From 99cdd7ab93566e1170a81a38f139e47fba47d350 Mon Sep 17 00:00:00 2001 From: delageniere Date: Fri, 15 Sep 2017 11:01:11 +0200 Subject: [PATCH 01/38] closes #167 --- ispyb-bcr-ear/pom.xml | 202 +- ispyb-bcr/pom.xml | 9 +- ispyb-ear/pom.xml | 5 +- ispyb-ejb/pom.xml | 28 +- .../ispyb/common/util/upload/ISPyBParser.java | 7 +- .../biosaxs/services/BiosaxsServices.java | 1 + .../core/experiment/Experiment3Service.java | 3 + .../experiment/Experiment3ServiceBean.java | 705 +- .../core/robot/Robot3ServiceBean.java | 2090 +- .../webservice/ATSASPipeline3ServiceBean.java | 2099 +- .../vos/dataAcquisition/Experiment3VO.java | 1006 +- ispyb-ui/pom.xml | 9 +- .../biosaxs/dataAdapter/BiosaxsActions.java | 1 + .../src/main/webapp/js/ispyb/min/ispyb-bx.js | 42726 ++++++++-------- ispyb-ws/pom.xml | 3 +- 15 files changed, 24447 insertions(+), 24447 deletions(-) diff --git a/ispyb-bcr-ear/pom.xml b/ispyb-bcr-ear/pom.xml index c072129af..cdac8b23b 100644 --- a/ispyb-bcr-ear/pom.xml +++ b/ispyb-bcr-ear/pom.xml @@ -1,112 +1,90 @@ - - 4.0.0 - - ispyb - ispyb-parent - 5.2.0 - - ispyb-bcr-ear - ear - - - - - - ispyb - ispyb-ejb3 - ejb - 5.2.0 - provided - - - - ispyb - ispyb-bcr - 5.0.3 - war - - - - org.apache.httpcomponents - httpclient - 4.4 - - - - - bcr - - - src/main/resources - - - - - - org.apache.maven.plugins - maven-ear-plugin - ${version.ear.plugin} - - - - 6 - true - - lib - - - - - ispyb - ispyb-ejb3 - / - - - - - ispyb - ispyb-bcr - /bcr/bcr - - - - no-version - - - - - org.wildfly.plugins - wildfly-maven-plugin - ${version.wildfly.maven.plugin} - - bcr.ear - false - - - - - + + 4.0.0 + + ispyb + ispyb-parent + 5.2.0 + + ispyb-bcr-ear + ear + + + + + ispyb + ispyb-ejb3 + ejb + 5.2.0 + provided + + + + ispyb + ispyb-bcr + 5.0.3 + war + + + + org.apache.httpcomponents + httpclient + 4.4 + + + + + bcr + + + src/main/resources + + + + + + org.apache.maven.plugins + maven-ear-plugin + ${version.ear.plugin} + + + + 6 + true + + lib + + + + + ispyb + ispyb-ejb3 + / + + + + + ispyb + ispyb-bcr + /bcr/bcr + + + + no-version + + + + + org.wildfly.plugins + wildfly-maven-plugin + ${version.wildfly.maven.plugin} + + bcr.ear + false + + + + + diff --git a/ispyb-bcr/pom.xml b/ispyb-bcr/pom.xml index 915e82467..a3a64ce4b 100644 --- a/ispyb-bcr/pom.xml +++ b/ispyb-bcr/pom.xml @@ -133,7 +133,7 @@ commons-collections commons-collections - 3.2.1 + 3.2.2 com.sun.mail @@ -200,12 +200,17 @@ org.hibernate hibernate-core - 4.0.0.Final + 5.0.10.Final + provided antlr antlr + + dom4j + dom4j + diff --git a/ispyb-ear/pom.xml b/ispyb-ear/pom.xml index 7ce68d16a..ce16ed6b7 100644 --- a/ispyb-ear/pom.xml +++ b/ispyb-ear/pom.xml @@ -15,6 +15,7 @@ ejb 5.2.0 + ispyb ispyb-ui @@ -27,6 +28,7 @@ war 5.2.0 + @@ -58,6 +60,7 @@ ispyb-ejb3 / + ispyb ispyb-ws @@ -69,7 +72,7 @@ ispyb-ui /ispyb - + no-version diff --git a/ispyb-ejb/pom.xml b/ispyb-ejb/pom.xml index 35777fab1..c6632b948 100644 --- a/ispyb-ejb/pom.xml +++ b/ispyb-ejb/pom.xml @@ -53,14 +53,6 @@ provided - - - - - - - @@ -69,16 +61,20 @@ provided - org.hibernate hibernate-core - 4.0.0.Final + 5.0.10.Final + provided antlr antlr + + dom4j + dom4j + @@ -90,13 +86,18 @@ org.jboss.ejb3 jboss-ejb3-ext-api - 2.1.0 + 2.2.0.Final org.jboss.as jboss-as-security 7.1.1.Final + + org.jboss.ws + jbossws-spi + 2.3.1.Final + org.apache.axis @@ -108,11 +109,6 @@ httpclient 4.4 - - org.jboss.ws - jbossws-spi - 2.3.1.Final - jhdf jhdf diff --git a/ispyb-ejb/src/main/java/ispyb/common/util/upload/ISPyBParser.java b/ispyb-ejb/src/main/java/ispyb/common/util/upload/ISPyBParser.java index f6a25a0cd..7038cc588 100644 --- a/ispyb-ejb/src/main/java/ispyb/common/util/upload/ISPyBParser.java +++ b/ispyb-ejb/src/main/java/ispyb/common/util/upload/ISPyBParser.java @@ -73,6 +73,8 @@ public class ISPyBParser extends XLSParser { */ private HSSFWorkbook mWorkbook = null; + + private final String PWD = "ispyb"; private static final Ejb3ServiceLocator ejb3ServiceLocator = Ejb3ServiceLocator.getInstance(); @@ -515,7 +517,7 @@ public void populateExistingShipment(String templateFileName, String populatedTe workbook.setSheetName(s, dewarCode + "_" + puckNumber); HSSFSheet sheet = workbook.getSheetAt(s); - sheet.setProtect(false); + sheet.protectSheet(PWD); // Dewar Code HSSFRow row = sheet.getRow(dewarRow); @@ -599,7 +601,8 @@ public void populateExistingShipment(String templateFileName, String populatedTe cell = row.createCell(shippingDateCol); cell.setCellValue(new HSSFRichTextString(shippingDate)); - sheet.setProtect(true); + //sheet.setProtect(true); + sheet.protectSheet(PWD); puckNumber++; } } diff --git a/ispyb-ejb/src/main/java/ispyb/server/biosaxs/services/BiosaxsServices.java b/ispyb-ejb/src/main/java/ispyb/server/biosaxs/services/BiosaxsServices.java index cb0803db9..0ee508c83 100644 --- a/ispyb-ejb/src/main/java/ispyb/server/biosaxs/services/BiosaxsServices.java +++ b/ispyb-ejb/src/main/java/ispyb/server/biosaxs/services/BiosaxsServices.java @@ -487,6 +487,7 @@ public Integer createHPLC(String proposalCode, String proposalNumber, String nam } Experiment3VO experiment = new Experiment3VO(); + experiment = this.experiment3Service.initPlates(experiment); experiment.setProposalId(proposal.getProposalId()); experiment.setName(name); experiment.setSessionId(sessionId); diff --git a/ispyb-ejb/src/main/java/ispyb/server/biosaxs/services/core/experiment/Experiment3Service.java b/ispyb-ejb/src/main/java/ispyb/server/biosaxs/services/core/experiment/Experiment3Service.java index 29d3ae30b..0dbc0ce7c 100644 --- a/ispyb-ejb/src/main/java/ispyb/server/biosaxs/services/core/experiment/Experiment3Service.java +++ b/ispyb-ejb/src/main/java/ispyb/server/biosaxs/services/core/experiment/Experiment3Service.java @@ -72,5 +72,8 @@ public interface Experiment3Service { public abstract void saveStructure(Structure3VO structure3vo); public List> getExperimentDescription(Integer experimentId); + + public Experiment3VO initPlates(Experiment3VO vo); + } \ No newline at end of file diff --git a/ispyb-ejb/src/main/java/ispyb/server/biosaxs/services/core/experiment/Experiment3ServiceBean.java b/ispyb-ejb/src/main/java/ispyb/server/biosaxs/services/core/experiment/Experiment3ServiceBean.java index 084d8769c..ca577d69d 100644 --- a/ispyb-ejb/src/main/java/ispyb/server/biosaxs/services/core/experiment/Experiment3ServiceBean.java +++ b/ispyb-ejb/src/main/java/ispyb/server/biosaxs/services/core/experiment/Experiment3ServiceBean.java @@ -1,348 +1,357 @@ -/******************************************************************************* - * This file is part of ISPyB. - * - * ISPyB is free software: you can redistribute it and/or modify - * it under the terms of the GNU Lesser General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * ISPyB is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public License - * along with ISPyB. If not, see . - * - * Contributors : S. Delageniere, R. Leal, L. Launer, K. Levik, S. Veyrier, P. Brenchereau, M. Bodin, A. De Maria Antolinos - ******************************************************************************************************************************/ - -package ispyb.server.biosaxs.services.core.experiment; - - -import ispyb.server.biosaxs.services.core.ExperimentScope; -import ispyb.server.biosaxs.services.core.proposal.SaxsProposal3Service; -import ispyb.server.biosaxs.services.sql.SQLQueryKeeper; -import ispyb.server.biosaxs.vos.assembly.Macromolecule3VO; -import ispyb.server.biosaxs.vos.assembly.Stoichiometry3VO; -import ispyb.server.biosaxs.vos.assembly.Structure3VO; -import ispyb.server.biosaxs.vos.dataAcquisition.Buffer3VO; -import ispyb.server.biosaxs.vos.dataAcquisition.Experiment3VO; -import ispyb.server.biosaxs.vos.dataAcquisition.Measurement3VO; -import ispyb.server.biosaxs.vos.datacollection.MeasurementTodataCollection3VO; -import ispyb.server.biosaxs.vos.datacollection.SaxsDataCollection3VO; -import ispyb.server.biosaxs.vos.utils.comparator.SaxsDataCollectionComparator; -import ispyb.server.biosaxs.vos.utils.parser.RobotXMLParser; -import ispyb.server.mx.services.ws.rest.WsServiceBean; - -import java.io.File; -import java.util.Arrays; -import java.util.Calendar; -import java.util.Collections; -import java.util.Comparator; -import java.util.GregorianCalendar; -import java.util.List; -import java.util.Map; -import java.util.Set; - -import javax.ejb.EJB; -import javax.ejb.Stateless; -import javax.persistence.EntityManager; -import javax.persistence.NoResultException; -import javax.persistence.PersistenceContext; -import javax.persistence.TypedQuery; - -import org.apache.log4j.Logger; -import org.hibernate.SQLQuery; -import org.hibernate.Session; -import org.hibernate.transform.AliasToEntityMapResultTransformer; - - - -@Stateless -public class Experiment3ServiceBean extends WsServiceBean implements Experiment3Service, Experiment3ServiceLocal { - - private final static Logger log = Logger.getLogger(Experiment3ServiceBean.class); - - - /** - * QUERIES - */ - private String GetExperimentDescriptionByExperimentId = getViewExperimentDescriptionTableQuery() + " where experimentId = :experimentId"; - - - - @PersistenceContext(unitName = "ispyb_db") - private EntityManager entityManager; - - @EJB - private SaxsProposal3Service saxsProposal3Service; - - @Override - public void persist(Experiment3VO transientInstance) { - try { - entityManager.persist(transientInstance); - } catch (RuntimeException re) { - throw re; - } - } - - @Override - public Experiment3VO merge(Experiment3VO detachedInstance) { - try { - Experiment3VO result = entityManager.merge(detachedInstance); - return result; - } catch (RuntimeException re) { - throw re; - } - } - - private String getViewExperimentDescriptionTableQuery(){ - return this.getQueryFromResourceFile("/queries/biosaxs/Experiment3ServiceBean/getViewExperimentDescriptionTableQuery.sql"); - } - - - @Override - public List findByProposalId(int proposalId, ExperimentScope scope) { - StringBuilder ejbQLQuery = Experiment3ServiceBean.getQueryByScope(scope); - ejbQLQuery.append("WHERE experiment.proposalId = :proposalId"); - TypedQuery query = entityManager.createQuery(ejbQLQuery.toString(), Experiment3VO.class).setParameter("proposalId", proposalId); - return query.getResultList(); - } - - @Override - public Experiment3VO findById(Integer experimentId, ExperimentScope scope, Integer proposalId) { - try { - StringBuilder ejbQLQuery = Experiment3ServiceBean.getQueryByScope(scope); - ejbQLQuery.append("WHERE experiment.experimentId = :experimentId "); - // if coming from manager account, proposalId can be null - if (proposalId != null) { - ejbQLQuery.append(" and experiment.proposalId = :proposalId"); - } - TypedQuery query = entityManager.createQuery(ejbQLQuery.toString(), Experiment3VO.class); - query.setParameter("experimentId", experimentId); - if (proposalId != null) { - query.setParameter("proposalId", proposalId); - } - return query.getSingleResult(); - } catch (NoResultException e) { - return null; - } - } - - public static StringBuilder getQueryByScope(ExperimentScope scope){ - StringBuilder ejbQLQuery = new StringBuilder(); - ejbQLQuery.append("SELECT DISTINCT(experiment) FROM Experiment3VO experiment "); - - switch (scope) { - case MINIMAL: - break; - case MEDIUM: - ejbQLQuery.append("LEFT JOIN FETCH experiment.samples samples "); - ejbQLQuery.append("LEFT JOIN FETCH samples.macromolecule3VO macromolecule "); - ejbQLQuery.append("LEFT JOIN FETCH macromolecule.stoichiometry st "); -// ejbQLQuery.append("LEFT JOIN FETCH st.macromolecule3VO "); - ejbQLQuery.append("LEFT JOIN FETCH macromolecule.structure3VOs "); - ejbQLQuery.append("LEFT JOIN FETCH samples.measurements specimens "); - ejbQLQuery.append("LEFT JOIN FETCH experiment.samplePlate3VOs samplePlates "); - ejbQLQuery.append("LEFT JOIN FETCH samplePlates.plategroup3VO "); - ejbQLQuery.append("LEFT JOIN FETCH samplePlates.sampleplateposition3VOs "); - - ejbQLQuery.append("LEFT JOIN FETCH specimens.merge3VOs merges "); - ejbQLQuery.append("LEFT JOIN FETCH specimens.run3VO "); - break; - case PREPARE_EXPERIMENT: - ejbQLQuery.append("LEFT JOIN FETCH experiment.samples samples "); - ejbQLQuery.append("LEFT JOIN FETCH samples.macromolecule3VO "); - ejbQLQuery.append("LEFT JOIN FETCH samples.measurements specimens "); - ejbQLQuery.append("LEFT JOIN FETCH experiment.samplePlate3VOs samplePlates "); - ejbQLQuery.append("LEFT JOIN FETCH samplePlates.plategroup3VO "); - ejbQLQuery.append("LEFT JOIN FETCH samplePlates.sampleplateposition3VOs "); - ejbQLQuery.append("LEFT JOIN FETCH experiment.dataCollections dataCollections "); - ejbQLQuery.append("LEFT JOIN FETCH dataCollections.measurementtodatacollection3VOs "); - break; - default: - break; - } - return ejbQLQuery; - } - - - @Override - public Experiment3VO findByMeasurementId(int measurementId){ - StringBuilder ejbQLQuery = Experiment3ServiceBean.getQueryByScope(ExperimentScope.MEDIUM); - ejbQLQuery.append(" wHERE specimens.measurementId = " + measurementId); - TypedQuery query = entityManager.createQuery(ejbQLQuery.toString(), Experiment3VO.class); - return query.getSingleResult(); - } - - - @Override - public List test(String ejbQL) { - try { - TypedQuery query = entityManager.createQuery(ejbQL, Experiment3VO.class); - return query.getResultList(); - } catch (RuntimeException re) { - log.error("get failed", re); - throw re; - } - } - - @Override - public Experiment3VO findById(Integer experimentId, ExperimentScope scope) { - StringBuilder ejbQLQuery = Experiment3ServiceBean.getQueryByScope(scope); - ejbQLQuery.append("WHERE experiment.experimentId = :experimentId"); - TypedQuery query = entityManager.createQuery(ejbQLQuery.toString(), Experiment3VO.class); - query.setParameter("experimentId", experimentId); - List results = query.getResultList(); - if (results.isEmpty()) { - return null; // handle no-results case - } else { - return results.get(0); - } - } - - - @Override - public List> getExperimentDescription(Integer experimentId) { - Session session = (Session) this.entityManager.getDelegate(); - SQLQuery query = session.createSQLQuery(GetExperimentDescriptionByExperimentId); - query.setParameter("experimentId", experimentId); - return executeSQLQuery(query); - } - - - - /** - * It returns the xml as String of the robot.xml file - * This xml format is used on BsxCube for load sample changer experiments - * - */ - @Override - public String toRobotXML(Integer experimentId, int proposalId, final SaxsDataCollectionComparator... multipleOptions) { - this.setPriorities(experimentId, proposalId, multipleOptions); - return this.toRobotXML(experimentId, proposalId); - } - - @Override - public String toRobotXML(Integer experimentId, int proposalId) { - Experiment3VO experiment = this.findById(experimentId, ExperimentScope.MEDIUM); - List buffers = saxsProposal3Service.findBuffersByProposalId(proposalId); - return RobotXMLParser.toRobotXML(experiment, experiment.getSamplePlate3VOs(), buffers); - } - - - - @Override - public void remove(Experiment3VO experiment) { - Experiment3VO result = entityManager.merge(experiment); - this.entityManager.remove(result); - } - - /** - * Sets the order for each data collection based on SaxsDataCollectionComparator - */ - @Override - public Experiment3VO setPriorities(int experimentId, int proposalId, SaxsDataCollectionComparator[] multipleOptions) { - Experiment3VO experiment = this.findById(experimentId, ExperimentScope.MEDIUM, proposalId); - List dataCollectionList = experiment.getDataCollectionList(); - /** Sort data collections by the priority order **/ - Collections.sort(dataCollectionList, SaxsDataCollectionComparator.compare(experiment, SaxsDataCollectionComparator.getComparator(multipleOptions))); - - int priority = 1; - for (int i = 0; i < dataCollectionList.size(); i++) { - SaxsDataCollection3VO datacollection = dataCollectionList.get(i); - List measurementsToDatacollection = this.getMeasurementToDataCollectionOrdered(datacollection); - for (MeasurementTodataCollection3VO m : measurementsToDatacollection) { - Measurement3VO measurement = experiment.getMeasurementById(m.getMeasurementId()); - measurement.setPriority(priority); - measurement = this.entityManager.merge(measurement); - priority ++; - } - } - return experiment; - - } - /** Sort two measurements by their dataCollectionOrder field **/ - private static Comparator MeasurementTodataCollectionComparatorOrder = new Comparator(){ - public int compare(MeasurementTodataCollection3VO o1, MeasurementTodataCollection3VO o2) { - return o1.getDataCollectionOrder() - o2.getDataCollectionOrder(); - } - }; - - /** Sort a data collection by its dataCollectionOrder field **/ - private List getMeasurementToDataCollectionOrdered(SaxsDataCollection3VO dataCollection){ - Set measurements = dataCollection.getMeasurementtodatacollection3VOs(); - List list = Arrays.asList(measurements.toArray(new MeasurementTodataCollection3VO[measurements.size()])); - Collections.sort(list, MeasurementTodataCollectionComparatorOrder); - return list; - } - - @Override - public void saveStructure(Integer macromoleculeId, String fileName, String filePath, String type, String symmetry, String multiplicity) { - Structure3VO structure = new Structure3VO(); - structure.setMacromoleculeId(macromoleculeId); - structure.setFilePath(filePath); - structure.setName(fileName); - structure.setType(type); - structure.setSymmetry(symmetry); - structure.setMultiplicity(multiplicity); - structure.setCreationDate(GregorianCalendar.getInstance().getTime()); - entityManager.merge(structure); - } - - @Override - public void removeStructure(int structureId) { - Structure3VO structure = this.entityManager.find(Structure3VO.class, structureId); - this.entityManager.remove(structure); - } - - @Override - public Structure3VO findStructureById(int structureId) { - return this.entityManager.find(Structure3VO.class, structureId); - } - - @Override - public void removeStoichiometry(int stoichiometryId) { - Stoichiometry3VO st = this.entityManager.find(Stoichiometry3VO.class, stoichiometryId); - this.entityManager.remove(st); - } - - @Override - public void saveStoichiometry(int macromoleculeId, int hostmacromoleculeId, String ratio, String comments) { - Stoichiometry3VO stoi = new Stoichiometry3VO(); - stoi.setMacromolecule3VOByHostMacromoleculeId(macromoleculeId); - stoi.setHostmacromoleculeId(hostmacromoleculeId); - stoi.setRatio(ratio); - this.entityManager.merge(stoi); - } - -// @Override -// public Macromolecule3VO findMacromoleculeById(Integer macromoleculeId) { -// StringBuilder ejbQLQuery = new StringBuilder(); -// ejbQLQuery.append("SELECT DISTINCT(macromolecule) FROM Macromolecule3VO macromolecule "); -// ejbQLQuery.append("LEFT JOIN FETCH macromolecule.stoichiometry st "); -// ejbQLQuery.append("LEFT JOIN FETCH st.macromolecule3VO "); -// ejbQLQuery.append("LEFT JOIN FETCH macromolecule.structure3VOs "); -// ejbQLQuery.append("WHERE macromolecule.macromoleculeId = :macromoleculeId"); -// TypedQuery query = entityManager.createQuery(ejbQLQuery.toString(), Macromolecule3VO.class); -// query.setParameter("macromoleculeId", macromoleculeId); -// return query.getSingleResult(); -// } - - @Override - public Structure3VO findStructureByFilePathId(String filePath, int experimentId) { -// Experiment3VO experiment = this.findById(experimentId, ExperimentScope.MINIMAL); -// List macromolecules = saxsProposal3Service.findMacromoleculesByProposalId(experiment.getProposalId()); -// for (Macromolecule3VO macromolecule3vo : macromolecules) { -// -// } - return null; - } - - @Override - public void saveStructure(Structure3VO structure3vo) { - this.entityManager.merge(structure3vo); - - } -} +/******************************************************************************* + * This file is part of ISPyB. + * + * ISPyB is free software: you can redistribute it and/or modify + * it under the terms of the GNU Lesser General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * ISPyB is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with ISPyB. If not, see . + * + * Contributors : S. Delageniere, R. Leal, L. Launer, K. Levik, S. Veyrier, P. Brenchereau, M. Bodin, A. De Maria Antolinos + ******************************************************************************************************************************/ + +package ispyb.server.biosaxs.services.core.experiment; + + +import java.util.Arrays; +import java.util.Collections; +import java.util.Comparator; +import java.util.GregorianCalendar; +import java.util.List; +import java.util.Map; +import java.util.Set; + +import javax.ejb.EJB; +import javax.ejb.Stateless; +import javax.naming.NamingException; +import javax.persistence.EntityManager; +import javax.persistence.NoResultException; +import javax.persistence.PersistenceContext; +import javax.persistence.TypedQuery; + +import org.apache.log4j.Logger; +import org.hibernate.SQLQuery; +import org.hibernate.Session; + +import ispyb.server.biosaxs.services.core.ExperimentScope; +import ispyb.server.biosaxs.services.core.plateType.PlateType3Service; +import ispyb.server.biosaxs.services.core.proposal.SaxsProposal3Service; +import ispyb.server.biosaxs.vos.assembly.Stoichiometry3VO; +import ispyb.server.biosaxs.vos.assembly.Structure3VO; +import ispyb.server.biosaxs.vos.dataAcquisition.Buffer3VO; +import ispyb.server.biosaxs.vos.dataAcquisition.Experiment3VO; +import ispyb.server.biosaxs.vos.dataAcquisition.Measurement3VO; +import ispyb.server.biosaxs.vos.datacollection.MeasurementTodataCollection3VO; +import ispyb.server.biosaxs.vos.datacollection.SaxsDataCollection3VO; +import ispyb.server.biosaxs.vos.utils.comparator.SaxsDataCollectionComparator; +import ispyb.server.biosaxs.vos.utils.parser.RobotXMLParser; +import ispyb.server.mx.services.ws.rest.WsServiceBean; + + + +@Stateless +public class Experiment3ServiceBean extends WsServiceBean implements Experiment3Service, Experiment3ServiceLocal { + + private final static Logger log = Logger.getLogger(Experiment3ServiceBean.class); + + + /** + * QUERIES + */ + private String GetExperimentDescriptionByExperimentId = getViewExperimentDescriptionTableQuery() + " where experimentId = :experimentId"; + + + + @PersistenceContext(unitName = "ispyb_db") + private EntityManager entityManager; + + @EJB + private SaxsProposal3Service saxsProposal3Service; + + @EJB + private PlateType3Service plateType3Service; + + @Override + public void persist(Experiment3VO transientInstance) { + try { + entityManager.persist(transientInstance); + } catch (RuntimeException re) { + throw re; + } + } + + @Override + public Experiment3VO merge(Experiment3VO detachedInstance) { + try { + Experiment3VO result = entityManager.merge(detachedInstance); + return result; + } catch (RuntimeException re) { + throw re; + } + } + + private String getViewExperimentDescriptionTableQuery(){ + return this.getQueryFromResourceFile("/queries/biosaxs/Experiment3ServiceBean/getViewExperimentDescriptionTableQuery.sql"); + } + + + @Override + public List findByProposalId(int proposalId, ExperimentScope scope) { + StringBuilder ejbQLQuery = Experiment3ServiceBean.getQueryByScope(scope); + ejbQLQuery.append("WHERE experiment.proposalId = :proposalId"); + TypedQuery query = entityManager.createQuery(ejbQLQuery.toString(), Experiment3VO.class).setParameter("proposalId", proposalId); + return query.getResultList(); + } + + @Override + public Experiment3VO findById(Integer experimentId, ExperimentScope scope, Integer proposalId) { + try { + StringBuilder ejbQLQuery = Experiment3ServiceBean.getQueryByScope(scope); + ejbQLQuery.append("WHERE experiment.experimentId = :experimentId "); + // if coming from manager account, proposalId can be null + if (proposalId != null) { + ejbQLQuery.append(" and experiment.proposalId = :proposalId"); + } + TypedQuery query = entityManager.createQuery(ejbQLQuery.toString(), Experiment3VO.class); + query.setParameter("experimentId", experimentId); + if (proposalId != null) { + query.setParameter("proposalId", proposalId); + } + return query.getSingleResult(); + } catch (NoResultException e) { + return null; + } + } + + public Experiment3VO initPlates(Experiment3VO vo){ + try { + vo.setPlatetype3VOs(this.plateType3Service.findAll()); + } catch (Exception e) { + e.printStackTrace(); + } + return vo; + } + + public static StringBuilder getQueryByScope(ExperimentScope scope){ + StringBuilder ejbQLQuery = new StringBuilder(); + ejbQLQuery.append("SELECT DISTINCT(experiment) FROM Experiment3VO experiment "); + + switch (scope) { + case MINIMAL: + break; + case MEDIUM: + ejbQLQuery.append("LEFT JOIN FETCH experiment.samples samples "); + ejbQLQuery.append("LEFT JOIN FETCH samples.macromolecule3VO macromolecule "); + ejbQLQuery.append("LEFT JOIN FETCH macromolecule.stoichiometry st "); +// ejbQLQuery.append("LEFT JOIN FETCH st.macromolecule3VO "); + ejbQLQuery.append("LEFT JOIN FETCH macromolecule.structure3VOs "); + ejbQLQuery.append("LEFT JOIN FETCH samples.measurements specimens "); + ejbQLQuery.append("LEFT JOIN FETCH experiment.samplePlate3VOs samplePlates "); + ejbQLQuery.append("LEFT JOIN FETCH samplePlates.plategroup3VO "); + ejbQLQuery.append("LEFT JOIN FETCH samplePlates.sampleplateposition3VOs "); + + ejbQLQuery.append("LEFT JOIN FETCH specimens.merge3VOs merges "); + ejbQLQuery.append("LEFT JOIN FETCH specimens.run3VO "); + break; + case PREPARE_EXPERIMENT: + ejbQLQuery.append("LEFT JOIN FETCH experiment.samples samples "); + ejbQLQuery.append("LEFT JOIN FETCH samples.macromolecule3VO "); + ejbQLQuery.append("LEFT JOIN FETCH samples.measurements specimens "); + ejbQLQuery.append("LEFT JOIN FETCH experiment.samplePlate3VOs samplePlates "); + ejbQLQuery.append("LEFT JOIN FETCH samplePlates.plategroup3VO "); + ejbQLQuery.append("LEFT JOIN FETCH samplePlates.sampleplateposition3VOs "); + ejbQLQuery.append("LEFT JOIN FETCH experiment.dataCollections dataCollections "); + ejbQLQuery.append("LEFT JOIN FETCH dataCollections.measurementtodatacollection3VOs "); + break; + default: + break; + } + return ejbQLQuery; + } + + + @Override + public Experiment3VO findByMeasurementId(int measurementId){ + StringBuilder ejbQLQuery = Experiment3ServiceBean.getQueryByScope(ExperimentScope.MEDIUM); + ejbQLQuery.append(" wHERE specimens.measurementId = " + measurementId); + TypedQuery query = entityManager.createQuery(ejbQLQuery.toString(), Experiment3VO.class); + return query.getSingleResult(); + } + + + @Override + public List test(String ejbQL) { + try { + TypedQuery query = entityManager.createQuery(ejbQL, Experiment3VO.class); + return query.getResultList(); + } catch (RuntimeException re) { + log.error("get failed", re); + throw re; + } + } + + @Override + public Experiment3VO findById(Integer experimentId, ExperimentScope scope) { + StringBuilder ejbQLQuery = Experiment3ServiceBean.getQueryByScope(scope); + ejbQLQuery.append("WHERE experiment.experimentId = :experimentId"); + TypedQuery query = entityManager.createQuery(ejbQLQuery.toString(), Experiment3VO.class); + query.setParameter("experimentId", experimentId); + List results = query.getResultList(); + if (results.isEmpty()) { + return null; // handle no-results case + } else { + return results.get(0); + } + } + + + @Override + public List> getExperimentDescription(Integer experimentId) { + Session session = (Session) this.entityManager.getDelegate(); + SQLQuery query = session.createSQLQuery(GetExperimentDescriptionByExperimentId); + query.setParameter("experimentId", experimentId); + return executeSQLQuery(query); + } + + + + /** + * It returns the xml as String of the robot.xml file + * This xml format is used on BsxCube for load sample changer experiments + * + */ + @Override + public String toRobotXML(Integer experimentId, int proposalId, final SaxsDataCollectionComparator... multipleOptions) { + this.setPriorities(experimentId, proposalId, multipleOptions); + return this.toRobotXML(experimentId, proposalId); + } + + @Override + public String toRobotXML(Integer experimentId, int proposalId) { + Experiment3VO experiment = this.findById(experimentId, ExperimentScope.MEDIUM); + List buffers = saxsProposal3Service.findBuffersByProposalId(proposalId); + return RobotXMLParser.toRobotXML(experiment, experiment.getSamplePlate3VOs(), buffers); + } + + + + @Override + public void remove(Experiment3VO experiment) { + Experiment3VO result = entityManager.merge(experiment); + this.entityManager.remove(result); + } + + /** + * Sets the order for each data collection based on SaxsDataCollectionComparator + */ + @Override + public Experiment3VO setPriorities(int experimentId, int proposalId, SaxsDataCollectionComparator[] multipleOptions) { + Experiment3VO experiment = this.findById(experimentId, ExperimentScope.MEDIUM, proposalId); + List dataCollectionList = experiment.getDataCollectionList(); + /** Sort data collections by the priority order **/ + Collections.sort(dataCollectionList, SaxsDataCollectionComparator.compare(experiment, SaxsDataCollectionComparator.getComparator(multipleOptions))); + + int priority = 1; + for (int i = 0; i < dataCollectionList.size(); i++) { + SaxsDataCollection3VO datacollection = dataCollectionList.get(i); + List measurementsToDatacollection = this.getMeasurementToDataCollectionOrdered(datacollection); + for (MeasurementTodataCollection3VO m : measurementsToDatacollection) { + Measurement3VO measurement = experiment.getMeasurementById(m.getMeasurementId()); + measurement.setPriority(priority); + measurement = this.entityManager.merge(measurement); + priority ++; + } + } + return experiment; + + } + /** Sort two measurements by their dataCollectionOrder field **/ + private static Comparator MeasurementTodataCollectionComparatorOrder = new Comparator(){ + public int compare(MeasurementTodataCollection3VO o1, MeasurementTodataCollection3VO o2) { + return o1.getDataCollectionOrder() - o2.getDataCollectionOrder(); + } + }; + + /** Sort a data collection by its dataCollectionOrder field **/ + private List getMeasurementToDataCollectionOrdered(SaxsDataCollection3VO dataCollection){ + Set measurements = dataCollection.getMeasurementtodatacollection3VOs(); + List list = Arrays.asList(measurements.toArray(new MeasurementTodataCollection3VO[measurements.size()])); + Collections.sort(list, MeasurementTodataCollectionComparatorOrder); + return list; + } + + @Override + public void saveStructure(Integer macromoleculeId, String fileName, String filePath, String type, String symmetry, String multiplicity) { + Structure3VO structure = new Structure3VO(); + structure.setMacromoleculeId(macromoleculeId); + structure.setFilePath(filePath); + structure.setName(fileName); + structure.setType(type); + structure.setSymmetry(symmetry); + structure.setMultiplicity(multiplicity); + structure.setCreationDate(GregorianCalendar.getInstance().getTime()); + entityManager.merge(structure); + } + + @Override + public void removeStructure(int structureId) { + Structure3VO structure = this.entityManager.find(Structure3VO.class, structureId); + this.entityManager.remove(structure); + } + + @Override + public Structure3VO findStructureById(int structureId) { + return this.entityManager.find(Structure3VO.class, structureId); + } + + @Override + public void removeStoichiometry(int stoichiometryId) { + Stoichiometry3VO st = this.entityManager.find(Stoichiometry3VO.class, stoichiometryId); + this.entityManager.remove(st); + } + + @Override + public void saveStoichiometry(int macromoleculeId, int hostmacromoleculeId, String ratio, String comments) { + Stoichiometry3VO stoi = new Stoichiometry3VO(); + stoi.setMacromolecule3VOByHostMacromoleculeId(macromoleculeId); + stoi.setHostmacromoleculeId(hostmacromoleculeId); + stoi.setRatio(ratio); + this.entityManager.merge(stoi); + } + +// @Override +// public Macromolecule3VO findMacromoleculeById(Integer macromoleculeId) { +// StringBuilder ejbQLQuery = new StringBuilder(); +// ejbQLQuery.append("SELECT DISTINCT(macromolecule) FROM Macromolecule3VO macromolecule "); +// ejbQLQuery.append("LEFT JOIN FETCH macromolecule.stoichiometry st "); +// ejbQLQuery.append("LEFT JOIN FETCH st.macromolecule3VO "); +// ejbQLQuery.append("LEFT JOIN FETCH macromolecule.structure3VOs "); +// ejbQLQuery.append("WHERE macromolecule.macromoleculeId = :macromoleculeId"); +// TypedQuery query = entityManager.createQuery(ejbQLQuery.toString(), Macromolecule3VO.class); +// query.setParameter("macromoleculeId", macromoleculeId); +// return query.getSingleResult(); +// } + + @Override + public Structure3VO findStructureByFilePathId(String filePath, int experimentId) { +// Experiment3VO experiment = this.findById(experimentId, ExperimentScope.MINIMAL); +// List macromolecules = saxsProposal3Service.findMacromoleculesByProposalId(experiment.getProposalId()); +// for (Macromolecule3VO macromolecule3vo : macromolecules) { +// +// } + return null; + } + + @Override + public void saveStructure(Structure3VO structure3vo) { + this.entityManager.merge(structure3vo); + + } +} diff --git a/ispyb-ejb/src/main/java/ispyb/server/biosaxs/services/core/robot/Robot3ServiceBean.java b/ispyb-ejb/src/main/java/ispyb/server/biosaxs/services/core/robot/Robot3ServiceBean.java index b05cecc55..60a952618 100644 --- a/ispyb-ejb/src/main/java/ispyb/server/biosaxs/services/core/robot/Robot3ServiceBean.java +++ b/ispyb-ejb/src/main/java/ispyb/server/biosaxs/services/core/robot/Robot3ServiceBean.java @@ -1,1045 +1,1045 @@ -/******************************************************************************* - * This file is part of ISPyB. - * - * ISPyB is free software: you can redistribute it and/or modify - * it under the terms of the GNU Lesser General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * ISPyB is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public License - * along with ISPyB. If not, see . - * - * Contributors : S. Delageniere, R. Leal, L. Launer, K. Levik, S. Veyrier, P. Brenchereau, M. Bodin, A. De Maria Antolinos - ******************************************************************************************************************************/ - -package ispyb.server.biosaxs.services.core.robot; - -import ispyb.common.util.Constants; -import ispyb.server.biosaxs.services.core.ExperimentScope; -import ispyb.server.biosaxs.services.core.experiment.Experiment3ServiceLocal; -import ispyb.server.biosaxs.services.core.measurement.Measurement3ServiceLocal; -import ispyb.server.biosaxs.services.core.measurementToDataCollection.MeasurementToDatacollection3ServiceLocal; -import ispyb.server.biosaxs.services.core.plateType.PlateType3ServiceLocal; -import ispyb.server.biosaxs.services.core.proposal.SaxsProposal3ServiceLocal; -import ispyb.server.biosaxs.services.core.samplePlate.Sampleplate3ServiceLocal; -import ispyb.server.biosaxs.services.core.specimen.Specimen3Service; -import ispyb.server.biosaxs.vos.assembly.Macromolecule3VO; -import ispyb.server.biosaxs.vos.dataAcquisition.Buffer3VO; -import ispyb.server.biosaxs.vos.dataAcquisition.Experiment3VO; -import ispyb.server.biosaxs.vos.dataAcquisition.Measurement3VO; -import ispyb.server.biosaxs.vos.dataAcquisition.Specimen3VO; -import ispyb.server.biosaxs.vos.dataAcquisition.plate.PlateGroup3VO; -import ispyb.server.biosaxs.vos.dataAcquisition.plate.Platetype3VO; -import ispyb.server.biosaxs.vos.dataAcquisition.plate.Sampleplate3VO; -import ispyb.server.biosaxs.vos.dataAcquisition.plate.Sampleplateposition3VO; -import ispyb.server.biosaxs.vos.datacollection.MeasurementTodataCollection3VO; -import ispyb.server.biosaxs.vos.datacollection.SaxsDataCollection3VO; - -import java.lang.reflect.Modifier; -import java.util.ArrayList; -import java.util.Calendar; -import java.util.Date; -import java.util.GregorianCalendar; -import java.util.HashMap; -import java.util.HashSet; -import java.util.List; - -import javax.ejb.EJB; -import javax.ejb.Stateless; -import javax.persistence.EntityManager; -import javax.persistence.PersistenceContext; - -import org.apache.log4j.Logger; - -import com.google.gson.GsonBuilder; - -@Stateless -public class Robot3ServiceBean implements Robot3Service, Robot3ServiceLocal { - - private final static Logger log = Logger.getLogger(Robot3ServiceBean.class); - - /** The specimen3 service local. */ - @EJB - private Measurement3ServiceLocal measurement3ServiceLocal; - - /** The experiment3 service local. */ - @EJB - private Experiment3ServiceLocal experiment3ServiceLocal; - - /** The macromolecule3 service. */ - @EJB - private SaxsProposal3ServiceLocal proposal3Service; - - /** The sample plate3 service. */ - @EJB - private Sampleplate3ServiceLocal samplePlate3Service; - - /** The plate type3 service. */ - @EJB - private PlateType3ServiceLocal plateType3Service; - - /** The measurement to data collection3 service. */ - @EJB - private MeasurementToDatacollection3ServiceLocal measurementToDataCollection3Service; - - @EJB - private Specimen3Service specimen3Service; - - /** The entity manager. */ - @PersistenceContext(unitName = "ispyb_db") - private EntityManager entityManager; - - /** The now. */ - protected static Calendar NOW; - - /** - * Gets the now. - * - * @return the now - */ - private Date getNow() { - NOW = GregorianCalendar.getInstance(); - return NOW.getTime(); - } - - /** - * Gets the buffers. It returns a hashmap - * - * @param samples - * the samples - * @return the buffers - */ - private HashMap parseBuffers(ArrayList> samples, int proposalId) { - List buffersProposal = proposal3Service.findBuffersByProposalId(proposalId); - Robot3ServiceBean.log.info("----------------- parseBuffers ------------ "); - HashMap bufferNameToBuffer3VO = new HashMap(); - - /** Store the name of the macromolecules **/ - HashMap bufferNameToBufferAcronym = new HashMap(); - - /** - * It is possible that users make a mistake and for the same specimen in the same position they set a different - * buffer's name - */ - HashMap bufferPositionToBufferAcronym = new HashMap(); - - for (HashMap sample : samples) { - if (sample.get("type").equals("Buffer")) { - Buffer3VO buffer = new Buffer3VO(); - buffer.setName(sample.get("macromolecule").trim()); - buffer.setAcronym(sample.get("macromolecule").trim()); - buffer.setComment(sample.get("comments")); - - Robot3ServiceBean.log.info("sample: " + sample.toString()); - Robot3ServiceBean.log.info("buffername: " + sample.get("buffername")); - - String positionCode = this.getSamplePositionKey(sample); - if (bufferPositionToBufferAcronym.get(positionCode) == null) { - bufferNameToBufferAcronym.put(sample.get("buffername").trim(), sample.get("macromolecule").trim()); - bufferPositionToBufferAcronym.put(positionCode, sample.get("macromolecule").trim()); - } else { - Robot3ServiceBean.log.info("Buffers detected in the same position with different macromolecule name"); - log.warn("Buffers detected in the same position with different macromolecule name"); - bufferNameToBufferAcronym.put(sample.get("buffername").trim(), - bufferPositionToBufferAcronym.get(positionCode)); - } - } - } - - for (String bufferName : bufferNameToBufferAcronym.keySet()) { - Buffer3VO bufferExists = this - .getBufferByAcronym(buffersProposal, bufferNameToBufferAcronym.get(bufferName)); - if (bufferExists != null) { - bufferNameToBuffer3VO.put(bufferName, bufferExists); - } else { - Buffer3VO buffer = new Buffer3VO(); - buffer.setAcronym(bufferNameToBufferAcronym.get(bufferName)); - buffer.setName(bufferNameToBufferAcronym.get(bufferName)); - bufferNameToBuffer3VO.put(bufferName, buffer); - } - } - - return bufferNameToBuffer3VO; - } - - /** If the acronym exists in the list the macromolecule is returned **/ - private Macromolecule3VO getMacromoleculeByAcronym(List macromolecules, String acronym) { - for (Macromolecule3VO macromolecule : macromolecules) { - if (macromolecule.getAcronym().toLowerCase().equals(acronym.toLowerCase())) { - return macromolecule; - } - } - return null; - } - - /** If the acronym exists in the list the buffer is returned **/ - private Buffer3VO getBufferByAcronym(List buffers, String acronym) { - for (Buffer3VO buffer : buffers) { - if (buffer.getAcronym().toLowerCase().equals(acronym.toLowerCase())) { - return buffer; - } - } - return null; - } - - /** - * Gets the macromolecules. If there are two with the same name it means that they are the same macromolecules - * - * @param samples - * the samples - * @return the macromolecules - */ - private HashMap parseMacromolecules(ArrayList> samples, - int proposalId) { - List macromoleculesProposalList = proposal3Service.findMacromoleculesByProposalId(proposalId); - Robot3ServiceBean.log.info("----------------- parseMacromolecules ------------ "); - HashMap acronymToMacromolecule3VO = new HashMap(); - /** Store the name of the macromolecules **/ - HashSet macromoleculeAcronyms = new HashSet(); - for (HashMap sample : samples) { - if (sample.get("type").equals("Sample")) { - /** If not macromolecule is defined we use the code **/ - if (sample.get("macromolecule") == null) { - macromoleculeAcronyms.add(sample.get("code").trim()); - } else { - macromoleculeAcronyms.add(sample.get("macromolecule").trim()); - } - } - } - - for (String acronym : macromoleculeAcronyms) { - Macromolecule3VO macromoleculeExists = this.getMacromoleculeByAcronym(macromoleculesProposalList, acronym); - if (macromoleculeExists != null) { - acronymToMacromolecule3VO.put(acronym, macromoleculeExists); - } else { - Macromolecule3VO macromolecule = new Macromolecule3VO(); - macromolecule.setAcronym(acronym); - macromolecule.setName(acronym); - acronymToMacromolecule3VO.put(acronym, macromolecule); - } - } - return acronymToMacromolecule3VO; - } - - private String getSamplePositionKey(HashMap sample) { - return sample.get("plate") + "_" + sample.get("row") + "_" + sample.get("well"); - } - - /** - * Gets the specimens. - * - * @param samples - * the samples - * @param acronymToMacromolecule3VO - * the macromolecules - * @param bufferNameToBuffer3VO - * the buffers - * @param plateIndexToSamplePlate3VO - * the plates - * @return HashMap where String is bufferName for the buffers and position for the Samples - */ - private HashMap getSpecimens(ArrayList> samples, - HashMap acronymToMacromolecule3VO, - HashMap bufferNameToBuffer3VO, HashMap plateIndexToSamplePlate3VO) { - - HashMap specimenIdToSpecimen3VO = new HashMap(); - - /** Looking for positions **/ - for (HashMap sample : samples) { - // String positionCode = sample.get("plate") + "_" + sample.get("row") + "_" + sample.get("well"); - String positionCode = this.getSamplePositionKey(sample); - Specimen3VO specimen = null; - - if (specimenIdToSpecimen3VO.get(positionCode) == null) { - /** Creating new Sample for the experiment **/ - specimen = new Specimen3VO(); - /** Buffer **/ - Buffer3VO buffer = bufferNameToBuffer3VO.get(sample.get("buffername").trim()); - if (buffer == null) { - log.error("Buffer not found with buffer name: " + sample.get("buffername")); - } - specimen.setBufferId(buffer.getBufferId()); - - /** Macromolecule **/ - if (sample.get("type").equals("Sample")) { - Macromolecule3VO macromolecule3VO = acronymToMacromolecule3VO.get(sample.get("macromolecule")); - specimen.setMacromolecule3VO(macromolecule3VO); - } - - /** Position **/ - if (plateIndexToSamplePlate3VO != null) { - Sampleplate3VO plate = plateIndexToSamplePlate3VO.get(sample.get("plate")); - if (plate != null) { - Sampleplateposition3VO position = new Sampleplateposition3VO(); - position.setSamplePlateId(plate.getSamplePlateId()); - position.setRowNumber(Integer.parseInt(sample.get("row"))); - position.setColumnNumber(Integer.parseInt(sample.get("well"))); - position = entityManager.merge(position); - specimen.setSampleplateposition3VO(position); - } - } - /** Specimen properties **/ - specimen.setConcentration(sample.get("concentration")); - specimen.setVolume(sample.get("volume")); -// specimen.setCode(sample.get("macromolecule")); - } else { - /** Updating volume to load **/ - specimen = specimenIdToSpecimen3VO.get(positionCode); - specimen.setVolume(String.valueOf(Integer.parseInt(specimen.getVolume()) - + Integer.parseInt(sample.get("volume")))); - } - - /** it is a buffer we keep the code of the buffername **/ - if (specimen.getMacromolecule3VO() == null) { - specimenIdToSpecimen3VO.put(sample.get("buffername"), specimen); - } else { - specimenIdToSpecimen3VO.put(positionCode, specimen); - } - } - return specimenIdToSpecimen3VO; - } - - /** - * Gets the plates. This should be changed depending on the bm configuration - * - * @param samples - * the samples - * @param storageTemperature - * the storage temperature - * @return the plates - */ -// private HashMap parsePlates(ArrayList> samples, String storageTemperature) { -// /** There is always three Plates **/ -// HashMap platePositionToSamplePlate3VO = new HashMap(); -// -// /** Plate 1 **/ -// Platetype3VO type = this.plateType3Service.findById(1); -// Sampleplate3VO samplePlate_1 = new Sampleplate3VO(); -// samplePlate_1.setStorageTemperature(storageTemperature); -// samplePlate_1.setName(type.getName()); -// samplePlate_1.setSlotPositionRow("1"); -// samplePlate_1.setSlotPositionColumn("1"); -// samplePlate_1.setPlatetype3VO(type); -// platePositionToSamplePlate3VO.put("1", samplePlate_1); -// -// /** Plate 2 **/ -// Platetype3VO type_2 = this.plateType3Service.findById(2); -// Sampleplate3VO samplePlate_2 = new Sampleplate3VO(); -// samplePlate_2.setStorageTemperature(storageTemperature); -// samplePlate_2.setName(type_2.getName()); -// samplePlate_2.setPlatetype3VO(type_2); -// samplePlate_2.setSlotPositionRow("1"); -// samplePlate_2.setSlotPositionColumn("2"); -// platePositionToSamplePlate3VO.put("2", samplePlate_2); -// -// /** Plate 3 **/ -// Platetype3VO type_3 = this.plateType3Service.findById(4); -// Sampleplate3VO samplePlate_3 = new Sampleplate3VO(); -// samplePlate_3.setStorageTemperature(storageTemperature); -// samplePlate_3.setName(type_3.getName()); -// samplePlate_3.setSlotPositionRow("1"); -// samplePlate_3.setSlotPositionColumn("3"); -// samplePlate_3.setPlatetype3VO(type_3); -// platePositionToSamplePlate3VO.put("3", samplePlate_3); -// -// return platePositionToSamplePlate3VO; -// } - - /** - * Parses the specimen. - * - * @param sample - * the sample - * @return the specimen3 vo - */ - private Measurement3VO parseSpecimen(HashMap sample) { - String waittime = sample.get("waittime"); - - /** - * Problem is that from BsxCube there is not any parameters for volume, volume in this case means volumeToLoad - * however from WUI there are both for indicating in buffers specially the volume and the volumeToLoad - * **/ - String volumeToLoad = sample.get("volume"); - if (sample.containsKey("volumeToLoad")) { - volumeToLoad = sample.get("volumeToLoad"); - } - String comments = sample.get("comments"); - String transmission = sample.get("transmission"); - String viscosity = sample.get("viscosity"); - String flow = sample.get("flow"); - String code = sample.get("code"); - - Measurement3VO measurement = new Measurement3VO(); -// measurement.setCode(code); - measurement.setWaitTime(waittime); - measurement.setVolumeToLoad(volumeToLoad); - measurement.setComment(comments); - measurement.setTransmission(transmission); - measurement.setViscosity(viscosity); - measurement.setFlow(Boolean.valueOf(flow)); - - return measurement; - } - - /** - * Creates the measurements. - * - * @param samples - * the samples - * @param sample3vOs - * the sample3v os - * @param experiment - * the experiment - * @param buffers - * the buffers - * @param mode - * the mode - * @param extraFlowTime - * the extra flow time - * @return the list - * @throws Exception - * the exception - */ - public List createMeasurements(ArrayList> samples, - HashMap sample3vOs, Experiment3VO experiment, HashMap buffers, - String mode, String extraFlowTime) throws Exception { - List dataCollections = new ArrayList(); - - /** Creating for measurements **/ - for (HashMap sample : samples) { - String positionCode = sample.get("plate") + "_" + sample.get("row") + "_" + sample.get("well"); - if (sample.get("type").equals("Sample")) { - - Specimen3VO specimen = sample3vOs.get(positionCode); - String exposureTemperature = sample.get("SEUtemperature"); - Measurement3VO measurement = this.parseSpecimen(sample); - measurement.setSpecimenId(specimen.getSpecimenId()); - measurement.setExtraFlowTime(extraFlowTime); - measurement.setExposureTemperature(exposureTemperature); - -// try{ - /** Code should be runNumber otherwise set as acronym + concentration **/ -// if (sample.get("code") != null){ -// measurement.setCode(sample.get("code")); -// } -// else{ -// measurement.setCode(specimen.getMacromolecule3VO().getAcronym() + "_" + specimen.getConcentration()); -// } -// } -// catch(Exception exp){ -// exp.printStackTrace(); -// System.out.println("It has not been possible to set the code to the measurement"); -// } - - /** Buffer **/ - Specimen3VO buffer = sample3vOs.get(sample.get("buffername")); - - if (buffer == null) { - throw new Exception("Buffer not found: " + sample.get("buffername")); - } - - /** MODE: Before and After **/ - if (mode.equals("BeforeAndAfter")) { - for (HashMap sampleBuffer : samples) { - if (sampleBuffer.get("type").equals("Buffer")) { - if (sampleBuffer.get("buffername").equals(sample.get("buffername"))) { - - /** Measurement Before **/ - Measurement3VO measurementBufferBefore = this.parseSpecimen(sampleBuffer); - measurementBufferBefore.setSpecimenId(buffer.getSpecimenId()); - measurementBufferBefore.setExtraFlowTime(extraFlowTime); - measurementBufferBefore.setExposureTemperature(exposureTemperature); - - /** Copying parameters of the sample measurement **/ - /** Update, buffer's parameter may be different **/ - measurementBufferBefore.setVolumeToLoad(measurement.getVolumeToLoad()); - measurementBufferBefore.setTransmission(measurement.getTransmission()); - measurementBufferBefore.setFlow(measurement.getFlow()); - measurementBufferBefore.setViscosity(measurement.getViscosity()); - measurementBufferBefore.setWaitTime(measurement.getWaitTime()); - - /** But not exposure temperature **/ - measurementBufferBefore.setExposureTemperature(measurement.getExposureTemperature()); - - measurementBufferBefore = this.measurement3ServiceLocal.merge(measurementBufferBefore); - buffer.getMeasurements().add(measurementBufferBefore); - - /** Sample **/ - measurement = this.measurement3ServiceLocal.merge(measurement); - specimen.getMeasurements().add(measurement); - - /** After **/ - Measurement3VO specimenBufferAfter = this.parseSpecimen(sampleBuffer); - specimenBufferAfter.setSpecimenId(buffer.getSpecimenId()); - specimenBufferAfter.setExtraFlowTime(extraFlowTime); - specimenBufferAfter.setExposureTemperature(exposureTemperature); - /** Specimen After Code **/ - // specimenBufferAfter.setCode(experiment.getCodeSpecimen(buffer, specimenBufferAfter)); - - /** Copying parameters of the sample measurement **/ - specimenBufferAfter.setVolumeToLoad(measurement.getVolumeToLoad()); - specimenBufferAfter.setTransmission(measurement.getTransmission()); - specimenBufferAfter.setFlow(measurement.getFlow()); - specimenBufferAfter.setViscosity(measurement.getViscosity()); - specimenBufferAfter.setWaitTime(measurement.getWaitTime()); - - specimenBufferAfter.setExposureTemperature(measurement.getExposureTemperature()); - - specimenBufferAfter = this.measurement3ServiceLocal.merge(specimenBufferAfter); - buffer.getMeasurements().add(specimenBufferAfter); - - /** Creating Data Collections **/ - List dataCollectionSpecimens = new ArrayList(); - dataCollectionSpecimens.add(measurementBufferBefore); - dataCollectionSpecimens.add(measurement); - dataCollectionSpecimens.add(specimenBufferAfter); - dataCollections.add(this.createDataCollection(dataCollectionSpecimens, experiment)); - } - } - } - } - - if (mode.equals("After")) { - for (HashMap sampleBuffer : samples) { - if (sampleBuffer.get("type").equals("Buffer")) { - if (sampleBuffer.get("buffername").equals(sample.get("buffername"))) { - - /** Sample **/ - measurement = this.measurement3ServiceLocal.merge(measurement); - - /** After **/ - Measurement3VO measurementBufferAfter = this.parseSpecimen(sampleBuffer); - measurementBufferAfter.setSpecimenId(buffer.getSpecimenId()); - measurementBufferAfter.setExtraFlowTime(extraFlowTime); - measurementBufferAfter.setExposureTemperature(exposureTemperature); - - /** Specimen code **/ - // measurementBufferAfter.setCode(experiment.getCodeSpecimen(buffer, - // measurementBufferAfter)); - measurementBufferAfter = this.measurement3ServiceLocal.merge(measurementBufferAfter); - - /** Creating Data Collections **/ - List dataCollectionSpecimens = new ArrayList(); - dataCollectionSpecimens.add(measurement); - dataCollections.add(this.createDataCollection(dataCollectionSpecimens, experiment)); - } - } - } - } - - if (mode.equals("Before")) { - for (HashMap sampleBuffer : samples) { - if (sampleBuffer.get("type").equals("Buffer")) { - if (sampleBuffer.get("buffername").equals(sample.get("buffername"))) { - Measurement3VO specimenBufferBefore = this.parseSpecimen(sampleBuffer); - specimenBufferBefore.setSpecimenId(buffer.getSpecimenId()); - specimenBufferBefore.setExtraFlowTime(extraFlowTime); - specimenBufferBefore.setExposureTemperature(exposureTemperature); - - /** Specimen Before **/ - // specimenBufferBefore.setCode(experiment.getCodeSpecimen(buffer, - // specimenBufferBefore)); - specimenBufferBefore = this.measurement3ServiceLocal.merge(specimenBufferBefore); - buffer.getMeasurements().add(specimenBufferBefore); - - /** Sample **/ - measurement = this.measurement3ServiceLocal.merge(measurement); - specimen.getMeasurements().add(measurement); - - /** Creating Data Collections **/ - List dataCollectionSpecimens = new ArrayList(); - dataCollectionSpecimens.add(specimenBufferBefore); - dataCollectionSpecimens.add(measurement); - dataCollections.add(this.createDataCollection(dataCollectionSpecimens, experiment)); - } - } - } - } - - if (mode.equals("None")) { - /** Single sample with no data collection **/ - measurement = this.measurement3ServiceLocal.merge(measurement); - specimen.getMeasurements().add(measurement); - - } - } - } - return dataCollections; - } - - /** - * Creates the data collection. - * - * @param specimens - * the specimens - * @param experiment - * the experiment - * @return the saxs data collection3 vo - */ - private SaxsDataCollection3VO createDataCollection(List specimens, Experiment3VO experiment) { - SaxsDataCollection3VO dc = new SaxsDataCollection3VO(); - dc.setExperimentId(experiment.getExperimentId()); - dc = this.entityManager.merge(dc); - - int order = 1; - for (Measurement3VO specimen3vo : specimens) { - MeasurementTodataCollection3VO mc = new MeasurementTodataCollection3VO(); - mc.setDataCollectionId(dc.getDataCollectionId()); - mc.setMeasurementId(specimen3vo.getMeasurementId()); - mc.setDataCollectionOrder(order); - dc.getMeasurementtodatacollection3VOs().add(this.measurementToDataCollection3Service.merge(mc)); - order++; - - } - return dc; - } - - private Specimen3VO isAlreadyCreatedByPosition(Specimen3VO specimen, List specimens) { - if (specimen.getSampleplateposition3VO() != null) { - /** Checking for position of the specimen **/ - for (Specimen3VO existingSpecimen : specimens) { - if (existingSpecimen.getSampleplateposition3VO() != null) { - if (existingSpecimen.getSampleplateposition3VO().getSamplePlateId() - .equals(specimen.getSampleplateposition3VO().getSamplePlateId())) { - if (existingSpecimen.getSampleplateposition3VO().getColumnNumber() == specimen - .getSampleplateposition3VO().getColumnNumber()) { - if (existingSpecimen.getSampleplateposition3VO().getRowNumber() == specimen - .getSampleplateposition3VO().getRowNumber()) { - return existingSpecimen; - } - } - } - } - } - } - return null; - } - - private Experiment3VO createExperimentFromRobotParams(Experiment3VO experiment, - ArrayList> samples, int proposalId, String mode, String storageTemperature, - String extraFlowTime, Boolean optimize) throws Exception { - - try { - ArrayList bufferList = new ArrayList(); - HashMap bufferNameToBuffer3VO = parseBuffers(samples, proposalId); - HashMap bufferIdToBuffer3VO = new HashMap(); - for (String key : bufferNameToBuffer3VO.keySet()) { - Buffer3VO buffer3VO = bufferNameToBuffer3VO.get(key); - buffer3VO.setProposalId(proposalId); - buffer3VO = this.proposal3Service.merge(buffer3VO); - bufferNameToBuffer3VO.put(key, buffer3VO); - bufferIdToBuffer3VO.put(buffer3VO.getBufferId(), buffer3VO); - bufferList.add(buffer3VO); - } - - HashMap acronymToMacromolecule3VO = parseMacromolecules(samples, proposalId); - log.debug("----------------- MACROMOLECULES ------------"); - log.debug(acronymToMacromolecule3VO.toString()); - for (String key : acronymToMacromolecule3VO.keySet()) { - Macromolecule3VO macromolecule3VO = acronymToMacromolecule3VO.get(key); - macromolecule3VO.setProposalId(proposalId); - macromolecule3VO = this.proposal3Service.merge(macromolecule3VO); - acronymToMacromolecule3VO.put(key, macromolecule3VO); - } - - /** There is only one plate group **/ - PlateGroup3VO plateGroup = new PlateGroup3VO(); - plateGroup.setName("BsxCube Group 1"); - plateGroup.setStorageTemperature(storageTemperature); - plateGroup = this.samplePlate3Service.merge(plateGroup); - - /** Plate index is the position in the plate in the sample changer: 1,2,3 for bm29 **/ -// HashMap plateIndexToSamplePlate3VO = parsePlates(samples, storageTemperature); - HashMap plateIndexToSamplePlate3VO = getDefaultSampleChangerPlateconfiguration(storageTemperature); - System.out.println(new GsonBuilder().excludeFieldsWithModifiers(Modifier.PRIVATE).create().toJson(plateIndexToSamplePlate3VO)); - - /** Creating plates **/ - for (String key : plateIndexToSamplePlate3VO.keySet()) { - Sampleplate3VO plate = plateIndexToSamplePlate3VO.get(key); - plate.setExperimentId(experiment.getExperimentId()); - plate.setStorageTemperature(storageTemperature); - plate.setPlategroup3VO(plateGroup); - plate = this.samplePlate3Service.merge(plate); - plateIndexToSamplePlate3VO.put(key, plate); - experiment.getSamplePlate3VOs().add(plate); - } - - log.debug("----------------- buffers ------------"); - log.debug(bufferNameToBuffer3VO.toString()); - - log.debug("----------------- samples ------------"); - log.debug(samples.toString()); - - HashMap specimens = getSpecimens(samples, acronymToMacromolecule3VO, - bufferNameToBuffer3VO, plateIndexToSamplePlate3VO); - log.debug("----------------- specimens ------------"); - log.debug(specimens.toString()); - - HashMap sampleBuffersVOs = new HashMap(); - - List specimensCreated = new ArrayList(); - /** - * Key: For buffers is the buffer name For samples is the position - */ - for (String key : specimens.keySet()) { - Specimen3VO specimen = specimens.get(key); - if (specimen.getSampleplateposition3VO() != null) { - specimen.setSampleplateposition3VO(entityManager.merge(specimen.getSampleplateposition3VO())); - } - specimen.setExperimentId(experiment.getExperimentId()); - - /** - * Feature when samples contains macromolecule and buffername is the backgroundId Before doing the merge - * we have to check that this is not the case: BUFFERNAME PLATE ROW WELL BUFFER 1 1 1 1 BBSA 2 1 1 1 - * BBSA - * **/ - Specimen3VO existingSpecimenAtSamePosition = isAlreadyCreatedByPosition(specimen, specimensCreated); - if (existingSpecimenAtSamePosition == null) { - specimen = specimen3Service.merge(specimen); - specimensCreated.add(specimen); - experiment.getSamples().add(specimen); - } else { - specimen = existingSpecimenAtSamePosition; - } - - specimens.put(key, specimen); - if (specimen.getMacromolecule3VO() == null) { - sampleBuffersVOs.put(bufferIdToBuffer3VO.get(specimen.getBufferId()).getAcronym(), specimen); - } - } - - List dataCollectionList = createMeasurements(samples, specimens, experiment, - bufferNameToBuffer3VO, mode, extraFlowTime); - - /** Set the priorities but also optimize the buffers **/ - if (optimize) { - // measurement3ServiceLocal.optimizeAndPrioritize(experiment, dataCollections, 1); - measurement3ServiceLocal.resetAllPriorities(experiment, dataCollectionList); - measurement3ServiceLocal.optimizeDatacollectionByRemovingDuplicatedBuffers(experiment, - dataCollectionList, 1); - } - return experiment; - } catch (Exception e) { - throw e; - } - - } - - /** - * createExperimentFromRobotParams - * - * Create the macromolecule, buffer, plates, samples, measurement and executes the prioritizer in order to optimize - * the buffers duplicated When a data collection is: buffer1 sample1 buffer1 buffer1 sample2 buffer1 - * - * Because there are two buffer1 together the prioritizer will remove one like: buffer1 sample1 buffer1 sample2 - * buffer1 - * - * @param samples - * ArrayList> containing the hashmaps with all the values required to generate an - * experiment samples = "[{'code': 'Buff1', 'plate': '2', 'enable': True, 'title': 'P2-1:9', - * 'transmission': 20.0, 'viscosity': 'Low', 'recuperate': False, 'SEUtemperature': 4.0, 'flow': False, - * 'comments': 'test', 'volume': 20, 'buffername': 'testot', 'typen': 0, 'waittime': 0.0, - * 'concentration': 0.0, 'type': 'Buffer', 'well': '9', 'row': 1}] - * - * Coming form WUI we add a new parameter called volumeToLoad in order to distinguish both specially for - * buffer measurements - * - * @param proposalId - * the proposal id - * @param mode - * the mode: "BeforeAndAfter", "None", "Before" and "After" - * @param storageTemperature - * the storage temperature - * @param extraFlowTime - * the extra flow time - * @return the experiment3VO - * - * TODO: Mode should replaced by enumeration - */ - @Override - public Experiment3VO createExperimentFromRobotParams(ArrayList> samples, Integer sessionId, - int proposalId, String mode, String storageTemperature, String extraFlowTime, String type, - String sourceFilePath, String name, String comments) throws Exception { - return this.createExperimentFromRobotParams(samples, sessionId, proposalId, mode, storageTemperature, - extraFlowTime, type, sourceFilePath, name, true, comments); - } - - @Override - public Experiment3VO createExperimentFromRobotParams(ArrayList> samples, Integer sessionId, - int proposalId, String mode, String storageTemperature, String extraFlowTime, String type, - String sourceFilePath, String name, Boolean optimize, String comments) throws Exception { - - Experiment3VO experiment = new Experiment3VO(); - experiment.setType(type); - - experiment.setSourceFilePath(sourceFilePath); - experiment.setCreationDate(getNow()); - experiment.setName(name); - experiment.setProposalId(proposalId); - experiment.setSessionId(sessionId); - experiment.setComments(comments); - experiment = this.experiment3ServiceLocal.merge(experiment); - - if (sourceFilePath != null) { - /** Modifying the path if contains __ID__ then we replace __ID__ by the real id of the experiment **/ - experiment.setSourceFilePath(experiment.getSourceFilePath().replace("__ID__", - String.valueOf(experiment.getExperimentId()))); - experiment = this.experiment3ServiceLocal.merge(experiment); - } - - /** Triming all values **/ - for (HashMap hashMap : samples) { - for (String key : hashMap.keySet()) { - /** It may be null when creating template and plate = null **/ - if (hashMap.get(key) != null) { - hashMap.put(key, hashMap.get(key).trim()); - } - } - } - - /** Dealing with macromolecule **/ - for (HashMap hashMap : samples) { - if (!hashMap.containsKey("macromolecule")) { - hashMap.put("macromolecule", hashMap.get("code")); - } - } - - experiment = this.createExperimentFromRobotParams(experiment, samples, proposalId, mode, storageTemperature, - extraFlowTime, optimize); - return experiment; - } - - @Override - public Experiment3VO addMeasurementsToExperiment(int experimentId, int proposalId, - ArrayList> samples) throws Exception { - System.out.println("addMeasurementsToExperiment"); - this.log.info("addMeasurementsToExperiment"); -// Experiment3VO experiment = this.experiment3ServiceLocal.findById(experimentId, ExperimentScope.PREPARE_EXPERIMENT, proposalId); - Experiment3VO experiment = this.experiment3ServiceLocal.findById(experimentId, ExperimentScope.MINIMAL, proposalId); - System.out.println("PREPARE_EXPERIMENT"); - this.log.info("PREPARE_EXPERIMENT"); - /** Triming all values **/ - for (HashMap hashMap : samples) { - for (String key : hashMap.keySet()) { - /** It may be null when creating template and plate = null **/ - if (hashMap.get(key) != null) { - hashMap.put(key, hashMap.get(key).trim()); - } - } - } - - HashMap buffers = this.parseBuffers(samples, proposalId); - for (String key : buffers.keySet()) { - System.out.println(buffers.get(key)); - } - - HashMap macromolecules = this.parseMacromolecules(samples, proposalId); - for (String key : macromolecules.keySet()) { - System.out.println(macromolecules.get(key)); - } - - HashMap specimens = this.getSpecimens(samples, macromolecules, buffers); - for (String key : specimens.keySet()) { - System.out.println(specimens.get(key)); - } - - for (String key : specimens.keySet()) { - Specimen3VO sample = specimens.get(key); - sample.setExperimentId(experiment.getExperimentId()); - sample.setSampleplateposition3VO(null); - sample = specimen3Service.merge(sample); - experiment.getSamples().add(sample); - specimens.put(key, sample); - } - this.createMeasurements(samples, specimens, experiment, buffers, "BeforeAndAfter", "0"); - experiment = this.experiment3ServiceLocal.findById(experimentId, ExperimentScope.MEDIUM, proposalId); - return experiment; - } - - private HashMap getSpecimens(ArrayList> samples, - HashMap macromolecules, HashMap buffers) { - - HashMap sample3VOs = new HashMap(); - - /** Looking for positions **/ - for (HashMap sample : samples) { - String positionCode = sample.get("plate") + "_" + sample.get("row") + "_" + sample.get("well"); - Specimen3VO sample3VO = null; - - if (sample3VOs.get(positionCode) == null) { - /** Creating new Sample for the experiment **/ - sample3VO = new Specimen3VO(); - - /** Buffer **/ - Buffer3VO buffer = buffers.get(sample.get("buffername").trim()); - if (buffer == null) { - log.error("Buffer not found with buffer name: " + sample.get("buffername")); - } - sample3VO.setBufferId(buffer.getBufferId()); - - /** Macromolecule **/ - if (sample.get("type").equals("Sample")) { - Macromolecule3VO macromolecule3VO = macromolecules.get(sample.get("macromolecule")); - sample3VO.setMacromolecule3VO(macromolecule3VO); - } - - /** Sample properties **/ - sample3VO.setConcentration(sample.get("concentration")); - sample3VO.setVolume(sample.get("volume")); -// sample3VO.setCode(sample.get("macromolecule")); - - } else { - /** Updating volume to load **/ - sample3VO = sample3VOs.get(positionCode); - sample3VO.setVolume(String.valueOf(Integer.parseInt(sample3VO.getVolume()) - + Integer.parseInt(sample.get("volume")))); - } - - /** it is a buffer we keep the code of the buffername **/ - if (sample3VO.getMacromolecule3VO() == null) { - sample3VOs.put(sample.get("buffername"), sample3VO); - } else { - sample3VOs.put(positionCode, sample3VO); - } - - } - return sample3VOs; - } - - - /** - * Gets the plates. This should be changed depending on the bm configuration - * - * @param samples - * the samples - * @param storageTemperature - * the storage temperature - * @return the plates - */ - @Override - public HashMap getDefaultSampleChangerPlateconfiguration( String storageTemperature) { - /** There is always three Plates **/ - HashMap platePositionToSamplePlate3VO = new HashMap(); - - /** Plate 1 **/ - Platetype3VO type = this.plateType3Service.findById(1); - Sampleplate3VO samplePlate_1 = new Sampleplate3VO(); - samplePlate_1.setStorageTemperature(storageTemperature); - samplePlate_1.setName(type.getName()); - samplePlate_1.setSlotPositionRow("1"); - samplePlate_1.setSlotPositionColumn("1"); - samplePlate_1.setPlatetype3VO(type); - platePositionToSamplePlate3VO.put("1", samplePlate_1); - - /** Plate 2 **/ - Platetype3VO type_2 = this.plateType3Service.findById(2); - Sampleplate3VO samplePlate_2 = new Sampleplate3VO(); - samplePlate_2.setStorageTemperature(storageTemperature); - samplePlate_2.setName(type_2.getName()); - samplePlate_2.setPlatetype3VO(type_2); - samplePlate_2.setSlotPositionRow("1"); - samplePlate_2.setSlotPositionColumn("2"); - platePositionToSamplePlate3VO.put("2", samplePlate_2); - - /** Plate 3 **/ - Platetype3VO type_3 = this.plateType3Service.findById(4); - Sampleplate3VO samplePlate_3 = new Sampleplate3VO(); - samplePlate_3.setStorageTemperature(storageTemperature); - samplePlate_3.setName(type_3.getName()); - samplePlate_3.setSlotPositionRow("1"); - samplePlate_3.setSlotPositionColumn("3"); - samplePlate_3.setPlatetype3VO(type_3); - platePositionToSamplePlate3VO.put("3", samplePlate_3); - - /** At EMBL Layout is vertical instead of horizontal **/ - if (Constants.SITE_IS_EMBL()){ - samplePlate_1.setSlotPositionRow("1"); - samplePlate_1.setSlotPositionColumn("1"); - samplePlate_2.setSlotPositionRow("2"); - samplePlate_2.setSlotPositionColumn("1"); - samplePlate_3.setSlotPositionRow("3"); - samplePlate_3.setSlotPositionColumn("1"); - } - return platePositionToSamplePlate3VO; - } - - public ArrayList createOrUpdateMacromolecule(ArrayList> samples, int proposalId) throws Exception { - Robot3ServiceBean.log.info("createOrUpdateMacromolecule"); - - ArrayList macromoleculeList = new ArrayList(); - - /** Triming all values **/ - for (HashMap hashMap : samples) { - for (String key : hashMap.keySet()) { - /** It may be null when creating template and plate = null **/ - if (hashMap.get(key) != null) { - hashMap.put(key, hashMap.get(key).trim()); - } - } - } - - HashMap macromolecules = this.parseMacromolecules(samples, proposalId); - for (String key : macromolecules.keySet()) { - Robot3ServiceBean.log.info("createOrUpdateMacromolecule: " + macromolecules.get(key)); - } - - /** Macromolecule **/ - for (HashMap sample : samples) { - if (sample.get("type").equals("Sample")) { - Macromolecule3VO macromolecule3VO = macromolecules.get(sample.get("macromolecule")); - Robot3ServiceBean.log.info("createOrUpdateMacromolecule macromolecule.acronym = " + macromolecule3VO.getAcronym()); - if (macromolecule3VO != null) { - macromolecule3VO.setProposalId(proposalId); - macromolecule3VO = this.proposal3Service.merge(macromolecule3VO); - macromoleculeList.add(macromolecule3VO); - } - } - } - Robot3ServiceBean.log.info("createOrUpdateMacromolecule size = " + macromoleculeList.size()); - - return macromoleculeList; - } - - public ArrayList createOrUpdateBuffer(ArrayList> samples, int proposalId) throws Exception { - Robot3ServiceBean.log.info("createOrUpdateBuffer"); - - ArrayList bufferList = new ArrayList(); - - /** Triming all values **/ - for (HashMap hashMap : samples) { - for (String key : hashMap.keySet()) { - /** It may be null when creating template and plate = null **/ - if (hashMap.get(key) != null) { - hashMap.put(key, hashMap.get(key).trim()); - } - } - } - - HashMap buffers = this.parseBuffers(samples, proposalId); - for (String key : buffers.keySet()) { - Robot3ServiceBean.log.info("createOrUpdateBuffer: key= " + key + " | value= " + buffers.get(key)); - } - - /** Buffer **/ - for (HashMap sample : samples) { - Buffer3VO buffer3VO = buffers.get(sample.get("buffername").trim()); - if (buffer3VO == null) { - log.error("Buffer not found with buffer name: " + sample.get("buffername")); - } - - if (buffer3VO != null) { - buffer3VO.setProposalId(proposalId); - buffer3VO = this.proposal3Service.merge(buffer3VO); - bufferList.add(buffer3VO); - } - } - Robot3ServiceBean.log.info("createOrUpdateBuffer size = " + bufferList.size()); - - return bufferList; - } -} +/******************************************************************************* + * This file is part of ISPyB. + * + * ISPyB is free software: you can redistribute it and/or modify + * it under the terms of the GNU Lesser General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * ISPyB is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with ISPyB. If not, see . + * + * Contributors : S. Delageniere, R. Leal, L. Launer, K. Levik, S. Veyrier, P. Brenchereau, M. Bodin, A. De Maria Antolinos + ******************************************************************************************************************************/ + +package ispyb.server.biosaxs.services.core.robot; + +import java.lang.reflect.Modifier; +import java.util.ArrayList; +import java.util.Calendar; +import java.util.Date; +import java.util.GregorianCalendar; +import java.util.HashMap; +import java.util.HashSet; +import java.util.List; + +import javax.ejb.EJB; +import javax.ejb.Stateless; +import javax.persistence.EntityManager; +import javax.persistence.PersistenceContext; + +import org.apache.log4j.Logger; + +import com.google.gson.GsonBuilder; + +import ispyb.common.util.Constants; +import ispyb.server.biosaxs.services.core.ExperimentScope; +import ispyb.server.biosaxs.services.core.experiment.Experiment3ServiceLocal; +import ispyb.server.biosaxs.services.core.measurement.Measurement3ServiceLocal; +import ispyb.server.biosaxs.services.core.measurementToDataCollection.MeasurementToDatacollection3ServiceLocal; +import ispyb.server.biosaxs.services.core.plateType.PlateType3ServiceLocal; +import ispyb.server.biosaxs.services.core.proposal.SaxsProposal3ServiceLocal; +import ispyb.server.biosaxs.services.core.samplePlate.Sampleplate3ServiceLocal; +import ispyb.server.biosaxs.services.core.specimen.Specimen3Service; +import ispyb.server.biosaxs.vos.assembly.Macromolecule3VO; +import ispyb.server.biosaxs.vos.dataAcquisition.Buffer3VO; +import ispyb.server.biosaxs.vos.dataAcquisition.Experiment3VO; +import ispyb.server.biosaxs.vos.dataAcquisition.Measurement3VO; +import ispyb.server.biosaxs.vos.dataAcquisition.Specimen3VO; +import ispyb.server.biosaxs.vos.dataAcquisition.plate.PlateGroup3VO; +import ispyb.server.biosaxs.vos.dataAcquisition.plate.Platetype3VO; +import ispyb.server.biosaxs.vos.dataAcquisition.plate.Sampleplate3VO; +import ispyb.server.biosaxs.vos.dataAcquisition.plate.Sampleplateposition3VO; +import ispyb.server.biosaxs.vos.datacollection.MeasurementTodataCollection3VO; +import ispyb.server.biosaxs.vos.datacollection.SaxsDataCollection3VO; + +@Stateless +public class Robot3ServiceBean implements Robot3Service, Robot3ServiceLocal { + + private final static Logger log = Logger.getLogger(Robot3ServiceBean.class); + + /** The specimen3 service local. */ + @EJB + private Measurement3ServiceLocal measurement3ServiceLocal; + + /** The experiment3 service local. */ + @EJB + private Experiment3ServiceLocal experiment3ServiceLocal; + + /** The macromolecule3 service. */ + @EJB + private SaxsProposal3ServiceLocal proposal3Service; + + /** The sample plate3 service. */ + @EJB + private Sampleplate3ServiceLocal samplePlate3Service; + + /** The plate type3 service. */ + @EJB + private PlateType3ServiceLocal plateType3Service; + + /** The measurement to data collection3 service. */ + @EJB + private MeasurementToDatacollection3ServiceLocal measurementToDataCollection3Service; + + @EJB + private Specimen3Service specimen3Service; + + /** The entity manager. */ + @PersistenceContext(unitName = "ispyb_db") + private EntityManager entityManager; + + /** The now. */ + protected static Calendar NOW; + + /** + * Gets the now. + * + * @return the now + */ + private Date getNow() { + NOW = GregorianCalendar.getInstance(); + return NOW.getTime(); + } + + /** + * Gets the buffers. It returns a hashmap + * + * @param samples + * the samples + * @return the buffers + */ + private HashMap parseBuffers(ArrayList> samples, int proposalId) { + List buffersProposal = proposal3Service.findBuffersByProposalId(proposalId); + Robot3ServiceBean.log.info("----------------- parseBuffers ------------ "); + HashMap bufferNameToBuffer3VO = new HashMap(); + + /** Store the name of the macromolecules **/ + HashMap bufferNameToBufferAcronym = new HashMap(); + + /** + * It is possible that users make a mistake and for the same specimen in the same position they set a different + * buffer's name + */ + HashMap bufferPositionToBufferAcronym = new HashMap(); + + for (HashMap sample : samples) { + if (sample.get("type").equals("Buffer")) { + Buffer3VO buffer = new Buffer3VO(); + buffer.setName(sample.get("macromolecule").trim()); + buffer.setAcronym(sample.get("macromolecule").trim()); + buffer.setComment(sample.get("comments")); + + Robot3ServiceBean.log.info("sample: " + sample.toString()); + Robot3ServiceBean.log.info("buffername: " + sample.get("buffername")); + + String positionCode = this.getSamplePositionKey(sample); + if (bufferPositionToBufferAcronym.get(positionCode) == null) { + bufferNameToBufferAcronym.put(sample.get("buffername").trim(), sample.get("macromolecule").trim()); + bufferPositionToBufferAcronym.put(positionCode, sample.get("macromolecule").trim()); + } else { + Robot3ServiceBean.log.info("Buffers detected in the same position with different macromolecule name"); + log.warn("Buffers detected in the same position with different macromolecule name"); + bufferNameToBufferAcronym.put(sample.get("buffername").trim(), + bufferPositionToBufferAcronym.get(positionCode)); + } + } + } + + for (String bufferName : bufferNameToBufferAcronym.keySet()) { + Buffer3VO bufferExists = this + .getBufferByAcronym(buffersProposal, bufferNameToBufferAcronym.get(bufferName)); + if (bufferExists != null) { + bufferNameToBuffer3VO.put(bufferName, bufferExists); + } else { + Buffer3VO buffer = new Buffer3VO(); + buffer.setAcronym(bufferNameToBufferAcronym.get(bufferName)); + buffer.setName(bufferNameToBufferAcronym.get(bufferName)); + bufferNameToBuffer3VO.put(bufferName, buffer); + } + } + + return bufferNameToBuffer3VO; + } + + /** If the acronym exists in the list the macromolecule is returned **/ + private Macromolecule3VO getMacromoleculeByAcronym(List macromolecules, String acronym) { + for (Macromolecule3VO macromolecule : macromolecules) { + if (macromolecule.getAcronym().toLowerCase().equals(acronym.toLowerCase())) { + return macromolecule; + } + } + return null; + } + + /** If the acronym exists in the list the buffer is returned **/ + private Buffer3VO getBufferByAcronym(List buffers, String acronym) { + for (Buffer3VO buffer : buffers) { + if (buffer.getAcronym().toLowerCase().equals(acronym.toLowerCase())) { + return buffer; + } + } + return null; + } + + /** + * Gets the macromolecules. If there are two with the same name it means that they are the same macromolecules + * + * @param samples + * the samples + * @return the macromolecules + */ + private HashMap parseMacromolecules(ArrayList> samples, + int proposalId) { + List macromoleculesProposalList = proposal3Service.findMacromoleculesByProposalId(proposalId); + Robot3ServiceBean.log.info("----------------- parseMacromolecules ------------ "); + HashMap acronymToMacromolecule3VO = new HashMap(); + /** Store the name of the macromolecules **/ + HashSet macromoleculeAcronyms = new HashSet(); + for (HashMap sample : samples) { + if (sample.get("type").equals("Sample")) { + /** If not macromolecule is defined we use the code **/ + if (sample.get("macromolecule") == null) { + macromoleculeAcronyms.add(sample.get("code").trim()); + } else { + macromoleculeAcronyms.add(sample.get("macromolecule").trim()); + } + } + } + + for (String acronym : macromoleculeAcronyms) { + Macromolecule3VO macromoleculeExists = this.getMacromoleculeByAcronym(macromoleculesProposalList, acronym); + if (macromoleculeExists != null) { + acronymToMacromolecule3VO.put(acronym, macromoleculeExists); + } else { + Macromolecule3VO macromolecule = new Macromolecule3VO(); + macromolecule.setAcronym(acronym); + macromolecule.setName(acronym); + acronymToMacromolecule3VO.put(acronym, macromolecule); + } + } + return acronymToMacromolecule3VO; + } + + private String getSamplePositionKey(HashMap sample) { + return sample.get("plate") + "_" + sample.get("row") + "_" + sample.get("well"); + } + + /** + * Gets the specimens. + * + * @param samples + * the samples + * @param acronymToMacromolecule3VO + * the macromolecules + * @param bufferNameToBuffer3VO + * the buffers + * @param plateIndexToSamplePlate3VO + * the plates + * @return HashMap where String is bufferName for the buffers and position for the Samples + */ + private HashMap getSpecimens(ArrayList> samples, + HashMap acronymToMacromolecule3VO, + HashMap bufferNameToBuffer3VO, HashMap plateIndexToSamplePlate3VO) { + + HashMap specimenIdToSpecimen3VO = new HashMap(); + + /** Looking for positions **/ + for (HashMap sample : samples) { + // String positionCode = sample.get("plate") + "_" + sample.get("row") + "_" + sample.get("well"); + String positionCode = this.getSamplePositionKey(sample); + Specimen3VO specimen = null; + + if (specimenIdToSpecimen3VO.get(positionCode) == null) { + /** Creating new Sample for the experiment **/ + specimen = new Specimen3VO(); + /** Buffer **/ + Buffer3VO buffer = bufferNameToBuffer3VO.get(sample.get("buffername").trim()); + if (buffer == null) { + log.error("Buffer not found with buffer name: " + sample.get("buffername")); + } + specimen.setBufferId(buffer.getBufferId()); + + /** Macromolecule **/ + if (sample.get("type").equals("Sample")) { + Macromolecule3VO macromolecule3VO = acronymToMacromolecule3VO.get(sample.get("macromolecule")); + specimen.setMacromolecule3VO(macromolecule3VO); + } + + /** Position **/ + if (plateIndexToSamplePlate3VO != null) { + Sampleplate3VO plate = plateIndexToSamplePlate3VO.get(sample.get("plate")); + if (plate != null) { + Sampleplateposition3VO position = new Sampleplateposition3VO(); + position.setSamplePlateId(plate.getSamplePlateId()); + position.setRowNumber(Integer.parseInt(sample.get("row"))); + position.setColumnNumber(Integer.parseInt(sample.get("well"))); + position = entityManager.merge(position); + specimen.setSampleplateposition3VO(position); + } + } + /** Specimen properties **/ + specimen.setConcentration(sample.get("concentration")); + specimen.setVolume(sample.get("volume")); +// specimen.setCode(sample.get("macromolecule")); + } else { + /** Updating volume to load **/ + specimen = specimenIdToSpecimen3VO.get(positionCode); + specimen.setVolume(String.valueOf(Integer.parseInt(specimen.getVolume()) + + Integer.parseInt(sample.get("volume")))); + } + + /** it is a buffer we keep the code of the buffername **/ + if (specimen.getMacromolecule3VO() == null) { + specimenIdToSpecimen3VO.put(sample.get("buffername"), specimen); + } else { + specimenIdToSpecimen3VO.put(positionCode, specimen); + } + } + return specimenIdToSpecimen3VO; + } + + /** + * Gets the plates. This should be changed depending on the bm configuration + * + * @param samples + * the samples + * @param storageTemperature + * the storage temperature + * @return the plates + */ +// private HashMap parsePlates(ArrayList> samples, String storageTemperature) { +// /** There is always three Plates **/ +// HashMap platePositionToSamplePlate3VO = new HashMap(); +// +// /** Plate 1 **/ +// Platetype3VO type = this.plateType3Service.findById(1); +// Sampleplate3VO samplePlate_1 = new Sampleplate3VO(); +// samplePlate_1.setStorageTemperature(storageTemperature); +// samplePlate_1.setName(type.getName()); +// samplePlate_1.setSlotPositionRow("1"); +// samplePlate_1.setSlotPositionColumn("1"); +// samplePlate_1.setPlatetype3VO(type); +// platePositionToSamplePlate3VO.put("1", samplePlate_1); +// +// /** Plate 2 **/ +// Platetype3VO type_2 = this.plateType3Service.findById(2); +// Sampleplate3VO samplePlate_2 = new Sampleplate3VO(); +// samplePlate_2.setStorageTemperature(storageTemperature); +// samplePlate_2.setName(type_2.getName()); +// samplePlate_2.setPlatetype3VO(type_2); +// samplePlate_2.setSlotPositionRow("1"); +// samplePlate_2.setSlotPositionColumn("2"); +// platePositionToSamplePlate3VO.put("2", samplePlate_2); +// +// /** Plate 3 **/ +// Platetype3VO type_3 = this.plateType3Service.findById(4); +// Sampleplate3VO samplePlate_3 = new Sampleplate3VO(); +// samplePlate_3.setStorageTemperature(storageTemperature); +// samplePlate_3.setName(type_3.getName()); +// samplePlate_3.setSlotPositionRow("1"); +// samplePlate_3.setSlotPositionColumn("3"); +// samplePlate_3.setPlatetype3VO(type_3); +// platePositionToSamplePlate3VO.put("3", samplePlate_3); +// +// return platePositionToSamplePlate3VO; +// } + + /** + * Parses the specimen. + * + * @param sample + * the sample + * @return the specimen3 vo + */ + private Measurement3VO parseSpecimen(HashMap sample) { + String waittime = sample.get("waittime"); + + /** + * Problem is that from BsxCube there is not any parameters for volume, volume in this case means volumeToLoad + * however from WUI there are both for indicating in buffers specially the volume and the volumeToLoad + * **/ + String volumeToLoad = sample.get("volume"); + if (sample.containsKey("volumeToLoad")) { + volumeToLoad = sample.get("volumeToLoad"); + } + String comments = sample.get("comments"); + String transmission = sample.get("transmission"); + String viscosity = sample.get("viscosity"); + String flow = sample.get("flow"); + String code = sample.get("code"); + + Measurement3VO measurement = new Measurement3VO(); +// measurement.setCode(code); + measurement.setWaitTime(waittime); + measurement.setVolumeToLoad(volumeToLoad); + measurement.setComment(comments); + measurement.setTransmission(transmission); + measurement.setViscosity(viscosity); + measurement.setFlow(Boolean.valueOf(flow)); + + return measurement; + } + + /** + * Creates the measurements. + * + * @param samples + * the samples + * @param sample3vOs + * the sample3v os + * @param experiment + * the experiment + * @param buffers + * the buffers + * @param mode + * the mode + * @param extraFlowTime + * the extra flow time + * @return the list + * @throws Exception + * the exception + */ + public List createMeasurements(ArrayList> samples, + HashMap sample3vOs, Experiment3VO experiment, HashMap buffers, + String mode, String extraFlowTime) throws Exception { + List dataCollections = new ArrayList(); + + /** Creating for measurements **/ + for (HashMap sample : samples) { + String positionCode = sample.get("plate") + "_" + sample.get("row") + "_" + sample.get("well"); + if (sample.get("type").equals("Sample")) { + + Specimen3VO specimen = sample3vOs.get(positionCode); + String exposureTemperature = sample.get("SEUtemperature"); + Measurement3VO measurement = this.parseSpecimen(sample); + measurement.setSpecimenId(specimen.getSpecimenId()); + measurement.setExtraFlowTime(extraFlowTime); + measurement.setExposureTemperature(exposureTemperature); + +// try{ + /** Code should be runNumber otherwise set as acronym + concentration **/ +// if (sample.get("code") != null){ +// measurement.setCode(sample.get("code")); +// } +// else{ +// measurement.setCode(specimen.getMacromolecule3VO().getAcronym() + "_" + specimen.getConcentration()); +// } +// } +// catch(Exception exp){ +// exp.printStackTrace(); +// System.out.println("It has not been possible to set the code to the measurement"); +// } + + /** Buffer **/ + Specimen3VO buffer = sample3vOs.get(sample.get("buffername")); + + if (buffer == null) { + throw new Exception("Buffer not found: " + sample.get("buffername")); + } + + /** MODE: Before and After **/ + if (mode.equals("BeforeAndAfter")) { + for (HashMap sampleBuffer : samples) { + if (sampleBuffer.get("type").equals("Buffer")) { + if (sampleBuffer.get("buffername").equals(sample.get("buffername"))) { + + /** Measurement Before **/ + Measurement3VO measurementBufferBefore = this.parseSpecimen(sampleBuffer); + measurementBufferBefore.setSpecimenId(buffer.getSpecimenId()); + measurementBufferBefore.setExtraFlowTime(extraFlowTime); + measurementBufferBefore.setExposureTemperature(exposureTemperature); + + /** Copying parameters of the sample measurement **/ + /** Update, buffer's parameter may be different **/ + measurementBufferBefore.setVolumeToLoad(measurement.getVolumeToLoad()); + measurementBufferBefore.setTransmission(measurement.getTransmission()); + measurementBufferBefore.setFlow(measurement.getFlow()); + measurementBufferBefore.setViscosity(measurement.getViscosity()); + measurementBufferBefore.setWaitTime(measurement.getWaitTime()); + + /** But not exposure temperature **/ + measurementBufferBefore.setExposureTemperature(measurement.getExposureTemperature()); + + measurementBufferBefore = this.measurement3ServiceLocal.merge(measurementBufferBefore); + buffer.getMeasurements().add(measurementBufferBefore); + + /** Sample **/ + measurement = this.measurement3ServiceLocal.merge(measurement); + specimen.getMeasurements().add(measurement); + + /** After **/ + Measurement3VO specimenBufferAfter = this.parseSpecimen(sampleBuffer); + specimenBufferAfter.setSpecimenId(buffer.getSpecimenId()); + specimenBufferAfter.setExtraFlowTime(extraFlowTime); + specimenBufferAfter.setExposureTemperature(exposureTemperature); + /** Specimen After Code **/ + // specimenBufferAfter.setCode(experiment.getCodeSpecimen(buffer, specimenBufferAfter)); + + /** Copying parameters of the sample measurement **/ + specimenBufferAfter.setVolumeToLoad(measurement.getVolumeToLoad()); + specimenBufferAfter.setTransmission(measurement.getTransmission()); + specimenBufferAfter.setFlow(measurement.getFlow()); + specimenBufferAfter.setViscosity(measurement.getViscosity()); + specimenBufferAfter.setWaitTime(measurement.getWaitTime()); + + specimenBufferAfter.setExposureTemperature(measurement.getExposureTemperature()); + + specimenBufferAfter = this.measurement3ServiceLocal.merge(specimenBufferAfter); + buffer.getMeasurements().add(specimenBufferAfter); + + /** Creating Data Collections **/ + List dataCollectionSpecimens = new ArrayList(); + dataCollectionSpecimens.add(measurementBufferBefore); + dataCollectionSpecimens.add(measurement); + dataCollectionSpecimens.add(specimenBufferAfter); + dataCollections.add(this.createDataCollection(dataCollectionSpecimens, experiment)); + } + } + } + } + + if (mode.equals("After")) { + for (HashMap sampleBuffer : samples) { + if (sampleBuffer.get("type").equals("Buffer")) { + if (sampleBuffer.get("buffername").equals(sample.get("buffername"))) { + + /** Sample **/ + measurement = this.measurement3ServiceLocal.merge(measurement); + + /** After **/ + Measurement3VO measurementBufferAfter = this.parseSpecimen(sampleBuffer); + measurementBufferAfter.setSpecimenId(buffer.getSpecimenId()); + measurementBufferAfter.setExtraFlowTime(extraFlowTime); + measurementBufferAfter.setExposureTemperature(exposureTemperature); + + /** Specimen code **/ + // measurementBufferAfter.setCode(experiment.getCodeSpecimen(buffer, + // measurementBufferAfter)); + measurementBufferAfter = this.measurement3ServiceLocal.merge(measurementBufferAfter); + + /** Creating Data Collections **/ + List dataCollectionSpecimens = new ArrayList(); + dataCollectionSpecimens.add(measurement); + dataCollections.add(this.createDataCollection(dataCollectionSpecimens, experiment)); + } + } + } + } + + if (mode.equals("Before")) { + for (HashMap sampleBuffer : samples) { + if (sampleBuffer.get("type").equals("Buffer")) { + if (sampleBuffer.get("buffername").equals(sample.get("buffername"))) { + Measurement3VO specimenBufferBefore = this.parseSpecimen(sampleBuffer); + specimenBufferBefore.setSpecimenId(buffer.getSpecimenId()); + specimenBufferBefore.setExtraFlowTime(extraFlowTime); + specimenBufferBefore.setExposureTemperature(exposureTemperature); + + /** Specimen Before **/ + // specimenBufferBefore.setCode(experiment.getCodeSpecimen(buffer, + // specimenBufferBefore)); + specimenBufferBefore = this.measurement3ServiceLocal.merge(specimenBufferBefore); + buffer.getMeasurements().add(specimenBufferBefore); + + /** Sample **/ + measurement = this.measurement3ServiceLocal.merge(measurement); + specimen.getMeasurements().add(measurement); + + /** Creating Data Collections **/ + List dataCollectionSpecimens = new ArrayList(); + dataCollectionSpecimens.add(specimenBufferBefore); + dataCollectionSpecimens.add(measurement); + dataCollections.add(this.createDataCollection(dataCollectionSpecimens, experiment)); + } + } + } + } + + if (mode.equals("None")) { + /** Single sample with no data collection **/ + measurement = this.measurement3ServiceLocal.merge(measurement); + specimen.getMeasurements().add(measurement); + + } + } + } + return dataCollections; + } + + /** + * Creates the data collection. + * + * @param specimens + * the specimens + * @param experiment + * the experiment + * @return the saxs data collection3 vo + */ + private SaxsDataCollection3VO createDataCollection(List specimens, Experiment3VO experiment) { + SaxsDataCollection3VO dc = new SaxsDataCollection3VO(); + dc.setExperimentId(experiment.getExperimentId()); + dc = this.entityManager.merge(dc); + + int order = 1; + for (Measurement3VO specimen3vo : specimens) { + MeasurementTodataCollection3VO mc = new MeasurementTodataCollection3VO(); + mc.setDataCollectionId(dc.getDataCollectionId()); + mc.setMeasurementId(specimen3vo.getMeasurementId()); + mc.setDataCollectionOrder(order); + dc.getMeasurementtodatacollection3VOs().add(this.measurementToDataCollection3Service.merge(mc)); + order++; + + } + return dc; + } + + private Specimen3VO isAlreadyCreatedByPosition(Specimen3VO specimen, List specimens) { + if (specimen.getSampleplateposition3VO() != null) { + /** Checking for position of the specimen **/ + for (Specimen3VO existingSpecimen : specimens) { + if (existingSpecimen.getSampleplateposition3VO() != null) { + if (existingSpecimen.getSampleplateposition3VO().getSamplePlateId() + .equals(specimen.getSampleplateposition3VO().getSamplePlateId())) { + if (existingSpecimen.getSampleplateposition3VO().getColumnNumber() == specimen + .getSampleplateposition3VO().getColumnNumber()) { + if (existingSpecimen.getSampleplateposition3VO().getRowNumber() == specimen + .getSampleplateposition3VO().getRowNumber()) { + return existingSpecimen; + } + } + } + } + } + } + return null; + } + + private Experiment3VO createExperimentFromRobotParams(Experiment3VO experiment, + ArrayList> samples, int proposalId, String mode, String storageTemperature, + String extraFlowTime, Boolean optimize) throws Exception { + + try { + ArrayList bufferList = new ArrayList(); + HashMap bufferNameToBuffer3VO = parseBuffers(samples, proposalId); + HashMap bufferIdToBuffer3VO = new HashMap(); + for (String key : bufferNameToBuffer3VO.keySet()) { + Buffer3VO buffer3VO = bufferNameToBuffer3VO.get(key); + buffer3VO.setProposalId(proposalId); + buffer3VO = this.proposal3Service.merge(buffer3VO); + bufferNameToBuffer3VO.put(key, buffer3VO); + bufferIdToBuffer3VO.put(buffer3VO.getBufferId(), buffer3VO); + bufferList.add(buffer3VO); + } + + HashMap acronymToMacromolecule3VO = parseMacromolecules(samples, proposalId); + log.debug("----------------- MACROMOLECULES ------------"); + log.debug(acronymToMacromolecule3VO.toString()); + for (String key : acronymToMacromolecule3VO.keySet()) { + Macromolecule3VO macromolecule3VO = acronymToMacromolecule3VO.get(key); + macromolecule3VO.setProposalId(proposalId); + macromolecule3VO = this.proposal3Service.merge(macromolecule3VO); + acronymToMacromolecule3VO.put(key, macromolecule3VO); + } + + /** There is only one plate group **/ + PlateGroup3VO plateGroup = new PlateGroup3VO(); + plateGroup.setName("BsxCube Group 1"); + plateGroup.setStorageTemperature(storageTemperature); + plateGroup = this.samplePlate3Service.merge(plateGroup); + + /** Plate index is the position in the plate in the sample changer: 1,2,3 for bm29 **/ +// HashMap plateIndexToSamplePlate3VO = parsePlates(samples, storageTemperature); + HashMap plateIndexToSamplePlate3VO = getDefaultSampleChangerPlateconfiguration(storageTemperature); + System.out.println(new GsonBuilder().excludeFieldsWithModifiers(Modifier.PRIVATE).create().toJson(plateIndexToSamplePlate3VO)); + + /** Creating plates **/ + for (String key : plateIndexToSamplePlate3VO.keySet()) { + Sampleplate3VO plate = plateIndexToSamplePlate3VO.get(key); + plate.setExperimentId(experiment.getExperimentId()); + plate.setStorageTemperature(storageTemperature); + plate.setPlategroup3VO(plateGroup); + plate = this.samplePlate3Service.merge(plate); + plateIndexToSamplePlate3VO.put(key, plate); + experiment.getSamplePlate3VOs().add(plate); + } + + log.debug("----------------- buffers ------------"); + log.debug(bufferNameToBuffer3VO.toString()); + + log.debug("----------------- samples ------------"); + log.debug(samples.toString()); + + HashMap specimens = getSpecimens(samples, acronymToMacromolecule3VO, + bufferNameToBuffer3VO, plateIndexToSamplePlate3VO); + log.debug("----------------- specimens ------------"); + log.debug(specimens.toString()); + + HashMap sampleBuffersVOs = new HashMap(); + + List specimensCreated = new ArrayList(); + /** + * Key: For buffers is the buffer name For samples is the position + */ + for (String key : specimens.keySet()) { + Specimen3VO specimen = specimens.get(key); + if (specimen.getSampleplateposition3VO() != null) { + specimen.setSampleplateposition3VO(entityManager.merge(specimen.getSampleplateposition3VO())); + } + specimen.setExperimentId(experiment.getExperimentId()); + + /** + * Feature when samples contains macromolecule and buffername is the backgroundId Before doing the merge + * we have to check that this is not the case: BUFFERNAME PLATE ROW WELL BUFFER 1 1 1 1 BBSA 2 1 1 1 + * BBSA + * **/ + Specimen3VO existingSpecimenAtSamePosition = isAlreadyCreatedByPosition(specimen, specimensCreated); + if (existingSpecimenAtSamePosition == null) { + specimen = specimen3Service.merge(specimen); + specimensCreated.add(specimen); + experiment.getSamples().add(specimen); + } else { + specimen = existingSpecimenAtSamePosition; + } + + specimens.put(key, specimen); + if (specimen.getMacromolecule3VO() == null) { + sampleBuffersVOs.put(bufferIdToBuffer3VO.get(specimen.getBufferId()).getAcronym(), specimen); + } + } + + List dataCollectionList = createMeasurements(samples, specimens, experiment, + bufferNameToBuffer3VO, mode, extraFlowTime); + + /** Set the priorities but also optimize the buffers **/ + if (optimize) { + // measurement3ServiceLocal.optimizeAndPrioritize(experiment, dataCollections, 1); + measurement3ServiceLocal.resetAllPriorities(experiment, dataCollectionList); + measurement3ServiceLocal.optimizeDatacollectionByRemovingDuplicatedBuffers(experiment, + dataCollectionList, 1); + } + return experiment; + } catch (Exception e) { + throw e; + } + + } + + /** + * createExperimentFromRobotParams + * + * Create the macromolecule, buffer, plates, samples, measurement and executes the prioritizer in order to optimize + * the buffers duplicated When a data collection is: buffer1 sample1 buffer1 buffer1 sample2 buffer1 + * + * Because there are two buffer1 together the prioritizer will remove one like: buffer1 sample1 buffer1 sample2 + * buffer1 + * + * @param samples + * ArrayList> containing the hashmaps with all the values required to generate an + * experiment samples = "[{'code': 'Buff1', 'plate': '2', 'enable': True, 'title': 'P2-1:9', + * 'transmission': 20.0, 'viscosity': 'Low', 'recuperate': False, 'SEUtemperature': 4.0, 'flow': False, + * 'comments': 'test', 'volume': 20, 'buffername': 'testot', 'typen': 0, 'waittime': 0.0, + * 'concentration': 0.0, 'type': 'Buffer', 'well': '9', 'row': 1}] + * + * Coming form WUI we add a new parameter called volumeToLoad in order to distinguish both specially for + * buffer measurements + * + * @param proposalId + * the proposal id + * @param mode + * the mode: "BeforeAndAfter", "None", "Before" and "After" + * @param storageTemperature + * the storage temperature + * @param extraFlowTime + * the extra flow time + * @return the experiment3VO + * + * TODO: Mode should replaced by enumeration + */ + @Override + public Experiment3VO createExperimentFromRobotParams(ArrayList> samples, Integer sessionId, + int proposalId, String mode, String storageTemperature, String extraFlowTime, String type, + String sourceFilePath, String name, String comments) throws Exception { + return this.createExperimentFromRobotParams(samples, sessionId, proposalId, mode, storageTemperature, + extraFlowTime, type, sourceFilePath, name, true, comments); + } + + @Override + public Experiment3VO createExperimentFromRobotParams(ArrayList> samples, Integer sessionId, + int proposalId, String mode, String storageTemperature, String extraFlowTime, String type, + String sourceFilePath, String name, Boolean optimize, String comments) throws Exception { + + Experiment3VO experiment = new Experiment3VO(); + experiment = this.experiment3ServiceLocal.initPlates(experiment); + experiment.setType(type); + experiment.setSourceFilePath(sourceFilePath); + experiment.setCreationDate(getNow()); + experiment.setName(name); + experiment.setProposalId(proposalId); + experiment.setSessionId(sessionId); + experiment.setComments(comments); + experiment = this.experiment3ServiceLocal.merge(experiment); + + if (sourceFilePath != null) { + /** Modifying the path if contains __ID__ then we replace __ID__ by the real id of the experiment **/ + experiment.setSourceFilePath(experiment.getSourceFilePath().replace("__ID__", + String.valueOf(experiment.getExperimentId()))); + experiment = this.experiment3ServiceLocal.merge(experiment); + } + + /** Triming all values **/ + for (HashMap hashMap : samples) { + for (String key : hashMap.keySet()) { + /** It may be null when creating template and plate = null **/ + if (hashMap.get(key) != null) { + hashMap.put(key, hashMap.get(key).trim()); + } + } + } + + /** Dealing with macromolecule **/ + for (HashMap hashMap : samples) { + if (!hashMap.containsKey("macromolecule")) { + hashMap.put("macromolecule", hashMap.get("code")); + } + } + + experiment = this.createExperimentFromRobotParams(experiment, samples, proposalId, mode, storageTemperature, + extraFlowTime, optimize); + return experiment; + } + + @Override + public Experiment3VO addMeasurementsToExperiment(int experimentId, int proposalId, + ArrayList> samples) throws Exception { + System.out.println("addMeasurementsToExperiment"); + this.log.info("addMeasurementsToExperiment"); +// Experiment3VO experiment = this.experiment3ServiceLocal.findById(experimentId, ExperimentScope.PREPARE_EXPERIMENT, proposalId); + Experiment3VO experiment = this.experiment3ServiceLocal.findById(experimentId, ExperimentScope.MINIMAL, proposalId); + System.out.println("PREPARE_EXPERIMENT"); + this.log.info("PREPARE_EXPERIMENT"); + /** Triming all values **/ + for (HashMap hashMap : samples) { + for (String key : hashMap.keySet()) { + /** It may be null when creating template and plate = null **/ + if (hashMap.get(key) != null) { + hashMap.put(key, hashMap.get(key).trim()); + } + } + } + + HashMap buffers = this.parseBuffers(samples, proposalId); + for (String key : buffers.keySet()) { + System.out.println(buffers.get(key)); + } + + HashMap macromolecules = this.parseMacromolecules(samples, proposalId); + for (String key : macromolecules.keySet()) { + System.out.println(macromolecules.get(key)); + } + + HashMap specimens = this.getSpecimens(samples, macromolecules, buffers); + for (String key : specimens.keySet()) { + System.out.println(specimens.get(key)); + } + + for (String key : specimens.keySet()) { + Specimen3VO sample = specimens.get(key); + sample.setExperimentId(experiment.getExperimentId()); + sample.setSampleplateposition3VO(null); + sample = specimen3Service.merge(sample); + experiment.getSamples().add(sample); + specimens.put(key, sample); + } + this.createMeasurements(samples, specimens, experiment, buffers, "BeforeAndAfter", "0"); + experiment = this.experiment3ServiceLocal.findById(experimentId, ExperimentScope.MEDIUM, proposalId); + return experiment; + } + + private HashMap getSpecimens(ArrayList> samples, + HashMap macromolecules, HashMap buffers) { + + HashMap sample3VOs = new HashMap(); + + /** Looking for positions **/ + for (HashMap sample : samples) { + String positionCode = sample.get("plate") + "_" + sample.get("row") + "_" + sample.get("well"); + Specimen3VO sample3VO = null; + + if (sample3VOs.get(positionCode) == null) { + /** Creating new Sample for the experiment **/ + sample3VO = new Specimen3VO(); + + /** Buffer **/ + Buffer3VO buffer = buffers.get(sample.get("buffername").trim()); + if (buffer == null) { + log.error("Buffer not found with buffer name: " + sample.get("buffername")); + } + sample3VO.setBufferId(buffer.getBufferId()); + + /** Macromolecule **/ + if (sample.get("type").equals("Sample")) { + Macromolecule3VO macromolecule3VO = macromolecules.get(sample.get("macromolecule")); + sample3VO.setMacromolecule3VO(macromolecule3VO); + } + + /** Sample properties **/ + sample3VO.setConcentration(sample.get("concentration")); + sample3VO.setVolume(sample.get("volume")); +// sample3VO.setCode(sample.get("macromolecule")); + + } else { + /** Updating volume to load **/ + sample3VO = sample3VOs.get(positionCode); + sample3VO.setVolume(String.valueOf(Integer.parseInt(sample3VO.getVolume()) + + Integer.parseInt(sample.get("volume")))); + } + + /** it is a buffer we keep the code of the buffername **/ + if (sample3VO.getMacromolecule3VO() == null) { + sample3VOs.put(sample.get("buffername"), sample3VO); + } else { + sample3VOs.put(positionCode, sample3VO); + } + + } + return sample3VOs; + } + + + /** + * Gets the plates. This should be changed depending on the bm configuration + * + * @param samples + * the samples + * @param storageTemperature + * the storage temperature + * @return the plates + */ + @Override + public HashMap getDefaultSampleChangerPlateconfiguration( String storageTemperature) { + /** There is always three Plates **/ + HashMap platePositionToSamplePlate3VO = new HashMap(); + + /** Plate 1 **/ + Platetype3VO type = this.plateType3Service.findById(1); + Sampleplate3VO samplePlate_1 = new Sampleplate3VO(); + samplePlate_1.setStorageTemperature(storageTemperature); + samplePlate_1.setName(type.getName()); + samplePlate_1.setSlotPositionRow("1"); + samplePlate_1.setSlotPositionColumn("1"); + samplePlate_1.setPlatetype3VO(type); + platePositionToSamplePlate3VO.put("1", samplePlate_1); + + /** Plate 2 **/ + Platetype3VO type_2 = this.plateType3Service.findById(2); + Sampleplate3VO samplePlate_2 = new Sampleplate3VO(); + samplePlate_2.setStorageTemperature(storageTemperature); + samplePlate_2.setName(type_2.getName()); + samplePlate_2.setPlatetype3VO(type_2); + samplePlate_2.setSlotPositionRow("1"); + samplePlate_2.setSlotPositionColumn("2"); + platePositionToSamplePlate3VO.put("2", samplePlate_2); + + /** Plate 3 **/ + Platetype3VO type_3 = this.plateType3Service.findById(4); + Sampleplate3VO samplePlate_3 = new Sampleplate3VO(); + samplePlate_3.setStorageTemperature(storageTemperature); + samplePlate_3.setName(type_3.getName()); + samplePlate_3.setSlotPositionRow("1"); + samplePlate_3.setSlotPositionColumn("3"); + samplePlate_3.setPlatetype3VO(type_3); + platePositionToSamplePlate3VO.put("3", samplePlate_3); + + /** At EMBL Layout is vertical instead of horizontal **/ + if (Constants.SITE_IS_EMBL()){ + samplePlate_1.setSlotPositionRow("1"); + samplePlate_1.setSlotPositionColumn("1"); + samplePlate_2.setSlotPositionRow("2"); + samplePlate_2.setSlotPositionColumn("1"); + samplePlate_3.setSlotPositionRow("3"); + samplePlate_3.setSlotPositionColumn("1"); + } + return platePositionToSamplePlate3VO; + } + + public ArrayList createOrUpdateMacromolecule(ArrayList> samples, int proposalId) throws Exception { + Robot3ServiceBean.log.info("createOrUpdateMacromolecule"); + + ArrayList macromoleculeList = new ArrayList(); + + /** Triming all values **/ + for (HashMap hashMap : samples) { + for (String key : hashMap.keySet()) { + /** It may be null when creating template and plate = null **/ + if (hashMap.get(key) != null) { + hashMap.put(key, hashMap.get(key).trim()); + } + } + } + + HashMap macromolecules = this.parseMacromolecules(samples, proposalId); + for (String key : macromolecules.keySet()) { + Robot3ServiceBean.log.info("createOrUpdateMacromolecule: " + macromolecules.get(key)); + } + + /** Macromolecule **/ + for (HashMap sample : samples) { + if (sample.get("type").equals("Sample")) { + Macromolecule3VO macromolecule3VO = macromolecules.get(sample.get("macromolecule")); + Robot3ServiceBean.log.info("createOrUpdateMacromolecule macromolecule.acronym = " + macromolecule3VO.getAcronym()); + if (macromolecule3VO != null) { + macromolecule3VO.setProposalId(proposalId); + macromolecule3VO = this.proposal3Service.merge(macromolecule3VO); + macromoleculeList.add(macromolecule3VO); + } + } + } + Robot3ServiceBean.log.info("createOrUpdateMacromolecule size = " + macromoleculeList.size()); + + return macromoleculeList; + } + + public ArrayList createOrUpdateBuffer(ArrayList> samples, int proposalId) throws Exception { + Robot3ServiceBean.log.info("createOrUpdateBuffer"); + + ArrayList bufferList = new ArrayList(); + + /** Triming all values **/ + for (HashMap hashMap : samples) { + for (String key : hashMap.keySet()) { + /** It may be null when creating template and plate = null **/ + if (hashMap.get(key) != null) { + hashMap.put(key, hashMap.get(key).trim()); + } + } + } + + HashMap buffers = this.parseBuffers(samples, proposalId); + for (String key : buffers.keySet()) { + Robot3ServiceBean.log.info("createOrUpdateBuffer: key= " + key + " | value= " + buffers.get(key)); + } + + /** Buffer **/ + for (HashMap sample : samples) { + Buffer3VO buffer3VO = buffers.get(sample.get("buffername").trim()); + if (buffer3VO == null) { + log.error("Buffer not found with buffer name: " + sample.get("buffername")); + } + + if (buffer3VO != null) { + buffer3VO.setProposalId(proposalId); + buffer3VO = this.proposal3Service.merge(buffer3VO); + bufferList.add(buffer3VO); + } + } + Robot3ServiceBean.log.info("createOrUpdateBuffer size = " + bufferList.size()); + + return bufferList; + } +} diff --git a/ispyb-ejb/src/main/java/ispyb/server/biosaxs/services/webservice/ATSASPipeline3ServiceBean.java b/ispyb-ejb/src/main/java/ispyb/server/biosaxs/services/webservice/ATSASPipeline3ServiceBean.java index 702368ff6..63ce622a9 100644 --- a/ispyb-ejb/src/main/java/ispyb/server/biosaxs/services/webservice/ATSASPipeline3ServiceBean.java +++ b/ispyb-ejb/src/main/java/ispyb/server/biosaxs/services/webservice/ATSASPipeline3ServiceBean.java @@ -1,1049 +1,1050 @@ -/******************************************************************************* - * This file is part of ISPyB. - * - * ISPyB is free software: you can redistribute it and/or modify - * it under the terms of the GNU Lesser General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * ISPyB is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public License - * along with ISPyB. If not, see . - * - * Contributors : S. Delageniere, R. Leal, L. Launer, K. Levik, S. Veyrier, P. Brenchereau, M. Bodin, A. De Maria Antolinos - ******************************************************************************************************************************/ - -package ispyb.server.biosaxs.services.webservice; - -import ispyb.common.util.Constants; -import ispyb.server.biosaxs.services.core.ExperimentScope; -import ispyb.server.biosaxs.services.core.analysis.abInitioModelling.AbInitioModelling3Service; -import ispyb.server.biosaxs.services.core.analysis.advanced.AdvancedAnalysis3Service; -import ispyb.server.biosaxs.services.core.analysis.primaryDataProcessing.PrimaryDataProcessing3Service; -import ispyb.server.biosaxs.services.core.experiment.Experiment3Service; -import ispyb.server.biosaxs.services.core.measurement.Measurement3Service; -import ispyb.server.biosaxs.services.core.measurementToDataCollection.MeasurementToDataCollection3Service; -import ispyb.server.biosaxs.services.core.proposal.SaxsProposal3Service; -import ispyb.server.biosaxs.services.core.robot.Robot3Service; -import ispyb.server.biosaxs.services.core.samplePlate.Sampleplate3Service; -import ispyb.server.biosaxs.services.core.specimen.Specimen3Service; -import ispyb.server.biosaxs.vos.advanced.FitStructureToExperimentalData3VO; -import ispyb.server.biosaxs.vos.advanced.MixtureToStructure; -import ispyb.server.biosaxs.vos.advanced.RigidBodyModeling3VO; -import ispyb.server.biosaxs.vos.advanced.Superposition3VO; -import ispyb.server.biosaxs.vos.assembly.Macromolecule3VO; -import ispyb.server.biosaxs.vos.assembly.Structure3VO; -import ispyb.server.biosaxs.vos.dataAcquisition.Buffer3VO; -import ispyb.server.biosaxs.vos.dataAcquisition.Experiment3VO; -import ispyb.server.biosaxs.vos.dataAcquisition.Measurement3VO; -import ispyb.server.biosaxs.vos.dataAcquisition.Specimen3VO; -import ispyb.server.biosaxs.vos.dataAcquisition.plate.PlateGroup3VO; -import ispyb.server.biosaxs.vos.dataAcquisition.plate.Sampleplate3VO; -import ispyb.server.biosaxs.vos.dataAcquisition.plate.Sampleplateposition3VO; -import ispyb.server.biosaxs.vos.datacollection.Framelist3VO; -import ispyb.server.biosaxs.vos.datacollection.MeasurementTodataCollection3VO; -import ispyb.server.biosaxs.vos.datacollection.Merge3VO; -import ispyb.server.biosaxs.vos.datacollection.Model3VO; -import ispyb.server.biosaxs.vos.datacollection.SaxsDataCollection3VO; -import ispyb.server.biosaxs.vos.datacollection.Subtraction3VO; -import ispyb.server.common.services.proposals.Proposal3Service; -import ispyb.server.common.services.sessions.Session3Service; -import ispyb.server.common.util.LoggerFormatter; -import ispyb.server.common.vos.proposals.Proposal3VO; -import ispyb.server.common.vos.proposals.ProposalWS3VO; -import ispyb.server.mx.vos.collections.Session3VO; -import ispyb.server.mx.vos.collections.SessionWS3VO; - -import java.io.File; -import java.lang.reflect.Type; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.Calendar; -import java.util.Date; -import java.util.GregorianCalendar; -import java.util.HashMap; -import java.util.HashSet; -import java.util.Iterator; -import java.util.List; -import java.util.Set; - -import javax.ejb.EJB; -import javax.ejb.Stateless; -import javax.persistence.EntityManager; -import javax.persistence.PersistenceContext; - -import org.apache.log4j.Logger; - -import com.google.gson.Gson; -import com.google.gson.JsonElement; -import com.google.gson.reflect.TypeToken; - -@Stateless -public class ATSASPipeline3ServiceBean implements ATSASPipeline3Service, DesySampleChangerConnectorServiceLocal { - private final static Logger LOG = Logger.getLogger("ATSASPipeline3ServiceBean"); - - /** The entity manager. */ - @PersistenceContext(unitName = "ispyb_db") - private EntityManager entityManager; - - @EJB - private Proposal3Service proposalService; - - @EJB - private SaxsProposal3Service saxsProposal3Service; - - @EJB - private AbInitioModelling3Service AbInitioModelling3Service; - - @EJB - private Experiment3Service experiment3Service; - - @EJB - private Measurement3Service measurement3Service; - - @EJB - private Specimen3Service specimen3Service; - - @EJB - private Sampleplate3Service sampleplate3Service; - - @EJB - private Robot3Service robot3Service; - - @EJB - private MeasurementToDataCollection3Service measurementToDataCollection3Service; - - @EJB - private PrimaryDataProcessing3Service primaryDataProcessing3Service; - - @EJB - private AdvancedAnalysis3Service advancedAnalysis3Service; - - private long now; - - @EJB - private Session3Service sessionService; - - /** The now. */ - protected static Calendar NOW; - - private Date getNow(){ - NOW = GregorianCalendar.getInstance(); - return NOW.getTime(); - } - - private Integer getSessionIdForExperiment(ProposalWS3VO proposal) throws Exception { - Calendar cal = Calendar.getInstance(); - Date today = cal.getTime(); - cal.add(Calendar.HOUR_OF_DAY, 24); - // by default the session created contains 3 shifts of 8hours each. - Date endTime = cal.getTime(); - - Integer sessionId = null; - - SessionWS3VO[] sessionTab = sessionService.findForWSByProposalCodeAndNumber(proposal.getCode(), - proposal.getNumber(), Constants.getSAXSBeamline()); - - if (sessionTab == null || sessionTab.length == 0) { - // No session found we have to create one to attach the experiment data to it - Session3VO ses = new Session3VO(); - ses.setBeamlineName(Constants.getSAXSBeamline()); - ses.setProposalVO(proposalService.findByPk(proposal.getProposalId())); - ses.setStartDate(today); - ses.setEndDate(endTime); - ses.setComments("session created by ISPyBB"); - ses.setScheduled((byte) 0); - ses.setNbShifts(3); - ses.setUsedFlag((byte) 1); - ses.setTimeStamp(today); - ses.setLastUpdate(endTime); - ses = sessionService.create(ses); - sessionId = ses.getSessionId(); - } else { - sessionId = sessionTab[0].getSessionId(); - } - - return sessionId; - } - - @Override - public Experiment3VO createEmptyExperiment(String proposalCode, String proposalNumber, String name) throws Exception { - ProposalWS3VO proposal = proposalService.findForWSByCodeAndNumber(proposalCode, proposalNumber); - - Experiment3VO experiment = new Experiment3VO(); - experiment.setName(name); - experiment.setType("STATIC"); - try{ - experiment.setSessionId(getSessionIdForExperiment(proposal)); - } - catch(Exception exp){ - /** Non-blocking exception **/ - exp.printStackTrace(); - } - experiment.setCreationDate(GregorianCalendar.getInstance().getTime()); - - - experiment.setProposalId(proposal.getProposalId()); - experiment = this.experiment3Service.merge(experiment); - HashMap plates = robot3Service.getDefaultSampleChangerPlateconfiguration("20"); - - PlateGroup3VO plateGroup = new PlateGroup3VO(); - plateGroup.setStorageTemperature("20"); - plateGroup = sampleplate3Service.merge(plateGroup); - - for (String key : plates.keySet()) { - Sampleplate3VO plate = plates.get(key); - plate.setExperimentId(experiment.getExperimentId()); - plate.setPlategroup3VO(plateGroup); - plate = sampleplate3Service.merge(plate); - sampleplate3Service.merge(plate); - } - - /** Creating a session **/ - Integer sessionId = null; - - - return experiment; - } - - @Override - public Measurement3VO appendMeasurementToExperiment(String experimentId, - String runNumber, String type, String plate, String row, String well, String name, String bufferName, - String concentration, String sEUtemperature, String viscosity, String volume, String volumeToLoad, String waitTime, String transmission, String comments) { - - // return experiment3Service.appendMeasurementToExperiment(experimentId, - // runNumber, type, plate, row, well, name, bufferName, concentration, - // sEUtemperature, viscosity, volume, volumeToLoad, waitTime, - // transmission, comments); - Experiment3VO experiment = experiment3Service.findById(Integer.parseInt(experimentId), ExperimentScope.MEDIUM); - System.out.println("Getting Experiment:" + experiment.getExperimentId()); - System.out.println("NAME:" + name); - System.out.println("proposal:" + experiment.getProposalId()); - - List macromolecules = new ArrayList(); - try { - List macromoleculeList = saxsProposal3Service.findMacromoleculesBy(name, experiment.getProposalId()); - System.out.println(macromoleculeList); - if (macromoleculeList != null) { - for (Macromolecule3VO macromolecule3vo : macromoleculeList) { - if (macromolecule3vo.getAcronym() != null) { - if (macromolecule3vo.getAcronym().toLowerCase().trim().equals(name.toLowerCase().trim())) { - macromolecules.add(macromolecule3vo); - System.out.println("Found"); - } - } - } - } - } catch (Exception e) { - e.printStackTrace(); - macromolecules = new ArrayList(); - } - - Specimen3VO specimen = new Specimen3VO(); - - /** - * - * We don't check location of the specimen for ATSAS - * http://forge.epn-campus.eu/issues/2095 - * - */ - Set plates = experiment.getSamplePlate3VOs(); - - - - - specimen.setConcentration(concentration); - if (type.toUpperCase().equals("SAMPLE")) { - Macromolecule3VO macromolecule = null; - if (macromolecules.size() == 0) { - if (name == null) { - name = ""; - } - Macromolecule3VO m = new Macromolecule3VO(experiment.getProposalId(), name, name, ""); - m.setCreationDate(GregorianCalendar.getInstance().getTime()); - macromolecule = entityManager.merge(m); - } else { - macromolecule = macromolecules.get(0); - } - specimen.setMacromolecule3VO(macromolecule); - } - - List buffers = saxsProposal3Service.findBuffersByProposalId(experiment.getProposalId()); - for (Buffer3VO buffer3vo : buffers) { - if (buffer3vo.getAcronym() != null) { - if (buffer3vo.getAcronym().equals(bufferName)) { - specimen.setBufferId(buffer3vo.getBufferId()); - } - } - } - /** If buffer not found **/ - if (specimen.getBufferId() == null) { - Buffer3VO buffer3VO = new Buffer3VO(); - if (bufferName == null) { - bufferName = ""; - } - buffer3VO.setAcronym(bufferName); - buffer3VO.setName(bufferName); - buffer3VO.setProposalId(experiment.getProposalId()); - buffer3VO = entityManager.merge(buffer3VO); - specimen.setBufferId(buffer3VO.getBufferId()); - } - - /** Sample plate position **/ - LOG.info("getSampleplateposition3VO: " + specimen.getSampleplateposition3VO()); - LOG.info("plates: " + plates.size()); - if (specimen.getSampleplateposition3VO() == null) { - /** this specimen is new because has no position **/ - for (Sampleplate3VO samplePlate : plates) { - if (samplePlate.getSlotPositionColumn().equals(plate)) { - Sampleplateposition3VO position = new Sampleplateposition3VO(); - position.setColumnNumber(Integer.parseInt(well)); - position.setRowNumber(Integer.parseInt(row)); - position.setSamplePlateId(samplePlate.getSamplePlateId()); - position = entityManager.merge(position); - specimen.setSampleplateposition3VO(position); - } - } - } - - specimen.setExperimentId(experiment.getExperimentId()); - specimen.setVolume(volume); - - specimen = entityManager.merge(specimen); - - Measurement3VO measurement = new Measurement3VO(); - measurement.setCode(runNumber); - measurement.setSpecimenId(specimen.getSpecimenId()); - measurement.setExposureTemperature(sEUtemperature); - measurement.setTransmission(transmission); - measurement.setComment(comments); - measurement.setViscosity(viscosity); - measurement.setVolumeToLoad(volumeToLoad); - measurement.setWaitTime(waitTime); - measurement.setPriority(experiment.getMeasurements().size() + 1); - measurement = entityManager.merge(measurement); - return measurement; - } - - public void updateAverage(int measurementId, int averagedCount, int framesCount, String oneDimensionalDataFilePathArray, String discardedCurves, String averageFilePath) { - List curveList = Arrays.asList(oneDimensionalDataFilePathArray.split(",")); - List mergeList = this.primaryDataProcessing3Service.findByMeasurementId(measurementId); - if (mergeList != null){ - if (mergeList.size() > 0){ - Merge3VO merge = mergeList.get(0); - if (Integer.parseInt(merge.getFramesCount()) >= framesCount){ - LOG.info("Same number of frames count. No update"); - return; - } - else{ - this.primaryDataProcessing3Service.addMerge(measurementId, averagedCount, framesCount, oneDimensionalDataFilePathArray, null, averageFilePath); - } - } - } - } - - @Override - public void addAveraged(String measurementId, String averaged, String discarded, String averageFile) { - - Type listType = new TypeToken>>() { - }.getType(); - List> averageFrames = new Gson().fromJson(averaged, listType); - List> discardeFrames = new Gson().fromJson(discarded, listType); - - - ArrayList oneDimensionalFiles = new ArrayList(); - LOG.info("########### Averaged Frames ############# "); - for (HashMap frame : averageFrames) { - if (frame.containsKey("filePath")) { - oneDimensionalFiles.add(frame.get("filePath")); - LOG.info("\t" + frame.get("filePath")); - } - } - - LOG.info("########### Discarded Frames ############# "); - for (HashMap frame : discardeFrames) { - if (frame.containsKey("filePath")) { - oneDimensionalFiles.add(frame.get("filePath")); - LOG.info("\t" + frame.get("filePath")); - } - } - - /** Does it contains already a average **/ - List merges = primaryDataProcessing3Service.findByMeasurementId(Integer.parseInt(measurementId)); - LOG.info("------ Number of Averages by measurementId --------"); - LOG.info(merges.size()); - - if (merges.size() == 0) { - LOG.info("\t Creating a new average"); - /** Not any average found so we create a new one **/ - this.primaryDataProcessing3Service.addMerge(Integer.parseInt(measurementId), averageFrames.size(), oneDimensionalFiles.size(), - oneDimensionalFiles.toString().replace("[", "").replace("]", ""), null, averageFile); - } else { - LOG.info("\t Updating a new average"); - /** It is an update of the average **/ - - this.updateAverage(Integer.parseInt(measurementId), averageFrames.size(), oneDimensionalFiles.size(), - oneDimensionalFiles.toString().replace("[", "").replace("]", ""), null, averageFile); - - } - } - -// private void removeFrameListById(int frameListId) { -// Framelist3VO frameList = this.entityManager.find(Framelist3VO.class, frameListId); -// /** Looking for FrameToListObjects **/ -// -// String query = "select f from Frametolist3VO f where f.frameListId=:frameListId"; -// Query EJBQuery = this.entityManager.createQuery(query).setParameter("frameListId", frameListId); -// List frameToListList = (List)EJBQuery.getResultList(); -// for (Frametolist3VO frametolist3vo : frameToListList) { -// System.out.println("Found " + frametolist3vo.getFrameToListId()); -// } -// -// } - - /** - * True if a datacollection contains all the measurementIds otherwise false - * - * @param dataCollection - * @param measurementIds - * @return - */ - private Boolean containsSameMeasurements(SaxsDataCollection3VO dataCollection, List measurementIds) { - Iterator mIterator = dataCollection.getMeasurementtodatacollection3VOs().iterator(); - HashSet measurementDataCollectionSet = new HashSet(); - while (mIterator.hasNext()) { - MeasurementTodataCollection3VO measurementToDataCollection = mIterator.next(); - measurementDataCollectionSet.add(measurementToDataCollection.getMeasurementId()); - } - for (Integer measurementId : measurementIds) { - if (!measurementDataCollectionSet.contains(measurementId)) { - return false; - } - } - return true; - } - - private SaxsDataCollection3VO getDataCollectionByMeasurementsId(Experiment3VO experiment, List measurementIds) { - Iterator iterator = experiment.getDataCollections().iterator(); - while (iterator.hasNext()) { - SaxsDataCollection3VO dataCollection = iterator.next(); - if (this.containsSameMeasurements(dataCollection, measurementIds)) { - /** - * Returning the existing one - */ - return dataCollection; - } - } - return null; - } - /** - * Returns the measurement id corresponding to a sample or null if all measurementIds are buffers - * @param experiment - * @param measurementIds - * @return - */ - private Integer getSampleFromMeasurementList(Experiment3VO experiment, List measurementIds) { - for (Integer measurementId : measurementIds) { - Specimen3VO specimen = experiment.getSampleById(experiment.getMeasurementById(measurementId).getSpecimenId()); - if (specimen.getMacromolecule3VO() != null){ - return measurementId; - } - } - return null; - } - - /** - * return a existing datacollection if found containing the same - * measurements or create a new one - * - * @param experiment - * @param measurementIds - * @return - */ - private SaxsDataCollection3VO getSaxsDataCollectionByMeasurementIds(Experiment3VO experiment, List measurementIds) { -// SaxsDataCollection3VO datacollection = this.getDataCollectionByMeasurementsId(experiment, measurementIds); - SaxsDataCollection3VO datacollection = null; - LOG.info("Getting data collection"); - LOG.info("Getting data collection: " + measurementIds.toString()); - Integer sampleMeasurementId = this.getSampleFromMeasurementList(experiment, measurementIds); - LOG.info("sampleMeasurementId: " + sampleMeasurementId); - if (sampleMeasurementId == null){ - datacollection = this.getDataCollectionByMeasurementsId(experiment, measurementIds); - } - else{ - /** Look for a subtraction already containing this sample **/ - datacollection = experiment.getDataCollectionByMeasurementId(sampleMeasurementId); - - if (datacollection != null){ - /** Adding extra measurements **/ - Set measurementToDatacollectionList = datacollection.getMeasurementtodatacollection3VOs(); - Set measurementKeys = new HashSet(); - for (MeasurementTodataCollection3VO measurementToDatacollection : measurementToDatacollectionList) { - measurementKeys.add(measurementToDatacollection.getMeasurementId()); - } - LOG.info("measurementKeys:" + measurementKeys.toString()); - for (Integer measurementId : measurementIds) { - LOG.info("measurementKeys:" + measurementId + " " + measurementKeys.toString()); - if(!measurementKeys.contains(measurementId)){ - /** This measurement does not belong to the data collection yet **/ - MeasurementTodataCollection3VO measurementToDataCollection = new MeasurementTodataCollection3VO(); - measurementToDataCollection.setDataCollectionId(datacollection.getDataCollectionId()); - measurementToDataCollection.setMeasurementId(measurementId); - measurementToDataCollection.setDataCollectionOrder(datacollection.getMeasurementtodatacollection3VOs().size() + 1); - LOG.info("setDataCollectionOrder:" + datacollection.getMeasurementtodatacollection3VOs().size() + 1); - this.entityManager.merge(measurementToDataCollection); - } - } - } - } - - if (datacollection != null) { - return datacollection; - } else { - /** We create a new one **/ - SaxsDataCollection3VO dataCollection = new SaxsDataCollection3VO(); - dataCollection.setExperimentId(experiment.getExperimentId()); - dataCollection = entityManager.merge(dataCollection); - int dataCollectionOrder = 1; - for (Integer measurementId : measurementIds) { - MeasurementTodataCollection3VO measurementToDataCollection = new MeasurementTodataCollection3VO(); - measurementToDataCollection.setDataCollectionId(dataCollection.getDataCollectionId()); - measurementToDataCollection.setMeasurementId(measurementId); - measurementToDataCollection.setDataCollectionOrder(dataCollectionOrder); - this.entityManager.merge(measurementToDataCollection); - dataCollectionOrder++; - } - return dataCollection; - } - } - - private Framelist3VO createFrames(List sampleOneDimensionalFilesList){ - if (sampleOneDimensionalFilesList.size() > 0){ - return this.primaryDataProcessing3Service.addFrameList(sampleOneDimensionalFilesList); - } - return null; - } - - private void addSubtraction(Integer dataCollectionId, String rgStdev, String i0, String i0Stdev, String firstPointUsed, - String lastPointUsed, String quality, String isagregated, String rgGuinier, String rgGnom, String dmax, String total, - String volume, String sampleOneDimensionalFiles, String bufferOneDimensionalFiles, String sampleAverageFilePath, - String bestBufferFilePath, String subtractedFilePath, String experimentalDataPlotFilePath, String densityPlotFilePath, - String guinierPlotFilePath, String kratkyPlotFilePath, String gnomOutputFilePath, Subtraction3VO subtraction) { - - HashMap params = new HashMap(); - - long start = this.logInit("addSubtraction_CP_3.1", new Gson().toJson(params)); - - /** Getting the frames **/ - Type typeOfHash = new TypeToken>>() {}.getType(); - List> sampleOneDimensionalFilesListObject = new Gson().fromJson(sampleOneDimensionalFiles, typeOfHash); - List> bufferOneDimensionalFilesListObject = new Gson().fromJson(bufferOneDimensionalFiles, typeOfHash); - - List sampleOneDimensionalFilesList = new ArrayList(); - List bufferOneDimensionalFilesList = new ArrayList(); - - for (HashMap fileObject : sampleOneDimensionalFilesListObject) { - if (fileObject.get("filePath")!= null){ - sampleOneDimensionalFilesList.add(fileObject.get("filePath")); - } - } - - for (HashMap fileObject : bufferOneDimensionalFilesListObject) { - if (fileObject.get("filePath")!= null){ - bufferOneDimensionalFilesList.add(fileObject.get("filePath")); - } - } - - LOG.info(sampleOneDimensionalFilesList); - Framelist3VO sampleFiles = this.createFrames(sampleOneDimensionalFilesList); - this.logFinish("addSubtraction_CP_3.1", start); - - start = this.logInit("addSubtraction_CP_3.2", new Gson().toJson(params)); - Framelist3VO bufferFiles = this.createFrames(bufferOneDimensionalFilesList); - this.logFinish("addSubtraction_CP_3.2", start); - - - start = this.logInit("addSubtraction_CP_3.3", new Gson().toJson(params)); - subtraction.setDataCollectionId(dataCollectionId); - subtraction.setRg(rgGuinier); - subtraction.setRgStdev(rgStdev); - subtraction.setI0(i0); - subtraction.setI0stdev(i0Stdev); - subtraction.setFirstPointUsed(firstPointUsed); - subtraction.setLastPointUsed(lastPointUsed); - subtraction.setQuality(quality); - subtraction.setIsagregated(isagregated); - subtraction.setGnomFilePath(densityPlotFilePath); - subtraction.setRgGuinier(rgGuinier); - subtraction.setRgGnom(rgGnom); - subtraction.setDmax(dmax); - subtraction.setTotal(total); - subtraction.setVolume(volume); - subtraction.setKratkyFilePath(kratkyPlotFilePath); - subtraction.setScatteringFilePath(experimentalDataPlotFilePath); - subtraction.setGuinierFilePath(guinierPlotFilePath); - subtraction.setSubstractedFilePath(subtractedFilePath); - subtraction.setGnomFilePathOutput(gnomOutputFilePath); - subtraction.setCreationTime(getNow()); - - if (sampleFiles != null){ - subtraction.setSampleOneDimensionalFiles(sampleFiles); - } - if (bufferFiles != null){ - subtraction.setBufferOneDimensionalFiles(bufferFiles); - } - subtraction.setSampleAverageFilePath(sampleAverageFilePath); - subtraction.setBufferAverageFilePath(bestBufferFilePath); - - this.entityManager.merge(subtraction); - this.logFinish("addSubtraction_CP_3.3", start); - - } - - private void addSubtraction(int dataCollectionId, String rgStdev, String i0, String i0Stdev, String firstPointUsed, - String lastPointUsed, String quality, String isagregated, String rgGuinier, String rgGnom, String dmax, String total, - String volume, String sampleOneDimensionalFiles, String bufferOneDimensionalFiles, String sampleAverageFilePath, - String bestBufferFilePath, String subtractedFilePath, String experimentalDataPlotFilePath, String densityPlotFilePath, - String guinierPlotFilePath, String kratkyPlotFilePath, String gnomOutputFilePath) { - - Subtraction3VO subtraction = new Subtraction3VO(); - this.addSubtraction(dataCollectionId, rgStdev, i0, i0Stdev, firstPointUsed, lastPointUsed, quality, isagregated, rgGuinier, rgGnom, dmax, total, volume, sampleOneDimensionalFiles, bufferOneDimensionalFiles, sampleAverageFilePath, bestBufferFilePath, subtractedFilePath, experimentalDataPlotFilePath, densityPlotFilePath, guinierPlotFilePath, kratkyPlotFilePath, gnomOutputFilePath, subtraction); - - } - - - @Override - public void addSubtraction(String sampleMeasurementId, String rgStdev, String i0, String i0Stdev, String firstPointUsed, - String lastPointUsed, String quality, String isagregated, String rgGuinier, String rgGnom, String dmax, String total, - String volume, String sampleOneDimensionalFiles, String bufferOneDimensionalFiles, String sampleAverageFilePath, - String bestBufferFilePath, String subtractedFilePath, String experimentalDataPlotFilePath, String densityPlotFilePath, - String guinierPlotFilePath, String kratkyPlotFilePath, String gnomOutputFilePath) { - - - - HashMap params = new HashMap(); - long start = this.logInit("addSubtraction_CP_1", new Gson().toJson(params)); - if (sampleMeasurementId != null){ - // TODO: To be changed, performace problems!!! - Experiment3VO experiment = experiment3Service.findByMeasurementId(Integer.parseInt(sampleMeasurementId)); - this.logFinish("addSubtraction_CP_1", start); - - - if (experiment != null) { - start = this.logInit("addSubtraction_CP_2", new Gson().toJson(params)); - int dataCollectionId = experiment.getDataCollectionByMeasurementId(Integer.parseInt(sampleMeasurementId)).getDataCollectionId(); - this.logFinish("addSubtraction_CP_2", start); - - - start = this.logInit("addSubtraction_CP_3", new Gson().toJson(params)); - this.addSubtraction(dataCollectionId, rgStdev, i0, i0Stdev, firstPointUsed, lastPointUsed, quality, isagregated, rgGuinier, rgGnom, dmax, total, volume, sampleOneDimensionalFiles, bufferOneDimensionalFiles, sampleAverageFilePath, bestBufferFilePath, subtractedFilePath, experimentalDataPlotFilePath, densityPlotFilePath, guinierPlotFilePath, kratkyPlotFilePath, gnomOutputFilePath); - this.logFinish("addSubtraction_CP_3", start); - - } - } - } - - - /** - * Adds a new subtraction to several measurements To note: there are not any data collection yet - */ - public void addSubtraction( - String experimentId, - String runNumberList, - String rgStdev, - String i0, - String i0Stdev, - String firstPointUsed, - String lastPointUsed, - String quality, - String isagregated, - String rgGuinier, - String rgGnom, - String dmax, - String total, - String volume, - String sampleOneDimensionalFiles, - String bufferOneDimensionalFiles, - String sampleAverageFilePath, - String bestBufferFilePath, - String subtractedFilePath, - String experimentalDataPlotFilePath, - String densityPlotFilePath, - String guinierPlotFilePath, - String kratkyPlotFilePath, - String gnomOutputFilePath) throws Exception { - - Type typeOfList = new TypeToken>() {}.getType(); - List ids = new Gson().fromJson(runNumberList, typeOfList); - - /** Finding measurement by experimentId and run number **/ - List measurementIds = new ArrayList(); - for (String runNumber : ids) { - Measurement3VO measurement = measurement3Service.findMeasurementByCode(Integer.parseInt(experimentId), runNumber.toString()); - if (measurement != null) { - measurementIds.add(measurement.getMeasurementId()); - } else { - throw new Exception("No measurement found for runNumber: " + runNumber + " and experimentId: " + experimentId); - } - } - - System.out.println("Adding data collection and subtraction"); - - /** Adding data collection and subtraction **/ - if (measurementIds != null) { - if (measurementIds.size() > 0) { - Experiment3VO experiment = experiment3Service.findById(Integer.parseInt(experimentId), ExperimentScope.MEDIUM); - if (experiment != null) { - /** This method creates the data collection if it does not exist yet **/ - SaxsDataCollection3VO dataCollection = getSaxsDataCollectionByMeasurementIds(experiment, measurementIds); - - if (dataCollection.getSubstraction3VOs().size() == 0){ - this.addSubtraction(dataCollection.getDataCollectionId(), rgStdev, i0, i0Stdev, firstPointUsed, lastPointUsed, quality, isagregated, rgGuinier, rgGnom, dmax, total, volume, sampleOneDimensionalFiles, bufferOneDimensionalFiles, sampleAverageFilePath, bestBufferFilePath, subtractedFilePath, experimentalDataPlotFilePath, densityPlotFilePath, guinierPlotFilePath, kratkyPlotFilePath, gnomOutputFilePath); - } - else{ - /** - * Upgrading subtraction - */ - Subtraction3VO subtraction = (Subtraction3VO) Arrays.asList(dataCollection.getSubstraction3VOs().toArray()).get(0); - this.addSubtraction(dataCollection.getDataCollectionId(), rgStdev, i0, i0Stdev, firstPointUsed, lastPointUsed, quality, isagregated, rgGuinier, rgGnom, dmax, total, volume, sampleOneDimensionalFiles, bufferOneDimensionalFiles, sampleAverageFilePath, bestBufferFilePath, subtractedFilePath, experimentalDataPlotFilePath, densityPlotFilePath, guinierPlotFilePath, kratkyPlotFilePath, gnomOutputFilePath, subtraction); - } - } - } - } - } - - - - @Override - public void addAbinitioModelling(String experimentId, String runNumber, - ArrayList models3vo, Model3VO referenceModel, - Model3VO refinedModel) throws Exception { - - Measurement3VO measurement = measurement3Service.findMeasurementByCode(Integer.parseInt(experimentId), (runNumber)); - if (measurement != null){ - ArrayList measurementIds = new ArrayList(); - measurementIds.add(measurement.getMeasurementId()); - AbInitioModelling3Service.addAbinitioModeling(measurementIds, - models3vo, - referenceModel, - refinedModel); - - } - else{ - throw new Exception("No measurement found for " + experimentId + " and " + runNumber); - } - } - - @Override - public Model3VO getModel(String experimentId, String runNumber, String pdbfilepath) throws Exception { - Measurement3VO measurement = measurement3Service.findMeasurementByCode(Integer.parseInt(experimentId), (runNumber)); - if (measurement != null){ - return AbInitioModelling3Service.getModel(measurement.getMeasurementId(), pdbfilepath); - } - else{ - throw new Exception("Not measurement found for " + experimentId + " and " + runNumber); - } - } - - @Override - public Model3VO merge(Model3VO model) { - return this.entityManager.merge(model); - } - - @Override - public List getMacromoleculeByAcronym(String proposal, String acronym) { - List proposal3VOs = this.proposalService.findProposalByLoginName(proposal); - if (proposal3VOs != null){ - if (proposal3VOs.size() > 0){ - Proposal3VO proposal3VO = proposal3VOs.get(0); - List macromolecules = this.saxsProposal3Service.findMacromoleculesBy(acronym, proposal3VO.getProposalId()); - return macromolecules; - } - } - return new ArrayList(); - } - - public List getSubtractionByCode(String experimentId, String runNumber) { - Measurement3VO measurement = measurement3Service.findMeasurementByCode(Integer.valueOf(experimentId), runNumber); - System.out.println("measurement " + measurement); - if (measurement != null){ - return primaryDataProcessing3Service.getSubstractionsByMeasurementId(measurement.getMeasurementId()); - } - System.out.println("measurement not found "); - return null; - } - - public Macromolecule3VO getMacromoleculeByCode(String experimentId, String runNumber) { - Measurement3VO measurement = measurement3Service.findMeasurementByCode(Integer.valueOf(experimentId), runNumber); - if (measurement != null){ - Specimen3VO specimen = entityManager.find(Specimen3VO.class, measurement.getSpecimenId()); - if (specimen != null){ - return saxsProposal3Service.findMacromoleculesById(specimen.getMacromolecule3VO().getMacromoleculeId()); -// return experiment3Service.findMacromoleculeById(specimen.getMacromolecule3VO().getMacromoleculeId()); - } - } - return null; - } - - /** - * - * @param experimentId - * @param runNumber - * @param filePath {filePath:"/filepath.dat"} - * @return - */ - public Structure3VO getStructuresByCode(String experimentId, String runNumber, String filePath) { - Macromolecule3VO macromolecule = this.getMacromoleculeByCode(experimentId, runNumber); - for (Structure3VO structure : macromolecule.getStructure3VOs()) { - if (structure.getFilePath().trim().equals(filePath.trim())){ - return structure; - } - } - - return null; - } - - @Override - public void addMixture(String experimentId, String runNumber, String fitFilePath, String pdb) throws Exception { - List subtractions = this.getSubtractionByCode(experimentId, runNumber); - System.out.println("+++addMixture " + experimentId + " " + runNumber); - if (subtractions != null){ - if (subtractions.size() > 0){ - /** Getting last one are they should come by order **/ - Subtraction3VO subtraction = subtractions.get(subtractions.size() - 1); - - System.out.println("+++Subtraction Found"); - /** Getting Structure **/ - - Type ListType = new TypeToken>>() {}.getType(); - - /** Reading pdbs **/ - List> pdbFilePath = new Gson().fromJson(pdb, ListType); - - List mixtures = new ArrayList(); - if (pdbFilePath.size() > 0){ - for (HashMap pdbHash : pdbFilePath) { - MixtureToStructure mixture = new MixtureToStructure(); - - if (pdbHash.containsKey("filePath")){ - /** Finding the structue linked to such filePath */ - Structure3VO structure = this.getStructuresByCode(experimentId, runNumber, pdbHash.get("filePath")); - /** If structure does not exist we create a new one **/ - if (structure == null){ - structure = new Structure3VO(); - Macromolecule3VO macromolecule = this.getMacromoleculeByCode(experimentId, runNumber); - System.out.println("Macromolecule found"); - if (macromolecule != null){ - structure.setMacromoleculeId(macromolecule.getMacromoleculeId()); - structure.setFilePath(pdbHash.get("filePath")); - if (pdbHash.get("filePath") != null){ - String name = new File(pdbHash.get("filePath")).getName(); - structure.setName(name); - } - structure.setType("PDB"); - structure.setCreationDate(getNow()); - structure = this.entityManager.merge(structure); - System.out.println("Structure created"); - } - else{ - throw new Exception("Macromolecule not found for experimentId " + experimentId + " and runNumber " + runNumber ); - } - } - - /** Structure exists here **/ - mixture.setStructureId(structure.getStructureId()); - mixture.setCreationDate(getNow()); - - } - - if (pdbHash.containsKey("volumeFraction")){ - System.out.println("+++" +"Volume: " + pdbHash.get("volumeFraction")); - mixture.setVolumeFraction(pdbHash.get("volumeFraction")); - } - - mixtures.add(mixture); - } - - System.out.println( "+++Mixtures --- " + mixtures.size()); - System.out.println("+++" +fitFilePath + " --- " + fitFilePath); - - - /** Creating FitStructureToExperimentalData **/ - FitStructureToExperimentalData3VO fit = new FitStructureToExperimentalData3VO(); - fit.setSubtractionId(subtraction.getSubtractionId()); - fit.setCreationDate(getNow()); - fit.setFitFilePath(fitFilePath); - fit = entityManager.merge(fit); - System.out.println("+++Merging fit " + fit.getFitFilePath() + " " + fit.getFitStructureToExperimentalDataId()); - - /** Creating MixtureToStructures **/ - for (MixtureToStructure mixtureToStructure : mixtures) { - mixtureToStructure.setMixtureId(fit.getFitStructureToExperimentalDataId()); - mixtureToStructure = this.entityManager.merge(mixtureToStructure); - System.out.println("+++Merging mixturetoStructure " + mixtureToStructure.getVolumeFraction() + " " + mixtureToStructure.getStructureId() + " " + mixtureToStructure.getFitToStructureId()); - } - } - - /** Reading fitFilePath **/ -// Type HashType = new TypeToken>() {}.getType(); -// HashMap fitFilePathHash = new Gson().fromJson(fitFilePath, HashType); -// if (fitFilePathHash.containsKey("filePath")){ -// fitFilePath = fitFilePathHash.get("filePath"); -// } - - - } - else{ - throw new Exception("0 subtractions has been found for experimentId= " + experimentId + " and runNumber= " + runNumber); - } - - } - else{ - throw new Exception("No subtraction has been found for experimentId= " + experimentId + " and runNumber= " + runNumber); - } -// if (fitStructure == null){ -// fitStructure = new FitStructureToExperimentalData(); -// } -// -// fitStructure.setFitFilePath(fitFilePath); -//// fitStructure.setLogFilePath(logFile); -// fitStructure.setOutputFilePath(summaryFile); -//// fitStructure.setStructureId(Integer.parseInt(structureId)); -// fitStructure.setSubtractionId(Integer.parseInt(subtractionId)); -// fitStructure.setWorkflowId(Integer.parseInt(workflowId)); -// fitStructure.setComments("Finished at " + getNow()); -// fitStructure = advancedAnalysis3Service.merge(fitStructure); - - } - - @Override - public void addRigidBodyModeling(String experimentId, String runNumber, String fitFilePath, String rigidBodyModelFilePath, - String logFilePath, String curveConfigFilePath, String subunitConfigFilePath, String crosscorrConfigFilePath, - String contactConditionsFilePath, String masterSymmetry) throws Exception { - - List subtractions = this.getSubtractionByCode(experimentId, runNumber); - if (subtractions != null){ - if (subtractions.size() > 0){ - RigidBodyModeling3VO rigid = new RigidBodyModeling3VO(); - rigid.setSubtractionId(subtractions.get(subtractions.size() - 1).getSubtractionId()); - rigid.setFitFilePath(fitFilePath); - rigid.setRigidBodyModelFilePath(rigidBodyModelFilePath); - rigid.setLogFilePath(logFilePath); - rigid.setCurveConfigFilePath(curveConfigFilePath); - rigid.setSubUnitConfigFilePath(subunitConfigFilePath); - rigid.setCrossCorrConfigFilePath(crosscorrConfigFilePath); - rigid.setContactDescriptionFilePath(contactConditionsFilePath); - rigid.setSymmetry(masterSymmetry); - rigid.setCreationDate(getNow()); - this.entityManager.merge(rigid); - } - else{ - throw new Exception("No subtraction found for " + experimentId + " " + runNumber); - } - } - else{ - throw new Exception("No subtraction found for " + experimentId + " " + runNumber + "(null)"); - } - } - - @Override - public void addSuperposition(String experimentId, String runNumber, String abinitioModelPdbFilePath, String aprioriPdbFilePath, - String alignedPdbFilePath) throws Exception { - - List subtractions = this.getSubtractionByCode(experimentId, runNumber); - if (subtractions != null){ - Superposition3VO superposition = new Superposition3VO(); - superposition.setSubtractionId(subtractions.get(subtractions.size() - 1).getSubtractionId()); - superposition.setAbinitioModelPdbFilePath(abinitioModelPdbFilePath); - superposition.setAprioriPdbFilePath(aprioriPdbFilePath); - superposition.setAlignedPdbFilePath(alignedPdbFilePath); - superposition.setCreationDate(getNow()); - this.entityManager.merge(superposition); - } - else{ - throw new Exception("No subtraction found for " + experimentId + " " + runNumber + "(null)"); - } - - - } - - @Override - public HashMap getAprioriInformationByRunNumber(String proposal, String acronym) throws Exception { - HashMap info = new HashMap(); - List macromolecules = this.getMacromoleculeByAcronym(proposal, acronym); - if (macromolecules.size() == 1){ - Macromolecule3VO macromolecule = macromolecules.get(0); - if (macromolecule != null){ - info.put("ACRONYM", macromolecule.getAcronym()); - List> pdb = new ArrayList>(); - List> fasta = new ArrayList>(); - List> rbms = new ArrayList>(); - if (macromolecule.getStructure3VOs() != null){ - for (Structure3VO structure : macromolecule.getStructure3VOs()) { - if (structure.getType().equals("PDB")){ - HashMap pdbEntry = new HashMap(); - pdbEntry.put("FILEPATH", structure.getFilePath()); - pdbEntry.put("SYMMETRY", structure.getSymmetry()); - pdbEntry.put("MULTIPLICITY", structure.getMultiplicity()); - pdb.add(pdbEntry); - } - if (structure.getType().equals("SEQUENCE")){ - HashMap fastaEntry = new HashMap(); - fastaEntry.put("FILEPATH", structure.getFilePath()); - fasta.add(fastaEntry); - } - } - } - - HashMap rbm = new HashMap(); - rbm.put("FILEPATH", macromolecule.getContactsDescriptionFilePath()); - rbm.put("SYMMETRY", macromolecule.getSymmetry()); - rbms.add(rbm); - - info.put("PDB", pdb); - info.put("SEQUENCE", fasta); - info.put("RIGIDBODY", rbms); - return info; - } - else{ - throw new Exception("macromolecule not found"); - } - } - else{ - throw new Exception(macromolecules.size() + " macromolecules found"); - } - } - - - private void logFinish(String methodName, long id) { - LOG.debug("### [" + methodName.toUpperCase() + "] Execution time was " + (System.currentTimeMillis() - this.now) + " ms."); - LoggerFormatter.log(LOG, LoggerFormatter.Package.BIOSAXS_WS, methodName, id, System.currentTimeMillis(), - System.currentTimeMillis() - this.now); - - } - - protected long logInit(String methodName, String params) { - LOG.info("-----------------------"); - this.now = System.currentTimeMillis(); - LOG.info(methodName.toUpperCase()); - LoggerFormatter.log(LOG, LoggerFormatter.Package.BIOSAXS_WS, methodName, System.currentTimeMillis(), - System.currentTimeMillis(), params); - return this.now; - } - - @Override - public List getMacromoleculesByProposal(String code, String number) throws Exception { - ProposalWS3VO proposal = proposalService.findForWSByCodeAndNumber(code, number); - return this.saxsProposal3Service.findMacromoleculesByProposalId(proposal.getProposalId()); - } - - @Override - public List getBuffersByProposal(String code, String number) throws Exception { - ProposalWS3VO proposal = proposalService.findForWSByCodeAndNumber(code, number); - return this.saxsProposal3Service.findBuffersByProposalId(proposal.getProposalId()); - } -} +/******************************************************************************* + * This file is part of ISPyB. + * + * ISPyB is free software: you can redistribute it and/or modify + * it under the terms of the GNU Lesser General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * ISPyB is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with ISPyB. If not, see . + * + * Contributors : S. Delageniere, R. Leal, L. Launer, K. Levik, S. Veyrier, P. Brenchereau, M. Bodin, A. De Maria Antolinos + ******************************************************************************************************************************/ + +package ispyb.server.biosaxs.services.webservice; + +import ispyb.common.util.Constants; +import ispyb.server.biosaxs.services.core.ExperimentScope; +import ispyb.server.biosaxs.services.core.analysis.abInitioModelling.AbInitioModelling3Service; +import ispyb.server.biosaxs.services.core.analysis.advanced.AdvancedAnalysis3Service; +import ispyb.server.biosaxs.services.core.analysis.primaryDataProcessing.PrimaryDataProcessing3Service; +import ispyb.server.biosaxs.services.core.experiment.Experiment3Service; +import ispyb.server.biosaxs.services.core.measurement.Measurement3Service; +import ispyb.server.biosaxs.services.core.measurementToDataCollection.MeasurementToDataCollection3Service; +import ispyb.server.biosaxs.services.core.proposal.SaxsProposal3Service; +import ispyb.server.biosaxs.services.core.robot.Robot3Service; +import ispyb.server.biosaxs.services.core.samplePlate.Sampleplate3Service; +import ispyb.server.biosaxs.services.core.specimen.Specimen3Service; +import ispyb.server.biosaxs.vos.advanced.FitStructureToExperimentalData3VO; +import ispyb.server.biosaxs.vos.advanced.MixtureToStructure; +import ispyb.server.biosaxs.vos.advanced.RigidBodyModeling3VO; +import ispyb.server.biosaxs.vos.advanced.Superposition3VO; +import ispyb.server.biosaxs.vos.assembly.Macromolecule3VO; +import ispyb.server.biosaxs.vos.assembly.Structure3VO; +import ispyb.server.biosaxs.vos.dataAcquisition.Buffer3VO; +import ispyb.server.biosaxs.vos.dataAcquisition.Experiment3VO; +import ispyb.server.biosaxs.vos.dataAcquisition.Measurement3VO; +import ispyb.server.biosaxs.vos.dataAcquisition.Specimen3VO; +import ispyb.server.biosaxs.vos.dataAcquisition.plate.PlateGroup3VO; +import ispyb.server.biosaxs.vos.dataAcquisition.plate.Sampleplate3VO; +import ispyb.server.biosaxs.vos.dataAcquisition.plate.Sampleplateposition3VO; +import ispyb.server.biosaxs.vos.datacollection.Framelist3VO; +import ispyb.server.biosaxs.vos.datacollection.MeasurementTodataCollection3VO; +import ispyb.server.biosaxs.vos.datacollection.Merge3VO; +import ispyb.server.biosaxs.vos.datacollection.Model3VO; +import ispyb.server.biosaxs.vos.datacollection.SaxsDataCollection3VO; +import ispyb.server.biosaxs.vos.datacollection.Subtraction3VO; +import ispyb.server.common.services.proposals.Proposal3Service; +import ispyb.server.common.services.sessions.Session3Service; +import ispyb.server.common.util.LoggerFormatter; +import ispyb.server.common.vos.proposals.Proposal3VO; +import ispyb.server.common.vos.proposals.ProposalWS3VO; +import ispyb.server.mx.vos.collections.Session3VO; +import ispyb.server.mx.vos.collections.SessionWS3VO; + +import java.io.File; +import java.lang.reflect.Type; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Calendar; +import java.util.Date; +import java.util.GregorianCalendar; +import java.util.HashMap; +import java.util.HashSet; +import java.util.Iterator; +import java.util.List; +import java.util.Set; + +import javax.ejb.EJB; +import javax.ejb.Stateless; +import javax.persistence.EntityManager; +import javax.persistence.PersistenceContext; + +import org.apache.log4j.Logger; + +import com.google.gson.Gson; +import com.google.gson.JsonElement; +import com.google.gson.reflect.TypeToken; + +@Stateless +public class ATSASPipeline3ServiceBean implements ATSASPipeline3Service, DesySampleChangerConnectorServiceLocal { + private final static Logger LOG = Logger.getLogger("ATSASPipeline3ServiceBean"); + + /** The entity manager. */ + @PersistenceContext(unitName = "ispyb_db") + private EntityManager entityManager; + + @EJB + private Proposal3Service proposalService; + + @EJB + private SaxsProposal3Service saxsProposal3Service; + + @EJB + private AbInitioModelling3Service AbInitioModelling3Service; + + @EJB + private Experiment3Service experiment3Service; + + @EJB + private Measurement3Service measurement3Service; + + @EJB + private Specimen3Service specimen3Service; + + @EJB + private Sampleplate3Service sampleplate3Service; + + @EJB + private Robot3Service robot3Service; + + @EJB + private MeasurementToDataCollection3Service measurementToDataCollection3Service; + + @EJB + private PrimaryDataProcessing3Service primaryDataProcessing3Service; + + @EJB + private AdvancedAnalysis3Service advancedAnalysis3Service; + + private long now; + + @EJB + private Session3Service sessionService; + + /** The now. */ + protected static Calendar NOW; + + private Date getNow(){ + NOW = GregorianCalendar.getInstance(); + return NOW.getTime(); + } + + private Integer getSessionIdForExperiment(ProposalWS3VO proposal) throws Exception { + Calendar cal = Calendar.getInstance(); + Date today = cal.getTime(); + cal.add(Calendar.HOUR_OF_DAY, 24); + // by default the session created contains 3 shifts of 8hours each. + Date endTime = cal.getTime(); + + Integer sessionId = null; + + SessionWS3VO[] sessionTab = sessionService.findForWSByProposalCodeAndNumber(proposal.getCode(), + proposal.getNumber(), Constants.getSAXSBeamline()); + + if (sessionTab == null || sessionTab.length == 0) { + // No session found we have to create one to attach the experiment data to it + Session3VO ses = new Session3VO(); + ses.setBeamlineName(Constants.getSAXSBeamline()); + ses.setProposalVO(proposalService.findByPk(proposal.getProposalId())); + ses.setStartDate(today); + ses.setEndDate(endTime); + ses.setComments("session created by ISPyBB"); + ses.setScheduled((byte) 0); + ses.setNbShifts(3); + ses.setUsedFlag((byte) 1); + ses.setTimeStamp(today); + ses.setLastUpdate(endTime); + ses = sessionService.create(ses); + sessionId = ses.getSessionId(); + } else { + sessionId = sessionTab[0].getSessionId(); + } + + return sessionId; + } + + @Override + public Experiment3VO createEmptyExperiment(String proposalCode, String proposalNumber, String name) throws Exception { + ProposalWS3VO proposal = proposalService.findForWSByCodeAndNumber(proposalCode, proposalNumber); + + Experiment3VO experiment = new Experiment3VO(); + experiment = this.experiment3Service.initPlates(experiment); + experiment.setName(name); + experiment.setType("STATIC"); + try{ + experiment.setSessionId(getSessionIdForExperiment(proposal)); + } + catch(Exception exp){ + /** Non-blocking exception **/ + exp.printStackTrace(); + } + experiment.setCreationDate(GregorianCalendar.getInstance().getTime()); + + + experiment.setProposalId(proposal.getProposalId()); + experiment = this.experiment3Service.merge(experiment); + HashMap plates = robot3Service.getDefaultSampleChangerPlateconfiguration("20"); + + PlateGroup3VO plateGroup = new PlateGroup3VO(); + plateGroup.setStorageTemperature("20"); + plateGroup = sampleplate3Service.merge(plateGroup); + + for (String key : plates.keySet()) { + Sampleplate3VO plate = plates.get(key); + plate.setExperimentId(experiment.getExperimentId()); + plate.setPlategroup3VO(plateGroup); + plate = sampleplate3Service.merge(plate); + sampleplate3Service.merge(plate); + } + + /** Creating a session **/ + Integer sessionId = null; + + + return experiment; + } + + @Override + public Measurement3VO appendMeasurementToExperiment(String experimentId, + String runNumber, String type, String plate, String row, String well, String name, String bufferName, + String concentration, String sEUtemperature, String viscosity, String volume, String volumeToLoad, String waitTime, String transmission, String comments) { + + // return experiment3Service.appendMeasurementToExperiment(experimentId, + // runNumber, type, plate, row, well, name, bufferName, concentration, + // sEUtemperature, viscosity, volume, volumeToLoad, waitTime, + // transmission, comments); + Experiment3VO experiment = experiment3Service.findById(Integer.parseInt(experimentId), ExperimentScope.MEDIUM); + System.out.println("Getting Experiment:" + experiment.getExperimentId()); + System.out.println("NAME:" + name); + System.out.println("proposal:" + experiment.getProposalId()); + + List macromolecules = new ArrayList(); + try { + List macromoleculeList = saxsProposal3Service.findMacromoleculesBy(name, experiment.getProposalId()); + System.out.println(macromoleculeList); + if (macromoleculeList != null) { + for (Macromolecule3VO macromolecule3vo : macromoleculeList) { + if (macromolecule3vo.getAcronym() != null) { + if (macromolecule3vo.getAcronym().toLowerCase().trim().equals(name.toLowerCase().trim())) { + macromolecules.add(macromolecule3vo); + System.out.println("Found"); + } + } + } + } + } catch (Exception e) { + e.printStackTrace(); + macromolecules = new ArrayList(); + } + + Specimen3VO specimen = new Specimen3VO(); + + /** + * + * We don't check location of the specimen for ATSAS + * http://forge.epn-campus.eu/issues/2095 + * + */ + Set plates = experiment.getSamplePlate3VOs(); + + + + + specimen.setConcentration(concentration); + if (type.toUpperCase().equals("SAMPLE")) { + Macromolecule3VO macromolecule = null; + if (macromolecules.size() == 0) { + if (name == null) { + name = ""; + } + Macromolecule3VO m = new Macromolecule3VO(experiment.getProposalId(), name, name, ""); + m.setCreationDate(GregorianCalendar.getInstance().getTime()); + macromolecule = entityManager.merge(m); + } else { + macromolecule = macromolecules.get(0); + } + specimen.setMacromolecule3VO(macromolecule); + } + + List buffers = saxsProposal3Service.findBuffersByProposalId(experiment.getProposalId()); + for (Buffer3VO buffer3vo : buffers) { + if (buffer3vo.getAcronym() != null) { + if (buffer3vo.getAcronym().equals(bufferName)) { + specimen.setBufferId(buffer3vo.getBufferId()); + } + } + } + /** If buffer not found **/ + if (specimen.getBufferId() == null) { + Buffer3VO buffer3VO = new Buffer3VO(); + if (bufferName == null) { + bufferName = ""; + } + buffer3VO.setAcronym(bufferName); + buffer3VO.setName(bufferName); + buffer3VO.setProposalId(experiment.getProposalId()); + buffer3VO = entityManager.merge(buffer3VO); + specimen.setBufferId(buffer3VO.getBufferId()); + } + + /** Sample plate position **/ + LOG.info("getSampleplateposition3VO: " + specimen.getSampleplateposition3VO()); + LOG.info("plates: " + plates.size()); + if (specimen.getSampleplateposition3VO() == null) { + /** this specimen is new because has no position **/ + for (Sampleplate3VO samplePlate : plates) { + if (samplePlate.getSlotPositionColumn().equals(plate)) { + Sampleplateposition3VO position = new Sampleplateposition3VO(); + position.setColumnNumber(Integer.parseInt(well)); + position.setRowNumber(Integer.parseInt(row)); + position.setSamplePlateId(samplePlate.getSamplePlateId()); + position = entityManager.merge(position); + specimen.setSampleplateposition3VO(position); + } + } + } + + specimen.setExperimentId(experiment.getExperimentId()); + specimen.setVolume(volume); + + specimen = entityManager.merge(specimen); + + Measurement3VO measurement = new Measurement3VO(); + measurement.setCode(runNumber); + measurement.setSpecimenId(specimen.getSpecimenId()); + measurement.setExposureTemperature(sEUtemperature); + measurement.setTransmission(transmission); + measurement.setComment(comments); + measurement.setViscosity(viscosity); + measurement.setVolumeToLoad(volumeToLoad); + measurement.setWaitTime(waitTime); + measurement.setPriority(experiment.getMeasurements().size() + 1); + measurement = entityManager.merge(measurement); + return measurement; + } + + public void updateAverage(int measurementId, int averagedCount, int framesCount, String oneDimensionalDataFilePathArray, String discardedCurves, String averageFilePath) { + List curveList = Arrays.asList(oneDimensionalDataFilePathArray.split(",")); + List mergeList = this.primaryDataProcessing3Service.findByMeasurementId(measurementId); + if (mergeList != null){ + if (mergeList.size() > 0){ + Merge3VO merge = mergeList.get(0); + if (Integer.parseInt(merge.getFramesCount()) >= framesCount){ + LOG.info("Same number of frames count. No update"); + return; + } + else{ + this.primaryDataProcessing3Service.addMerge(measurementId, averagedCount, framesCount, oneDimensionalDataFilePathArray, null, averageFilePath); + } + } + } + } + + @Override + public void addAveraged(String measurementId, String averaged, String discarded, String averageFile) { + + Type listType = new TypeToken>>() { + }.getType(); + List> averageFrames = new Gson().fromJson(averaged, listType); + List> discardeFrames = new Gson().fromJson(discarded, listType); + + + ArrayList oneDimensionalFiles = new ArrayList(); + LOG.info("########### Averaged Frames ############# "); + for (HashMap frame : averageFrames) { + if (frame.containsKey("filePath")) { + oneDimensionalFiles.add(frame.get("filePath")); + LOG.info("\t" + frame.get("filePath")); + } + } + + LOG.info("########### Discarded Frames ############# "); + for (HashMap frame : discardeFrames) { + if (frame.containsKey("filePath")) { + oneDimensionalFiles.add(frame.get("filePath")); + LOG.info("\t" + frame.get("filePath")); + } + } + + /** Does it contains already a average **/ + List merges = primaryDataProcessing3Service.findByMeasurementId(Integer.parseInt(measurementId)); + LOG.info("------ Number of Averages by measurementId --------"); + LOG.info(merges.size()); + + if (merges.size() == 0) { + LOG.info("\t Creating a new average"); + /** Not any average found so we create a new one **/ + this.primaryDataProcessing3Service.addMerge(Integer.parseInt(measurementId), averageFrames.size(), oneDimensionalFiles.size(), + oneDimensionalFiles.toString().replace("[", "").replace("]", ""), null, averageFile); + } else { + LOG.info("\t Updating a new average"); + /** It is an update of the average **/ + + this.updateAverage(Integer.parseInt(measurementId), averageFrames.size(), oneDimensionalFiles.size(), + oneDimensionalFiles.toString().replace("[", "").replace("]", ""), null, averageFile); + + } + } + +// private void removeFrameListById(int frameListId) { +// Framelist3VO frameList = this.entityManager.find(Framelist3VO.class, frameListId); +// /** Looking for FrameToListObjects **/ +// +// String query = "select f from Frametolist3VO f where f.frameListId=:frameListId"; +// Query EJBQuery = this.entityManager.createQuery(query).setParameter("frameListId", frameListId); +// List frameToListList = (List)EJBQuery.getResultList(); +// for (Frametolist3VO frametolist3vo : frameToListList) { +// System.out.println("Found " + frametolist3vo.getFrameToListId()); +// } +// +// } + + /** + * True if a datacollection contains all the measurementIds otherwise false + * + * @param dataCollection + * @param measurementIds + * @return + */ + private Boolean containsSameMeasurements(SaxsDataCollection3VO dataCollection, List measurementIds) { + Iterator mIterator = dataCollection.getMeasurementtodatacollection3VOs().iterator(); + HashSet measurementDataCollectionSet = new HashSet(); + while (mIterator.hasNext()) { + MeasurementTodataCollection3VO measurementToDataCollection = mIterator.next(); + measurementDataCollectionSet.add(measurementToDataCollection.getMeasurementId()); + } + for (Integer measurementId : measurementIds) { + if (!measurementDataCollectionSet.contains(measurementId)) { + return false; + } + } + return true; + } + + private SaxsDataCollection3VO getDataCollectionByMeasurementsId(Experiment3VO experiment, List measurementIds) { + Iterator iterator = experiment.getDataCollections().iterator(); + while (iterator.hasNext()) { + SaxsDataCollection3VO dataCollection = iterator.next(); + if (this.containsSameMeasurements(dataCollection, measurementIds)) { + /** + * Returning the existing one + */ + return dataCollection; + } + } + return null; + } + /** + * Returns the measurement id corresponding to a sample or null if all measurementIds are buffers + * @param experiment + * @param measurementIds + * @return + */ + private Integer getSampleFromMeasurementList(Experiment3VO experiment, List measurementIds) { + for (Integer measurementId : measurementIds) { + Specimen3VO specimen = experiment.getSampleById(experiment.getMeasurementById(measurementId).getSpecimenId()); + if (specimen.getMacromolecule3VO() != null){ + return measurementId; + } + } + return null; + } + + /** + * return a existing datacollection if found containing the same + * measurements or create a new one + * + * @param experiment + * @param measurementIds + * @return + */ + private SaxsDataCollection3VO getSaxsDataCollectionByMeasurementIds(Experiment3VO experiment, List measurementIds) { +// SaxsDataCollection3VO datacollection = this.getDataCollectionByMeasurementsId(experiment, measurementIds); + SaxsDataCollection3VO datacollection = null; + LOG.info("Getting data collection"); + LOG.info("Getting data collection: " + measurementIds.toString()); + Integer sampleMeasurementId = this.getSampleFromMeasurementList(experiment, measurementIds); + LOG.info("sampleMeasurementId: " + sampleMeasurementId); + if (sampleMeasurementId == null){ + datacollection = this.getDataCollectionByMeasurementsId(experiment, measurementIds); + } + else{ + /** Look for a subtraction already containing this sample **/ + datacollection = experiment.getDataCollectionByMeasurementId(sampleMeasurementId); + + if (datacollection != null){ + /** Adding extra measurements **/ + Set measurementToDatacollectionList = datacollection.getMeasurementtodatacollection3VOs(); + Set measurementKeys = new HashSet(); + for (MeasurementTodataCollection3VO measurementToDatacollection : measurementToDatacollectionList) { + measurementKeys.add(measurementToDatacollection.getMeasurementId()); + } + LOG.info("measurementKeys:" + measurementKeys.toString()); + for (Integer measurementId : measurementIds) { + LOG.info("measurementKeys:" + measurementId + " " + measurementKeys.toString()); + if(!measurementKeys.contains(measurementId)){ + /** This measurement does not belong to the data collection yet **/ + MeasurementTodataCollection3VO measurementToDataCollection = new MeasurementTodataCollection3VO(); + measurementToDataCollection.setDataCollectionId(datacollection.getDataCollectionId()); + measurementToDataCollection.setMeasurementId(measurementId); + measurementToDataCollection.setDataCollectionOrder(datacollection.getMeasurementtodatacollection3VOs().size() + 1); + LOG.info("setDataCollectionOrder:" + datacollection.getMeasurementtodatacollection3VOs().size() + 1); + this.entityManager.merge(measurementToDataCollection); + } + } + } + } + + if (datacollection != null) { + return datacollection; + } else { + /** We create a new one **/ + SaxsDataCollection3VO dataCollection = new SaxsDataCollection3VO(); + dataCollection.setExperimentId(experiment.getExperimentId()); + dataCollection = entityManager.merge(dataCollection); + int dataCollectionOrder = 1; + for (Integer measurementId : measurementIds) { + MeasurementTodataCollection3VO measurementToDataCollection = new MeasurementTodataCollection3VO(); + measurementToDataCollection.setDataCollectionId(dataCollection.getDataCollectionId()); + measurementToDataCollection.setMeasurementId(measurementId); + measurementToDataCollection.setDataCollectionOrder(dataCollectionOrder); + this.entityManager.merge(measurementToDataCollection); + dataCollectionOrder++; + } + return dataCollection; + } + } + + private Framelist3VO createFrames(List sampleOneDimensionalFilesList){ + if (sampleOneDimensionalFilesList.size() > 0){ + return this.primaryDataProcessing3Service.addFrameList(sampleOneDimensionalFilesList); + } + return null; + } + + private void addSubtraction(Integer dataCollectionId, String rgStdev, String i0, String i0Stdev, String firstPointUsed, + String lastPointUsed, String quality, String isagregated, String rgGuinier, String rgGnom, String dmax, String total, + String volume, String sampleOneDimensionalFiles, String bufferOneDimensionalFiles, String sampleAverageFilePath, + String bestBufferFilePath, String subtractedFilePath, String experimentalDataPlotFilePath, String densityPlotFilePath, + String guinierPlotFilePath, String kratkyPlotFilePath, String gnomOutputFilePath, Subtraction3VO subtraction) { + + HashMap params = new HashMap(); + + long start = this.logInit("addSubtraction_CP_3.1", new Gson().toJson(params)); + + /** Getting the frames **/ + Type typeOfHash = new TypeToken>>() {}.getType(); + List> sampleOneDimensionalFilesListObject = new Gson().fromJson(sampleOneDimensionalFiles, typeOfHash); + List> bufferOneDimensionalFilesListObject = new Gson().fromJson(bufferOneDimensionalFiles, typeOfHash); + + List sampleOneDimensionalFilesList = new ArrayList(); + List bufferOneDimensionalFilesList = new ArrayList(); + + for (HashMap fileObject : sampleOneDimensionalFilesListObject) { + if (fileObject.get("filePath")!= null){ + sampleOneDimensionalFilesList.add(fileObject.get("filePath")); + } + } + + for (HashMap fileObject : bufferOneDimensionalFilesListObject) { + if (fileObject.get("filePath")!= null){ + bufferOneDimensionalFilesList.add(fileObject.get("filePath")); + } + } + + LOG.info(sampleOneDimensionalFilesList); + Framelist3VO sampleFiles = this.createFrames(sampleOneDimensionalFilesList); + this.logFinish("addSubtraction_CP_3.1", start); + + start = this.logInit("addSubtraction_CP_3.2", new Gson().toJson(params)); + Framelist3VO bufferFiles = this.createFrames(bufferOneDimensionalFilesList); + this.logFinish("addSubtraction_CP_3.2", start); + + + start = this.logInit("addSubtraction_CP_3.3", new Gson().toJson(params)); + subtraction.setDataCollectionId(dataCollectionId); + subtraction.setRg(rgGuinier); + subtraction.setRgStdev(rgStdev); + subtraction.setI0(i0); + subtraction.setI0stdev(i0Stdev); + subtraction.setFirstPointUsed(firstPointUsed); + subtraction.setLastPointUsed(lastPointUsed); + subtraction.setQuality(quality); + subtraction.setIsagregated(isagregated); + subtraction.setGnomFilePath(densityPlotFilePath); + subtraction.setRgGuinier(rgGuinier); + subtraction.setRgGnom(rgGnom); + subtraction.setDmax(dmax); + subtraction.setTotal(total); + subtraction.setVolume(volume); + subtraction.setKratkyFilePath(kratkyPlotFilePath); + subtraction.setScatteringFilePath(experimentalDataPlotFilePath); + subtraction.setGuinierFilePath(guinierPlotFilePath); + subtraction.setSubstractedFilePath(subtractedFilePath); + subtraction.setGnomFilePathOutput(gnomOutputFilePath); + subtraction.setCreationTime(getNow()); + + if (sampleFiles != null){ + subtraction.setSampleOneDimensionalFiles(sampleFiles); + } + if (bufferFiles != null){ + subtraction.setBufferOneDimensionalFiles(bufferFiles); + } + subtraction.setSampleAverageFilePath(sampleAverageFilePath); + subtraction.setBufferAverageFilePath(bestBufferFilePath); + + this.entityManager.merge(subtraction); + this.logFinish("addSubtraction_CP_3.3", start); + + } + + private void addSubtraction(int dataCollectionId, String rgStdev, String i0, String i0Stdev, String firstPointUsed, + String lastPointUsed, String quality, String isagregated, String rgGuinier, String rgGnom, String dmax, String total, + String volume, String sampleOneDimensionalFiles, String bufferOneDimensionalFiles, String sampleAverageFilePath, + String bestBufferFilePath, String subtractedFilePath, String experimentalDataPlotFilePath, String densityPlotFilePath, + String guinierPlotFilePath, String kratkyPlotFilePath, String gnomOutputFilePath) { + + Subtraction3VO subtraction = new Subtraction3VO(); + this.addSubtraction(dataCollectionId, rgStdev, i0, i0Stdev, firstPointUsed, lastPointUsed, quality, isagregated, rgGuinier, rgGnom, dmax, total, volume, sampleOneDimensionalFiles, bufferOneDimensionalFiles, sampleAverageFilePath, bestBufferFilePath, subtractedFilePath, experimentalDataPlotFilePath, densityPlotFilePath, guinierPlotFilePath, kratkyPlotFilePath, gnomOutputFilePath, subtraction); + + } + + + @Override + public void addSubtraction(String sampleMeasurementId, String rgStdev, String i0, String i0Stdev, String firstPointUsed, + String lastPointUsed, String quality, String isagregated, String rgGuinier, String rgGnom, String dmax, String total, + String volume, String sampleOneDimensionalFiles, String bufferOneDimensionalFiles, String sampleAverageFilePath, + String bestBufferFilePath, String subtractedFilePath, String experimentalDataPlotFilePath, String densityPlotFilePath, + String guinierPlotFilePath, String kratkyPlotFilePath, String gnomOutputFilePath) { + + + + HashMap params = new HashMap(); + long start = this.logInit("addSubtraction_CP_1", new Gson().toJson(params)); + if (sampleMeasurementId != null){ + // TODO: To be changed, performace problems!!! + Experiment3VO experiment = experiment3Service.findByMeasurementId(Integer.parseInt(sampleMeasurementId)); + this.logFinish("addSubtraction_CP_1", start); + + + if (experiment != null) { + start = this.logInit("addSubtraction_CP_2", new Gson().toJson(params)); + int dataCollectionId = experiment.getDataCollectionByMeasurementId(Integer.parseInt(sampleMeasurementId)).getDataCollectionId(); + this.logFinish("addSubtraction_CP_2", start); + + + start = this.logInit("addSubtraction_CP_3", new Gson().toJson(params)); + this.addSubtraction(dataCollectionId, rgStdev, i0, i0Stdev, firstPointUsed, lastPointUsed, quality, isagregated, rgGuinier, rgGnom, dmax, total, volume, sampleOneDimensionalFiles, bufferOneDimensionalFiles, sampleAverageFilePath, bestBufferFilePath, subtractedFilePath, experimentalDataPlotFilePath, densityPlotFilePath, guinierPlotFilePath, kratkyPlotFilePath, gnomOutputFilePath); + this.logFinish("addSubtraction_CP_3", start); + + } + } + } + + + /** + * Adds a new subtraction to several measurements To note: there are not any data collection yet + */ + public void addSubtraction( + String experimentId, + String runNumberList, + String rgStdev, + String i0, + String i0Stdev, + String firstPointUsed, + String lastPointUsed, + String quality, + String isagregated, + String rgGuinier, + String rgGnom, + String dmax, + String total, + String volume, + String sampleOneDimensionalFiles, + String bufferOneDimensionalFiles, + String sampleAverageFilePath, + String bestBufferFilePath, + String subtractedFilePath, + String experimentalDataPlotFilePath, + String densityPlotFilePath, + String guinierPlotFilePath, + String kratkyPlotFilePath, + String gnomOutputFilePath) throws Exception { + + Type typeOfList = new TypeToken>() {}.getType(); + List ids = new Gson().fromJson(runNumberList, typeOfList); + + /** Finding measurement by experimentId and run number **/ + List measurementIds = new ArrayList(); + for (String runNumber : ids) { + Measurement3VO measurement = measurement3Service.findMeasurementByCode(Integer.parseInt(experimentId), runNumber.toString()); + if (measurement != null) { + measurementIds.add(measurement.getMeasurementId()); + } else { + throw new Exception("No measurement found for runNumber: " + runNumber + " and experimentId: " + experimentId); + } + } + + System.out.println("Adding data collection and subtraction"); + + /** Adding data collection and subtraction **/ + if (measurementIds != null) { + if (measurementIds.size() > 0) { + Experiment3VO experiment = experiment3Service.findById(Integer.parseInt(experimentId), ExperimentScope.MEDIUM); + if (experiment != null) { + /** This method creates the data collection if it does not exist yet **/ + SaxsDataCollection3VO dataCollection = getSaxsDataCollectionByMeasurementIds(experiment, measurementIds); + + if (dataCollection.getSubstraction3VOs().size() == 0){ + this.addSubtraction(dataCollection.getDataCollectionId(), rgStdev, i0, i0Stdev, firstPointUsed, lastPointUsed, quality, isagregated, rgGuinier, rgGnom, dmax, total, volume, sampleOneDimensionalFiles, bufferOneDimensionalFiles, sampleAverageFilePath, bestBufferFilePath, subtractedFilePath, experimentalDataPlotFilePath, densityPlotFilePath, guinierPlotFilePath, kratkyPlotFilePath, gnomOutputFilePath); + } + else{ + /** + * Upgrading subtraction + */ + Subtraction3VO subtraction = (Subtraction3VO) Arrays.asList(dataCollection.getSubstraction3VOs().toArray()).get(0); + this.addSubtraction(dataCollection.getDataCollectionId(), rgStdev, i0, i0Stdev, firstPointUsed, lastPointUsed, quality, isagregated, rgGuinier, rgGnom, dmax, total, volume, sampleOneDimensionalFiles, bufferOneDimensionalFiles, sampleAverageFilePath, bestBufferFilePath, subtractedFilePath, experimentalDataPlotFilePath, densityPlotFilePath, guinierPlotFilePath, kratkyPlotFilePath, gnomOutputFilePath, subtraction); + } + } + } + } + } + + + + @Override + public void addAbinitioModelling(String experimentId, String runNumber, + ArrayList models3vo, Model3VO referenceModel, + Model3VO refinedModel) throws Exception { + + Measurement3VO measurement = measurement3Service.findMeasurementByCode(Integer.parseInt(experimentId), (runNumber)); + if (measurement != null){ + ArrayList measurementIds = new ArrayList(); + measurementIds.add(measurement.getMeasurementId()); + AbInitioModelling3Service.addAbinitioModeling(measurementIds, + models3vo, + referenceModel, + refinedModel); + + } + else{ + throw new Exception("No measurement found for " + experimentId + " and " + runNumber); + } + } + + @Override + public Model3VO getModel(String experimentId, String runNumber, String pdbfilepath) throws Exception { + Measurement3VO measurement = measurement3Service.findMeasurementByCode(Integer.parseInt(experimentId), (runNumber)); + if (measurement != null){ + return AbInitioModelling3Service.getModel(measurement.getMeasurementId(), pdbfilepath); + } + else{ + throw new Exception("Not measurement found for " + experimentId + " and " + runNumber); + } + } + + @Override + public Model3VO merge(Model3VO model) { + return this.entityManager.merge(model); + } + + @Override + public List getMacromoleculeByAcronym(String proposal, String acronym) { + List proposal3VOs = this.proposalService.findProposalByLoginName(proposal); + if (proposal3VOs != null){ + if (proposal3VOs.size() > 0){ + Proposal3VO proposal3VO = proposal3VOs.get(0); + List macromolecules = this.saxsProposal3Service.findMacromoleculesBy(acronym, proposal3VO.getProposalId()); + return macromolecules; + } + } + return new ArrayList(); + } + + public List getSubtractionByCode(String experimentId, String runNumber) { + Measurement3VO measurement = measurement3Service.findMeasurementByCode(Integer.valueOf(experimentId), runNumber); + System.out.println("measurement " + measurement); + if (measurement != null){ + return primaryDataProcessing3Service.getSubstractionsByMeasurementId(measurement.getMeasurementId()); + } + System.out.println("measurement not found "); + return null; + } + + public Macromolecule3VO getMacromoleculeByCode(String experimentId, String runNumber) { + Measurement3VO measurement = measurement3Service.findMeasurementByCode(Integer.valueOf(experimentId), runNumber); + if (measurement != null){ + Specimen3VO specimen = entityManager.find(Specimen3VO.class, measurement.getSpecimenId()); + if (specimen != null){ + return saxsProposal3Service.findMacromoleculesById(specimen.getMacromolecule3VO().getMacromoleculeId()); +// return experiment3Service.findMacromoleculeById(specimen.getMacromolecule3VO().getMacromoleculeId()); + } + } + return null; + } + + /** + * + * @param experimentId + * @param runNumber + * @param filePath {filePath:"/filepath.dat"} + * @return + */ + public Structure3VO getStructuresByCode(String experimentId, String runNumber, String filePath) { + Macromolecule3VO macromolecule = this.getMacromoleculeByCode(experimentId, runNumber); + for (Structure3VO structure : macromolecule.getStructure3VOs()) { + if (structure.getFilePath().trim().equals(filePath.trim())){ + return structure; + } + } + + return null; + } + + @Override + public void addMixture(String experimentId, String runNumber, String fitFilePath, String pdb) throws Exception { + List subtractions = this.getSubtractionByCode(experimentId, runNumber); + System.out.println("+++addMixture " + experimentId + " " + runNumber); + if (subtractions != null){ + if (subtractions.size() > 0){ + /** Getting last one are they should come by order **/ + Subtraction3VO subtraction = subtractions.get(subtractions.size() - 1); + + System.out.println("+++Subtraction Found"); + /** Getting Structure **/ + + Type ListType = new TypeToken>>() {}.getType(); + + /** Reading pdbs **/ + List> pdbFilePath = new Gson().fromJson(pdb, ListType); + + List mixtures = new ArrayList(); + if (pdbFilePath.size() > 0){ + for (HashMap pdbHash : pdbFilePath) { + MixtureToStructure mixture = new MixtureToStructure(); + + if (pdbHash.containsKey("filePath")){ + /** Finding the structue linked to such filePath */ + Structure3VO structure = this.getStructuresByCode(experimentId, runNumber, pdbHash.get("filePath")); + /** If structure does not exist we create a new one **/ + if (structure == null){ + structure = new Structure3VO(); + Macromolecule3VO macromolecule = this.getMacromoleculeByCode(experimentId, runNumber); + System.out.println("Macromolecule found"); + if (macromolecule != null){ + structure.setMacromoleculeId(macromolecule.getMacromoleculeId()); + structure.setFilePath(pdbHash.get("filePath")); + if (pdbHash.get("filePath") != null){ + String name = new File(pdbHash.get("filePath")).getName(); + structure.setName(name); + } + structure.setType("PDB"); + structure.setCreationDate(getNow()); + structure = this.entityManager.merge(structure); + System.out.println("Structure created"); + } + else{ + throw new Exception("Macromolecule not found for experimentId " + experimentId + " and runNumber " + runNumber ); + } + } + + /** Structure exists here **/ + mixture.setStructureId(structure.getStructureId()); + mixture.setCreationDate(getNow()); + + } + + if (pdbHash.containsKey("volumeFraction")){ + System.out.println("+++" +"Volume: " + pdbHash.get("volumeFraction")); + mixture.setVolumeFraction(pdbHash.get("volumeFraction")); + } + + mixtures.add(mixture); + } + + System.out.println( "+++Mixtures --- " + mixtures.size()); + System.out.println("+++" +fitFilePath + " --- " + fitFilePath); + + + /** Creating FitStructureToExperimentalData **/ + FitStructureToExperimentalData3VO fit = new FitStructureToExperimentalData3VO(); + fit.setSubtractionId(subtraction.getSubtractionId()); + fit.setCreationDate(getNow()); + fit.setFitFilePath(fitFilePath); + fit = entityManager.merge(fit); + System.out.println("+++Merging fit " + fit.getFitFilePath() + " " + fit.getFitStructureToExperimentalDataId()); + + /** Creating MixtureToStructures **/ + for (MixtureToStructure mixtureToStructure : mixtures) { + mixtureToStructure.setMixtureId(fit.getFitStructureToExperimentalDataId()); + mixtureToStructure = this.entityManager.merge(mixtureToStructure); + System.out.println("+++Merging mixturetoStructure " + mixtureToStructure.getVolumeFraction() + " " + mixtureToStructure.getStructureId() + " " + mixtureToStructure.getFitToStructureId()); + } + } + + /** Reading fitFilePath **/ +// Type HashType = new TypeToken>() {}.getType(); +// HashMap fitFilePathHash = new Gson().fromJson(fitFilePath, HashType); +// if (fitFilePathHash.containsKey("filePath")){ +// fitFilePath = fitFilePathHash.get("filePath"); +// } + + + } + else{ + throw new Exception("0 subtractions has been found for experimentId= " + experimentId + " and runNumber= " + runNumber); + } + + } + else{ + throw new Exception("No subtraction has been found for experimentId= " + experimentId + " and runNumber= " + runNumber); + } +// if (fitStructure == null){ +// fitStructure = new FitStructureToExperimentalData(); +// } +// +// fitStructure.setFitFilePath(fitFilePath); +//// fitStructure.setLogFilePath(logFile); +// fitStructure.setOutputFilePath(summaryFile); +//// fitStructure.setStructureId(Integer.parseInt(structureId)); +// fitStructure.setSubtractionId(Integer.parseInt(subtractionId)); +// fitStructure.setWorkflowId(Integer.parseInt(workflowId)); +// fitStructure.setComments("Finished at " + getNow()); +// fitStructure = advancedAnalysis3Service.merge(fitStructure); + + } + + @Override + public void addRigidBodyModeling(String experimentId, String runNumber, String fitFilePath, String rigidBodyModelFilePath, + String logFilePath, String curveConfigFilePath, String subunitConfigFilePath, String crosscorrConfigFilePath, + String contactConditionsFilePath, String masterSymmetry) throws Exception { + + List subtractions = this.getSubtractionByCode(experimentId, runNumber); + if (subtractions != null){ + if (subtractions.size() > 0){ + RigidBodyModeling3VO rigid = new RigidBodyModeling3VO(); + rigid.setSubtractionId(subtractions.get(subtractions.size() - 1).getSubtractionId()); + rigid.setFitFilePath(fitFilePath); + rigid.setRigidBodyModelFilePath(rigidBodyModelFilePath); + rigid.setLogFilePath(logFilePath); + rigid.setCurveConfigFilePath(curveConfigFilePath); + rigid.setSubUnitConfigFilePath(subunitConfigFilePath); + rigid.setCrossCorrConfigFilePath(crosscorrConfigFilePath); + rigid.setContactDescriptionFilePath(contactConditionsFilePath); + rigid.setSymmetry(masterSymmetry); + rigid.setCreationDate(getNow()); + this.entityManager.merge(rigid); + } + else{ + throw new Exception("No subtraction found for " + experimentId + " " + runNumber); + } + } + else{ + throw new Exception("No subtraction found for " + experimentId + " " + runNumber + "(null)"); + } + } + + @Override + public void addSuperposition(String experimentId, String runNumber, String abinitioModelPdbFilePath, String aprioriPdbFilePath, + String alignedPdbFilePath) throws Exception { + + List subtractions = this.getSubtractionByCode(experimentId, runNumber); + if (subtractions != null){ + Superposition3VO superposition = new Superposition3VO(); + superposition.setSubtractionId(subtractions.get(subtractions.size() - 1).getSubtractionId()); + superposition.setAbinitioModelPdbFilePath(abinitioModelPdbFilePath); + superposition.setAprioriPdbFilePath(aprioriPdbFilePath); + superposition.setAlignedPdbFilePath(alignedPdbFilePath); + superposition.setCreationDate(getNow()); + this.entityManager.merge(superposition); + } + else{ + throw new Exception("No subtraction found for " + experimentId + " " + runNumber + "(null)"); + } + + + } + + @Override + public HashMap getAprioriInformationByRunNumber(String proposal, String acronym) throws Exception { + HashMap info = new HashMap(); + List macromolecules = this.getMacromoleculeByAcronym(proposal, acronym); + if (macromolecules.size() == 1){ + Macromolecule3VO macromolecule = macromolecules.get(0); + if (macromolecule != null){ + info.put("ACRONYM", macromolecule.getAcronym()); + List> pdb = new ArrayList>(); + List> fasta = new ArrayList>(); + List> rbms = new ArrayList>(); + if (macromolecule.getStructure3VOs() != null){ + for (Structure3VO structure : macromolecule.getStructure3VOs()) { + if (structure.getType().equals("PDB")){ + HashMap pdbEntry = new HashMap(); + pdbEntry.put("FILEPATH", structure.getFilePath()); + pdbEntry.put("SYMMETRY", structure.getSymmetry()); + pdbEntry.put("MULTIPLICITY", structure.getMultiplicity()); + pdb.add(pdbEntry); + } + if (structure.getType().equals("SEQUENCE")){ + HashMap fastaEntry = new HashMap(); + fastaEntry.put("FILEPATH", structure.getFilePath()); + fasta.add(fastaEntry); + } + } + } + + HashMap rbm = new HashMap(); + rbm.put("FILEPATH", macromolecule.getContactsDescriptionFilePath()); + rbm.put("SYMMETRY", macromolecule.getSymmetry()); + rbms.add(rbm); + + info.put("PDB", pdb); + info.put("SEQUENCE", fasta); + info.put("RIGIDBODY", rbms); + return info; + } + else{ + throw new Exception("macromolecule not found"); + } + } + else{ + throw new Exception(macromolecules.size() + " macromolecules found"); + } + } + + + private void logFinish(String methodName, long id) { + LOG.debug("### [" + methodName.toUpperCase() + "] Execution time was " + (System.currentTimeMillis() - this.now) + " ms."); + LoggerFormatter.log(LOG, LoggerFormatter.Package.BIOSAXS_WS, methodName, id, System.currentTimeMillis(), + System.currentTimeMillis() - this.now); + + } + + protected long logInit(String methodName, String params) { + LOG.info("-----------------------"); + this.now = System.currentTimeMillis(); + LOG.info(methodName.toUpperCase()); + LoggerFormatter.log(LOG, LoggerFormatter.Package.BIOSAXS_WS, methodName, System.currentTimeMillis(), + System.currentTimeMillis(), params); + return this.now; + } + + @Override + public List getMacromoleculesByProposal(String code, String number) throws Exception { + ProposalWS3VO proposal = proposalService.findForWSByCodeAndNumber(code, number); + return this.saxsProposal3Service.findMacromoleculesByProposalId(proposal.getProposalId()); + } + + @Override + public List getBuffersByProposal(String code, String number) throws Exception { + ProposalWS3VO proposal = proposalService.findForWSByCodeAndNumber(code, number); + return this.saxsProposal3Service.findBuffersByProposalId(proposal.getProposalId()); + } +} diff --git a/ispyb-ejb/src/main/java/ispyb/server/biosaxs/vos/dataAcquisition/Experiment3VO.java b/ispyb-ejb/src/main/java/ispyb/server/biosaxs/vos/dataAcquisition/Experiment3VO.java index c68884135..4610826b9 100644 --- a/ispyb-ejb/src/main/java/ispyb/server/biosaxs/vos/dataAcquisition/Experiment3VO.java +++ b/ispyb-ejb/src/main/java/ispyb/server/biosaxs/vos/dataAcquisition/Experiment3VO.java @@ -1,505 +1,501 @@ -/******************************************************************************* - * This file is part of ISPyB. - * - * ISPyB is free software: you can redistribute it and/or modify - * it under the terms of the GNU Lesser General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * ISPyB is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public License - * along with ISPyB. If not, see . - * - * Contributors : S. Delageniere, R. Leal, L. Launer, K. Levik, S. Veyrier, P. Brenchereau, M. Bodin, A. De Maria Antolinos - ******************************************************************************************************************************/ - -package ispyb.server.biosaxs.vos.dataAcquisition; - -import static javax.persistence.GenerationType.IDENTITY; -import ispyb.server.biosaxs.services.core.plateType.PlateType3Service; -import ispyb.server.biosaxs.vos.assembly.Macromolecule3VO; -import ispyb.server.biosaxs.vos.dataAcquisition.plate.Platetype3VO; -import ispyb.server.biosaxs.vos.dataAcquisition.plate.Sampleplate3VO; -import ispyb.server.biosaxs.vos.dataAcquisition.plate.Sampleplateposition3VO; -import ispyb.server.biosaxs.vos.datacollection.MeasurementTodataCollection3VO; -import ispyb.server.biosaxs.vos.datacollection.SaxsDataCollection3VO; -import ispyb.server.common.util.ejb.Ejb3ServiceLocator; - -import java.util.ArrayList; -import java.util.Date; -import java.util.HashSet; -import java.util.Iterator; -import java.util.List; -import java.util.Set; - -import javax.naming.NamingException; -import javax.persistence.CascadeType; -import javax.persistence.Column; -import javax.persistence.Entity; -import javax.persistence.FetchType; -import javax.persistence.GeneratedValue; -import javax.persistence.Id; -import javax.persistence.JoinColumn; -import javax.persistence.OneToMany; -import javax.persistence.Table; -import javax.persistence.Temporal; -import javax.persistence.TemporalType; -import javax.persistence.Transient; - -/** - * Experiment3VO generated by hbm2java - */ -@Entity -@Table(name = "Experiment") -public class Experiment3VO implements java.io.Serializable { - - private static final long serialVersionUID = 1L; - - protected Integer experimentId; - - protected Integer sessionId; - - protected String name; - - protected Date creationDate; - - protected String sourceFilePath; - - protected String type; - - protected String comments; - - protected String dataAcquisitionFilePath; - - protected String status; - - protected int proposalId; - - protected Set samplePlate3VOs = new HashSet(0); - - protected List platetype3VOs = new ArrayList(); - - protected Set samples3VOs = new HashSet(0); - - protected Set dataCollections = new HashSet(0); - - /** Services for filling up plate types **/ - private static final Ejb3ServiceLocator ejb3ServiceLocator = Ejb3ServiceLocator.getInstance(); - - private PlateType3Service plateType3Service; - - public Experiment3VO() { - try { - this.plateType3Service = (PlateType3Service) ejb3ServiceLocator.getLocalService(PlateType3Service.class); - this.platetype3VOs = this.plateType3Service.findAll(); - } catch (NamingException e) { - // //e.printStackTrace(); - } - } - - @Id - @GeneratedValue(strategy = IDENTITY) - @Column(name = "experimentId", unique = true, nullable = false) - public Integer getExperimentId() { - return this.experimentId; - } - - public void setExperimentId(Integer experimentId) { - this.experimentId = experimentId; - } - - @Column(name = "name") - public String getName() { - return this.name; - } - - public void setName(String name) { - this.name = name; - } - - @Column(name = "sessionId") - public Integer getSessionId() { - return this.sessionId; - } - - public void setSessionId(Integer sessionId) { - this.sessionId = sessionId; - } - - @Temporal(TemporalType.TIMESTAMP) - @Column(name = "creationDate", length = 0) - public Date getCreationDate() { - return this.creationDate; - } - - public void setCreationDate(Date creationDate) { - this.creationDate = creationDate; - } - - @Column(name = "comments", length = 512) - public String getComments() { - return this.comments; - } - - public void setComments(String comments) { - this.comments = comments; - } - - @Column(name = "proposalId") - public int getProposalId() { - return this.proposalId; - } - - public void setProposalId(int proposalId) { - this.proposalId = proposalId; - } - - /** - * TRANSIENT METHODS *. - * - * @param macromolecules - * List of all the macromolecules of the proposal which this experiment belongs to - * @return the macromolecules - */ - @Transient - public Set getMacromolecules() { - Set macromolecules = new HashSet(); - for (Specimen3VO sample : this.getSamples()) { - if (sample.getMacromolecule3VO() != null) { - macromolecules.add(sample.getMacromolecule3VO()); - } - } - return macromolecules; - } - - @Transient - public List getMeasurements() { - List specimen3VOs = new ArrayList(); - for (Specimen3VO sample : this.getSamples()) { - specimen3VOs.addAll(sample.getMeasurements()); - } - - return specimen3VOs; - } - - @Transient - public Specimen3VO getSampleWithThisBufferId(int bufferId) { - for (Specimen3VO sample : this.getSamples()) { - if (sample.getBufferId().equals(bufferId) && (sample.getMacromolecule3VO() == null)) { - return sample; - } - } - return null; - } - - @OneToMany(fetch = FetchType.LAZY, cascade = CascadeType.REMOVE) - @JoinColumn(name = "experimentId") - public Set getSamplePlate3VOs() { - return samplePlate3VOs; - } - - public void setSamplePlate3VOs(Set samplePlate3VOs) { - this.samplePlate3VOs = samplePlate3VOs; - } - - @Transient - public List getPlatetype3VOs() { - if (this.platetype3VOs == null) { - try { - this.plateType3Service = (PlateType3Service) ejb3ServiceLocator - .getLocalService(PlateType3Service.class); - this.platetype3VOs = this.plateType3Service.findAll(); - } catch (NamingException e) { - e.printStackTrace(); - } - } - return this.platetype3VOs; - } - - @Transient - public Measurement3VO getMeasurementById(Integer measurementId) { - List measurements = this.getMeasurements(); - for (Measurement3VO measurement : measurements) { - // System.out.println("Experiment3VO.getSpecimenById: " + measurement); - if (measurement.getMeasurementId() != null) { - if (measurement.getMeasurementId().equals(measurementId)) { - return measurement; - } - } - } - return null; - } - - @Transient - public Sampleplate3VO getSamplePlateById(Integer samplePlateId) { - Set samplePlates = this.getSamplePlate3VOs(); - for (Sampleplate3VO samplePlate : samplePlates) { - if (samplePlate.getSamplePlateId().equals(samplePlateId)) { - return samplePlate; - } - } - return null; - } - - @Transient - public Sampleplateposition3VO getPosition(Integer samplePlateId, int row, int well) { - Sampleplate3VO samplePlate = this.getSamplePlateById(samplePlateId); - if (samplePlate != null) { - for (Sampleplateposition3VO position : samplePlate.getSampleplateposition3VOs()) { - if ((position.getRowNumber() == row) && (well == position.getColumnNumber())) { - return position; - } - } - } - - /** If not found **/ - return null; - - } - - - @Transient - public String getCodeSample(Specimen3VO sample) { - int count = 1; - String name = new String(); - do { - if (sample.getMacromolecule3VO() != null) { - name = sample.getMacromolecule3VO().getAcronym() + "_" + "Buffer_Not-Know";// this.getBufferById(sample.getBufferId()).getAcronym(); - } else { - name = "Buffer_Not-Know"; // this.getBufferById(sample.getBufferId()).getAcronym(); - } - if (count > 0) { - name = name + "-" + count; - } - count++; - } while (this.isSpecimenCodeUsed(name, sample)); - return name; - - } - - @Transient - public boolean isSpecimenCodeUsed(String code, Specimen3VO specimen) { - Set samples = this.getSamples(); - for (Specimen3VO sample3vo : samples) { - if (sample3vo.getCode().equals(code)) { - if (specimen.getSpecimenId() == null) { - return true; - } else { - if (specimen.getSpecimenId().equals(sample3vo.getSpecimenId())) { - return false; - } else { - return true; - } - } - } - } - return false; - } - - @OneToMany(fetch = FetchType.EAGER) - @JoinColumn(name = "experimentId") - public Set getDataCollections() { - return dataCollections; - } - - public void setDataCollections(Set dataCollections) { - this.dataCollections = dataCollections; - } - - @Transient - public List getDataCollectionList() { - List list = new ArrayList(); - Iterator iterator = this.getDataCollections().iterator(); - while (iterator.hasNext()) { - list.add(iterator.next()); - } - return list; - } - - @OneToMany(fetch = FetchType.LAZY) - @JoinColumn(name = "experimentId") - public Set getSamples() { - return samples3VOs; - } - - public void setSamples(Set samples) { - this.samples3VOs = samples; - } - - @Transient - public Specimen3VO getSampleById(int sampleId) { - for (Specimen3VO sample : this.getSamples()) { - if (sample.getSpecimenId().equals(sampleId)) { - return sample; - } - } - return null; - - } - - public String getCodeSpecimen(Measurement3VO specimen) { - Specimen3VO sample = this.getSampleById(specimen.getSpecimenId()); - return this.getCodeSpecimen(sample, specimen); - } - - public String getCodeSpecimen(Specimen3VO sample3vo, Measurement3VO specimen) { - String code = sample3vo.getCode();// this.getCodeSample(sample3vo); - if (sample3vo.getMacromolecule3VO() == null) { - return code + "_" + specimen.getExposureTemperature(); - } else { - return code + "_" + specimen.getExposureTemperature() + "_" + sample3vo.getConcentration(); - } - } - - @Transient - public Specimen3VO getSampleByPosition(Sampleplateposition3VO position) { - Set specimens = this.getSamples(); - for (Specimen3VO sample : specimens) { - if (sample.getSampleplateposition3VO() != null) { - Sampleplateposition3VO specimenPosition = sample.getSampleplateposition3VO(); - if (specimenPosition.getSamplePlateId().equals(position.getSamplePlateId())) { - if (specimenPosition.getRowNumber() == position.getRowNumber() - && specimenPosition.getColumnNumber() == position.getColumnNumber()) { - return sample; - } - } - } - } - return null; - } - - @Transient - public SaxsDataCollection3VO getDataCollectionByMeasurementId(int measurementId) { - Measurement3VO measurement = this.getMeasurementById(measurementId); - Set dataCollections = this.getDataCollections(); - for (SaxsDataCollection3VO saxsDataCollection3VO : dataCollections) { - for (MeasurementTodataCollection3VO measurementToDataCollection : saxsDataCollection3VO - .getMeasurementtodatacollection3VOs()) { - if (measurement.getMeasurementId().equals(measurementToDataCollection.getMeasurementId())) { - return saxsDataCollection3VO; - } - } - } - return null; - } - - @Transient - public List getDataCollectionListByMeasurementId(int measurementId) { - List list = new ArrayList(); - Measurement3VO measurement = this.getMeasurementById(measurementId); - Set dataCollections = this.getDataCollections(); - for (SaxsDataCollection3VO saxsDataCollection3VO : dataCollections) { - for (MeasurementTodataCollection3VO measurementToDataCollection : saxsDataCollection3VO - .getMeasurementtodatacollection3VOs()) { - if (measurement.getMeasurementId().equals(measurementToDataCollection.getMeasurementId())) { - list.add(saxsDataCollection3VO); - } - } - } - return list; - } - - @Transient - public List getMeasurementsOfDataCollectionByMeasurementId(int measurementId) { - SaxsDataCollection3VO dc = getDataCollectionByMeasurementId(measurementId); - List list = new ArrayList(); - for (MeasurementTodataCollection3VO iterable_element : dc.getMeasurementtodatacollection3VOs()) { - list.add(iterable_element); - } - return list; - } - - @Transient - public SaxsDataCollection3VO getDataCollectionById(int dataCollectionId) { - Set dataCollections = this.getDataCollections(); - for (SaxsDataCollection3VO saxsDataCollection3VO : dataCollections) { - if (saxsDataCollection3VO.equals(dataCollectionId)) { - return saxsDataCollection3VO; - } - } - return null; - } - - @Transient - public Measurement3VO getMeasurementBefore(int measurementId) { - Integer measurementBeforeId = this.getMeasurementIdBefore(measurementId); - if (measurementBeforeId != null) - return this.getMeasurementById(measurementBeforeId); - return null; - } - - @Transient - public Integer getMeasurementIdBefore(int measurementId) { - SaxsDataCollection3VO dataCollection = this.getDataCollectionByMeasurementId(measurementId); - if (dataCollection != null) { - for (MeasurementTodataCollection3VO measurement : dataCollection.getMeasurementtodatacollection3VOs()) { - if (measurement.getDataCollectionOrder() == 1) { - return measurement.getMeasurementId(); - } - } - } - return null; - } - - @Transient - public Measurement3VO getMeasurementAfter(int measurementId) { - Integer measurementAfterId = this.getMeasurementIdAfter(measurementId); - if (measurementAfterId != null) - return this.getMeasurementById(measurementAfterId); - return null; - } - - @Transient - public Integer getMeasurementIdAfter(int measurementId) { - SaxsDataCollection3VO dataCollection = this.getDataCollectionByMeasurementId(measurementId); - if (dataCollection != null) { - for (MeasurementTodataCollection3VO measurement : dataCollection.getMeasurementtodatacollection3VOs()) { - if (measurement.getDataCollectionOrder() == 3) { - return measurement.getMeasurementId(); - } - } - } - return null; - } - - @Column(name = "sourceFilePath") - public String getSourceFilePath() { - return sourceFilePath; - } - - public void setSourceFilePath(String sourceFilePath) { - this.sourceFilePath = sourceFilePath; - } - - @Column(name = "experimentType") - public String getType() { - return type; - } - - public void setType(String type) { - this.type = type; - } - - @Column(name = "dataAcquisitionFilePath") - public String getDataAcquisitionFilePath() { - return dataAcquisitionFilePath; - } - - public void setDataAcquisitionFilePath(String dataAcquisitionFilePath) { - this.dataAcquisitionFilePath = dataAcquisitionFilePath; - } - - @Column(name = "status") - public String getStatus() { - return status; - } - - public void setStatus(String status) { - this.status = status; - } - -} +/******************************************************************************* + * This file is part of ISPyB. + * + * ISPyB is free software: you can redistribute it and/or modify + * it under the terms of the GNU Lesser General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * ISPyB is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with ISPyB. If not, see . + * + * Contributors : S. Delageniere, R. Leal, L. Launer, K. Levik, S. Veyrier, P. Brenchereau, M. Bodin, A. De Maria Antolinos + ******************************************************************************************************************************/ + +package ispyb.server.biosaxs.vos.dataAcquisition; + +import static javax.persistence.GenerationType.IDENTITY; +//import ispyb.server.biosaxs.services.core.plateType.PlateType3Service; +import ispyb.server.biosaxs.vos.assembly.Macromolecule3VO; +import ispyb.server.biosaxs.vos.dataAcquisition.plate.Platetype3VO; +import ispyb.server.biosaxs.vos.dataAcquisition.plate.Sampleplate3VO; +import ispyb.server.biosaxs.vos.dataAcquisition.plate.Sampleplateposition3VO; +import ispyb.server.biosaxs.vos.datacollection.MeasurementTodataCollection3VO; +import ispyb.server.biosaxs.vos.datacollection.SaxsDataCollection3VO; +import ispyb.server.common.util.ejb.Ejb3ServiceLocator; + +import java.util.ArrayList; +import java.util.Date; +import java.util.HashSet; +import java.util.Iterator; +import java.util.List; +import java.util.Set; + +import javax.naming.NamingException; +import javax.persistence.CascadeType; +import javax.persistence.Column; +import javax.persistence.Entity; +import javax.persistence.FetchType; +import javax.persistence.GeneratedValue; +import javax.persistence.Id; +import javax.persistence.JoinColumn; +import javax.persistence.OneToMany; +import javax.persistence.Table; +import javax.persistence.Temporal; +import javax.persistence.TemporalType; +import javax.persistence.Transient; + +/** + * Experiment3VO generated by hbm2java + */ +@Entity +@Table(name = "Experiment") +public class Experiment3VO implements java.io.Serializable { + + private static final long serialVersionUID = 1L; + + protected Integer experimentId; + + protected Integer sessionId; + + protected String name; + + protected Date creationDate; + + protected String sourceFilePath; + + protected String type; + + protected String comments; + + protected String dataAcquisitionFilePath; + + protected String status; + + protected int proposalId; + + protected Set samplePlate3VOs = new HashSet(0); + + protected List platetype3VOs = new ArrayList(); + + protected Set samples3VOs = new HashSet(0); + + protected Set dataCollections = new HashSet(0); + + /** Services for filling up plate types **/ + private static final Ejb3ServiceLocator ejb3ServiceLocator = Ejb3ServiceLocator.getInstance(); + + //private PlateType3Service plateType3Service; + + public Experiment3VO() { + // TODO remove this : not correct design no service should be called from a VO to be replaced by the init method of ExperimentService +// try { +// this.plateType3Service = (PlateType3Service) ejb3ServiceLocator.getLocalService(PlateType3Service.class); +// this.platetype3VOs = this.plateType3Service.findAll(); +// } catch (NamingException e) { +// e.printStackTrace(); +// } + } + + @Id + @GeneratedValue(strategy = IDENTITY) + @Column(name = "experimentId", unique = true, nullable = false) + public Integer getExperimentId() { + return this.experimentId; + } + + public void setExperimentId(Integer experimentId) { + this.experimentId = experimentId; + } + + @Column(name = "name") + public String getName() { + return this.name; + } + + public void setName(String name) { + this.name = name; + } + + @Column(name = "sessionId") + public Integer getSessionId() { + return this.sessionId; + } + + public void setSessionId(Integer sessionId) { + this.sessionId = sessionId; + } + + @Temporal(TemporalType.TIMESTAMP) + @Column(name = "creationDate", length = 0) + public Date getCreationDate() { + return this.creationDate; + } + + public void setCreationDate(Date creationDate) { + this.creationDate = creationDate; + } + + @Column(name = "comments", length = 512) + public String getComments() { + return this.comments; + } + + public void setComments(String comments) { + this.comments = comments; + } + + @Column(name = "proposalId") + public int getProposalId() { + return this.proposalId; + } + + public void setProposalId(int proposalId) { + this.proposalId = proposalId; + } + + /** + * TRANSIENT METHODS *. + * + * @param macromolecules + * List of all the macromolecules of the proposal which this experiment belongs to + * @return the macromolecules + */ + @Transient + public Set getMacromolecules() { + Set macromolecules = new HashSet(); + for (Specimen3VO sample : this.getSamples()) { + if (sample.getMacromolecule3VO() != null) { + macromolecules.add(sample.getMacromolecule3VO()); + } + } + return macromolecules; + } + + @Transient + public List getMeasurements() { + List specimen3VOs = new ArrayList(); + for (Specimen3VO sample : this.getSamples()) { + specimen3VOs.addAll(sample.getMeasurements()); + } + + return specimen3VOs; + } + + @Transient + public Specimen3VO getSampleWithThisBufferId(int bufferId) { + for (Specimen3VO sample : this.getSamples()) { + if (sample.getBufferId().equals(bufferId) && (sample.getMacromolecule3VO() == null)) { + return sample; + } + } + return null; + } + + @OneToMany(fetch = FetchType.LAZY, cascade = CascadeType.REMOVE) + @JoinColumn(name = "experimentId") + public Set getSamplePlate3VOs() { + return samplePlate3VOs; + } + + public void setSamplePlate3VOs(Set samplePlate3VOs) { + this.samplePlate3VOs = samplePlate3VOs; + } + + @Transient + public List getPlatetype3VOs() { + return this.platetype3VOs; + } + + public void setPlatetype3VOs(List platetype3vOs) { + platetype3VOs = platetype3vOs; + } + + @Transient + public Measurement3VO getMeasurementById(Integer measurementId) { + List measurements = this.getMeasurements(); + for (Measurement3VO measurement : measurements) { + // System.out.println("Experiment3VO.getSpecimenById: " + measurement); + if (measurement.getMeasurementId() != null) { + if (measurement.getMeasurementId().equals(measurementId)) { + return measurement; + } + } + } + return null; + } + + @Transient + public Sampleplate3VO getSamplePlateById(Integer samplePlateId) { + Set samplePlates = this.getSamplePlate3VOs(); + for (Sampleplate3VO samplePlate : samplePlates) { + if (samplePlate.getSamplePlateId().equals(samplePlateId)) { + return samplePlate; + } + } + return null; + } + + @Transient + public Sampleplateposition3VO getPosition(Integer samplePlateId, int row, int well) { + Sampleplate3VO samplePlate = this.getSamplePlateById(samplePlateId); + if (samplePlate != null) { + for (Sampleplateposition3VO position : samplePlate.getSampleplateposition3VOs()) { + if ((position.getRowNumber() == row) && (well == position.getColumnNumber())) { + return position; + } + } + } + + /** If not found **/ + return null; + + } + + + @Transient + public String getCodeSample(Specimen3VO sample) { + int count = 1; + String name = new String(); + do { + if (sample.getMacromolecule3VO() != null) { + name = sample.getMacromolecule3VO().getAcronym() + "_" + "Buffer_Not-Know";// this.getBufferById(sample.getBufferId()).getAcronym(); + } else { + name = "Buffer_Not-Know"; // this.getBufferById(sample.getBufferId()).getAcronym(); + } + if (count > 0) { + name = name + "-" + count; + } + count++; + } while (this.isSpecimenCodeUsed(name, sample)); + return name; + + } + + @Transient + public boolean isSpecimenCodeUsed(String code, Specimen3VO specimen) { + Set samples = this.getSamples(); + for (Specimen3VO sample3vo : samples) { + if (sample3vo.getCode().equals(code)) { + if (specimen.getSpecimenId() == null) { + return true; + } else { + if (specimen.getSpecimenId().equals(sample3vo.getSpecimenId())) { + return false; + } else { + return true; + } + } + } + } + return false; + } + + @OneToMany(fetch = FetchType.EAGER) + @JoinColumn(name = "experimentId") + public Set getDataCollections() { + return dataCollections; + } + + public void setDataCollections(Set dataCollections) { + this.dataCollections = dataCollections; + } + + @Transient + public List getDataCollectionList() { + List list = new ArrayList(); + Iterator iterator = this.getDataCollections().iterator(); + while (iterator.hasNext()) { + list.add(iterator.next()); + } + return list; + } + + @OneToMany(fetch = FetchType.LAZY) + @JoinColumn(name = "experimentId") + public Set getSamples() { + return samples3VOs; + } + + public void setSamples(Set samples) { + this.samples3VOs = samples; + } + + @Transient + public Specimen3VO getSampleById(int sampleId) { + for (Specimen3VO sample : this.getSamples()) { + if (sample.getSpecimenId().equals(sampleId)) { + return sample; + } + } + return null; + + } + + public String getCodeSpecimen(Measurement3VO specimen) { + Specimen3VO sample = this.getSampleById(specimen.getSpecimenId()); + return this.getCodeSpecimen(sample, specimen); + } + + public String getCodeSpecimen(Specimen3VO sample3vo, Measurement3VO specimen) { + String code = sample3vo.getCode();// this.getCodeSample(sample3vo); + if (sample3vo.getMacromolecule3VO() == null) { + return code + "_" + specimen.getExposureTemperature(); + } else { + return code + "_" + specimen.getExposureTemperature() + "_" + sample3vo.getConcentration(); + } + } + + @Transient + public Specimen3VO getSampleByPosition(Sampleplateposition3VO position) { + Set specimens = this.getSamples(); + for (Specimen3VO sample : specimens) { + if (sample.getSampleplateposition3VO() != null) { + Sampleplateposition3VO specimenPosition = sample.getSampleplateposition3VO(); + if (specimenPosition.getSamplePlateId().equals(position.getSamplePlateId())) { + if (specimenPosition.getRowNumber() == position.getRowNumber() + && specimenPosition.getColumnNumber() == position.getColumnNumber()) { + return sample; + } + } + } + } + return null; + } + + @Transient + public SaxsDataCollection3VO getDataCollectionByMeasurementId(int measurementId) { + Measurement3VO measurement = this.getMeasurementById(measurementId); + Set dataCollections = this.getDataCollections(); + for (SaxsDataCollection3VO saxsDataCollection3VO : dataCollections) { + for (MeasurementTodataCollection3VO measurementToDataCollection : saxsDataCollection3VO + .getMeasurementtodatacollection3VOs()) { + if (measurement.getMeasurementId().equals(measurementToDataCollection.getMeasurementId())) { + return saxsDataCollection3VO; + } + } + } + return null; + } + + @Transient + public List getDataCollectionListByMeasurementId(int measurementId) { + List list = new ArrayList(); + Measurement3VO measurement = this.getMeasurementById(measurementId); + Set dataCollections = this.getDataCollections(); + for (SaxsDataCollection3VO saxsDataCollection3VO : dataCollections) { + for (MeasurementTodataCollection3VO measurementToDataCollection : saxsDataCollection3VO + .getMeasurementtodatacollection3VOs()) { + if (measurement.getMeasurementId().equals(measurementToDataCollection.getMeasurementId())) { + list.add(saxsDataCollection3VO); + } + } + } + return list; + } + + @Transient + public List getMeasurementsOfDataCollectionByMeasurementId(int measurementId) { + SaxsDataCollection3VO dc = getDataCollectionByMeasurementId(measurementId); + List list = new ArrayList(); + for (MeasurementTodataCollection3VO iterable_element : dc.getMeasurementtodatacollection3VOs()) { + list.add(iterable_element); + } + return list; + } + + @Transient + public SaxsDataCollection3VO getDataCollectionById(int dataCollectionId) { + Set dataCollections = this.getDataCollections(); + for (SaxsDataCollection3VO saxsDataCollection3VO : dataCollections) { + if (saxsDataCollection3VO.equals(dataCollectionId)) { + return saxsDataCollection3VO; + } + } + return null; + } + + @Transient + public Measurement3VO getMeasurementBefore(int measurementId) { + Integer measurementBeforeId = this.getMeasurementIdBefore(measurementId); + if (measurementBeforeId != null) + return this.getMeasurementById(measurementBeforeId); + return null; + } + + @Transient + public Integer getMeasurementIdBefore(int measurementId) { + SaxsDataCollection3VO dataCollection = this.getDataCollectionByMeasurementId(measurementId); + if (dataCollection != null) { + for (MeasurementTodataCollection3VO measurement : dataCollection.getMeasurementtodatacollection3VOs()) { + if (measurement.getDataCollectionOrder() == 1) { + return measurement.getMeasurementId(); + } + } + } + return null; + } + + @Transient + public Measurement3VO getMeasurementAfter(int measurementId) { + Integer measurementAfterId = this.getMeasurementIdAfter(measurementId); + if (measurementAfterId != null) + return this.getMeasurementById(measurementAfterId); + return null; + } + + @Transient + public Integer getMeasurementIdAfter(int measurementId) { + SaxsDataCollection3VO dataCollection = this.getDataCollectionByMeasurementId(measurementId); + if (dataCollection != null) { + for (MeasurementTodataCollection3VO measurement : dataCollection.getMeasurementtodatacollection3VOs()) { + if (measurement.getDataCollectionOrder() == 3) { + return measurement.getMeasurementId(); + } + } + } + return null; + } + + @Column(name = "sourceFilePath") + public String getSourceFilePath() { + return sourceFilePath; + } + + public void setSourceFilePath(String sourceFilePath) { + this.sourceFilePath = sourceFilePath; + } + + @Column(name = "experimentType") + public String getType() { + return type; + } + + public void setType(String type) { + this.type = type; + } + + @Column(name = "dataAcquisitionFilePath") + public String getDataAcquisitionFilePath() { + return dataAcquisitionFilePath; + } + + public void setDataAcquisitionFilePath(String dataAcquisitionFilePath) { + this.dataAcquisitionFilePath = dataAcquisitionFilePath; + } + + @Column(name = "status") + public String getStatus() { + return status; + } + + public void setStatus(String status) { + this.status = status; + } + +} diff --git a/ispyb-ui/pom.xml b/ispyb-ui/pom.xml index 7d2baa67a..8710e2a4b 100644 --- a/ispyb-ui/pom.xml +++ b/ispyb-ui/pom.xml @@ -179,12 +179,17 @@ org.hibernate hibernate-core - 4.0.0.Final + 5.0.10.Final + provided antlr antlr + + dom4j + dom4j + @@ -470,4 +475,4 @@ - + \ No newline at end of file diff --git a/ispyb-ui/src/main/java/ispyb/client/biosaxs/dataAdapter/BiosaxsActions.java b/ispyb-ui/src/main/java/ispyb/client/biosaxs/dataAdapter/BiosaxsActions.java index 5f865c402..3e1b36c2e 100644 --- a/ispyb-ui/src/main/java/ispyb/client/biosaxs/dataAdapter/BiosaxsActions.java +++ b/ispyb-ui/src/main/java/ispyb/client/biosaxs/dataAdapter/BiosaxsActions.java @@ -179,6 +179,7 @@ public Experiment3VO getExperimentById(Integer experimentId, ExperimentScope exp */ public Experiment3VO createExperiment(Integer proposalId, Integer sessionId, String name, String comments, Date createTime) { Experiment3VO experiment = new Experiment3VO(); + experiment = experiment3Service.initPlates(experiment); experiment.setCreationDate(createTime); experiment.setComments(comments); experiment.setName(name); diff --git a/ispyb-ui/src/main/webapp/js/ispyb/min/ispyb-bx.js b/ispyb-ui/src/main/webapp/js/ispyb/min/ispyb-bx.js index a98a06520..23e07209a 100644 --- a/ispyb-ui/src/main/webapp/js/ispyb/min/ispyb-bx.js +++ b/ispyb-ui/src/main/webapp/js/ispyb/min/ispyb-bx.js @@ -38,321 +38,321 @@ Event.prototype = { } }; -function GenericGraph(args) { - this.width = 600; - this.height = 400; - - this.targetId = null; - /** Free spaces in the borders * */ - this.top = 10; - this.left = 10; - this.bottom = 50; - this.right = 40; - - /** Ruler * */ - this.rulerHeight = 50; - this.rulerWidth = 50; - this.rulerStroke = 2; - this.rulerVerticalMarksNumber = 5; - - this.rulerMaxValue = null; - this.rulerMinValue = null; - - /** plot options * */ - this.plotPoints = true; - this.pointRadius = 2; - this.fillOpacityPoint = 0.2; - this.strokeOpacityPoint = 0.2; - - /** Cluster titles * */ - this.clusterTitleHeight = 20; - this.interClassesSpace = 2; - this.interClustersSpace = 4; - this.fontSize = 7; - - /** - * If true classes and title will be rendender in the rule otherwise will be - * integer values - */ - this.plotHorizontalByCluster = true; - - if (args != null) { - if (args.targetId != null) { - this.targetId = args.targetId; - } - if (args.plotHorizontalByCluster != null) { - this.plotHorizontalByCluster = args.plotHorizontalByCluster; - } - if (args.height != null) { - this.height = args.height; - } - if (args.width != null) { - this.width = args.width; - } - if (args.rulerMinValue != null) { - this.rulerMinValue = args.rulerMinValue; - } - if (args.rulerMaxValue != null) { - this.rulerMaxValue = args.rulerMaxValue; - } - if (args.rulerHeight != null) { - this.rulerHeight = args.rulerHeight; - } - - } -} - -GenericGraph.prototype.calculate = function(data) { - var result = {}; - - var checked = this.cleanArray(data); - - /** sorting array * */ - checked.sort(function(a, b) { - return a - b; - }); - - var median = this.getMedian(checked); - - result.median = median; - result.Q1 = Number(this.getQ1(checked)); - result.Q2 = Number(this.getQ2(checked)); - result.Q3 = Number(this.getQ3(checked)); - result.population = checked; - - result.IQR = Number(result.Q3 - result.Q1); - result.outlier_below_limit = result.Q1 - (1.5 * result.IQR); - result.outlier_above_limit = result.Q3 + (1.5 * result.IQR); - result.below_outliers = this.getBelowOutliers(result.outlier_below_limit, checked); - result.above_outliers = this.getAboveOutliers(result.outlier_above_limit, checked); - - result.min_whisker = this.minValueWhisker(result.outlier_below_limit, result.Q1, checked); - result.max_whisker = this.maxValueWhisker(result.outlier_above_limit, result.Q3, checked); - - return result; -}; - -GenericGraph.prototype.drawSVGVerticalText = function(x, y, text, properties) { - var transform = [ "transform", "translate(" + x + ", " + y + "), rotate(-90) " ]; - properties.push(transform); - SVG.drawText(0, 0, text, this.svg, properties); -}; - -/** Plot the numbers on the axis * */ -GenericGraph.prototype.plotRuler = function(rulerProperties) { - - SVG.drawRectangle(rulerProperties.vertical.x, rulerProperties.vertical.y, rulerProperties.vertical.width, rulerProperties.vertical.height, - this.svg, [ [ "fill", "black" ] ]); - var distance = rulerProperties.vertical.height / (this.rulerVerticalMarksNumber + 1); - for ( var i = 0; i <= this.rulerVerticalMarksNumber + 1; i++) { - var deltaHeight = distance * i; - var aux = rulerProperties.vertical.height - deltaHeight; - - var text = Number((aux / rulerProperties.vertical.height) * (rulerProperties.maxPoint - rulerProperties.minPoint) + rulerProperties.minPoint) - .toFixed(3); - - SVG.drawLine(rulerProperties.horizontal.x, this.top + deltaHeight, rulerProperties.horizontal.x - rulerProperties.markWidth, - this.top + deltaHeight, this.svg, [ [ "stroke", "black" ] ]); - SVG.drawText(this.left, this.top + distance * i + 5, text, this.svg, [ [ "style", "font-size:xx-small" ] ]); - /** Drawing the mark up to the end * */ - SVG.drawLine(rulerProperties.horizontal.x, this.top + deltaHeight, this.width - this.right, this.top + deltaHeight, this.svg, [ - [ "stroke", rulerProperties.markColor ], [ "stroke-width", "0.3" ] ]); - - if (i == this.rulerVerticalMarksNumber + 1) { - SVG.drawLine(rulerProperties.horizontal.x, this.top + deltaHeight, this.width - this.right, this.top + deltaHeight, this.svg, [ [ - "stroke", rulerProperties.markColor ] ]); - } - } - - /** Drawing horizontal rulers * */ - if (!this.plotHorizontalByCluster) { - var width = rulerProperties.horizontal.width; - var ratio = width / (rulerProperties.horizontal.xValues.range); - for ( i = 0; i < rulerProperties.horizontal.xValues.values.length; i++) { - var coorX = rulerProperties.horizontal.xValues.values[i] - rulerProperties.horizontal.xValues.min; - SVG.drawText(rulerProperties.horizontal.x + coorX * ratio, this.height - (this.bottom + (this.clusterTitleHeight)), - rulerProperties.horizontal.xValues.values[i], this.svg, [ [ "style", "font-size:small" ] ]); - } - } -}; - -GenericGraph.prototype.plotAxes = function(properties) { - /** - * Drawing canvas plot-free spaces SVG.drawRectangle(0, this.top, this.left, - * this.height, this.svg, [["fill", "pink"]]); SVG.drawRectangle(this.width - - * this.right, this.top, plot.width, plot.height, this.svg, [["fill", - * "pink"]]); SVG.drawRectangle(0, 0, this.width, this.top, this.svg, - * [["fill", "red"]]); SVG.drawRectangle(0, this.height - this.bottom, - * this.width, this.bottom, this.svg, [["fill", "red"]]); - */ - - /** Drawing ruler Space * */ - this.plotRuler({ - minPoint : Number(properties.minPoint), - maxPoint : Number(properties.maxPoint), - markColor : "black", - markWidth : 20, - vertical : { - x : this.left + this.rulerWidth - this.rulerStroke, - y : this.top, - width : this.rulerStroke, - height : this.height - (this.top + this.bottom + this.clusterTitleHeight) - this.rulerHeight - }, - horizontal : { - x : this.left + this.rulerWidth - this.rulerStroke, - y : this.height - (this.bottom + this.clusterTitleHeight + this.rulerHeight), - width : properties.width, - height : this.rulerStroke, - xValues : properties.xValues - } - }); - -}; - -/** Remove nulls and NaN elements in the array * */ -GenericGraph.prototype.cleanArray = function(data) { - var checked = []; - - /** checking data are numbers * */ - for ( var i = 0; i < data.length; i++) { - if (data[i] != null) { - if (!isNaN(data[i])) { - checked.push(data[i]); - } - } - } - return checked; -}; - -GenericGraph.prototype.refresh = function(data) { - document.getElementById(this.targetId).innerHTML = ""; - this.draw(this.targetId, data); -}; - -GenericGraph.prototype.getClassColor = function(className) { - for ( var i = 0; i < this.data.clusters.length; i++) { - var cluster = this.data.clusters[i]; - for ( var j = 0; j < cluster.classes.length; j++) { - var classes = cluster.classes[j]; - if (classes.name == className) { - if (classes.color != null) { - return classes.color; - } - } - } - } - return "black"; -}; - -GenericGraph.prototype.getDimensions = function(data) { - var results = {}; - var points = []; - - this.data = data; - var classesNumber = 0; - var xValues = []; - - for ( var i = 0; i < data.clusters.length; i++) { - var cluster = data.clusters[i]; - if (!this.plotHorizontalByCluster) { - xValues.push(data.clusters[i].x); - } - for ( var j = 0; j < cluster.classes.length; j++) { - var classes = cluster.classes[j]; - points = points.concat(classes.values); - classesNumber = classesNumber + 1; - } - } - - var checked = this.cleanArray(points); - - checked.sort(function(a, b) { - return a - b; - }); - - results.minPoint = checked[0]; - if (this.rulerMinValue != null) { - results.minPoint = this.rulerMinValue; - } - results.maxPoint = checked[checked.length - 1]; - if (this.rulerMaxValue != null) { - results.maxPoint = this.rulerMaxValue; - } - - results.classesNumber = classesNumber; - results.clusterNumber = data.clusters.length; - - var totalInterClassesFreeSpace = (classesNumber - data.clusters.length) * this.interClassesSpace; - var totalInterClusterFreeSpace = (data.clusters.length) * this.interClustersSpace; - results.classWidth = (this.width - (this.rulerWidth + this.left + this.right + totalInterClassesFreeSpace + totalInterClusterFreeSpace))/ classesNumber; - results.width = this.width - (this.right + this.left) - this.rulerWidth + this.rulerStroke; - - results.xValues = {}; - - xValues.sort(function(a, b) { - return a - b; - }); - results.xValues.values = xValues; - if (xValues.length > 0) { - results.xValues.min = xValues[0]; - results.xValues.max = xValues[xValues.length - 1]; - results.xValues.range = results.xValues.max - results.xValues.min; - } - return results; - -}; - -GenericGraph.prototype.draw = function(targetId, data) { - this.targetId = targetId; - var properties = (this.getDimensions(data)); - this.svg = SVG.createSVGCanvas(document.getElementById(this.targetId), [ [ "width", this.width ], [ "height", this.height ] ]); - this.plotAxes(properties); -}; - -GenericGraph.prototype.getMedian = function(checked) { - /** Calculating median * */ - if (checked.length % 2 == 1) { - return checked[Math.floor(checked.length / 2)]; - } else { - return (Number(checked[(checked.length / 2) - 1]) + Number(checked[checked.length / 2])) / 2; - } -}; - -GenericGraph.prototype.pointToPixel = function(value, boxProperties) { - var ratio = (value - boxProperties.minPoint) / (boxProperties.maxPoint - boxProperties.minPoint); - var pixelLength = boxProperties.height - boxProperties.y + this.top; - return (-1 * ratio) * (pixelLength) + (boxProperties.y + boxProperties.height); -}; - -GenericGraph.prototype.maxValueWhisker = function(aboveLimit, q3, array) { - var points = []; - for ( var i = 0; i < array.length; i++) { - if ((array[i] > q3) && (array[i]) <= aboveLimit) { - points.push(array[i]); - } - } - if (points.length > 0) { - points.sort(function(a, b) { - return a - b; - }); - return points[points.length - 1]; - } - return null; -}; - -GenericGraph.prototype.input = function() { - return DATADOC.getBoxWhikerData(); -}; - -GenericGraph.prototype.test = function(targetId) { - var plot = new GenericGraph({ - targetId : targetId, - height : 350, - width : 450, - maxBoxWidth : 25 - }); - plot.refresh(this.input()); -}; +function GenericGraph(args) { + this.width = 600; + this.height = 400; + + this.targetId = null; + /** Free spaces in the borders * */ + this.top = 10; + this.left = 10; + this.bottom = 50; + this.right = 40; + + /** Ruler * */ + this.rulerHeight = 50; + this.rulerWidth = 50; + this.rulerStroke = 2; + this.rulerVerticalMarksNumber = 5; + + this.rulerMaxValue = null; + this.rulerMinValue = null; + + /** plot options * */ + this.plotPoints = true; + this.pointRadius = 2; + this.fillOpacityPoint = 0.2; + this.strokeOpacityPoint = 0.2; + + /** Cluster titles * */ + this.clusterTitleHeight = 20; + this.interClassesSpace = 2; + this.interClustersSpace = 4; + this.fontSize = 7; + + /** + * If true classes and title will be rendender in the rule otherwise will be + * integer values + */ + this.plotHorizontalByCluster = true; + + if (args != null) { + if (args.targetId != null) { + this.targetId = args.targetId; + } + if (args.plotHorizontalByCluster != null) { + this.plotHorizontalByCluster = args.plotHorizontalByCluster; + } + if (args.height != null) { + this.height = args.height; + } + if (args.width != null) { + this.width = args.width; + } + if (args.rulerMinValue != null) { + this.rulerMinValue = args.rulerMinValue; + } + if (args.rulerMaxValue != null) { + this.rulerMaxValue = args.rulerMaxValue; + } + if (args.rulerHeight != null) { + this.rulerHeight = args.rulerHeight; + } + + } +} + +GenericGraph.prototype.calculate = function(data) { + var result = {}; + + var checked = this.cleanArray(data); + + /** sorting array * */ + checked.sort(function(a, b) { + return a - b; + }); + + var median = this.getMedian(checked); + + result.median = median; + result.Q1 = Number(this.getQ1(checked)); + result.Q2 = Number(this.getQ2(checked)); + result.Q3 = Number(this.getQ3(checked)); + result.population = checked; + + result.IQR = Number(result.Q3 - result.Q1); + result.outlier_below_limit = result.Q1 - (1.5 * result.IQR); + result.outlier_above_limit = result.Q3 + (1.5 * result.IQR); + result.below_outliers = this.getBelowOutliers(result.outlier_below_limit, checked); + result.above_outliers = this.getAboveOutliers(result.outlier_above_limit, checked); + + result.min_whisker = this.minValueWhisker(result.outlier_below_limit, result.Q1, checked); + result.max_whisker = this.maxValueWhisker(result.outlier_above_limit, result.Q3, checked); + + return result; +}; + +GenericGraph.prototype.drawSVGVerticalText = function(x, y, text, properties) { + var transform = [ "transform", "translate(" + x + ", " + y + "), rotate(-90) " ]; + properties.push(transform); + SVG.drawText(0, 0, text, this.svg, properties); +}; + +/** Plot the numbers on the axis * */ +GenericGraph.prototype.plotRuler = function(rulerProperties) { + + SVG.drawRectangle(rulerProperties.vertical.x, rulerProperties.vertical.y, rulerProperties.vertical.width, rulerProperties.vertical.height, + this.svg, [ [ "fill", "black" ] ]); + var distance = rulerProperties.vertical.height / (this.rulerVerticalMarksNumber + 1); + for ( var i = 0; i <= this.rulerVerticalMarksNumber + 1; i++) { + var deltaHeight = distance * i; + var aux = rulerProperties.vertical.height - deltaHeight; + + var text = Number((aux / rulerProperties.vertical.height) * (rulerProperties.maxPoint - rulerProperties.minPoint) + rulerProperties.minPoint) + .toFixed(3); + + SVG.drawLine(rulerProperties.horizontal.x, this.top + deltaHeight, rulerProperties.horizontal.x - rulerProperties.markWidth, + this.top + deltaHeight, this.svg, [ [ "stroke", "black" ] ]); + SVG.drawText(this.left, this.top + distance * i + 5, text, this.svg, [ [ "style", "font-size:xx-small" ] ]); + /** Drawing the mark up to the end * */ + SVG.drawLine(rulerProperties.horizontal.x, this.top + deltaHeight, this.width - this.right, this.top + deltaHeight, this.svg, [ + [ "stroke", rulerProperties.markColor ], [ "stroke-width", "0.3" ] ]); + + if (i == this.rulerVerticalMarksNumber + 1) { + SVG.drawLine(rulerProperties.horizontal.x, this.top + deltaHeight, this.width - this.right, this.top + deltaHeight, this.svg, [ [ + "stroke", rulerProperties.markColor ] ]); + } + } + + /** Drawing horizontal rulers * */ + if (!this.plotHorizontalByCluster) { + var width = rulerProperties.horizontal.width; + var ratio = width / (rulerProperties.horizontal.xValues.range); + for ( i = 0; i < rulerProperties.horizontal.xValues.values.length; i++) { + var coorX = rulerProperties.horizontal.xValues.values[i] - rulerProperties.horizontal.xValues.min; + SVG.drawText(rulerProperties.horizontal.x + coorX * ratio, this.height - (this.bottom + (this.clusterTitleHeight)), + rulerProperties.horizontal.xValues.values[i], this.svg, [ [ "style", "font-size:small" ] ]); + } + } +}; + +GenericGraph.prototype.plotAxes = function(properties) { + /** + * Drawing canvas plot-free spaces SVG.drawRectangle(0, this.top, this.left, + * this.height, this.svg, [["fill", "pink"]]); SVG.drawRectangle(this.width - + * this.right, this.top, plot.width, plot.height, this.svg, [["fill", + * "pink"]]); SVG.drawRectangle(0, 0, this.width, this.top, this.svg, + * [["fill", "red"]]); SVG.drawRectangle(0, this.height - this.bottom, + * this.width, this.bottom, this.svg, [["fill", "red"]]); + */ + + /** Drawing ruler Space * */ + this.plotRuler({ + minPoint : Number(properties.minPoint), + maxPoint : Number(properties.maxPoint), + markColor : "black", + markWidth : 20, + vertical : { + x : this.left + this.rulerWidth - this.rulerStroke, + y : this.top, + width : this.rulerStroke, + height : this.height - (this.top + this.bottom + this.clusterTitleHeight) - this.rulerHeight + }, + horizontal : { + x : this.left + this.rulerWidth - this.rulerStroke, + y : this.height - (this.bottom + this.clusterTitleHeight + this.rulerHeight), + width : properties.width, + height : this.rulerStroke, + xValues : properties.xValues + } + }); + +}; + +/** Remove nulls and NaN elements in the array * */ +GenericGraph.prototype.cleanArray = function(data) { + var checked = []; + + /** checking data are numbers * */ + for ( var i = 0; i < data.length; i++) { + if (data[i] != null) { + if (!isNaN(data[i])) { + checked.push(data[i]); + } + } + } + return checked; +}; + +GenericGraph.prototype.refresh = function(data) { + document.getElementById(this.targetId).innerHTML = ""; + this.draw(this.targetId, data); +}; + +GenericGraph.prototype.getClassColor = function(className) { + for ( var i = 0; i < this.data.clusters.length; i++) { + var cluster = this.data.clusters[i]; + for ( var j = 0; j < cluster.classes.length; j++) { + var classes = cluster.classes[j]; + if (classes.name == className) { + if (classes.color != null) { + return classes.color; + } + } + } + } + return "black"; +}; + +GenericGraph.prototype.getDimensions = function(data) { + var results = {}; + var points = []; + + this.data = data; + var classesNumber = 0; + var xValues = []; + + for ( var i = 0; i < data.clusters.length; i++) { + var cluster = data.clusters[i]; + if (!this.plotHorizontalByCluster) { + xValues.push(data.clusters[i].x); + } + for ( var j = 0; j < cluster.classes.length; j++) { + var classes = cluster.classes[j]; + points = points.concat(classes.values); + classesNumber = classesNumber + 1; + } + } + + var checked = this.cleanArray(points); + + checked.sort(function(a, b) { + return a - b; + }); + + results.minPoint = checked[0]; + if (this.rulerMinValue != null) { + results.minPoint = this.rulerMinValue; + } + results.maxPoint = checked[checked.length - 1]; + if (this.rulerMaxValue != null) { + results.maxPoint = this.rulerMaxValue; + } + + results.classesNumber = classesNumber; + results.clusterNumber = data.clusters.length; + + var totalInterClassesFreeSpace = (classesNumber - data.clusters.length) * this.interClassesSpace; + var totalInterClusterFreeSpace = (data.clusters.length) * this.interClustersSpace; + results.classWidth = (this.width - (this.rulerWidth + this.left + this.right + totalInterClassesFreeSpace + totalInterClusterFreeSpace))/ classesNumber; + results.width = this.width - (this.right + this.left) - this.rulerWidth + this.rulerStroke; + + results.xValues = {}; + + xValues.sort(function(a, b) { + return a - b; + }); + results.xValues.values = xValues; + if (xValues.length > 0) { + results.xValues.min = xValues[0]; + results.xValues.max = xValues[xValues.length - 1]; + results.xValues.range = results.xValues.max - results.xValues.min; + } + return results; + +}; + +GenericGraph.prototype.draw = function(targetId, data) { + this.targetId = targetId; + var properties = (this.getDimensions(data)); + this.svg = SVG.createSVGCanvas(document.getElementById(this.targetId), [ [ "width", this.width ], [ "height", this.height ] ]); + this.plotAxes(properties); +}; + +GenericGraph.prototype.getMedian = function(checked) { + /** Calculating median * */ + if (checked.length % 2 == 1) { + return checked[Math.floor(checked.length / 2)]; + } else { + return (Number(checked[(checked.length / 2) - 1]) + Number(checked[checked.length / 2])) / 2; + } +}; + +GenericGraph.prototype.pointToPixel = function(value, boxProperties) { + var ratio = (value - boxProperties.minPoint) / (boxProperties.maxPoint - boxProperties.minPoint); + var pixelLength = boxProperties.height - boxProperties.y + this.top; + return (-1 * ratio) * (pixelLength) + (boxProperties.y + boxProperties.height); +}; + +GenericGraph.prototype.maxValueWhisker = function(aboveLimit, q3, array) { + var points = []; + for ( var i = 0; i < array.length; i++) { + if ((array[i] > q3) && (array[i]) <= aboveLimit) { + points.push(array[i]); + } + } + if (points.length > 0) { + points.sort(function(a, b) { + return a - b; + }); + return points[points.length - 1]; + } + return null; +}; + +GenericGraph.prototype.input = function() { + return DATADOC.getBoxWhikerData(); +}; + +GenericGraph.prototype.test = function(targetId) { + var plot = new GenericGraph({ + targetId : targetId, + height : 350, + width : 450, + maxBoxWidth : 25 + }); + plot.refresh(this.input()); +}; /** * Using dygraph it plots a chart. Params: targetId, labelsContainerId, args @@ -2087,338 +2087,338 @@ MacromoleculeConditionGrid.prototype.test = function(targetId) { panel.render(targetId); }; - -function ItemGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ - this.id = id; - this.args = new Object(); - - this.defaultFormat = new ItemFormat(defaultFormat); - - if(selectedFormat != null){ - this.selected = new ItemFormat(selectedFormat); - } - else{ - this.selected = new ItemFormat(defaultFormat); - } - - if(overFormat != null){ - this.over = new ItemFormat(overFormat); - } - else{ - this.over = new ItemFormat(defaultFormat); - } - - if(draggingFormat != null){ - this.dragging = new ItemFormat(draggingFormat); - } - else{ - this.dragging = new ItemFormat(defaultFormat); - } - - //Events - this.stateChanged = new Event(this); - - - //Attaching events - var _this = this; - this._setEvents(); -}; - -ItemGraphFormatter.prototype.getType = function(){ - return this.args.type; -}; - - -ItemGraphFormatter.prototype.toJSON = function(){ - var json = this.args; - json.defaultFormat = this.getDefault().toJSON(); - json.over = this.getOver().toJSON(); - json.selected = this.getSelected().toJSON(); - json.dragging = this.getDragging().toJSON(); - json.id = this.id; - return json; -}; - -ItemGraphFormatter.prototype.loadFromJSON = function(json){ - this.args = json; - this.defaultFormat = new ItemFormat(json.defaultFormat); - this.over = new ItemFormat(json.over); - this.selected = new ItemFormat(json.selected); - this.dragging = new ItemFormat(json.dragging); - this._setEvents(); -}; - -ItemGraphFormatter.prototype._setEvents = function(){ - //Attaching events - var _this = this; - - this.defaultFormat.changed.attach(function (sender, item){ - _this.over.setSize(_this.defaultFormat.getSize()); - _this.selected.setSize(_this.defaultFormat.getSize()); - _this.dragging.setSize(_this.defaultFormat.getSize()); - _this.stateChanged.notify(_this); - }); - - this.selected.changed.attach(function (sender, item){ - _this.stateChanged.notify(_this); - }); - - this.over.changed.attach(function (sender, item){ - _this.stateChanged.notify(_this); - }); - - this.dragging.changed.attach(function (sender, item){ - _this.stateChanged.notify(_this); - }); -}; - -/** Getters **/ -ItemGraphFormatter.prototype.getId = function(){return this.id;}; -ItemGraphFormatter.prototype.getDefault = function(){return this.defaultFormat;}; -ItemGraphFormatter.prototype.getSelected = function(){return this.selected;}; -ItemGraphFormatter.prototype.getOver = function(){return this.over;}; -ItemGraphFormatter.prototype.getDragging = function(){return this.dragging;}; - -function ItemFormat(args){ - this.defaultFormat = new Object(); - this.args = new Object(); - this.args.title = new Object(); - //Defult properties - this.args.visible = true; - this.args.hidden = false; - this.args.stroke = "#000000"; - this.args.strokeOpacity = 0.8; - this.args["stroke-width"] = 1; - this.args.fill = "#000000"; - this.args["fill-opacity"] = 1; - this.args.size = 1; - this.args.opacity = 1; - this.args.fontSize = "8"; - this.args.fontColor = "#000000"; - - /** For directed edge with arrow **/ - //this.args.arrowSize = 1; - - - if (args != null){ - if (args.visible != null){ - this.args.visible = args.visible; - } - if (args.opacity != null){ - this.args.opacity = args.opacity; - } - if (args.size != null){ - this.args.size = args.size; - } - if (args.hidden != null){ - this.args.hidden = args.hidden; - } - if (args.stroke != null){ - this.args.stroke = this._fixColor(args.stroke); - } - if (args.strokeOpacity != null){ - this.args.strokeOpacity = args.strokeOpacity; - } - if (args["stroke-width"]!=null){ - this.args["stroke-width"] = args["stroke-width"]; - } - if (args["fill-opacity"]!=null){ - this.args["fill-opacity"] = args["fill-opacity"]; - } - if (args.shape!=null){ - this.args.shape = args.shape; - } - if (args.fill!=null){ - this.args.fill = this._fixColor(args.fill); - } - - - if (args.title!=null){ - if (args.title.fontSize!=null){ - this.args.title.fontSize = args.title.fontSize; - } - if (args.title.fill!=null){ - this.args.title.fill = this._fixColor(args.title.fill); - } - } - - /** For directed edge with arrow **/ - /*if (args.arrowSize!=null){ - this.args.arrowSize = args.arrowSize; - }*/ - - } - - this.changed = new Event(); -}; - -ItemFormat.prototype._fixColor = function(color){ - var fixed = color; - if (color.indexOf("green") != -1){ - fixed = '#04B431'; - } - - if (color.indexOf("blue") != -1){ - fixed = '#045FB4'; - } - - if (color.indexOf("red") != -1){ - fixed = '#DF0101'; - } - - if (color.indexOf("black") != -1){ - fixed = '#000000'; - } - - if (color.indexOf("white") != -1){ - fixed = '#FFFFFF'; - } - - if (color.indexOf("#") == -1){ - fixed = "#" + color; - } - return fixed; -}; - -ItemFormat.prototype.toJSON = function(){ - if(this.args.strokeOpacity != null){ - this.args["stroke-opacity"] = this.args.strokeOpacity; - delete this.args.strokeOpacity; - } - -// if(this.args.strokeWidth != null){ -// this.args["stroke-width"] = this.args.strokeWidth; -// delete this.args["stroke-width"]; -// } - - if(this.args.title.fontColor != null){ - this.args.title["font-color"] = this.args.title.fontColor; - } - else{ - this.args.title["font-color"] = this.args.fontColor;//;this.args.title.fontColor; - } - - if(this.args.title.fontSize != null){ - this.args.title["font-size"] = this.args.title.fontSize;//;this.args.title.fontColor; - } - else{ - this.args.title["font-size"] = this.args.fontSize;//;this.args.title.fontColor; - } - //return this.args; - return this.args; -}; - -ItemFormat.prototype.getAttribute = function(name){return this.args[name];}; - -//Getters and Setters -ItemFormat.prototype.setVisible = function(visible){ - if (this.args.visible != visible){ - this.args.visible = visible; - this.changed.notify(this); - } -}; - -ItemFormat.prototype.getVisible = function(){return this.args.visible;}; - -ItemFormat.prototype.setHidden = function(hidden){ - if (this.args.hidden != hidden){ - this.args.hidden = hidden; - this.changed.notify(this); - } -}; - -ItemFormat.prototype.getHidden = function(){return this.args.hidden;}; - - -ItemFormat.prototype.setStroke = function(stroke){ - if (this.args.stroke != stroke){ - this.args.stroke = stroke; - this.changed.notify(this); - } -}; - -ItemFormat.prototype.getStroke = function(){return this.args.stroke;}; - -ItemFormat.prototype.setStrokeOpacity = function(strokeOpacity){ - if (this.args.strokeOpacity != strokeOpacity){ - this.args.strokeOpacity = strokeOpacity; - this.changed.notify(this); - } -}; - -ItemFormat.prototype.getStrokeOpacity = function(){return this.args["stroke-opacity"];}; - -ItemFormat.prototype.setStrokeWidth = function(strokeWidth){ - if (this.args["stroke-width"] != strokeWidth){ - this.args["stroke-width"] = strokeWidth; - this.changed.notify(this); - } -}; - - -ItemFormat.prototype.getFillOpacity = function(){return this.args["fill-opacity"];}; - -ItemFormat.prototype.setfillOpacity = function(strokeWidth){ - if (this.args["fill-opacity"] != strokeWidth){ - this.args["fill-opacity"] = strokeWidth; - this.changed.notify(this); - } -}; - - -ItemFormat.prototype.getStrokeWidth = function(){ - return this.args["stroke-width"]; -}; - -ItemFormat.prototype.setFill = function(fill){ - if (this.args.fill != fill){ - this.args.fill = fill; - this.changed.notify(this); - } -}; - -ItemFormat.prototype.getFill = function(){return this.args.fill;}; - -ItemFormat.prototype.setSize = function(size){ - if (this.args.size != size){ - this.args.size = size; - this.changed.notify(this); - } -}; - -ItemFormat.prototype.getSize = function(){return this.args.size;}; - -ItemFormat.prototype.setOpacity = function(opacity){ - if (this.args.opacity != opacity){ - this.args.opacity = opacity; - this.changed.notify(this); - } -}; - -ItemFormat.prototype.getOpacity = function(){return this.args.opacity;}; - -ItemFormat.prototype.getArrowSize = function(){return this.args.arrowSize;}; - -ItemFormat.prototype.setArrowSize = function(arrowSize){ - if (this.args.arrowSize != arrowSize){ - this.args.arrowSize = arrowSize; - this.changed.notify(this); - } -}; - -ItemFormat.prototype.getFontSize = function(){return this.args.title.fontSize;}; - -ItemFormat.prototype.setFontSize = function(fontSize){ - - if (this.args.title.fontSize != fontSize){ - this.args.title.fontSize = fontSize; - this.changed.notify(this); - } -}; - - - - + +function ItemGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ + this.id = id; + this.args = new Object(); + + this.defaultFormat = new ItemFormat(defaultFormat); + + if(selectedFormat != null){ + this.selected = new ItemFormat(selectedFormat); + } + else{ + this.selected = new ItemFormat(defaultFormat); + } + + if(overFormat != null){ + this.over = new ItemFormat(overFormat); + } + else{ + this.over = new ItemFormat(defaultFormat); + } + + if(draggingFormat != null){ + this.dragging = new ItemFormat(draggingFormat); + } + else{ + this.dragging = new ItemFormat(defaultFormat); + } + + //Events + this.stateChanged = new Event(this); + + + //Attaching events + var _this = this; + this._setEvents(); +}; + +ItemGraphFormatter.prototype.getType = function(){ + return this.args.type; +}; + + +ItemGraphFormatter.prototype.toJSON = function(){ + var json = this.args; + json.defaultFormat = this.getDefault().toJSON(); + json.over = this.getOver().toJSON(); + json.selected = this.getSelected().toJSON(); + json.dragging = this.getDragging().toJSON(); + json.id = this.id; + return json; +}; + +ItemGraphFormatter.prototype.loadFromJSON = function(json){ + this.args = json; + this.defaultFormat = new ItemFormat(json.defaultFormat); + this.over = new ItemFormat(json.over); + this.selected = new ItemFormat(json.selected); + this.dragging = new ItemFormat(json.dragging); + this._setEvents(); +}; + +ItemGraphFormatter.prototype._setEvents = function(){ + //Attaching events + var _this = this; + + this.defaultFormat.changed.attach(function (sender, item){ + _this.over.setSize(_this.defaultFormat.getSize()); + _this.selected.setSize(_this.defaultFormat.getSize()); + _this.dragging.setSize(_this.defaultFormat.getSize()); + _this.stateChanged.notify(_this); + }); + + this.selected.changed.attach(function (sender, item){ + _this.stateChanged.notify(_this); + }); + + this.over.changed.attach(function (sender, item){ + _this.stateChanged.notify(_this); + }); + + this.dragging.changed.attach(function (sender, item){ + _this.stateChanged.notify(_this); + }); +}; + +/** Getters **/ +ItemGraphFormatter.prototype.getId = function(){return this.id;}; +ItemGraphFormatter.prototype.getDefault = function(){return this.defaultFormat;}; +ItemGraphFormatter.prototype.getSelected = function(){return this.selected;}; +ItemGraphFormatter.prototype.getOver = function(){return this.over;}; +ItemGraphFormatter.prototype.getDragging = function(){return this.dragging;}; + +function ItemFormat(args){ + this.defaultFormat = new Object(); + this.args = new Object(); + this.args.title = new Object(); + //Defult properties + this.args.visible = true; + this.args.hidden = false; + this.args.stroke = "#000000"; + this.args.strokeOpacity = 0.8; + this.args["stroke-width"] = 1; + this.args.fill = "#000000"; + this.args["fill-opacity"] = 1; + this.args.size = 1; + this.args.opacity = 1; + this.args.fontSize = "8"; + this.args.fontColor = "#000000"; + + /** For directed edge with arrow **/ + //this.args.arrowSize = 1; + + + if (args != null){ + if (args.visible != null){ + this.args.visible = args.visible; + } + if (args.opacity != null){ + this.args.opacity = args.opacity; + } + if (args.size != null){ + this.args.size = args.size; + } + if (args.hidden != null){ + this.args.hidden = args.hidden; + } + if (args.stroke != null){ + this.args.stroke = this._fixColor(args.stroke); + } + if (args.strokeOpacity != null){ + this.args.strokeOpacity = args.strokeOpacity; + } + if (args["stroke-width"]!=null){ + this.args["stroke-width"] = args["stroke-width"]; + } + if (args["fill-opacity"]!=null){ + this.args["fill-opacity"] = args["fill-opacity"]; + } + if (args.shape!=null){ + this.args.shape = args.shape; + } + if (args.fill!=null){ + this.args.fill = this._fixColor(args.fill); + } + + + if (args.title!=null){ + if (args.title.fontSize!=null){ + this.args.title.fontSize = args.title.fontSize; + } + if (args.title.fill!=null){ + this.args.title.fill = this._fixColor(args.title.fill); + } + } + + /** For directed edge with arrow **/ + /*if (args.arrowSize!=null){ + this.args.arrowSize = args.arrowSize; + }*/ + + } + + this.changed = new Event(); +}; + +ItemFormat.prototype._fixColor = function(color){ + var fixed = color; + if (color.indexOf("green") != -1){ + fixed = '#04B431'; + } + + if (color.indexOf("blue") != -1){ + fixed = '#045FB4'; + } + + if (color.indexOf("red") != -1){ + fixed = '#DF0101'; + } + + if (color.indexOf("black") != -1){ + fixed = '#000000'; + } + + if (color.indexOf("white") != -1){ + fixed = '#FFFFFF'; + } + + if (color.indexOf("#") == -1){ + fixed = "#" + color; + } + return fixed; +}; + +ItemFormat.prototype.toJSON = function(){ + if(this.args.strokeOpacity != null){ + this.args["stroke-opacity"] = this.args.strokeOpacity; + delete this.args.strokeOpacity; + } + +// if(this.args.strokeWidth != null){ +// this.args["stroke-width"] = this.args.strokeWidth; +// delete this.args["stroke-width"]; +// } + + if(this.args.title.fontColor != null){ + this.args.title["font-color"] = this.args.title.fontColor; + } + else{ + this.args.title["font-color"] = this.args.fontColor;//;this.args.title.fontColor; + } + + if(this.args.title.fontSize != null){ + this.args.title["font-size"] = this.args.title.fontSize;//;this.args.title.fontColor; + } + else{ + this.args.title["font-size"] = this.args.fontSize;//;this.args.title.fontColor; + } + //return this.args; + return this.args; +}; + +ItemFormat.prototype.getAttribute = function(name){return this.args[name];}; + +//Getters and Setters +ItemFormat.prototype.setVisible = function(visible){ + if (this.args.visible != visible){ + this.args.visible = visible; + this.changed.notify(this); + } +}; + +ItemFormat.prototype.getVisible = function(){return this.args.visible;}; + +ItemFormat.prototype.setHidden = function(hidden){ + if (this.args.hidden != hidden){ + this.args.hidden = hidden; + this.changed.notify(this); + } +}; + +ItemFormat.prototype.getHidden = function(){return this.args.hidden;}; + + +ItemFormat.prototype.setStroke = function(stroke){ + if (this.args.stroke != stroke){ + this.args.stroke = stroke; + this.changed.notify(this); + } +}; + +ItemFormat.prototype.getStroke = function(){return this.args.stroke;}; + +ItemFormat.prototype.setStrokeOpacity = function(strokeOpacity){ + if (this.args.strokeOpacity != strokeOpacity){ + this.args.strokeOpacity = strokeOpacity; + this.changed.notify(this); + } +}; + +ItemFormat.prototype.getStrokeOpacity = function(){return this.args["stroke-opacity"];}; + +ItemFormat.prototype.setStrokeWidth = function(strokeWidth){ + if (this.args["stroke-width"] != strokeWidth){ + this.args["stroke-width"] = strokeWidth; + this.changed.notify(this); + } +}; + + +ItemFormat.prototype.getFillOpacity = function(){return this.args["fill-opacity"];}; + +ItemFormat.prototype.setfillOpacity = function(strokeWidth){ + if (this.args["fill-opacity"] != strokeWidth){ + this.args["fill-opacity"] = strokeWidth; + this.changed.notify(this); + } +}; + + +ItemFormat.prototype.getStrokeWidth = function(){ + return this.args["stroke-width"]; +}; + +ItemFormat.prototype.setFill = function(fill){ + if (this.args.fill != fill){ + this.args.fill = fill; + this.changed.notify(this); + } +}; + +ItemFormat.prototype.getFill = function(){return this.args.fill;}; + +ItemFormat.prototype.setSize = function(size){ + if (this.args.size != size){ + this.args.size = size; + this.changed.notify(this); + } +}; + +ItemFormat.prototype.getSize = function(){return this.args.size;}; + +ItemFormat.prototype.setOpacity = function(opacity){ + if (this.args.opacity != opacity){ + this.args.opacity = opacity; + this.changed.notify(this); + } +}; + +ItemFormat.prototype.getOpacity = function(){return this.args.opacity;}; + +ItemFormat.prototype.getArrowSize = function(){return this.args.arrowSize;}; + +ItemFormat.prototype.setArrowSize = function(arrowSize){ + if (this.args.arrowSize != arrowSize){ + this.args.arrowSize = arrowSize; + this.changed.notify(this); + } +}; + +ItemFormat.prototype.getFontSize = function(){return this.args.title.fontSize;}; + +ItemFormat.prototype.setFontSize = function(fontSize){ + + if (this.args.title.fontSize != fontSize){ + this.args.title.fontSize = fontSize; + this.changed.notify(this); + } +}; + + + + /** * This class executes the actions @@ -4952,1101 +4952,2095 @@ function openExperiment(experimentId) { BIOSAXS.openExperiment(experimentId); } -var SITE_CONF = { - SAMPLE_CHANGER_CONFIGURATION : { - "3":{ - "platetype3VO": {"plateTypeId":4,"name":"96 Well plate","rowCount":8,"columnCount":12,"shape":"REC"}, - "name":"96 Well plate", - "slotPositionRow":"1", - "slotPositionColumn":"3", - "storageTemperature":"0", - "sampleplateposition3VOs":[], - "experimentId":0 - }, - "2":{ - "platetype3VO":{"plateTypeId":2,"name":" 4 x ( 8 + 3 ) Block","rowCount":4,"columnCount":11,"shape":"REC"}, - "name":" 4 x ( 8 + 3 ) Block", - "slotPositionRow":"1", - "slotPositionColumn":"2", - "storageTemperature":"0", - "sampleplateposition3VOs":[],"experimentId":0 - }, - "1":{ - "platetype3VO":{"plateTypeId":1,"name":"Deep Well","rowCount":8,"columnCount":12,"shape":"REC"}, - "name":"Deep Well", - "slotPositionRow":"1", - "slotPositionColumn":"1", - "storageTemperature":"0", - "sampleplateposition3VOs":[], - "experimentId":0 - } - } +var SITE_CONF = { + SAMPLE_CHANGER_CONFIGURATION : { + "3":{ + "platetype3VO": {"plateTypeId":4,"name":"96 Well plate","rowCount":8,"columnCount":12,"shape":"REC"}, + "name":"96 Well plate", + "slotPositionRow":"1", + "slotPositionColumn":"3", + "storageTemperature":"0", + "sampleplateposition3VOs":[], + "experimentId":0 + }, + "2":{ + "platetype3VO":{"plateTypeId":2,"name":" 4 x ( 8 + 3 ) Block","rowCount":4,"columnCount":11,"shape":"REC"}, + "name":" 4 x ( 8 + 3 ) Block", + "slotPositionRow":"1", + "slotPositionColumn":"2", + "storageTemperature":"0", + "sampleplateposition3VOs":[],"experimentId":0 + }, + "1":{ + "platetype3VO":{"plateTypeId":1,"name":"Deep Well","rowCount":8,"columnCount":12,"shape":"REC"}, + "name":"Deep Well", + "slotPositionRow":"1", + "slotPositionColumn":"1", + "storageTemperature":"0", + "sampleplateposition3VOs":[], + "experimentId":0 + } + } }; - -var ISPYB_CONF = { - load : function(config) { - for (var key in config) { - ISPYB_CONF[key] = config[key]; - } - }, - SAMPLE_CHANGER_CONFIGURATION : { - "1": { - "platetype3VO": {"plateTypeId": 1, "name": "Deep Well", "rowCount": 8, "columnCount": 12, "shape": "REC"}, - "name": "Deep Well", - "slotPositionRow": "1", - "slotPositionColumn": "1", - "storageTemperature": "0", - "sampleplateposition3VOs": [], - "experimentId": 0 - } - } + +var ISPYB_CONF = { + load : function(config) { + for (var key in config) { + ISPYB_CONF[key] = config[key]; + } + }, + SAMPLE_CHANGER_CONFIGURATION : { + "1": { + "platetype3VO": {"plateTypeId": 1, "name": "Deep Well", "rowCount": 8, "columnCount": 12, "shape": "REC"}, + "name": "Deep Well", + "slotPositionRow": "1", + "slotPositionColumn": "1", + "storageTemperature": "0", + "sampleplateposition3VOs": [], + "experimentId": 0 + } + } }; -var SITE_CONF = { - -}; +var SITE_CONF = { + +}; -/** - * Example form - * - * @witdh - * @height - */ -function AbinitioForm(args) { - this.id = BUI.id(); - this.width = null; - this.height = null; - - if (args != null) { - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; - } - } - - var _this = this; - /** Widgets **/ - this.abinitioGrid = new AbinitioGrid({ - width : null, - height : 200 - }); - - this.abinitioGrid.onSelected.attach(function(sender, models) { - var modelsIdList = []; - for ( var i in models) { - modelsIdList.push(models[i].modelId); - } - _this._renderPlot(_this.subtractions[0].subtractionId, modelsIdList); - _this._renderPDB(modelsIdList); - }); - - /** Dygraph Widget that plots fir files**/ - this.plotWidget = new PlotWidget({ - width : 745 / 2, - height : 300, - margin : "10 0 5 10" - }); - - /** PDB viewer **/ - this.viewer = new PDBViewer({ - width : 745 / 2, - height : 300 - }); - -} - -AbinitioForm.prototype._renderPlot = function(subtractionId, modelsIdList) { - /** Trying to plot tje subtraction and the models **/ - try { - var colors = [ "#669900", "#0000FF" ]; - this.plotWidget.refresh([], [ ], modelsIdList, [], [], colors); - } catch (e) { - console.log(e); - } -}; - -AbinitioForm.prototype._renderPDB = function(modelsIdList) { - /** Trying to plot the PDB file **/ - try { - var viz = []; - for (var i = 0; i < modelsIdList.length; i++) { - viz.push({ - modelId : modelsIdList[i], - color : "0xFF6600", - opacity : 0.8 - }); - } - this.viewer.refresh(viz); - } catch (e) { - console.log(e); - } -}; - -AbinitioForm.prototype._getItems = function() { - var _this = this; - return [ { - xtype : 'label', - forId : 'myFieldId', - text : 'INLINE HELP: To be updated', - margin : '15 0 20 10', - cls : "inline-help" - }, this.abinitioGrid.getPanel(), { - xtype : 'container', - layout : 'hbox', - items : [ this.plotWidget.getPanel(), this.viewer.getPanel() ] - } ] -}; - -AbinitioForm.prototype._getButtons = function() { - return []; -}; - -AbinitioForm.prototype.getPanel = function() { - var _this = this; - this.panel = Ext.create('Ext.form.Panel', { - width : this.width, - height : this.height, - margin : 10, - border : 1, - defaultType : 'textfield', - items : this._getItems(), - buttons : this._getButtons(), - listeners : { - afterrender : function() { - _this._populate(); - - } - } - }); - return this.panel; -}; - -/** Populates could be call when the DOM is not filled yet **/ -AbinitioForm.prototype._populate = function() { -}; - -/** It populates the form * */ -AbinitioForm.prototype.refresh = function(subtractions) { - this.subtractions = subtractions; - this.abinitioGrid.refresh(subtractions); -}; - -AbinitioForm.prototype.input = function() { - return {}; -}; - -/** It populates the form **/ -AbinitioForm.prototype.test = function(targetId) { - var macromoleculeForm = new AbinitioForm(); - var panel = macromoleculeForm.getPanel(); - panel.render(targetId); -}; +/** + * Example form + * + * @witdh + * @height + */ +function AbinitioForm(args) { + this.id = BUI.id(); + this.width = null; + this.height = null; -/** - * Example form - * - * @witdh - * @height - */ -function DataReductionForm(args) { - this.id = BUI.id(); - this.width = null; - this.height = null; - - if (args != null) { - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; - } - } - + if (args != null) { + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + } + + var _this = this; + /** Widgets **/ + this.abinitioGrid = new AbinitioGrid({ + width : null, + height : 200 + }); + + this.abinitioGrid.onSelected.attach(function(sender, models) { + var modelsIdList = []; + for ( var i in models) { + modelsIdList.push(models[i].modelId); + } + _this._renderPlot(_this.subtractions[0].subtractionId, modelsIdList); + _this._renderPDB(modelsIdList); + }); + + /** Dygraph Widget that plots fir files**/ + this.plotWidget = new PlotWidget({ + width : 745 / 2, + height : 300, + margin : "10 0 5 10" + }); + + /** PDB viewer **/ + this.viewer = new PDBViewer({ + width : 745 / 2, + height : 300 + }); + +} + +AbinitioForm.prototype._renderPlot = function(subtractionId, modelsIdList) { + /** Trying to plot tje subtraction and the models **/ + try { + var colors = [ "#669900", "#0000FF" ]; + this.plotWidget.refresh([], [ ], modelsIdList, [], [], colors); + } catch (e) { + console.log(e); + } +}; + +AbinitioForm.prototype._renderPDB = function(modelsIdList) { + /** Trying to plot the PDB file **/ + try { + var viz = []; + for (var i = 0; i < modelsIdList.length; i++) { + viz.push({ + modelId : modelsIdList[i], + color : "0xFF6600", + opacity : 0.8 + }); + } + this.viewer.refresh(viz); + } catch (e) { + console.log(e); + } +}; + +AbinitioForm.prototype._getItems = function() { + var _this = this; + return [ { + xtype : 'label', + forId : 'myFieldId', + text : 'INLINE HELP: To be updated', + margin : '15 0 20 10', + cls : "inline-help" + }, this.abinitioGrid.getPanel(), { + xtype : 'container', + layout : 'hbox', + items : [ this.plotWidget.getPanel(), this.viewer.getPanel() ] + } ] +}; + +AbinitioForm.prototype._getButtons = function() { + return []; +}; + +AbinitioForm.prototype.getPanel = function() { + var _this = this; + this.panel = Ext.create('Ext.form.Panel', { + width : this.width, + height : this.height, + margin : 10, + border : 1, + defaultType : 'textfield', + items : this._getItems(), + buttons : this._getButtons(), + listeners : { + afterrender : function() { + _this._populate(); + + } + } + }); + return this.panel; +}; + +/** Populates could be call when the DOM is not filled yet **/ +AbinitioForm.prototype._populate = function() { +}; + +/** It populates the form * */ +AbinitioForm.prototype.refresh = function(subtractions) { + this.subtractions = subtractions; + this.abinitioGrid.refresh(subtractions); +}; + +AbinitioForm.prototype.input = function() { + return {}; +}; + +/** It populates the form **/ +AbinitioForm.prototype.test = function(targetId) { + var macromoleculeForm = new AbinitioForm(); + var panel = macromoleculeForm.getPanel(); + panel.render(targetId); +}; + +/** + * Example form + * + * @witdh + * @height + */ +function DataReductionForm(args) { + this.id = BUI.id(); + this.width = null; + this.height = null; + + if (args != null) { + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + } + + var _this = this; + + /** Widgets **/ + this.plotWidget = new PlotWidget({ + width : 650, + height : 490 + }); + + /** Selected frames to be displayed **/ + this.selectedItems = { + frames : [], + averages : [], + subtractions : [] + }; + +} + +DataReductionForm.prototype._parseSelectedItemsToIds = function(selectedArray) { + var ids = []; + if (selectedArray != null) { + for (var i = 0; i < selectedArray.length; i++) { + ids.push(selectedArray[i].id); + } + } + return ids; +}; + +DataReductionForm.prototype.onSelectionChanged = function(columnName, selected) { + if (selected != null) { + if (columnName == "Frames") { + this.selectedItems.frames = selected; + this.selectedItems.subtractions = []; + } + if (columnName == "Averages") { + this.selectedItems.averages = selected; + } + if (columnName == "Subtractions") { + this.selectedItems.frames = []; + this.selectedItems.subtractions = selected; + } + } + this.plotWidget.refresh(this._parseSelectedItemsToIds(this.selectedItems.frames), this._parseSelectedItemsToIds(this.selectedItems.subtractions)); +}; + +DataReductionForm.prototype._getFramesExtPanel = function(store, columnName, height) { + var _this = this; + + var selModel = Ext.create('Ext.selection.RowModel', { + allowDeselect : true, + mode : 'MULTI', + listeners : { + selectionchange : function(sm, selections) { + var selected = []; + for (var i = 0; i < selections.length; i++) { + selected.push(selections[i].raw); + } + _this.onSelectionChanged(columnName, selected); + } + } + }); + + return Ext.create('Ext.grid.Panel', { + store : store, + margin : 10, + height : height, + width : 200, + selModel : selModel, + columns : [ { + text : columnName, + dataIndex : 'fileName', + flex : 1 + } ], + viewConfig : { + } + }); +}; + +DataReductionForm.prototype._getFramesPanel = function() { + var fields = [ 'fileName', 'type', 'id' ]; + + this.framesStore = Ext.create('Ext.data.Store', { + fields : fields, + sorters : 'fileName' + }); + + this.averagesStore = Ext.create('Ext.data.Store', { + fields : fields + }); + + this.subtractionStore = Ext.create('Ext.data.Store', { + fields : fields + }); + + var gridFrames = this._getFramesExtPanel(this.framesStore, "Frames", 375); + var gridAvgs = this._getFramesExtPanel(this.averagesStore, "Averages", 125); + var subtractionAvgs = this._getFramesExtPanel(this.subtractionStore, "Subtractions", 75); + + return { + xtype : 'container', + layout : 'vbox', + items : [ gridFrames, subtractionAvgs ] + }; +}; + +DataReductionForm.prototype._getImageContainer = function(name, help) { + var html = "
" + name + "
" + return { + xtype : 'container', + layout : 'vbox', + items : [ { + html : html, + margin : "5 0 0 0", + height : 95, + width : 100 + }, { + xtype : 'label', + forId : 'myFieldId', + text : help, + margin : '5 0 0 0', + cls : "inline-help" + } ] + } +}; + +DataReductionForm.prototype._getItems = function() { + var _this = this; + return [ { + xtype : 'container', + layout : 'hbox', + items : [ + this._getFramesPanel(), + this.plotWidget.getPanel(), + { + xtype : 'panel', + width : 110, + frame : true, + margin : "10 5 5 5", + border : 0, + layout : 'vbox', + items : [ this._getImageContainer("scattering", "Scattering"), this._getImageContainer("guinier", "Guinier Region"), + this._getImageContainer("kratky", "Kratky Plot"), this._getImageContainer("gnom", "P(r) distribution") ] + } ] + } ] +}; + +DataReductionForm.prototype._getButtons = function() { + return []; +}; + +DataReductionForm.prototype.getPanel = function() { + var _this = this; + this.panel = Ext.create('Ext.form.Panel', { + width : this.width, + height : this.height, + border : 0, + items : this._getItems(), + buttons : this._getButtons(), + listeners : { + afterrender : function() { + _this._populate(); + } + } + }); + return this.panel; +}; + +/** Populates could be call when the DOM is not filled yet **/ +DataReductionForm.prototype._populate = function() { +}; + +/** It populates the form * */ +DataReductionForm.prototype.refresh = function(subtractions) { + if (subtractions != null) { + for (var i = 0; i < subtractions.length; i++) { + /** Loading frame grids **/ + var subtraction = subtractions[i]; + var averages = [ { + fileName : BUI.getFileName(subtraction.bufferAverageFilePath), + type : 'bufferAvg', + id : subtraction.subtractionId + }, { + fileName : BUI.getFileName(subtraction.sampleAverageFilePath), + type : 'sampleAvg', + id : subtraction.subtractionId + } + + ]; + this.averagesStore.loadData(averages, true); + this.subtractionStore.loadData([ { + fileName : BUI.getFileName(subtraction.substractedFilePath), + type : 'SUBTRACTION', + id : subtraction.subtractionId + } ], true); + + var frames = []; + /** Buffers **/ + if (subtraction.bufferOneDimensionalFiles != null) { + if (subtraction.bufferOneDimensionalFiles.frametolist3VOs != null) { + for (var j = 0; j < subtraction.bufferOneDimensionalFiles.frametolist3VOs.length; j++) { + var frametolist3VO = subtraction.bufferOneDimensionalFiles.frametolist3VOs[j]; + if (frametolist3VO.frame3VO != null) { + frames.push({ + fileName : BUI.getFileName(frametolist3VO.frame3VO.filePath), + type : 'BUFFER', + id : frametolist3VO.frame3VO.frameId + }); + } + } + } + } + /** Samples **/ + if (subtraction.sampleOneDimensionalFiles != null) { + if (subtraction.sampleOneDimensionalFiles.frametolist3VOs != null) { + for (var j = 0; j < subtraction.sampleOneDimensionalFiles.frametolist3VOs.length; j++) { + var frametolist3VO = subtraction.sampleOneDimensionalFiles.frametolist3VOs[j]; + if (frametolist3VO.frame3VO != null) { + frames.push({ + fileName : BUI.getFileName(frametolist3VO.frame3VO.filePath), + type : 'SAMPLE', + id : frametolist3VO.frame3VO.frameId + }); + } + } + } + } + + this.framesStore.loadData(frames, true); + + /** Loading images **/ + this._displayImage("scattering", subtraction.subtractionId); + this._displayImage("kratky", subtraction.subtractionId); + this._displayImage("guinier", subtraction.subtractionId); + this._displayImage("gnom", subtraction.subtractionId); + } + } +}; + +DataReductionForm.prototype._displayImage = function(name, subtractionId) { + var url = BUI.getURL() + '&type=' + name + '&subtractionId=' + subtractionId; + var event = "OnClick= window.open('" + url + "')"; + document.getElementById(this.id + "_" + name).innerHTML = ''; +}; + +DataReductionForm.prototype.input = function() { + return {}; +}; + +/** It populates the form **/ +DataReductionForm.prototype.test = function(targetId) { + var macromoleculeForm = new DataReductionForm(); + var panel = macromoleculeForm.getPanel(); + panel.render(targetId); +}; + +function PlotWidget(args) { + this.width = 600; + this.height = 600; + this.id = BUI.id(); + + this.linear = false; + + this.margin = "10 0 0 0"; + /** for each stat the max and minimum value when it is scaled in order to show correctly in the legend **/ + this.ranges = {}; + if (args != null) { + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + if (args.margin != null) { + this.margin = args.margin; + } + } + +} + +PlotWidget.prototype.getMenu = function() { + var _this = this; + /** Actions buttons **/ + var actions = []; + actions.push("->"); + actions.push({ + text : "Export as Image", + scope : this, + icon : '../images/save.gif', + handler : function(item, pressed) { + var largeImage = document.createElement("img"); + largeImage.style.display = 'block'; + largeImage.style.width = 200 + "px"; + largeImage.style.height = 200 + "px"; + largeImage.setAttribute('src', Dygraph.Export.asCanvas(this.dygraphObject.dygraph).toDataURL()); + window.open(Dygraph.Export.asCanvas(this.dygraphObject.dygraph).toDataURL(), 'Image', ''); + } + }); + + return actions; +}; + +/** Looks for the maximum value and then divide everything but that value **/ +PlotWidget.prototype.scaledData = function(data) { + for (var i = 0; i < data.length; i++) { + var values = this.getMaxAndMinValue(data[i]); + data[i] = this.divideValuesByMax(data[i], values.max); + this.ranges[data[i].label] = values; + } + return data; +}; + +/** Given a stat float[] and a max number it will divide each value by max **/ +PlotWidget.prototype.divideValuesByMax = function(stat, max) { + for (var j = 0; j < stat.data.length; j++) { + if (max != 0) { + stat.data[j] = Number(stat.data[j]) / max; + stat.std[j] = Number(stat.std[j]) / max; + } + } + return stat; +}; + +/** returns max value of a stat **/ +PlotWidget.prototype.getMaxAndMinValue = function(stat) { + var max = 0; + var min = stat.data[0]; + for (var j = 0; j < stat.data.length; j++) { + if (Number(stat.data[j]) > max) { + max = Number(stat.data[j]); + } + if (Number(stat.std[j]) > max) { + max = Number(stat.std[j]); + } + if (Number(stat.data[j]) < min) { + min = Number(stat.data[j]); + } + } + return { + max : Number(max), + min : Number(min) + }; +}; + +PlotWidget.prototype._renderDygraph = function(parsed, colors, labels) { + this.dygraphObject = new StdDevDyGraph(this.id, { + width : this.width - 20, + height : this.height - 40, + xlabel : "", + }); + + this.dygraphObject.draw(parsed, colors, labels); + +}; + +PlotWidget.prototype.getPanel = function() { + this.panel = Ext.create('Ext.panel.Panel', { + width : this.width, + height : this.height, + margin : this.margin, + tbar : this.getMenu(), + items : [ { + html : "", + id : this.id, + width : this.width, + height : this.height, + padding : 10, + margin : "0 0 0 -30", + border : 0 + } ] + }); + + return this.panel; +}; + +PlotWidget.prototype.getPoint = function(y, error) { + var minus = y - error; + var max = y + error; + + if (this.linear) { + return [ Math.abs(minus), y, Math.abs(max) ]; + } + if ((minus != 0) && (max != 0)) { + return [ Math.log(Math.abs(minus)), Math.log(y), Math.log(Math.abs(max)) ]; + } else { + return [ Math.log(y), Math.log(y), Math.log(y) ]; + } + +}; + +PlotWidget.prototype.getDataPlot = function(frames, subtractions, models, fits, rbms) { + var files = []; + var labels = [ "Intensity" ]; + if (frames != null) { + for (var i = 0; i < frames.length; i++) { + files.push(frames[i].data); + labels.push(frames[i].fileName); + } + } + function splitData(data, column, errorColumn, name){ + var result = [] + for (var j = 0; j < data.length; j++) { + console.log(data[j][column]); + result.push([j,data[j][column],data[j][errorColumn]]);//[0, data[i][column],0]]); + } + files.push(result); + labels.push(name); + } + + if (subtractions != null) { + for (var i = 0; i < subtractions.length; i++) { + /** For subtraction **/ + files.push(subtractions[i].subtraction.data); + labels.push(subtractions[i].subtraction.fileName); + /** For sample average **/ +// files.push(subtractions[i].sampleAvg.data); +// labels.push(subtractions[i].sampleAvg.fileName); + /** For buffer average **/ +// files.push(subtractions[i].bufferAvg.data); +// labels.push(subtractions[i].bufferAvg.fileName); + } + } + + if (models != null) { + for (var i = 0; i < models.length; i++) { + for ( var key in models[i]) { + splitData(models[i][key].fir.data, 1, 2, "Intensity"); + splitData(models[i][key].fir.data, 3, 3, "Fit"); + } + } + } + + if (fits != null) { + for (var i = 0; i < fits.length; i++) { + for ( var key in fits[i]) { + + /** adding fit file to be plotted **/ + if (fits[i][key].fit.data[0].length == 3){ + splitData(fits[i][key].fit.data, 1, 1, "Intensity"); + splitData(fits[i][key].fit.data, 2, 2, "Fit"); + } + + /** s, Iexp(s), err, Ifit(s). **/ + if (fits[i][key].fit.data[0].length == 4){ + splitData(fits[i][key].fit.data, 1, 2, "Intensity"); + splitData(fits[i][key].fit.data, 3, 3, "Fit"); + } + + if (fits[i][key].fit.data[0].length == 5){ + /** X Intensity Fit Error Residues **/ + + splitData(fits[i][key].fit.data, 1, 3, "Intensity"); + splitData(fits[i][key].fit.data, 2, 2, "Fit"); + } + } + } + } + + var dataPoints = []; + if (files.length > 0) { + for (var i = 0; i < files[0].length; i++) { + dataPoints.push([ files[0][i][0], this.getPoint(files[0][i][1], files[0][i][2]) ]); + } + if (files.length > 1) { + for (var i = 1; i < files.length; i++) { + for (var j = 0; j < dataPoints.length; j++) { + if (files[i][j] != null){ + dataPoints[j].push(this.getPoint(files[i][j][1], files[i][j][2])); + } + else{ + dataPoints[j].push([0,0,0]); + } + } + } + } + } + + return { + dataPoints : dataPoints, + labels : labels + } +}; + +PlotWidget.prototype.refresh = function(frames, subtractions, models, fits, rbms, colors) { + + var _this = this; + this.panel.setLoading("Reading Files"); + + var dataAdapter = new BiosaxsDataAdapter(); + dataAdapter.onSuccess.attach(function(sender, data) { + _this.panel.setLoading("Rendering"); + var parsed = _this.getDataPlot(data.frames, data.subtractions, data.models, data.fits, rbms); + _this._renderDygraph(parsed.dataPoints, colors, parsed.labels); + _this.panel.setLoading(false); + }); + dataAdapter.onError.attach(function(sender, data) { + _this.panel.setLoading(false); + }); + dataAdapter.getDataPlot(frames, subtractions, models, fits, rbms); +}; + +PlotWidget.prototype.input = function() { + return DATADOC.getHPLCData(); +}; + + +/** + * Fit form + * + * @witdh + * @height + */ +function FitForm(args) { + this.id = BUI.id(); + this.width = null; + this.height = null; + + if (args != null) { + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + } + + var _this = this; + + /** Widgets **/ + this.fitGrid = new FitStructureToExperimentDataGrid({ + width : null, + height : 200 + }); + + this.fitGrid.onSelected.attach(function(sender, fits) { + var modelsIdList = []; + for ( var i in fits) { + modelsIdList.push(fits[i].fitStructureToExperimentalDataId); + } + _this._renderPlot(_this.subtractions[0].subtractionId, modelsIdList); +// var adapter = new BiosaxsDataAdapter(); +// adapter.onSuccess.attach(function(sender, data) { +// +// }); +// adapter.getScatteringCurveByFrameIdsList([], [], [], ids); + }); + + + /** Dygraph Widget that plots fir files**/ + this.plotWidget = new PlotWidget({ + width : 745, + height : 300, + margin : "10 0 10 10" + }); +} + +FitForm.prototype._renderPlot = function(subtractionId, modelsIdList) { + /** Trying to plot tje subtraction and the models **/ + try { + var colors = [ "#669900", "#0000FF" ]; + + this.plotWidget.refresh([], [ ], [], modelsIdList, [], colors); + } catch (e) { + console.log(e); + } +}; + +FitForm.prototype._getItems = function() { + var _this = this; + return [ { + xtype : 'label', + forId : 'myFieldId', + text : 'INLINE HELP: To be updated', + margin : '15 0 20 10', + cls : "inline-help" + }, this.fitGrid.getPanel(), this.plotWidget.getPanel() ] + +}; + +FitForm.prototype._getButtons = function() { + return []; +}; + +FitForm.prototype.getPanel = function() { + var _this = this; + this.panel = Ext.create('Ext.form.Panel', { + width : this.width, + height : this.height, + margin : 10, + border : 1, + defaultType : 'textfield', + items : this._getItems(), + buttons : this._getButtons(), + listeners : { + afterrender : function() { + _this._populate(); + + } + } + }); + return this.panel; +}; + +/** Populates could be call when the DOM is not filled yet **/ +FitForm.prototype._populate = function() { +}; + +/** It populates the form * */ +FitForm.prototype.refresh = function(subtractions) { + this.subtractions = subtractions; + this.fitGrid.refresh(subtractions); +}; + +FitForm.prototype.input = function() { + return {}; +}; + +/** It populates the form **/ +FitForm.prototype.test = function(targetId) { + var macromoleculeForm = new FitForm(); + var panel = macromoleculeForm.getPanel(); + panel.render(targetId); +}; + +/** + * Example form + * + * @witdh + * @height + */ +function RigidBodyModelingResultForm(args) { + this.id = BUI.id(); + this.width = null; + this.height = null; + + if (args != null) { + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + } + + var _this = this; + /** Widgets **/ + this.rigidModelGrid = new RigidModelGrid({ + width : null, + height : 200 + }); + + this.rigidModelGrid.onSelected.attach(function(sender, fits){ + var ids = []; + for ( var i in fits) { + ids.push(fits[i].fitStructureToExperimentalDataId); + } + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data){ +// debugger + + }); + + adapter.getScatteringCurveByFrameIdsList([], [], [], ids); + }); + +} + +RigidBodyModelingResultForm.prototype._getItems = function() { + var _this = this; + return [ { + xtype : 'label', + forId : 'myFieldId', + text : 'INLINE HELP: To be updated', + margin : '15 0 20 10', + cls : "inline-help" + }, this.rigidModelGrid.getPanel() ] + +}; + +RigidBodyModelingResultForm.prototype._getButtons = function() { + return []; +}; + +RigidBodyModelingResultForm.prototype.getPanel = function() { + var _this = this; + this.panel = Ext.create('Ext.form.Panel', { + width : this.width, + height : this.height, + margin : 10, + border : 1, + defaultType : 'textfield', + items : this._getItems(), + buttons : this._getButtons(), + listeners : { + afterrender : function() { + _this._populate(); + + } + } + }); + return this.panel; +}; + +/** Populates could be call when the DOM is not filled yet **/ +RigidBodyModelingResultForm.prototype._populate = function() { +}; + +/** It populates the form * */ +RigidBodyModelingResultForm.prototype.refresh = function(subtractions) { + this.rigidModelGrid.refresh(subtractions); +}; + +RigidBodyModelingResultForm.prototype.input = function() { + return {}; +}; + +/** It populates the form **/ +RigidBodyModelingResultForm.prototype.test = function(targetId) { + var macromoleculeForm = new RigidBodyModelingResultForm(); + var panel = macromoleculeForm.getPanel(); + panel.render(targetId); +}; + +/** + * Example form + * + * @witdh + * @height + */ +function SuperpositionForm(args) { + this.id = BUI.id(); + this.width = null; + this.height = null; + + if (args != null) { + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + } + + var _this = this; + + /** Widgets **/ + this.superpositionGrid = new SuperpositionGrid({ + width : null, + height : 200 + }); + + this.superpositionGrid.onSelected.attach(function(sender, superpositions) { + var ids = []; + for ( var i in superpositions) { + ids.push(superpositions[i].superpositionId); + } +// _this._renderAbinitio(ids); +// _this.aprioriPDBViewer.refresh(); + _this._renderAligned(ids); + // getAlignedPDBContentBySuperpositionList + }); + + /** PDB viewer **/ +// this.abinitioPDBViewer = new PDBViewer({ +// width : 860 / 2, +// height : 300 / 2, +// margin : 0 +// }); +// +// /** PDB viewer **/ +// this.aprioriPDBViewer = new StructurePDBViewer({ +// width : 860 / 2, +// height : 300 / 2, +// margin : 0 +// }); + + this.alignedPDBViewer = new AlignedSuperpositionPDBViewer({ + width : 860 , + height : 300 + }); + +} + +SuperpositionForm.prototype._renderAligned = function(modelsIdList) { + /** Trying to plot the PDB file **/ + try { + this.alignedPDBViewer.refresh(modelsIdList); + } catch (e) { + console.log(e); + } +}; + +SuperpositionForm.prototype._renderAbinitio = function(modelsIdList) { + /** Trying to plot the PDB file **/ + try { + var viz = []; + for (var i = 0; i < modelsIdList.length; i++) { + viz.push({ + modelId : modelsIdList[i], + color : "0xFF6600", + opacity : 0.8 + }); + } + this.abinitioPDBViewer.refresh(viz); + } catch (e) { + console.log(e); + } +}; + +SuperpositionForm.prototype._getItems = function() { + var _this = this; + return [ { + xtype : 'label', + forId : 'myFieldId', + text : 'INLINE HELP: To be updated', + margin : '15 0 20 10', + cls : "inline-help" + }, this.superpositionGrid.getPanel(), { + xtype : 'container', + layout : 'hbox', + items : [ +// { +// xtype : 'container', +// layout : 'vbox', +// items : [ this.abinitioPDBViewer.getPanel(), this.aprioriPDBViewer.getPanel() +// +// ] +// }, + + this.alignedPDBViewer.getPanel() ] + } ] + +}; + +SuperpositionForm.prototype._getButtons = function() { + return []; +}; + +SuperpositionForm.prototype.getPanel = function() { + var _this = this; + this.panel = Ext.create('Ext.form.Panel', { + width : this.width, + height : this.height, + margin : 10, + border : 1, + defaultType : 'textfield', + items : this._getItems(), + buttons : this._getButtons(), + listeners : { + afterrender : function() { + _this._populate(); + + } + } + }); + return this.panel; +}; + +/** Populates could be call when the DOM is not filled yet **/ +SuperpositionForm.prototype._populate = function() { +}; + +/** It populates the form * */ +SuperpositionForm.prototype.refresh = function(subtractions) { + this.subtractions = subtractions; + this.superpositionGrid.refresh(subtractions); +}; + +SuperpositionForm.prototype.input = function() { + return {}; +}; + +/** It populates the form **/ +SuperpositionForm.prototype.test = function(targetId) { + var macromoleculeForm = new SuperpositionForm(); + var panel = macromoleculeForm.getPanel(); + panel.render(targetId); +}; + +/** + * Example form + * + * @witdh + * @height + */ +function AssemblyForm(args) { + this.id = BUI.id(); + this.width = 700; + this.height = 500; + + if (args != null) { + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + } + + this.molarityGrid = new MolarityGrid({height : this.height - 50}); +} + +AssemblyForm.prototype._getItems = function() { + return [ { + xtype : 'label', + forId : 'myFieldId', + text : 'List of previously defined macromolecules present in the assembly. This information will be used for additional cross-checks where possible', + margin : '15 0 20 10', + cls : "inline-help" + }, this.molarityGrid.getPanel() ]; +}; + +AssemblyForm.prototype._getButtons = function() { + return []; +}; + +AssemblyForm.prototype.getPanel = function() { + this.panel = Ext.create('Ext.form.Panel', { + width : this.width, + height : this.height, + margin : 10, + border : 0, + defaultType : 'textfield', + items : this._getItems(), + buttons : this._getButtons() + }); + return this.panel; +}; + + +/** It populates the form **/ +AssemblyForm.prototype.refresh = function(macromolecule) { + this.macromolecule = macromolecule; + this.molarityGrid.refresh(macromolecule); +}; + +AssemblyForm.prototype.input = function() { + return {}; +}; + + +AssemblyForm.prototype.test = function(targetId) { + var assemblyForm = new AssemblyForm(); + + var panel = assemblyForm.getPanel(); + panel.render(targetId); +}; +/** + * Edit the information of a buffer + * + * #onSaved + * #onRemoveAdditive + */ +function BufferForm() { var _this = this; - /** Widgets **/ - this.plotWidget = new PlotWidget({ - width : 650, - height : 490 + this.additiveGrid = new AdditiveGrid(); + this.additiveGrid.onRemoveButtonClicked.attach(function(sender, args) { + _this.onRemoveAdditive.notify(args); }); - /** Selected frames to be displayed **/ - this.selectedItems = { - frames : [], - averages : [], - subtractions : [] - }; - + this.onSaved = new Event(this); + this.onRemoveAdditive = new Event(this); } -DataReductionForm.prototype._parseSelectedItemsToIds = function(selectedArray) { - var ids = []; - if (selectedArray != null) { - for (var i = 0; i < selectedArray.length; i++) { - ids.push(selectedArray[i].id); - } - } - return ids; -}; - -DataReductionForm.prototype.onSelectionChanged = function(columnName, selected) { - if (selected != null) { - if (columnName == "Frames") { - this.selectedItems.frames = selected; - this.selectedItems.subtractions = []; - } - if (columnName == "Averages") { - this.selectedItems.averages = selected; - } - if (columnName == "Subtractions") { - this.selectedItems.frames = []; - this.selectedItems.subtractions = selected; - } - } - this.plotWidget.refresh(this._parseSelectedItemsToIds(this.selectedItems.frames), this._parseSelectedItemsToIds(this.selectedItems.subtractions)); -}; - -DataReductionForm.prototype._getFramesExtPanel = function(store, columnName, height) { - var _this = this; - - var selModel = Ext.create('Ext.selection.RowModel', { - allowDeselect : true, - mode : 'MULTI', - listeners : { - selectionchange : function(sm, selections) { - var selected = []; - for (var i = 0; i < selections.length; i++) { - selected.push(selections[i].raw); - } - _this.onSelectionChanged(columnName, selected); - } - } - }); - - return Ext.create('Ext.grid.Panel', { - store : store, - margin : 10, - height : height, - width : 200, - selModel : selModel, - columns : [ { - text : columnName, - dataIndex : 'fileName', - flex : 1 - } ], - viewConfig : { - } - }); +BufferForm.prototype.getBuffer = function() { + this.buffer.name = Ext.getCmp("buffer_name").getValue(); + this.buffer.acronym = Ext.getCmp("buffer_acronym").getValue(); + this.buffer.comments = Ext.getCmp("buffer_comments").getValue(); + this.buffer.ph = Ext.getCmp("buffer_ph").getValue(); + this.buffer.composition = Ext.getCmp("buffer_composition").getValue(); + this.buffer.bufferhasadditive3VOs = this.additiveGrid.getAdditives(); + return this.buffer; }; -DataReductionForm.prototype._getFramesPanel = function() { - var fields = [ 'fileName', 'type', 'id' ]; - - this.framesStore = Ext.create('Ext.data.Store', { - fields : fields, - sorters : 'fileName' - }); - - this.averagesStore = Ext.create('Ext.data.Store', { - fields : fields - }); - - this.subtractionStore = Ext.create('Ext.data.Store', { - fields : fields - }); - - var gridFrames = this._getFramesExtPanel(this.framesStore, "Frames", 375); - var gridAvgs = this._getFramesExtPanel(this.averagesStore, "Averages", 125); - var subtractionAvgs = this._getFramesExtPanel(this.subtractionStore, "Subtractions", 75); - - return { - xtype : 'container', - layout : 'vbox', - items : [ gridFrames, subtractionAvgs ] - }; -}; - -DataReductionForm.prototype._getImageContainer = function(name, help) { - var html = "
" + name + "
" +BufferForm.prototype._getTopPanel = function() { return { xtype : 'container', - layout : 'vbox', + layout : 'hbox', + border : 0, + frame : true, items : [ { - html : html, - margin : "5 0 0 0", - height : 95, - width : 100 + xtype : 'container', + layout : 'hbox', + items : [ { + xtype : 'container', + flex : 1, + border : false, + layout : 'anchor', + defaultType : 'textfield', + items : [ { + xtype : 'requiredtext', + id : 'buffer_name', + fieldLabel : 'Name', + name : 'name', + width : '200px', + value : this.buffer.name + }, { + xtype : 'requiredtext', + id : 'buffer_acronym', + fieldLabel : 'Acronym', + name : 'acronym', + width : '200px', + value : this.buffer.acronym + } ] + } ] }, { - xtype : 'label', - forId : 'myFieldId', - text : help, - margin : '5 0 0 0', - cls : "inline-help" + xtype : 'container', + flex : 1, + layout : 'anchor', + defaultType : 'textfield', + margin : '0 0 0 10', + items : [ { + id : 'buffer_ph', + fieldLabel : 'pH', + name : 'ph', + value : this.buffer.ph, + xtype : 'numberfield', + width : 200, + minValue : 0, + maxValue : 15 + }, { + xtype : 'requiredtext', + id : 'buffer_composition', + fieldLabel : 'Composition', + name : 'composition', + width : 200, + value : this.buffer.composition + } ] } ] - } + }; }; -DataReductionForm.prototype._getItems = function() { - var _this = this; - return [ { +BufferForm.prototype.getPanel = function(buffer) { + this.buffer = buffer; + this.panel = Ext.createWidget({ xtype : 'container', - layout : 'hbox', - items : [ - this._getFramesPanel(), - this.plotWidget.getPanel(), - { - xtype : 'panel', - width : 110, - frame : true, - margin : "10 5 5 5", - border : 0, - layout : 'vbox', - items : [ this._getImageContainer("scattering", "Scattering"), this._getImageContainer("guinier", "Guinier Region"), - this._getImageContainer("kratky", "Kratky Plot"), this._getImageContainer("gnom", "P(r) distribution") ] - } ] - } ] -}; - -DataReductionForm.prototype._getButtons = function() { - return []; -}; + layout : 'vbox', + style : { + padding : '10px' + }, + fieldDefaults : { + labelAlign : 'left', + labelWidth : 50 -DataReductionForm.prototype.getPanel = function() { - var _this = this; - this.panel = Ext.create('Ext.form.Panel', { - width : this.width, - height : this.height, - border : 0, - items : this._getItems(), - buttons : this._getButtons(), - listeners : { - afterrender : function() { - _this._populate(); - } - } + }, + items : [ this._getTopPanel(), { + id : 'buffer_comments', + xtype : 'textareafield', + name : 'comments', + fieldLabel : 'Comments', + width : '100%', + value : buffer.comments + }, this.additiveGrid.getPanel(buffer) ] }); return this.panel; }; -/** Populates could be call when the DOM is not filled yet **/ -DataReductionForm.prototype._populate = function() { -}; - -/** It populates the form * */ -DataReductionForm.prototype.refresh = function(subtractions) { - if (subtractions != null) { - for (var i = 0; i < subtractions.length; i++) { - /** Loading frame grids **/ - var subtraction = subtractions[i]; - var averages = [ { - fileName : BUI.getFileName(subtraction.bufferAverageFilePath), - type : 'bufferAvg', - id : subtraction.subtractionId - }, { - fileName : BUI.getFileName(subtraction.sampleAverageFilePath), - type : 'sampleAvg', - id : subtraction.subtractionId - } - - ]; - this.averagesStore.loadData(averages, true); - this.subtractionStore.loadData([ { - fileName : BUI.getFileName(subtraction.substractedFilePath), - type : 'SUBTRACTION', - id : subtraction.subtractionId - } ], true); - - var frames = []; - /** Buffers **/ - if (subtraction.bufferOneDimensionalFiles != null) { - if (subtraction.bufferOneDimensionalFiles.frametolist3VOs != null) { - for (var j = 0; j < subtraction.bufferOneDimensionalFiles.frametolist3VOs.length; j++) { - var frametolist3VO = subtraction.bufferOneDimensionalFiles.frametolist3VOs[j]; - if (frametolist3VO.frame3VO != null) { - frames.push({ - fileName : BUI.getFileName(frametolist3VO.frame3VO.filePath), - type : 'BUFFER', - id : frametolist3VO.frame3VO.frameId - }); - } - } - } - } - /** Samples **/ - if (subtraction.sampleOneDimensionalFiles != null) { - if (subtraction.sampleOneDimensionalFiles.frametolist3VOs != null) { - for (var j = 0; j < subtraction.sampleOneDimensionalFiles.frametolist3VOs.length; j++) { - var frametolist3VO = subtraction.sampleOneDimensionalFiles.frametolist3VOs[j]; - if (frametolist3VO.frame3VO != null) { - frames.push({ - fileName : BUI.getFileName(frametolist3VO.frame3VO.filePath), - type : 'SAMPLE', - id : frametolist3VO.frame3VO.frameId - }); - } - } - } - } - - this.framesStore.loadData(frames, true); - - /** Loading images **/ - this._displayImage("scattering", subtraction.subtractionId); - this._displayImage("kratky", subtraction.subtractionId); - this._displayImage("guinier", subtraction.subtractionId); - this._displayImage("gnom", subtraction.subtractionId); +BufferForm.prototype.input = function() { + return { + buffer : { + "bufferId" : 422, + "proposalId" : 10, + "safetyLevelId" : null, + "name" : "B1", + "acronym" : "B1", + "ph" : null, + "composition" : null, + "bufferhasadditive3VOs" : [], + "comments" : null } - } -}; - -DataReductionForm.prototype._displayImage = function(name, subtractionId) { - var url = BUI.getURL() + '&type=' + name + '&subtractionId=' + subtractionId; - var event = "OnClick= window.open('" + url + "')"; - document.getElementById(this.id + "_" + name).innerHTML = ''; -}; - -DataReductionForm.prototype.input = function() { - return {}; + }; }; -/** It populates the form **/ -DataReductionForm.prototype.test = function(targetId) { - var macromoleculeForm = new DataReductionForm(); - var panel = macromoleculeForm.getPanel(); +BufferForm.prototype.test = function(targetId) { + var bufferForm = new BufferForm(); + var panel = bufferForm.getPanel(bufferForm.input().buffer); panel.render(targetId); }; - -function PlotWidget(args) { - this.width = 600; - this.height = 600; - this.id = BUI.id(); - - this.linear = false; - - this.margin = "10 0 0 0"; - /** for each stat the max and minimum value when it is scaled in order to show correctly in the legend **/ - this.ranges = {}; + +/** + * @showTitle + * + * #onSaved + * #onAddPlates + * #onRemovePlates + **/ +function CaseForm(args) { + this.width = 700; + this.showTitle = true; if (args != null) { - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; - } - if (args.margin != null) { - this.margin = args.margin; + if (args.showTitle != null) { + this.showTitle = args.showTitle; } } -} - -PlotWidget.prototype.getMenu = function() { var _this = this; - /** Actions buttons **/ - var actions = []; - actions.push("->"); - actions.push({ - text : "Export as Image", - scope : this, - icon : '../images/save.gif', - handler : function(item, pressed) { - var largeImage = document.createElement("img"); - largeImage.style.display = 'block'; - largeImage.style.width = 200 + "px"; - largeImage.style.height = 200 + "px"; - largeImage.setAttribute('src', Dygraph.Export.asCanvas(this.dygraphObject.dygraph).toDataURL()); - window.open(Dygraph.Export.asCanvas(this.dygraphObject.dygraph).toDataURL(), 'Image', ''); + this.stockSolutionGrid = new StockSolutionGrid({ + width : this.width - 10, + minHeight : 300, + height : 300, + tbar : true, + showTitle : true, + isPackedVisible : false, + btnAddExisting : true, + btnRemoveVisible : false, + btnUnpackVisible : true + }); + + /** When selecting existing stock solutions **/ + this.stockSolutionGrid.onStockSolutionSelected.attach(function(sender, stockSolutions) { + if (stockSolutions != null) { + for ( var i = 0; i < stockSolutions.length; i++) { + _this.saveStockSolution(stockSolutions[i]); + } } }); - return actions; -}; + /** it can be because it has been added a new one or removed **/ + this.stockSolutionGrid.onProposalChanged.attach(function(sender, stockSolution) { + if (stockSolution != null) { + _this.saveStockSolution(stockSolution); + } else { + BIOSAXS.proposal.onInitialized.attach(function() { + _this.stockSolutionGrid.refresh(BIOSAXS.proposal.getStockSolutionsByDewarId(_this.dewar.dewarId)); -/** Looks for the maximum value and then divide everything but that value **/ -PlotWidget.prototype.scaledData = function(data) { - for (var i = 0; i < data.length; i++) { - var values = this.getMaxAndMinValue(data[i]); - data[i] = this.divideValuesByMax(data[i], values.max); - this.ranges[data[i].label] = values; - } - return data; -}; + _this.stockSolutionGrid.grid.setLoading(false); + }); + BIOSAXS.proposal.init(); -/** Given a stat float[] and a max number it will divide each value by max **/ -PlotWidget.prototype.divideValuesByMax = function(stat, max) { - for (var j = 0; j < stat.data.length; j++) { - if (max != 0) { - stat.data[j] = Number(stat.data[j]) / max; - stat.std[j] = Number(stat.std[j]) / max; } - } - return stat; -}; -/** returns max value of a stat **/ -PlotWidget.prototype.getMaxAndMinValue = function(stat) { - var max = 0; - var min = stat.data[0]; - for (var j = 0; j < stat.data.length; j++) { - if (Number(stat.data[j]) > max) { - max = Number(stat.data[j]); - } - if (Number(stat.std[j]) > max) { - max = Number(stat.std[j]); - } - if (Number(stat.data[j]) < min) { - min = Number(stat.data[j]); - } - } - return { - max : Number(max), - min : Number(min) - }; -}; - -PlotWidget.prototype._renderDygraph = function(parsed, colors, labels) { - this.dygraphObject = new StdDevDyGraph(this.id, { - width : this.width - 20, - height : this.height - 40, - xlabel : "", }); - this.dygraphObject.draw(parsed, colors, labels); + this.onSaved = new Event(this); + this.onAddPlates = new Event(this); + this.onRemovePlates = new Event(this); +} +CaseForm.prototype.saveStockSolution = function(stockSolution) { + var _this = this; + var adapter = new BiosaxsDataAdapter(); + this.stockSolutionGrid.grid.setLoading("ISPyB: setting case to Stock solution"); + adapter.onSuccess.attach(function(sender, stockSolution) { + BIOSAXS.proposal.onInitialized.attach(function() { + _this.stockSolutionGrid.refresh(BIOSAXS.proposal.getStockSolutionsByDewarId(_this.dewar.dewarId)); + _this.stockSolutionGrid.grid.setLoading(false); + }); + BIOSAXS.proposal.init(); + }); + adapter.onError.attach(function(sender, data) { + _this.stockSolutionGrid.grid.setLoading(false); + BUI.showError(data); + }); + stockSolution.boxId = _this.dewar.dewarId; + adapter.saveStockSolution(stockSolution); }; -PlotWidget.prototype.getPanel = function() { - this.panel = Ext.create('Ext.panel.Panel', { - width : this.width, - height : this.height, - margin : this.margin, - tbar : this.getMenu(), - items : [ { - html : "", - id : this.id, - width : this.width, - height : this.height, - padding : 10, - margin : "0 0 0 -30", - border : 0 - } ] +CaseForm.prototype.fillStores = function() { + var _this = this; + this.panel.setLoading("Loading Labcontacts from database"); + + var proposal = BUI.getProposal(); + proposal.onDataRetrieved.attach(function(sender, data) { + _this.labContactForSendingStore.loadData(data, false); + _this.labContactForReturnStore.loadData(data, false); + _this.panel.setLoading(false); }); + proposal.getLabContactsByProposalId(); - return this.panel; }; -PlotWidget.prototype.getPoint = function(y, error) { - var minus = y - error; - var max = y + error; - - if (this.linear) { - return [ Math.abs(minus), y, Math.abs(max) ]; - } - if ((minus != 0) && (max != 0)) { - return [ Math.log(Math.abs(minus)), Math.log(y), Math.log(Math.abs(max)) ]; - } else { - return [ Math.log(y), Math.log(y), Math.log(y) ]; - } - +CaseForm.prototype.refresh = function(dewar) { + this.setDewar(dewar); + this.stockSolutionGrid.refresh(BIOSAXS.proposal.getStockSolutionsByDewarId(dewar.dewarId)); }; -PlotWidget.prototype.getDataPlot = function(frames, subtractions, models, fits, rbms) { - var files = []; - var labels = [ "Intensity" ]; - if (frames != null) { - for (var i = 0; i < frames.length; i++) { - files.push(frames[i].data); - labels.push(frames[i].fileName); - } - } - function splitData(data, column, errorColumn, name){ - var result = [] - for (var j = 0; j < data.length; j++) { - console.log(data[j][column]); - result.push([j,data[j][column],data[j][errorColumn]]);//[0, data[i][column],0]]); - } - files.push(result); - labels.push(name); - } - - if (subtractions != null) { - for (var i = 0; i < subtractions.length; i++) { - /** For subtraction **/ - files.push(subtractions[i].subtraction.data); - labels.push(subtractions[i].subtraction.fileName); - /** For sample average **/ -// files.push(subtractions[i].sampleAvg.data); -// labels.push(subtractions[i].sampleAvg.fileName); - /** For buffer average **/ -// files.push(subtractions[i].bufferAvg.data); -// labels.push(subtractions[i].bufferAvg.fileName); - } - } - - if (models != null) { - for (var i = 0; i < models.length; i++) { - for ( var key in models[i]) { - splitData(models[i][key].fir.data, 1, 2, "Intensity"); - splitData(models[i][key].fir.data, 3, 3, "Fit"); - } - } - } - - if (fits != null) { - for (var i = 0; i < fits.length; i++) { - for ( var key in fits[i]) { - - /** adding fit file to be plotted **/ - if (fits[i][key].fit.data[0].length == 3){ - splitData(fits[i][key].fit.data, 1, 1, "Intensity"); - splitData(fits[i][key].fit.data, 2, 2, "Fit"); - } - - /** s, Iexp(s), err, Ifit(s). **/ - if (fits[i][key].fit.data[0].length == 4){ - splitData(fits[i][key].fit.data, 1, 2, "Intensity"); - splitData(fits[i][key].fit.data, 3, 3, "Fit"); - } - - if (fits[i][key].fit.data[0].length == 5){ - /** X Intensity Fit Error Residues **/ - - splitData(fits[i][key].fit.data, 1, 3, "Intensity"); - splitData(fits[i][key].fit.data, 2, 2, "Fit"); - } - } - } - } - - var dataPoints = []; - if (files.length > 0) { - for (var i = 0; i < files[0].length; i++) { - dataPoints.push([ files[0][i][0], this.getPoint(files[0][i][1], files[0][i][2]) ]); - } - if (files.length > 1) { - for (var i = 1; i < files.length; i++) { - for (var j = 0; j < dataPoints.length; j++) { - if (files[i][j] != null){ - dataPoints[j].push(this.getPoint(files[i][j][1], files[i][j][2])); - } - else{ - dataPoints[j].push([0,0,0]); - } - } - } - } - } +CaseForm.prototype.getDewar = function() { + this.dewar.code = Ext.getCmp("dewar_code").getValue(); + this.dewar.comments = Ext.getCmp("dewar_comments").getValue(); + this.dewar.trackingNumberFromSynchrotron = Ext.getCmp("dewar_trackingNumberFromSynchrotron").getValue(); + this.dewar.trackingNumberToSynchrotron = Ext.getCmp("dewar_trackingNumberToSynchrotron").getValue(); + this.dewar.transportValue = Ext.getCmp("dewar_transportValue").getValue(); + this.dewar.storageLocation = Ext.getCmp("dewar_storageLocation").getValue(); + this.dewar.firstExperimentId = this.macromoleculeCombo.getValue(); + return this.dewar; +}; - return { - dataPoints : dataPoints, - labels : labels +CaseForm.prototype.setDewar = function(dewar) { + this.dewar = dewar; + Ext.getCmp("dewar_code").setValue(this.dewar.code); + Ext.getCmp("dewar_dewarStatus").setText(new String(this.dewar.dewarStatus).toUpperCase()); + Ext.getCmp("dewar_comments").setValue(this.dewar.comments); + Ext.getCmp("dewar_trackingNumberFromSynchrotron").setValue(this.dewar.trackingNumberFromSynchrotron); + Ext.getCmp("dewar_trackingNumberToSynchrotron").setValue(this.dewar.trackingNumberToSynchrotron); + Ext.getCmp("dewar_transportValue").setValue(this.dewar.transportValue); + Ext.getCmp("dewar_storageLocation").setValue(this.dewar.storageLocation); + if (dewar.sessionVO != null) { + this.macromoleculeCombo.setValue(dewar.sessionVO.sessionId); } }; -PlotWidget.prototype.refresh = function(frames, subtractions, models, fits, rbms, colors) { - - var _this = this; - this.panel.setLoading("Reading Files"); - - var dataAdapter = new BiosaxsDataAdapter(); - dataAdapter.onSuccess.attach(function(sender, data) { - _this.panel.setLoading("Rendering"); - var parsed = _this.getDataPlot(data.frames, data.subtractions, data.models, data.fits, rbms); - _this._renderDygraph(parsed.dataPoints, colors, parsed.labels); - _this.panel.setLoading(false); - }); - dataAdapter.onError.attach(function(sender, data) { - _this.panel.setLoading(false); +CaseForm.prototype.getSessionCombo = function() { + this.macromoleculeCombo = BIOSAXS_COMBOMANAGER.getComboSessions(BIOSAXS.proposal.getSessions(), { + labelWidth : 100, + margin : '5 0 00 0', + width : 250 }); - dataAdapter.getDataPlot(frames, subtractions, models, fits, rbms); -}; - -PlotWidget.prototype.input = function() { - return DATADOC.getHPLCData(); + return this.macromoleculeCombo; }; - -/** - * Fit form - * - * @witdh - * @height - */ -function FitForm(args) { - this.id = BUI.id(); - this.width = null; - this.height = null; - - if (args != null) { - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; - } - } +CaseForm.prototype.getInformationPanel = function() { + if (this.panel == null) { + this.informationPanel = Ext.create('Ext.form.Panel', { + width : this.width - 10, + border : 0, + items : [ { + xtype : 'container', + margin : "2 2 2 2", + collapsible : false, + defaultType : 'textfield', + layout : 'anchor', + items : [ { + xtype : 'container', + layout : 'hbox', + items : [ { + xtype : 'requiredtext', + fieldLabel : 'Code', + allowBlank : false, + name : 'code', + id : 'dewar_code', + anchor : '50%' + }, { + xtype : 'label', + margin : '0 0 0 20', + readOnly : true, + id : 'dewar_dewarStatus', + anchor : '50%' + } ] + }, this.getSessionCombo(), { + margin : '5 0 0 0', + xtype : 'textareafield', + name : 'comments', + id : 'dewar_comments', + width : this.width - 50, + fieldLabel : 'Comments' + } ] + }, { + xtype : 'fieldset', + title : 'Courier Accounts Details for Return', + collapsible : false, + layout : 'anchor', + defaults : { + anchor : '100%' + }, + items : [ { + xtype : 'container', + layout : 'hbox', + items : [ { + xtype : 'textfield', + labelWidth : 200, + width : 280, + fieldLabel : 'Track Number From Synchrotron', + id : 'dewar_trackingNumberFromSynchrotron' + }, { + xtype : 'numberfield', + width : 190, + labelWidth : 110, + margin : '0 0 0 30', + fieldLabel : 'Transport Value', + id : 'dewar_transportValue' + } - var _this = this; - - /** Widgets **/ - this.fitGrid = new FitStructureToExperimentDataGrid({ - width : null, - height : 200 - }); + ] + }, { + xtype : 'container', + layout : 'hbox', + margin : '10 0 0 0', + items : [ - this.fitGrid.onSelected.attach(function(sender, fits) { - var modelsIdList = []; - for ( var i in fits) { - modelsIdList.push(fits[i].fitStructureToExperimentalDataId); - } - _this._renderPlot(_this.subtractions[0].subtractionId, modelsIdList); -// var adapter = new BiosaxsDataAdapter(); -// adapter.onSuccess.attach(function(sender, data) { -// -// }); -// adapter.getScatteringCurveByFrameIdsList([], [], [], ids); - }); - - - /** Dygraph Widget that plots fir files**/ - this.plotWidget = new PlotWidget({ - width : 745, - height : 300, - margin : "10 0 10 10" - }); -} + { + xtype : 'textfield', + labelWidth : 200, + width : 280, + fieldLabel : 'Track Number To Synchrotron', + id : 'dewar_trackingNumberToSynchrotron' + }, { + xtype : 'textfield', + margin : '0 0 0 30', + width : 190, + labelWidth : 110, + fieldLabel : 'Storage Location', + id : 'dewar_storageLocation' + } -FitForm.prototype._renderPlot = function(subtractionId, modelsIdList) { - /** Trying to plot tje subtraction and the models **/ - try { - var colors = [ "#669900", "#0000FF" ]; - - this.plotWidget.refresh([], [ ], [], modelsIdList, [], colors); - } catch (e) { - console.log(e); + ] + } ] + } ] + }); } -}; - -FitForm.prototype._getItems = function() { - var _this = this; - return [ { - xtype : 'label', - forId : 'myFieldId', - text : 'INLINE HELP: To be updated', - margin : '15 0 20 10', - cls : "inline-help" - }, this.fitGrid.getPanel(), this.plotWidget.getPanel() ] - -}; -FitForm.prototype._getButtons = function() { - return []; + return this.informationPanel; }; -FitForm.prototype.getPanel = function() { - var _this = this; - this.panel = Ext.create('Ext.form.Panel', { +CaseForm.prototype.getPanel = function(dewar) { + this.dewar = dewar; + this.panel = Ext.createWidget({ + xtype : 'container', + layout : 'vbox', width : this.width, - height : this.height, - margin : 10, - border : 1, - defaultType : 'textfield', - items : this._getItems(), - buttons : this._getButtons(), - listeners : { - afterrender : function() { - _this._populate(); + border : 0, + items : [ { + items : { + xtype : "container", + layout : "vbox", + margin : "5 5 5 5", + items : [ this.getInformationPanel(dewar), this.stockSolutionGrid.getPanel() ] } - } + } ] }); + + this.refresh(dewar); return this.panel; -}; -/** Populates could be call when the DOM is not filled yet **/ -FitForm.prototype._populate = function() { }; -/** It populates the form * */ -FitForm.prototype.refresh = function(subtractions) { - this.subtractions = subtractions; - this.fitGrid.refresh(subtractions); -}; +CaseForm.prototype.input = function() { + return { + dewar : { + "dewarId" : 305861, + "code" : "ESRF-TEST", + "comments" : "comments", + "storageLocation" : "FRIDGE", + "dewarStatus" : "opened", + "timeStamp" : null, + "isStorageDewar" : null, + "barCode" : "ESRF305861", + "customsValue" : null, + "transportValue" : null, + "trackingNumberToSynchrotron" : "3333", + "trackingNumberFromSynchrotron" : "224466", + "type" : "Dewar", + "sessionVO" : { + "sessionId" : 31697, + "expSessionPk" : null, + "projectCode" : null, + "startDate" : "2012 07 21", + "endDate" : "2012 07 23", + "beamlineName" : "BM29", + "scheduled" : 1, + "nbShifts" : 2, + "comments" : null, + "beamlineOperator" : "PERNOT P", + "usedFlag" : null, + "sessionTitle" : null, + "structureDeterminations" : null, + "dewarTransport" : null, + "databackupFrance" : null, + "databackupEurope" : null, + "visit_number" : null, + "operatorSiteNumber" : "14061", + "timeStamp" : "2012 04 25" + } + }, + proposal : { + "assemblies" : [], + "sessions" : [ { + "sessionId" : 31697, + "expSessionPk" : null, + "projectCode" : null, + "startDate" : "2012 07 21", + "endDate" : "2012 07 23", + "beamlineName" : "BM29", + "scheduled" : 1, + "nbShifts" : 2, + "comments" : null, + "beamlineOperator" : "PERNOT P", + "usedFlag" : null, + "sessionTitle" : null, + "structureDeterminations" : null, + "dewarTransport" : null, + "databackupFrance" : null, + "databackupEurope" : null, + "visit_number" : null, + "operatorSiteNumber" : "14061", + "timeStamp" : "2012 04 25" + } ], + "labcontacts" : [ { + "labContactId" : 787, + "personVO" : { + "personId" : 304252, + "personUUID" : null, + "familyName" : "KIM", + "givenName" : "Henry", + "title" : null, + "emailAddress" : "henry-sung.kim@ibs.fr", + "phoneNumber" : "", + "login" : "", + "passwd" : "", + "faxNumber" : "" + }, + "cardName" : "KIM-Institut de Bio", + "defaultCourrierCompany" : "22", + "courierAccount" : "", + "billingReference" : "", + "dewarAvgCustomsValue" : 0, + "dewarAvgTransportValue" : 0 + } ], + "buffers" : [ { + "bufferId" : 811, + "proposalId" : 3124, + "safetyLevelId" : null, + "name" : "EDTA", + "acronym" : "EDTA", + "ph" : null, + "composition" : "", + "bufferhasadditive3VOs" : [], + "comments" : "" + }, { + "bufferId" : 810, + "proposalId" : 3124, + "safetyLevelId" : null, + "name" : "HEPES", + "acronym" : "HEPES", + "ph" : null, + "composition" : "", + "bufferhasadditive3VOs" : [], + "comments" : "" + } ], + "shippings" : [ { + "shippingId" : 304107, + "shippingName" : "TEST", + "deliveryAgentAgentName" : null, + "deliveryAgentShippingDate" : null, + "deliveryAgentDeliveryDate" : null, + "deliveryAgentAgentCode" : null, + "deliveryAgentFlightCode" : null, + "shippingStatus" : "opened", + "timeStamp" : "2013 09 25", + "laboratoryId" : null, + "isStorageShipping" : null, + "creationDate" : "2013 09 25", + "comments" : "test", + "sendingLabContactVO" : { + "labContactId" : 787, + "personVO" : { + "personId" : 304252, + "personUUID" : null, + "familyName" : "KIM", + "givenName" : "Henry", + "title" : null, + "emailAddress" : "henry-sung.kim@ibs.fr", + "phoneNumber" : "", + "login" : "", + "passwd" : "", + "faxNumber" : "" + }, + "cardName" : "KIM-Institut de Bio", + "defaultCourrierCompany" : "22", + "courierAccount" : "", + "billingReference" : "", + "dewarAvgCustomsValue" : 0, + "dewarAvgTransportValue" : 0 + }, + "returnLabContactVO" : { + "labContactId" : 787, + "personVO" : { + "personId" : 304252, + "personUUID" : null, + "familyName" : "KIM", + "givenName" : "Henry", + "title" : null, + "emailAddress" : "henry-sung.kim@ibs.fr", + "phoneNumber" : "", + "login" : "", + "passwd" : "", + "faxNumber" : "" + }, + "cardName" : "KIM-Institut de Bio", + "defaultCourrierCompany" : "22", + "courierAccount" : "", + "billingReference" : "", + "dewarAvgCustomsValue" : 0, + "dewarAvgTransportValue" : 0 + }, + "returnCourier" : null, + "dateOfShippingToUser" : null, + "shippingType" : "DewarTracking", + "dewarVOs" : [ { + "dewarId" : 305861, + "code" : "ESRF-TEST", + "comments" : "comments", + "storageLocation" : "FRIDGE", + "dewarStatus" : "opened", + "timeStamp" : null, + "isStorageDewar" : null, + "barCode" : "ESRF305861", + "customsValue" : null, + "transportValue" : null, + "trackingNumberToSynchrotron" : "3333", + "trackingNumberFromSynchrotron" : "224466", + "type" : "Dewar", + "sessionVO" : { + "sessionId" : 31697, + "expSessionPk" : null, + "projectCode" : null, + "startDate" : "2012 07 21", + "endDate" : "2012 07 23", + "beamlineName" : "BM29", + "scheduled" : 1, + "nbShifts" : 2, + "comments" : null, + "beamlineOperator" : "PERNOT P", + "usedFlag" : null, + "sessionTitle" : null, + "structureDeterminations" : null, + "dewarTransport" : null, + "databackupFrance" : null, + "databackupEurope" : null, + "visit_number" : null, + "operatorSiteNumber" : "14061", + "timeStamp" : "2012 04 25" + } + } ] + } ], + "macromolecules" : [ { + "macromoleculeId" : 5933, + "safetylevelId" : null, + "proposalId" : 3124, + "name" : "A", + "acronym" : "A", + "molecularMass" : "", + "extintionCoefficient" : "", + "sequence" : null, + "creationDate" : null, + "comments" : "", + "macromoleculeregion3VOs" : [], + "stoichiometry3VOsForHostMacromoleculeId" : [], + "structure3VOs" : [] + } ], + "stockSolutions" : [ { + "stockSolutionId" : 6, + "proposalId" : 3124, + "macromoleculeId" : 5933, + "bufferId" : 811, + "instructionSet3VO" : null, + "boxId" : 305861, + "storageTemperature" : "20", + "volume" : "300", + "concentration" : "1.2", + "comments" : "Buffer EDTA with A", + "name" : "A_EDTA_1.2", + "samples" : [] + } ] + } -FitForm.prototype.input = function() { - return {}; + }; }; -/** It populates the form **/ -FitForm.prototype.test = function(targetId) { - var macromoleculeForm = new FitForm(); - var panel = macromoleculeForm.getPanel(); - panel.render(targetId); -}; - -/** - * Example form - * - * @witdh - * @height - */ -function RigidBodyModelingResultForm(args) { +CaseForm.prototype.test = function(targetId) { + var caseForm = new CaseForm(); + BIOSAXS.proposal = new Proposal(caseForm.input().proposal); + var panel = caseForm.getPanel(caseForm.input().dewar); + panel.render(targetId); +}; + +/** + * Example form + * + * @witdh + * @height + */ +function ExampleForm(args) { + this.id = BUI.id(); + this.width = 700; + this.height = 500; + + if (args != null) { + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + } +} + +ExampleForm.prototype._getItems = function() { + return [{ + fieldLabel : 'First Name', + name : 'first', + allowBlank : false + }, { + fieldLabel : 'Last Name', + name : 'last', + allowBlank : false + } ]; +}; + +ExampleForm.prototype._getItems = function() { + return [ ]; +}; + +ExampleForm.prototype._getButtons = function() { + return [ ]; +}; + +ExampleForm.prototype.getPanel = function() { + this.panel = Ext.create('Ext.form.Panel', { + width : this.width, + height : this.height, + margin : 10, + border : 1, + defaultType : 'textfield', + items : this._getItems(), + buttons : this._getButtons() + }); + return this.panel; +}; + +/** It populates the form **/ +ExampleForm.prototype.refresh = function(macromolecule) { +}; + +function ExperimentForm(args) { this.id = BUI.id(); - this.width = null; - this.height = null; if (args != null) { - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; - } } - var _this = this; - /** Widgets **/ - this.rigidModelGrid = new RigidModelGrid({ - width : null, - height : 200 + this.onSaved = new Event(this); +} + +ExperimentForm.prototype._getItems = function(experiment) { + this.experiment = experiment; + var typeCombo = Ext.create('Ext.form.ComboBox', { + id : this.id + 'type', + fieldLabel : 'Type', + store : [ "STATIC", "CALIBRATION", "HPLC" ], + queryMode : 'local', + labelWidth : 120, + displayField : 'name', + valueField : 'name', + value : experiment.json.type, + disabled : (experiment.json.type == 'TEMPLATE') }); - this.rigidModelGrid.onSelected.attach(function(sender, fits){ - var ids = []; - for ( var i in fits) { - ids.push(fits[i].fitStructureToExperimentalDataId); + var items = []; + + + if (experiment.json.type == "HPLC" ){ + var typeMacromolecule = BIOSAXS_COMBOMANAGER.getComboMacromoleculeByMacromolecules(BIOSAXS.proposal.getMacromolecules(), {labelWidth : 120, width: "120px"}); + if (experiment.getHPLCMacromolecule() != null){ + typeMacromolecule.setValue(experiment.getHPLCMacromolecule().macromoleculeId); + items.push(typeMacromolecule); } - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data){ -// debugger - - }); - - adapter.getScatteringCurveByFrameIdsList([], [], [], ids); + } + + + items.push(typeCombo, { + id : this.id + 'name', + xtype : 'textfield', + fieldLabel : 'Name', + labelWidth : 120, + width : '100%', + value : experiment.json.name + }, { + id : this.id + 'comments', + xtype : 'textareafield', + name : 'comments', + fieldLabel : 'Comments', + labelWidth : 120, + height : 120, + width : '100%', + value : experiment.json.comments }); - -} - -RigidBodyModelingResultForm.prototype._getItems = function() { - var _this = this; - return [ { - xtype : 'label', - forId : 'myFieldId', - text : 'INLINE HELP: To be updated', - margin : '15 0 20 10', - cls : "inline-help" - }, this.rigidModelGrid.getPanel() ] - -}; - -RigidBodyModelingResultForm.prototype._getButtons = function() { - return []; + return items; }; - -RigidBodyModelingResultForm.prototype.getPanel = function() { +ExperimentForm.prototype.getPanel = function(experiment) { var _this = this; - this.panel = Ext.create('Ext.form.Panel', { - width : this.width, - height : this.height, - margin : 10, - border : 1, - defaultType : 'textfield', - items : this._getItems(), - buttons : this._getButtons(), - listeners : { - afterrender : function() { - _this._populate(); - - } - } + + this.panel = Ext.createWidget({ + xtype : 'container', + layout : 'vbox', + border : 0, + style : { + padding : '10px' + }, + fieldDefaults : { + labelAlign : 'left', + labelWidth : 50 + }, + items : this._getItems(experiment) }); return this.panel; }; -/** Populates could be call when the DOM is not filled yet **/ -RigidBodyModelingResultForm.prototype._populate = function() { -}; - -/** It populates the form * */ -RigidBodyModelingResultForm.prototype.refresh = function(subtractions) { - this.rigidModelGrid.refresh(subtractions); -}; - -RigidBodyModelingResultForm.prototype.input = function() { - return {}; +ExperimentForm.prototype.input = function() { + return new ExperimentHeaderForm().input(); }; -/** It populates the form **/ -RigidBodyModelingResultForm.prototype.test = function(targetId) { - var macromoleculeForm = new RigidBodyModelingResultForm(); - var panel = macromoleculeForm.getPanel(); +ExperimentForm.prototype.test = function(targetId) { + var experimentForm = new ExperimentForm(); + var panel = experimentForm.getPanel(new Experiment(experimentForm.input().experiment)); panel.render(targetId); }; /** - * Example form + * Shows the header for the experiments changing the color and parameters depending on experiment type * - * @witdh - * @height */ -function SuperpositionForm(args) { +function ExperimentHeaderForm(args) { this.id = BUI.id(); - this.width = null; - this.height = null; + this.backgroundColor = '#FFFFFF'; +} - if (args != null) { - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; +ExperimentHeaderForm.prototype.getHTMLSource = function(experiment) { + var html = BUI.createFormLabel("Name :", experiment.json.name, 75, 400, this.backgroundColor); + if (experiment.json.type == "HPLC") { + if (experiment.getHPLCMacromolecule() != null){ + html = html + BUI.createFormLabel("Molecule :", experiment.getHPLCMacromolecule().acronym, 75, 400, this.backgroundColor); } } + else{ + html = html + BUI.createFormLabel("Type :", experiment.json.type, 75, 400, this.backgroundColor); + } + + html = html + BUI.createFormLabel("Date :", experiment.json.creationDate, 75, 400, this.backgroundColor); + return html; +}; - var _this = this; - - /** Widgets **/ - this.superpositionGrid = new SuperpositionGrid({ - width : null, - height : 200 - }); - - this.superpositionGrid.onSelected.attach(function(sender, superpositions) { - var ids = []; - for ( var i in superpositions) { - ids.push(superpositions[i].superpositionId); - } -// _this._renderAbinitio(ids); -// _this.aprioriPDBViewer.refresh(); - _this._renderAligned(ids); - // getAlignedPDBContentBySuperpositionList - }); - - /** PDB viewer **/ -// this.abinitioPDBViewer = new PDBViewer({ -// width : 860 / 2, -// height : 300 / 2, -// margin : 0 -// }); -// -// /** PDB viewer **/ -// this.aprioriPDBViewer = new StructurePDBViewer({ -// width : 860 / 2, -// height : 300 / 2, -// margin : 0 -// }); +ExperimentHeaderForm.prototype.getHTMLDownload = function(experiment) { + var bgcolor = "background-color:" + this.backgroundColor + ";"; + var html = "
"; + if ((experiment.json.type == "CALIBATION") || (experiment.json.type == "STATIC")) { + html = html + " Download Source File
"; + html = html + + ""; + } + if (experiment.json.type == "TEMPLATE") { + html = html + + " Download Source File"; + } - this.alignedPDBViewer = new AlignedSuperpositionPDBViewer({ - width : 860 , - height : 300 - }); + if (experiment.json.type == "HPLC") { + html = html + " Download h5 File"; + } -} + return html; +}; -SuperpositionForm.prototype._renderAligned = function(modelsIdList) { - /** Trying to plot the PDB file **/ - try { - this.alignedPDBViewer.refresh(modelsIdList); - } catch (e) { - console.log(e); - } +ExperimentHeaderForm.prototype.getTopPanel = function(experiment) { + return { + xtype : 'container', + layout : 'hbox', + items : [ { + margin : "0 0 0 0", + width : 475, + border : 0, + html : this.getHTMLSource(experiment) + }, { + margin : "0 0 0 0", + width : 475, + border : 0, + html : this.getHTMLDownload(experiment) + } ] + }; }; -SuperpositionForm.prototype._renderAbinitio = function(modelsIdList) { - /** Trying to plot the PDB file **/ - try { - var viz = []; - for (var i = 0; i < modelsIdList.length; i++) { - viz.push({ - modelId : modelsIdList[i], - color : "0xFF6600", - opacity : 0.8 +ExperimentHeaderForm.prototype.getButton = function(experiment) { + var _this = this; + return Ext.create('Ext.Button', { + text : 'EDIT', + minWidth : '100', + margin : '10 0 0 30', + handler : function() { + var experimentWindow = new ExperimentWindow(); + experimentWindow.onSaved.attach(function(sender, data) { + _this.experiment.json.name = data.name; + _this.experiment.json.type = data.type; + _this.experiment.json.comments = data.comments; + _this.panel.remove(_this.panel.items.items[0]); + _this.panel.remove(_this.panel.items.items[0]); + _this.panel.insert(_this.getTopPanel(_this.experiment)); + _this.panel.insert(_this.getBottomPanel(_this.experiment)); }); + experimentWindow.show(experiment); } - this.abinitioPDBViewer.refresh(viz); - } catch (e) { - console.log(e); - } + }); }; -SuperpositionForm.prototype._getItems = function() { - var _this = this; - return [ { - xtype : 'label', - forId : 'myFieldId', - text : 'INLINE HELP: To be updated', - margin : '15 0 20 10', - cls : "inline-help" - }, this.superpositionGrid.getPanel(), { +ExperimentHeaderForm.prototype.getBottomPanel = function(experiment) { + return { xtype : 'container', layout : 'hbox', - items : [ -// { -// xtype : 'container', -// layout : 'vbox', -// items : [ this.abinitioPDBViewer.getPanel(), this.aprioriPDBViewer.getPanel() -// -// ] -// }, - - this.alignedPDBViewer.getPanel() ] - } ] - -}; - -SuperpositionForm.prototype._getButtons = function() { - return []; + margin : '10 0 0 0', + items : [ this.getComments(experiment), this.getButton(experiment) ] + }; }; -SuperpositionForm.prototype.getPanel = function() { - var _this = this; - this.panel = Ext.create('Ext.form.Panel', { - width : this.width, - height : this.height, - margin : 10, - border : 1, - defaultType : 'textfield', - items : this._getItems(), - buttons : this._getButtons(), - listeners : { - afterrender : function() { - _this._populate(); - - } - } - }); - return this.panel; +ExperimentHeaderForm.prototype.getComments = function(experiment) { + return { + xtype : 'textareafield', + labelStyle : 'font-weight: bold;', + name : 'comments', + fieldLabel : 'Comments', + labelWidth : 70, + height : 40, + minWidth : '450', + readOnly : true, + value : experiment.json.comments + }; }; -/** Populates could be call when the DOM is not filled yet **/ -SuperpositionForm.prototype._populate = function() { -}; +ExperimentHeaderForm.prototype.getPanel = function(experiment) { + this.experiment = experiment; + + if (experiment.json.type == 'CALIBRATION') { + this.backgroundColor = '#EFFBFB'; + } + if (experiment.json.type == 'TEMPLATE') { + this.backgroundColor = '#E0F8E6'; + } -/** It populates the form * */ -SuperpositionForm.prototype.refresh = function(subtractions) { - this.subtractions = subtractions; - this.superpositionGrid.refresh(subtractions); + this.panel = Ext.create('Ext.container.Container', { + frame : false, + layout : 'vbox', + padding : 5, + bodyPadding : '5 5 0 0', + width : 890, + margin : '0 0 10 0', + height : 120, + style : { + borderColor : '#99bce8', + borderStyle : 'solid', + borderWidth : '1px', + 'background-color' : this.backgroundColor + }, + fieldDefaults : { + msgTarget : 'side', + labelWidth : 100 + }, + items : [ this.getTopPanel(experiment), this.getBottomPanel(experiment) ] + }); + return this.panel; }; -SuperpositionForm.prototype.input = function() { - return {}; +ExperimentHeaderForm.prototype.input = function() { + return { + experiment : DATADOC.getExperiment_10() + }; }; -/** It populates the form **/ -SuperpositionForm.prototype.test = function(targetId) { - var macromoleculeForm = new SuperpositionForm(); - var panel = macromoleculeForm.getPanel(); +ExperimentHeaderForm.prototype.test = function(targetId) { + var experimentHeaderForm = new ExperimentHeaderForm(); + var panel = experimentHeaderForm.getPanel(new Experiment(experimentHeaderForm.input().experiment)); panel.render(targetId); + }; /** - * Example form + * Macromolecule form with the general parameters of a macromolecule * * @witdh * @height + * + * #onSave button save has been clicked + * #onClose button close has been clicked */ -function AssemblyForm(args) { +function MacromoleculeForm(args) { this.id = BUI.id(); this.width = 700; this.height = 500; @@ -6059,15944 +7053,9793 @@ function AssemblyForm(args) { this.height = args.height; } } - - this.molarityGrid = new MolarityGrid({height : this.height - 50}); + + /** Events **/ + this.onSave = new Event(this); + this.onClose = new Event(this); } -AssemblyForm.prototype._getItems = function() { - return [ { - xtype : 'label', - forId : 'myFieldId', - text : 'List of previously defined macromolecules present in the assembly. This information will be used for additional cross-checks where possible', - margin : '15 0 20 10', - cls : "inline-help" - }, this.molarityGrid.getPanel() ]; -}; - -AssemblyForm.prototype._getButtons = function() { - return []; +/** Type : is the Ext type then requiredtext or textfield * */ +MacromoleculeForm.prototype._getFieldTextWithHelp = function(type, fieldLabel, fieldName, help) { + return Ext.create('Ext.container.Container', { + margin : "10 0 0 10", + items : [ { + xtype : type, + fieldLabel : fieldLabel, + name : fieldName, + id : this.id + fieldName + }, { + xtype : 'label', + forId : 'myFieldId', + text : help, + margin : "5 0 0 105", + cls : "inline-help" + } ] + }); }; -AssemblyForm.prototype.getPanel = function() { - this.panel = Ext.create('Ext.form.Panel', { - width : this.width, - height : this.height, - margin : 10, - border : 0, - defaultType : 'textfield', - items : this._getItems(), - buttons : this._getButtons() +MacromoleculeForm.prototype._getNumericWithHelp = function(type, fieldLabel, fieldName, help) { + return Ext.create('Ext.container.Container', { + margin : "0 0 0 10", + items : [ { + xtype : type, + fieldLabel : fieldLabel, + name : fieldName, + id : this.id + fieldName, + decimalPrecision : 6, + width : 220 + }, { + xtype : 'label', + forId : 'myFieldId', + text : help, + margin : "5 0 0 10", + cls : "inline-help" + } ] }); - return this.panel; }; - -/** It populates the form **/ -AssemblyForm.prototype.refresh = function(macromolecule) { - this.macromolecule = macromolecule; - this.molarityGrid.refresh(macromolecule); +MacromoleculeForm.prototype._getButtons = function() { + var _this = this; + return [ { + text : 'Save', + handler : function() { + _this._save(); + } + },{ + text : 'Close', + handler : function() { + _this.onClose.notify(); + + } + } ]; }; -AssemblyForm.prototype.input = function() { - return {}; +/** It persits the macromolecule in the database **/ +MacromoleculeForm.prototype._persist = function(macromoleculeId, acronym, name, molecularMass, extintionCoefficient, comments, refractiveIndex, solventViscosity) { + + /** Checking not duplicated acronym **/ + if (((macromoleculeId == null) && (BIOSAXS.proposal.getMacromoleculeByAcronym(acronym) != null))== true){ + BUI.showError("Duplicated acronym"); + return; + } + + + if (macromoleculeId == null){ + /** new macromolecule **/ + this.macromolecule = {}; + this.macromolecule.macromoleculeId = null; + } + else{ + this.macromolecule.macromoleculeId = macromoleculeId; + } + + this.macromolecule["acronym"] = acronym; + this.macromolecule["name"] = name; + this.macromolecule["molecularMass"] = molecularMass; + this.macromolecule["extintionCoefficient"] = extintionCoefficient; + this.macromolecule["comments"] = comments; + this.macromolecule["symmetry"] = Ext.getCmp(this.id + 'comboSym').getValue(); + this.macromolecule["refractiveIndex"] = refractiveIndex; + this.macromolecule["solventViscosity"] = solventViscosity; + + var _this = this; + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, proposal) { + /** Updating the proposal global object **/ + BIOSAXS.proposal.setItems(proposal); + _this.panel.setLoading(false); + + var saved = BIOSAXS.proposal.getMacromoleculeByAcronym(acronym); + /** Refreshing to check that everything is ok **/ + _this.refresh(saved); + _this.onSave.notify(saved); + }); + + this.panel.setLoading("Saving Macromolecule") + adapter.saveMacromolecule(this.macromolecule); }; - -AssemblyForm.prototype.test = function(targetId) { - var assemblyForm = new AssemblyForm(); +/** Save the macromolecule in the DB **/ +MacromoleculeForm.prototype._save = function() { - var panel = assemblyForm.getPanel(); - panel.render(targetId); -}; -/** - * Edit the information of a buffer - * - * #onSaved - * #onRemoveAdditive - */ -function BufferForm() { var _this = this; + + var acronym = this._getField("acronym"); + var name = this._getField("name"); + var molecularMass = this._getField("molecularMass"); + var extintionCoefficient = this._getField("extintionCoefficient"); + var comments = this._getField("comments"); + + var refractiveIndex = this._getField("refractiveIndex"); + var solventViscosity = this._getField("solventViscosity"); + + /** Checking required fields **/ + if (name == "") { + BUI.showError("Name field is mandatory"); + return; + } + if (acronym == "") { + BUI.showError("Acroynm field is mandatory"); + return; + } - this.additiveGrid = new AdditiveGrid(); - this.additiveGrid.onRemoveButtonClicked.attach(function(sender, args) { - _this.onRemoveAdditive.notify(args); - }); + if (this.macromolecule != null){ + /** Checking if it is a new macromolecule **/ + if (this.macromolecule.macromoleculeId == null){ + /** Check if the acronym exists already **/ + this._persist(null, acronym, name, molecularMass, extintionCoefficient, comments, refractiveIndex, solventViscosity); + } + else{ + /** It is an update **/ + this._persist(this.macromolecule.macromoleculeId, acronym, name, molecularMass, extintionCoefficient, comments, refractiveIndex, solventViscosity); + } + } + else{ + /** It is a new macromolecule **/ + this._persist(null, acronym, name, molecularMass, extintionCoefficient, comments, refractiveIndex, solventViscosity); + } +}; - this.onSaved = new Event(this); - this.onRemoveAdditive = new Event(this); -} -BufferForm.prototype.getBuffer = function() { - this.buffer.name = Ext.getCmp("buffer_name").getValue(); - this.buffer.acronym = Ext.getCmp("buffer_acronym").getValue(); - this.buffer.comments = Ext.getCmp("buffer_comments").getValue(); - this.buffer.ph = Ext.getCmp("buffer_ph").getValue(); - this.buffer.composition = Ext.getCmp("buffer_composition").getValue(); - this.buffer.bufferhasadditive3VOs = this.additiveGrid.getAdditives(); - return this.buffer; -}; -BufferForm.prototype._getTopPanel = function() { - return { - xtype : 'container', - layout : 'hbox', - border : 0, - frame : true, - items : [ { - xtype : 'container', - layout : 'hbox', - items : [ { +MacromoleculeForm.prototype._getItems = function() { + var _this = this; + /** Symmetry combo box **/ + var symmetry = Ext.create('Ext.data.Store', { + fields : [ 's' ], + data : this._getSymmetries() + }); + + this.symmetryComboBox = Ext.create('Ext.form.ComboBox', { + fieldLabel : 'Symmetry', + store : symmetry, + id : this.id + 'comboSym', + queryMode : 'local', + displayField : 's', + valueField : 's', + value : "P1", + margin : "0 0 0 30", + width : 220 + }); + + return [this._getFieldTextWithHelp("requiredtext", "Name", "name", "Long name. i.e: Bovine serum albumin"), + this._getFieldTextWithHelp("requiredtext", "Acronym", "acronym", "Acronym will be used in the files and analisys. i.e: BSA"), + this._getFieldTextWithHelp("textfield", "Mol. Mass (Da)", "molecularMass", "Atomic mass estimation measured in Da"), + { xtype : 'container', - flex : 1, - border : false, - layout : 'anchor', - defaultType : 'textfield', - items : [ { - xtype : 'requiredtext', - id : 'buffer_name', - fieldLabel : 'Name', - name : 'name', - width : '200px', - value : this.buffer.name - }, { - xtype : 'requiredtext', - id : 'buffer_acronym', - fieldLabel : 'Acronym', - name : 'acronym', - width : '200px', - value : this.buffer.acronym - } ] - } ] - }, { - xtype : 'container', - flex : 1, - layout : 'anchor', - defaultType : 'textfield', - margin : '0 0 0 10', - items : [ { - id : 'buffer_ph', - fieldLabel : 'pH', - name : 'ph', - value : this.buffer.ph, - xtype : 'numberfield', - width : 200, - minValue : 0, - maxValue : 15 - }, { - xtype : 'requiredtext', - id : 'buffer_composition', - fieldLabel : 'Composition', - name : 'composition', - width : 200, - value : this.buffer.composition - } ] - } ] - }; + layout : 'hbox', + margin : "10 0 0 0", + items :[ + this._getNumericWithHelp("numberfield", "Extinction coef.", "extintionCoefficient", ""), + this.symmetryComboBox + ] + }, + { + xtype : 'container', + layout : 'hbox', + margin : "5 0 0 0", + items :[ + this._getNumericWithHelp("numberfield", "Refractive Index", "refractiveIndex", "How radiation propagates through the medium"), + this._getNumericWithHelp("numberfield", "Solvent Viscosity", "solventViscosity", "") + ] + }, + { + id : this.id + "comments", + xtype : 'textareafield', + name : 'comments', + margin : '35 0 0 10', + fieldLabel : 'Comments', + width : this.width - 100 + } ]; }; -BufferForm.prototype.getPanel = function(buffer) { - this.buffer = buffer; - this.panel = Ext.createWidget({ - xtype : 'container', - layout : 'vbox', - style : { - padding : '10px' - }, - fieldDefaults : { - labelAlign : 'left', - labelWidth : 50 +MacromoleculeForm.prototype._getSymmetries = function() { + return [ { + "s" : "P1" + }, { + "s" : "P2" + }, { + "s" : "P3" + }, { + "s" : "P4" + }, { + "s" : "P5" + }, { + "s" : "P6" + }, { + "s" : "P32" + }, { + "s" : "P42" + }, { + "s" : "P52" + }, { + "s" : "P62" + }, { + "s" : "P222" + } ] +}; - }, - items : [ this._getTopPanel(), { - id : 'buffer_comments', - xtype : 'textareafield', - name : 'comments', - fieldLabel : 'Comments', - width : '100%', - value : buffer.comments - }, this.additiveGrid.getPanel(buffer) ] +MacromoleculeForm.prototype.getPanel = function() { + this.panel = Ext.create('Ext.form.Panel', { + width : this.width, + height : this.height, + margin : 10, + border : 1, + defaultType : 'textfield', + items : this._getItems(), + buttons : this._getButtons() }); return this.panel; }; -BufferForm.prototype.input = function() { - return { - buffer : { - "bufferId" : 422, - "proposalId" : 10, - "safetyLevelId" : null, - "name" : "B1", - "acronym" : "B1", - "ph" : null, - "composition" : null, - "bufferhasadditive3VOs" : [], - "comments" : null - } - }; + +/** Populates each text field by field name and value **/ +MacromoleculeForm.prototype._populateField = function(fieldName, value) { + if (value != null){ + Ext.getCmp(this.id + fieldName).setValue(value); + } }; -BufferForm.prototype.test = function(targetId) { - var bufferForm = new BufferForm(); - var panel = bufferForm.getPanel(bufferForm.input().buffer); - panel.render(targetId); +/** Gets the value of a textfield **/ +MacromoleculeForm.prototype._getField = function(fieldName) { + return Ext.getCmp(this.id + fieldName).getValue(); }; - -/** - * @showTitle - * - * #onSaved - * #onAddPlates - * #onRemovePlates - **/ -function CaseForm(args) { - this.width = 700; - this.showTitle = true; - if (args != null) { - if (args.showTitle != null) { - this.showTitle = args.showTitle; - } - } - var _this = this; - this.stockSolutionGrid = new StockSolutionGrid({ - width : this.width - 10, - minHeight : 300, - height : 300, - tbar : true, - showTitle : true, - isPackedVisible : false, - btnAddExisting : true, - btnRemoveVisible : false, - btnUnpackVisible : true - }); - /** When selecting existing stock solutions **/ - this.stockSolutionGrid.onStockSolutionSelected.attach(function(sender, stockSolutions) { - if (stockSolutions != null) { - for ( var i = 0; i < stockSolutions.length; i++) { - _this.saveStockSolution(stockSolutions[i]); - } +/** It populates the form **/ +MacromoleculeForm.prototype.refresh = function(macromolecule) { + this.macromolecule = macromolecule; + if (macromolecule != null){ + this._populateField("name", macromolecule.name); + this._populateField("acronym", macromolecule.acronym); + this._populateField("extintionCoefficient", macromolecule.extintionCoefficient); + this._populateField("molecularMass", macromolecule.molecularMass); + this._populateField("comments", macromolecule.comments); + this._populateField("refractiveIndex", macromolecule.refractiveIndex); + this._populateField("solventViscosity", macromolecule.solventViscosity); + if (macromolecule.symmetry != null){ + Ext.getCmp(this.id + 'comboSym').setValue(macromolecule.symmetry); } - }); + } +}; - /** it can be because it has been added a new one or removed **/ - this.stockSolutionGrid.onProposalChanged.attach(function(sender, stockSolution) { - if (stockSolution != null) { - _this.saveStockSolution(stockSolution); - } else { - BIOSAXS.proposal.onInitialized.attach(function() { - _this.stockSolutionGrid.refresh(BIOSAXS.proposal.getStockSolutionsByDewarId(_this.dewar.dewarId)); - _this.stockSolutionGrid.grid.setLoading(false); - }); - BIOSAXS.proposal.init(); +MacromoleculeForm.prototype.input = function() { + return {}; +}; - } +/** It populates the form **/ +MacromoleculeForm.prototype.test = function(targetId) { + var macromoleculeForm = new MacromoleculeForm(); + macromoleculeForm.onClose.attach(function(sender){ + alert("Click on close"); }); + var panel = macromoleculeForm.getPanel(); + panel.render(targetId); +}; - this.onSaved = new Event(this); - this.onAddPlates = new Event(this); - this.onRemovePlates = new Event(this); -} -CaseForm.prototype.saveStockSolution = function(stockSolution) { - var _this = this; - var adapter = new BiosaxsDataAdapter(); - this.stockSolutionGrid.grid.setLoading("ISPyB: setting case to Stock solution"); - adapter.onSuccess.attach(function(sender, stockSolution) { - BIOSAXS.proposal.onInitialized.attach(function() { - _this.stockSolutionGrid.refresh(BIOSAXS.proposal.getStockSolutionsByDewarId(_this.dewar.dewarId)); - _this.stockSolutionGrid.grid.setLoading(false); - }); - BIOSAXS.proposal.init(); - }); - adapter.onError.attach(function(sender, data) { - _this.stockSolutionGrid.grid.setLoading(false); - BUI.showError(data); - }); - stockSolution.boxId = _this.dewar.dewarId; - adapter.saveStockSolution(stockSolution); -}; - -CaseForm.prototype.fillStores = function() { - var _this = this; - this.panel.setLoading("Loading Labcontacts from database"); + - var proposal = BUI.getProposal(); - proposal.onDataRetrieved.attach(function(sender, data) { - _this.labContactForSendingStore.loadData(data, false); - _this.labContactForReturnStore.loadData(data, false); - _this.panel.setLoading(false); - }); - proposal.getLabContactsByProposalId(); +function ModelVisualizerForm(args){ + this.id =BUI.id(); + this.width = 600; + this.height = 400; + if (args!= null){ + if (args.width != null){ + this.width = args.width; + } + if (args.height != null){ + this.height = args.height; + } + } }; -CaseForm.prototype.refresh = function(dewar) { - this.setDewar(dewar); - this.stockSolutionGrid.refresh(BIOSAXS.proposal.getStockSolutionsByDewarId(dewar.dewarId)); +ModelVisualizerForm.prototype._getFirHTML = function(modelId, width, height, type, desc) { + var html = ""; + html = html + ''; + html = html + ''; + html = html + ''; + html = html + '
dammin.' + type + '
' + desc + '
'; + return html; }; -CaseForm.prototype.getDewar = function() { - this.dewar.code = Ext.getCmp("dewar_code").getValue(); - this.dewar.comments = Ext.getCmp("dewar_comments").getValue(); - this.dewar.trackingNumberFromSynchrotron = Ext.getCmp("dewar_trackingNumberFromSynchrotron").getValue(); - this.dewar.trackingNumberToSynchrotron = Ext.getCmp("dewar_trackingNumberToSynchrotron").getValue(); - this.dewar.transportValue = Ext.getCmp("dewar_transportValue").getValue(); - this.dewar.storageLocation = Ext.getCmp("dewar_storageLocation").getValue(); - this.dewar.firstExperimentId = this.macromoleculeCombo.getValue(); - return this.dewar; +ModelVisualizerForm.prototype.getItems = function(modelPanel){ + _this = this; + var height = _this.height/2 - 60; + var width = _this.width/2 - 10; + + return Ext.create('Ext.container.Container', { + layout: { + type: 'vbox', // Arrange child items vertically + }, + items: [ + modelPanel, + { + xtype : 'container', + layout: { + type: 'hbox', // Arrange child items vertically + }, + items : [{ + html : this._getFirHTML("id", width, height, "fir", "Fit of the simulated scattering curve versus a smoothed experimental data (spline interpolation)"), + height :height, + width : width, + padding: 2 + }, + { + html : this._getFirHTML("id", width, height, "fit", "Fit of the simulated scattering curve versus the experimental data."), + height : height, + width : width, + padding: 2 + }] + } + + ] + }); }; -CaseForm.prototype.setDewar = function(dewar) { - this.dewar = dewar; - Ext.getCmp("dewar_code").setValue(this.dewar.code); - Ext.getCmp("dewar_dewarStatus").setText(new String(this.dewar.dewarStatus).toUpperCase()); - Ext.getCmp("dewar_comments").setValue(this.dewar.comments); - Ext.getCmp("dewar_trackingNumberFromSynchrotron").setValue(this.dewar.trackingNumberFromSynchrotron); - Ext.getCmp("dewar_trackingNumberToSynchrotron").setValue(this.dewar.trackingNumberToSynchrotron); - Ext.getCmp("dewar_transportValue").setValue(this.dewar.transportValue); - Ext.getCmp("dewar_storageLocation").setValue(this.dewar.storageLocation); - if (dewar.sessionVO != null) { - this.macromoleculeCombo.setValue(dewar.sessionVO.sessionId); +ModelVisualizerForm.prototype.refresh = function(models){ + var input = []; +// var colors = ["008000", "F0A804", "0000FF", "800080", "C0C0C0"]; + for (var i = 0; i < models.length; i++) { + console.log(BUI.rainbow(models.length, i).replace("#", "0x")); + input.push({ + color: BUI.rainbow(models.length, i).replace("#", "0x"), + modelId: models[i].modelId, + opacity: 0.8, + radius: 3, + title: BUI.getFileNameByPath(models[i].pdbFile), + type: "SHAPEDETERMINATIONMODEL" + + }); } + + this.panel.removeAll(); + this.panel.add( + _this.getItems( + new PDBViewer({ + width : this.width - 10, + height : (this.height/2) - 10, + title : "" + }).draw(input) + ) + ); + + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + var splitted = data.toString().split("\n"); + var array = []; + for ( var i = 0; i < splitted.length; i++) { + var line = splitted[i].trim(); + var line_splited = line.split(/\s*[\s,]\s*/); + if (line_splited.length == 4) { + array.push([ Number(line_splited[0]), BUI.getStvArray(line_splited[1], line_splited[2]), BUI.getStvArray(line_splited[3], 0) ]); + } + } + + var id = (_this.id + "firid"); + var dygraphWidget = new StdDevDyGraph(id, { + width : (_this.width/2) - 10, + height :(_this.height/2) -110, + xlabel : 'q(nm-1)' + }); + dygraphWidget.draw(array, [ "#FF0000", "#0000FF", "#FF00FF" ], [ 's', 'I(exp)', 'I(sim)' ]); + }); + + adapter.getModelFile("FIR", models[0].modelId); + + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + var splitted = data.toString().split("\n"); + var array = []; + for ( var i = 0; i < splitted.length; i++) { + var line = splitted[i].trim(); + var line_splited = line.split(/\s*[\s,]\s*/); + if (line_splited.length == 3) { + array.push([ Number(line_splited[0]), BUI.getStvArray(line_splited[1], 0), BUI.getStvArray(line_splited[2], 0) ]); + } + } + + var id = (_this.id + "fitid"); + + var dygraphWidget = new StdDevDyGraph(id, { + width : (_this.width/2) - 10, + height : (_this.height/2) - 110, + xlabel : 'q(nm-1)' + }); + dygraphWidget.draw(array, [ "#FF0000", "#0000FF" ], [ "s", "I(exp)", "I(sim)" ]); + }); + adapter.getModelFile("FIT", models[0].modelId); }; -CaseForm.prototype.getSessionCombo = function() { - this.macromoleculeCombo = BIOSAXS_COMBOMANAGER.getComboSessions(BIOSAXS.proposal.getSessions(), { - labelWidth : 100, - margin : '5 0 00 0', - width : 250 +ModelVisualizerForm.prototype.getPanel = function(modelList){ + _this = this; + this.modelList = modelList; + this.panel = Ext.create('Ext.Panel', { + title: 'Results', + width: this.width, + height: this.height, + layout: { + type: 'vbox', // Arrange child items vertically +// align: 'stretch' // Each takes up full width + }, + items: [ + + ], + listeners : { + afterrender : function(grid, eOpts) { +// alert(_this.modelList) + } + } }); - return this.macromoleculeCombo; + + return this.panel; + }; -CaseForm.prototype.getInformationPanel = function() { - if (this.panel == null) { - this.informationPanel = Ext.create('Ext.form.Panel', { - width : this.width - 10, - border : 0, - items : [ { - xtype : 'container', - margin : "2 2 2 2", - collapsible : false, - defaultType : 'textfield', - layout : 'anchor', - items : [ { - xtype : 'container', - layout : 'hbox', - items : [ { - xtype : 'requiredtext', - fieldLabel : 'Code', - allowBlank : false, - name : 'code', - id : 'dewar_code', - anchor : '50%' - }, { - xtype : 'label', - margin : '0 0 0 20', - readOnly : true, - id : 'dewar_dewarStatus', - anchor : '50%' - } ] - }, this.getSessionCombo(), { - margin : '5 0 0 0', - xtype : 'textareafield', - name : 'comments', - id : 'dewar_comments', - width : this.width - 50, - fieldLabel : 'Comments' - } ] - }, { - xtype : 'fieldset', - title : 'Courier Accounts Details for Return', - collapsible : false, - layout : 'anchor', - defaults : { - anchor : '100%' - }, - items : [ { - xtype : 'container', - layout : 'hbox', - items : [ { - xtype : 'textfield', - labelWidth : 200, - width : 280, - fieldLabel : 'Track Number From Synchrotron', - id : 'dewar_trackingNumberFromSynchrotron' - }, { - xtype : 'numberfield', - width : 190, - labelWidth : 110, - margin : '0 0 0 30', - fieldLabel : 'Transport Value', - id : 'dewar_transportValue' - } - - ] - }, { - xtype : 'container', - layout : 'hbox', - margin : '10 0 0 0', - items : [ - - { - xtype : 'textfield', - labelWidth : 200, - width : 280, - fieldLabel : 'Track Number To Synchrotron', - id : 'dewar_trackingNumberToSynchrotron' - }, { - xtype : 'textfield', - margin : '0 0 0 30', - width : 190, - labelWidth : 110, - fieldLabel : 'Storage Location', - id : 'dewar_storageLocation' - } - - ] - } ] - } ] - }); - } - - return this.informationPanel; -}; - -CaseForm.prototype.getPanel = function(dewar) { - this.dewar = dewar; - this.panel = Ext.createWidget({ - xtype : 'container', - layout : 'vbox', - width : this.width, - border : 0, - items : [ { - items : { - xtype : "container", - layout : "vbox", - margin : "5 5 5 5", - items : [ this.getInformationPanel(dewar), this.stockSolutionGrid.getPanel() ] - - } - } ] - }); - - this.refresh(dewar); - return this.panel; - -}; - -CaseForm.prototype.input = function() { - return { - dewar : { - "dewarId" : 305861, - "code" : "ESRF-TEST", - "comments" : "comments", - "storageLocation" : "FRIDGE", - "dewarStatus" : "opened", - "timeStamp" : null, - "isStorageDewar" : null, - "barCode" : "ESRF305861", - "customsValue" : null, - "transportValue" : null, - "trackingNumberToSynchrotron" : "3333", - "trackingNumberFromSynchrotron" : "224466", - "type" : "Dewar", - "sessionVO" : { - "sessionId" : 31697, - "expSessionPk" : null, - "projectCode" : null, - "startDate" : "2012 07 21", - "endDate" : "2012 07 23", - "beamlineName" : "BM29", - "scheduled" : 1, - "nbShifts" : 2, - "comments" : null, - "beamlineOperator" : "PERNOT P", - "usedFlag" : null, - "sessionTitle" : null, - "structureDeterminations" : null, - "dewarTransport" : null, - "databackupFrance" : null, - "databackupEurope" : null, - "visit_number" : null, - "operatorSiteNumber" : "14061", - "timeStamp" : "2012 04 25" - } - }, - proposal : { - "assemblies" : [], - "sessions" : [ { - "sessionId" : 31697, - "expSessionPk" : null, - "projectCode" : null, - "startDate" : "2012 07 21", - "endDate" : "2012 07 23", - "beamlineName" : "BM29", - "scheduled" : 1, - "nbShifts" : 2, - "comments" : null, - "beamlineOperator" : "PERNOT P", - "usedFlag" : null, - "sessionTitle" : null, - "structureDeterminations" : null, - "dewarTransport" : null, - "databackupFrance" : null, - "databackupEurope" : null, - "visit_number" : null, - "operatorSiteNumber" : "14061", - "timeStamp" : "2012 04 25" - } ], - "labcontacts" : [ { - "labContactId" : 787, - "personVO" : { - "personId" : 304252, - "personUUID" : null, - "familyName" : "KIM", - "givenName" : "Henry", - "title" : null, - "emailAddress" : "henry-sung.kim@ibs.fr", - "phoneNumber" : "", - "login" : "", - "passwd" : "", - "faxNumber" : "" - }, - "cardName" : "KIM-Institut de Bio", - "defaultCourrierCompany" : "22", - "courierAccount" : "", - "billingReference" : "", - "dewarAvgCustomsValue" : 0, - "dewarAvgTransportValue" : 0 - } ], - "buffers" : [ { - "bufferId" : 811, - "proposalId" : 3124, - "safetyLevelId" : null, - "name" : "EDTA", - "acronym" : "EDTA", - "ph" : null, - "composition" : "", - "bufferhasadditive3VOs" : [], - "comments" : "" - }, { - "bufferId" : 810, - "proposalId" : 3124, - "safetyLevelId" : null, - "name" : "HEPES", - "acronym" : "HEPES", - "ph" : null, - "composition" : "", - "bufferhasadditive3VOs" : [], - "comments" : "" - } ], - "shippings" : [ { - "shippingId" : 304107, - "shippingName" : "TEST", - "deliveryAgentAgentName" : null, - "deliveryAgentShippingDate" : null, - "deliveryAgentDeliveryDate" : null, - "deliveryAgentAgentCode" : null, - "deliveryAgentFlightCode" : null, - "shippingStatus" : "opened", - "timeStamp" : "2013 09 25", - "laboratoryId" : null, - "isStorageShipping" : null, - "creationDate" : "2013 09 25", - "comments" : "test", - "sendingLabContactVO" : { - "labContactId" : 787, - "personVO" : { - "personId" : 304252, - "personUUID" : null, - "familyName" : "KIM", - "givenName" : "Henry", - "title" : null, - "emailAddress" : "henry-sung.kim@ibs.fr", - "phoneNumber" : "", - "login" : "", - "passwd" : "", - "faxNumber" : "" - }, - "cardName" : "KIM-Institut de Bio", - "defaultCourrierCompany" : "22", - "courierAccount" : "", - "billingReference" : "", - "dewarAvgCustomsValue" : 0, - "dewarAvgTransportValue" : 0 - }, - "returnLabContactVO" : { - "labContactId" : 787, - "personVO" : { - "personId" : 304252, - "personUUID" : null, - "familyName" : "KIM", - "givenName" : "Henry", - "title" : null, - "emailAddress" : "henry-sung.kim@ibs.fr", - "phoneNumber" : "", - "login" : "", - "passwd" : "", - "faxNumber" : "" - }, - "cardName" : "KIM-Institut de Bio", - "defaultCourrierCompany" : "22", - "courierAccount" : "", - "billingReference" : "", - "dewarAvgCustomsValue" : 0, - "dewarAvgTransportValue" : 0 - }, - "returnCourier" : null, - "dateOfShippingToUser" : null, - "shippingType" : "DewarTracking", - "dewarVOs" : [ { - "dewarId" : 305861, - "code" : "ESRF-TEST", - "comments" : "comments", - "storageLocation" : "FRIDGE", - "dewarStatus" : "opened", - "timeStamp" : null, - "isStorageDewar" : null, - "barCode" : "ESRF305861", - "customsValue" : null, - "transportValue" : null, - "trackingNumberToSynchrotron" : "3333", - "trackingNumberFromSynchrotron" : "224466", - "type" : "Dewar", - "sessionVO" : { - "sessionId" : 31697, - "expSessionPk" : null, - "projectCode" : null, - "startDate" : "2012 07 21", - "endDate" : "2012 07 23", - "beamlineName" : "BM29", - "scheduled" : 1, - "nbShifts" : 2, - "comments" : null, - "beamlineOperator" : "PERNOT P", - "usedFlag" : null, - "sessionTitle" : null, - "structureDeterminations" : null, - "dewarTransport" : null, - "databackupFrance" : null, - "databackupEurope" : null, - "visit_number" : null, - "operatorSiteNumber" : "14061", - "timeStamp" : "2012 04 25" - } - } ] - } ], - "macromolecules" : [ { - "macromoleculeId" : 5933, - "safetylevelId" : null, - "proposalId" : 3124, - "name" : "A", - "acronym" : "A", - "molecularMass" : "", - "extintionCoefficient" : "", - "sequence" : null, - "creationDate" : null, - "comments" : "", - "macromoleculeregion3VOs" : [], - "stoichiometry3VOsForHostMacromoleculeId" : [], - "structure3VOs" : [] - } ], - "stockSolutions" : [ { - "stockSolutionId" : 6, - "proposalId" : 3124, - "macromoleculeId" : 5933, - "bufferId" : 811, - "instructionSet3VO" : null, - "boxId" : 305861, - "storageTemperature" : "20", - "volume" : "300", - "concentration" : "1.2", - "comments" : "Buffer EDTA with A", - "name" : "A_EDTA_1.2", - "samples" : [] - } ] - } - - }; -}; - -CaseForm.prototype.test = function(targetId) { - var caseForm = new CaseForm(); - BIOSAXS.proposal = new Proposal(caseForm.input().proposal); - var panel = caseForm.getPanel(caseForm.input().dewar); - panel.render(targetId); -}; - -/** - * Example form - * - * @witdh - * @height - */ -function ExampleForm(args) { - this.id = BUI.id(); - this.width = 700; - this.height = 500; - - if (args != null) { - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; - } - } -} - -ExampleForm.prototype._getItems = function() { - return [{ - fieldLabel : 'First Name', - name : 'first', - allowBlank : false - }, { - fieldLabel : 'Last Name', - name : 'last', - allowBlank : false - } ]; -}; - -ExampleForm.prototype._getItems = function() { - return [ ]; -}; - -ExampleForm.prototype._getButtons = function() { - return [ ]; -}; - -ExampleForm.prototype.getPanel = function() { - this.panel = Ext.create('Ext.form.Panel', { - width : this.width, - height : this.height, - margin : 10, - border : 1, - defaultType : 'textfield', - items : this._getItems(), - buttons : this._getButtons() - }); - return this.panel; -}; - -/** It populates the form **/ -ExampleForm.prototype.refresh = function(macromolecule) { -}; - -function ExperimentForm(args) { - this.id = BUI.id(); - - if (args != null) { - } - - this.onSaved = new Event(this); -} - -ExperimentForm.prototype._getItems = function(experiment) { - this.experiment = experiment; - var typeCombo = Ext.create('Ext.form.ComboBox', { - id : this.id + 'type', - fieldLabel : 'Type', - store : [ "STATIC", "CALIBRATION", "HPLC" ], - queryMode : 'local', - labelWidth : 120, - displayField : 'name', - valueField : 'name', - value : experiment.json.type, - disabled : (experiment.json.type == 'TEMPLATE') - }); - - var items = []; - - - if (experiment.json.type == "HPLC" ){ - var typeMacromolecule = BIOSAXS_COMBOMANAGER.getComboMacromoleculeByMacromolecules(BIOSAXS.proposal.getMacromolecules(), {labelWidth : 120, width: "120px"}); - if (experiment.getHPLCMacromolecule() != null){ - typeMacromolecule.setValue(experiment.getHPLCMacromolecule().macromoleculeId); - items.push(typeMacromolecule); - } - } - - - items.push(typeCombo, { - id : this.id + 'name', - xtype : 'textfield', - fieldLabel : 'Name', - labelWidth : 120, - width : '100%', - value : experiment.json.name - }, { - id : this.id + 'comments', - xtype : 'textareafield', - name : 'comments', - fieldLabel : 'Comments', - labelWidth : 120, - height : 120, - width : '100%', - value : experiment.json.comments - }); - return items; -}; -ExperimentForm.prototype.getPanel = function(experiment) { - var _this = this; - - this.panel = Ext.createWidget({ - xtype : 'container', - layout : 'vbox', - border : 0, - style : { - padding : '10px' - }, - fieldDefaults : { - labelAlign : 'left', - labelWidth : 50 - }, - items : this._getItems(experiment) - }); - return this.panel; -}; - -ExperimentForm.prototype.input = function() { - return new ExperimentHeaderForm().input(); -}; - -ExperimentForm.prototype.test = function(targetId) { - var experimentForm = new ExperimentForm(); - var panel = experimentForm.getPanel(new Experiment(experimentForm.input().experiment)); - panel.render(targetId); -}; - -/** - * Shows the header for the experiments changing the color and parameters depending on experiment type - * - */ -function ExperimentHeaderForm(args) { - this.id = BUI.id(); - this.backgroundColor = '#FFFFFF'; -} - -ExperimentHeaderForm.prototype.getHTMLSource = function(experiment) { - var html = BUI.createFormLabel("Name :", experiment.json.name, 75, 400, this.backgroundColor); - if (experiment.json.type == "HPLC") { - if (experiment.getHPLCMacromolecule() != null){ - html = html + BUI.createFormLabel("Molecule :", experiment.getHPLCMacromolecule().acronym, 75, 400, this.backgroundColor); - } - } - else{ - html = html + BUI.createFormLabel("Type :", experiment.json.type, 75, 400, this.backgroundColor); - } - - html = html + BUI.createFormLabel("Date :", experiment.json.creationDate, 75, 400, this.backgroundColor); - return html; -}; - -ExperimentHeaderForm.prototype.getHTMLDownload = function(experiment) { - var bgcolor = "background-color:" + this.backgroundColor + ";"; - var html = "
"; - if ((experiment.json.type == "CALIBATION") || (experiment.json.type == "STATIC")) { - html = html + " Download Source File
"; - html = html - + ""; - } - if (experiment.json.type == "TEMPLATE") { - html = html - + " Download Source File"; - } - - if (experiment.json.type == "HPLC") { - html = html + " Download h5 File"; - } - - return html; -}; - -ExperimentHeaderForm.prototype.getTopPanel = function(experiment) { - return { - xtype : 'container', - layout : 'hbox', - items : [ { - margin : "0 0 0 0", - width : 475, - border : 0, - html : this.getHTMLSource(experiment) - }, { - margin : "0 0 0 0", - width : 475, - border : 0, - html : this.getHTMLDownload(experiment) - } ] - }; -}; - -ExperimentHeaderForm.prototype.getButton = function(experiment) { - var _this = this; - return Ext.create('Ext.Button', { - text : 'EDIT', - minWidth : '100', - margin : '10 0 0 30', - handler : function() { - var experimentWindow = new ExperimentWindow(); - experimentWindow.onSaved.attach(function(sender, data) { - _this.experiment.json.name = data.name; - _this.experiment.json.type = data.type; - _this.experiment.json.comments = data.comments; - _this.panel.remove(_this.panel.items.items[0]); - _this.panel.remove(_this.panel.items.items[0]); - _this.panel.insert(_this.getTopPanel(_this.experiment)); - _this.panel.insert(_this.getBottomPanel(_this.experiment)); - }); - experimentWindow.show(experiment); - } - }); -}; - -ExperimentHeaderForm.prototype.getBottomPanel = function(experiment) { - return { - xtype : 'container', - layout : 'hbox', - margin : '10 0 0 0', - items : [ this.getComments(experiment), this.getButton(experiment) ] - }; -}; - -ExperimentHeaderForm.prototype.getComments = function(experiment) { - return { - xtype : 'textareafield', - labelStyle : 'font-weight: bold;', - name : 'comments', - fieldLabel : 'Comments', - labelWidth : 70, - height : 40, - minWidth : '450', - readOnly : true, - value : experiment.json.comments - }; -}; - -ExperimentHeaderForm.prototype.getPanel = function(experiment) { - this.experiment = experiment; - - if (experiment.json.type == 'CALIBRATION') { - this.backgroundColor = '#EFFBFB'; - } - if (experiment.json.type == 'TEMPLATE') { - this.backgroundColor = '#E0F8E6'; - } - - this.panel = Ext.create('Ext.container.Container', { - frame : false, - layout : 'vbox', - padding : 5, - bodyPadding : '5 5 0 0', - width : 890, - margin : '0 0 10 0', - height : 120, - style : { - borderColor : '#99bce8', - borderStyle : 'solid', - borderWidth : '1px', - 'background-color' : this.backgroundColor - }, - fieldDefaults : { - msgTarget : 'side', - labelWidth : 100 - }, - items : [ this.getTopPanel(experiment), this.getBottomPanel(experiment) ] - }); - return this.panel; -}; - -ExperimentHeaderForm.prototype.input = function() { - return { - experiment : DATADOC.getExperiment_10() - }; -}; - -ExperimentHeaderForm.prototype.test = function(targetId) { - var experimentHeaderForm = new ExperimentHeaderForm(); - var panel = experimentHeaderForm.getPanel(new Experiment(experimentHeaderForm.input().experiment)); - panel.render(targetId); - -}; - -/** - * Macromolecule form with the general parameters of a macromolecule - * - * @witdh - * @height - * - * #onSave button save has been clicked - * #onClose button close has been clicked - */ -function MacromoleculeForm(args) { - this.id = BUI.id(); - this.width = 700; - this.height = 500; - - if (args != null) { - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; - } - } - - /** Events **/ - this.onSave = new Event(this); - this.onClose = new Event(this); -} - -/** Type : is the Ext type then requiredtext or textfield * */ -MacromoleculeForm.prototype._getFieldTextWithHelp = function(type, fieldLabel, fieldName, help) { - return Ext.create('Ext.container.Container', { - margin : "10 0 0 10", - items : [ { - xtype : type, - fieldLabel : fieldLabel, - name : fieldName, - id : this.id + fieldName - }, { - xtype : 'label', - forId : 'myFieldId', - text : help, - margin : "5 0 0 105", - cls : "inline-help" - } ] - }); -}; - -MacromoleculeForm.prototype._getNumericWithHelp = function(type, fieldLabel, fieldName, help) { - return Ext.create('Ext.container.Container', { - margin : "0 0 0 10", - items : [ { - xtype : type, - fieldLabel : fieldLabel, - name : fieldName, - id : this.id + fieldName, - decimalPrecision : 6, - width : 220 - }, { - xtype : 'label', - forId : 'myFieldId', - text : help, - margin : "5 0 0 10", - cls : "inline-help" - } ] - }); -}; - -MacromoleculeForm.prototype._getButtons = function() { - var _this = this; - return [ { - text : 'Save', - handler : function() { - _this._save(); - } - },{ - text : 'Close', - handler : function() { - _this.onClose.notify(); - - } - } ]; -}; - -/** It persits the macromolecule in the database **/ -MacromoleculeForm.prototype._persist = function(macromoleculeId, acronym, name, molecularMass, extintionCoefficient, comments, refractiveIndex, solventViscosity) { - - /** Checking not duplicated acronym **/ - if (((macromoleculeId == null) && (BIOSAXS.proposal.getMacromoleculeByAcronym(acronym) != null))== true){ - BUI.showError("Duplicated acronym"); - return; - } - - - if (macromoleculeId == null){ - /** new macromolecule **/ - this.macromolecule = {}; - this.macromolecule.macromoleculeId = null; - } - else{ - this.macromolecule.macromoleculeId = macromoleculeId; - } - - this.macromolecule["acronym"] = acronym; - this.macromolecule["name"] = name; - this.macromolecule["molecularMass"] = molecularMass; - this.macromolecule["extintionCoefficient"] = extintionCoefficient; - this.macromolecule["comments"] = comments; - this.macromolecule["symmetry"] = Ext.getCmp(this.id + 'comboSym').getValue(); - this.macromolecule["refractiveIndex"] = refractiveIndex; - this.macromolecule["solventViscosity"] = solventViscosity; - - var _this = this; - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, proposal) { - /** Updating the proposal global object **/ - BIOSAXS.proposal.setItems(proposal); - _this.panel.setLoading(false); - - var saved = BIOSAXS.proposal.getMacromoleculeByAcronym(acronym); - /** Refreshing to check that everything is ok **/ - _this.refresh(saved); - _this.onSave.notify(saved); - }); - - this.panel.setLoading("Saving Macromolecule") - adapter.saveMacromolecule(this.macromolecule); -}; - -/** Save the macromolecule in the DB **/ -MacromoleculeForm.prototype._save = function() { - - var _this = this; - - var acronym = this._getField("acronym"); - var name = this._getField("name"); - var molecularMass = this._getField("molecularMass"); - var extintionCoefficient = this._getField("extintionCoefficient"); - var comments = this._getField("comments"); - - var refractiveIndex = this._getField("refractiveIndex"); - var solventViscosity = this._getField("solventViscosity"); - - /** Checking required fields **/ - if (name == "") { - BUI.showError("Name field is mandatory"); - return; - } - if (acronym == "") { - BUI.showError("Acroynm field is mandatory"); - return; - } - - if (this.macromolecule != null){ - /** Checking if it is a new macromolecule **/ - if (this.macromolecule.macromoleculeId == null){ - /** Check if the acronym exists already **/ - this._persist(null, acronym, name, molecularMass, extintionCoefficient, comments, refractiveIndex, solventViscosity); - } - else{ - /** It is an update **/ - this._persist(this.macromolecule.macromoleculeId, acronym, name, molecularMass, extintionCoefficient, comments, refractiveIndex, solventViscosity); - } - } - else{ - /** It is a new macromolecule **/ - this._persist(null, acronym, name, molecularMass, extintionCoefficient, comments, refractiveIndex, solventViscosity); - } -}; - - - -MacromoleculeForm.prototype._getItems = function() { - var _this = this; - /** Symmetry combo box **/ - var symmetry = Ext.create('Ext.data.Store', { - fields : [ 's' ], - data : this._getSymmetries() - }); - - this.symmetryComboBox = Ext.create('Ext.form.ComboBox', { - fieldLabel : 'Symmetry', - store : symmetry, - id : this.id + 'comboSym', - queryMode : 'local', - displayField : 's', - valueField : 's', - value : "P1", - margin : "0 0 0 30", - width : 220 - }); - - return [this._getFieldTextWithHelp("requiredtext", "Name", "name", "Long name. i.e: Bovine serum albumin"), - this._getFieldTextWithHelp("requiredtext", "Acronym", "acronym", "Acronym will be used in the files and analisys. i.e: BSA"), - this._getFieldTextWithHelp("textfield", "Mol. Mass (Da)", "molecularMass", "Atomic mass estimation measured in Da"), - { - xtype : 'container', - layout : 'hbox', - margin : "10 0 0 0", - items :[ - this._getNumericWithHelp("numberfield", "Extinction coef.", "extintionCoefficient", ""), - this.symmetryComboBox - ] - }, - { - xtype : 'container', - layout : 'hbox', - margin : "5 0 0 0", - items :[ - this._getNumericWithHelp("numberfield", "Refractive Index", "refractiveIndex", "How radiation propagates through the medium"), - this._getNumericWithHelp("numberfield", "Solvent Viscosity", "solventViscosity", "") - ] - }, - { - id : this.id + "comments", - xtype : 'textareafield', - name : 'comments', - margin : '35 0 0 10', - fieldLabel : 'Comments', - width : this.width - 100 - } ]; -}; - -MacromoleculeForm.prototype._getSymmetries = function() { - return [ { - "s" : "P1" - }, { - "s" : "P2" - }, { - "s" : "P3" - }, { - "s" : "P4" - }, { - "s" : "P5" - }, { - "s" : "P6" - }, { - "s" : "P32" - }, { - "s" : "P42" - }, { - "s" : "P52" - }, { - "s" : "P62" - }, { - "s" : "P222" - } ] -}; - -MacromoleculeForm.prototype.getPanel = function() { - this.panel = Ext.create('Ext.form.Panel', { - width : this.width, - height : this.height, - margin : 10, - border : 1, - defaultType : 'textfield', - items : this._getItems(), - buttons : this._getButtons() - }); - return this.panel; -}; - - -/** Populates each text field by field name and value **/ -MacromoleculeForm.prototype._populateField = function(fieldName, value) { - if (value != null){ - Ext.getCmp(this.id + fieldName).setValue(value); - } -}; - -/** Gets the value of a textfield **/ -MacromoleculeForm.prototype._getField = function(fieldName) { - return Ext.getCmp(this.id + fieldName).getValue(); -}; - - -/** It populates the form **/ -MacromoleculeForm.prototype.refresh = function(macromolecule) { - this.macromolecule = macromolecule; - if (macromolecule != null){ - this._populateField("name", macromolecule.name); - this._populateField("acronym", macromolecule.acronym); - this._populateField("extintionCoefficient", macromolecule.extintionCoefficient); - this._populateField("molecularMass", macromolecule.molecularMass); - this._populateField("comments", macromolecule.comments); - this._populateField("refractiveIndex", macromolecule.refractiveIndex); - this._populateField("solventViscosity", macromolecule.solventViscosity); - if (macromolecule.symmetry != null){ - Ext.getCmp(this.id + 'comboSym').setValue(macromolecule.symmetry); - } - } -}; - - -MacromoleculeForm.prototype.input = function() { - return {}; -}; - - -/** It populates the form **/ -MacromoleculeForm.prototype.test = function(targetId) { - var macromoleculeForm = new MacromoleculeForm(); - macromoleculeForm.onClose.attach(function(sender){ - alert("Click on close"); - }); - var panel = macromoleculeForm.getPanel(); - panel.render(targetId); -}; - - - - - -function ModelVisualizerForm(args){ - this.id =BUI.id(); - this.width = 600; - this.height = 400; - if (args!= null){ - if (args.width != null){ - this.width = args.width; - } - if (args.height != null){ - this.height = args.height; - } - } -}; - -ModelVisualizerForm.prototype._getFirHTML = function(modelId, width, height, type, desc) { - var html = ""; - html = html + ''; - html = html + ''; - html = html + ''; - html = html + '
dammin.' + type + '
' + desc + '
'; - return html; -}; - -ModelVisualizerForm.prototype.getItems = function(modelPanel){ - _this = this; - var height = _this.height/2 - 60; - var width = _this.width/2 - 10; - - return Ext.create('Ext.container.Container', { - layout: { - type: 'vbox', // Arrange child items vertically - }, - items: [ - modelPanel, - { - xtype : 'container', - layout: { - type: 'hbox', // Arrange child items vertically - }, - items : [{ - html : this._getFirHTML("id", width, height, "fir", "Fit of the simulated scattering curve versus a smoothed experimental data (spline interpolation)"), - height :height, - width : width, - padding: 2 - }, - { - html : this._getFirHTML("id", width, height, "fit", "Fit of the simulated scattering curve versus the experimental data."), - height : height, - width : width, - padding: 2 - }] - } - - ] - }); -}; - -ModelVisualizerForm.prototype.refresh = function(models){ - var input = []; -// var colors = ["008000", "F0A804", "0000FF", "800080", "C0C0C0"]; - for (var i = 0; i < models.length; i++) { - console.log(BUI.rainbow(models.length, i).replace("#", "0x")); - input.push({ - color: BUI.rainbow(models.length, i).replace("#", "0x"), - modelId: models[i].modelId, - opacity: 0.8, - radius: 3, - title: BUI.getFileNameByPath(models[i].pdbFile), - type: "SHAPEDETERMINATIONMODEL" - - }); - } - - this.panel.removeAll(); - this.panel.add( - _this.getItems( - new PDBViewer({ - width : this.width - 10, - height : (this.height/2) - 10, - title : "" - }).draw(input) - ) - ); - - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - var splitted = data.toString().split("\n"); - var array = []; - for ( var i = 0; i < splitted.length; i++) { - var line = splitted[i].trim(); - var line_splited = line.split(/\s*[\s,]\s*/); - if (line_splited.length == 4) { - array.push([ Number(line_splited[0]), BUI.getStvArray(line_splited[1], line_splited[2]), BUI.getStvArray(line_splited[3], 0) ]); - } - } - - var id = (_this.id + "firid"); - var dygraphWidget = new StdDevDyGraph(id, { - width : (_this.width/2) - 10, - height :(_this.height/2) -110, - xlabel : 'q(nm-1)' - }); - dygraphWidget.draw(array, [ "#FF0000", "#0000FF", "#FF00FF" ], [ 's', 'I(exp)', 'I(sim)' ]); - }); - - adapter.getModelFile("FIR", models[0].modelId); - - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - var splitted = data.toString().split("\n"); - var array = []; - for ( var i = 0; i < splitted.length; i++) { - var line = splitted[i].trim(); - var line_splited = line.split(/\s*[\s,]\s*/); - if (line_splited.length == 3) { - array.push([ Number(line_splited[0]), BUI.getStvArray(line_splited[1], 0), BUI.getStvArray(line_splited[2], 0) ]); - } - } - - var id = (_this.id + "fitid"); - - var dygraphWidget = new StdDevDyGraph(id, { - width : (_this.width/2) - 10, - height : (_this.height/2) - 110, - xlabel : 'q(nm-1)' - }); - dygraphWidget.draw(array, [ "#FF0000", "#0000FF" ], [ "s", "I(exp)", "I(sim)" ]); - }); - adapter.getModelFile("FIT", models[0].modelId); -}; - -ModelVisualizerForm.prototype.getPanel = function(modelList){ - _this = this; - this.modelList = modelList; - this.panel = Ext.create('Ext.Panel', { - title: 'Results', - width: this.width, - height: this.height, - layout: { - type: 'vbox', // Arrange child items vertically -// align: 'stretch' // Each takes up full width - }, - items: [ - - ], - listeners : { - afterrender : function(grid, eOpts) { -// alert(_this.modelList) - } - } - }); - - return this.panel; - -}; - - -/** - * Example form - * - * @witdh - * @height - */ -function MolarityForm(args) { - this.id = BUI.id(); - this.width = 700; - this.height = 500; - - if (args != null) { - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; - } - } - - this.onSave = new Event(this); - this.onClose = new Event(this); -} - - -MolarityForm.prototype._getNumericWithHelp = function(type, fieldLabel, fieldName, help) { - return Ext.create('Ext.container.Container', { - margin : "10 0 0 10", - items : [ { - xtype : type, - fieldLabel : fieldLabel, - name : fieldName, - id : this.id + fieldName, - decimalPrecision : 6 - }, { - xtype : 'label', - forId : 'myFieldId', - text : help, - margin : "5 0 0 105", - cls : "inline-help" - } ] - }); -}; - - -MolarityForm.prototype._getItems = function() { - this.macromoleculeCombo = BIOSAXS_COMBOMANAGER.getComboMacromoleculeByMacromolecules(this.getMacromuleculesCandidates(this.macromolecule), { - width : 250, - labelWidth : 100, - margin : 10 - }); - - return [ { - xtype : 'container', - flex : 1, - margin : '10 0 0 10', - border : 0, - layout : 'anchor', - defaultType : 'requiredtext', - items : [ this.macromoleculeCombo, - this._getNumericWithHelp("textfield", "Ratio", "ratio", "Number in assymmetric units") - ] - } ]; -}; - -MolarityForm.prototype._persist = function() { - var _this = this; - var macromoleculeId = this.macromoleculeCombo.getValue(); - var ratio = Ext.getCmp(this.id + "ratio").getValue(); - var comments = "Not used yet"; - var dataAdapter = new BiosaxsDataAdapter(); - this.panel.setLoading("Saving"); - dataAdapter.onSuccess.attach(function(sender, args) { - _this.onSave.notify(); - }); - dataAdapter.saveStoichiometry(this.macromolecule.macromoleculeId, macromoleculeId, ratio, comments); -}; - -MolarityForm.prototype._getButtons = function() { - var _this = this; - - function onClose() { - _this.onClose.notify(); - } - - return [ { - text : 'Save', - handler : function() { - _this._persist(); - } - }, { - text : 'Cancel', - handler : function() { - onClose(); - } - } ]; -}; - -MolarityForm.prototype.getPanel = function() { - this.panel = Ext.create('Ext.form.Panel', { -// width : null, - height : this.height, - margin : 2, - border : 1, - defaultType : 'requiredtext', - items : this._getItems(), - buttons : this._getButtons() - }); - return this.panel; -}; - -/** macromolecules contains all macromolecules except this one **/ -MolarityForm.prototype.getMacromuleculesCandidates = function(macromolecule) { - var macromolecules = []; - if ( BIOSAXS.proposal.macromolecules){ - for (var i = 0; i < BIOSAXS.proposal.macromolecules.length; i++) { - var m = BIOSAXS.proposal.macromolecules[i]; - if (this.macromolecule != null){ - if (m.macromoleculeId != this.macromolecule.macromoleculeId) { - macromolecules.push(m); - } - } - } - } - return macromolecules; -}; - - -/** It populates the form **/ -MolarityForm.prototype.refresh = function(macromolecule) { - this.macromolecule = macromolecule; - -}; - - -MolarityForm.prototype.input = function() { - return {}; -}; - - -/** It populates the form **/ -MolarityForm.prototype.test = function(targetId) { - var macromoleculeForm = new MolarityForm(); - var panel = macromoleculeForm.getPanel(); - panel.render(targetId); -}; - -///** -// * -// * @witdh -// * @height -// */ -//function MacromoleculeForm(args) { -// this.id = BUI.id(); -// this.width = 700; -// this.height = 500; -// -// if (args != null) { -// if (args.width != null) { -// this.width = args.width; -// } -// if (args.height != null) { -// this.height = args.height; -// } -// } -// -// this.onClose = new Event(this); -//} -// -//MacromoleculeForm.prototype.getMacromolecule = function() { -// this.macromolecule.name = Ext.getCmp(this.panel.getItemId()).getValues().name; -// this.macromolecule.acronym = Ext.getCmp(this.panel.getItemId()).getValues().acronym; -// this.macromolecule.comments = Ext.getCmp(this.panel.getItemId()).getValues().comments; -// this.macromolecule.extintionCoefficient = Ext.getCmp(this.panel.getItemId()).getValues().extintionCoefficient; -// this.macromolecule.molecularMass = Ext.getCmp(this.panel.getItemId()).getValues().molecularMass; -// return this.macromolecule; -//}; -// -//MacromoleculeForm.prototype.setMacromolecule = function(macromolecule) { -// this.pdbStore.loadData(macromolecule.structure3VOs); -// -//}; -// -//MacromoleculeForm.prototype.getForm = function(macromolecule) { -// this.panel = Ext.createWidget('form', { -// frame : false, -// border : 0, -// padding : 15, -// width : 550, -// height : 350, -// items : [ { -// xtype : 'container', -// layout : 'hbox', -// items : [ { -// xtype : 'container', -// flex : 1, -// border : false, -// layout : 'anchor', -// defaultType : 'requiredtext', -// items : [ { -// fieldLabel : 'Name', -// name : 'name', -// anchor : '95%', -// tooltip : "Name of the macromolecule", -// value : macromolecule.name -// }, { -// fieldLabel : 'Acronym', -// name : 'acronym', -// anchor : '95%', -// value : macromolecule.acronym -// } ] -// }, { -// xtype : 'container', -// flex : 1, -// layout : 'anchor', -// defaultType : 'textfield', -// items : [ { -// xtype : 'numberfield', -// fieldLabel : 'Mol. Mass (Da)', -// name : 'molecularMass', -// value : macromolecule.molecularMass, -// decimalPrecision : 6 -// }, { -// xtype : 'numberfield', -// fieldLabel : 'Extinction coef.', -// name : 'extintionCoefficient', -// value : macromolecule.extintionCoefficient, -// decimalPrecision : 6 -// } ] -// } ] -// }, { -// xtype : 'textareafield', -// name : 'comments', -// fieldLabel : 'Comments', -// value : macromolecule.comments, -// width : this.width - 10 -// }, -// -// { -// html : BUI.getWarningHTML("The macromolecule is unsaved. Save the macromolecule to get access to other tabs"), -// margin : "150 10 10 10", -// id : this.id + "unsavedWarning", -// hidden : !(!macromolecule.macromoleculeId) -// } -// -// ] -// }); -// return this.panel; -//}; -// -//MacromoleculeForm.prototype.save = function() { -// var _this = this; -// -// var adapter = new BiosaxsDataAdapter(); -// adapter.onSuccess.attach(function(sender, proposal) { -// BIOSAXS.proposal.setItems(proposal); -// _this.panel.setLoading(false); -// -// Ext.getCmp(_this.id + "assembly").enable() -// Ext.getCmp(_this.id + "advanced").enable(); -// Ext.getCmp(_this.id + "unsavedWarning").hide(); -// }); -// -// if (this.getMacromolecule().name == "") { -// BUI.showError("Name field is mandatory"); -// return; -// } -// if (this.getMacromolecule().acronym == "") { -// BUI.showError("Acroynm field is mandatory"); -// return; -// } -// -// /** Check if acronym is unique * */ -// if (this.getMacromolecule().macromoleculeId == null) { -// if (BIOSAXS.proposal.getMacromoleculeByAcronym(this.getMacromolecule().acronym) == null) { -// this.panel.setLoading("ISPyB: Saving Macromolecule") -// adapter.saveMacromolecule(this.getMacromolecule()); -// } else { -// alert("There is already an existing macromolecule with the same acronym"); -// -// } -// } else { -// this.panel.setLoading("ISPyB: Saving Macromolecule") -// adapter.saveMacromolecule(this.getMacromolecule()); -// } -// -//}; -// -//MacromoleculeForm.prototype.getPanel = function(macromolecule) { -// var _this = this; -// this.macromolecule = macromolecule; -// return Ext.createWidget('tabpanel', { -// height : this.height, -// margin : 5, -// plain : true, -// style : { -// padding : 5 -// }, -// items : [ { -// tabConfig : { -// title : "General", -// disabled : false -// }, -// items : [ this.getForm(macromolecule) ], -// bbar : [ "->", { -// text : 'Save', -// cls : 'btn-with-border', -// style : { -// -// border : 1 -// }, -// handler : function() { -// _this.save(); -// } -// }, { -// text : 'Close', -// cls : 'btn-with-border', -// handler : function() { -// _this.onClose.notify(); -// } -// } ] -// }, { -// tabConfig : { -// id : this.id + "assembly", -// title : "Assembly", -// tooltip : 'Description of subunits present in the macromolecule', -// // hidden : (!macromolecule.macromoleculeId), -// disabled : (!macromolecule.macromoleculeId) -// }, -// items : [ this.getMolarityGrid(macromolecule) ] -// }, { -// tabConfig : { -// id : this.id + "advanced", -// title : "Advanced Modeling", -// // hidden : (!macromolecule.macromoleculeId), -// tooltip : 'Definition of the description contacts and symetries', -// disabled : (!macromolecule.macromoleculeId) -// }, -// items : [ this.getRigidBodyForm(macromolecule) ] -// } ] -// }); -//}; -// -//MacromoleculeForm.prototype.getRigidBodyForm = function(macromolecule) { -// var _this = this; -// -// // [P1, P2, P3, P4 ,P5 ,P6 ,32, P42, P52, P62] + P222 -// var symmetry = Ext.create('Ext.data.Store', { -// fields : [ 's' ], -// data : [ { -// "s" : "P1" -// }, { -// "s" : "P2" -// }, { -// "s" : "P3" -// }, { -// "s" : "P4" -// }, { -// "s" : "P5" -// }, { -// "s" : "P6" -// }, { -// "s" : "P32" -// }, { -// "s" : "P42" -// }, { -// "s" : "P52" -// }, { -// "s" : "P62" -// }, { -// "s" : "P222" -// } ] -// }); -// -// if (macromolecule.symmetry == null) { -// macromolecule.symmetry = "P1"; -// } -// var comboBox = Ext.create('Ext.form.ComboBox', { -// fieldLabel : 'Symmetry', -// store : symmetry, -// id : 'comboSym', -// queryMode : 'local', -// displayField : 's', -// valueField : 's', -// value : macromolecule.symmetry, -// margin : "10 0 0 0", -// listeners : { -// change : function(combo, newValue, oldValue, eOpts) { -// macromolecule.symmetry = newValue; -// } -// } -// }); -// -// this.rigidBodyPanel = Ext.createWidget('form', { -// frame : false, -// border : 0, -// padding : 10, -// width : 550, -// height : 400, -// items : [ { -// xtype : 'container', -// layout : 'hbox', -// items : [ { -// xtype : 'container', -// border : false, -// layout : 'hbox', -// items : [ { -// xtype : 'label', -// forId : 'myFieldId', -// text : 'Contact Desc:', -// width : 105, -// margin : '0 0 0 0' -// }, { -// xtype : 'textfield', -// hideLabel : true, -// id : "contactsDescriptionFilePath", -// margin : '0 0 0 0', -// width : 300, -// value : macromolecule.contactsDescriptionFilePath -// }, { -// text : 'Upload', -// xtype : 'button', -// margin : "0 0 0 20", -// width : 100, -// handler : function() { -// _this._openUploadDialog(macromolecule.macromoleculeId, "CONTACTS", "Upload Contact Description File"); -// } -// } ] -// } ] -// }, -// -// comboBox, { -// xtype : 'checkbox', -// margin : '10 0 0 5', -// boxLabel : "I want rigid body modeling run on this stuff", -// checked : true, -// width : 300 -// }, _this.getPDBGrid(macromolecule) ] -// }); -// return this.rigidBodyPanel; -//}; -// -//MacromoleculeForm.prototype.update = function() { -// var _this = this; -// BIOSAXS.proposal.onInitialized.attach(function() { -// if (BIOSAXS.proposal != null) { -// var macromolecules = BIOSAXS.proposal.macromolecules; -// for (var i = 0; i < macromolecules.length; i++) { -// if (macromolecules[i].macromoleculeId == _this.macromolecule.macromoleculeId) { -// _this.macromolecule = macromolecules[i]; -// _this.setMacromolecule(_this.macromolecule); -// _this.molarityStore.loadData(_this.parseMolarityData(_this.macromolecule)); -// _this.pdbGrid.setLoading(false); -// Ext.getCmp("contactsDescriptionFilePath").setValue(_this.macromolecule.contactsDescriptionFilePath) -// _this.molarityGrid.setLoading(false); -// -// } -// } -// } -// }); -// this.molarityGrid.setLoading("Updating"); -// this.pdbGrid.setLoading("Updating"); -// BIOSAXS.proposal.init(); -//}; -// -///******************************************************************************* -// * MOLARITY GRID -// ******************************************************************************/ -// -//MacromoleculeForm.prototype.parseMolarityData = function(macromolecule) { -// var data = []; -// if (macromolecule.stoichiometry != null) { -// for (var i = 0; i < macromolecule.stoichiometry.length; i++) { -// data.push({ -// ratio : macromolecule.stoichiometry[i].ratio, -// acronym : macromolecule.stoichiometry[i].macromolecule3VO.acronym, -// comments : macromolecule.stoichiometry[i].macromolecule3VO.comments, -// stoichiometryId : macromolecule.stoichiometry[i].stoichiometryId, -// name : macromolecule.stoichiometry[i].macromolecule3VO.name -// }); -// } -// } -// return data; -//}; -// -//MacromoleculeForm.prototype.getMolarityGrid = function(macromolecule) { -// var _this = this; -// -// this.molarityStore = Ext.create('Ext.data.Store', { -// fields : [ 'acronym', 'ratio', 'comments', 'stoichiometryId', 'name' ], -// data : this.parseMolarityData(macromolecule), -// sorters : { -// property : 'ratio', -// direction : 'DESC' -// } -// }); -// -// this.molarityGrid = Ext.create('Ext.grid.Panel', { -// store : this.molarityStore, -// height : 350, -// padding : 5, -// columns : [ -// -// { -// text : 'Subunit', -// columns : [ { -// text : "Acronym", -// width : 100, -// hidden : false, -// dataIndex : 'acronym', -// sortable : true -// }, { -// text : "Name", -// width : 100, -// hidden : false, -// dataIndex : 'name', -// sortable : true -// }, { -// text : "Comments", -// width : 100, -// dataIndex : 'comments', -// sortable : true -// } ] -// }, { -// text : "Number
in assymmetric units", -// width : 150, -// dataIndex : 'ratio', -// tooltip : 'Number of times this subunit is present in the macromolecule', -// sortable : true -// }, { -// id : this.id + 'MOLARITY_REMOVE', -// flex : 0.1, -// sortable : false, -// renderer : function(value, metaData, record, rowIndex, colIndex, store) { -// return BUI.getRedButton('REMOVE'); -// } -// } ], -// listeners : { -// cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { -// if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'MOLARITY_REMOVE') { -// var dataAdapter = new BiosaxsDataAdapter(); -// dataAdapter.onSuccess.attach(function() { -// _this.molarityGrid.setLoading(false); -// _this.update(); -// }); -// dataAdapter.removeStoichiometry(record.data.stoichiometryId); -// _this.molarityGrid.setLoading("Removing Structure"); -// } -// } -// }, -// buttons : [ { -// text : 'Add molarity', -// handler : function() { -// -// function onClose() { -// w.destroy(); -// _this.update(); -// } -// var w = Ext.create('Ext.window.Window', { -// title : 'Molarity', -// height : 300, -// width : 500, -// modal : true, -// buttons : [ { -// text : 'Save', -// handler : function() { -// var macromoleculeId = (_this.macromoleculeCombo.getValue()); -// var ratio = Ext.getCmp(_this.id + "ratio").getValue(); -// var comments = ""; -// var dataAdapter = new BiosaxsDataAdapter(); -// dataAdapter.onSuccess.attach(function(sender, args) { -// _this.update(); -// w.destroy(); -// }); -// dataAdapter.saveStoichiometry(_this.macromolecule.macromoleculeId, macromoleculeId, ratio, comments); -// } -// }, { -// text : 'Cancel', -// handler : function() { -// onClose(); -// } -// } ], -// items : [ _this.getMolarityForm(macromolecule) ], -// listeners : { -// onEsc : function() { -// onClose(); -// }, -// close : function() { -// onClose(); -// } -// } -// }).show(); -// } -// } ] -// }); -// return this.molarityGrid; -//}; -// -///******************************************************************************* -// * PDB GRID -// ******************************************************************************/ -// -//MacromoleculeForm.prototype._openUploadDialog = function(macromoleculeId, type, title) { -// var _this = this; -// function onClose() { -// w.destroy(); -// _this.update(); -// } -// -// var w = Ext.create('Ext.window.Window', { -// title : title, -// height : 200, -// width : 400, -// modal : true, -// buttons : [ { -// text : 'Close', -// handler : function() { -// onClose(); -// } -// } ], -// layout : 'fit', -// items : { -// html : "" -// }, -// listeners : { -// onEsc : function() { -// onClose(); -// }, -// close : function() { -// onClose(); -// } -// } -// }).show(); -//}; -// -//MacromoleculeForm.prototype._getPlugins = function() { -// var _this = this; -// var plugins = []; -// // if (this.updateRowEnabled) { -// plugins.push(Ext.create('Ext.grid.plugin.RowEditing', { -// clicksToEdit : 1, -// listeners : { -// validateedit : function(grid, e) { -// /** Comments are always updatable* */ -// e.record.raw.symmetry = e.newValues.symmetry; -// e.record.raw.multiplicity = e.newValues.multiplicity; -// -// var adapter = new BiosaxsDataAdapter(); -// adapter.onSuccess.attach(function(sender, measurement) { -// // _this.grid.setLoading(false); -// }); -// adapter.onError.attach(function() { -// alert("Error"); -// // _this.grid.setLoading(false); -// }); -// -// // _this.grid.setLoading(); -// adapter.saveStructure(e.record.raw); -// } -// } -// })); -// // } -// return plugins; -//}; -// -//MacromoleculeForm.prototype.getPDBGrid = function(macromolecule) { -// var _this = this; -// -// var data = macromolecule.structure3VOs; -// -// // /** Getting PDB from subunits **/ -// // if (macromolecule != null){ -// // if (macromolecule.stoichiometry != null){ -// // for (var i =0; i < macromolecule.stoichiometry.length; i++){ -// // var stoichiometry = macromolecule.stoichiometry[i]; -// // if (stoichiometry.macromolecule3VO != null){ -// // if (stoichiometry.macromolecule3VO.structure3VOs != null){ -// // for (var j = 0; j < stoichiometry.macromolecule3VO.structure3VOs.length; -// // j++) { -// // var structure = stoichiometry.macromolecule3VO.structure3VOs[j]; -// // structure["isSubunit"] = stoichiometry.macromolecule3VO.acronym; -// // data.push(structure) -// // } -// // } -// // } -// // } -// // } -// // } -// -// this.pdbStore = Ext.create('Ext.data.Store', { -// fields : [ 'filePath', 'structureId', 'structureType', 'symmetry', 'structureId', 'name', 'multiplicity' ], -// data : macromolecule.structure3VOs, -// groupField : 'structureType', -// sorters : { -// property : 'structureId', -// direction : 'DESC' -// } -// }); -// -// var groupingFeature = Ext.create('Ext.grid.feature.Grouping', { -// groupHeaderTpl : Ext.create('Ext.XTemplate', -// "
{name:this.formatName}
", { -// formatName : function(name) { -// return name; -// } -// }), -// hideGroupedHeader : true, -// startCollapsed : false -// }); -// -// this.pdbGrid = Ext.create('Ext.grid.Panel', { -// margin : "15 0 0 5", -// height : 250, -// store : this.pdbStore, -// plugins : _this._getPlugins(), -// buttons : [ { -// // text : 'Add PDB file', -// text : 'Add Modeling Option', -// handler : function() { -// _this._openUploadDialog(macromolecule.macromoleculeId, "PDB", 'Upload PDB File'); -// } -// } -// -// ], -// columns : [ -// { -// text : "structureId", -// flex : 0.2, -// hidden : true, -// dataIndex : 'structureId', -// sortable : true -// }, -// { -// text : "File", -// flex : 0.5, -// dataIndex : 'filePath', -// sortable : true, -// hidden : true -// }, -// { -// text : "PDB", -// flex : 0.4, -// dataIndex : 'name', -// sortable : true -// }, -// { -// text : "Symmetry", -// flex : 0.4, -// dataIndex : 'symmetry', -// sortable : true, -// editor : { -// xtype : 'combobox', -// typeAhead : true, -// triggerAction : 'all', -// selectOnTab : true, -// store : [ [ "P1", "P1" ], [ "P2", "P2" ], [ "P3", "P3" ], [ "P4", "P4" ], [ "P5", "P5" ], [ "P6", "P6" ], [ "P32", "P32" ], [ "P42", "P42" ], -// [ "P52", "P52" ], [ "P62", "P62" ], [ "P222", "P222" ] ], -// } -// }, { -// text : "Multiplicity", -// flex : 0.4, -// dataIndex : 'multiplicity', -// sortable : true, -// editor : { -// xtype : 'textfield' -// } -// -// }, { -// text : "Subunit", -// flex : 0.2, -// dataIndex : 'isSubunit', -// sortable : true, -// hidden : true -// }, { -// text : "Type", -// flex : 0.2, -// dataIndex : 'structureType', -// sortable : true, -// hidden : true -// }, -// -// { -// id : this.id + 'REMOVE', -// flex : 0.2, -// hidden : true, -// sortable : false, -// renderer : function(value, metaData, record, rowIndex, colIndex, store) { -// return BUI.getRedButton('REMOVE'); -// } -// }, ], -// -// listeners : { -// itemdblclick : function(dataview, record, item, e) { -// _this._editExperiment(record.raw.experimentId); -// }, -// cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { -// -// if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'REMOVE') { -// var dataAdapter = new BiosaxsDataAdapter(); -// dataAdapter.onSuccess.attach(function() { -// _this.pdbGrid.setLoading(false); -// _this.update(); -// }); -// dataAdapter.removeStructure(record.data.structureId); -// _this.pdbGrid.setLoading("Removing PDB file"); -// } -// -// } -// }, -// viewConfig : { -// getRowClass : function(record, rowIdx, params, store) { -// if (record.raw.isSubunit != null) { -// return "blue-row"; -// } -// } -// } -// }); -// -// return this.pdbGrid; -//}; -// -//MacromoleculeForm.prototype.getMolarityForm = function(macromolecule) { -// var _this = this; -// var data = []; -// for (var i = 0; i < BIOSAXS.proposal.macromolecules.length; i++) { -// var m = BIOSAXS.proposal.macromolecules[i]; -// if (m.macromoleculeId != macromolecule.macromoleculeId) { -// data.push(m); -// } -// -// } -// this.macromoleculeCombo = BIOSAXS_COMBOMANAGER.getComboMacromoleculeByMacromolecules(data, { -// width : 250, -// labelWidth : 100, -// margin : 10 -// }); -// -// return Ext.createWidget('form', { -// -// frame : false, -// border : 0, -// // padding : 15, -// width : 550, -// height : 350, -// items : [ { -// xtype : 'container', -// flex : 1, -// border : false, -// layout : 'anchor', -// defaultType : 'requiredtext', -// items : [ this.macromoleculeCombo, { -// xtype : 'numberfield', -// name : 'Ratio', -// id : _this.id + "ratio", -// fieldLabel : 'Number in assymmetric units', -// value : 1, -// decimalPrecision : 6, -// margin : 10 -// }, { -// xtype : 'textareafield', -// name : 'comments', -// fieldLabel : 'Comments', -// margin : 10, -// width : 400, -// value : "" -// -// } ] -// } ] -// }); -// -//}; -// -///******************************************************************************* -// * JAVASCRIPT DOC -// ******************************************************************************/ -//MacromoleculeForm.prototype.input = function() { -// return { -// macromolecule : DATADOC.getMacromolecule_10() -// }; -//}; -// -//MacromoleculeForm.prototype.test = function(targetId) { -// var macromoleculeForm = new MacromoleculeForm(); -// var panel = macromoleculeForm.getPanel(macromoleculeForm.input().macromolecule); -// panel.render(targetId); -//}; - -function ResultSummaryForm() { - this.radiationDamageThreshold = BUI.getRadiationDamageThreshold(); - this.qualityThreshold = BUI.getQualityThreshold(); - - /** Data clusters with bufers **/ - this.clusterByBuffers = false; - - /** Visualization are groupeb by concenttrations. Ex: 4.5mg/ml and 4.7mg/ml will be clusterized together **/ - this.collapseConcentrations = true; - - this.summaryHeight = 350; - this.id = BUI.id(); - - var _this = this; - - this.qualityControlResultsWidget = new QualityControlResultsWidget({ - qualityThreshold : this.radiationDamageThreshold, - radiationDamageThreshold : this.qualityThreshold - - }); - this.qualityControlResultsWidget.onQualityChanged.attach(function(sender, value) { - _this.qualityThreshold = value; - _this.thresholdsChanged(); - }); - - this.qualityControlResultsWidget.onRadiationDatamageChanged.attach(function(sender, value) { - _this.radiationDamageThreshold = value; - _this.thresholdsChanged(); - - }); - this.concentrationHTMLTableWidget = new ConcentrationHTMLTableWidget({ - height : 250, - showBufferColumns : this.clusterByBuffers - }); - - this.plot = new BoxWhiskerGraph({ - targetId : _this.id + '_boxPlot', - height : 350, - width : 450, - maxBoxWidth : 25 - }); - - this.rangePlot = new RangeWhiskerGraph({ - targetId : _this.id + '_rangePlot', - height : 350, - width : 450, - maxBoxWidth : 25 - }); -} - -ResultSummaryForm.prototype.thresholdsChanged = function() { - var parsedData = this.prepareData(this.rawData); - - var filtered = JSON.parse(JSON.stringify(parsedData)); - filtered.concentration.concentrations = []; - for ( var conc in parsedData.concentration.concentrations) { - if (parsedData.concentration.concentrations[conc].calculation.rgGnom.validNumber > 0) { - filtered.concentration.concentrations.push(parsedData.concentration.concentrations[conc]); - } - } - - this.plotWhisker(filtered); - this.plotRange(filtered); - - this.concentrationHTMLTableWidget.refresh(parsedData); -}; - -/** Given a frame object (object returned by analyzeFrames()) and depending of the threshold indicates if a datacollection has radiation damage **/ -ResultSummaryForm.prototype.hasRadiationDamage = function(frameObject) { - var bb = frameObject.bufferBeforeFramesMerged / frameObject.framesCount; - var ba = frameObject.bufferAfterFramesMerged / frameObject.framesCount; - var mol = frameObject.framesMerge / frameObject.framesCount; - return !((bb >= this.radiationDamageThreshold) && (ba >= this.radiationDamageThreshold) && (mol >= this.radiationDamageThreshold)); -}; - -/** Return (frameObject) an object with the information about the frames for a data collection**/ -ResultSummaryForm.prototype.analyzeFrames = function(dataCollectionRow) { - return { - bufferAfterFramesMerged : dataCollectionRow.bufferAfterFramesMerged, - bufferBeforeFramesMerged : dataCollectionRow.bufferBeforeFramesMerged, - framesCount : dataCollectionRow.framesCount, - framesMerge : dataCollectionRow.framesMerge - }; -}; - -ResultSummaryForm.prototype.detectDataCollectionWarnings = function(dataCollectionRow) { - var frameObject = this.analyzeFrames(dataCollectionRow); - var warnings = { - count : 0, - type : [] - }; - - if (this.hasRadiationDamage(frameObject)) { - warnings.count = warnings.count + 1; - warnings.type.push("RADIATION DAMAGE"); - } - - if (Number(dataCollectionRow.quality) < this.qualityThreshold) { - warnings.count = 1;//warnings.count + 1; - warnings.type.push("Quality <" + this.qualityThreshold); - } - return warnings; -}; - -/** Return array composed by {concentration} objects **/ -ResultSummaryForm.prototype.getConcentrations = function(data) { - var concentrationsId = {}; - - for ( var i = 0; i < data.length; i++) { - var warning = this.detectDataCollectionWarnings(data[i]); - var id = data[i].conc;// + "_" + data[i].bufferId; - if (this.clusterByBuffers) { - id = data[i].conc + "_" + data[i].bufferId; - } - - if (concentrationsId[id] == null) { - concentrationsId[id] = { - id : id, - concentration : Number(data[i].conc).toFixed(2), - bufferId : data[i].bufferId, - bufferAcronym : data[i].bufferAcronym, - rgGuinier : [], - i0Guinier : [], - rgGnom : [], - dMax : [], - quality : [], - frames : [], - frames_warning : warning.count - }; - } else { - concentrationsId[id].frames_warning = concentrationsId[id].frames_warning + warning.count; - } - - concentrationsId[id].frames.push(data[i]); - - if (warning.count == 0) { - concentrationsId[id].rgGuinier.push(data[i].rgGuinier); - concentrationsId[id].i0Guinier.push(data[i].I0); - concentrationsId[id].quality.push(data[i].quality); - concentrationsId[id].rgGnom.push(data[i].rgGnom); - concentrationsId[id].dMax.push(data[i].dmax); - } - - } - var concentrations = []; - for ( var item in concentrationsId) { - if (concentrationsId.hasOwnProperty(item)) { - concentrations.push({ - concentration : concentrationsId[item].concentration, - id : item, - bufferId : Number(concentrationsId[item].bufferId).toFixed(2), - bufferAcronym : concentrationsId[item].bufferAcronym, - rgGuinier : concentrationsId[item].rgGuinier, - /** Frames **/ - frames : concentrationsId[item].frames, - frames_warning : concentrationsId[item].frames_warning, - /** Calculation **/ - calculation : { - rgGuinier : BUI.getStandardDeviation(concentrationsId[item].rgGuinier), - i0Guinier : BUI.getStandardDeviation(concentrationsId[item].i0Guinier), - quality : BUI.getStandardDeviation(concentrationsId[item].quality), - rgGnom : BUI.getStandardDeviation(concentrationsId[item].rgGnom), - dMax : BUI.getStandardDeviation(concentrationsId[item].dMax) - - } - }); - } - } - - return { - concentrations : concentrations - }; -}; - -ResultSummaryForm.prototype.prepareData = function(data) { - /** Return array composed by {acronym, bufferId} objects **/ - function getBuffers(data) { - var buffersId = {}; - for ( var i = 0; i < data.length; i++) { - buffersId[data[i].bufferId] = data[i].acronym; - } - var buffers = []; - for ( var id in buffersId) { - if (buffersId.hasOwnProperty(id)) { - buffers.push({ - acronym : buffersId[id], - bufferId : id - }); - } - } - return buffers; - } - - /** Get a string with all the concentrations **/ - function getConcentrationString(parseConcentrations) { - var concentrations = []; - for ( var i = 0; i < parseConcentrations.concentrations.length; i++) { - concentrations.push(parseConcentrations.concentrations[i].concentration + " mg/ml "); - } - return concentrations.toString(); - } - - var parseConcentrations = this.getConcentrations(data); - - return { - dataCollectionCount : data.length, - buffers : getBuffers(data), - concentration : parseConcentrations, - concentrationLabel : getConcentrationString(parseConcentrations) - }; -}; - -ResultSummaryForm.prototype.getDataForWhisker = function(data) { - var clusters = []; - - var concentrations = {}; - var i = 0; - var conc = 0; - if (this.collapseConcentrations) { - for (i = 0; i < data.concentration.concentrations.length; i++) { - conc = data.concentration.concentrations[i]; - var concentration = Number(conc.concentration).toFixed(0); - if (concentrations[concentration] == null) { - concentrations[concentration] = {}; - concentrations[concentration].concentration = concentration; - concentrations[concentration].calculation = {}; - concentrations[concentration].calculation.rgGuinier = {}; - concentrations[concentration].calculation.rgGuinier.values = []; - concentrations[concentration].calculation.rgGuinier.values = conc.calculation.rgGuinier.values; - concentrations[concentration].calculation.rgGnom = {}; - concentrations[concentration].calculation.rgGnom.values = []; - concentrations[concentration].calculation.rgGnom.values = conc.calculation.rgGnom.values; - } else { - concentrations[concentration].calculation.rgGuinier.values = concentrations[concentration].calculation.rgGuinier.values - .concat(conc.calculation.rgGuinier.values); - concentrations[concentration].calculation.rgGnom.values = concentrations[concentration].calculation.rgGnom.values - .concat(conc.calculation.rgGnom.values); - } - } - - /** From object to array **/ - var array = []; - for ( var key in concentrations) { - if (concentrations.hasOwnProperty(key)) { - array.push(concentrations[key]); - } - } - data.concentration.concentrations = array; - } - - for (i = 0; i < data.concentration.concentrations.length; i++) { - conc = data.concentration.concentrations[i]; - clusters.push({ - name : conc.concentration + "mg/ml", - concentration : Number(conc.concentration), - x : Number(conc.concentration), - classes : [] - }); - clusters[clusters.length - 1].classes.push({ - name : "Guinier", - color : '#9A2EFE', - values : conc.calculation.rgGuinier.values - - }); - clusters[clusters.length - 1].classes.push({ - name : "P(r)", - color : '#2E64FE', - values : conc.calculation.rgGnom.values - - }); - } - return { - clusters : clusters.sort(function(a, b) { - return a.concentration - b.concentration; - }) - }; -}; - -ResultSummaryForm.prototype.getDataForWhiskerQuality = function(data) { - var clusters = []; - - for ( var i = 0; i < data.concentration.concentrations.length; i++) { - var conc = data.concentration.concentrations[i]; - clusters.push({ - name : conc.concentration + "mg/ml", - classes : [] - }); - clusters[clusters.length - 1].classes.push({ - name : "Quality", - values : conc.calculation.quality.values - - }); - } - - return { - clusters : clusters - }; -}; - -ResultSummaryForm.prototype.plotQualityWhisker = function(parsedData) { - this.qualityPlot.refresh(this.getDataForWhiskerQuality(parsedData)); -}; - -ResultSummaryForm.prototype.plotWhisker = function(parsedData) { - this.plot.refresh(this.getDataForWhisker(parsedData)); -}; - -ResultSummaryForm.prototype.plotRange = function(parsedData) { - this.rangePlot.refresh(this.getDataForWhisker(parsedData)); -}; - -ResultSummaryForm.prototype.getPanel = function(data) { - var _this = this; - _this.rawData = data; - var parsedData = this.prepareData(data); - - this.panel = Ext - .createWidget( - 'form', - { - bodyPadding : 20, - frame : false, - border : 0, - width : this.width, - height : this.summaryHeight + 1000, - items : [ { - xtype : 'container', - layout : 'hbox', - items : [ { - xtype : 'container', - flex : 1, - border : false, - layout : 'anchor', - defaultType : 'textfield', - items : [ - _this.qualityControlResultsWidget.getPanel(), - { - xtype : 'fieldset', - width : 950, - margin : "20, 0 0 0", - height : this.summaryHeight + 500, - items : [ - { - html : "
Concentration Analysis
", - border : 0, - width : 900 - - }, - { - html : this.concentrationHTMLTableWidget.getPanel(parsedData), - border : 0, - width : 900, - margin : "10, 0 0 10" - - }, - { - xtype : 'container', - layout : 'vbox', - border : 5, - items : [ - { - html : "
Rg based on Guinier and Gnom
", - border : 8, - width : 900, - margin : "20 0 0 10" - - }, { - xtype : 'container', - layout : 'hbox', - items : [ { - xtype : 'container', - layout : 'vbox', - items : [ { - html : "
", - border : 0, - width : this.plot.width, - padding : "10 0 0 20", - listeners : { - afterrender : function() { - _this.plotWhisker(parsedData); - - } - } - }, { - html : "
Concentration (mg/ml)
", - width : 450, - border : 0, - margin : "-50 0 0 0" - - } ] - }, { - xtype : 'container', - layout : 'vbox', - items : [ { - html : "
", - border : 0, - width : this.rangePlot.width, - padding : "10 0 0 10", - listeners : { - afterrender : function() { - _this.plotRange(parsedData); - } - } - }, { - html : "
Concentration (mg/ml)
", - width : 450, - border : 0, - margin : "-50 0 0 0" - - } ] - } ] - } ] - } ] - } ] - } - - ] - } ] - }); - return this.panel; - -}; - -ResultSummaryForm.prototype.input = function() { - return { - data : DATADOC.getData_3367() - }; -}; - -ResultSummaryForm.prototype.test = function(targetId) { - var resultSummaryForm = new ResultSummaryForm(); - var panel = resultSummaryForm.getPanel(resultSummaryForm.input().data); - panel.render(targetId); - -}; - -/** - * Example form - * - * @witdh - * @height - */ -function RigibBodyModelingForm(args) { - this.id = BUI.id(); - this.width = 700; - this.height = 500; - - if (args != null) { - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; - } - } - - var _this = this; - this.rigidBodyGrid = new AprioriRigidBodyGrid(); - - this.rigidBodyGrid.onUploadFile.attach(function(sender, type, title){ - _this._openUploadDialog(_this.macromolecule.macromoleculeId, type, title); - }); - - this.rigidBodyGrid.onRemove.attach(function(sender, type, title){ - _this._update(); - }); - - this.onSave = new Event(this); - -} - -RigibBodyModelingForm.prototype._getItems = function() { - var _this = this; - - - return [ { - xtype : 'label', - forId : 'myFieldId', - text : 'Information for model fit, mixture analysis and rigid body modeling', - margin : '15 0 20 10', - cls : "inline-help" - }, - this.rigidBodyGrid.getPanel(), - { - xtype : 'label', - forId : 'myFieldId', - text : 'Distance restraints may be imposed on the model using contacts conditions file (OPTIONAL)', - margin : '25 0 5 10', - cls : "inline-help" - }, - { - xtype : 'container', - layout : 'hbox', - items : [ { - xtype : 'container', - border : false, - layout : 'hbox', - items : [ { - xtype : 'label', - forId : 'myFieldId', - text : 'Contact Description File: (Optional)', - width : 150, - margin : '10 0 0 10' - }, { - id : this.id + "contactsDescriptionFilePath", - xtype : 'textfield', - hideLabel : true, - margin : '10 0 0 0', - width : 200, - disabled: true - }, { - text : 'Upload', - xtype : 'button', - margin : "10 0 0 10", - width : 80, - handler : function() { - - _this._openUploadDialog(_this.macromolecule.macromoleculeId, "CONTACTS", "Upload Contact Description File"); - } - }, { - text : 'Remove', - id : _this.id + "_remove", - xtype : 'button', - margin : "10 0 0 10", - width : 80, - handler : function() { - _this.macromolecule.contactsDescriptionFilePath = null; - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, proposal) { - /** Updating the proposal global object **/ - BIOSAXS.proposal.setItems(proposal); - _this.panel.setLoading(false); - - var saved = BIOSAXS.proposal.getMacromoleculeByAcronym(_this.macromolecule.acronym); - /** Refreshing to check that everything is ok **/ - _this.refresh(saved); - _this.onSave.notify(saved); - }); - - _this.panel.setLoading("Saving Macromolecule") - adapter.saveMacromolecule(_this.macromolecule); - } - } ] - } ] - }, { - xtype : 'panel', - html : "Go to SASREF manual for further information", - margin : "10 0 0 160", - border : 0 - - }, - { - xtype : 'checkbox', - margin : '10 0 0 5', - boxLabel : "I want rigid body modeling run on this stuff", - checked : true, - width : 300 - } ] - -}; - -/** Because update is a jsp page we don't know if the user has uploaded a file or not then we need to refresh **/ -RigibBodyModelingForm.prototype._update = function(macromoleculeId, type, title) { - var _this = this; - BIOSAXS.proposal.onInitialized.attach(function() { - if (BIOSAXS.proposal != null) { - _this.refresh(BIOSAXS.proposal.getMacromoleculeById(_this.macromolecule.macromoleculeId)); - _this.panel.setLoading(false); - } - }); - this.panel.setLoading(); - BIOSAXS.proposal.init(); -}; - -RigibBodyModelingForm.prototype._openUploadDialog = function(macromoleculeId, type, title) { - var _this = this; - function onClose() { - w.destroy(); - _this._update(); - - } - - var w = Ext.create('Ext.window.Window', { - title : title, - height : 200, - width : 400, - modal : true, - buttons : [ { - text : 'Close', - handler : function() { - onClose(); - } - } ], - layout : 'fit', - items : { - html : "" - }, - listeners : { - onEsc : function() { - onClose(); - }, - close : function() { - onClose(); - } - } - }).show(); -}; - -RigibBodyModelingForm.prototype._getButtons = function() { - return []; -}; - -RigibBodyModelingForm.prototype.getPanel = function() { - var _this = this; - this.panel = Ext.create('Ext.form.Panel', { - width : this.width, - height : this.height, - margin : 10, - border : 1, - defaultType : 'textfield', - items : this._getItems(), - buttons : this._getButtons(), - listeners : { - afterrender : function(){ - _this._populate(); - - } - } - }); - return this.panel; -}; - -/** Populates could be call when the DOM is not filled yet **/ -RigibBodyModelingForm.prototype._populate = function() { - if (this.macromolecule != null){ - if (Ext.getCmp(this.id + "contactsDescriptionFilePath") != null){ - if (this.macromolecule.contactsDescriptionFilePath != null){ - Ext.getCmp(this.id + "contactsDescriptionFilePath").setValue(this.macromolecule.contactsDescriptionFilePath); - Ext.getCmp(this.id + "_remove").enable(); - } - else{ - Ext.getCmp(this.id + "_remove").disable(); - Ext.getCmp(this.id + "contactsDescriptionFilePath").setValue(""); - - } - } - } -}; - -/** It populates the form * */ -RigibBodyModelingForm.prototype.refresh = function(macromolecule) { - this.macromolecule = macromolecule; - this.rigidBodyGrid.refresh(macromolecule); - this._populate(); -}; - -RigibBodyModelingForm.prototype.input = function() { - return {}; -}; - - -/** It populates the form **/ -RigibBodyModelingForm.prototype.test = function(targetId) { - var macromoleculeForm = new RigibBodyModelingForm(); - var panel = macromoleculeForm.getPanel(); - panel.render(targetId); -}; - - -/** - * Same form as MX part - * - * @creationMode if true a create button appears instead of save - * @showTitle true or false - */ -function ShipmentForm(args) { - this.id = BUI.id(); - - this.creationMode = false; - this.showTitle = true; - if (args != null) { - if (args.creationMode != null) { - this.creationMode = args.creationMode; - } - if (args.showTitle != null) { - this.showTitle = args.showTitle; - } - } - - this.onSaved = new Event(this); -} - -ShipmentForm.prototype.fillStores = function() { - this.panel.setLoading("Loading Labcontacts from database"); - this.labContactForSendingStore.loadData(BIOSAXS.proposal.getLabcontacts(), false); - this.labContactForReturnStore.loadData(BIOSAXS.proposal.getLabcontacts(), false); - this.panel.setLoading(false); - if (this.shipment != null) { - this.setShipment(this.shipment); - } -}; - -ShipmentForm.prototype.draw = function(targetId) { - this.getPanel().render(targetId); -}; - -ShipmentForm.prototype.setShipment = function(shipment) { - this.shipment = shipment; - var _this = this; - Ext.getCmp(_this.id + "shippingName").setValue(shipment.json.shippingName); - Ext.getCmp(_this.id + "shippingStatus").setValue(shipment.json.shippingStatus); - Ext.getCmp(_this.id + "comments").setValue(shipment.json.comments); - if (shipment.json.sendingLabContactVO != null) { - this.labContactsSendingCombo.setValue(shipment.json.sendingLabContactVO.labContactId); - } - if (shipment.json.returnLabContactVO != null) { - this.labContactsReturnCombo.setValue(shipment.json.returnLabContactVO.labContactId); - } - -}; - -ShipmentForm.prototype._saveShipment = function() { - var _this = this; - var shippingId = null; - if (this.shipment != null) { - shippingId = this.shipment.json.shippingId; - } - var json = { - shippingId : shippingId, - name : Ext.getCmp(_this.id + "shippingName").getValue(), - status : Ext.getCmp(_this.id + "shippingStatus").getValue(), - sendingLabContactId : Ext.getCmp(_this.id + "shipmentform_sendingLabContactId").getValue(), - returnLabContactId : Ext.getCmp(_this.id + "returnLabContactId").getValue(), - returnCourier : Ext.getCmp(_this.id + "returnCourier").getValue(), - courierAccount : Ext.getCmp(_this.id + "courierAccount").getValue(), - BillingReference : Ext.getCmp(_this.id + "BillingReference").getValue(), - dewarAvgCustomsValue : Ext.getCmp(_this.id + "dewarAvgCustomsValue").getValue(), - dewarAvgTransportValue : Ext.getCmp(_this.id + "dewarAvgTransportValue").getValue(), - comments : Ext.getCmp(_this.id + "comments").getValue() - }; - - var dataAdapter = new BiosaxsDataAdapter(); - dataAdapter.onSuccess.attach(function(sender, shipment) { - window.location = BUI.getShippingURL(shipment.shippingId); - }); - - dataAdapter.onError.attach(function(sender, error) { - _this.onError.notify(error); - }); - - /** Cheking params **/ - if (json.name == "") { - BUI.showError("Name field is mandatory"); - return; - } - - if (json.sendingLabContactId == null) { - BUI.showError("Lab contact for sending field is mandatory"); - return; - } - - if (json.returnLabContactId == null) { - BUI.showError("Lab contact for return field is mandatory"); - return; - } - - dataAdapter.createShipment(json.shippingId, json.name, json.status, json.comments, json.sendingLabContactId, json.returnLabContactId, - json.returnCourier, json.courierAccount, json.BillingReference, json.dewarAvgCustomsValue, json.dewarAvgTransportValue); - -}; - -ShipmentForm.prototype.getPanel = function(shipment) { - var _this = this; - this.shipment = shipment; - var required = '*'; - var buttons = []; - - if (_this.creationMode) { - buttons.push({ - text : 'Create', - scope : this, - handler : function() { - _this._saveShipment(); - } - }); - } else { - buttons.push({ - text : 'Save', - scope : this, - handler : function() { - _this._saveShipment(); - } - }); - - } - - this.labContactForSendingStore = Ext.create('Ext.data.Store', { - fields : [ 'cardName', 'labContactId' ] - }); - - this.labContactForReturnStore = Ext.create('Ext.data.Store', { - fields : [ 'cardName', 'labContactId' ] - }); - - // Create the combo box, attached to the states data store - this.labContactsSendingCombo = Ext.create('Ext.form.ComboBox', { - id : _this.id + "shipmentform_sendingLabContactId", - fieldLabel : 'Lab contact for sending', - afterLabelTextTpl : required, - store : this.labContactForSendingStore, - queryMode : 'local', - labelWidth : 200, - displayField : 'cardName', - valueField : 'labContactId' - }); - - this.labContactsReturnCombo = Ext.create('Ext.form.ComboBox', { - id : _this.id + "returnLabContactId", - fieldLabel : 'If No, Lab-Contact for Return', - afterLabelTextTpl : required, - store : this.labContactForReturnStore, - queryMode : 'local', - labelWidth : 200, - displayField : 'cardName', - valueField : 'labContactId', - listeners : { - change : function(x, newValue) { - for ( var i = 0; i < x.getStore().data.items.length; i++) { - if (x.getStore().data.items[i].raw.labContactId == newValue) { - Ext.getCmp(_this.id + "returnCourier").setValue(x.getStore().data.items[i].raw.defaultCourrierCompany); - Ext.getCmp(_this.id + "courierAccount").setValue(x.getStore().data.items[i].raw.courierAccount); - Ext.getCmp(_this.id + "BillingReference").setValue(x.getStore().data.items[i].raw.billingReference); - Ext.getCmp(_this.id + "dewarAvgCustomsValue").setValue(x.getStore().data.items[i].raw.dewarAvgCustomsValue); - Ext.getCmp(_this.id + "dewarAvgTransportValue").setValue(x.getStore().data.items[i].raw.dewarAvgTransportValue); - } - } - } - } - }); - - if (this.panel == null) { - this.panel = Ext.create('Ext.form.Panel', { - bodyPadding : 5, - width : 600, - border : 1, - items : [ { - xtype : 'fieldset', - title : 'Details', - collapsible : false, - defaultType : 'textfield', - layout : 'anchor', - defaults : { - anchor : '100%' - }, - items : [ { - xtype : 'requiredtext', - fieldLabel : 'Shipment Label', - allowBlank : false, - name : 'shippingName', - id : _this.id + 'shippingName', - value : '', - anchor : '50%' - }, { - - xtype : 'textareafield', - name : 'comments', - id : _this.id + 'comments', - fieldLabel : 'Comments', - value : '' - }, { - fieldLabel : 'Status', - readOnly : true, - id : _this.id + 'shippingStatus', - value : 'Opened', - anchor : '50%' - } ] - }, { - xtype : 'fieldset', - title : 'Lab-Contacts', - collapsible : false, - defaultType : 'textfield', - layout : 'anchor', - defaults : { - anchor : '100%' - }, - items : [ this.labContactsSendingCombo, this.labContactsReturnCombo ] - }, { - border : 0, - html : BUI.getWarningHTML("These informations are relevant for all shipments") - }, { - xtype : 'fieldset', - title : 'Courier accounts details for return', - collapsible : false, - layout : 'anchor', - defaults : { - anchor : '100%' - }, - items : [ { - xtype : 'textfield', - labelWidth : 400, - fieldLabel : 'Courier company for return (if ESRF sends a dewar back)', - id : _this.id + 'returnCourier', - value : '' - }, { - xtype : 'textfield', - labelWidth : 400, - fieldLabel : 'Courier account', - id : _this.id + 'courierAccount', - value : '' - }, { - xtype : 'textfield', - labelWidth : 400, - fieldLabel : 'Billing reference', - id : _this.id + 'BillingReference', - value : '' - }, { - xtype : 'numberfield', - labelWidth : 400, - fieldLabel : 'Average Customs value of a dewar (Euro)', - id : _this.id + 'dewarAvgCustomsValue', - value : '' - }, { - xtype : 'numberfield', - labelWidth : 400, - fieldLabel : 'Average Transport value of a dewar (Euro)', - id : _this.id + 'dewarAvgTransportValue', - value : '' - } ] - } ], - buttons : buttons - }); - } - this.fillStores(); - if (this.showTitle) { - this.panel.setTitle('Create a new Shipment'); - } - return this.panel; -}; - -ShipmentForm.prototype.input = function() { - return { - proposal : DATADOC.getProposal_10() - - }; -}; - -ShipmentForm.prototype.test = function(targetId) { - var shipmentForm = new ShipmentForm({ - creationMode : true - - }); - BIOSAXS.proposal = new Proposal(shipmentForm.input().proposal); - shipmentForm.getPanel().render(targetId); -}; - -/** - * #onSaved - */ -function StockSolutionForm(args) { - this.id = BUI.id(); - this.actions = []; - - if (args != null) { - if (args.actions != null) { - this.actions = args.actions; - } - } - this.onSaved = new Event(this); -} - -StockSolutionForm.prototype.getStockSolution = function() { - if (this.stockSolution != null) { - this.stockSolution.concentration = Ext.getCmp(this.id + "stockSolution_concentration").getValue(); - this.stockSolution.storageTemperature = Ext.getCmp(this.id + "stockSolution_storageTemperature").getValue(); - this.stockSolution.volume = Ext.getCmp(this.id + "stockSolution_volume").getValue(); - this.stockSolution.comments = Ext.getCmp(this.id + "stockSolution_comments").getValue(); - this.stockSolution.name = Ext.getCmp(this.id + "stockSolution_name").getValue(); - this.stockSolution.bufferId = this.bufferCombo.getValue(); - - if (this.macromoleculeCombo.getValue() != null) { - this.stockSolution.macromoleculeId = this.macromoleculeCombo.getValue(); - } else { - this.stockSolution.macromolecule3VO = null; - } - - } else { - return { - concentration : Ext.getCmp(this.id + "stockSolution_concentration").getValue(), - storageTemperature : Ext.getCmp(this.id + "stockSolution_storageTemperature").getValue(), - volume : Ext.getCmp(this.id + "stockSolution_volume").getValue(), - comments : Ext.getCmp(this.id + "stockSolution_comments").getValue(), - name : Ext.getCmp(this.id + "stockSolution_name").getValue(), - bufferId : this.bufferCombo.getValue(), - macromoleculeId : this.macromoleculeCombo.getValue() - }; - } - return this.stockSolution; -}; - -StockSolutionForm.prototype.setStockSolution = function(stockSolution) { - if (stockSolution != null) { - if (stockSolution.macromoleculeId != null) { - this.macromoleculeCombo.setValue(stockSolution.macromoleculeId); - } - this.bufferCombo.setValue(stockSolution.bufferId); - Ext.getCmp(this.id + "stockSolution_concentration").setValue(this.stockSolution.concentration); - Ext.getCmp(this.id + "stockSolution_storageTemperature").setValue(this.stockSolution.storageTemperature); - Ext.getCmp(this.id + "stockSolution_volume").setValue(this.stockSolution.volume); - Ext.getCmp(this.id + "stockSolution_name").setValue(this.stockSolution.name); - Ext.getCmp(this.id + "stockSolution_comments").setValue(this.stockSolution.comments); - } -}; - -StockSolutionForm.prototype.getBufferCombo = function() { - this.bufferCombo = BIOSAXS_COMBOMANAGER.getComboBuffers(BIOSAXS.proposal.getBuffers(), { - labelWidth : 120, - margin : '0 0 10 0', - width : 220 - - }); - return this.bufferCombo; -}; - -StockSolutionForm.prototype.getMacromoleculeCombo = function() { - this.macromoleculeCombo = BIOSAXS_COMBOMANAGER.getComboMacromoleculeByMacromolecules(BIOSAXS.proposal.getMacromolecules(), { - labelWidth : 120, - margin : '0 0 10 0', - width : 220 - - }); - return this.macromoleculeCombo; -}; - -StockSolutionForm.prototype.refresh = function() { -}; - -StockSolutionForm.prototype._getTopPanel = function() { - return { - xtype : 'container', - layout : 'hbox', - border : 0, - items : [ { - xtype : 'container', - layout : 'hbox', - items : [ { - xtype : 'container', - flex : 1, - border : false, - layout : 'anchor', - defaultType : 'textfield', - items : [ - - this.getMacromoleculeCombo(), { - xtype : 'requiredtext', - id : this.id + 'stockSolution_name', - fieldLabel : 'Acronym', - labelWidth : 120, - width : 250 - }, { - xtype : 'requiredtext', - id : this.id + 'stockSolution_concentration', - fieldLabel : 'Conc. (mg/ml)', - labelWidth : 120, - width : 250 - }, - - { - id : this.id + 'stockSolution_storageTemperature', - fieldLabel : 'Storage Temp.(C)', - labelWidth : 120, - width : 250 - }, { - xtype : 'requiredtext', - id : this.id + 'stockSolution_volume', - fieldLabel : 'Volume in Well (µl)', - labelWidth : 120, - width : 250 - } ] - } ] - }, { - xtype : 'container', - flex : 1, - layout : 'anchor', - defaultType : 'textfield', - margin : '0 0 0 10', - items : [ this.getBufferCombo() ] - } ] - }; - -}; - -StockSolutionForm.prototype.getPanel = function(stockSolution) { - this.stockSolution = stockSolution; - this.panel = Ext.createWidget({ - xtype : 'container', - layout : 'vbox', - border : 0, - style : { - padding : '10px' - }, - fieldDefaults : { - labelAlign : 'left', - labelWidth : 50 - }, - items : [ this._getTopPanel(stockSolution), { - id : this.id + 'stockSolution_comments', - xtype : 'textareafield', - name : 'comments', - fieldLabel : 'Comments', - labelWidth : 120, - width : '100%' - } ] - }); - - this.setStockSolution(stockSolution); - return this.panel; -}; - -StockSolutionForm.prototype.input = function() { - return { - stock : { - "stockSolutionId" : 6, - "proposalId" : 3124, - "macromoleculeId" : 5933, - "bufferId" : 811, - "instructionSet3VO" : null, - "boxId" : 305861, - "storageTemperature" : "20", - "volume" : "300", - "concentration" : "1.2", - "comments" : "Buffer EDTA with A", - "name" : "A_EDTA_1.2", - "samples" : [], - "buffer" : "EDTA", - "macromolecule" : "A" - }, - proposal : new MeasurementGrid().input().proposal - }; -}; - -StockSolutionForm.prototype.test = function(targetId) { - var stockSolutionForm = new StockSolutionForm(); - BIOSAXS.proposal = new Proposal(stockSolutionForm.input().proposal); - var panel = stockSolutionForm.getPanel(new Shipment(stockSolutionForm.input().stock)); - panel.render(targetId); -}; - - -BoxWhiskerGraph.prototype.cleanArray = GenericGraph.prototype.cleanArray; -BoxWhiskerGraph.prototype.plotAxes = GenericGraph.prototype.plotAxes; -BoxWhiskerGraph.prototype.plotRuler = GenericGraph.prototype.plotRuler; -BoxWhiskerGraph.prototype.drawSVGVerticalText = GenericGraph.prototype.drawSVGVerticalText; -BoxWhiskerGraph.prototype.getClassColor = GenericGraph.prototype.getClassColor; -BoxWhiskerGraph.prototype.getDimensions = GenericGraph.prototype.getDimensions; -BoxWhiskerGraph.prototype.calculate = GenericGraph.prototype.calculate; -BoxWhiskerGraph.prototype.getMedian = GenericGraph.prototype.getMedian; -BoxWhiskerGraph.prototype.pointToPixel = GenericGraph.prototype.pointToPixel; -BoxWhiskerGraph.prototype.maxValueWhisker = GenericGraph.prototype.maxValueWhisker; -BoxWhiskerGraph.prototype.refresh = GenericGraph.prototype.refresh; - -/** - * Subclass of GenericGraph - * - * @maxBoxWidth - */ -function BoxWhiskerGraph(args){ - this.maxBoxWidth = 25; - - if (args == null){ - args = new Object(); - } - args["plotHorizontalByCluster"] = true; - - GenericGraph.call(this, args); - - if (args.maxBoxWidth != null){ - this.maxBoxWidth = args.maxBoxWidth; - } -}; - - - -/** -There are several different methods for calculating quartiles.[1] This calculator uses a method described by Moore and McCabe to find quartile values. -The same method also used by The TI-83 to calculate quartile values. -With this method, the first quartile is the median of the numbers below the median, the third quartile is the median of the numbers above the median. - -http://www.miniwebtool.com/quartile-calculator/ -http://www.alcula.com/calculators/statistics/box-plot/ -**/ -BoxWhiskerGraph.prototype.getQ1 = function(array){ - array = array.slice(0, array.length/2); - return this.getMedian(array); -}; - -BoxWhiskerGraph.prototype.getQ3 = function(array){ - array = array.slice((array.length + 1)/2); - return this.getMedian(array); - -}; - -BoxWhiskerGraph.prototype.getQ2 = function(array){ - return this.getMedian(array); -}; - -BoxWhiskerGraph.prototype.getBelowOutliers = function(belowLimit, array){ - var points = new Array(); - for (var i = 0; i < array.length; i++){ - if (array[i] <= belowLimit){ - points.push(array[i]); - } - } - return points; -}; - -BoxWhiskerGraph.prototype.getAboveOutliers = function(aboveLimit, array){ - var points = new Array(); - for (var i = 0; i < array.length; i++){ - if (array[i] >= aboveLimit){ - points.push(array[i]); - } - } - return points; -}; - - -BoxWhiskerGraph.prototype.minValueWhisker = function(belowLimit, q1, array){ - var points = new Array(); - - for (var i = 0; i < array.length; i++){ - if ((array[i] < q1) && (array[i]) > belowLimit){ - points.push(array[i]); - } - } - - if (points.length > 0){ - points.sort(function(a, b){return a - b;}); - return points[0]; - } - return null; -}; - -BoxWhiskerGraph.prototype.isNumber = function(value){ - if (value=="") return false; - - var d = parseInt(value); - if (!isNaN(d)) return true; else return false; - -}; - -BoxWhiskerGraph.prototype.plotBoxWhisker = function(boxProperties){ - if (this.maxBoxWidth != null){ - if (boxProperties.width > this.maxBoxWidth){ - boxProperties.x = boxProperties.x + (boxProperties.width/2) - (this.maxBoxWidth/2); - boxProperties.width = this.maxBoxWidth; - } - - } - - if (this.plotPoints){ - for(var i = 0; i < boxProperties.values.length; i++){ - var value = boxProperties.values[i]; - var toPixel = this.pointToPixel(value, boxProperties); - SVG.drawCircle(boxProperties.x + (boxProperties.width/2) + 2, toPixel, this.pointRadius, this.svg, [["fill", "green"], ["fill-opacity", this.fillOpacityPoint],['stroke-opacity', this.strokeOpacityPoint], ["stroke", "black"]]); - } - } - - - var boxColor = this.getClassColor(boxProperties.name); - var result = this.calculate(boxProperties.values); - /** Q1 **/ - - if (this.isNumber(result.Q1)){ - SVG.drawLine(boxProperties.x, this.pointToPixel(result.Q1, boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result.Q1, boxProperties), this.svg, [["stroke", boxColor]]); - } - /** Q2 **/ - if (this.isNumber(result.Q2)){ - SVG.drawLine(boxProperties.x, this.pointToPixel(result.Q2, boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result.Q2, boxProperties), this.svg, [["stroke", "blue"], ["stroke-width", "2"]]); - } - - /** Q3 **/ - if (this.isNumber(result.Q3)){ - SVG.drawLine(boxProperties.x, this.pointToPixel(result.Q3, boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result.Q3, boxProperties), this.svg, [["stroke", boxColor]]); - } - - /** Concenting Q1 and Q3 **/ - if (this.isNumber(result.Q1)&&this.isNumber(result.Q3)){ - SVG.drawLine(boxProperties.x, this.pointToPixel(result.Q1, boxProperties), boxProperties.x, this.pointToPixel(result.Q3, boxProperties), this.svg, [["stroke", boxColor]]); - SVG.drawLine(boxProperties.x + boxProperties.width, this.pointToPixel(result.Q1, boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result.Q3, boxProperties), this.svg, [["stroke", boxColor]]); - } - - /** min-whisker **/ - if (result["min-whisker"] != null){ - if (this.isNumber(result.Q1)){ - SVG.drawLine(boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result.Q1, boxProperties), boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result["min-whisker"], boxProperties), this.svg, [["stroke", boxColor]]); - } - SVG.drawLine(boxProperties.x,this.pointToPixel(result["min-whisker"], boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result["min-whisker"], boxProperties) , this.svg, [["stroke", boxColor]]); - - } - - /** max-whisker **/ - if (result["max-whisker"] != null){ - if (this.isNumber(result.Q3)){ - SVG.drawLine(boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result.Q3, boxProperties), boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result["max-whisker"], boxProperties), this.svg, [["stroke", boxColor]]); - } - SVG.drawLine(boxProperties.x , this.pointToPixel(result["max-whisker"], boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result["max-whisker"], boxProperties), this.svg, [["stroke", boxColor]]); - - } - - /** outliners **/ - if (result["above-outliers"] != null){ - for (var point in result["above-outliers"]){ - SVG.drawCircle(boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result["above-outliers"][point], boxProperties), this.pointRadius, this.svg, [["fill", "red"], ["fill-opacity", "1"]]); - //SVG.drawText(boxProperties.x + (boxProperties.width/2) - 2, this.pointToPixel(result["above-outliers"][point], boxProperties) + 2, "x",this.svg, [["fill", "black"], ["font-size", "x-small"]]); - } - } - if (result["below-outliers"] != null){ - for (var point in result["below-outliers"]){ - SVG.drawCircle(boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result["below-outliers"][point], boxProperties), this.pointRadius, this.svg, [["fill", "red"], ["fill-opacity", "1"]]); - //SVG.drawText(boxProperties.x + (boxProperties.width/2) - 2, this.pointToPixel(result["below-outliers"][point], boxProperties) + 2, "x",this.svg, [["fill", "black"], ["font-size", "x-small"]]); - } - } -}; - - - -BoxWhiskerGraph.prototype.plotClusterTitles = function(properties){ - /** Cluster Titles **/ - var posX = this.left + this.rulerWidth; - var data = this.data; - for(var i = 0; i < data.clusters.length; i++ ){ - /** title for the clusters **/ - posX = posX + this.interClustersSpace; - - /** Drawing title of classes **/ - var cluster = data.clusters[i]; - var posXClasses = posX; - for(var j = 0; j < cluster.classes.length; j++){ - //SVG.drawRectangle(posXClasses, this.height - (this.bottom + this.clusterTitleHeight + this.rulerHeight), properties.classWidth, this.rulerHeight, this.svg, [["fill", "green"]]); -// SVG.drawText(posXClasses + 1/6*properties.classWidth, this.height - (this.bottom + this.clusterTitleHeight + (this.rulerHeight*1/4)), cluster.classes[j].name, this.svg, [["style", "font-size:xx-small"]]); - var color = cluster.classes[j].color; - this.drawSVGVerticalText(posXClasses + 1/2*(properties.classWidth), this.height - (this.bottom - this.clusterTitleHeight + (this.rulerHeight)), cluster.classes[j].name , [["style", "font-size:x-small;"], ["fill", color]]); - - // SVG.drawRectangle(posXClasses, this.height - (this.bottom + this.clusterTitleHeight), properties.classWidth, 2, this.svg, [["fill", "black"]]); - posXClasses = posXClasses + properties.classWidth + this.interClassesSpace; - } - - var clusterTitleSpace = (data.clusters[i].classes.length * properties.classWidth) + ((data.clusters[i].classes.length - 1) * this.interClassesSpace); - //SVG.drawRectangle(posX, this.height - (this.bottom + this.clusterTitleHeight), clusterTitleSpace, this.clusterTitleHeight, this.svg, [["fill", "pink"]]); - SVG.drawRectangle(posX, this.height - (this.clusterTitleHeight+this.bottom), clusterTitleSpace, 1, this.svg, []); - -// var transform = ["translate", "(" + posX + 1/3*clusterTitleSpace +", " + this.height - (this.bottom + (this.clusterTitleHeight*1/4)) +")"], ["transform", "rotate(180)"]; -// var transform = ["transform", "translate(" + (posX + 1/3*clusterTitleSpace) +", " + (this.height - (this.bottom + (this.clusterTitleHeight*1/4))) + "), rotate(-90) "]; -// this.drawSVGVerticalText(posX + 1/3*clusterTitleSpace, this.height - (this.bottom + (this.clusterTitleHeight*1/4)),data.clusters[i].name, [["style", "font-size:x-small"]]); - SVG.drawText(posX , this.height - (this.bottom + (this.clusterTitleHeight*1/4)),data.clusters[i].name ,this.svg, [["style", "font-size:x-small"]]); - posX = posX + clusterTitleSpace; - } -}; - -BoxWhiskerGraph.prototype.plotWhisters = function(data, properties){ - var colors = ["yellow", "orange", "green"]; - var posX = this.left + this.rulerWidth; - for(var i = 0; i < data.clusters.length; i++ ){ - var cluster = data.clusters[i]; - /** inter cluster space **/ - //SVG.drawRectangle(posX, this.top, this.interClustersSpace, this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight, this.svg, [["fill", "black"]]); - posX = posX + this.interClustersSpace; - - for (var j = 0; j < cluster.classes.length; j ++){ - - //SVG.drawRectangle(posX, this.top, properties.classWidth, this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight, this.svg, [["fill", colors[j]]]); - this.plotBoxWhisker( - { - name : cluster.classes[j].name, - values : cluster.classes[j].values, - minPoint : properties.minPoint, - maxPoint : properties.maxPoint, - x : posX, - y : this.top, - width : properties.classWidth, - height : this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight - - - } - ); - posX = posX + properties.classWidth; - //SVG.drawRectangle(posX, this.top, this.interClassesSpace, this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight, this.svg, [["fill", "black"]]); - if (j < cluster.classes.length - 1){ - posX = posX + this.interClassesSpace; - } - } - } -}; - -BoxWhiskerGraph.prototype.draw = function(targetId, data){ - this.targetId = targetId; - var properties = (this.getDimensions(data)); - this.svg = SVG.createSVGCanvas(document.getElementById(this.targetId), [["width", this.width], ["height", this.height]]); - this.plotAxes(properties); - this.plotClusterTitles(properties); - this.plotWhisters(data,properties); -}; - -BoxWhiskerGraph.prototype.input = function(){ - return DATADOC.getBoxWhikerData(); -}; - -BoxWhiskerGraph.prototype.test = function(targetId){ - var plot = new BoxWhiskerGraph( - { - targetId : targetId, - height : 350, - width : 450, - maxBoxWidth : 25 - } - ); - plot.refresh(this.input()); -}; - - - - - - - -function DataSet(){ - this.json = null; - -}; - - -DataSet.prototype.loadFromJSON = function(json){ - if(json != null) { - if(this.validate(json)) { - this.json = json; - } - } -}; - - -DataSet.prototype.toJSON = function(json){ - return this.json; -}; - - -/** Abstract method to be override on childs classes **/ -DataSet.prototype.validate = function(json){ - if (true){ - return true; - } - /*else{ - throw "Data validation failed"; - }*/ -}; - - - - -Edge.prototype.getName = GraphItem.prototype.getName; -Edge.prototype.setName = GraphItem.prototype.setName; -Edge.prototype.getId = GraphItem.prototype.getId; - -function Edge(id, name, nodeSource, nodeTarget, args){ - GraphItem.prototype.constructor.call(this, id, name, args); - - this.sourceNode = nodeSource; - this.targetNode = nodeTarget; - -}; - -Edge.prototype.toJSON = function(){ - return {"index": this.id,"sourceIndex":this.sourceNode.getId(),"targetIndex":this.targetNode.getId(),"args":this.args}; -}; - -Edge.prototype.getNodeSource = function(){ - return this.sourceNode; -}; - -Edge.prototype.getNodeTarget = function(){ - return this.targetNode; -}; - -Edge.prototype.remove = function(){ - //Remove edge object in the nodes - this.getNodeSource().removeEdge(this); - this.getNodeTarget().removeEdge(this); - - this.deleted.notify(this); -}; - - -EdgeGraphFormatter.prototype.setProperties = ItemGraphFormatter.prototype.setProperties; -EdgeGraphFormatter.prototype.getDefault = ItemGraphFormatter.prototype.getDefault; -EdgeGraphFormatter.prototype.getSelected = ItemGraphFormatter.prototype.getSelected; -EdgeGraphFormatter.prototype.getOver = ItemGraphFormatter.prototype.getOver; -EdgeGraphFormatter.prototype.getDragging = ItemGraphFormatter.prototype.getDragging; -EdgeGraphFormatter.prototype.getId = ItemGraphFormatter.prototype.getId; -EdgeGraphFormatter.prototype.toJSON = ItemGraphFormatter.prototype.toJSON; -EdgeGraphFormatter.prototype.loadFromJSON = ItemGraphFormatter.prototype.loadFromJSON; -EdgeGraphFormatter.prototype._setEvents = ItemGraphFormatter.prototype._setEvents; - -function EdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ - ItemGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); - - this.getDefault().args.type = "EdgeGraphFormatter"; -}; - - - - -LineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; -LineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; -LineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; -LineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; -LineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; -LineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; -LineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; -LineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; -LineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; - -function LineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ - EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); - this.args.type = "LineEdgeGraphFormatter"; -}; - -/** DIRECTED **/ -DirectedLineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; -DirectedLineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; -DirectedLineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; -DirectedLineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; -DirectedLineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; -DirectedLineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; -DirectedLineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; -DirectedLineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; -DirectedLineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; - -function DirectedLineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ - EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); - this.args.type = "DirectedLineEdgeGraphFormatter"; - this.args.arrowSize = "3"; -}; -DirectedLineEdgeGraphFormatter.prototype.getArrowSize = function(){ - return this.args.arrowSize; -}; - -OdirectedLineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; -OdirectedLineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; -OdirectedLineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; -OdirectedLineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; -OdirectedLineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; -OdirectedLineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; -OdirectedLineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; -OdirectedLineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; -OdirectedLineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; - -function OdirectedLineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ - EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); - this.args.type = "DirectedLineEdgeGraphFormatter"; - this.args.arrowSize = "3"; -}; - -OdirectedLineEdgeGraphFormatter.prototype.getArrowSize = function(){ - return this.args.arrowSize; -}; - - -/** CUT (inhibition) **/ -CutDirectedLineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; -CutDirectedLineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; -CutDirectedLineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; -CutDirectedLineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; -CutDirectedLineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; -CutDirectedLineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; -CutDirectedLineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; -CutDirectedLineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; -CutDirectedLineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; - -function CutDirectedLineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ - EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); - this.args.type = "CutDirectedLineEdgeGraphFormatter"; -}; - - - - -BezierEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; -BezierEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; -BezierEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; -BezierEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; -BezierEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; -BezierEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; -BezierEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; -BezierEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; -BezierEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; -BezierEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; - -function BezierEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ - EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); - this.args.type = "BezierEdgeGraphFormatter"; -}; - - - -DotDirectedLineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; -DotDirectedLineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; -DotDirectedLineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; -DotDirectedLineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; -DotDirectedLineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; -DotDirectedLineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; -DotDirectedLineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; -DotDirectedLineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; -DotDirectedLineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; - -function DotDirectedLineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ - EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); - this.args.type = "DotDirectedLineEdgeGraphFormatter"; -}; - - -OdotDirectedLineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; -OdotDirectedLineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; -OdotDirectedLineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; -OdotDirectedLineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; -OdotDirectedLineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; -OdotDirectedLineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; -OdotDirectedLineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; -OdotDirectedLineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; -OdotDirectedLineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; - -function OdotDirectedLineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ - EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); - this.args.type = "OdotDirectedLineEdgeGraphFormatter"; -}; - - - -function GraphDataset(){ - DataSet.prototype.constructor.call(this); - this.edges = new Object(); - this.vertices = new Object(); - this.verticesIndex = new Object(); - - //Events - this.newVertex = new Event(this); - this.vertexNameChanged = new Event(this); - this.vertexDeleted = new Event(this); - - this.newEdge = new Event(this); - this.edgeNameChanged = new Event(this); - this.edgeDeleted = new Event(this); - - this.json = new Object(); - this.json.vertices = new Array(); - this.json.edges = new Array(); - this.json.relations = new Array(); -}; - -GraphDataset.prototype.loadFromJSON = DataSet.prototype.loadFromJSON; -GraphDataset.prototype.toJSON = DataSet.prototype.toJSON; -GraphDataset.prototype.validate = DataSet.prototype.validate; - -/** Devuelve el numero de edges incidentes sobre el nodo con mas edges **/ -GraphDataset.prototype.getMaxClass = function(){ - var maxClassNode = 0; - for ( var node in this.vertices) { - if (this.vertices[node].getEdgesCount() > maxClassNode){ - maxClassNode = this.vertices[node].getEdgesCount(); - } - } - return maxClassNode; -}; - -/** Devuelve el numero de edges incidentes sobre el nodo con mas edges **/ -GraphDataset.prototype.getMinClass = function(){ - var minClassNode = Math.min(); - for ( var node in this.vertices) { - if (this.vertices[node].getEdgesCount() < minClassNode){ - minClassNode = this.vertices[node].getEdgesCount(); - } - } - return minClassNode; -}; - -GraphDataset.prototype.getVertexByName = function(nodeName){ - var results = new Array(); - - for (var vertexId in this.verticesIndex[nodeName]){ - var vertexByid = this.getVertexById(this.verticesIndex[nodeName][vertexId]); - results.push(vertexByid); - //* añadido nuevo porque fallaba el anterior codigo - return vertexByid - } - - if (results <= 1){ - return this.getVertexById(this.verticesIndex[nodeName]); - } - else{ - return results; - } -}; - -GraphDataset.prototype.getVertexById = function(id){ - return this.vertices[id]; -}; - -GraphDataset.prototype.toSIF = function(){ - var sifDataAdapter = new SifFileDataAdapter(); - return sifDataAdapter.toSIF(this); -}; - -GraphDataset.prototype.toSIFID = function(){ - var sifDataAdapter = new SifFileDataAdapter(); - return sifDataAdapter.toSIFID(this); -}; - -GraphDataset.prototype.toDOT = function(){ - var dotFileDataAdapter = new DotFileDataAdapter(); - return dotFileDataAdapter.toDOT(this); -}; - -GraphDataset.prototype.toDOTID = function(){ - var dotFileDataAdapter = new DotFileDataAdapter(); - return dotFileDataAdapter.toDOTID(this); -}; - -GraphDataset.prototype._addNode = function(nodeName, args){ - return new Vertex(this._getVerticesCount()-1, nodeName, args); -}; - -GraphDataset.prototype.addNode = function(nodeName, args){ - this.json.vertices.push(nodeName); - this._addVerticesIndex(nodeName, this._getVerticesCount() - 1); - var vertex = this._addNode(nodeName, args); - this.vertices[this._getVerticesCount()-1] = vertex; - this._setNodeEvents(vertex); - this.newVertex.notify(vertex); -}; - -GraphDataset.prototype._addVerticesIndex = function(nodeName, id){ - if (this.verticesIndex[nodeName] == null){ - this.verticesIndex[nodeName] = new Array(); - } - this.verticesIndex[nodeName].push(id); -}; - -GraphDataset.prototype.addEdge = function(edgeName, nodeSourceId, nodeTargetId, args){ - this.json.edges.push(edgeName); - var nodeSource = this.getVertexById(nodeSourceId); - var nodeTarget = this.getVertexById(nodeTargetId); - var index = this.getEdgesCount() - 1; - this.edges[index] = new Edge(index, edgeName, nodeSource, nodeTarget, args); - this.json.relations.push({"index": index, "sourceIndex": nodeSourceId, "targetIndex": nodeTargetId, "args": args }); - - nodeSource.addEdge(this.edges[index]); - nodeTarget.addEdge(this.edges[index]); - this._setEdgeEvents(this.edges[index]); - this.newEdge.notify(this.edges[index]); -}; - -GraphDataset.prototype.getVertices = function(){ - return this.vertices; -}; - -GraphDataset.prototype.getEdges = function(){ - return this.edges; -}; - -GraphDataset.prototype.getEdgeById = function(edgeId){ - return this.edges[edgeId]; -}; - -GraphDataset.prototype._getVerticesCount = function(){ - return this.json.vertices.length; -}; - - -GraphDataset.prototype.getVerticesCount = function(){ - var count = 0; - for ( var vertex in this.getVertices()) { - count ++; - } - return count; -}; - - -GraphDataset.prototype.getEdgesCount = function(){ - return this.json.edges.length; -}; - -GraphDataset.prototype.init = function(){ - this.edges = new Object(); - this.vertices = new Object(); -}; - -GraphDataset.prototype._setNodeEvents = function(node){ - var _this = this; - //NODE EVENTS - node.deleted.attach(function (sender, node){ - _this._removeNode(node); - }); - - node.nameChanged.attach(function (sender, args){ - var item = args.item; - var newName = item.name; - var indexes = _this.verticesIndex[args.previousName]; - for(var i = 0; i < indexes.length; i++){ - if(indexes[i] == item.id) - indexes.splice(i,1); - } - if(indexes.length == 0){ - delete _this.verticesIndex[args.previousName]; - } - _this._addVerticesIndex(newName, item.id); - _this.json.vertices[item.id] = newName; - _this.vertexNameChanged.notify(args); - }); -}; - -GraphDataset.prototype._setEdgeEvents = function(edge){ - var _this = this; - //EDGE EVENTS - edge.nameChanged.attach(function (sender, edge){ - _this.edgeNameChanged.notify(edge); - - }); - - edge.deleted.attach(function (sender, edge){ - _this._removeEdge(edge); - }); -}; - -GraphDataset.prototype._connectVerticesByName = function(nodeNameSource, nodeNameTarget){ - var source = this.getVertexByName(nodeNameSource); - var target = this.getVertexByName(nodeNameTarget); - - if ((source != null)&&(target!=null)){ - this.addEdge(source.getName() +"_" + target.getName(), source.getId(), target.getId(), {}); - } - else{ - if (source == null){ - console.log("No encontrado: " + nodeNameSource) - } - if (target == null){ - console.log("No encontrado: " + nodeNameTarget) - } - } -}; - -GraphDataset.prototype.loadFromJSON = function(json){ - var json = json; - this.init(); - this.json = new Object(); - this.json.vertices = new Array(); - this.json.edges = new Array(); - this.json.relations = new Array(); - - for ( var i = 0; i < json.nodes.length; i++) { - if (json.nodes[i] != null){ - var name = json.nodes[i]; - this.addNode(name); - } - else{ - this.json.vertices.push(null); - } - } - - for ( var i = 0; i < json.edges.length; i++) { - if (json.edges[i] != null){ - if (json.relations[i] != null){ - var name = json.edges[i]; - this.addEdge(name, json.relations[i].sourceIndex, json.relations[i].targetIndex, json.relations[i].args); - } - } - else{ - this.json.edges.push(null); - this.json.relations.push(null); - } - } -}; - -GraphDataset.prototype.prettyPrint = function(){ - for ( var node in this.vertices) { - console.log(this.vertices[node].getName() ); - for ( var j = 0; j < this.vertices[node].getEdgesIn().length; j++) { - console.log(" --> " + this.vertices[node].getEdgesIn()[j].getNodeTarget().getName() ); - } - } -}; - -GraphDataset.prototype._removeEdge = function(edge){ - this.json.edges[edge.getId()] = null; - this.json.relations[edge.getId()] = null; - - delete this.edges[edge.getId()]; - this.edgeDeleted.notify(edge); - - -}; - -GraphDataset.prototype._removeNode = function(node){ - this.json.vertices[node.getId()] = null; - delete this.vertices[node.getId()]; - this.vertexDeleted.notify(node); -}; - -GraphDataset.prototype.toJSON = function(){ - var json = new Object(); - var nodes = new Array(); - json.nodes = this.json.vertices; //nodes; - json.edges = this.json.edges; //edges; - json.relations = this.json.relations; - return json; -}; - -GraphDataset.prototype.clone = function(){ - var dsDataset = new GraphDataset(); - dsDataset.loadFromJSON(this.toJSON()); - return dsDataset; -}; -//GraphDataset.prototype.test = function(){ -// this.loadFromJSON(this.toJSON()); -//}; - -function labels(){ - var names = new Array(); - - var dataset = interactomeViewer.graphEditorWidget.dataset; - var layout = interactomeViewer.graphEditorWidget.layout; - - for ( var vertexId in interactomeViewer.graphEditorWidget.dataset.getVertices()) { - names.push(interactomeViewer.graphEditorWidget.dataset.getVertexById(vertexId).getName()); - } - - var sorted = (names.sort()); - console.log(sorted) - var distance = 0.01; - var altura = 0.6; - for ( var i = 0; i < names.length; i++) { - var id =dataset.getVertexByName(names[i]).getId(); - - layout.getNodeById(id).setCoordenates(distance, altura); - - - distance = parseFloat(distance) + parseFloat(0.03); - - altura = parseFloat(altura) + parseFloat(0.02); - - if (parseFloat(altura) == 0.9800000000000003){ - - altura = 0.6; - distance = distance - 0.51; - } - - } - - -}; - -function GraphItem(id, name, args){ - this.id = id; - this.name = name; - this.type = "NONE"; - - this.args = new Object(); - - - if (args!=null){ - this.args = args; - if (args.type !=null){ - this.type = args.type; - } - } - - //Events - this.nameChanged = new Event(this); - this.deleted = new Event(this); -} - -GraphItem.prototype.getName = function(){ - return this.name; -}; - -GraphItem.prototype.getId = function(){ - return this.id; -}; - -GraphItem.prototype.setName = function(name){ - var oldName = this.getName(); - this.name = name; - this.nameChanged.notify({"item": this, "previousName" : oldName}); -}; - - - - - -function LayoutDataset(){ - this.dataset = null; - this.vertices = new Object(); - this.changed = new Event(this); - - - this.args = new Object(); - - //RANDOM, CIRCLE - this.args.type = "CIRCLE"; -}; - -LayoutDataset.prototype.loadFromJSON = function(dataset, json){ - var _this = this; - this.vertices = new Object(); - this.dataset = dataset; //new GraphDataset(); - for ( var vertex in json) { - this.vertices[vertex] = new NodeLayout(vertex, json[vertex].x, json[vertex].y); - this.vertices[vertex].changed.attach(function (sender, item){ - _this.changed.notify(item); - }); - } - this._attachDatasetEvents(); -}; - - -LayoutDataset.prototype.toJSON = function(){ - var serialize = new Object(); - for ( var vertex in this.vertices) { - serialize[vertex] = new Object(); - serialize[vertex].x = this.vertices[vertex].x; - serialize[vertex].y = this.vertices[vertex].y; - } - serialize.dataset = new Object(); - serialize.dataset =this.dataset.toJSON(); - return serialize; -}; - -LayoutDataset.prototype.dataBind = function(graphDataset){ - this.dataset = graphDataset; - this._attachDatasetEvents(); - this._calculateLayout(); -}; - -LayoutDataset.prototype._removeVertex = function(vertexId){ - delete this.vertices[vertexId]; -}; - -LayoutDataset.prototype._attachDatasetEvents = function(){ - var _this = this; - - this.dataset.vertexDeleted.attach(function (sender, item){ - _this._removeVertex(item.getId()); - }); - - this.dataset.newVertex.attach(function (sender, item){ - _this.vertices[item.getId()] = new NodeLayout(item.getId(), 0.5, 0.5); - _this.vertices[item.getId()].changed.attach(function (sender, item){ - _this.changed.notify(item); - }); - }); -}; - -LayoutDataset.prototype.getType = function(){ - return this.args.type; -}; - -LayoutDataset.prototype._calculateLayoutVertices = function(type, count){ - - if (type == "CIRCLE"){ - var radius = 0.4; - var centerX = 0.5; - var centerY = 0.5; - var verticesCoordinates = new Array(); - for(var i = 0; i < count; i++){ - x = centerX + radius * Math.sin(i * 2 * Math.PI/count); - y = centerY + radius * Math.cos(i * 2 * Math.PI/count); - verticesCoordinates.push({'x':x,'y':y}); - } - return verticesCoordinates; - } -}; - - -LayoutDataset.prototype._calculateLayout = function(){ - var _this = this; - if (this.getType() == "RANDOM"){ - for ( var vertex in this.dataset.getVertices()) { - if (this.vertices[vertex] == null){ - this.vertices[vertex] = new NodeLayout(vertex, 0, 0); - } - this.vertices[vertex].setCoordinates(Math.random(), Math.random()); - this.vertices[vertex].changed.attach(function (sender, item){ - _this.changed.notify(item); - }); - } - } - - if ( this.getType() == "CIRCLE"){ - - var count = this.dataset._getVerticesCount(); - var verticesCoordinates = this._calculateLayoutVertices(this.getType(), count); - - var aux = 0; - for ( var vertex in this.dataset.getVertices()) { - if (this.vertices[vertex] == null){ - this.vertices[vertex] = new NodeLayout(vertex, 0, 0); - } - this.vertices[vertex].setCoordinates(verticesCoordinates[aux].x, verticesCoordinates[aux].y);//{"x":, "y":}; - aux++; - this.vertices[vertex].changed.attach(function (sender, item){ - _this.changed.notify(item); - }); - } - } - - - if (this.getType() == "SQUARE"){ - - var count = this.dataset._getVerticesCount(); - var xMin = 0.1; - var xMax = 0.9; - var yMin = 0.1; - var yMax = 0.9; - - var rows = Math.sqrt(count); - var step = (xMax - xMin) / rows; - - var verticesCoordinates = new Array(); - for(var i = 0; i < rows; i ++){ - for ( var j = 0; j < rows; j++) { - x = i * step + xMin; - y = j * step + yMin; - verticesCoordinates.push({'x':x,'y':y}); - } - } - - var aux = 0; - for ( var vertex in this.dataset.getVertices()) { - if (this.vertices[vertex] == null){ - this.vertices[vertex] = new NodeLayout(vertex, 0, 0); - } - this.vertices[vertex].setCoordinates(verticesCoordinates[aux].x, verticesCoordinates[aux].y);//{"x":, "y":}; - aux++; - this.vertices[vertex].changed.attach(function (sender, item){ - _this.changed.notify(item); - }); - } - } - -}; - -LayoutDataset.prototype.getNodeById = function(id){ - return this.vertices[id]; -}; - -LayoutDataset.prototype.getVerticesByArea = function(x1, y1, x2, y2){ - var vertices = new Array(); - for ( var vertex in this.dataset.getVertices()) { - if ((this.vertices[vertex].x >= x1)&&(this.vertices[vertex].x <= x2)){ - if ((this.vertices[vertex].y >= y1)&&(this.vertices[vertex].y <= y2)){ - vertices.push(this.vertices[vertex]); - } - } - } - return vertices; -}; - - - - -LayoutDataset.prototype.getLayout = function(type){ - - if (type == "CIRCLE"){ - this.args.type = "CIRCLE"; - this._calculateLayout(); - return; - } - - if (type == "SQUARE"){ - this.args.type = "SQUARE"; - this._calculateLayout(); - return; - } - - if (type == "RANDOM"){ - this.args.type = "RANDOM"; - this._calculateLayout(); - return; - } - - - var dotText = this.dataset.toDOTID(); - var url = "http://bioinfo.cipf.es/utils/ws/rest/network/layout/"+type+".coords"; - var _this = this; - - $.ajax({ - async: true, - type: "POST", - url: url, - dataType: "text", - data: { - dot :dotText - }, - cache: false, - success: function(data){ - var response = JSON.parse(data); - for ( var vertexId in response) { - _this.vertices[vertexId].setCoordinates(response[vertexId].x, response[vertexId].y); - } - } - }); - -// $.ajax({ -// async: true, -// type: "POST", -// url: url, -// dataType: "script", -// data: { -// dot :dotText -// }, -// cache: false, -// success: function(data){ -// var response = JSON.parse(data); -// for ( var vertexId in response) { -// _this.vertices[vertexId].setCoordinates(response[vertexId].x, response[vertexId].y); -// } -// } -// }); - -}; - -function NodeLayout(id, x, y, args){ - this.id = id; - this.x = x; - this.y = y; - this.changed = new Event(this); -}; - -NodeLayout.prototype.getId = function(id){ - return this.id; -}; - -NodeLayout.prototype.setCoordinates = function(x, y){ - this.x = x; - this.y = y; - this.changed.notify(this); -}; - - - -function NetworkDataSetFormatter(vertexFormatProperties, defaultEdgeProperties, args){ - DataSet.prototype.constructor.call(this); - - this.args = new Object(); - - this.vertices = new Object(); - this.edges = new Object(); - this.dataset = null; - this.maxClass = 0; - this.minClass = 0; - - /** Coordenates with default Setting */ - this.args.width = 1100; - this.args.height = 500; - - /** Optional parameters */ - this.args.backgroundColor = "#FFFFFF"; - this.args.backgroundImage = null; - this.args.backgroundImageHeight = null; - this.args.backgroundImageWidth = null; - this.args.backgroundImageX = null; - this.args.backgroundImageY = null; - - - this.args.balanceNodes = false; - this.args.nodesMaxSize = 3; - this.args.nodesMinSize = 0.5; - - - /** Zoom **/ - this.args.zoomScale = 1; - this.args.zoomScaleStepFactor = 0.4; - - if (args != null){ - if (args.backgroundImage != null){ - this.args.backgroundImage = args.backgroundImage; - } - - if (args.width != null){ - this.args.width = args.width; - } - - if (args.height != null){ - this.args.height = args.height; - this.args.svgHeight = args.height; - } - - if (args.svgHeight != null){ - this.args.svgHeight = args.svgHeight; - } - - if (args.backgroundColor != null){ - this.args.backgroundColor = args.backgroundColor; - } - - if(args.balanceNodes != null){ - this.args.balanceNodes = args.balanceNodes; - } - - if(args.nodesMaxSize != null){ - this.args.nodesMaxSize = args.nodesMaxSize; - } - if(args.nodesMinSize != null){ - this.args.nodesMinSize = args.nodesMinSize; - } - } - - this.args.defaultEdgeProperties = {"fill":"#000000", "radius":"1", "stroke":"#000000", "size":1, "title":{"fontSize":10, "fontColor":"#000000"}}; - this.args.vertexFormatProperties = { "fill":"#000000", "stroke":"#000000", "stroke-opacity":"#000000"}; - - if (vertexFormatProperties!= null){ - this.args.vertexFormatProperties = vertexFormatProperties; - } - if (defaultEdgeProperties!= null){ - this.args.defaultEdgeProperties = defaultEdgeProperties; - } - - /** Events **/ - this.changed = new Event(this); - this.edgeChanged = new Event(this); - this.resized = new Event(this); - this.backgroundImageChanged= new Event(this); - this.backgroundColorChanged= new Event(this); -}; - -NetworkDataSetFormatter.prototype.loadFromJSON = function(dataset, json){ - this.args = new Object(); - this.vertices = new Object(); - this.args = json; - this._setDataset(dataset); - var _this = this; - - for ( var vertex in json.vertices) { - this.addVertex(vertex, json.vertices[vertex]); - } - - for ( var edgeId in json.edges) { - this.addEdge(edgeId, json.edges[edgeId]); - } -}; - - -NetworkDataSetFormatter.prototype.toJSON = function(){ - - -// this.args.vertices = new Object(); -// this.args.edges = new Object(); -// -// for ( var vertex in this.vertices) { -// this.args.vertices[vertex] = this.getVertexById(vertex).toJSON(); -// } -// for ( var edge in this.edges) { -// this.args.edges[edge] = this.getEdgeById(edge).toJSON(); -// } -// -// return (this.args); - - - var serialize = new Object(); - serialize = JSON.parse(JSON.stringify(this.args)); - serialize.vertices = new Object(); - serialize.edges = new Object(); - - for ( var vertex in this.vertices) { - serialize.vertices[vertex] = this.getVertexById(vertex).toJSON(); - } - for ( var edge in this.edges) { - serialize.edges[edge] = this.getEdgeById(edge).toJSON(); - } - - return (serialize); -}; - - - -NetworkDataSetFormatter.prototype._getNodeSize = function(nodeId){ - if (this.isVerticesBalanced()){ - var total = this.maxClass - this.minClass; - if (total == 0){ total = 1;} - var nodeConnection = this.dataset.getVertexById(nodeId).getEdges().length; - return ((nodeConnection*this.args.nodesMaxSize)/total) + this.args.nodesMinSize; - } - return this.getVertexById(nodeId).getDefault().getSize(); -}; - -NetworkDataSetFormatter.prototype._recalculateSize = function(){ - if (this.isVerticesBalanced()){ - this.maxClass = this.dataset.getMaxClass(); - this.minClass = this.dataset.getMinClass(); - for ( var vertexIdAll in this.vertices) { - var size = this._getNodeSize(vertexIdAll); - this.vertices[vertexIdAll].getDefault().setSize(size); - this.vertices[vertexIdAll].getSelected().setSize(size); - this.vertices[vertexIdAll].getOver().setSize(size); - } - } -}; - - -NetworkDataSetFormatter.prototype.addVertex = function(vertexId, json){ - - - if (json == null){ - this.vertices[vertexId] = new CircleVertexGraphFormatter(vertexId, this.args.vertexFormatProperties.defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); - } - else{ - - /** Cargo los attributos desde el json **/ - if (json.type == null){ - this.vertices[vertexId] = new CircleVertexGraphFormatter(vertexId, this.args.vertexFormatProperties.defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); - } - - if ((json.type == "SquareVertexGraphFormatter")||(json.type == "SquareVertexNetworkFormatter")){ - this.vertices[vertexId] = new SquareVertexGraphFormatter(vertexId); - this.vertices[vertexId].loadFromJSON(json); - } - - if ((json.type == "CircleVertexGraphFormatter")||(json.type == "CircleVertexNetworkFormatter")){ - this.vertices[vertexId] = new CircleVertexGraphFormatter(vertexId); - this.vertices[vertexId].loadFromJSON(json); - } - - if ((json.type == "EllipseVertexGraphFormatter")||(json.type == "EllipseVertexNetworkFormatter")){ - this.vertices[vertexId] = new EllipseVertexGraphFormatter(vertexId); - this.vertices[vertexId].loadFromJSON(json); - } - - if ((json.type == "RectangleVertexGraphFormatter")||(json.type == "RectangleVertexNetworkFormatter")){ - this.vertices[vertexId] = new RectangleVertexGraphFormatter(vertexId); - this.vertices[vertexId].loadFromJSON(json); - } - - if ((json.type == "RoundedVertexGraphFormatter")||(json.type == "RoundedVertexNetworkFormatter")){ - this.vertices[vertexId] = new RoundedVertexGraphFormatter(vertexId); - this.vertices[vertexId].loadFromJSON(json); - } - - } - - - var _this = this; - this.vertices[vertexId].stateChanged.attach(function (sender, item){ - _this.changed.notify(item); - }); - - var size = this._getNodeSize(vertexId); - this.vertices[vertexId].defaultFormat.args.size = size; - this.vertices[vertexId].selected.args.size = size; - this.vertices[vertexId].over.args.size = size; - -}; - -NetworkDataSetFormatter.prototype.addEdge = function(edgeId, json){ - - /** Es un edge nuevo que le doy los atributos por defecto **/ - if (json == null){ - if (this.dataset.getEdgeById(edgeId).getNodeSource().getId() == this.dataset.getEdgeById(edgeId).getNodeTarget().getId()){ - this.edges[edgeId] = new BezierEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); - }else{ - this.edges[edgeId] = new DirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); - } - } - else{ - /** Cargo los attributos desde el json **/ - if (json.type == null){ - this.edges[edgeId] = new LineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); - } - - if ((json.type == "LineEdgeGraphFormatter")||(json.type == "LineEdgeNetworkFormatter")){ - this.edges[edgeId] = new LineEdgeGraphFormatter(edgeId); - this.edges[edgeId].loadFromJSON(json); - } - if ((json.type == "DirectedLineEdgeGraphFormatter")||(json.type == "DirectedLineEdgeNetworkFormatter")){ - this.edges[edgeId] = new DirectedLineEdgeGraphFormatter(edgeId); - this.edges[edgeId].loadFromJSON(json); - } - - if ((json.type == "BezierEdgeGraphFormatter")||(json.type == "BezierEdgeNetworkFormatter")){ - this.edges[edgeId] = new BezierEdgeGraphFormatter(edgeId); - this.edges[edgeId].loadFromJSON(json); - } - - - if ((json.type == "CutDirectedLineEdgeGraphFormatter")||(json.type == "CutDirectedLineEdgeNetworkFormatter")){ - this.edges[edgeId] = new CutDirectedLineEdgeGraphFormatter(edgeId); - this.edges[edgeId].loadFromJSON(json); - } - - if ((json.type == "DotDirectedLineEdgeGraphFormatter")||(json.type == "DotDirectedLineEdgeNetworkFormatter")){ - this.edges[edgeId] = new DotDirectedLineEdgeGraphFormatter(edgeId); - this.edges[edgeId].loadFromJSON(json); - } - if ((json.type == "OdotDirectedLineEdgeGraphFormatter")||(json.type == "OdotDirectedLineEdgeNetworkFormatter")){ - this.edges[edgeId] = new OdotDirectedLineEdgeGraphFormatter(edgeId); - this.edges[edgeId].loadFromJSON(json); - } - - if ((json.type == "OdirectedLineEdgeGraphFormatter")||(json.type == "OdirectedLineEdgeNetworkFormatter")){ - this.edges[edgeId] = new OdirectedLineEdgeGraphFormatter(edgeId); - this.edges[edgeId].loadFromJSON(json); - } - } - - var _this = this; - this.edges[edgeId].stateChanged.attach(function (sender, item){ - _this.edgeChanged.notify(item); - }); - - this._recalculateSize(); -}; - -NetworkDataSetFormatter.prototype._setDataset = function(dataset){ - this.dataset = dataset; - this.maxClass = dataset.getMaxClass(); - this.minClass = dataset.getMinClass(); - this._attachDatasetEvents(); -}; - -NetworkDataSetFormatter.prototype.changeEdgeType = function(edgeId, type){ - if ((type == "LineEdgeGraphFormatter")||(type == "LineEdgeNetworkFormatter")){ - this.edges[edgeId] = new LineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); - - } - if ((type == "DirectedLineEdgeGraphFormatter")||(type == "DirectedLineEdgeNetworkFormatter")){ - this.edges[edgeId] = new DirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); - } - - if ((type == "CutDirectedLineEdgeGraphFormatter")||(type == "CutDirectedLineEdgeNetworkFormatter")){ - this.edges[edgeId] = new CutDirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); - } - - if ((type == "DotDirectedLineEdgeGraphFormatter")||(type == "DotDirectedLineEdgeNetworkFormatter")){ - this.edges[edgeId] = new DotDirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); - } - - if ((type == "OdotDirectedLineEdgeGraphFormatter")||(type == "OdotDirectedLineEdgeNetworkFormatter")){ - this.edges[edgeId] = new OdotDirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); - } - - if ((type == "OdirectedLineEdgeGraphFormatter")||(type == "OdirectedLineEdgeNetworkFormatter")){ - this.edges[edgeId] = new OdirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); - } - - - - var _this = this; - this.edges[edgeId].stateChanged.attach(function (sender, item){ - _this.edgeChanged.notify(item); - }); - _this.edgeChanged.notify(this.edges[edgeId]); -}; -/* -classe = "SquareNetworkNodeFormatter"; -} -if (value == "circle"){ - classe = "CircleNetworkNodeFormatter"; - **/ -NetworkDataSetFormatter.prototype.changeNodeType = function(vertexId, type){ - var defaultFormat = JSON.parse(JSON.stringify(this.vertices[vertexId].getDefault())); - var selectedFormat = JSON.parse(JSON.stringify(this.vertices[vertexId].getSelected())); - var defaultFormat = JSON.parse(JSON.stringify(this.vertices[vertexId].getDefault())); - var defaultFormat = JSON.parse(JSON.stringify(this.vertices[vertexId].getDefault())); - - if ((type == "SquareVertexGraphFormatter")||(type == "SquareVertexNetworkFormatter")){ - this.vertices[vertexId] = new SquareVertexGraphFormatter(vertexId,defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); - } - - if ((type == "CircleVertexGraphFormatter")||(type == "CircleVertexNetworkFormatter")){ - this.vertices[vertexId] = new CircleVertexGraphFormatter(vertexId, defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); - } - - if ((type == "EllipseVertexGraphFormatter")||(type == "EllipseVertexNetworkFormatter")){ - this.vertices[vertexId] = new EllipseVertexGraphFormatter(vertexId, defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); - } - - if ((type == "RectangleVertexGraphFormatter")||(type == "RectangleVertexNetworkFormatter")){ - this.vertices[vertexId] = new RectangleVertexGraphFormatter(vertexId, defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); - } - - if ((type == "RoundedVertexGraphFormatter")||(type == "RoundedVertexNetworkFormatter")){ - this.vertices[vertexId] = new RoundedVertexGraphFormatter(vertexId, defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); - } - - if ((type == "OctagonVertexGraphFormatter")||(type == "OctagonVertexNetworkhFormatter")){ - this.vertices[vertexId] = new OctagonVertexGraphFormatter(vertexId, defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); - } - - - var _this = this; - this.vertices[vertexId].stateChanged.attach(function (sender, item){ - _this.changed.notify(item); - }); - _this.changed.notify(this.vertices[vertexId]); -}; - - - -NetworkDataSetFormatter.prototype.dataBind = function(networkDataSet){ - var _this = this; - this._setDataset(networkDataSet); - - for ( var vertex in this.dataset.getVertices()) { - this.addVertex(vertex); - } - - for ( var edge in this.dataset.getEdges()) { - this.addEdge(edge); - } -}; - -NetworkDataSetFormatter.prototype._removeEdge = function(edgeId){ - delete this.edges[edgeId]; -}; - -NetworkDataSetFormatter.prototype._removeVertex = function(vertexId){ - delete this.vertices[vertexId]; -}; - -NetworkDataSetFormatter.prototype._attachDatasetEvents = function(id){ - var _this = this; - this.dataset.vertexDeleted.attach(function (sender, item){ - _this._removeVertex(item.getId()); - }); - - this.dataset.edgeDeleted.attach(function (sender, item){ - _this._removeEdge(item.getId()); - }); - - this.dataset.newVertex.attach(function (sender, item){ - _this.addVertex(item.getId()); - }); - - this.dataset.newEdge.attach(function (sender, item){ - _this.addEdge(item.getId()); - }); -}; - - -NetworkDataSetFormatter.prototype.getVertexById = function(id){ - return this.vertices[id]; -}; - -NetworkDataSetFormatter.prototype.getEdgeById = function(id){ - return this.edges[id]; -}; - -NetworkDataSetFormatter.prototype.makeLabelsBigger = function(){ -for ( var vertexId in this.vertices) { - var fontSize = this.vertices[vertexId].getDefault().getFontSize() + 2; - this.vertices[vertexId].getDefault().setFontSize(fontSize); - } -}; - -NetworkDataSetFormatter.prototype.makeLabelsSmaller = function(){ - for ( var vertexId in this.vertices) { - var fontSize = this.vertices[vertexId].getDefault().getFontSize() - 2; - this.vertices[vertexId].getDefault().setFontSize(fontSize); - } -}; - - -NetworkDataSetFormatter.prototype.resize = function(width, height){ - this.args.width = width; - this.args.height = height; - this.resized.notify(); -}; - -/** ZOOM GETTERS **/ -NetworkDataSetFormatter.prototype.getZoomScaleStepFactor = function(){return this.args.zoomScaleStepFactor;}; -NetworkDataSetFormatter.prototype.setZoomScaleStepFactor = function(scaleFactor){this.args.zoomScaleStepFactor = scaleFactor;}; -NetworkDataSetFormatter.prototype.getZoomScale = function(){return this.args.zoomScale;}; -NetworkDataSetFormatter.prototype.setZoomScale = function(scale){this.args.zoomScale = scale;}; - -NetworkDataSetFormatter.prototype.getNodesMaxSize = function(){return this.args.nodesMaxSize;}; -NetworkDataSetFormatter.prototype.getNodesMinSize = function(){return this.args.nodesMinSize;}; - -/** SIZE SETTERS AND GETTERS **/ -NetworkDataSetFormatter.prototype.isVerticesBalanced = function(){return this.args.balanceNodes;}; -NetworkDataSetFormatter.prototype.getWidth = function(){return this.args.width;}; -NetworkDataSetFormatter.prototype.getHeight = function(){return this.args.height;}; - -/** OPTIONAL PARAMETERS GETTERS AND SETTERS **/ -NetworkDataSetFormatter.prototype.getBackgroundImage = function(){return this.args.backgroundImage;}; -NetworkDataSetFormatter.prototype.setBackgroundImage = function(value){this.args.backgroundImage = value; this.backgroundImageChanged.notify(this);}; - - -NetworkDataSetFormatter.prototype.getBackgroundImageWidth = function(){return this.args.backgroundImageWidth;}; -NetworkDataSetFormatter.prototype.setBackgroundImageWidth = function(value){this.args.backgroundImageWidth = value; this.backgroundImageChanged.notify(this);}; - -NetworkDataSetFormatter.prototype.getBackgroundImageHeight = function(){return this.args.backgroundImageHeight;}; -NetworkDataSetFormatter.prototype.setBackgroundImageHeight = function(value){this.args.backgroundImageHeight = value; this.backgroundImageChanged.notify(this);}; - -NetworkDataSetFormatter.prototype.getBackgroundImageX = function(){return this.args.backgroundImageX;}; -NetworkDataSetFormatter.prototype.setBackgroundImageX = function(value){this.args.backgroundImageX = value; this.backgroundImageChanged.notify(this);}; - -NetworkDataSetFormatter.prototype.getBackgroundImageY = function(){return this.args.backgroundImageX;}; -NetworkDataSetFormatter.prototype.setBackgroundImageY = function(value){this.args.backgroundImageY = value; this.backgroundImageChanged.notify(this);}; - - - -NetworkDataSetFormatter.prototype.getBackgroundColor = function(){return this.args.backgroundColor;}; -NetworkDataSetFormatter.prototype.setBackgroundColor = function(value){this.args.backgroundColor = value; this.backgroundColorChanged.notify(this);}; - -NetworkDataSetFormatter.prototype.getWidth = function(){return this.args.width;}; -NetworkDataSetFormatter.prototype.setWidth = function(value){this.args.width = value;}; - -NetworkDataSetFormatter.prototype.getHeight = function(){return this.args.height;}; -NetworkDataSetFormatter.prototype.setHeight = function(value){this.args.height = value;}; - - - - -Vertex.prototype.getName = GraphItem.prototype.getName; -Vertex.prototype.setName = GraphItem.prototype.setName; -Vertex.prototype.getId = GraphItem.prototype.getId; - -function Vertex(id, name, args){ - GraphItem.prototype.constructor.call(this, id, name, args); - this.edgesIn= new Array(); - this.edgesOut= new Array(); -}; - -Vertex.prototype.getEdges = function(){ - return this.edgesIn.concat(this.edgesOut); -}; - -Vertex.prototype.getEdgesCount = function(){ - return this.getEdges().length; -}; - -Vertex.prototype.getEdgesIn = function(){ - return this.edgesIn; -}; - -Vertex.prototype.getEdgesOut = function(){ - return this.edgesOut; -}; - -Vertex.prototype.addEdge = function(edge){ - if (edge.getNodeSource().getId() == this.id){ - this.edgesIn.push(edge); - } - else{ - this.edgesOut.push(edge); - } -}; - -Vertex.prototype.removeEdge = function(edge){ - for ( var i = 0; i < this.getEdgesIn().length; i++) { - var edgeIn = this.edgesIn[i]; - if (edgeIn.getId() == edge.getId()){ - this.edgesIn.splice(i, 1); - } - } - for ( var i = 0; i < this.getEdgesOut().length; i++) { - var edgeIn = this.edgesOut[i]; - if (edgeIn.getId() == edge.getId()){ - this.edgesOut.splice(i, 1); - } - } -}; - -Vertex.prototype.remove = function(){ - var edges = this.getEdges(); - for ( var i = 0; i < edges.length; i++) { - var edge = edges[i]; - edge.remove(); - } - this.deleted.notify(this); -}; - - - - - -VertexGraphFormatter.prototype.getDefault = ItemGraphFormatter.prototype.getDefault; -VertexGraphFormatter.prototype.getSelected = ItemGraphFormatter.prototype.getSelected; -VertexGraphFormatter.prototype.getOver = ItemGraphFormatter.prototype.getOver; -VertexGraphFormatter.prototype.getDragging = ItemGraphFormatter.prototype.getDragging; -VertexGraphFormatter.prototype.getId = ItemGraphFormatter.prototype.getId; -VertexGraphFormatter.prototype.toJSON = ItemGraphFormatter.prototype.toJSON; -VertexGraphFormatter.prototype.loadFromJSON = ItemGraphFormatter.prototype.loadFromJSON; -VertexGraphFormatter.prototype._setEvents = ItemGraphFormatter.prototype._setEvents; - - -function VertexGraphFormatter(defaultFormat, selectedFormat, overFormat, draggingFormat){ - ItemGraphFormatter.prototype.constructor.call(this, defaultFormat, selectedFormat, overFormat, draggingFormat); -}; - - -CircleVertexGraphFormatter.prototype.getDefault = VertexGraphFormatter.prototype.getDefault; -CircleVertexGraphFormatter.prototype.getSelected = VertexGraphFormatter.prototype.getSelected; -CircleVertexGraphFormatter.prototype.getOver = VertexGraphFormatter.prototype.getOver; -CircleVertexGraphFormatter.prototype.getDragging = VertexGraphFormatter.prototype.getDragging; -CircleVertexGraphFormatter.prototype.getId = VertexGraphFormatter.prototype.getId; -CircleVertexGraphFormatter.prototype.toJSON = VertexGraphFormatter.prototype.toJSON; -CircleVertexGraphFormatter.prototype.loadFromJSON = VertexGraphFormatter.prototype.loadFromJSON; -CircleVertexGraphFormatter.prototype._setEvents = VertexGraphFormatter.prototype._setEvents; - -function CircleVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ - VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); - this.args.type = "CircleVertexGraphFormatter"; - if (defaultFormat != null){ - if (defaultFormat.radius != null){ - this.defaultFormat.args.radius = defaultFormat.radius; - } - } - - if (selectedFormat != null){ - if (selectedFormat.radius != null){ - this.selected.args.radius = selectedFormat.radius; - } - } - - if (overFormat != null){ - if (overFormat.radius != null){ - this.over.args.radius = overFormat.radius; - } - } - - if (draggingFormat != null){ - if (draggingFormat.radius != null){ - this.dragging.args.draggingFormat = draggingFormat.radius; - } - } -}; - - - -SquareVertexGraphFormatter.prototype.getDefault = VertexGraphFormatter.prototype.getDefault; -SquareVertexGraphFormatter.prototype.getSelected = VertexGraphFormatter.prototype.getSelected; -SquareVertexGraphFormatter.prototype.getOver = VertexGraphFormatter.prototype.getOver; -SquareVertexGraphFormatter.prototype.getDragging = VertexGraphFormatter.prototype.getDragging; -SquareVertexGraphFormatter.prototype.getId = VertexGraphFormatter.prototype.getId; -SquareVertexGraphFormatter.prototype.toJSON = VertexGraphFormatter.prototype.toJSON; -SquareVertexGraphFormatter.prototype.loadFromJSON = VertexGraphFormatter.prototype.loadFromJSON; -SquareVertexGraphFormatter.prototype._setEvents = VertexGraphFormatter.prototype._setEvents; - -function SquareVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ - VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); - this.args.type = "SquareVertexGraphFormatter"; - if (defaultFormat != null){ - if (defaultFormat.radius != null){ - this.defaultFormat.args.radius = defaultFormat.radius; - } - } - - if (selectedFormat != null){ - if (selectedFormat.radius != null){ - this.selected.args.radius = selectedFormat.radius; - } - } - - if (overFormat != null){ - if (overFormat.radius != null){ - this.over.args.radius = overFormat.radius; - } - } - - if (draggingFormat != null){ - if (draggingFormat.radius != null){ - this.dragging.args.draggingFormat = draggingFormat.radius; - } - } -}; - - -EllipseVertexGraphFormatter.prototype.getDefault = VertexGraphFormatter.prototype.getDefault; -EllipseVertexGraphFormatter.prototype.getSelected = VertexGraphFormatter.prototype.getSelected; -EllipseVertexGraphFormatter.prototype.getOver = VertexGraphFormatter.prototype.getOver; -EllipseVertexGraphFormatter.prototype.getDragging = VertexGraphFormatter.prototype.getDragging; -EllipseVertexGraphFormatter.prototype.getId = VertexGraphFormatter.prototype.getId; -EllipseVertexGraphFormatter.prototype.toJSON = VertexGraphFormatter.prototype.toJSON; -EllipseVertexGraphFormatter.prototype.loadFromJSON = VertexGraphFormatter.prototype.loadFromJSON; -EllipseVertexGraphFormatter.prototype._setEvents = VertexGraphFormatter.prototype._setEvents; - -function EllipseVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ - VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); - this.args.type = "EllipseVertexGraphFormatter"; - if (defaultFormat != null){ - if (defaultFormat.radius != null){ - this.defaultFormat.args.radius = defaultFormat.radius; - } - } - - if (selectedFormat != null){ - if (selectedFormat.radius != null){ - this.selected.args.radius = selectedFormat.radius; - } - } - - if (overFormat != null){ - if (overFormat.radius != null){ - this.over.args.radius = overFormat.radius; - } - } - - if (draggingFormat != null){ - if (draggingFormat.radius != null){ - this.dragging.args.draggingFormat = draggingFormat.radius; - } - } -}; - - - -RectangleVertexGraphFormatter.prototype.getDefault = ItemGraphFormatter.prototype.getDefault; -RectangleVertexGraphFormatter.prototype.getSelected = ItemGraphFormatter.prototype.getSelected; -RectangleVertexGraphFormatter.prototype.getOver = ItemGraphFormatter.prototype.getOver; -RectangleVertexGraphFormatter.prototype.getDragging = ItemGraphFormatter.prototype.getDragging; -RectangleVertexGraphFormatter.prototype.getId = ItemGraphFormatter.prototype.getId; -RectangleVertexGraphFormatter.prototype.toJSON = ItemGraphFormatter.prototype.toJSON; -RectangleVertexGraphFormatter.prototype.loadFromJSON = ItemGraphFormatter.prototype.loadFromJSON; -RectangleVertexGraphFormatter.prototype._setEvents = ItemGraphFormatter.prototype._setEvents; - -function RectangleVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ - VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); - this.args.type = "RectangleVertexGraphFormatter"; - if (defaultFormat != null){ - if (defaultFormat.radius != null){ - this.defaultFormat.args.radius = defaultFormat.radius; - } - } - - if (selectedFormat != null){ - if (selectedFormat.radius != null){ - this.selected.args.radius = selectedFormat.radius; - } - } - - if (overFormat != null){ - if (overFormat.radius != null){ - this.over.args.radius = overFormat.radius; - } - } - - if (draggingFormat != null){ - if (draggingFormat.radius != null){ - this.dragging.args.draggingFormat = draggingFormat.radius; - } - } -}; - - - -RoundedVertexGraphFormatter.prototype.getDefault = ItemGraphFormatter.prototype.getDefault; -RoundedVertexGraphFormatter.prototype.getSelected = ItemGraphFormatter.prototype.getSelected; -RoundedVertexGraphFormatter.prototype.getOver = ItemGraphFormatter.prototype.getOver; -RoundedVertexGraphFormatter.prototype.getDragging = ItemGraphFormatter.prototype.getDragging; -RoundedVertexGraphFormatter.prototype.getId = ItemGraphFormatter.prototype.getId; -RoundedVertexGraphFormatter.prototype.toJSON = ItemGraphFormatter.prototype.toJSON; -RoundedVertexGraphFormatter.prototype.loadFromJSON = ItemGraphFormatter.prototype.loadFromJSON; -RoundedVertexGraphFormatter.prototype._setEvents = ItemGraphFormatter.prototype._setEvents; - -function RoundedVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ - VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); - this.args.type = "RoundedVertexGraphFormatter"; - if (defaultFormat != null){ - if (defaultFormat.radius != null){ - this.defaultFormat.args.radius = defaultFormat.radius; - } - } - - if (selectedFormat != null){ - if (selectedFormat.radius != null){ - this.selected.args.radius = selectedFormat.radius; - } - } - - if (overFormat != null){ - if (overFormat.radius != null){ - this.over.args.radius = overFormat.radius; - } - } - - if (draggingFormat != null){ - if (draggingFormat.radius != null){ - this.dragging.args.draggingFormat = draggingFormat.radius; - } - } -}; - - - -OctagonVertexGraphFormatter.prototype.getDefault = ItemGraphFormatter.prototype.getDefault; -OctagonVertexGraphFormatter.prototype.getSelected = ItemGraphFormatter.prototype.getSelected; -OctagonVertexGraphFormatter.prototype.getOver = ItemGraphFormatter.prototype.getOver; -OctagonVertexGraphFormatter.prototype.getDragging = ItemGraphFormatter.prototype.getDragging; -OctagonVertexGraphFormatter.prototype.getId = ItemGraphFormatter.prototype.getId; -OctagonVertexGraphFormatter.prototype.toJSON = ItemGraphFormatter.prototype.toJSON; -OctagonVertexGraphFormatter.prototype.loadFromJSON = ItemGraphFormatter.prototype.loadFromJSON; -OctagonVertexGraphFormatter.prototype._setEvents = ItemGraphFormatter.prototype._setEvents; - -function OctagonVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ - VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); - this.args.type = "OctagonVertexGraphFormatter"; - if (defaultFormat != null){ - if (defaultFormat.radius != null){ - this.defaultFormat.args.radius = defaultFormat.radius; - } - } - - if (selectedFormat != null){ - if (selectedFormat.radius != null){ - this.selected.args.radius = selectedFormat.radius; - } - } - - if (overFormat != null){ - if (overFormat.radius != null){ - this.over.args.radius = overFormat.radius; - } - } - - if (draggingFormat != null){ - if (draggingFormat.radius != null){ - this.dragging.args.draggingFormat = draggingFormat.radius; - } - } -}; - - - -var Colors = new function() -{ - this.hashColor = []; - this.getColorByScoreArrayValue = function (arrayScore) - { - var array = new Array(); - - for (var i = 0; i< arrayScore.length; i++) - { - - var color = this.getColorByScoreValue(arrayScore[i]) - array.push( color); - - } - return array; - }; - - this.getHexStringByScoreArrayValue = function (arrayScore) - { - var arrayColor = this.getColorByScoreArrayValue(arrayScore); - var arrayHex = new Array(); - for (var i = 0; i< arrayColor.length; i++) - { - arrayHex.push( arrayColor[i].HexString()); - } - return arrayHex; - }; - - this.getColorByScoreValue = function (score) - { - - var truncate = score.toString().substr(0,4); - if (this.hashColor[truncate]!=null) - { - return this.hashColor[truncate]; - } - - - if(isNaN(score)) { - return Colors.ColorFromRGB(0,0,0); - } - var value; - - var from, to; - if(score < 0.5) { - from = Colors.ColorFromRGB(0,0,255); - to = Colors.ColorFromRGB(255,255,255); - value = (score * 2); - } else { - from = Colors.ColorFromRGB(255,255,255); - to = Colors.ColorFromRGB(255,0,0); - value = (score * 2) - 1; - } - - var x = value; - var y = 1.0 - value; - var color = Colors.ColorFromRGB(y * from.Red() + x * to.Red(), y * from.Green() + x * to.Green(), y * from.Blue() + x * to.Blue()); - - this.hashColor[truncate] = color; - - return color; - }; - - this.ColorFromHSV = function(hue, sat, val) - { - var color = new Color(); - color.SetHSV(hue,sat,val); - return color; - }; - - this.ColorFromRGB = function(r, g, b) - { - var color = new Color(); - color.SetRGB(r,g,b); - return color; - }; - - this.ColorFromHex = function(hexStr) - { - var color = new Color(); - color.SetHexString(hexStr); - return color; - }; - - function Color() { - //Stored as values between 0 and 1 - var red = 0; - var green = 0; - var blue = 0; - - //Stored as values between 0 and 360 - var hue = 0; - - //Strored as values between 0 and 1 - var saturation = 0; - var value = 0; - - this.SetRGB = function(r, g, b) - { - red = r/255.0; - green = g/255.0; - blue = b/255.0; - calculateHSV(); - }; - - this.Red = function() { return Math.round(red*255); }; - - this.Green = function() { return Math.round(green*255); }; - - this.Blue = function() { return Math.round(blue*255); }; - - this.SetHSV = function(h, s, v) - { - hue = h; - saturation = s; - value = v; - calculateRGB(); - }; - - this.Hue = function() - { return hue; }; - - this.Saturation = function() - { return saturation; }; - - this.Value = function() - { return value; }; - - this.SetHexString = function(hexString) - { - if(hexString == null || typeof(hexString) != "string") - { - this.SetRGB(0,0,0); - return; - } - - if (hexString.substr(0, 1) == '#') - hexString = hexString.substr(1); - - if(hexString.length != 6) - { - this.SetRGB(0,0,0); - return; - } - - var r = parseInt(hexString.substr(0, 2), 16); - var g = parseInt(hexString.substr(2, 2), 16); - var b = parseInt(hexString.substr(4, 2), 16); - if (isNaN(r) || isNaN(g) || isNaN(b)) - { - this.SetRGB(0,0,0); - return; - } - - this.SetRGB(r,g,b); - }; - - this.HexString = function() - { - - var rStr = this.Red().toString(16); - if (rStr.length == 1) - rStr = '0' + rStr; - var gStr = this.Green().toString(16); - if (gStr.length == 1) - gStr = '0' + gStr; - var bStr = this.Blue().toString(16); - if (bStr.length == 1) - bStr = '0' + bStr; - return ('#' + rStr + gStr + bStr).toUpperCase(); - }; - - this.Complement = function() - { - var newHue = (hue >= 180) ? hue - 180 : hue + 180; - var newVal = (value * (saturation - 1) + 1); - var newSat = (value*saturation) / newVal; - var newColor = new Color(); - newColor.SetHSV(newHue, newSat, newVal); - return newColor; - } ; - - function calculateHSV() - { - var max = Math.max(Math.max(red, green), blue); - var min = Math.min(Math.min(red, green), blue); - - value = max; - - saturation = 0; - if(max != 0) - saturation = 1 - min/max; - - hue = 0; - if(min == max) - return; - - var delta = (max - min); - if (red == max) - hue = (green - blue) / delta; - else if (green == max) - hue = 2 + ((blue - red) / delta); - else - hue = 4 + ((red - green) / delta); - hue = hue * 60; - if(hue < 0) - hue += 360; - } - - function calculateRGB() - { - red = value; - green = value; - blue = value; - - if(value == 0 || saturation == 0) - return; - - var tHue = (hue / 60); - var i = Math.floor(tHue); - var f = tHue - i; - var p = value * (1 - saturation); - var q = value * (1 - saturation * f); - var t = value * (1 - saturation * (1 - f)); - switch(i) - { - case 0: - red = value; green = t; blue = p; - break; - case 1: - red = q; green = value; blue = p; - break; - case 2: - red = p; green = value; blue = t; - break; - case 3: - red = p; green = q; blue = value; - break; - case 4: - red = t; green = p; blue = value; - break; - default: - red = value; green = p; blue = q; - break; - } - } - } -} -(); -/* - * Clase gestiona la insercción, eliminación de los elementos en el DOM - * - * Vital hacerla SIEMPRE compatible hacia atrás - * - * Last update: 28-10-2010 - * - */ - - -var DOM = {}; - -DOM.createNewElement = function(type, nodeParent, attributes) -{ - - var node = document.createElement(type); - for (var i=0; i0) - { - parent.removeChild(parent.childNodes[0]); - - } -}; - -DOM.select = function(targetID) -{ - return document.getElementById(targetID); -// return $("#"+targetID); -}; -var Geometry = -{ - - /** From tow points obtains the angles formed with the cartesian side **/ - getAngleBetweenTwoPoints : function(x1, y1, x2, y2){ - //var m = (y1 - y2)/ (x1 - x2); - return Math.atan2(y2-y1, x2-x1); - }, - - getAdjacentSideOfRectangleRight : function(angle, hypotenuse){ - return Math.abs(Math.cos(angle)*hypotenuse); - }, - - getOppositeSideOfRectangleRight : function(angle, hypotenuse){ - return Math.abs(Math.sin(angle)*hypotenuse); - }, - - toDegree: function(radian){ - return radian*180/Math.PI; - - } - - -}; - -var SVG = -{ - svgns : 'http://www.w3.org/2000/svg', - xlinkns : "http://www.w3.org/1999/xlink", - - createSVGCanvas: function(parentNode, attributes) - { - - attributes.push( ['xmlns', SVG.svgns], ['xmlns:xlink', 'http://www.w3.org/1999/xlink']); - var svg = document.createElementNS("http://www.w3.org/2000/svg", "svg"); - this._setProperties(svg, attributes); - parentNode.appendChild( svg); - return svg; - - }, - - createRectangle : function (x, y, width, height, attributes){ - var rect = document.createElementNS(this.svgns, "rect"); - rect.setAttribute("x",x); - rect.setAttribute("y",y); - rect.setAttribute("width",width); - rect.setAttribute("height",height); - SVG._setProperties(rect, attributes); - return rect; - }, - - drawImage64 : function (x, y, width, height, base64, svgNode, attributes) { - var node = SVG.createImage64(x, y, width, height, base64, attributes); - svgNode.appendChild(node); - return node; - }, - - createImage64 : function (x, y, width, height, base64, attributes) { - var img = document.createElementNS(this.svgns, "image"); - img.setAttribute("x",x); - img.setAttribute("y",y); - img.setAttribute("width",width); - img.setAttribute("height",height); - img.setAttribute("xlink:href",base64); - SVG._setProperties(img, attributes); - return img; - }, - - createLine: function (x1, y1, x2, y2, attributes){ - var line = document.createElementNS(this.svgns,"line"); - line.setAttribute("x1",x1); - line.setAttribute("y1",y1); - line.setAttribute("x2", x2); - line.setAttribute("y2", y2); - SVG._setProperties(line, attributes); - return line; - }, - - createClip: function (id, nodeToClip, attributes){ - var clip = document.createElementNS(this.svgns,"clipPath"); - clip.setAttribute("id",id); - clip.appendChild(nodeToClip); - return clip; - }, - - drawClip : function (id, nodeToClip, svgNode) { - var node = SVG.createClip(id, nodeToClip); - svgNode.appendChild(node); - return node; - }, - - drawRectangle : function (cx, cy, width, height, svgNode, attributes) { - try{ - var node = SVG.createRectangle(cx, cy, width, height, attributes); - svgNode.appendChild(node); - } - catch(e){ - - console.log("-------------------- "); - console.log("Error on drawRectangle " + e); - console.log(attributes); - console.log("-------------------- "); - } - return node; - }, - - createEllipse : function (x, y, rx, ry, attributes){ - var rect = document.createElementNS(this.svgns, "ellipse"); - rect.setAttribute("cx",x); - rect.setAttribute("cy",y); - rect.setAttribute("rx",rx); - rect.setAttribute("ry",ry); - SVG._setProperties(rect, attributes); - return rect; - }, - - drawEllipse : function (cx, cy, rx, ry, svgNode, attributes) { - var node = SVG.createEllipse(cx, cy, rx, ry, attributes); - svgNode.appendChild(node); - return node; - }, - - drawImage : function (x, y, canvasSVG, attributes) { - var image = document.createElementNS(this.svgns, "image"); - image.setAttribute("x",x); - image.setAttribute("y",y); - canvasSVG.appendChild(image); - SVG._setProperties(image, attributes); - }, - - drawLine : function (x1, y1, x2, y2, nodeSVG, attributes) { - try{ - var line = SVG.createLine(x1, y1, x2, y2, attributes); - nodeSVG.appendChild(line); - }catch(e){ - } - return line; - }, - - - drawPath: function (d, nodeSVG, attributes) { - var path = SVG.createPath(d, attributes); - nodeSVG.appendChild(path); - return path; - }, - - createPoligon : function (points, attributes){ - var poligon = document.createElementNS(this.svgns, "polygon"); - poligon.setAttribute("points",points); - SVG._setProperties(poligon, attributes); - return poligon; - }, - - drawPoligon : function (points, canvasSVG, attributes){ - var poligon = SVG.createPoligon(points, attributes); - canvasSVG.appendChild(poligon); - return poligon; - }, - // - - createPath : function (d, attributes){ - var path = document.createElementNS(this.svgns, "path"); - path.setAttribute("d",d); - SVG._setProperties(path, attributes); - return path; - }, - - drawCircle : function (x, y, radio, canvasSVG, attributes) { - - var newText = document.createElementNS(this.svgns,"circle"); - newText.setAttribute("cx",x); - newText.setAttribute("cy",y); - newText.setAttribute("r",radio); - - canvasSVG.appendChild(newText); - attributes["cursor"] = "pointer"; - this._setProperties(newText, attributes); - return newText; - }, - - - _setProperties: function(node, attributes) - { - if (attributes instanceof Array){ - for (var i=0; i< attributes.length; i++) - { - node.setAttribute(attributes[i][0], attributes[i][1]); - } - } - else{ - for ( var key in attributes){ - node.setAttribute(key, attributes[key]); - } - } - }, - -/* drawPath: function(pointsArray, canvasSVG, attributes){ - var path = document.createElementNS(this.svgns,"polyline"); - path.setAttribute ('id', id); - - var d= pointsArray[0].x+ " "+ pointsArray[0].y; - for (var i=1; i< pointsArray.length; i++) - { - d=d+" "+pointsArray[i].x+" "+pointsArray[i].y; - } - path.setAttribute ('points', d); - canvasSVG.appendChild(path); - },*/ - - createText : function (x, y, text, attributes) { - var node = document.createElementNS(this.svgns,"text"); - node.setAttributeNS(null , "x",x); - node.setAttributeNS(null, "y",y); - - var textNode = document.createTextNode(text); - node.appendChild(textNode); - - this._setProperties(node, attributes); - return node; - }, - - drawText : function (x, y, text, canvasSVG, attributes) { - var text = SVG.createText(x, y, text, attributes); - canvasSVG.appendChild(text); - return text; - }, - - - - drawGroup: function(svgNode, attributes) - { - var group = SVG.createGroup(attributes); - svgNode.appendChild(group); - return group; - }, - - createGroup: function(attributes){ - var group = document.createElementNS(this.svgns,"g"); - this._setProperties(group, attributes); - return group; - } - -}; - - - -var CanvasToSVG = { - - convert: function(sourceCanvas, targetSVG, x, y, id, attributes) { - - var img = this._convert(sourceCanvas, targetSVG, x, y, id); - - for (var i=0; i< attributes.length; i++) - { - img.setAttribute(attributes[i][0], attributes[i][1]); - } - }, - - _convert: function(sourceCanvas, targetSVG, x, y, id) { - var svgNS = "http://www.w3.org/2000/svg"; - var xlinkNS = "http://www.w3.org/1999/xlink"; - // get base64 encoded png from Canvas - var image = sourceCanvas.toDataURL(); - - // must be careful with the namespaces - var svgimg = document.createElementNS(svgNS, "image"); - - svgimg.setAttribute('id', id); - - //svgimg.setAttribute('class', class); - //svgimg.setAttribute('xlink:href', image); - svgimg.setAttributeNS(xlinkNS, 'xlink:href', image); - - - - - svgimg.setAttribute('x', x ? x : 0); - svgimg.setAttribute('y', y ? y : 0); - svgimg.setAttribute('width', sourceCanvas.width); - svgimg.setAttribute('height', sourceCanvas.height); - //svgimg.setAttribute('cursor', 'pointer'); - svgimg.imageData = image; - - targetSVG.appendChild(svgimg); - return svgimg; - }, - - importSVG: function(sourceSVG, targetCanvas) { - svg_xml = sourceSVG;//(new XMLSerializer()).serializeToString(sourceSVG); - var ctx = targetCanvas.getContext('2d'); - - var img = new Image(); - img.src = "data:image/svg+xml;base64," + btoa(svg_xml); -// img.onload = function() { - ctx.drawImage(img, 0, 0); -// }; - } - -}; -/* -Graph.prototype.importSVG = function(sourceSVG, targetCanvas) { - sourceSVG = this._svg; - targetCanvas = document.createElementNS('canvas'); - // https://developer.mozilla.org/en/XMLSerializer - svg_xml = (new XMLSerializer()).serializeToString(sourceSVG); - var ctx = targetCanvas.getContext('2d'); - // this is just a JavaScript (HTML) image - var img = new Image(); - // http://en.wikipedia.org/wiki/SVG#Native_support - // https://developer.mozilla.org/en/DOM/window.btoa - img.src = "data:image/svg+xml;base64," + btoa(svg_xml); - img.onload = function() { - // after this, Canvas’ origin-clean is DIRTY - ctx.drawImage(img, 0, 0); - } -}; -*/ - -/* - -Normalizacion de datos para dibujar colores -Issues: - No sé como debería llamarse esta libreria - No sé si ya existe una funciçon en javascript que lo haga - - -*/ - - -var Normalizer = new function() -{ - this.normalizeArray = function (arrayData) - { - - return this.standardizeArray(this.normal(arrayData)); - -// var result = this._getMaxAndMin(arrayData); -// var min =result[0]; -// var max = result[1]; -// -// -// //los hacemos todos positivos -// for (var i = 0; i< arrayData.length; i++) -// { -// arrayData[i]= Math.abs(min) + parseFloat(arrayData[i]); -// } -// -// var result = this._getMaxAndMin(arrayData); -// var min =result[0]; -// var max = result[1]; -// -// -// var resultArray = new Array(); -// for (var i = 0; i< arrayData.length; i++) -// { -// resultArray.push(arrayData[i]*1/max); -// } -// return resultArray; - }; - - this.normal = function(arrayData){ - var mean = this._getMean(arrayData); - var deviation = this._getStdDeviation(arrayData); - var result = this._getMaxAndMin(arrayData); - var min = result[0]; - var max = result[1]; - - var resultArray = new Array(); - for (var i = 0; i< arrayData.length; i++) { - if (deviation!=0){ - resultArray.push((arrayData[i]-mean)/deviation); - }else{ - resultArray.push(arrayData[i]); - } - } - return resultArray; - }; - - this.standardizeArray = function(arrayData) - { - var result = this._getMaxAndMin(arrayData); - var min = result[0]; - var max = result[1]; - - var offset = ( min <= 0 ) ? Math.abs(min) : (-1 * min); - var resultArray = new Array(); - for (var i = 0; i< arrayData.length; i++) { - if(max + offset!=0){ - resultArray.push((arrayData[i] + offset) / (max + offset)); - }else{ - resultArray.push(arrayData[i]+offset); - } - } - return resultArray; - }; - - - this._getMean = function(arrayData) { - var sum = 0; - for (var i = 0; i< arrayData.length; i++) { - sum = sum + parseFloat(arrayData[i]); - } - return sum/arrayData.length; - }; - - this._getStdDeviation = function(arrayData) { - var mean = this._getMean(arrayData); - var acum = 0.0; - for(var i=0; i max) max = parseFloat(arrayData[i]); - } - - return [min, max]; - }; -}; -function GraphCanvas(componentID, targetNode, args) { - this.args = {}; - /** target */ - this.targetID = targetNode.id; - - /** id manage */ - this.id = componentID; - this.args.idGraph = this.id + "main"; - this.args.idBackgroundNode = this.id + "background"; - - this.args.idEdgesGraph = this.id + "edges"; - this.args.idNodesGraph = this.id + "vertices"; - this.args.idLabelGraph = this.id + "label"; - this.args.idBackground = this.id + "background"; - - /** Objects Graph **/ - this.dataset = null; - this.formatter = null; - this.layout = null; - - /** Drawing **/ - this.circleDefaultRadius = 2; - this.squareDefaultSide = this.circleDefaultRadius * 1.5; - - /** Directed Arrow **/ - this.arrowDefaultSize = this.circleDefaultRadius; - - /** Groups **/ - this.GraphGroup = null; - this.GraphNodeGroup = null; - this.GraphLabelGroup = null; - this.GraphBackground = null; - - /** SETTINGS FLAGS **/ - this.args.draggingCanvasEnabled = false; //Flag to set if the canvas can be dragged - this.args.multipleSelectionEnabled = false; - this.args.interactive = false; - this.args.labeled = false; - this.args.linkEnabled = false; - - /** If numberEdge > maxNumberEdgesMoving then only it will move edges when mouse up **/ - this.args.maxNumberEdgesMoving = 3; - this.args.maxNumberEdgesFiringEvents = 50; - - /** Linking edges **/ - this.args.linking = false; - this.linkStartX = 0; - this.linkStartY = 0; - this.linkSVGNode = null; - this.linkNodeSource = null; - this.linkNodeTarget = null; - - /** Dragging Control **/ - this.draggingElement = null; - this.dragging = false; - this.nMouseOffsetX = 0; - this.nMouseOffsetY = 0; - this.dragStartX = 0; - this.dragStartY = 0; - this.desplazamientoX = 0; - this.desplazamientoY = 0; - - /** Selection Control **/ - this.selecting = false; - this.selectorX = null; - this.selectorY = null; - this.selectorSVGNode = null; - - /** Node status **/ - this.args.isVertexSelected = {}; - this.args.selectedVertices = []; - - /** Edges status **/ - this.args.isEdgeSelected = {}; - //this.args.selectedEdges = []; - - if (args != null) { - if (args.multipleSelectionEnabled != null) { - this.args.multipleSelectionEnabled = args.multipleSelectionEnabled; - this.args.draggingCanvasEnabled = !(this.args.multipleSelectionEnabled); - } - if (args.draggingCanvasEnabled != null) { - this.args.draggingCanvasEnabled = args.draggingCanvasEnabled; - this.args.multipleSelectionEnabled = !(this.args.draggingCanvasEnabled); - } - if (args.interactive != null) { - this.args.interactive = args.interactive; - } - if (args.labeled != null) { - this.args.labeled = args.labeled; - } - - } - - /** Hashmap with the svg node labels **/ - this.svgLabels = {}; - - /** EVENTS **/ - this.onVertexOut = new Event(this); - this.onVertexOver = new Event(this); - this.onVertexSelect = new Event(this); - this.onEdgeSelect = new Event(this); - this.onCanvasClicked = new Event(this); - this.onVertexUp = new Event(this); -} - -GraphCanvas.prototype.showLabels = function(value) { - this.args.labeled = value; - this.removeLabels(); - if (value) { - this.renderLabels(); - } -}; - -GraphCanvas.prototype.getSelectedVertices = function() { - return this.args.selectedVertices; -}; - -GraphCanvas.prototype.getSelectedEdges = function() { - var selected = []; - for ( var selectedEdge in this.args.isEdgeSelected) { - selected.push(selectedEdge); - } - return selected; -}; - -GraphCanvas.prototype.createSVGDom = function(targetID, id, width, height, backgroundColor) { - var container = document.getElementById(targetID); - this._svg = SVG.createSVGCanvas(container, [ - [ "style", "background-color:" + backgroundColor + ";" ], [ "id", id ], [ "dragx", 0 ], [ "dragy", 0 ], - [ "height", this.getFormatter().getHeight() ], [ "width", this.getFormatter().getWidth() ] ]); - return this._svg; -}; - -/** MULTIPLE SELECTION **/ -GraphCanvas.prototype.isMultipleSelectionEnabled = function() { - return this.args.multipleSelectionEnabled; -}; - -GraphCanvas.prototype.setMultipleSelection = function(value) { - this.args.multipleSelectionEnabled = value; - this.args.draggingCanvasEnabled = (!value); -}; - -GraphCanvas.prototype.setSelecting = function(value) { - this.selecting = value; -}; - -/** linking **/ -GraphCanvas.prototype.setLinking = function(value) { - this.args.linkEnabled = value; - this.selecting = !value; - this.dragging = !value; -}; - -/** CANVAS MOVING **/ -GraphCanvas.prototype.setDraggingCanvas = function(value) { - this.args.draggingCanvasEnabled = value; - this.args.multipleSelectionEnabled = !value; -}; - -GraphCanvas.prototype.isDraggingCanvasEnabled = function() { - return this.args.draggingCanvasEnabled; -}; -/** ZOOM **/ -GraphCanvas.prototype.getScale = function() { - return this.getFormatter().getZoomScale(); -}; - -GraphCanvas.prototype.setScale = function(scale) { - var graphNode = document.getElementById(this.args.idGraph); - graphNode.setAttribute("transform", graphNode.getAttribute("transform").replace("scale(" + this.getScale() + ")", "scale(" + scale + ")")); - this.getFormatter().setZoomScale(scale); -}; - -GraphCanvas.prototype.zoomIn = function() { - this.setScale(this.getScale() + this.getFormatter().getZoomScaleStepFactor()); -}; - -GraphCanvas.prototype.zoomOut = function() { - this.setScale(this.getScale() - this.getFormatter().getZoomScaleStepFactor()); - -}; - -/** SVG COORDENATES **/ -GraphCanvas.prototype.getSVGCoordenates = function(evt) { - var p = this._svg.createSVGPoint(); - p.x = evt.clientX; - p.y = evt.clientY; - - var m = this._svg.getScreenCTM(document.documentElement); - p = p.matrixTransform(m.inverse()); - return p; -}; - -/** SVG EVENTS **/ -GraphCanvas.prototype.mouseClick = function(event) { - if (event.button == 0) { - if (!this.args.interactive) { - return; - } - - if (this.isVertex(event.target)) { - this.clickNode(this.getVertexIdFromSVGId(event.target.id)); - } - /** Como el evento mouseClick viene despues del mouse up es aqui donde manejo el tema de deseccionar los elementos que estoy dragging **/ - if (this.dragging) { - this.dragging = false; - } - } -}; - -GraphCanvas.prototype.mouseMove = function(evt) { - if (this.selecting) { - this.clearLabels(); - - var width = (this.getSVGCoordenates(evt).x - this.selectorX); - var height = (this.getSVGCoordenates(evt).y - this.selectorY); - if ((width > 0) && (height > 0)) { - this.displaySelection(this.selectorX, this.selectorY, width, height); - } - if ((width > 0) && (height < 0)) { - this.displaySelection(this.selectorX, this.getSVGCoordenates(evt).y, width, Math.abs(height)); - } - if ((width < 0) && (height < 0)) { - this.displaySelection(this.getSVGCoordenates(evt).x, this.getSVGCoordenates(evt).y, Math.abs(width), Math.abs(height)); - } - if ((width < 0) && (height > 0)) { - this.displaySelection(this.selectorX + width, this.selectorY, Math.abs(width), Math.abs(height)); - } - - var x1 = (parseFloat(this.selectorSVGNode.getAttribute("x")) - DOM.select(this.id).getAttribute("dragx")) / this.getFormatter().getWidth(); - var y1 = (parseFloat(this.selectorSVGNode.getAttribute("y")) - DOM.select(this.id).getAttribute("dragy")) / this.getFormatter().getHeight(); - var x2 = (x1 + parseFloat(this.selectorSVGNode.getAttribute("width") / this.getFormatter().getWidth())); - var y2 = (y1 + parseFloat(this.selectorSVGNode.getAttribute("height") / this.getFormatter().getHeight())); - - this.deselectNodes(this.getLayout()); - var verticesSelected = this.getLayout().getVerticesByArea(x1 / this.getFormatter().getZoomScale(), y1 / this.getFormatter().getZoomScale(), - x2 / this.getFormatter().getZoomScale(), y2 / this.getFormatter().getZoomScale()); - for ( var i = 0; i < verticesSelected.length; i++) { - this.selectNode(verticesSelected[i].getId()); - this.renderLabel(verticesSelected[i].getId()); - } - - } - var p = null; - if (this.args.linking) { - p = this.getSVGCoordenates(evt); - if (this.linkSVGNode != null) { - this.linkSVGNode.setAttribute("x2", p.x - 2); - this.linkSVGNode.setAttribute("y2", p.y - 2); - } - } - - if (this.dragging) { - p = this.getSVGCoordenates(evt); - p.x -= this.nMouseOffsetX; - p.y -= this.nMouseOffsetY; - this.desplazamientoX = (this.getSVGCoordenates(evt).x - this.dragStartX);// + parseFloat(DOM.select(this.id).getAttribute("dragx")); - this.desplazamientoY = (this.getSVGCoordenates(evt).y - this.dragStartY);// + parseFloat(DOM.select(this.id).getAttribute("dragy")); - - if (this.draggingElement != null) { - /** Click sobre el recct del banground que provoca que mueva todo el canvas **/ - if (this.isNodeCanvas(this.draggingElement)) { - - p = this.getSVGCoordenates(evt); - p.x = this.desplazamientoX; - p.y = this.desplazamientoY; - - this.draggingElement.setAttribute("dragx", p.x); - this.draggingElement.setAttribute("dragy", p.y); - this.draggingElement = document.getElementById(this.args.idGraph); - this.draggingElement.setAttribute("transform", "translate(" + p.x + "," + p.y + "), scale(" + this.getScale() + ")"); - - DOM.select(this.id).setAttribute("dragx", p.x); - DOM.select(this.id).setAttribute("dragy", p.y); - - if (this.NodeSVGbackgroundImage != null) { - this.NodeSVGbackgroundImage.setAttribute("dragx", p.x); - this.NodeSVGbackgroundImage.setAttribute("dragy", p.y); - } - } else { - if (this.isVertex(this.draggingElement)) { - this.selectNode(this.getVertexIdFromSVGId(this.draggingElement.id)); - this.desplazamientoX = this.desplazamientoX / this.getFormatter().getZoomScale(); - this.desplazamientoY = this.desplazamientoY / this.getFormatter().getZoomScale(); - this.moveSelectedNodes(this.desplazamientoX, this.desplazamientoY); - - this.dragStartX = this.getSVGCoordenates(evt).x; - this.dragStartY = this.getSVGCoordenates(evt).y; - } else { - if (this.isNodeBackground(this.draggingElement)) { - - this.draggingElement.setAttribute("dragx", p.x); - this.draggingElement.setAttribute("dragy", p.y); - this.draggingElement = document.getElementById(this.args.idGraph); - this.draggingElement.setAttribute("transform", "translate(" + p.x + "," + p.y + "), scale(" + this.getScale() + ")"); - } else { - this.draggingElement.setAttribute("transform", "translate(" + p.x + "," + p.y + ")"); - } - } - } - } - } -}; - -GraphCanvas.prototype.moveSelectedNodes = function(offsetX, offsetY) { - for ( var i = 0; i < this.getSelectedVertices().length; i++) { - - var nodeId = this.getSelectedVertices()[i]; - var svgNodeId = this.getSVGNodeId(nodeId); - - var x = parseFloat(DOM.select(svgNodeId).getAttribute("dragx")) + parseFloat(offsetX);// - parseFloat(DOM.select(this.id).getAttribute("dragx")); - var y = parseFloat(DOM.select(svgNodeId).getAttribute("dragy")) + parseFloat(offsetY);// + parseFloat(DOM.select(this.id).getAttribute("dragy")); - - this._movingNode(DOM.select(svgNodeId), x, y); - } -}; - -GraphCanvas.prototype.mouseDown = function(evt) { - if (event.button == 0) { - - /** if !no interactive mouse events do anything **/ - if (!this.args.interactive) { - return; - } - - var p = this.getSVGCoordenates(evt); - - /** When click on canvas or background deselect all **/ - if (this.isNodeCanvas(evt.target) || this.isNodeBackground(evt.target)) { - this.deselectNodes(); - this.deselectEdges(); - this.onCanvasClicked.notify(); - } - - /** if I am linking vertices **/ - if (this.args.linkEnabled) { - - if (!this.args.linking) { - this.args.linking = true; - if (this.isVertex(evt.target)) { - this.linkStartX = p.x; - this.linkStartY = p.y; - this.linkSVGNode = SVG.drawLine(p.x, p.y, p.x, p.y, this._svg, { - "stroke" : "#FF0000" - }); - this.linkNodeSource = this.getVertexIdFromSVGId(evt.target.id); - } - } else { - this.linkNodeTarget = this.getVertexIdFromSVGId(evt.target.id); - this.args.linking = false; - this.args.linkEnabled = false; - if (this.isVertex(evt.target)) { - this.getDataset().addEdge(this.linkNodeSource + "_" + this.linkNodeTarget, this.linkNodeSource, this.linkNodeTarget, {}); - } - this.linkSVGNode.parentNode.removeChild(this.linkSVGNode); - } - return; - } - - /** Id is a vertex or the canvas **/ - if (this.isVertex(evt.target) || this.isNodeCanvas(evt.target) || this.isNodeBackground(evt.target)) { - this._startDragging(evt); - } - /** if i is edge **/ - if (this.isEdge(evt.target)) { - this.selectEdge(this.getEdgeIdFromSVGId(evt.target.getAttribute("id"))); - } - - if (this.args.multipleSelectionEnabled) { - if (!this.dragging) { - this.setSelecting(true); - this.selectorX = p.x; - this.selectorY = p.y; - this.displaySelection(p.x, p.y, 1, 1); - } - } - - } - if (event.button == 1) { - this.setLinking(false); - this.setMultipleSelection(false); - this.selecting = false; - - /** Id is a vertex or the canvas **/ - if (this.isVertex(evt.target) || this.isNodeCanvas(evt.target) || this.isNodeBackground(evt.target)) { - this._startDragging(evt); - } - } -}; - -GraphCanvas.prototype.mouseUp = function(event) { - if (!this.args.interactive) { - return; - } - - if (this.dragging) { - this._stopDragging(event); - if (this.isVertex(event.target)) { - var vertexId = this.getVertexIdFromSVGId(event.target.id); - if (this.getDataset().getVertexById(vertexId).getEdges().length >= this.args.maxNumberEdgesMoving) { - this.moveEdge(vertexId); - } - } - } - - if (this.selecting) { - this.setSelecting(false); - - var x1 = (parseFloat(this.selectorSVGNode.getAttribute("x")) - DOM.select(this.id).getAttribute("dragx")) / this.getFormatter().getWidth(); - var y1 = (parseFloat(this.selectorSVGNode.getAttribute("y")) - DOM.select(this.id).getAttribute("dragy")) / this.getFormatter().getHeight(); - var x2 = (x1 + parseFloat(this.selectorSVGNode.getAttribute("width") / this.formatter.getWidth())); - var y2 = (y1 + parseFloat(this.selectorSVGNode.getAttribute("height") / this.formatter.getHeight())); - - var verticesSelected = this.getLayout().getVerticesByArea(x1 / this.getFormatter().getZoomScale, y1 / this.getFormatter().getZoomScale, - x2 / this.getFormatter().getZoomScale, y2 / this.getFormatter().getZoomScale); - - for ( var i = 0; i < verticesSelected.length; i++) { - this.selectNode(verticesSelected[i].getId()); - } - - if (this.selectorSVGNode != null) { - this._svg.removeChild(this.selectorSVGNode); - } - - if (this.args.labeled) { - this.clearLabels(); - this.renderLabels(); - } - - this.selectorSVGNode = null; - // this.renderLabels(); - } -}; - -/** SELECTION **/ -GraphCanvas.prototype.displaySelection = function(x, y, width, height) { - if (this.selectorSVGNode != null) { - this.selectorSVGNode.setAttribute("x", x); - this.selectorSVGNode.setAttribute("y", y); - this.selectorSVGNode.setAttribute("width", width); - this.selectorSVGNode.setAttribute("height", height); - } else { - this.selectorSVGNode = SVG.drawRectangle(x, y, width, height, this._svg, { - "fill" : "red", - "stroke" : "black", - "opacity" : "0.2", - "stroke-opacity" : "1" - }); - } -}; - -/** DRAGGING **/ -GraphCanvas.prototype._startDragging = function(evt) { - if (!this.isDraggingCanvasEnabled()) { - if (this.isNodeCanvas(evt.target)) { - this.draggingElement = null; - } - } - - if (this.isVertex(evt.target) || (this.isNodeBackground(evt.target) && (this.isDraggingCanvasEnabled()))|| (this.isNodeCanvas(evt.target) && (this.isDraggingCanvasEnabled()))) { - this.clearLabels(); - this.draggingElement = evt.target; - this.dragging = true; - var p = this.getSVGCoordenates(evt); - - this.nMouseOffsetX = p.x - parseInt(evt.target.getAttribute("dragx")); - this.nMouseOffsetY = p.y - parseInt(evt.target.getAttribute("dragy")); - - if (this.isVertex(evt.target)) { - this.dragStartX = parseInt(this.draggingElement.getAttribute("dragx")) * this.getFormatter().getZoomScale() - + parseFloat(DOM.select(this.id).getAttribute("dragx")); - this.dragStartY = parseInt(this.draggingElement.getAttribute("dragy")) * this.getFormatter().getZoomScale() - + parseFloat(DOM.select(this.id).getAttribute("dragy")); - } else { - this.dragStartX = p.x - parseInt(this.draggingElement.getAttribute("dragx"));// + parseFloat(DOM.select(this.id).getAttribute("dragx")); - this.dragStartY = p.y - parseInt(this.draggingElement.getAttribute("dragy"));// + parseFloat(DOM.select(this.id).getAttribute("dragy")); - } - } -}; - -GraphCanvas.prototype._stopDragging = function(event) { - this.nMouseOffsetX = 0; - this.nMouseOffsetX = 0; - /** despues del evento up viene el evento click entonces acabo el dragging en el mouseclick **/ - this.dragging = false; - this.draggingElement = null; - this.renderLabels(); - - this.setLinking(false); - this.setMultipleSelection(true); - this.selecting = false; - -}; - -/** Move the edges of the vertex with the vertexId indicado **/ -GraphCanvas.prototype.moveEdge = function(vertexId) { - var x = this.getLayout().getNodeById(vertexId).x * this.getFormatter().getWidth(); - var y = this.getLayout().getNodeById(vertexId).y * this.getFormatter().getHeight(); - - /** Moving edges out **/ - for ( var i = 0; i < this.getDataset().getVertexById(vertexId).getEdgesOut().length; i++) { - var edgeId = this.getDataset().getVertexById(vertexId).getEdgesOut()[i].getId(); - var svgEdgeId = this.getSVGEdgeId(edgeId); - var edgeFormatter = this.getFormatter().getEdgeById(edgeId); - if (edgeFormatter instanceof LineEdgeGraphFormatter) { - DOM.select(svgEdgeId + "_shadow").setAttribute("x2", x); - DOM.select(svgEdgeId + "_shadow").setAttribute("y2", y); - DOM.select(svgEdgeId).setAttribute("x2", x); - DOM.select(svgEdgeId).setAttribute("y2", y); - } - - if ((edgeFormatter instanceof DirectedLineEdgeGraphFormatter) || (edgeFormatter instanceof OdirectedLineEdgeGraphFormatter) - || (edgeFormatter instanceof OdotDirectedLineEdgeGraphFormatter) || (edgeFormatter instanceof DotDirectedLineEdgeGraphFormatter) - || (edgeFormatter instanceof CutDirectedLineEdgeGraphFormatter)) { - this.removeEdge(edgeId); - this.renderEdge(edgeId); - } - } - - /** Moving edges in **/ - for ( var i = 0; i < this.getDataset().getVertexById(vertexId).getEdgesIn().length; i++) { - var edgeId = this.getDataset().getVertexById(vertexId).getEdgesIn()[i].getId(); - var svgEdgeId = this.getSVGEdgeId(edgeId); - var edgeFormatter = this.getFormatter().getEdgeById(edgeId); - if (edgeFormatter instanceof LineEdgeGraphFormatter) { - DOM.select(svgEdgeId).setAttribute("x1", x); - DOM.select(svgEdgeId).setAttribute("y1", y); - DOM.select(svgEdgeId + "_shadow").setAttribute("x1", x); - DOM.select(svgEdgeId + "_shadow").setAttribute("y1", y); - } - - if ((edgeFormatter instanceof DirectedLineEdgeGraphFormatter) || (edgeFormatter instanceof OdirectedLineEdgeGraphFormatter) - || (edgeFormatter instanceof OdotDirectedLineEdgeGraphFormatter) || (edgeFormatter instanceof DotDirectedLineEdgeGraphFormatter) - || (edgeFormatter instanceof CutDirectedLineEdgeGraphFormatter)) { - this.removeEdge(edgeId); - this.renderEdge(edgeId); - } - - if (edgeFormatter instanceof BezierEdgeGraphFormatter) { - var radius = this.getFormatter().getVertexById(vertexId).getDefault().getSize() * this.getFormatter().getNodesMaxSize(); - var d = this.calculateCoordenatesBezier(radius, x, y); - DOM.select(svgEdgeId).setAttribute("d", d); - } - } -}; - -GraphCanvas.prototype.moveNode = function(vertexId) { - var x = this.getLayout().getNodeById(vertexId).x * this.getFormatter().getWidth(); - var y = this.getLayout().getNodeById(vertexId).y * this.getFormatter().getHeight(); - var svgNodeElement = DOM.select(this.getSVGNodeId(vertexId)); - - svgNodeElement.setAttribute("dragx", x); - svgNodeElement.setAttribute("dragy", y); - svgNodeElement.setAttribute("transform", "translate(" + x + "," + y + ")"); - - if (this.getDataset().getVertexById(vertexId).getEdges().length < this.args.maxNumberEdgesMoving) { - this.moveEdge(vertexId); - } -}; - -GraphCanvas.prototype._movingNode = function(svgNodeElement, x, y) { - var vertexId = this.getVertexIdFromSVGId(svgNodeElement.getAttribute("id")); - this.getLayout().getNodeById(vertexId).setCoordinates(x / this.getFormatter().getWidth(), y / this.getFormatter().getHeight()); - this.desplazamientoX = 0; - this.desplazamientoY = 0; - this.removeLabel(vertexId); - this.renderLabel(vertexId); -}; - -/** INIT **/ -GraphCanvas.prototype.init = function() { - - this._svg = this.createSVGDom(this.targetID, this.id, this.getFormatter().getWidth(), this.getFormatter().getHeight(), this.getFormatter() - .getBackgroundColor()); - this.GraphGroup = SVG.drawGroup(this._svg, [ [ "id", this.args.idGraph ], [ "transform", "translate(0,0), scale(1)" ] ]); - this.GraphBackground = SVG.drawGroup(this.GraphGroup, [ [ "id", this.args.idBackground ] ]); - this.GraphEdgeGroup = SVG.drawGroup(this.GraphGroup, [ [ "id", this.args.idEdgesGraph ] ]); - this.GraphNodeGroup = SVG.drawGroup(this.GraphGroup, [ [ "id", this.args.idNodesGraph ] ]); - this.GraphLabelGroup = SVG.drawGroup(this.GraphGroup, [ [ "id", this.args.idLabelGraph ] ]); - - if ((this.getFormatter().getBackgroundImage() != null) && (this.getFormatter().getBackgroundImage() != "")) { - this.setBackgroundImage(this.getFormatter().getBackgroundImage()); - } - /** SVG Events listener */ - var _this = this; - this._svg.addEventListener("click", function(event) { - _this.mouseClick(event); - }, false); - this._svg.addEventListener("mousemove", function(event) { - _this.mouseMove(event, _this); - }, false); - this._svg.addEventListener("mousedown", function(event) { - _this.mouseDown(event, _this); - }, false); - this._svg.addEventListener("mouseup", function(event) { - _this.mouseUp(event, _this); - }, false); -}; - -/* - GraphCanvas.prototype.backgroungToSVG = function(){ - var _this = this; - var canvas = document.createElement('canvas'); - canvas.setAttribute("id", "canvas"); - canvas.width = this.formatter.getWidth(); - canvas.height = this.formatter.getHeight(); - - this._svg.parentNode.parentNode.appendChild(canvas); - var ctx = document.getElementById('canvas').getContext('2d'); - var img = new Image(); - - img.src = this.formatter.getBackgroundImage(); - ctx.drawImage(img,0,0 ,_this.formatter.getWidth(), _this.formatter.getHeight()); - - - img.onload = function() { - canvas.parentNode.removeChild(canvas); - } - - this.NodeSVGbackgroundImage.setAttribute("xlink:href", document.getElementById("canvas").toDataURL()); - this.NodeSVGbackgroundImage.removeAttribute("href"); - - // - - };*/ - -GraphCanvas.prototype.setBackgroundImage = function() { - if (this.NodeSVGbackgroundImage != null) { - this.NodeSVGbackgroundImage.parentNode.removeChild(this.NodeSVGbackgroundImage); - } - $('#' + this.targetID).svg(); - $('#' + this.targetID).svg("get"); - - $('#' + this.targetID).svg("get")._svg = document.getElementById(this.id); - - var svg = $('#' + this.targetID).svg("get"); - this.NodeSVGbackgroundImage = svg.image(0, 0, this.getFormatter().getWidth(), this.getFormatter().getHeight(), this.getFormatter() - .getBackgroundImage()); - this.NodeSVGbackgroundImage.setAttribute("id", this.args.idBackgroundNode); - - this.NodeSVGbackgroundImage.setAttribute("x", 0); - this.NodeSVGbackgroundImage.setAttribute("y", 0); - - this.NodeSVGbackgroundImage.setAttribute("dragx", 0); - this.NodeSVGbackgroundImage.setAttribute("dragy", 0); - - if (this.getFormatter().args.backgroundImageHeight != null) { - this.NodeSVGbackgroundImage.setAttribute("height", this.getFormatter().args.backgroundImageHeight); - } - if (this.getFormatter().args.backgroundImageWidth != null) { - this.NodeSVGbackgroundImage.setAttribute("width", this.getFormatter().args.backgroundImageWidth); - } - - if (this.getFormatter().args.backgroundImageX != null) { - this.NodeSVGbackgroundImage.setAttribute("x", this.getFormatter().args.backgroundImageX); - } - if (this.getFormatter().args.backgroundImageY != null) { - this.NodeSVGbackgroundImage.setAttribute("y", this.getFormatter().args.backgroundImageY); - } - - this.GraphBackground.appendChild(this.NodeSVGbackgroundImage); - this.NodeSVGbackgroundImage.removeAttribute("href"); - this.NodeSVGbackgroundImage.setAttribute("xlink:href", this.getFormatter().getBackgroundImage()); -}; - -GraphCanvas.prototype.removeBackgroundImage = function() { - if (this.NodeSVGbackgroundImage != null) { - this.NodeSVGbackgroundImage.parentNode.removeChild(this.NodeSVGbackgroundImage); - } -}; - -GraphCanvas.prototype._setBackgroundColor = function(color) { - var attributes = [ [ "fill", color ] ]; - SVG.drawRectangle(0, 0, this.getFormatter().getWidth(), this.getFormatter().getHeight(), this.GraphBackground, attributes); -}; - -/** Serialize **/ -GraphCanvas.prototype.toJSON = function() { - var json = {}; - json.dataset = {}; - json.formatter = {}; - json.layout = {}; - json.dataset = this.getDataset().toJSON(); - json.formatter = this.getFormatter().toJSON(); - json.layout = this.getLayout().toJSON(); - return json; -}; - -GraphCanvas.prototype.toHTML = function() { - //this.backgroungToSVG(); - var html = this._svg.parentElement.innerHTML; - - var start = html.indexOf("") + 6; - - return html.substr(start, end); -}; - -/** DRAW **/ -GraphCanvas.prototype.draw = function(graphdataset, graphformatter, graphlayout) { - this.setDataset(graphdataset); - this.setFormatter(graphformatter); - this.setLayout(graphlayout); - - var _this = this; - this.getFormatter().changed.attach(function(sender, item) { - _this.removeNode(item.getId()); - _this.renderNode(item.getId()); - if (_this.args.labeled) { - _this.removeLabel(item.getId()); - _this.renderLabel(item.getId()); - } - - }); - //TODO - this.getFormatter().edgeChanged.attach(function(sender, item) { - _this.removeEdge(item.getId()); - _this.renderEdge(item.getId()); - }); - - this.getFormatter().resized.attach(function(sender, item) { - _this.resize(_this.getFormatter().getWidth(), _this.getFormatter().getHeight()); - }); - - this.getFormatter().backgroundImageChanged.attach(function(sender, item) { - _this.setBackgroundImage(_this.getFormatter().getBackgroundImage()); - }); - - this.getFormatter().backgroundColorChanged.attach(function(sender, item) { - _this._setBackgroundColor(_this.getFormatter().getBackgroundColor()); - }); - - this.getLayout().changed.attach(function(sender, item) { - _this.moveNode(item.getId()); - _this.moveEdge(item.getId()); - if (_this.args.labeled) { - _this.removeLabel(item.getId()); - _this.renderLabel(item.getId()); - } - }); - - this.getDataset().newVertex.attach(function(sender, item) { - - _this.renderNode(item.getId()); - if (_this.args.labeled) { - _this.renderLabel(item.getId()); - } - }); - - this.getDataset().newEdge.attach(function(sender, item) { - _this.renderEdge(item.getId()); - }); - - this.getDataset().vertexDeleted.attach(function(sender, item) { - _this.removeNode(item.getId()); - if (_this.args.labeled) { - _this.removeLabel(item.getId()); - } - }); - - this.getDataset().edgeDeleted.attach(function(sender, item) { - _this.removeEdge(item.getId()); - }); - - this.getDataset().vertexNameChanged.attach(function(sender, args) { - if (_this.args.labeled) { - _this.removeLabel(args.item.getId()); - _this.removeLabel(args.item.getId()); - _this.renderLabel(args.item.getId()); - } - }); - this.init(); - this.render(); -}; - -GraphCanvas.prototype.render = function() { - for ( var id in this.getDataset().getVertices()) { - this.renderNode(id); - } - this.renderLabels(); - this.renderEdges(); -}; - -GraphCanvas.prototype.renderLabels = function() { - if (this.args.labeled) { - for ( var id in this.getDataset().getVertices()) { - this.renderLabel(id); - } - } -}; - -GraphCanvas.prototype.removeLabels = function() { - for ( var id in this.getDataset().getVertices()) { - this.removeLabel(id); - } -}; - -/** Utilities method for nodes **/ -GraphCanvas.prototype.isNodeCanvas = function(node) { - return ((node.id == this.args.idGraph) || (node.id == this.id)); -}; - -GraphCanvas.prototype.isNodeBackground = function(node) { - return ((node.id == this.args.idBackgroundNode)); -}; - -GraphCanvas.prototype.isVertex = function(node) { - if (node.getAttribute("id") != null) { - if (node.getAttribute("id").indexOf("_v_") != -1) { - return true; - } - } - return false; -}; - -GraphCanvas.prototype.isLabel = function(node) { - if (node.getAttribute("id") != null) { - if (node.getAttribute("id").indexOf("_l_") != -1) { - return true; - } - } - return false; -}; - -GraphCanvas.prototype.isEdge = function(node) { - if (node.getAttribute("id") != null) { - if (node.getAttribute("id").indexOf("_e_") != -1) { - return true; - } - } - return false; -}; - -/** Resize **/ -GraphCanvas.prototype.resize = function(width, height) { - // this._svg.setAttribute("width", width); - // this._svg.setAttribute("height", height); - if (this.NodeSVGbackgroundImage != null) { - this.NodeSVGbackgroundImage.setAttribute("width", width); - this.NodeSVGbackgroundImage.setAttribute("height", height); - } - - this._svg.setAttribute("width", width); - this._svg.setAttribute("height", height); - - this.clearCanvas(); - this.render(); -}; - -GraphCanvas.prototype.clearCanvas = function() { - DOM.removeChilds(this.GraphEdgeGroup.getAttribute("id")); - DOM.removeChilds(this.GraphNodeGroup.getAttribute("id")); - this.clearLabels(); -}; - -GraphCanvas.prototype.clearLabels = function() { - DOM.removeChilds(this.GraphLabelGroup.getAttribute("id")); -}; - -/** ID'S converter **/ -GraphCanvas.prototype.getSVGNodeId = function(nodeId) { - return this.id + "_v_" + nodeId; -}; - -GraphCanvas.prototype.getSVGEdgeId = function(edgeId) { - return this.id + "_e_" + edgeId; -}; - -GraphCanvas.prototype.getSVGArrowEdgeId = function(edgeId) { - return this.id + "_arrow_" + edgeId; -}; - -GraphCanvas.prototype.getSVGLabelId = function(edgeId) { - return this.id + "_l_" + edgeId; -}; - -GraphCanvas.prototype.blinkVertexById = function(vertexId) { - $("#" + this.getSVGNodeId(vertexId)).fadeIn().fadeOut().fadeIn().fadeOut().fadeIn().fadeOut(); -}; - -GraphCanvas.prototype.getVertexIdFromSVGId = function(svgVertexId) { - return svgVertexId.replace(this.id, "").replace("_v_", ""); -}; - -GraphCanvas.prototype.getEdgeIdFromSVGId = function(svgEdgeId) { - return svgEdgeId.replace(this.id, "").replace("_e_", ""); -}; - -/** VERTEX **/ -GraphCanvas.prototype.getVertexById = function(id) { - return document.getElementById(this.getSVGNodeId(id)); -}; - -GraphCanvas.prototype.renderNodes = function() { - for ( var id in this.getDataset().getVertices()) { - this.renderNode(id); - } -}; - -GraphCanvas.prototype.overNode = function(nodeId) { - if (!this.args.interactive) { - return; - } - /** If selected we don't change the format **/ - if (this.args.isVertexSelected[nodeId] == null) { - var args = this.getFormatter().getVertexById(nodeId).getOver(); - args.args["cursor"] = 'pointer'; - this.changeVertexFormat(nodeId, args); - } -}; - -GraphCanvas.prototype.outNode = function(nodeId) { - if (!this.args.interactive) { - return; - } - - /** If selected we don't change the format **/ - if (this.args.isVertexSelected[nodeId] == null) { - this.changeVertexFormat(nodeId, this.getFormatter().getVertexById(nodeId).getDefault()); - } -}; - -GraphCanvas.prototype.overLabel = function(nodeId) { - this.overNode(nodeId); - // this.svgLabels[nodeId].setAttribute("cursor", "pointer"); -}; - -GraphCanvas.prototype.outLabel = function(nodeId) { - this.outNode(nodeId); - // this.svgLabels[nodeId].setAttribute("cursor", ""); -}; - -GraphCanvas.prototype.clickNode = function(nodeId) { - if (!this.args.interactive) { - return; - } - - /** si el evento se dispara oprque estaba dragging entonces no activo nada **/ - if (this.args.isVertexSelected[nodeId] == null) { - this.selectNode(nodeId); - } else { - this.deselectNode(nodeId); - } -}; - -GraphCanvas.prototype.selectNode = function(nodeId) { - for ( var i = 0; i < this.args.selectedVertices.length; i++) { - var format = this.getFormatter().getVertexById(nodeId).getSelected(); - format.opacity = 0.2; - this.changeVertexFormat(nodeId, this.getFormatter().getVertexById(nodeId).getSelected()); - } - - if (this.args.isVertexSelected[nodeId] == null) { - var format = this.getFormatter().getVertexById(nodeId).getSelected(); - format.opacity = 1; - this.changeVertexFormat(nodeId, this.getFormatter().getVertexById(nodeId).getSelected()); - this.args.selectedVertices.push(nodeId); - this.args.isVertexSelected[nodeId] = this.args.selectedVertices.length - 1; - this.onVertexSelect.notify(nodeId); - } -}; - -GraphCanvas.prototype.selectAllEdges = function() { - this.deselectNodes(); - this.deselectEdges(); - - for ( var edgesId in this.getDataset().edges) { - this.selectEdge(edgesId); - } -}; - -GraphCanvas.prototype.selectAllNodes = function() { - this.deselectNodes(); - this.deselectEdges(); - - for ( var vertexId in this.getDataset().vertices) { - this.selectNode(vertexId); - } -}; - -GraphCanvas.prototype.selectAll = function() { - this.deselectNodes(); - this.deselectEdges(); - - for ( var vertexId in this.getDataset().vertices) { - this.selectNode(vertexId); - } - - for ( var edgesId in this.getDataset().edges) { - this.selectEdge(edgesId); - } -}; - -GraphCanvas.prototype.selectEdge = function(edgeId) { - if (this.args.isEdgeSelected[edgeId] == null) { - this.changeEdgeFormat(edgeId, this.getFormatter().getEdgeById(edgeId).getSelected()); - //this.args.selectedEdges.push(edgeId); - this.args.isEdgeSelected[edgeId] = true; //this.args.selectedEdges.length - 1; - this.onEdgeSelect.notify(edgeId); - } -}; - -GraphCanvas.prototype.selectEdges = function(edges) { - - for ( var i = 0; i < edges.length; i++) { - this.selectEdge(edges[i]); - } -}; - -GraphCanvas.prototype.deselectNode = function(nodeId) { - if (this.args.isVertexSelected[nodeId] != null) { - this.changeVertexFormat(nodeId, this.getFormatter().getVertexById(nodeId).getDefault()); - this.args.selectedVertices.splice(this.args.isVertexSelected[nodeId], 1); - var index = this.args.isVertexSelected[nodeId]; - delete this.args.isVertexSelected[nodeId]; - - for ( var vertex in this.args.isVertexSelected) { - if (this.args.isVertexSelected[vertex] > index) { - this.args.isVertexSelected[vertex] = this.args.isVertexSelected[vertex] - 1; - } - } - } -}; - -GraphCanvas.prototype.deselectNodes = function() { - var selected = JSON.parse(JSON.stringify(this.getSelectedVertices())); - for ( var i = 0; i < selected.length; i++) { - this.deselectNode(selected[i]); - } -}; -GraphCanvas.prototype.selectNodes = function(idNodes) { - - for ( var i = 0; i < idNodes.length; i++) { - this.selectNode(idNodes[i]); - } - - // for ( var vertex in this.args.isVertexSelected) { - // if (this.args.isVertexSelected[vertex] > index){ - // this.args.isVertexSelected[vertex] = this.args.isVertexSelected[vertex] - 1; - // } - // } - -}; - -GraphCanvas.prototype.changeVertexFormat = function(nodeId, format) { - var svgNode = DOM.select(this.getSVGNodeId(nodeId)); - if (svgNode != null) { - var properties = format.toJSON(); - for ( var item in properties) { - svgNode.setAttribute(item, properties[item]); - } - - if (this.getFormatter().getVertexById(nodeId) instanceof CircleVertexGraphFormatter) { - var transform = "translate(" + svgNode.getAttribute("dragx") + "," + svgNode.getAttribute("dragy") + "), scale(" + format.getSize() + ")"; - svgNode.setAttribute("transform", transform); - } - } -}; - -GraphCanvas.prototype.renderLabel = function(nodeId) { - var x = Math.ceil(this.getLayout().getNodeById(nodeId).x * this.getFormatter().getWidth()); - var y = Math.ceil(this.getLayout().getNodeById(nodeId).y * this.getFormatter().getHeight()); - - var svgAttributesNode = JSON.parse(JSON.stringify(this.getFormatter().getVertexById(nodeId).getDefault().toJSON().title)); - svgAttributesNode.id = this.getSVGLabelId(this.getDataset().getVertexById(nodeId).getId()); - svgAttributesNode.dx = (-1) * (this.getDataset().getVertexById(nodeId).getName().length * svgAttributesNode["font-size"]) / 4 - 4; - - svgAttributesNode.dy = parseFloat((this.getFormatter().getVertexById(nodeId).getDefault().getSize())) - + parseFloat(svgAttributesNode["font-size"]) + parseFloat(this.getFormatter().getVertexById(nodeId).getDefault().getStrokeWidth()) - 4; - svgAttributesNode.dragx = Math.ceil(this.getLayout().getNodeById(nodeId).x * this.getFormatter().getWidth()); - - var gragy = parseFloat(this.getFormatter().getVertexById(nodeId).getDefault().getSize()) - + Math.ceil(this.getLayout().getNodeById(nodeId).y * this.getFormatter().getHeight()); - svgAttributesNode.dragy = gragy; - svgAttributesNode.transform = "translate(" + svgAttributesNode.dragx + "," + svgAttributesNode.dragy + ")";//, scale("+this.formatter.getVertexById(nodeId).getDefault().getSize()+")"; - - var nodeSVG = SVG.drawText(0, 0, this.getDataset().getVertexById(nodeId).getName(), this.GraphLabelGroup, svgAttributesNode); - - this.svgLabels[nodeId] = nodeSVG; - - /** Events for the SVG node **/ - var _this = this; - if (nodeSVG != null) { - nodeSVG.addEventListener("mouseover", function() { - _this.overLabel(nodeId); - }, false); - nodeSVG.addEventListener("mouseout", function() { - _this.outLabel(nodeId); - }, false); - } - -}; - -GraphCanvas.prototype.removeLabel = function(labelId) { - if (DOM.select(this.getSVGLabelId(labelId)) != null) { - DOM.select(this.getSVGLabelId(labelId)).parentNode.removeChild(DOM.select(this.getSVGLabelId(labelId))); - } -}; - -GraphCanvas.prototype.renderNode = function(nodeId) { - var svgAttributesNode = JSON.parse(JSON.stringify(this.getFormatter().getVertexById(nodeId).getDefault().toJSON())); - svgAttributesNode.dragx = Math.ceil(this.getLayout().getNodeById(nodeId).x * this.getFormatter().getWidth()); - svgAttributesNode.dragy = Math.ceil(this.getLayout().getNodeById(nodeId).y * this.getFormatter().getHeight()); - svgAttributesNode.transform = "translate(" + svgAttributesNode.dragx + "," + svgAttributesNode.dragy + ")"; - svgAttributesNode.id = this.getSVGNodeId(nodeId); - /*svgAttributesNode["stroke-width"] = 3 ; - svgAttributesNode["stroke-opacity"] = 1 ; - svgAttributesNode["fill-opacity"] = svgAttributesNode["opacity"] ; - svgAttributesNode["opacity"] = 1 ;*/ - this.circleDefaultRadius = this.getFormatter().getVertexById(nodeId).getDefault().getSize(); - var nodeSVG; - - if (this.getFormatter().getVertexById(nodeId) instanceof CircleVertexGraphFormatter) { - nodeSVG = SVG.drawCircle(0, 0, this.circleDefaultRadius, this.GraphNodeGroup, svgAttributesNode); - } - - if (this.getFormatter().getVertexById(nodeId) instanceof SquareVertexGraphFormatter) { - //nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius) ,0 - (this.formatter.getVertexById(nodeId).getDefault().getSize()) , (this.getFormatter().getVertexById(nodeId).getDefault().getSize()*2), (this.getFormatter().getVertexById(nodeId).getDefault().getSize()*2), this.GraphNodeGroup, svgAttributesNode); - nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius), 0 - (this.circleDefaultRadius), (this.circleDefaultRadius * 2), - (this.circleDefaultRadius * 2), this.GraphNodeGroup, svgAttributesNode); - } - - if (this.getFormatter().getVertexById(nodeId) instanceof EllipseVertexGraphFormatter) { - nodeSVG = SVG.drawEllipse(0, 0, this.circleDefaultRadius * 1.5, this.circleDefaultRadius, this.GraphNodeGroup, svgAttributesNode); - } - - if (this.getFormatter().getVertexById(nodeId) instanceof RectangleVertexGraphFormatter) { - //nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius) ,0 - ((this.circleDefaultRadius*2)/2) , (this.circleDefaultRadius*2), (this.circleDefaultRadius), this.GraphNodeGroup, svgAttributesNode); - nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius * 1.5), 0 - (this.circleDefaultRadius), (this.circleDefaultRadius * 2 * 1.5), - (this.circleDefaultRadius * 2), this.GraphNodeGroup, svgAttributesNode); - - } - - if (this.getFormatter().getVertexById(nodeId) instanceof RoundedVertexGraphFormatter) { - svgAttributesNode.ry = 2;// this.formatter.getVertexById(nodeId).getDefault().getSize()/4; - svgAttributesNode.rx = 2;// this.formatter.getVertexById(nodeId).getDefault().getSize()/4; - nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius * 1.5), 0 - (this.circleDefaultRadius), (this.circleDefaultRadius * 2 * 1.5), - (this.circleDefaultRadius * 2), this.GraphNodeGroup, svgAttributesNode); - } - - // - - if (this.getFormatter().getVertexById(nodeId) instanceof OctagonVertexGraphFormatter) { - svgAttributesNode.ry = 2; - svgAttributesNode.rx = 2; - nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius * 1.5), 0 - (this.circleDefaultRadius), (this.circleDefaultRadius * 2 * 1.5), - (this.circleDefaultRadius * 2), this.GraphNodeGroup, svgAttributesNode); - } - - nodeSVG.internalId = nodeId; - // - var _this = this; - - /** Events for the SVG node **/ - if (nodeSVG != null) { - nodeSVG.addEventListener("mouseover", function() { - _this.onVertexOver.notify(nodeId); - _this.overNode(nodeId); - }, false); - nodeSVG.addEventListener("mouseout", function() { - _this.onVertexOut.notify(nodeId); - _this.outNode(nodeId); - }, false); - //nodeSVG.addEventListener("click", function(){_this.clickNode(nodeId);}, false); - // - nodeSVG.addEventListener("mouseup", function() { - _this.onVertexUp.notify(nodeId); - }, false); - } -}; - -GraphCanvas.prototype.removeNode = function(nodeId) { - DOM.select(this.getSVGNodeId(nodeId)).parentNode.removeChild(DOM.select(this.getSVGNodeId(nodeId))); - if (this.args.labeled) { - this.removeLabel(nodeId); - } -}; - -/** REMOVING **/ -GraphCanvas.prototype.removeSelected = function() { - /** El orden importa **/ - this.removeSelectedEdges(); - this.removeSelectedNode(); - -}; - -GraphCanvas.prototype.removeSelectedNode = function() { - var selected = JSON.parse(JSON.stringify(this.getSelectedVertices())); - this.deselectNodes(); - var sorted = selected.sort(function(a, b) { - return a - b - }); - for ( var i = 0; i < sorted.length; i++) { - if (this.getDataset().getVertexById(sorted[i]) != null) { - this.getDataset().getVertexById(sorted[i]).remove(); - } - } -}; - -/** EDGES **/ -GraphCanvas.prototype.removeEdge = function(edgeId) { - if (DOM.select(this.getSVGEdgeId(edgeId)) != null) { - DOM.select(this.getSVGEdgeId(edgeId)).parentNode.removeChild(DOM.select(this.getSVGEdgeId(edgeId))); - } - - if (DOM.select(this.getSVGEdgeId(edgeId) + "_shadow") != null) { - DOM.select(this.getSVGEdgeId(edgeId) + "_shadow").parentNode.removeChild(DOM.select(this.getSVGEdgeId(edgeId) + "_shadow")); - } - - if (DOM.select(this.getSVGArrowEdgeId(edgeId)) != null) { - DOM.select(this.getSVGArrowEdgeId(edgeId)).parentNode.removeChild(DOM.select(this.getSVGArrowEdgeId(edgeId))); - } -}; - -GraphCanvas.prototype.overEdge = function(edgeId) { - if ((!this.args.interactive) || this.dragging || this.selecting) { - return; - } - - /** If selected we don't change the format **/ - if (this.args.isEdgeSelected[edgeId] == null) { - var format = this.getFormatter().getEdgeById(edgeId).getOver(); - format.args["cursor"] = "pointer"; - this.changeEdgeFormat(edgeId, format); - } -}; - -GraphCanvas.prototype.outEdge = function(edgeId) { - if (!this.args.interactive) { - return; - } - - /** If selected we don't change the format **/ - if (this.args.isEdgeSelected[edgeId] == null) { - this.changeEdgeFormat(edgeId, this.getFormatter().getEdgeById(edgeId).getDefault()); - } -}; - -GraphCanvas.prototype.changeEdgeFormat = function(edgeId, format) { - var svgEdge = DOM.select(this.getSVGEdgeId(edgeId) + "_shadow"); - if (svgEdge != null) { - var properties = format.toJSON(); - for ( var item in properties) { - svgEdge.setAttribute(item, properties[item]); - } - } -}; - -GraphCanvas.prototype.deselectEdge = function(edgeID) { - if (this.args.isEdgeSelected[edgeID] != null) { - this.changeEdgeFormat(edgeID, this.getFormatter().getEdgeById(edgeID).getDefault()); - var index = this.args.isEdgeSelected[edgeID]; - delete this.args.isEdgeSelected[edgeID]; - } -}; - -GraphCanvas.prototype.deselectEdges = function() { - var selected = JSON.parse(JSON.stringify(this.getSelectedEdges())); - for ( var i = 0; i < selected.length; i++) { - this.deselectEdge(selected[i]); - } -}; - -GraphCanvas.prototype.removeSelectedEdges = function() { - var selected = JSON.parse(JSON.stringify(this.getSelectedEdges())); - this.deselectEdges(); - for ( var i = 0; i < selected.length; i++) { - if (this.getDataset().getEdgeById(selected[i]) != null) { - this.getDataset().getEdgeById(selected[i]).remove(); - } - } -}; - -GraphCanvas.prototype.renderEdge = function(edgeId) { - var svgAttributesEdge = this.getFormatter().getEdgeById(edgeId).getDefault().toJSON(); - var edge = this.getDataset().getEdgeById(edgeId); - - var svgNodeTarget = this.getVertexById(edge.getNodeTarget().getId()); - var svgNodeSource = this.getVertexById(edge.getNodeSource().getId()); - svgAttributesEdge.id = this.getSVGEdgeId(edge.getId()) + "_shadow"; - - var svgEdge = null; - - if (this.getFormatter().getEdgeById(edgeId) instanceof LineEdgeGraphFormatter) { - var coordenateSourceX = svgNodeSource.getAttribute("dragx"); - var coordenateSourceY = svgNodeSource.getAttribute("dragy"); - var coordenateTargetX = svgNodeTarget.getAttribute("dragx"); - var coordenateTargetY = svgNodeTarget.getAttribute("dragy"); - - SVG.drawLine(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, this.GraphEdgeGroup, svgAttributesEdge); - var attributesShadow = {}; - attributesShadow.id = this.getSVGEdgeId(edge.getId()); - attributesShadow["stroke-opacity"] = 0; - attributesShadow["stroke-width"] = 4; - attributesShadow["stroke"] = "black"; - svgEdge = SVG.drawLine(svgNodeSource.getAttribute("dragx"), svgNodeSource.getAttribute("dragy"), svgNodeTarget.getAttribute("dragx"), - svgNodeTarget.getAttribute("dragy"), this.GraphEdgeGroup, attributesShadow); - } - - if (this.getFormatter().getEdgeById(edgeId) instanceof BezierEdgeGraphFormatter) { - var nodeId = edge.getNodeTarget().getId(); - var nodeSize = this.formatter.getVertexById(nodeId).getDefault().getSize() * this.getFormatter().getNodesMaxSize(); - svgAttributesEdge.fill = "none"; - svgAttributesEdge.id = this.getSVGEdgeId(edgeId); - var d = this.calculateCoordenatesBezier(nodeSize, svgNodeSource.getAttribute("dragx"), svgNodeSource.getAttribute("dragy")); - svgEdge = SVG.drawPath(d, this.GraphEdgeGroup, svgAttributesEdge); - } - ; - - if ((this.getFormatter().getEdgeById(edgeId) instanceof DirectedLineEdgeGraphFormatter) - || (this.getFormatter().getEdgeById(edgeId) instanceof CutDirectedLineEdgeGraphFormatter) - || (this.getFormatter().getEdgeById(edgeId) instanceof DotDirectedLineEdgeGraphFormatter) - || (this.getFormatter().getEdgeById(edgeId) instanceof OdotDirectedLineEdgeGraphFormatter) - || (this.getFormatter().getEdgeById(edgeId) instanceof OdirectedLineEdgeGraphFormatter)) { - var coordenateSourceX = svgNodeSource.getAttribute("dragx"); - var coordenateSourceY = svgNodeSource.getAttribute("dragy"); - var coordenateTargetX = svgNodeTarget.getAttribute("dragx"); - var coordenateTargetY = svgNodeTarget.getAttribute("dragy"); - - var offset = parseFloat(this.getFormatter().getVertexById(this.getDataset().getEdgeById(edgeId).getNodeTarget().getId()).getDefault() - .getSize() - * this.circleDefaultRadius); - var point = this._calculateEdgePointerPosition(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, offset); - coordenateTargetX = point.x; - coordenateTargetY = point.y; - SVG.drawLine(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, this.GraphEdgeGroup, svgAttributesEdge); - - var attributesShadow = {}; - attributesShadow.id = this.getSVGEdgeId(edge.getId()); - attributesShadow["stroke-opacity"] = 0; - attributesShadow["stroke-width"] = 4; - attributesShadow["stroke"] = "black"; - svgEdge = SVG.drawLine(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, this.GraphEdgeGroup, attributesShadow); - } - - if (this.getFormatter().getEdgeById(edgeId) instanceof DirectedLineEdgeGraphFormatter - || (this.getFormatter().getEdgeById(edgeId) instanceof OdirectedLineEdgeGraphFormatter)) { - var coordenateSourceX = svgNodeSource.getAttribute("dragx"); - var coordenateSourceY = svgNodeSource.getAttribute("dragy"); - var coordenateTargetX = svgNodeTarget.getAttribute("dragx"); - var coordenateTargetY = svgNodeTarget.getAttribute("dragy"); - - var point = this._calculateEdgePointerPosition(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, offset); - coordenateTargetX = point.x; - coordenateTargetY = point.y; - - var angle = Geometry.toDegree(point.angle) + 90; - this.arrowDefaultSize = this.getFormatter().getEdgeById(edgeId).getArrowSize(); //getDefault().getArrowSize(); - var d = "-" + this.arrowDefaultSize + ",0 0,-" + parseFloat(this.arrowDefaultSize) * 2 + " " + this.arrowDefaultSize + ",0"; - - var attributes; - - if (this.getFormatter().getEdgeById(edgeId) instanceof DirectedLineEdgeGraphFormatter) { - attributes = [ - [ "fill", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], - [ "stroke", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], [ "id", this.getSVGArrowEdgeId(edgeId) ] ]; - } else { - attributes = [ - [ "fill", "#FFFFFF" ], [ "stroke", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], - [ "id", this.getSVGArrowEdgeId(edgeId) ] ]; - } - - var flechaSVGNode = SVG.drawPoligon(d, this.GraphEdgeGroup, attributes);//, ["transform", "rotate("+angle+"), translate(0,0)"]]); - flechaSVGNode.setAttribute("transform", " translate(" + coordenateTargetX + ", " + coordenateTargetY + "), rotate(" + angle + ")"); - } - ; - - if (this.getFormatter().getEdgeById(edgeId) instanceof CutDirectedLineEdgeGraphFormatter) { - var coordenateSourceX = svgNodeSource.getAttribute("dragx"); - var coordenateSourceY = svgNodeSource.getAttribute("dragy"); - var coordenateTargetX = svgNodeTarget.getAttribute("dragx"); - var coordenateTargetY = svgNodeTarget.getAttribute("dragy"); - - var point = this._calculateEdgePointerPosition(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, offset); - coordenateTargetX = point.x; - coordenateTargetY = point.y; - - var angle = Geometry.toDegree(point.angle) + 90; - - //this.arrowDefaultSize = 2; //getDefault().getArrowSize(); - var d = "-4,0 4,0 4,-2 -4,-2"; - - var flechaSVGNode = SVG.drawPoligon(d, this.GraphEdgeGroup, [ - [ "fill", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], - [ "stroke", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], [ "id", this.getSVGArrowEdgeId(edgeId) ] ]);//, ["transform", "rotate("+angle+"), translate(0,0)"]]); - flechaSVGNode.setAttribute("transform", " translate(" + coordenateTargetX + ", " + coordenateTargetY + "), rotate(" + angle + ")"); - } - ; - - if ((this.getFormatter().getEdgeById(edgeId) instanceof DotDirectedLineEdgeGraphFormatter) - || (this.getFormatter().getEdgeById(edgeId) instanceof OdotDirectedLineEdgeGraphFormatter)) { - var coordenateSourceX = svgNodeSource.getAttribute("dragx"); - var coordenateSourceY = svgNodeSource.getAttribute("dragy"); - var coordenateTargetX = svgNodeTarget.getAttribute("dragx"); - var coordenateTargetY = svgNodeTarget.getAttribute("dragy"); - var point = this._calculateEdgePointerPosition(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, offset); - coordenateTargetX = point.x; - coordenateTargetY = point.y; - var angle = Geometry.toDegree(point.angle) + 90; - // this.arrowDefaultSize = this.formatter.getEdgeById(edgeId).getArrowSize(); //getDefault().getArrowSize(); - var attributes = []; - if (this.getFormatter().getEdgeById(edgeId) instanceof OdotDirectedLineEdgeGraphFormatter) { - attributes = [ - [ "fill", "#FFFFFF" ], [ "stroke", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], - [ "id", this.getSVGArrowEdgeId(edgeId) ] ]; - } else { - attributes = [ - [ "fill", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], - [ "stroke", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], [ "id", this.getSVGArrowEdgeId(edgeId) ] ]; - } - var flechaSVGNode = SVG.drawCircle(0, 0, 4, this.GraphEdgeGroup, attributes); - flechaSVGNode.setAttribute("transform", " translate(" + coordenateTargetX + ", " + coordenateTargetY + "), rotate(" + angle + ")"); - } - ; - - var _this = this; - /** Events for the SVG edge **/ - if (svgEdge != null) { - if (this.getDataset().getEdgesCount() < this.args.maxNumberEdgesFiringEvents) { - svgEdge.addEventListener("mouseover", function() { - _this.overEdge(edgeId); - }, false); - svgEdge.addEventListener("mouseout", function() { - _this.outEdge(edgeId); - }, false); - } - } -}; - -GraphCanvas.prototype._calculateEdgePointerPosition = function(sourceX, sourceY, targetX, targetY, radius) { - var angle = Geometry.getAngleBetweenTwoPoints(sourceX, sourceY, targetX, targetY); - - /** Suponiendo el node source que este a la derecha **/ - if ((targetX - sourceX) < 0) { - var b = Geometry.getAdjacentSideOfRectangleRight(angle, radius); - targetX = parseFloat(targetX) + parseFloat(b); - arrowX = parseFloat(targetX) + parseFloat(b) + this.arrowDefaultSize / 2; - } else { - var b = Geometry.getAdjacentSideOfRectangleRight(angle, radius); - targetX = parseFloat(targetX) - parseFloat(b); - arrowX = parseFloat(targetX) - parseFloat(b) - this.arrowDefaultSize / 2; - } - - /** Suponiendo el node source que este a la arriba **/ - if ((targetY - sourceY) > 0) { - var a = Geometry.getOppositeSideOfRectangleRight(angle, radius); - targetY = parseFloat(targetY) - parseFloat(a); - arrowY = parseFloat(targetY) - parseFloat(a) - this.arrowDefaultSize / 2; - } else { - var a = Geometry.getOppositeSideOfRectangleRight(angle, radius); - targetY = parseFloat(targetY) + parseFloat(a); - arrowY = parseFloat(targetY) + parseFloat(a) - this.arrowDefaultSize / 2; - - } - - return { - "x" : arrowX, - "y" : arrowY, - "angle" : angle - }; -}; - -GraphCanvas.prototype.calculateCoordenatesBezier = function(nodeSize, x1, y1) { - var x11 = x1 - (nodeSize / 2); - var y11 = y1 - (nodeSize / 2); - - var x12 = parseFloat(x1) + parseFloat(nodeSize / 2); - var y12 = y1 - (nodeSize / 2); - - var curvePointX = (x12 - x11) / 2 + x11; - var curvePointY = y1 - (nodeSize * 2); - var d = "M" + x11 + "," + y11 + " T" + curvePointX + "," + curvePointY + " " + x12 + "," + y12; - return d; - -}; - -GraphCanvas.prototype.renderEdges = function() { - for ( var edge in this.getDataset().getEdges()) { - this.renderEdge(this.getDataset().getEdgeById(edge).getId()); - - } -}; - -GraphCanvas.prototype.getLastSelectedNode = function() { - var node = null; - if (this.getSelectedVertices().length > 0) { - var nodeId = this.getSelectedVertices()[this.getSelectedVertices().length - 1]; - node = this.getDataset().getVertexById(nodeId); - } - return node; -}; -/* - GraphCanvas.prototype.getNodeByNameAndIndex = function(node, index){ - var nodeId = this.getDataset().verticesIndex[node][index]; - var nodeItem = this.getDataset().getVertexById(nodeId); - return nodeItem; - }; - */ - -GraphCanvas.prototype.setDataset = function(dataset) { - this.dataset = dataset; -}; - -GraphCanvas.prototype.setFormatter = function(formatter) { - this.formatter = formatter; -}; - -GraphCanvas.prototype.setLayout = function(layout) { - this.layout = layout; -}; - -/** API **/ -GraphCanvas.prototype.getDataset = function() { - return this.dataset; -}; - -GraphCanvas.prototype.getFormatter = function() { - return this.formatter; -}; - -GraphCanvas.prototype.getLayout = function() { - return this.layout; -}; - -/** API DATASET **/ -GraphCanvas.prototype.addVertex = function(name, args) { - this.getDataset().addNode(name, args); -}; - -GraphCanvas.prototype.removeVertex = function(vertexId) { - this.getDataset().getVertexById(vertexId).remove(); -}; - -GraphCanvas.prototype.addEdge = function(edgeName, nodeSourceId, nodeTargetId, args) { - this.getDataset().addEdge(edgeName, nodeSourceId, nodeTargetId, args); -}; -/* - GraphCanvas.prototype.removeEdge = function(edgeId){ - this.getDataset().getEdgeById(edgeId).remove(); - }; - */ - -/** API FORMATTER **/ -GraphCanvas.prototype.getWidth = function() { - return this.getFormatter().getWidth(); -}; - -GraphCanvas.prototype.getHeight = function() { - return this.getFormatter().getHeight(); -}; - -GraphCanvas.prototype.getBackgroundImage = function() { - return this.getFormatter().getBackgroundImage(); -}; - -//GraphCanvas.prototype.setBackgroundImage = function(value){ -// this.getFormatter().setBackgroundImage(value); -//}; - -GraphCanvas.prototype.getBackgroundColor = function() { - return this.getFormatter().getBackgroundColor(); -}; - -GraphCanvas.prototype.setBackgroundColor = function() { - this.getFormatter().setBackgroundColor(value); -}; - -//GraphCanvas.prototype.setEdgeFill = function(edgeId, value){ -// this.getFormatter().getEdgeById(edgeId).getDefault().setFill(value); -//}; -// -//GraphCanvas.prototype.getEdgeFill = function(edgeId){ -// return this.getFormatter().getEdgeById(edgeId).getDefault().getFill(); -//}; - -/** VERTICES FORMATTER **/ -GraphCanvas.prototype.setVertexSize = function(vertexId, value) { - this.getFormatter().getVertexById(vertexId).getDefault().setSize(value); -}; - -GraphCanvas.prototype.getVertexSize = function(vertexId) { - return this.getFormatter().getVertexById(vertexId).getDefault().getSize(); -}; - -GraphCanvas.prototype.setVertexStroke = function(vertexId, value) { - this.getFormatter().getVertexById(vertexId).getDefault().setStroke(value); -}; - -GraphCanvas.prototype.getVertexStroke = function(vertexId) { - return this.getFormatter().getVertexById(vertexId).getDefault().getStroke(); -}; - -GraphCanvas.prototype.setVertexStrokeOpacity = function(vertexId, value) { - this.getFormatter().getVertexById(vertexId).getDefault().setStrokeOpacity(value); -}; - -GraphCanvas.prototype.getVertexStrokeOpacity = function(vertexId) { - return this.getFormatter().getVertexById(vertexId).getDefault().getStrokeOpacity(); -}; - -GraphCanvas.prototype.setVertexOpacity = function(vertexId, value) { - this.getFormatter().getVertexById(vertexId).getDefault().setOpacity(value); -}; - -GraphCanvas.prototype.getVertexOpacity = function(vertexId) { - return this.getFormatter().getVertexById(vertexId).getDefault().getOpacity(); -}; - -GraphCanvas.prototype.setVertexFill = function(vertexId, color) { - this.getFormatter().getVertexById(vertexId).getDefault().setFill(color); -}; - -GraphCanvas.prototype.getVertexFill = function(vertexId) { - return this.getFormatter().getVertexById(vertexId).getDefault().getFill(); -}; - -/** EDGES FORMATTER **/ -GraphCanvas.prototype.setEdgeSize = function(edgeId, value) { - this.getFormatter().getEdgeById(edgeId).getDefault().setSize(value); -}; - -GraphCanvas.prototype.getEdgeSize = function(edgeId) { - return this.getFormatter().getEdgeById(edgeId).getDefault().getSize(); -}; - -GraphCanvas.prototype.setEdgeStroke = function(edgeId, value) { - this.getFormatter().getEdgeById(edgeId).getDefault().setStroke(value); -}; - -GraphCanvas.prototype.getEdgeStroke = function(edgeId) { - return this.getFormatter().getEdgeById(edgeId).getDefault().getStroke(); -}; - -GraphCanvas.prototype.setEdgeStrokeOpacity = function(edgeId, value) { - this.getFormatter().getEdgeById(edgeId).getDefault().setStrokeOpacity(value); -}; - -GraphCanvas.prototype.getEdgeStrokeOpacity = function(edgeId) { - return this.getFormatter().getEdgeById(edgeId).getDefault().getStrokeOpacity(); -}; - -GraphCanvas.prototype.setEdgeFill = function(edgeId, color) { - this.getFormatter().getEdgeById(edgeId).getDefault().setFill(color); -}; - -GraphCanvas.prototype.getEdgeFill = function(edgeId) { - return this.getFormatter().getEdgeById(edgeId).getDefault().getFill(); -}; - -/** API LAYOUT **/ -GraphCanvas.prototype.setCoordinates = function(vertexId, x, y) { - return this.getLayout().getEdgeById(vertexId).setCoordinates(x, y); -}; - - - -function HPLCGraph(args) { - this.width = 600; - this.height = 600; - this.title = ''; - this.bbar = false; - this.plotInnerPanelPadding = 10; - this.plotPanelPadding = 5; - this.id = BUI.id(); - - this.hidePlots = null; - this.xlabel = ""; - this.scaled = false; - this.xParam = null; - this.showRangeSelector = true; - this.interactionModel = null; - - /** for each stat the max and minimum value when it is scaled in order to show correctly in the legend **/ - this.ranges = {}; - if (args != null) { - if (args.interactionModel != null) { - this.interactionModel = args.interactionModel; - } - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; - } - if (args.bbar != null) { - this.bbar = args.bbar; - } - if (args.title != null) { - this.title = args.title; - } - if (args.plots != null) { - this.plots = args.plots; - } - - if (args.scaled != null) { - this.scaled = args.scaled; - } - if (args.xlabel != null) { - this.xlabel = args.xlabel; - } - if (args.xParam != null) { - this.xParam = args.xParam; - } - if (args.showRangeSelector != null) { - this.showRangeSelector = args.showRangeSelector; - } - } - - this.onZoomX = new Event(this); - this.onResetZoom = new Event(this); - this.dblclick = new Event(this); -} - -HPLCGraph.prototype.getMenu = function () { - var _this = this; - /** Actions buttons **/ - var actions = []; - - function toggle(item, pressed) { - if (pressed) { - _this.plots[item.param] = true; - } else { - delete _this.plots[item.param]; - } - _this.reloadData(this.hplcData); - } - - for (var i = 0; i < this.hplcData.length; i++) { - if (this.hplcData[i].showOnMenu != false) { - var param = this.hplcData[i].param; - var style = "style='padding:0 0px 0 5px;'"; - actions.push({ - text : "
" + BUI.getRectangleColorDIV(this.hplcData[i].color, 10, 10) + " " + this.hplcData[i].label + "
", - id : _this.id + param, - param : param, - enableToggle : true, - scope : this, - toggleHandler : toggle, - pressed : (_this.plots[param] != null) - }); - } - } - actions.push("-"); - - actions.push({ - text : "Scale", - enableToggle : true, - scope : this, - pressed : this.scaled, - icon : '../images/icon_graph.png', - toggleHandler : function (item, pressed) { - _this.scaled = pressed; - _this.reloadData(this.hplcData); - } - }); - - actions.push("->"); - actions.push({ - text : "Save", - scope : this, - icon : '../images/save.gif', - handler : function (item, pressed) { - var largeImage = document.createElement("img"); - largeImage.style.display = 'block'; - largeImage.style.width = 200 + "px"; - largeImage.style.height = 200 + "px"; - largeImage.setAttribute('src', Dygraph.Export.asCanvas(this.dygraphObject.dygraph).toDataURL()); - window.open(Dygraph.Export.asCanvas(this.dygraphObject.dygraph).toDataURL(), 'Image', ''); - } - }); - - return actions; -}; - -/** Looks for the maximum value and then divide everything but that value **/ -HPLCGraph.prototype.scaledData = function (data) { - for (var i = 0; i < data.length; i++) { - var values = this.getMaxAndMinValue(data[i]); - data[i] = this.divideValuesByMax(data[i], values.max); - this.ranges[data[i].label] = values; - } - return data; -}; - - -/** Given a stat float[] and a max number it will divide each value by max **/ -HPLCGraph.prototype.divideValuesByMax = function (stat, max) { - for (var j = 0; j < stat.data.length; j++) { - if (max != 0) { - stat.data[j] = Number(stat.data[j]) / max; - stat.std[j] = Number(stat.std[j]) / max; - } - } - return stat; -}; - -/** returns max value of a stat **/ -HPLCGraph.prototype.getMaxAndMinValue = function (stat) { - var max = 0; - var min = stat.data[0]; - for (var j = 0; j < stat.data.length; j++) { - if (Number(stat.data[j]) > max) { - max = Number(stat.data[j]); - } - if (Number(stat.std[j]) > max) { - max = Number(stat.std[j]); - } - if (Number(stat.data[j]) < min) { - min = Number(stat.data[j]); - } - } - return { - max : Number(max), - min : Number(min) - }; -}; - -HPLCGraph.prototype.getPoint = function (data, i) { - var point = [ 10, 10, 10 ]; - var y = parseFloat(data.data[i]); - var error = parseFloat(data.std[i]); - if (data.fdata == null) { - return [ y - error, y, y + error ]; - } else { - if (data.fstd != null) { - return [ data.fstd(y - error), data.fdata(y), data.fstd(y + error) ]; - } - return [ data.fdata(y) - error, data.fdata(y), data.fdata(y) + error ]; - } - return point; -}; - -HPLCGraph.prototype.reloadData = function(hplcData) { - this.panel.setLoading(false); - this.hplcData = hplcData; - - var data = hplcData; - - - /** In case of having peaks **/ - if (this.peaks != null) { - for (var peak in this.peaks) { - var values = []; - var std = []; - for (var i = 0; i < this.peaks[peak].length; i++) { - values.push(this.peaks[peak][i][1]); - std.push(this.peaks[peak][i][2]); - } - data.push({ - param : peak, - data : values, - showOnMenu : false, - fdata : function (a) { - var value = (Math.log(parseFloat(a))); - if (isNumber(value)) { - return value; - } - }, - fstd : function (a) { - var value = Math.log(Math.abs(parseFloat(a))); - if (isNumber(value)) - return value; - }, - std : std, - color : this.colorPeak[peak], - label : peak - }); - - } - } - - - if (this.scaled) { - data = this.scaledData(JSON.parse(JSON.stringify(hplcData))); - } - - var paramIndex = {}; - var parsed = []; - var j = 0; - for (var i = 0; i < data[0].data.length - 1; i++) { - var aux = []; - for (j = 0; j < data.length; j++) { - if (this.plots != null) { - if (this.plots[data[j].param] != null) { - aux.push(this.getPoint(data[j], i)); - paramIndex[data[j].param] = aux.length - 1; - } - } else { - aux.push([ data[j].data[i] - data[j].std[i], data[j].data[i], data[j].data[i] + data[j].std[i] ]); - } - } - parsed.push([]); - - var index = i; - if (this.xParam != null) { - index = parseFloat(data[this.xParam].data[i]); - } - - parsed[parsed.length - 1].push(index); - - for (j = 0; j < data.length; j++) { - if (this.plots != null) { - if (this.plots[data[j].param] != null) { - parsed[parsed.length - 1].push(aux[paramIndex[data[j].param]]); - } - } else { - parsed[parsed.length - 1].push(aux[j]); - } - } - } - - var colors = []; - var labels = [ "" ]; - for (j = 0; j < data.length; j++) { - if (this.plots != null) { - if (this.plots[data[j].param] != null) { - colors.push(data[j].color); - labels.push(data[j].label); - } - } else { - parsed[parsed.length - 1].push(aux[j]); - } - } - - this._renderDygraph(parsed, colors, labels); -}; - -HPLCGraph.prototype._renderDygraph = function (parsed, colors, labels) { - this.dygraphObject = new StdDevDyGraph(this.id, { - width : this.width, - height : this.height - 10, - xlabel : this.xlabel, - showRangeSelector : this.showRangeSelector, - interactionModel : this.interactionModel, - scaled : this.scaled, - ranges : this.ranges - }); - this.dygraphObject.draw(parsed, colors, labels); - - var _this = this; - this.dygraphObject.onZoomX.attach(function (sender, args) { - try { - _this.onZoomX.notify(args); - } catch (e) { - } - }); - - this.dygraphObject.onResetZoom.attach(function (sender, args) { - try { - _this.onResetZoom.notify(args); - } catch (e) { - } - }); - - this.dygraphObject.dblclick.attach(function (sender, args) { - try { - _this.dblclick.notify(args); - } catch (e) { - } - }); - -}; - -HPLCGraph.prototype.loadData = function (data) { - var _this = this; - this.reloadData(data); - this.panel.addDocked({ - xtype : 'toolbar', - items : this.getMenu() - }); - - - if (this.bbar == true){ - this.panel.addDocked({ - xtype : 'toolbar', - dock: 'bottom', - items : [ - { - xtype: 'numberfield', - id: 'main_field_start', - fieldLabel: 'Range from', - width: 170, - labelWidth : 70, - value: 0, - minValue: 0 - }, - { - xtype: 'numberfield', - id: 'main_field_end', - fieldLabel: 'to', - width: 130, - labelWidth : 30, - value: 0, - minValue: 0 - }, - { - xtype: 'button', - text: 'Go', - handler: function () { - var start = parseFloat(Ext.getCmp("main_field_start").getValue()); - var end = parseFloat(Ext.getCmp("main_field_end").getValue()); - - if (start < 0) { - start = 0; - } - if (end < 0) { - end = 0; - } - if (start > end) { - var aux = end; - end = start; - start = aux; - } - - _this.dygraphObject.dygraph.updateOptions({ isZoomedIgnoreProgrammaticZoom: true, dateWindow: [start, end] }); - } - } - ] - }); - } -}; - -HPLCGraph.prototype.getPanel = function () { - this.panel = Ext.create('Ext.panel.Panel', { - padding : this.plotPanelPadding, - width : this.width + 4 * this.plotInnerPanelPadding, - height : this.height + 4 * this.plotInnerPanelPadding, - items : [ { - html : "", - id : this.id, - width : this.width, - height : this.height - } ] - }); - - return this.panel; -}; - -HPLCGraph.prototype.input = function () { - return DATADOC.getHPLCData(); -}; - -HPLCGraph.prototype.getDataByFrameNumber = function (frameNumber) { - var data = {}; - data.frameNumber = frameNumber; - for (var key in this.hplcData){ - data[this.hplcData[key].label] = this.hplcData[key].data[frameNumber]; - } - console.log(data); - return data; -}; - - -HPLCGraph.prototype.test = function (targetId) { - var mainPlotPanel = new HPLCGraph({ - title : 'I0', - width : 800, - height : 400, - plots : { - "I0" : true, - "Rg" : true, - "Mass" : true - }, - xlabel : "HPLC Frames", - scaled : this.scaled, - interactionModel : { - 'dblclick' : function (event, g, context) { - } - } - }); - mainPlotPanel.getPanel().render(targetId); - mainPlotPanel.loadData(mainPlotPanel.input()); - -}; - - -function MergesHPLCGraph(args) { - HPLCGraph.prototype.constructor.call(this, args); - -// this.peakColors = ["#00FB42", "#00BA31", "#007C21", "#003E10"]; - this.peakColors = ["#DEBD00", "#6D9100", "#872900", "#0092CC"]; -} - - -MergesHPLCGraph.prototype.scaledData = HPLCGraph.prototype.scaledData; -MergesHPLCGraph.prototype.divideValuesByMax = HPLCGraph.prototype.divideValuesByMax; -MergesHPLCGraph.prototype.getMaxAndMinValue = HPLCGraph.prototype.getMaxAndMinValue; -MergesHPLCGraph.prototype.getPoint = HPLCGraph.prototype.getPoint; -MergesHPLCGraph.prototype.reloadData = HPLCGraph.prototype.reloadData; -MergesHPLCGraph.prototype._renderDygraph = HPLCGraph.prototype._renderDygraph; -MergesHPLCGraph.prototype.loadData = HPLCGraph.prototype.loadData; -MergesHPLCGraph.prototype.getPanel = HPLCGraph.prototype.getPanel; -MergesHPLCGraph.prototype.getDataByFrameNumber = HPLCGraph.prototype.getDataByFrameNumber; - - -MergesHPLCGraph.prototype.setPeaks = function (data) { - this.peaks = data; - /** get size of peaks **/ - this.peakKeys = []; - this.colorPeak = {}; - var colorCount = 1; - for (var key in this.peaks) { - if (this.peaks.hasOwnProperty(key)) { - var color = this.peakColors[colorCount % this.peakColors.length]; - colorCount = colorCount + 1; - this.peakKeys.push(key); - this.colorPeak[key] = color; - } - } - this.peakKeys.sort(); -}; - - -MergesHPLCGraph.prototype.getMenu = function () { - var _this = this; - /** Actions buttons **/ - var actions = []; - - function toggle(item, pressed) { - if (pressed) { - _this.plots[item.param] = true; - } else { - delete _this.plots[item.param]; - } - _this.reloadData(_this.hplcData); - } - - - /** Toolbar for peaks Average **/ - if (this.peaks != null) { - var items = []; - for (var i = 0; i < this.peakKeys.length; i++) { - var color = this.colorPeak[this.peakKeys[i]]; - items.push({ - text: "Peak #" + i + " " + this.peakKeys[i].replace("- ", " to #").replace(".0", "").replace(".0", "") + "", - peakid : this.peakKeys[i], - checked: false, - checkHandler: function (sender, pressed) { - var item = new Object(); - item.param = sender.peakid; - toggle(item, pressed); - } - }); - } - - var menu = Ext.create('Ext.menu.Menu', { - id: 'mainMenu', - style: { - overflow: 'visible' - }, - items: items - }); - var tb = Ext.create('Ext.toolbar.Toolbar'); - tb.add({ - text: 'Peaks Avg.', - menu: menu - }); - actions.push(tb); - } - - - - for (var i = 0; i < this.hplcData.length; i++) { - if (this.hplcData[i].showOnMenu != false) { - var param = this.hplcData[i].param; - var style = "style='padding:0 0px 0 5px;'"; - actions.push({ - text : "
" + BUI.getRectangleColorDIV(this.hplcData[i].color, 10, 10) + " " + this.hplcData[i].label + "
", - id : _this.id + param, - param : param, - enableToggle : true, - scope : this, - margin : 5, - toggleHandler : toggle, - pressed : (_this.plots[param] != null) - }); - } - } - - actions.push("->"); - actions.push({ - text : "Save", - scope : this, - icon : '../images/save.gif', - handler : function (item, pressed) { - var largeImage = document.createElement("img"); - largeImage.style.display = 'block'; - largeImage.style.width = 200 + "px"; - largeImage.style.height = 200 + "px"; - largeImage.setAttribute('src', Dygraph.Export.asCanvas(this.dygraphObject.dygraph).toDataURL()); - window.open(Dygraph.Export.asCanvas(this.dygraphObject.dygraph).toDataURL(), 'Image', ''); - } - }); - - return actions; -}; - - -MergesHPLCGraph.prototype.input = function () { - return DATADOC.getScatteringHPLCFrameData(); -}; - -MergesHPLCGraph.prototype.test = function (targetId) { - var mainPlotPanel = new MergesHPLCGraph({ - title : 'Scattering', - width : this.plotWidth, - height : 500, - showRangeSelector : false, - xParam : 0, - xlabel : "scattering_I", - plots : { - "scattering_I" : true, - "subtracted_I" : true, - "buffer_I" : true - } - }); - mainPlotPanel.getPanel().render(targetId); - mainPlotPanel.loadData(mainPlotPanel.input()); -}; - - -function NetworkWidget(args) { - this.id = "NetworkViewer_" + Math.random().toString().replace(".", "_"); - - this.label = true; - if (args != null) { - if (args.targetId != null) { - this.targetId = args.targetId; - } - if (args.label != null) { - this.label = args.label; - } - } - - this.onVertexOver = new Event(this); - this.onVertexOut = new Event(this); -} - -NetworkWidget.prototype.draw = function(dataset, formatter, layout) { - - this.graphCanvas = new GraphCanvas(this.id, document.getElementById(this.targetId), { - "labeled" : this.label, - "multipleSelectionEnabled" : false, - "draggingCanvasEnabled" : false - }); - this.graphCanvas.draw(dataset, formatter, layout); - - var _this = this; - this.graphCanvas.onVertexOver.attach(function(sender, nodeId) { - _this.onVertexOver.notify(nodeId); - }); - - this.graphCanvas.onVertexOut.attach(function(sender, nodeId) { - _this.onVertexOut.notify(nodeId); - }); -}; - -/** SELECT VERTICES BY NAME * */ -NetworkWidget.prototype.selectVertexByName = function(vertexName) { - var vertices = this.getDataset().getVertexByName(vertexName); - if (vertices != null) { - for ( var nodeId in vertices) { - if (vertices.hasOwnProperty(nodeId)) { - var vertexId = vertices[nodeId].getId(); - this.selectVertexById(vertexId); - } - } - } -}; - -NetworkWidget.prototype.selectVerticesByName = function(verticesName) { - for ( var i = 0; i < verticesName.length; i++) { - this.selectVertexByName(verticesName[i]); - } -}; - -/** SELECT VERTICES BY ID * */ -NetworkWidget.prototype.selectVertexById = function(vertexId) { - this.graphCanvas.selectNode(vertexId); - this.blinkVertexById(vertexId); -}; - -NetworkWidget.prototype.selectVerticesById = function(verticesId) { - for ( var i = 0; i < verticesId.length; i++) { - this.selectVertexById(verticesId[i]); - } -}; - -/** VECINDARIO * */ -NetworkWidget.prototype.selectNeighbourhood = function() { - this.selectEdgesFromVertices(); - this.selectAdjacent(); -}; - -/** DESELECT * */ -NetworkWidget.prototype.deselectNodes = function() { - this.graphCanvas.deselectNodes(); -}; - -/** SELECT ALL NODES * */ -NetworkWidget.prototype.selectAllNodes = function() { - this.getGraphCanvas().selectAllNodes(); -}; - -/** SELECT EVERYTHING * */ -NetworkWidget.prototype.selectAll = function() { - this.getGraphCanvas().selectAll(); -}; - -/** SELECT ALL EDGES * */ -NetworkWidget.prototype.selectAllEdges = function() { - this.getGraphCanvas().selectAllEdges(); -}; - -/** ZOOM * */ -NetworkWidget.prototype.setScale = function(value) { - this.graphCanvas.setScale(value); -}; - -NetworkWidget.prototype.getScale = function() { - return this.graphCanvas.getScale(value); -}; - -/** SELECT ADJACENT VERTICES FROM SELECTED VERTICES * */ -NetworkWidget.prototype.selectAdjacent = function() { - var selectedVertices = this.getGraphCanvas().getSelectedVertices(); - var edges = []; - for ( var i = 0; i < selectedVertices.length; i++) { - edges = edges.concat(this.getGraphCanvas().getDataset().getVertexById(selectedVertices[i]).getEdges()); - } - var vertices = []; - for ( i = 0; i < edges.length; i++) { - vertices.push(edges[i].getNodeSource().getId()); - vertices.push(edges[i].getNodeTarget().getId()); - } - - this.selectVerticesById(vertices); -}; - -/** SELECT EDGES FROM SELECTED VERTICES * */ -NetworkWidget.prototype.selectEdgesFromVertices = function() { - var selectedVertices = this.getGraphCanvas().getSelectedVertices(); - var edges = []; - for ( var i = 0; i < selectedVertices.length; i++) { - edges = edges.concat(this.getGraphCanvas().getDataset().getVertexById(selectedVertices[i]).getEdges()); - } - var edgesId = []; - for ( i = 0; i < edges.length; i++) { - edgesId.push(edges[i].getId()); - } - this.getGraphCanvas().selectEdges(edgesId); -}; - -/** BLINKING * */ -NetworkWidget.prototype.blinkVertexById = function(vertexId) { - this.graphCanvas.blinkVertexById(vertexId); -}; - -/** COMPONENTE CONEXA DE LOS NODOS SELECCIONADOS * */ -NetworkWidget.prototype.selectConnectedComponent = function() { - var elements = this.getConnectedComponent(); - this.selectVerticesById(elements.nodes); - this.graphCanvas.selectEdges(elements.edges); -}; - -NetworkWidget.prototype.getConnectedComponent = function() { - var nodosVisitados = {}; - var aristasVisitadas = {}; - var arrNodos = []; - var arrAristas = []; - var selectedGraphNodesId = this.getGraphCanvas().getSelectedVertices(); - for ( var i = 0; i < selectedGraphNodesId.length; i++) { - this.visitNode(selectedGraphNodesId[i], nodosVisitados, aristasVisitadas, arrNodos, arrAristas); - } - return { - nodes : arrNodos, - edges : arrAristas - }; -}; - -NetworkWidget.prototype.visitNode = function(nodeId, nodosVisitados, aristasVisitadas, arrNodos, arrAristas) { - nodosVisitados[nodeId] = true; - arrNodos.push(nodeId); - var nodeEdges = this.getDataset().getVertexById(nodeId).getEdges(); - for ( var j = 0; j < nodeEdges.length; j++) { - var edge = nodeEdges[j]; - var edgeId = edge.getId(); - if (aristasVisitadas[edgeId] == null) { - aristasVisitadas[edgeId] = true; - arrAristas.push(edgeId); - var nodeTargetId = edge.getNodeTarget().getId(); - if (nodosVisitados[nodeTargetId] == null) { - this.visitNode(nodeTargetId, nodosVisitados, aristasVisitadas, arrNodos, arrAristas); - } - var nodeSourceId = edge.getNodeSource().getId(); - if (nodosVisitados[nodeSourceId] == null) { - this.visitNode(nodeSourceId, nodosVisitados, aristasVisitadas, arrNodos, arrAristas); - } - } - } -}; - -/** COLLAPSE SELECTED VERTICES * */ -NetworkWidget.prototype.collapse = function() { - var selectedVertices = this.getGraphCanvas().getSelectedVertices(); - var xMin = -Infinity; - var xMax = Infinity; - var yMin = -Infinity; - var yMax = Infinity; - - for ( var i = 0; i < selectedVertices.length; i++) { - var vertex = this.getGraphCanvas().getLayout().getNodeById(selectedVertices[i]); - if (xMin < vertex.x) { - xMin = vertex.x; - } - if (xMax > vertex.x) { - xMax = vertex.x; - } - if (yMin < vertex.y) { - yMin = vertex.y; - } - if (yMax > vertex.y) { - yMax = vertex.y; - } - } - - var centerX = xMin - xMax; - var centerY = yMin - yMax; - var radius = (xMax - xMin) / 4; - - var count = selectedVertices.length; - var verticesCoordinates = []; - - for ( i = 0; i < selectedVertices.length; i++) { - x = centerX + radius * Math.sin(i * 2 * Math.PI / count); - y = centerY + radius * Math.cos(i * 2 * Math.PI / count); - verticesCoordinates.push({ - 'x' : x, - 'y' : y - }); - } - - for ( i = 0; i < selectedVertices.length; i++) { - this.getGraphCanvas().getLayout().getNodeById(selectedVertices[i]).setCoordinates(verticesCoordinates[i].x, verticesCoordinates[i].y); - } -}; - -/** SETTER FONT SIZE * */ -NetworkWidget.prototype.setVerticesFontSize = function(value) { - for ( var nodeId in this.getDataset().getVertices()) { - if (this.getDataset().getVertices().hasOwnProperty(nodeId)) { - this.getFormatter().getVertexById(nodeId).getDefault().setFontSize(value); - } - } -}; - -/** GETTERS * */ -NetworkWidget.prototype.getFormatter = function() { - return this.getGraphCanvas().getFormatter(); -}; -NetworkWidget.prototype.getLayout = function() { - return this.getGraphCanvas().getLayout(); -}; - -NetworkWidget.prototype.getDataset = function() { - return this.getGraphCanvas().getDataset(); -}; - -NetworkWidget.prototype.getGraphCanvas = function() { - return this.graphCanvas; -}; - -RangeWhiskerGraph.prototype.cleanArray = GenericGraph.prototype.cleanArray; -RangeWhiskerGraph.prototype.plotAxes = GenericGraph.prototype.plotAxes; -RangeWhiskerGraph.prototype.plotRuler = GenericGraph.prototype.plotRuler; -RangeWhiskerGraph.prototype.drawSVGVerticalText = GenericGraph.prototype.drawSVGVerticalText; -RangeWhiskerGraph.prototype.getClassColor = GenericGraph.prototype.getClassColor; -RangeWhiskerGraph.prototype.getDimensions = GenericGraph.prototype.getDimensions; -RangeWhiskerGraph.prototype.calculate = GenericGraph.prototype.calculate; -RangeWhiskerGraph.prototype.getMedian = GenericGraph.prototype.getMedian; -RangeWhiskerGraph.prototype.pointToPixel = GenericGraph.prototype.pointToPixel; -RangeWhiskerGraph.prototype.maxValueWhisker = GenericGraph.prototype.maxValueWhisker; -RangeWhiskerGraph.prototype.refresh = GenericGraph.prototype.refresh; - -/** - * Subclass of GenericGraph - * - * @plotHorizontalByCluster - */ -function RangeWhiskerGraph(args) { - this.maxBoxWidth = 25; - - if (args == null) { - args = {}; - } - args.plotHorizontalByCluster = false; - - GenericGraph.call(this, args); - - if (args.maxBoxWidth != null) { - this.maxBoxWidth = args.maxBoxWidth; - } -} - -RangeWhiskerGraph.prototype.refresh = function(data) { - document.getElementById(this.targetId).innerHTML = ""; - this.draw(this.targetId, data); -}; - -RangeWhiskerGraph.prototype.isNumber = function(value) { - if (value == "") - return false; - - var d = parseInt(value); - if (!isNaN(d)) - return true; - else - return false; - -}; - -/** - There are several different methods for calculating quartiles.[1] This calculator uses a method described by Moore and McCabe to find quartile values. - The same method also used by The TI-83 to calculate quartile values. - With this method, the first quartile is the median of the numbers below the median, the third quartile is the median of the numbers above the median. - - http://www.miniwebtool.com/quartile-calculator/ - http://www.alcula.com/calculators/statistics/box-plot/ - - **/ -RangeWhiskerGraph.prototype.getQ1 = function(array) { - array = array.slice(0, array.length / 2); - return this.getMedian(array); -}; - -RangeWhiskerGraph.prototype.getQ3 = function(array) { - array = array.slice((array.length + 1) / 2); - return this.getMedian(array); - -}; - -RangeWhiskerGraph.prototype.getQ2 = function(array) { - return this.getMedian(array); -}; - -RangeWhiskerGraph.prototype.getBelowOutliers = function(belowLimit, array) { - var points = []; - for ( var i = 0; i < array.length; i++) { - if (array[i] <= belowLimit) { - points.push(array[i]); - } - } - return points; -}; - -RangeWhiskerGraph.prototype.getAboveOutliers = function(aboveLimit, array) { - var points = []; - for ( var i = 0; i < array.length; i++) { - if (array[i] >= aboveLimit) { - points.push(array[i]); - } - } - return points; -}; - -RangeWhiskerGraph.prototype.minValueWhisker = function(belowLimit, q1, array) { - var points = []; - - for ( var i = 0; i < array.length; i++) { - if ((array[i] < q1) && (array[i]) > belowLimit) { - points.push(array[i]); - } - } - - if (points.length > 0) { - points.sort(function(a, b) { - return a - b; - }); - return points[0]; - } - return null; -}; - -//RangeWhiskerGraph.prototype.maxValueWhisker = function(aboveLimit, q3, array){ -// var points = []; -// for (var i = 0; i < array.length; i++){ -// if ((array[i] > q3) && (array[i]) <= aboveLimit){ -// points.push(array[i]); -// } -// } -// if (points.length > 0){ -// points.sort(function(a, b){return a - b;}); -// return points[points.length - 1]; -// } -// return null; -//}; - -RangeWhiskerGraph.prototype.drawPoints = function(boxProperties) { - if (this.plotPoints) { - for ( var i = 0; i < boxProperties.values.length; i++) { - var value = boxProperties.values[i]; - var toPixel = this.pointToPixel(value, boxProperties); - SVG.drawCircle(boxProperties.x, toPixel, this.pointRadius, this.svg, - [ - [ "fill", "green" ], [ "fill-opacity", this.fillOpacityPoint ], [ 'stroke-opacity', this.strokeOpacityPoint ], - [ "stroke", "black" ] ]); - } - } -}; - -RangeWhiskerGraph.prototype.plotRangeQ1Q3 = function(data, properties) { - var posX = this.left + this.rulerWidth; - - var boxBordersPointsQ1 = []; - var boxBordersPointsQ3 = []; - var Q2 = []; - - for ( var i = 0; i < data.clusters.length; i++) { - var cluster = data.clusters[i]; - /** inter cluster space **/ - posX = posX + this.interClustersSpace; - - for ( var j = 0; j < cluster.classes.length; j++) { - var ratio = properties.width / (properties.xValues.range); - var coorX = (cluster.x - properties.xValues.min) * ratio + this.rulerWidth; - var boxProperties = { - name : cluster.classes[j].name, - values : cluster.classes[j].values, - minPoint : properties.minPoint, - maxPoint : properties.maxPoint, - x : coorX + this.left, - y : this.top, - width : properties.classWidth, - height : this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight - }; - - var result = this.calculate(boxProperties.values); - var boxColor = this.getClassColor(boxProperties.name); - - if (this.isNumber(result.Q1) && this.isNumber(result.Q3)) { - var x = boxProperties.x; - var y = this.pointToPixel(result.Q1, boxProperties); - if (boxBordersPointsQ1[cluster.classes[j].name] == null) { - boxBordersPointsQ1[cluster.classes[j].name] = []; - } - boxBordersPointsQ1[cluster.classes[j].name].push({ - x : x, - y : y - }); - - x = boxProperties.x; - y = this.pointToPixel(result.Q3, boxProperties); - if (boxBordersPointsQ3[cluster.classes[j].name] == null) { - boxBordersPointsQ3[cluster.classes[j].name] = []; - } - boxBordersPointsQ3[cluster.classes[j].name].push({ - x : x, - y : y - }); - } else { - - if (this.isNumber(result.Q2)) { - - if (boxBordersPointsQ1[cluster.classes[j].name] == null) { - boxBordersPointsQ1[cluster.classes[j].name] = []; - } - - if (boxBordersPointsQ3[cluster.classes[j].name] == null) { - boxBordersPointsQ3[cluster.classes[j].name] = []; - } - - boxBordersPointsQ1[cluster.classes[j].name].push({ - x : boxProperties.x, - y : this.pointToPixel(result.Q2, boxProperties) - }); - boxBordersPointsQ3[cluster.classes[j].name].push({ - x : boxProperties.x, - y : this.pointToPixel(result.Q2, boxProperties) - }); - } - } - } - } - for ( var classe in boxBordersPointsQ1) { - var points = boxBordersPointsQ1[classe]; - var pointsSVG = ""; - for (var k = 0; k < points.length; k++) { - pointsSVG = Number(points[k].x).toFixed(1) + "," + Number(points[k].y).toFixed(1) + " " + pointsSVG; - } - - points = boxBordersPointsQ3[classe]; - for (var z = points.length - 1; z >= 0; z--) { - pointsSVG = Number(points[z].x).toFixed(1) + "," + Number(points[z].y).toFixed(1) + " " + pointsSVG; - } - - SVG.drawPoligon(pointsSVG, this.svg, [ - [ "fill", this.getClassColor(classe) ], [ "opacity", "0.3" ], [ "stroke", "black" ], [ "stroke-width", 1 ] ]); - } -}; - -RangeWhiskerGraph.prototype.plotWhisters = function(data, properties) { - var colors = [ "yellow", "orange", "green" ]; - - this.plotRangeQ1Q3(data, properties); - var Q2 = {}; - - for ( var i = 0; i < data.clusters.length; i++) { - var cluster = data.clusters[i]; - for ( var j = 0; j < cluster.classes.length; j++) { - var ratio = properties.width / (properties.xValues.range); - var coorX = (cluster.x - properties.xValues.min) * ratio + this.left + this.rulerWidth - this.rulerStroke; - var boxProperties = { - name : cluster.classes[j].name, - values : cluster.classes[j].values, - minPoint : properties.minPoint, - maxPoint : properties.maxPoint, - x : coorX, - y : this.top, - width : properties.classWidth, - height : this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight - }; - - this.drawPoints(boxProperties); - - /** PLOTTING Q2 **/ - var result = this.calculate(boxProperties.values); - var boxColor = this.getClassColor(boxProperties.name); - if (this.isNumber(result.Q2)) { - if (Q2[boxProperties.name] != null) { - SVG.drawLine(boxProperties.x, this.pointToPixel(result.Q2, boxProperties), Q2[boxProperties.name].x, Q2[boxProperties.name].y, - this.svg, [ [ "stroke", boxColor ], [ "stroke-width", "2" ] ]); - } - Q2[boxProperties.name] = { - x : boxProperties.x, - y : this.pointToPixel(result.Q2, boxProperties) - } - } - } - } - -}; - -RangeWhiskerGraph.prototype.draw = function(targetId, data) { - //this.calculate(data); - this.targetId = targetId; - var properties = (this.getDimensions(data)); - this.svg = SVG.createSVGCanvas(document.getElementById(this.targetId), [ [ "width", this.width ], [ "height", this.height ] ]); - this.plotAxes(properties); - this.plotWhisters(data, properties); -}; - -RangeWhiskerGraph.prototype.input = function() { - return DATADOC.getBoxWhikerData(); -}; - -RangeWhiskerGraph.prototype.test = function(targetId) { - var plot = new RangeWhiskerGraph({ - targetId : targetId, - height : 350, - width : 450, - maxBoxWidth : 25 - }); - plot.refresh(this.input()); -}; - -StdDevDyGraph.prototype.dblclick = DygraphWidget.prototype.dblclick; -StdDevDyGraph.prototype._createHTLMWrapper = DygraphWidget.prototype._createHTLMWrapper; -StdDevDyGraph.prototype.draw = DygraphWidget.prototype.draw; - -function StdDevDyGraph(targetId, args) { - this.scaled = false; - if (args == null) { - args = {}; - } - args.customBars = true; - DygraphWidget.prototype.constructor.call(this, targetId, args); -} - -StdDevDyGraph.prototype.input = function () { - return { - data : [ [ 1, [ 2, 3, 3.5 ], [ 4, 4.2, 5 ] ], [ 2, [ 5, 5.5, 5.7 ], [ 4, 4.2, 5 ] ] ], - colors : [ "blue", "red" ], - labels : [ "", 'data1', 'data2' ] - }; -}; - -StdDevDyGraph.prototype.test = function (targetId) { - var dygraphObject = new StdDevDyGraph(targetId, { - width : 500, - height : 400, - xlabel : "xLabel", - showRangeSelector : false - }); - - dygraphObject.draw(dygraphObject.input().data, dygraphObject.input().colors, dygraphObject.input().labels); -}; - - - -function AbinitioGrid(args) { - this.height = null; - this.width = null; - this.id = BUI.id(); - - if (args != null) { - if (args.height != null) { - this.height = args.height; - - if (args.width != null) { - this.width = args.width; - } - } - } - - this.onSelected = new Event(this); -}; - - -AbinitioGrid.prototype.refresh = function(subtractions){ - this.store.loadData(this._prepareData(subtractions)); -}; - -AbinitioGrid.prototype._prepareData = function(subtractions){ - /** Parsing data * */ - var models = []; - for (var l = 0; l < subtractions.length; l++) { - var subtraction = subtractions[l]; - for (var k = 0; k < subtraction.substractionToAbInitioModel3VOs.length; k++) { - var data = subtraction.substractionToAbInitioModel3VOs[k].abinitiomodel3VO; - if (data.averagedModel != null) { - models.push(data.averagedModel); - models[models.length - 1].type = "Reference"; - } - - if (data.shapeDeterminationModel != null) { - models.push(data.shapeDeterminationModel); - models[models.length - 1].type = "Refined"; - } - - if (data.modelList3VO != null) { - if (data.modelList3VO.modeltolist3VOs != null) { - for (var i = 0; i < data.modelList3VO.modeltolist3VOs.length; i++) { - models.push(data.modelList3VO.modeltolist3VOs[i].model3VO); - models[models.length - 1].type = "Model"; - } - } - } - } - } - return models; -}; - -AbinitioGrid.prototype.getPanel = function(){ - var _this = this; - - - var modelFields = [ "modelId", "type", "chiSqrt", "dmax", "firFile", "logFile", "fitFile", "pdbFile", "rfactor", "rg", "volume" ]; - Ext.define('AbinitioModel', { - extend : 'Ext.data.Model', - fields : modelFields - - }); - - /** - * Store in Memory - */ - this.store = Ext.create('Ext.data.Store', { - model : 'AbinitioModel', - autoload : true, - groupField : 'type' - }); - - - var groupingFeature = Ext.create('Ext.grid.feature.Grouping',{ - groupHeaderTpl: '{name} ({rows.length} model{[values.rows.length > 1 ? "s" : ""]})', - startCollapsed: true, - collapsible : true - }); - - this.grid = Ext.create('Ext.grid.Panel', { - collapsible : false, - resizable : true, - features: [groupingFeature], - autoscroll : true, - multiSelect : true, - store : this.store, - height : this.height, - width : this.width, - margin : 10, - columns : [ { - text : "Type", - dataindex : "type", - hidden : true, - renderer : function(a, b, record) { - return record.data.type; - }, - flex : 1 - }, - { - text : "ModelId", - dataindex : "modelId", - hidden : true, - renderer : function(a, b, record) { - return record.data.modelId; - - }, - flex : 1 - }, - - { - text : "chiSqrt", - dataindex : "chiSqrt", - renderer : function(a, b, record) { - if (record.data.dmax != null) { - return BUI.formatValuesUnits(record.data.chiSqrt, "", 12, this.decimals); - } - - }, - flex : 1 - }, - { - text : "Dmax", - dataindex : "dmax", - renderer : function(a, b, record) { - if (record.data.dmax != null) { - return BUI.formatValuesUnits(record.data.dmax, "nm", 12, this.decimals); - } - - }, - flex : 1 - }, { - text : "rFactor", - dataindex : "rfactor", - hidden : true, - renderer : function(a, b, record) { - if (record.data.rfactor != null) { - return record.data.rfactor; - } - }, - flex : 1 - }, { - text : "Rg", - dataindex : "rg", - renderer : function(a, b, record) { - if (record.data.rg != null) { - return BUI.formatValuesUnits(record.data.rg, "nm", 12, this.decimals); - } - - }, - flex : 1 - }, - { - text : "Volume", - dataindex : "volume", - renderer : function(a, b, record) { - if (record.raw.volume != null){ - return BUI.formatValuesUnits(record.raw.volume, '') + " nm3"; - } - }, - flex : 1 - }, - { - text : "PDB", - dataindex : "pdbFile", - renderer : function(a, b, record) { - if (record.data.pdbFile != null){ - return record.data.pdbFile.split("/")[record.data.pdbFile.split("/").length - 1]; - } - }, - flex : 1 - }, { - text : "Fir", - dataindex : "firFile", - renderer : function(a, b, record) { - if (record.data.firFile != null){ - return record.data.firFile.split("/")[record.data.firFile.split("/").length - 1]; - } - }, - flex : 1 - }, { - text : "LOG", - dataindex : "logFile", - hidden : true, - renderer : function(a, b, record) { - if (record.data.logFile != null){ - return record.data.logFile.split("/")[record.data.logFile.split("/").length - 1]; - } - }, - flex : 1 - } - ], - viewConfig : { - enableTextSelection : true, - preserveScrollOnRefresh : true, - stripeRows : true, - listeners : { - 'celldblclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - }, - 'cellclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - var models = []; - for (var i = 0; i < grid.getSelectionModel().selected.items.length; i++) { - models.push(grid.getSelectionModel().selected.items[i].raw); - } - _this.onSelected.notify(models); - } - } - } - }); - return this.grid; - -}; - - -function AdditiveGrid(args) { - this.onRemoveButtonClicked = new Event(this); -} - -AdditiveGrid.prototype.getBuffer = function() { - return this.buffer; -}; - -AdditiveGrid.prototype._getActions = function() { - var _this = this; - /** Actions buttons **/ - var actions = []; - - actions.push(Ext.create('Ext.Action', { - icon : '../images/add.png', - text : 'Add', - disabled : true, - alwaysEnabled : true, - handler : function(widget, event) { - _this.buffer.bufferhasadditive3VOs.push(BIOSAXS_BEANS.getBufferhasAdditive3VO()); - _this.refresh(_this.buffer, _this.experiment); - } - })); - - return actions; -}; - -AdditiveGrid.prototype.refresh = function(buffer, experiment) { - this.buffer = buffer; - this.experiment = experiment; - if (buffer) { - if (buffer.bufferhasadditive3VOs) { - this.features = buffer.bufferhasadditive3VOs; - } - } - this.experiment = experiment; - this.store.loadData(this._prepareData(), false); -}; - -AdditiveGrid.prototype.getAdditives = function() { - var additives = []; - for ( var i = 0; i < this.store.getCount(); i++) { - var bufferHasAdditive = BIOSAXS_BEANS.getBufferhasAdditive3VO(); - var data = this.store.getAt(i).getData(); - - bufferHasAdditive.additive3VO.name = data.name; - bufferHasAdditive.additive3VO.comments = data.comments; - bufferHasAdditive.additive3VO.additiveType = data.additiveType; - - bufferHasAdditive.bufferId = this.buffer.bufferId; - bufferHasAdditive.bufferHasAdditiveId = data.bufferHasAdditiveId; - bufferHasAdditive.quantity = data.quantity; - additives.push(bufferHasAdditive); - } - - return additives; -}; - -AdditiveGrid.prototype._getFields = function(buffers) { - var columns = [ - - { - header : 'Name', - dataIndex : 'name', - type : 'string', - editor : { - allowBlank : true - }, - flex : 1 - }, - { - header : 'Type', - name : 'additiveType', - dataIndex : 'additiveType', - editor : { - xtype : 'combobox', - typeAhead : true, - triggerAction : 'all', - selectOnTab : true, - store : BIOSAXS.proposal.getAdditiveTypes(), - lazyRender : true, - listClass : 'x-combo-list-small' - }, - flex : 0.6 - }, - { - header : 'Quantity', - dataIndex : 'quantity', - name : 'quantity', - editor : { - allowBlank : true - }, - type : 'string', - flex : 1 - }, - { - xtype : 'actioncolumn', - items : [ { - icon : '../images/cancel.png', - tooltip : 'Delete additive', - scope : this, - handler : function(grid, rowIndex, colIndex) { - if ((grid.getStore().getAt(rowIndex).data.bufferHasAdditiveId == null)|| (grid.getStore().getAt(rowIndex).data.bufferHasAdditiveId == "")) { - grid.getStore().removeAt(rowIndex); - } else { - this.onRemoveButtonClicked.notify({ - 'bufferId' : this.buffer.bufferId, - 'bufferHasAdditiveId' : this.store.getAt(rowIndex).data.bufferHasAdditiveId - }); - } - } - } ] - } ]; - - return columns; -}; - -AdditiveGrid.prototype._prepareData = function() { - var data = []; - if (this.features == null) { - this.features = []; - } - for (var i = 0; i < this.features.length; i++) { - var object = this.features[i]; - object.name = this.features[i].additive3VO.name; - object.additiveType = this.features[i].additive3VO.additiveType; - object.comments = this.features[i].additive3VO.comments; - object.additiveId = this.features[i].additive3VO.additiveId; - data.push(object); - } - return data; -}; - -AdditiveGrid.prototype.getPanel = function(buffer, experiment) { - this.buffer = buffer; - this.features = buffer.bufferhasadditive3VOs; - this.experiment = experiment; - return this._renderGrid(); -}; - -AdditiveGrid.prototype.getStore = function() { - var _this = this; - var store = Ext.create('Ext.data.Store', { - fields : [ "name", "additiveType", "comments", "additiveId", "bufferHasAdditiveId", "quantity" ], - autoload : false, - data : this._prepareData(), - listeners : { - update : function(store, record) { - record.index = _this.grid.getSelectionModel().getCurrentPosition().row; - _this.buffer.bufferhasadditive3VOs[record.index].additive3VO.name = record.data.name; - _this.buffer.bufferhasadditive3VOs[record.index].additive3VO.additiveType = record.data.additiveType; - _this.buffer.bufferhasadditive3VOs[record.index].additive3VO.comments = record.data.comments; - _this.buffer.bufferhasadditive3VOs[record.index].quantity = record.data.quantity; - } - } - }); - - // store.sort('bufferHasAdditiveId', 'ASC'); - store.loadData(this._prepareData(), false); - return store; -}; - -AdditiveGrid.prototype._renderGrid = function() { - var _this = this; - this.store = this.getStore(); - - var cellEditing = Ext.create('Ext.grid.plugin.CellEditing', { - clicksToEdit : 1 - }); - - this.grid = Ext.create('Ext.grid.Panel', { - dockedItems : [ { - xtype : 'toolbar', - items : this._getActions() - } ], - store : this.store, - height : 230, - title : "Additives", - width : "100%", - columns : _this._getFields(), - plugins : [ cellEditing ], - viewConfig : { - stripeRows : true, - listeners : { - itemcontextmenu : function(view, rec, node, index, e) { - e.stopEvent(); - contextMenu.showAt(e.getXY()); - return false; - } - } - }, - selModel : { - mode : 'SINGLE' - } - }); - - return this.grid; -}; - -AdditiveGrid.prototype.input = function() { -}; - -AdditiveGrid.prototype.test = function(targetId) { - var grid = new AdditiveGrid(); - var panel = grid.getPanel([]); - panel.render(targetId); - -}; - -/** AnalysisGrid **/ -function AnalysisGrid(args) { - var _this = this; - - this.id = BUI.id(); - if (Ext.get("mainPanel")){ - this.width = Ext.get("mainPanel").getWidth(); - } - else{ - this.width = this.maxWidth; - } - this.maxWidth = 1500; - - /** Visibles **/ - this.isGuinierTabVisible = true; - this.isGnomTabVisible = true; - this.isPorodTabVisible = true; - this.isScatteringPlotVisible = true; - this.isAbinitioTabVisible = true; - this.showButtonsVisible = true; - this.isI0Visible = true; - - this.margin = null; - this.grouped = true; - - this.hideNulls = false; - this.decimals = 4; - this.height = null; - this.sorters = [ { - property : 'conc', - direction : 'ASC' - } ]; - - if (args != null) { - if (args.grouped != null) { - this.grouped = args.grouped; - } - - if (args.showButtonsVisible != null) { - this.showButtonsVisible = args.showButtonsVisible; - } - if (args.isI0Visible != null) { - this.isI0Visible = args.isI0Visible; - } - if (args.sorters != null) { - this.sorters = args.sorters; - } - if (args.isScatteringPlotVisible != null) { - this.isScatteringPlotVisible = args.isScatteringPlotVisible; - } - if (args.isGuinierTabVisible != null) { - this.isGuinierTabVisible = args.isGuinierTabVisible; - } - if (args.isGnomTabVisible != null) { - this.isGnomTabVisible = args.isGnomTabVisible; - } - if (args.isPorodTabVisible != null) { - this.isPorodTabVisible = args.isPorodTabVisible; - } - if (args.hideNulls != null) { - this.hideNulls = args.hideNulls; - } - if (args.height != null) { - this.height = args.height; - } - if (args.width != null) { - this.width = args.width; - } - if (args.maxWidth != null) { - this.maxWidth = args.maxWidth; - } - } -} - -AnalysisGrid.prototype.refresh = function(data, args) { - this.store.loadData(this._prepareData(data), false); - if (args != null){ - if (args.experiment != null){ - this.experiment = args.experiment; - } - } -}; - -AnalysisGrid.prototype._getPorod = function() { - return { - text : 'Porod', - name : 'Porod', - columns : [ - { - text : 'Volume', - dataIndex : 'volumeEdna', - width : 75, - sortable : true, - hidden : !this.isPorodTabVisible, - renderer : function(val, y, sample) { - if (sample.raw.volume != null) - return BUI.formatValuesUnits(sample.raw.volume, '') + " nm3"; - } - }, - { - text : 'MM Vol. est.', - dataIndex : 'volumeEdna', - tooltip : '[Volume/2 - Volume/1.5] (Guinier)', - sortable : true, - width : 95, - hidden : !this.isPorodTabVisible, - renderer : function(val, y, sample) { - if (sample.raw.volume != null) - return Number(sample.raw.volume / 2).toFixed(1) + " - " + Number(sample.raw.volume / 1.5).toFixed(1)+ "kD"; - } - } ] - }; -}; - - -AnalysisGrid.prototype._getFramesColumn = function() { - var _this = this; - return { - text : 'Frames (Averaged/Total)', - dataIndex : 'datacollection', - name : 'datacollection', - sortable : true, - width : 150, - renderer : function(dataCollections, y, data) { - /** Bug of Webservices: frames count were swapped with frames averages **/ - if (data.raw.bufferAfterFramesCount){ - if (data.raw.bufferAfterFramesMerged){ - if (parseInt(data.raw.bufferAfterFramesMerged) > parseInt(data.raw.bufferAfterFramesCount)){ - var aux = parseInt(data.raw.bufferAfterFramesCount); - data.raw.bufferAfterFramesCount= data.raw.bufferAfterFramesMerged; - data.raw.bufferAfterFramesMerged = aux; - } - } - } - - if (data.raw.bufferBeforeFramesCount){ - if (data.raw.bufferBeforeFramesMerged){ - if (parseInt(data.raw.bufferBeforeFramesMerged) > parseInt(data.raw.bufferBeforeFramesCount)){ - var aux = parseInt(data.raw.bufferBeforeFramesCount); - data.raw.bufferBeforeFramesCount= data.raw.bufferBeforeFramesMerged; - data.raw.bufferBeforeFramesMerged = aux; - } - } - - } - - var bufferAcronym = data.raw.bufferAcronym; - var macromoleculeAcronym = data.raw.macromoleculeAcronym; - var bbmerges = data.raw.bufferBeforeFramesMerged; - var molmerges = data.raw.framesMerge; - var bamerges = data.raw.bufferAfterFramesMerged; - var totalframes = data.raw.framesCount; - var bufferId = data.raw.bufferId; - var macromoleculeId = data.raw.macromoleculeId; - var macromoleculeColor = null; - if (_this.experiment != null){ - macromoleculeColor = _this.experiment.macromoleculeColors[data.raw.macromoleculeId]; - } - - /** BUG in the database to be fixed **/ - try{ - if (totalframes != null){ - if(molmerges != null){ - if (parseFloat(totalframes) < parseFloat(molmerges)){ - var aux = totalframes; - totalframes = molmerges; - molmerges = aux; - } - } - } - } - catch(e){ - - } - - return BUI.getHTMLTableForFrameAveraged(bufferAcronym, - macromoleculeAcronym, - bbmerges, - molmerges, - bamerges, - totalframes, - bufferId, - macromoleculeId, - macromoleculeColor); - } - }; -}; - -AnalysisGrid.prototype._getColumns = function() { - var _this = this; - return [ - { - name : 'groupeField', - dataIndex : 'groupeField', - hidden : true - - }, - { - "header" : "subtractionId", - hidden : true, - "dataIndex" : "subtractionId", - "name" : "subtractionId" - }, - { - header : "Macromolecule", - dataIndex : "macromoleculeAcronym", - name : "macromoleculeAcronym", - renderer : function(val, y, sample) { - return '
' + val + '
' + - BUI.formatValuesUnits(sample.raw.conc, "mg/ml", 10, this.decimals) + '
' + - BUI.formatValuesUnits(sample.raw.exposureTemperature, "C", 10, this.decimals) + '
' - } - }, - { - header : "Order", - dataIndex : "priorityLevelId", - name : "priorityLevelId", - hidden : true - }, - { - header : "Code", - dataIndex : "code", - name : "code", - hidden : true - }, - { - header : "Conc.", - dataIndex : "conc", - width : 80, - name : "conc", - type : "number", - hidden : true, - renderer : function(val, y, sample) { - return BUI.formatValuesUnits(val, "mg/ml", 10, this.decimals); - } - }, - { - text : 'Scattering', - width : 100, - dataIndex : 'subtractionId', - name : 'subtractionId', - hidden : !this.isScatteringPlotVisible, - renderer : function(val, y, sample) { - var url = BUI.getURL() + '&type=scattering&subtractionId=' + sample.raw.subtractionId; - var event = "OnClick= window.open('" + url + "')"; - return ''; - } - }, - { - text : 'Kratky', - width : 100, - dataIndex : 'subtractionId', - hidden : true, - name : 'subtractionId', - renderer : function(val, y, sample) { - var url = BUI.getURL() + '&type=kratky&subtractionId=' + sample.raw.subtractionId; - var event = "OnClick= window.open('" + url + "')"; - return ''; - } - }, - this._getFramesColumn(), - { - text : 'File Name', - dataIndex : 'averageFilePath', - name : 'averageFilePath', - sortable : true, - width : 150, - hidden : true, - renderer : function(dataCollections, y, data) { - return BUI.getHTMLTableForPrefixes(data.raw.bufferBeforeAverageFilePath, data.raw.averageFilePath, - data.raw.bufferAfterAverageFilePath); - } - }, - - { - text : 'Guinier', - name : 'Guinier', - columns : [ - { - text : 'Rg', - dataIndex : 'rgGuinier', - name : 'rgGuinier', - hidden : !this.isGuinierTabVisible, - width : 75, - tooltip : 'In polymer physics, the radius of gyration is used to describe the dimensions of a polymer chain.', - sortable : true, - renderer : function(val, y, sample) { - if (sample.raw.rgGuinier != null) { - /** Show warning if rgGuinier and rgGnom differ more than 10% **/ - if (Math.abs(sample.raw.rgGuinier - sample.raw.rgGnom) > (sample.raw.rgGuinier * 0.1)) { - return "" + BUI.formatValuesUnits(sample.raw.rgGuinier, "") + ""; - - } - return BUI.formatValuesUnits(sample.raw.rgGuinier, "nm", 12, this.decimals); - } - } - }, - { - text : 'Points', - dataIndex : 'points', - sortable : true, - width : 100, - type : 'string', - hidden : !this.isGuinierTabVisible, - renderer : function(val, y, sample) { - if ((sample.raw.firstPointUsed == "") || (sample.raw.firstPointUsed == null)) - return; - return "" + sample.raw.firstPointUsed + " - " + sample.raw.lastPointUsed + " (" + - (sample.raw.lastPointUsed - sample.raw.firstPointUsed) + " )"; - } - }, - { - text : 'Quality', - dataIndex : 'quality', - hidden : !this.isGuinierTabVisible, - tooltip : 'Estimated data quality. 1.0 - means ideal quality, 0.0 - unusable data. In table format it is given in percent (100% - ideal quality, 0% - unusable data). Please note that this estimation is based only on the Guinier interval (very low angles).', - width : 60, - sortable : true, - renderer : function(val, y, sample) { - if (sample.raw.quality != null) { - val = sample.raw.quality; - if ((val != null) && (val != "")) { - return "" + (Number(val) * 100).toFixed(2) + " %"; - } - } - } - }, { - text : 'I(0)', - dataIndex : 'I0', - sortable : true, - hidden : !this.isI0Visible, - tooltip : 'Extrapolated scattering intensity at zero angle I(0) (forward scattering)', - width : 75, - type : 'string', - renderer : function(val, y, sample) { - if (sample.raw.I0 != null) { - return BUI.formatValuesErrorUnitsScientificFormat(sample.raw.I0, sample.raw.i0stdev, ""); - } - } - }, { - text : 'Aggregated', - tooltip : "If aggregation was detected from the slope of the data curve at low angles the value is '1', otherwise '0'.", - dataIndex : 'isagregated', - hidden : true, - width : 75, - renderer : function(val, y, sample) { - if ((sample.raw.isagregated != null)) { - if (val == true) { - return "Yes"; - } else { - return "No"; - } - } - } - }, { - text : 'Guinier', - sortable : true, - dataIndex : 'subtractionId', - type : 'string', - width : 100, - hidden : true, - renderer : function(val, y, sample) { - - if (sample.raw.subtractionId != null) { - var url = BUI.getURL() + '&type=guinier&subtractionId=' + sample.raw.subtractionId; - var event = "OnClick= window.open('" + url + "')"; - return ''; - } - } - } ] - }, - { - text : 'Gnom', - name : 'Gnom', - - columns : [ { - text : 'Rg', - dataIndex : 'rgGnom', - type : 'string', - width : 65, - hidden : !this.isGnomTabVisible, - sortable : true, - renderer : function(val, y, sample) { - /** Show warning if rgGuinier and rgGnom differ more than 10% **/ - if (sample.raw.rgGnom != null) { - if (Math.abs(sample.raw.rgGuinier - sample.raw.rgGnom) > (sample.raw.rgGuinier * 0.1)) { - return "" + BUI.formatValuesUnits(sample.raw.rgGnom, "") + ""; - - } - return BUI.formatValuesUnits(sample.raw.rgGnom, "nm"); - } - } - }, { - text : 'Total', - dataIndex : 'total', - width : 65, - hidden : !this.isGnomTabVisible, - sortable : true, - renderer : function(val, y, sample) { - if (sample.raw.total != null) - return BUI.formatValuesUnits(sample.raw.total, ''); - } - }, { - text : 'Dmax', - dataIndex : 'dmax', - sortable : true, - width : 75, - hidden : !this.isGnomTabVisible, - renderer : function(val, y, sample) { - if (sample.raw.dmax != null) - return BUI.formatValuesUnits(sample.raw.dmax, "") + " nm"; - } - }, { - text : 'P(r)', - sortable : true, - hidden : true, - width : 100, - dataIndex : 'subtractionId', - type : 'string', - renderer : function(val, y, sample) { - var url = BUI.getURL() + '&type=gnom&subtractionId=' + sample.raw.subtractionId; - var event = "OnClick= window.open('" + url + "')"; - return ''; - } - } ] - }, - this._getPorod(), - { - text : 'AbInitio Modeling', - name : 'AbInitio_modeling', - - columns : [ - { - text : 'NSD', - dataIndex : 'volumeEdna', - width : 100, - sortable : true, - hidden : true, - renderer : function(val, y, sample) { - var url = BUI.getNSDImageURL(sample.raw.modelListId); - var event = "OnClick= window.open('" + url + "')"; - return ''; - } - }, - { - text : 'Chi2', - dataIndex : 'volumeEdna', - sortable : true, - hidden : true, - width : 100, - renderer : function(val, y, sample) { - var url = BUI.getCHI2ImageURL(sample.raw.modelListId); - var event = "OnClick= window.open('" + url + "')"; - return ''; - } - }, - { - text : 'Pdb', - dataIndex : 'volumeEdna', - tooltip : 'Damaver: The program suite DAMAVER is a set of programs to align ab initio models, select the most typical one and build an averaged model. Dammif : Rapid ab initio shape determination by simulated annealing using a single phase dummy atom model. Dammin :Ab initio shape determination by simulated annealing using a single phase dummy atom model', - sortable : true, - width : 125, - hidden : !this.isAbinitioTabVisible, - renderer : function(val, y, sample) { - var html = new String(); - var split = null; - var url = null; - var file = sample.raw.averagedModel; - if (file != null) { - split = file.split("/"); - if (split.length > 0) { - url = BUI.getPdbURL() + '&type=AVERAGED&abInitioModelId=' + sample.raw.abInitioModelId; - html = html + ''+ split[split.length - 1] + '

'; - - } - } - - file = sample.raw.rapidShapeDeterminationModel; - if (file != null) { - split = file.split("/"); - if (split.length > 0) { - url = BUI.getPdbURL() + '&type=RAPIDSHAPEDETERMINATIONMODEL&abInitioModelId=' + sample.raw.abInitioModelId; - html = html + '' + split[split.length - 1] + '

'; - } - } - - file = sample.raw.shapeDeterminationModel; - if (file != null) { - split = file.split("/"); - if (split.length > 0) { - url = BUI.getPdbURL() + '&type=SHAPEDETERMINATIONMODEL&abInitioModelId=' + sample.raw.abInitioModelId; - html = html + ''+ split[split.length - 1] + ''; - } - } - return html; - } - }, - { - text : 'Damaver', - dataIndex : 'volumeEdna', - hidden : true, - tooltip : 'Damaver: The program suite DAMAVER is a set of programs to align ab initio models, select the most typical one and build an averaged model. ', - sortable : true, - width : 125, - renderer : function(val, y, sample) { - var file = sample.raw.averagedModel; - if (file != null) { - var split = file.split("/"); - if (split.length > 0) { - var url = BUI.getPdbURL() + '&type=AVERAGED&abInitioModelId=' + sample.raw.abInitioModelId; - return '' + split[split.length - 1]+ ''; - } - } - return sample.raw.averagedModel; - } - }, - { - text : 'Dammif', - dataIndex : 'volumeEdna', - hidden : true, - tooltip : 'Dammif : Rapid ab initio shape determination by simulated annealing using a single phase dummy atom model', - sortable : true, - width : 125, - renderer : function(val, y, sample) { - var file = sample.raw.rapidShapeDeterminationModel; - if (file != null) { - var split = file.split("/"); - if (split.length > 0) { - var url = BUI.getPdbURL() + '&type=RAPIDSHAPEDETERMINATIONMODEL&abInitioModelId=' + sample.raw.abInitioModelId; - return '' + split[split.length - 1] + ''; - } - } - return sample.raw.averagedModel; - } - }, - { - text : 'Dammin', - dataIndex : 'volumeEdna', - hidden : true, - tooltip : 'Dammin :Ab initio shape determination by simulated annealing using a single phase dummy atom model', - sortable : true, - width : 125, - renderer : function(val, y, sample) { - var file = sample.raw.shapeDeterminationModel; - if (file != null) { - var split = file.split("/"); - if (split.length > 0) { - var url = BUI.getPdbURL() + '&type=SHAPEDETERMINATIONMODEL&abInitioModelId=' + sample.raw.abInitioModelId; - return '' + split[split.length - 1]+ ''; - } - } - return sample.raw.averagedModel; - } - } ] - }, { - text : 'Time', - dataIndex : 'substractionCreationTime', - name : 'substractionCreationTime', - hidden : true, - width : 80, - sortable : true, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - try { - if (record.raw.substractionCreationTime != null) { - return moment(record.raw.substractionCreationTime).format('h:mm:ss a'); - } - } catch (e) { - return "NA"; - } - } - }, { - text : 'Date', - dataIndex : 'substractionCreationTime', - name : 'substractionCreationTime', - hidden : true, - width : 80, - sortable : true, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - try { - if (record.raw.substractionCreationTime != null) { - return moment(record.raw.substractionCreationTime).format("LL"); - } - } catch (e) { - return "NA"; - } - } - }, - this._getButtons()]; -}; - -AnalysisGrid.prototype._getButtons = function() { - return { - id : this.id + 'buttonPlot', - name : 'buttonPlot', - hidden : !this.showButtonsVisible, - width : 110, - sortable : false, - renderer : function(value, metaData, sample, rowIndex, colIndex, store) { - var html = ""; - - if (sample.raw.subtractionId) { - html = html + ""; - if (sample.raw.rapidShapeDeterminationModelId != null) { - html = html + ""; - } - } - return html + "
" + BUI.getGreenButton('Calibration', { - height : 20, - width : 100 - }) + "
" + BUI.getGreenButton('Primary Data Proc.', { - height : 20, - width : 100 - }) + "
" + BUI.getGreenButton('AbInitio Modeling', { - height : 20, - width : 100 - }) + "
"; - } - }; -}; -AnalysisGrid.prototype._prepareData = function(data) { - if (this.hideNulls) { - var result = []; - for ( var i = 0; i < data.length; i++) { - if (data[i].subtractionId != null) { - data[i].groupeField = data[i].macromoleculeAcronym + " " + data[i].bufferAcronym; - result.push(data[i]); - } - } - return result; - } else { - return data; - } -}; - -AnalysisGrid.prototype.getPanel = function(data) { - var _this = this; - var columns = this._getColumns(); - - var fields = JSON.parse(JSON.stringify(columns)); - fields.push({ - name : 'experimentId', - dataIndex : 'experimentId' - - }); - this.store = Ext.create('Ext.data.Store', { - fields : fields, - autoload : true, - data : this._prepareData(data), - groupField : 'groupeField' - }); - - this.store.sort(this.sorters); - - var features = []; - - if (this.grouped) { - features.push({ - ftype : 'grouping', - groupHeaderTpl : '{name}', - hideGroupedHeader : false, - startCollapsed : false - }); - } - - this.grid = Ext.create('Ext.grid.Panel', { - style : { - padding : 5 - }, - maxWidth : this.maxWidth, - width : this.width, - height : this.height, - store : this.store, - columns : columns, - resizable : true, - features : features, - viewConfig : { - preserveScrollOnRefresh : true, - stripeRows : true, - listeners : { - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonPlot') { - if (e.target.defaultValue == 'AbInitio Modeling') { - var url = BUI.getPDBVisualizerURL(record.raw.averagedModelId, record.raw.subtractionId, record.raw.experimentId); - window.open(url, "_blank"); - } - - if (e.target.defaultValue == 'Primary Data Proc.') { - _this._edit(record.raw); - } - - if (e.target.defaultValue == 'Calibration') { - _this._showCalibration(record.raw); - } - } - } - } - }, - selModel : { - mode : 'SINGLE' - } - }); - - return this.grid; - -}; - -AnalysisGrid.prototype._openVisualizarBySubstractionId = function(record) { - //experimentId, subtractionId) { - var experimentId = record.experimentId; - var subtractionId = record.subtractionId; - - var _this = this; - var adapter = new BiosaxsDataAdapter(); - this.subtractionId = subtractionId; - - adapter.onSuccess.attach(function(sender, data) { - var experiment = new Experiment(data); - var experimentList = new ExperimentList([ experiment ]); - var subtraction = experiment.getSubtractionById(_this.subtractionId); - _this.grid.setLoading(false); - _this._openVisualizer(experimentList, subtraction, record); - }); - this.grid.setLoading("ISPyB: Fetching experiment"); - adapter.getExperimentById(experimentId, "MEDIUM"); -}; - -AnalysisGrid.prototype._edit = function(record) { - var experimentId = record.experimentId; - var _this = this; - - if (BIOSAXS.proposal.macromolecules == null) { - this.grid.setLoading("ISPyB: Fetching proposal"); - BIOSAXS.proposal.onInitialized.attach(function(sender, data) { - _this._openVisualizarBySubstractionId(record); - }); - BIOSAXS.proposal.init(); - } else { - this._openVisualizarBySubstractionId(record); - } -}; - - -AnalysisGrid.prototype._showCalibration = function(row) { - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - Ext.create('Ext.window.Window', { - title : 'Calibration', - width : 900, - resizable : true, - height : 400, - modal : true, - frame : false, - draggable : true, - closable : true, - autoscroll : true, - paddin : 5, - layout : { - type : 'vbox', - align : 'stretch' - }, - items : [ new AnalysisGrid({ - isGuinierTabVisible : false, - isGnomTabVisible : false, - isPorodTabVisible : false, - isAbinitioTabVisible : false, - isI0Visible : true, - showButtonsVisible : false, - height : 350, - sorters : [ { - property : 'experimentId', - direction : 'DESC' - } ] - }).getPanel(data) ] - }).show(); - }); - adapter.getAnalysisCalibrationByProposalId(); -}; - -AnalysisGrid.prototype._openVisualizer = function(experimentList, subtraction, record) { - var merges = experimentList.getMergesByDataCollectionId(subtraction.dataCollectionId); - var mergeIdList = []; - for ( var i = 0; i < merges.length; i++) { - mergeIdList.push(merges[i].mergeId); - } - - var dataAdapter = new BiosaxsDataAdapter(); - dataAdapter.onSuccess.attach(function(sender, merges) { - var dataCollectionCurveVisualizer = new DataCollectionCurveVisualizer(); - dataCollectionCurveVisualizer.draw(); - dataCollectionCurveVisualizer.refresh(merges, experimentList, subtraction.dataCollectionId, record); - }); - - dataAdapter.onError.attach(function(sender, error) { - }); - - dataAdapter.getMergesByIdsList(mergeIdList); -}; - -AnalysisGrid.prototype.input = function() { - return { - data : DATADOC.getData_3367().slice(20, 30),//[{"total":"0.447505552082","bufferBeforeMeasurementId":22150,"sampleMergeId":12373,"averagedModelId":43636,"I0":"32.50776","proposalCode":"OPD","averagedModel":"/data/pyarch/bm29/opd29/1137/1d/damaver.pdb","bufferAfterMergeId":12374,"framesCount":"10","bufferBeforeMergeId":12372,"averageFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_016_ave.dat","bufferAfterMeasurementId":22152,"rgGuinier":"2.96883","subtractedFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_016_sub.dat","firstPointUsed":"30","chi2RgFilePath":"/data/pyarch/bm29/opd29/1137/1d/chi2_R.png","abInitioModelId":272,"macromoleculeId":112,"code":"_20.0_1.25","transmission":"100.0","timeStart":"2013-07-17 17:10:25.743734","bufferAcronym":"MES","quality":"0.87091","shapeDeterminationModelId":43638,"expermientComments":"[BsxCube] Generated from BsxCube","bufferId":707,"isagregated":"False","dmax":"10.390905","bufferBeforeAverageFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_015_ave.dat","exposureTemperature":"20.0","subtractionId":5165,"conc":"1.25","rapidShapeDeterminationModel":"/data/pyarch/bm29/opd29/1137/1d/damfilt.pdb","experimentCreationDate":"Jul 17, 2013 5:08:37 PM","lastPointUsed":"92","modelListId":272,"framesMerge":"10","rapidShapeDeterminationModelId":43637,"bufferAfterAverageFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_017_ave.dat","nsdFilePath":"/data/pyarch/bm29/opd29/1137/1d/nsd.png","bufferAfterFramesMerged":"10","experimentId":1137,"macromoleculeAcronym":"MG386","i0stdev":"0.05726128","sampleMeasurementId":22151,"measurementComments":"[1] MES","priorityLevelId":2,"bufferBeforeFramesMerged":"10","substractionCreationTime":"Jul 17, 2013 5:12:32 PM","proposalNumber":"29","rgGnom":"3.05242714339","volume":"44.1406","shapeDeterminationModel":"/data/pyarch/bm29/opd29/1137/1d/dammin.pdb","comments":null},{"total":"0.582641941147","bufferBeforeMeasurementId":22152,"sampleMergeId":12375,"averagedModelId":43809,"I0":"31.4366153846","proposalCode":"OPD","averagedModel":"/data/pyarch/bm29/opd29/1137/1d/damaver.pdb","bufferAfterMergeId":12376,"framesCount":"10","bufferBeforeMergeId":12374,"averageFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_018_ave.dat","bufferAfterMeasurementId":22155,"rgGuinier":"2.95541","subtractedFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_018_sub.dat","firstPointUsed":"21","chi2RgFilePath":"/data/pyarch/bm29/opd29/1137/1d/chi2_R.png","abInitioModelId":273,"macromoleculeId":112,"code":"_20.0_0.65000000000000002","transmission":"100.0","timeStart":"2013-07-17 17:12:55.837462","bufferAcronym":"MES","quality":"0.870164","shapeDeterminationModelId":43811,"expermientComments":"[BsxCube] Generated from BsxCube","bufferId":707,"isagregated":"False","dmax":"10.343935","bufferBeforeAverageFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_017_ave.dat","exposureTemperature":"20.0","subtractionId":5166,"conc":"0.65000000000000002","rapidShapeDeterminationModel":"/data/pyarch/bm29/opd29/1137/1d/damfilt.pdb","experimentCreationDate":"Jul 17, 2013 5:08:37 PM","lastPointUsed":"80","modelListId":273,"framesMerge":"10","rapidShapeDeterminationModelId":43810,"bufferAfterAverageFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_019_ave.dat","nsdFilePath":"/data/pyarch/bm29/opd29/1137/1d/nsd.png","bufferAfterFramesMerged":"10","experimentId":1137,"macromoleculeAcronym":"MG386","i0stdev":"0.100250461538","sampleMeasurementId":22154,"measurementComments":"[2] MES","priorityLevelId":4,"bufferBeforeFramesMerged":"10","substractionCreationTime":"Jul 17, 2013 5:15:02 PM","proposalNumber":"29","rgGnom":"2.9963404542","volume":"42.2255","shapeDeterminationModel":"/data/pyarch/bm29/opd29/1137/1d/dammin.pdb","comments":null}], - proposal : new ResultsAssemblyGrid().input().proposal - }; -}; - -AnalysisGrid.prototype.test = function(targetId) { - var analysisGrid = new AnalysisGrid(); - BIOSAXS.proposal = new Proposal(analysisGrid.input().proposal); - var panel = analysisGrid.getPanel(analysisGrid.input().data); - panel.render(targetId); -}; - - -function HPLCAnalysisGrid(args) { - AnalysisGrid.prototype.constructor.call(this, args); -} - -HPLCAnalysisGrid.prototype._edit = AnalysisGrid.prototype._edit; -HPLCAnalysisGrid.prototype._getColumns = AnalysisGrid.prototype._getColumns; -HPLCAnalysisGrid.prototype._openVisualizarBySubstractionId = AnalysisGrid.prototype._openVisualizarBySubstractionId; -HPLCAnalysisGrid.prototype._openVisualizer = AnalysisGrid.prototype._openVisualizer; -HPLCAnalysisGrid.prototype._prepareData = AnalysisGrid.prototype._prepareData; -HPLCAnalysisGrid.prototype._showCalibration = AnalysisGrid.prototype._showCalibration; -HPLCAnalysisGrid.prototype.getPanel = AnalysisGrid.prototype.getPanel; -HPLCAnalysisGrid.prototype.input = AnalysisGrid.prototype.input; -HPLCAnalysisGrid.prototype.test = AnalysisGrid.prototype.test; -HPLCAnalysisGrid.prototype.refresh = AnalysisGrid.prototype.refresh; -HPLCAnalysisGrid.prototype._getPorod = AnalysisGrid.prototype._getPorod; - -HPLCAnalysisGrid.prototype._getButtons = function() { - return { - id : this.id + 'buttonPlot', - name : 'buttonPlot', - hidden : !this.showButtonsVisible, - width : 110, - sortable : false, - renderer : function(value, metaData, sample, rowIndex, colIndex, store) { - var html = ""; - - if (sample.raw.subtractionId) { - if (sample.raw.rapidShapeDeterminationModelId != null) { - html = html + ""; - } - } - return html + "
" + BUI.getGreenButton('AbInitio Modeling', { - height : 20, - width : 100 - }) + "
"; - } - }; -}; - -HPLCAnalysisGrid.prototype._getFramesColumn = function() { - return { - text : 'Frames', - dataIndex : 'datacollection', - name : 'datacollection', - sortable : true, - width : 150, - renderer : function(dataCollections, y, data) { - molmerges = data.raw.framesMerge; - totalframes = data.raw.framesCount; - return molmerges +" - "+ totalframes; - } - }; -}; - - - - -/** - * Rigid body grid to show PDB, symmetry and multiplicity - * - * - * #onUploadFile click on upload file - */ -function AprioriRigidBodyGrid(args) { - - this.height = 250; - this.btnEditVisible = true; - this.btnRemoveVisible = true; - - if (args != null) { - if (args.height != null) { - this.height = args.height; - } - if (args.btnEditVisible != null) { - this.btnEditVisible = args.btnEditVisible; - } - if (args.btnRemoveVisible != null) { - this.btnRemoveVisible = args.btnRemoveVisible; - } - } - - /** Events **/ - this.onUploadFile = new Event(this); - this.onRemove = new Event(this); -} - -AprioriRigidBodyGrid.prototype._getColumns = function() { -}; - -AprioriRigidBodyGrid.prototype._getTopButtons = function() { - var _this = this; - /** Actions buttons **/ - var actions = []; - - /** ADD BUTTON **/ - actions.push(Ext.create('Ext.Action', { - icon : '../images/add.png', - text : 'Add', - disabled : false, - handler : function(widget, event) { - _this.onAddButtonClicked.notify(); - } - })); - - return actions; -}; - -AprioriRigidBodyGrid.prototype.refresh = function(macromolecule) { - this.macromolecule = macromolecule; - if (macromolecule != null){ - this.pdbStore.loadData(macromolecule.structure3VOs); - } -}; - -AprioriRigidBodyGrid.prototype._prepareData = function() { - var data = []; - for ( var i = 0; i < this.features.length; i++) { - data.push(this.features[i]); - } - return data; -}; - -AprioriRigidBodyGrid.prototype._getPlugins = function() { - var _this = this; - var plugins = []; - plugins.push(Ext.create('Ext.grid.plugin.RowEditing', { - clicksToEdit : 1, - listeners : { - validateedit : function(grid, e) { - /** Comments are always updatable* */ - e.record.raw.symmetry = e.newValues.symmetry; - e.record.raw.multiplicity = e.newValues.multiplicity; - - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, proposal) { - BIOSAXS.proposal.setItems(proposal); - _this.refresh(BIOSAXS.proposal.getMacromoleculeById(_this.macromolecule.macromoleculeId)); - _this.panel.setLoading(false); - }); - adapter.onError.attach(function() { - alert("Error"); - }); - - _this.panel.setLoading(); - adapter.saveStructure(e.record.raw); - } - } - })); - return plugins; -}; - -AprioriRigidBodyGrid.prototype.getPanel = function() { - var _this = this; - - this.pdbStore = Ext.create('Ext.data.Store', { - fields : [ 'filePath', 'structureId', 'structureType', 'symmetry', 'structureId', 'name', 'multiplicity' ], - groupField : 'structureType', - sorters : { - property : 'structureId', - direction : 'DESC' - } - }); - - var groupingFeature = Ext.create('Ext.grid.feature.Grouping', { - groupHeaderTpl : Ext.create('Ext.XTemplate', - "
{name:this.formatName}
", { - formatName : function(name) { - return name; - } - }), - hideGroupedHeader : true, - startCollapsed : false - }); - - this.panel = Ext.create('Ext.grid.Panel', { - margin : "15 10 0 10", - height : this.height, - store : this.pdbStore, - plugins : _this._getPlugins(), - tbar : [ { - text : 'Add Modeling Option (PDB)', - icon : '../images/add.png', - handler : function() { - _this.onUploadFile.notify('PDB', 'Upload PDB File'); - } - } - - ], - columns : [ - { - text : "structureId", - flex : 0.2, - hidden : true, - dataIndex : 'structureId', - sortable : true - }, - { - text : "File", - flex : 0.5, - dataIndex : 'filePath', - sortable : true, - hidden : true - }, - { - text : "PDB", - flex : 0.4, - dataIndex : 'name', - sortable : true - }, - { - text : "Symmetry", - flex : 0.2, - dataIndex : 'symmetry', - sortable : true, - editor : { - xtype : 'combobox', - typeAhead : true, - triggerAction : 'all', - selectOnTab : true, - store : [ [ "P1", "P1" ], [ "P2", "P2" ], [ "P3", "P3" ], [ "P4", "P4" ], [ "P5", "P5" ], [ "P6", "P6" ], [ "P32", "P32" ], [ "P42", "P42" ], - [ "P52", "P52" ], [ "P62", "P62" ], [ "P222", "P222" ] ], - } - }, { - text : "Multiplicity", - flex : 0.2, - dataIndex : 'multiplicity', - sortable : true, - editor : { - xtype : 'textfield' - } - - }, { - text : "Subunit", - flex : 0.2, - dataIndex : 'isSubunit', - sortable : true, - hidden : true - }, { - text : "Type", - flex : 0.2, - dataIndex : 'structureType', - sortable : true, - hidden : true - }, - - { - id : this.id + 'REMOVE', - flex : 0.2, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - return BUI.getRedButton('REMOVE'); - } - }, ], - - listeners : { - itemdblclick : function(dataview, record, item, e) { - _this._editExperiment(record.raw.experimentId); - }, - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'REMOVE') { - var dataAdapter = new BiosaxsDataAdapter(); - dataAdapter.onSuccess.attach(function() { - _this.panel.setLoading(false); - _this.onRemove.notify(); - }); - _this.panel.setLoading("Removing PDB file"); - dataAdapter.removeStructure(record.data.structureId); - } - - } - }, - viewConfig : { - getRowClass : function(record, rowIdx, params, store) { - if (record.raw.isSubunit != null) { - return "blue-row"; - } - } - } - }); - - return this.panel; -}; - - - - -AprioriRigidBodyGrid.prototype.input = function() { - return { - proposal : DATADOC.getProposal_10(), - dewars : DATADOC.getDewars_10() - - }; -}; - -AprioriRigidBodyGrid.prototype.test = function(targetId) { - var AprioriRigidBodyGrid = new AprioriRigidBodyGrid({ - height : 150 - }); - BIOSAXS.proposal = new Proposal(AprioriRigidBodyGrid.input().proposal); - var panel = AprioriRigidBodyGrid.getPanel(AprioriRigidBodyGrid.input().dewars); - panel.render(targetId); - -}; - -/** - * It shows buffer grid with a top bar with "Add" button - * - * @height - * @searchBar - * @collapsed - * @width - */ -function BufferGrid(args) { - this.height = 500; - this.searchBar = false; - this.tbar = false; - this.collapsed = false; - this.id = BUI.id(); - - if (args != null) { - if (args.height != null) { - this.height = args.height; - } - if (args.searchBar != null) { - this.searchBar = args.searchBar; - } - - if (args.tbar != null) { - this.tbar = args.tbar; - } - - if (args.collapsed != null) { - this.collapsed = args.collapsed; - } - - if (args.width != null) { - this.width = args.width; - } - } -} - -BufferGrid.prototype._edit = function(bufferId) { - var _this = this; - var window = new BufferWindow(); - window.onSuccess.attach(function(sender, proposal) { - _this.store.loadData(BIOSAXS.proposal.getBuffers()); - }); - window.draw(BIOSAXS.proposal.getBufferById(bufferId)); -}; - -BufferGrid.prototype.refresh = function(buffers) { - this.store.loadData(this._prepareData(buffers), false); -}; - -BufferGrid.prototype._prepareData = function(buffers) { - return buffers; -}; - -BufferGrid.prototype._getTbar = function() { - var _this = this; - var actions = []; - - actions.push(Ext.create('Ext.Action', { - icon : '../images/add.png', - text : 'Add buffer', - disabled : false, - handler : function(widget, event) { - var window = new BufferWindow(); - window.onSuccess.attach(function(sender) { - _this.store.loadData(BIOSAXS.proposal.getBuffers()); - }); - window.draw({}); - } - })); - return actions; -}; - -BufferGrid.prototype.getPanel = function(buffers) { - var _this = this; - - this.store = Ext.create('Ext.data.Store', { - fields : [ 'bufferId', 'acronym', 'name', 'composition' ], - data : buffers - }); - - this.store.sort('acronym'); - - var type = 'Ext.grid.Panel'; - if (this.searchBar == true) { - type = 'Ext.ux.LiveSearchGridPanel'; - } - - this.grid = Ext.create(type, { - title : 'Buffers', - collapsible : true, - collapsed : this.collapsed, - store : this.store, - height : this.height, - width : this.width, - columns : [ - /*{ - text : '', - dataIndex : 'bufferId', - width : 20, - renderer : function(val, y, sample) { - return BUI.getRectangleColorDIV(BIOSAXS.proposal.bufferColors[val], 10, 10); - } - },*/ - { - text : 'Acronym', - dataIndex : 'acronym', - flex : 1 - }, { - text : 'Name', - dataIndex : 'name', - flex : 1, - hidden : true - }, { - text : 'Composition', - dataIndex : 'composition', - flex : 1, - hidden : true - }, { - id : _this.id + 'buttonEditBuffer', - width : 80, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - return BUI.getGreenButton('EDIT'); - } - }, { - id : _this.id + 'buttonRemoveBuffer', - width : 85, - hidden : true, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - return BUI.getRedButton('REMOVE'); - } - } ], - flex : 1, - viewConfig : { - stripeRows : true, - listeners : { - 'celldblclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - _this._edit(record.data.bufferId); - }, - 'cellclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEditBuffer') { - _this._edit(record.data.bufferId); - } - - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemoveBuffer') { - BUI.showBetaWarning(); - } - } - - } - } - }); - - /** Adding the tbar **/ - if (this.tbar) { - this.grid.addDocked({ - xtype : 'toolbar', - items : this._getTbar() - }); - } - return this.grid; -}; - -BufferGrid.prototype.input = function() { - return new MacromoleculeGrid().input(); -}; - -BufferGrid.prototype.test = function(targetId) { - var bufferGrid = new BufferGrid({ - width : 800, - height : 350, - collapsed : false, - tbar : true - }); - - BIOSAXS.proposal = new Proposal(bufferGrid.input().proposal); - var panel = bufferGrid.getPanel(BIOSAXS.proposal.macromolecules); - panel.render(targetId); -}; - -/** - * A shipment may contains one or more cases where stock solutions and sample plates are stored - * - * @height - * @btnEditVisible - * @btnRemoveVisible - * - * #onEditButtonClicked - * #onAddButtonClicked - * #onRemoveButtonClicked - * #onDuplicateButtonClicked - */ -function CaseGrid(args) { - - this.height = 100; - this.btnEditVisible = true; - this.btnRemoveVisible = true; - - if (args != null) { - if (args.height != null) { - this.height = args.height; - } - if (args.btnEditVisible != null) { - this.btnEditVisible = args.btnEditVisible; - } - if (args.btnRemoveVisible != null) { - this.btnRemoveVisible = args.btnRemoveVisible; - } - } - - /** Events **/ - this.onEditButtonClicked = new Event(this); - this.onAddButtonClicked = new Event(this); - this.onRemoveButtonClicked = new Event(this); - this.onDuplicateButtonClicked = new Event(this); -} - -CaseGrid.prototype._getColumns = function() { - var _this = this; - - function actionItemRenderer(value, meta, record, rowIx, ColIx, store) { - /*if (record.raw.specimen3VOs.length > 0){ - return 'x-hide-display'; - }*/ - } - - var columns = [ - { - header : 'Code', - dataIndex : 'code', - name : 'code', - type : 'string', - flex : 1 - }, - { - header : 'Bar Code', - dataIndex : 'barCode', - name : 'barCode', - type : 'string', - flex : 1, - hidden : true - }, - { - header : 'BeamLine', - dataIndex : 'barCode', - type : 'string', - flex : 1, - renderer : function(comp, val, record) { - if (record.raw.sessionVO != null) { - return "" + record.raw.sessionVO.beamlineName + ""; - } - } - }, - { - header : 'Session', - dataIndex : 'barCode', - type : 'string', - flex : 1, - renderer : function(comp, val, record) { - if (record.raw.sessionVO != null) { - return "" + moment(record.raw.sessionVO.startDate).format("MMM Do YY") + ""; - } - } - }, - { - header : 'Status', - dataIndex : 'dewarStatus', - name : 'dewarStatus', - type : 'string', - flex : 1, - renderer : function(comp, val, record) { - if (new String(record.raw.dewarStatus).toUpperCase() == 'OPENED') { - return "" + new String(record.raw.dewarStatus).toUpperCase() + ""; - } - return "" + new String(record.raw.dewarStatus).toUpperCase() + ""; - } - }, - { - header : 'Type', - dataIndex : 'type', - name : 'type', - type : 'string', - flex : 1, - hidden : true - }, - { - header : 'Sample Plates', - dataIndex : 'plates', - name : 'plates', - type : 'string', - flex : 1, - hidden : true - }, - { - header : 'Stock Solutions', - dataIndex : 'plates', - name : 'plates', - type : 'string', - width : 100, - renderer : function(comp, val, record) { - var html = "
"; - var stockSolutions = BIOSAXS.proposal.getStockSolutionsByDewarId(record.raw.dewarId); - html = html + "" + stockSolutions.length + " x"; - return html + "
"; - } - }, { - header : 'isStorageDewar', - dataIndex : 'isStorageDewar', - name : 'isStorageDewar', - type : 'string', - flex : 1, - hidden : true - }, { - header : 'Tracking Number From Synchrotron', - dataIndex : 'trackingNumberFromSynchrotron', - name : 'trackingNumberFromSynchrotron', - type : 'string', - flex : 1, - hidden : true - }, { - header : 'Tracking Number To Synchrotron', - dataIndex : 'trackingNumberToSynchrotron', - name : 'trackingNumberToSynchrotron', - type : 'string', - flex : 1, - hidden : true - }, { - header : 'Storage Location', - dataIndex : 'storageLocation', - name : 'storageLocation', - type : 'string', - flex : 1, - hidden : false - }, { - header : 'Comments', - dataIndex : 'comments', - name : 'comments', - type : 'string', - flex : 1, - hidden : false - } - ]; - - if (this.btnEditVisible) { - columns.push({ - id : _this.id + 'buttonEdit', - text : '', - hidden : !_this.btnEditVisible, - width : 85, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - return BUI.getGreenButton('EDIT'); - } - }); - } - - if (this.btnRemoveVisible) { - columns.push({ - id : _this.id + 'buttonRemove', - width : 85, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - if (_this.btnRemoveVisible) { - return BUI.getRedButton('REMOVE'); - } - } - }); - } - - columns.push({ - dataIndex : 'comments', - type : 'string', - width : 85, - hidden : false, - renderer : function(comp, val, record) { - return BUI.getBlueButton("LABELS", { - href : BUI.getPrintcomponentURL(record.raw.dewarId) - }); - } - }); - - return columns; -}; - -CaseGrid.prototype._getTopButtons = function() { - var _this = this; - /** Actions buttons **/ - var actions = []; - - /** ADD BUTTON **/ - actions.push(Ext.create('Ext.Action', { - icon : '../images/add.png', - text : 'Add', - disabled : false, - handler : function(widget, event) { - _this.onAddButtonClicked.notify(); - } - })); - - return actions; -}; - -CaseGrid.prototype.refresh = function(dewars) { - this.features = dewars; - this.store.loadData(this._prepareData(dewars), false); -}; - -CaseGrid.prototype._sort = function(store) { - store.sort('dewarId', 'DESC'); -}; - -CaseGrid.prototype._prepareData = function() { - var data = []; - for ( var i = 0; i < this.features.length; i++) { - data.push(this.features[i]); - } - return data; -}; - -CaseGrid.prototype.getPanel = function(dewars, plates) { - this.features = dewars; - this.plates = plates; - return this._renderGrid(); -}; - -CaseGrid.prototype._edit = function(dewar) { - var _this = this; - var caseWindow = new CaseWindow(); - /**SAVED **/ - caseWindow.onSaved.attach(function(sender, dewar) { - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, shipment) { - _this.refresh(shipment.dewarVOs); - }); - adapter.saveCase(BIOSAXS.proposal.getShipmentByDewarId(dewar.dewarId).shippingId, dewar); - }); - caseWindow.draw(dewar); -}; - -CaseGrid.prototype._getStoreFields = function(data) { - return [ { - name : 'dewarId', - type : 'string' - }, { - name : 'barCode', - type : 'string' - }, { - name : 'code', - type : 'string' - }, { - name : 'comments', - type : 'string' - }, { - name : 'dewarStatus', - type : 'string' - }, { - name : 'isStorageDewar', - type : 'string' - }, { - name : 'plates', - type : 'string' - }, { - name : 'transportValue', - type : 'string' - }, { - name : 'trackingNumberFromSynchrotron', - type : 'string' - }, { - name : 'trackingNumberToSynchrotron', - type : 'string' - }, { - name : 'timeStamp', - type : 'string' - }, { - name : 'storageLocation', - type : 'string' - }, { - name : 'type', - type : 'string' - } - - ]; -}; - -CaseGrid.prototype._renderGrid = function() { - var _this = this; - - /** Store **/ - var data = this._prepareData(); - this.store = Ext.create('Ext.data.Store', { - fields : this._getStoreFields(data), - autoload : true, - data : data - }); - this._sort(this.store); - - this.store.loadData(data, false); - - this.grid = Ext.create('Ext.grid.Panel', { - style : { - padding : 5 - }, - height : this.height, - store : this.store, - columns : this._getColumns(), - viewConfig : { - stripeRows : true, - listeners : { - itemdblclick : function(dataview, record, item, e) { - _this._edit(record.raw); - }, - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEdit') { - _this._edit(record.raw); - } - - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemove') { - _this.onRemoveButtonClicked.notify(_this.store.getAt(rowIndex).raw.dewarId); - } - } - } - }, - selModel : { - mode : 'SINGLE' - } - }); - - var actions = _this._getTopButtons(); - this.grid.addDocked({ - xtype : 'toolbar', - items : actions - }); - - this.grid.getSelectionModel().on({ - selectionchange : function(sm, selections) { - if (selections.length) { - for ( var i = 0; i < actions.length; i++) { - if (actions[i].enable) { - actions[i].enable(); - } - } - } else { - for ( var i = 0; i < actions.length; i++) { - if (actions[i].alwaysEnabled == false) { - if (actions[i].disable) { - actions[i].disable(); - } - } - } - } - } - }); - return this.grid; -}; - -CaseGrid.prototype.input = function() { - return { - proposal : DATADOC.getProposal_10(), - dewars : DATADOC.getDewars_10() - - }; -}; - -CaseGrid.prototype.test = function(targetId) { - var CaseGrid = new CaseGrid({ - height : 150 - }); - BIOSAXS.proposal = new Proposal(CaseGrid.input().proposal); - var panel = CaseGrid.getPanel(CaseGrid.input().dewars); - panel.render(targetId); - -}; - -/** - * A shipment may contains one or more cases where stock solutions and sample plates are stored - * - * @height - * @btnEditVisible - * @btnRemoveVisible - * - * #onEditButtonClicked - * #onAddButtonClicked - * #onRemoveButtonClicked - * #onDuplicateButtonClicked - */ -function ExampleGrid(args) { - - this.height = 100; - this.btnEditVisible = true; - this.btnRemoveVisible = true; - - if (args != null) { - if (args.height != null) { - this.height = args.height; - } - if (args.btnEditVisible != null) { - this.btnEditVisible = args.btnEditVisible; - } - if (args.btnRemoveVisible != null) { - this.btnRemoveVisible = args.btnRemoveVisible; - } - } - - /** Events **/ - this.onEditButtonClicked = new Event(this); - this.onAddButtonClicked = new Event(this); - this.onRemoveButtonClicked = new Event(this); - this.onDuplicateButtonClicked = new Event(this); -} - -ExampleGrid.prototype._getColumns = function() { - var _this = this; - - function actionItemRenderer(value, meta, record, rowIx, ColIx, store) { - /*if (record.raw.specimen3VOs.length > 0){ - return 'x-hide-display'; - }*/ - } - - var columns = [ - { - header : 'Code', - dataIndex : 'code', - name : 'code', - type : 'string', - flex : 1 - }, - { - header : 'Bar Code', - dataIndex : 'barCode', - name : 'barCode', - type : 'string', - flex : 1, - hidden : true - }, - { - header : 'BeamLine', - dataIndex : 'barCode', - type : 'string', - flex : 1, - renderer : function(comp, val, record) { - if (record.raw.sessionVO != null) { - return "" + record.raw.sessionVO.beamlineName + ""; - } - } - }, - { - header : 'Session', - dataIndex : 'barCode', - type : 'string', - flex : 1, - renderer : function(comp, val, record) { - if (record.raw.sessionVO != null) { - return "" + moment(record.raw.sessionVO.startDate).format("MMM Do YY") + ""; - } - } - }, - { - header : 'Status', - dataIndex : 'dewarStatus', - name : 'dewarStatus', - type : 'string', - flex : 1, - renderer : function(comp, val, record) { - if (new String(record.raw.dewarStatus).toUpperCase() == 'OPENED') { - return "" + new String(record.raw.dewarStatus).toUpperCase() + ""; - } - return "" + new String(record.raw.dewarStatus).toUpperCase() + ""; - } - }, - { - header : 'Type', - dataIndex : 'type', - name : 'type', - type : 'string', - flex : 1, - hidden : true - }, - { - header : 'Sample Plates', - dataIndex : 'plates', - name : 'plates', - type : 'string', - flex : 1, - hidden : true - }, - { - header : 'Stock Solutions', - dataIndex : 'plates', - name : 'plates', - type : 'string', - width : 100, - renderer : function(comp, val, record) { - var html = "
"; - var stockSolutions = BIOSAXS.proposal.getStockSolutionsByDewarId(record.raw.dewarId); - html = html + "" + stockSolutions.length + " x"; - return html + "
"; - } - }, { - header : 'isStorageDewar', - dataIndex : 'isStorageDewar', - name : 'isStorageDewar', - type : 'string', - flex : 1, - hidden : true - }, { - header : 'Tracking Number From Synchrotron', - dataIndex : 'trackingNumberFromSynchrotron', - name : 'trackingNumberFromSynchrotron', - type : 'string', - flex : 1, - hidden : true - }, { - header : 'Tracking Number To Synchrotron', - dataIndex : 'trackingNumberToSynchrotron', - name : 'trackingNumberToSynchrotron', - type : 'string', - flex : 1, - hidden : true - }, { - header : 'Storage Location', - dataIndex : 'storageLocation', - name : 'storageLocation', - type : 'string', - flex : 1, - hidden : false - }, { - header : 'Comments', - dataIndex : 'comments', - name : 'comments', - type : 'string', - flex : 1, - hidden : false - } - ]; - - if (this.btnEditVisible) { - columns.push({ - id : _this.id + 'buttonEdit', - text : '', - hidden : !_this.btnEditVisible, - width : 85, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - return BUI.getGreenButton('EDIT'); - } - }); - } - - if (this.btnRemoveVisible) { - columns.push({ - id : _this.id + 'buttonRemove', - width : 85, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - if (_this.btnRemoveVisible) { - return BUI.getRedButton('REMOVE'); - } - } - }); - } - - columns.push({ - dataIndex : 'comments', - type : 'string', - width : 85, - hidden : false, - renderer : function(comp, val, record) { - return BUI.getBlueButton("LABELS", { - href : BUI.getPrintcomponentURL(record.raw.dewarId) - }); - } - }); - - return columns; -}; - -ExampleGrid.prototype._getTopButtons = function() { - var _this = this; - /** Actions buttons **/ - var actions = []; - - /** ADD BUTTON **/ - actions.push(Ext.create('Ext.Action', { - icon : '../images/add.png', - text : 'Add', - disabled : false, - handler : function(widget, event) { - _this.onAddButtonClicked.notify(); - } - })); - - return actions; -}; - -ExampleGrid.prototype.refresh = function(dewars) { - this.features = dewars; - this.store.loadData(this._prepareData(dewars), false); -}; - -ExampleGrid.prototype._sort = function(store) { - store.sort('dewarId', 'DESC'); -}; - -ExampleGrid.prototype._prepareData = function() { - var data = []; - for ( var i = 0; i < this.features.length; i++) { - data.push(this.features[i]); - } - return data; -}; - -ExampleGrid.prototype.getPanel = function() { - this.grid = Ext.create('Ext.grid.Panel', { - style : { - padding : 5 - }, - height : this.height, - store : this.store, - columns : this._getColumns(), - viewConfig : { - stripeRows : true, - listeners : { - itemdblclick : function(dataview, record, item, e) { - _this._edit(record.raw); - }, - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEdit') { - _this._edit(record.raw); - } - - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemove') { - _this.onRemoveButtonClicked.notify(_this.store.getAt(rowIndex).raw.dewarId); - } - } - } - }, - selModel : { - mode : 'SINGLE' - } - }); - - var actions = _this._getTopButtons(); - this.grid.addDocked({ - xtype : 'toolbar', - items : actions - }); - - this.grid.getSelectionModel().on({ - selectionchange : function(sm, selections) { - if (selections.length) { - for ( var i = 0; i < actions.length; i++) { - if (actions[i].enable) { - actions[i].enable(); - } - } - } else { - for ( var i = 0; i < actions.length; i++) { - if (actions[i].alwaysEnabled == false) { - if (actions[i].disable) { - actions[i].disable(); - } - } - } - } - } - }); - return this.grid; -}; - - -ExampleGrid.prototype._getStoreFields = function(data) { - return [ { - name : 'dewarId', - type : 'string' - }, { - name : 'barCode', - type : 'string' - }, { - name : 'code', - type : 'string' - }, { - name : 'comments', - type : 'string' - }, { - name : 'dewarStatus', - type : 'string' - }, { - name : 'isStorageDewar', - type : 'string' - }, { - name : 'plates', - type : 'string' - }, { - name : 'transportValue', - type : 'string' - }, { - name : 'trackingNumberFromSynchrotron', - type : 'string' - }, { - name : 'trackingNumberToSynchrotron', - type : 'string' - }, { - name : 'timeStamp', - type : 'string' - }, { - name : 'storageLocation', - type : 'string' - }, { - name : 'type', - type : 'string' - } - - ]; -}; - -ExampleGrid.prototype._renderGrid = function() { - var _this = this; - - /** Store **/ - var data = this._prepareData(); - this.store = Ext.create('Ext.data.Store', { - fields : this._getStoreFields(data), - autoload : true, - data : data - }); - this._sort(this.store); - - this.store.loadData(data, false); - - this.grid = Ext.create('Ext.grid.Panel', { - style : { - padding : 5 - }, - height : this.height, - store : this.store, - columns : this._getColumns(), - viewConfig : { - stripeRows : true, - listeners : { - itemdblclick : function(dataview, record, item, e) { - _this._edit(record.raw); - }, - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEdit') { - _this._edit(record.raw); - } - - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemove') { - _this.onRemoveButtonClicked.notify(_this.store.getAt(rowIndex).raw.dewarId); - } - } - } - }, - selModel : { - mode : 'SINGLE' - } - }); - - var actions = _this._getTopButtons(); - this.grid.addDocked({ - xtype : 'toolbar', - items : actions - }); - - this.grid.getSelectionModel().on({ - selectionchange : function(sm, selections) { - if (selections.length) { - for ( var i = 0; i < actions.length; i++) { - if (actions[i].enable) { - actions[i].enable(); - } - } - } else { - for ( var i = 0; i < actions.length; i++) { - if (actions[i].alwaysEnabled == false) { - if (actions[i].disable) { - actions[i].disable(); - } - } - } - } - } - }); - return this.grid; -}; - -ExampleGrid.prototype.input = function() { - return { - proposal : DATADOC.getProposal_10(), - dewars : DATADOC.getDewars_10() - - }; -}; - -ExampleGrid.prototype.test = function(targetId) { - var ExampleGrid = new ExampleGrid({ - height : 150 - }); - BIOSAXS.proposal = new Proposal(ExampleGrid.input().proposal); - var panel = ExampleGrid.getPanel(ExampleGrid.input().dewars); - panel.render(targetId); - -}; - - -/** - * Shows a list of experiment AKA data acquisitions - * @height - * @sorters - * @minHeight - * @gridType: Ext.ux.LiveSearchGridPanel or Ext.grid.Panel - * @tbar true or false - * @grouping true or false - * @width - * @title - * #onEditButtonClicked - */ -function ExperimentGrid(args) { - this.width = "100%"; - this.height = 700; - this.minHeight = 500; - - this.id = BUI.id(); - this.gridType = 'Ext.grid.Panel'; //'Ext.ux.LiveSearchGridPanel'; - this.tbar = false; - this.hideHeaders = false; - this.grouping = true; - this.title = null; - - this.filtered = null; - - /** maximum row count **/ - this.limit = 100; - - this.sessionIdFilter = null; - - /** if not null filtered by date **/ - this.date = null; - - this.sorters = [ { - property : 'date', - direction : 'DESC' - }, { - property : 'time', - direction : 'DESC' - } ]; - - this.dates = {}; - if (args != null) { - if (args.height != null) { - this.height = args.height; - } - if (args.limit != null) { - this.limit = args.limit; - } - if (args.sorters != null) { - this.sorters = args.sorters; - } - if (args.sessionId != null){ - this.sessionIdFilter = args.sessionId; - } - if (args.filtered != null) { - this.filtered = args.filtered; - } - if (args.minHeight != null) { - this.minHeight = args.minHeight; - } - if (args.gridType != null) { - this.gridType = args.gridType; - } - if (args.tbar != null) { - this.tbar = args.tbar; - } - if (args.grouping != null) { - this.grouping = args.grouping; - } - if (args.width != null) { - this.width = args.width; - } - if (args.title != null) { - this.title = args.title; - } - - } - /** Events **/ - this.onEditButtonClicked = new Event(this); -} - -ExperimentGrid.prototype._getFilterTypes = function() { - return []; -}; - -ExperimentGrid.prototype._prepareData = function(rows) { - var data = []; - var count = 0; - - rows.sort(function(a,b){return b.experimentId - a.experimentId;}); - for ( var i = 0; i < rows.length; i++) { - var row = rows[i]; - this.dates[moment(row.creationDate).format("YYYYMMDD")] = moment(row.creationDate).format("MMM Do YY"); - if ( - ( this.filtered == null || row.experimentType == this.filtered ) && (count < this.limit || this.limit == null ) && (this.sessionIdFilter == null || this.date != null || (this.date == null && this.sessionIdFilter == row.sessionId)) - ){ - - data.push({ - experimentId : row.experimentId, - status : row.status, - dataAcquisitionFilePath : row.dataAcquisitionFilePath, - type : row.experimentType, - name : row.name, - macromolecules_names : row.macromolecules, - percentageAnalysed : { - value : (row.dataCollectionDoneCount / row.dataCollectionCount) * 100, - text : row.dataCollectionDoneCount + " of " + row.dataCollectionCount - }, - percentageCollected : { - value : (row.measurementDoneCount / row.measurementCount) * 100, - text : row.measurementDoneCount + " of " + row.measurementCount - }, - percentageMerged : { - value : (row.measurementAveragedCount / row.measurementCount) * 100, - text : row.measurementAveragedCount + " of " + row.measurementCount - }, - date : moment(row.creationDate).format("YYYYMMDD"), - time : moment(row.creationDate).format("YYYYMMDDHHmmss"), - creationDate : row.creationDate - }); - count ++; - } - } - return data; -}; - -ExperimentGrid.prototype.getPanel = function(experiments) { - this.features = experiments; - return this._renderGrid(experiments); -}; - -ExperimentGrid.prototype.refresh = function(experiments) { - this.experiments = experiments; - var filtered = []; - for ( var i = 0; i < experiments.length; i++) { - if (experiments[i].experimentType != "TEMPLATE") { - filtered.push(experiments[i]); - } - } - - this.parsedData = this._prepareData(filtered); - - var day = {}; - var dates = []; - for ( var i = 0; i < this.experiments.length; i++) { - var date = moment(this.experiments[i].creationDate).format("MMM Do YYYY"); - if (day[date] == null){ - dates.push({ - date : date, - value : moment(this.experiments[i].creationDate) - }); - day[date] = true; - } - } - - this.storeDate.loadData(dates, false); - this.store.loadData(this.parsedData, false); - - /** If it has already been filtered by date we keep the filter **/ - if (this.date != null){ - this._filterByDate(this.date); - } -}; - -ExperimentGrid.prototype._getTopButtons = function() { - var _this = this; - /** Actions buttons **/ - var actions = []; - - actions.push(Ext.create('Ext.Action', { - icon : '../images/calendar_icon.png', - text : 'Show Calendar', - disabled : false, - handler : function(widget, event) { - var window = Ext.create('Ext.window.Window', { - title : 'Calendar', - width : 600, - height : 600, - modal : true, - closable : true, - layout : { - type : 'vbox', - align : 'stretch' - }, - items : [ { - xtype : 'label', - html : 'Click on a data acquisition to select:', - margin : '5 5 5 5' - }, { - html : '
', - margin : '5 5 5 5' - } - - ] - }).show(); - - var calendarWidget = new CalendarWidget({ - height : 450 - }); - var aux = _this.limit; - /** we remove the limit temporarily **/ - _this.limit = null; - _this.sessionIdFilter = null; - calendarWidget.loadData(_this._prepareData(_this.experiments)); - _this.limit = aux; - calendarWidget.draw('calendar'); - calendarWidget.onClick.attach(function(sender, date) { - date = moment(date, "YYYY-MM-DD"); - _this._filterByDate(date); - window.close(); - - }); - - } - })); - this.storeDate = Ext.create('Ext.data.ArrayStore', { - fields: ['date', 'value'], - data : [] - }); - - this.dateMenu = Ext.create('Ext.form.field.ComboBox', { - hideLabel: true, - store: this.storeDate, - displayField: 'date', - typeAhead: true, - queryMode: 'local', - margin : '0 0 0 30', - triggerAction: 'all', - emptyText:'Select a date...', - selectOnFocus:true, - width:135, - listeners:{ - scope: this, - 'select': function (a,b,c){ - _this.limit = null; - _this._filterByDate(moment(b[0].raw.value, "YYYY-MM-DD")); - } - } - }); - - actions.push(this.dateMenu); - - actions.push("->"); - if (_this.filtered != null){ - actions.push({ - html : "Experiment Type: " + _this.filtered +"" - }); - } - else{ - actions.push({ - html : "Experiment Type: ALL" - }); - } - return actions; -}; - -/** - * Date format: "YYYY-MM-DD" - */ -ExperimentGrid.prototype._filterByDate = function(date) { - var experimentsFiltered = []; - /** Getting all the experiments of date**/ - for ( var i = 0; i < this.experiments.length; i++) { - var experiment = this.experiments[i]; - if (experiment.creationDate != null) { - var experimentDate = moment(experiment.creationDate); - if (experimentDate.year() == date.year()) { - if (experimentDate.month() == date.month()) { - if (experimentDate.date() == date.date()) { - experimentsFiltered.push(experiment); - } - } - } - } - } - var parsedData = this._prepareData(experimentsFiltered); - this.store.loadData(parsedData); - this.date = date; -}; - -/** Only for templates **/ -ExperimentGrid.prototype._removeExperimentById = function(experimentId) { - var _this = this; - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(evt, args) { - _this.grid.setLoading(false); - document.getElementById(BIOSAXS.targetId).innerHTML = ""; - BIOSAXS.start(BIOSAXS.targetId); - }); - this.grid.setLoading("Removing experiment "); - adapter.removeExperimentById(experimentId); -}; - -ExperimentGrid.prototype._renderGrid = function() { - var _this = this; - - /** Store **/ - this.store = Ext.create('Ext.data.Store', { - fields : this._getColumns(), - groupField : 'date', - autoload : true, - data : [], - remoteSort: false, - sorters : this.sorters - }); - - - - - var groupingFeature = Ext.create('Ext.grid.feature.Grouping', { - groupHeaderTpl : Ext.create('Ext.XTemplate', - "
{name:this.formatName}
", { - formatName : function(name) { - return _this.dates[name]; - } - }), - hideGroupedHeader : true, - startCollapsed : false - }); - - this.features = []; - if (this.grouping) { - this.features.push(groupingFeature); - } - - /** Grid **/ - this.grid = Ext.create(this.gridType, { - hideHeaders : this.hideHeaders, - resizable : true, - title : this.title, - width : this.width, - minHeight : this.minHeight, - height : this.height, - features : this.features, - store : this.store, - columns : this._getColumns(), - selModel : { - mode : 'SINGLE' - }, - viewConfig : { - stripeRows : true, - getRowClass : function(record, rowIdx, params, store) { - if (record.raw.type == "TEMPLATE") { - return "template-color-row"; - } - if ((record.raw.type == "CALIBRATION") && (record.raw.status == "FINISHED")) { - return "blue-row"; - } - }, - listeners : { - itemdblclick : function(dataview, record, item, e) { - _this._editExperiment(record.raw.experimentId); - }, - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'GO') { - _this._editExperiment(record.raw.experimentId); - } - - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'REMOVE') { - _this._removeExperimentById(record.raw.experimentId); - } - - } - } - } - }); - - var actions = _this._getTopButtons(); - - if (this.tbar) { - this.grid.addDocked({ - xtype : 'toolbar', - items : actions - }); - this.grid.getSelectionModel().on({ - selectionchange : function(sm, selections) { - if (selections.length) { - for ( var i = 0; i < actions.length; i++) { - if (actions[i].enable) { - actions[i].enable(); - } - } - } else { - for ( var i = 0; i < actions.length; i++) { - if (actions[i].alwaysEnabled == false) { - if (actions[i].disable) { - actions[i].disable(); - } - } - } - } - } - }); - } - - return this.grid; -}; - -ExperimentGrid.prototype._getColumns = function() { - var _this = this; - function actionItemRenderer(value, meta, record, rowIx, ColIx, store) { - if (record.raw.buffer3VOs != null) { - if (record.raw.buffer3VOs.length > 0) { - return 'x-hide-display'; - } - } - - if (record.data.platesCount > 0) { - return 'x-hide-display'; - } - } - - return [ - { - text : 'experimentId', - dataIndex : 'experimentId', - name : 'experimentId', - type : 'string', - hidden : true - }, - { - xtype : 'rownumberer', - width : 40 - }, - { - text : 'Name', - dataIndex : 'name', - name : 'name', - type : 'string', - flex : 1 - }, - - { - text : 'Type', - dataIndex : 'type', - name : 'type', - type : 'string', - flex : 1, - renderer : function(val) { - if (val == "CALIBRATION") { - return "" + val + ""; - } - - return val; - } - }, - { - text : 'Macromolecules', - name : 'macromolecules_names', - dataIndex : 'macromolecules_names', - flex : 1, - renderer : function(val) { - if (val != null) { - return " " + val + ""; - } - return " Information not available"; - } - }, - { - text : 'Buffers', - dataIndex : 'buffer_names', - name : 'buffer_names', - flex : 1, - hidden : true, - renderer : function(val) { - return "Buffer/s: " + val + ""; - } - }, - { - text : 'Status', - dataIndex : 'status', - name : 'status', - type : 'string', - flex : 1, - renderer : function(val, x, sample) { - if (sample.raw.type == "TEMPLATE") { - return "READY"; - } - if (sample.raw.status == "ABORTED") { - return "" + val + ""; - } - return "" + val + ""; - } - }, - { - text : 'Download', - dataIndex : 'creationDate', - name : 'creationDate', - renderer : function(val, x, sample) { - if (sample != null) { - if (sample.raw.type == "HPLC") { - return; - } - return BUI.getZipHTMLByExperimentId(sample.raw.experimentId, sample.raw.name); - } - }, - width : 100 - - }, - { - header : 'Measurements', - dataIndex : 'percentageCollected', - name : 'percentageCollected', - type : 'string', - renderer : function(val, y, sample) { - if ((sample.raw.type == "TEMPLATE") || (sample.raw.type == "HPLC")) { - return; - } - return "
" + BUI.getProgessBar(sample.raw.percentageCollected.value, sample.raw.percentageCollected.text) + "
"; - }, - width : 100 - }, - { - header : 'Averaged', - dataIndex : 'percentageMerged', - name : 'percentageMerged', - type : 'string', - renderer : function(val, y, sample) { - if ((sample.raw.type == "TEMPLATE") || (sample.raw.type == "HPLC")) { - return; - } - return "
" + BUI.getProgessBar(sample.raw.percentageMerged.value, sample.raw.percentageMerged.text) + "
"; - }, - width : 100 - }, - { - header : 'Subtractions', - dataIndex : 'percentageAnalysed', - name : 'percentageAnalysed', - type : 'string', - renderer : function(val, y, sample) { - if ((sample.raw.type == "TEMPLATE") || (sample.raw.type == "HPLC")) { - return; - } - return "
" + BUI.getProgessBar(sample.raw.percentageAnalysed.value, sample.raw.percentageAnalysed.text) + "
"; - }, - width : 100 - }, - - { - text : 'time', - dataIndex : 'time', - name : 'time', - hidden : true, - renderer : function(val) { - return val; - }, - width : 100 - - }, { - text : 'Date', - dataIndex : 'date', - name : 'date', - renderer : function(val) { - return val; - }, - width : 100 - - }, - - { - text : 'Time', - dataIndex : 'creationDate', - name : 'creationDate', - renderer : function(val) { - return moment(val).format(" HH:mm:ss"); - }, - width : 100 - - }, { - id : _this.id + 'GO', - width : 80, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - return BUI.getGreenButton('GO'); - } - } ]; -}; - -/** Changes location.href in order to edit the experiment **/ -ExperimentGrid.prototype._editExperiment = function(experimentId) { - if (Ext.urlDecode(window.location.href).sessionId != null) { - location.href = 'viewProjectList.do?reqCode=display&experimentId=' + experimentId + '&sessionId='+ Ext.urlDecode(window.location.href).sessionId; - } else { - location.href = 'viewProjectList.do?reqCode=display&experimentId=' + experimentId; - } -}; - -ExperimentGrid.prototype.input = function() { - var experiments = DATADOC.getExperimentList_10(); - return { - experiments : experiments, - proposal : new MeasurementGrid().input().proposal - - }; -}; - -ExperimentGrid.prototype.test = function(targetId) { - var experimentGrid = new ExperimentGrid({ - height : 350, - minHeight : 350, - width : 1000 - - }); - BIOSAXS.proposal = new Proposal(experimentGrid.input().proposal); - var panel = experimentGrid.getPanel(experimentGrid.input().experiments); - experimentGrid.refresh(experimentGrid.input().experiments); - panel.render(targetId); -}; - -function FitStructureToExperimentDataGrid(args) { - this.height = null; - this.width = null; - this.id = BUI.id(); - - if (args != null) { - if (args.height != null) { - this.height = args.height; - - if (args.width != null) { - this.width = args.width; - } - } - } - - this.onSelected = new Event(this); -} - -FitStructureToExperimentDataGrid.prototype.getStructuresByMacromolecule = function(macromolecule) { - var structures = []; - if (macromolecule.structure3VOs != null) { - if (macromolecule.structure3VOs.length > 0) { - for (var i = 0; i < macromolecule.structure3VOs.length; i++) { - structures.push(macromolecule.structure3VOs[i]); - } - } - } - return structures; -}; - -FitStructureToExperimentDataGrid.prototype._prepareData = function(subtractions) { - var data = []; - for (var i = 0; i < subtractions.length; i++) { - - for (var j = 0; j < subtractions[i].fitStructureToExperimentalData3VOs.length; j++) { - var fit = subtractions[i].fitStructureToExperimentalData3VOs[j]; - data.push({ - fit : fit.fitFilePath, - fitStructureToExperimentalDataId : fit.fitStructureToExperimentalDataId, - mixtureToStructure3VOs : fit.mixtureToStructure3VOs, - subtractedFile : subtractions[i].substractedFilePath - }); - } - } - return data; - -}; - -FitStructureToExperimentDataGrid.prototype.refresh = function(subtractions) { - this.store.loadData(this._prepareData(subtractions), false); -}; - -FitStructureToExperimentDataGrid.prototype.getPanel = function() { - var _this = this; - this.store = Ext.create('Ext.data.Store', { - fields : [ 'fit', 'subtractedFile', 'structureId', 'fitFilePath', 'mixtureToStructure3VOs' ], - data : [] - }); - - this.store.sort([ { - property : 'name', - direction : 'ASC' - } ]); - - this.selModel = Ext.create('Ext.selection.RowModel', { - allowDeselect : true, - mode : 'MULTI', - listeners : { - selectionchange : function(sm, selections) { - var selected = []; - for (var i = 0; i < selections.length; i++) { - selected.push(selections[i].raw); - } - _this.onSelected.notify(selected); - } - } - }); - - this.panel = Ext.create('Ext.grid.Panel', { - store : this.store, - deferredRender : false, - width : this.width, - height : this.height, - margin : 10, - selModel : this.selModel, - columns : [ { - text : 'Name', - dataIndex : 'fit', - flex : 1, - renderer : function(val, b, record) { - return BUI.getFileName(val); - } - }, { - text : 'PDB', - dataIndex : 'mixtureToStructure3VOs', - flex : 1, - renderer : function(values, b, record) { - var html = ""; - for (var i = 0; i < values.length; i++) { - var structure = BIOSAXS.proposal.getStructuresById(values[i].structureId); - html = html + ""; - if (structure != null){ - html = html + ""; - } - html = html + ""; - } - return html + "
" + structure.name + "
"; - } - }, { - text : 'Volume Fraction', - dataIndex : 'mixtureToStructure3VOs', - flex : 1, - renderer : function(values, b, record) { - var html = ""; - for (var i = 0; i < values.length; i++) { - html = html + ""; - html = html + ""; - html = html + ""; - } - - return html + "
" + values[i].volumeFraction + "
"; - } - },{ - text : 'Subtraction', - dataIndex : 'subtractedFile', - flex : 1, - renderer : function(values, b, record) { - return values.split("/")[values.split("/").length - 1]; - } - },], - - viewConfig : { - enableTextSelection : true, - preserveScrollOnRefresh : true - }, - listeners : { - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - }, - afterrender : function() { - } - } - }); - return this.panel; -}; - -/** Static method **/ -FitStructureToExperimentDataGrid.prototype.RUNFitScattering = function(subtractionId, structureId) { - var _this = this; - /** Add to Workflow **/ - var adapter = new BiosaxsDataAdapter(); - var workflow = { - 'workflowTitle' : 'FitExperimentalDatatoStructure', - 'comments' : 'FitExperimentalDatatoStructure run from ISPyB for subtractionId: ' + subtractionId + ' and structureId ' + structureId - } - - var inputs = [ { - name : 'subtractionId', - value : subtractionId - }, { - name : 'structureId', - value : structureId - } ]; - - adapter.onSuccess.attach(function(sender, data) { - /** Add to Fit **/ - var adapter2 = new BiosaxsDataAdapter(); - var fit = { - 'workflowId' : data.workflowId, - 'subtractionId' : subtractionId, - 'structureId' : structureId, - 'comments' : 'Sent to workflow engine' - } - adapter2.onSuccess.attach(function(sender, fit) { - _this.refresh(_this.subtractionId, _this.macromolecule); - }); - adapter2.addFitStructureData(fit); - - }); - adapter.addWorkflow(workflow, inputs); - -}; +/** + * Example form + * + * @witdh + * @height + */ +function MolarityForm(args) { + this.id = BUI.id(); + this.width = 700; + this.height = 500; + + if (args != null) { + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + } + + this.onSave = new Event(this); + this.onClose = new Event(this); +} + -/** - * It shows buffer grid with a top bar with "Add" button - * - * @height - * @searchBar - * @collapsed - * @width - */ -function FrameGrid(args) { - this.height = 500; - this.width = 500; - this.searchBar = false; - this.tbar = false; - this.collapsed = false; - - - if (args != null) { - if (args.height != null) { - this.height = args.height; - } - - if (args.searchBar != null) { - this.searchBar = args.searchBar; - } - - if (args.tbar != null) { - this.tbar = args.tbar; - } - - if (args.collapsed != null) { - this.collapsed = args.collapsed; - } - - if (args.width != null) { - this.width = args.width; - } - } -} - -FrameGrid.prototype._edit = function(bufferId) { - var _this = this; - var window = new BufferWindow(); - window.onSuccess.attach(function(sender, proposal) { - _this.store.loadData(BIOSAXS.proposal.getBuffers()); - }); - window.draw(BIOSAXS.proposal.getBufferById(bufferId)); -}; - -FrameGrid.prototype.refresh = function(buffers, experimentId) { - this.experimentId = experimentId; - this.store.loadData(this._prepareData(buffers), false); -}; - -FrameGrid.prototype._prepareData = function(buffers) { - return buffers; -}; - -FrameGrid.prototype._getTbar = function() { - var _this = this; - var actions = []; - - actions.push(Ext.create('Ext.Action', { - icon : '../images/add.png', - text : 'Add Buffer', - disabled : false, - handler : function(widget, event) { - var window = new BufferWindow(); - window.onSuccess.attach(function(sender) { - _this.store.loadData(BIOSAXS.proposal.getBuffers()); - }); - window.draw({}); - } - })); - return actions; -}; - -FrameGrid.prototype.getPanel = function(buffers) { - var _this = this; - - this.store = Ext.create('Ext.data.Store', { - fields : [ 'frameNumber', 'I0', 'Rg', 'Mass', 'Vc', 'Qr', 'quality'], - data : buffers - }); - - this.store.sort('frameNumber'); - - var type = 'Ext.grid.Panel'; - if (this.searchBar == true) { - type = 'Ext.ux.LiveSearchGridPanel'; - } - - this.grid = Ext.create(type, { - store : this.store, - height : this.height, - width : this.width, - margin : 5, - columns : [{ - text : 'Frame', - dataIndex : 'frameNumber', - flex : 1 - },{ - text : 'I0', - dataIndex : 'I0', - flex : 1, - renderer : function(val, y, sample) { - return BUI.formatValuesUnits(sample.data.I0, "", 12, 3); - } - },{ - text : 'Rg', - dataIndex : 'Rg', - flex : 1, - renderer : function(val, y, sample) { - return BUI.formatValuesUnits(sample.data.Rg, "nm", 12, 3); - } - },{ - text : 'Mass', - dataIndex : 'Mass', - flex : 1, - renderer : function(val, y, sample) { - return BUI.formatValuesUnits(sample.data.Mass, "", 12, 3); - } - },{ - text : 'Vc', - dataIndex : 'Vc', - flex : 1, - renderer : function(val, y, sample) { - return BUI.formatValuesUnits(sample.data.Vc, "", 12, 3); - } - },{ - text : 'Qr', - dataIndex : 'Qr', - flex : 1, - renderer : function(val, y, sample) { - return BUI.formatValuesUnits(sample.data.Qr, "", 12, 3); - } - },{ - text : 'Quality', - dataIndex : 'quality', - flex : 1, - renderer : function(val, y, sample) { - return (Number(sample.data.quality) * 100).toFixed(2) + "%"; - } - }, - { - text : '', - renderer : function(val, x, sample) { - if (sample != null) { - return BUI.getZipHTMLByFrameRangeId(_this.experimentId, sample.raw.frameNumber, sample.raw.frameNumber); - } - }, - width : 100 - }], - flex : 1, - viewConfig : { - stripeRows : true - } - }); - - /** Adding the tbar **/ - if (this.tbar) { - this.grid.addDocked({ - xtype : 'toolbar', - items : this._getTbar() - }); - } - return this.grid; -}; - -FrameGrid.prototype.input = function() { - return []; -}; - -FrameGrid.prototype.test = function(targetId) { - var frameGrid = new FrameGrid({ - width : 800, - height : 350, - collapsed : false, - tbar : true - }); - - var panel = frameGrid.getPanel([]); - panel.render(targetId); -}; - - -function PeakGrid(args) { - this.height = 500; - this.searchBar = false; - this.tbar = false; - this.collapsed = false; - this.width = 500; - this.showExtendedColumns = false; - - if (args != null) { - if (args.showExtendedColumns != null) { - this.showExtendedColumns = args.showExtendedColumns; - } - if (args.height != null) { - this.height = args.height; - } - if (args.searchBar != null) { - this.searchBar = args.searchBar; - } - - if (args.tbar != null) { - this.tbar = args.tbar; - } - - if (args.collapsed != null) { - this.collapsed = args.collapsed; - } - - if (args.width != null) { - this.width = args.width; - } - } -} - - -PeakGrid.prototype.refresh = function(buffers) { - this.store.loadData(this._prepareData(buffers), false); -}; - -PeakGrid.prototype._prepareData = function(buffers) { - -// for ( var i = 0; i < buffers.length; i++) { -// buffers[i].name = "Peak #" + (i+1); +MolarityForm.prototype._getNumericWithHelp = function(type, fieldLabel, fieldName, help) { + return Ext.create('Ext.container.Container', { + margin : "10 0 0 10", + items : [ { + xtype : type, + fieldLabel : fieldLabel, + name : fieldName, + id : this.id + fieldName, + decimalPrecision : 6 + }, { + xtype : 'label', + forId : 'myFieldId', + text : help, + margin : "5 0 0 105", + cls : "inline-help" + } ] + }); +}; + + +MolarityForm.prototype._getItems = function() { + this.macromoleculeCombo = BIOSAXS_COMBOMANAGER.getComboMacromoleculeByMacromolecules(this.getMacromuleculesCandidates(this.macromolecule), { + width : 250, + labelWidth : 100, + margin : 10 + }); + + return [ { + xtype : 'container', + flex : 1, + margin : '10 0 0 10', + border : 0, + layout : 'anchor', + defaultType : 'requiredtext', + items : [ this.macromoleculeCombo, + this._getNumericWithHelp("textfield", "Ratio", "ratio", "Number in assymmetric units") + ] + } ]; +}; + +MolarityForm.prototype._persist = function() { + var _this = this; + var macromoleculeId = this.macromoleculeCombo.getValue(); + var ratio = Ext.getCmp(this.id + "ratio").getValue(); + var comments = "Not used yet"; + var dataAdapter = new BiosaxsDataAdapter(); + this.panel.setLoading("Saving"); + dataAdapter.onSuccess.attach(function(sender, args) { + _this.onSave.notify(); + }); + dataAdapter.saveStoichiometry(this.macromolecule.macromoleculeId, macromoleculeId, ratio, comments); +}; + +MolarityForm.prototype._getButtons = function() { + var _this = this; + + function onClose() { + _this.onClose.notify(); + } + + return [ { + text : 'Save', + handler : function() { + _this._persist(); + } + }, { + text : 'Cancel', + handler : function() { + onClose(); + } + } ]; +}; + +MolarityForm.prototype.getPanel = function() { + this.panel = Ext.create('Ext.form.Panel', { +// width : null, + height : this.height, + margin : 2, + border : 1, + defaultType : 'requiredtext', + items : this._getItems(), + buttons : this._getButtons() + }); + return this.panel; +}; + +/** macromolecules contains all macromolecules except this one **/ +MolarityForm.prototype.getMacromuleculesCandidates = function(macromolecule) { + var macromolecules = []; + if ( BIOSAXS.proposal.macromolecules){ + for (var i = 0; i < BIOSAXS.proposal.macromolecules.length; i++) { + var m = BIOSAXS.proposal.macromolecules[i]; + if (this.macromolecule != null){ + if (m.macromoleculeId != this.macromolecule.macromoleculeId) { + macromolecules.push(m); + } + } + } + } + return macromolecules; +}; + + +/** It populates the form **/ +MolarityForm.prototype.refresh = function(macromolecule) { + this.macromolecule = macromolecule; + +}; + + +MolarityForm.prototype.input = function() { + return {}; +}; + + +/** It populates the form **/ +MolarityForm.prototype.test = function(targetId) { + var macromoleculeForm = new MolarityForm(); + var panel = macromoleculeForm.getPanel(); + panel.render(targetId); +}; + +///** +// * +// * @witdh +// * @height +// */ +//function MacromoleculeForm(args) { +// this.id = BUI.id(); +// this.width = 700; +// this.height = 500; +// +// if (args != null) { +// if (args.width != null) { +// this.width = args.width; +// } +// if (args.height != null) { +// this.height = args.height; +// } +// } +// +// this.onClose = new Event(this); +//} +// +//MacromoleculeForm.prototype.getMacromolecule = function() { +// this.macromolecule.name = Ext.getCmp(this.panel.getItemId()).getValues().name; +// this.macromolecule.acronym = Ext.getCmp(this.panel.getItemId()).getValues().acronym; +// this.macromolecule.comments = Ext.getCmp(this.panel.getItemId()).getValues().comments; +// this.macromolecule.extintionCoefficient = Ext.getCmp(this.panel.getItemId()).getValues().extintionCoefficient; +// this.macromolecule.molecularMass = Ext.getCmp(this.panel.getItemId()).getValues().molecularMass; +// return this.macromolecule; +//}; +// +//MacromoleculeForm.prototype.setMacromolecule = function(macromolecule) { +// this.pdbStore.loadData(macromolecule.structure3VOs); +// +//}; +// +//MacromoleculeForm.prototype.getForm = function(macromolecule) { +// this.panel = Ext.createWidget('form', { +// frame : false, +// border : 0, +// padding : 15, +// width : 550, +// height : 350, +// items : [ { +// xtype : 'container', +// layout : 'hbox', +// items : [ { +// xtype : 'container', +// flex : 1, +// border : false, +// layout : 'anchor', +// defaultType : 'requiredtext', +// items : [ { +// fieldLabel : 'Name', +// name : 'name', +// anchor : '95%', +// tooltip : "Name of the macromolecule", +// value : macromolecule.name +// }, { +// fieldLabel : 'Acronym', +// name : 'acronym', +// anchor : '95%', +// value : macromolecule.acronym +// } ] +// }, { +// xtype : 'container', +// flex : 1, +// layout : 'anchor', +// defaultType : 'textfield', +// items : [ { +// xtype : 'numberfield', +// fieldLabel : 'Mol. Mass (Da)', +// name : 'molecularMass', +// value : macromolecule.molecularMass, +// decimalPrecision : 6 +// }, { +// xtype : 'numberfield', +// fieldLabel : 'Extinction coef.', +// name : 'extintionCoefficient', +// value : macromolecule.extintionCoefficient, +// decimalPrecision : 6 +// } ] +// } ] +// }, { +// xtype : 'textareafield', +// name : 'comments', +// fieldLabel : 'Comments', +// value : macromolecule.comments, +// width : this.width - 10 +// }, +// +// { +// html : BUI.getWarningHTML("The macromolecule is unsaved. Save the macromolecule to get access to other tabs"), +// margin : "150 10 10 10", +// id : this.id + "unsavedWarning", +// hidden : !(!macromolecule.macromoleculeId) +// } +// +// ] +// }); +// return this.panel; +//}; +// +//MacromoleculeForm.prototype.save = function() { +// var _this = this; +// +// var adapter = new BiosaxsDataAdapter(); +// adapter.onSuccess.attach(function(sender, proposal) { +// BIOSAXS.proposal.setItems(proposal); +// _this.panel.setLoading(false); +// +// Ext.getCmp(_this.id + "assembly").enable() +// Ext.getCmp(_this.id + "advanced").enable(); +// Ext.getCmp(_this.id + "unsavedWarning").hide(); +// }); +// +// if (this.getMacromolecule().name == "") { +// BUI.showError("Name field is mandatory"); +// return; +// } +// if (this.getMacromolecule().acronym == "") { +// BUI.showError("Acroynm field is mandatory"); +// return; +// } +// +// /** Check if acronym is unique * */ +// if (this.getMacromolecule().macromoleculeId == null) { +// if (BIOSAXS.proposal.getMacromoleculeByAcronym(this.getMacromolecule().acronym) == null) { +// this.panel.setLoading("ISPyB: Saving Macromolecule") +// adapter.saveMacromolecule(this.getMacromolecule()); +// } else { +// alert("There is already an existing macromolecule with the same acronym"); +// +// } +// } else { +// this.panel.setLoading("ISPyB: Saving Macromolecule") +// adapter.saveMacromolecule(this.getMacromolecule()); +// } +// +//}; +// +//MacromoleculeForm.prototype.getPanel = function(macromolecule) { +// var _this = this; +// this.macromolecule = macromolecule; +// return Ext.createWidget('tabpanel', { +// height : this.height, +// margin : 5, +// plain : true, +// style : { +// padding : 5 +// }, +// items : [ { +// tabConfig : { +// title : "General", +// disabled : false +// }, +// items : [ this.getForm(macromolecule) ], +// bbar : [ "->", { +// text : 'Save', +// cls : 'btn-with-border', +// style : { +// +// border : 1 +// }, +// handler : function() { +// _this.save(); +// } +// }, { +// text : 'Close', +// cls : 'btn-with-border', +// handler : function() { +// _this.onClose.notify(); +// } +// } ] +// }, { +// tabConfig : { +// id : this.id + "assembly", +// title : "Assembly", +// tooltip : 'Description of subunits present in the macromolecule', +// // hidden : (!macromolecule.macromoleculeId), +// disabled : (!macromolecule.macromoleculeId) +// }, +// items : [ this.getMolarityGrid(macromolecule) ] +// }, { +// tabConfig : { +// id : this.id + "advanced", +// title : "Advanced Modeling", +// // hidden : (!macromolecule.macromoleculeId), +// tooltip : 'Definition of the description contacts and symetries', +// disabled : (!macromolecule.macromoleculeId) +// }, +// items : [ this.getRigidBodyForm(macromolecule) ] +// } ] +// }); +//}; +// +//MacromoleculeForm.prototype.getRigidBodyForm = function(macromolecule) { +// var _this = this; +// +// // [P1, P2, P3, P4 ,P5 ,P6 ,32, P42, P52, P62] + P222 +// var symmetry = Ext.create('Ext.data.Store', { +// fields : [ 's' ], +// data : [ { +// "s" : "P1" +// }, { +// "s" : "P2" +// }, { +// "s" : "P3" +// }, { +// "s" : "P4" +// }, { +// "s" : "P5" +// }, { +// "s" : "P6" +// }, { +// "s" : "P32" +// }, { +// "s" : "P42" +// }, { +// "s" : "P52" +// }, { +// "s" : "P62" +// }, { +// "s" : "P222" +// } ] +// }); +// +// if (macromolecule.symmetry == null) { +// macromolecule.symmetry = "P1"; +// } +// var comboBox = Ext.create('Ext.form.ComboBox', { +// fieldLabel : 'Symmetry', +// store : symmetry, +// id : 'comboSym', +// queryMode : 'local', +// displayField : 's', +// valueField : 's', +// value : macromolecule.symmetry, +// margin : "10 0 0 0", +// listeners : { +// change : function(combo, newValue, oldValue, eOpts) { +// macromolecule.symmetry = newValue; +// } +// } +// }); +// +// this.rigidBodyPanel = Ext.createWidget('form', { +// frame : false, +// border : 0, +// padding : 10, +// width : 550, +// height : 400, +// items : [ { +// xtype : 'container', +// layout : 'hbox', +// items : [ { +// xtype : 'container', +// border : false, +// layout : 'hbox', +// items : [ { +// xtype : 'label', +// forId : 'myFieldId', +// text : 'Contact Desc:', +// width : 105, +// margin : '0 0 0 0' +// }, { +// xtype : 'textfield', +// hideLabel : true, +// id : "contactsDescriptionFilePath", +// margin : '0 0 0 0', +// width : 300, +// value : macromolecule.contactsDescriptionFilePath +// }, { +// text : 'Upload', +// xtype : 'button', +// margin : "0 0 0 20", +// width : 100, +// handler : function() { +// _this._openUploadDialog(macromolecule.macromoleculeId, "CONTACTS", "Upload Contact Description File"); +// } +// } ] +// } ] +// }, +// +// comboBox, { +// xtype : 'checkbox', +// margin : '10 0 0 5', +// boxLabel : "I want rigid body modeling run on this stuff", +// checked : true, +// width : 300 +// }, _this.getPDBGrid(macromolecule) ] +// }); +// return this.rigidBodyPanel; +//}; +// +//MacromoleculeForm.prototype.update = function() { +// var _this = this; +// BIOSAXS.proposal.onInitialized.attach(function() { +// if (BIOSAXS.proposal != null) { +// var macromolecules = BIOSAXS.proposal.macromolecules; +// for (var i = 0; i < macromolecules.length; i++) { +// if (macromolecules[i].macromoleculeId == _this.macromolecule.macromoleculeId) { +// _this.macromolecule = macromolecules[i]; +// _this.setMacromolecule(_this.macromolecule); +// _this.molarityStore.loadData(_this.parseMolarityData(_this.macromolecule)); +// _this.pdbGrid.setLoading(false); +// Ext.getCmp("contactsDescriptionFilePath").setValue(_this.macromolecule.contactsDescriptionFilePath) +// _this.molarityGrid.setLoading(false); +// +// } +// } +// } +// }); +// this.molarityGrid.setLoading("Updating"); +// this.pdbGrid.setLoading("Updating"); +// BIOSAXS.proposal.init(); +//}; +// +///******************************************************************************* +// * MOLARITY GRID +// ******************************************************************************/ +// +//MacromoleculeForm.prototype.parseMolarityData = function(macromolecule) { +// var data = []; +// if (macromolecule.stoichiometry != null) { +// for (var i = 0; i < macromolecule.stoichiometry.length; i++) { +// data.push({ +// ratio : macromolecule.stoichiometry[i].ratio, +// acronym : macromolecule.stoichiometry[i].macromolecule3VO.acronym, +// comments : macromolecule.stoichiometry[i].macromolecule3VO.comments, +// stoichiometryId : macromolecule.stoichiometry[i].stoichiometryId, +// name : macromolecule.stoichiometry[i].macromolecule3VO.name +// }); +// } +// } +// return data; +//}; +// +//MacromoleculeForm.prototype.getMolarityGrid = function(macromolecule) { +// var _this = this; +// +// this.molarityStore = Ext.create('Ext.data.Store', { +// fields : [ 'acronym', 'ratio', 'comments', 'stoichiometryId', 'name' ], +// data : this.parseMolarityData(macromolecule), +// sorters : { +// property : 'ratio', +// direction : 'DESC' +// } +// }); +// +// this.molarityGrid = Ext.create('Ext.grid.Panel', { +// store : this.molarityStore, +// height : 350, +// padding : 5, +// columns : [ +// +// { +// text : 'Subunit', +// columns : [ { +// text : "Acronym", +// width : 100, +// hidden : false, +// dataIndex : 'acronym', +// sortable : true +// }, { +// text : "Name", +// width : 100, +// hidden : false, +// dataIndex : 'name', +// sortable : true +// }, { +// text : "Comments", +// width : 100, +// dataIndex : 'comments', +// sortable : true +// } ] +// }, { +// text : "Number
in assymmetric units", +// width : 150, +// dataIndex : 'ratio', +// tooltip : 'Number of times this subunit is present in the macromolecule', +// sortable : true +// }, { +// id : this.id + 'MOLARITY_REMOVE', +// flex : 0.1, +// sortable : false, +// renderer : function(value, metaData, record, rowIndex, colIndex, store) { +// return BUI.getRedButton('REMOVE'); +// } +// } ], +// listeners : { +// cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { +// if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'MOLARITY_REMOVE') { +// var dataAdapter = new BiosaxsDataAdapter(); +// dataAdapter.onSuccess.attach(function() { +// _this.molarityGrid.setLoading(false); +// _this.update(); +// }); +// dataAdapter.removeStoichiometry(record.data.stoichiometryId); +// _this.molarityGrid.setLoading("Removing Structure"); +// } +// } +// }, +// buttons : [ { +// text : 'Add molarity', +// handler : function() { +// +// function onClose() { +// w.destroy(); +// _this.update(); +// } +// var w = Ext.create('Ext.window.Window', { +// title : 'Molarity', +// height : 300, +// width : 500, +// modal : true, +// buttons : [ { +// text : 'Save', +// handler : function() { +// var macromoleculeId = (_this.macromoleculeCombo.getValue()); +// var ratio = Ext.getCmp(_this.id + "ratio").getValue(); +// var comments = ""; +// var dataAdapter = new BiosaxsDataAdapter(); +// dataAdapter.onSuccess.attach(function(sender, args) { +// _this.update(); +// w.destroy(); +// }); +// dataAdapter.saveStoichiometry(_this.macromolecule.macromoleculeId, macromoleculeId, ratio, comments); +// } +// }, { +// text : 'Cancel', +// handler : function() { +// onClose(); +// } +// } ], +// items : [ _this.getMolarityForm(macromolecule) ], +// listeners : { +// onEsc : function() { +// onClose(); +// }, +// close : function() { +// onClose(); +// } +// } +// }).show(); +// } +// } ] +// }); +// return this.molarityGrid; +//}; +// +///******************************************************************************* +// * PDB GRID +// ******************************************************************************/ +// +//MacromoleculeForm.prototype._openUploadDialog = function(macromoleculeId, type, title) { +// var _this = this; +// function onClose() { +// w.destroy(); +// _this.update(); +// } +// +// var w = Ext.create('Ext.window.Window', { +// title : title, +// height : 200, +// width : 400, +// modal : true, +// buttons : [ { +// text : 'Close', +// handler : function() { +// onClose(); +// } +// } ], +// layout : 'fit', +// items : { +// html : "" +// }, +// listeners : { +// onEsc : function() { +// onClose(); +// }, +// close : function() { +// onClose(); +// } +// } +// }).show(); +//}; +// +//MacromoleculeForm.prototype._getPlugins = function() { +// var _this = this; +// var plugins = []; +// // if (this.updateRowEnabled) { +// plugins.push(Ext.create('Ext.grid.plugin.RowEditing', { +// clicksToEdit : 1, +// listeners : { +// validateedit : function(grid, e) { +// /** Comments are always updatable* */ +// e.record.raw.symmetry = e.newValues.symmetry; +// e.record.raw.multiplicity = e.newValues.multiplicity; +// +// var adapter = new BiosaxsDataAdapter(); +// adapter.onSuccess.attach(function(sender, measurement) { +// // _this.grid.setLoading(false); +// }); +// adapter.onError.attach(function() { +// alert("Error"); +// // _this.grid.setLoading(false); +// }); +// +// // _this.grid.setLoading(); +// adapter.saveStructure(e.record.raw); +// } +// } +// })); +// // } +// return plugins; +//}; +// +//MacromoleculeForm.prototype.getPDBGrid = function(macromolecule) { +// var _this = this; +// +// var data = macromolecule.structure3VOs; +// +// // /** Getting PDB from subunits **/ +// // if (macromolecule != null){ +// // if (macromolecule.stoichiometry != null){ +// // for (var i =0; i < macromolecule.stoichiometry.length; i++){ +// // var stoichiometry = macromolecule.stoichiometry[i]; +// // if (stoichiometry.macromolecule3VO != null){ +// // if (stoichiometry.macromolecule3VO.structure3VOs != null){ +// // for (var j = 0; j < stoichiometry.macromolecule3VO.structure3VOs.length; +// // j++) { +// // var structure = stoichiometry.macromolecule3VO.structure3VOs[j]; +// // structure["isSubunit"] = stoichiometry.macromolecule3VO.acronym; +// // data.push(structure) +// // } +// // } +// // } +// // } +// // } +// // } +// +// this.pdbStore = Ext.create('Ext.data.Store', { +// fields : [ 'filePath', 'structureId', 'structureType', 'symmetry', 'structureId', 'name', 'multiplicity' ], +// data : macromolecule.structure3VOs, +// groupField : 'structureType', +// sorters : { +// property : 'structureId', +// direction : 'DESC' +// } +// }); +// +// var groupingFeature = Ext.create('Ext.grid.feature.Grouping', { +// groupHeaderTpl : Ext.create('Ext.XTemplate', +// "
{name:this.formatName}
", { +// formatName : function(name) { +// return name; +// } +// }), +// hideGroupedHeader : true, +// startCollapsed : false +// }); +// +// this.pdbGrid = Ext.create('Ext.grid.Panel', { +// margin : "15 0 0 5", +// height : 250, +// store : this.pdbStore, +// plugins : _this._getPlugins(), +// buttons : [ { +// // text : 'Add PDB file', +// text : 'Add Modeling Option', +// handler : function() { +// _this._openUploadDialog(macromolecule.macromoleculeId, "PDB", 'Upload PDB File'); +// } +// } +// +// ], +// columns : [ +// { +// text : "structureId", +// flex : 0.2, +// hidden : true, +// dataIndex : 'structureId', +// sortable : true +// }, +// { +// text : "File", +// flex : 0.5, +// dataIndex : 'filePath', +// sortable : true, +// hidden : true +// }, +// { +// text : "PDB", +// flex : 0.4, +// dataIndex : 'name', +// sortable : true +// }, +// { +// text : "Symmetry", +// flex : 0.4, +// dataIndex : 'symmetry', +// sortable : true, +// editor : { +// xtype : 'combobox', +// typeAhead : true, +// triggerAction : 'all', +// selectOnTab : true, +// store : [ [ "P1", "P1" ], [ "P2", "P2" ], [ "P3", "P3" ], [ "P4", "P4" ], [ "P5", "P5" ], [ "P6", "P6" ], [ "P32", "P32" ], [ "P42", "P42" ], +// [ "P52", "P52" ], [ "P62", "P62" ], [ "P222", "P222" ] ], +// } +// }, { +// text : "Multiplicity", +// flex : 0.4, +// dataIndex : 'multiplicity', +// sortable : true, +// editor : { +// xtype : 'textfield' +// } +// +// }, { +// text : "Subunit", +// flex : 0.2, +// dataIndex : 'isSubunit', +// sortable : true, +// hidden : true +// }, { +// text : "Type", +// flex : 0.2, +// dataIndex : 'structureType', +// sortable : true, +// hidden : true +// }, +// +// { +// id : this.id + 'REMOVE', +// flex : 0.2, +// hidden : true, +// sortable : false, +// renderer : function(value, metaData, record, rowIndex, colIndex, store) { +// return BUI.getRedButton('REMOVE'); +// } +// }, ], +// +// listeners : { +// itemdblclick : function(dataview, record, item, e) { +// _this._editExperiment(record.raw.experimentId); +// }, +// cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { +// +// if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'REMOVE') { +// var dataAdapter = new BiosaxsDataAdapter(); +// dataAdapter.onSuccess.attach(function() { +// _this.pdbGrid.setLoading(false); +// _this.update(); +// }); +// dataAdapter.removeStructure(record.data.structureId); +// _this.pdbGrid.setLoading("Removing PDB file"); +// } +// +// } +// }, +// viewConfig : { +// getRowClass : function(record, rowIdx, params, store) { +// if (record.raw.isSubunit != null) { +// return "blue-row"; +// } +// } +// } +// }); +// +// return this.pdbGrid; +//}; +// +//MacromoleculeForm.prototype.getMolarityForm = function(macromolecule) { +// var _this = this; +// var data = []; +// for (var i = 0; i < BIOSAXS.proposal.macromolecules.length; i++) { +// var m = BIOSAXS.proposal.macromolecules[i]; +// if (m.macromoleculeId != macromolecule.macromoleculeId) { +// data.push(m); +// } +// // } - /** Adding information of buffer **/ - if (buffers.length > 0){ - buffers.unshift({ - name : "BUFFER", - start : 0, - experimentId : buffers[0].experimentId, - end : buffers[0].start - 1 - }); - } - - - return buffers; -}; - -PeakGrid.prototype._getTbar = function() { - var _this = this; - var actions = []; +// this.macromoleculeCombo = BIOSAXS_COMBOMANAGER.getComboMacromoleculeByMacromolecules(data, { +// width : 250, +// labelWidth : 100, +// margin : 10 +// }); +// +// return Ext.createWidget('form', { +// +// frame : false, +// border : 0, +// // padding : 15, +// width : 550, +// height : 350, +// items : [ { +// xtype : 'container', +// flex : 1, +// border : false, +// layout : 'anchor', +// defaultType : 'requiredtext', +// items : [ this.macromoleculeCombo, { +// xtype : 'numberfield', +// name : 'Ratio', +// id : _this.id + "ratio", +// fieldLabel : 'Number in assymmetric units', +// value : 1, +// decimalPrecision : 6, +// margin : 10 +// }, { +// xtype : 'textareafield', +// name : 'comments', +// fieldLabel : 'Comments', +// margin : 10, +// width : 400, +// value : "" +// +// } ] +// } ] +// }); +// +//}; +// +///******************************************************************************* +// * JAVASCRIPT DOC +// ******************************************************************************/ +//MacromoleculeForm.prototype.input = function() { +// return { +// macromolecule : DATADOC.getMacromolecule_10() +// }; +//}; +// +//MacromoleculeForm.prototype.test = function(targetId) { +// var macromoleculeForm = new MacromoleculeForm(); +// var panel = macromoleculeForm.getPanel(macromoleculeForm.input().macromolecule); +// panel.render(targetId); +//}; + +function ResultSummaryForm() { + this.radiationDamageThreshold = BUI.getRadiationDamageThreshold(); + this.qualityThreshold = BUI.getQualityThreshold(); - actions.push(Ext.create('Ext.Action', { - icon : '../images/add.png', - text : 'Add Buffer', - disabled : false, - handler : function(widget, event) { - var window = new BufferWindow(); - window.onSuccess.attach(function(sender) { - _this.store.loadData(BIOSAXS.proposal.getBuffers()); - }); - window.draw({}); - } - })); - return actions; -}; + /** Data clusters with bufers **/ + this.clusterByBuffers = false; + + /** Visualization are groupeb by concenttrations. Ex: 4.5mg/ml and 4.7mg/ml will be clusterized together **/ + this.collapseConcentrations = true; + + this.summaryHeight = 350; + this.id = BUI.id(); -PeakGrid.prototype.getPanel = function(buffers) { var _this = this; - this.peakCount = 0; - this.store = Ext.create('Ext.data.Store', { - fields : ['name', {name:'start', type : 'int'}, {name:'end', type : 'int'}], - data : buffers - - }); - - this.store.sort('start'); - var type = 'Ext.grid.Panel'; - if (this.searchBar == true) { - type = 'Ext.ux.LiveSearchGridPanel'; - } - this.grid = Ext.create(type, { - store : this.store, - height : this.height, - width : this.width, - margin : 5, - columns : [ - { - text : '', - dataIndex : 'name', - width : 100, - hidden : _this.showExtendedColumns, - renderer : function(val, y, sample) { - if (sample.data.name == "BUFFER") - return "BUFFER"; - _this.peakCount++; - return "Peak #" + _this.peakCount; - } - - - }, - { - text : 'Peaks', - dataIndex : 'start', - sortable : true, - width : 100, - hidden: !_this.showExtendedColumns, - renderer : function(val, y, sample) { - return "From " + Number(sample.raw.start) + " to " + Number(sample.raw.end); - } - }, - { - text : 'Frames', - hidden : _this.showExtendedColumns, - columns : [ - { - text : 'Start', - dataIndex : 'start', - sortable : true, - hidden : _this.showExtendedColumns, - width : 100, - renderer : function(val, y, sample) { - return Number(val); - } - },{ - text : 'End', - dataIndex : 'end', - width : 100, - hidden : _this.showExtendedColumns, - renderer : function(val, y, sample) { - return Number(val); - } - },{ - text : 'Total', - dataIndex : 'end', - width : 100, - hidden : _this.showExtendedColumns, - renderer : function(val, y, sample) { - return "" + (sample.raw.end - sample.raw.start) + " frames"; - } - } - ] - } -// , -// { -// text : '', -// hidden : _this.showExtendedColumns, -// renderer : function(val, x, sample) { -// if (sample != null) { -// return BUI.getZipHTMLByFrameRangeId(sample.raw.experimentId, sample.raw.start, sample.raw.end); -// } -// }, -// width : 100 -// } - ], - flex : 1, - viewConfig : { - stripeRows : true, - getRowClass : function(record, rowIdx, params, store) { - if (record.raw.name == "BUFFER") { - return "blue-row"; - } - } - } + this.qualityControlResultsWidget = new QualityControlResultsWidget({ + qualityThreshold : this.radiationDamageThreshold, + radiationDamageThreshold : this.qualityThreshold + + }); + this.qualityControlResultsWidget.onQualityChanged.attach(function(sender, value) { + _this.qualityThreshold = value; + _this.thresholdsChanged(); }); - /** Adding the tbar **/ - if (this.tbar) { - this.grid.addDocked({ - xtype : 'toolbar', - items : this._getTbar() - }); - } - return this.grid; -}; + this.qualityControlResultsWidget.onRadiationDatamageChanged.attach(function(sender, value) { + _this.radiationDamageThreshold = value; + _this.thresholdsChanged(); -PeakGrid.prototype.input = function() { - return []; -}; + }); + this.concentrationHTMLTableWidget = new ConcentrationHTMLTableWidget({ + height : 250, + showBufferColumns : this.clusterByBuffers + }); -PeakGrid.prototype.test = function(targetId) { - var PeakGrid = new PeakGrid({ - width : 800, + this.plot = new BoxWhiskerGraph({ + targetId : _this.id + '_boxPlot', height : 350, - collapsed : false, - tbar : true + width : 450, + maxBoxWidth : 25 }); - var panel = PeakGrid.getPanel([]); - panel.render(targetId); -}; - -/** - * Macromolecule Grid showing macromolecules and adding anb updating buttons - * - * @height - * @maxHeight - * @width - * @cssFontStyle - * @searchBar makes this grid as Ext.ux.LiveSearchGridPanel - * @tbar top bar containing "Add" and "Update From SMIS" button - * @collapsed - * @collapsible - * @btnEditVisible - * @btnRemoveVisible - * @multiselect makes it multiselect using Ext.selection.CheckboxModel - * - * #onSelected - * #onMacromoleculesChanged - */ -function MacromoleculeGrid(args) { - this.height = 500; - this.width = 500; - this.id = BUI.id(); - this.maxHeight = this.height; + this.rangePlot = new RangeWhiskerGraph({ + targetId : _this.id + '_rangePlot', + height : 350, + width : 450, + maxBoxWidth : 25 + }); +} - this.searchBar = false; - this.tbar = false; +ResultSummaryForm.prototype.thresholdsChanged = function() { + var parsedData = this.prepareData(this.rawData); - this.collapsible = true; - this.collapsed = true; + var filtered = JSON.parse(JSON.stringify(parsedData)); + filtered.concentration.concentrations = []; + for ( var conc in parsedData.concentration.concentrations) { + if (parsedData.concentration.concentrations[conc].calculation.rgGnom.validNumber > 0) { + filtered.concentration.concentrations.push(parsedData.concentration.concentrations[conc]); + } + } - this.btnEditVisible = true; - this.btnRemoveVisible = false; - this.multiselect = false; + this.plotWhisker(filtered); + this.plotRange(filtered); - /** Font style applied to the acronym column **/ - this.cssFontStyle = null; + this.concentrationHTMLTableWidget.refresh(parsedData); +}; - if (args != null) { - if (args.height != null) { - this.height = args.height; - this.maxHeight = this.height; - } - if (args.maxHeight != null) { - this.maxHeight = args.maxHeight; - } - if (args.width != null) { - this.width = args.width; - } - if (args.cssFontStyle != null) { - this.cssFontStyle = args.cssFontStyle; - } +/** Given a frame object (object returned by analyzeFrames()) and depending of the threshold indicates if a datacollection has radiation damage **/ +ResultSummaryForm.prototype.hasRadiationDamage = function(frameObject) { + var bb = frameObject.bufferBeforeFramesMerged / frameObject.framesCount; + var ba = frameObject.bufferAfterFramesMerged / frameObject.framesCount; + var mol = frameObject.framesMerge / frameObject.framesCount; + return !((bb >= this.radiationDamageThreshold) && (ba >= this.radiationDamageThreshold) && (mol >= this.radiationDamageThreshold)); +}; - if (args.searchBar != null) { - this.searchBar = args.searchBar; - } - if (args.tbar != null) { - this.tbar = args.tbar; - } - if (args.collapsible != null) { - this.collapsible = args.collapsible; - } - if (args.collapsed != null) { - this.collapsed = args.collapsed; - } - if (args.btnEditVisible != null) { - this.btnEditVisible = args.btnEditVisible; - } - if (args.btnRemoveVisible != null) { - this.btnRemoveVisible = args.btnRemoveVisible; - } - if (args.multiselect != null) { - this.multiselect = args.multiselect; - } +/** Return (frameObject) an object with the information about the frames for a data collection**/ +ResultSummaryForm.prototype.analyzeFrames = function(dataCollectionRow) { + return { + bufferAfterFramesMerged : dataCollectionRow.bufferAfterFramesMerged, + bufferBeforeFramesMerged : dataCollectionRow.bufferBeforeFramesMerged, + framesCount : dataCollectionRow.framesCount, + framesMerge : dataCollectionRow.framesMerge + }; +}; + +ResultSummaryForm.prototype.detectDataCollectionWarnings = function(dataCollectionRow) { + var frameObject = this.analyzeFrames(dataCollectionRow); + var warnings = { + count : 0, + type : [] + }; + + if (this.hasRadiationDamage(frameObject)) { + warnings.count = warnings.count + 1; + warnings.type.push("RADIATION DAMAGE"); } - this.onSelected = new Event(); - - this.onMacromoleculesChanged = new Event(); -} + if (Number(dataCollectionRow.quality) < this.qualityThreshold) { + warnings.count = 1;//warnings.count + 1; + warnings.type.push("Quality <" + this.qualityThreshold); + } + return warnings; +}; +/** Return array composed by {concentration} objects **/ +ResultSummaryForm.prototype.getConcentrations = function(data) { + var concentrationsId = {}; + for ( var i = 0; i < data.length; i++) { + var warning = this.detectDataCollectionWarnings(data[i]); + var id = data[i].conc;// + "_" + data[i].bufferId; + if (this.clusterByBuffers) { + id = data[i].conc + "_" + data[i].bufferId; + } + if (concentrationsId[id] == null) { + concentrationsId[id] = { + id : id, + concentration : Number(data[i].conc).toFixed(2), + bufferId : data[i].bufferId, + bufferAcronym : data[i].bufferAcronym, + rgGuinier : [], + i0Guinier : [], + rgGnom : [], + dMax : [], + quality : [], + frames : [], + frames_warning : warning.count + }; + } else { + concentrationsId[id].frames_warning = concentrationsId[id].frames_warning + warning.count; + } + concentrationsId[id].frames.push(data[i]); -MacromoleculeGrid.prototype.edit = function(macromolecule) { - var _this = this; - var window = new MacromoleculeWindow(); - window.onSave.attach(function(sender) { - _this.store.loadData(BIOSAXS.proposal.getMacromolecules()); - _this.onMacromoleculesChanged.notify(); - }); - window.draw(macromolecule); -}; + if (warning.count == 0) { + concentrationsId[id].rgGuinier.push(data[i].rgGuinier); + concentrationsId[id].i0Guinier.push(data[i].I0); + concentrationsId[id].quality.push(data[i].quality); + concentrationsId[id].rgGnom.push(data[i].rgGnom); + concentrationsId[id].dMax.push(data[i].dmax); + } -MacromoleculeGrid.prototype.getTbar = function() { - var _this = this; - var actions = []; + } + var concentrations = []; + for ( var item in concentrationsId) { + if (concentrationsId.hasOwnProperty(item)) { + concentrations.push({ + concentration : concentrationsId[item].concentration, + id : item, + bufferId : Number(concentrationsId[item].bufferId).toFixed(2), + bufferAcronym : concentrationsId[item].bufferAcronym, + rgGuinier : concentrationsId[item].rgGuinier, + /** Frames **/ + frames : concentrationsId[item].frames, + frames_warning : concentrationsId[item].frames_warning, + /** Calculation **/ + calculation : { + rgGuinier : BUI.getStandardDeviation(concentrationsId[item].rgGuinier), + i0Guinier : BUI.getStandardDeviation(concentrationsId[item].i0Guinier), + quality : BUI.getStandardDeviation(concentrationsId[item].quality), + rgGnom : BUI.getStandardDeviation(concentrationsId[item].rgGnom), + dMax : BUI.getStandardDeviation(concentrationsId[item].dMax) - actions.push(Ext.create('Ext.Action', { - icon : '../images/add.png', - text : 'Add macromolecule', - disabled : false, - handler : function(widget, event) { - _this.edit(); - } - })); - actions.push("->"); - actions.push(Ext.create('Ext.Action', { - icon : '../images/folder_go.png', - text : 'Update From SMIS', - tooltip : "Retrieve all the macromolecules of your proposal from SMIS database", - disabled : false, - handler : function(widget, event) { - _this.grid.setLoading("Connecting to SMIS"); - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - BIOSAXS.proposal.setMacromolecules(data.macromolecules); - _this.refresh(BIOSAXS.proposal.macromolecules); - _this.grid.setLoading(false); - }); - adapter.onError.attach(function(sender, data) { - _this.grid.setLoading(false); + } }); - adapter.updateDataBaseFromSMIS(); } - })); - return actions; -}; + } -MacromoleculeGrid.prototype.deselectAll = function() { - this.grid.getSelectionModel().deselectAll(); + return { + concentrations : concentrations + }; }; -MacromoleculeGrid.prototype.selectById = function(macromoleculeId) { - this.grid.getSelectionModel().deselectAll(); - for ( var i = 0; i < this.grid.getStore().data.items.length; i++) { - var item = this.grid.getStore().data.items[i].raw; - if (item.macromoleculeId == macromoleculeId) { - this.grid.getSelectionModel().select(i); +ResultSummaryForm.prototype.prepareData = function(data) { + /** Return array composed by {acronym, bufferId} objects **/ + function getBuffers(data) { + var buffersId = {}; + for ( var i = 0; i < data.length; i++) { + buffersId[data[i].bufferId] = data[i].acronym; + } + var buffers = []; + for ( var id in buffersId) { + if (buffersId.hasOwnProperty(id)) { + buffers.push({ + acronym : buffersId[id], + bufferId : id + }); + } } + return buffers; } -}; -MacromoleculeGrid.prototype.refresh = function(macromolecules) { - this.store.loadData(macromolecules, false); + /** Get a string with all the concentrations **/ + function getConcentrationString(parseConcentrations) { + var concentrations = []; + for ( var i = 0; i < parseConcentrations.concentrations.length; i++) { + concentrations.push(parseConcentrations.concentrations[i].concentration + " mg/ml "); + } + return concentrations.toString(); + } + + var parseConcentrations = this.getConcentrations(data); + + return { + dataCollectionCount : data.length, + buffers : getBuffers(data), + concentration : parseConcentrations, + concentrationLabel : getConcentrationString(parseConcentrations) + }; }; -MacromoleculeGrid.prototype.getColumns = function() { - var _this = this; - var columns = [ - { - text : 'Acronym', - dataIndex : 'acronym', - id : this.id + "acronym", - flex : 1, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - if (_this.cssFontStyle != null) { - return "" + value + ""; +ResultSummaryForm.prototype.getDataForWhisker = function(data) { + var clusters = []; + + var concentrations = {}; + var i = 0; + var conc = 0; + if (this.collapseConcentrations) { + for (i = 0; i < data.concentration.concentrations.length; i++) { + conc = data.concentration.concentrations[i]; + var concentration = Number(conc.concentration).toFixed(0); + if (concentrations[concentration] == null) { + concentrations[concentration] = {}; + concentrations[concentration].concentration = concentration; + concentrations[concentration].calculation = {}; + concentrations[concentration].calculation.rgGuinier = {}; + concentrations[concentration].calculation.rgGuinier.values = []; + concentrations[concentration].calculation.rgGuinier.values = conc.calculation.rgGuinier.values; + concentrations[concentration].calculation.rgGnom = {}; + concentrations[concentration].calculation.rgGnom.values = []; + concentrations[concentration].calculation.rgGnom.values = conc.calculation.rgGnom.values; + } else { + concentrations[concentration].calculation.rgGuinier.values = concentrations[concentration].calculation.rgGuinier.values + .concat(conc.calculation.rgGuinier.values); + concentrations[concentration].calculation.rgGnom.values = concentrations[concentration].calculation.rgGnom.values + .concat(conc.calculation.rgGnom.values); } - return value; } - }, { - text : 'Name', - dataIndex : 'name', - id : this.id + "name", - flex : 1, - hidden : true - } ]; - if (this.btnEditVisible) { - columns.push({ - id : _this.id + 'buttonEditMacromolecule', - width : 85, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - if (_this.btnEditVisible) { - return BUI.getGreenButton('EDIT'); - } - return null; + /** From object to array **/ + var array = []; + for ( var key in concentrations) { + if (concentrations.hasOwnProperty(key)) { + array.push(concentrations[key]); } + } + data.concentration.concentrations = array; + } + + for (i = 0; i < data.concentration.concentrations.length; i++) { + conc = data.concentration.concentrations[i]; + clusters.push({ + name : conc.concentration + "mg/ml", + concentration : Number(conc.concentration), + x : Number(conc.concentration), + classes : [] + }); + clusters[clusters.length - 1].classes.push({ + name : "Guinier", + color : '#9A2EFE', + values : conc.calculation.rgGuinier.values + + }); + clusters[clusters.length - 1].classes.push({ + name : "P(r)", + color : '#2E64FE', + values : conc.calculation.rgGnom.values + }); } - if (this.btnRemoveVisible) { - columns.push({ - id : _this.id + 'buttonRemoveMacromolecule', - width : 85, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - if (_this.btnRemoveVisible) { - return BUI.getRedButton('REMOVE'); - } - return null; - } + return { + clusters : clusters.sort(function(a, b) { + return a.concentration - b.concentration; + }) + }; +}; + +ResultSummaryForm.prototype.getDataForWhiskerQuality = function(data) { + var clusters = []; + + for ( var i = 0; i < data.concentration.concentrations.length; i++) { + var conc = data.concentration.concentrations[i]; + clusters.push({ + name : conc.concentration + "mg/ml", + classes : [] + }); + clusters[clusters.length - 1].classes.push({ + name : "Quality", + values : conc.calculation.quality.values + }); } - return columns; + return { + clusters : clusters + }; +}; + +ResultSummaryForm.prototype.plotQualityWhisker = function(parsedData) { + this.qualityPlot.refresh(this.getDataForWhiskerQuality(parsedData)); }; +ResultSummaryForm.prototype.plotWhisker = function(parsedData) { + this.plot.refresh(this.getDataForWhisker(parsedData)); +}; -/** Returns the grid **/ -MacromoleculeGrid.prototype.getPanel = function() { +ResultSummaryForm.prototype.plotRange = function(parsedData) { + this.rangePlot.refresh(this.getDataForWhisker(parsedData)); +}; + +ResultSummaryForm.prototype.getPanel = function(data) { var _this = this; + _this.rawData = data; + var parsedData = this.prepareData(data); - this.store = Ext.create('Ext.data.Store', { - fields : [ 'macromoleculeId', 'name', 'acronym' ] - }); + this.panel = Ext + .createWidget( + 'form', + { + bodyPadding : 20, + frame : false, + border : 0, + width : this.width, + height : this.summaryHeight + 1000, + items : [ { + xtype : 'container', + layout : 'hbox', + items : [ { + xtype : 'container', + flex : 1, + border : false, + layout : 'anchor', + defaultType : 'textfield', + items : [ + _this.qualityControlResultsWidget.getPanel(), + { + xtype : 'fieldset', + width : 950, + margin : "20, 0 0 0", + height : this.summaryHeight + 500, + items : [ + { + html : "
Concentration Analysis
", + border : 0, + width : 900 - var type = 'Ext.grid.Panel'; - if (this.searchBar == true) { - type = 'Ext.ux.LiveSearchGridPanel'; - } + }, + { + html : this.concentrationHTMLTableWidget.getPanel(parsedData), + border : 0, + width : 900, + margin : "10, 0 0 10" - this.selModel = Ext.create('Ext.selection.RowModel', { -// allowDeselect : true, -// mode : 'MULTI', - listeners : { - selectionchange : function(sm, selections) { - var selected = []; - for (var i = 0; i < selections.length; i++) { - selected.push(selections[i].raw); - } - _this.onSelected.notify(selected); - } - } - }); + }, + { + xtype : 'container', + layout : 'vbox', + border : 5, + items : [ + { + html : "
Rg based on Guinier and Gnom
", + border : 8, + width : 900, + margin : "20 0 0 10" - this.grid = Ext.create(type, { - id : this.id, - title : 'Macromolecules', - collapsible : this.collapsible, - collapsed : this.collapsed, - store : this.store, - height : this.height, - maxHeight : this.maxHeight, - selModel : this.selModel, - columns : this.getColumns(), - width : this.width, - viewConfig : { - stripeRows : true, - listeners : { - 'celldblclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - _this.edit(BIOSAXS.proposal.getMacromoleculeById(record.data.macromoleculeId)); - }, - 'cellclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEditMacromolecule') { - _this.edit(BIOSAXS.proposal.getMacromoleculeById(record.data.macromoleculeId)); - } - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemoveMacromolecule') { - BUI.showBetaWarning(); - } - } + }, { + xtype : 'container', + layout : 'hbox', + items : [ { + xtype : 'container', + layout : 'vbox', + items : [ { + html : "
", + border : 0, + width : this.plot.width, + padding : "10 0 0 20", + listeners : { + afterrender : function() { + _this.plotWhisker(parsedData); - } - } - }); + } + } + }, { + html : "
Concentration (mg/ml)
", + width : 450, + border : 0, + margin : "-50 0 0 0" + + } ] + }, { + xtype : 'container', + layout : 'vbox', + items : [ { + html : "
", + border : 0, + width : this.rangePlot.width, + padding : "10 0 0 10", + listeners : { + afterrender : function() { + _this.plotRange(parsedData); + } + } + }, { + html : "
Concentration (mg/ml)
", + width : 450, + border : 0, + margin : "-50 0 0 0" + + } ] + } ] + } ] + } ] + } ] + } + + ] + } ] + }); + return this.panel; - /** Adding the tbar **/ - if (this.tbar) { - this.grid.addDocked({ - xtype : 'toolbar', - items : this.getTbar() - }); - } - return this.grid; }; -MacromoleculeGrid.prototype.input = function() { +ResultSummaryForm.prototype.input = function() { return { - proposal : DATADOC.getProposal_10() + data : DATADOC.getData_3367() }; }; -MacromoleculeGrid.prototype.test = function(targetId) { - var macromoleculeGrid = new MacromoleculeGrid({ - width : 800, - height : 350, - collapsed : false, - tbar : true - }); - - BIOSAXS.proposal = new Proposal(macromoleculeGrid.input().proposal); - var panel = macromoleculeGrid.getPanel(BIOSAXS.proposal.macromolecules); +ResultSummaryForm.prototype.test = function(targetId) { + var resultSummaryForm = new ResultSummaryForm(); + var panel = resultSummaryForm.getPanel(resultSummaryForm.input().data); panel.render(targetId); + }; -/** - * Shows measurements with their attributes as specimen, exposure temperature, - * volume to load, transmission etc... - * - * @addBtnMultipleEdit: if true add a button for changing measurements' - * parameters by choosing multiple measurements. It opens - * MultipleEditMeasurementGridWindow - * @collapsed: if true it doesn't show buffer's measurements - * @editor: hashmap containing columns to be edited. It is an array of a json - * like editor of Ext - * @selModel - * @collapseBtnEnable - * @removeBtnEnabled Ext.selection.RowModel - * @addBtnEnable - * @updateRowEnabled true/false if update plugin is set to the grid - * @showTitle - * @title - * @isStatusColumnHidden - * @isPriorityColumnHidden - * @isTimeColumnHidden - * @estimateTime - * @margin - * @tbar - * @height - * @maxHeight - * @minHeight - * @width - * @maxWidth - * @resizable - * @experimentColorBased when colors for buffers and macromolecules are not - * selected by the proposal but by experiment, so the - * number of colors is smaller +/** + * Example form + * + * @witdh + * @height + */ +function RigibBodyModelingForm(args) { + this.id = BUI.id(); + this.width = 700; + this.height = 500; + + if (args != null) { + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + } + + var _this = this; + this.rigidBodyGrid = new AprioriRigidBodyGrid(); + + this.rigidBodyGrid.onUploadFile.attach(function(sender, type, title){ + _this._openUploadDialog(_this.macromolecule.macromoleculeId, type, title); + }); + + this.rigidBodyGrid.onRemove.attach(function(sender, type, title){ + _this._update(); + }); + + this.onSave = new Event(this); + +} + +RigibBodyModelingForm.prototype._getItems = function() { + var _this = this; + + + return [ { + xtype : 'label', + forId : 'myFieldId', + text : 'Information for model fit, mixture analysis and rigid body modeling', + margin : '15 0 20 10', + cls : "inline-help" + }, + this.rigidBodyGrid.getPanel(), + { + xtype : 'label', + forId : 'myFieldId', + text : 'Distance restraints may be imposed on the model using contacts conditions file (OPTIONAL)', + margin : '25 0 5 10', + cls : "inline-help" + }, + { + xtype : 'container', + layout : 'hbox', + items : [ { + xtype : 'container', + border : false, + layout : 'hbox', + items : [ { + xtype : 'label', + forId : 'myFieldId', + text : 'Contact Description File: (Optional)', + width : 150, + margin : '10 0 0 10' + }, { + id : this.id + "contactsDescriptionFilePath", + xtype : 'textfield', + hideLabel : true, + margin : '10 0 0 0', + width : 200, + disabled: true + }, { + text : 'Upload', + xtype : 'button', + margin : "10 0 0 10", + width : 80, + handler : function() { + + _this._openUploadDialog(_this.macromolecule.macromoleculeId, "CONTACTS", "Upload Contact Description File"); + } + }, { + text : 'Remove', + id : _this.id + "_remove", + xtype : 'button', + margin : "10 0 0 10", + width : 80, + handler : function() { + _this.macromolecule.contactsDescriptionFilePath = null; + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, proposal) { + /** Updating the proposal global object **/ + BIOSAXS.proposal.setItems(proposal); + _this.panel.setLoading(false); + + var saved = BIOSAXS.proposal.getMacromoleculeByAcronym(_this.macromolecule.acronym); + /** Refreshing to check that everything is ok **/ + _this.refresh(saved); + _this.onSave.notify(saved); + }); + + _this.panel.setLoading("Saving Macromolecule") + adapter.saveMacromolecule(_this.macromolecule); + } + } ] + } ] + }, { + xtype : 'panel', + html : "Go to SASREF manual for further information", + margin : "10 0 0 160", + border : 0 + + }, + { + xtype : 'checkbox', + margin : '10 0 0 5', + boxLabel : "I want rigid body modeling run on this stuff", + checked : true, + width : 300 + } ] + +}; + +/** Because update is a jsp page we don't know if the user has uploaded a file or not then we need to refresh **/ +RigibBodyModelingForm.prototype._update = function(macromoleculeId, type, title) { + var _this = this; + BIOSAXS.proposal.onInitialized.attach(function() { + if (BIOSAXS.proposal != null) { + _this.refresh(BIOSAXS.proposal.getMacromoleculeById(_this.macromolecule.macromoleculeId)); + _this.panel.setLoading(false); + } + }); + this.panel.setLoading(); + BIOSAXS.proposal.init(); +}; + +RigibBodyModelingForm.prototype._openUploadDialog = function(macromoleculeId, type, title) { + var _this = this; + function onClose() { + w.destroy(); + _this._update(); + + } + + var w = Ext.create('Ext.window.Window', { + title : title, + height : 200, + width : 400, + modal : true, + buttons : [ { + text : 'Close', + handler : function() { + onClose(); + } + } ], + layout : 'fit', + items : { + html : "" + }, + listeners : { + onEsc : function() { + onClose(); + }, + close : function() { + onClose(); + } + } + }).show(); +}; + +RigibBodyModelingForm.prototype._getButtons = function() { + return []; +}; + +RigibBodyModelingForm.prototype.getPanel = function() { + var _this = this; + this.panel = Ext.create('Ext.form.Panel', { + width : this.width, + height : this.height, + margin : 10, + border : 1, + defaultType : 'textfield', + items : this._getItems(), + buttons : this._getButtons(), + listeners : { + afterrender : function(){ + _this._populate(); + + } + } + }); + return this.panel; +}; + +/** Populates could be call when the DOM is not filled yet **/ +RigibBodyModelingForm.prototype._populate = function() { + if (this.macromolecule != null){ + if (Ext.getCmp(this.id + "contactsDescriptionFilePath") != null){ + if (this.macromolecule.contactsDescriptionFilePath != null){ + Ext.getCmp(this.id + "contactsDescriptionFilePath").setValue(this.macromolecule.contactsDescriptionFilePath); + Ext.getCmp(this.id + "_remove").enable(); + } + else{ + Ext.getCmp(this.id + "_remove").disable(); + Ext.getCmp(this.id + "contactsDescriptionFilePath").setValue(""); + + } + } + } +}; + +/** It populates the form * */ +RigibBodyModelingForm.prototype.refresh = function(macromolecule) { + this.macromolecule = macromolecule; + this.rigidBodyGrid.refresh(macromolecule); + this._populate(); +}; + +RigibBodyModelingForm.prototype.input = function() { + return {}; +}; + + +/** It populates the form **/ +RigibBodyModelingForm.prototype.test = function(targetId) { + var macromoleculeForm = new RigibBodyModelingForm(); + var panel = macromoleculeForm.getPanel(); + panel.render(targetId); +}; + + +/** + * Same form as MX part * - * #onClick #onSelected #onRemoved #onUpdateTime #onMeasurementChanged - * #onExperimentChanged + * @creationMode if true a create button appears instead of save + * @showTitle true or false */ -function MeasurementGrid(args) { +function ShipmentForm(args) { this.id = BUI.id(); - this.height = 500; - this.width = 900; - - this.maxWidth = 1200; - this.maxHeight = 600; - this.minHeight = 500; - - this.unitsFontSize = 9; - this.title = "Measurements"; - this.estimateTime = false; - this.collapsed = true; - this.tbar = true; - + this.creationMode = false; this.showTitle = true; - this.resizable = true; - this.updateRowEnabled = true; - - /** - * Hash map containing the keys of the editable columns. Ex: - * 'exposureTemperature' * - */ - this.editor = { - comments : { - xtype : 'textfield', - allowBlank : true + if (args != null) { + if (args.creationMode != null) { + this.creationMode = args.creationMode; } - }; + if (args.showTitle != null) { + this.showTitle = args.showTitle; + } + } - this.isTimeColumnHidden = false; - this.isStatusColumnHidden = false; - this.isPriorityColumnHidden = true; - this.margin = "0 0 0 0"; + this.onSaved = new Event(this); +} - this.addBtnEnable = true; - this.sorter = [ { - property : 'priority', - direction : 'ASC' - } ]; +ShipmentForm.prototype.fillStores = function() { + this.panel.setLoading("Loading Labcontacts from database"); + this.labContactForSendingStore.loadData(BIOSAXS.proposal.getLabcontacts(), false); + this.labContactForReturnStore.loadData(BIOSAXS.proposal.getLabcontacts(), false); + this.panel.setLoading(false); + if (this.shipment != null) { + this.setShipment(this.shipment); + } +}; - this.removeBtnEnabled = false; - this.collapseBtnEnable = true; - this.addBtnMultipleEdit = false; - this.sortingBtnEnable = false; +ShipmentForm.prototype.draw = function(targetId) { + this.getPanel().render(targetId); +}; +ShipmentForm.prototype.setShipment = function(shipment) { + this.shipment = shipment; var _this = this; - this.selModel = Ext.create('Ext.selection.RowModel', { - allowDeselect : true, - mode : 'MULTI', - listeners : { - selectionchange : function(sm, selections) { - var selected = []; - for (var i = 0; i < selections.length; i++) { - selected.push(selections[i].raw); - } - _this.onSelected.notify(selected); - } - } - }); - - if (args != null) { - - if (args.selModel != null) { - this.selModel = args.selModel; - } + Ext.getCmp(_this.id + "shippingName").setValue(shipment.json.shippingName); + Ext.getCmp(_this.id + "shippingStatus").setValue(shipment.json.shippingStatus); + Ext.getCmp(_this.id + "comments").setValue(shipment.json.comments); + if (shipment.json.sendingLabContactVO != null) { + this.labContactsSendingCombo.setValue(shipment.json.sendingLabContactVO.labContactId); + } + if (shipment.json.returnLabContactVO != null) { + this.labContactsReturnCombo.setValue(shipment.json.returnLabContactVO.labContactId); + } - if (args.removeBtnEnabled != null) { - this.removeBtnEnabled = args.removeBtnEnabled; - } +}; - if (args.addBtnMultipleEdit != null) { - this.addBtnMultipleEdit = args.addBtnMultipleEdit; - } +ShipmentForm.prototype._saveShipment = function() { + var _this = this; + var shippingId = null; + if (this.shipment != null) { + shippingId = this.shipment.json.shippingId; + } + var json = { + shippingId : shippingId, + name : Ext.getCmp(_this.id + "shippingName").getValue(), + status : Ext.getCmp(_this.id + "shippingStatus").getValue(), + sendingLabContactId : Ext.getCmp(_this.id + "shipmentform_sendingLabContactId").getValue(), + returnLabContactId : Ext.getCmp(_this.id + "returnLabContactId").getValue(), + returnCourier : Ext.getCmp(_this.id + "returnCourier").getValue(), + courierAccount : Ext.getCmp(_this.id + "courierAccount").getValue(), + BillingReference : Ext.getCmp(_this.id + "BillingReference").getValue(), + dewarAvgCustomsValue : Ext.getCmp(_this.id + "dewarAvgCustomsValue").getValue(), + dewarAvgTransportValue : Ext.getCmp(_this.id + "dewarAvgTransportValue").getValue(), + comments : Ext.getCmp(_this.id + "comments").getValue() + }; - // if (args.experimentColorBased != null) { - // this.experimentColorBased = args.experimentColorBased; - // } + var dataAdapter = new BiosaxsDataAdapter(); + dataAdapter.onSuccess.attach(function(sender, shipment) { + window.location = BUI.getShippingURL(shipment.shippingId); + }); - if (args.collapsed != null) { - this.collapsed = args.collapsed; - } - if (args.resizable != null) { - this.resizable = args.resizable; - } + dataAdapter.onError.attach(function(sender, error) { + _this.onError.notify(error); + }); - if (args.editor != null) { - this.editor = args.editor; - } + /** Cheking params **/ + if (json.name == "") { + BUI.showError("Name field is mandatory"); + return; + } - if (args.collapseBtnEnable != null) { - this.collapseBtnEnable = args.collapseBtnEnable; - } + if (json.sendingLabContactId == null) { + BUI.showError("Lab contact for sending field is mandatory"); + return; + } - if (args.addBtnEnable != null) { - this.addBtnEnable = args.addBtnEnable; - } - if (args.sortingBtnEnable != null) { - this.sortingBtnEnable = args.sortingBtnEnable; - } + if (json.returnLabContactId == null) { + BUI.showError("Lab contact for return field is mandatory"); + return; + } - if (args.isPriorityColumnHidden != null) { - this.isPriorityColumnHidden = args.isPriorityColumnHidden; - } + dataAdapter.createShipment(json.shippingId, json.name, json.status, json.comments, json.sendingLabContactId, json.returnLabContactId, + json.returnCourier, json.courierAccount, json.BillingReference, json.dewarAvgCustomsValue, json.dewarAvgTransportValue); - if (args.width != null) { - this.width = args.width; - } +}; - if (args.updateRowEnabled != null) { - this.updateRowEnabled = args.updateRowEnabled; - } +ShipmentForm.prototype.getPanel = function(shipment) { + var _this = this; + this.shipment = shipment; + var required = '*'; + var buttons = []; - if (args.showTitle != null) { - this.showTitle = args.showTitle; - if (this.showTitle == false) { - this.title = null; + if (_this.creationMode) { + buttons.push({ + text : 'Create', + scope : this, + handler : function() { + _this._saveShipment(); } - } - - if (args.height != null) { - this.height = args.height; - } - - if (args.maxHeight != null) { - this.maxHeight = args.maxHeight; - } - - if (args.minHeight != null) { - this.minHeight = args.minHeight; - } + }); + } else { + buttons.push({ + text : 'Save', + scope : this, + handler : function() { + _this._saveShipment(); + } + }); - if (args.maxWidth != null) { - this.maxWidth = args.maxWidth; - } + } - if (args.isStatusColumnHidden != null) { - this.isStatusColumnHidden = args.isStatusColumnHidden; - } - if (args.isTimeColumnHidden != null) { - this.isTimeColumnHidden = args.isTimeColumnHidden; - } + this.labContactForSendingStore = Ext.create('Ext.data.Store', { + fields : [ 'cardName', 'labContactId' ] + }); - if (args.title != null) { - this.title = args.title; - } - if (args.estimateTime != null) { - this.estimateTime = args.estimateTime; - } + this.labContactForReturnStore = Ext.create('Ext.data.Store', { + fields : [ 'cardName', 'labContactId' ] + }); - if (args.margin != null) { - this.margin = args.margin; - } + // Create the combo box, attached to the states data store + this.labContactsSendingCombo = Ext.create('Ext.form.ComboBox', { + id : _this.id + "shipmentform_sendingLabContactId", + fieldLabel : 'Lab contact for sending', + afterLabelTextTpl : required, + store : this.labContactForSendingStore, + queryMode : 'local', + labelWidth : 200, + displayField : 'cardName', + valueField : 'labContactId' + }); - if (args.tbar != null) { - this.tbar = args.tbar; + this.labContactsReturnCombo = Ext.create('Ext.form.ComboBox', { + id : _this.id + "returnLabContactId", + fieldLabel : 'If No, Lab-Contact for Return', + afterLabelTextTpl : required, + store : this.labContactForReturnStore, + queryMode : 'local', + labelWidth : 200, + displayField : 'cardName', + valueField : 'labContactId', + listeners : { + change : function(x, newValue) { + for ( var i = 0; i < x.getStore().data.items.length; i++) { + if (x.getStore().data.items[i].raw.labContactId == newValue) { + Ext.getCmp(_this.id + "returnCourier").setValue(x.getStore().data.items[i].raw.defaultCourrierCompany); + Ext.getCmp(_this.id + "courierAccount").setValue(x.getStore().data.items[i].raw.courierAccount); + Ext.getCmp(_this.id + "BillingReference").setValue(x.getStore().data.items[i].raw.billingReference); + Ext.getCmp(_this.id + "dewarAvgCustomsValue").setValue(x.getStore().data.items[i].raw.dewarAvgCustomsValue); + Ext.getCmp(_this.id + "dewarAvgTransportValue").setValue(x.getStore().data.items[i].raw.dewarAvgTransportValue); + } + } + } } + }); - if (args.sorter != null) { - this.sorter = args.sorter; - } + if (this.panel == null) { + this.panel = Ext.create('Ext.form.Panel', { + bodyPadding : 5, + width : 600, + border : 1, + items : [ { + xtype : 'fieldset', + title : 'Details', + collapsible : false, + defaultType : 'textfield', + layout : 'anchor', + defaults : { + anchor : '100%' + }, + items : [ { + xtype : 'requiredtext', + fieldLabel : 'Shipment Label', + allowBlank : false, + name : 'shippingName', + id : _this.id + 'shippingName', + value : '', + anchor : '50%' + }, { + xtype : 'textareafield', + name : 'comments', + id : _this.id + 'comments', + fieldLabel : 'Comments', + value : '' + }, { + fieldLabel : 'Status', + readOnly : true, + id : _this.id + 'shippingStatus', + value : 'Opened', + anchor : '50%' + } ] + }, { + xtype : 'fieldset', + title : 'Lab-Contacts', + collapsible : false, + defaultType : 'textfield', + layout : 'anchor', + defaults : { + anchor : '100%' + }, + items : [ this.labContactsSendingCombo, this.labContactsReturnCombo ] + }, { + border : 0, + html : BUI.getWarningHTML("These informations are relevant for all shipments") + }, { + xtype : 'fieldset', + title : 'Courier accounts details for return', + collapsible : false, + layout : 'anchor', + defaults : { + anchor : '100%' + }, + items : [ { + xtype : 'textfield', + labelWidth : 400, + fieldLabel : 'Courier company for return (if ESRF sends a dewar back)', + id : _this.id + 'returnCourier', + value : '' + }, { + xtype : 'textfield', + labelWidth : 400, + fieldLabel : 'Courier account', + id : _this.id + 'courierAccount', + value : '' + }, { + xtype : 'textfield', + labelWidth : 400, + fieldLabel : 'Billing reference', + id : _this.id + 'BillingReference', + value : '' + }, { + xtype : 'numberfield', + labelWidth : 400, + fieldLabel : 'Average Customs value of a dewar (Euro)', + id : _this.id + 'dewarAvgCustomsValue', + value : '' + }, { + xtype : 'numberfield', + labelWidth : 400, + fieldLabel : 'Average Transport value of a dewar (Euro)', + id : _this.id + 'dewarAvgTransportValue', + value : '' + } ] + } ], + buttons : buttons + }); } - this.onClick = new Event(this); - this.onSelected = new Event(this); - this.onRemoved = new Event(this); - this.onUpdateTime = new Event(this); - this.onMeasurementChanged = new Event(this); - this.onExperimentChanged = new Event(this); -} - -MeasurementGrid.prototype._sortBy = function(sort) { - var _this = this; - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - _this.onExperimentChanged.notify(data); - _this.grid.setLoading(false); - // wizardWidget.window.close(); - }); - adapter.onError.attach(function(sender, data) { - _this.grid.setLoading(false); - alert("Oops, there was a problem"); - }); - _this.grid.setLoading("Sorting"); - adapter.sortMeasurements(this.experiments.experiments[0].experimentId, sort); + this.fillStores(); + if (this.showTitle) { + this.panel.setTitle('Create a new Shipment'); + } + return this.panel; }; -MeasurementGrid.prototype._getMenu = function() { - var _this = this; - if (this.tbar) { +ShipmentForm.prototype.input = function() { + return { + proposal : DATADOC.getProposal_10() - var items = []; - if (_this.addBtnEnable) { - items.push({ - icon : '../images/add.png', - text : 'Add measurements', - handler : function() { - _this._openAddMeasurementWindow(); - } - }); - } + }; +}; - if (_this.addBtnMultipleEdit) { - items.push({ - icon : '../images/Edit_16x16_01.png', - text : 'Multiple Edit', - handler : function() { - var multipleEditMeasurementGridWindow = new MultipleEditMeasurementGridWindow(); - multipleEditMeasurementGridWindow.onExperimentChanged.attach(function(sender, data) { - _this.onExperimentChanged.notify(data); - }); +ShipmentForm.prototype.test = function(targetId) { + var shipmentForm = new ShipmentForm({ + creationMode : true - multipleEditMeasurementGridWindow.draw(_this.measurements, _this.experiments); + }); + BIOSAXS.proposal = new Proposal(shipmentForm.input().proposal); + shipmentForm.getPanel().render(targetId); +}; + +/** + * #onSaved + */ +function StockSolutionForm(args) { + this.id = BUI.id(); + this.actions = []; - } - }); + if (args != null) { + if (args.actions != null) { + this.actions = args.actions; } + } + this.onSaved = new Event(this); +} - items.push("->"); +StockSolutionForm.prototype.getStockSolution = function() { + if (this.stockSolution != null) { + this.stockSolution.concentration = Ext.getCmp(this.id + "stockSolution_concentration").getValue(); + this.stockSolution.storageTemperature = Ext.getCmp(this.id + "stockSolution_storageTemperature").getValue(); + this.stockSolution.volume = Ext.getCmp(this.id + "stockSolution_volume").getValue(); + this.stockSolution.comments = Ext.getCmp(this.id + "stockSolution_comments").getValue(); + this.stockSolution.name = Ext.getCmp(this.id + "stockSolution_name").getValue(); + this.stockSolution.bufferId = this.bufferCombo.getValue(); - if (_this.sortingBtnEnable) { - var split = Ext.create('Ext.button.Split', { - text : 'Sort by', - // handle a click on the button itself - handler : function() { - // alert("The button was clicked"); - }, - menu : new Ext.menu.Menu({ - items : [ - { - text : 'First Created First Measured', - handler : function() { - _this._sortBy("FIFO"); - } - }, "-", { - text : 'Default', - handler : function() { - _this._sortBy("DEFAULT"); - } - } ] - }) - }); - items.push(split); + if (this.macromoleculeCombo.getValue() != null) { + this.stockSolution.macromoleculeId = this.macromoleculeCombo.getValue(); + } else { + this.stockSolution.macromolecule3VO = null; } - if (_this.collapseBtnEnable) { - items.push({ - text : 'Collapse buffers', - enableToggle : true, - scope : this, - toggleHandler : function(item, pressed) { - this.collapsed = pressed; - this.grid.getStore().loadData(this._prepareData(this.measurements, this.experiments), false); - }, - pressed : this.collapsed - }); + } else { + return { + concentration : Ext.getCmp(this.id + "stockSolution_concentration").getValue(), + storageTemperature : Ext.getCmp(this.id + "stockSolution_storageTemperature").getValue(), + volume : Ext.getCmp(this.id + "stockSolution_volume").getValue(), + comments : Ext.getCmp(this.id + "stockSolution_comments").getValue(), + name : Ext.getCmp(this.id + "stockSolution_name").getValue(), + bufferId : this.bufferCombo.getValue(), + macromoleculeId : this.macromoleculeCombo.getValue() + }; + } + return this.stockSolution; +}; + +StockSolutionForm.prototype.setStockSolution = function(stockSolution) { + if (stockSolution != null) { + if (stockSolution.macromoleculeId != null) { + this.macromoleculeCombo.setValue(stockSolution.macromoleculeId); } - var tb = Ext.create('Ext.toolbar.Toolbar', { - items : items - }); - return tb; + this.bufferCombo.setValue(stockSolution.bufferId); + Ext.getCmp(this.id + "stockSolution_concentration").setValue(this.stockSolution.concentration); + Ext.getCmp(this.id + "stockSolution_storageTemperature").setValue(this.stockSolution.storageTemperature); + Ext.getCmp(this.id + "stockSolution_volume").setValue(this.stockSolution.volume); + Ext.getCmp(this.id + "stockSolution_name").setValue(this.stockSolution.name); + Ext.getCmp(this.id + "stockSolution_comments").setValue(this.stockSolution.comments); } - return null; }; -/** Opens WizardWidget for adding new measurements * */ -MeasurementGrid.prototype._openAddMeasurementWindow = function(measurements, experiments) { - var _this = this; - var wizardWidget = new WizardWidget(); - wizardWidget.onFinished.attach(function(sender, result) { - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - _this.onExperimentChanged.notify(data); - _this.grid.setLoading(false); - wizardWidget.window.close(); - }); - wizardWidget.current.setLoading("ISPyB: Adding measurements"); - adapter.addMeasurements(result.name, "comments", result.data, _this.experiments.experiments[0].experimentId); +StockSolutionForm.prototype.getBufferCombo = function() { + this.bufferCombo = BIOSAXS_COMBOMANAGER.getComboBuffers(BIOSAXS.proposal.getBuffers(), { + labelWidth : 120, + margin : '0 0 10 0', + width : 220 + }); + return this.bufferCombo; +}; - wizardWidget.draw(null, new MeasurementCreatorStepWizardForm(BIOSAXS.proposal.getMacromolecules(), { - noNext : true - })); +StockSolutionForm.prototype.getMacromoleculeCombo = function() { + this.macromoleculeCombo = BIOSAXS_COMBOMANAGER.getComboMacromoleculeByMacromolecules(BIOSAXS.proposal.getMacromolecules(), { + labelWidth : 120, + margin : '0 0 10 0', + width : 220 + + }); + return this.macromoleculeCombo; }; -/******************************************************************************* - * Opens WizardWidget for adding new measurements - * - * @Measurements - * @Experiments experimentList Object - ******************************************************************************/ -MeasurementGrid.prototype._prepareData = function(measurements, experiments) { - var data = []; - for (var i = 0; i < measurements.length; i++) { - var measurement = measurements[i]; - var specimen = experiments.getSampleById(measurement.specimenId); - var buffer = experiments.getBufferById(specimen.bufferId); - measurement.buffer_acronym = buffer.acronym; - measurement.bufferId = buffer.bufferId; - measurement.volume = specimen.volume; - if (specimen.macromolecule3VO != null) { - measurement.acronym = specimen.macromolecule3VO.acronym; - measurement.macromoleculeId = specimen.macromolecule3VO.macromoleculeId; - } - measurement.concentration = specimen.concentration; - if (measurement.run3VO != null) { - measurement.energy = measurement.run3VO.energy; - measurement.expExposureTemperature = measurement.run3VO.exposureTemperature; - measurement.storageTemperature = measurement.run3VO.storageTemperature; - measurement.timePerFrame = measurement.run3VO.timePerFrame; - measurement.radiationAbsolute = measurement.run3VO.radiationAbsolute; - measurement.radiationRelative = measurement.run3VO.radiationRelative; - measurement.status = "DONE"; +StockSolutionForm.prototype.refresh = function() { +}; - try { - if (measurement.run3VO.timeStart != null) { - if (measurement.run3VO.timeStart != "") { - measurement.miliseconds = moment(measurement.run3VO.timeStart).format("X"); - } - } - } catch (E) { - console.log(E); - } - } +StockSolutionForm.prototype._getTopPanel = function() { + return { + xtype : 'container', + layout : 'hbox', + border : 0, + items : [ { + xtype : 'container', + layout : 'hbox', + items : [ { + xtype : 'container', + flex : 1, + border : false, + layout : 'anchor', + defaultType : 'textfield', + items : [ - if (experiments.getDataCollectionByMeasurementId(measurement.measurementId).length > 0) { - var measurementtodatacollection3VOs = experiments.getDataCollectionByMeasurementId(measurement.measurementId)[0].measurementtodatacollection3VOs; - for (var k = 0; k < measurementtodatacollection3VOs.length; k++) { - if (measurementtodatacollection3VOs[k].dataCollectionOrder == 1) { - var specimenBuffer = experiments.getSampleById(experiments.getMeasurementById(measurementtodatacollection3VOs[k].measurementId).specimenId); - if (specimenBuffer.sampleplateposition3VO != null) { - measurement.bufferSampleplateposition3VO = specimenBuffer.sampleplateposition3VO; - measurement.bufferSampleplate = (experiments.getSamplePlateById(specimenBuffer.sampleplateposition3VO.samplePlateId)); - } - } - } - } + this.getMacromoleculeCombo(), { + xtype : 'requiredtext', + id : this.id + 'stockSolution_name', + fieldLabel : 'Acronym', + labelWidth : 120, + width : 250 + }, { + xtype : 'requiredtext', + id : this.id + 'stockSolution_concentration', + fieldLabel : 'Conc. (mg/ml)', + labelWidth : 120, + width : 250 + }, - if (this.collapsed) { - /** If collapsed only the samples * */ - if (specimen.macromolecule3VO != null) { - data.push(measurement); - } - } else { - data.push(measurement); - } + { + id : this.id + 'stockSolution_storageTemperature', + fieldLabel : 'Storage Temp.(C)', + labelWidth : 120, + width : 250 + }, { + xtype : 'requiredtext', + id : this.id + 'stockSolution_volume', + fieldLabel : 'Volume in Well (µl)', + labelWidth : 120, + width : 250 + } ] + } ] + }, { + xtype : 'container', + flex : 1, + layout : 'anchor', + defaultType : 'textfield', + margin : '0 0 0 10', + items : [ this.getBufferCombo() ] + } ] + }; - } - return data; }; -/** - * Refresh data grid with the measurements and the experiments - * - * @measurements array with measurement3VO objects - * @experiments array with experiments objects - */ -MeasurementGrid.prototype.refresh = function(measurements, experiments) { - this.experiments = experiments; - this.measurements = measurements; - this.store.loadData(this._prepareData(measurements, experiments), false); +StockSolutionForm.prototype.getPanel = function(stockSolution) { + this.stockSolution = stockSolution; + this.panel = Ext.createWidget({ + xtype : 'container', + layout : 'vbox', + border : 0, + style : { + padding : '10px' + }, + fieldDefaults : { + labelAlign : 'left', + labelWidth : 50 + }, + items : [ this._getTopPanel(stockSolution), { + id : this.id + 'stockSolution_comments', + xtype : 'textareafield', + name : 'comments', + fieldLabel : 'Comments', + labelWidth : 120, + width : '100%' + } ] + }); + + this.setStockSolution(stockSolution); + return this.panel; +}; + +StockSolutionForm.prototype.input = function() { + return { + stock : { + "stockSolutionId" : 6, + "proposalId" : 3124, + "macromoleculeId" : 5933, + "bufferId" : 811, + "instructionSet3VO" : null, + "boxId" : 305861, + "storageTemperature" : "20", + "volume" : "300", + "concentration" : "1.2", + "comments" : "Buffer EDTA with A", + "name" : "A_EDTA_1.2", + "samples" : [], + "buffer" : "EDTA", + "macromolecule" : "A" + }, + proposal : new MeasurementGrid().input().proposal + }; +}; + +StockSolutionForm.prototype.test = function(targetId) { + var stockSolutionForm = new StockSolutionForm(); + BIOSAXS.proposal = new Proposal(stockSolutionForm.input().proposal); + var panel = stockSolutionForm.getPanel(new Shipment(stockSolutionForm.input().stock)); + panel.render(targetId); }; + + +BoxWhiskerGraph.prototype.cleanArray = GenericGraph.prototype.cleanArray; +BoxWhiskerGraph.prototype.plotAxes = GenericGraph.prototype.plotAxes; +BoxWhiskerGraph.prototype.plotRuler = GenericGraph.prototype.plotRuler; +BoxWhiskerGraph.prototype.drawSVGVerticalText = GenericGraph.prototype.drawSVGVerticalText; +BoxWhiskerGraph.prototype.getClassColor = GenericGraph.prototype.getClassColor; +BoxWhiskerGraph.prototype.getDimensions = GenericGraph.prototype.getDimensions; +BoxWhiskerGraph.prototype.calculate = GenericGraph.prototype.calculate; +BoxWhiskerGraph.prototype.getMedian = GenericGraph.prototype.getMedian; +BoxWhiskerGraph.prototype.pointToPixel = GenericGraph.prototype.pointToPixel; +BoxWhiskerGraph.prototype.maxValueWhisker = GenericGraph.prototype.maxValueWhisker; +BoxWhiskerGraph.prototype.refresh = GenericGraph.prototype.refresh; /** - * Set status bar to busy (refreshing icon) + * Subclass of GenericGraph * - * @msg message to be displayed on the bar + * @maxBoxWidth */ -MeasurementGrid.prototype._showStatusBarBusy = function(msg) { - var statusBar = Ext.getCmp(this.id + 'basic-statusbar'); - statusBar.setStatus({ - text : msg, - iconCls : 'x-status-busy', - clear : false - }); +function BoxWhiskerGraph(args){ + this.maxBoxWidth = 25; + + if (args == null){ + args = new Object(); + } + args["plotHorizontalByCluster"] = true; + + GenericGraph.call(this, args); + + if (args.maxBoxWidth != null){ + this.maxBoxWidth = args.maxBoxWidth; + } }; + + /** - * Set status bar to ready (ok icon) - * - * @msg message to be displayed on the bar - */ -MeasurementGrid.prototype._showStatusBarReady = function(msg) { - var statusBar = Ext.getCmp(this.id + 'basic-statusbar'); - statusBar.setStatus({ - text : msg, - iconCls : 'x-status-valid', - clear : false - }); +There are several different methods for calculating quartiles.[1] This calculator uses a method described by Moore and McCabe to find quartile values. +The same method also used by The TI-83 to calculate quartile values. +With this method, the first quartile is the median of the numbers below the median, the third quartile is the median of the numbers above the median. + +http://www.miniwebtool.com/quartile-calculator/ +http://www.alcula.com/calculators/statistics/box-plot/ +**/ +BoxWhiskerGraph.prototype.getQ1 = function(array){ + array = array.slice(0, array.length/2); + return this.getMedian(array); }; -/** - * If updateRowEnabled returns an array with Ext.grid.plugin.RowEditing - */ -MeasurementGrid.prototype._getPlugins = function() { - var _this = this; - var plugins = []; - if (this.updateRowEnabled) { - plugins.push(Ext.create('Ext.grid.plugin.RowEditing', { - clicksToEdit : 1, - listeners : { - validateedit : function(grid, e) { - /** Setting values * */ - for ( var key in _this.editor) { - e.record.raw[key] = e.newValues[key]; - } - /** Comments are always updatable* */ - e.record.raw.comments = e.newValues.comments; +BoxWhiskerGraph.prototype.getQ3 = function(array){ + array = array.slice((array.length + 1)/2); + return this.getMedian(array); + +}; - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, measurement) { - _this.onMeasurementChanged.notify(measurement); - _this.grid.setLoading(false); - }); - adapter.onError.attach(function() { - alert("Error"); - _this.grid.setLoading(false); - }); +BoxWhiskerGraph.prototype.getQ2 = function(array){ + return this.getMedian(array); +}; - _this.grid.setLoading(); - adapter.saveMeasurement(e.record.raw, _this.experiments.experiments[0]); - } - } - })); +BoxWhiskerGraph.prototype.getBelowOutliers = function(belowLimit, array){ + var points = new Array(); + for (var i = 0; i < array.length; i++){ + if (array[i] <= belowLimit){ + points.push(array[i]); + } } - return plugins; + return points; }; -/** - * @key name of the columns mathing the this.editor[key] - */ -MeasurementGrid.prototype._getEditor = function(key) { - if (this.editor[key] != null) { - return this.editor[key]; +BoxWhiskerGraph.prototype.getAboveOutliers = function(aboveLimit, array){ + var points = new Array(); + for (var i = 0; i < array.length; i++){ + if (array[i] >= aboveLimit){ + points.push(array[i]); + } } - return null; + return points; }; -MeasurementGrid.prototype.getPanel = function(measurements, experiments) { - this.experiments = experiments; - this.measurements = measurements; - var _this = this; - this.store = Ext.create('Ext.data.Store', { - fields : [ { - name : 'miliseconds', - type : 'int' - }, 'priority', 'bufferId', { - name : 'exposureTemperature', - type : 'numeric' - }, 'volumeToLoad','code', 'transmission', 'viscosity', 'waitTime', 'flow', 'buffer_acronym', 'macromoleculeId', 'acronym', 'concentration', 'extraFlowTime', 'volume', 'energy', - 'expExposureTemperature', 'storageTemperature', 'timePerFrame', 'radiationAbsolute', 'radiationRelative', 'status', 'comments' ], - data : this._prepareData(measurements, experiments) - }); - this.store.sort(this.sorter); - var bbar = {}; - try { - bbar = Ext.create('Ext.ux.StatusBar', { - id : _this.id + 'basic-statusbar', - defaultText : 'Ready', - text : 'Ready', - iconCls : 'x-status-valid', - items : [] - }); - } catch (exp) { - console.log("bbar error"); + +BoxWhiskerGraph.prototype.minValueWhisker = function(belowLimit, q1, array){ + var points = new Array(); + + for (var i = 0; i < array.length; i++){ + if ((array[i] < q1) && (array[i]) > belowLimit){ + points.push(array[i]); + } + } + + if (points.length > 0){ + points.sort(function(a, b){return a - b;}); + return points[0]; } + return null; +}; - this.grid = Ext - .create( - 'Ext.grid.Panel', - { - id : this.id, - title : this.title, - store : this.store, - selModel : this.selModel, - plugins : this._getPlugins(), - resizable : this.resizable, - margin : this.margin, - maxHeight : this.maxHeight, - minHeight : this.minHeight, - maxWidth : this.maxWidth, - width : this.width, - tbar : this._getMenu(), - columns : [ - { - text : 'Order', - dataIndex : 'priority', - width : 50, - hidden : _this.isPriorityColumnHidden, - sortable : true +BoxWhiskerGraph.prototype.isNumber = function(value){ + if (value=="") return false; - }, - { - text : 'Run Number', - dataIndex : 'code', - width : 50, - hidden : true, - sortable : true + var d = parseInt(value); + if (!isNaN(d)) return true; else return false; - }, +}; - { - text : 'Specimen', - columns : [ +BoxWhiskerGraph.prototype.plotBoxWhisker = function(boxProperties){ + if (this.maxBoxWidth != null){ + if (boxProperties.width > this.maxBoxWidth){ + boxProperties.x = boxProperties.x + (boxProperties.width/2) - (this.maxBoxWidth/2); + boxProperties.width = this.maxBoxWidth; + } + + } - { - text : '', - dataIndex : 'macromoleculeId', - width : 30, - renderer : function(val, y, sample) { - if (val != null) { - if (_this.experiments == null) { - return BUI.getRectangleColorDIV(BIOSAXS.proposal.macromoleculeColors[val], 10, 10); - } else { - return BUI.getRectangleColorDIV(_this.experiments.macromoleculeColors[val], 10, 10); - } - } - }, - sortable : true - }, - { - text : 'Macromo.', - dataIndex : 'acronym', - width : 80, - renderer : function(val, y, sample) { - return val; - }, - sortable : true - }, - { - text : 'Conc. ', - dataIndex : 'concentration', - width : 80, - renderer : function(val, y, sample) { - if (sample.raw.macromoleculeId == null) { - return ""; - } - if (isNaN(val)) - return val; + if (this.plotPoints){ + for(var i = 0; i < boxProperties.values.length; i++){ + var value = boxProperties.values[i]; + var toPixel = this.pointToPixel(value, boxProperties); + SVG.drawCircle(boxProperties.x + (boxProperties.width/2) + 2, toPixel, this.pointRadius, this.svg, [["fill", "green"], ["fill-opacity", this.fillOpacityPoint],['stroke-opacity', this.strokeOpacityPoint], ["stroke", "black"]]); + } + } + - if (val != 0) { - return BUI.formatValuesUnits(val, '', { - fontSize : 16, - decimals : 3, - unitsFontSize : this.unitsFontSize - }); - } else { - return; - } + var boxColor = this.getClassColor(boxProperties.name); + var result = this.calculate(boxProperties.values); + /** Q1 **/ + + if (this.isNumber(result.Q1)){ + SVG.drawLine(boxProperties.x, this.pointToPixel(result.Q1, boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result.Q1, boxProperties), this.svg, [["stroke", boxColor]]); + } + /** Q2 **/ + if (this.isNumber(result.Q2)){ + SVG.drawLine(boxProperties.x, this.pointToPixel(result.Q2, boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result.Q2, boxProperties), this.svg, [["stroke", "blue"], ["stroke-width", "2"]]); + } + + /** Q3 **/ + if (this.isNumber(result.Q3)){ + SVG.drawLine(boxProperties.x, this.pointToPixel(result.Q3, boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result.Q3, boxProperties), this.svg, [["stroke", boxColor]]); + } + + /** Concenting Q1 and Q3 **/ + if (this.isNumber(result.Q1)&&this.isNumber(result.Q3)){ + SVG.drawLine(boxProperties.x, this.pointToPixel(result.Q1, boxProperties), boxProperties.x, this.pointToPixel(result.Q3, boxProperties), this.svg, [["stroke", boxColor]]); + SVG.drawLine(boxProperties.x + boxProperties.width, this.pointToPixel(result.Q1, boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result.Q3, boxProperties), this.svg, [["stroke", boxColor]]); + } + + /** min-whisker **/ + if (result["min-whisker"] != null){ + if (this.isNumber(result.Q1)){ + SVG.drawLine(boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result.Q1, boxProperties), boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result["min-whisker"], boxProperties), this.svg, [["stroke", boxColor]]); + } + SVG.drawLine(boxProperties.x,this.pointToPixel(result["min-whisker"], boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result["min-whisker"], boxProperties) , this.svg, [["stroke", boxColor]]); + + } + + /** max-whisker **/ + if (result["max-whisker"] != null){ + if (this.isNumber(result.Q3)){ + SVG.drawLine(boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result.Q3, boxProperties), boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result["max-whisker"], boxProperties), this.svg, [["stroke", boxColor]]); + } + SVG.drawLine(boxProperties.x , this.pointToPixel(result["max-whisker"], boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result["max-whisker"], boxProperties), this.svg, [["stroke", boxColor]]); + + } + + /** outliners **/ + if (result["above-outliers"] != null){ + for (var point in result["above-outliers"]){ + SVG.drawCircle(boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result["above-outliers"][point], boxProperties), this.pointRadius, this.svg, [["fill", "red"], ["fill-opacity", "1"]]); + //SVG.drawText(boxProperties.x + (boxProperties.width/2) - 2, this.pointToPixel(result["above-outliers"][point], boxProperties) + 2, "x",this.svg, [["fill", "black"], ["font-size", "x-small"]]); + } + } + if (result["below-outliers"] != null){ + for (var point in result["below-outliers"]){ + SVG.drawCircle(boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result["below-outliers"][point], boxProperties), this.pointRadius, this.svg, [["fill", "red"], ["fill-opacity", "1"]]); + //SVG.drawText(boxProperties.x + (boxProperties.width/2) - 2, this.pointToPixel(result["below-outliers"][point], boxProperties) + 2, "x",this.svg, [["fill", "black"], ["font-size", "x-small"]]); + } + } +}; - }, - sortable : true - }, - { - text : '', - dataIndex : 'bufferId', - width : 30, - hidden : false, - renderer : function(val, y, sample) { - if (val != null) { - var color = '#FFCCFF'; - if (_this.experiments != null) { - var dc = _this.experiments.getDataCollectionByMeasurementId(sample.raw.measurementId); - if (dc != null) { - if (dc.length > 0) { - color = _this.experiments.getSpecimenColorByBufferId(_this.experiments - .getMeasurementById(dc[0].measurementtodatacollection3VOs[0].measurementId).specimenId); - } - } - } else { - color = BIOSAXS.proposal.bufferColors[val]; - } - return BUI.getRectangleColorDIV(color, 10, 10); - } - }, - sortable : true - }, - { - text : 'Buffer', - dataIndex : 'buffer_acronym', - width : 120, - renderer : function(val, y, sample) { - if (sample.raw.bufferSampleplateposition3VO != null) { - return BIOSAXS.proposal.getBufferById(sample.raw.bufferId).acronym + " Plate: [" - + sample.raw.bufferSampleplate.slotPositionColumn + ", " - + BUI.getSamplePlateLetters()[sample.raw.bufferSampleplateposition3VO.rowNumber - 1] + "-" - + sample.raw.bufferSampleplateposition3VO.columnNumber + "]"; - } - return val; - }, - sortable : true - }, { - text : 'Position', - width : 100, - hidden : true, - renderer : function(val, y, sample) { - if (_this.experiments != null) { - return BUI.getSamplePositionHTML(_this.experiments.getSampleById(sample.raw.specimenId), _this.experiments.experiments[0]); - } - } - } ] - }, - { - text : 'Parameters', - columns : [ - { - text : 'Ex. Flow. time (s)', - dataIndex : 'extraFlowTime', - width : 100, - hidden : true, - renderer : function(val, y, sample) { - return BUI.formatValuesUnits(val, 's', { - fontSize : 12, - decimals : 0, - unitsFontSize : this.unitsFontSize - }); - } - }, - { - text : 'Exp. Temp.', - dataIndex : 'exposureTemperature', - width : 70, - renderer : function(val, y, sample) { - if (Number(val)) { - return BUI.formatValuesUnits(val, 'C', { - fontSize : 12, - decimals : 2, - unitsFontSize : this.unitsFontSize - }); - } - return null; - }, - sortable : true, - editor : this._getEditor("exposureTemperature") - }, - { - text : 'Vol. Load', - dataIndex : 'volumeToLoad', - width : 60, - hidden : false, - editor : this._getEditor("volumeToLoad"), - renderer : function(val, y, sample) { - // return val+ " µl"; - return BUI.formatValuesUnits(val, 'µl', { - fontSize : 12, - decimals : 2, - unitsFontSize : this.unitsFontSize - }); - } - }, - { - text : 'Volume in Well', - dataIndex : 'volume', - hidden : true, - editor : this._getEditor("volume"), - width : 80, - renderer : function(val, y, sample) { - // return val + "(µl)"; - return BUI.formatValuesUnits(val, 'µl', { - fontSize : 12, - decimals : 2, - unitsFontSize : this.unitsFontSize - }); - } - }, - { - text : 'Trans.', - dataIndex : 'transmission', - width : 60, - editor : this._getEditor("transmission"), - renderer : function(val, y, sample) { - return BUI.formatValuesUnits(val, '%', { - fontSize : 12, - decimals : 0, - unitsFontSize : this.unitsFontSize - }); - } - }, - { - text : 'Wait T.', - dataIndex : 'waitTime', - editor : this._getEditor("waitTime"), - width : 50, - renderer : function(val, y, sample) { - // if (val != 0) { - return BUI.formatValuesUnits(val, 's', { - fontSize : 12, - decimals : 0, - unitsFontSize : this.unitsFontSize - }); - // } - } - }, - { - text : 'Flow', - dataIndex : 'flow', - editor : this._getEditor("flow"), - width : 50, - renderer : function(val, y, sample) { - if (val == true) { - return "yes"; - } - return null; - } - }, - { - text : 'Viscosity', - dataIndex : 'viscosity', - tooltip : 'The viscosity of a fluid is a measure of its resistance to gradual deformation by shear stress or tensile stress. For liquids, it corresponds to the informal notion of "thickness"', - editor : this._getEditor("viscosity"), - width : 50, - renderer : function(val, y, sample) { - return val; - } - } ] - }, { - text : 'Status', - dataIndex : 'status', - width : 50, - hidden : _this.isStatusColumnHidden, - renderer : function(val, y, sample) { - if (val != null) { - if (val == 'DONE') { - return "" + val + " "; - } - } - } - }, { - text : 'Time', - dataIndex : 'time', - width : 80, - hidden : _this.isTimeColumnHidden, - renderer : function(val, y, sample) { - if (sample.raw.run3VO != null) { - if (sample.raw.run3VO.timeStart != null) { - if (sample.raw.run3VO.timeStart != "") { - var m = moment(sample.raw.run3VO.timeStart); - return m.format("hh:mm:ss a"); - } - } - } - } - }, { - text : 'Energy', - dataIndex : 'energy', - width : 100, - hidden : true - }, { - text : 'Real Exp. Temp.(C)', - width : 100, - dataIndex : 'expExposureTemperature', - hidden : true - }, { - text : 'Storage Temp.(C)', - width : 100, - dataIndex : 'storageTemperature', - hidden : true - }, { - text : 'Time/Frame (s)', - width : 100, - dataIndex : 'timePerFrame', - hidden : true - }, { - text : 'Radiation Relative', - dataIndex : 'radiationRelative', - width : 100, - hidden : true - }, { - text : 'Radiation Absolute', - dataIndex : 'radiationAbsolute', - width : 100, - hidden : true - }, { - text : 'Comments', - dataIndex : 'comments', - flex : 1, - hidden : false, - editor : this._getEditor("comments") - }, { - id : _this.id + 'buttonRemoveSample', - text : '', - hidden : !_this.removeBtnEnabled, - width : 100, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - if (record.raw.macromoleculeId != null) { - if (_this.removeBtnEnabled) { - return BUI.getRedButton('REMOVE'); - } - } - } - } ], - bbar : bbar, - viewConfig : { - stripeRows : true, - getRowClass : function(record, index, rowParams, store) { - if (record.data.status == "DONE") { - return 'green-row'; - } - }, - listeners : { - 'itemclick' : function(grid, record, item, index, e, eOpts) { - _this.onClick.notify({ - specimen : record.raw - }); - }, - 'cellclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemoveSample') { - grid.getStore().removeAt(rowIndex); +BoxWhiskerGraph.prototype.plotClusterTitles = function(properties){ + /** Cluster Titles **/ + var posX = this.left + this.rulerWidth; + var data = this.data; + for(var i = 0; i < data.clusters.length; i++ ){ + /** title for the clusters **/ + posX = posX + this.interClustersSpace; + + /** Drawing title of classes **/ + var cluster = data.clusters[i]; + var posXClasses = posX; + for(var j = 0; j < cluster.classes.length; j++){ + //SVG.drawRectangle(posXClasses, this.height - (this.bottom + this.clusterTitleHeight + this.rulerHeight), properties.classWidth, this.rulerHeight, this.svg, [["fill", "green"]]); +// SVG.drawText(posXClasses + 1/6*properties.classWidth, this.height - (this.bottom + this.clusterTitleHeight + (this.rulerHeight*1/4)), cluster.classes[j].name, this.svg, [["style", "font-size:xx-small"]]); + var color = cluster.classes[j].color; + this.drawSVGVerticalText(posXClasses + 1/2*(properties.classWidth), this.height - (this.bottom - this.clusterTitleHeight + (this.rulerHeight)), cluster.classes[j].name , [["style", "font-size:x-small;"], ["fill", color]]); + + // SVG.drawRectangle(posXClasses, this.height - (this.bottom + this.clusterTitleHeight), properties.classWidth, 2, this.svg, [["fill", "black"]]); + posXClasses = posXClasses + properties.classWidth + this.interClassesSpace; + } + + var clusterTitleSpace = (data.clusters[i].classes.length * properties.classWidth) + ((data.clusters[i].classes.length - 1) * this.interClassesSpace); + //SVG.drawRectangle(posX, this.height - (this.bottom + this.clusterTitleHeight), clusterTitleSpace, this.clusterTitleHeight, this.svg, [["fill", "pink"]]); + SVG.drawRectangle(posX, this.height - (this.clusterTitleHeight+this.bottom), clusterTitleSpace, 1, this.svg, []); + +// var transform = ["translate", "(" + posX + 1/3*clusterTitleSpace +", " + this.height - (this.bottom + (this.clusterTitleHeight*1/4)) +")"], ["transform", "rotate(180)"]; +// var transform = ["transform", "translate(" + (posX + 1/3*clusterTitleSpace) +", " + (this.height - (this.bottom + (this.clusterTitleHeight*1/4))) + "), rotate(-90) "]; +// this.drawSVGVerticalText(posX + 1/3*clusterTitleSpace, this.height - (this.bottom + (this.clusterTitleHeight*1/4)),data.clusters[i].name, [["style", "font-size:x-small"]]); + SVG.drawText(posX , this.height - (this.bottom + (this.clusterTitleHeight*1/4)),data.clusters[i].name ,this.svg, [["style", "font-size:x-small"]]); + posX = posX + clusterTitleSpace; + } +}; + +BoxWhiskerGraph.prototype.plotWhisters = function(data, properties){ + var colors = ["yellow", "orange", "green"]; + var posX = this.left + this.rulerWidth; + for(var i = 0; i < data.clusters.length; i++ ){ + var cluster = data.clusters[i]; + /** inter cluster space **/ + //SVG.drawRectangle(posX, this.top, this.interClustersSpace, this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight, this.svg, [["fill", "black"]]); + posX = posX + this.interClustersSpace; + + for (var j = 0; j < cluster.classes.length; j ++){ + + //SVG.drawRectangle(posX, this.top, properties.classWidth, this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight, this.svg, [["fill", colors[j]]]); + this.plotBoxWhisker( + { + name : cluster.classes[j].name, + values : cluster.classes[j].values, + minPoint : properties.minPoint, + maxPoint : properties.maxPoint, + x : posX, + y : this.top, + width : properties.classWidth, + height : this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight + + + } + ); + posX = posX + properties.classWidth; + //SVG.drawRectangle(posX, this.top, this.interClassesSpace, this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight, this.svg, [["fill", "black"]]); + if (j < cluster.classes.length - 1){ + posX = posX + this.interClassesSpace; + } + } + } +}; + +BoxWhiskerGraph.prototype.draw = function(targetId, data){ + this.targetId = targetId; + var properties = (this.getDimensions(data)); + this.svg = SVG.createSVGCanvas(document.getElementById(this.targetId), [["width", this.width], ["height", this.height]]); + this.plotAxes(properties); + this.plotClusterTitles(properties); + this.plotWhisters(data,properties); +}; + +BoxWhiskerGraph.prototype.input = function(){ + return DATADOC.getBoxWhikerData(); +}; + +BoxWhiskerGraph.prototype.test = function(targetId){ + var plot = new BoxWhiskerGraph( + { + targetId : targetId, + height : 350, + width : 450, + maxBoxWidth : 25 + } + ); + plot.refresh(this.input()); +}; + + + + + + + +function DataSet(){ + this.json = null; + +}; + + +DataSet.prototype.loadFromJSON = function(json){ + if(json != null) { + if(this.validate(json)) { + this.json = json; + } + } +}; + + +DataSet.prototype.toJSON = function(json){ + return this.json; +}; + + +/** Abstract method to be override on childs classes **/ +DataSet.prototype.validate = function(json){ + if (true){ + return true; + } + /*else{ + throw "Data validation failed"; + }*/ +}; + + + + +Edge.prototype.getName = GraphItem.prototype.getName; +Edge.prototype.setName = GraphItem.prototype.setName; +Edge.prototype.getId = GraphItem.prototype.getId; + +function Edge(id, name, nodeSource, nodeTarget, args){ + GraphItem.prototype.constructor.call(this, id, name, args); + + this.sourceNode = nodeSource; + this.targetNode = nodeTarget; + +}; + +Edge.prototype.toJSON = function(){ + return {"index": this.id,"sourceIndex":this.sourceNode.getId(),"targetIndex":this.targetNode.getId(),"args":this.args}; +}; + +Edge.prototype.getNodeSource = function(){ + return this.sourceNode; +}; + +Edge.prototype.getNodeTarget = function(){ + return this.targetNode; +}; + +Edge.prototype.remove = function(){ + //Remove edge object in the nodes + this.getNodeSource().removeEdge(this); + this.getNodeTarget().removeEdge(this); + + this.deleted.notify(this); +}; + + +EdgeGraphFormatter.prototype.setProperties = ItemGraphFormatter.prototype.setProperties; +EdgeGraphFormatter.prototype.getDefault = ItemGraphFormatter.prototype.getDefault; +EdgeGraphFormatter.prototype.getSelected = ItemGraphFormatter.prototype.getSelected; +EdgeGraphFormatter.prototype.getOver = ItemGraphFormatter.prototype.getOver; +EdgeGraphFormatter.prototype.getDragging = ItemGraphFormatter.prototype.getDragging; +EdgeGraphFormatter.prototype.getId = ItemGraphFormatter.prototype.getId; +EdgeGraphFormatter.prototype.toJSON = ItemGraphFormatter.prototype.toJSON; +EdgeGraphFormatter.prototype.loadFromJSON = ItemGraphFormatter.prototype.loadFromJSON; +EdgeGraphFormatter.prototype._setEvents = ItemGraphFormatter.prototype._setEvents; + +function EdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ + ItemGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); + + this.getDefault().args.type = "EdgeGraphFormatter"; +}; + + + + +LineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; +LineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; +LineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; +LineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; +LineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; +LineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; +LineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; +LineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; +LineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; + +function LineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ + EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); + this.args.type = "LineEdgeGraphFormatter"; +}; + +/** DIRECTED **/ +DirectedLineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; +DirectedLineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; +DirectedLineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; +DirectedLineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; +DirectedLineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; +DirectedLineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; +DirectedLineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; +DirectedLineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; +DirectedLineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; + +function DirectedLineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ + EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); + this.args.type = "DirectedLineEdgeGraphFormatter"; + this.args.arrowSize = "3"; +}; +DirectedLineEdgeGraphFormatter.prototype.getArrowSize = function(){ + return this.args.arrowSize; +}; + +OdirectedLineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; +OdirectedLineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; +OdirectedLineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; +OdirectedLineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; +OdirectedLineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; +OdirectedLineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; +OdirectedLineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; +OdirectedLineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; +OdirectedLineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; + +function OdirectedLineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ + EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); + this.args.type = "DirectedLineEdgeGraphFormatter"; + this.args.arrowSize = "3"; +}; + +OdirectedLineEdgeGraphFormatter.prototype.getArrowSize = function(){ + return this.args.arrowSize; +}; + + +/** CUT (inhibition) **/ +CutDirectedLineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; +CutDirectedLineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; +CutDirectedLineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; +CutDirectedLineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; +CutDirectedLineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; +CutDirectedLineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; +CutDirectedLineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; +CutDirectedLineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; +CutDirectedLineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; + +function CutDirectedLineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ + EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); + this.args.type = "CutDirectedLineEdgeGraphFormatter"; +}; + + + + +BezierEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; +BezierEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; +BezierEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; +BezierEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; +BezierEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; +BezierEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; +BezierEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; +BezierEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; +BezierEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; +BezierEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; + +function BezierEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ + EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); + this.args.type = "BezierEdgeGraphFormatter"; +}; + + + +DotDirectedLineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; +DotDirectedLineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; +DotDirectedLineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; +DotDirectedLineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; +DotDirectedLineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; +DotDirectedLineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; +DotDirectedLineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; +DotDirectedLineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; +DotDirectedLineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; + +function DotDirectedLineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ + EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); + this.args.type = "DotDirectedLineEdgeGraphFormatter"; +}; + + +OdotDirectedLineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; +OdotDirectedLineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; +OdotDirectedLineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; +OdotDirectedLineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; +OdotDirectedLineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; +OdotDirectedLineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; +OdotDirectedLineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; +OdotDirectedLineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; +OdotDirectedLineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; + +function OdotDirectedLineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ + EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); + this.args.type = "OdotDirectedLineEdgeGraphFormatter"; +}; + + + +function GraphDataset(){ + DataSet.prototype.constructor.call(this); + this.edges = new Object(); + this.vertices = new Object(); + this.verticesIndex = new Object(); + + //Events + this.newVertex = new Event(this); + this.vertexNameChanged = new Event(this); + this.vertexDeleted = new Event(this); + + this.newEdge = new Event(this); + this.edgeNameChanged = new Event(this); + this.edgeDeleted = new Event(this); + + this.json = new Object(); + this.json.vertices = new Array(); + this.json.edges = new Array(); + this.json.relations = new Array(); +}; + +GraphDataset.prototype.loadFromJSON = DataSet.prototype.loadFromJSON; +GraphDataset.prototype.toJSON = DataSet.prototype.toJSON; +GraphDataset.prototype.validate = DataSet.prototype.validate; + +/** Devuelve el numero de edges incidentes sobre el nodo con mas edges **/ +GraphDataset.prototype.getMaxClass = function(){ + var maxClassNode = 0; + for ( var node in this.vertices) { + if (this.vertices[node].getEdgesCount() > maxClassNode){ + maxClassNode = this.vertices[node].getEdgesCount(); + } + } + return maxClassNode; +}; + +/** Devuelve el numero de edges incidentes sobre el nodo con mas edges **/ +GraphDataset.prototype.getMinClass = function(){ + var minClassNode = Math.min(); + for ( var node in this.vertices) { + if (this.vertices[node].getEdgesCount() < minClassNode){ + minClassNode = this.vertices[node].getEdgesCount(); + } + } + return minClassNode; +}; + +GraphDataset.prototype.getVertexByName = function(nodeName){ + var results = new Array(); + + for (var vertexId in this.verticesIndex[nodeName]){ + var vertexByid = this.getVertexById(this.verticesIndex[nodeName][vertexId]); + results.push(vertexByid); + //* añadido nuevo porque fallaba el anterior codigo + return vertexByid + } + + if (results <= 1){ + return this.getVertexById(this.verticesIndex[nodeName]); + } + else{ + return results; + } +}; + +GraphDataset.prototype.getVertexById = function(id){ + return this.vertices[id]; +}; + +GraphDataset.prototype.toSIF = function(){ + var sifDataAdapter = new SifFileDataAdapter(); + return sifDataAdapter.toSIF(this); +}; + +GraphDataset.prototype.toSIFID = function(){ + var sifDataAdapter = new SifFileDataAdapter(); + return sifDataAdapter.toSIFID(this); +}; + +GraphDataset.prototype.toDOT = function(){ + var dotFileDataAdapter = new DotFileDataAdapter(); + return dotFileDataAdapter.toDOT(this); +}; + +GraphDataset.prototype.toDOTID = function(){ + var dotFileDataAdapter = new DotFileDataAdapter(); + return dotFileDataAdapter.toDOTID(this); +}; + +GraphDataset.prototype._addNode = function(nodeName, args){ + return new Vertex(this._getVerticesCount()-1, nodeName, args); +}; + +GraphDataset.prototype.addNode = function(nodeName, args){ + this.json.vertices.push(nodeName); + this._addVerticesIndex(nodeName, this._getVerticesCount() - 1); + var vertex = this._addNode(nodeName, args); + this.vertices[this._getVerticesCount()-1] = vertex; + this._setNodeEvents(vertex); + this.newVertex.notify(vertex); +}; + +GraphDataset.prototype._addVerticesIndex = function(nodeName, id){ + if (this.verticesIndex[nodeName] == null){ + this.verticesIndex[nodeName] = new Array(); + } + this.verticesIndex[nodeName].push(id); +}; + +GraphDataset.prototype.addEdge = function(edgeName, nodeSourceId, nodeTargetId, args){ + this.json.edges.push(edgeName); + var nodeSource = this.getVertexById(nodeSourceId); + var nodeTarget = this.getVertexById(nodeTargetId); + var index = this.getEdgesCount() - 1; + this.edges[index] = new Edge(index, edgeName, nodeSource, nodeTarget, args); + this.json.relations.push({"index": index, "sourceIndex": nodeSourceId, "targetIndex": nodeTargetId, "args": args }); + + nodeSource.addEdge(this.edges[index]); + nodeTarget.addEdge(this.edges[index]); + this._setEdgeEvents(this.edges[index]); + this.newEdge.notify(this.edges[index]); +}; + +GraphDataset.prototype.getVertices = function(){ + return this.vertices; +}; + +GraphDataset.prototype.getEdges = function(){ + return this.edges; +}; + +GraphDataset.prototype.getEdgeById = function(edgeId){ + return this.edges[edgeId]; +}; + +GraphDataset.prototype._getVerticesCount = function(){ + return this.json.vertices.length; +}; + + +GraphDataset.prototype.getVerticesCount = function(){ + var count = 0; + for ( var vertex in this.getVertices()) { + count ++; + } + return count; +}; + + +GraphDataset.prototype.getEdgesCount = function(){ + return this.json.edges.length; +}; + +GraphDataset.prototype.init = function(){ + this.edges = new Object(); + this.vertices = new Object(); +}; + +GraphDataset.prototype._setNodeEvents = function(node){ + var _this = this; + //NODE EVENTS + node.deleted.attach(function (sender, node){ + _this._removeNode(node); + }); + + node.nameChanged.attach(function (sender, args){ + var item = args.item; + var newName = item.name; + var indexes = _this.verticesIndex[args.previousName]; + for(var i = 0; i < indexes.length; i++){ + if(indexes[i] == item.id) + indexes.splice(i,1); + } + if(indexes.length == 0){ + delete _this.verticesIndex[args.previousName]; + } + _this._addVerticesIndex(newName, item.id); + _this.json.vertices[item.id] = newName; + _this.vertexNameChanged.notify(args); + }); +}; + +GraphDataset.prototype._setEdgeEvents = function(edge){ + var _this = this; + //EDGE EVENTS + edge.nameChanged.attach(function (sender, edge){ + _this.edgeNameChanged.notify(edge); + + }); + + edge.deleted.attach(function (sender, edge){ + _this._removeEdge(edge); + }); +}; + +GraphDataset.prototype._connectVerticesByName = function(nodeNameSource, nodeNameTarget){ + var source = this.getVertexByName(nodeNameSource); + var target = this.getVertexByName(nodeNameTarget); + + if ((source != null)&&(target!=null)){ + this.addEdge(source.getName() +"_" + target.getName(), source.getId(), target.getId(), {}); + } + else{ + if (source == null){ + console.log("No encontrado: " + nodeNameSource) + } + if (target == null){ + console.log("No encontrado: " + nodeNameTarget) + } + } +}; + +GraphDataset.prototype.loadFromJSON = function(json){ + var json = json; + this.init(); + this.json = new Object(); + this.json.vertices = new Array(); + this.json.edges = new Array(); + this.json.relations = new Array(); + + for ( var i = 0; i < json.nodes.length; i++) { + if (json.nodes[i] != null){ + var name = json.nodes[i]; + this.addNode(name); + } + else{ + this.json.vertices.push(null); + } + } + + for ( var i = 0; i < json.edges.length; i++) { + if (json.edges[i] != null){ + if (json.relations[i] != null){ + var name = json.edges[i]; + this.addEdge(name, json.relations[i].sourceIndex, json.relations[i].targetIndex, json.relations[i].args); + } + } + else{ + this.json.edges.push(null); + this.json.relations.push(null); + } + } +}; + +GraphDataset.prototype.prettyPrint = function(){ + for ( var node in this.vertices) { + console.log(this.vertices[node].getName() ); + for ( var j = 0; j < this.vertices[node].getEdgesIn().length; j++) { + console.log(" --> " + this.vertices[node].getEdgesIn()[j].getNodeTarget().getName() ); + } + } +}; + +GraphDataset.prototype._removeEdge = function(edge){ + this.json.edges[edge.getId()] = null; + this.json.relations[edge.getId()] = null; + + delete this.edges[edge.getId()]; + this.edgeDeleted.notify(edge); + + +}; + +GraphDataset.prototype._removeNode = function(node){ + this.json.vertices[node.getId()] = null; + delete this.vertices[node.getId()]; + this.vertexDeleted.notify(node); +}; + +GraphDataset.prototype.toJSON = function(){ + var json = new Object(); + var nodes = new Array(); + json.nodes = this.json.vertices; //nodes; + json.edges = this.json.edges; //edges; + json.relations = this.json.relations; + return json; +}; + +GraphDataset.prototype.clone = function(){ + var dsDataset = new GraphDataset(); + dsDataset.loadFromJSON(this.toJSON()); + return dsDataset; +}; +//GraphDataset.prototype.test = function(){ +// this.loadFromJSON(this.toJSON()); +//}; + +function labels(){ + var names = new Array(); + + var dataset = interactomeViewer.graphEditorWidget.dataset; + var layout = interactomeViewer.graphEditorWidget.layout; + + for ( var vertexId in interactomeViewer.graphEditorWidget.dataset.getVertices()) { + names.push(interactomeViewer.graphEditorWidget.dataset.getVertexById(vertexId).getName()); + } + + var sorted = (names.sort()); + console.log(sorted) + var distance = 0.01; + var altura = 0.6; + for ( var i = 0; i < names.length; i++) { + var id =dataset.getVertexByName(names[i]).getId(); + + layout.getNodeById(id).setCoordenates(distance, altura); + + + distance = parseFloat(distance) + parseFloat(0.03); + + altura = parseFloat(altura) + parseFloat(0.02); + + if (parseFloat(altura) == 0.9800000000000003){ + + altura = 0.6; + distance = distance - 0.51; + } + + } + + +}; + +function GraphItem(id, name, args){ + this.id = id; + this.name = name; + this.type = "NONE"; + + this.args = new Object(); + + + if (args!=null){ + this.args = args; + if (args.type !=null){ + this.type = args.type; + } + } + + //Events + this.nameChanged = new Event(this); + this.deleted = new Event(this); +} + +GraphItem.prototype.getName = function(){ + return this.name; +}; + +GraphItem.prototype.getId = function(){ + return this.id; +}; + +GraphItem.prototype.setName = function(name){ + var oldName = this.getName(); + this.name = name; + this.nameChanged.notify({"item": this, "previousName" : oldName}); +}; + + + + + +function LayoutDataset(){ + this.dataset = null; + this.vertices = new Object(); + this.changed = new Event(this); + + + this.args = new Object(); + + //RANDOM, CIRCLE + this.args.type = "CIRCLE"; +}; + +LayoutDataset.prototype.loadFromJSON = function(dataset, json){ + var _this = this; + this.vertices = new Object(); + this.dataset = dataset; //new GraphDataset(); + for ( var vertex in json) { + this.vertices[vertex] = new NodeLayout(vertex, json[vertex].x, json[vertex].y); + this.vertices[vertex].changed.attach(function (sender, item){ + _this.changed.notify(item); + }); + } + this._attachDatasetEvents(); +}; + + +LayoutDataset.prototype.toJSON = function(){ + var serialize = new Object(); + for ( var vertex in this.vertices) { + serialize[vertex] = new Object(); + serialize[vertex].x = this.vertices[vertex].x; + serialize[vertex].y = this.vertices[vertex].y; + } + serialize.dataset = new Object(); + serialize.dataset =this.dataset.toJSON(); + return serialize; +}; + +LayoutDataset.prototype.dataBind = function(graphDataset){ + this.dataset = graphDataset; + this._attachDatasetEvents(); + this._calculateLayout(); +}; + +LayoutDataset.prototype._removeVertex = function(vertexId){ + delete this.vertices[vertexId]; +}; + +LayoutDataset.prototype._attachDatasetEvents = function(){ + var _this = this; + + this.dataset.vertexDeleted.attach(function (sender, item){ + _this._removeVertex(item.getId()); + }); + + this.dataset.newVertex.attach(function (sender, item){ + _this.vertices[item.getId()] = new NodeLayout(item.getId(), 0.5, 0.5); + _this.vertices[item.getId()].changed.attach(function (sender, item){ + _this.changed.notify(item); + }); + }); +}; + +LayoutDataset.prototype.getType = function(){ + return this.args.type; +}; + +LayoutDataset.prototype._calculateLayoutVertices = function(type, count){ + + if (type == "CIRCLE"){ + var radius = 0.4; + var centerX = 0.5; + var centerY = 0.5; + var verticesCoordinates = new Array(); + for(var i = 0; i < count; i++){ + x = centerX + radius * Math.sin(i * 2 * Math.PI/count); + y = centerY + radius * Math.cos(i * 2 * Math.PI/count); + verticesCoordinates.push({'x':x,'y':y}); + } + return verticesCoordinates; + } +}; + + +LayoutDataset.prototype._calculateLayout = function(){ + var _this = this; + if (this.getType() == "RANDOM"){ + for ( var vertex in this.dataset.getVertices()) { + if (this.vertices[vertex] == null){ + this.vertices[vertex] = new NodeLayout(vertex, 0, 0); + } + this.vertices[vertex].setCoordinates(Math.random(), Math.random()); + this.vertices[vertex].changed.attach(function (sender, item){ + _this.changed.notify(item); + }); + } + } + + if ( this.getType() == "CIRCLE"){ + + var count = this.dataset._getVerticesCount(); + var verticesCoordinates = this._calculateLayoutVertices(this.getType(), count); + + var aux = 0; + for ( var vertex in this.dataset.getVertices()) { + if (this.vertices[vertex] == null){ + this.vertices[vertex] = new NodeLayout(vertex, 0, 0); + } + this.vertices[vertex].setCoordinates(verticesCoordinates[aux].x, verticesCoordinates[aux].y);//{"x":, "y":}; + aux++; + this.vertices[vertex].changed.attach(function (sender, item){ + _this.changed.notify(item); + }); + } + } + + + if (this.getType() == "SQUARE"){ + + var count = this.dataset._getVerticesCount(); + var xMin = 0.1; + var xMax = 0.9; + var yMin = 0.1; + var yMax = 0.9; + + var rows = Math.sqrt(count); + var step = (xMax - xMin) / rows; + + var verticesCoordinates = new Array(); + for(var i = 0; i < rows; i ++){ + for ( var j = 0; j < rows; j++) { + x = i * step + xMin; + y = j * step + yMin; + verticesCoordinates.push({'x':x,'y':y}); + } + } + + var aux = 0; + for ( var vertex in this.dataset.getVertices()) { + if (this.vertices[vertex] == null){ + this.vertices[vertex] = new NodeLayout(vertex, 0, 0); + } + this.vertices[vertex].setCoordinates(verticesCoordinates[aux].x, verticesCoordinates[aux].y);//{"x":, "y":}; + aux++; + this.vertices[vertex].changed.attach(function (sender, item){ + _this.changed.notify(item); + }); + } + } + +}; + +LayoutDataset.prototype.getNodeById = function(id){ + return this.vertices[id]; +}; + +LayoutDataset.prototype.getVerticesByArea = function(x1, y1, x2, y2){ + var vertices = new Array(); + for ( var vertex in this.dataset.getVertices()) { + if ((this.vertices[vertex].x >= x1)&&(this.vertices[vertex].x <= x2)){ + if ((this.vertices[vertex].y >= y1)&&(this.vertices[vertex].y <= y2)){ + vertices.push(this.vertices[vertex]); + } + } + } + return vertices; +}; + + + + +LayoutDataset.prototype.getLayout = function(type){ + + if (type == "CIRCLE"){ + this.args.type = "CIRCLE"; + this._calculateLayout(); + return; + } + + if (type == "SQUARE"){ + this.args.type = "SQUARE"; + this._calculateLayout(); + return; + } + + if (type == "RANDOM"){ + this.args.type = "RANDOM"; + this._calculateLayout(); + return; + } + + + var dotText = this.dataset.toDOTID(); + var url = "http://bioinfo.cipf.es/utils/ws/rest/network/layout/"+type+".coords"; + var _this = this; + + $.ajax({ + async: true, + type: "POST", + url: url, + dataType: "text", + data: { + dot :dotText + }, + cache: false, + success: function(data){ + var response = JSON.parse(data); + for ( var vertexId in response) { + _this.vertices[vertexId].setCoordinates(response[vertexId].x, response[vertexId].y); + } + } + }); + +// $.ajax({ +// async: true, +// type: "POST", +// url: url, +// dataType: "script", +// data: { +// dot :dotText +// }, +// cache: false, +// success: function(data){ +// var response = JSON.parse(data); +// for ( var vertexId in response) { +// _this.vertices[vertexId].setCoordinates(response[vertexId].x, response[vertexId].y); +// } +// } +// }); + +}; + +function NodeLayout(id, x, y, args){ + this.id = id; + this.x = x; + this.y = y; + this.changed = new Event(this); +}; + +NodeLayout.prototype.getId = function(id){ + return this.id; +}; + +NodeLayout.prototype.setCoordinates = function(x, y){ + this.x = x; + this.y = y; + this.changed.notify(this); +}; + + + +function NetworkDataSetFormatter(vertexFormatProperties, defaultEdgeProperties, args){ + DataSet.prototype.constructor.call(this); + + this.args = new Object(); + + this.vertices = new Object(); + this.edges = new Object(); + this.dataset = null; + this.maxClass = 0; + this.minClass = 0; + + /** Coordenates with default Setting */ + this.args.width = 1100; + this.args.height = 500; + + /** Optional parameters */ + this.args.backgroundColor = "#FFFFFF"; + this.args.backgroundImage = null; + this.args.backgroundImageHeight = null; + this.args.backgroundImageWidth = null; + this.args.backgroundImageX = null; + this.args.backgroundImageY = null; + + + this.args.balanceNodes = false; + this.args.nodesMaxSize = 3; + this.args.nodesMinSize = 0.5; + + + /** Zoom **/ + this.args.zoomScale = 1; + this.args.zoomScaleStepFactor = 0.4; + + if (args != null){ + if (args.backgroundImage != null){ + this.args.backgroundImage = args.backgroundImage; + } + + if (args.width != null){ + this.args.width = args.width; + } + + if (args.height != null){ + this.args.height = args.height; + this.args.svgHeight = args.height; + } + + if (args.svgHeight != null){ + this.args.svgHeight = args.svgHeight; + } + + if (args.backgroundColor != null){ + this.args.backgroundColor = args.backgroundColor; + } + + if(args.balanceNodes != null){ + this.args.balanceNodes = args.balanceNodes; + } + + if(args.nodesMaxSize != null){ + this.args.nodesMaxSize = args.nodesMaxSize; + } + if(args.nodesMinSize != null){ + this.args.nodesMinSize = args.nodesMinSize; + } + } + + this.args.defaultEdgeProperties = {"fill":"#000000", "radius":"1", "stroke":"#000000", "size":1, "title":{"fontSize":10, "fontColor":"#000000"}}; + this.args.vertexFormatProperties = { "fill":"#000000", "stroke":"#000000", "stroke-opacity":"#000000"}; + + if (vertexFormatProperties!= null){ + this.args.vertexFormatProperties = vertexFormatProperties; + } + if (defaultEdgeProperties!= null){ + this.args.defaultEdgeProperties = defaultEdgeProperties; + } + + /** Events **/ + this.changed = new Event(this); + this.edgeChanged = new Event(this); + this.resized = new Event(this); + this.backgroundImageChanged= new Event(this); + this.backgroundColorChanged= new Event(this); +}; + +NetworkDataSetFormatter.prototype.loadFromJSON = function(dataset, json){ + this.args = new Object(); + this.vertices = new Object(); + this.args = json; + this._setDataset(dataset); + var _this = this; + + for ( var vertex in json.vertices) { + this.addVertex(vertex, json.vertices[vertex]); + } + + for ( var edgeId in json.edges) { + this.addEdge(edgeId, json.edges[edgeId]); + } +}; + + +NetworkDataSetFormatter.prototype.toJSON = function(){ + + +// this.args.vertices = new Object(); +// this.args.edges = new Object(); +// +// for ( var vertex in this.vertices) { +// this.args.vertices[vertex] = this.getVertexById(vertex).toJSON(); +// } +// for ( var edge in this.edges) { +// this.args.edges[edge] = this.getEdgeById(edge).toJSON(); +// } +// +// return (this.args); + + + var serialize = new Object(); + serialize = JSON.parse(JSON.stringify(this.args)); + serialize.vertices = new Object(); + serialize.edges = new Object(); + + for ( var vertex in this.vertices) { + serialize.vertices[vertex] = this.getVertexById(vertex).toJSON(); + } + for ( var edge in this.edges) { + serialize.edges[edge] = this.getEdgeById(edge).toJSON(); + } + + return (serialize); +}; + + + +NetworkDataSetFormatter.prototype._getNodeSize = function(nodeId){ + if (this.isVerticesBalanced()){ + var total = this.maxClass - this.minClass; + if (total == 0){ total = 1;} + var nodeConnection = this.dataset.getVertexById(nodeId).getEdges().length; + return ((nodeConnection*this.args.nodesMaxSize)/total) + this.args.nodesMinSize; + } + return this.getVertexById(nodeId).getDefault().getSize(); +}; + +NetworkDataSetFormatter.prototype._recalculateSize = function(){ + if (this.isVerticesBalanced()){ + this.maxClass = this.dataset.getMaxClass(); + this.minClass = this.dataset.getMinClass(); + for ( var vertexIdAll in this.vertices) { + var size = this._getNodeSize(vertexIdAll); + this.vertices[vertexIdAll].getDefault().setSize(size); + this.vertices[vertexIdAll].getSelected().setSize(size); + this.vertices[vertexIdAll].getOver().setSize(size); + } + } +}; + + +NetworkDataSetFormatter.prototype.addVertex = function(vertexId, json){ + + + if (json == null){ + this.vertices[vertexId] = new CircleVertexGraphFormatter(vertexId, this.args.vertexFormatProperties.defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); + } + else{ + + /** Cargo los attributos desde el json **/ + if (json.type == null){ + this.vertices[vertexId] = new CircleVertexGraphFormatter(vertexId, this.args.vertexFormatProperties.defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); + } + + if ((json.type == "SquareVertexGraphFormatter")||(json.type == "SquareVertexNetworkFormatter")){ + this.vertices[vertexId] = new SquareVertexGraphFormatter(vertexId); + this.vertices[vertexId].loadFromJSON(json); + } + + if ((json.type == "CircleVertexGraphFormatter")||(json.type == "CircleVertexNetworkFormatter")){ + this.vertices[vertexId] = new CircleVertexGraphFormatter(vertexId); + this.vertices[vertexId].loadFromJSON(json); + } + + if ((json.type == "EllipseVertexGraphFormatter")||(json.type == "EllipseVertexNetworkFormatter")){ + this.vertices[vertexId] = new EllipseVertexGraphFormatter(vertexId); + this.vertices[vertexId].loadFromJSON(json); + } + + if ((json.type == "RectangleVertexGraphFormatter")||(json.type == "RectangleVertexNetworkFormatter")){ + this.vertices[vertexId] = new RectangleVertexGraphFormatter(vertexId); + this.vertices[vertexId].loadFromJSON(json); + } + + if ((json.type == "RoundedVertexGraphFormatter")||(json.type == "RoundedVertexNetworkFormatter")){ + this.vertices[vertexId] = new RoundedVertexGraphFormatter(vertexId); + this.vertices[vertexId].loadFromJSON(json); + } + + } + + + var _this = this; + this.vertices[vertexId].stateChanged.attach(function (sender, item){ + _this.changed.notify(item); + }); + + var size = this._getNodeSize(vertexId); + this.vertices[vertexId].defaultFormat.args.size = size; + this.vertices[vertexId].selected.args.size = size; + this.vertices[vertexId].over.args.size = size; + +}; + +NetworkDataSetFormatter.prototype.addEdge = function(edgeId, json){ + + /** Es un edge nuevo que le doy los atributos por defecto **/ + if (json == null){ + if (this.dataset.getEdgeById(edgeId).getNodeSource().getId() == this.dataset.getEdgeById(edgeId).getNodeTarget().getId()){ + this.edges[edgeId] = new BezierEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); + }else{ + this.edges[edgeId] = new DirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); + } + } + else{ + /** Cargo los attributos desde el json **/ + if (json.type == null){ + this.edges[edgeId] = new LineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); + } + + if ((json.type == "LineEdgeGraphFormatter")||(json.type == "LineEdgeNetworkFormatter")){ + this.edges[edgeId] = new LineEdgeGraphFormatter(edgeId); + this.edges[edgeId].loadFromJSON(json); + } + if ((json.type == "DirectedLineEdgeGraphFormatter")||(json.type == "DirectedLineEdgeNetworkFormatter")){ + this.edges[edgeId] = new DirectedLineEdgeGraphFormatter(edgeId); + this.edges[edgeId].loadFromJSON(json); + } + + if ((json.type == "BezierEdgeGraphFormatter")||(json.type == "BezierEdgeNetworkFormatter")){ + this.edges[edgeId] = new BezierEdgeGraphFormatter(edgeId); + this.edges[edgeId].loadFromJSON(json); + } + + + if ((json.type == "CutDirectedLineEdgeGraphFormatter")||(json.type == "CutDirectedLineEdgeNetworkFormatter")){ + this.edges[edgeId] = new CutDirectedLineEdgeGraphFormatter(edgeId); + this.edges[edgeId].loadFromJSON(json); + } + + if ((json.type == "DotDirectedLineEdgeGraphFormatter")||(json.type == "DotDirectedLineEdgeNetworkFormatter")){ + this.edges[edgeId] = new DotDirectedLineEdgeGraphFormatter(edgeId); + this.edges[edgeId].loadFromJSON(json); + } + if ((json.type == "OdotDirectedLineEdgeGraphFormatter")||(json.type == "OdotDirectedLineEdgeNetworkFormatter")){ + this.edges[edgeId] = new OdotDirectedLineEdgeGraphFormatter(edgeId); + this.edges[edgeId].loadFromJSON(json); + } + + if ((json.type == "OdirectedLineEdgeGraphFormatter")||(json.type == "OdirectedLineEdgeNetworkFormatter")){ + this.edges[edgeId] = new OdirectedLineEdgeGraphFormatter(edgeId); + this.edges[edgeId].loadFromJSON(json); + } + } + + var _this = this; + this.edges[edgeId].stateChanged.attach(function (sender, item){ + _this.edgeChanged.notify(item); + }); + + this._recalculateSize(); +}; + +NetworkDataSetFormatter.prototype._setDataset = function(dataset){ + this.dataset = dataset; + this.maxClass = dataset.getMaxClass(); + this.minClass = dataset.getMinClass(); + this._attachDatasetEvents(); +}; + +NetworkDataSetFormatter.prototype.changeEdgeType = function(edgeId, type){ + if ((type == "LineEdgeGraphFormatter")||(type == "LineEdgeNetworkFormatter")){ + this.edges[edgeId] = new LineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); + + } + if ((type == "DirectedLineEdgeGraphFormatter")||(type == "DirectedLineEdgeNetworkFormatter")){ + this.edges[edgeId] = new DirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); + } + + if ((type == "CutDirectedLineEdgeGraphFormatter")||(type == "CutDirectedLineEdgeNetworkFormatter")){ + this.edges[edgeId] = new CutDirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); + } + + if ((type == "DotDirectedLineEdgeGraphFormatter")||(type == "DotDirectedLineEdgeNetworkFormatter")){ + this.edges[edgeId] = new DotDirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); + } + + if ((type == "OdotDirectedLineEdgeGraphFormatter")||(type == "OdotDirectedLineEdgeNetworkFormatter")){ + this.edges[edgeId] = new OdotDirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); + } + + if ((type == "OdirectedLineEdgeGraphFormatter")||(type == "OdirectedLineEdgeNetworkFormatter")){ + this.edges[edgeId] = new OdirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); + } + + + + var _this = this; + this.edges[edgeId].stateChanged.attach(function (sender, item){ + _this.edgeChanged.notify(item); + }); + _this.edgeChanged.notify(this.edges[edgeId]); +}; +/* +classe = "SquareNetworkNodeFormatter"; +} +if (value == "circle"){ + classe = "CircleNetworkNodeFormatter"; + **/ +NetworkDataSetFormatter.prototype.changeNodeType = function(vertexId, type){ + var defaultFormat = JSON.parse(JSON.stringify(this.vertices[vertexId].getDefault())); + var selectedFormat = JSON.parse(JSON.stringify(this.vertices[vertexId].getSelected())); + var defaultFormat = JSON.parse(JSON.stringify(this.vertices[vertexId].getDefault())); + var defaultFormat = JSON.parse(JSON.stringify(this.vertices[vertexId].getDefault())); + + if ((type == "SquareVertexGraphFormatter")||(type == "SquareVertexNetworkFormatter")){ + this.vertices[vertexId] = new SquareVertexGraphFormatter(vertexId,defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); + } + + if ((type == "CircleVertexGraphFormatter")||(type == "CircleVertexNetworkFormatter")){ + this.vertices[vertexId] = new CircleVertexGraphFormatter(vertexId, defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); + } + + if ((type == "EllipseVertexGraphFormatter")||(type == "EllipseVertexNetworkFormatter")){ + this.vertices[vertexId] = new EllipseVertexGraphFormatter(vertexId, defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); + } + + if ((type == "RectangleVertexGraphFormatter")||(type == "RectangleVertexNetworkFormatter")){ + this.vertices[vertexId] = new RectangleVertexGraphFormatter(vertexId, defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); + } + + if ((type == "RoundedVertexGraphFormatter")||(type == "RoundedVertexNetworkFormatter")){ + this.vertices[vertexId] = new RoundedVertexGraphFormatter(vertexId, defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); + } + + if ((type == "OctagonVertexGraphFormatter")||(type == "OctagonVertexNetworkhFormatter")){ + this.vertices[vertexId] = new OctagonVertexGraphFormatter(vertexId, defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); + } + + + var _this = this; + this.vertices[vertexId].stateChanged.attach(function (sender, item){ + _this.changed.notify(item); + }); + _this.changed.notify(this.vertices[vertexId]); +}; + + + +NetworkDataSetFormatter.prototype.dataBind = function(networkDataSet){ + var _this = this; + this._setDataset(networkDataSet); + + for ( var vertex in this.dataset.getVertices()) { + this.addVertex(vertex); + } + + for ( var edge in this.dataset.getEdges()) { + this.addEdge(edge); + } +}; + +NetworkDataSetFormatter.prototype._removeEdge = function(edgeId){ + delete this.edges[edgeId]; +}; + +NetworkDataSetFormatter.prototype._removeVertex = function(vertexId){ + delete this.vertices[vertexId]; +}; + +NetworkDataSetFormatter.prototype._attachDatasetEvents = function(id){ + var _this = this; + this.dataset.vertexDeleted.attach(function (sender, item){ + _this._removeVertex(item.getId()); + }); + + this.dataset.edgeDeleted.attach(function (sender, item){ + _this._removeEdge(item.getId()); + }); + + this.dataset.newVertex.attach(function (sender, item){ + _this.addVertex(item.getId()); + }); + + this.dataset.newEdge.attach(function (sender, item){ + _this.addEdge(item.getId()); + }); +}; + + +NetworkDataSetFormatter.prototype.getVertexById = function(id){ + return this.vertices[id]; +}; + +NetworkDataSetFormatter.prototype.getEdgeById = function(id){ + return this.edges[id]; +}; + +NetworkDataSetFormatter.prototype.makeLabelsBigger = function(){ +for ( var vertexId in this.vertices) { + var fontSize = this.vertices[vertexId].getDefault().getFontSize() + 2; + this.vertices[vertexId].getDefault().setFontSize(fontSize); + } +}; + +NetworkDataSetFormatter.prototype.makeLabelsSmaller = function(){ + for ( var vertexId in this.vertices) { + var fontSize = this.vertices[vertexId].getDefault().getFontSize() - 2; + this.vertices[vertexId].getDefault().setFontSize(fontSize); + } +}; + + +NetworkDataSetFormatter.prototype.resize = function(width, height){ + this.args.width = width; + this.args.height = height; + this.resized.notify(); +}; + +/** ZOOM GETTERS **/ +NetworkDataSetFormatter.prototype.getZoomScaleStepFactor = function(){return this.args.zoomScaleStepFactor;}; +NetworkDataSetFormatter.prototype.setZoomScaleStepFactor = function(scaleFactor){this.args.zoomScaleStepFactor = scaleFactor;}; +NetworkDataSetFormatter.prototype.getZoomScale = function(){return this.args.zoomScale;}; +NetworkDataSetFormatter.prototype.setZoomScale = function(scale){this.args.zoomScale = scale;}; + +NetworkDataSetFormatter.prototype.getNodesMaxSize = function(){return this.args.nodesMaxSize;}; +NetworkDataSetFormatter.prototype.getNodesMinSize = function(){return this.args.nodesMinSize;}; + +/** SIZE SETTERS AND GETTERS **/ +NetworkDataSetFormatter.prototype.isVerticesBalanced = function(){return this.args.balanceNodes;}; +NetworkDataSetFormatter.prototype.getWidth = function(){return this.args.width;}; +NetworkDataSetFormatter.prototype.getHeight = function(){return this.args.height;}; + +/** OPTIONAL PARAMETERS GETTERS AND SETTERS **/ +NetworkDataSetFormatter.prototype.getBackgroundImage = function(){return this.args.backgroundImage;}; +NetworkDataSetFormatter.prototype.setBackgroundImage = function(value){this.args.backgroundImage = value; this.backgroundImageChanged.notify(this);}; + + +NetworkDataSetFormatter.prototype.getBackgroundImageWidth = function(){return this.args.backgroundImageWidth;}; +NetworkDataSetFormatter.prototype.setBackgroundImageWidth = function(value){this.args.backgroundImageWidth = value; this.backgroundImageChanged.notify(this);}; + +NetworkDataSetFormatter.prototype.getBackgroundImageHeight = function(){return this.args.backgroundImageHeight;}; +NetworkDataSetFormatter.prototype.setBackgroundImageHeight = function(value){this.args.backgroundImageHeight = value; this.backgroundImageChanged.notify(this);}; + +NetworkDataSetFormatter.prototype.getBackgroundImageX = function(){return this.args.backgroundImageX;}; +NetworkDataSetFormatter.prototype.setBackgroundImageX = function(value){this.args.backgroundImageX = value; this.backgroundImageChanged.notify(this);}; + +NetworkDataSetFormatter.prototype.getBackgroundImageY = function(){return this.args.backgroundImageX;}; +NetworkDataSetFormatter.prototype.setBackgroundImageY = function(value){this.args.backgroundImageY = value; this.backgroundImageChanged.notify(this);}; + + + +NetworkDataSetFormatter.prototype.getBackgroundColor = function(){return this.args.backgroundColor;}; +NetworkDataSetFormatter.prototype.setBackgroundColor = function(value){this.args.backgroundColor = value; this.backgroundColorChanged.notify(this);}; + +NetworkDataSetFormatter.prototype.getWidth = function(){return this.args.width;}; +NetworkDataSetFormatter.prototype.setWidth = function(value){this.args.width = value;}; + +NetworkDataSetFormatter.prototype.getHeight = function(){return this.args.height;}; +NetworkDataSetFormatter.prototype.setHeight = function(value){this.args.height = value;}; + + + + +Vertex.prototype.getName = GraphItem.prototype.getName; +Vertex.prototype.setName = GraphItem.prototype.setName; +Vertex.prototype.getId = GraphItem.prototype.getId; + +function Vertex(id, name, args){ + GraphItem.prototype.constructor.call(this, id, name, args); + this.edgesIn= new Array(); + this.edgesOut= new Array(); +}; + +Vertex.prototype.getEdges = function(){ + return this.edgesIn.concat(this.edgesOut); +}; + +Vertex.prototype.getEdgesCount = function(){ + return this.getEdges().length; +}; + +Vertex.prototype.getEdgesIn = function(){ + return this.edgesIn; +}; + +Vertex.prototype.getEdgesOut = function(){ + return this.edgesOut; +}; + +Vertex.prototype.addEdge = function(edge){ + if (edge.getNodeSource().getId() == this.id){ + this.edgesIn.push(edge); + } + else{ + this.edgesOut.push(edge); + } +}; + +Vertex.prototype.removeEdge = function(edge){ + for ( var i = 0; i < this.getEdgesIn().length; i++) { + var edgeIn = this.edgesIn[i]; + if (edgeIn.getId() == edge.getId()){ + this.edgesIn.splice(i, 1); + } + } + for ( var i = 0; i < this.getEdgesOut().length; i++) { + var edgeIn = this.edgesOut[i]; + if (edgeIn.getId() == edge.getId()){ + this.edgesOut.splice(i, 1); + } + } +}; + +Vertex.prototype.remove = function(){ + var edges = this.getEdges(); + for ( var i = 0; i < edges.length; i++) { + var edge = edges[i]; + edge.remove(); + } + this.deleted.notify(this); +}; + + + + + +VertexGraphFormatter.prototype.getDefault = ItemGraphFormatter.prototype.getDefault; +VertexGraphFormatter.prototype.getSelected = ItemGraphFormatter.prototype.getSelected; +VertexGraphFormatter.prototype.getOver = ItemGraphFormatter.prototype.getOver; +VertexGraphFormatter.prototype.getDragging = ItemGraphFormatter.prototype.getDragging; +VertexGraphFormatter.prototype.getId = ItemGraphFormatter.prototype.getId; +VertexGraphFormatter.prototype.toJSON = ItemGraphFormatter.prototype.toJSON; +VertexGraphFormatter.prototype.loadFromJSON = ItemGraphFormatter.prototype.loadFromJSON; +VertexGraphFormatter.prototype._setEvents = ItemGraphFormatter.prototype._setEvents; + + +function VertexGraphFormatter(defaultFormat, selectedFormat, overFormat, draggingFormat){ + ItemGraphFormatter.prototype.constructor.call(this, defaultFormat, selectedFormat, overFormat, draggingFormat); +}; + + +CircleVertexGraphFormatter.prototype.getDefault = VertexGraphFormatter.prototype.getDefault; +CircleVertexGraphFormatter.prototype.getSelected = VertexGraphFormatter.prototype.getSelected; +CircleVertexGraphFormatter.prototype.getOver = VertexGraphFormatter.prototype.getOver; +CircleVertexGraphFormatter.prototype.getDragging = VertexGraphFormatter.prototype.getDragging; +CircleVertexGraphFormatter.prototype.getId = VertexGraphFormatter.prototype.getId; +CircleVertexGraphFormatter.prototype.toJSON = VertexGraphFormatter.prototype.toJSON; +CircleVertexGraphFormatter.prototype.loadFromJSON = VertexGraphFormatter.prototype.loadFromJSON; +CircleVertexGraphFormatter.prototype._setEvents = VertexGraphFormatter.prototype._setEvents; + +function CircleVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ + VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); + this.args.type = "CircleVertexGraphFormatter"; + if (defaultFormat != null){ + if (defaultFormat.radius != null){ + this.defaultFormat.args.radius = defaultFormat.radius; + } + } + + if (selectedFormat != null){ + if (selectedFormat.radius != null){ + this.selected.args.radius = selectedFormat.radius; + } + } + + if (overFormat != null){ + if (overFormat.radius != null){ + this.over.args.radius = overFormat.radius; + } + } + + if (draggingFormat != null){ + if (draggingFormat.radius != null){ + this.dragging.args.draggingFormat = draggingFormat.radius; + } + } +}; + + + +SquareVertexGraphFormatter.prototype.getDefault = VertexGraphFormatter.prototype.getDefault; +SquareVertexGraphFormatter.prototype.getSelected = VertexGraphFormatter.prototype.getSelected; +SquareVertexGraphFormatter.prototype.getOver = VertexGraphFormatter.prototype.getOver; +SquareVertexGraphFormatter.prototype.getDragging = VertexGraphFormatter.prototype.getDragging; +SquareVertexGraphFormatter.prototype.getId = VertexGraphFormatter.prototype.getId; +SquareVertexGraphFormatter.prototype.toJSON = VertexGraphFormatter.prototype.toJSON; +SquareVertexGraphFormatter.prototype.loadFromJSON = VertexGraphFormatter.prototype.loadFromJSON; +SquareVertexGraphFormatter.prototype._setEvents = VertexGraphFormatter.prototype._setEvents; + +function SquareVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ + VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); + this.args.type = "SquareVertexGraphFormatter"; + if (defaultFormat != null){ + if (defaultFormat.radius != null){ + this.defaultFormat.args.radius = defaultFormat.radius; + } + } + + if (selectedFormat != null){ + if (selectedFormat.radius != null){ + this.selected.args.radius = selectedFormat.radius; + } + } + + if (overFormat != null){ + if (overFormat.radius != null){ + this.over.args.radius = overFormat.radius; + } + } + + if (draggingFormat != null){ + if (draggingFormat.radius != null){ + this.dragging.args.draggingFormat = draggingFormat.radius; + } + } +}; + + +EllipseVertexGraphFormatter.prototype.getDefault = VertexGraphFormatter.prototype.getDefault; +EllipseVertexGraphFormatter.prototype.getSelected = VertexGraphFormatter.prototype.getSelected; +EllipseVertexGraphFormatter.prototype.getOver = VertexGraphFormatter.prototype.getOver; +EllipseVertexGraphFormatter.prototype.getDragging = VertexGraphFormatter.prototype.getDragging; +EllipseVertexGraphFormatter.prototype.getId = VertexGraphFormatter.prototype.getId; +EllipseVertexGraphFormatter.prototype.toJSON = VertexGraphFormatter.prototype.toJSON; +EllipseVertexGraphFormatter.prototype.loadFromJSON = VertexGraphFormatter.prototype.loadFromJSON; +EllipseVertexGraphFormatter.prototype._setEvents = VertexGraphFormatter.prototype._setEvents; + +function EllipseVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ + VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); + this.args.type = "EllipseVertexGraphFormatter"; + if (defaultFormat != null){ + if (defaultFormat.radius != null){ + this.defaultFormat.args.radius = defaultFormat.radius; + } + } + + if (selectedFormat != null){ + if (selectedFormat.radius != null){ + this.selected.args.radius = selectedFormat.radius; + } + } + + if (overFormat != null){ + if (overFormat.radius != null){ + this.over.args.radius = overFormat.radius; + } + } + + if (draggingFormat != null){ + if (draggingFormat.radius != null){ + this.dragging.args.draggingFormat = draggingFormat.radius; + } + } +}; + + + +RectangleVertexGraphFormatter.prototype.getDefault = ItemGraphFormatter.prototype.getDefault; +RectangleVertexGraphFormatter.prototype.getSelected = ItemGraphFormatter.prototype.getSelected; +RectangleVertexGraphFormatter.prototype.getOver = ItemGraphFormatter.prototype.getOver; +RectangleVertexGraphFormatter.prototype.getDragging = ItemGraphFormatter.prototype.getDragging; +RectangleVertexGraphFormatter.prototype.getId = ItemGraphFormatter.prototype.getId; +RectangleVertexGraphFormatter.prototype.toJSON = ItemGraphFormatter.prototype.toJSON; +RectangleVertexGraphFormatter.prototype.loadFromJSON = ItemGraphFormatter.prototype.loadFromJSON; +RectangleVertexGraphFormatter.prototype._setEvents = ItemGraphFormatter.prototype._setEvents; + +function RectangleVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ + VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); + this.args.type = "RectangleVertexGraphFormatter"; + if (defaultFormat != null){ + if (defaultFormat.radius != null){ + this.defaultFormat.args.radius = defaultFormat.radius; + } + } + + if (selectedFormat != null){ + if (selectedFormat.radius != null){ + this.selected.args.radius = selectedFormat.radius; + } + } + + if (overFormat != null){ + if (overFormat.radius != null){ + this.over.args.radius = overFormat.radius; + } + } + + if (draggingFormat != null){ + if (draggingFormat.radius != null){ + this.dragging.args.draggingFormat = draggingFormat.radius; + } + } +}; + + + +RoundedVertexGraphFormatter.prototype.getDefault = ItemGraphFormatter.prototype.getDefault; +RoundedVertexGraphFormatter.prototype.getSelected = ItemGraphFormatter.prototype.getSelected; +RoundedVertexGraphFormatter.prototype.getOver = ItemGraphFormatter.prototype.getOver; +RoundedVertexGraphFormatter.prototype.getDragging = ItemGraphFormatter.prototype.getDragging; +RoundedVertexGraphFormatter.prototype.getId = ItemGraphFormatter.prototype.getId; +RoundedVertexGraphFormatter.prototype.toJSON = ItemGraphFormatter.prototype.toJSON; +RoundedVertexGraphFormatter.prototype.loadFromJSON = ItemGraphFormatter.prototype.loadFromJSON; +RoundedVertexGraphFormatter.prototype._setEvents = ItemGraphFormatter.prototype._setEvents; + +function RoundedVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ + VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); + this.args.type = "RoundedVertexGraphFormatter"; + if (defaultFormat != null){ + if (defaultFormat.radius != null){ + this.defaultFormat.args.radius = defaultFormat.radius; + } + } + + if (selectedFormat != null){ + if (selectedFormat.radius != null){ + this.selected.args.radius = selectedFormat.radius; + } + } + + if (overFormat != null){ + if (overFormat.radius != null){ + this.over.args.radius = overFormat.radius; + } + } + + if (draggingFormat != null){ + if (draggingFormat.radius != null){ + this.dragging.args.draggingFormat = draggingFormat.radius; + } + } +}; + + + +OctagonVertexGraphFormatter.prototype.getDefault = ItemGraphFormatter.prototype.getDefault; +OctagonVertexGraphFormatter.prototype.getSelected = ItemGraphFormatter.prototype.getSelected; +OctagonVertexGraphFormatter.prototype.getOver = ItemGraphFormatter.prototype.getOver; +OctagonVertexGraphFormatter.prototype.getDragging = ItemGraphFormatter.prototype.getDragging; +OctagonVertexGraphFormatter.prototype.getId = ItemGraphFormatter.prototype.getId; +OctagonVertexGraphFormatter.prototype.toJSON = ItemGraphFormatter.prototype.toJSON; +OctagonVertexGraphFormatter.prototype.loadFromJSON = ItemGraphFormatter.prototype.loadFromJSON; +OctagonVertexGraphFormatter.prototype._setEvents = ItemGraphFormatter.prototype._setEvents; + +function OctagonVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ + VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); + this.args.type = "OctagonVertexGraphFormatter"; + if (defaultFormat != null){ + if (defaultFormat.radius != null){ + this.defaultFormat.args.radius = defaultFormat.radius; + } + } + + if (selectedFormat != null){ + if (selectedFormat.radius != null){ + this.selected.args.radius = selectedFormat.radius; + } + } + + if (overFormat != null){ + if (overFormat.radius != null){ + this.over.args.radius = overFormat.radius; + } + } + + if (draggingFormat != null){ + if (draggingFormat.radius != null){ + this.dragging.args.draggingFormat = draggingFormat.radius; + } + } +}; + + + +var Colors = new function() +{ + this.hashColor = []; + this.getColorByScoreArrayValue = function (arrayScore) + { + var array = new Array(); + + for (var i = 0; i< arrayScore.length; i++) + { + + var color = this.getColorByScoreValue(arrayScore[i]) + array.push( color); + + } + return array; + }; + + this.getHexStringByScoreArrayValue = function (arrayScore) + { + var arrayColor = this.getColorByScoreArrayValue(arrayScore); + var arrayHex = new Array(); + for (var i = 0; i< arrayColor.length; i++) + { + arrayHex.push( arrayColor[i].HexString()); + } + return arrayHex; + }; + + this.getColorByScoreValue = function (score) + { + + var truncate = score.toString().substr(0,4); + if (this.hashColor[truncate]!=null) + { + return this.hashColor[truncate]; + } + + + if(isNaN(score)) { + return Colors.ColorFromRGB(0,0,0); + } + var value; + + var from, to; + if(score < 0.5) { + from = Colors.ColorFromRGB(0,0,255); + to = Colors.ColorFromRGB(255,255,255); + value = (score * 2); + } else { + from = Colors.ColorFromRGB(255,255,255); + to = Colors.ColorFromRGB(255,0,0); + value = (score * 2) - 1; + } + + var x = value; + var y = 1.0 - value; + var color = Colors.ColorFromRGB(y * from.Red() + x * to.Red(), y * from.Green() + x * to.Green(), y * from.Blue() + x * to.Blue()); + + this.hashColor[truncate] = color; + + return color; + }; + + this.ColorFromHSV = function(hue, sat, val) + { + var color = new Color(); + color.SetHSV(hue,sat,val); + return color; + }; + + this.ColorFromRGB = function(r, g, b) + { + var color = new Color(); + color.SetRGB(r,g,b); + return color; + }; + + this.ColorFromHex = function(hexStr) + { + var color = new Color(); + color.SetHexString(hexStr); + return color; + }; + + function Color() { + //Stored as values between 0 and 1 + var red = 0; + var green = 0; + var blue = 0; + + //Stored as values between 0 and 360 + var hue = 0; + + //Strored as values between 0 and 1 + var saturation = 0; + var value = 0; + + this.SetRGB = function(r, g, b) + { + red = r/255.0; + green = g/255.0; + blue = b/255.0; + calculateHSV(); + }; + + this.Red = function() { return Math.round(red*255); }; + + this.Green = function() { return Math.round(green*255); }; + + this.Blue = function() { return Math.round(blue*255); }; + + this.SetHSV = function(h, s, v) + { + hue = h; + saturation = s; + value = v; + calculateRGB(); + }; + + this.Hue = function() + { return hue; }; + + this.Saturation = function() + { return saturation; }; + + this.Value = function() + { return value; }; + + this.SetHexString = function(hexString) + { + if(hexString == null || typeof(hexString) != "string") + { + this.SetRGB(0,0,0); + return; + } + + if (hexString.substr(0, 1) == '#') + hexString = hexString.substr(1); + + if(hexString.length != 6) + { + this.SetRGB(0,0,0); + return; + } + + var r = parseInt(hexString.substr(0, 2), 16); + var g = parseInt(hexString.substr(2, 2), 16); + var b = parseInt(hexString.substr(4, 2), 16); + if (isNaN(r) || isNaN(g) || isNaN(b)) + { + this.SetRGB(0,0,0); + return; + } + + this.SetRGB(r,g,b); + }; + + this.HexString = function() + { + + var rStr = this.Red().toString(16); + if (rStr.length == 1) + rStr = '0' + rStr; + var gStr = this.Green().toString(16); + if (gStr.length == 1) + gStr = '0' + gStr; + var bStr = this.Blue().toString(16); + if (bStr.length == 1) + bStr = '0' + bStr; + return ('#' + rStr + gStr + bStr).toUpperCase(); + }; + + this.Complement = function() + { + var newHue = (hue >= 180) ? hue - 180 : hue + 180; + var newVal = (value * (saturation - 1) + 1); + var newSat = (value*saturation) / newVal; + var newColor = new Color(); + newColor.SetHSV(newHue, newSat, newVal); + return newColor; + } ; + + function calculateHSV() + { + var max = Math.max(Math.max(red, green), blue); + var min = Math.min(Math.min(red, green), blue); + + value = max; + + saturation = 0; + if(max != 0) + saturation = 1 - min/max; + + hue = 0; + if(min == max) + return; + + var delta = (max - min); + if (red == max) + hue = (green - blue) / delta; + else if (green == max) + hue = 2 + ((blue - red) / delta); + else + hue = 4 + ((red - green) / delta); + hue = hue * 60; + if(hue < 0) + hue += 360; + } + + function calculateRGB() + { + red = value; + green = value; + blue = value; + + if(value == 0 || saturation == 0) + return; + + var tHue = (hue / 60); + var i = Math.floor(tHue); + var f = tHue - i; + var p = value * (1 - saturation); + var q = value * (1 - saturation * f); + var t = value * (1 - saturation * (1 - f)); + switch(i) + { + case 0: + red = value; green = t; blue = p; + break; + case 1: + red = q; green = value; blue = p; + break; + case 2: + red = p; green = value; blue = t; + break; + case 3: + red = p; green = q; blue = value; + break; + case 4: + red = t; green = p; blue = value; + break; + default: + red = value; green = p; blue = q; + break; + } + } + } +} +(); +/* + * Clase gestiona la insercción, eliminación de los elementos en el DOM + * + * Vital hacerla SIEMPRE compatible hacia atrás + * + * Last update: 28-10-2010 + * + */ + + +var DOM = {}; + +DOM.createNewElement = function(type, nodeParent, attributes) +{ + + var node = document.createElement(type); + for (var i=0; i0) + { + parent.removeChild(parent.childNodes[0]); + + } +}; + +DOM.select = function(targetID) +{ + return document.getElementById(targetID); +// return $("#"+targetID); +}; +var Geometry = +{ + + /** From tow points obtains the angles formed with the cartesian side **/ + getAngleBetweenTwoPoints : function(x1, y1, x2, y2){ + //var m = (y1 - y2)/ (x1 - x2); + return Math.atan2(y2-y1, x2-x1); + }, + + getAdjacentSideOfRectangleRight : function(angle, hypotenuse){ + return Math.abs(Math.cos(angle)*hypotenuse); + }, + + getOppositeSideOfRectangleRight : function(angle, hypotenuse){ + return Math.abs(Math.sin(angle)*hypotenuse); + }, + + toDegree: function(radian){ + return radian*180/Math.PI; + + } + + +}; + +var SVG = +{ + svgns : 'http://www.w3.org/2000/svg', + xlinkns : "http://www.w3.org/1999/xlink", + + createSVGCanvas: function(parentNode, attributes) + { + + attributes.push( ['xmlns', SVG.svgns], ['xmlns:xlink', 'http://www.w3.org/1999/xlink']); + var svg = document.createElementNS("http://www.w3.org/2000/svg", "svg"); + this._setProperties(svg, attributes); + parentNode.appendChild( svg); + return svg; + + }, + + createRectangle : function (x, y, width, height, attributes){ + var rect = document.createElementNS(this.svgns, "rect"); + rect.setAttribute("x",x); + rect.setAttribute("y",y); + rect.setAttribute("width",width); + rect.setAttribute("height",height); + SVG._setProperties(rect, attributes); + return rect; + }, + + drawImage64 : function (x, y, width, height, base64, svgNode, attributes) { + var node = SVG.createImage64(x, y, width, height, base64, attributes); + svgNode.appendChild(node); + return node; + }, + + createImage64 : function (x, y, width, height, base64, attributes) { + var img = document.createElementNS(this.svgns, "image"); + img.setAttribute("x",x); + img.setAttribute("y",y); + img.setAttribute("width",width); + img.setAttribute("height",height); + img.setAttribute("xlink:href",base64); + SVG._setProperties(img, attributes); + return img; + }, + + createLine: function (x1, y1, x2, y2, attributes){ + var line = document.createElementNS(this.svgns,"line"); + line.setAttribute("x1",x1); + line.setAttribute("y1",y1); + line.setAttribute("x2", x2); + line.setAttribute("y2", y2); + SVG._setProperties(line, attributes); + return line; + }, + + createClip: function (id, nodeToClip, attributes){ + var clip = document.createElementNS(this.svgns,"clipPath"); + clip.setAttribute("id",id); + clip.appendChild(nodeToClip); + return clip; + }, + + drawClip : function (id, nodeToClip, svgNode) { + var node = SVG.createClip(id, nodeToClip); + svgNode.appendChild(node); + return node; + }, + + drawRectangle : function (cx, cy, width, height, svgNode, attributes) { + try{ + var node = SVG.createRectangle(cx, cy, width, height, attributes); + svgNode.appendChild(node); + } + catch(e){ + + console.log("-------------------- "); + console.log("Error on drawRectangle " + e); + console.log(attributes); + console.log("-------------------- "); + } + return node; + }, + + createEllipse : function (x, y, rx, ry, attributes){ + var rect = document.createElementNS(this.svgns, "ellipse"); + rect.setAttribute("cx",x); + rect.setAttribute("cy",y); + rect.setAttribute("rx",rx); + rect.setAttribute("ry",ry); + SVG._setProperties(rect, attributes); + return rect; + }, + + drawEllipse : function (cx, cy, rx, ry, svgNode, attributes) { + var node = SVG.createEllipse(cx, cy, rx, ry, attributes); + svgNode.appendChild(node); + return node; + }, + + drawImage : function (x, y, canvasSVG, attributes) { + var image = document.createElementNS(this.svgns, "image"); + image.setAttribute("x",x); + image.setAttribute("y",y); + canvasSVG.appendChild(image); + SVG._setProperties(image, attributes); + }, + + drawLine : function (x1, y1, x2, y2, nodeSVG, attributes) { + try{ + var line = SVG.createLine(x1, y1, x2, y2, attributes); + nodeSVG.appendChild(line); + }catch(e){ + } + return line; + }, + + + drawPath: function (d, nodeSVG, attributes) { + var path = SVG.createPath(d, attributes); + nodeSVG.appendChild(path); + return path; + }, + + createPoligon : function (points, attributes){ + var poligon = document.createElementNS(this.svgns, "polygon"); + poligon.setAttribute("points",points); + SVG._setProperties(poligon, attributes); + return poligon; + }, + + drawPoligon : function (points, canvasSVG, attributes){ + var poligon = SVG.createPoligon(points, attributes); + canvasSVG.appendChild(poligon); + return poligon; + }, + // + + createPath : function (d, attributes){ + var path = document.createElementNS(this.svgns, "path"); + path.setAttribute("d",d); + SVG._setProperties(path, attributes); + return path; + }, + + drawCircle : function (x, y, radio, canvasSVG, attributes) { + + var newText = document.createElementNS(this.svgns,"circle"); + newText.setAttribute("cx",x); + newText.setAttribute("cy",y); + newText.setAttribute("r",radio); + + canvasSVG.appendChild(newText); + attributes["cursor"] = "pointer"; + this._setProperties(newText, attributes); + return newText; + }, + + + _setProperties: function(node, attributes) + { + if (attributes instanceof Array){ + for (var i=0; i< attributes.length; i++) + { + node.setAttribute(attributes[i][0], attributes[i][1]); + } + } + else{ + for ( var key in attributes){ + node.setAttribute(key, attributes[key]); + } + } + }, + +/* drawPath: function(pointsArray, canvasSVG, attributes){ + var path = document.createElementNS(this.svgns,"polyline"); + path.setAttribute ('id', id); + + var d= pointsArray[0].x+ " "+ pointsArray[0].y; + for (var i=1; i< pointsArray.length; i++) + { + d=d+" "+pointsArray[i].x+" "+pointsArray[i].y; + } + path.setAttribute ('points', d); + canvasSVG.appendChild(path); + },*/ + + createText : function (x, y, text, attributes) { + var node = document.createElementNS(this.svgns,"text"); + node.setAttributeNS(null , "x",x); + node.setAttributeNS(null, "y",y); + + var textNode = document.createTextNode(text); + node.appendChild(textNode); + + this._setProperties(node, attributes); + return node; + }, + + drawText : function (x, y, text, canvasSVG, attributes) { + var text = SVG.createText(x, y, text, attributes); + canvasSVG.appendChild(text); + return text; + }, + + + + drawGroup: function(svgNode, attributes) + { + var group = SVG.createGroup(attributes); + svgNode.appendChild(group); + return group; + }, + + createGroup: function(attributes){ + var group = document.createElementNS(this.svgns,"g"); + this._setProperties(group, attributes); + return group; + } + +}; + + + +var CanvasToSVG = { + + convert: function(sourceCanvas, targetSVG, x, y, id, attributes) { + + var img = this._convert(sourceCanvas, targetSVG, x, y, id); + + for (var i=0; i< attributes.length; i++) + { + img.setAttribute(attributes[i][0], attributes[i][1]); + } + }, + + _convert: function(sourceCanvas, targetSVG, x, y, id) { + var svgNS = "http://www.w3.org/2000/svg"; + var xlinkNS = "http://www.w3.org/1999/xlink"; + // get base64 encoded png from Canvas + var image = sourceCanvas.toDataURL(); + + // must be careful with the namespaces + var svgimg = document.createElementNS(svgNS, "image"); + + svgimg.setAttribute('id', id); + + //svgimg.setAttribute('class', class); + //svgimg.setAttribute('xlink:href', image); + svgimg.setAttributeNS(xlinkNS, 'xlink:href', image); + + + + + svgimg.setAttribute('x', x ? x : 0); + svgimg.setAttribute('y', y ? y : 0); + svgimg.setAttribute('width', sourceCanvas.width); + svgimg.setAttribute('height', sourceCanvas.height); + //svgimg.setAttribute('cursor', 'pointer'); + svgimg.imageData = image; + + targetSVG.appendChild(svgimg); + return svgimg; + }, + + importSVG: function(sourceSVG, targetCanvas) { + svg_xml = sourceSVG;//(new XMLSerializer()).serializeToString(sourceSVG); + var ctx = targetCanvas.getContext('2d'); + + var img = new Image(); + img.src = "data:image/svg+xml;base64," + btoa(svg_xml); +// img.onload = function() { + ctx.drawImage(img, 0, 0); +// }; + } + +}; +/* +Graph.prototype.importSVG = function(sourceSVG, targetCanvas) { + sourceSVG = this._svg; + targetCanvas = document.createElementNS('canvas'); + // https://developer.mozilla.org/en/XMLSerializer + svg_xml = (new XMLSerializer()).serializeToString(sourceSVG); + var ctx = targetCanvas.getContext('2d'); + // this is just a JavaScript (HTML) image + var img = new Image(); + // http://en.wikipedia.org/wiki/SVG#Native_support + // https://developer.mozilla.org/en/DOM/window.btoa + img.src = "data:image/svg+xml;base64," + btoa(svg_xml); + img.onload = function() { + // after this, Canvas’ origin-clean is DIRTY + ctx.drawImage(img, 0, 0); + } +}; +*/ + +/* + +Normalizacion de datos para dibujar colores +Issues: + No sé como debería llamarse esta libreria + No sé si ya existe una funciçon en javascript que lo haga + + +*/ + + +var Normalizer = new function() +{ + this.normalizeArray = function (arrayData) + { + + return this.standardizeArray(this.normal(arrayData)); + +// var result = this._getMaxAndMin(arrayData); +// var min =result[0]; +// var max = result[1]; +// +// +// //los hacemos todos positivos +// for (var i = 0; i< arrayData.length; i++) +// { +// arrayData[i]= Math.abs(min) + parseFloat(arrayData[i]); +// } +// +// var result = this._getMaxAndMin(arrayData); +// var min =result[0]; +// var max = result[1]; +// +// +// var resultArray = new Array(); +// for (var i = 0; i< arrayData.length; i++) +// { +// resultArray.push(arrayData[i]*1/max); +// } +// return resultArray; + }; + + this.normal = function(arrayData){ + var mean = this._getMean(arrayData); + var deviation = this._getStdDeviation(arrayData); + var result = this._getMaxAndMin(arrayData); + var min = result[0]; + var max = result[1]; + + var resultArray = new Array(); + for (var i = 0; i< arrayData.length; i++) { + if (deviation!=0){ + resultArray.push((arrayData[i]-mean)/deviation); + }else{ + resultArray.push(arrayData[i]); + } + } + return resultArray; + }; + + this.standardizeArray = function(arrayData) + { + var result = this._getMaxAndMin(arrayData); + var min = result[0]; + var max = result[1]; + + var offset = ( min <= 0 ) ? Math.abs(min) : (-1 * min); + var resultArray = new Array(); + for (var i = 0; i< arrayData.length; i++) { + if(max + offset!=0){ + resultArray.push((arrayData[i] + offset) / (max + offset)); + }else{ + resultArray.push(arrayData[i]+offset); + } + } + return resultArray; + }; + + + this._getMean = function(arrayData) { + var sum = 0; + for (var i = 0; i< arrayData.length; i++) { + sum = sum + parseFloat(arrayData[i]); + } + return sum/arrayData.length; + }; + + this._getStdDeviation = function(arrayData) { + var mean = this._getMean(arrayData); + var acum = 0.0; + for(var i=0; i max) max = parseFloat(arrayData[i]); + } + + return [min, max]; + }; +}; +function GraphCanvas(componentID, targetNode, args) { + this.args = {}; + /** target */ + this.targetID = targetNode.id; + + /** id manage */ + this.id = componentID; + this.args.idGraph = this.id + "main"; + this.args.idBackgroundNode = this.id + "background"; + + this.args.idEdgesGraph = this.id + "edges"; + this.args.idNodesGraph = this.id + "vertices"; + this.args.idLabelGraph = this.id + "label"; + this.args.idBackground = this.id + "background"; + + /** Objects Graph **/ + this.dataset = null; + this.formatter = null; + this.layout = null; + + /** Drawing **/ + this.circleDefaultRadius = 2; + this.squareDefaultSide = this.circleDefaultRadius * 1.5; + + /** Directed Arrow **/ + this.arrowDefaultSize = this.circleDefaultRadius; + + /** Groups **/ + this.GraphGroup = null; + this.GraphNodeGroup = null; + this.GraphLabelGroup = null; + this.GraphBackground = null; + + /** SETTINGS FLAGS **/ + this.args.draggingCanvasEnabled = false; //Flag to set if the canvas can be dragged + this.args.multipleSelectionEnabled = false; + this.args.interactive = false; + this.args.labeled = false; + this.args.linkEnabled = false; + + /** If numberEdge > maxNumberEdgesMoving then only it will move edges when mouse up **/ + this.args.maxNumberEdgesMoving = 3; + this.args.maxNumberEdgesFiringEvents = 50; + + /** Linking edges **/ + this.args.linking = false; + this.linkStartX = 0; + this.linkStartY = 0; + this.linkSVGNode = null; + this.linkNodeSource = null; + this.linkNodeTarget = null; + + /** Dragging Control **/ + this.draggingElement = null; + this.dragging = false; + this.nMouseOffsetX = 0; + this.nMouseOffsetY = 0; + this.dragStartX = 0; + this.dragStartY = 0; + this.desplazamientoX = 0; + this.desplazamientoY = 0; + + /** Selection Control **/ + this.selecting = false; + this.selectorX = null; + this.selectorY = null; + this.selectorSVGNode = null; + + /** Node status **/ + this.args.isVertexSelected = {}; + this.args.selectedVertices = []; + + /** Edges status **/ + this.args.isEdgeSelected = {}; + //this.args.selectedEdges = []; + + if (args != null) { + if (args.multipleSelectionEnabled != null) { + this.args.multipleSelectionEnabled = args.multipleSelectionEnabled; + this.args.draggingCanvasEnabled = !(this.args.multipleSelectionEnabled); + } + if (args.draggingCanvasEnabled != null) { + this.args.draggingCanvasEnabled = args.draggingCanvasEnabled; + this.args.multipleSelectionEnabled = !(this.args.draggingCanvasEnabled); + } + if (args.interactive != null) { + this.args.interactive = args.interactive; + } + if (args.labeled != null) { + this.args.labeled = args.labeled; + } + + } + + /** Hashmap with the svg node labels **/ + this.svgLabels = {}; + + /** EVENTS **/ + this.onVertexOut = new Event(this); + this.onVertexOver = new Event(this); + this.onVertexSelect = new Event(this); + this.onEdgeSelect = new Event(this); + this.onCanvasClicked = new Event(this); + this.onVertexUp = new Event(this); +} + +GraphCanvas.prototype.showLabels = function(value) { + this.args.labeled = value; + this.removeLabels(); + if (value) { + this.renderLabels(); + } +}; + +GraphCanvas.prototype.getSelectedVertices = function() { + return this.args.selectedVertices; +}; + +GraphCanvas.prototype.getSelectedEdges = function() { + var selected = []; + for ( var selectedEdge in this.args.isEdgeSelected) { + selected.push(selectedEdge); + } + return selected; +}; + +GraphCanvas.prototype.createSVGDom = function(targetID, id, width, height, backgroundColor) { + var container = document.getElementById(targetID); + this._svg = SVG.createSVGCanvas(container, [ + [ "style", "background-color:" + backgroundColor + ";" ], [ "id", id ], [ "dragx", 0 ], [ "dragy", 0 ], + [ "height", this.getFormatter().getHeight() ], [ "width", this.getFormatter().getWidth() ] ]); + return this._svg; +}; + +/** MULTIPLE SELECTION **/ +GraphCanvas.prototype.isMultipleSelectionEnabled = function() { + return this.args.multipleSelectionEnabled; +}; + +GraphCanvas.prototype.setMultipleSelection = function(value) { + this.args.multipleSelectionEnabled = value; + this.args.draggingCanvasEnabled = (!value); +}; + +GraphCanvas.prototype.setSelecting = function(value) { + this.selecting = value; +}; + +/** linking **/ +GraphCanvas.prototype.setLinking = function(value) { + this.args.linkEnabled = value; + this.selecting = !value; + this.dragging = !value; +}; + +/** CANVAS MOVING **/ +GraphCanvas.prototype.setDraggingCanvas = function(value) { + this.args.draggingCanvasEnabled = value; + this.args.multipleSelectionEnabled = !value; +}; + +GraphCanvas.prototype.isDraggingCanvasEnabled = function() { + return this.args.draggingCanvasEnabled; +}; +/** ZOOM **/ +GraphCanvas.prototype.getScale = function() { + return this.getFormatter().getZoomScale(); +}; + +GraphCanvas.prototype.setScale = function(scale) { + var graphNode = document.getElementById(this.args.idGraph); + graphNode.setAttribute("transform", graphNode.getAttribute("transform").replace("scale(" + this.getScale() + ")", "scale(" + scale + ")")); + this.getFormatter().setZoomScale(scale); +}; + +GraphCanvas.prototype.zoomIn = function() { + this.setScale(this.getScale() + this.getFormatter().getZoomScaleStepFactor()); +}; + +GraphCanvas.prototype.zoomOut = function() { + this.setScale(this.getScale() - this.getFormatter().getZoomScaleStepFactor()); + +}; + +/** SVG COORDENATES **/ +GraphCanvas.prototype.getSVGCoordenates = function(evt) { + var p = this._svg.createSVGPoint(); + p.x = evt.clientX; + p.y = evt.clientY; + + var m = this._svg.getScreenCTM(document.documentElement); + p = p.matrixTransform(m.inverse()); + return p; +}; + +/** SVG EVENTS **/ +GraphCanvas.prototype.mouseClick = function(event) { + if (event.button == 0) { + if (!this.args.interactive) { + return; + } + + if (this.isVertex(event.target)) { + this.clickNode(this.getVertexIdFromSVGId(event.target.id)); + } + /** Como el evento mouseClick viene despues del mouse up es aqui donde manejo el tema de deseccionar los elementos que estoy dragging **/ + if (this.dragging) { + this.dragging = false; + } + } +}; + +GraphCanvas.prototype.mouseMove = function(evt) { + if (this.selecting) { + this.clearLabels(); + + var width = (this.getSVGCoordenates(evt).x - this.selectorX); + var height = (this.getSVGCoordenates(evt).y - this.selectorY); + if ((width > 0) && (height > 0)) { + this.displaySelection(this.selectorX, this.selectorY, width, height); + } + if ((width > 0) && (height < 0)) { + this.displaySelection(this.selectorX, this.getSVGCoordenates(evt).y, width, Math.abs(height)); + } + if ((width < 0) && (height < 0)) { + this.displaySelection(this.getSVGCoordenates(evt).x, this.getSVGCoordenates(evt).y, Math.abs(width), Math.abs(height)); + } + if ((width < 0) && (height > 0)) { + this.displaySelection(this.selectorX + width, this.selectorY, Math.abs(width), Math.abs(height)); + } + + var x1 = (parseFloat(this.selectorSVGNode.getAttribute("x")) - DOM.select(this.id).getAttribute("dragx")) / this.getFormatter().getWidth(); + var y1 = (parseFloat(this.selectorSVGNode.getAttribute("y")) - DOM.select(this.id).getAttribute("dragy")) / this.getFormatter().getHeight(); + var x2 = (x1 + parseFloat(this.selectorSVGNode.getAttribute("width") / this.getFormatter().getWidth())); + var y2 = (y1 + parseFloat(this.selectorSVGNode.getAttribute("height") / this.getFormatter().getHeight())); + + this.deselectNodes(this.getLayout()); + var verticesSelected = this.getLayout().getVerticesByArea(x1 / this.getFormatter().getZoomScale(), y1 / this.getFormatter().getZoomScale(), + x2 / this.getFormatter().getZoomScale(), y2 / this.getFormatter().getZoomScale()); + for ( var i = 0; i < verticesSelected.length; i++) { + this.selectNode(verticesSelected[i].getId()); + this.renderLabel(verticesSelected[i].getId()); + } + + } + var p = null; + if (this.args.linking) { + p = this.getSVGCoordenates(evt); + if (this.linkSVGNode != null) { + this.linkSVGNode.setAttribute("x2", p.x - 2); + this.linkSVGNode.setAttribute("y2", p.y - 2); + } + } + + if (this.dragging) { + p = this.getSVGCoordenates(evt); + p.x -= this.nMouseOffsetX; + p.y -= this.nMouseOffsetY; + this.desplazamientoX = (this.getSVGCoordenates(evt).x - this.dragStartX);// + parseFloat(DOM.select(this.id).getAttribute("dragx")); + this.desplazamientoY = (this.getSVGCoordenates(evt).y - this.dragStartY);// + parseFloat(DOM.select(this.id).getAttribute("dragy")); + + if (this.draggingElement != null) { + /** Click sobre el recct del banground que provoca que mueva todo el canvas **/ + if (this.isNodeCanvas(this.draggingElement)) { + + p = this.getSVGCoordenates(evt); + p.x = this.desplazamientoX; + p.y = this.desplazamientoY; + + this.draggingElement.setAttribute("dragx", p.x); + this.draggingElement.setAttribute("dragy", p.y); + this.draggingElement = document.getElementById(this.args.idGraph); + this.draggingElement.setAttribute("transform", "translate(" + p.x + "," + p.y + "), scale(" + this.getScale() + ")"); + + DOM.select(this.id).setAttribute("dragx", p.x); + DOM.select(this.id).setAttribute("dragy", p.y); + + if (this.NodeSVGbackgroundImage != null) { + this.NodeSVGbackgroundImage.setAttribute("dragx", p.x); + this.NodeSVGbackgroundImage.setAttribute("dragy", p.y); + } + } else { + if (this.isVertex(this.draggingElement)) { + this.selectNode(this.getVertexIdFromSVGId(this.draggingElement.id)); + this.desplazamientoX = this.desplazamientoX / this.getFormatter().getZoomScale(); + this.desplazamientoY = this.desplazamientoY / this.getFormatter().getZoomScale(); + this.moveSelectedNodes(this.desplazamientoX, this.desplazamientoY); + + this.dragStartX = this.getSVGCoordenates(evt).x; + this.dragStartY = this.getSVGCoordenates(evt).y; + } else { + if (this.isNodeBackground(this.draggingElement)) { + + this.draggingElement.setAttribute("dragx", p.x); + this.draggingElement.setAttribute("dragy", p.y); + this.draggingElement = document.getElementById(this.args.idGraph); + this.draggingElement.setAttribute("transform", "translate(" + p.x + "," + p.y + "), scale(" + this.getScale() + ")"); + } else { + this.draggingElement.setAttribute("transform", "translate(" + p.x + "," + p.y + ")"); + } + } + } + } + } +}; + +GraphCanvas.prototype.moveSelectedNodes = function(offsetX, offsetY) { + for ( var i = 0; i < this.getSelectedVertices().length; i++) { + + var nodeId = this.getSelectedVertices()[i]; + var svgNodeId = this.getSVGNodeId(nodeId); + + var x = parseFloat(DOM.select(svgNodeId).getAttribute("dragx")) + parseFloat(offsetX);// - parseFloat(DOM.select(this.id).getAttribute("dragx")); + var y = parseFloat(DOM.select(svgNodeId).getAttribute("dragy")) + parseFloat(offsetY);// + parseFloat(DOM.select(this.id).getAttribute("dragy")); + + this._movingNode(DOM.select(svgNodeId), x, y); + } +}; + +GraphCanvas.prototype.mouseDown = function(evt) { + if (event.button == 0) { + + /** if !no interactive mouse events do anything **/ + if (!this.args.interactive) { + return; + } + + var p = this.getSVGCoordenates(evt); + + /** When click on canvas or background deselect all **/ + if (this.isNodeCanvas(evt.target) || this.isNodeBackground(evt.target)) { + this.deselectNodes(); + this.deselectEdges(); + this.onCanvasClicked.notify(); + } + + /** if I am linking vertices **/ + if (this.args.linkEnabled) { + + if (!this.args.linking) { + this.args.linking = true; + if (this.isVertex(evt.target)) { + this.linkStartX = p.x; + this.linkStartY = p.y; + this.linkSVGNode = SVG.drawLine(p.x, p.y, p.x, p.y, this._svg, { + "stroke" : "#FF0000" + }); + this.linkNodeSource = this.getVertexIdFromSVGId(evt.target.id); + } + } else { + this.linkNodeTarget = this.getVertexIdFromSVGId(evt.target.id); + this.args.linking = false; + this.args.linkEnabled = false; + if (this.isVertex(evt.target)) { + this.getDataset().addEdge(this.linkNodeSource + "_" + this.linkNodeTarget, this.linkNodeSource, this.linkNodeTarget, {}); + } + this.linkSVGNode.parentNode.removeChild(this.linkSVGNode); + } + return; + } + + /** Id is a vertex or the canvas **/ + if (this.isVertex(evt.target) || this.isNodeCanvas(evt.target) || this.isNodeBackground(evt.target)) { + this._startDragging(evt); + } + /** if i is edge **/ + if (this.isEdge(evt.target)) { + this.selectEdge(this.getEdgeIdFromSVGId(evt.target.getAttribute("id"))); + } + + if (this.args.multipleSelectionEnabled) { + if (!this.dragging) { + this.setSelecting(true); + this.selectorX = p.x; + this.selectorY = p.y; + this.displaySelection(p.x, p.y, 1, 1); + } + } + + } + if (event.button == 1) { + this.setLinking(false); + this.setMultipleSelection(false); + this.selecting = false; + + /** Id is a vertex or the canvas **/ + if (this.isVertex(evt.target) || this.isNodeCanvas(evt.target) || this.isNodeBackground(evt.target)) { + this._startDragging(evt); + } + } +}; + +GraphCanvas.prototype.mouseUp = function(event) { + if (!this.args.interactive) { + return; + } + + if (this.dragging) { + this._stopDragging(event); + if (this.isVertex(event.target)) { + var vertexId = this.getVertexIdFromSVGId(event.target.id); + if (this.getDataset().getVertexById(vertexId).getEdges().length >= this.args.maxNumberEdgesMoving) { + this.moveEdge(vertexId); + } + } + } + + if (this.selecting) { + this.setSelecting(false); + + var x1 = (parseFloat(this.selectorSVGNode.getAttribute("x")) - DOM.select(this.id).getAttribute("dragx")) / this.getFormatter().getWidth(); + var y1 = (parseFloat(this.selectorSVGNode.getAttribute("y")) - DOM.select(this.id).getAttribute("dragy")) / this.getFormatter().getHeight(); + var x2 = (x1 + parseFloat(this.selectorSVGNode.getAttribute("width") / this.formatter.getWidth())); + var y2 = (y1 + parseFloat(this.selectorSVGNode.getAttribute("height") / this.formatter.getHeight())); + + var verticesSelected = this.getLayout().getVerticesByArea(x1 / this.getFormatter().getZoomScale, y1 / this.getFormatter().getZoomScale, + x2 / this.getFormatter().getZoomScale, y2 / this.getFormatter().getZoomScale); + + for ( var i = 0; i < verticesSelected.length; i++) { + this.selectNode(verticesSelected[i].getId()); + } + + if (this.selectorSVGNode != null) { + this._svg.removeChild(this.selectorSVGNode); + } + + if (this.args.labeled) { + this.clearLabels(); + this.renderLabels(); + } + + this.selectorSVGNode = null; + // this.renderLabels(); + } +}; + +/** SELECTION **/ +GraphCanvas.prototype.displaySelection = function(x, y, width, height) { + if (this.selectorSVGNode != null) { + this.selectorSVGNode.setAttribute("x", x); + this.selectorSVGNode.setAttribute("y", y); + this.selectorSVGNode.setAttribute("width", width); + this.selectorSVGNode.setAttribute("height", height); + } else { + this.selectorSVGNode = SVG.drawRectangle(x, y, width, height, this._svg, { + "fill" : "red", + "stroke" : "black", + "opacity" : "0.2", + "stroke-opacity" : "1" + }); + } +}; + +/** DRAGGING **/ +GraphCanvas.prototype._startDragging = function(evt) { + if (!this.isDraggingCanvasEnabled()) { + if (this.isNodeCanvas(evt.target)) { + this.draggingElement = null; + } + } + + if (this.isVertex(evt.target) || (this.isNodeBackground(evt.target) && (this.isDraggingCanvasEnabled()))|| (this.isNodeCanvas(evt.target) && (this.isDraggingCanvasEnabled()))) { + this.clearLabels(); + this.draggingElement = evt.target; + this.dragging = true; + var p = this.getSVGCoordenates(evt); + + this.nMouseOffsetX = p.x - parseInt(evt.target.getAttribute("dragx")); + this.nMouseOffsetY = p.y - parseInt(evt.target.getAttribute("dragy")); + + if (this.isVertex(evt.target)) { + this.dragStartX = parseInt(this.draggingElement.getAttribute("dragx")) * this.getFormatter().getZoomScale() + + parseFloat(DOM.select(this.id).getAttribute("dragx")); + this.dragStartY = parseInt(this.draggingElement.getAttribute("dragy")) * this.getFormatter().getZoomScale() + + parseFloat(DOM.select(this.id).getAttribute("dragy")); + } else { + this.dragStartX = p.x - parseInt(this.draggingElement.getAttribute("dragx"));// + parseFloat(DOM.select(this.id).getAttribute("dragx")); + this.dragStartY = p.y - parseInt(this.draggingElement.getAttribute("dragy"));// + parseFloat(DOM.select(this.id).getAttribute("dragy")); + } + } +}; + +GraphCanvas.prototype._stopDragging = function(event) { + this.nMouseOffsetX = 0; + this.nMouseOffsetX = 0; + /** despues del evento up viene el evento click entonces acabo el dragging en el mouseclick **/ + this.dragging = false; + this.draggingElement = null; + this.renderLabels(); + + this.setLinking(false); + this.setMultipleSelection(true); + this.selecting = false; + +}; + +/** Move the edges of the vertex with the vertexId indicado **/ +GraphCanvas.prototype.moveEdge = function(vertexId) { + var x = this.getLayout().getNodeById(vertexId).x * this.getFormatter().getWidth(); + var y = this.getLayout().getNodeById(vertexId).y * this.getFormatter().getHeight(); + + /** Moving edges out **/ + for ( var i = 0; i < this.getDataset().getVertexById(vertexId).getEdgesOut().length; i++) { + var edgeId = this.getDataset().getVertexById(vertexId).getEdgesOut()[i].getId(); + var svgEdgeId = this.getSVGEdgeId(edgeId); + var edgeFormatter = this.getFormatter().getEdgeById(edgeId); + if (edgeFormatter instanceof LineEdgeGraphFormatter) { + DOM.select(svgEdgeId + "_shadow").setAttribute("x2", x); + DOM.select(svgEdgeId + "_shadow").setAttribute("y2", y); + DOM.select(svgEdgeId).setAttribute("x2", x); + DOM.select(svgEdgeId).setAttribute("y2", y); + } + + if ((edgeFormatter instanceof DirectedLineEdgeGraphFormatter) || (edgeFormatter instanceof OdirectedLineEdgeGraphFormatter) + || (edgeFormatter instanceof OdotDirectedLineEdgeGraphFormatter) || (edgeFormatter instanceof DotDirectedLineEdgeGraphFormatter) + || (edgeFormatter instanceof CutDirectedLineEdgeGraphFormatter)) { + this.removeEdge(edgeId); + this.renderEdge(edgeId); + } + } + + /** Moving edges in **/ + for ( var i = 0; i < this.getDataset().getVertexById(vertexId).getEdgesIn().length; i++) { + var edgeId = this.getDataset().getVertexById(vertexId).getEdgesIn()[i].getId(); + var svgEdgeId = this.getSVGEdgeId(edgeId); + var edgeFormatter = this.getFormatter().getEdgeById(edgeId); + if (edgeFormatter instanceof LineEdgeGraphFormatter) { + DOM.select(svgEdgeId).setAttribute("x1", x); + DOM.select(svgEdgeId).setAttribute("y1", y); + DOM.select(svgEdgeId + "_shadow").setAttribute("x1", x); + DOM.select(svgEdgeId + "_shadow").setAttribute("y1", y); + } + + if ((edgeFormatter instanceof DirectedLineEdgeGraphFormatter) || (edgeFormatter instanceof OdirectedLineEdgeGraphFormatter) + || (edgeFormatter instanceof OdotDirectedLineEdgeGraphFormatter) || (edgeFormatter instanceof DotDirectedLineEdgeGraphFormatter) + || (edgeFormatter instanceof CutDirectedLineEdgeGraphFormatter)) { + this.removeEdge(edgeId); + this.renderEdge(edgeId); + } + + if (edgeFormatter instanceof BezierEdgeGraphFormatter) { + var radius = this.getFormatter().getVertexById(vertexId).getDefault().getSize() * this.getFormatter().getNodesMaxSize(); + var d = this.calculateCoordenatesBezier(radius, x, y); + DOM.select(svgEdgeId).setAttribute("d", d); + } + } +}; + +GraphCanvas.prototype.moveNode = function(vertexId) { + var x = this.getLayout().getNodeById(vertexId).x * this.getFormatter().getWidth(); + var y = this.getLayout().getNodeById(vertexId).y * this.getFormatter().getHeight(); + var svgNodeElement = DOM.select(this.getSVGNodeId(vertexId)); + + svgNodeElement.setAttribute("dragx", x); + svgNodeElement.setAttribute("dragy", y); + svgNodeElement.setAttribute("transform", "translate(" + x + "," + y + ")"); + + if (this.getDataset().getVertexById(vertexId).getEdges().length < this.args.maxNumberEdgesMoving) { + this.moveEdge(vertexId); + } +}; + +GraphCanvas.prototype._movingNode = function(svgNodeElement, x, y) { + var vertexId = this.getVertexIdFromSVGId(svgNodeElement.getAttribute("id")); + this.getLayout().getNodeById(vertexId).setCoordinates(x / this.getFormatter().getWidth(), y / this.getFormatter().getHeight()); + this.desplazamientoX = 0; + this.desplazamientoY = 0; + this.removeLabel(vertexId); + this.renderLabel(vertexId); +}; + +/** INIT **/ +GraphCanvas.prototype.init = function() { + + this._svg = this.createSVGDom(this.targetID, this.id, this.getFormatter().getWidth(), this.getFormatter().getHeight(), this.getFormatter() + .getBackgroundColor()); + this.GraphGroup = SVG.drawGroup(this._svg, [ [ "id", this.args.idGraph ], [ "transform", "translate(0,0), scale(1)" ] ]); + this.GraphBackground = SVG.drawGroup(this.GraphGroup, [ [ "id", this.args.idBackground ] ]); + this.GraphEdgeGroup = SVG.drawGroup(this.GraphGroup, [ [ "id", this.args.idEdgesGraph ] ]); + this.GraphNodeGroup = SVG.drawGroup(this.GraphGroup, [ [ "id", this.args.idNodesGraph ] ]); + this.GraphLabelGroup = SVG.drawGroup(this.GraphGroup, [ [ "id", this.args.idLabelGraph ] ]); + + if ((this.getFormatter().getBackgroundImage() != null) && (this.getFormatter().getBackgroundImage() != "")) { + this.setBackgroundImage(this.getFormatter().getBackgroundImage()); + } + /** SVG Events listener */ + var _this = this; + this._svg.addEventListener("click", function(event) { + _this.mouseClick(event); + }, false); + this._svg.addEventListener("mousemove", function(event) { + _this.mouseMove(event, _this); + }, false); + this._svg.addEventListener("mousedown", function(event) { + _this.mouseDown(event, _this); + }, false); + this._svg.addEventListener("mouseup", function(event) { + _this.mouseUp(event, _this); + }, false); +}; + +/* + GraphCanvas.prototype.backgroungToSVG = function(){ + var _this = this; + var canvas = document.createElement('canvas'); + canvas.setAttribute("id", "canvas"); + canvas.width = this.formatter.getWidth(); + canvas.height = this.formatter.getHeight(); + + this._svg.parentNode.parentNode.appendChild(canvas); + var ctx = document.getElementById('canvas').getContext('2d'); + var img = new Image(); + + img.src = this.formatter.getBackgroundImage(); + ctx.drawImage(img,0,0 ,_this.formatter.getWidth(), _this.formatter.getHeight()); + + + img.onload = function() { + canvas.parentNode.removeChild(canvas); + } + + this.NodeSVGbackgroundImage.setAttribute("xlink:href", document.getElementById("canvas").toDataURL()); + this.NodeSVGbackgroundImage.removeAttribute("href"); + + // + + };*/ + +GraphCanvas.prototype.setBackgroundImage = function() { + if (this.NodeSVGbackgroundImage != null) { + this.NodeSVGbackgroundImage.parentNode.removeChild(this.NodeSVGbackgroundImage); + } + $('#' + this.targetID).svg(); + $('#' + this.targetID).svg("get"); + + $('#' + this.targetID).svg("get")._svg = document.getElementById(this.id); + + var svg = $('#' + this.targetID).svg("get"); + this.NodeSVGbackgroundImage = svg.image(0, 0, this.getFormatter().getWidth(), this.getFormatter().getHeight(), this.getFormatter() + .getBackgroundImage()); + this.NodeSVGbackgroundImage.setAttribute("id", this.args.idBackgroundNode); + + this.NodeSVGbackgroundImage.setAttribute("x", 0); + this.NodeSVGbackgroundImage.setAttribute("y", 0); + + this.NodeSVGbackgroundImage.setAttribute("dragx", 0); + this.NodeSVGbackgroundImage.setAttribute("dragy", 0); + + if (this.getFormatter().args.backgroundImageHeight != null) { + this.NodeSVGbackgroundImage.setAttribute("height", this.getFormatter().args.backgroundImageHeight); + } + if (this.getFormatter().args.backgroundImageWidth != null) { + this.NodeSVGbackgroundImage.setAttribute("width", this.getFormatter().args.backgroundImageWidth); + } + + if (this.getFormatter().args.backgroundImageX != null) { + this.NodeSVGbackgroundImage.setAttribute("x", this.getFormatter().args.backgroundImageX); + } + if (this.getFormatter().args.backgroundImageY != null) { + this.NodeSVGbackgroundImage.setAttribute("y", this.getFormatter().args.backgroundImageY); + } + + this.GraphBackground.appendChild(this.NodeSVGbackgroundImage); + this.NodeSVGbackgroundImage.removeAttribute("href"); + this.NodeSVGbackgroundImage.setAttribute("xlink:href", this.getFormatter().getBackgroundImage()); +}; + +GraphCanvas.prototype.removeBackgroundImage = function() { + if (this.NodeSVGbackgroundImage != null) { + this.NodeSVGbackgroundImage.parentNode.removeChild(this.NodeSVGbackgroundImage); + } +}; + +GraphCanvas.prototype._setBackgroundColor = function(color) { + var attributes = [ [ "fill", color ] ]; + SVG.drawRectangle(0, 0, this.getFormatter().getWidth(), this.getFormatter().getHeight(), this.GraphBackground, attributes); +}; + +/** Serialize **/ +GraphCanvas.prototype.toJSON = function() { + var json = {}; + json.dataset = {}; + json.formatter = {}; + json.layout = {}; + json.dataset = this.getDataset().toJSON(); + json.formatter = this.getFormatter().toJSON(); + json.layout = this.getLayout().toJSON(); + return json; +}; + +GraphCanvas.prototype.toHTML = function() { + //this.backgroungToSVG(); + var html = this._svg.parentElement.innerHTML; + + var start = html.indexOf("") + 6; + + return html.substr(start, end); +}; + +/** DRAW **/ +GraphCanvas.prototype.draw = function(graphdataset, graphformatter, graphlayout) { + this.setDataset(graphdataset); + this.setFormatter(graphformatter); + this.setLayout(graphlayout); + + var _this = this; + this.getFormatter().changed.attach(function(sender, item) { + _this.removeNode(item.getId()); + _this.renderNode(item.getId()); + if (_this.args.labeled) { + _this.removeLabel(item.getId()); + _this.renderLabel(item.getId()); + } + + }); + //TODO + this.getFormatter().edgeChanged.attach(function(sender, item) { + _this.removeEdge(item.getId()); + _this.renderEdge(item.getId()); + }); + + this.getFormatter().resized.attach(function(sender, item) { + _this.resize(_this.getFormatter().getWidth(), _this.getFormatter().getHeight()); + }); + + this.getFormatter().backgroundImageChanged.attach(function(sender, item) { + _this.setBackgroundImage(_this.getFormatter().getBackgroundImage()); + }); + + this.getFormatter().backgroundColorChanged.attach(function(sender, item) { + _this._setBackgroundColor(_this.getFormatter().getBackgroundColor()); + }); + + this.getLayout().changed.attach(function(sender, item) { + _this.moveNode(item.getId()); + _this.moveEdge(item.getId()); + if (_this.args.labeled) { + _this.removeLabel(item.getId()); + _this.renderLabel(item.getId()); + } + }); + + this.getDataset().newVertex.attach(function(sender, item) { + + _this.renderNode(item.getId()); + if (_this.args.labeled) { + _this.renderLabel(item.getId()); + } + }); + + this.getDataset().newEdge.attach(function(sender, item) { + _this.renderEdge(item.getId()); + }); + + this.getDataset().vertexDeleted.attach(function(sender, item) { + _this.removeNode(item.getId()); + if (_this.args.labeled) { + _this.removeLabel(item.getId()); + } + }); + + this.getDataset().edgeDeleted.attach(function(sender, item) { + _this.removeEdge(item.getId()); + }); + + this.getDataset().vertexNameChanged.attach(function(sender, args) { + if (_this.args.labeled) { + _this.removeLabel(args.item.getId()); + _this.removeLabel(args.item.getId()); + _this.renderLabel(args.item.getId()); + } + }); + this.init(); + this.render(); +}; + +GraphCanvas.prototype.render = function() { + for ( var id in this.getDataset().getVertices()) { + this.renderNode(id); + } + this.renderLabels(); + this.renderEdges(); +}; + +GraphCanvas.prototype.renderLabels = function() { + if (this.args.labeled) { + for ( var id in this.getDataset().getVertices()) { + this.renderLabel(id); + } + } +}; + +GraphCanvas.prototype.removeLabels = function() { + for ( var id in this.getDataset().getVertices()) { + this.removeLabel(id); + } +}; + +/** Utilities method for nodes **/ +GraphCanvas.prototype.isNodeCanvas = function(node) { + return ((node.id == this.args.idGraph) || (node.id == this.id)); +}; + +GraphCanvas.prototype.isNodeBackground = function(node) { + return ((node.id == this.args.idBackgroundNode)); +}; + +GraphCanvas.prototype.isVertex = function(node) { + if (node.getAttribute("id") != null) { + if (node.getAttribute("id").indexOf("_v_") != -1) { + return true; + } + } + return false; +}; + +GraphCanvas.prototype.isLabel = function(node) { + if (node.getAttribute("id") != null) { + if (node.getAttribute("id").indexOf("_l_") != -1) { + return true; + } + } + return false; +}; + +GraphCanvas.prototype.isEdge = function(node) { + if (node.getAttribute("id") != null) { + if (node.getAttribute("id").indexOf("_e_") != -1) { + return true; + } + } + return false; +}; + +/** Resize **/ +GraphCanvas.prototype.resize = function(width, height) { + // this._svg.setAttribute("width", width); + // this._svg.setAttribute("height", height); + if (this.NodeSVGbackgroundImage != null) { + this.NodeSVGbackgroundImage.setAttribute("width", width); + this.NodeSVGbackgroundImage.setAttribute("height", height); + } + + this._svg.setAttribute("width", width); + this._svg.setAttribute("height", height); + + this.clearCanvas(); + this.render(); +}; + +GraphCanvas.prototype.clearCanvas = function() { + DOM.removeChilds(this.GraphEdgeGroup.getAttribute("id")); + DOM.removeChilds(this.GraphNodeGroup.getAttribute("id")); + this.clearLabels(); +}; + +GraphCanvas.prototype.clearLabels = function() { + DOM.removeChilds(this.GraphLabelGroup.getAttribute("id")); +}; + +/** ID'S converter **/ +GraphCanvas.prototype.getSVGNodeId = function(nodeId) { + return this.id + "_v_" + nodeId; +}; + +GraphCanvas.prototype.getSVGEdgeId = function(edgeId) { + return this.id + "_e_" + edgeId; +}; + +GraphCanvas.prototype.getSVGArrowEdgeId = function(edgeId) { + return this.id + "_arrow_" + edgeId; +}; + +GraphCanvas.prototype.getSVGLabelId = function(edgeId) { + return this.id + "_l_" + edgeId; +}; + +GraphCanvas.prototype.blinkVertexById = function(vertexId) { + $("#" + this.getSVGNodeId(vertexId)).fadeIn().fadeOut().fadeIn().fadeOut().fadeIn().fadeOut(); +}; + +GraphCanvas.prototype.getVertexIdFromSVGId = function(svgVertexId) { + return svgVertexId.replace(this.id, "").replace("_v_", ""); +}; + +GraphCanvas.prototype.getEdgeIdFromSVGId = function(svgEdgeId) { + return svgEdgeId.replace(this.id, "").replace("_e_", ""); +}; + +/** VERTEX **/ +GraphCanvas.prototype.getVertexById = function(id) { + return document.getElementById(this.getSVGNodeId(id)); +}; + +GraphCanvas.prototype.renderNodes = function() { + for ( var id in this.getDataset().getVertices()) { + this.renderNode(id); + } +}; + +GraphCanvas.prototype.overNode = function(nodeId) { + if (!this.args.interactive) { + return; + } + /** If selected we don't change the format **/ + if (this.args.isVertexSelected[nodeId] == null) { + var args = this.getFormatter().getVertexById(nodeId).getOver(); + args.args["cursor"] = 'pointer'; + this.changeVertexFormat(nodeId, args); + } +}; + +GraphCanvas.prototype.outNode = function(nodeId) { + if (!this.args.interactive) { + return; + } + + /** If selected we don't change the format **/ + if (this.args.isVertexSelected[nodeId] == null) { + this.changeVertexFormat(nodeId, this.getFormatter().getVertexById(nodeId).getDefault()); + } +}; + +GraphCanvas.prototype.overLabel = function(nodeId) { + this.overNode(nodeId); + // this.svgLabels[nodeId].setAttribute("cursor", "pointer"); +}; + +GraphCanvas.prototype.outLabel = function(nodeId) { + this.outNode(nodeId); + // this.svgLabels[nodeId].setAttribute("cursor", ""); +}; + +GraphCanvas.prototype.clickNode = function(nodeId) { + if (!this.args.interactive) { + return; + } + + /** si el evento se dispara oprque estaba dragging entonces no activo nada **/ + if (this.args.isVertexSelected[nodeId] == null) { + this.selectNode(nodeId); + } else { + this.deselectNode(nodeId); + } +}; + +GraphCanvas.prototype.selectNode = function(nodeId) { + for ( var i = 0; i < this.args.selectedVertices.length; i++) { + var format = this.getFormatter().getVertexById(nodeId).getSelected(); + format.opacity = 0.2; + this.changeVertexFormat(nodeId, this.getFormatter().getVertexById(nodeId).getSelected()); + } + + if (this.args.isVertexSelected[nodeId] == null) { + var format = this.getFormatter().getVertexById(nodeId).getSelected(); + format.opacity = 1; + this.changeVertexFormat(nodeId, this.getFormatter().getVertexById(nodeId).getSelected()); + this.args.selectedVertices.push(nodeId); + this.args.isVertexSelected[nodeId] = this.args.selectedVertices.length - 1; + this.onVertexSelect.notify(nodeId); + } +}; + +GraphCanvas.prototype.selectAllEdges = function() { + this.deselectNodes(); + this.deselectEdges(); + + for ( var edgesId in this.getDataset().edges) { + this.selectEdge(edgesId); + } +}; + +GraphCanvas.prototype.selectAllNodes = function() { + this.deselectNodes(); + this.deselectEdges(); + + for ( var vertexId in this.getDataset().vertices) { + this.selectNode(vertexId); + } +}; + +GraphCanvas.prototype.selectAll = function() { + this.deselectNodes(); + this.deselectEdges(); + + for ( var vertexId in this.getDataset().vertices) { + this.selectNode(vertexId); + } + + for ( var edgesId in this.getDataset().edges) { + this.selectEdge(edgesId); + } +}; + +GraphCanvas.prototype.selectEdge = function(edgeId) { + if (this.args.isEdgeSelected[edgeId] == null) { + this.changeEdgeFormat(edgeId, this.getFormatter().getEdgeById(edgeId).getSelected()); + //this.args.selectedEdges.push(edgeId); + this.args.isEdgeSelected[edgeId] = true; //this.args.selectedEdges.length - 1; + this.onEdgeSelect.notify(edgeId); + } +}; + +GraphCanvas.prototype.selectEdges = function(edges) { + + for ( var i = 0; i < edges.length; i++) { + this.selectEdge(edges[i]); + } +}; + +GraphCanvas.prototype.deselectNode = function(nodeId) { + if (this.args.isVertexSelected[nodeId] != null) { + this.changeVertexFormat(nodeId, this.getFormatter().getVertexById(nodeId).getDefault()); + this.args.selectedVertices.splice(this.args.isVertexSelected[nodeId], 1); + var index = this.args.isVertexSelected[nodeId]; + delete this.args.isVertexSelected[nodeId]; + + for ( var vertex in this.args.isVertexSelected) { + if (this.args.isVertexSelected[vertex] > index) { + this.args.isVertexSelected[vertex] = this.args.isVertexSelected[vertex] - 1; + } + } + } +}; + +GraphCanvas.prototype.deselectNodes = function() { + var selected = JSON.parse(JSON.stringify(this.getSelectedVertices())); + for ( var i = 0; i < selected.length; i++) { + this.deselectNode(selected[i]); + } +}; +GraphCanvas.prototype.selectNodes = function(idNodes) { + + for ( var i = 0; i < idNodes.length; i++) { + this.selectNode(idNodes[i]); + } + + // for ( var vertex in this.args.isVertexSelected) { + // if (this.args.isVertexSelected[vertex] > index){ + // this.args.isVertexSelected[vertex] = this.args.isVertexSelected[vertex] - 1; + // } + // } + +}; + +GraphCanvas.prototype.changeVertexFormat = function(nodeId, format) { + var svgNode = DOM.select(this.getSVGNodeId(nodeId)); + if (svgNode != null) { + var properties = format.toJSON(); + for ( var item in properties) { + svgNode.setAttribute(item, properties[item]); + } + + if (this.getFormatter().getVertexById(nodeId) instanceof CircleVertexGraphFormatter) { + var transform = "translate(" + svgNode.getAttribute("dragx") + "," + svgNode.getAttribute("dragy") + "), scale(" + format.getSize() + ")"; + svgNode.setAttribute("transform", transform); + } + } +}; + +GraphCanvas.prototype.renderLabel = function(nodeId) { + var x = Math.ceil(this.getLayout().getNodeById(nodeId).x * this.getFormatter().getWidth()); + var y = Math.ceil(this.getLayout().getNodeById(nodeId).y * this.getFormatter().getHeight()); + + var svgAttributesNode = JSON.parse(JSON.stringify(this.getFormatter().getVertexById(nodeId).getDefault().toJSON().title)); + svgAttributesNode.id = this.getSVGLabelId(this.getDataset().getVertexById(nodeId).getId()); + svgAttributesNode.dx = (-1) * (this.getDataset().getVertexById(nodeId).getName().length * svgAttributesNode["font-size"]) / 4 - 4; + + svgAttributesNode.dy = parseFloat((this.getFormatter().getVertexById(nodeId).getDefault().getSize())) + + parseFloat(svgAttributesNode["font-size"]) + parseFloat(this.getFormatter().getVertexById(nodeId).getDefault().getStrokeWidth()) - 4; + svgAttributesNode.dragx = Math.ceil(this.getLayout().getNodeById(nodeId).x * this.getFormatter().getWidth()); + + var gragy = parseFloat(this.getFormatter().getVertexById(nodeId).getDefault().getSize()) + + Math.ceil(this.getLayout().getNodeById(nodeId).y * this.getFormatter().getHeight()); + svgAttributesNode.dragy = gragy; + svgAttributesNode.transform = "translate(" + svgAttributesNode.dragx + "," + svgAttributesNode.dragy + ")";//, scale("+this.formatter.getVertexById(nodeId).getDefault().getSize()+")"; + + var nodeSVG = SVG.drawText(0, 0, this.getDataset().getVertexById(nodeId).getName(), this.GraphLabelGroup, svgAttributesNode); + + this.svgLabels[nodeId] = nodeSVG; + + /** Events for the SVG node **/ + var _this = this; + if (nodeSVG != null) { + nodeSVG.addEventListener("mouseover", function() { + _this.overLabel(nodeId); + }, false); + nodeSVG.addEventListener("mouseout", function() { + _this.outLabel(nodeId); + }, false); + } + +}; + +GraphCanvas.prototype.removeLabel = function(labelId) { + if (DOM.select(this.getSVGLabelId(labelId)) != null) { + DOM.select(this.getSVGLabelId(labelId)).parentNode.removeChild(DOM.select(this.getSVGLabelId(labelId))); + } +}; + +GraphCanvas.prototype.renderNode = function(nodeId) { + var svgAttributesNode = JSON.parse(JSON.stringify(this.getFormatter().getVertexById(nodeId).getDefault().toJSON())); + svgAttributesNode.dragx = Math.ceil(this.getLayout().getNodeById(nodeId).x * this.getFormatter().getWidth()); + svgAttributesNode.dragy = Math.ceil(this.getLayout().getNodeById(nodeId).y * this.getFormatter().getHeight()); + svgAttributesNode.transform = "translate(" + svgAttributesNode.dragx + "," + svgAttributesNode.dragy + ")"; + svgAttributesNode.id = this.getSVGNodeId(nodeId); + /*svgAttributesNode["stroke-width"] = 3 ; + svgAttributesNode["stroke-opacity"] = 1 ; + svgAttributesNode["fill-opacity"] = svgAttributesNode["opacity"] ; + svgAttributesNode["opacity"] = 1 ;*/ + this.circleDefaultRadius = this.getFormatter().getVertexById(nodeId).getDefault().getSize(); + var nodeSVG; + + if (this.getFormatter().getVertexById(nodeId) instanceof CircleVertexGraphFormatter) { + nodeSVG = SVG.drawCircle(0, 0, this.circleDefaultRadius, this.GraphNodeGroup, svgAttributesNode); + } + + if (this.getFormatter().getVertexById(nodeId) instanceof SquareVertexGraphFormatter) { + //nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius) ,0 - (this.formatter.getVertexById(nodeId).getDefault().getSize()) , (this.getFormatter().getVertexById(nodeId).getDefault().getSize()*2), (this.getFormatter().getVertexById(nodeId).getDefault().getSize()*2), this.GraphNodeGroup, svgAttributesNode); + nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius), 0 - (this.circleDefaultRadius), (this.circleDefaultRadius * 2), + (this.circleDefaultRadius * 2), this.GraphNodeGroup, svgAttributesNode); + } + + if (this.getFormatter().getVertexById(nodeId) instanceof EllipseVertexGraphFormatter) { + nodeSVG = SVG.drawEllipse(0, 0, this.circleDefaultRadius * 1.5, this.circleDefaultRadius, this.GraphNodeGroup, svgAttributesNode); + } + + if (this.getFormatter().getVertexById(nodeId) instanceof RectangleVertexGraphFormatter) { + //nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius) ,0 - ((this.circleDefaultRadius*2)/2) , (this.circleDefaultRadius*2), (this.circleDefaultRadius), this.GraphNodeGroup, svgAttributesNode); + nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius * 1.5), 0 - (this.circleDefaultRadius), (this.circleDefaultRadius * 2 * 1.5), + (this.circleDefaultRadius * 2), this.GraphNodeGroup, svgAttributesNode); + + } + + if (this.getFormatter().getVertexById(nodeId) instanceof RoundedVertexGraphFormatter) { + svgAttributesNode.ry = 2;// this.formatter.getVertexById(nodeId).getDefault().getSize()/4; + svgAttributesNode.rx = 2;// this.formatter.getVertexById(nodeId).getDefault().getSize()/4; + nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius * 1.5), 0 - (this.circleDefaultRadius), (this.circleDefaultRadius * 2 * 1.5), + (this.circleDefaultRadius * 2), this.GraphNodeGroup, svgAttributesNode); + } + + // + + if (this.getFormatter().getVertexById(nodeId) instanceof OctagonVertexGraphFormatter) { + svgAttributesNode.ry = 2; + svgAttributesNode.rx = 2; + nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius * 1.5), 0 - (this.circleDefaultRadius), (this.circleDefaultRadius * 2 * 1.5), + (this.circleDefaultRadius * 2), this.GraphNodeGroup, svgAttributesNode); + } + + nodeSVG.internalId = nodeId; + // + var _this = this; + + /** Events for the SVG node **/ + if (nodeSVG != null) { + nodeSVG.addEventListener("mouseover", function() { + _this.onVertexOver.notify(nodeId); + _this.overNode(nodeId); + }, false); + nodeSVG.addEventListener("mouseout", function() { + _this.onVertexOut.notify(nodeId); + _this.outNode(nodeId); + }, false); + //nodeSVG.addEventListener("click", function(){_this.clickNode(nodeId);}, false); + // + nodeSVG.addEventListener("mouseup", function() { + _this.onVertexUp.notify(nodeId); + }, false); + } +}; + +GraphCanvas.prototype.removeNode = function(nodeId) { + DOM.select(this.getSVGNodeId(nodeId)).parentNode.removeChild(DOM.select(this.getSVGNodeId(nodeId))); + if (this.args.labeled) { + this.removeLabel(nodeId); + } +}; + +/** REMOVING **/ +GraphCanvas.prototype.removeSelected = function() { + /** El orden importa **/ + this.removeSelectedEdges(); + this.removeSelectedNode(); + +}; + +GraphCanvas.prototype.removeSelectedNode = function() { + var selected = JSON.parse(JSON.stringify(this.getSelectedVertices())); + this.deselectNodes(); + var sorted = selected.sort(function(a, b) { + return a - b + }); + for ( var i = 0; i < sorted.length; i++) { + if (this.getDataset().getVertexById(sorted[i]) != null) { + this.getDataset().getVertexById(sorted[i]).remove(); + } + } +}; + +/** EDGES **/ +GraphCanvas.prototype.removeEdge = function(edgeId) { + if (DOM.select(this.getSVGEdgeId(edgeId)) != null) { + DOM.select(this.getSVGEdgeId(edgeId)).parentNode.removeChild(DOM.select(this.getSVGEdgeId(edgeId))); + } + + if (DOM.select(this.getSVGEdgeId(edgeId) + "_shadow") != null) { + DOM.select(this.getSVGEdgeId(edgeId) + "_shadow").parentNode.removeChild(DOM.select(this.getSVGEdgeId(edgeId) + "_shadow")); + } + + if (DOM.select(this.getSVGArrowEdgeId(edgeId)) != null) { + DOM.select(this.getSVGArrowEdgeId(edgeId)).parentNode.removeChild(DOM.select(this.getSVGArrowEdgeId(edgeId))); + } +}; + +GraphCanvas.prototype.overEdge = function(edgeId) { + if ((!this.args.interactive) || this.dragging || this.selecting) { + return; + } + + /** If selected we don't change the format **/ + if (this.args.isEdgeSelected[edgeId] == null) { + var format = this.getFormatter().getEdgeById(edgeId).getOver(); + format.args["cursor"] = "pointer"; + this.changeEdgeFormat(edgeId, format); + } +}; + +GraphCanvas.prototype.outEdge = function(edgeId) { + if (!this.args.interactive) { + return; + } + + /** If selected we don't change the format **/ + if (this.args.isEdgeSelected[edgeId] == null) { + this.changeEdgeFormat(edgeId, this.getFormatter().getEdgeById(edgeId).getDefault()); + } +}; + +GraphCanvas.prototype.changeEdgeFormat = function(edgeId, format) { + var svgEdge = DOM.select(this.getSVGEdgeId(edgeId) + "_shadow"); + if (svgEdge != null) { + var properties = format.toJSON(); + for ( var item in properties) { + svgEdge.setAttribute(item, properties[item]); + } + } +}; + +GraphCanvas.prototype.deselectEdge = function(edgeID) { + if (this.args.isEdgeSelected[edgeID] != null) { + this.changeEdgeFormat(edgeID, this.getFormatter().getEdgeById(edgeID).getDefault()); + var index = this.args.isEdgeSelected[edgeID]; + delete this.args.isEdgeSelected[edgeID]; + } +}; + +GraphCanvas.prototype.deselectEdges = function() { + var selected = JSON.parse(JSON.stringify(this.getSelectedEdges())); + for ( var i = 0; i < selected.length; i++) { + this.deselectEdge(selected[i]); + } +}; + +GraphCanvas.prototype.removeSelectedEdges = function() { + var selected = JSON.parse(JSON.stringify(this.getSelectedEdges())); + this.deselectEdges(); + for ( var i = 0; i < selected.length; i++) { + if (this.getDataset().getEdgeById(selected[i]) != null) { + this.getDataset().getEdgeById(selected[i]).remove(); + } + } +}; + +GraphCanvas.prototype.renderEdge = function(edgeId) { + var svgAttributesEdge = this.getFormatter().getEdgeById(edgeId).getDefault().toJSON(); + var edge = this.getDataset().getEdgeById(edgeId); + + var svgNodeTarget = this.getVertexById(edge.getNodeTarget().getId()); + var svgNodeSource = this.getVertexById(edge.getNodeSource().getId()); + svgAttributesEdge.id = this.getSVGEdgeId(edge.getId()) + "_shadow"; + + var svgEdge = null; + + if (this.getFormatter().getEdgeById(edgeId) instanceof LineEdgeGraphFormatter) { + var coordenateSourceX = svgNodeSource.getAttribute("dragx"); + var coordenateSourceY = svgNodeSource.getAttribute("dragy"); + var coordenateTargetX = svgNodeTarget.getAttribute("dragx"); + var coordenateTargetY = svgNodeTarget.getAttribute("dragy"); + + SVG.drawLine(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, this.GraphEdgeGroup, svgAttributesEdge); + var attributesShadow = {}; + attributesShadow.id = this.getSVGEdgeId(edge.getId()); + attributesShadow["stroke-opacity"] = 0; + attributesShadow["stroke-width"] = 4; + attributesShadow["stroke"] = "black"; + svgEdge = SVG.drawLine(svgNodeSource.getAttribute("dragx"), svgNodeSource.getAttribute("dragy"), svgNodeTarget.getAttribute("dragx"), + svgNodeTarget.getAttribute("dragy"), this.GraphEdgeGroup, attributesShadow); + } + + if (this.getFormatter().getEdgeById(edgeId) instanceof BezierEdgeGraphFormatter) { + var nodeId = edge.getNodeTarget().getId(); + var nodeSize = this.formatter.getVertexById(nodeId).getDefault().getSize() * this.getFormatter().getNodesMaxSize(); + svgAttributesEdge.fill = "none"; + svgAttributesEdge.id = this.getSVGEdgeId(edgeId); + var d = this.calculateCoordenatesBezier(nodeSize, svgNodeSource.getAttribute("dragx"), svgNodeSource.getAttribute("dragy")); + svgEdge = SVG.drawPath(d, this.GraphEdgeGroup, svgAttributesEdge); + } + ; + + if ((this.getFormatter().getEdgeById(edgeId) instanceof DirectedLineEdgeGraphFormatter) + || (this.getFormatter().getEdgeById(edgeId) instanceof CutDirectedLineEdgeGraphFormatter) + || (this.getFormatter().getEdgeById(edgeId) instanceof DotDirectedLineEdgeGraphFormatter) + || (this.getFormatter().getEdgeById(edgeId) instanceof OdotDirectedLineEdgeGraphFormatter) + || (this.getFormatter().getEdgeById(edgeId) instanceof OdirectedLineEdgeGraphFormatter)) { + var coordenateSourceX = svgNodeSource.getAttribute("dragx"); + var coordenateSourceY = svgNodeSource.getAttribute("dragy"); + var coordenateTargetX = svgNodeTarget.getAttribute("dragx"); + var coordenateTargetY = svgNodeTarget.getAttribute("dragy"); + + var offset = parseFloat(this.getFormatter().getVertexById(this.getDataset().getEdgeById(edgeId).getNodeTarget().getId()).getDefault() + .getSize() + * this.circleDefaultRadius); + var point = this._calculateEdgePointerPosition(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, offset); + coordenateTargetX = point.x; + coordenateTargetY = point.y; + SVG.drawLine(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, this.GraphEdgeGroup, svgAttributesEdge); + + var attributesShadow = {}; + attributesShadow.id = this.getSVGEdgeId(edge.getId()); + attributesShadow["stroke-opacity"] = 0; + attributesShadow["stroke-width"] = 4; + attributesShadow["stroke"] = "black"; + svgEdge = SVG.drawLine(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, this.GraphEdgeGroup, attributesShadow); + } + + if (this.getFormatter().getEdgeById(edgeId) instanceof DirectedLineEdgeGraphFormatter + || (this.getFormatter().getEdgeById(edgeId) instanceof OdirectedLineEdgeGraphFormatter)) { + var coordenateSourceX = svgNodeSource.getAttribute("dragx"); + var coordenateSourceY = svgNodeSource.getAttribute("dragy"); + var coordenateTargetX = svgNodeTarget.getAttribute("dragx"); + var coordenateTargetY = svgNodeTarget.getAttribute("dragy"); + + var point = this._calculateEdgePointerPosition(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, offset); + coordenateTargetX = point.x; + coordenateTargetY = point.y; + + var angle = Geometry.toDegree(point.angle) + 90; + this.arrowDefaultSize = this.getFormatter().getEdgeById(edgeId).getArrowSize(); //getDefault().getArrowSize(); + var d = "-" + this.arrowDefaultSize + ",0 0,-" + parseFloat(this.arrowDefaultSize) * 2 + " " + this.arrowDefaultSize + ",0"; + + var attributes; + + if (this.getFormatter().getEdgeById(edgeId) instanceof DirectedLineEdgeGraphFormatter) { + attributes = [ + [ "fill", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], + [ "stroke", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], [ "id", this.getSVGArrowEdgeId(edgeId) ] ]; + } else { + attributes = [ + [ "fill", "#FFFFFF" ], [ "stroke", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], + [ "id", this.getSVGArrowEdgeId(edgeId) ] ]; + } + + var flechaSVGNode = SVG.drawPoligon(d, this.GraphEdgeGroup, attributes);//, ["transform", "rotate("+angle+"), translate(0,0)"]]); + flechaSVGNode.setAttribute("transform", " translate(" + coordenateTargetX + ", " + coordenateTargetY + "), rotate(" + angle + ")"); + } + ; + + if (this.getFormatter().getEdgeById(edgeId) instanceof CutDirectedLineEdgeGraphFormatter) { + var coordenateSourceX = svgNodeSource.getAttribute("dragx"); + var coordenateSourceY = svgNodeSource.getAttribute("dragy"); + var coordenateTargetX = svgNodeTarget.getAttribute("dragx"); + var coordenateTargetY = svgNodeTarget.getAttribute("dragy"); + + var point = this._calculateEdgePointerPosition(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, offset); + coordenateTargetX = point.x; + coordenateTargetY = point.y; + + var angle = Geometry.toDegree(point.angle) + 90; + + //this.arrowDefaultSize = 2; //getDefault().getArrowSize(); + var d = "-4,0 4,0 4,-2 -4,-2"; + + var flechaSVGNode = SVG.drawPoligon(d, this.GraphEdgeGroup, [ + [ "fill", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], + [ "stroke", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], [ "id", this.getSVGArrowEdgeId(edgeId) ] ]);//, ["transform", "rotate("+angle+"), translate(0,0)"]]); + flechaSVGNode.setAttribute("transform", " translate(" + coordenateTargetX + ", " + coordenateTargetY + "), rotate(" + angle + ")"); + } + ; + + if ((this.getFormatter().getEdgeById(edgeId) instanceof DotDirectedLineEdgeGraphFormatter) + || (this.getFormatter().getEdgeById(edgeId) instanceof OdotDirectedLineEdgeGraphFormatter)) { + var coordenateSourceX = svgNodeSource.getAttribute("dragx"); + var coordenateSourceY = svgNodeSource.getAttribute("dragy"); + var coordenateTargetX = svgNodeTarget.getAttribute("dragx"); + var coordenateTargetY = svgNodeTarget.getAttribute("dragy"); + var point = this._calculateEdgePointerPosition(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, offset); + coordenateTargetX = point.x; + coordenateTargetY = point.y; + var angle = Geometry.toDegree(point.angle) + 90; + // this.arrowDefaultSize = this.formatter.getEdgeById(edgeId).getArrowSize(); //getDefault().getArrowSize(); + var attributes = []; + if (this.getFormatter().getEdgeById(edgeId) instanceof OdotDirectedLineEdgeGraphFormatter) { + attributes = [ + [ "fill", "#FFFFFF" ], [ "stroke", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], + [ "id", this.getSVGArrowEdgeId(edgeId) ] ]; + } else { + attributes = [ + [ "fill", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], + [ "stroke", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], [ "id", this.getSVGArrowEdgeId(edgeId) ] ]; + } + var flechaSVGNode = SVG.drawCircle(0, 0, 4, this.GraphEdgeGroup, attributes); + flechaSVGNode.setAttribute("transform", " translate(" + coordenateTargetX + ", " + coordenateTargetY + "), rotate(" + angle + ")"); + } + ; + + var _this = this; + /** Events for the SVG edge **/ + if (svgEdge != null) { + if (this.getDataset().getEdgesCount() < this.args.maxNumberEdgesFiringEvents) { + svgEdge.addEventListener("mouseover", function() { + _this.overEdge(edgeId); + }, false); + svgEdge.addEventListener("mouseout", function() { + _this.outEdge(edgeId); + }, false); + } + } +}; + +GraphCanvas.prototype._calculateEdgePointerPosition = function(sourceX, sourceY, targetX, targetY, radius) { + var angle = Geometry.getAngleBetweenTwoPoints(sourceX, sourceY, targetX, targetY); + + /** Suponiendo el node source que este a la derecha **/ + if ((targetX - sourceX) < 0) { + var b = Geometry.getAdjacentSideOfRectangleRight(angle, radius); + targetX = parseFloat(targetX) + parseFloat(b); + arrowX = parseFloat(targetX) + parseFloat(b) + this.arrowDefaultSize / 2; + } else { + var b = Geometry.getAdjacentSideOfRectangleRight(angle, radius); + targetX = parseFloat(targetX) - parseFloat(b); + arrowX = parseFloat(targetX) - parseFloat(b) - this.arrowDefaultSize / 2; + } + + /** Suponiendo el node source que este a la arriba **/ + if ((targetY - sourceY) > 0) { + var a = Geometry.getOppositeSideOfRectangleRight(angle, radius); + targetY = parseFloat(targetY) - parseFloat(a); + arrowY = parseFloat(targetY) - parseFloat(a) - this.arrowDefaultSize / 2; + } else { + var a = Geometry.getOppositeSideOfRectangleRight(angle, radius); + targetY = parseFloat(targetY) + parseFloat(a); + arrowY = parseFloat(targetY) + parseFloat(a) - this.arrowDefaultSize / 2; + + } + + return { + "x" : arrowX, + "y" : arrowY, + "angle" : angle + }; +}; + +GraphCanvas.prototype.calculateCoordenatesBezier = function(nodeSize, x1, y1) { + var x11 = x1 - (nodeSize / 2); + var y11 = y1 - (nodeSize / 2); + + var x12 = parseFloat(x1) + parseFloat(nodeSize / 2); + var y12 = y1 - (nodeSize / 2); + + var curvePointX = (x12 - x11) / 2 + x11; + var curvePointY = y1 - (nodeSize * 2); + var d = "M" + x11 + "," + y11 + " T" + curvePointX + "," + curvePointY + " " + x12 + "," + y12; + return d; + +}; + +GraphCanvas.prototype.renderEdges = function() { + for ( var edge in this.getDataset().getEdges()) { + this.renderEdge(this.getDataset().getEdgeById(edge).getId()); + + } +}; + +GraphCanvas.prototype.getLastSelectedNode = function() { + var node = null; + if (this.getSelectedVertices().length > 0) { + var nodeId = this.getSelectedVertices()[this.getSelectedVertices().length - 1]; + node = this.getDataset().getVertexById(nodeId); + } + return node; +}; +/* + GraphCanvas.prototype.getNodeByNameAndIndex = function(node, index){ + var nodeId = this.getDataset().verticesIndex[node][index]; + var nodeItem = this.getDataset().getVertexById(nodeId); + return nodeItem; + }; + */ + +GraphCanvas.prototype.setDataset = function(dataset) { + this.dataset = dataset; +}; + +GraphCanvas.prototype.setFormatter = function(formatter) { + this.formatter = formatter; +}; + +GraphCanvas.prototype.setLayout = function(layout) { + this.layout = layout; +}; + +/** API **/ +GraphCanvas.prototype.getDataset = function() { + return this.dataset; +}; + +GraphCanvas.prototype.getFormatter = function() { + return this.formatter; +}; + +GraphCanvas.prototype.getLayout = function() { + return this.layout; +}; + +/** API DATASET **/ +GraphCanvas.prototype.addVertex = function(name, args) { + this.getDataset().addNode(name, args); +}; + +GraphCanvas.prototype.removeVertex = function(vertexId) { + this.getDataset().getVertexById(vertexId).remove(); +}; + +GraphCanvas.prototype.addEdge = function(edgeName, nodeSourceId, nodeTargetId, args) { + this.getDataset().addEdge(edgeName, nodeSourceId, nodeTargetId, args); +}; +/* + GraphCanvas.prototype.removeEdge = function(edgeId){ + this.getDataset().getEdgeById(edgeId).remove(); + }; + */ + +/** API FORMATTER **/ +GraphCanvas.prototype.getWidth = function() { + return this.getFormatter().getWidth(); +}; + +GraphCanvas.prototype.getHeight = function() { + return this.getFormatter().getHeight(); +}; + +GraphCanvas.prototype.getBackgroundImage = function() { + return this.getFormatter().getBackgroundImage(); +}; + +//GraphCanvas.prototype.setBackgroundImage = function(value){ +// this.getFormatter().setBackgroundImage(value); +//}; + +GraphCanvas.prototype.getBackgroundColor = function() { + return this.getFormatter().getBackgroundColor(); +}; + +GraphCanvas.prototype.setBackgroundColor = function() { + this.getFormatter().setBackgroundColor(value); +}; + +//GraphCanvas.prototype.setEdgeFill = function(edgeId, value){ +// this.getFormatter().getEdgeById(edgeId).getDefault().setFill(value); +//}; +// +//GraphCanvas.prototype.getEdgeFill = function(edgeId){ +// return this.getFormatter().getEdgeById(edgeId).getDefault().getFill(); +//}; + +/** VERTICES FORMATTER **/ +GraphCanvas.prototype.setVertexSize = function(vertexId, value) { + this.getFormatter().getVertexById(vertexId).getDefault().setSize(value); +}; + +GraphCanvas.prototype.getVertexSize = function(vertexId) { + return this.getFormatter().getVertexById(vertexId).getDefault().getSize(); +}; + +GraphCanvas.prototype.setVertexStroke = function(vertexId, value) { + this.getFormatter().getVertexById(vertexId).getDefault().setStroke(value); +}; + +GraphCanvas.prototype.getVertexStroke = function(vertexId) { + return this.getFormatter().getVertexById(vertexId).getDefault().getStroke(); +}; + +GraphCanvas.prototype.setVertexStrokeOpacity = function(vertexId, value) { + this.getFormatter().getVertexById(vertexId).getDefault().setStrokeOpacity(value); +}; + +GraphCanvas.prototype.getVertexStrokeOpacity = function(vertexId) { + return this.getFormatter().getVertexById(vertexId).getDefault().getStrokeOpacity(); +}; + +GraphCanvas.prototype.setVertexOpacity = function(vertexId, value) { + this.getFormatter().getVertexById(vertexId).getDefault().setOpacity(value); +}; + +GraphCanvas.prototype.getVertexOpacity = function(vertexId) { + return this.getFormatter().getVertexById(vertexId).getDefault().getOpacity(); +}; + +GraphCanvas.prototype.setVertexFill = function(vertexId, color) { + this.getFormatter().getVertexById(vertexId).getDefault().setFill(color); +}; + +GraphCanvas.prototype.getVertexFill = function(vertexId) { + return this.getFormatter().getVertexById(vertexId).getDefault().getFill(); +}; + +/** EDGES FORMATTER **/ +GraphCanvas.prototype.setEdgeSize = function(edgeId, value) { + this.getFormatter().getEdgeById(edgeId).getDefault().setSize(value); +}; + +GraphCanvas.prototype.getEdgeSize = function(edgeId) { + return this.getFormatter().getEdgeById(edgeId).getDefault().getSize(); +}; + +GraphCanvas.prototype.setEdgeStroke = function(edgeId, value) { + this.getFormatter().getEdgeById(edgeId).getDefault().setStroke(value); +}; + +GraphCanvas.prototype.getEdgeStroke = function(edgeId) { + return this.getFormatter().getEdgeById(edgeId).getDefault().getStroke(); +}; + +GraphCanvas.prototype.setEdgeStrokeOpacity = function(edgeId, value) { + this.getFormatter().getEdgeById(edgeId).getDefault().setStrokeOpacity(value); +}; + +GraphCanvas.prototype.getEdgeStrokeOpacity = function(edgeId) { + return this.getFormatter().getEdgeById(edgeId).getDefault().getStrokeOpacity(); +}; + +GraphCanvas.prototype.setEdgeFill = function(edgeId, color) { + this.getFormatter().getEdgeById(edgeId).getDefault().setFill(color); +}; + +GraphCanvas.prototype.getEdgeFill = function(edgeId) { + return this.getFormatter().getEdgeById(edgeId).getDefault().getFill(); +}; + +/** API LAYOUT **/ +GraphCanvas.prototype.setCoordinates = function(vertexId, x, y) { + return this.getLayout().getEdgeById(vertexId).setCoordinates(x, y); +}; + + + +function HPLCGraph(args) { + this.width = 600; + this.height = 600; + this.title = ''; + this.bbar = false; + this.plotInnerPanelPadding = 10; + this.plotPanelPadding = 5; + this.id = BUI.id(); - if (record.raw.measurementId != null) { - /** For testing * */ - grid.setLoading("ISPyB: Removing measurement"); - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - grid.setLoading(false); - /** - * We get and refresh experiment - * because specimens has changed * - */ - var adapter2 = new BiosaxsDataAdapter(); - adapter2.onSuccess.attach(function(sender, experiment) { - _this.onRemoved.notify(experiment); - _this._showStatusBarReady('Ready'); - }); - if (_this.experiments.experiments[0].experimentId != null) { - adapter2.getExperimentById(_this.experiments.experiments[0].experimentId, "MEDIUM"); - _this._showStatusBarBusy("ISPyB: Removing Unused Specimens"); - } - }); + this.hidePlots = null; + this.xlabel = ""; + this.scaled = false; + this.xParam = null; + this.showRangeSelector = true; + this.interactionModel = null; + + /** for each stat the max and minimum value when it is scaled in order to show correctly in the legend **/ + this.ranges = {}; + if (args != null) { + if (args.interactionModel != null) { + this.interactionModel = args.interactionModel; + } + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + if (args.bbar != null) { + this.bbar = args.bbar; + } + if (args.title != null) { + this.title = args.title; + } + if (args.plots != null) { + this.plots = args.plots; + } + + if (args.scaled != null) { + this.scaled = args.scaled; + } + if (args.xlabel != null) { + this.xlabel = args.xlabel; + } + if (args.xParam != null) { + this.xParam = args.xParam; + } + if (args.showRangeSelector != null) { + this.showRangeSelector = args.showRangeSelector; + } + } + + this.onZoomX = new Event(this); + this.onResetZoom = new Event(this); + this.dblclick = new Event(this); +} + +HPLCGraph.prototype.getMenu = function () { + var _this = this; + /** Actions buttons **/ + var actions = []; + + function toggle(item, pressed) { + if (pressed) { + _this.plots[item.param] = true; + } else { + delete _this.plots[item.param]; + } + _this.reloadData(this.hplcData); + } + + for (var i = 0; i < this.hplcData.length; i++) { + if (this.hplcData[i].showOnMenu != false) { + var param = this.hplcData[i].param; + var style = "style='padding:0 0px 0 5px;'"; + actions.push({ + text : "
" + BUI.getRectangleColorDIV(this.hplcData[i].color, 10, 10) + " " + this.hplcData[i].label + "
", + id : _this.id + param, + param : param, + enableToggle : true, + scope : this, + toggleHandler : toggle, + pressed : (_this.plots[param] != null) + }); + } + } + actions.push("-"); + + actions.push({ + text : "Scale", + enableToggle : true, + scope : this, + pressed : this.scaled, + icon : '../images/icon_graph.png', + toggleHandler : function (item, pressed) { + _this.scaled = pressed; + _this.reloadData(this.hplcData); + } + }); + + actions.push("->"); + actions.push({ + text : "Save", + scope : this, + icon : '../images/save.gif', + handler : function (item, pressed) { + var largeImage = document.createElement("img"); + largeImage.style.display = 'block'; + largeImage.style.width = 200 + "px"; + largeImage.style.height = 200 + "px"; + largeImage.setAttribute('src', Dygraph.Export.asCanvas(this.dygraphObject.dygraph).toDataURL()); + window.open(Dygraph.Export.asCanvas(this.dygraphObject.dygraph).toDataURL(), 'Image', ''); + } + }); + + return actions; +}; - adapter.onError.attach(function(sender, data) { - alert("Error: " + data); - grid.setLoading(false); - }); +/** Looks for the maximum value and then divide everything but that value **/ +HPLCGraph.prototype.scaledData = function (data) { + for (var i = 0; i < data.length; i++) { + var values = this.getMaxAndMinValue(data[i]); + data[i] = this.divideValuesByMax(data[i], values.max); + this.ranges[data[i].label] = values; + } + return data; +}; - adapter.removeMeasurement(record.raw); - } - } - } +/** Given a stat float[] and a max number it will divide each value by max **/ +HPLCGraph.prototype.divideValuesByMax = function (stat, max) { + for (var j = 0; j < stat.data.length; j++) { + if (max != 0) { + stat.data[j] = Number(stat.data[j]) / max; + stat.std[j] = Number(stat.std[j]) / max; + } + } + return stat; +}; - } - } - }); +/** returns max value of a stat **/ +HPLCGraph.prototype.getMaxAndMinValue = function (stat) { + var max = 0; + var min = stat.data[0]; + for (var j = 0; j < stat.data.length; j++) { + if (Number(stat.data[j]) > max) { + max = Number(stat.data[j]); + } + if (Number(stat.std[j]) > max) { + max = Number(stat.std[j]); + } + if (Number(stat.data[j]) < min) { + min = Number(stat.data[j]); + } + } + return { + max : Number(max), + min : Number(min) + }; +}; - this.grid.on("afterrender", function() { +HPLCGraph.prototype.getPoint = function (data, i) { + var point = [ 10, 10, 10 ]; + var y = parseFloat(data.data[i]); + var error = parseFloat(data.std[i]); + if (data.fdata == null) { + return [ y - error, y, y + error ]; + } else { + if (data.fstd != null) { + return [ data.fstd(y - error), data.fdata(y), data.fstd(y + error) ]; + } + return [ data.fdata(y) - error, data.fdata(y), data.fdata(y) + error ]; + } + return point; +}; - function updateTime() { - try { - _this.estimatedTime = _this.estimatedTime - 1; +HPLCGraph.prototype.reloadData = function(hplcData) { + this.panel.setLoading(false); + this.hplcData = hplcData; - _this.onUpdateTime.notify({ - hours : (Number(_this.estimatedTime / 3600).toFixed()), - minutes : (Number((_this.estimatedTime / 60) % 60).toFixed()), - seconds : (Number(_this.estimatedTime % 60).toFixed()) + var data = hplcData; + - }); + /** In case of having peaks **/ + if (this.peaks != null) { + for (var peak in this.peaks) { + var values = []; + var std = []; + for (var i = 0; i < this.peaks[peak].length; i++) { + values.push(this.peaks[peak][i][1]); + std.push(this.peaks[peak][i][2]); + } + data.push({ + param : peak, + data : values, + showOnMenu : false, + fdata : function (a) { + var value = (Math.log(parseFloat(a))); + if (isNumber(value)) { + return value; + } + }, + fstd : function (a) { + var value = Math.log(Math.abs(parseFloat(a))); + if (isNumber(value)) + return value; + }, + std : std, + color : this.colorPeak[peak], + label : peak + }); + + } + } + + + if (this.scaled) { + data = this.scaledData(JSON.parse(JSON.stringify(hplcData))); + } - if (Number(_this.estimatedTime) < 0) { - _this.timer = null; - grid.setTitle(_this.title); + var paramIndex = {}; + var parsed = []; + var j = 0; + for (var i = 0; i < data[0].data.length - 1; i++) { + var aux = []; + for (j = 0; j < data.length; j++) { + if (this.plots != null) { + if (this.plots[data[j].param] != null) { + aux.push(this.getPoint(data[j], i)); + paramIndex[data[j].param] = aux.length - 1; } + } else { + aux.push([ data[j].data[i] - data[j].std[i], data[j].data[i], data[j].data[i] + data[j].std[i] ]); + } + } + parsed.push([]); - } catch (e) { - console.log(e); - _this.timer = null; + var index = i; + if (this.xParam != null) { + index = parseFloat(data[this.xParam].data[i]); + } + + parsed[parsed.length - 1].push(index); + + for (j = 0; j < data.length; j++) { + if (this.plots != null) { + if (this.plots[data[j].param] != null) { + parsed[parsed.length - 1].push(aux[paramIndex[data[j].param]]); + } + } else { + parsed[parsed.length - 1].push(aux[j]); } } + } - if (_this.estimateTime) { - var experimentList = _this.experiments; - var collected = experimentList.getMeasurementsCollected(); - if (collected.length > 0) { - if (collected[0].run3VO != null) { - try { - var end = collected[0].run3VO.timeEnd; - var start = collected[0].run3VO.timeStart; - var dstart = moment(start); - var dend = moment(end); - var seconds = Number(dend.diff(dstart) / 1000).toFixed(); + var colors = []; + var labels = [ "" ]; + for (j = 0; j < data.length; j++) { + if (this.plots != null) { + if (this.plots[data[j].param] != null) { + colors.push(data[j].color); + labels.push(data[j].label); + } + } else { + parsed[parsed.length - 1].push(aux[j]); + } + } - _this.estimatedTime = (seconds * experimentList.getMeasurementsNotCollected().length); + this._renderDygraph(parsed, colors, labels); +}; - if (_this.estimatedTime > 0) { - updateTime(); - _this.timer = setInterval(function() { - updateTime(); - }, 1000); +HPLCGraph.prototype._renderDygraph = function (parsed, colors, labels) { + this.dygraphObject = new StdDevDyGraph(this.id, { + width : this.width, + height : this.height - 10, + xlabel : this.xlabel, + showRangeSelector : this.showRangeSelector, + interactionModel : this.interactionModel, + scaled : this.scaled, + ranges : this.ranges + }); + this.dygraphObject.draw(parsed, colors, labels); + + var _this = this; + this.dygraphObject.onZoomX.attach(function (sender, args) { + try { + _this.onZoomX.notify(args); + } catch (e) { + } + }); + + this.dygraphObject.onResetZoom.attach(function (sender, args) { + try { + _this.onResetZoom.notify(args); + } catch (e) { + } + }); + + this.dygraphObject.dblclick.attach(function (sender, args) { + try { + _this.dblclick.notify(args); + } catch (e) { + } + }); + +}; + +HPLCGraph.prototype.loadData = function (data) { + var _this = this; + this.reloadData(data); + this.panel.addDocked({ + xtype : 'toolbar', + items : this.getMenu() + }); + + + if (this.bbar == true){ + this.panel.addDocked({ + xtype : 'toolbar', + dock: 'bottom', + items : [ + { + xtype: 'numberfield', + id: 'main_field_start', + fieldLabel: 'Range from', + width: 170, + labelWidth : 70, + value: 0, + minValue: 0 + }, + { + xtype: 'numberfield', + id: 'main_field_end', + fieldLabel: 'to', + width: 130, + labelWidth : 30, + value: 0, + minValue: 0 + }, + { + xtype: 'button', + text: 'Go', + handler: function () { + var start = parseFloat(Ext.getCmp("main_field_start").getValue()); + var end = parseFloat(Ext.getCmp("main_field_end").getValue()); + + if (start < 0) { + start = 0; + } + if (end < 0) { + end = 0; + } + if (start > end) { + var aux = end; + end = start; + start = aux; + } + + _this.dygraphObject.dygraph.updateOptions({ isZoomedIgnoreProgrammaticZoom: true, dateWindow: [start, end] }); + } } + ] + }); + } +}; - } catch (e) { - } - } - } - } +HPLCGraph.prototype.getPanel = function () { + this.panel = Ext.create('Ext.panel.Panel', { + padding : this.plotPanelPadding, + width : this.width + 4 * this.plotInnerPanelPadding, + height : this.height + 4 * this.plotInnerPanelPadding, + items : [ { + html : "", + id : this.id, + width : this.width, + height : this.height + } ] }); - return this.grid; + return this.panel; }; -/** Method for testing * */ -MeasurementGrid.prototype.input = function() { - var experiment = DATADOC.getExperiment_10(); - var measurements = DATADOC.getMeasurements_10(); - var proposal = DATADOC.getProposal_10(); - return { - experiment : experiment, - measurements : measurements, - proposal : proposal - }; +HPLCGraph.prototype.input = function () { + return DATADOC.getHPLCData(); }; -MeasurementGrid.prototype.test = function(targetId) { - var measurementGrid = new MeasurementGrid({ - tbar : true - - }); - BIOSAXS.proposal = new Proposal(measurementGrid.input().proposal); - var panel = measurementGrid.getPanel(measurementGrid.input().measurements, new ExperimentList([ new Experiment(measurementGrid.input().experiment) ])); - panel.render(targetId); +HPLCGraph.prototype.getDataByFrameNumber = function (frameNumber) { + var data = {}; + data.frameNumber = frameNumber; + for (var key in this.hplcData){ + data[this.hplcData[key].label] = this.hplcData[key].data[frameNumber]; + } + console.log(data); + return data; }; - -/** - * A shipment may contains one or more cases where stock solutions and sample - * plates are stored - * - * @height - * @btnEditVisible - * @btnRemoveVisible - * - * #onEditButtonClicked - */ -function MolarityGrid(args) { - this.height = 100; - this.width = 100; - if (args != null) { - if (args.height != null) { - this.height = args.height; - } - if (args.width != null) { - this.width = args.width; + +HPLCGraph.prototype.test = function (targetId) { + var mainPlotPanel = new HPLCGraph({ + title : 'I0', + width : 800, + height : 400, + plots : { + "I0" : true, + "Rg" : true, + "Mass" : true + }, + xlabel : "HPLC Frames", + scaled : this.scaled, + interactionModel : { + 'dblclick' : function (event, g, context) { + } } - } + }); + mainPlotPanel.getPanel().render(targetId); + mainPlotPanel.loadData(mainPlotPanel.input()); - var _this = this; - - this.molarityForm = new MolarityForm({height : 180, width : 455}); +}; - this.molarityForm.onSave.attach(function(sender){ - _this.molarityWindow.destroy(); - _this.updateProposal(); - - }); - - this.molarityForm.onClose.attach(function(sender){ - _this.molarityWindow.destroy(); - - }); + +function MergesHPLCGraph(args) { + HPLCGraph.prototype.constructor.call(this, args); - /** Events * */ - this.onEditButtonClicked = new Event(this); +// this.peakColors = ["#00FB42", "#00BA31", "#007C21", "#003E10"]; + this.peakColors = ["#DEBD00", "#6D9100", "#872900", "#0092CC"]; } -MolarityGrid.prototype._getColumns = function() { - return [ { - text : 'Subunit', - columns : [ { - text : "Acronym", - width : 100, - hidden : false, - dataIndex : 'acronym', - sortable : true - }, { - text : "Name", - width : 125, - hidden : false, - dataIndex : 'name', - sortable : true - }, { - text : "MM Est.", - width : 100, - dataIndex : 'molecularMass', - sortable : true, - renderer : function(grid, cls, record){ - return BUI.formatValuesUnits(record.data.molecularMass , "Da", 10, 2); - - } - } ] - }, { -// text : "Number
in assymmetric units", - text : "Ratio", - width : 100, - dataIndex : 'ratio', - tooltip : 'Number of times the subunit is present in the macromolecule', - sortable : true - }, { - id : this.id + 'MOLARITY_REMOVE', - flex : 0.1, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - return BUI.getRedButton('REMOVE'); - } - } ]; -}; -MolarityGrid.prototype._openMolarityWindow = function() { - this.molarityWindow = Ext.create('Ext.window.Window', { - title : 'Molarity', - height : 220, - width : 500, - modal : true, - items : [this.molarityForm.getPanel() ] - }).show(); -}; +MergesHPLCGraph.prototype.scaledData = HPLCGraph.prototype.scaledData; +MergesHPLCGraph.prototype.divideValuesByMax = HPLCGraph.prototype.divideValuesByMax; +MergesHPLCGraph.prototype.getMaxAndMinValue = HPLCGraph.prototype.getMaxAndMinValue; +MergesHPLCGraph.prototype.getPoint = HPLCGraph.prototype.getPoint; +MergesHPLCGraph.prototype.reloadData = HPLCGraph.prototype.reloadData; +MergesHPLCGraph.prototype._renderDygraph = HPLCGraph.prototype._renderDygraph; +MergesHPLCGraph.prototype.loadData = HPLCGraph.prototype.loadData; +MergesHPLCGraph.prototype.getPanel = HPLCGraph.prototype.getPanel; +MergesHPLCGraph.prototype.getDataByFrameNumber = HPLCGraph.prototype.getDataByFrameNumber; -MolarityGrid.prototype._getButtons = function() { - var _this = this; - return [ { - text : 'Add subunit', - icon : '../images/add.png', - handler : function() { - _this._openMolarityWindow(); + +MergesHPLCGraph.prototype.setPeaks = function (data) { + this.peaks = data; + /** get size of peaks **/ + this.peakKeys = []; + this.colorPeak = {}; + var colorCount = 1; + for (var key in this.peaks) { + if (this.peaks.hasOwnProperty(key)) { + var color = this.peakColors[colorCount % this.peakColors.length]; + colorCount = colorCount + 1; + this.peakKeys.push(key); + this.colorPeak[key] = color; } - }]; + } + this.peakKeys.sort(); }; -MolarityGrid.prototype.updateProposal = function() { +MergesHPLCGraph.prototype.getMenu = function () { var _this = this; - this.panel.setLoading(); - BIOSAXS.proposal.onInitialized.attach(function() { - if (BIOSAXS.proposal != null) { - var macromolecules = BIOSAXS.proposal.macromolecules; - for (var i = 0; i < macromolecules.length; i++) { - - if (macromolecules[i].macromoleculeId == _this.macromolecule.macromoleculeId) { - _this.refresh(macromolecules[i]); - _this.panel.setLoading(false); + /** Actions buttons **/ + var actions = []; + + function toggle(item, pressed) { + if (pressed) { + _this.plots[item.param] = true; + } else { + delete _this.plots[item.param]; + } + _this.reloadData(_this.hplcData); + } + + + /** Toolbar for peaks Average **/ + if (this.peaks != null) { + var items = []; + for (var i = 0; i < this.peakKeys.length; i++) { + var color = this.colorPeak[this.peakKeys[i]]; + items.push({ + text: "Peak #" + i + " " + this.peakKeys[i].replace("- ", " to #").replace(".0", "").replace(".0", "") + "", + peakid : this.peakKeys[i], + checked: false, + checkHandler: function (sender, pressed) { + var item = new Object(); + item.param = sender.peakid; + toggle(item, pressed); } - } + }); } - }); - BIOSAXS.proposal.init(); -}; - + + var menu = Ext.create('Ext.menu.Menu', { + id: 'mainMenu', + style: { + overflow: 'visible' + }, + items: items + }); + var tb = Ext.create('Ext.toolbar.Toolbar'); + tb.add({ + text: 'Peaks Avg.', + menu: menu + }); + actions.push(tb); + } -MolarityGrid.prototype.getPanel = function() { - var _this = this; + - this.molarityStore = Ext.create('Ext.data.Store', { - fields : [ 'acronym', 'ratio', 'comments', 'stoichiometryId', 'name', 'molecularMass' ], - sorters : { - property : 'ratio', - direction : 'DESC' + for (var i = 0; i < this.hplcData.length; i++) { + if (this.hplcData[i].showOnMenu != false) { + var param = this.hplcData[i].param; + var style = "style='padding:0 0px 0 5px;'"; + actions.push({ + text : "
" + BUI.getRectangleColorDIV(this.hplcData[i].color, 10, 10) + " " + this.hplcData[i].label + "
", + id : _this.id + param, + param : param, + enableToggle : true, + scope : this, + margin : 5, + toggleHandler : toggle, + pressed : (_this.plots[param] != null) + }); } - }); - - this.panel = Ext.create('Ext.grid.Panel', { - store : this.molarityStore, - height : this.height, - padding : 5, - columns : this._getColumns(), - listeners : { - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - - /** Remove entry * */ - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'MOLARITY_REMOVE') { - var dataAdapter = new BiosaxsDataAdapter(); - dataAdapter.onSuccess.attach(function(sender) { - _this.updateProposal(); - - }); - dataAdapter.removeStoichiometry(record.data.stoichiometryId); - _this.panel.setLoading("Removing Structure"); - } - } - }, - tbar : this._getButtons() - }); - return this.panel; -}; + } -MolarityGrid.prototype._prepareData = function(macromolecule) { - /** Return an array of [{ratio,acronym, stoichiometryId, name}] **/ - var data = []; - if (macromolecule.stoichiometry != null) { - for (var i = 0; i < macromolecule.stoichiometry.length; i++) { - var hostMacromolecule = BIOSAXS.proposal.getMacromoleculeById(macromolecule.stoichiometry[i].macromoleculeId); - data.push({ - ratio : macromolecule.stoichiometry[i].ratio, - acronym : hostMacromolecule.acronym, - comments : hostMacromolecule.comments, - molecularMass : hostMacromolecule.molecularMass, - stoichiometryId : macromolecule.stoichiometry[i].stoichiometryId, - name : hostMacromolecule.name - }); - } + actions.push("->"); + actions.push({ + text : "Save", + scope : this, + icon : '../images/save.gif', + handler : function (item, pressed) { + var largeImage = document.createElement("img"); + largeImage.style.display = 'block'; + largeImage.style.width = 200 + "px"; + largeImage.style.height = 200 + "px"; + largeImage.setAttribute('src', Dygraph.Export.asCanvas(this.dygraphObject.dygraph).toDataURL()); + window.open(Dygraph.Export.asCanvas(this.dygraphObject.dygraph).toDataURL(), 'Image', ''); } - return data; -}; + }); -MolarityGrid.prototype.refresh = function(macromolecule) { - if (macromolecule != null){ - this.molarityStore.loadData(this._prepareData(macromolecule)); - this.molarityForm.refresh(macromolecule); - this.macromolecule = macromolecule; - } + return actions; }; -MolarityGrid.prototype.input = function() { - return { - proposal : DATADOC.getProposal_10(), - dewars : DATADOC.getDewars_10() - }; +MergesHPLCGraph.prototype.input = function () { + return DATADOC.getScatteringHPLCFrameData(); }; -MolarityGrid.prototype.test = function(targetId) { - var MolarityGrid = new MolarityGrid({ - height : 150 +MergesHPLCGraph.prototype.test = function (targetId) { + var mainPlotPanel = new MergesHPLCGraph({ + title : 'Scattering', + width : this.plotWidth, + height : 500, + showRangeSelector : false, + xParam : 0, + xlabel : "scattering_I", + plots : { + "scattering_I" : true, + "subtracted_I" : true, + "buffer_I" : true + } }); - BIOSAXS.proposal = new Proposal(MolarityGrid.input().proposal); - var panel = MolarityGrid.getPanel(MolarityGrid.input().dewars); - panel.render(targetId); - + mainPlotPanel.getPanel().render(targetId); + mainPlotPanel.loadData(mainPlotPanel.input()); }; + + +function NetworkWidget(args) { + this.id = "NetworkViewer_" + Math.random().toString().replace(".", "_"); + + this.label = true; + if (args != null) { + if (args.targetId != null) { + this.targetId = args.targetId; + } + if (args.label != null) { + this.label = args.label; + } + } + + this.onVertexOver = new Event(this); + this.onVertexOut = new Event(this); +} + +NetworkWidget.prototype.draw = function(dataset, formatter, layout) { + + this.graphCanvas = new GraphCanvas(this.id, document.getElementById(this.targetId), { + "labeled" : this.label, + "multipleSelectionEnabled" : false, + "draggingCanvasEnabled" : false + }); + this.graphCanvas.draw(dataset, formatter, layout); + + var _this = this; + this.graphCanvas.onVertexOver.attach(function(sender, nodeId) { + _this.onVertexOver.notify(nodeId); + }); + + this.graphCanvas.onVertexOut.attach(function(sender, nodeId) { + _this.onVertexOut.notify(nodeId); + }); +}; + +/** SELECT VERTICES BY NAME * */ +NetworkWidget.prototype.selectVertexByName = function(vertexName) { + var vertices = this.getDataset().getVertexByName(vertexName); + if (vertices != null) { + for ( var nodeId in vertices) { + if (vertices.hasOwnProperty(nodeId)) { + var vertexId = vertices[nodeId].getId(); + this.selectVertexById(vertexId); + } + } + } +}; + +NetworkWidget.prototype.selectVerticesByName = function(verticesName) { + for ( var i = 0; i < verticesName.length; i++) { + this.selectVertexByName(verticesName[i]); + } +}; + +/** SELECT VERTICES BY ID * */ +NetworkWidget.prototype.selectVertexById = function(vertexId) { + this.graphCanvas.selectNode(vertexId); + this.blinkVertexById(vertexId); +}; + +NetworkWidget.prototype.selectVerticesById = function(verticesId) { + for ( var i = 0; i < verticesId.length; i++) { + this.selectVertexById(verticesId[i]); + } +}; + +/** VECINDARIO * */ +NetworkWidget.prototype.selectNeighbourhood = function() { + this.selectEdgesFromVertices(); + this.selectAdjacent(); +}; +/** DESELECT * */ +NetworkWidget.prototype.deselectNodes = function() { + this.graphCanvas.deselectNodes(); +}; + +/** SELECT ALL NODES * */ +NetworkWidget.prototype.selectAllNodes = function() { + this.getGraphCanvas().selectAllNodes(); +}; + +/** SELECT EVERYTHING * */ +NetworkWidget.prototype.selectAll = function() { + this.getGraphCanvas().selectAll(); +}; + +/** SELECT ALL EDGES * */ +NetworkWidget.prototype.selectAllEdges = function() { + this.getGraphCanvas().selectAllEdges(); +}; + +/** ZOOM * */ +NetworkWidget.prototype.setScale = function(value) { + this.graphCanvas.setScale(value); +}; + +NetworkWidget.prototype.getScale = function() { + return this.graphCanvas.getScale(value); +}; + +/** SELECT ADJACENT VERTICES FROM SELECTED VERTICES * */ +NetworkWidget.prototype.selectAdjacent = function() { + var selectedVertices = this.getGraphCanvas().getSelectedVertices(); + var edges = []; + for ( var i = 0; i < selectedVertices.length; i++) { + edges = edges.concat(this.getGraphCanvas().getDataset().getVertexById(selectedVertices[i]).getEdges()); + } + var vertices = []; + for ( i = 0; i < edges.length; i++) { + vertices.push(edges[i].getNodeSource().getId()); + vertices.push(edges[i].getNodeTarget().getId()); + } + + this.selectVerticesById(vertices); +}; + +/** SELECT EDGES FROM SELECTED VERTICES * */ +NetworkWidget.prototype.selectEdgesFromVertices = function() { + var selectedVertices = this.getGraphCanvas().getSelectedVertices(); + var edges = []; + for ( var i = 0; i < selectedVertices.length; i++) { + edges = edges.concat(this.getGraphCanvas().getDataset().getVertexById(selectedVertices[i]).getEdges()); + } + var edgesId = []; + for ( i = 0; i < edges.length; i++) { + edgesId.push(edges[i].getId()); + } + this.getGraphCanvas().selectEdges(edgesId); +}; + +/** BLINKING * */ +NetworkWidget.prototype.blinkVertexById = function(vertexId) { + this.graphCanvas.blinkVertexById(vertexId); +}; + +/** COMPONENTE CONEXA DE LOS NODOS SELECCIONADOS * */ +NetworkWidget.prototype.selectConnectedComponent = function() { + var elements = this.getConnectedComponent(); + this.selectVerticesById(elements.nodes); + this.graphCanvas.selectEdges(elements.edges); +}; + +NetworkWidget.prototype.getConnectedComponent = function() { + var nodosVisitados = {}; + var aristasVisitadas = {}; + var arrNodos = []; + var arrAristas = []; + var selectedGraphNodesId = this.getGraphCanvas().getSelectedVertices(); + for ( var i = 0; i < selectedGraphNodesId.length; i++) { + this.visitNode(selectedGraphNodesId[i], nodosVisitados, aristasVisitadas, arrNodos, arrAristas); + } + return { + nodes : arrNodos, + edges : arrAristas + }; +}; + +NetworkWidget.prototype.visitNode = function(nodeId, nodosVisitados, aristasVisitadas, arrNodos, arrAristas) { + nodosVisitados[nodeId] = true; + arrNodos.push(nodeId); + var nodeEdges = this.getDataset().getVertexById(nodeId).getEdges(); + for ( var j = 0; j < nodeEdges.length; j++) { + var edge = nodeEdges[j]; + var edgeId = edge.getId(); + if (aristasVisitadas[edgeId] == null) { + aristasVisitadas[edgeId] = true; + arrAristas.push(edgeId); + var nodeTargetId = edge.getNodeTarget().getId(); + if (nodosVisitados[nodeTargetId] == null) { + this.visitNode(nodeTargetId, nodosVisitados, aristasVisitadas, arrNodos, arrAristas); + } + var nodeSourceId = edge.getNodeSource().getId(); + if (nodosVisitados[nodeSourceId] == null) { + this.visitNode(nodeSourceId, nodosVisitados, aristasVisitadas, arrNodos, arrAristas); + } + } + } +}; + +/** COLLAPSE SELECTED VERTICES * */ +NetworkWidget.prototype.collapse = function() { + var selectedVertices = this.getGraphCanvas().getSelectedVertices(); + var xMin = -Infinity; + var xMax = Infinity; + var yMin = -Infinity; + var yMax = Infinity; + + for ( var i = 0; i < selectedVertices.length; i++) { + var vertex = this.getGraphCanvas().getLayout().getNodeById(selectedVertices[i]); + if (xMin < vertex.x) { + xMin = vertex.x; + } + if (xMax > vertex.x) { + xMax = vertex.x; + } + if (yMin < vertex.y) { + yMin = vertex.y; + } + if (yMax > vertex.y) { + yMax = vertex.y; + } + } + + var centerX = xMin - xMax; + var centerY = yMin - yMax; + var radius = (xMax - xMin) / 4; + + var count = selectedVertices.length; + var verticesCoordinates = []; + + for ( i = 0; i < selectedVertices.length; i++) { + x = centerX + radius * Math.sin(i * 2 * Math.PI / count); + y = centerY + radius * Math.cos(i * 2 * Math.PI / count); + verticesCoordinates.push({ + 'x' : x, + 'y' : y + }); + } + + for ( i = 0; i < selectedVertices.length; i++) { + this.getGraphCanvas().getLayout().getNodeById(selectedVertices[i]).setCoordinates(verticesCoordinates[i].x, verticesCoordinates[i].y); + } +}; +/** SETTER FONT SIZE * */ +NetworkWidget.prototype.setVerticesFontSize = function(value) { + for ( var nodeId in this.getDataset().getVertices()) { + if (this.getDataset().getVertices().hasOwnProperty(nodeId)) { + this.getFormatter().getVertexById(nodeId).getDefault().setFontSize(value); + } + } +}; + +/** GETTERS * */ +NetworkWidget.prototype.getFormatter = function() { + return this.getGraphCanvas().getFormatter(); +}; +NetworkWidget.prototype.getLayout = function() { + return this.getGraphCanvas().getLayout(); +}; + +NetworkWidget.prototype.getDataset = function() { + return this.getGraphCanvas().getDataset(); +}; + +NetworkWidget.prototype.getGraphCanvas = function() { + return this.graphCanvas; +}; + +RangeWhiskerGraph.prototype.cleanArray = GenericGraph.prototype.cleanArray; +RangeWhiskerGraph.prototype.plotAxes = GenericGraph.prototype.plotAxes; +RangeWhiskerGraph.prototype.plotRuler = GenericGraph.prototype.plotRuler; +RangeWhiskerGraph.prototype.drawSVGVerticalText = GenericGraph.prototype.drawSVGVerticalText; +RangeWhiskerGraph.prototype.getClassColor = GenericGraph.prototype.getClassColor; +RangeWhiskerGraph.prototype.getDimensions = GenericGraph.prototype.getDimensions; +RangeWhiskerGraph.prototype.calculate = GenericGraph.prototype.calculate; +RangeWhiskerGraph.prototype.getMedian = GenericGraph.prototype.getMedian; +RangeWhiskerGraph.prototype.pointToPixel = GenericGraph.prototype.pointToPixel; +RangeWhiskerGraph.prototype.maxValueWhisker = GenericGraph.prototype.maxValueWhisker; +RangeWhiskerGraph.prototype.refresh = GenericGraph.prototype.refresh; + /** - * Given data analysis parsed with ResultsAssemblyWidget makes a selector grid with buffer/protein - **/ -function SpecimenSelectorResultGrid() { - this.id = BUI.id(); -} + * Subclass of GenericGraph + * + * @plotHorizontalByCluster + */ +function RangeWhiskerGraph(args) { + this.maxBoxWidth = 25; -SpecimenSelectorResultGrid.prototype._prepareData = function(data) { - var parsed = []; - for ( var i = 0; i < data.length; i++) { - var row = data[i]; - for ( var j = 0; j < row.conditions.length; j++) { - parsed.push({ - bufferId : row.conditions[j].bufferId, - macromoleculeId : row.macromoleculeId, - macromoleculeAcronym : BIOSAXS.proposal.getMacromoleculeById(row.macromoleculeId).acronym, - bufferAcronym : BIOSAXS.proposal.getBufferById(row.conditions[j].bufferId).acronym - }); - } + if (args == null) { + args = {}; } - return parsed; -}; - -SpecimenSelectorResultGrid.prototype.refresh = function(data) { - this.store.loadData(this._prepareData(data)); -}; - -SpecimenSelectorResultGrid.prototype.getPanel = function(data) { - var _this = this; - this.store = Ext.create('Ext.data.Store', { - fields : [ 'macromoleculeId', 'bufferId', 'macromoleculeAcronym', 'bufferAcronym', 'concentration' ], - data : this._prepareData(data), - groupField : 'macromoleculeAcronym' - }); + args.plotHorizontalByCluster = false; - this.store.sort('concentration'); - this.grid = Ext.create('Ext.grid.Panel', { - id : this.id, - store : this.store, - width : this.width, - height : this.height, - maxHeight : this.maxHeight, - border : 1, - features : [ { - ftype : 'grouping', - groupHeaderTpl : '{name}', - hideGroupedHeader : true, - startCollapsed : false - } ], - selModel : Ext.create('Ext.selection.CheckboxModel', { - allowDeselect : true, - mode : 'MULTI', - listeners : { - selectionchange : function(sm, selections) { - _this.selected = []; - for ( var i = 0; i < selections.length; i++) { - _this.selected.push(selections[i].raw); - } - } - } - }), - margin : 10, - sortableColumns : true, - columns : [ { - text : 'Macromolecule', - dataIndex : 'macromoleculeAcronym', - flex : 1 - }, { - text : '', - dataIndex : 'bufferId', - width : 20, - hidden : false, - renderer : function(val, y, sample) { - return BUI.getRectangleColorDIV(BIOSAXS.proposal.bufferColors[val], 10, 10); - } - }, { - text : 'Buffer', - dataIndex : 'bufferAcronym', - flex : 1 - }, { - text : 'Concentration', - dataIndex : 'concentration', - flex : 1, - renderer : function(val, y, sample) { - return val + " mg/ml"; - } - } ] - }); + GenericGraph.call(this, args); - /** Adding the tbar **/ - if (this.tbar) { - this.grid.addDocked({ - xtype : 'toolbar', - items : this.getTbar() - }); + if (args.maxBoxWidth != null) { + this.maxBoxWidth = args.maxBoxWidth; } - return this.grid; -}; +} -SpecimenSelectorResultGrid.prototype.input = function() { - return { - data : new ResultsAssemblyGrid()._prepareData(new ResultsAssemblyGrid().input().data), - proposal : new ResultsAssemblyGrid().input().proposal - }; +RangeWhiskerGraph.prototype.refresh = function(data) { + document.getElementById(this.targetId).innerHTML = ""; + this.draw(this.targetId, data); }; -SpecimenSelectorResultGrid.prototype.test = function(targetId) { - var specimenSelectorResultGrid = new SpecimenSelectorResultGrid(); - BIOSAXS.proposal = new Proposal(specimenSelectorResultGrid.input().proposal); - var panel = specimenSelectorResultGrid.getPanel(specimenSelectorResultGrid.input().data); - panel.render(targetId); -}; +RangeWhiskerGraph.prototype.isNumber = function(value) { + if (value == "") + return false; -/** - * Show all buffer conditions for each macromolecules pointing out the measurements quality - * - * @height - * @maxHeight - * @width - * @searchBar - * @tbar - * @btnResultVisible - * - * #onClick - */ -function ResultsAssemblyGrid(args) { - this.height = 500; - this.id = BUI.id(); - this.maxHeight = this.height; + var d = parseInt(value); + if (!isNaN(d)) + return true; + else + return false; - this.width = 900; - this.searchBar = false; - this.tbar = false; - this.btnResultVisible = false; +}; - /** For processing **/ - this.processed = {}; - this.renderedPlotIndex = 0; +/** + There are several different methods for calculating quartiles.[1] This calculator uses a method described by Moore and McCabe to find quartile values. + The same method also used by The TI-83 to calculate quartile values. + With this method, the first quartile is the median of the numbers below the median, the third quartile is the median of the numbers above the median. - this.plotWidth = 210; - this.plotHeight = 80; + http://www.miniwebtool.com/quartile-calculator/ + http://www.alcula.com/calculators/statistics/box-plot/ - /** Colors **/ - this.validColor = BUI.getValidColor(); - this.warningColor = BUI.getWarningColor(); - this.notValidColor = BUI.getErrorColor(); + **/ +RangeWhiskerGraph.prototype.getQ1 = function(array) { + array = array.slice(0, array.length / 2); + return this.getMedian(array); +}; - /** Show warning if guinier quality less than **/ - this.guinierQuality = BUI.getQualityThreshold(); - this.framePercentageThreshold = BUI.getRadiationDamageThreshold(); +RangeWhiskerGraph.prototype.getQ3 = function(array) { + array = array.slice((array.length + 1) / 2); + return this.getMedian(array); - if (args != null) { - if (args.height != null) { - this.height = args.height; - this.maxHeight = this.height; - } - if (args.maxHeight != null) { - this.maxHeight = args.maxHeight; - } - if (args.width != null) { - this.width = args.width; - } - if (args.searchBar != null) { - this.searchBar = args.searchBar; +}; + +RangeWhiskerGraph.prototype.getQ2 = function(array) { + return this.getMedian(array); +}; + +RangeWhiskerGraph.prototype.getBelowOutliers = function(belowLimit, array) { + var points = []; + for ( var i = 0; i < array.length; i++) { + if (array[i] <= belowLimit) { + points.push(array[i]); } + } + return points; +}; - if (args.tbar != null) { - this.tbar = args.tbar; +RangeWhiskerGraph.prototype.getAboveOutliers = function(aboveLimit, array) { + var points = []; + for ( var i = 0; i < array.length; i++) { + if (array[i] >= aboveLimit) { + points.push(array[i]); } - if (args.btnResultVisible != null) { - this.btnResultVisible = args.btnResultVisible; + } + return points; +}; + +RangeWhiskerGraph.prototype.minValueWhisker = function(belowLimit, q1, array) { + var points = []; + + for ( var i = 0; i < array.length; i++) { + if ((array[i] < q1) && (array[i]) > belowLimit) { + points.push(array[i]); } + } + if (points.length > 0) { + points.sort(function(a, b) { + return a - b; + }); + return points[0]; } + return null; +}; - this.onClick = new Event(); -} +//RangeWhiskerGraph.prototype.maxValueWhisker = function(aboveLimit, q3, array){ +// var points = []; +// for (var i = 0; i < array.length; i++){ +// if ((array[i] > q3) && (array[i]) <= aboveLimit){ +// points.push(array[i]); +// } +// } +// if (points.length > 0){ +// points.sort(function(a, b){return a - b;}); +// return points[points.length - 1]; +// } +// return null; +//}; -ResultsAssemblyGrid.prototype.edit = function(macromoleculeId) { - var _this = this; - var window = new MacromoleculeWindow(); - window.onSuccess.attach(function(sender, proposal) { - _this.store.loadData(_this._prepareData(BIOSAXS.proposal.getMacromolecules())); - }); - window.draw(BIOSAXS.proposal.getMacromoleculeById(macromoleculeId)); +RangeWhiskerGraph.prototype.drawPoints = function(boxProperties) { + if (this.plotPoints) { + for ( var i = 0; i < boxProperties.values.length; i++) { + var value = boxProperties.values[i]; + var toPixel = this.pointToPixel(value, boxProperties); + SVG.drawCircle(boxProperties.x, toPixel, this.pointRadius, this.svg, + [ + [ "fill", "green" ], [ "fill-opacity", this.fillOpacityPoint ], [ 'stroke-opacity', this.strokeOpacityPoint ], + [ "stroke", "black" ] ]); + } + } }; -ResultsAssemblyGrid.prototype.getTbar = function() { - var _this = this; - var actions = []; +RangeWhiskerGraph.prototype.plotRangeQ1Q3 = function(data, properties) { + var posX = this.left + this.rulerWidth; - actions.push(Ext.create('Ext.Action', { - icon : '../images/add.png', - text : 'Add Macromolecule', - disabled : false, - handler : function(widget, event) { - var window = new MacromoleculeWindow(); - window.onSuccess.attach(function(sender) { - _this.refresh(); - }); - window.draw({}); - } - })); + var boxBordersPointsQ1 = []; + var boxBordersPointsQ3 = []; + var Q2 = []; - actions.push(Ext.create('Ext.Action', { - icon : '../images/add.png', - text : 'Define an Assembly', - disabled : false, - handler : function(widget, event) { - var createAssemblywindow = new CreateAssemblyWindow(); - createAssemblywindow.onSaved.attach(function(evt, args) { - if (args.macromoleculeIds.length > 0) { - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, proposal) { - _this.refresh(); - }); - adapter.saveAssembly(args.assemblyId, args.macromoleculeIds); + for ( var i = 0; i < data.clusters.length; i++) { + var cluster = data.clusters[i]; + /** inter cluster space **/ + posX = posX + this.interClustersSpace; - } + for ( var j = 0; j < cluster.classes.length; j++) { + var ratio = properties.width / (properties.xValues.range); + var coorX = (cluster.x - properties.xValues.min) * ratio + this.rulerWidth; + var boxProperties = { + name : cluster.classes[j].name, + values : cluster.classes[j].values, + minPoint : properties.minPoint, + maxPoint : properties.maxPoint, + x : coorX + this.left, + y : this.top, + width : properties.classWidth, + height : this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight + }; - }); - createAssemblywindow.draw(_this.experiment); - } - })); + var result = this.calculate(boxProperties.values); + var boxColor = this.getClassColor(boxProperties.name); - return actions; -}; + if (this.isNumber(result.Q1) && this.isNumber(result.Q3)) { + var x = boxProperties.x; + var y = this.pointToPixel(result.Q1, boxProperties); + if (boxBordersPointsQ1[cluster.classes[j].name] == null) { + boxBordersPointsQ1[cluster.classes[j].name] = []; + } + boxBordersPointsQ1[cluster.classes[j].name].push({ + x : x, + y : y + }); -ResultsAssemblyGrid.prototype.refresh = function() { - this.store.loadData(this._prepareData()); -}; + x = boxProperties.x; + y = this.pointToPixel(result.Q3, boxProperties); + if (boxBordersPointsQ3[cluster.classes[j].name] == null) { + boxBordersPointsQ3[cluster.classes[j].name] = []; + } + boxBordersPointsQ3[cluster.classes[j].name].push({ + x : x, + y : y + }); + } else { -ResultsAssemblyGrid.prototype.addCondition = function(record, data_parsed, i) { - function getCondition(record) { - return { - concentration : record.conc, - quality : record.quality, - bufferBeforeFramesMerged : record.bufferBeforeFramesMerged, - bufferAfterFramesMerged : record.bufferAfterFramesMerged, - framesCount : record.framesCount, - framesMerge : record.framesMerge - }; - } + if (this.isNumber(result.Q2)) { - if (data_parsed[i].conditions != null) { - var bufferFound = false; - for ( var index in data_parsed[i].conditions) { - condition = data_parsed[i].conditions[index]; + if (boxBordersPointsQ1[cluster.classes[j].name] == null) { + boxBordersPointsQ1[cluster.classes[j].name] = []; + } - if ((condition.macromoleculeId == record.macromoleculeId) && (condition.bufferId == record.bufferId)) { - data_parsed[i].conditions[index].concentrations.push(getCondition(record)); - bufferFound = true; + if (boxBordersPointsQ3[cluster.classes[j].name] == null) { + boxBordersPointsQ3[cluster.classes[j].name] = []; + } + + boxBordersPointsQ1[cluster.classes[j].name].push({ + x : boxProperties.x, + y : this.pointToPixel(result.Q2, boxProperties) + }); + boxBordersPointsQ3[cluster.classes[j].name].push({ + x : boxProperties.x, + y : this.pointToPixel(result.Q2, boxProperties) + }); + } } } - if (!bufferFound) { - data_parsed[i].conditions.push({ - macromoleculeId : record.macromoleculeId, - bufferId : record.bufferId, - concentrations : [ getCondition(record) ] - }); + } + for ( var classe in boxBordersPointsQ1) { + var points = boxBordersPointsQ1[classe]; + var pointsSVG = ""; + for (var k = 0; k < points.length; k++) { + pointsSVG = Number(points[k].x).toFixed(1) + "," + Number(points[k].y).toFixed(1) + " " + pointsSVG; + } + + points = boxBordersPointsQ3[classe]; + for (var z = points.length - 1; z >= 0; z--) { + pointsSVG = Number(points[z].x).toFixed(1) + "," + Number(points[z].y).toFixed(1) + " " + pointsSVG; } + + SVG.drawPoligon(pointsSVG, this.svg, [ + [ "fill", this.getClassColor(classe) ], [ "opacity", "0.3" ], [ "stroke", "black" ], [ "stroke-width", 1 ] ]); } }; -ResultsAssemblyGrid.prototype.process = function(record, data_parsed) { - if (this.processed[record.macromoleculeId] == null) { - this.processed[record.macromoleculeId] = true; - record.measurementCount = 1; - record.subtractionCount = 1; - record.averageCount = 1; - record.conditions = []; - data_parsed.push(record); - } +RangeWhiskerGraph.prototype.plotWhisters = function(data, properties) { + var colors = [ "yellow", "orange", "green" ]; - for ( var i = 0; i < data_parsed.length; i++) { - if (data_parsed[i].macromoleculeId == record.macromoleculeId) { - data_parsed[i].measurementCount = data_parsed[i].measurementCount + 1; + this.plotRangeQ1Q3(data, properties); + var Q2 = {}; - if (record.subtractionId != null) { - data_parsed[i].subtractionCount = data_parsed[i].subtractionCount + 1; - this.addCondition(record, data_parsed, i); - } + for ( var i = 0; i < data.clusters.length; i++) { + var cluster = data.clusters[i]; + for ( var j = 0; j < cluster.classes.length; j++) { + var ratio = properties.width / (properties.xValues.range); + var coorX = (cluster.x - properties.xValues.min) * ratio + this.left + this.rulerWidth - this.rulerStroke; + var boxProperties = { + name : cluster.classes[j].name, + values : cluster.classes[j].values, + minPoint : properties.minPoint, + maxPoint : properties.maxPoint, + x : coorX, + y : this.top, + width : properties.classWidth, + height : this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight + }; - if (record.framesMerge != null) { - data_parsed[i].averageCount = data_parsed[i].averageCount + 1; - } + this.drawPoints(boxProperties); - if (record.timeStart != null) { - if (data_parsed[i].timeStart != null) { - if (moment(data_parsed[i].timeStart).format("X") > moment(record.timeStart).format("X")) { - data_parsed[i].timeStart = record.timeStart; - } + /** PLOTTING Q2 **/ + var result = this.calculate(boxProperties.values); + var boxColor = this.getClassColor(boxProperties.name); + if (this.isNumber(result.Q2)) { + if (Q2[boxProperties.name] != null) { + SVG.drawLine(boxProperties.x, this.pointToPixel(result.Q2, boxProperties), Q2[boxProperties.name].x, Q2[boxProperties.name].y, + this.svg, [ [ "stroke", boxColor ], [ "stroke-width", "2" ] ]); + } + Q2[boxProperties.name] = { + x : boxProperties.x, + y : this.pointToPixel(result.Q2, boxProperties) } } } } - return data_parsed; - }; -ResultsAssemblyGrid.prototype._prepareData = function(data) { - var data_parsed = []; - for ( var i = 0; i < data.length; i++) { - data_parsed = this.process(data[i], data_parsed); - } - this.data = data_parsed; - return data_parsed; +RangeWhiskerGraph.prototype.draw = function(targetId, data) { + //this.calculate(data); + this.targetId = targetId; + var properties = (this.getDimensions(data)); + this.svg = SVG.createSVGCanvas(document.getElementById(this.targetId), [ [ "width", this.width ], [ "height", this.height ] ]); + this.plotAxes(properties); + this.plotWhisters(data, properties); }; -/** Given an array of conditions it returns distinct(concentrations) order by concentration and hash map with number of ocurrences**/ -ResultsAssemblyGrid.prototype.parseConcentrations = function(val, conditions, differentConcentration, quality) { - var conditions = []; - var differentConcentration = {}; - var quality = []; - for ( var i = 0; i < val.length; i++) { - var conc = Number(val[i].concentration).toFixed(1); - var quality = Number(val[i].quality).toFixed(2); - if (differentConcentration[conc] == null) { - differentConcentration[conc] = 0; - conditions.push({ - concentration : conc, - quality : [ quality ], - frames : [ { - bufferAfterFramesMerged : val[i].bufferAfterFramesMerged, - bufferBeforeFramesMerged : val[i].bufferBeforeFramesMerged, - framesMerge : val[i].framesMerge, - framesCount : val[i].framesCount - } ] - }); - } else { - /** Add quality **/ - for ( var j = 0; j < conditions.length; j++) { - if (conditions[j].concentration == conc) { - conditions[j].quality.push(quality); - conditions[j].frames.push({ - bufferAfterFramesMerged : val[i].bufferAfterFramesMerged, - bufferBeforeFramesMerged : val[i].bufferBeforeFramesMerged, - framesMerge : val[i].framesMerge, - framesCount : val[i].framesCount - }); - } - } - } +RangeWhiskerGraph.prototype.input = function() { + return DATADOC.getBoxWhikerData(); +}; - differentConcentration[conc] = differentConcentration[conc] + 1; - } - /** sorting concentrations **/ - conditions.sort(function(a, b) { - return a.concentration - b.concentration; +RangeWhiskerGraph.prototype.test = function(targetId) { + var plot = new RangeWhiskerGraph({ + targetId : targetId, + height : 350, + width : 450, + maxBoxWidth : 25 }); - return { - concentrations : conditions, - differentConcentration : differentConcentration - }; + plot.refresh(this.input()); }; + +StdDevDyGraph.prototype.dblclick = DygraphWidget.prototype.dblclick; +StdDevDyGraph.prototype._createHTLMWrapper = DygraphWidget.prototype._createHTLMWrapper; +StdDevDyGraph.prototype.draw = DygraphWidget.prototype.draw; -ResultsAssemblyGrid.prototype.getConditionWarnings = function(condition) { - - var withWarnings = 0; - - for ( var i = 0; i < condition.frames.length; i++) { - if (condition.quality[i] == null) { - withWarnings = withWarnings + 1; - continue; - } else { - if (Number(condition.quality[i]) < this.guinierQuality) { - withWarnings = withWarnings + 1; - continue; - } - } - - if (condition.frames[i].bufferBeforeFramesMerged / condition.frames[i].framesCount < this.framePercentageThreshold|| condition.frames[i].framesMerged / condition.frames[i].framesCount < this.framePercentageThreshold|| condition.frames[i].bufferAfterFramesMerged / condition.frames[i].framesCount < this.framePercentageThreshold) { - withWarnings = withWarnings + 1; - continue; - } +function StdDevDyGraph(targetId, args) { + this.scaled = false; + if (args == null) { + args = {}; } + args.customBars = true; + DygraphWidget.prototype.constructor.call(this, targetId, args); +} +StdDevDyGraph.prototype.input = function () { return { - withWarnings : withWarnings, - withoutWarnings : condition.frames.length - withWarnings + data : [ [ 1, [ 2, 3, 3.5 ], [ 4, 4.2, 5 ] ], [ 2, [ 5, 5.5, 5.7 ], [ 4, 4.2, 5 ] ] ], + colors : [ "blue", "red" ], + labels : [ "", 'data1', 'data2' ] }; }; -ResultsAssemblyGrid.prototype.getFrameHTMLTable = function(warnings) { - var html = ""; - if (warnings.withWarnings > 0) { - html = html + "
" + warnings.withWarnings + - "x
"; - } - - if (warnings.withoutWarnings > 0) { - html = html + "
" + warnings.withoutWarnings + - "x
"; - } - return html; -}; +StdDevDyGraph.prototype.test = function (targetId) { + var dygraphObject = new StdDevDyGraph(targetId, { + width : 500, + height : 400, + xlabel : "xLabel", + showRangeSelector : false + }); -ResultsAssemblyGrid.prototype.createConcentrationRow = function(numberOcu, condition, warnings){ - var html = ""; - if (numberOcu > 1){ - html = html + "" +numberOcu + "x " + BUI.formatConcentration(condition.concentration); - } - else{ - html = html + BUI.formatConcentration(condition.concentration); - } - html = html + ""; - html = html + this.getFrameHTMLTable(warnings); + ""; - html = html + ""; - return html; + dygraphObject.draw(dygraphObject.input().data, dygraphObject.input().colors, dygraphObject.input().labels); }; + + + +function AbinitioGrid(args) { + this.height = null; + this.width = null; + this.id = BUI.id(); + + if (args != null) { + if (args.height != null) { + this.height = args.height; + + if (args.width != null) { + this.width = args.width; + } + } + } + + this.onSelected = new Event(this); +}; + + +AbinitioGrid.prototype.refresh = function(subtractions){ + this.store.loadData(this._prepareData(subtractions)); +}; + +AbinitioGrid.prototype._prepareData = function(subtractions){ + /** Parsing data * */ + var models = []; + for (var l = 0; l < subtractions.length; l++) { + var subtraction = subtractions[l]; + for (var k = 0; k < subtraction.substractionToAbInitioModel3VOs.length; k++) { + var data = subtraction.substractionToAbInitioModel3VOs[k].abinitiomodel3VO; + if (data.averagedModel != null) { + models.push(data.averagedModel); + models[models.length - 1].type = "Reference"; + } + + if (data.shapeDeterminationModel != null) { + models.push(data.shapeDeterminationModel); + models[models.length - 1].type = "Refined"; + } + + if (data.modelList3VO != null) { + if (data.modelList3VO.modeltolist3VOs != null) { + for (var i = 0; i < data.modelList3VO.modeltolist3VOs.length; i++) { + models.push(data.modelList3VO.modeltolist3VOs[i].model3VO); + models[models.length - 1].type = "Model"; + } + } + } + } + } + return models; +}; + +AbinitioGrid.prototype.getPanel = function(){ + var _this = this; + + + var modelFields = [ "modelId", "type", "chiSqrt", "dmax", "firFile", "logFile", "fitFile", "pdbFile", "rfactor", "rg", "volume" ]; + Ext.define('AbinitioModel', { + extend : 'Ext.data.Model', + fields : modelFields + + }); + + /** + * Store in Memory + */ + this.store = Ext.create('Ext.data.Store', { + model : 'AbinitioModel', + autoload : true, + groupField : 'type' + }); + + + var groupingFeature = Ext.create('Ext.grid.feature.Grouping',{ + groupHeaderTpl: '{name} ({rows.length} model{[values.rows.length > 1 ? "s" : ""]})', + startCollapsed: true, + collapsible : true + }); + + this.grid = Ext.create('Ext.grid.Panel', { + collapsible : false, + resizable : true, + features: [groupingFeature], + autoscroll : true, + multiSelect : true, + store : this.store, + height : this.height, + width : this.width, + margin : 10, + columns : [ { + text : "Type", + dataindex : "type", + hidden : true, + renderer : function(a, b, record) { + return record.data.type; + }, + flex : 1 + }, + { + text : "ModelId", + dataindex : "modelId", + hidden : true, + renderer : function(a, b, record) { + return record.data.modelId; + + }, + flex : 1 + }, + + { + text : "chiSqrt", + dataindex : "chiSqrt", + renderer : function(a, b, record) { + if (record.data.dmax != null) { + return BUI.formatValuesUnits(record.data.chiSqrt, "", 12, this.decimals); + } + + }, + flex : 1 + }, + { + text : "Dmax", + dataindex : "dmax", + renderer : function(a, b, record) { + if (record.data.dmax != null) { + return BUI.formatValuesUnits(record.data.dmax, "nm", 12, this.decimals); + } + + }, + flex : 1 + }, { + text : "rFactor", + dataindex : "rfactor", + hidden : true, + renderer : function(a, b, record) { + if (record.data.rfactor != null) { + return record.data.rfactor; + } + }, + flex : 1 + }, { + text : "Rg", + dataindex : "rg", + renderer : function(a, b, record) { + if (record.data.rg != null) { + return BUI.formatValuesUnits(record.data.rg, "nm", 12, this.decimals); + } + + }, + flex : 1 + }, + { + text : "Volume", + dataindex : "volume", + renderer : function(a, b, record) { + if (record.raw.volume != null){ + return BUI.formatValuesUnits(record.raw.volume, '') + " nm3"; + } + }, + flex : 1 + }, + { + text : "PDB", + dataindex : "pdbFile", + renderer : function(a, b, record) { + if (record.data.pdbFile != null){ + return record.data.pdbFile.split("/")[record.data.pdbFile.split("/").length - 1]; + } + }, + flex : 1 + }, { + text : "Fir", + dataindex : "firFile", + renderer : function(a, b, record) { + if (record.data.firFile != null){ + return record.data.firFile.split("/")[record.data.firFile.split("/").length - 1]; + } + }, + flex : 1 + }, { + text : "LOG", + dataindex : "logFile", + hidden : true, + renderer : function(a, b, record) { + if (record.data.logFile != null){ + return record.data.logFile.split("/")[record.data.logFile.split("/").length - 1]; + } + }, + flex : 1 + } + ], + viewConfig : { + enableTextSelection : true, + preserveScrollOnRefresh : true, + stripeRows : true, + listeners : { + 'celldblclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + }, + 'cellclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + var models = []; + for (var i = 0; i < grid.getSelectionModel().selected.items.length; i++) { + models.push(grid.getSelectionModel().selected.items[i].raw); + } + _this.onSelected.notify(models); + } + } + } + }); + return this.grid; + +}; + +function AdditiveGrid(args) { + this.onRemoveButtonClicked = new Event(this); +} -ResultsAssemblyGrid.prototype.getConditionHTMLTable = function(val, style, record) { - var maxNumberColumns = 2; - var html = "
"; - var nColumns = 0; - for ( var r = 0; r < val.length; r++) { - if (nColumns == maxNumberColumns) { - nColumns = 0; - html = html + ""; - } - html = html + ""; - nColumns = nColumns + 1; - } - html = html + "
"; - var value = val[r]; - - var bufferAcronym = (BIOSAXS.proposal.getBufferById(value.bufferId).acronym); - - var parsed = (this.parseConcentrations(value.concentrations)); - var conditions = parsed.concentrations; - var differentConcentration = parsed.differentConcentration; - - /** Checking warnings **/ - var warnings = []; - var concentrationValidPerconcentration = 0; - var measurements = 0; - for ( var i = 0; i < conditions.length; i++) { - measurements = measurements + conditions[i].frames.length; - var warning = this.getConditionWarnings(conditions[i]); - warnings.push(warning); - if (warning.withoutWarnings > 0) { - concentrationValidPerconcentration = concentrationValidPerconcentration + 1; - } - } - - this.validColor = '#E0F8E0'; - this.warningColor = '#F5DA81'; - this.notValidColor = '#F6CED8'; - - var color = this.warningColor; - if (concentrationValidPerconcentration > 2) { - color = this.validColor; - } - /** More measurement need to be done **/ - if (measurements < 3) { - color = this.notValidColor; - } - - html = html + ""; - html = html + ""; - for ( var i = 0; i < conditions.length; i++) { - html = html + this.createConcentrationRow(differentConcentration[conditions[i].concentration], conditions[i], warnings[i]); - } - - html = html + ""; - html = html + "
" + bufferAcronym.toUpperCase() + - "
"; - - html = html + "
"; - return html; +AdditiveGrid.prototype.getBuffer = function() { + return this.buffer; }; -ResultsAssemblyGrid.prototype._getTbar = function() { - function goTo(url) { - window.location = url; - } - +AdditiveGrid.prototype._getActions = function() { var _this = this; - return [ { - icon : '../images/application_view_list.png', - text : 'Multiple Select', - handler : function() { - var specimenSelectorResultGrid = new SpecimenSelectorResultGrid(); - var window = Ext.create('Ext.window.Window', { - title : 'Multiple select', - height : 600, - width : 600, - layout : 'fit', - items : [ specimenSelectorResultGrid.getPanel(_this.data) ], - buttons : [ { - text : 'Go', - handler : function() { - var array = []; - for ( var i = 0; i < specimenSelectorResultGrid.selected.length; i++) { - var row = specimenSelectorResultGrid.selected[i]; - array.push({ - macromoleculeId : row.macromoleculeId, - bufferId : row.bufferId - }); - } - goTo(BUI.getMacromoleculeResultsURLByMultipleSearch(array)); + /** Actions buttons **/ + var actions = []; - } - }, { - text : 'Cancel', - handler : function() { - window.close(); - } - } ] + actions.push(Ext.create('Ext.Action', { + icon : '../images/add.png', + text : 'Add', + disabled : true, + alwaysEnabled : true, + handler : function(widget, event) { + _this.buffer.bufferhasadditive3VOs.push(BIOSAXS_BEANS.getBufferhasAdditive3VO()); + _this.refresh(_this.buffer, _this.experiment); + } + })); - }).show(); + return actions; +}; +AdditiveGrid.prototype.refresh = function(buffer, experiment) { + this.buffer = buffer; + this.experiment = experiment; + if (buffer) { + if (buffer.bufferhasadditive3VOs) { + this.features = buffer.bufferhasadditive3VOs; } - } ]; + } + this.experiment = experiment; + this.store.loadData(this._prepareData(), false); }; -ResultsAssemblyGrid.prototype.getLegendPanel = function() { - return { - html : '
' + BUI.getRectangleColorDIV(this.validColor, 10, 10) + - 'Good quality measurements' + - BUI.getRectangleColorDIV(this.warningColor, 10, 10) + - 'Probably valid with manual processing' + - BUI.getRectangleColorDIV(this.notValidColor, 10, 10) + - 'More measurements need to be done
' - }; -}; -/** Returns the grid **/ -ResultsAssemblyGrid.prototype.getPanel = function(macromolecules) { - var _this = this; +AdditiveGrid.prototype.getAdditives = function() { + var additives = []; + for ( var i = 0; i < this.store.getCount(); i++) { + var bufferHasAdditive = BIOSAXS_BEANS.getBufferhasAdditive3VO(); + var data = this.store.getAt(i).getData(); - this.store = Ext.create('Ext.data.Store', { - fields : [ - 'macromoleculeId', 'macromoleculeAcronym', 'measurementCount', 'subtractionCount', 'averageCount', 'timeStart', 'concentrationArray', - 'bufferConditions', 'conditions' ], - data : this._prepareData(macromolecules) - }); + bufferHasAdditive.additive3VO.name = data.name; + bufferHasAdditive.additive3VO.comments = data.comments; + bufferHasAdditive.additive3VO.additiveType = data.additiveType; - this.store.sort('macromoleculeAcronym'); + bufferHasAdditive.bufferId = this.buffer.bufferId; + bufferHasAdditive.bufferHasAdditiveId = data.bufferHasAdditiveId; + bufferHasAdditive.quantity = data.quantity; + additives.push(bufferHasAdditive); + } - this.grid = Ext.create('Ext.grid.Panel', { - id : this.id, - title : 'Macromolecules', - store : this.store, - tbar : this._getTbar(), - bbar : [ this.getLegendPanel() ], - width : this.width, - height : this.height, - maxHeight : this.maxHeight, - sortableColumns : true, - columns : [ - { - text : '', - dataIndex : 'macromoleculeId', - width : 20, - hidden : false, - renderer : function(val, y, sample) { - return BUI.getRectangleColorDIV(BIOSAXS.proposal.macromoleculeColors[val], 10, 10); - } - }, - { - text : 'Macromolecule', - dataIndex : 'macromoleculeAcronym', - width : 200 + return additives; +}; + +AdditiveGrid.prototype._getFields = function(buffers) { + var columns = [ + + { + header : 'Name', + dataIndex : 'name', + type : 'string', + editor : { + allowBlank : true }, - { - text : 'Buffer Conditions', - dataIndex : 'conditions', - flex : 1, - renderer : function(val, style, record) { - return _this.getConditionHTMLTable(val, style, record); - } + flex : 1 + }, + { + header : 'Type', + name : 'additiveType', + dataIndex : 'additiveType', + editor : { + xtype : 'combobox', + typeAhead : true, + triggerAction : 'all', + selectOnTab : true, + store : BIOSAXS.proposal.getAdditiveTypes(), + lazyRender : true, + listClass : 'x-combo-list-small' }, - { - header : 'Average', - dataIndex : 'percentageCollected', - name : 'percentageCollected', - type : 'string', - hidden : true, - renderer : function(val, y, sample) { - return "
" + - BUI.getProgessBar((sample.raw.averageCount / sample.raw.measurementCount) * 100, sample.raw.averageCount + "/" + - sample.raw.measurementCount) + "
"; - }, - width : 100, - sorter : false + flex : 0.6 + }, + { + header : 'Quantity', + dataIndex : 'quantity', + name : 'quantity', + editor : { + allowBlank : true }, - { - header : 'Subtractions', - dataIndex : 'percentageCollected', - name : 'percentageCollected', - type : 'string', - hidden : true, - renderer : function(val, y, sample) { - return "
"+ BUI.getProgessBar((sample.raw.subtractionCount / sample.raw.measurementCount) * 100, sample.raw.subtractionCount + "/" + - sample.raw.measurementCount) + "
"; - }, - width : 100 - }, { - header : 'Date', - dataIndex : 'timeStart', - name : 'timeStart', - type : 'string', - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - if (record.raw.timeStart != null) { - return moment(record.raw.timeStart).format("MMM Do YY"); + type : 'string', + flex : 1 + }, + { + xtype : 'actioncolumn', + items : [ { + icon : '../images/cancel.png', + tooltip : 'Delete additive', + scope : this, + handler : function(grid, rowIndex, colIndex) { + if ((grid.getStore().getAt(rowIndex).data.bufferHasAdditiveId == null)|| (grid.getStore().getAt(rowIndex).data.bufferHasAdditiveId == "")) { + grid.getStore().removeAt(rowIndex); + } else { + this.onRemoveButtonClicked.notify({ + 'bufferId' : this.buffer.bufferId, + 'bufferHasAdditiveId' : this.store.getAt(rowIndex).data.bufferHasAdditiveId + }); } } - }, { - header : 'Download', - dataIndex : 'percentageCollected', - name : 'percentageCollected', - type : 'string', - renderer : function(val, y, sample) { - return BUI.getZipHTMLByMacromoleculeId(sample.raw.macromoleculeId); - }, - width : 100 - }, + } ] + } ]; + + return columns; +}; + +AdditiveGrid.prototype._prepareData = function() { + var data = []; + if (this.features == null) { + this.features = []; + } + for (var i = 0; i < this.features.length; i++) { + var object = this.features[i]; + object.name = this.features[i].additive3VO.name; + object.additiveType = this.features[i].additive3VO.additiveType; + object.comments = this.features[i].additive3VO.comments; + object.additiveId = this.features[i].additive3VO.additiveId; + data.push(object); + } + return data; +}; - { - id : 'btnResultVisible', - width : 85, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - return BUI.getGreenButton('GO'); - } - } ], +AdditiveGrid.prototype.getPanel = function(buffer, experiment) { + this.buffer = buffer; + this.features = buffer.bufferhasadditive3VOs; + this.experiment = experiment; + return this._renderGrid(); +}; + +AdditiveGrid.prototype.getStore = function() { + var _this = this; + var store = Ext.create('Ext.data.Store', { + fields : [ "name", "additiveType", "comments", "additiveId", "bufferHasAdditiveId", "quantity" ], + autoload : false, + data : this._prepareData(), + listeners : { + update : function(store, record) { + record.index = _this.grid.getSelectionModel().getCurrentPosition().row; + _this.buffer.bufferhasadditive3VOs[record.index].additive3VO.name = record.data.name; + _this.buffer.bufferhasadditive3VOs[record.index].additive3VO.additiveType = record.data.additiveType; + _this.buffer.bufferhasadditive3VOs[record.index].additive3VO.comments = record.data.comments; + _this.buffer.bufferhasadditive3VOs[record.index].quantity = record.data.quantity; + } + } + }); + + // store.sort('bufferHasAdditiveId', 'ASC'); + store.loadData(this._prepareData(), false); + return store; +}; + +AdditiveGrid.prototype._renderGrid = function() { + var _this = this; + this.store = this.getStore(); + + var cellEditing = Ext.create('Ext.grid.plugin.CellEditing', { + clicksToEdit : 1 + }); + + this.grid = Ext.create('Ext.grid.Panel', { + dockedItems : [ { + xtype : 'toolbar', + items : this._getActions() + } ], + store : this.store, + height : 230, + title : "Additives", + width : "100%", + columns : _this._getFields(), + plugins : [ cellEditing ], viewConfig : { stripeRows : true, listeners : { - afterrender : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - }, - celldblclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - _this.edit(record.data.macromoleculeId); - }, - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - if (grid.getGridColumns()[cellIndex].getId() == 'buttonEditMacromolecule') { - _this.edit(record.data.macromoleculeId); - } - if (grid.getGridColumns()[cellIndex].getId() == 'buttonRemoveMacromolecule') { - BUI.showBetaWarning(); - } - if (grid.getGridColumns()[cellIndex].getId() == 'btnResultVisible') { - window.location = BUI.getMacromoleculeResultsURL(record.data.macromoleculeId); - } + itemcontextmenu : function(view, rec, node, index, e) { + e.stopEvent(); + contextMenu.showAt(e.getXY()); + return false; } } + }, + selModel : { + mode : 'SINGLE' } }); - /** Adding the tbar **/ - if (this.tbar) { - this.grid.addDocked({ - xtype : 'toolbar', - items : this.getTbar() - }); - } return this.grid; }; -ResultsAssemblyGrid.prototype.input = function(targetId) { - return { - data : DATADOC.getData_3367(), - proposal : DATADOC.getProposal_3367() - }; +AdditiveGrid.prototype.input = function() { }; -ResultsAssemblyGrid.prototype.test = function(targetId) { - var grid = new ResultsAssemblyGrid({ - height : 600, - searchBar : false, - tbar : false, - btnResultVisible : true, - width : 1000 - }); - BIOSAXS.proposal = new Proposal(grid.input().proposal); - var panel = grid.getPanel(grid.input().data); +AdditiveGrid.prototype.test = function(targetId) { + var grid = new AdditiveGrid(); + var panel = grid.getPanel([]); panel.render(targetId); }; +/** AnalysisGrid **/ +function AnalysisGrid(args) { + var _this = this; -function RigidModelGrid(args) { - this.height = null; - this.width = null; this.id = BUI.id(); + if (Ext.get("mainPanel")){ + this.width = Ext.get("mainPanel").getWidth(); + } + else{ + this.width = this.maxWidth; + } + this.maxWidth = 1500; + + /** Visibles **/ + this.isGuinierTabVisible = true; + this.isGnomTabVisible = true; + this.isPorodTabVisible = true; + this.isScatteringPlotVisible = true; + this.isAbinitioTabVisible = true; + this.showButtonsVisible = true; + this.isI0Visible = true; + + this.margin = null; + this.grouped = true; + + this.hideNulls = false; + this.decimals = 4; + this.height = null; + this.sorters = [ { + property : 'conc', + direction : 'ASC' + } ]; if (args != null) { + if (args.grouped != null) { + this.grouped = args.grouped; + } + + if (args.showButtonsVisible != null) { + this.showButtonsVisible = args.showButtonsVisible; + } + if (args.isI0Visible != null) { + this.isI0Visible = args.isI0Visible; + } + if (args.sorters != null) { + this.sorters = args.sorters; + } + if (args.isScatteringPlotVisible != null) { + this.isScatteringPlotVisible = args.isScatteringPlotVisible; + } + if (args.isGuinierTabVisible != null) { + this.isGuinierTabVisible = args.isGuinierTabVisible; + } + if (args.isGnomTabVisible != null) { + this.isGnomTabVisible = args.isGnomTabVisible; + } + if (args.isPorodTabVisible != null) { + this.isPorodTabVisible = args.isPorodTabVisible; + } + if (args.hideNulls != null) { + this.hideNulls = args.hideNulls; + } if (args.height != null) { this.height = args.height; + } + if (args.width != null) { + this.width = args.width; + } + if (args.maxWidth != null) { + this.maxWidth = args.maxWidth; + } + } +} - if (args.width != null) { - this.width = args.width; +AnalysisGrid.prototype.refresh = function(data, args) { + this.store.loadData(this._prepareData(data), false); + if (args != null){ + if (args.experiment != null){ + this.experiment = args.experiment; + } + } +}; + +AnalysisGrid.prototype._getPorod = function() { + return { + text : 'Porod', + name : 'Porod', + columns : [ + { + text : 'Volume', + dataIndex : 'volumeEdna', + width : 75, + sortable : true, + hidden : !this.isPorodTabVisible, + renderer : function(val, y, sample) { + if (sample.raw.volume != null) + return BUI.formatValuesUnits(sample.raw.volume, '') + " nm3"; + } + }, + { + text : 'MM Vol. est.', + dataIndex : 'volumeEdna', + tooltip : '[Volume/2 - Volume/1.5] (Guinier)', + sortable : true, + width : 95, + hidden : !this.isPorodTabVisible, + renderer : function(val, y, sample) { + if (sample.raw.volume != null) + return Number(sample.raw.volume / 2).toFixed(1) + " - " + Number(sample.raw.volume / 1.5).toFixed(1)+ "kD"; + } + } ] + }; +}; + + +AnalysisGrid.prototype._getFramesColumn = function() { + var _this = this; + return { + text : 'Frames (Averaged/Total)', + dataIndex : 'datacollection', + name : 'datacollection', + sortable : true, + width : 150, + renderer : function(dataCollections, y, data) { + /** Bug of Webservices: frames count were swapped with frames averages **/ + if (data.raw.bufferAfterFramesCount){ + if (data.raw.bufferAfterFramesMerged){ + if (parseInt(data.raw.bufferAfterFramesMerged) > parseInt(data.raw.bufferAfterFramesCount)){ + var aux = parseInt(data.raw.bufferAfterFramesCount); + data.raw.bufferAfterFramesCount= data.raw.bufferAfterFramesMerged; + data.raw.bufferAfterFramesMerged = aux; + } + } + } + + if (data.raw.bufferBeforeFramesCount){ + if (data.raw.bufferBeforeFramesMerged){ + if (parseInt(data.raw.bufferBeforeFramesMerged) > parseInt(data.raw.bufferBeforeFramesCount)){ + var aux = parseInt(data.raw.bufferBeforeFramesCount); + data.raw.bufferBeforeFramesCount= data.raw.bufferBeforeFramesMerged; + data.raw.bufferBeforeFramesMerged = aux; + } + } + + } + + var bufferAcronym = data.raw.bufferAcronym; + var macromoleculeAcronym = data.raw.macromoleculeAcronym; + var bbmerges = data.raw.bufferBeforeFramesMerged; + var molmerges = data.raw.framesMerge; + var bamerges = data.raw.bufferAfterFramesMerged; + var totalframes = data.raw.framesCount; + var bufferId = data.raw.bufferId; + var macromoleculeId = data.raw.macromoleculeId; + var macromoleculeColor = null; + if (_this.experiment != null){ + macromoleculeColor = _this.experiment.macromoleculeColors[data.raw.macromoleculeId]; } - } - } - - this.onSelected = new Event(this); -} - - -RigidModelGrid.prototype.refresh = function(subtractions) { - var data = []; - if (subtractions != null){ - if (subtractions.length > 0){ - for (j in subtractions){ - var subtraction = subtractions[j]; - if (subtraction.rigidBodyModeling3VOs != null){ - for (i in subtraction.rigidBodyModeling3VOs){ - data.push(subtraction.rigidBodyModeling3VOs[i]); + + /** BUG in the database to be fixed **/ + try{ + if (totalframes != null){ + if(molmerges != null){ + if (parseFloat(totalframes) < parseFloat(molmerges)){ + var aux = totalframes; + totalframes = molmerges; + molmerges = aux; + } } } } + catch(e){ + + } + + return BUI.getHTMLTableForFrameAveraged(bufferAcronym, + macromoleculeAcronym, + bbmerges, + molmerges, + bamerges, + totalframes, + bufferId, + macromoleculeId, + macromoleculeColor); } - } - this.store.loadData(data); + }; }; -RigidModelGrid.prototype.getPanel = function() { +AnalysisGrid.prototype._getColumns = function() { var _this = this; - this.store = Ext.create('Ext.data.Store', { - fields : [ 'symmetry', 'subtractionId', 'subUnitConfigFilePath', 'rigidBodyModelingId', 'rigidBodyModelFilePath', 'logFilePath', 'fitFilePath', 'curveConfigFilePath', - 'crossCorrConfigFilePath', 'contactDescriptionFilePath' ], - data : [] - }); - - this.store.sort([ { - property : 'name', - direction : 'ASC' - } ]); + return [ + { + name : 'groupeField', + dataIndex : 'groupeField', + hidden : true - this.panel = Ext.create('Ext.grid.Panel', { - store : this.store, - width : this.width, - height : this.height, - margin : 10, - deferredRender : false, - columns : [ { - text : 'RBM', - dataIndex : 'rigidBodyModelFilePath', - hidden : false, - flex : 1, - renderer : function(val){ - return BUI.getFileName(val); - } - }, { - text : 'Sub Unit Conf.', - dataIndex : 'subUnitConfigFilePath', + }, + { + "header" : "subtractionId", hidden : true, - flex : 1, - renderer : function(val){ - return BUI.getFileName(val); + "dataIndex" : "subtractionId", + "name" : "subtractionId" + }, + { + header : "Macromolecule", + dataIndex : "macromoleculeAcronym", + name : "macromoleculeAcronym", + renderer : function(val, y, sample) { + return '
' + val + '
' + + BUI.formatValuesUnits(sample.raw.conc, "mg/ml", 10, this.decimals) + '
' + + BUI.formatValuesUnits(sample.raw.exposureTemperature, "C", 10, this.decimals) + '
' } - }, { - text : 'Log', - dataIndex : 'logFilePath', + }, + { + header : "Order", + dataIndex : "priorityLevelId", + name : "priorityLevelId", + hidden : true + }, + { + header : "Code", + dataIndex : "code", + name : "code", + hidden : true + }, + { + header : "Conc.", + dataIndex : "conc", + width : 80, + name : "conc", + type : "number", hidden : true, - flex : 1, - renderer : function(val){ - return BUI.getFileName(val); - } - }, { - text : 'Fit', - dataIndex : 'fitFilePath', - hidden : false, - flex : 1, - renderer : function(val){ - return BUI.getFileName(val); - } - }, { - text : 'Curve Conf.', - dataIndex : 'curveConfigFilePath', - hidden : false, - flex : 1, - renderer : function(val){ - return BUI.getFileName(val); + renderer : function(val, y, sample) { + return BUI.formatValuesUnits(val, "mg/ml", 10, this.decimals); } - }, { - text : 'Cross Corr.', - dataIndex : 'crossCorrConfigFilePath', - hidden : false, - flex : 1, - renderer : function(val){ - return BUI.getFileName(val); + }, + { + text : 'Scattering', + width : 100, + dataIndex : 'subtractionId', + name : 'subtractionId', + hidden : !this.isScatteringPlotVisible, + renderer : function(val, y, sample) { + var url = BUI.getURL() + '&type=scattering&subtractionId=' + sample.raw.subtractionId; + var event = "OnClick= window.open('" + url + "')"; + return ''; } - }, { - text : 'Contact Desc.', - dataIndex : 'contactDescriptionFilePath', + }, + { + text : 'Kratky', + width : 100, + dataIndex : 'subtractionId', hidden : true, - flex : 1, - renderer : function(val){ - return BUI.getFileName(val); + name : 'subtractionId', + renderer : function(val, y, sample) { + var url = BUI.getURL() + '&type=kratky&subtractionId=' + sample.raw.subtractionId; + var event = "OnClick= window.open('" + url + "')"; + return ''; } - } ], - - viewConfig : { - enableTextSelection : true, - preserveScrollOnRefresh : true }, - listeners : { - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - - }, - afterrender : function() { + this._getFramesColumn(), + { + text : 'File Name', + dataIndex : 'averageFilePath', + name : 'averageFilePath', + sortable : true, + width : 150, + hidden : true, + renderer : function(dataCollections, y, data) { + return BUI.getHTMLTableForPrefixes(data.raw.bufferBeforeAverageFilePath, data.raw.averageFilePath, + data.raw.bufferAfterAverageFilePath); } - } - }); - return this.panel; -}; + }, - -/** - * shows shipments - * - * @height - * @width - * @minHeight - * @btnEditVisible - */ -function ShipmentGrid(args) { - this.id = BUI.id(); - this.height = 100; - this.width = null; - this.minHeight = null; - this.btnEditVisible = true; + { + text : 'Guinier', + name : 'Guinier', + columns : [ + { + text : 'Rg', + dataIndex : 'rgGuinier', + name : 'rgGuinier', + hidden : !this.isGuinierTabVisible, + width : 75, + tooltip : 'In polymer physics, the radius of gyration is used to describe the dimensions of a polymer chain.', + sortable : true, + renderer : function(val, y, sample) { + if (sample.raw.rgGuinier != null) { + /** Show warning if rgGuinier and rgGnom differ more than 10% **/ + if (Math.abs(sample.raw.rgGuinier - sample.raw.rgGnom) > (sample.raw.rgGuinier * 0.1)) { + return "" + BUI.formatValuesUnits(sample.raw.rgGuinier, "") + ""; - if (args != null) { - if (args.height != null) { - this.height = args.height; - } - if (args.width != null) { - this.width = args.width; - } - if (args.minHeight != null) { - this.minHeight = args.minHeight; - } - if (args.btnEditVisible != null) { - this.btnEditVisible = args.btnEditVisible; - } - } -} + } + return BUI.formatValuesUnits(sample.raw.rgGuinier, "nm", 12, this.decimals); + } + } + }, + { + text : 'Points', + dataIndex : 'points', + sortable : true, + width : 100, + type : 'string', + hidden : !this.isGuinierTabVisible, + renderer : function(val, y, sample) { + if ((sample.raw.firstPointUsed == "") || (sample.raw.firstPointUsed == null)) + return; + return "" + sample.raw.firstPointUsed + " - " + sample.raw.lastPointUsed + " (" + + (sample.raw.lastPointUsed - sample.raw.firstPointUsed) + " )"; + } + }, + { + text : 'Quality', + dataIndex : 'quality', + hidden : !this.isGuinierTabVisible, + tooltip : 'Estimated data quality. 1.0 - means ideal quality, 0.0 - unusable data. In table format it is given in percent (100% - ideal quality, 0% - unusable data). Please note that this estimation is based only on the Guinier interval (very low angles).', + width : 60, + sortable : true, + renderer : function(val, y, sample) { + if (sample.raw.quality != null) { + val = sample.raw.quality; + if ((val != null) && (val != "")) { + return "" + (Number(val) * 100).toFixed(2) + " %"; + } + } + } + }, { + text : 'I(0)', + dataIndex : 'I0', + sortable : true, + hidden : !this.isI0Visible, + tooltip : 'Extrapolated scattering intensity at zero angle I(0) (forward scattering)', + width : 75, + type : 'string', + renderer : function(val, y, sample) { + if (sample.raw.I0 != null) { + return BUI.formatValuesErrorUnitsScientificFormat(sample.raw.I0, sample.raw.i0stdev, ""); + } + } + }, { + text : 'Aggregated', + tooltip : "If aggregation was detected from the slope of the data curve at low angles the value is '1', otherwise '0'.", + dataIndex : 'isagregated', + hidden : true, + width : 75, + renderer : function(val, y, sample) { + if ((sample.raw.isagregated != null)) { + if (val == true) { + return "Yes"; + } else { + return "No"; + } + } + } + }, { + text : 'Guinier', + sortable : true, + dataIndex : 'subtractionId', + type : 'string', + width : 100, + hidden : true, + renderer : function(val, y, sample) { -ShipmentGrid.prototype._getColumns = function() { - var _this = this; - var columns = [ - { - text : 'Name', - dataIndex : 'shippingName', - flex : 1 + if (sample.raw.subtractionId != null) { + var url = BUI.getURL() + '&type=guinier&subtractionId=' + sample.raw.subtractionId; + var event = "OnClick= window.open('" + url + "')"; + return ''; + } + } + } ] }, { - header : 'Type', - dataIndex : 'shippingType', - flex : 1, - hidden : true, - renderer : function(val, comp, record) { - if (val != null) { - return val.toUpperCase(); - } + text : 'Gnom', + name : 'Gnom', - } - }, - { - header : 'Status', - type : 'string', - flex : 1, - hidden : false, - renderer : function(comp, val, record) { - if (record.raw.shippingStatus != null) { - if (new String(record.raw.shippingStatus).toUpperCase() == 'OPENED') { - return "" + new String(record.raw.shippingStatus).toUpperCase() + ""; + columns : [ { + text : 'Rg', + dataIndex : 'rgGnom', + type : 'string', + width : 65, + hidden : !this.isGnomTabVisible, + sortable : true, + renderer : function(val, y, sample) { + /** Show warning if rgGuinier and rgGnom differ more than 10% **/ + if (sample.raw.rgGnom != null) { + if (Math.abs(sample.raw.rgGuinier - sample.raw.rgGnom) > (sample.raw.rgGuinier * 0.1)) { + return "" + BUI.formatValuesUnits(sample.raw.rgGnom, "") + ""; + + } + return BUI.formatValuesUnits(sample.raw.rgGnom, "nm"); } - return "" + new String(record.raw.shippingStatus).toUpperCase() + ""; } - } + }, { + text : 'Total', + dataIndex : 'total', + width : 65, + hidden : !this.isGnomTabVisible, + sortable : true, + renderer : function(val, y, sample) { + if (sample.raw.total != null) + return BUI.formatValuesUnits(sample.raw.total, ''); + } + }, { + text : 'Dmax', + dataIndex : 'dmax', + sortable : true, + width : 75, + hidden : !this.isGnomTabVisible, + renderer : function(val, y, sample) { + if (sample.raw.dmax != null) + return BUI.formatValuesUnits(sample.raw.dmax, "") + " nm"; + } + }, { + text : 'P(r)', + sortable : true, + hidden : true, + width : 100, + dataIndex : 'subtractionId', + type : 'string', + renderer : function(val, y, sample) { + var url = BUI.getURL() + '&type=gnom&subtractionId=' + sample.raw.subtractionId; + var event = "OnClick= window.open('" + url + "')"; + return ''; + } + } ] }, + this._getPorod(), { - text : 'Cases', - flex : 1, - hidden : false, - renderer : function(comp, val, record) { - var shipment = BIOSAXS.proposal.getShipmentById(record.data.shippingId); - var container = ""; - if (shipment.dewarVOs.length > 0) { - container = container + ""; - } else { - return "Empty"; - } - return container + "
" + shipment.dewarVOs.length + "x
"; - } - }, { - header : 'Comments', - dataIndex : 'comments', - flex : 1, - hidden : false - }, { - header : 'Creation Date', - dataIndex : 'creationDate', - hidden : true - } ]; - - if (this.btnEditVisible) { - columns.push({ - id : _this.id + 'buttonEdit', - text : '', - hidden : !_this.btnEditVisible, - width : 100, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - return BUI.getGreenButton('EDIT'); - } - }); - } - - columns.push({ - id : _this.id + 'buttonRemove', - text : '', - width : 100, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - var shipment = BIOSAXS.proposal.getShipmentById(record.data.shippingId); - if (shipment.dewarVOs.length == 0) { - return BUI.getRedButton('REMOVE'); - } - - } - }); - - return columns; -}; - -ShipmentGrid.prototype._getTopButtons = function() { - var _this = this; - /** Actions buttons **/ - var actions = []; - actions.push(Ext.create('Ext.Action', { - icon : '../images/add.png', - text : 'Add Shipment', - handler : function(widget, event) { - //window.location = BUI.getCreateShipmentURL(); - var _this = this; - - var shipmentForm = new ShipmentForm({ - creationMode : true, - showTitle : false - }); - shipmentForm.onSaved.attach(function(sender, shipment) { - _this.showShipmentTabs(shipment, targetId); - }); - - var window = Ext.create('Ext.window.Window', { - title : 'New Shipment', - height : 600, - width : 800, - layout : 'fit', - items : [ shipmentForm.getPanel() ] - }).show(); - - } - })); - return actions; -}; - -ShipmentGrid.prototype.refresh = function(shippings) { - this.features = shippings; - this.store.loadData(this._prepareData(), false); -}; - -ShipmentGrid.prototype._prepareData = function() { - var data = []; - for ( var i = 0; i < this.features.length; i++) { - data.push(this.features[i]); - } - return data; -}; - -ShipmentGrid.prototype.getPanel = function(shipments) { - this.features = shipments; - return this._renderGrid(); -}; - -ShipmentGrid.prototype.edit = function(shippingId) { - window.location = BUI.getShippingURL(shippingId); -}; - -ShipmentGrid.prototype._getStoreFields = function(data) { - var _this = this; - return [ { - name : 'shippingId' - }, { - name : 'shippingName' - }, { - name : 'shippingStatus' - }, { - name : 'shippingType' - }, { - name : 'creationDate' - }, { - name : 'comments' - } ]; -}; - -ShipmentGrid.prototype._renderGrid = function() { - var _this = this; - - /** Store **/ - var data = this._prepareData(); - this.store = Ext.create('Ext.data.Store', { - fields : this._getStoreFields(data), - autoload : true, - data : data - }); - - this.store.loadData(data, false); + text : 'AbInitio Modeling', + name : 'AbInitio_modeling', - this.grid = Ext.create('Ext.grid.Panel', { - title : "Shipping", - icon : '/ispyb/images/plane.gif', - width : this.width, - minWidth : this.minWidth, - height : this.height, - store : this.store, - columns : this._getColumns(), - viewConfig : { - stripeRows : true, - listeners : { - itemdblclick : function(dataview, record, item, e) { - _this.edit(record.raw.shippingId); + columns : [ + { + text : 'NSD', + dataIndex : 'volumeEdna', + width : 100, + sortable : true, + hidden : true, + renderer : function(val, y, sample) { + var url = BUI.getNSDImageURL(sample.raw.modelListId); + var event = "OnClick= window.open('" + url + "')"; + return ''; + } }, - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEdit') { - _this.edit(record.data.shippingId); + { + text : 'Chi2', + dataIndex : 'volumeEdna', + sortable : true, + hidden : true, + width : 100, + renderer : function(val, y, sample) { + var url = BUI.getCHI2ImageURL(sample.raw.modelListId); + var event = "OnClick= window.open('" + url + "')"; + return ''; } + }, + { + text : 'Pdb', + dataIndex : 'volumeEdna', + tooltip : 'Damaver: The program suite DAMAVER is a set of programs to align ab initio models, select the most typical one and build an averaged model. Dammif : Rapid ab initio shape determination by simulated annealing using a single phase dummy atom model. Dammin :Ab initio shape determination by simulated annealing using a single phase dummy atom model', + sortable : true, + width : 125, + hidden : !this.isAbinitioTabVisible, + renderer : function(val, y, sample) { + var html = new String(); + var split = null; + var url = null; + var file = sample.raw.averagedModel; + if (file != null) { + split = file.split("/"); + if (split.length > 0) { + url = BUI.getPdbURL() + '&type=AVERAGED&abInitioModelId=' + sample.raw.abInitioModelId; + html = html + ''+ split[split.length - 1] + '

'; - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemove') { - var shipment = BIOSAXS.proposal.getShipmentById(record.data.shippingId); - if (shipment.dewarVOs.length == 0) { + } + } - var adapter = new BiosaxsDataAdapter(); - _this.grid.setLoading("ISPyB: Removing shipment"); - adapter.onSuccess.attach(function(sender) { - BIOSAXS.proposal.onInitialized.attach(function(sender) { - _this.refresh(BIOSAXS.proposal.getShipments()); - _this.grid.setLoading(false); - }); - BIOSAXS.proposal.init(); - }); + file = sample.raw.rapidShapeDeterminationModel; + if (file != null) { + split = file.split("/"); + if (split.length > 0) { + url = BUI.getPdbURL() + '&type=RAPIDSHAPEDETERMINATIONMODEL&abInitioModelId=' + sample.raw.abInitioModelId; + html = html + '' + split[split.length - 1] + '

'; + } + } - adapter.onError.attach(function(sender) { - alert("Error"); - _this.grid.setLoading(false); - }); - adapter.removeShipment(record.data.shippingId); + file = sample.raw.shapeDeterminationModel; + if (file != null) { + split = file.split("/"); + if (split.length > 0) { + url = BUI.getPdbURL() + '&type=SHAPEDETERMINATIONMODEL&abInitioModelId=' + sample.raw.abInitioModelId; + html = html + ''+ split[split.length - 1] + ''; + } } + return html; } - } - } - }, - selModel : { - mode : 'SINGLE' - } - }); - - var actions = _this._getTopButtons(); - this.grid.addDocked({ - xtype : 'toolbar', - items : actions - }); - - this.grid.getSelectionModel().on({ - selectionchange : function(sm, selections) { - if (selections.length) { - for ( var i = 0; i < actions.length; i++) { - if (actions[i].enable) { - actions[i].enable(); + }, + { + text : 'Damaver', + dataIndex : 'volumeEdna', + hidden : true, + tooltip : 'Damaver: The program suite DAMAVER is a set of programs to align ab initio models, select the most typical one and build an averaged model. ', + sortable : true, + width : 125, + renderer : function(val, y, sample) { + var file = sample.raw.averagedModel; + if (file != null) { + var split = file.split("/"); + if (split.length > 0) { + var url = BUI.getPdbURL() + '&type=AVERAGED&abInitioModelId=' + sample.raw.abInitioModelId; + return '' + split[split.length - 1]+ ''; + } + } + return sample.raw.averagedModel; } - } - } else { - for ( var i = 0; i < actions.length; i++) { - if (actions[i].alwaysEnabled == false) { - if (actions[i].disable) { - actions[i].disable(); + }, + { + text : 'Dammif', + dataIndex : 'volumeEdna', + hidden : true, + tooltip : 'Dammif : Rapid ab initio shape determination by simulated annealing using a single phase dummy atom model', + sortable : true, + width : 125, + renderer : function(val, y, sample) { + var file = sample.raw.rapidShapeDeterminationModel; + if (file != null) { + var split = file.split("/"); + if (split.length > 0) { + var url = BUI.getPdbURL() + '&type=RAPIDSHAPEDETERMINATIONMODEL&abInitioModelId=' + sample.raw.abInitioModelId; + return '' + split[split.length - 1] + ''; + } } + return sample.raw.averagedModel; } - } - } - } - }); - return this.grid; -}; - -ShipmentGrid.prototype.input = function() { - return { - proposal : new MeasurementGrid().input().proposal, - shippings : DATADOC.getShippings_10() - }; -}; - -ShipmentGrid.prototype.test = function(targetId) { - var shipmentGrid = new ShipmentGrid({ - minHeight : 300, - height : 440 - }); - BIOSAXS.proposal = new Proposal(shipmentGrid.input().proposal); - var panel = shipmentGrid.getPanel(targetId); - panel.render(targetId); - shipmentGrid.refresh(shipmentGrid.input().shippings); -}; - -function SpecimenGrid(args) { - this.id = BUI.id(); - this.height = 500; - this.unitsFontSize = 9; - this.editEnabled = false; - this.isPositionColumnHidden = false; - this.removeBtnEnabled = false; - - this.selectionMode = "MULTI"; - this.updateRowEnabled = false; - this.grouped = true; - this.width = 900; - this.title = 'Specimens'; - - this.margin = "0 0 0 0"; -// this.experimentColorBased = false; - - if (args != null) { - if (args.height != null) { - this.height = args.height; - } - - if (args.showTitle == false) { - this.title = null; - } - - if (args.margin == false) { - this.margin = args.margin; - } - - if (args.grouped == false) { - this.grouped = null; - } - - if (args.width != null) { - this.width = args.width; - } - - - if (args.editEnabled != null) { - this.editEnabled = args.editEnabled; - } - if (args.removeBtnEnabled != null) { - this.removeBtnEnabled = args.removeBtnEnabled; - } - if (args.isPositionColumnHidden != null) { - this.isPositionColumnHidden = args.isPositionColumnHidden; - } - if (args.selectionMode != null) { - this.selectionMode = args.selectionMode; - } - if (args.updateRowEnabled != null) { - this.updateRowEnabled = args.updateRowEnabled; - } - - } - this.onClick = new Event(this); - this.onSelected = new Event(this); - this.onRemoved = new Event(this); - this.onSpecimenChanged = new Event(); -} - -SpecimenGrid.prototype._prepareData = function(experiment) { - var data = []; - - var samples = experiment.getSamples(); - for ( var i = 0; i < samples.length; i++) { - var sample = samples[i]; - if (sample.macromolecule3VO != null) { - sample.macromolecule = sample.macromolecule3VO.acronym; - sample.exposureTemperature = []; - sample.macromoleculeId = sample.macromolecule3VO.macromoleculeId; - } + }, + { + text : 'Dammin', + dataIndex : 'volumeEdna', + hidden : true, + tooltip : 'Dammin :Ab initio shape determination by simulated annealing using a single phase dummy atom model', + sortable : true, + width : 125, + renderer : function(val, y, sample) { + var file = sample.raw.shapeDeterminationModel; + if (file != null) { + var split = file.split("/"); + if (split.length > 0) { + var url = BUI.getPdbURL() + '&type=SHAPEDETERMINATIONMODEL&abInitioModelId=' + sample.raw.abInitioModelId; + return '' + split[split.length - 1]+ ''; + } + } + return sample.raw.averagedModel; + } + } ] + }, { + text : 'Time', + dataIndex : 'substractionCreationTime', + name : 'substractionCreationTime', + hidden : true, + width : 80, + sortable : true, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + try { + if (record.raw.substractionCreationTime != null) { + return moment(record.raw.substractionCreationTime).format('h:mm:ss a'); + } + } catch (e) { + return "NA"; + } + } + }, { + text : 'Date', + dataIndex : 'substractionCreationTime', + name : 'substractionCreationTime', + hidden : true, + width : 80, + sortable : true, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + try { + if (record.raw.substractionCreationTime != null) { + return moment(record.raw.substractionCreationTime).format("LL"); + } + } catch (e) { + return "NA"; + } + } + }, + this._getButtons()]; +}; - if (sample.sampleplateposition3VO != null) { - if (sample.sampleplateposition3VO.samplePlateId != null) { - sample.samplePlateId = sample.sampleplateposition3VO.samplePlateId; - sample.rowNumber = sample.sampleplateposition3VO.rowNumber; - sample.columnNumber = sample.sampleplateposition3VO.columnNumber; - if (experiment.getSamplePlateById(sample.sampleplateposition3VO.samplePlateId).plategroup3VO != null) { - sample.plateGroupName = experiment.getSamplePlateById(sample.sampleplateposition3VO.samplePlateId).plategroup3VO.name; - sample.samplePlateName = experiment.getSamplePlateById(sample.sampleplateposition3VO.samplePlateId).name + " [" + sample.plateGroupName + "]"; - sample.slotPositionColumn = experiment.getSamplePlateById(sample.sampleplateposition3VO.samplePlateId).slotPositionColumn; +AnalysisGrid.prototype._getButtons = function() { + return { + id : this.id + 'buttonPlot', + name : 'buttonPlot', + hidden : !this.showButtonsVisible, + width : 110, + sortable : false, + renderer : function(value, metaData, sample, rowIndex, colIndex, store) { + var html = ""; + + if (sample.raw.subtractionId) { + html = html + ""; + if (sample.raw.rapidShapeDeterminationModelId != null) { + html = html + ""; } } - } else { - sample.samplePlateName = "Unallocated Specimens"; + return html + "
" + BUI.getGreenButton('Calibration', { + height : 20, + width : 100 + }) + "
" + BUI.getGreenButton('Primary Data Proc.', { + height : 20, + width : 100 + }) + "
" + BUI.getGreenButton('AbInitio Modeling', { + height : 20, + width : 100 + }) + "
"; } - - /** For grouping, because sencha has not option for multiple grouping I add a field to your store with a convert function that concatenates these two fields and then group by that field.**/ - sample.groupIndex = sample.bufferId + sample.macromoleculeId; - var macromolecule = BIOSAXS.proposal.getMacromoleculeById(sample.macromoleculeId); - - sample.acronym = "Buffers"; - if (macromolecule != null) { - sample.acronym = BIOSAXS.proposal.getMacromoleculeById(sample.macromoleculeId).acronym; + }; +}; +AnalysisGrid.prototype._prepareData = function(data) { + if (this.hideNulls) { + var result = []; + for ( var i = 0; i < data.length; i++) { + if (data[i].subtractionId != null) { + data[i].groupeField = data[i].macromoleculeAcronym + " " + data[i].bufferAcronym; + result.push(data[i]); + } } - - sample.buffer = experiment.getBufferById(sample.bufferId); - - sample.volumeToLoad = experiment.getVolumeToLoadBySampleId(sample.sampleId); - data.push(sample); + return result; + } else { + return data; } - return data; }; -SpecimenGrid.prototype.deselectAll = function() { - this.grid.getSelectionModel().deselectAll(); -}; +AnalysisGrid.prototype.getPanel = function(data) { + var _this = this; + var columns = this._getColumns(); -SpecimenGrid.prototype.selectById = function(specimenId) { - this.grid.getSelectionModel().deselectAll(); - for ( var i = 0; i < this.grid.getStore().data.items.length; i++) { - var item = this.grid.getStore().data.items[i].raw; - if (item.specimenId == specimenId) { - this.grid.getSelectionModel().select(i); - } - } -}; + var fields = JSON.parse(JSON.stringify(columns)); + fields.push({ + name : 'experimentId', + dataIndex : 'experimentId' -SpecimenGrid.prototype.getStore = function() { - return this.store; -}; + }); + this.store = Ext.create('Ext.data.Store', { + fields : fields, + autoload : true, + data : this._prepareData(data), + groupField : 'groupeField' + }); -SpecimenGrid.prototype.getPlugins = function() { - var _this = this; + this.store.sort(this.sorters); - var plugins = []; + var features = []; - if (this.updateRowEnabled) { - plugins.push(Ext.create('Ext.grid.plugin.RowEditing', { - clicksToEdit : 1, + if (this.grouped) { + features.push({ + ftype : 'grouping', + groupHeaderTpl : '{name}', + hideGroupedHeader : false, + startCollapsed : false + }); + } + + this.grid = Ext.create('Ext.grid.Panel', { + style : { + padding : 5 + }, + maxWidth : this.maxWidth, + width : this.width, + height : this.height, + store : this.store, + columns : columns, + resizable : true, + features : features, + viewConfig : { + preserveScrollOnRefresh : true, + stripeRows : true, listeners : { - validateedit : function(grid, e) { - var measurements = []; + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - if (e.newValues.bufferId != e.record.raw.bufferId) { - /** If buffer has changed we have to change all the specimens sharing same datacollection **/ - var dataCollections = []; - if (e.record.raw.macromoleculeId == null) { - dataCollections = dataCollections.concat(_this.experiment.getDataCollectionsBySpecimenId(e.record.raw.specimenId)); - } else { - var sampleDataCollections = _this.experiment.getDataCollectionsBySpecimenId(e.record.raw.specimenId); - for ( var i = 0; i < sampleDataCollections.length; i++) { - var sampleDataCollection = sampleDataCollections[i]; - if (sampleDataCollection != null) { - for ( var j = 0; j < sampleDataCollection.measurementtodatacollection3VOs.length; j++) { - var measurementTODc = sampleDataCollection.measurementtodatacollection3VOs[j]; - if (measurementTODc.dataCollectionOrder == 1) { - dataCollections = dataCollections.concat(_this.experiment.getDataCollectionsBySpecimenId(_this.experiment - .getMeasurementById(measurementTODc.measurementId).specimenId)); - } - } - } - } - } - var i = null; - for ( i = 0; i < dataCollections.length; i++) { - var dataCollection = dataCollections[i]; - var specimens = _this.experiment.getSpecimenByDataCollectionId(dataCollection.dataCollectionId); - measurements = measurements.concat(specimens); + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonPlot') { + if (e.target.defaultValue == 'AbInitio Modeling') { + var url = BUI.getPDBVisualizerURL(record.raw.averagedModelId, record.raw.subtractionId, record.raw.experimentId); + window.open(url, "_blank"); } - for ( i = 0; i < measurements.length; i++) { - var measurement = measurements[i]; - var specimen = _this.experiment.getSpecimenById(measurement.specimenId); - specimen.bufferId = e.newValues.bufferId; - new BiosaxsDataAdapter().saveSpecimen(specimen, _this.experiment); + if (e.target.defaultValue == 'Primary Data Proc.') { + _this._edit(record.raw); } - } - - /** Setting values **/ - e.record.raw.concentration = e.newValues.concentration; - e.record.raw.volume = e.newValues.volume; - /** Position **/ - if (e.record.raw.sampleplateposition3VO != null) { - var samplePlate = _this.experiment.getSamplePlateBySlotPositionColumn(e.newValues.slotPositionColumn); - if (samplePlate != null) { - e.record.raw.sampleplateposition3VO = { - columnNumber : e.newValues.columnNumber, - rowNumber : e.newValues.rowNumber, - samplePlateId : samplePlate.samplePlateId - }; - } - } else { - if (e.newValues.slotPositionColumn != null) { - var samplePlate = _this.experiment.getSamplePlateBySlotPositionColumn(e.newValues.slotPositionColumn); - if (samplePlate != null) { - e.record.raw.sampleplateposition3VO = { - columnNumber : e.newValues.columnNumber, - rowNumber : e.newValues.rowNumber, - samplePlateId : samplePlate.samplePlateId - }; - } + if (e.target.defaultValue == 'Calibration') { + _this._showCalibration(record.raw); } } - - var macromoleculeId = e.record.data.macromoleculeId; - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, specimen) { - /** Because macromolecule3VO is fecthed LAZY **/ - if (macromoleculeId != null) { - specimen.macromolecule3VO = BIOSAXS.proposal.getMacromoleculeById(macromoleculeId); - } - _this.onSpecimenChanged.notify(specimen); - _this.grid.setLoading(false); - }); - adapter.onError.attach(function() { - alert("Error"); - _this.grid.setLoading(false); - }); - _this.grid.setLoading(); - adapter.saveSpecimen(e.record.raw, _this.experiment); } } - })); - } - return plugins; + }, + selModel : { + mode : 'SINGLE' + } + }); + + return this.grid; + +}; + +AnalysisGrid.prototype._openVisualizarBySubstractionId = function(record) { + //experimentId, subtractionId) { + var experimentId = record.experimentId; + var subtractionId = record.subtractionId; + + var _this = this; + var adapter = new BiosaxsDataAdapter(); + this.subtractionId = subtractionId; + + adapter.onSuccess.attach(function(sender, data) { + var experiment = new Experiment(data); + var experimentList = new ExperimentList([ experiment ]); + var subtraction = experiment.getSubtractionById(_this.subtractionId); + _this.grid.setLoading(false); + _this._openVisualizer(experimentList, subtraction, record); + }); + this.grid.setLoading("ISPyB: Fetching experiment"); + adapter.getExperimentById(experimentId, "MEDIUM"); }; -SpecimenGrid.prototype._getRowCombo = function() { - var data = []; - for ( var i = 1; i <= 8; i++) { - data.push({ - rowNumber : i, - name : BUI.getSamplePlateLetters()[i - 1] +AnalysisGrid.prototype._edit = function(record) { + var experimentId = record.experimentId; + var _this = this; + + if (BIOSAXS.proposal.macromolecules == null) { + this.grid.setLoading("ISPyB: Fetching proposal"); + BIOSAXS.proposal.onInitialized.attach(function(sender, data) { + _this._openVisualizarBySubstractionId(record); }); + BIOSAXS.proposal.init(); + } else { + this._openVisualizarBySubstractionId(record); } +}; - var positionsStore = Ext.create('Ext.data.Store', { - fields : [ 'rowNumber', 'name' ], - data : data - }); - return Ext.create('Ext.form.ComboBox', { - store : positionsStore, - queryMode : 'local', - displayField : 'name', - valueField : 'rowNumber' +AnalysisGrid.prototype._showCalibration = function(row) { + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + Ext.create('Ext.window.Window', { + title : 'Calibration', + width : 900, + resizable : true, + height : 400, + modal : true, + frame : false, + draggable : true, + closable : true, + autoscroll : true, + paddin : 5, + layout : { + type : 'vbox', + align : 'stretch' + }, + items : [ new AnalysisGrid({ + isGuinierTabVisible : false, + isGnomTabVisible : false, + isPorodTabVisible : false, + isAbinitioTabVisible : false, + isI0Visible : true, + showButtonsVisible : false, + height : 350, + sorters : [ { + property : 'experimentId', + direction : 'DESC' + } ] + }).getPanel(data) ] + }).show(); }); + adapter.getAnalysisCalibrationByProposalId(); }; -SpecimenGrid.prototype._getColumnCombo = function() { - var data = []; - for ( var i = 1; i <= 12; i++) { - data.push({ - columnNumber : i - }); +AnalysisGrid.prototype._openVisualizer = function(experimentList, subtraction, record) { + var merges = experimentList.getMergesByDataCollectionId(subtraction.dataCollectionId); + var mergeIdList = []; + for ( var i = 0; i < merges.length; i++) { + mergeIdList.push(merges[i].mergeId); } - var positionsStore = Ext.create('Ext.data.Store', { - fields : [ 'columnNumber' ], - data : data + var dataAdapter = new BiosaxsDataAdapter(); + dataAdapter.onSuccess.attach(function(sender, merges) { + var dataCollectionCurveVisualizer = new DataCollectionCurveVisualizer(); + dataCollectionCurveVisualizer.draw(); + dataCollectionCurveVisualizer.refresh(merges, experimentList, subtraction.dataCollectionId, record); }); - return Ext.create('Ext.form.ComboBox', { - store : positionsStore, - queryMode : 'local', - displayField : 'columnNumber', - valueField : 'columnNumber' + dataAdapter.onError.attach(function(sender, error) { }); + + dataAdapter.getMergesByIdsList(mergeIdList); }; -SpecimenGrid.prototype._getSlotColumBombo = function() { - if (this.experiment){ - var length = this.experiment.getSamplePlates().length; - - var data = []; - for ( var i = 1; i <= length; i++) { - data.push({ - slotPositionColumn : i - }); - } +AnalysisGrid.prototype.input = function() { + return { + data : DATADOC.getData_3367().slice(20, 30),//[{"total":"0.447505552082","bufferBeforeMeasurementId":22150,"sampleMergeId":12373,"averagedModelId":43636,"I0":"32.50776","proposalCode":"OPD","averagedModel":"/data/pyarch/bm29/opd29/1137/1d/damaver.pdb","bufferAfterMergeId":12374,"framesCount":"10","bufferBeforeMergeId":12372,"averageFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_016_ave.dat","bufferAfterMeasurementId":22152,"rgGuinier":"2.96883","subtractedFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_016_sub.dat","firstPointUsed":"30","chi2RgFilePath":"/data/pyarch/bm29/opd29/1137/1d/chi2_R.png","abInitioModelId":272,"macromoleculeId":112,"code":"_20.0_1.25","transmission":"100.0","timeStart":"2013-07-17 17:10:25.743734","bufferAcronym":"MES","quality":"0.87091","shapeDeterminationModelId":43638,"expermientComments":"[BsxCube] Generated from BsxCube","bufferId":707,"isagregated":"False","dmax":"10.390905","bufferBeforeAverageFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_015_ave.dat","exposureTemperature":"20.0","subtractionId":5165,"conc":"1.25","rapidShapeDeterminationModel":"/data/pyarch/bm29/opd29/1137/1d/damfilt.pdb","experimentCreationDate":"Jul 17, 2013 5:08:37 PM","lastPointUsed":"92","modelListId":272,"framesMerge":"10","rapidShapeDeterminationModelId":43637,"bufferAfterAverageFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_017_ave.dat","nsdFilePath":"/data/pyarch/bm29/opd29/1137/1d/nsd.png","bufferAfterFramesMerged":"10","experimentId":1137,"macromoleculeAcronym":"MG386","i0stdev":"0.05726128","sampleMeasurementId":22151,"measurementComments":"[1] MES","priorityLevelId":2,"bufferBeforeFramesMerged":"10","substractionCreationTime":"Jul 17, 2013 5:12:32 PM","proposalNumber":"29","rgGnom":"3.05242714339","volume":"44.1406","shapeDeterminationModel":"/data/pyarch/bm29/opd29/1137/1d/dammin.pdb","comments":null},{"total":"0.582641941147","bufferBeforeMeasurementId":22152,"sampleMergeId":12375,"averagedModelId":43809,"I0":"31.4366153846","proposalCode":"OPD","averagedModel":"/data/pyarch/bm29/opd29/1137/1d/damaver.pdb","bufferAfterMergeId":12376,"framesCount":"10","bufferBeforeMergeId":12374,"averageFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_018_ave.dat","bufferAfterMeasurementId":22155,"rgGuinier":"2.95541","subtractedFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_018_sub.dat","firstPointUsed":"21","chi2RgFilePath":"/data/pyarch/bm29/opd29/1137/1d/chi2_R.png","abInitioModelId":273,"macromoleculeId":112,"code":"_20.0_0.65000000000000002","transmission":"100.0","timeStart":"2013-07-17 17:12:55.837462","bufferAcronym":"MES","quality":"0.870164","shapeDeterminationModelId":43811,"expermientComments":"[BsxCube] Generated from BsxCube","bufferId":707,"isagregated":"False","dmax":"10.343935","bufferBeforeAverageFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_017_ave.dat","exposureTemperature":"20.0","subtractionId":5166,"conc":"0.65000000000000002","rapidShapeDeterminationModel":"/data/pyarch/bm29/opd29/1137/1d/damfilt.pdb","experimentCreationDate":"Jul 17, 2013 5:08:37 PM","lastPointUsed":"80","modelListId":273,"framesMerge":"10","rapidShapeDeterminationModelId":43810,"bufferAfterAverageFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_019_ave.dat","nsdFilePath":"/data/pyarch/bm29/opd29/1137/1d/nsd.png","bufferAfterFramesMerged":"10","experimentId":1137,"macromoleculeAcronym":"MG386","i0stdev":"0.100250461538","sampleMeasurementId":22154,"measurementComments":"[2] MES","priorityLevelId":4,"bufferBeforeFramesMerged":"10","substractionCreationTime":"Jul 17, 2013 5:15:02 PM","proposalNumber":"29","rgGnom":"2.9963404542","volume":"42.2255","shapeDeterminationModel":"/data/pyarch/bm29/opd29/1137/1d/dammin.pdb","comments":null}], + proposal : new ResultsAssemblyGrid().input().proposal + }; +}; + +AnalysisGrid.prototype.test = function(targetId) { + var analysisGrid = new AnalysisGrid(); + BIOSAXS.proposal = new Proposal(analysisGrid.input().proposal); + var panel = analysisGrid.getPanel(analysisGrid.input().data); + panel.render(targetId); +}; + + +function HPLCAnalysisGrid(args) { + AnalysisGrid.prototype.constructor.call(this, args); +} - var positionsStore = Ext.create('Ext.data.Store', { - fields : [ 'slotPositionColumn' ], - data : data - }); +HPLCAnalysisGrid.prototype._edit = AnalysisGrid.prototype._edit; +HPLCAnalysisGrid.prototype._getColumns = AnalysisGrid.prototype._getColumns; +HPLCAnalysisGrid.prototype._openVisualizarBySubstractionId = AnalysisGrid.prototype._openVisualizarBySubstractionId; +HPLCAnalysisGrid.prototype._openVisualizer = AnalysisGrid.prototype._openVisualizer; +HPLCAnalysisGrid.prototype._prepareData = AnalysisGrid.prototype._prepareData; +HPLCAnalysisGrid.prototype._showCalibration = AnalysisGrid.prototype._showCalibration; +HPLCAnalysisGrid.prototype.getPanel = AnalysisGrid.prototype.getPanel; +HPLCAnalysisGrid.prototype.input = AnalysisGrid.prototype.input; +HPLCAnalysisGrid.prototype.test = AnalysisGrid.prototype.test; +HPLCAnalysisGrid.prototype.refresh = AnalysisGrid.prototype.refresh; +HPLCAnalysisGrid.prototype._getPorod = AnalysisGrid.prototype._getPorod; + +HPLCAnalysisGrid.prototype._getButtons = function() { + return { + id : this.id + 'buttonPlot', + name : 'buttonPlot', + hidden : !this.showButtonsVisible, + width : 110, + sortable : false, + renderer : function(value, metaData, sample, rowIndex, colIndex, store) { + var html = ""; - return Ext.create('Ext.form.ComboBox', { - store : positionsStore, - queryMode : 'local', - displayField : 'slotPositionColumn', - valueField : 'slotPositionColumn' - }); + if (sample.raw.subtractionId) { + if (sample.raw.rapidShapeDeterminationModelId != null) { + html = html + ""; + } + } + return html + "
" + BUI.getGreenButton('AbInitio Modeling', { + height : 20, + width : 100 + }) + "
"; + } + }; +}; + +HPLCAnalysisGrid.prototype._getFramesColumn = function() { + return { + text : 'Frames', + dataIndex : 'datacollection', + name : 'datacollection', + sortable : true, + width : 150, + renderer : function(dataCollections, y, data) { + molmerges = data.raw.framesMerge; + totalframes = data.raw.framesCount; + return molmerges +" - "+ totalframes; + } + }; +}; + + + + +/** + * Rigid body grid to show PDB, symmetry and multiplicity + * + * + * #onUploadFile click on upload file + */ +function AprioriRigidBodyGrid(args) { + + this.height = 250; + this.btnEditVisible = true; + this.btnRemoveVisible = true; + + if (args != null) { + if (args.height != null) { + this.height = args.height; + } + if (args.btnEditVisible != null) { + this.btnEditVisible = args.btnEditVisible; + } + if (args.btnRemoveVisible != null) { + this.btnRemoveVisible = args.btnRemoveVisible; + } + } + + /** Events **/ + this.onUploadFile = new Event(this); + this.onRemove = new Event(this); +} + +AprioriRigidBodyGrid.prototype._getColumns = function() { +}; + +AprioriRigidBodyGrid.prototype._getTopButtons = function() { + var _this = this; + /** Actions buttons **/ + var actions = []; + + /** ADD BUTTON **/ + actions.push(Ext.create('Ext.Action', { + icon : '../images/add.png', + text : 'Add', + disabled : false, + handler : function(widget, event) { + _this.onAddButtonClicked.notify(); + } + })); + + return actions; +}; + +AprioriRigidBodyGrid.prototype.refresh = function(macromolecule) { + this.macromolecule = macromolecule; + if (macromolecule != null){ + this.pdbStore.loadData(macromolecule.structure3VOs); + } +}; + +AprioriRigidBodyGrid.prototype._prepareData = function() { + var data = []; + for ( var i = 0; i < this.features.length; i++) { + data.push(this.features[i]); + } + return data; +}; + +AprioriRigidBodyGrid.prototype._getPlugins = function() { + var _this = this; + var plugins = []; + plugins.push(Ext.create('Ext.grid.plugin.RowEditing', { + clicksToEdit : 1, + listeners : { + validateedit : function(grid, e) { + /** Comments are always updatable* */ + e.record.raw.symmetry = e.newValues.symmetry; + e.record.raw.multiplicity = e.newValues.multiplicity; + + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, proposal) { + BIOSAXS.proposal.setItems(proposal); + _this.refresh(BIOSAXS.proposal.getMacromoleculeById(_this.macromolecule.macromoleculeId)); + _this.panel.setLoading(false); + }); + adapter.onError.attach(function() { + alert("Error"); + }); + + _this.panel.setLoading(); + adapter.saveStructure(e.record.raw); + } + } + })); + return plugins; +}; + +AprioriRigidBodyGrid.prototype.getPanel = function() { + var _this = this; + + this.pdbStore = Ext.create('Ext.data.Store', { + fields : [ 'filePath', 'structureId', 'structureType', 'symmetry', 'structureId', 'name', 'multiplicity' ], + groupField : 'structureType', + sorters : { + property : 'structureId', + direction : 'DESC' + } + }); + + var groupingFeature = Ext.create('Ext.grid.feature.Grouping', { + groupHeaderTpl : Ext.create('Ext.XTemplate', + "
{name:this.formatName}
", { + formatName : function(name) { + return name; + } + }), + hideGroupedHeader : true, + startCollapsed : false + }); + + this.panel = Ext.create('Ext.grid.Panel', { + margin : "15 10 0 10", + height : this.height, + store : this.pdbStore, + plugins : _this._getPlugins(), + tbar : [ { + text : 'Add Modeling Option (PDB)', + icon : '../images/add.png', + handler : function() { + _this.onUploadFile.notify('PDB', 'Upload PDB File'); + } + } + + ], + columns : [ + { + text : "structureId", + flex : 0.2, + hidden : true, + dataIndex : 'structureId', + sortable : true + }, + { + text : "File", + flex : 0.5, + dataIndex : 'filePath', + sortable : true, + hidden : true + }, + { + text : "PDB", + flex : 0.4, + dataIndex : 'name', + sortable : true + }, + { + text : "Symmetry", + flex : 0.2, + dataIndex : 'symmetry', + sortable : true, + editor : { + xtype : 'combobox', + typeAhead : true, + triggerAction : 'all', + selectOnTab : true, + store : [ [ "P1", "P1" ], [ "P2", "P2" ], [ "P3", "P3" ], [ "P4", "P4" ], [ "P5", "P5" ], [ "P6", "P6" ], [ "P32", "P32" ], [ "P42", "P42" ], + [ "P52", "P52" ], [ "P62", "P62" ], [ "P222", "P222" ] ], + } + }, { + text : "Multiplicity", + flex : 0.2, + dataIndex : 'multiplicity', + sortable : true, + editor : { + xtype : 'textfield' + } + + }, { + text : "Subunit", + flex : 0.2, + dataIndex : 'isSubunit', + sortable : true, + hidden : true + }, { + text : "Type", + flex : 0.2, + dataIndex : 'structureType', + sortable : true, + hidden : true + }, + + { + id : this.id + 'REMOVE', + flex : 0.2, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + return BUI.getRedButton('REMOVE'); + } + }, ], + + listeners : { + itemdblclick : function(dataview, record, item, e) { + _this._editExperiment(record.raw.experimentId); + }, + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'REMOVE') { + var dataAdapter = new BiosaxsDataAdapter(); + dataAdapter.onSuccess.attach(function() { + _this.panel.setLoading(false); + _this.onRemove.notify(); + }); + _this.panel.setLoading("Removing PDB file"); + dataAdapter.removeStructure(record.data.structureId); + } + + } + }, + viewConfig : { + getRowClass : function(record, rowIdx, params, store) { + if (record.raw.isSubunit != null) { + return "blue-row"; + } + } + } + }); + + return this.panel; +}; + + + + +AprioriRigidBodyGrid.prototype.input = function() { + return { + proposal : DATADOC.getProposal_10(), + dewars : DATADOC.getDewars_10() + + }; +}; + +AprioriRigidBodyGrid.prototype.test = function(targetId) { + var AprioriRigidBodyGrid = new AprioriRigidBodyGrid({ + height : 150 + }); + BIOSAXS.proposal = new Proposal(AprioriRigidBodyGrid.input().proposal); + var panel = AprioriRigidBodyGrid.getPanel(AprioriRigidBodyGrid.input().dewars); + panel.render(targetId); + +}; + +/** + * It shows buffer grid with a top bar with "Add" button + * + * @height + * @searchBar + * @collapsed + * @width + */ +function BufferGrid(args) { + this.height = 500; + this.searchBar = false; + this.tbar = false; + this.collapsed = false; + this.id = BUI.id(); + + if (args != null) { + if (args.height != null) { + this.height = args.height; + } + if (args.searchBar != null) { + this.searchBar = args.searchBar; + } + + if (args.tbar != null) { + this.tbar = args.tbar; + } + + if (args.collapsed != null) { + this.collapsed = args.collapsed; + } + + if (args.width != null) { + this.width = args.width; + } } +} + +BufferGrid.prototype._edit = function(bufferId) { + var _this = this; + var window = new BufferWindow(); + window.onSuccess.attach(function(sender, proposal) { + _this.store.loadData(BIOSAXS.proposal.getBuffers()); + }); + window.draw(BIOSAXS.proposal.getBufferById(bufferId)); }; -SpecimenGrid.prototype.getPanelByExperiment = function(experiment) { - this.experiment = experiment; - var data = this._prepareData(experiment); - return this.getPanel(data); +BufferGrid.prototype.refresh = function(buffers) { + this.store.loadData(this._prepareData(buffers), false); }; -SpecimenGrid.prototype.refresh = function(experiment) { - this.experiment = experiment; - var data = this._prepareData(experiment); - this.store.loadData(data); +BufferGrid.prototype._prepareData = function(buffers) { + return buffers; }; -SpecimenGrid.prototype.getPanel = function() { +BufferGrid.prototype._getTbar = function() { var _this = this; - this.store = Ext.create('Ext.data.Store', { - fields : [ - 'buffer', 'bufferId', 'code', 'macromolecule', 'acronym', 'macromoleculeId', 'concentration', 'volume', 'samplePlateId', - 'slotPositionColumn', 'rowNumber', 'columnNumber', 'groupIndex' ], - data : [], - groupField : 'acronym' - }); - this.store.sort([ { - property : 'concentration', - direction : 'ASC' - }, { - property : 'buffer', - direction : 'ASC' - } ]); + var actions = []; - var selModel = Ext.create('Ext.selection.RowModel', { - allowDeselect : true, - mode : this.selectionMode, - listeners : { - selectionchange : function(sm, selections) { - var selected = []; - for ( var i = 0; i < selections.length; i++) { - selected.push(selections[i].raw); - } - _this.onSelected.notify(selected); - } + actions.push(Ext.create('Ext.Action', { + icon : '../images/add.png', + text : 'Add buffer', + disabled : false, + handler : function(widget, event) { + var window = new BufferWindow(); + window.onSuccess.attach(function(sender) { + _this.store.loadData(BIOSAXS.proposal.getBuffers()); + }); + window.draw({}); } - }); - - var features = []; - - if (this.grouped) { - features.push({ - ftype : 'grouping', - groupHeaderTpl : '{name}', - hideGroupedHeader : false, - startCollapsed : false, - id : 'myGroupedStore' - }); - } + })); + return actions; +}; - this.grid = Ext.create( - 'Ext.grid.Panel', - { - title : this.title, - height : this.height, - width : this.width, - selModel : selModel, - store : this.store, - features : features, - margin : this.margin, - plugins : this.getPlugins(), - columns : [ - { - text : '', - dataIndex : 'macromolecule', - width : 20, - renderer : function(val, y, sample) { - var macromoleculeId = null; - if (sample.raw.macromolecule3VO != null) { - macromoleculeId = sample.raw.macromolecule3VO.macromoleculeId; - } - else{ - macromoleculeId = sample.raw.macromoleculeId; - } - - if (macromoleculeId == null) return; - return BUI.getRectangleColorDIV(_this.experiment.macromoleculeColors[macromoleculeId], 10, 10); - } - }, - { - text : 'Macromolecule', - dataIndex : 'macromolecule', - width : 100 - }, - { - text : '', - dataIndex : 'buffer', - width : 20, - renderer : function(val, y, sample) { - var color = "black"; - if (sample.raw.bufferId != null) { - if (_this.experiment.getDataCollectionsBySpecimenId(sample.raw.specimenId)[0] != null){ - color = _this.experiment.getSpecimenColorByBufferId(_this.experiment.getMeasurementById(_this.experiment.getDataCollectionsBySpecimenId(sample.raw.specimenId)[0].measurementtodatacollection3VOs[0].measurementId).specimenId); - } - return BUI.getRectangleColorDIV(color, 10, 10); - } - } - }, { - text : 'Buffer', - dataIndex : 'bufferId', - width : 140, - renderer : function(val, y, sample) { - if (sample.raw.bufferId != null) { - return BIOSAXS.proposal.getBufferById(val).acronym; - } - }, - editor : BIOSAXS_COMBOMANAGER.getComboBuffers(BIOSAXS.proposal.getBuffers(), { - noLabel : true, - width : 300 - }) - }, { - text : 'Conc.', - dataIndex : 'concentration', - width : 100, - editor : { - allowBlank : false - }, - renderer : function(val, meta, sample) { - if (isNaN(val)) { - meta.tdCls = 'yellow-cell'; - return val; - } else { - if (val != 0) { - return BUI.formatValuesUnits(val, 'mg/ml', { - fontSize : 16, - decimals : 3, - unitsFontSize : this.unitsFontSize - }); - } else { - return; - } - } - } - }, { - text : 'Vol. Well', - dataIndex : 'volume', - width : 70, - editor : { - allowBlank : true - }, - renderer : function(val, y, sample) { - return BUI.formatValuesUnits(sample.data.volume, 'µl', { - fontSize : 12, - decimals : 2, - unitsFontSize : this.unitsFontSize - }); - } - }, { - text : 'Position', - hidden : true, - flex : 1, - renderer : function(val, y, sample) { - return BUI.getSamplePositionHTML(sample.raw, _this.experiment); - } - }, { - text : 'samplePlateId', - dataIndex : 'samplePlateId', - hidden : true - }, { - text : 'Plate', - hidden : this.isPositionColumnHidden, - dataIndex : 'slotPositionColumn', - editor : _this._getSlotColumBombo(), - flex : 1, - renderer : function(val, meta, sample) { - if ((val != null) & (val != "")) { - return val; - } else { - meta.tdCls = 'yellow-cell'; - } - } - }, { - text : 'Row', - hidden : this.isPositionColumnHidden, - dataIndex : 'rowNumber', - editor : this._getRowCombo(), - flex : 1, - renderer : function(val, meta, sample) { - if ((val != null) && (val != "")) { - return BUI.getSamplePlateLetters()[val - 1]; - } else { - meta.tdCls = 'yellow-cell'; - } - } - }, { - text : 'Well', - hidden : this.isPositionColumnHidden, - dataIndex : 'columnNumber', - editor : this._getColumnCombo(), - flex : 1, - renderer : function(val, meta, sample) { - if ((val != null) && (val != "")) { - return val; - } else { - meta.tdCls = 'yellow-cell'; - } - } - }, { - id : _this.id + 'buttonEditSample', - text : 'Edit', - width : 80, - sortable : false, - hidden : !_this.editEnabled, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - if (_this.editEnabled) { - return BUI.getGreenButton('EDIT'); - } - } - }, { - id : _this.id + 'buttonRemoveSample', - text : '', - hidden : !_this.removeBtnEnabled, - width : 100, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - if (_this.removeBtnEnabled) { - return BUI.getRedButton('REMOVE'); - } - } - } +BufferGrid.prototype.getPanel = function(buffers) { + var _this = this; - ], - viewConfig : { - preserveScrollOnRefresh : true, - stripeRows : true, - getRowClass : function(record) { - var specimens = _this.experiment.getSampleByPosition(record.data.samplePlateId, record.data.rowNumber, - record.data.columnNumber); - if (specimens.length > 1) { - return 'red-row'; + this.store = Ext.create('Ext.data.Store', { + fields : [ 'bufferId', 'acronym', 'name', 'composition' ], + data : buffers + }); - } - }, - listeners : { - selectionchange : function(grid, selected) { - _this.onClick.notify(record.raw); - }, - cellclick : function(grid, td, cellIndex, record, tr) { - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEditSample') { - } - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemoveSample') { - grid.getStore().removeAt(rowIndex); - _this.onRemoved.notify(); - } + this.store.sort('acronym'); - } + var type = 'Ext.grid.Panel'; + if (this.searchBar == true) { + type = 'Ext.ux.LiveSearchGridPanel'; + } - } - } - }); + this.grid = Ext.create(type, { + title : 'Buffers', + collapsible : true, + collapsed : this.collapsed, + store : this.store, + height : this.height, + width : this.width, + columns : [ + /*{ + text : '', + dataIndex : 'bufferId', + width : 20, + renderer : function(val, y, sample) { + return BUI.getRectangleColorDIV(BIOSAXS.proposal.bufferColors[val], 10, 10); + } + },*/ + { + text : 'Acronym', + dataIndex : 'acronym', + flex : 1 + }, { + text : 'Name', + dataIndex : 'name', + flex : 1, + hidden : true + }, { + text : 'Composition', + dataIndex : 'composition', + flex : 1, + hidden : true + }, { + id : _this.id + 'buttonEditBuffer', + width : 80, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + return BUI.getGreenButton('EDIT'); + } + }, { + id : _this.id + 'buttonRemoveBuffer', + width : 85, + hidden : true, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + return BUI.getRedButton('REMOVE'); + } + } ], + flex : 1, + viewConfig : { + stripeRows : true, + listeners : { + 'celldblclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + _this._edit(record.data.bufferId); + }, + 'cellclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEditBuffer') { + _this._edit(record.data.bufferId); + } + + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemoveBuffer') { + BUI.showBetaWarning(); + } + } + + } + } + }); + + /** Adding the tbar **/ + if (this.tbar) { + this.grid.addDocked({ + xtype : 'toolbar', + items : this._getTbar() + }); + } return this.grid; }; -SpecimenGrid.prototype.input = function() { - return { - experiment : DATADOC.getExperiment_10(), - proposal : DATADOC.getProposal_10() - }; +BufferGrid.prototype.input = function() { + return new MacromoleculeGrid().input(); }; -SpecimenGrid.prototype.test = function(targetId) { - var specimenGrid = new SpecimenGrid({ - height : 400, - maxHeight : 400, - width : 1000 +BufferGrid.prototype.test = function(targetId) { + var bufferGrid = new BufferGrid({ + width : 800, + height : 350, + collapsed : false, + tbar : true }); - BIOSAXS.proposal = new Proposal(specimenGrid.input().proposal); - var experiment = new Experiment(specimenGrid.input().experiment); - var panel = specimenGrid.getPanelByExperiment(experiment); + BIOSAXS.proposal = new Proposal(bufferGrid.input().proposal); + var panel = bufferGrid.getPanel(BIOSAXS.proposal.macromolecules); panel.render(targetId); - }; /** - * Shows a list of stock solutions with macromolecule, buffer, storage temperature, concentration, shipment and comments + * A shipment may contains one or more cases where stock solutions and sample plates are stored * - * @multiselect allows multiple selection - * @height - * @minHeight - * @width - * @tbar - * @showTitle - * @isPackedVisible shows is stock solution is in a box - * @btnEditVisible shows edit button - * @btnAddVisible - * @btnAddExisting - * @btnUnpackVisible allows to unpack a stock solution - * @btnRemoveVisible allow to remove a stock solution + * @height + * @btnEditVisible + * @btnRemoveVisible + * + * #onEditButtonClicked + * #onAddButtonClicked + * #onRemoveButtonClicked + * #onDuplicateButtonClicked */ +function CaseGrid(args) { -function StockSolutionGrid(args) { - this.id = BUI.id(); this.height = 100; - this.width = null; - this.minHeight = null; - this.tbar = true; - - this.title = "Stock Solutions"; - - /** Visible buttons and actions **/ this.btnEditVisible = true; this.btnRemoveVisible = true; - this.btnAddVisible = true; - this.btnAddExisting = false; - this.isPackedVisible = true; - this.btnUnpackVisible = false; - - /** Selectors **/ - this.multiselect = false; - this.selectedStockSolutions = []; if (args != null) { - if (args.btnUnpackVisible != null) { - this.btnUnpackVisible = args.btnUnpackVisible; - } - if (args.multiselect != null) { - this.multiselect = args.multiselect; - } if (args.height != null) { this.height = args.height; } if (args.btnEditVisible != null) { this.btnEditVisible = args.btnEditVisible; } - if (args.btnAddVisible != null) { - this.btnAddVisible = args.btnAddVisible; - } - if (args.btnAddExisting != null) { - this.btnAddExisting = args.btnAddExisting; - } - if (args.width != null) { - this.width = args.width; - } - if (args.minHeight != null) { - this.minHeight = args.minHeight; - } - if (args.tbar != null) { - this.tbar = args.tbar; - } if (args.btnRemoveVisible != null) { this.btnRemoveVisible = args.btnRemoveVisible; } - if (args.isPackedVisible != null) { - this.isPackedVisible = args.isPackedVisible; - } - if (args.showTitle != null) { - this.showTitle = args.showTitle; - if (this.showTitle == false) { - this.title = null; + } + + /** Events **/ + this.onEditButtonClicked = new Event(this); + this.onAddButtonClicked = new Event(this); + this.onRemoveButtonClicked = new Event(this); + this.onDuplicateButtonClicked = new Event(this); +} + +CaseGrid.prototype._getColumns = function() { + var _this = this; + + function actionItemRenderer(value, meta, record, rowIx, ColIx, store) { + /*if (record.raw.specimen3VOs.length > 0){ + return 'x-hide-display'; + }*/ + } + + var columns = [ + { + header : 'Code', + dataIndex : 'code', + name : 'code', + type : 'string', + flex : 1 + }, + { + header : 'Bar Code', + dataIndex : 'barCode', + name : 'barCode', + type : 'string', + flex : 1, + hidden : true + }, + { + header : 'BeamLine', + dataIndex : 'barCode', + type : 'string', + flex : 1, + renderer : function(comp, val, record) { + if (record.raw.sessionVO != null) { + return "" + record.raw.sessionVO.beamlineName + ""; + } + } + }, + { + header : 'Session', + dataIndex : 'barCode', + type : 'string', + flex : 1, + renderer : function(comp, val, record) { + if (record.raw.sessionVO != null) { + return "" + moment(record.raw.sessionVO.startDate).format("MMM Do YY") + ""; + } } - } - - } - - /** Events **/ - this.onProposalChanged = new Event(this); - this.onStockSolutionSelected = new Event(this); -} - -StockSolutionGrid.prototype._getColumns = function() { - var _this = this; - var columns = [ - - { - header : 'Macromolecule', - dataIndex : 'macromolecule', - id : _this.id + 'macromolecule', - type : 'string', - renderer : function(val, y, specimen) { - return '' + val + ''; }, - hidden : false, - flex : 1 - }, { - header : 'Buffer', - dataIndex : 'buffer', - name : 'buffer', - hidden : false, - renderer : function(val, y, specimen) { - return '' + val + ''; + { + header : 'Status', + dataIndex : 'dewarStatus', + name : 'dewarStatus', + type : 'string', + flex : 1, + renderer : function(comp, val, record) { + if (new String(record.raw.dewarStatus).toUpperCase() == 'OPENED') { + return "" + new String(record.raw.dewarStatus).toUpperCase() + ""; + } + return "" + new String(record.raw.dewarStatus).toUpperCase() + ""; + } }, - type : 'string', - flex : 1 - }, { - header : 'Acronym', - dataIndex : 'name', - name : 'name', - type : 'string', - flex : 1, - hidden : true - }, { - header : 'Storage Temp.', - dataIndex : 'storageTemperature', - name : 'storageTemperature', - type : 'string', - flex : 1, - hidden : false, - renderer : function(val) { - return BUI.formatValuesUnits(val, 'C', { - fontSize : 12, - decimals : 2, - unitsFontSize : 10 - }); - } - }, { - header : 'Volume', - dataIndex : 'volume', - type : 'string', - flex : 1, - hidden : false, - renderer : function(val) { - return BUI.formatValuesUnits(val, 'µl', { - fontSize : 12, - decimals : 2, - unitsFontSize : 10 - }); - } - }, { - header : 'Concentration', - dataIndex : 'concentration', - name : 'concentration', - type : 'string', - flex : 1, - renderer : function(val) { - return BUI.formatValuesUnits(val, 'mg/ml', { - fontSize : 12, - decimals : 2, - unitsFontSize : 10 - }); - } - }, { - header : 'Packed', - dataIndex : 'comments', - id : _this.id + "box", - type : 'string', - width : 50, - hidden : !this.isPackedVisible, - renderer : function(val, cmp, a) { - if (a.raw.boxId != null) { - return "
"; + { + header : 'Type', + dataIndex : 'type', + name : 'type', + type : 'string', + flex : 1, + hidden : true + }, + { + header : 'Sample Plates', + dataIndex : 'plates', + name : 'plates', + type : 'string', + flex : 1, + hidden : true + }, + { + header : 'Stock Solutions', + dataIndex : 'plates', + name : 'plates', + type : 'string', + width : 100, + renderer : function(comp, val, record) { + var html = "
"; + var stockSolutions = BIOSAXS.proposal.getStockSolutionsByDewarId(record.raw.dewarId); + html = html + "" + stockSolutions.length + " x"; + return html + "
"; } - + }, { + header : 'isStorageDewar', + dataIndex : 'isStorageDewar', + name : 'isStorageDewar', + type : 'string', + flex : 1, + hidden : true + }, { + header : 'Tracking Number From Synchrotron', + dataIndex : 'trackingNumberFromSynchrotron', + name : 'trackingNumberFromSynchrotron', + type : 'string', + flex : 1, + hidden : true + }, { + header : 'Tracking Number To Synchrotron', + dataIndex : 'trackingNumberToSynchrotron', + name : 'trackingNumberToSynchrotron', + type : 'string', + flex : 1, + hidden : true + }, { + header : 'Storage Location', + dataIndex : 'storageLocation', + name : 'storageLocation', + type : 'string', + flex : 1, + hidden : false + }, { + header : 'Comments', + dataIndex : 'comments', + name : 'comments', + type : 'string', + flex : 1, + hidden : false } - }, { - header : 'Comments', - dataIndex : 'comments', - type : 'string', - flex : 1 - } ]; + ]; if (this.btnEditVisible) { columns.push({ id : _this.id + 'buttonEdit', + text : '', + hidden : !_this.btnEditVisible, width : 85, sortable : false, renderer : function(value, metaData, record, rowIndex, colIndex, store) { - if (_this.btnEditVisible) { - return BUI.getGreenButton('EDIT'); - } + return BUI.getGreenButton('EDIT'); } }); } @@ -22014,4646 +16857,9803 @@ StockSolutionGrid.prototype._getColumns = function() { }); } - if (this.btnUnpackVisible) { - columns.push({ - id : _this.id + 'buttonUnpack', - width : 85, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - if (_this.btnUnpackVisible) { - return BUI.getBlueButton('UNPACK'); - } - } - }); - } + columns.push({ + dataIndex : 'comments', + type : 'string', + width : 85, + hidden : false, + renderer : function(comp, val, record) { + return BUI.getBlueButton("LABELS", { + href : BUI.getPrintcomponentURL(record.raw.dewarId) + }); + } + }); + return columns; }; -StockSolutionGrid.prototype._getTopButtons = function() { - var _this = this; - /** Actions buttons **/ - var actions = []; - - /** ADD BUTTON **/ - if (this.btnAddVisible) { - actions.push(Ext.create('Ext.Action', { - icon : '../images/add.png', - text : 'Add Stock Solution', - tooltip : 'Will create a new stock solution', - disabled : false, - alwaysEnabled : true, - handler : function(widget, event) { - _this.edit(); - } - })); - } - - if (this.btnAddExisting) { - actions.push(Ext.create('Ext.Action', { - icon : '../images/add.png', - text : 'Add Existing', - tooltip : 'Allows to select upacked stock solutions', - disabled : false, - alwaysEnabled : true, - handler : function(widget, event) { - var stockSolutionGrid = new StockSolutionGrid({ - btnAddVisible : false, - btnEditVisible : false, - btnRemoveVisible : false, - btnAddExisting : false, - isPackedVisible : true, - multiselect : true - }); - - var window = Ext.create('Ext.window.Window', { - title : 'Select', - height : 400, - width : 800, - layout : 'fit', - items : [ stockSolutionGrid.getPanel() ], - buttons : [ { - text : 'Pack', - handler : function() { - _this.onStockSolutionSelected.notify(stockSolutionGrid.selectedStockSolutions); - window.close(); - } - }, { - text : 'Cancel', - handler : function() { - window.close(); - } - } ] - - }).show(); +CaseGrid.prototype._getTopButtons = function() { + var _this = this; + /** Actions buttons **/ + var actions = []; - stockSolutionGrid.refresh(BIOSAXS.proposal.getUnpackedStockSolutions()); - } - })); - } + /** ADD BUTTON **/ + actions.push(Ext.create('Ext.Action', { + icon : '../images/add.png', + text : 'Add', + disabled : false, + handler : function(widget, event) { + _this.onAddButtonClicked.notify(); + } + })); return actions; }; -StockSolutionGrid.prototype.refresh = function(stockSolutions) { - this.features = stockSolutions; - this.store.loadData(this._prepareData(), false); +CaseGrid.prototype.refresh = function(dewars) { + this.features = dewars; + this.store.loadData(this._prepareData(dewars), false); }; -StockSolutionGrid.prototype._prepareData = function() { +CaseGrid.prototype._sort = function(store) { + store.sort('dewarId', 'DESC'); +}; + +CaseGrid.prototype._prepareData = function() { var data = []; for ( var i = 0; i < this.features.length; i++) { - var stockSolution = this.features[i]; - stockSolution.buffer = BIOSAXS.proposal.getBufferById(stockSolution.bufferId).acronym; - if (stockSolution.macromoleculeId != null) { - stockSolution.macromolecule = BIOSAXS.proposal.getMacromoleculeById(stockSolution.macromoleculeId).acronym; - } - data.push(stockSolution); + data.push(this.features[i]); } return data; }; -StockSolutionGrid.prototype.getPanel = function() { +CaseGrid.prototype.getPanel = function(dewars, plates) { + this.features = dewars; + this.plates = plates; return this._renderGrid(); }; -StockSolutionGrid.prototype.edit = function(stockSolutionId) { +CaseGrid.prototype._edit = function(dewar) { var _this = this; - var stockSolutionWindow = new StockSolutionWindow(); - /** On stock solution SAVED **/ - stockSolutionWindow.onSaved.attach(function(sender, stockSolution) { - _this.onProposalChanged.notify(stockSolution); + var caseWindow = new CaseWindow(); + /**SAVED **/ + caseWindow.onSaved.attach(function(sender, dewar) { + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, shipment) { + _this.refresh(shipment.dewarVOs); + }); + adapter.saveCase(BIOSAXS.proposal.getShipmentByDewarId(dewar.dewarId).shippingId, dewar); }); - stockSolutionWindow.draw(BIOSAXS.proposal.getStockSolutionById(stockSolutionId)); + caseWindow.draw(dewar); }; -StockSolutionGrid.prototype._getStoreFields = function() { +CaseGrid.prototype._getStoreFields = function(data) { return [ { - name : 'name', + name : 'dewarId', type : 'string' }, { - name : 'stockSolutionId', + name : 'barCode', type : 'string' }, { - name : 'macromolecule', + name : 'code', type : 'string' }, { - name : 'buffer', + name : 'comments', type : 'string' }, { - name : 'storageTemperature', - type : 'numeric' + name : 'dewarStatus', + type : 'string' }, { - name : 'volume', + name : 'isStorageDewar', type : 'string' }, { - name : 'concentration', + name : 'plates', type : 'string' }, { - name : 'buffer', + name : 'transportValue', type : 'string' }, { - name : 'comments', + name : 'trackingNumberFromSynchrotron', type : 'string' - } ]; -}; + }, { + name : 'trackingNumberToSynchrotron', + type : 'string' + }, { + name : 'timeStamp', + type : 'string' + }, { + name : 'storageLocation', + type : 'string' + }, { + name : 'type', + type : 'string' + } -//StockSolutionGrid.prototype.refresh = function() { -// this.proposal.onInitialized.attach(function(sender){ -// -// }); -// this.proposal.init(Ext.urlDecode(window.location.href).sessionId); -//}; + ]; +}; -StockSolutionGrid.prototype._renderGrid = function() { +CaseGrid.prototype._renderGrid = function() { var _this = this; /** Store **/ + var data = this._prepareData(); this.store = Ext.create('Ext.data.Store', { - fields : this._getStoreFields(), //columns, - autoload : true + fields : this._getStoreFields(data), + autoload : true, + data : data }); + this._sort(this.store); - var filters = { - ftype : 'filters', - local : true, - filters : this.filters - }; - - var selModel = null; - - if (this.multiselect) { - selModel = Ext.create('Ext.selection.CheckboxModel', { - //multiSelect : false,//this.multiselect, - mode : 'SINGLE', - listeners : { - selectionchange : function(sm, selections) { - _this.selectedStockSolutions = []; - for ( var i = 0; i < selections.length; i++) { - _this.selectedStockSolutions.push(selections[i].raw); - } - } - } - }); - } else { - selModel = { - mode : 'SINGLE' - }; - } - - this.store.sort("stockSolutionId", "desc"); + this.store.loadData(data, false); this.grid = Ext.create('Ext.grid.Panel', { style : { padding : 5 }, - icon : '/ispyb/images/SampleHolder_24x24_01.png', - title : this.title, height : this.height, - width : this.width, - minWidth : this.minWidth, - selModel : selModel, store : this.store, columns : this._getColumns(), viewConfig : { stripeRows : true, listeners : { itemdblclick : function(dataview, record, item, e) { - _this.edit(record.raw.stockSolutionId); - }, - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - var adapter = null; - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonUnpack') { - _this.grid.setLoading("ISPyB: Unpacking stock solution"); - adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender) { - _this.onProposalChanged.notify(); - _this.grid.setLoading(false); - }); - adapter.onError.attach(function(sender) { - _this.onProposalChanged.notify(); - _this.grid.setLoading(false); - }); - record.raw.boxId = null; - adapter.saveStockSolution(record.raw); - } - - if (grid.getGridColumns()[cellIndex].getId() == _this.id + "box") { - window.location = BUI.getShippingURL(BIOSAXS.proposal.getShipmentByDewarId(record.raw.boxId).shippingId); - } - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEdit') { - _this.edit(record.data.stockSolutionId); - } - - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemove') { - _this.grid.setLoading("ISPyB: Removing stock solution"); - adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender) { - _this.onProposalChanged.notify(); - _this.grid.setLoading(false); - }); - adapter.onError.attach(function(sender) { - _this.onProposalChanged.notify(); - _this.grid.setLoading(false); - }); - adapter.removeStockSolution(record.data.stockSolutionId); - } - } - } - } - - }); - - var actions = _this._getTopButtons(); - this.grid.addDocked({ - xtype : 'toolbar', - items : actions - }); - - var i = null; - this.grid.getSelectionModel().on({ - selectionchange : function(sm, selections) { - if (selections.length) { - for ( i = 0; i < actions.length; i++) { - if (actions[i].enable) { - actions[i].enable(); - } - } - } else { - for ( i = 0; i < actions.length; i++) { - if (actions[i].alwaysEnabled == false) { - if (actions[i].disable) { - actions[i].disable(); - } - } - } - } - } - }); - return this.grid; -}; - -StockSolutionGrid.prototype.input = function() { - return { - proposal : DATADOC.getProposal_10() - }; -}; - -StockSolutionGrid.prototype.test = function(targetId) { - var stockSolutionGrid = new StockSolutionGrid({ - height : 300, - width : 900 - }); - BIOSAXS.proposal = new Proposal(stockSolutionGrid.input().proposal); - var panel = stockSolutionGrid.getPanel(); - stockSolutionGrid.refresh(BIOSAXS.proposal.getStockSolutions()); - panel.render(targetId); -}; - - -function SuperpositionGrid(args) { - this.height = null; - this.width = null; - this.id = BUI.id(); - - if (args != null) { - if (args.height != null) { - this.height = args.height; - - if (args.width != null) { - this.width = args.width; - } - } - } - - this.onSelected = new Event(this); -} - -SuperpositionGrid.prototype._prepareData = function(data) { - return data; -}; + _this._edit(record.raw); + }, + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEdit') { + _this._edit(record.raw); + } -SuperpositionGrid.prototype.refresh = function(subtractions) { - var data = []; - if (subtractions != null){ - if (subtractions.length > 0){ - for (j in subtractions){ - var subtraction = subtractions[j]; - if (subtraction.superposition3VOs != null){ - for (i in subtraction.superposition3VOs){ - data.push(subtraction.superposition3VOs[i]); + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemove') { + _this.onRemoveButtonClicked.notify(_this.store.getAt(rowIndex).raw.dewarId); } } } + }, + selModel : { + mode : 'SINGLE' } - } - this.store.loadData(data); -}; + }); -SuperpositionGrid.prototype.getPanel = function() { - var _this = this; - this.store = Ext.create('Ext.data.Store', { - fields : [ 'abinitioModelPdbFilePath', 'aprioriPdbFilePath', 'alignedPdbFilePath' ], - data : [] + var actions = _this._getTopButtons(); + this.grid.addDocked({ + xtype : 'toolbar', + items : actions }); - this.selModel = Ext.create('Ext.selection.RowModel', { - allowDeselect : true, - mode : 'MULTI', - listeners : { - selectionchange : function(sm, selections) { - var selected = []; - for (var i = 0; i < selections.length; i++) { - selected.push(selections[i].raw); + this.grid.getSelectionModel().on({ + selectionchange : function(sm, selections) { + if (selections.length) { + for ( var i = 0; i < actions.length; i++) { + if (actions[i].enable) { + actions[i].enable(); + } + } + } else { + for ( var i = 0; i < actions.length; i++) { + if (actions[i].alwaysEnabled == false) { + if (actions[i].disable) { + actions[i].disable(); + } + } } - _this.onSelected.notify(selected); } } }); - - this.store.sort([ { - property : 'name', - direction : 'ASC' - } ]); + return this.grid; +}; - this.panel = Ext.create('Ext.grid.Panel', { - store : this.store, - selModel : this.selModel, - width : this.width, - height : this.height, - margin : 10, - deferredRender : false, - columns : [ { - text : 'Abinitio', - dataIndex : 'abinitioModelPdbFilePath', - hidden : false, - flex : 1, - renderer : function(val){ - return BUI.getFileName(val); - } - }, { - text : 'Apriori', - dataIndex : 'aprioriPdbFilePath', - hidden : false, - flex : 1, - renderer : function(val){ - return BUI.getFileName(val); - } - }, { - text : 'Aligned', - dataIndex : 'alignedPdbFilePath', - hidden : false, - flex : 1, - renderer : function(val){ - return BUI.getFileName(val); - } - } ], +CaseGrid.prototype.input = function() { + return { + proposal : DATADOC.getProposal_10(), + dewars : DATADOC.getDewars_10() - viewConfig : { - enableTextSelection : true, - preserveScrollOnRefresh : true - }, - listeners : { - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + }; +}; - }, - afterrender : function() { - } - } +CaseGrid.prototype.test = function(targetId) { + var CaseGrid = new CaseGrid({ + height : 150 }); - return this.panel; + BIOSAXS.proposal = new Proposal(CaseGrid.input().proposal); + var panel = CaseGrid.getPanel(CaseGrid.input().dewars); + panel.render(targetId); + }; +/** + * A shipment may contains one or more cases where stock solutions and sample plates are stored + * + * @height + * @btnEditVisible + * @btnRemoveVisible + * + * #onEditButtonClicked + * #onAddButtonClicked + * #onRemoveButtonClicked + * #onDuplicateButtonClicked + */ +function ExampleGrid(args) { + + this.height = 100; + this.btnEditVisible = true; + this.btnRemoveVisible = true; + + if (args != null) { + if (args.height != null) { + this.height = args.height; + } + if (args.btnEditVisible != null) { + this.btnEditVisible = args.btnEditVisible; + } + if (args.btnRemoveVisible != null) { + this.btnRemoveVisible = args.btnRemoveVisible; + } + } + + /** Events **/ + this.onEditButtonClicked = new Event(this); + this.onAddButtonClicked = new Event(this); + this.onRemoveButtonClicked = new Event(this); + this.onDuplicateButtonClicked = new Event(this); +} + +ExampleGrid.prototype._getColumns = function() { + var _this = this; + + function actionItemRenderer(value, meta, record, rowIx, ColIx, store) { + /*if (record.raw.specimen3VOs.length > 0){ + return 'x-hide-display'; + }*/ + } + + var columns = [ + { + header : 'Code', + dataIndex : 'code', + name : 'code', + type : 'string', + flex : 1 + }, + { + header : 'Bar Code', + dataIndex : 'barCode', + name : 'barCode', + type : 'string', + flex : 1, + hidden : true + }, + { + header : 'BeamLine', + dataIndex : 'barCode', + type : 'string', + flex : 1, + renderer : function(comp, val, record) { + if (record.raw.sessionVO != null) { + return "" + record.raw.sessionVO.beamlineName + ""; + } + } + }, + { + header : 'Session', + dataIndex : 'barCode', + type : 'string', + flex : 1, + renderer : function(comp, val, record) { + if (record.raw.sessionVO != null) { + return "" + moment(record.raw.sessionVO.startDate).format("MMM Do YY") + ""; + } + } + }, + { + header : 'Status', + dataIndex : 'dewarStatus', + name : 'dewarStatus', + type : 'string', + flex : 1, + renderer : function(comp, val, record) { + if (new String(record.raw.dewarStatus).toUpperCase() == 'OPENED') { + return "" + new String(record.raw.dewarStatus).toUpperCase() + ""; + } + return "" + new String(record.raw.dewarStatus).toUpperCase() + ""; + } + }, + { + header : 'Type', + dataIndex : 'type', + name : 'type', + type : 'string', + flex : 1, + hidden : true + }, + { + header : 'Sample Plates', + dataIndex : 'plates', + name : 'plates', + type : 'string', + flex : 1, + hidden : true + }, + { + header : 'Stock Solutions', + dataIndex : 'plates', + name : 'plates', + type : 'string', + width : 100, + renderer : function(comp, val, record) { + var html = "
"; + var stockSolutions = BIOSAXS.proposal.getStockSolutionsByDewarId(record.raw.dewarId); + html = html + "" + stockSolutions.length + " x"; + return html + "
"; + } + }, { + header : 'isStorageDewar', + dataIndex : 'isStorageDewar', + name : 'isStorageDewar', + type : 'string', + flex : 1, + hidden : true + }, { + header : 'Tracking Number From Synchrotron', + dataIndex : 'trackingNumberFromSynchrotron', + name : 'trackingNumberFromSynchrotron', + type : 'string', + flex : 1, + hidden : true + }, { + header : 'Tracking Number To Synchrotron', + dataIndex : 'trackingNumberToSynchrotron', + name : 'trackingNumberToSynchrotron', + type : 'string', + flex : 1, + hidden : true + }, { + header : 'Storage Location', + dataIndex : 'storageLocation', + name : 'storageLocation', + type : 'string', + flex : 1, + hidden : false + }, { + header : 'Comments', + dataIndex : 'comments', + name : 'comments', + type : 'string', + flex : 1, + hidden : false + } + ]; + + if (this.btnEditVisible) { + columns.push({ + id : _this.id + 'buttonEdit', + text : '', + hidden : !_this.btnEditVisible, + width : 85, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + return BUI.getGreenButton('EDIT'); + } + }); + } + + if (this.btnRemoveVisible) { + columns.push({ + id : _this.id + 'buttonRemove', + width : 85, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + if (_this.btnRemoveVisible) { + return BUI.getRedButton('REMOVE'); + } + } + }); + } + + columns.push({ + dataIndex : 'comments', + type : 'string', + width : 85, + hidden : false, + renderer : function(comp, val, record) { + return BUI.getBlueButton("LABELS", { + href : BUI.getPrintcomponentURL(record.raw.dewarId) + }); + } + }); + + return columns; +}; + +ExampleGrid.prototype._getTopButtons = function() { + var _this = this; + /** Actions buttons **/ + var actions = []; + + /** ADD BUTTON **/ + actions.push(Ext.create('Ext.Action', { + icon : '../images/add.png', + text : 'Add', + disabled : false, + handler : function(widget, event) { + _this.onAddButtonClicked.notify(); + } + })); + + return actions; +}; + +ExampleGrid.prototype.refresh = function(dewars) { + this.features = dewars; + this.store.loadData(this._prepareData(dewars), false); +}; + +ExampleGrid.prototype._sort = function(store) { + store.sort('dewarId', 'DESC'); +}; + +ExampleGrid.prototype._prepareData = function() { + var data = []; + for ( var i = 0; i < this.features.length; i++) { + data.push(this.features[i]); + } + return data; +}; + +ExampleGrid.prototype.getPanel = function() { + this.grid = Ext.create('Ext.grid.Panel', { + style : { + padding : 5 + }, + height : this.height, + store : this.store, + columns : this._getColumns(), + viewConfig : { + stripeRows : true, + listeners : { + itemdblclick : function(dataview, record, item, e) { + _this._edit(record.raw); + }, + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEdit') { + _this._edit(record.raw); + } + + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemove') { + _this.onRemoveButtonClicked.notify(_this.store.getAt(rowIndex).raw.dewarId); + } + } + } + }, + selModel : { + mode : 'SINGLE' + } + }); + + var actions = _this._getTopButtons(); + this.grid.addDocked({ + xtype : 'toolbar', + items : actions + }); + + this.grid.getSelectionModel().on({ + selectionchange : function(sm, selections) { + if (selections.length) { + for ( var i = 0; i < actions.length; i++) { + if (actions[i].enable) { + actions[i].enable(); + } + } + } else { + for ( var i = 0; i < actions.length; i++) { + if (actions[i].alwaysEnabled == false) { + if (actions[i].disable) { + actions[i].disable(); + } + } + } + } + } + }); + return this.grid; +}; + + +ExampleGrid.prototype._getStoreFields = function(data) { + return [ { + name : 'dewarId', + type : 'string' + }, { + name : 'barCode', + type : 'string' + }, { + name : 'code', + type : 'string' + }, { + name : 'comments', + type : 'string' + }, { + name : 'dewarStatus', + type : 'string' + }, { + name : 'isStorageDewar', + type : 'string' + }, { + name : 'plates', + type : 'string' + }, { + name : 'transportValue', + type : 'string' + }, { + name : 'trackingNumberFromSynchrotron', + type : 'string' + }, { + name : 'trackingNumberToSynchrotron', + type : 'string' + }, { + name : 'timeStamp', + type : 'string' + }, { + name : 'storageLocation', + type : 'string' + }, { + name : 'type', + type : 'string' + } + + ]; +}; + +ExampleGrid.prototype._renderGrid = function() { + var _this = this; + + /** Store **/ + var data = this._prepareData(); + this.store = Ext.create('Ext.data.Store', { + fields : this._getStoreFields(data), + autoload : true, + data : data + }); + this._sort(this.store); + + this.store.loadData(data, false); + + this.grid = Ext.create('Ext.grid.Panel', { + style : { + padding : 5 + }, + height : this.height, + store : this.store, + columns : this._getColumns(), + viewConfig : { + stripeRows : true, + listeners : { + itemdblclick : function(dataview, record, item, e) { + _this._edit(record.raw); + }, + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEdit') { + _this._edit(record.raw); + } + + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemove') { + _this.onRemoveButtonClicked.notify(_this.store.getAt(rowIndex).raw.dewarId); + } + } + } + }, + selModel : { + mode : 'SINGLE' + } + }); + + var actions = _this._getTopButtons(); + this.grid.addDocked({ + xtype : 'toolbar', + items : actions + }); + + this.grid.getSelectionModel().on({ + selectionchange : function(sm, selections) { + if (selections.length) { + for ( var i = 0; i < actions.length; i++) { + if (actions[i].enable) { + actions[i].enable(); + } + } + } else { + for ( var i = 0; i < actions.length; i++) { + if (actions[i].alwaysEnabled == false) { + if (actions[i].disable) { + actions[i].disable(); + } + } + } + } + } + }); + return this.grid; +}; + +ExampleGrid.prototype.input = function() { + return { + proposal : DATADOC.getProposal_10(), + dewars : DATADOC.getDewars_10() + + }; +}; + +ExampleGrid.prototype.test = function(targetId) { + var ExampleGrid = new ExampleGrid({ + height : 150 + }); + BIOSAXS.proposal = new Proposal(ExampleGrid.input().proposal); + var panel = ExampleGrid.getPanel(ExampleGrid.input().dewars); + panel.render(targetId); + +}; + + /** - * See ExperimentGrid - * + * Shows a list of experiment AKA data acquisitions + * @height + * @sorters + * @minHeight + * @gridType: Ext.ux.LiveSearchGridPanel or Ext.grid.Panel + * @tbar true or false + * @grouping true or false + * @width + * @title + * #onEditButtonClicked */ -function TemplateGrid(args) { - - if (args == null) { - args = {}; - } - args.sorters = [ { - property : 'experimentId', - direction : 'DESC' - } ]; - - ExperimentGrid.prototype.constructor.call(this, args); -} - -TemplateGrid.prototype._getFilterTypes = ExperimentGrid.prototype._getFilterTypes; -TemplateGrid.prototype._prettyPrintMacromolecules = ExperimentGrid.prototype._prettyPrintMacromolecules; -TemplateGrid.prototype._getPercentage = ExperimentGrid.prototype._getPercentage; -TemplateGrid.prototype._getPercentageCollected = ExperimentGrid.prototype._getPercentageCollected; -TemplateGrid.prototype.getPercentageMerged = ExperimentGrid.prototype.getPercentageMerged; -TemplateGrid.prototype._prepareData = ExperimentGrid.prototype._prepareData; -TemplateGrid.prototype.getPanel = ExperimentGrid.prototype.getPanel; -TemplateGrid.prototype._renderGrid = ExperimentGrid.prototype._renderGrid; -TemplateGrid.prototype._editExperiment = ExperimentGrid.prototype._editExperiment; -TemplateGrid.prototype._removeExperimentById = ExperimentGrid.prototype._removeExperimentById; - -TemplateGrid.prototype._getTopButtons = function() { - /** Actions buttons * */ - var actions = []; - - actions.push(Ext.create('Ext.Action', { - icon : '../images/add.png', - text : 'Add experiment', - handler : function(widget, event) { - var wizardWidget = new WizardWidget({ - windowMode : true - }); - - wizardWidget.onFinished.attach(function(sender, result) { - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - var experiment = new Experiment(data); - BIOSAXS.openExperimentByExperiment(experiment); - wizardWidget.window.close(); - }); - wizardWidget.current.setLoading("ISPyB: Creating experiment"); - adapter.createTemplate(result.name, "comments", result.data); - }); - -// wizardWidget.draw(this.targetId, new ExperimentTypeWizardForm()); - wizardWidget.draw(this.targetId, new MeasurementCreatorStepWizardForm(BIOSAXS.proposal.getMacromolecules())); - } - })); - return actions; -}; - -TemplateGrid.prototype.refresh = function(data) { - var filtered = []; - for ( var i = 0; i < data.length; i++) { - if (data[i].experimentType == "TEMPLATE") { - filtered.push(data[i]); - } - } - this.store.loadData(this._prepareData(filtered), false); -}; - -TemplateGrid.prototype._getColumns = function() { - var _this = this; - function actionItemRenderer(value, meta, record, rowIx, ColIx, store) { - if (record.raw.buffer3VOs != null) { - if (record.raw.buffer3VOs.length > 0) { - return 'x-hide-display'; - } - } +function ExperimentGrid(args) { + this.width = "100%"; + this.height = 700; + this.minHeight = 500; - if (record.data.platesCount > 0) { - return 'x-hide-display'; - } - } + this.id = BUI.id(); + this.gridType = 'Ext.grid.Panel'; //'Ext.ux.LiveSearchGridPanel'; + this.tbar = false; + this.hideHeaders = false; + this.grouping = true; + this.title = null; - return [ { - xtype : 'rownumberer', - width : 40 - }, { - text : 'experimentId', - dataIndex : 'experimentId', - name : 'experimentId', - type : 'string', - hidden : true + this.filtered = null; + + /** maximum row count **/ + this.limit = 100; + + this.sessionIdFilter = null; + + /** if not null filtered by date **/ + this.date = null; + + this.sorters = [ { + property : 'date', + direction : 'DESC' }, { - text : 'Name', - dataIndex : 'name', - name : 'name', - type : 'string', - flex : 1 - }, + property : 'time', + direction : 'DESC' + } ]; - { - text : 'Type', - dataIndex : 'type', - name : 'type', - type : 'string', - hidden : true, - flex : 1, - renderer : function(val) { - return val; + this.dates = {}; + if (args != null) { + if (args.height != null) { + this.height = args.height; } - }, { - text : 'Macromolecules', - name : 'macromolecules_names', - dataIndex : 'macromolecules_names', - flex : 1, - renderer : function(val) { - return " " + val + ""; + if (args.limit != null) { + this.limit = args.limit; } - }, { - id : _this.id + 'GO', - width : 80, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - return BUI.getGreenButton('EDIT'); + if (args.sorters != null) { + this.sorters = args.sorters; } - }, { - id : _this.id + 'REMOVE', - width : 100, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - return BUI.getRedButton('REMOVE'); + if (args.sessionId != null){ + this.sessionIdFilter = args.sessionId; + } + if (args.filtered != null) { + this.filtered = args.filtered; + } + if (args.minHeight != null) { + this.minHeight = args.minHeight; + } + if (args.gridType != null) { + this.gridType = args.gridType; + } + if (args.tbar != null) { + this.tbar = args.tbar; + } + if (args.grouping != null) { + this.grouping = args.grouping; + } + if (args.width != null) { + this.width = args.width; + } + if (args.title != null) { + this.title = args.title; } - } ]; -}; - -TemplateGrid.prototype.input = function() { - var experiments = DATADOC.getExperimentList_10(); - return { - experiments : experiments, - proposal : new MeasurementGrid().input().proposal - - }; -}; - -TemplateGrid.prototype.test = function(targetId) { - var experimentGrid = new TemplateGrid({ - height : 350, - minHeight : 350, - width : 1000, - gridType : 'Ext.grid.Panel', - title : 'Experiments', - grouping : false, - tbar : true - }); - BIOSAXS.proposal = new Proposal(experimentGrid.input().proposal); - var panel = experimentGrid.getPanel(experimentGrid.input().experiments); - experimentGrid.refresh(experimentGrid.input().experiments); - panel.render(targetId); -}; - -function VolumeGrid() { - this.id = BUI.id(); + } + /** Events **/ + this.onEditButtonClicked = new Event(this); } -VolumeGrid.prototype.getPanel = function(experiment) { - this.experiment = experiment; - return this.render(); +ExperimentGrid.prototype._getFilterTypes = function() { + return []; }; -VolumeGrid.prototype.getVolumesPanel = function(data, title) { - var _this = this; - var store = Ext.create('Ext.data.Store', { - fields : [ 'name', 'volume', 'macromoleculeId', 'bufferId' ], - data : data - }); - store.sort([ { - property : 'name', - direction : 'ASC' - } ]); - - var grid = Ext.create('Ext.grid.Panel', { - title : title, - height : 400, - maxHeight : 400, - width : 900, - store : store, - margin : '10 0 50 10', - tbar : [ { - text : 'Go to Shipment', - icon : '../images/plane-small.gif', - handler : function() { - window.location = BUI.getCreateShipmentList(); - } - } ], - viewConfig : { - stripeRows : true, - listeners : { - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonCreate') { - var stockSolutionWindow = new StockSolutionWindow(); - /** On stock solution SAVED **/ - stockSolutionWindow.onSaved.attach(function(sender, stockSolution) { - BIOSAXS.proposal.onInitialized.attach(function(sender, data) { - _this.refresh(_this.experiment); - }); - BIOSAXS.proposal.init(); - }); - var acronym = "ST"; - if (record.raw.macromoleculeId != null) { - acronym = acronym + "_" + BIOSAXS.proposal.getMacromoleculeById(record.raw.macromoleculeId).acronym; - } - if (record.raw.bufferId != null) { - acronym = acronym + "_" + BIOSAXS.proposal.getBufferById(record.raw.bufferId).acronym; - } - stockSolutionWindow.draw({ - concentration : record.raw.concentration, - macromoleculeId : record.raw.macromoleculeId, - bufferId : record.raw.bufferId, - name : acronym, - volume : record.raw.volume - }); - } - - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonStockSolutions') { - var stockSolutionGrid = new StockSolutionGrid({ - btnAddVisible : false, - btnEditVisible : false, - btnRemoveVisible : false, - btnAddExisting : false, - isPackedVisible : true, - multiselect : false - }); - - var window = Ext.create('Ext.window.Window', { - title : 'Stock solutions by specimen', - height : 400, - width : 800, - layout : 'fit', - items : [ stockSolutionGrid.getPanel() ], - buttons : [ { - text : 'Close', - handler : function() { - window.close(); - } - } ] - - }).show(); - stockSolutionGrid.refresh(BIOSAXS.proposal.getStockSolutionsBySpecimen(record.raw.macromoleculeId, record.raw.bufferId)); - } - } - } - }, - columns : [ -// { -// text : '', -// dataIndex : 'macromoleculeId', -// width : 20, -// renderer : function(val, y, sample) { -// if (val != null) { -//// return BUI.getRectangleColorDIV(BIOSAXS.proposal.macromoleculeColors[val], 10, 10); -// return BUI.getRectangleColorDIV(_this.experiment.macromoleculeColors[val], 10, 10); -// } -// } -// }, -// { -// text : '', -// dataIndex : 'bufferId', -// width : 20, -// renderer : function(val, y, sample) { -// if (val != null) { -// return BUI.getRectangleColorDIV(_this.experiment.getSpecimenColorByBufferId(val), 10, 10); -// } -// } -// }, - { - text : 'Specimen', - dataIndex : 'name', - flex : 0.5 - }, - { - text : 'Estimated Volume', - dataIndex : 'volume', - tooltip : 'Estimation of the maximum volume needed for making this experiment', - flex : 0.5, - editor : { - allowBlank : true - }, - renderer : function(val, y, sample) { - return BUI.formatValuesUnits(sample.data.volume, 'µl', { - fontSize : 16, - decimals : 2, - unitsFontSize : this.unitsFontSize - }); - } - }, - { - text : 'Stock Solution', - id : _this.id + 'buttonStockSolutions', - dataIndex : 'name', - flex : 0.5, - tooltip : 'Stock Solutions containing this specimen in this proposal', - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - var macromoleculeId = record.raw.macromoleculeId; - var bufferId = record.raw.bufferId; - var stockSolutions = BIOSAXS.proposal.getStockSolutionsBySpecimen(macromoleculeId, bufferId); - if (stockSolutions.length > 0) { - return "
" + stockSolutions.length + " x
"; - } +ExperimentGrid.prototype._prepareData = function(rows) { + var data = []; + var count = 0; + + rows.sort(function(a,b){return b.experimentId - a.experimentId;}); + for ( var i = 0; i < rows.length; i++) { + var row = rows[i]; + this.dates[moment(row.creationDate).format("YYYYMMDD")] = moment(row.creationDate).format("MMM Do YY"); + if ( + ( this.filtered == null || row.experimentType == this.filtered ) && (count < this.limit || this.limit == null ) && (this.sessionIdFilter == null || this.date != null || (this.date == null && this.sessionIdFilter == row.sessionId)) + ){ - } - }, { - id : _this.id + 'buttonCreate', - text : '', - tooltip : 'Create a new stock solution for shipping', - width : 170, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - return BUI.getGreenButton('NEW STOCK SOLUTION', { - width : 160 + data.push({ + experimentId : row.experimentId, + status : row.status, + dataAcquisitionFilePath : row.dataAcquisitionFilePath, + type : row.experimentType, + name : row.name, + macromolecules_names : row.macromolecules, + percentageAnalysed : { + value : (row.dataCollectionDoneCount / row.dataCollectionCount) * 100, + text : row.dataCollectionDoneCount + " of " + row.dataCollectionCount + }, + percentageCollected : { + value : (row.measurementDoneCount / row.measurementCount) * 100, + text : row.measurementDoneCount + " of " + row.measurementCount + }, + percentageMerged : { + value : (row.measurementAveragedCount / row.measurementCount) * 100, + text : row.measurementAveragedCount + " of " + row.measurementCount + }, + date : moment(row.creationDate).format("YYYYMMDD"), + time : moment(row.creationDate).format("YYYYMMDDHHmmss"), + creationDate : row.creationDate }); - } - } ] - }); - return grid; + count ++; + } + } + return data; +}; +ExperimentGrid.prototype.getPanel = function(experiments) { + this.features = experiments; + return this._renderGrid(experiments); }; -VolumeGrid.prototype._prepareData = function(experiment) { - var keys = {}; - for ( var i = 0; i < experiment.getSamples().length; i++) { - var sample = experiment.getSamples()[i]; - var key = ""; - if (sample.macromoleculeId == null) { - key = experiment.getBufferById(sample.bufferId).acronym; - if (keys[key] == null) { - keys[key] = { - macromoleculeId : sample.macromoleculeId, - name : key, - bufferId : sample.bufferId, - volume : 0 - }; - } - keys[key].volume = Number(sample.volume) + Number(keys[key].volume); +ExperimentGrid.prototype.refresh = function(experiments) { + this.experiments = experiments; + var filtered = []; + for ( var i = 0; i < experiments.length; i++) { + if (experiments[i].experimentType != "TEMPLATE") { + filtered.push(experiments[i]); } + } - if ((sample.macromolecule3VO != null) || (sample.macromoleculeId != null)) { - macromoleculeId = sample.macromoleculeId; - if (sample.macromoleculeId == null) { - sample.macromoleculeId = sample.macromolecule3VO.macromoleculeId; - } - key = BIOSAXS.proposal.getMacromoleculeById(sample.macromoleculeId).acronym + " + " + experiment.getBufferById(sample.bufferId).acronym; - if (keys[key] == null) { - keys[key] = { - macromoleculeId : sample.macromoleculeId, - name : key, - bufferId : sample.bufferId, - volume : 0 - }; - } - keys[key].volume = Number(sample.volume) + Number(keys[key].volume); + this.parsedData = this._prepareData(filtered); + + var day = {}; + var dates = []; + for ( var i = 0; i < this.experiments.length; i++) { + var date = moment(this.experiments[i].creationDate).format("MMM Do YYYY"); + if (day[date] == null){ + dates.push({ + date : date, + value : moment(this.experiments[i].creationDate) + }); + day[date] = true; } } - var data = []; - for (var keyId in keys) { - data.push(keys[keyId]); + + this.storeDate.loadData(dates, false); + this.store.loadData(this.parsedData, false); + + /** If it has already been filtered by date we keep the filter **/ + if (this.date != null){ + this._filterByDate(this.date); } - - return data; }; -VolumeGrid.prototype.refresh = function(experiment) { - this.experiment = experiment; - this.macromoleculeGrid.getStore().loadData(this._prepareData(this.experiment), false); -}; +ExperimentGrid.prototype._getTopButtons = function() { + var _this = this; + /** Actions buttons **/ + var actions = []; -VolumeGrid.prototype.render = function() { - this.macromoleculeGrid = this.getVolumesPanel(this._prepareData(this.experiment), "Estimation of required Volume"); + actions.push(Ext.create('Ext.Action', { + icon : '../images/calendar_icon.png', + text : 'Show Calendar', + disabled : false, + handler : function(widget, event) { + var window = Ext.create('Ext.window.Window', { + title : 'Calendar', + width : 600, + height : 600, + modal : true, + closable : true, + layout : { + type : 'vbox', + align : 'stretch' + }, + items : [ { + xtype : 'label', + html : 'Click on a data acquisition to select:', + margin : '5 5 5 5' + }, { + html : '
', + margin : '5 5 5 5' + } - return { - xtype : 'container', - layout : 'vbox', - margin : "0, 0, 0, 5", - items : [ { - xtype : 'container', - layout : 'hbox', - margin : "0, 0, 0, 0", - items : [ this.macromoleculeGrid ] - } ] - }; + ] + }).show(); + + var calendarWidget = new CalendarWidget({ + height : 450 + }); + var aux = _this.limit; + /** we remove the limit temporarily **/ + _this.limit = null; + _this.sessionIdFilter = null; + calendarWidget.loadData(_this._prepareData(_this.experiments)); + _this.limit = aux; + calendarWidget.draw('calendar'); + calendarWidget.onClick.attach(function(sender, date) { + date = moment(date, "YYYY-MM-DD"); + _this._filterByDate(date); + window.close(); + + }); + + } + })); + this.storeDate = Ext.create('Ext.data.ArrayStore', { + fields: ['date', 'value'], + data : [] + }); + + this.dateMenu = Ext.create('Ext.form.field.ComboBox', { + hideLabel: true, + store: this.storeDate, + displayField: 'date', + typeAhead: true, + queryMode: 'local', + margin : '0 0 0 30', + triggerAction: 'all', + emptyText:'Select a date...', + selectOnFocus:true, + width:135, + listeners:{ + scope: this, + 'select': function (a,b,c){ + _this.limit = null; + _this._filterByDate(moment(b[0].raw.value, "YYYY-MM-DD")); + } + } + }); + + actions.push(this.dateMenu); + + actions.push("->"); + if (_this.filtered != null){ + actions.push({ + html : "Experiment Type: " + _this.filtered +"" + }); + } + else{ + actions.push({ + html : "Experiment Type: ALL" + }); + } + return actions; }; -VolumeGrid.prototype.input = function(experiment) { - return { - experiment : DATADOC.getExperiment_10() - }; +/** + * Date format: "YYYY-MM-DD" + */ +ExperimentGrid.prototype._filterByDate = function(date) { + var experimentsFiltered = []; + /** Getting all the experiments of date**/ + for ( var i = 0; i < this.experiments.length; i++) { + var experiment = this.experiments[i]; + if (experiment.creationDate != null) { + var experimentDate = moment(experiment.creationDate); + if (experimentDate.year() == date.year()) { + if (experimentDate.month() == date.month()) { + if (experimentDate.date() == date.date()) { + experimentsFiltered.push(experiment); + } + } + } + } + } + var parsedData = this._prepareData(experimentsFiltered); + this.store.loadData(parsedData); + this.date = date; }; -VolumeGrid.prototype.test = function(targetId) { - var volumeGrid = new VolumeGrid(); - BIOSAXS.proposal = new Proposal(new MeasurementGrid().input().proposal); - var panel = volumeGrid.getPanel(new Experiment(new VolumeGrid().input().experiment)); - Ext.create('Ext.panel.Panel', { - height : 500, - width : 1000, - renderTo : targetId, - items : [ panel ] +/** Only for templates **/ +ExperimentGrid.prototype._removeExperimentById = function(experimentId) { + var _this = this; + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(evt, args) { + _this.grid.setLoading(false); + document.getElementById(BIOSAXS.targetId).innerHTML = ""; + BIOSAXS.start(BIOSAXS.targetId); }); + this.grid.setLoading("Removing experiment "); + adapter.removeExperimentById(experimentId); }; - -/** - * Example of a tab panel to be populated with widgets - * - * @width width in pixels - * @height height in pixels - * - * #myEvent event that this class is supposed to throw - * - **/ -function ExampleTabs(args) { - this.width = 500; - this.height = 500; + +ExperimentGrid.prototype._renderGrid = function() { + var _this = this; + + /** Store **/ + this.store = Ext.create('Ext.data.Store', { + fields : this._getColumns(), + groupField : 'date', + autoload : true, + data : [], + remoteSort: false, + sorters : this.sorters + }); + - if (args != null){ - if (args.width != null){ - this.width= args.width; - } - if (args.height != null){ - this.height= args.height; - } - } - /** Events **/ - this.myEvent = new Event(); -} - -/** Populate the widget **/ -ExampleTabs.prototype.refresh = function(macromolecule) { -}; + var groupingFeature = Ext.create('Ext.grid.feature.Grouping', { + groupHeaderTpl : Ext.create('Ext.XTemplate', + "
{name:this.formatName}
", { + formatName : function(name) { + return _this.dates[name]; + } + }), + hideGroupedHeader : true, + startCollapsed : false + }); -/** It creates a tab panel with the specified with and height **/ -ExampleTabs.prototype.getPanel = function() { - this.panel = Ext.createWidget('tabpanel', { - height : this.height, - width : this.width, - style : { - padding : 2 + this.features = []; + if (this.grouping) { + this.features.push(groupingFeature); + } + + /** Grid **/ + this.grid = Ext.create(this.gridType, { + hideHeaders : this.hideHeaders, + resizable : true, + title : this.title, + width : this.width, + minHeight : this.minHeight, + height : this.height, + features : this.features, + store : this.store, + columns : this._getColumns(), + selModel : { + mode : 'SINGLE' }, - items : [ { - tabConfig : { - title : 'Test', - icon : '/ispyb/images/plane-small.gif' + viewConfig : { + stripeRows : true, + getRowClass : function(record, rowIdx, params, store) { + if (record.raw.type == "TEMPLATE") { + return "template-color-row"; + } + if ((record.raw.type == "CALIBRATION") && (record.raw.status == "FINISHED")) { + return "blue-row"; + } }, - items : [ { - xtype : 'container', - margin : '5 5 5 5', - items : [ ] - } ] - } ] + listeners : { + itemdblclick : function(dataview, record, item, e) { + _this._editExperiment(record.raw.experimentId); + }, + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'GO') { + _this._editExperiment(record.raw.experimentId); + } + + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'REMOVE') { + _this._removeExperimentById(record.raw.experimentId); + } + + } + } + } }); - return this.panel; -}; - -/** - * Shows an experiments with the specimens, measurements, analysis tabs where - * results are shown and the frames widget - * - * @targetId - */ -function ExperimentTabs(targetId) { - this.height = 900; - this.targetId = targetId; + var actions = _this._getTopButtons(); - this.id = BUI.id(); - var _this = this; + if (this.tbar) { + this.grid.addDocked({ + xtype : 'toolbar', + items : actions + }); + this.grid.getSelectionModel().on({ + selectionchange : function(sm, selections) { + if (selections.length) { + for ( var i = 0; i < actions.length; i++) { + if (actions[i].enable) { + actions[i].enable(); + } + } + } else { + for ( var i = 0; i < actions.length; i++) { + if (actions[i].alwaysEnabled == false) { + if (actions[i].disable) { + actions[i].disable(); + } + } + } + } + } + }); + } - this.INTERVAL_UPDATE = BUI.getUpdateInterval(); + return this.grid; +}; - this.gridHeight = 1000; - /** data * */ - this.experiment = null; +ExperimentGrid.prototype._getColumns = function() { + var _this = this; + function actionItemRenderer(value, meta, record, rowIx, ColIx, store) { + if (record.raw.buffer3VOs != null) { + if (record.raw.buffer3VOs.length > 0) { + return 'x-hide-display'; + } + } - - /** Specimen Widget contains a specimenGrid and a sampleChangerWidget than can be displayed with are vertical or horizontal layout **/ - this.specimenWidget = new SpecimenWidget({ - height : 600 - }); - - - /** For Overview * */ - /*this.samplePlateGroupWidget = new SamplePlateGroupWidget({ - showTitle : false, - height : 250, - margin : 5, - border : 0 + if (record.data.platesCount > 0) { + return 'x-hide-display'; + } + } - });*/ + return [ + { + text : 'experimentId', + dataIndex : 'experimentId', + name : 'experimentId', + type : 'string', + hidden : true + }, + { + xtype : 'rownumberer', + width : 40 + }, + { + text : 'Name', + dataIndex : 'name', + name : 'name', + type : 'string', + flex : 1 + }, - /** For Measurements * */ - /*this.measurementSamplePlateGroupWidget = new SamplePlateGroupWidget({ - showTitle : false, - height : 250, - margin : '5 0 0 0', - border : 0 - });*/ + { + text : 'Type', + dataIndex : 'type', + name : 'type', + type : 'string', + flex : 1, + renderer : function(val) { + if (val == "CALIBRATION") { + return "" + val + ""; + } + + return val; + } + }, + { + text : 'Macromolecules', + name : 'macromolecules_names', + dataIndex : 'macromolecules_names', + flex : 1, + renderer : function(val) { + if (val != null) { + return " " + val + ""; + } + return " Information not available"; + } + }, + { + text : 'Buffers', + dataIndex : 'buffer_names', + name : 'buffer_names', + flex : 1, + hidden : true, + renderer : function(val) { + return "Buffer/s: " + val + ""; + } + }, + { + text : 'Status', + dataIndex : 'status', + name : 'status', + type : 'string', + flex : 1, + renderer : function(val, x, sample) { + if (sample.raw.type == "TEMPLATE") { + return "READY"; + } + if (sample.raw.status == "ABORTED") { + return "" + val + ""; + } + return "" + val + ""; + } + }, + { + text : 'Download', + dataIndex : 'creationDate', + name : 'creationDate', + renderer : function(val, x, sample) { + if (sample != null) { + if (sample.raw.type == "HPLC") { + return; + } + return BUI.getZipHTMLByExperimentId(sample.raw.experimentId, sample.raw.name); + } + }, + width : 100 - this.measurementGridDone = new MeasurementGrid({ - height : 600, - minHeight : 400, - maxHeight : 800, - positionColumnsHidden : true, - showTitle : false, - estimateTime : true, - width : 900, - maxWidth : 1500, - addBtnEnable : false, - markDone : true, - removeBtnEnabled : false - }); - this.measurementGridDone.onSelected.attach(function(sender, measurements) { - var specimens = []; - for ( var i = 0; i < measurements.length; i++) { - specimens.push(_this.experiment.getSampleById(measurements[i].specimenId)); - } - //_this.measurementSamplePlateGroupWidget.selectSpecimens(specimens); - }); + }, + { + header : 'Measurements', + dataIndex : 'percentageCollected', + name : 'percentageCollected', + type : 'string', + renderer : function(val, y, sample) { + if ((sample.raw.type == "TEMPLATE") || (sample.raw.type == "HPLC")) { + return; + } + return "
" + BUI.getProgessBar(sample.raw.percentageCollected.value, sample.raw.percentageCollected.text) + "
"; + }, + width : 100 + }, + { + header : 'Averaged', + dataIndex : 'percentageMerged', + name : 'percentageMerged', + type : 'string', + renderer : function(val, y, sample) { + if ((sample.raw.type == "TEMPLATE") || (sample.raw.type == "HPLC")) { + return; + } + return "
" + BUI.getProgessBar(sample.raw.percentageMerged.value, sample.raw.percentageMerged.text) + "
"; + }, + width : 100 + }, + { + header : 'Subtractions', + dataIndex : 'percentageAnalysed', + name : 'percentageAnalysed', + type : 'string', + renderer : function(val, y, sample) { + if ((sample.raw.type == "TEMPLATE") || (sample.raw.type == "HPLC")) { + return; + } + return "
" + BUI.getProgessBar(sample.raw.percentageAnalysed.value, sample.raw.percentageAnalysed.text) + "
"; + }, + width : 100 + }, - /** AnalysisGrid * */ - this.analysisGrid = new AnalysisGrid({ - height : Ext.getBody().getViewSize().height * 0.9 - 300, - positionColumnsHidden : true, - sorters : [ { - property : 'priorityLevelId', - direction : 'ASC' - } ] - }); - - - /** Queue * */ - this.queueGrid = new QueueGrid({ - url : BUI.getQueueUrlByExperiment(), - height : Ext.getBody().getViewSize().height * 0.9 - 300, - width : Ext.getBody().getViewSize().width * 0.9 - 300, - isGrouped : true, - tbar : false, - bbar : false, - sorter : [{ - property: 'measurementId', - direction: 'DESC' - }] - }); + { + text : 'time', + dataIndex : 'time', + name : 'time', + hidden : true, + renderer : function(val) { + return val; + }, + width : 100 -} + }, { + text : 'Date', + dataIndex : 'date', + name : 'date', + renderer : function(val) { + return val; + }, + width : 100 -ExperimentTabs.prototype.error = function(error) { - var e = JSON.parse(error); - showError(e); - this.panel.setLoading(false); -}; + }, -ExperimentTabs.prototype.draw = function(experiment) { - this.renderDataAcquisition(experiment); -}; + { + text : 'Time', + dataIndex : 'creationDate', + name : 'creationDate', + renderer : function(val) { + return moment(val).format(" HH:mm:ss"); + }, + width : 100 -ExperimentTabs.prototype.refreshAnalysisData = function() { - var _this = this; - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - _this.analysisGrid.refresh(data, {experiment : _this.experiment}); - }); - adapter.getAnalysisInformationByExperimentId(this.experiment.experimentId); - - /** Auto load **/ - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - _this.queueGrid.refresh(data); - }); - adapter.getCompactAnalysisByExperimentId(this.experiment.experimentId); - this.queueGrid.store.proxy.url = BUI.getQueueUrlByExperiment(this.experiment.experimentId); - this.queueGrid.refresh(); + }, { + id : _this.id + 'GO', + width : 80, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + return BUI.getGreenButton('GO'); + } + } ]; }; -ExperimentTabs.prototype.getSpecimenContainerHeight = function(experiment) { - var maxItems = 0; - if (maxItems < experiment.getSamples().length + 1) { - maxItems = experiment.getSamples().length + 1; - } - - var height = (maxItems + 1) * 40 + 40; - if (height > 400) { - height = 400; +/** Changes location.href in order to edit the experiment **/ +ExperimentGrid.prototype._editExperiment = function(experimentId) { + if (Ext.urlDecode(window.location.href).sessionId != null) { + location.href = 'viewProjectList.do?reqCode=display&experimentId=' + experimentId + '&sessionId='+ Ext.urlDecode(window.location.href).sessionId; + } else { + location.href = 'viewProjectList.do?reqCode=display&experimentId=' + experimentId; } - return height; -}; - -ExperimentTabs.prototype.getExperimentTitle = function() { - var experimentHeaderForm = new ExperimentHeaderForm(); - return experimentHeaderForm.getPanel(this.experiment); }; -ExperimentTabs.prototype.renderDataAcquisition = function(experiment) { - var _this = this; - this.experiment = experiment; +ExperimentGrid.prototype.input = function() { + var experiments = DATADOC.getExperimentList_10(); + return { + experiments : experiments, + proposal : new MeasurementGrid().input().proposal - var specimenGrid = new SpecimenGrid({ - height : 400, - maxHeight : 500, - width : 890 - }); + }; +}; - specimenGrid.onClick.attach(function(sender, args) { - }); +ExperimentGrid.prototype.test = function(targetId) { + var experimentGrid = new ExperimentGrid({ + height : 350, + minHeight : 350, + width : 1000 - specimenGrid.onSelected.attach(function(sender, specimens) { - //_this.samplePlateGroupWidget.selectSpecimens(specimens); - }); - var specimenContainer = this.specimenWidget.getPanel(); - this.specimenWidget.refresh(experiment); - /* - var specimenContainer = Ext.create('Ext.container.Container', { - layout : 'hbox', - width : 900, - padding : '10 0 0 2', - items : [ specimenGrid.getPanel() ] }); + BIOSAXS.proposal = new Proposal(experimentGrid.input().proposal); + var panel = experimentGrid.getPanel(experimentGrid.input().experiments); + experimentGrid.refresh(experimentGrid.input().experiments); + panel.render(targetId); +}; + + +function FitStructureToExperimentDataGrid(args) { + this.height = null; + this.width = null; + this.id = BUI.id(); + + if (args != null) { + if (args.height != null) { + this.height = args.height; + + if (args.width != null) { + this.width = args.width; + } + } + } + + this.onSelected = new Event(this); +} + +FitStructureToExperimentDataGrid.prototype.getStructuresByMacromolecule = function(macromolecule) { + var structures = []; + if (macromolecule.structure3VOs != null) { + if (macromolecule.structure3VOs.length > 0) { + for (var i = 0; i < macromolecule.structure3VOs.length; i++) { + structures.push(macromolecule.structure3VOs[i]); + } + } + } + return structures; +}; + +FitStructureToExperimentDataGrid.prototype._prepareData = function(subtractions) { + var data = []; + for (var i = 0; i < subtractions.length; i++) { + + for (var j = 0; j < subtractions[i].fitStructureToExperimentalData3VOs.length; j++) { + var fit = subtractions[i].fitStructureToExperimentalData3VOs[j]; + data.push({ + fit : fit.fitFilePath, + fitStructureToExperimentalDataId : fit.fitStructureToExperimentalDataId, + mixtureToStructure3VOs : fit.mixtureToStructure3VOs, + subtractedFile : subtractions[i].substractedFilePath + }); + } + } + return data; + +}; + +FitStructureToExperimentDataGrid.prototype.refresh = function(subtractions) { + this.store.loadData(this._prepareData(subtractions), false); +}; + +FitStructureToExperimentDataGrid.prototype.getPanel = function() { + var _this = this; + this.store = Ext.create('Ext.data.Store', { + fields : [ 'fit', 'subtractedFile', 'structureId', 'fitFilePath', 'mixtureToStructure3VOs' ], + data : [] + }); + + this.store.sort([ { + property : 'name', + direction : 'ASC' + } ]); + + this.selModel = Ext.create('Ext.selection.RowModel', { + allowDeselect : true, + mode : 'MULTI', + listeners : { + selectionchange : function(sm, selections) { + var selected = []; + for (var i = 0; i < selections.length; i++) { + selected.push(selections[i].raw); + } + _this.onSelected.notify(selected); + } + } + }); + + this.panel = Ext.create('Ext.grid.Panel', { + store : this.store, + deferredRender : false, + width : this.width, + height : this.height, + margin : 10, + selModel : this.selModel, + columns : [ { + text : 'Name', + dataIndex : 'fit', + flex : 1, + renderer : function(val, b, record) { + return BUI.getFileName(val); + } + }, { + text : 'PDB', + dataIndex : 'mixtureToStructure3VOs', + flex : 1, + renderer : function(values, b, record) { + var html = ""; + for (var i = 0; i < values.length; i++) { + var structure = BIOSAXS.proposal.getStructuresById(values[i].structureId); + html = html + ""; + if (structure != null){ + html = html + ""; + } + html = html + ""; + } + return html + "
" + structure.name + "
"; + } + }, { + text : 'Volume Fraction', + dataIndex : 'mixtureToStructure3VOs', + flex : 1, + renderer : function(values, b, record) { + var html = ""; + for (var i = 0; i < values.length; i++) { + html = html + ""; + html = html + ""; + html = html + ""; + } + + return html + "
" + values[i].volumeFraction + "
"; + } + },{ + text : 'Subtraction', + dataIndex : 'subtractedFile', + flex : 1, + renderer : function(values, b, record) { + return values.split("/")[values.split("/").length - 1]; + } + },], + + viewConfig : { + enableTextSelection : true, + preserveScrollOnRefresh : true + }, + listeners : { + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + }, + afterrender : function() { + } + } + }); + return this.panel; +}; + +/** Static method **/ +FitStructureToExperimentDataGrid.prototype.RUNFitScattering = function(subtractionId, structureId) { + var _this = this; + /** Add to Workflow **/ + var adapter = new BiosaxsDataAdapter(); + var workflow = { + 'workflowTitle' : 'FitExperimentalDatatoStructure', + 'comments' : 'FitExperimentalDatatoStructure run from ISPyB for subtractionId: ' + subtractionId + ' and structureId ' + structureId + } + + var inputs = [ { + name : 'subtractionId', + value : subtractionId + }, { + name : 'structureId', + value : structureId + } ]; + + adapter.onSuccess.attach(function(sender, data) { + /** Add to Fit **/ + var adapter2 = new BiosaxsDataAdapter(); + var fit = { + 'workflowId' : data.workflowId, + 'subtractionId' : subtractionId, + 'structureId' : structureId, + 'comments' : 'Sent to workflow engine' + } + adapter2.onSuccess.attach(function(sender, fit) { + _this.refresh(_this.subtractionId, _this.macromolecule); + }); + adapter2.addFitStructureData(fit); + + }); + adapter.addWorkflow(workflow, inputs); + +}; + +/** + * It shows buffer grid with a top bar with "Add" button + * + * @height + * @searchBar + * @collapsed + * @width + */ +function FrameGrid(args) { + this.height = 500; + this.width = 500; + this.searchBar = false; + this.tbar = false; + this.collapsed = false; - specimenGrid.refresh(experiment);*/ - var experimentList = new ExperimentList([ _this.experiment ]); - var measurementContainer = Ext.create('Ext.container.Container', { - layout : 'vbox', - padding : '5px 0px 0px 10px', - items : [] - }); - measurementContainer.insert(0, _this.measurementGridDone.getPanel(this.experiment.getMeasurements(), experimentList)); -// measurementContainer.insert(1, _this.measurementSamplePlateGroupWidget.getPanel(experiment)); + if (args != null) { + if (args.height != null) { + this.height = args.height; + } + + if (args.searchBar != null) { + this.searchBar = args.searchBar; + } - // this.dataCollectionCurveVisualizer = new DataCollectionCurveVisualizer(); - // this.dataCollectionCurveVisualizer.experiments = [experiment]; - // this.dataCollectionCurveVisualizer.dataCollectionFrameTree.experiments = - // [experiment]; - // this.dataCollectionCurveVisualizer.dataCollections = - // experiment.getDataCollections(); + if (args.tbar != null) { + this.tbar = args.tbar; + } - this.panel = Ext.createWidget('tabpanel', { - plain : true, - style : { - padding : 2 - }, - items : [ { - tabConfig : { - id : 'genralTabl', - title : "Overview" - }, - items : [ specimenContainer ] - }, { - tabConfig : { - title : 'Measurements' - }, - items : [ measurementContainer] - }, { - tabConfig : { - id : 'SpecimenTab', - title : 'Analysis', - hidden : this.isTemplate() - }, - items : [ { - xtype : 'container', - layout : 'vbox', - padding : '5px 0px 10px 10px', - items : [ _this.analysisGrid.getPanel([]) ] - } ] - }, - { - tabConfig : { - id : 'newAnalysisTab', - title : 'Analysis BETA', - hidden : this.isTemplate() - }, - items : [ { - xtype : 'container', - layout : 'vbox', - padding : '5px 0px 10px 10px', - items : [ _this.queueGrid.getPanel([]) ] - } ] + if (args.collapsed != null) { + this.collapsed = args.collapsed; } - ] + + if (args.width != null) { + this.width = args.width; + } + } +} + +FrameGrid.prototype._edit = function(bufferId) { + var _this = this; + var window = new BufferWindow(); + window.onSuccess.attach(function(sender, proposal) { + _this.store.loadData(BIOSAXS.proposal.getBuffers()); }); + window.draw(BIOSAXS.proposal.getBufferById(bufferId)); +}; - return this.getPanel(this.panel); +FrameGrid.prototype.refresh = function(buffers, experimentId) { + this.experimentId = experimentId; + this.store.loadData(this._prepareData(buffers), false); }; -ExperimentTabs.prototype.isTemplate = function() { - if (this.experiment.json.type == "TEMPLATE") { - return true; - } - return false; +FrameGrid.prototype._prepareData = function(buffers) { + return buffers; }; -ExperimentTabs.prototype.update = function() { +FrameGrid.prototype._getTbar = function() { var _this = this; - var inter; - if (!_this.isTemplate()) { - function updateExperiments() { - _this.refreshAnalysisData(); - window.clearInterval(inter); - inter = setInterval(function() { - updateExperiments(); - }, _this.INTERVAL_UPDATE); - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - var experiment = new Experiment(data); - _this.measurementGridDone.refresh(experiment.getMeasurements(), new ExperimentList([ experiment ])); + var actions = []; + + actions.push(Ext.create('Ext.Action', { + icon : '../images/add.png', + text : 'Add Buffer', + disabled : false, + handler : function(widget, event) { + var window = new BufferWindow(); + window.onSuccess.attach(function(sender) { + _this.store.loadData(BIOSAXS.proposal.getBuffers()); }); - adapter.getExperimentById(_this.experiment.json.experimentId, "MEDIUM"); + window.draw({}); } - inter = setInterval(function() { - updateExperiments(); - }, _this.INTERVAL_UPDATE); - } + })); + return actions; }; -ExperimentTabs.prototype.getPanel = function(panel) { +FrameGrid.prototype.getPanel = function(buffers) { var _this = this; - if (this.experimentPanel == null) { - this.experimentPanel = Ext.create('Ext.container.Container', { - bodyPadding : 2, - width : Ext.getBody().getViewSize().width * 0.9, - renderTo : this.targetId, - style : { - padding : 2 - }, - items : [ this.getExperimentTitle(), this.panel ], - listeners : { - afterrender : function() { - _this.refreshAnalysisData(); - _this.update(); - } - } - }); - } - - return this.experimentPanel; -}; - -ExperimentTabs.prototype.input = function() { - return { - experiment : DATADOC.getExperiment_10(), - proposal : DATADOC.getProposal_10() - }; -}; - -ExperimentTabs.prototype.test = function(targetId) { - var experimentTabs = new ExperimentTabs(targetId); - BIOSAXS.proposal = new Proposal(experimentTabs.input().proposal); - experimentTabs.draw(new Experiment(experimentTabs.input().experiment)); -}; + this.store = Ext.create('Ext.data.Store', { + fields : [ 'frameNumber', 'I0', 'Rg', 'Mass', 'Vc', 'Qr', 'quality'], + data : buffers + }); - -/** - * Shows an experiments with the specimens, measurements, analysis tabs where results are shown and the frames widget - * - * @targetId - */ -function HPLCTabs(targetId) { - this.height = 1400; - this.targetId = targetId; + this.store.sort('frameNumber'); - this.id = BUI.id(); + var type = 'Ext.grid.Panel'; + if (this.searchBar == true) { + type = 'Ext.ux.LiveSearchGridPanel'; + } - this.gridHeight = 600; - this.pointsCount = 1036; - this.plotHeight = 350; - this.plotWidth = 800; - this.plotPanelPadding = 5; + this.grid = Ext.create(type, { + store : this.store, + height : this.height, + width : this.width, + margin : 5, + columns : [{ + text : 'Frame', + dataIndex : 'frameNumber', + flex : 1 + },{ + text : 'I0', + dataIndex : 'I0', + flex : 1, + renderer : function(val, y, sample) { + return BUI.formatValuesUnits(sample.data.I0, "", 12, 3); + } + },{ + text : 'Rg', + dataIndex : 'Rg', + flex : 1, + renderer : function(val, y, sample) { + return BUI.formatValuesUnits(sample.data.Rg, "nm", 12, 3); + } + },{ + text : 'Mass', + dataIndex : 'Mass', + flex : 1, + renderer : function(val, y, sample) { + return BUI.formatValuesUnits(sample.data.Mass, "", 12, 3); + } + },{ + text : 'Vc', + dataIndex : 'Vc', + flex : 1, + renderer : function(val, y, sample) { + return BUI.formatValuesUnits(sample.data.Vc, "", 12, 3); + } + },{ + text : 'Qr', + dataIndex : 'Qr', + flex : 1, + renderer : function(val, y, sample) { + return BUI.formatValuesUnits(sample.data.Qr, "", 12, 3); + } + },{ + text : 'Quality', + dataIndex : 'quality', + flex : 1, + renderer : function(val, y, sample) { + return (Number(sample.data.quality) * 100).toFixed(2) + "%"; + } + }, + { + text : '', + renderer : function(val, x, sample) { + if (sample != null) { + return BUI.getZipHTMLByFrameRangeId(_this.experimentId, sample.raw.frameNumber, sample.raw.frameNumber); + } + }, + width : 100 + }], + flex : 1, + viewConfig : { + stripeRows : true + } + }); - var _this = this; + /** Adding the tbar **/ + if (this.tbar) { + this.grid.addDocked({ + xtype : 'toolbar', + items : this._getTbar() + }); + } + return this.grid; +}; - this.analysisGrid = new HPLCAnalysisGrid({ - height : Ext.getBody().getViewSize().height * 0.9 - 300, - positionColumnsHidden : true, - sorters : [ { - property : 'priorityLevelId', - direction : 'ASC' - } ] - }); +FrameGrid.prototype.input = function() { + return []; +}; - this.frameGrid = new FrameGrid({ - width : 600, - height : 60, - collapsed : false, - tbar : false - }); - - this.peakGrid = new PeakGrid({ - width : 550, - height : 500, - collapsed : false, - tbar : false - }); - - this.peakGrid2 = new PeakGrid({ - width : 102, - height : this.plotHeight, +FrameGrid.prototype.test = function(targetId) { + var frameGrid = new FrameGrid({ + width : 800, + height : 350, collapsed : false, - tbar : false, - showExtendedColumns : true + tbar : true }); - - this.mainPlotPanel = new HPLCGraph({ - title : 'I0', - width : this.plotWidth - 110, - height : this.plotHeight, - bbar : true, - plots : { - "I0" : true, - "Rg" : true - }, - xlabel : "HPLC Frames", - scaled : true, - interactionModel : { - 'dblclick' : function(event, g, context) { - _this._selectFrame(g.lastx_); - var annotations = []; - annotations.push({ - series : g.selPoints_[0].name, - x : g.lastx_, - width : 100, - height : 23, - tickHeight : 4, - shortText : g.lastx_, - text : g.lastx_, - attachAtBottom : true - }); - g.setAnnotations(annotations); - } + var panel = frameGrid.getPanel([]); + panel.render(targetId); +}; + + +function PeakGrid(args) { + this.height = 500; + this.searchBar = false; + this.tbar = false; + this.collapsed = false; + this.width = 500; + this.showExtendedColumns = false; + + if (args != null) { + if (args.showExtendedColumns != null) { + this.showExtendedColumns = args.showExtendedColumns; + } + if (args.height != null) { + this.height = args.height; + } + if (args.searchBar != null) { + this.searchBar = args.searchBar; } - }); - this.intensityPlotPanel = new MergesHPLCGraph({ - title : 'Scattering', - width : this.plotWidth, - height : 500, - showRangeSelector : false, - xParam : 0, - xlabel : "scattering_I", - plots : { - "scattering_I" : true, - "subtracted_I" : true, - "buffer_I" : true + if (args.tbar != null) { + this.tbar = args.tbar; } - }); -} + if (args.collapsed != null) { + this.collapsed = args.collapsed; + } -HPLCTabs.prototype._selectFrame = function(frameNumber) { - try{ - this._renderScatteringCurve(frameNumber); - this.frameGrid.refresh([this.mainPlotPanel.getDataByFrameNumber(frameNumber)], this.experiment.experimentId); - } - catch(e){ - console.log(e); + if (args.width != null) { + this.width = args.width; + } } -}; +} -HPLCTabs.prototype.error = function(error) { - var e = JSON.parse(error); - showError(e); - this.panel.setLoading(false); -}; -HPLCTabs.prototype.loadDataMainPlot = function(data) { - var zeroArray = []; - for ( var i = 0; i < data.I0.length; i++) { - zeroArray.push(0); - } - data = [ { - param : "I0", - data : data.I0, - std : data.I0_Stdev, - color : '#0066CC', - label : "I0" - }, - { - param : "sum_I", - label : "sum_I", - color : "#00FF00", - data : data.sum_I, - std : zeroArray - }, - { - param : "Rg", - label : "Rg", - color : "#21610B", - data : data.Rg, - std : data.Rg_Stdev - }, { - param : "Mass", - data : data.mass, - std : data.mass_Stdev, - color : '#FF9900', - label : "Mass" - }, { - param : "Vc", - data : data.Vc, - std : data.Vc_Stdev, - color : '#990099', - label : "Vc" - }, { - param : "Qr", - data : data.Qr, - std : data.Qr_Stdev, - color : '#FF0066', - label : "Qr" - }, { - param : "quality", - label : "quality", - color : "#FF00FF", - data : data.quality, - std : zeroArray - } ]; - this.data = data; - this.mainPlotPanel.loadData(data); +PeakGrid.prototype.refresh = function(buffers) { + this.store.loadData(this._prepareData(buffers), false); }; -HPLCTabs.prototype._loadIntensityPlotByFrameNumber = function(frameNumber) { - var _this = this; +PeakGrid.prototype._prepareData = function(buffers) { - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - var array = []; - data = [ { - param : "q", - data : data[frameNumber].q, - std : data[frameNumber].q, - fstd : function(a) { - return parseFloat(a); - }, - color : '#green', - label : "q", - showOnMenu : false - }, - { - param : "scattering_I", - data : data[frameNumber].scattering_I, - fdata : function(a) { - return Math.log(parseFloat(a)); - }, - std : data[frameNumber].scattering_Stdev, - fstd : function(a) { - return Math.log(Math.abs(parseFloat(a))); - }, - color : 'green', - label : "Log(I) Sample" - }, - { - param : "buffer_I", - data : data[frameNumber].buffer_I, - fdata : function(a) { - return Math.log(parseFloat(a)); - }, - fstd : function(a) { - return Math.log(Math.abs(parseFloat(a))); - }, - std : data[frameNumber].subtracted_Stdev, - color : '#0000FF', - label : "Log(I) Avg Buf." - }, - { - param : "subtracted_I", - data : data[frameNumber].subtracted_I, - fdata : function(a) { - var value = (Math.log(parseFloat(a))); - if (isNumber(value)) - return value; - }, - fstd : function(a) { - var value = Math.log(Math.abs(parseFloat(a))); - if (isNumber(value)) - return value; - }, - std : data[frameNumber].subtracted_Stdev, - color : 'red', - label : "Log(I) Sub." - } - ]; +// for ( var i = 0; i < buffers.length; i++) { +// buffers[i].name = "Peak #" + (i+1); +// } + /** Adding information of buffer **/ + if (buffers.length > 0){ + buffers.unshift({ + name : "BUFFER", + start : 0, + experimentId : buffers[0].experimentId, + end : buffers[0].start - 1 + }); + } + + + return buffers; +}; - _this.intensityPlotPanel.xlabel = "Frame " + frameNumber + " (q, nm-1)"; +PeakGrid.prototype._getTbar = function() { + var _this = this; + var actions = []; - if (_this.intensityPlotPanel.hplcData == null) { - /** It creates also top bar **/ - _this.intensityPlotPanel.loadData(data); - } else { - _this.intensityPlotPanel.reloadData(data); - + actions.push(Ext.create('Ext.Action', { + icon : '../images/add.png', + text : 'Add Buffer', + disabled : false, + handler : function(widget, event) { + var window = new BufferWindow(); + window.onSuccess.attach(function(sender) { + _this.store.loadData(BIOSAXS.proposal.getBuffers()); + }); + window.draw({}); } - _this.intensityPlotPanel.panel.setLoading(false); - }); - adapter.onError.attach(function(sender, data) { - _this.intensityPlotPanel.panel.setLoading(false); - }); - this.intensityPlotPanel.panel.setLoading("Retrieving Frame " + frameNumber); - adapter.getH5FrameScattering(this.experiment.json.experimentId, frameNumber); + })); + return actions; }; -HPLCTabs.prototype._renderScatteringCurve = function(frameNumber) { +PeakGrid.prototype.getPanel = function(buffers) { var _this = this; + this.peakCount = 0; + this.store = Ext.create('Ext.data.Store', { + fields : ['name', {name:'start', type : 'int'}, {name:'end', type : 'int'}], + data : buffers + + }); - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - _this.intensityPlotPanel.setPeaks(data); - _this._loadIntensityPlotByFrameNumber(frameNumber); - try{ - var peaks = []; - for(key in data){ - peaks.push({ - start : key.split("-")[0], - end : key.split("-")[1], - experimentId : _this.experiment.json.experimentId - }); + this.store.sort('start'); + + var type = 'Ext.grid.Panel'; + if (this.searchBar == true) { + type = 'Ext.ux.LiveSearchGridPanel'; + } + this.grid = Ext.create(type, { + store : this.store, + height : this.height, + width : this.width, + margin : 5, + columns : [ + { + text : '', + dataIndex : 'name', + width : 100, + hidden : _this.showExtendedColumns, + renderer : function(val, y, sample) { + if (sample.data.name == "BUFFER") + return "BUFFER"; + _this.peakCount++; + return "Peak #" + _this.peakCount; + } + + + }, + { + text : 'Peaks', + dataIndex : 'start', + sortable : true, + width : 100, + hidden: !_this.showExtendedColumns, + renderer : function(val, y, sample) { + return "From " + Number(sample.raw.start) + " to " + Number(sample.raw.end); + } + }, + { + text : 'Frames', + hidden : _this.showExtendedColumns, + columns : [ + { + text : 'Start', + dataIndex : 'start', + sortable : true, + hidden : _this.showExtendedColumns, + width : 100, + renderer : function(val, y, sample) { + return Number(val); + } + },{ + text : 'End', + dataIndex : 'end', + width : 100, + hidden : _this.showExtendedColumns, + renderer : function(val, y, sample) { + return Number(val); + } + },{ + text : 'Total', + dataIndex : 'end', + width : 100, + hidden : _this.showExtendedColumns, + renderer : function(val, y, sample) { + return "" + (sample.raw.end - sample.raw.start) + " frames"; + } + } + ] + } +// , +// { +// text : '', +// hidden : _this.showExtendedColumns, +// renderer : function(val, x, sample) { +// if (sample != null) { +// return BUI.getZipHTMLByFrameRangeId(sample.raw.experimentId, sample.raw.start, sample.raw.end); +// } +// }, +// width : 100 +// } + ], + flex : 1, + viewConfig : { + stripeRows : true, + getRowClass : function(record, rowIdx, params, store) { + if (record.raw.name == "BUFFER") { + return "blue-row"; + } } - _this.peakGrid2.refresh(JSON.parse(JSON.stringify(peaks))); - _this.peakGrid.refresh(peaks); -// console.log(peaks); - } - catch(e){ - showError(e); } }); - adapter.onError.attach(function(sender, data) { - _this.intensityPlotPanel.setLoading(false); + + /** Adding the tbar **/ + if (this.tbar) { + this.grid.addDocked({ + xtype : 'toolbar', + items : this._getTbar() + }); + } + return this.grid; +}; + +PeakGrid.prototype.input = function() { + return []; +}; + +PeakGrid.prototype.test = function(targetId) { + var PeakGrid = new PeakGrid({ + width : 800, + height : 350, + collapsed : false, + tbar : true }); - this.intensityPlotPanel.panel.setLoading("Reading HDF5 File "); - adapter.getH5FramesMerge(this.experiment.json.experimentId); + + var panel = PeakGrid.getPanel([]); + panel.render(targetId); }; + +/** + * Macromolecule Grid showing macromolecules and adding anb updating buttons + * + * @height + * @maxHeight + * @width + * @cssFontStyle + * @searchBar makes this grid as Ext.ux.LiveSearchGridPanel + * @tbar top bar containing "Add" and "Update From SMIS" button + * @collapsed + * @collapsible + * @btnEditVisible + * @btnRemoveVisible + * @multiselect makes it multiselect using Ext.selection.CheckboxModel + * + * #onSelected + * #onMacromoleculesChanged + */ +function MacromoleculeGrid(args) { + this.height = 500; + this.width = 500; + this.id = BUI.id(); + this.maxHeight = this.height; -HPLCTabs.prototype._postRenderOverviewPanel = function() { - var _this = this; - var adapter = new BiosaxsDataAdapter(); - adapter.onError.attach(function(sender, data) { - data = data.replace(/NaN/g, '0'); - _this.loadDataMainPlot(JSON.parse(data)); - + this.searchBar = false; + this.tbar = false; + + this.collapsible = true; + this.collapsed = true; + + this.btnEditVisible = true; + this.btnRemoveVisible = false; + this.multiselect = false; + + /** Font style applied to the acronym column **/ + this.cssFontStyle = null; + + if (args != null) { + if (args.height != null) { + this.height = args.height; + this.maxHeight = this.height; + } + if (args.maxHeight != null) { + this.maxHeight = args.maxHeight; + } + if (args.width != null) { + this.width = args.width; + } + if (args.cssFontStyle != null) { + this.cssFontStyle = args.cssFontStyle; + } + + if (args.searchBar != null) { + this.searchBar = args.searchBar; + } + if (args.tbar != null) { + this.tbar = args.tbar; + } + if (args.collapsible != null) { + this.collapsible = args.collapsible; + } + if (args.collapsed != null) { + this.collapsed = args.collapsed; + } + if (args.btnEditVisible != null) { + this.btnEditVisible = args.btnEditVisible; + } + if (args.btnRemoveVisible != null) { + this.btnRemoveVisible = args.btnRemoveVisible; + } + if (args.multiselect != null) { + this.multiselect = args.multiselect; + } + } - }); - adapter.onSuccess.attach(function(sender, data) { - _this.loadDataMainPlot(data); - _this._renderScatteringCurve(0); - }); - adapter.getH5fileParameters(this.experiment.json.experimentId, [ - "I0", "I0_Stdev", "sum_I","Rg", "Rg_Stdev", "Vc", "Vc_Stdev", "Qr", "Qr_Stdev", "mass", "mass_Stdev", "quality" ]); + this.onSelected = new Event(); -}; + this.onMacromoleculesChanged = new Event(); +} -HPLCTabs.prototype._postRenderDetailsPanel = function() { - if (this.data != null) { - this.I0PlotPanel.loadData(this.data); - this.RgPlotPanel.loadData(this.data); - this.MassPlotPanel.loadData(this.data); - this.VcPlotPanel.loadData(this.data); - } -}; -HPLCTabs.prototype.draw = function(experiment) { - var _this = this; - this.renderDataAcquisition(experiment); -}; -HPLCTabs.prototype.getExperimentTitle = function() { - var experimentHeaderForm = new ExperimentHeaderForm(); - return experimentHeaderForm.getPanel(this.experiment); -}; -HPLCTabs.prototype.renderDataAcquisition = function(experiment) { +MacromoleculeGrid.prototype.edit = function(macromolecule) { var _this = this; - this.experiment = experiment; - if (this.experimentPanel == null) { - this.experimentPanel = Ext.create('Ext.container.Container', { - bodyPadding : 2, - height : this.height, - width : Ext.getBody().getViewSize().width * 0.9, - renderTo : this.targetId, - style : { - padding : 2 - }, - items : [ this.getExperimentTitle(), this.getPanel() ], - listeners : { - afterrender : function() { - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - _this.analysisGrid.refresh(data); - }); - adapter.getAnalysisInformationByExperimentId(_this.experiment.experimentId); - } - } - }); - } - return this.experimentPanel; + var window = new MacromoleculeWindow(); + window.onSave.attach(function(sender) { + _this.store.loadData(BIOSAXS.proposal.getMacromolecules()); + _this.onMacromoleculesChanged.notify(); + }); + window.draw(macromolecule); }; -HPLCTabs.prototype.getPanel = function() { +MacromoleculeGrid.prototype.getTbar = function() { var _this = this; - this.panel = Ext.createWidget('tabpanel', - { - plain : true, - height : this.height, -// width : 900, - style : { - padding : 2 - }, - items : [ - { - tabConfig : { - title : "Overview" + var actions = []; - }, - items : [ { - xtype : 'container', - layout : 'hbox', - border : 1, - flex : 1, - items : [ { - xtype : 'container', - layout : 'vbox', - border : 1, - items : [ { - xtype : 'container', - margin : '10px', - border : 1, - items : [ - { - xtype : 'container', - margin : '0px', - layout : 'hbox', - border : 1, - items : [ - this.peakGrid2.getPanel([]), - this.mainPlotPanel.getPanel() - ] - }, - { - xtype : 'container', - layout : 'vbox', - border : 1, - items : [ - { - html: '
Select a frame by double-clicking on the HPLC Frames plot
', - margin: 5, - border : 0 - }, - this.frameGrid.getPanel([]), - this.intensityPlotPanel.getPanel() - ] - } - - ] - }], - listeners : { - afterrender : function() { - _this._postRenderOverviewPanel(); - } - } - } ] - } ] - }, -// { -// tabConfig : { -// title : "Details" -// }, -// items : [ { -// xtype : 'container', -// layout : 'hbox', -// border : 1, -// flex : 1, -// items : [ { -// xtype : 'container', -// layout : 'vbox', -// border : 1, -// items : [ { -// xtype : 'container', -// padding : '1px', -// items : [ -// this.I0PlotPanel.getPanel(), this.RgPlotPanel.getPanel(), this.MassPlotPanel.getPanel(), -// this.VcPlotPanel.getPanel() ] -// } ], -// listeners : { -// afterrender : function() { -// _this._postRenderDetailsPanel(); -// } -// } -// } ] -// } ] -// }, - { - tabConfig : { - title : "Analysis" - }, - items : [ { - xtype : 'container', - layout : 'vbox', - padding : '5px 0px 10px 10px', - items : [ _this.analysisGrid.getPanel([]) ] - } ] - }, - { - tabConfig : { - title : "File Manager" - }, - items : [ { - xtype : 'container', - layout : 'vbox', - padding : '5px 0px 10px 10px', - items : [ - { - html: '
Custom Download
', - margin : '10 0 10 5', - border : 0 - }, - { - html: '
Download has been temporary disabled. Contact your labcontact if you want to extract the frames from the HDF5 file
', - margin : '10 0 10 5', - hidden : _this.experiment.experimentId == 2602, - border : 0 - }, - { - xtype : 'container', - layout : 'hbox', - margin : '0 0 0 20', - flex : 1, - items :[ - { - xtype: 'numberfield', - id: 'field_start', - fieldLabel: 'Frames from', - value: 0, - minValue: 0 - }, - { - xtype: 'numberfield', - id: 'field_end', - fieldLabel: 'to', - labelWidth : 20, - margin : '0 0 0 10', - minValue: 0 - }, - { - xtype: 'button', - /** allowing test account to download frames **/ - disabled : _this.experiment.experimentId != 2602, - text : 'Download', - margin : '0 0 0 10', - handler : function() { - var experimentId = _this.experiment.experimentId; - var start = Ext.getCmp("field_start").getValue(); - var end = Ext.getCmp("field_end").getValue(); - /** Checking if start is bigger than end **/ - if (start > end){ - var aux = end; - end = start; - start = aux; - } - var url = BUI.getZipFrameHPLCUrl(experimentId, start, end); - window.open(url) - } - } - ] - }, - _this.peakGrid.getPanel([]) - - ] - } - ] - } - ] + actions.push(Ext.create('Ext.Action', { + icon : '../images/add.png', + text : 'Add macromolecule', + disabled : false, + handler : function(widget, event) { + _this.edit(); + } + })); + actions.push("->"); + actions.push(Ext.create('Ext.Action', { + icon : '../images/folder_go.png', + text : 'Update From SMIS', + tooltip : "Retrieve all the macromolecules of your proposal from SMIS database", + disabled : false, + handler : function(widget, event) { + _this.grid.setLoading("Connecting to SMIS"); + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + BIOSAXS.proposal.setMacromolecules(data.macromolecules); + _this.refresh(BIOSAXS.proposal.macromolecules); + _this.grid.setLoading(false); + }); + adapter.onError.attach(function(sender, data) { + _this.grid.setLoading(false); }); + adapter.updateDataBaseFromSMIS(); + } + })); + return actions; +}; - return this.panel; +MacromoleculeGrid.prototype.deselectAll = function() { + this.grid.getSelectionModel().deselectAll(); +}; + +MacromoleculeGrid.prototype.selectById = function(macromoleculeId) { + this.grid.getSelectionModel().deselectAll(); + for ( var i = 0; i < this.grid.getStore().data.items.length; i++) { + var item = this.grid.getStore().data.items[i].raw; + if (item.macromoleculeId == macromoleculeId) { + this.grid.getSelectionModel().select(i); + } + } +}; + +MacromoleculeGrid.prototype.refresh = function(macromolecules) { + this.store.loadData(macromolecules, false); +}; + +MacromoleculeGrid.prototype.getColumns = function() { + var _this = this; + var columns = [ + { + text : 'Acronym', + dataIndex : 'acronym', + id : this.id + "acronym", + flex : 1, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + if (_this.cssFontStyle != null) { + return "" + value + ""; + } + return value; + } + }, { + text : 'Name', + dataIndex : 'name', + id : this.id + "name", + flex : 1, + hidden : true + } ]; + + if (this.btnEditVisible) { + columns.push({ + id : _this.id + 'buttonEditMacromolecule', + width : 85, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + if (_this.btnEditVisible) { + return BUI.getGreenButton('EDIT'); + } + return null; + } + }); + } + if (this.btnRemoveVisible) { + columns.push({ + id : _this.id + 'buttonRemoveMacromolecule', + width : 85, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + if (_this.btnRemoveVisible) { + return BUI.getRedButton('REMOVE'); + } + return null; + } + }); + } + + return columns; +}; + + +/** Returns the grid **/ +MacromoleculeGrid.prototype.getPanel = function() { + var _this = this; + + this.store = Ext.create('Ext.data.Store', { + fields : [ 'macromoleculeId', 'name', 'acronym' ] + }); + + var type = 'Ext.grid.Panel'; + if (this.searchBar == true) { + type = 'Ext.ux.LiveSearchGridPanel'; + } + + this.selModel = Ext.create('Ext.selection.RowModel', { +// allowDeselect : true, +// mode : 'MULTI', + listeners : { + selectionchange : function(sm, selections) { + var selected = []; + for (var i = 0; i < selections.length; i++) { + selected.push(selections[i].raw); + } + _this.onSelected.notify(selected); + } + } + }); + + this.grid = Ext.create(type, { + id : this.id, + title : 'Macromolecules', + collapsible : this.collapsible, + collapsed : this.collapsed, + store : this.store, + height : this.height, + maxHeight : this.maxHeight, + selModel : this.selModel, + columns : this.getColumns(), + width : this.width, + viewConfig : { + stripeRows : true, + listeners : { + 'celldblclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + _this.edit(BIOSAXS.proposal.getMacromoleculeById(record.data.macromoleculeId)); + }, + 'cellclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEditMacromolecule') { + _this.edit(BIOSAXS.proposal.getMacromoleculeById(record.data.macromoleculeId)); + } + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemoveMacromolecule') { + BUI.showBetaWarning(); + } + } + + } + } + }); + + /** Adding the tbar **/ + if (this.tbar) { + this.grid.addDocked({ + xtype : 'toolbar', + items : this.getTbar() + }); + } + return this.grid; +}; + +MacromoleculeGrid.prototype.input = function() { + return { + proposal : DATADOC.getProposal_10() + }; +}; + +MacromoleculeGrid.prototype.test = function(targetId) { + var macromoleculeGrid = new MacromoleculeGrid({ + width : 800, + height : 350, + collapsed : false, + tbar : true + }); + + BIOSAXS.proposal = new Proposal(macromoleculeGrid.input().proposal); + var panel = macromoleculeGrid.getPanel(BIOSAXS.proposal.macromolecules); + panel.render(targetId); }; /** - * Main form tab for macromolecule + * Shows measurements with their attributes as specimen, exposure temperature, + * volume to load, transmission etc... * - * @width + * @addBtnMultipleEdit: if true add a button for changing measurements' + * parameters by choosing multiple measurements. It opens + * MultipleEditMeasurementGridWindow + * @collapsed: if true it doesn't show buffer's measurements + * @editor: hashmap containing columns to be edited. It is an array of a json + * like editor of Ext + * @selModel + * @collapseBtnEnable + * @removeBtnEnabled Ext.selection.RowModel + * @addBtnEnable + * @updateRowEnabled true/false if update plugin is set to the grid + * @showTitle + * @title + * @isStatusColumnHidden + * @isPriorityColumnHidden + * @isTimeColumnHidden + * @estimateTime + * @margin + * @tbar * @height + * @maxHeight + * @minHeight + * @width + * @maxWidth + * @resizable + * @experimentColorBased when colors for buffers and macromolecules are not + * selected by the proposal but by experiment, so the + * number of colors is smaller * - * #onClose when user clicks on close button in the MacromoleculeForm - * #onSave when macromole is saved by macromoleculeForm + * #onClick #onSelected #onRemoved #onUpdateTime #onMeasurementChanged + * #onExperimentChanged */ -function MacromoleculeTabs(args) { - this.width = 500; +function MeasurementGrid(args) { + this.id = BUI.id(); + this.height = 500; + this.width = 900; - if (args != null) { - if (args.width != null) { - this.width = args.width; + this.maxWidth = 1200; + this.maxHeight = 600; + this.minHeight = 500; + + this.unitsFontSize = 9; + this.title = "Measurements"; + this.estimateTime = false; + this.collapsed = true; + this.tbar = true; + + this.showTitle = true; + this.resizable = true; + this.updateRowEnabled = true; + + /** + * Hash map containing the keys of the editable columns. Ex: + * 'exposureTemperature' * + */ + this.editor = { + comments : { + xtype : 'textfield', + allowBlank : true } - if (args.height != null) { - this.height = args.height; + }; + + this.isTimeColumnHidden = false; + this.isStatusColumnHidden = false; + this.isPriorityColumnHidden = true; + this.margin = "0 0 0 0"; + + this.addBtnEnable = true; + this.sorter = [ { + property : 'priority', + direction : 'ASC' + } ]; + + this.removeBtnEnabled = false; + this.collapseBtnEnable = true; + this.addBtnMultipleEdit = false; + this.sortingBtnEnable = false; + + var _this = this; + this.selModel = Ext.create('Ext.selection.RowModel', { + allowDeselect : true, + mode : 'MULTI', + listeners : { + selectionchange : function(sm, selections) { + var selected = []; + for (var i = 0; i < selections.length; i++) { + selected.push(selections[i].raw); + } + _this.onSelected.notify(selected); + } } - } + }); - var _this = this; + if (args != null) { - /** Widgets **/ + if (args.selModel != null) { + this.selModel = args.selModel; + } - /** Macromolecule Form **/ - this.macromoleculeForm = new MacromoleculeForm({ - width : this.width - 30, - height : this.height - 50, - }); + if (args.removeBtnEnabled != null) { + this.removeBtnEnabled = args.removeBtnEnabled; + } - this.macromoleculeForm.onClose.attach(function(sender) { - _this.onClose.notify(); - }); + if (args.addBtnMultipleEdit != null) { + this.addBtnMultipleEdit = args.addBtnMultipleEdit; + } - this.macromoleculeForm.onSave.attach(function(sender, macromolecule) { - _this.onSave.notify(macromolecule); - }); + // if (args.experimentColorBased != null) { + // this.experimentColorBased = args.experimentColorBased; + // } - this.assemblyForm = new AssemblyForm({ - width : this.width - 30, - height : this.height - 50, - }); - - this.rigibBodyModelingForm = new RigibBodyModelingForm({ - width : this.width - 30, - height : this.height - 50, - }); - - this.rigibBodyModelingForm.onSave.attach(function(sender, macromolecule) { - _this.onSave.notify(macromolecule); - }); - + if (args.collapsed != null) { + this.collapsed = args.collapsed; + } + if (args.resizable != null) { + this.resizable = args.resizable; + } - /** Events **/ - this.onClose = new Event(this); - this.onSave = new Event(this); -} + if (args.editor != null) { + this.editor = args.editor; + } -/** Populate the widget **/ -MacromoleculeTabs.prototype.refresh = function(macromolecule) { - this.macromoleculeForm.refresh(macromolecule); - this.assemblyForm.refresh(macromolecule); - this.rigibBodyModelingForm.refresh(macromolecule); + if (args.collapseBtnEnable != null) { + this.collapseBtnEnable = args.collapseBtnEnable; + } - if (macromolecule != null){ - if (macromolecule.macromoleculeId == null){ - Ext.getCmp(this.id + "_advancedTab").disable(); - Ext.getCmp(this.id + "_assemblyTab").disable(); + if (args.addBtnEnable != null) { + this.addBtnEnable = args.addBtnEnable; } - else{ - Ext.getCmp(this.id + "_advancedTab").enable(); - Ext.getCmp(this.id + "_assemblyTab").enable(); + if (args.sortingBtnEnable != null) { + this.sortingBtnEnable = args.sortingBtnEnable; } - } - else{ - Ext.getCmp(this.id + "_advancedTab").disable(); - Ext.getCmp(this.id + "_assemblyTab").disable(); - } -}; -MacromoleculeTabs.prototype.getItems = function() { - return [ { - tabConfig : { - title : 'General' - }, - items : [ { - xtype : 'container', - items : [ this.macromoleculeForm.getPanel() ] - } ] - }, { - id : this.id + "_assemblyTab", - tabConfig : { - title : 'Assembly' - }, - items : [ { - xtype : 'container', - items : [ this.assemblyForm.getPanel() ] - } ] - },{ - id : this.id + "_advancedTab", - tabConfig : { - title : 'Advanced' - }, - items : [ this.rigibBodyModelingForm.getPanel() ] - } ]; -}; + if (args.isPriorityColumnHidden != null) { + this.isPriorityColumnHidden = args.isPriorityColumnHidden; + } -MacromoleculeTabs.prototype.getPanel = function() { - this.panel = Ext.createWidget('tabpanel', { - height : this.height, - width : this.width, - plain : true, - margin : 5, - border : 0, - items : this.getItems() - }); - return this.panel; -}; - -function ResultTabs() { -} + if (args.width != null) { + this.width = args.width; + } -ResultTabs.prototype.draw = function(targetId, data, macromoleculeId) { - var panel = this.getPanel(targetId, data, macromoleculeId); - return Ext.create('Ext.container.Container', { - renderTo : targetId, - items : [ BUI.getMacromoleculeHeader(macromoleculeId), panel ] - }); + if (args.updateRowEnabled != null) { + this.updateRowEnabled = args.updateRowEnabled; + } -}; + if (args.showTitle != null) { + this.showTitle = args.showTitle; + if (this.showTitle == false) { + this.title = null; + } + } -ResultTabs.prototype._splitBySpecimen = function(data) { - var splitted = {}; + if (args.height != null) { + this.height = args.height; + } - for ( var i = 0; i < data.length; i++) { - var row = data[i]; - if (splitted[row.macromoleculeId + "_" + row.bufferId] == null) { - splitted[row.macromoleculeId + "_" + row.bufferId] = []; + if (args.maxHeight != null) { + this.maxHeight = args.maxHeight; } - splitted[row.macromoleculeId + "_" + row.bufferId].push(row); - } - return splitted; -}; + if (args.minHeight != null) { + this.minHeight = args.minHeight; + } -ResultTabs.prototype._getTabTitle = function(key, data) { - var macromoleculeId = key.split("_")[0]; - var bufferId = key.split("_")[1]; + if (args.maxWidth != null) { + this.maxWidth = args.maxWidth; + } - return BIOSAXS.proposal.getMacromoleculeById(macromoleculeId).acronym + " + " + BIOSAXS.proposal.getBufferById(bufferId).acronym + "(" + data.length + ")"; -}; + if (args.isStatusColumnHidden != null) { + this.isStatusColumnHidden = args.isStatusColumnHidden; + } + if (args.isTimeColumnHidden != null) { + this.isTimeColumnHidden = args.isTimeColumnHidden; + } -ResultTabs.prototype.getPanel = function(targetId, data, macromoleculeId) { + if (args.title != null) { + this.title = args.title; + } + if (args.estimateTime != null) { + this.estimateTime = args.estimateTime; + } - var dataFiltered = new AnalysisGrid({ - hideNulls : true, - grouped : true, - sorters : [ { - property : 'quality', - direction : 'DESC' - } ] - })._prepareData(data); + if (args.margin != null) { + this.margin = args.margin; + } - var items = [ { - tabConfig : { - title : 'Analysis (' + dataFiltered.length + ')' - }, - items : [ { - xtype : 'container', - layout : 'vbox', - padding : 10, - items : [ new AnalysisGrid({ - isScatteringPlotVisible : false - }).getPanel(dataFiltered) ] - } ] - }, { - tabConfig : { - title : 'Concentration Effects' - }, - items : [ new ResultSummaryForm().getPanel(data) ] - } ]; + if (args.tbar != null) { + this.tbar = args.tbar; + } + + if (args.sorter != null) { + this.sorter = args.sorter; + } - var splitted = this._splitBySpecimen(dataFiltered); - for ( var key in splitted) { - items.push({ - tabConfig : { - title : this._getTabTitle(key, splitted[key]) - }, - items : [ new ResultSummaryForm().getPanel(splitted[key]) ] - }); } + this.onClick = new Event(this); + this.onSelected = new Event(this); + this.onRemoved = new Event(this); + this.onUpdateTime = new Event(this); + this.onMeasurementChanged = new Event(this); + this.onExperimentChanged = new Event(this); +} - this.panel = Ext.createWidget('tabpanel', { - style : { - padding : 2 - }, - items : items +MeasurementGrid.prototype._sortBy = function(sort) { + var _this = this; + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + _this.onExperimentChanged.notify(data); + _this.grid.setLoading(false); + // wizardWidget.window.close(); }); - return this.panel; - + adapter.onError.attach(function(sender, data) { + _this.grid.setLoading(false); + alert("Oops, there was a problem"); + }); + _this.grid.setLoading("Sorting"); + adapter.sortMeasurements(this.experiments.experiments[0].experimentId, sort); }; - - -function ShipmentTabs(targetId) { - this.targetId = targetId; +MeasurementGrid.prototype._getMenu = function() { var _this = this; - this.gridHeight = 500; - /** data **/ - this.shipment = null; - - /** Shipment Form **/ - this.shipmentForm = new ShipmentForm({ - creationMode : false, - showTitle : false - }); - this.shipmentForm.onSaved.attach(function(sender, data) { - _this.refresh(data); + if (this.tbar) { - }); + var items = []; + if (_this.addBtnEnable) { + items.push({ + icon : '../images/add.png', + text : 'Add measurements', + handler : function() { + _this._openAddMeasurementWindow(); + } + }); + } + if (_this.addBtnMultipleEdit) { + items.push({ + icon : '../images/Edit_16x16_01.png', + text : 'Multiple Edit', + handler : function() { + var multipleEditMeasurementGridWindow = new MultipleEditMeasurementGridWindow(); + multipleEditMeasurementGridWindow.onExperimentChanged.attach(function(sender, data) { + _this.onExperimentChanged.notify(data); + }); - /** Cases grid **/ - this.caseGrid = new CaseGrid({ - height : this.gridHeight - }); + multipleEditMeasurementGridWindow.draw(_this.measurements, _this.experiments); - this.caseGrid.onAddButtonClicked.attach(function(sender, dewar) { - _this.caseGrid.grid.setLoading("ISPyB: Creating a new case"); - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, shipment) { - /** updateing shipment on proposal **/ - for ( var i = 0; i < BIOSAXS.proposal.shippings.length; i++) { - if (BIOSAXS.proposal.shippings[i].shippingId == shipment.shippingId) { - BIOSAXS.proposal.shippings[i] = shipment; } - } - _this.refresh(shipment); - }); - adapter.onError.attach(function(sender, shipment) { - _this.caseGrid.grid.setLoading(false); - }); - adapter.addCase(_this.shipment.json.shippingId); - }); + }); + } - this.caseGrid.onRemoveButtonClicked.attach(function(sender, dewarId) { - _this.panel.setLoading("ISPyB: removing case"); - _this.shipment.onSaved.attach(function(sender, shipment) { - _this.refresh(shipment); + items.push("->"); - }); - _this.shipment.removeCase(dewarId); - }); -} + if (_this.sortingBtnEnable) { + var split = Ext.create('Ext.button.Split', { + text : 'Sort by', + // handle a click on the button itself + handler : function() { + // alert("The button was clicked"); + }, + menu : new Ext.menu.Menu({ + items : [ + { + text : 'First Created First Measured', + handler : function() { + _this._sortBy("FIFO"); + } + }, "-", { + text : 'Default', + handler : function() { + _this._sortBy("DEFAULT"); + } + } ] + }) + }); + items.push(split); + } -ShipmentTabs.prototype.refresh = function(shipment) { + if (_this.collapseBtnEnable) { + items.push({ + text : 'Collapse buffers', + enableToggle : true, + scope : this, + toggleHandler : function(item, pressed) { + this.collapsed = pressed; + this.grid.getStore().loadData(this._prepareData(this.measurements, this.experiments), false); + }, + pressed : this.collapsed + }); + } + var tb = Ext.create('Ext.toolbar.Toolbar', { + items : items + }); + return tb; + } + return null; +}; +/** Opens WizardWidget for adding new measurements * */ +MeasurementGrid.prototype._openAddMeasurementWindow = function(measurements, experiments) { var _this = this; - this.shipment = shipment; - var proposal = new Proposal(); - proposal.onDataRetrieved.attach(function(sender, plates) { - - _this.refreshWithPlates(shipment, plates); - _this.caseGrid.grid.setLoading(false); + var wizardWidget = new WizardWidget(); + wizardWidget.onFinished.attach(function(sender, result) { + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + _this.onExperimentChanged.notify(data); + _this.grid.setLoading(false); + wizardWidget.window.close(); + }); + wizardWidget.current.setLoading("ISPyB: Adding measurements"); + adapter.addMeasurements(result.name, "comments", result.data, _this.experiments.experiments[0].experimentId); }); - proposal.getPlatesByProposal(); + + wizardWidget.draw(null, new MeasurementCreatorStepWizardForm(BIOSAXS.proposal.getMacromolecules(), { + noNext : true + })); }; -ShipmentTabs.prototype.refreshWithPlates = function(shipment, plates) { - this.shipment = new Shipment(shipment); +/******************************************************************************* + * Opens WizardWidget for adding new measurements + * + * @Measurements + * @Experiments experimentList Object + ******************************************************************************/ +MeasurementGrid.prototype._prepareData = function(measurements, experiments) { + var data = []; + for (var i = 0; i < measurements.length; i++) { + var measurement = measurements[i]; + var specimen = experiments.getSampleById(measurement.specimenId); + var buffer = experiments.getBufferById(specimen.bufferId); + measurement.buffer_acronym = buffer.acronym; + measurement.bufferId = buffer.bufferId; + measurement.volume = specimen.volume; + if (specimen.macromolecule3VO != null) { + measurement.acronym = specimen.macromolecule3VO.acronym; + measurement.macromoleculeId = specimen.macromolecule3VO.macromoleculeId; + } + measurement.concentration = specimen.concentration; + if (measurement.run3VO != null) { + measurement.energy = measurement.run3VO.energy; + measurement.expExposureTemperature = measurement.run3VO.exposureTemperature; + measurement.storageTemperature = measurement.run3VO.storageTemperature; + measurement.timePerFrame = measurement.run3VO.timePerFrame; + measurement.radiationAbsolute = measurement.run3VO.radiationAbsolute; + measurement.radiationRelative = measurement.run3VO.radiationRelative; + measurement.status = "DONE"; - this.caseGrid.refresh(this.shipment.getDewars(), plates); - this.panel.setLoading(false); + try { + if (measurement.run3VO.timeStart != null) { + if (measurement.run3VO.timeStart != "") { + measurement.miliseconds = moment(measurement.run3VO.timeStart).format("X"); + } + } + } catch (E) { + console.log(E); + } + } + + if (experiments.getDataCollectionByMeasurementId(measurement.measurementId).length > 0) { + var measurementtodatacollection3VOs = experiments.getDataCollectionByMeasurementId(measurement.measurementId)[0].measurementtodatacollection3VOs; + for (var k = 0; k < measurementtodatacollection3VOs.length; k++) { + if (measurementtodatacollection3VOs[k].dataCollectionOrder == 1) { + var specimenBuffer = experiments.getSampleById(experiments.getMeasurementById(measurementtodatacollection3VOs[k].measurementId).specimenId); + if (specimenBuffer.sampleplateposition3VO != null) { + measurement.bufferSampleplateposition3VO = specimenBuffer.sampleplateposition3VO; + measurement.bufferSampleplate = (experiments.getSamplePlateById(specimenBuffer.sampleplateposition3VO.samplePlateId)); + } + } + } + } + + if (this.collapsed) { + /** If collapsed only the samples * */ + if (specimen.macromolecule3VO != null) { + data.push(measurement); + } + } else { + data.push(measurement); + } + + } + return data; }; -ShipmentTabs.prototype.error = function(error) { - var e = JSON.parse(error); - showError(e); - this.panel.setLoading(false); +/** + * Refresh data grid with the measurements and the experiments + * + * @measurements array with measurement3VO objects + * @experiments array with experiments objects + */ +MeasurementGrid.prototype.refresh = function(measurements, experiments) { + this.experiments = experiments; + this.measurements = measurements; + this.store.loadData(this._prepareData(measurements, experiments), false); }; -//ShipmentTabs.prototype.refreshTabTitles = function() { -/*Ext.getCmp("MacromoleculeTab").setText(this.getMacromoleculeTitle()); -Ext.getCmp("BufferTab").setText(this.getBuffersTitle()); -Ext.getCmp("SpecimenTab").setText(this.getSpecimenTitle()); -Ext.getCmp("PlatesTab").setText(this.getPlatesTitle()); -Ext.getCmp("AssembliesTab").setText(this.getShipmentTitle()); -Ext.getCmp("PlateGroupsTab").setText(this.getPlateGroupsTitle());*/ -//}; -ShipmentTabs.prototype.draw = function(shipment) { - var _this = this; - _this.plates = []; - _this.shipment = shipment; - _this.render(shipment); +/** + * Set status bar to busy (refreshing icon) + * + * @msg message to be displayed on the bar + */ +MeasurementGrid.prototype._showStatusBarBusy = function(msg) { + var statusBar = Ext.getCmp(this.id + 'basic-statusbar'); + statusBar.setStatus({ + text : msg, + iconCls : 'x-status-busy', + clear : false + }); +}; - // var proposal = new Proposal(); - // proposal.onDataRetrieved.attach(function(sender, plates){ - // _this.plates = plates; - // _this.shipment = shipment; - // _this.render(shipment); - // - // }); - // proposal.getPlatesByProposal(); +/** + * Set status bar to ready (ok icon) + * + * @msg message to be displayed on the bar + */ +MeasurementGrid.prototype._showStatusBarReady = function(msg) { + var statusBar = Ext.getCmp(this.id + 'basic-statusbar'); + statusBar.setStatus({ + text : msg, + iconCls : 'x-status-valid', + clear : false + }); }; -//ShipmentTabs.prototype.getShipmentTitle = function() { -// return 'Shipment'; -//}; +/** + * If updateRowEnabled returns an array with Ext.grid.plugin.RowEditing + */ +MeasurementGrid.prototype._getPlugins = function() { + var _this = this; + var plugins = []; + if (this.updateRowEnabled) { + plugins.push(Ext.create('Ext.grid.plugin.RowEditing', { + clicksToEdit : 1, + listeners : { + validateedit : function(grid, e) { + /** Setting values * */ + for ( var key in _this.editor) { + e.record.raw[key] = e.newValues[key]; + } + /** Comments are always updatable* */ + e.record.raw.comments = e.newValues.comments; -//ShipmentTabs.prototype.getMacromoleculeTitle = function() { -// return 'Macromolecules (' + this.experiment.getMacromolecules().length + ')'; -//}; + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, measurement) { + _this.onMeasurementChanged.notify(measurement); + _this.grid.setLoading(false); + }); + adapter.onError.attach(function() { + alert("Error"); + _this.grid.setLoading(false); + }); -//ShipmentTabs.prototype.getBuffersTitle = function() { -// return 'Buffers (' + this.experiment.getBuffers().length + ')'; -//}; + _this.grid.setLoading(); + adapter.saveMeasurement(e.record.raw, _this.experiments.experiments[0]); + } + } + })); + } + return plugins; +}; -//ShipmentTabs.prototype.getPlateGroupsTitle = function() { -// return 'Plate Groups (' + this.experiment.getPlateGroups().length + ')'; -//}; +/** + * @key name of the columns mathing the this.editor[key] + */ +MeasurementGrid.prototype._getEditor = function(key) { + if (this.editor[key] != null) { + return this.editor[key]; + } + return null; +}; -//ShipmentTabs.prototype.getSampleChangerTitle = function() { -// return 'Sample Changer'; -//}; +MeasurementGrid.prototype.getPanel = function(measurements, experiments) { + this.experiments = experiments; + this.measurements = measurements; + var _this = this; + this.store = Ext.create('Ext.data.Store', { + fields : [ { + name : 'miliseconds', + type : 'int' + }, 'priority', 'bufferId', { + name : 'exposureTemperature', + type : 'numeric' + }, 'volumeToLoad','code', 'transmission', 'viscosity', 'waitTime', 'flow', 'buffer_acronym', 'macromoleculeId', 'acronym', 'concentration', 'extraFlowTime', 'volume', 'energy', + 'expExposureTemperature', 'storageTemperature', 'timePerFrame', 'radiationAbsolute', 'radiationRelative', 'status', 'comments' ], + data : this._prepareData(measurements, experiments) + }); + this.store.sort(this.sorter); + var bbar = {}; + try { + bbar = Ext.create('Ext.ux.StatusBar', { + id : _this.id + 'basic-statusbar', + defaultText : 'Ready', + text : 'Ready', + iconCls : 'x-status-valid', + items : [] + }); + } catch (exp) { + console.log("bbar error"); + } -//ShipmentTabs.prototype.getSpecimenTitle = function() { -// return 'Specimens(' + this.experiment.getSpecimenCount() + ')'; -//}; + this.grid = Ext + .create( + 'Ext.grid.Panel', + { + id : this.id, + title : this.title, + store : this.store, + selModel : this.selModel, + plugins : this._getPlugins(), + resizable : this.resizable, + margin : this.margin, + maxHeight : this.maxHeight, + minHeight : this.minHeight, + maxWidth : this.maxWidth, + width : this.width, + tbar : this._getMenu(), + columns : [ + { + text : 'Order', + dataIndex : 'priority', + width : 50, + hidden : _this.isPriorityColumnHidden, + sortable : true -//ShipmentTabs.prototype.getPlatesTitle = function() { -// return 'Plates(' + this.experiment.getSamplePlates().length + ')'; -//}; + }, + { + text : 'Run Number', + dataIndex : 'code', + width : 50, + hidden : true, + sortable : true -//ShipmentTabs.prototype.getBuffersTip = function() { -/*if (this.experiment.getBuffers().length == 0){ - return BUI.getWarningHTML("There are no buffers. Click on add to create new ones. Click on edit button or double click to edit them"); - -} -else{ - return BUI.getTipHTML("Click on edit button or double click to edit them. Click on duplicate to create an identical buffer including its additives") -}*/ -//}; + }, -//ShipmentTabs.prototype.refreshTips = function() { -/*Ext.getCmp("BufferTabTip").update(this.getBuffersTip()); -Ext.getCmp("SpecimenTabTip").update(this.getSpecimensTip());*/ -//}; + { + text : 'Specimen', + columns : [ -ShipmentTabs.prototype.render = function(shipment) { - return this.getPanel(shipment); -}; + { + text : '', + dataIndex : 'macromoleculeId', + width : 30, + renderer : function(val, y, sample) { + if (val != null) { + if (_this.experiments == null) { + return BUI.getRectangleColorDIV(BIOSAXS.proposal.macromoleculeColors[val], 10, 10); + } else { + return BUI.getRectangleColorDIV(_this.experiments.macromoleculeColors[val], 10, 10); + } + } + }, + sortable : true + }, + { + text : 'Macromo.', + dataIndex : 'acronym', + width : 80, + renderer : function(val, y, sample) { + return val; + }, + sortable : true + }, + { + text : 'Conc. ', + dataIndex : 'concentration', + width : 80, + renderer : function(val, y, sample) { + if (sample.raw.macromoleculeId == null) { + return ""; + } + if (isNaN(val)) + return val; -ShipmentTabs.prototype.getShipmentHeader = function(shipment) { - var _this = this; - function getHTMLSource() { - var name = shipment.json.shippingName; - var status = shipment.json.shippingStatus; - var creationDate = shipment.json.creationDate; - var html = BUI.createFormLabel("Name :", name, 75, 400); - html = html + BUI.createFormLabel("Status :", status, 75, 400); - html = html + BUI.createFormLabel("Date :", creationDate, 75, 400); - return html; - } + if (val != 0) { + return BUI.formatValuesUnits(val, '', { + fontSize : 16, + decimals : 3, + unitsFontSize : this.unitsFontSize + }); + } else { + return; + } - return Ext.create('Ext.container.Container', { - frame : false, - layout : 'hbox', - title : 'General', - padding : 5, - bodyPadding : '5 5 0 0', - width : 890, - margin : '0 0 10 0', - height : 100, - style : { - borderColor : '#BDBDBD', - borderStyle : 'solid', - borderWidth : '1px' - }, - fieldDefaults : { - msgTarget : 'side', - labelWidth : 100 - }, - items : [ { - margin : "0 0 0 0", - width : 475, - border : 0, - html : getHTMLSource() - } - ] - }); -}; + }, + sortable : true + }, + { + text : '', + dataIndex : 'bufferId', + width : 30, + hidden : false, + renderer : function(val, y, sample) { + if (val != null) { + var color = '#FFCCFF'; + if (_this.experiments != null) { + var dc = _this.experiments.getDataCollectionByMeasurementId(sample.raw.measurementId); + if (dc != null) { + if (dc.length > 0) { + color = _this.experiments.getSpecimenColorByBufferId(_this.experiments + .getMeasurementById(dc[0].measurementtodatacollection3VOs[0].measurementId).specimenId); + } + } + } else { + color = BIOSAXS.proposal.bufferColors[val]; + } + return BUI.getRectangleColorDIV(color, 10, 10); + } + }, + sortable : true + }, + { + text : 'Buffer', + dataIndex : 'buffer_acronym', + width : 120, + renderer : function(val, y, sample) { + if (sample.raw.bufferSampleplateposition3VO != null) { + return BIOSAXS.proposal.getBufferById(sample.raw.bufferId).acronym + " Plate: [" + + sample.raw.bufferSampleplate.slotPositionColumn + ", " + + BUI.getSamplePlateLetters()[sample.raw.bufferSampleplateposition3VO.rowNumber - 1] + "-" + + sample.raw.bufferSampleplateposition3VO.columnNumber + "]"; + } + return val; + }, + sortable : true + }, { + text : 'Position', + width : 100, + hidden : true, + renderer : function(val, y, sample) { + if (_this.experiments != null) { + return BUI.getSamplePositionHTML(_this.experiments.getSampleById(sample.raw.specimenId), _this.experiments.experiments[0]); + } + } + } ] + }, + { + text : 'Parameters', + columns : [ + { + text : 'Ex. Flow. time (s)', + dataIndex : 'extraFlowTime', + width : 100, + hidden : true, + renderer : function(val, y, sample) { + return BUI.formatValuesUnits(val, 's', { + fontSize : 12, + decimals : 0, + unitsFontSize : this.unitsFontSize + }); + } + }, + { + text : 'Exp. Temp.', + dataIndex : 'exposureTemperature', + width : 70, + renderer : function(val, y, sample) { + if (Number(val)) { + return BUI.formatValuesUnits(val, 'C', { + fontSize : 12, + decimals : 2, + unitsFontSize : this.unitsFontSize + }); + } + return null; + }, + sortable : true, + editor : this._getEditor("exposureTemperature") + }, + { + text : 'Vol. Load', + dataIndex : 'volumeToLoad', + width : 60, + hidden : false, + editor : this._getEditor("volumeToLoad"), + renderer : function(val, y, sample) { + // return val+ " µl"; + return BUI.formatValuesUnits(val, 'µl', { + fontSize : 12, + decimals : 2, + unitsFontSize : this.unitsFontSize + }); + } + }, + { + text : 'Volume in Well', + dataIndex : 'volume', + hidden : true, + editor : this._getEditor("volume"), + width : 80, + renderer : function(val, y, sample) { + // return val + "(µl)"; + return BUI.formatValuesUnits(val, 'µl', { + fontSize : 12, + decimals : 2, + unitsFontSize : this.unitsFontSize + }); + } + }, + { + text : 'Trans.', + dataIndex : 'transmission', + width : 60, + editor : this._getEditor("transmission"), + renderer : function(val, y, sample) { + return BUI.formatValuesUnits(val, '%', { + fontSize : 12, + decimals : 0, + unitsFontSize : this.unitsFontSize + }); + } + }, + { + text : 'Wait T.', + dataIndex : 'waitTime', + editor : this._getEditor("waitTime"), + width : 50, + renderer : function(val, y, sample) { + // if (val != 0) { + return BUI.formatValuesUnits(val, 's', { + fontSize : 12, + decimals : 0, + unitsFontSize : this.unitsFontSize + }); + // } + } + }, + { + text : 'Flow', + dataIndex : 'flow', + editor : this._getEditor("flow"), + width : 50, + renderer : function(val, y, sample) { + if (val == true) { + return "yes"; + } + return null; + } + }, + { + text : 'Viscosity', + dataIndex : 'viscosity', + tooltip : 'The viscosity of a fluid is a measure of its resistance to gradual deformation by shear stress or tensile stress. For liquids, it corresponds to the informal notion of "thickness"', + editor : this._getEditor("viscosity"), + width : 50, + renderer : function(val, y, sample) { + return val; + } + } ] + }, { + text : 'Status', + dataIndex : 'status', + width : 50, + hidden : _this.isStatusColumnHidden, + renderer : function(val, y, sample) { + if (val != null) { + if (val == 'DONE') { + return "" + val + " "; + } + } + } + }, { + text : 'Time', + dataIndex : 'time', + width : 80, + hidden : _this.isTimeColumnHidden, + renderer : function(val, y, sample) { + if (sample.raw.run3VO != null) { + if (sample.raw.run3VO.timeStart != null) { + if (sample.raw.run3VO.timeStart != "") { + var m = moment(sample.raw.run3VO.timeStart); + return m.format("hh:mm:ss a"); + } + } + } + } + }, { + text : 'Energy', + dataIndex : 'energy', + width : 100, + hidden : true + }, { + text : 'Real Exp. Temp.(C)', + width : 100, + dataIndex : 'expExposureTemperature', + hidden : true + }, { + text : 'Storage Temp.(C)', + width : 100, + dataIndex : 'storageTemperature', + hidden : true + }, { + text : 'Time/Frame (s)', + width : 100, + dataIndex : 'timePerFrame', + hidden : true + }, { + text : 'Radiation Relative', + dataIndex : 'radiationRelative', + width : 100, + hidden : true + }, { + text : 'Radiation Absolute', + dataIndex : 'radiationAbsolute', + width : 100, + hidden : true + }, { + text : 'Comments', + dataIndex : 'comments', + flex : 1, + hidden : false, + editor : this._getEditor("comments") -ShipmentTabs.prototype.getTabPanel = function(shipment) { - this.panel = Ext.createWidget('tabpanel', { - height : 600, - style : { - padding : 2 - }, - items : [ { - tabConfig : { - id : 'Shipment', - title : 'Shipment', - icon : '/ispyb/images/plane-small.gif' - }, - items : [ { - xtype : 'container', - margin : '5 5 5 5', - items : [ this.shipmentForm.getPanel(shipment) ] - } ] - }, { - tabConfig : { - id : 'Cases', - title : 'Cases', - icon : '../images/box-icon-very-small.png' - }, - items : [ { - xtype : 'container', - margin : '5 5 5 5', - items : [ this.caseGrid.getPanel(shipment.getDewars(), this.plates) ] - } ] - } ] - }); - return this.panel; -}; + }, { + id : _this.id + 'buttonRemoveSample', + text : '', + hidden : !_this.removeBtnEnabled, + width : 100, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + if (record.raw.macromoleculeId != null) { + if (_this.removeBtnEnabled) { + return BUI.getRedButton('REMOVE'); + } + } + } + } ], + bbar : bbar, + viewConfig : { + stripeRows : true, + getRowClass : function(record, index, rowParams, store) { + if (record.data.status == "DONE") { + return 'green-row'; + } -ShipmentTabs.prototype.getPanel = function(shipment) { - var _this = this; - this.shipment = shipment; - if (this.plates == null) { - this.plates = []; - } + }, + listeners : { + 'itemclick' : function(grid, record, item, index, e, eOpts) { + _this.onClick.notify({ + specimen : record.raw + }); + }, + 'cellclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemoveSample') { + grid.getStore().removeAt(rowIndex); - if (this.shipPanel == null) { - this.shipPanel = Ext.create('Ext.container.Container', { - bodyPadding : 2, - width : Ext.getBody().getViewSize().width * 0.9, - renderTo : this.targetId, - style : { - padding : 2 - }, - items : [ this.getShipmentHeader(shipment), this.getTabPanel(shipment) ] - }); - } + if (record.raw.measurementId != null) { + /** For testing * */ + grid.setLoading("ISPyB: Removing measurement"); + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + grid.setLoading(false); + /** + * We get and refresh experiment + * because specimens has changed * + */ + var adapter2 = new BiosaxsDataAdapter(); + adapter2.onSuccess.attach(function(sender, experiment) { + _this.onRemoved.notify(experiment); + _this._showStatusBarReady('Ready'); + }); + if (_this.experiments.experiments[0].experimentId != null) { + adapter2.getExperimentById(_this.experiments.experiments[0].experimentId, "MEDIUM"); + _this._showStatusBarBusy("ISPyB: Removing Unused Specimens"); + } + }); - return this.shipPanel; -}; - -/** - * Shows an template with the specimens, measurements and the experiment's - * requirement - * - * @targetId - */ -function TemplateTabs(targetId) { - this.height = 600; - this.targetId = targetId; + adapter.onError.attach(function(sender, data) { + alert("Error: " + data); + grid.setLoading(false); + }); - this.id = BUI.id(); - var _this = this; + adapter.removeMeasurement(record.raw); + } + } - this.gridHeight = 1000; - /** data * */ - this.experiment = null; + } - this.specimenSelected = null; + } + } + }); - /** Specimen Widget contains a specimenGrid and a sampleChangerWidget than can be displayed with are vertical or horizontal layout **/ - this.specimenWidget = new SpecimenWidget({ - height : this.height - }); - - this.samplePlateGroupWidget = new SamplePlateGroupWidget({ - showTitle : false, - height : 250, - margin : 5, - bbar : true - }); - - this.samplePlateGroupWidget.onExperimentChanged.attach(function(sender, experiment) { - _this.refresh(experiment); - }); + this.grid.on("afterrender", function() { - this.samplePlateGroupWidget.onClick.attach(function(sender, args) { - }); + function updateTime() { + try { + _this.estimatedTime = _this.estimatedTime - 1; - this.volumePlanificator = new VolumeGrid(); + _this.onUpdateTime.notify({ + hours : (Number(_this.estimatedTime / 3600).toFixed()), + minutes : (Number((_this.estimatedTime / 60) % 60).toFixed()), + seconds : (Number(_this.estimatedTime % 60).toFixed()) - /** For Measurements * */ - var storeViscosity = Ext.create('Ext.data.Store', { - fields : [ 'name' ], - data : [ { - "name" : "low" - }, { - "name" : "medium" - }, { - "name" : "high" - } ] - }); + }); - // Create the combo box, attached to the states data store - var viscosityEditor = Ext.create('Ext.form.ComboBox', { - fieldLabel : '', - store : storeViscosity, - queryMode : 'local', - displayField : 'name', - valueField : 'name' - }); + if (Number(_this.estimatedTime) < 0) { + _this.timer = null; + grid.setTitle(_this.title); + } - this.measurementGrid = new MeasurementGrid({ - maxWidth : 1500, - estimateTime : false, - positionColumnsHidden : true, - isPriorityColumnHidden : true, - isStatusColumnHidden : true, - isTimeColumnHidden : true, - updateRowEnabled : true, - collapsed : true, - removeBtnEnabled : true, - showTitle : false, - collapseBtnEnable : false, - addBtnMultipleEdit : true, - sortingBtnEnable : true, - editor : { - exposureTemperature : { - xtype : 'textfield', - allowBlank : true - }, - comments : { - xtype : 'textfield', - allowBlank : true - }, - volumeToLoad : { - xtype : 'numberfield', - allowBlank : true - }, - transmission : { - xtype : 'numberfield', - allowBlank : true - }, - viscosity : viscosityEditor, - waitTime : { - xtype : 'numberfield', - allowBlank : true - }, - flow : { - xtype : 'checkbox', - allowBlank : true + } catch (e) { + console.log(e); + _this.timer = null; } } - }); - - this.measurementGrid.onSelected.attach(function(sender, measurements) { - var specimens = []; - for ( var i = 0; i < measurements.length; i++) { - specimens.push(_this.experiment.getSampleById(measurements[i].specimenId)); - } - }); - this.measurementGrid.onMeasurementChanged.attach(function(sender, measurement) { - _this.experiment.setMeasurement(measurement); - _this.refresh(_this.experiment); - }); + if (_this.estimateTime) { + var experimentList = _this.experiments; + var collected = experimentList.getMeasurementsCollected(); + if (collected.length > 0) { + if (collected[0].run3VO != null) { + try { + var end = collected[0].run3VO.timeEnd; + var start = collected[0].run3VO.timeStart; + var dstart = moment(start); + var dend = moment(end); + var seconds = Number(dend.diff(dstart) / 1000).toFixed(); - this.measurementGrid.onExperimentChanged.attach(function(sender, json) { - _this.refresh(new Experiment(json)); - }); + _this.estimatedTime = (seconds * experimentList.getMeasurementsNotCollected().length); - this.measurementGrid.onRemoved.attach(function(sender, experiment) { - _this.refreshSpecimen(new Experiment(experiment)); - }); + if (_this.estimatedTime > 0) { + updateTime(); + _this.timer = setInterval(function() { + updateTime(); + }, 1000); + } - this.measurementGrid.onUpdateTime.attach(function(sender, args) { - document.getElementById(_this.id + "_counter").innerHTML = args.hours + 'h, ' + args.minutes + 'min and ' + args.seconds + ' seconds'; + } catch (e) { + } + } + } + } }); - -} - -TemplateTabs.prototype.refreshMeasurement = function(experiment) { - this.experiment = experiment; - this.experiment.onSaved = new Event(this); - this.experiment.onSpecimenSaved = new Event(this); - var experimentList = new ExperimentList([ this.experiment ]); - this.measurementGrid.refresh(experimentList.getMeasurementsNotCollected(), experimentList); -}; -TemplateTabs.prototype.refreshSpecimen = function(experiment) { - this.experiment = experiment; - this.experiment.onSaved = new Event(this); - this.experiment.onSpecimenSaved = new Event(this); - this.samplePlateGroupWidget.refresh(this.experiment); - this.specimenWidget.refresh(this.experiment); - this.volumePlanificator.refresh(this.experiment); + return this.grid; }; -TemplateTabs.prototype.refresh = function(experiment) { - // var start = new Date().getTime(); - this.experiment = experiment; - this.experiment.onSaved = new Event(this); - this.experiment.onSpecimenSaved = new Event(this); - - // var experimentList = new ExperimentList([this.experiment]); - this.refreshMeasurement(experiment); - this.refreshSpecimen(experiment); - /** Refreshing grids * */ - this.panel.setLoading(false); - +/** Method for testing * */ +MeasurementGrid.prototype.input = function() { + var experiment = DATADOC.getExperiment_10(); + var measurements = DATADOC.getMeasurements_10(); + var proposal = DATADOC.getProposal_10(); + return { + experiment : experiment, + measurements : measurements, + proposal : proposal + }; }; -TemplateTabs.prototype.error = function(error) { - var e = JSON.parse(error); - showError(e); - this.panel.setLoading(false); +MeasurementGrid.prototype.test = function(targetId) { + var measurementGrid = new MeasurementGrid({ + tbar : true + }); + BIOSAXS.proposal = new Proposal(measurementGrid.input().proposal); + var panel = measurementGrid.getPanel(measurementGrid.input().measurements, new ExperimentList([ new Experiment(measurementGrid.input().experiment) ])); + panel.render(targetId); }; + +/** + * A shipment may contains one or more cases where stock solutions and sample + * plates are stored + * + * @height + * @btnEditVisible + * @btnRemoveVisible + * + * #onEditButtonClicked + */ +function MolarityGrid(args) { + this.height = 100; + this.width = 100; + + if (args != null) { + if (args.height != null) { + this.height = args.height; + } + if (args.width != null) { + this.width = args.width; + } + } + + var _this = this; + + this.molarityForm = new MolarityForm({height : 180, width : 455}); + + this.molarityForm.onSave.attach(function(sender){ + _this.molarityWindow.destroy(); + _this.updateProposal(); + + }); + + this.molarityForm.onClose.attach(function(sender){ + _this.molarityWindow.destroy(); + + }); + + /** Events * */ + this.onEditButtonClicked = new Event(this); +} + +MolarityGrid.prototype._getColumns = function() { + return [ { + text : 'Subunit', + columns : [ { + text : "Acronym", + width : 100, + hidden : false, + dataIndex : 'acronym', + sortable : true + }, { + text : "Name", + width : 125, + hidden : false, + dataIndex : 'name', + sortable : true + }, { + text : "MM Est.", + width : 100, + dataIndex : 'molecularMass', + sortable : true, + renderer : function(grid, cls, record){ + return BUI.formatValuesUnits(record.data.molecularMass , "Da", 10, 2); + + } + } ] + }, { +// text : "Number
in assymmetric units", + text : "Ratio", + width : 100, + dataIndex : 'ratio', + tooltip : 'Number of times the subunit is present in the macromolecule', + sortable : true + }, { + id : this.id + 'MOLARITY_REMOVE', + flex : 0.1, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + return BUI.getRedButton('REMOVE'); + } + } ]; +}; + +MolarityGrid.prototype._openMolarityWindow = function() { + this.molarityWindow = Ext.create('Ext.window.Window', { + title : 'Molarity', + height : 220, + width : 500, + modal : true, + items : [this.molarityForm.getPanel() ] + }).show(); +}; + +MolarityGrid.prototype._getButtons = function() { + var _this = this; + return [ { + text : 'Add subunit', + icon : '../images/add.png', + handler : function() { + _this._openMolarityWindow(); + } + }]; +}; + + +MolarityGrid.prototype.updateProposal = function() { + var _this = this; + this.panel.setLoading(); + BIOSAXS.proposal.onInitialized.attach(function() { + if (BIOSAXS.proposal != null) { + var macromolecules = BIOSAXS.proposal.macromolecules; + for (var i = 0; i < macromolecules.length; i++) { + + if (macromolecules[i].macromoleculeId == _this.macromolecule.macromoleculeId) { + _this.refresh(macromolecules[i]); + _this.panel.setLoading(false); + } + } + } + }); + BIOSAXS.proposal.init(); +}; + + +MolarityGrid.prototype.getPanel = function() { + var _this = this; + + this.molarityStore = Ext.create('Ext.data.Store', { + fields : [ 'acronym', 'ratio', 'comments', 'stoichiometryId', 'name', 'molecularMass' ], + sorters : { + property : 'ratio', + direction : 'DESC' + } + }); + + this.panel = Ext.create('Ext.grid.Panel', { + store : this.molarityStore, + height : this.height, + padding : 5, + columns : this._getColumns(), + listeners : { + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + + /** Remove entry * */ + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'MOLARITY_REMOVE') { + var dataAdapter = new BiosaxsDataAdapter(); + dataAdapter.onSuccess.attach(function(sender) { + _this.updateProposal(); + + }); + dataAdapter.removeStoichiometry(record.data.stoichiometryId); + _this.panel.setLoading("Removing Structure"); + } + } + }, + tbar : this._getButtons() + }); + return this.panel; +}; + +MolarityGrid.prototype._prepareData = function(macromolecule) { + /** Return an array of [{ratio,acronym, stoichiometryId, name}] **/ + var data = []; + if (macromolecule.stoichiometry != null) { + for (var i = 0; i < macromolecule.stoichiometry.length; i++) { + var hostMacromolecule = BIOSAXS.proposal.getMacromoleculeById(macromolecule.stoichiometry[i].macromoleculeId); + data.push({ + ratio : macromolecule.stoichiometry[i].ratio, + acronym : hostMacromolecule.acronym, + comments : hostMacromolecule.comments, + molecularMass : hostMacromolecule.molecularMass, + stoichiometryId : macromolecule.stoichiometry[i].stoichiometryId, + name : hostMacromolecule.name + }); + } + } + return data; +}; + +MolarityGrid.prototype.refresh = function(macromolecule) { + if (macromolecule != null){ + this.molarityStore.loadData(this._prepareData(macromolecule)); + this.molarityForm.refresh(macromolecule); + this.macromolecule = macromolecule; + } +}; + +MolarityGrid.prototype.input = function() { + return { + proposal : DATADOC.getProposal_10(), + dewars : DATADOC.getDewars_10() + + }; +}; + +MolarityGrid.prototype.test = function(targetId) { + var MolarityGrid = new MolarityGrid({ + height : 150 + }); + BIOSAXS.proposal = new Proposal(MolarityGrid.input().proposal); + var panel = MolarityGrid.getPanel(MolarityGrid.input().dewars); + panel.render(targetId); + +}; + + +/** + * Given data analysis parsed with ResultsAssemblyWidget makes a selector grid with buffer/protein + **/ +function SpecimenSelectorResultGrid() { + this.id = BUI.id(); +} -TemplateTabs.prototype.draw = function(experiment) { - this.render(experiment); +SpecimenSelectorResultGrid.prototype._prepareData = function(data) { + var parsed = []; + for ( var i = 0; i < data.length; i++) { + var row = data[i]; + for ( var j = 0; j < row.conditions.length; j++) { + parsed.push({ + bufferId : row.conditions[j].bufferId, + macromoleculeId : row.macromoleculeId, + macromoleculeAcronym : BIOSAXS.proposal.getMacromoleculeById(row.macromoleculeId).acronym, + bufferAcronym : BIOSAXS.proposal.getBufferById(row.conditions[j].bufferId).acronym + }); + } + } + return parsed; }; - -TemplateTabs.prototype.getExperimentTitle = function() { - var _this = this; - var experimentHeaderForm = new ExperimentHeaderForm(); - return experimentHeaderForm.getPanel(this.experiment); +SpecimenSelectorResultGrid.prototype.refresh = function(data) { + this.store.loadData(this._prepareData(data)); }; -TemplateTabs.prototype.render = function(experiment) { +SpecimenSelectorResultGrid.prototype.getPanel = function(data) { var _this = this; - this.experiment = experiment; + this.store = Ext.create('Ext.data.Store', { + fields : [ 'macromoleculeId', 'bufferId', 'macromoleculeAcronym', 'bufferAcronym', 'concentration' ], + data : this._prepareData(data), + groupField : 'macromoleculeAcronym' + }); - /** - * - * Depending on the sample Changer configuration we want to display the plates vertically or horizontally - * Default is vertical - * - * */ - - var specimenContainer = this.specimenWidget.getPanel(); - this.specimenWidget.refresh(experiment); - - var experimentList = new ExperimentList([ _this.experiment ]); - var measurementContainer = Ext.create('Ext.container.Container', { - layout : { - type : 'vbox' - }, - defaults : { - style : { - padding : '5px 0px 0px 10px' + this.store.sort('concentration'); + this.grid = Ext.create('Ext.grid.Panel', { + id : this.id, + store : this.store, + width : this.width, + height : this.height, + maxHeight : this.maxHeight, + border : 1, + features : [ { + ftype : 'grouping', + groupHeaderTpl : '{name}', + hideGroupedHeader : true, + startCollapsed : false + } ], + selModel : Ext.create('Ext.selection.CheckboxModel', { + allowDeselect : true, + mode : 'MULTI', + listeners : { + selectionchange : function(sm, selections) { + _this.selected = []; + for ( var i = 0; i < selections.length; i++) { + _this.selected.push(selections[i].raw); + } + } } - }, - items : [ _this.measurementGrid.getPanel(experimentList.getMeasurementsNotCollected(), experimentList) ] + }), + margin : 10, + sortableColumns : true, + columns : [ { + text : 'Macromolecule', + dataIndex : 'macromoleculeAcronym', + flex : 1 + }, { + text : '', + dataIndex : 'bufferId', + width : 20, + hidden : false, + renderer : function(val, y, sample) { + return BUI.getRectangleColorDIV(BIOSAXS.proposal.bufferColors[val], 10, 10); + } + }, { + text : 'Buffer', + dataIndex : 'bufferAcronym', + flex : 1 + }, { + text : 'Concentration', + dataIndex : 'concentration', + flex : 1, + renderer : function(val, y, sample) { + return val + " mg/ml"; + } + } ] }); - this.panel = Ext - .createWidget( - 'tabpanel', - { - plain : true, - items : [ - { - tabConfig : { - title : 'Measurements' - }, - items : [ { - xtype : 'container', - layout : 'vbox', - border : 1, -// height : _this.gridHeight, - margin : "0 0 10 0", - items : [ measurementContainer ] - } - - ] - }, - { - tabConfig : { - id : 'genralTabl', - title : "Specimens" - // width : 900, - // border : 3 - - }, - items : [ specimenContainer ] - }, - { - tabConfig : { - title : "Requirements" + /** Adding the tbar **/ + if (this.tbar) { + this.grid.addDocked({ + xtype : 'toolbar', + items : this.getTbar() + }); + } + return this.grid; +}; - }, - items : [ - { - html : BUI.getTipHTML("Estimated volume is the maximum volume required. Depending on the order of your measurements you may use less. Click on create stock solutions if you plan to ship these stock solutions"), - margin : "10 10 10 10", - border : 0 - }, this.volumePlanificator.getPanel(experiment) ] - } ] - }); - // ); - return this.getPanel(this.panel); +SpecimenSelectorResultGrid.prototype.input = function() { + return { + data : new ResultsAssemblyGrid()._prepareData(new ResultsAssemblyGrid().input().data), + proposal : new ResultsAssemblyGrid().input().proposal + }; }; -TemplateTabs.prototype.isTemplate = function() { - if (this.experiment.json.type == "TEMPLATE") { - return true; - } - return false; +SpecimenSelectorResultGrid.prototype.test = function(targetId) { + var specimenSelectorResultGrid = new SpecimenSelectorResultGrid(); + BIOSAXS.proposal = new Proposal(specimenSelectorResultGrid.input().proposal); + var panel = specimenSelectorResultGrid.getPanel(specimenSelectorResultGrid.input().data); + panel.render(targetId); }; +/** + * Show all buffer conditions for each macromolecules pointing out the measurements quality + * + * @height + * @maxHeight + * @width + * @searchBar + * @tbar + * @btnResultVisible + * + * #onClick + */ +function ResultsAssemblyGrid(args) { + this.height = 500; + this.id = BUI.id(); + this.maxHeight = this.height; -TemplateTabs.prototype.getPanel = function(panel) { - var _this = this; - if (this.experimentPanel == null) { - this.experimentPanel = Ext.create('Ext.container.Container', { - bodyPadding : 2, - width : 1000,//Ext.getBody().getViewSize().width * 0.9, - renderTo : this.targetId, - height : 500, -// style : { -// padding : 2 -// }, - items : [ - this.getExperimentTitle(), - this.panel - ], - listeners : { - afterrender : function(thisCmp) { - $("#SchemeReport" + _this.experiment.experimentId).click(function() { - $(this).target = "_blank"; - window.open('viewProjectList.do?reqCode=display&menu=platescheme&experimentId=' + _this.experiment.experimentId); - return false; - }); + this.width = 900; + this.searchBar = false; + this.tbar = false; + this.btnResultVisible = false; - } - } - }); - } - return this.experimentPanel; -}; + /** For processing **/ + this.processed = {}; + this.renderedPlotIndex = 0; -TemplateTabs.prototype.input = function(targetId) { - return new ExperimentTabs().input(); -}; + this.plotWidth = 210; + this.plotHeight = 80; -TemplateTabs.prototype.test = function(targetId) { - var experimentTabs = new TemplateTabs(targetId); - BIOSAXS.proposal = new Proposal(experimentTabs.input().proposal); - experimentTabs.draw(new Experiment(experimentTabs.input().experiment)); -}; - -var BUI = { - //interval : 60000, - interval : 40000, - rainbow : function(numOfSteps, step) { - // This function generates vibrant, "evenly spaced" colours (i.e. no clustering). This is ideal for creating easily distinguishable vibrant markers in Google Maps and other apps. - // Adam Cole, 2011-Sept-14 - // HSV to RBG adapted from: http://mjijackson.com/2008/02/rgb-to-hsl-and-rgb-to-hsv-color-model-conversion-algorithms-in-javascript - var r, g, b; - var h = step / numOfSteps; - var i = ~~(h * 6); - var f = h * 6 - i; - var q = 1 - f; - switch (i % 6) { - case 0: - r = 1, g = f, b = 0; - break; - case 1: - r = q, g = 1, b = 0; - break; - case 2: - r = 0, g = 1, b = f; - break; - case 3: - r = 0, g = q, b = 1; - break; - case 4: - r = f, g = 0, b = 1; - break; - case 5: - r = 1, g = 0, b = q; - break; + /** Colors **/ + this.validColor = BUI.getValidColor(); + this.warningColor = BUI.getWarningColor(); + this.notValidColor = BUI.getErrorColor(); + + /** Show warning if guinier quality less than **/ + this.guinierQuality = BUI.getQualityThreshold(); + this.framePercentageThreshold = BUI.getRadiationDamageThreshold(); + + if (args != null) { + if (args.height != null) { + this.height = args.height; + this.maxHeight = this.height; } - var c = "#" + ("00" + (~~(r * 255)).toString(16)).slice(-2) + ("00" + (~~(g * 255)).toString(16)).slice(-2) - + ("00" + (~~(b * 255)).toString(16)).slice(-2); - return (c); - }, - getFileNameByPath : function(filePath) { - if (filePath != null){ - var split = filePath.split("/"); - if (split.length > 0){ - return split[split.length - 1]; - } + if (args.maxHeight != null) { + this.maxHeight = args.maxHeight; + } + if (args.width != null) { + this.width = args.width; + } + if (args.searchBar != null) { + this.searchBar = args.searchBar; } - return "Not file"; - }, - getUpdateInterval : function() { - this.interval = this.interval + 2000; - return this.interval; - }, - getRadiationDamageThreshold : function() { - return 0.7; - }, - getQualityThreshold : function() { - return 0.7; - }, - getCreateShipmentURL : function() { - return '/ispyb/user/viewProjectList.do?reqCode=display&menu=create_shipment'; - }, - getCreateShipmentList : function() { - return '/ispyb/user/viewProjectList.do?reqCode=display&menu=list_shipment'; - }, - getShippingURL : function(shippingId) { - return '/ispyb/user/viewProjectList.do?reqCode=display&menu=shipment&shippingId=' + shippingId; - }, - getMacromoleculeResultsURLByMultipleSearch : function(array) { - return '/ispyb/user/viewProjectList.do?reqCode=display&menu=macromolecule&search=' - + JSON.stringify(array).replace(new RegExp("\"", 'g'), "'"); - }, - getMacromoleculeResultsURL : function(macromoleculeId) { - return '/ispyb/user/viewProjectList.do?reqCode=display&menu=macromolecule¯omoleculeId=' + macromoleculeId; - }, - getMacromoleculeBufferResultsURL : function(macromoleculeId, bufferId) { - return '/ispyb/user/viewProjectList.do?reqCode=display&menu=macromolecule&bufferId=' + bufferId + '¯omoleculeId=' + macromoleculeId; - }, + if (args.tbar != null) { + this.tbar = args.tbar; + } + if (args.btnResultVisible != null) { + this.btnResultVisible = args.btnResultVisible; + } - getMacromoleculeHeader : function(macromoleculeId) { + } - function getHTMLSource(macromoleculeId) { - if (macromoleculeId != null) { - var html = BUI.createFormLabel("Name :", BIOSAXS.proposal.getMacromoleculeById(macromoleculeId).name, 75, 400); - html = html + BUI.createFormLabel("Acronym :", BIOSAXS.proposal.getMacromoleculeById(macromoleculeId).acronym, 75, 400); - if (BIOSAXS.proposal.getMacromoleculeById(macromoleculeId).comments != null) { - html = html + BUI.createFormLabel("Comments :", BIOSAXS.proposal.getMacromoleculeById(macromoleculeId).comments, 75, 400); - } - return html; - } - } + this.onClick = new Event(); +} - return Ext.create('Ext.container.Container', { - frame : false, - layout : 'hbox', - title : 'Macromolecule', - bodyPadding : '5', - width : 890, - margin : '0 0 10 0', - height : 100, - style : { - borderColor : '#BDBDBD', - borderStyle : 'solid', - borderWidth : '1px' - }, - fieldDefaults : { - msgTarget : 'side', - labelWidth : 100 - }, - items : [ { - margin : "10 0 0 10", - width : 475, - border : 0, - html : getHTMLSource(macromoleculeId) - }, { - margin : "10 0 0 10", - width : 475, - border : 0, - html : BUI.getZipHTMLByMacromoleculeId(macromoleculeId) - } - ] - }); - }, +ResultsAssemblyGrid.prototype.edit = function(macromoleculeId) { + var _this = this; + var window = new MacromoleculeWindow(); + window.onSuccess.attach(function(sender, proposal) { + _this.store.loadData(_this._prepareData(BIOSAXS.proposal.getMacromolecules())); + }); + window.draw(BIOSAXS.proposal.getMacromoleculeById(macromoleculeId)); +}; - getZipHTMLByMacromoleculeId : function(macromoleculeId) { - if (macromoleculeId != null) { - var fileName = BIOSAXS.proposal.getMacromoleculeById(macromoleculeId).acronym; - return ""; - } - }, - getZipHTMLByExperimentId : function(experimentId, filename) { - if (filename == null){ - filename = "experiment"; - } - return ""; - }, - - getZipURLByAverageId : function(averageId, filename) { - if (filename == null){ - filename = "experiment"; - } - return "/ispyb/user/dataadapter.do?reqCode=getZipFileByAverageListId&f&mergeIdsList=" + averageId + "&fileName=" + filename; - }, - getZipURLBySubtractionId : function(subtractionId, filename) { - if (filename == null){ - filename = "experiment"; +ResultsAssemblyGrid.prototype.getTbar = function() { + var _this = this; + var actions = []; + + actions.push(Ext.create('Ext.Action', { + icon : '../images/add.png', + text : 'Add Macromolecule', + disabled : false, + handler : function(widget, event) { + var window = new MacromoleculeWindow(); + window.onSuccess.attach(function(sender) { + _this.refresh(); + }); + window.draw({}); } - return "/ispyb/user/dataadapter.do?reqCode=getZipFileByAverageListId&f&subtractionIdList=" + subtractionId + "&fileName=" + filename; - }, - - - getZipHTMLByFrameRangeId : function(experimentId, start, end) { - var fileName = "experiment"; - return ""; - }, - getZipFrameHPLCUrl : function(experimentId, start, end) { - return "/ispyb/user/dataadapter.do?reqCode=getZipFileH5ByFramesRange&f&experimentId=" + experimentId + "&start=" + Number(start) +"&end="+ Number(end); - }, - - getQueueUrl : function() { - return "/ispyb/user/dataadapter.do?reqCode=getPagingCompactAnalysisByProposalId"; - }, - - getQueueUrlByExperiment: function(experimentId) { - return "/ispyb/user/dataadapter.do?reqCode=getPagingCompactAnalysisByExperimentId&f&experimentId=" + experimentId; - }, - getStandardDeviation : function(values) { - var sum = 0; - var count = 0; - var avg = null; + })); + + actions.push(Ext.create('Ext.Action', { + icon : '../images/add.png', + text : 'Define an Assembly', + disabled : false, + handler : function(widget, event) { + var createAssemblywindow = new CreateAssemblyWindow(); + createAssemblywindow.onSaved.attach(function(evt, args) { + if (args.macromoleculeIds.length > 0) { + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, proposal) { + _this.refresh(); + }); + adapter.saveAssembly(args.assemblyId, args.macromoleculeIds); - var curatedValues = new Array(); - for ( var i = 0; i < values.length; i++) { - var value = values[i]; - if (value != null) { - if (!isNaN(value)) { - count = count + 1; - sum = sum + Number(value); - curatedValues.push(Number(value)); } - } - } - if (count > 0) { - avg = sum / count; - } else { - avg = sum; - } - var aux = 0; - for ( var i = 0; i < curatedValues.length; i++) { - var value = curatedValues[i]; - aux = aux + Math.pow(value - avg, 2); + }); + createAssemblywindow.draw(_this.experiment); } - /** std **/ - var std = Math.sqrt(aux / count); + })); + + return actions; +}; + +ResultsAssemblyGrid.prototype.refresh = function() { + this.store.loadData(this._prepareData()); +}; + +ResultsAssemblyGrid.prototype.addCondition = function(record, data_parsed, i) { + function getCondition(record) { return { - std : (std), - sum : (sum), - avg : (avg), - validNumber : count, - totalNumber : values.length, - values : values + concentration : record.conc, + quality : record.quality, + bufferBeforeFramesMerged : record.bufferBeforeFramesMerged, + bufferAfterFramesMerged : record.bufferAfterFramesMerged, + framesCount : record.framesCount, + framesMerge : record.framesMerge }; - }, - - getHTMLTableForFrameAveraged : function(bufferAcronym, macromoleculeAcronym, bbmerges, molmerges, bamerges, totalframes, bufferId,macromoleculeId, macromoleculeColor) { - - function getFrameSpan(framesMerged, total) { - return "(" + framesMerged + " of " + total + ")"; - } + } - function getColorFrame(framesMerged, total) { - if (framesMerged / total < 0.5) { - return "#FA5858"; - } - if ((framesMerged / total >= 0.5) && (framesMerged / total < 0.8)) { - return "#FF9900"; + if (data_parsed[i].conditions != null) { + var bufferFound = false; + for ( var index in data_parsed[i].conditions) { + condition = data_parsed[i].conditions[index]; + + if ((condition.macromoleculeId == record.macromoleculeId) && (condition.bufferId == record.bufferId)) { + data_parsed[i].conditions[index].concentrations.push(getCondition(record)); + bufferFound = true; } - return "white"; } - - function getRow(color, acroynm, framesMerged, totalframes) { - return " " - + BUI.getRectangleColorDIV(color, 10, 10) - + " " + acroynm + "" - + getFrameSpan(framesMerged, totalframes) + ""; + if (!bufferFound) { + data_parsed[i].conditions.push({ + macromoleculeId : record.macromoleculeId, + bufferId : record.bufferId, + concentrations : [ getCondition(record) ] + }); } + } +}; - var html = ""; +ResultsAssemblyGrid.prototype.process = function(record, data_parsed) { + if (this.processed[record.macromoleculeId] == null) { + this.processed[record.macromoleculeId] = true; + record.measurementCount = 1; + record.subtractionCount = 1; + record.averageCount = 1; + record.conditions = []; + data_parsed.push(record); + } - /** Buffer Before **/ - if (bufferAcronym != null) { - if (bbmerges != null) { - color = BIOSAXS.proposal.bufferColors[bufferId]; - html = html + getRow(color, bufferAcronym, bbmerges, totalframes); + for ( var i = 0; i < data_parsed.length; i++) { + if (data_parsed[i].macromoleculeId == record.macromoleculeId) { + data_parsed[i].measurementCount = data_parsed[i].measurementCount + 1; + + if (record.subtractionId != null) { + data_parsed[i].subtractionCount = data_parsed[i].subtractionCount + 1; + this.addCondition(record, data_parsed, i); } - } - /** Molecule **/ - if (macromoleculeAcronym != null) { - if (molmerges != null) { - if (macromoleculeColor == null){ - color = BIOSAXS.proposal.macromoleculeColors[macromoleculeId]; - } - else{ - color = macromoleculeColor; //BIOSAXS.proposal.macromoleculeColors[macromoleculeId]; + if (record.framesMerge != null) { + data_parsed[i].averageCount = data_parsed[i].averageCount + 1; + } + + if (record.timeStart != null) { + if (data_parsed[i].timeStart != null) { + if (moment(data_parsed[i].timeStart).format("X") > moment(record.timeStart).format("X")) { + data_parsed[i].timeStart = record.timeStart; + } } - html = html + getRow(color, macromoleculeAcronym, molmerges, totalframes); } } + } - /** Buffer After **/ - if (bufferAcronym != null) { - if (bamerges != null) { - color = BIOSAXS.proposal.bufferColors[bufferId]; - html = html + getRow(color, bufferAcronym, bamerges, totalframes); + return data_parsed; + +}; + +ResultsAssemblyGrid.prototype._prepareData = function(data) { + var data_parsed = []; + for ( var i = 0; i < data.length; i++) { + data_parsed = this.process(data[i], data_parsed); + } + this.data = data_parsed; + return data_parsed; +}; + +/** Given an array of conditions it returns distinct(concentrations) order by concentration and hash map with number of ocurrences**/ +ResultsAssemblyGrid.prototype.parseConcentrations = function(val, conditions, differentConcentration, quality) { + var conditions = []; + var differentConcentration = {}; + var quality = []; + for ( var i = 0; i < val.length; i++) { + var conc = Number(val[i].concentration).toFixed(1); + var quality = Number(val[i].quality).toFixed(2); + if (differentConcentration[conc] == null) { + differentConcentration[conc] = 0; + conditions.push({ + concentration : conc, + quality : [ quality ], + frames : [ { + bufferAfterFramesMerged : val[i].bufferAfterFramesMerged, + bufferBeforeFramesMerged : val[i].bufferBeforeFramesMerged, + framesMerge : val[i].framesMerge, + framesCount : val[i].framesCount + } ] + }); + } else { + /** Add quality **/ + for ( var j = 0; j < conditions.length; j++) { + if (conditions[j].concentration == conc) { + conditions[j].quality.push(quality); + conditions[j].frames.push({ + bufferAfterFramesMerged : val[i].bufferAfterFramesMerged, + bufferBeforeFramesMerged : val[i].bufferBeforeFramesMerged, + framesMerge : val[i].framesMerge, + framesCount : val[i].framesCount + }); + } } } - return html + "
"; - }, - isWebGLEnabled : function(return_context) { - if (!!window.WebGLRenderingContext) { - var canvas = document.createElement("canvas"); - names = [ "webgl", "experimental-webgl", "moz-webgl", "webkit-3d" ]; - context = false; - for ( var i = 0; i < 4; i++) { - try { - context = canvas.getContext(names[i]); - if (context && typeof context.getParameter == "function") { - // WebGL is enabled - if (return_context) { - // return WebGL object if the function's argument is present - return { - name : names[i], - gl : context - }; - } - // else, return just true - return true; - } - } catch (e) { - } + + differentConcentration[conc] = differentConcentration[conc] + 1; + } + /** sorting concentrations **/ + conditions.sort(function(a, b) { + return a.concentration - b.concentration; + }); + return { + concentrations : conditions, + differentConcentration : differentConcentration + }; +}; + +ResultsAssemblyGrid.prototype.getConditionWarnings = function(condition) { + + var withWarnings = 0; + + for ( var i = 0; i < condition.frames.length; i++) { + if (condition.quality[i] == null) { + withWarnings = withWarnings + 1; + continue; + } else { + if (Number(condition.quality[i]) < this.guinierQuality) { + withWarnings = withWarnings + 1; + continue; } - // WebGL is supported, but disabled - return false; } - // WebGL not supported28. - return false; - }, - getHTMLTableForPrefixes : function(bufferBeforeaverageFilePath, averageFilePath, bufferAfterAverageFilePath) { - function getRow(bufferBeforeaverageFilePath) { - file = bufferBeforeaverageFilePath; - try { - file = bufferBeforeaverageFilePath.split("/")[bufferBeforeaverageFilePath.split("/").length - 1]; - } catch (e) { - file = "NA"; + if (condition.frames[i].bufferBeforeFramesMerged / condition.frames[i].framesCount < this.framePercentageThreshold|| condition.frames[i].framesMerged / condition.frames[i].framesCount < this.framePercentageThreshold|| condition.frames[i].bufferAfterFramesMerged / condition.frames[i].framesCount < this.framePercentageThreshold) { + withWarnings = withWarnings + 1; + continue; + } + } + + return { + withWarnings : withWarnings, + withoutWarnings : condition.frames.length - withWarnings + }; +}; + +ResultsAssemblyGrid.prototype.getFrameHTMLTable = function(warnings) { + var html = ""; + if (warnings.withWarnings > 0) { + html = html + "
" + warnings.withWarnings + + "x
"; + } + + if (warnings.withoutWarnings > 0) { + html = html + "
" + warnings.withoutWarnings + + "x
"; + } + return html; +}; + +ResultsAssemblyGrid.prototype.createConcentrationRow = function(numberOcu, condition, warnings){ + var html = ""; + if (numberOcu > 1){ + html = html + "" +numberOcu + "x " + BUI.formatConcentration(condition.concentration); + } + else{ + html = html + BUI.formatConcentration(condition.concentration); + } + html = html + ""; + html = html + this.getFrameHTMLTable(warnings); + ""; + html = html + ""; + return html; +}; + + +ResultsAssemblyGrid.prototype.getConditionHTMLTable = function(val, style, record) { + var maxNumberColumns = 2; + var html = "
"; + var nColumns = 0; + for ( var r = 0; r < val.length; r++) { + if (nColumns == maxNumberColumns) { + nColumns = 0; + html = html + ""; + } + html = html + ""; } - var html = "
"; + var value = val[r]; + + var bufferAcronym = (BIOSAXS.proposal.getBufferById(value.bufferId).acronym); + + var parsed = (this.parseConcentrations(value.concentrations)); + var conditions = parsed.concentrations; + var differentConcentration = parsed.differentConcentration; + + /** Checking warnings **/ + var warnings = []; + var concentrationValidPerconcentration = 0; + var measurements = 0; + for ( var i = 0; i < conditions.length; i++) { + measurements = measurements + conditions[i].frames.length; + var warning = this.getConditionWarnings(conditions[i]); + warnings.push(warning); + if (warning.withoutWarnings > 0) { + concentrationValidPerconcentration = concentrationValidPerconcentration + 1; } - return "
" + file + "
"; - /** Buffer Before **/ - if (bufferBeforeaverageFilePath != null) { - html = html + getRow(bufferBeforeaverageFilePath); - } + this.validColor = '#E0F8E0'; + this.warningColor = '#F5DA81'; + this.notValidColor = '#F6CED8'; - /** Molecule **/ - if (averageFilePath != null) { - html = html + getRow(averageFilePath); + var color = this.warningColor; + if (concentrationValidPerconcentration > 2) { + color = this.validColor; + } + /** More measurement need to be done **/ + if (measurements < 3) { + color = this.notValidColor; } - /** Buffer After **/ - if (bufferAfterAverageFilePath != null) { - html = html + getRow(bufferAfterAverageFilePath); + html = html + "
"; + html = html + ""; + for ( var i = 0; i < conditions.length; i++) { + html = html + this.createConcentrationRow(differentConcentration[conditions[i].concentration], conditions[i], warnings[i]); } - return html + "
" + bufferAcronym.toUpperCase() + + "
"; - }, - getBaseURL : function() { - return '/ispyb/user/dataadapter.do'; - }, + html = html + ""; + html = html + ""; - getPrintcomponentURL : function(dewarId) { - return '/ispyb/user/viewDewarAction.do?reqCode=generateLabels&dewarId=' + dewarId; + html = html + ""; + nColumns = nColumns + 1; + } + html = html + "
"; + return html; +}; - }, - getPDBVisualizerURL : function(modelId, subtractionId, experimentId) { - return '/ispyb/user/viewProjectList.do?reqCode=display&menu=PDBVisualizer&modelId=' + modelId + '&experimentId=' + experimentId - + '&subtractionId=' + subtractionId; - }, +ResultsAssemblyGrid.prototype._getTbar = function() { + function goTo(url) { + window.location = url; + } - getURL : function() { - return this.getBaseURL() + '?reqCode=getImage'; + var _this = this; + return [ { + icon : '../images/application_view_list.png', + text : 'Multiple Select', + handler : function() { + var specimenSelectorResultGrid = new SpecimenSelectorResultGrid(); + var window = Ext.create('Ext.window.Window', { + title : 'Multiple select', + height : 600, + width : 600, + layout : 'fit', + items : [ specimenSelectorResultGrid.getPanel(_this.data) ], + buttons : [ { + text : 'Go', + handler : function() { + var array = []; + for ( var i = 0; i < specimenSelectorResultGrid.selected.length; i++) { + var row = specimenSelectorResultGrid.selected[i]; + array.push({ + macromoleculeId : row.macromoleculeId, + bufferId : row.bufferId + }); + } + goTo(BUI.getMacromoleculeResultsURLByMultipleSearch(array)); + + } + }, { + text : 'Cancel', + handler : function() { + window.close(); + } + } ] + + }).show(); - }, - getAbinitioImageURL : function() { - return this.getBaseURL() + '?reqCode=getAbinitioImage'; - }, - getNSDImageURL : function(modelListId) { - return BUI.getAbinitioImageURL() + '&type=NSD&modelListId=' + modelListId; - }, - getCHI2ImageURL : function(modelListId) { - return BUI.getAbinitioImageURL() + '&type=CHI2&modelListId=' + modelListId; - }, - getModelFile : function(type, modelId, format) { - return this.getBaseURL() + '?reqCode=getModelFile' + "&type=" + type + "&modelId=" + modelId + "&format=" + format; - }, - getPdbURL : function() { - return this.getBaseURL() + '?reqCode=getPdbFiles'; - }, - getStvArray : function(value, error) { - value = Number(value); - error = Number(error); - return [ value - error, value, value + error ]; - }, - getPointArrayForDygraph : function(x, y, error) { - return [ x, BUI.getStvArray(y, error) ]; - }, - createDIV : function(text, width, className, backgroundColor) { - var nameContainer = document.createElement("div"); - var nameSpan = document.createElement("span"); - if (className != null) { - nameSpan.setAttribute("class", className); - } - if (backgroundColor != null) { - nameSpan.setAttribute("style", "float:left;width:" + width + "px;height:18px;background-color:" + backgroundColor); - } else { - nameSpan.setAttribute("style", "float:left;width:" + width + "px;height:18px;"); } - nameSpan.appendChild(document.createTextNode(text)); - nameContainer.appendChild(nameSpan); - return nameContainer; - }, + } ]; +}; - createFormLabel : function(labelText, text, labelWidth, textWidth, backgroundColor) { - var div = document.createElement("div"); +ResultsAssemblyGrid.prototype.getLegendPanel = function() { + return { + html : '
' + BUI.getRectangleColorDIV(this.validColor, 10, 10) + + 'Good quality measurements' + + BUI.getRectangleColorDIV(this.warningColor, 10, 10) + + 'Probably valid with manual processing' + + BUI.getRectangleColorDIV(this.notValidColor, 10, 10) + + 'More measurements need to be done
' + }; +}; +/** Returns the grid **/ +ResultsAssemblyGrid.prototype.getPanel = function(macromolecules) { + var _this = this; - div.appendChild(BUI.createDIV(labelText, labelWidth, "bLabel", backgroundColor)); - div.appendChild(BUI.createDIV(text, textWidth, "btext", backgroundColor)); - return div.innerHTML; - }, + this.store = Ext.create('Ext.data.Store', { + fields : [ + 'macromoleculeId', 'macromoleculeAcronym', 'measurementCount', 'subtractionCount', 'averageCount', 'timeStart', 'concentrationArray', + 'bufferConditions', 'conditions' ], + data : this._prepareData(macromolecules) + }); - createTextArea : function(labelText, text, labelWidth, rows, cols) { - var div = document.createElement("div"); - div.appendChild(BUI.createDIV(labelText, labelWidth, "bLabel")); - var textArea = document.createElement("textarea"); - textArea.setAttribute("rows", rows); - textArea.setAttribute("cols", cols); - textArea.appendChild(document.createTextNode(text)); - div.appendChild(textArea); - return div.innerHTML; - }, + this.store.sort('macromoleculeAcronym'); - showBetaWarning : function() { - alert("ISPyB for Biosaxs version Beta has not this functionality enabled"); - }, + this.grid = Ext.create('Ext.grid.Panel', { + id : this.id, + title : 'Macromolecules', + store : this.store, + tbar : this._getTbar(), + bbar : [ this.getLegendPanel() ], + width : this.width, + height : this.height, + maxHeight : this.maxHeight, + sortableColumns : true, + columns : [ + { + text : '', + dataIndex : 'macromoleculeId', + width : 20, + hidden : false, + renderer : function(val, y, sample) { + return BUI.getRectangleColorDIV(BIOSAXS.proposal.macromoleculeColors[val], 10, 10); + } + }, + { + text : 'Macromolecule', + dataIndex : 'macromoleculeAcronym', + width : 200 + }, + { + text : 'Buffer Conditions', + dataIndex : 'conditions', + flex : 1, + renderer : function(val, style, record) { + return _this.getConditionHTMLTable(val, style, record); + } + }, + { + header : 'Average', + dataIndex : 'percentageCollected', + name : 'percentageCollected', + type : 'string', + hidden : true, + renderer : function(val, y, sample) { + return "
" + + BUI.getProgessBar((sample.raw.averageCount / sample.raw.measurementCount) * 100, sample.raw.averageCount + "/" + + sample.raw.measurementCount) + "
"; + }, + width : 100, + sorter : false + }, + { + header : 'Subtractions', + dataIndex : 'percentageCollected', + name : 'percentageCollected', + type : 'string', + hidden : true, + renderer : function(val, y, sample) { + return "
"+ BUI.getProgessBar((sample.raw.subtractionCount / sample.raw.measurementCount) * 100, sample.raw.subtractionCount + "/" + + sample.raw.measurementCount) + "
"; + }, + width : 100 + }, { + header : 'Date', + dataIndex : 'timeStart', + name : 'timeStart', + type : 'string', + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + if (record.raw.timeStart != null) { + return moment(record.raw.timeStart).format("MMM Do YY"); + } + } + }, { + header : 'Download', + dataIndex : 'percentageCollected', + name : 'percentageCollected', + type : 'string', + renderer : function(val, y, sample) { + return BUI.getZipHTMLByMacromoleculeId(sample.raw.macromoleculeId); + }, + width : 100 + }, - formatValuesErrorUnitsScientificFormat : function(val, error, unit, args) { - var fontSize = 14; - var decimals = 2; - var errorFontSize = 10; - /** line break **/ - var lineBreak = true; - if (args != null) { - if (args.fontSize != null) { - fontSize = args.fontSize; - } - if (args.decimals != null) { - decimals = args.decimals; - } - if (args.errorFontSize != null) { - errorFontSize = args.errorFontSize; - } - if (args.lineBreak != null) { - lineBreak = args.lineBreak; + { + id : 'btnResultVisible', + width : 85, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + return BUI.getGreenButton('GO'); + } + } ], + viewConfig : { + stripeRows : true, + listeners : { + afterrender : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + }, + celldblclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + _this.edit(record.data.macromoleculeId); + }, + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + if (grid.getGridColumns()[cellIndex].getId() == 'buttonEditMacromolecule') { + _this.edit(record.data.macromoleculeId); + } + if (grid.getGridColumns()[cellIndex].getId() == 'buttonRemoveMacromolecule') { + BUI.showBetaWarning(); + } + if (grid.getGridColumns()[cellIndex].getId() == 'btnResultVisible') { + window.location = BUI.getMacromoleculeResultsURL(record.data.macromoleculeId); + } + } } - } + }); - if (val == "") { - return ""; - } - if (error == null) { - return "" + Number(val).toFixed(decimals) + ""; - } - var html = "" + Number(val).toFixed(decimals) + " " + unit + ""; - if (lineBreak) { - html = html + "
"; - } - return html + " ± " + Number(Number(error).toFixed(3)).toExponential() - + ""; - }, + /** Adding the tbar **/ + if (this.tbar) { + this.grid.addDocked({ + xtype : 'toolbar', + items : this.getTbar() + }); + } + return this.grid; +}; - formatValuesErrorUnits : function(val, error, unit, args) { - var fontSize = 16; - var decimals = 2; - var errorFontSize = 10; - /** line break **/ - var lineBreak = true; - if (args != null) { - if (args.fontSize != null) { - fontSize = args.fontSize; - } - if (args.decimals != null) { - decimals = args.decimals; - } - if (args.errorFontSize != null) { - errorFontSize = args.errorFontSize; - } - if (args.lineBreak != null) { - lineBreak = args.lineBreak; - } +ResultsAssemblyGrid.prototype.input = function(targetId) { + return { + data : DATADOC.getData_3367(), + proposal : DATADOC.getProposal_3367() + }; +}; - } +ResultsAssemblyGrid.prototype.test = function(targetId) { + var grid = new ResultsAssemblyGrid({ + height : 600, + searchBar : false, + tbar : false, + btnResultVisible : true, + width : 1000 + }); + BIOSAXS.proposal = new Proposal(grid.input().proposal); + var panel = grid.getPanel(grid.input().data); + panel.render(targetId); - if (val == "") { - return ""; +}; + + +function RigidModelGrid(args) { + this.height = null; + this.width = null; + this.id = BUI.id(); + + if (args != null) { + if (args.height != null) { + this.height = args.height; + + if (args.width != null) { + this.width = args.width; + } + } + } + + this.onSelected = new Event(this); +} + + +RigidModelGrid.prototype.refresh = function(subtractions) { + var data = []; + if (subtractions != null){ + if (subtractions.length > 0){ + for (j in subtractions){ + var subtraction = subtractions[j]; + if (subtraction.rigidBodyModeling3VOs != null){ + for (i in subtraction.rigidBodyModeling3VOs){ + data.push(subtraction.rigidBodyModeling3VOs[i]); + } + } + } + } + } + this.store.loadData(data); +}; + +RigidModelGrid.prototype.getPanel = function() { + var _this = this; + this.store = Ext.create('Ext.data.Store', { + fields : [ 'symmetry', 'subtractionId', 'subUnitConfigFilePath', 'rigidBodyModelingId', 'rigidBodyModelFilePath', 'logFilePath', 'fitFilePath', 'curveConfigFilePath', + 'crossCorrConfigFilePath', 'contactDescriptionFilePath' ], + data : [] + }); + + this.store.sort([ { + property : 'name', + direction : 'ASC' + } ]); + + this.panel = Ext.create('Ext.grid.Panel', { + store : this.store, + width : this.width, + height : this.height, + margin : 10, + deferredRender : false, + columns : [ { + text : 'RBM', + dataIndex : 'rigidBodyModelFilePath', + hidden : false, + flex : 1, + renderer : function(val){ + return BUI.getFileName(val); + } + }, { + text : 'Sub Unit Conf.', + dataIndex : 'subUnitConfigFilePath', + hidden : true, + flex : 1, + renderer : function(val){ + return BUI.getFileName(val); + } + }, { + text : 'Log', + dataIndex : 'logFilePath', + hidden : true, + flex : 1, + renderer : function(val){ + return BUI.getFileName(val); + } + }, { + text : 'Fit', + dataIndex : 'fitFilePath', + hidden : false, + flex : 1, + renderer : function(val){ + return BUI.getFileName(val); + } + }, { + text : 'Curve Conf.', + dataIndex : 'curveConfigFilePath', + hidden : false, + flex : 1, + renderer : function(val){ + return BUI.getFileName(val); + } + }, { + text : 'Cross Corr.', + dataIndex : 'crossCorrConfigFilePath', + hidden : false, + flex : 1, + renderer : function(val){ + return BUI.getFileName(val); + } + }, { + text : 'Contact Desc.', + dataIndex : 'contactDescriptionFilePath', + hidden : true, + flex : 1, + renderer : function(val){ + return BUI.getFileName(val); + } + } ], + + viewConfig : { + enableTextSelection : true, + preserveScrollOnRefresh : true + }, + listeners : { + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + + }, + afterrender : function() { + } + } + }); + return this.panel; +}; + + +/** + * shows shipments + * + * @height + * @width + * @minHeight + * @btnEditVisible + */ +function ShipmentGrid(args) { + this.id = BUI.id(); + this.height = 100; + this.width = null; + this.minHeight = null; + this.btnEditVisible = true; + + if (args != null) { + if (args.height != null) { + this.height = args.height; } - if (error == null) { - return "" + Number(val).toFixed(decimals) + ""; + if (args.width != null) { + this.width = args.width; } - var html = "" + Number(val).toFixed(decimals) + " " + unit + ""; - if (lineBreak) { - html = html + "
"; + if (args.minHeight != null) { + this.minHeight = args.minHeight; } - return html + " ± " + Number(Number(error).toFixed(8)).toExponential() - + ""; - }, - - formatValuesUnits : function(val, unit, args) { - var fontSize = 12; - var decimals = 2; - var unitsFontSize = 10; - if (args != null) { - if (args.fontSize != null) { - fontSize = args.fontSize; - } - if (args.decimals != null) { - decimals = args.decimals; - } - if (args.unitsFontSize != null) { - unitsFontSize = args.unitsFontSize; - } - + if (args.btnEditVisible != null) { + this.btnEditVisible = args.btnEditVisible; } + } +} - if (val === "") { - return ""; - } - if (unit == null) { - return "" + Number(val).toFixed(decimals) + ""; - } - return "" + Number(val).toFixed(decimals) + " " + unit + ""; - }, +ShipmentGrid.prototype._getColumns = function() { + var _this = this; + var columns = [ + { + text : 'Name', + dataIndex : 'shippingName', + flex : 1 + }, + { + header : 'Type', + dataIndex : 'shippingType', + flex : 1, + hidden : true, + renderer : function(val, comp, record) { + if (val != null) { + return val.toUpperCase(); + } - getGreenButton : function(text, args) { - var width = 70; - var height = 20; - if (args != null) { - if (args.width != null) { - width = args.width; } - if (args.height != null) { - height = args.height; + }, + { + header : 'Status', + type : 'string', + flex : 1, + hidden : false, + renderer : function(comp, val, record) { + if (record.raw.shippingStatus != null) { + if (new String(record.raw.shippingStatus).toUpperCase() == 'OPENED') { + return "" + new String(record.raw.shippingStatus).toUpperCase() + ""; + } + return "" + new String(record.raw.shippingStatus).toUpperCase() + ""; + } + } + }, + { + text : 'Cases', + flex : 1, + hidden : false, + renderer : function(comp, val, record) { + var shipment = BIOSAXS.proposal.getShipmentById(record.data.shippingId); + var container = ""; + if (shipment.dewarVOs.length > 0) { + container = container + ""; + } else { + return "Empty"; + } + return container + "
" + shipment.dewarVOs.length + "x
"; } - } - - return ''; - }, -// getBlueButton : function(text, args) { -// var width = 70; -// var height = 20; -// if (args != null) { -// if (args.width != null) { -// width = args.width; -// } -// if (args.height != null) { -// height = args.height; -// } -// } -// -// return ''; -// }, + }, { + header : 'Comments', + dataIndex : 'comments', + flex : 1, + hidden : false + }, { + header : 'Creation Date', + dataIndex : 'creationDate', + hidden : true + } ]; - getBlueButton : function(text, args) { - var width = 70; - var height = 20; - var href = null; - if (args != null) { - if (args.width != null) { - width = args.width; - } - if (args.height != null) { - height = args.height; + if (this.btnEditVisible) { + columns.push({ + id : _this.id + 'buttonEdit', + text : '', + hidden : !_this.btnEditVisible, + width : 100, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + return BUI.getGreenButton('EDIT'); } - if (args.href != null) { - href = args.href; + }); + } + + columns.push({ + id : _this.id + 'buttonRemove', + text : '', + width : 100, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + var shipment = BIOSAXS.proposal.getShipmentById(record.data.shippingId); + if (shipment.dewarVOs.length == 0) { + return BUI.getRedButton('REMOVE'); } + } - if (href != null) { - return ''; - } else { - return ''; -// return ''; - } - }, - - getSubmitGreenButton : function(text) { - return ''; - }, + }); - getRedButton : function(text) { - return ''; + return columns; +}; - }, - getRectangleColorDIV : function(color, height, width) { - return '
'; - }, +ShipmentGrid.prototype._getTopButtons = function() { + var _this = this; + /** Actions buttons **/ + var actions = []; + actions.push(Ext.create('Ext.Action', { + icon : '../images/add.png', + text : 'Add Shipment', + handler : function(widget, event) { + //window.location = BUI.getCreateShipmentURL(); + var _this = this; - openBufferWindow : function(bufferId) { - var window = new BufferWindow(); - window.draw(tabs.experiment.getBufferById(bufferId), tabs.experiment); - }, + var shipmentForm = new ShipmentForm({ + creationMode : true, + showTitle : false + }); + shipmentForm.onSaved.attach(function(sender, shipment) { + _this.showShipmentTabs(shipment, targetId); + }); + + var window = Ext.create('Ext.window.Window', { + title : 'New Shipment', + height : 600, + width : 800, + layout : 'fit', + items : [ shipmentForm.getPanel() ] + }).show(); - /** Render for safety levels on grids **/ - safetyRenderer : function(val, y, specimen) { - var color = val; - if (val == "YELLOW") { - color = "#E9AB17"; } - return '' + val + ''; - }, + })); + return actions; +}; - getSampleColor : function() { - return '#CB181D'; - }, +ShipmentGrid.prototype.refresh = function(shippings) { + this.features = shippings; + this.store.loadData(this._prepareData(), false); +}; - getLightSampleColor : function() { - return '#FCBBA1'; - }, +ShipmentGrid.prototype._prepareData = function() { + var data = []; + for ( var i = 0; i < this.features.length; i++) { + data.push(this.features[i]); + } + return data; +}; - getBufferColor : function() { - return '#6A51A3'; - }, - getLightBufferColor : function() { - return '#BCBDDC'; - }, +ShipmentGrid.prototype.getPanel = function(shipments) { + this.features = shipments; + return this._renderGrid(); +}; - formatConcentration : function(val) { - if (val != null) { - return "" + Number(val).toFixed(2) + " mg/ml "; - } - return val; - }, +ShipmentGrid.prototype.edit = function(shippingId) { + window.location = BUI.getShippingURL(shippingId); +}; - formatVolume : function(sample, volume) { - if (Number(sample.data.volumeToLoad) > Number(sample.data.volume)) { - return "" + volume + " �l"; - } - if (Number(sample.data.volumeToLoad) == Number(sample.data.volume)) { - return "" + volume + " �l"; - } - return "" + volume + " �l"; - }, +ShipmentGrid.prototype._getStoreFields = function(data) { + var _this = this; + return [ { + name : 'shippingId' + }, { + name : 'shippingName' + }, { + name : 'shippingStatus' + }, { + name : 'shippingType' + }, { + name : 'creationDate' + }, { + name : 'comments' + } ]; +}; - getProposal : function() { - return new Proposal(); - }, +ShipmentGrid.prototype._renderGrid = function() { + var _this = this; - getSampleNameRenderer : function(val, y, record) { - var sample = record.data; - if (record.raw.macromolecule3VO == null) { - return '' + sample.code + ''; - } else { - return '' + sample.code + ''; - } - }, + /** Store **/ + var data = this._prepareData(); + this.store = Ext.create('Ext.data.Store', { + fields : this._getStoreFields(data), + autoload : true, + data : data + }); - getSafetyLevels : function() { - var safetyLevels = new Array(); - safetyLevels.push({ - safetyLevelId : "", - name : "UNKNOWN" - }); - safetyLevels.push({ - safetyLevelId : 1, - name : "GREEN" - }); - safetyLevels.push({ - safetyLevelId : 2, - name : "YELLOW" - }); - safetyLevels.push({ - safetyLevelId : 3, - name : "RED" - }); - return safetyLevels; - }, + this.store.loadData(data, false); + + this.grid = Ext.create('Ext.grid.Panel', { + title : "Shipping", + icon : '/ispyb/images/plane.gif', + width : this.width, + minWidth : this.minWidth, + height : this.height, + store : this.store, + columns : this._getColumns(), + viewConfig : { + stripeRows : true, + listeners : { + itemdblclick : function(dataview, record, item, e) { + _this.edit(record.raw.shippingId); + }, + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEdit') { + _this.edit(record.data.shippingId); + } - getErrorColor : function() { - return '#F6CED8'; - }, - getWarningColor : function() { - return '#F5DA81'; - }, - getValidColor : function() { - return '#E0F8E0'; - }, - getSamplePlateLetters : function() { - return [ "A", "B", "C", "D", "E", "F", "G", "H" ]; - }, - getSamplePositionHTML : function(sample, experiment) { - var plate = ""; - var row = ""; - var column = ""; - var rows = this.getSamplePlateLetters(); - if (sample.sampleplateposition3VO != null) { - var samplePlate = experiment.getSamplePlateById(sample.sampleplateposition3VO.samplePlateId); - if (samplePlate != null) { - plate = (samplePlate.slotPositionColumn); - row = (sample.sampleplateposition3VO.rowNumber); - column = (sample.sampleplateposition3VO.columnNumber); - // var html = "Plate: " + "" + plate + ""; - // html = html + ", Row: " + "" + rows[row - 1] + ""; - // html = html + ", Column: " + "" + column + ""; - var html = "Plate: " + plate - + "-" + rows[row - 1] + "" + column + ""; - return html; + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemove') { + var shipment = BIOSAXS.proposal.getShipmentById(record.data.shippingId); + if (shipment.dewarVOs.length == 0) { + + var adapter = new BiosaxsDataAdapter(); + _this.grid.setLoading("ISPyB: Removing shipment"); + adapter.onSuccess.attach(function(sender) { + BIOSAXS.proposal.onInitialized.attach(function(sender) { + _this.refresh(BIOSAXS.proposal.getShipments()); + _this.grid.setLoading(false); + }); + BIOSAXS.proposal.init(); + }); + + adapter.onError.attach(function(sender) { + alert("Error"); + _this.grid.setLoading(false); + }); + adapter.removeShipment(record.data.shippingId); + } + } + } } + }, + selModel : { + mode : 'SINGLE' } - return ""; - }, + }); - getSafetyLabelName : function(safetyLevelId) { - var safetyLevels = BUI.getSafetyLevels(); - for ( var i = 0; i < safetyLevels.length; i++) { - if (safetyLevels[i].safetyLevelId == safetyLevelId) { - return safetyLevels[i].name; + var actions = _this._getTopButtons(); + this.grid.addDocked({ + xtype : 'toolbar', + items : actions + }); + + this.grid.getSelectionModel().on({ + selectionchange : function(sm, selections) { + if (selections.length) { + for ( var i = 0; i < actions.length; i++) { + if (actions[i].enable) { + actions[i].enable(); + } + } + } else { + for ( var i = 0; i < actions.length; i++) { + if (actions[i].alwaysEnabled == false) { + if (actions[i].disable) { + actions[i].disable(); + } + } + } } } - return "UNKNOWN"; - }, - /** generate random id **/ - id : function() { - var text = ""; - var possible = "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789"; - - for ( var i = 0; i < 5; i++) - text += possible.charAt(Math.floor(Math.random() * possible.length)); + }); + return this.grid; +}; - return text; - }, - showWarning : function(message) { - Ext.Msg.show({ - title : 'Warning', - msg : message, - icon : Ext.Msg.WARNING, - animEl : 'elId' - }); - }, - showError : function(message) { - Ext.Msg.show({ - title : 'Warning', - msg : message, - icon : Ext.Msg.ERROR, - animEl : 'elId' - }); - }, - getTipHTML : function(message) { - //return "
Tip
" - // + message + "
"; - return "
Tip
" - + message + "
"; - }, +ShipmentGrid.prototype.input = function() { + return { + proposal : new MeasurementGrid().input().proposal, + shippings : DATADOC.getShippings_10() + }; +}; - getWarningHTML : function(message) { - return "
Warning
" - + message + "
"; - }, +ShipmentGrid.prototype.test = function(targetId) { + var shipmentGrid = new ShipmentGrid({ + minHeight : 300, + height : 440 + }); + BIOSAXS.proposal = new Proposal(shipmentGrid.input().proposal); + var panel = shipmentGrid.getPanel(targetId); + panel.render(targetId); + shipmentGrid.refresh(shipmentGrid.input().shippings); +}; + +function SpecimenGrid(args) { + this.id = BUI.id(); + this.height = 500; + this.unitsFontSize = 9; + this.editEnabled = false; + this.isPositionColumnHidden = false; + this.removeBtnEnabled = false; - getErrorHTML : function(message) { - return "
Error
" - + message + "
"; - }, + this.selectionMode = "MULTI"; + this.updateRowEnabled = false; + this.grouped = true; + this.width = 900; + this.title = 'Specimens'; + + this.margin = "0 0 0 0"; +// this.experimentColorBased = false; - getProgessBar : function(percentage, text) { - /** percentage 100% green **/ - var color = "#0a0"; + if (args != null) { + if (args.height != null) { + this.height = args.height; + } - color = "#99CC00"; - if (percentage > 100) { - color = "yellow"; - percentage = 100; + if (args.showTitle == false) { + this.title = null; } - if (isNaN(percentage)) { - color = "white"; - percentage = 0; + + if (args.margin == false) { + this.margin = args.margin; } - var defaultText = percentage + "%"; - if (text != null) { - defaultText = text; + if (args.grouped == false) { + this.grouped = null; } - return "
" + defaultText + "
"; - }, - getFileName : function(filePath){ - if (filePath != null){ - return filePath.split("/")[filePath.split("/").length - 1] + if (args.width != null) { + this.width = args.width; } - return ""; - } -}; -Ext.ux.form.RequiredCombo = Ext.extend(Ext.form.ComboBox, { - config : { - cls : 'custom-field-text-required' - }, - initComponent : function() { - Ext.ux.form.RequiredCombo.superclass.initComponent.apply(this, arguments); - }, - checkChange : function() { - if ((this.getValue() == null) || String(this.getValue()).length == 0) { - this.addCls('custom-field-text-required'); - } else { - this.removeCls('custom-field-text-required'); + if (args.editEnabled != null) { + this.editEnabled = args.editEnabled; + } + if (args.removeBtnEnabled != null) { + this.removeBtnEnabled = args.removeBtnEnabled; + } + if (args.isPositionColumnHidden != null) { + this.isPositionColumnHidden = args.isPositionColumnHidden; + } + if (args.selectionMode != null) { + this.selectionMode = args.selectionMode; + } + if (args.updateRowEnabled != null) { + this.updateRowEnabled = args.updateRowEnabled; } + } -}); + this.onClick = new Event(this); + this.onSelected = new Event(this); + this.onRemoved = new Event(this); + this.onSpecimenChanged = new Event(); +} -Ext.define('Ext.form.field.RequiredNumber', { - extend : 'Ext.form.field.Number', - alias : 'widget.requirednumberfield', - alternateClassName : [ 'Ext.form.RequiredNumberField', 'Ext.form.RequiredNumber' ], - config : { - cls : 'custom-field-text-required' - }, +SpecimenGrid.prototype._prepareData = function(experiment) { + var data = []; - initComponent : function() { - var me = this; - me.callParent(); - me.setMinValue(me.minValue); - me.setMaxValue(me.maxValue); - }, + var samples = experiment.getSamples(); + for ( var i = 0; i < samples.length; i++) { + var sample = samples[i]; + if (sample.macromolecule3VO != null) { + sample.macromolecule = sample.macromolecule3VO.acronym; + sample.exposureTemperature = []; + sample.macromoleculeId = sample.macromolecule3VO.macromoleculeId; + } - onChange : function() { - if ((this.getValue() == null) || String(this.getValue()).length == 0) { - this.addCls('custom-field-text-required'); + if (sample.sampleplateposition3VO != null) { + if (sample.sampleplateposition3VO.samplePlateId != null) { + sample.samplePlateId = sample.sampleplateposition3VO.samplePlateId; + sample.rowNumber = sample.sampleplateposition3VO.rowNumber; + sample.columnNumber = sample.sampleplateposition3VO.columnNumber; + if (experiment.getSamplePlateById(sample.sampleplateposition3VO.samplePlateId).plategroup3VO != null) { + sample.plateGroupName = experiment.getSamplePlateById(sample.sampleplateposition3VO.samplePlateId).plategroup3VO.name; + sample.samplePlateName = experiment.getSamplePlateById(sample.sampleplateposition3VO.samplePlateId).name + " [" + sample.plateGroupName + "]"; + sample.slotPositionColumn = experiment.getSamplePlateById(sample.sampleplateposition3VO.samplePlateId).slotPositionColumn; + } + } } else { - this.removeCls('custom-field-text-required'); + sample.samplePlateName = "Unallocated Specimens"; } - this.toggleSpinners(); - this.callParent(arguments); - } -}); -Ext.define('Ext.form.field.RequiredText', { - extend : 'Ext.form.field.Text', - alias : 'widget.requiredtext', - requires : [ 'Ext.form.field.VTypes', 'Ext.layout.component.field.Text' ], - alternateClassName : [ 'Ext.form.RequiredTextField', 'Ext.form.RequiredText' ], - config : { - cls : 'custom-field-text-required' - }, - initComponent : function() { - var me = this; - if (me.allowOnlyWhitespace === false) { - me.allowBlank = false; + /** For grouping, because sencha has not option for multiple grouping I add a field to your store with a convert function that concatenates these two fields and then group by that field.**/ + sample.groupIndex = sample.bufferId + sample.macromoleculeId; + var macromolecule = BIOSAXS.proposal.getMacromoleculeById(sample.macromoleculeId); + + sample.acronym = "Buffers"; + if (macromolecule != null) { + sample.acronym = BIOSAXS.proposal.getMacromoleculeById(sample.macromoleculeId).acronym; } - me.callParent(); - me.addEvents( - /** - * @event autosize - * Fires when the **{@link #autoSize}** function is triggered and the field is resized according to the - * {@link #grow}/{@link #growMin}/{@link #growMax} configs as a result. This event provides a hook for the - * developer to apply additional logic at runtime to resize the field if needed. - * @param {Ext.form.field.Text} this This text field - * @param {Number} width The new field width - */ - 'autosize', - /** - * @event keydown - * Keydown input field event. This event only fires if **{@link #enableKeyEvents}** is set to true. - * @param {Ext.form.field.Text} this This text field - * @param {Ext.EventObject} e - */ - 'keydown', - /** - * @event keyup - * Keyup input field event. This event only fires if **{@link #enableKeyEvents}** is set to true. - * @param {Ext.form.field.Text} this This text field - * @param {Ext.EventObject} e - */ - 'keyup', - /** - * @event keypress - * Keypress input field event. This event only fires if **{@link #enableKeyEvents}** is set to true. - * @param {Ext.form.field.Text} this This text field - * @param {Ext.EventObject} e - */ - 'keypress'); - me.addStateEvents('change'); - me.setGrowSizePolicy(); - }, - checkChange : function() { - if ((this.getValue() == null) || String(this.getValue()).length == 0) { - this.addCls('custom-field-text-required'); - } else { - this.removeCls('custom-field-text-required'); + sample.buffer = experiment.getBufferById(sample.bufferId); + + sample.volumeToLoad = experiment.getVolumeToLoadBySampleId(sample.sampleId); + data.push(sample); + } + return data; +}; + +SpecimenGrid.prototype.deselectAll = function() { + this.grid.getSelectionModel().deselectAll(); +}; + +SpecimenGrid.prototype.selectById = function(specimenId) { + this.grid.getSelectionModel().deselectAll(); + for ( var i = 0; i < this.grid.getStore().data.items.length; i++) { + var item = this.grid.getStore().data.items[i].raw; + if (item.specimenId == specimenId) { + this.grid.getSelectionModel().select(i); } } -}); +}; -var BIOSAXS_COMBOMANAGER = { +SpecimenGrid.prototype.getStore = function() { + return this.store; +}; - getComboMacromoleculeByMacromolecules : function(macromolecules, args) { - var labelWidth = 150; - var margin = "0 0 5 0"; - var width = 300; +SpecimenGrid.prototype.getPlugins = function() { + var _this = this; - if (args != null) { - if (args.labelWidth != null) { - labelWidth = args.labelWidth; - } - if (args.margin != null) { - margin = args.margin; - } - if (args.width != null) { - width = args.width; - } - } + var plugins = []; - var store = Ext.create('Ext.data.Store', { - fields : [ 'macromoleculeId', 'acronym' ], - data : macromolecules, - sorters : [ 'acronym' ] - }); + if (this.updateRowEnabled) { + plugins.push(Ext.create('Ext.grid.plugin.RowEditing', { + clicksToEdit : 1, + listeners : { + validateedit : function(grid, e) { + var measurements = []; - return Ext.create('Ext.form.ComboBox', { - fieldLabel : 'Macromolecules', - labelWidth : labelWidth, - width : width, - margin : margin, - store : store, - editable: false, - queryMode : 'local', - displayField : 'acronym', - valueField : 'macromoleculeId' - }); - }, - getComboBuffers : function(buffers, args) { - var labelWidth = 150; - var margin = "0 0 5 0"; - var width = 300; - var fieldLabel = 'Buffer'; + if (e.newValues.bufferId != e.record.raw.bufferId) { + /** If buffer has changed we have to change all the specimens sharing same datacollection **/ + var dataCollections = []; + if (e.record.raw.macromoleculeId == null) { + dataCollections = dataCollections.concat(_this.experiment.getDataCollectionsBySpecimenId(e.record.raw.specimenId)); + } else { + var sampleDataCollections = _this.experiment.getDataCollectionsBySpecimenId(e.record.raw.specimenId); + for ( var i = 0; i < sampleDataCollections.length; i++) { + var sampleDataCollection = sampleDataCollections[i]; + if (sampleDataCollection != null) { + for ( var j = 0; j < sampleDataCollection.measurementtodatacollection3VOs.length; j++) { + var measurementTODc = sampleDataCollection.measurementtodatacollection3VOs[j]; + if (measurementTODc.dataCollectionOrder == 1) { + dataCollections = dataCollections.concat(_this.experiment.getDataCollectionsBySpecimenId(_this.experiment + .getMeasurementById(measurementTODc.measurementId).specimenId)); + } + } + } + } + } + var i = null; + for ( i = 0; i < dataCollections.length; i++) { + var dataCollection = dataCollections[i]; + var specimens = _this.experiment.getSpecimenByDataCollectionId(dataCollection.dataCollectionId); + measurements = measurements.concat(specimens); + } - if (args != null) { - if (args.labelWidth != null) { - labelWidth = args.labelWidth; - } - if (args.margin != null) { - margin = args.margin; - } - if (args.width != null) { - width = args.width; - } - if (args.noLabel != null) { - fieldLabel = null; - } - } + for ( i = 0; i < measurements.length; i++) { + var measurement = measurements[i]; + var specimen = _this.experiment.getSpecimenById(measurement.specimenId); + specimen.bufferId = e.newValues.bufferId; + new BiosaxsDataAdapter().saveSpecimen(specimen, _this.experiment); + } + } - var store = Ext.create('Ext.data.Store', { - fields : [ 'bufferId', 'acronym' ], - data : buffers, - sorters : [ 'acronym' ] - }); + /** Setting values **/ + e.record.raw.concentration = e.newValues.concentration; + e.record.raw.volume = e.newValues.volume; - return Ext.create('Ext.form.ComboBox', { - fieldLabel : fieldLabel, - labelWidth : labelWidth, - width : width, - margin : margin, - editable: false, - store : store, - queryMode : 'local', - displayField : 'acronym', - valueField : 'bufferId' - }); - }, - getComboSessions : function(sessions, args) { - var labelWidth = 150; - var margin = "0 0 5 0"; - var width = 300; + /** Position **/ + if (e.record.raw.sampleplateposition3VO != null) { + var samplePlate = _this.experiment.getSamplePlateBySlotPositionColumn(e.newValues.slotPositionColumn); + if (samplePlate != null) { + e.record.raw.sampleplateposition3VO = { + columnNumber : e.newValues.columnNumber, + rowNumber : e.newValues.rowNumber, + samplePlateId : samplePlate.samplePlateId + }; + } + } else { + if (e.newValues.slotPositionColumn != null) { + var samplePlate = _this.experiment.getSamplePlateBySlotPositionColumn(e.newValues.slotPositionColumn); + if (samplePlate != null) { + e.record.raw.sampleplateposition3VO = { + columnNumber : e.newValues.columnNumber, + rowNumber : e.newValues.rowNumber, + samplePlateId : samplePlate.samplePlateId + }; + } + } + } - if (args != null) { - if (args.labelWidth != null) { - labelWidth = args.labelWidth; - } - if (args.margin != null) { - margin = args.margin; - } - if (args.width != null) { - width = args.width; + var macromoleculeId = e.record.data.macromoleculeId; + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, specimen) { + /** Because macromolecule3VO is fecthed LAZY **/ + if (macromoleculeId != null) { + specimen.macromolecule3VO = BIOSAXS.proposal.getMacromoleculeById(macromoleculeId); + } + _this.onSpecimenChanged.notify(specimen); + _this.grid.setLoading(false); + }); + adapter.onError.attach(function() { + alert("Error"); + _this.grid.setLoading(false); + }); + _this.grid.setLoading(); + adapter.saveSpecimen(e.record.raw, _this.experiment); + } } - } - - for ( var i = 0; i < sessions.length; i++) { - sessions[i]["startDateFormatted"] = moment(sessions[i].startDate).format("MMM Do YY"); - sessions[i]["sorter"] = moment(sessions[i].startDate).format("YYYYMMDD"); - } + })); + } + return plugins; +}; - var store = Ext.create('Ext.data.Store', { - fields : [ 'sessionId', 'startDateFormatted', 'beamlineName', 'startDate', 'endDate', 'beamlineOperator' ], - data : sessions, - sorters : [ 'sorter' ] +SpecimenGrid.prototype._getRowCombo = function() { + var data = []; + for ( var i = 1; i <= 8; i++) { + data.push({ + rowNumber : i, + name : BUI.getSamplePlateLetters()[i - 1] }); + } - return Ext.create('Ext.form.ComboBox', { - fieldLabel : 'Sessions', - labelWidth : labelWidth, - width : width, - margin : margin, - store : store, - queryMode : 'local', - // displayField : 'startDate', - valueField : 'sessionId', - // Template for the dropdown menu. - // Note the use of "x-boundlist-item" class, - // this is required to make the items selectable. - tpl : Ext.create('Ext.XTemplate', '', - '
{startDateFormatted} {beamlineName}
', ''), - // template for the content inside text field - displayTpl : Ext.create('Ext.XTemplate', '', '{startDateFormatted}', '') + var positionsStore = Ext.create('Ext.data.Store', { + fields : [ 'rowNumber', 'name' ], + data : data + }); - }); - } + return Ext.create('Ext.form.ComboBox', { + store : positionsStore, + queryMode : 'local', + displayField : 'name', + valueField : 'rowNumber' + }); }; - - function GenericWindow(args){ - this.title = "title"; - this.width = 700; - this.height = 500; - this.id = BUI.id(); - - this.close = false; - this.draggable = true; - this.modal = true; - - if (args != null){ - if (args.actions != null){ - this.actions = args.actions; - } - if (args.form != null){ - this.form = args.form; - } - if (args.width != null){ - this.width = args.width; - } - if (args.modal != null){ - this.modal = args.modal; - } - - if (args.height != null){ - this.height = args.height; - } - if (args.title != null){ - this.title = args.title; - } - if (args.form != null){ - this.form = args.form; - } - if (args.close != null){ - this.close = args.close; - } - if (args.draggable != null){ - this.draggable = args.draggable; - } - - } - /** Events **/ - this.onSaved = new Event(this); - }; - - -GenericWindow.prototype.getButtons = function() { - var _this = this; - - if (this.close){ - return [ { - text : 'Close', - handler : function() { - _this.panel.close(); - } - } ]; - } - else{ - return [ { - text : 'Save', - handler : function() { - _this.save(); - - } - }, { - text : 'Cancel', - handler : function() { - _this.panel.close(); - } - } ]; +SpecimenGrid.prototype._getColumnCombo = function() { + var data = []; + for ( var i = 1; i <= 12; i++) { + data.push({ + columnNumber : i + }); } -}; -GenericWindow.prototype.save = function (){ - alert("Method save of GenerciWindow class is abstract"); + var positionsStore = Ext.create('Ext.data.Store', { + fields : [ 'columnNumber' ], + data : data + }); + + return Ext.create('Ext.form.ComboBox', { + store : positionsStore, + queryMode : 'local', + displayField : 'columnNumber', + valueField : 'columnNumber' + }); }; -GenericWindow.prototype._postRender = function(data, experiment){ +SpecimenGrid.prototype._getSlotColumBombo = function() { + if (this.experiment){ + var length = this.experiment.getSamplePlates().length; + + var data = []; + for ( var i = 1; i <= length; i++) { + data.push({ + slotPositionColumn : i + }); + } + + var positionsStore = Ext.create('Ext.data.Store', { + fields : [ 'slotPositionColumn' ], + data : data + }); + return Ext.create('Ext.form.ComboBox', { + store : positionsStore, + queryMode : 'local', + displayField : 'slotPositionColumn', + valueField : 'slotPositionColumn' + }); + } }; - -GenericWindow.prototype.draw = function (data, experiment){ - this._render(data, experiment); +SpecimenGrid.prototype.getPanelByExperiment = function(experiment) { + this.experiment = experiment; + var data = this._prepareData(experiment); + return this.getPanel(data); }; -GenericWindow.prototype.refresh = function(data, experiment){ - this.data = data; - this.experiment = experiment; - this.form.refresh(data, experiment); +SpecimenGrid.prototype.refresh = function(experiment) { + this.experiment = experiment; + var data = this._prepareData(experiment); + this.store.loadData(data); }; -GenericWindow.prototype._render = function(data, experiment){ - this.data = data; - var _this = this; - if (this.panel == null){ - this.panel = Ext.create('Ext.Window', { - id : this.id, - title : this.title, - resizable : true, - constrain : true, - border : 1, - modal : this.modal, - frame : false, - draggable : this.draggable, - closable : true, - autoscroll : true, - layout : { type: 'vbox',align: 'stretch'}, - width : this.width, - height : this.form.height, - buttonAlign :'right', - buttons : this.getButtons(), - items : this.form.getPanel(data, experiment), - listeners: { - scope : this, - minimize : function(){ - this.panel.hide(); - }, - destroy : function(){ - delete this.panel; - } - } - }); - this.panel.setLoading(); - } - - this.panel.show(); - this._postRender(); -}; -function CalendarWidget(args) { - this.height = 740; +SpecimenGrid.prototype.getPanel = function() { + var _this = this; + this.store = Ext.create('Ext.data.Store', { + fields : [ + 'buffer', 'bufferId', 'code', 'macromolecule', 'acronym', 'macromoleculeId', 'concentration', 'volume', 'samplePlateId', + 'slotPositionColumn', 'rowNumber', 'columnNumber', 'groupIndex' ], + data : [], + groupField : 'acronym' + }); + this.store.sort([ { + property : 'concentration', + direction : 'ASC' + }, { + property : 'buffer', + direction : 'ASC' + } ]); - if (args != null) { - if (args.height != null) { - this.height = args.height; + var selModel = Ext.create('Ext.selection.RowModel', { + allowDeselect : true, + mode : this.selectionMode, + listeners : { + selectionchange : function(sm, selections) { + var selected = []; + for ( var i = 0; i < selections.length; i++) { + selected.push(selections[i].raw); + } + _this.onSelected.notify(selected); + } } + }); + + var features = []; + + if (this.grouped) { + features.push({ + ftype : 'grouping', + groupHeaderTpl : '{name}', + hideGroupedHeader : false, + startCollapsed : false, + id : 'myGroupedStore' + }); } - this.onClick = new Event(); -} + this.grid = Ext.create( + 'Ext.grid.Panel', + { + title : this.title, + height : this.height, + width : this.width, + selModel : selModel, + store : this.store, + features : features, + margin : this.margin, + plugins : this.getPlugins(), + columns : [ + { + text : '', + dataIndex : 'macromolecule', + width : 20, + renderer : function(val, y, sample) { + var macromoleculeId = null; + if (sample.raw.macromolecule3VO != null) { + macromoleculeId = sample.raw.macromolecule3VO.macromoleculeId; + } + else{ + macromoleculeId = sample.raw.macromoleculeId; + } + + if (macromoleculeId == null) return; + return BUI.getRectangleColorDIV(_this.experiment.macromoleculeColors[macromoleculeId], 10, 10); + } + }, + { + text : 'Macromolecule', + dataIndex : 'macromolecule', + width : 100 + }, + { + text : '', + dataIndex : 'buffer', + width : 20, + renderer : function(val, y, sample) { + var color = "black"; + if (sample.raw.bufferId != null) { + if (_this.experiment.getDataCollectionsBySpecimenId(sample.raw.specimenId)[0] != null){ + color = _this.experiment.getSpecimenColorByBufferId(_this.experiment.getMeasurementById(_this.experiment.getDataCollectionsBySpecimenId(sample.raw.specimenId)[0].measurementtodatacollection3VOs[0].measurementId).specimenId); + } + return BUI.getRectangleColorDIV(color, 10, 10); + } + } + }, { + text : 'Buffer', + dataIndex : 'bufferId', + width : 140, + renderer : function(val, y, sample) { + if (sample.raw.bufferId != null) { + return BIOSAXS.proposal.getBufferById(val).acronym; + } + }, + editor : BIOSAXS_COMBOMANAGER.getComboBuffers(BIOSAXS.proposal.getBuffers(), { + noLabel : true, + width : 300 + }) + }, { + text : 'Conc.', + dataIndex : 'concentration', + width : 100, + editor : { + allowBlank : false + }, + renderer : function(val, meta, sample) { + if (isNaN(val)) { + meta.tdCls = 'yellow-cell'; + return val; + } else { + if (val != 0) { + return BUI.formatValuesUnits(val, 'mg/ml', { + fontSize : 16, + decimals : 3, + unitsFontSize : this.unitsFontSize + }); + } else { + return; + } + } + } + }, { + text : 'Vol. Well', + dataIndex : 'volume', + width : 70, + editor : { + allowBlank : true + }, + renderer : function(val, y, sample) { + return BUI.formatValuesUnits(sample.data.volume, 'µl', { + fontSize : 12, + decimals : 2, + unitsFontSize : this.unitsFontSize + }); + } + }, { + text : 'Position', + hidden : true, + flex : 1, + renderer : function(val, y, sample) { + return BUI.getSamplePositionHTML(sample.raw, _this.experiment); + } + }, { + text : 'samplePlateId', + dataIndex : 'samplePlateId', + hidden : true + }, { + text : 'Plate', + hidden : this.isPositionColumnHidden, + dataIndex : 'slotPositionColumn', + editor : _this._getSlotColumBombo(), + flex : 1, + renderer : function(val, meta, sample) { + if ((val != null) & (val != "")) { + return val; + } else { + meta.tdCls = 'yellow-cell'; + } + } + }, { + text : 'Row', + hidden : this.isPositionColumnHidden, + dataIndex : 'rowNumber', + editor : this._getRowCombo(), + flex : 1, + renderer : function(val, meta, sample) { + if ((val != null) && (val != "")) { + return BUI.getSamplePlateLetters()[val - 1]; + } else { + meta.tdCls = 'yellow-cell'; + } + } + }, { + text : 'Well', + hidden : this.isPositionColumnHidden, + dataIndex : 'columnNumber', + editor : this._getColumnCombo(), + flex : 1, + renderer : function(val, meta, sample) { + if ((val != null) && (val != "")) { + return val; + } else { + meta.tdCls = 'yellow-cell'; + } + } + }, { + id : _this.id + 'buttonEditSample', + text : 'Edit', + width : 80, + sortable : false, + hidden : !_this.editEnabled, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + if (_this.editEnabled) { + return BUI.getGreenButton('EDIT'); + } + } + }, { + id : _this.id + 'buttonRemoveSample', + text : '', + hidden : !_this.removeBtnEnabled, + width : 100, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + if (_this.removeBtnEnabled) { + return BUI.getRedButton('REMOVE'); + } + } + } -CalendarWidget.prototype.loadData = function(data) { - this.events = []; + ], + viewConfig : { + preserveScrollOnRefresh : true, + stripeRows : true, + getRowClass : function(record) { + var specimens = _this.experiment.getSampleByPosition(record.data.samplePlateId, record.data.rowNumber, + record.data.columnNumber); + if (specimens.length > 1) { + return 'red-row'; - for ( var i = 0; i < data.length; i++) { - var date = moment(data[i].creationDate); - var textColor = 'black'; + } + }, + listeners : { + selectionchange : function(grid, selected) { + _this.onClick.notify(record.raw); + }, + cellclick : function(grid, td, cellIndex, record, tr) { + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEditSample') { + } + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemoveSample') { + grid.getStore().removeAt(rowIndex); + _this.onRemoved.notify(); + } - if (data[i].status == "FINISHED") { - textColor = 'green'; - } - if (data[i].status == "ABORTED") { - textColor = 'red'; - } - this.events.push({ - title : data[i].name, - start : date.format("YYYY-MM-DD HH:mm:ss"), - end : date.format("YYYY-MM-DD HH:mm:ss"), - date : date, - allDay : false, - color : textColor, - className : date.format("YYYY-MM-DD") - }); - } + } + } + } + }); + return this.grid; }; -CalendarWidget.prototype.draw = function(targetId) { - var _this = this; - $('#' + targetId).fullCalendar({ - eventClick : function(calEvent, jsEvent, view) { - _this.onClick.notify(calEvent.className[0]); - - }, - contentHeight : _this.height, - header : { - left : 'prev,next today', - center : 'title', - right : 'month,basicWeek,basicDay' - }, - editable : false, - events : this.events +SpecimenGrid.prototype.input = function() { + return { + experiment : DATADOC.getExperiment_10(), + proposal : DATADOC.getProposal_10() + }; +}; + +SpecimenGrid.prototype.test = function(targetId) { + var specimenGrid = new SpecimenGrid({ + height : 400, + maxHeight : 400, + width : 1000 }); + BIOSAXS.proposal = new Proposal(specimenGrid.input().proposal); + + var experiment = new Experiment(specimenGrid.input().experiment); + var panel = specimenGrid.getPanelByExperiment(experiment); + panel.render(targetId); }; /** - * It shows a table with the guinier and gnom data as well as passed and - * discarded measurements + * Shows a list of stock solutions with macromolecule, buffer, storage temperature, concentration, shipment and comments * - * @height - * @showBufferColumns + * @multiselect allows multiple selection + * @height + * @minHeight + * @width + * @tbar + * @showTitle + * @isPackedVisible shows is stock solution is in a box + * @btnEditVisible shows edit button + * @btnAddVisible + * @btnAddExisting + * @btnUnpackVisible allows to unpack a stock solution + * @btnRemoveVisible allow to remove a stock solution */ -function ConcentrationHTMLTableWidget(args) { + +function StockSolutionGrid(args) { this.id = BUI.id(); + this.height = 100; + this.width = null; + this.minHeight = null; + this.tbar = true; - this.showBufferColumns = true; + this.title = "Stock Solutions"; + + /** Visible buttons and actions **/ + this.btnEditVisible = true; + this.btnRemoveVisible = true; + this.btnAddVisible = true; + this.btnAddExisting = false; + this.isPackedVisible = true; + this.btnUnpackVisible = false; + + /** Selectors **/ + this.multiselect = false; + this.selectedStockSolutions = []; if (args != null) { + if (args.btnUnpackVisible != null) { + this.btnUnpackVisible = args.btnUnpackVisible; + } + if (args.multiselect != null) { + this.multiselect = args.multiselect; + } if (args.height != null) { this.height = args.height; } - if (args.showBufferColumns != null) { - this.showBufferColumns = args.showBufferColumns; + if (args.btnEditVisible != null) { + this.btnEditVisible = args.btnEditVisible; + } + if (args.btnAddVisible != null) { + this.btnAddVisible = args.btnAddVisible; + } + if (args.btnAddExisting != null) { + this.btnAddExisting = args.btnAddExisting; + } + if (args.width != null) { + this.width = args.width; + } + if (args.minHeight != null) { + this.minHeight = args.minHeight; + } + if (args.tbar != null) { + this.tbar = args.tbar; + } + if (args.btnRemoveVisible != null) { + this.btnRemoveVisible = args.btnRemoveVisible; + } + if (args.isPackedVisible != null) { + this.isPackedVisible = args.isPackedVisible; + } + if (args.showTitle != null) { + this.showTitle = args.showTitle; + if (this.showTitle == false) { + this.title = null; + } } - } -} - -ConcentrationHTMLTableWidget.prototype.refresh = function(parsedData) { - document.getElementById(this.id).innerHTML = this.getPanel(parsedData); -}; - -ConcentrationHTMLTableWidget.prototype.getPanel = function(parsedData) { - var html = "
"; - html = html + ""; - /** Title * */ - html = html + ""; - html = html + ""; - if (this.showBufferColumns) { - html = html + ""; } - html = html + ""; - html = html + ""; - html = html + ""; - html = html + ""; - html = html + ""; - html = html + ""; - html = html + ""; - html = html + ""; - html = html + ""; - html = html + ""; - html = html + ""; - html = html + ""; - html = html + ""; + /** Events **/ + this.onProposalChanged = new Event(this); + this.onStockSolutionSelected = new Event(this); +} - parsedData.concentration.concentrations.sort(function(a, b) { - return a.concentration - b.concentration; - }); - /** Row * */ - for ( var i = 0; i < parsedData.concentration.concentrations.length; i++) { - var row = parsedData[i]; +StockSolutionGrid.prototype._getColumns = function() { + var _this = this; + var columns = [ - var tr = ""; - if (i % 2 == 1) { - tr = ""; + { + header : 'Macromolecule', + dataIndex : 'macromolecule', + id : _this.id + 'macromolecule', + type : 'string', + renderer : function(val, y, specimen) { + return '' + val + ''; + }, + hidden : false, + flex : 1 + }, { + header : 'Buffer', + dataIndex : 'buffer', + name : 'buffer', + hidden : false, + renderer : function(val, y, specimen) { + return '' + val + ''; + }, + type : 'string', + flex : 1 + }, { + header : 'Acronym', + dataIndex : 'name', + name : 'name', + type : 'string', + flex : 1, + hidden : true + }, { + header : 'Storage Temp.', + dataIndex : 'storageTemperature', + name : 'storageTemperature', + type : 'string', + flex : 1, + hidden : false, + renderer : function(val) { + return BUI.formatValuesUnits(val, 'C', { + fontSize : 12, + decimals : 2, + unitsFontSize : 10 + }); } - var goodMeasurements = (parsedData.concentration.concentrations[i].frames.length - parsedData.concentration.concentrations[i].frames_warning); - if (goodMeasurements == 0) { - tr = ""; + }, { + header : 'Volume', + dataIndex : 'volume', + type : 'string', + flex : 1, + hidden : false, + renderer : function(val) { + return BUI.formatValuesUnits(val, 'µl', { + fontSize : 12, + decimals : 2, + unitsFontSize : 10 + }); } - html = html + tr; - html = html + ""; - if (this.showBufferColumns) { - html = html + ""; + }, { + header : 'Concentration', + dataIndex : 'concentration', + name : 'concentration', + type : 'string', + flex : 1, + renderer : function(val) { + return BUI.formatValuesUnits(val, 'mg/ml', { + fontSize : 12, + decimals : 2, + unitsFontSize : 10 + }); } - html = html + ""; - html = html + ""; - html = html + ""; - html = html + ""; - html = html + ""; - html = html + ""; - html = html + ""; - html = html + ""; + }, { + header : 'Packed', + dataIndex : 'comments', + id : _this.id + "box", + type : 'string', + width : 50, + hidden : !this.isPackedVisible, + renderer : function(val, cmp, a) { + if (a.raw.boxId != null) { + return "
"; + } + + } + }, { + header : 'Comments', + dataIndex : 'comments', + type : 'string', + flex : 1 + } ]; + + if (this.btnEditVisible) { + columns.push({ + id : _this.id + 'buttonEdit', + width : 85, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + if (_this.btnEditVisible) { + return BUI.getGreenButton('EDIT'); + } + } + }); + } + + if (this.btnRemoveVisible) { + columns.push({ + id : _this.id + 'buttonRemove', + width : 85, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + if (_this.btnRemoveVisible) { + return BUI.getRedButton('REMOVE'); + } + } + }); } - return html + "
ConcentrationBufferMeasurementsGuinierGnom
PassedDiscardedRgI0QualityRgdMax
" + parsedData.concentration.concentrations[i].concentration + "" + parsedData.concentration.concentrations[i].bufferAcronym + "" + goodMeasurements + " of " + parsedData.concentration.concentrations[i].frames.length + "" + parsedData.concentration.concentrations[i].frames_warning + "" + BUI.formatValuesErrorUnits(parsedData.concentration.concentrations[i].calculation.rgGuinier.avg, parsedData.concentration.concentrations[i].calculation.rgGuinier.std, "nm", { - lineBreak : false - }) + "" + BUI.formatValuesErrorUnits(parsedData.concentration.concentrations[i].calculation.i0Guinier.avg, parsedData.concentration.concentrations[i].calculation.i0Guinier.std, " ", { - lineBreak : false - }) + "" + BUI.formatValuesErrorUnits(parsedData.concentration.concentrations[i].calculation.quality.avg, parsedData.concentration.concentrations[i].calculation.quality.std, " ", { - lineBreak : false - }) + "" + BUI.formatValuesErrorUnits(parsedData.concentration.concentrations[i].calculation.rgGnom.avg, parsedData.concentration.concentrations[i].calculation.rgGnom.std, " ", { - lineBreak : false - }) + "" + BUI.formatValuesErrorUnits(parsedData.concentration.concentrations[i].calculation.dMax.avg, parsedData.concentration.concentrations[i].calculation.dMax.std, " ", { - lineBreak : false - }) + "
"; + + if (this.btnUnpackVisible) { + columns.push({ + id : _this.id + 'buttonUnpack', + width : 85, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + if (_this.btnUnpackVisible) { + return BUI.getBlueButton('UNPACK'); + } + } + }); + } + return columns; }; -ConcentrationHTMLTableWidget.prototype.input = function() { - return { - data : { - "dataCollectionCount" : 4, - "buffers" : [ { - "bufferId" : "422" - } ], - "concentration" : { - "concentrations" : [ { - "concentration" : "7.17", - "id" : "7.1699999999999999", - "bufferId" : "422.00", - "bufferAcronym" : "B1", - "rgGuinier" : [ "5.12723" ], - "frames" : [ { - "total" : "0.515705406286", - "bufferBeforeMeasurementId" : 15045, - "sampleMergeId" : 8176, - "averagedModelId" : null, - "I0" : "183.457461646", - "proposalCode" : "OPD", - "averagedModel" : null, - "bufferAfterMergeId" : 8177, - "framesCount" : "10", - "bufferBeforeMergeId" : 8175, - "averageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_065_ave.dat", - "bufferAfterMeasurementId" : 15048, - "rgGuinier" : "5.12723", - "subtractedFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_065_sub.dat", - "firstPointUsed" : "17", - "chi2RgFilePath" : null, - "abInitioModelId" : null, - "macromoleculeId" : 649, - "code" : "_4.0_7.17", - "transmission" : "100.0", - "timeStart" : "2013-06-05 15:43:54.348723", - "bufferAcronym" : "B1", - "quality" : "0.853011", - "shapeDeterminationModelId" : null, - "expermientComments" : "[BsxCube] Generated from BsxCube", - "bufferId" : 422, - "isagregated" : "False", - "dmax" : "25.63615", - "bufferBeforeAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_064_ave.dat", - "exposureTemperature" : "4.0", - "subtractionId" : 3377, - "conc" : "7.1699999999999999", - "rapidShapeDeterminationModel" : null, - "experimentCreationDate" : "Jun 5, 2013 3:30:30 PM", - "lastPointUsed" : "36", - "modelListId" : null, - "framesMerge" : "9", - "rapidShapeDeterminationModelId" : null, - "bufferAfterAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_066_ave.dat", - "nsdFilePath" : null, - "bufferAfterFramesMerged" : "10", - "experimentId" : 700, - "macromoleculeAcronym" : "L9", - "i0stdev" : "0.139364435146", - "sampleMeasurementId" : 15047, - "measurementComments" : "[5]", - "priorityLevelId" : 10, - "bufferBeforeFramesMerged" : "10", - "substractionCreationTime" : "Jun 5, 2013 3:46:31 PM", - "proposalNumber" : "29", - "rgGnom" : "5.40297914939", - "volume" : "475.302", - "shapeDeterminationModel" : null, - "comments" : null, - "groupeField" : "L9 B1" - } ], - "frames_warning" : 0, - "calculation" : { - "rgGuinier" : { - "std" : 0, - "sum" : 5.12723, - "avg" : 5.12723, - "validNumber" : 1, - "totalNumber" : 1, - "values" : [ "5.12723" ] - }, - "i0Guinier" : { - "std" : 0, - "sum" : 183.457461646, - "avg" : 183.457461646, - "validNumber" : 1, - "totalNumber" : 1, - "values" : [ "183.457461646" ] - }, - "quality" : { - "std" : 0, - "sum" : 0.853011, - "avg" : 0.853011, - "validNumber" : 1, - "totalNumber" : 1, - "values" : [ "0.853011" ] - }, - "rgGnom" : { - "std" : 0, - "sum" : 5.40297914939, - "avg" : 5.40297914939, - "validNumber" : 1, - "totalNumber" : 1, - "values" : [ "5.40297914939" ] - }, - "dMax" : { - "std" : 0, - "sum" : 25.63615, - "avg" : 25.63615, - "validNumber" : 1, - "totalNumber" : 1, - "values" : [ "25.63615" ] - } - } - }, { - "concentration" : "3.53", - "id" : "3.5299999999999998", - "bufferId" : "422.00", - "bufferAcronym" : "B1", - "rgGuinier" : [ "4.38278" ], - "frames" : [ { - "total" : "0.497164741078", - "bufferBeforeMeasurementId" : 15048, - "sampleMergeId" : 8178, - "averagedModelId" : null, - "I0" : "160.023229462", - "proposalCode" : "OPD", - "averagedModel" : null, - "bufferAfterMergeId" : 8179, - "framesCount" : "10", - "bufferBeforeMergeId" : 8177, - "averageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_067_ave.dat", - "bufferAfterMeasurementId" : 15051, - "rgGuinier" : "4.38278", - "subtractedFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_067_sub.dat", - "firstPointUsed" : "36", - "chi2RgFilePath" : null, - "abInitioModelId" : null, - "macromoleculeId" : 649, - "code" : "_4.0_3.53", - "transmission" : "100.0", - "timeStart" : "2013-06-05 15:47:04.630129", - "bufferAcronym" : "B1", - "quality" : "0.742825", - "shapeDeterminationModelId" : null, - "expermientComments" : "[BsxCube] Generated from BsxCube", - "bufferId" : 422, - "isagregated" : "False", - "dmax" : "15.33973", - "bufferBeforeAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_066_ave.dat", - "exposureTemperature" : "4.0", - "subtractionId" : 3378, - "conc" : "3.5299999999999998", - "rapidShapeDeterminationModel" : null, - "experimentCreationDate" : "Jun 5, 2013 3:30:30 PM", - "lastPointUsed" : "61", - "modelListId" : null, - "framesMerge" : "10", - "rapidShapeDeterminationModelId" : null, - "bufferAfterAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_068_ave.dat", - "nsdFilePath" : null, - "bufferAfterFramesMerged" : "10", - "experimentId" : 700, - "macromoleculeAcronym" : "L9", - "i0stdev" : "0.1499898017", - "sampleMeasurementId" : 15050, - "measurementComments" : "[6]", - "priorityLevelId" : 12, - "bufferBeforeFramesMerged" : "10", - "substractionCreationTime" : "Jun 5, 2013 3:49:42 PM", - "proposalNumber" : "29", - "rgGnom" : "4.40615474861", - "volume" : "372.656", - "shapeDeterminationModel" : null, - "comments" : null, - "groupeField" : "L9 B1" - } ], - "frames_warning" : 0, - "calculation" : { - "rgGuinier" : { - "std" : 0, - "sum" : 4.38278, - "avg" : 4.38278, - "validNumber" : 1, - "totalNumber" : 1, - "values" : [ "4.38278" ] - }, - "i0Guinier" : { - "std" : 0, - "sum" : 160.023229462, - "avg" : 160.023229462, - "validNumber" : 1, - "totalNumber" : 1, - "values" : [ "160.023229462" ] - }, - "quality" : { - "std" : 0, - "sum" : 0.742825, - "avg" : 0.742825, - "validNumber" : 1, - "totalNumber" : 1, - "values" : [ "0.742825" ] - }, - "rgGnom" : { - "std" : 0, - "sum" : 4.40615474861, - "avg" : 4.40615474861, - "validNumber" : 1, - "totalNumber" : 1, - "values" : [ "4.40615474861" ] - }, - "dMax" : { - "std" : 0, - "sum" : 15.33973, - "avg" : 15.33973, - "validNumber" : 1, - "totalNumber" : 1, - "values" : [ "15.33973" ] +StockSolutionGrid.prototype._getTopButtons = function() { + var _this = this; + /** Actions buttons **/ + var actions = []; + + /** ADD BUTTON **/ + if (this.btnAddVisible) { + actions.push(Ext.create('Ext.Action', { + icon : '../images/add.png', + text : 'Add Stock Solution', + tooltip : 'Will create a new stock solution', + disabled : false, + alwaysEnabled : true, + handler : function(widget, event) { + _this.edit(); + } + })); + } + + if (this.btnAddExisting) { + actions.push(Ext.create('Ext.Action', { + icon : '../images/add.png', + text : 'Add Existing', + tooltip : 'Allows to select upacked stock solutions', + disabled : false, + alwaysEnabled : true, + handler : function(widget, event) { + var stockSolutionGrid = new StockSolutionGrid({ + btnAddVisible : false, + btnEditVisible : false, + btnRemoveVisible : false, + btnAddExisting : false, + isPackedVisible : true, + multiselect : true + }); + + var window = Ext.create('Ext.window.Window', { + title : 'Select', + height : 400, + width : 800, + layout : 'fit', + items : [ stockSolutionGrid.getPanel() ], + buttons : [ { + text : 'Pack', + handler : function() { + _this.onStockSolutionSelected.notify(stockSolutionGrid.selectedStockSolutions); + window.close(); + } + }, { + text : 'Cancel', + handler : function() { + window.close(); } + } ] + + }).show(); + + stockSolutionGrid.refresh(BIOSAXS.proposal.getUnpackedStockSolutions()); + } + })); + } + + return actions; +}; + +StockSolutionGrid.prototype.refresh = function(stockSolutions) { + this.features = stockSolutions; + this.store.loadData(this._prepareData(), false); +}; + +StockSolutionGrid.prototype._prepareData = function() { + var data = []; + for ( var i = 0; i < this.features.length; i++) { + var stockSolution = this.features[i]; + stockSolution.buffer = BIOSAXS.proposal.getBufferById(stockSolution.bufferId).acronym; + if (stockSolution.macromoleculeId != null) { + stockSolution.macromolecule = BIOSAXS.proposal.getMacromoleculeById(stockSolution.macromoleculeId).acronym; + } + data.push(stockSolution); + } + return data; +}; + +StockSolutionGrid.prototype.getPanel = function() { + return this._renderGrid(); +}; + +StockSolutionGrid.prototype.edit = function(stockSolutionId) { + var _this = this; + var stockSolutionWindow = new StockSolutionWindow(); + /** On stock solution SAVED **/ + stockSolutionWindow.onSaved.attach(function(sender, stockSolution) { + _this.onProposalChanged.notify(stockSolution); + }); + stockSolutionWindow.draw(BIOSAXS.proposal.getStockSolutionById(stockSolutionId)); +}; + +StockSolutionGrid.prototype._getStoreFields = function() { + return [ { + name : 'name', + type : 'string' + }, { + name : 'stockSolutionId', + type : 'string' + }, { + name : 'macromolecule', + type : 'string' + }, { + name : 'buffer', + type : 'string' + }, { + name : 'storageTemperature', + type : 'numeric' + }, { + name : 'volume', + type : 'string' + }, { + name : 'concentration', + type : 'string' + }, { + name : 'buffer', + type : 'string' + }, { + name : 'comments', + type : 'string' + } ]; +}; + +//StockSolutionGrid.prototype.refresh = function() { +// this.proposal.onInitialized.attach(function(sender){ +// +// }); +// this.proposal.init(Ext.urlDecode(window.location.href).sessionId); +//}; + +StockSolutionGrid.prototype._renderGrid = function() { + var _this = this; + + /** Store **/ + this.store = Ext.create('Ext.data.Store', { + fields : this._getStoreFields(), //columns, + autoload : true + }); + + var filters = { + ftype : 'filters', + local : true, + filters : this.filters + }; + + var selModel = null; + + if (this.multiselect) { + selModel = Ext.create('Ext.selection.CheckboxModel', { + //multiSelect : false,//this.multiselect, + mode : 'SINGLE', + listeners : { + selectionchange : function(sm, selections) { + _this.selectedStockSolutions = []; + for ( var i = 0; i < selections.length; i++) { + _this.selectedStockSolutions.push(selections[i].raw); } - }, { - "concentration" : "1.75", - "id" : "1.75", - "bufferId" : "422.00", - "bufferAcronym" : "B1", - "rgGuinier" : [], - "frames" : [ { - "total" : "0.5538035065", - "bufferBeforeMeasurementId" : 15051, - "sampleMergeId" : 8180, - "averagedModelId" : null, - "I0" : "146.927428571", - "proposalCode" : "OPD", - "averagedModel" : null, - "bufferAfterMergeId" : 8181, - "framesCount" : "10", - "bufferBeforeMergeId" : 8179, - "averageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_069_ave.dat", - "bufferAfterMeasurementId" : 15054, - "rgGuinier" : "4.27139", - "subtractedFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_069_sub.dat", - "firstPointUsed" : "33", - "chi2RgFilePath" : null, - "abInitioModelId" : null, - "macromoleculeId" : 649, - "code" : "_4.0_1.75", - "transmission" : "100.0", - "timeStart" : "2013-06-05 15:50:09.395824", - "bufferAcronym" : "B1", - "quality" : "0.765999", - "shapeDeterminationModelId" : null, - "expermientComments" : "[BsxCube] Generated from BsxCube", - "bufferId" : 422, - "isagregated" : "False", - "dmax" : "14.949865", - "bufferBeforeAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_068_ave.dat", - "exposureTemperature" : "4.0", - "subtractionId" : 3379, - "conc" : "1.75", - "rapidShapeDeterminationModel" : null, - "experimentCreationDate" : "Jun 5, 2013 3:30:30 PM", - "lastPointUsed" : "62", - "modelListId" : null, - "framesMerge" : "6", - "rapidShapeDeterminationModelId" : null, - "bufferAfterAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_070_ave.dat", - "nsdFilePath" : null, - "bufferAfterFramesMerged" : "10", - "experimentId" : 700, - "macromoleculeAcronym" : "L9", - "i0stdev" : "0.191914285714", - "sampleMeasurementId" : 15053, - "measurementComments" : "[7]", - "priorityLevelId" : 14, - "bufferBeforeFramesMerged" : "10", - "substractionCreationTime" : "Jun 5, 2013 3:52:31 PM", - "proposalNumber" : "29", - "rgGnom" : "4.28379338749", - "volume" : "356.326", - "shapeDeterminationModel" : null, - "comments" : null, - "groupeField" : "L9 B1" - } ], - "frames_warning" : 1, - "calculation" : { - "rgGuinier" : { - "std" : null, - "sum" : 0, - "avg" : 0, - "validNumber" : 0, - "totalNumber" : 0, - "values" : [] - }, - "i0Guinier" : { - "std" : null, - "sum" : 0, - "avg" : 0, - "validNumber" : 0, - "totalNumber" : 0, - "values" : [] - }, - "quality" : { - "std" : null, - "sum" : 0, - "avg" : 0, - "validNumber" : 0, - "totalNumber" : 0, - "values" : [] - }, - "rgGnom" : { - "std" : null, - "sum" : 0, - "avg" : 0, - "validNumber" : 0, - "totalNumber" : 0, - "values" : [] - }, - "dMax" : { - "std" : null, - "sum" : 0, - "avg" : 0, - "validNumber" : 0, - "totalNumber" : 0, - "values" : [] + } + } + }); + } else { + selModel = { + mode : 'SINGLE' + }; + } + + this.store.sort("stockSolutionId", "desc"); + + this.grid = Ext.create('Ext.grid.Panel', { + style : { + padding : 5 + }, + icon : '/ispyb/images/SampleHolder_24x24_01.png', + title : this.title, + height : this.height, + width : this.width, + minWidth : this.minWidth, + selModel : selModel, + store : this.store, + columns : this._getColumns(), + viewConfig : { + stripeRows : true, + listeners : { + itemdblclick : function(dataview, record, item, e) { + _this.edit(record.raw.stockSolutionId); + }, + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + var adapter = null; + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonUnpack') { + _this.grid.setLoading("ISPyB: Unpacking stock solution"); + adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender) { + _this.onProposalChanged.notify(); + _this.grid.setLoading(false); + }); + adapter.onError.attach(function(sender) { + _this.onProposalChanged.notify(); + _this.grid.setLoading(false); + }); + record.raw.boxId = null; + adapter.saveStockSolution(record.raw); + } + + if (grid.getGridColumns()[cellIndex].getId() == _this.id + "box") { + window.location = BUI.getShippingURL(BIOSAXS.proposal.getShipmentByDewarId(record.raw.boxId).shippingId); + } + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEdit') { + _this.edit(record.data.stockSolutionId); + } + + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemove') { + _this.grid.setLoading("ISPyB: Removing stock solution"); + adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender) { + _this.onProposalChanged.notify(); + _this.grid.setLoading(false); + }); + adapter.onError.attach(function(sender) { + _this.onProposalChanged.notify(); + _this.grid.setLoading(false); + }); + adapter.removeStockSolution(record.data.stockSolutionId); + } + } + } + } + + }); + + var actions = _this._getTopButtons(); + this.grid.addDocked({ + xtype : 'toolbar', + items : actions + }); + + var i = null; + this.grid.getSelectionModel().on({ + selectionchange : function(sm, selections) { + if (selections.length) { + for ( i = 0; i < actions.length; i++) { + if (actions[i].enable) { + actions[i].enable(); + } + } + } else { + for ( i = 0; i < actions.length; i++) { + if (actions[i].alwaysEnabled == false) { + if (actions[i].disable) { + actions[i].disable(); + } + } + } + } + } + }); + return this.grid; +}; + +StockSolutionGrid.prototype.input = function() { + return { + proposal : DATADOC.getProposal_10() + }; +}; + +StockSolutionGrid.prototype.test = function(targetId) { + var stockSolutionGrid = new StockSolutionGrid({ + height : 300, + width : 900 + }); + BIOSAXS.proposal = new Proposal(stockSolutionGrid.input().proposal); + var panel = stockSolutionGrid.getPanel(); + stockSolutionGrid.refresh(BIOSAXS.proposal.getStockSolutions()); + panel.render(targetId); +}; + + +function SuperpositionGrid(args) { + this.height = null; + this.width = null; + this.id = BUI.id(); + + if (args != null) { + if (args.height != null) { + this.height = args.height; + + if (args.width != null) { + this.width = args.width; + } + } + } + + this.onSelected = new Event(this); +} + +SuperpositionGrid.prototype._prepareData = function(data) { + return data; +}; + +SuperpositionGrid.prototype.refresh = function(subtractions) { + var data = []; + if (subtractions != null){ + if (subtractions.length > 0){ + for (j in subtractions){ + var subtraction = subtractions[j]; + if (subtraction.superposition3VOs != null){ + for (i in subtraction.superposition3VOs){ + data.push(subtraction.superposition3VOs[i]); + } + } + } + } + } + this.store.loadData(data); +}; + +SuperpositionGrid.prototype.getPanel = function() { + var _this = this; + this.store = Ext.create('Ext.data.Store', { + fields : [ 'abinitioModelPdbFilePath', 'aprioriPdbFilePath', 'alignedPdbFilePath' ], + data : [] + }); + + this.selModel = Ext.create('Ext.selection.RowModel', { + allowDeselect : true, + mode : 'MULTI', + listeners : { + selectionchange : function(sm, selections) { + var selected = []; + for (var i = 0; i < selections.length; i++) { + selected.push(selections[i].raw); + } + _this.onSelected.notify(selected); + } + } + }); + + this.store.sort([ { + property : 'name', + direction : 'ASC' + } ]); + + this.panel = Ext.create('Ext.grid.Panel', { + store : this.store, + selModel : this.selModel, + width : this.width, + height : this.height, + margin : 10, + deferredRender : false, + columns : [ { + text : 'Abinitio', + dataIndex : 'abinitioModelPdbFilePath', + hidden : false, + flex : 1, + renderer : function(val){ + return BUI.getFileName(val); + } + }, { + text : 'Apriori', + dataIndex : 'aprioriPdbFilePath', + hidden : false, + flex : 1, + renderer : function(val){ + return BUI.getFileName(val); + } + }, { + text : 'Aligned', + dataIndex : 'alignedPdbFilePath', + hidden : false, + flex : 1, + renderer : function(val){ + return BUI.getFileName(val); + } + } ], + + viewConfig : { + enableTextSelection : true, + preserveScrollOnRefresh : true + }, + listeners : { + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + + }, + afterrender : function() { + } + } + }); + return this.panel; +}; + +/** + * See ExperimentGrid + * + */ +function TemplateGrid(args) { + + if (args == null) { + args = {}; + } + args.sorters = [ { + property : 'experimentId', + direction : 'DESC' + } ]; + + ExperimentGrid.prototype.constructor.call(this, args); +} + +TemplateGrid.prototype._getFilterTypes = ExperimentGrid.prototype._getFilterTypes; +TemplateGrid.prototype._prettyPrintMacromolecules = ExperimentGrid.prototype._prettyPrintMacromolecules; +TemplateGrid.prototype._getPercentage = ExperimentGrid.prototype._getPercentage; +TemplateGrid.prototype._getPercentageCollected = ExperimentGrid.prototype._getPercentageCollected; +TemplateGrid.prototype.getPercentageMerged = ExperimentGrid.prototype.getPercentageMerged; +TemplateGrid.prototype._prepareData = ExperimentGrid.prototype._prepareData; +TemplateGrid.prototype.getPanel = ExperimentGrid.prototype.getPanel; +TemplateGrid.prototype._renderGrid = ExperimentGrid.prototype._renderGrid; +TemplateGrid.prototype._editExperiment = ExperimentGrid.prototype._editExperiment; +TemplateGrid.prototype._removeExperimentById = ExperimentGrid.prototype._removeExperimentById; + +TemplateGrid.prototype._getTopButtons = function() { + /** Actions buttons * */ + var actions = []; + + actions.push(Ext.create('Ext.Action', { + icon : '../images/add.png', + text : 'Add experiment', + handler : function(widget, event) { + var wizardWidget = new WizardWidget({ + windowMode : true + }); + + wizardWidget.onFinished.attach(function(sender, result) { + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + var experiment = new Experiment(data); + BIOSAXS.openExperimentByExperiment(experiment); + wizardWidget.window.close(); + }); + wizardWidget.current.setLoading("ISPyB: Creating experiment"); + adapter.createTemplate(result.name, "comments", result.data); + }); + +// wizardWidget.draw(this.targetId, new ExperimentTypeWizardForm()); + wizardWidget.draw(this.targetId, new MeasurementCreatorStepWizardForm(BIOSAXS.proposal.getMacromolecules())); + } + })); + return actions; +}; + +TemplateGrid.prototype.refresh = function(data) { + var filtered = []; + for ( var i = 0; i < data.length; i++) { + if (data[i].experimentType == "TEMPLATE") { + filtered.push(data[i]); + } + } + this.store.loadData(this._prepareData(filtered), false); +}; + +TemplateGrid.prototype._getColumns = function() { + var _this = this; + function actionItemRenderer(value, meta, record, rowIx, ColIx, store) { + if (record.raw.buffer3VOs != null) { + if (record.raw.buffer3VOs.length > 0) { + return 'x-hide-display'; + } + } + + if (record.data.platesCount > 0) { + return 'x-hide-display'; + } + } + + return [ { + xtype : 'rownumberer', + width : 40 + }, { + text : 'experimentId', + dataIndex : 'experimentId', + name : 'experimentId', + type : 'string', + hidden : true + }, { + text : 'Name', + dataIndex : 'name', + name : 'name', + type : 'string', + flex : 1 + }, + + { + text : 'Type', + dataIndex : 'type', + name : 'type', + type : 'string', + hidden : true, + flex : 1, + renderer : function(val) { + return val; + } + }, { + text : 'Macromolecules', + name : 'macromolecules_names', + dataIndex : 'macromolecules_names', + flex : 1, + renderer : function(val) { + return " " + val + ""; + } + }, { + id : _this.id + 'GO', + width : 80, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + return BUI.getGreenButton('EDIT'); + } + }, { + id : _this.id + 'REMOVE', + width : 100, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + return BUI.getRedButton('REMOVE'); + } + } ]; +}; + +TemplateGrid.prototype.input = function() { + var experiments = DATADOC.getExperimentList_10(); + return { + experiments : experiments, + proposal : new MeasurementGrid().input().proposal + + }; +}; + +TemplateGrid.prototype.test = function(targetId) { + var experimentGrid = new TemplateGrid({ + height : 350, + minHeight : 350, + width : 1000, + gridType : 'Ext.grid.Panel', + title : 'Experiments', + grouping : false, + tbar : true + + }); + BIOSAXS.proposal = new Proposal(experimentGrid.input().proposal); + var panel = experimentGrid.getPanel(experimentGrid.input().experiments); + experimentGrid.refresh(experimentGrid.input().experiments); + panel.render(targetId); +}; + +function VolumeGrid() { + this.id = BUI.id(); +} + +VolumeGrid.prototype.getPanel = function(experiment) { + this.experiment = experiment; + return this.render(); +}; + +VolumeGrid.prototype.getVolumesPanel = function(data, title) { + var _this = this; + var store = Ext.create('Ext.data.Store', { + fields : [ 'name', 'volume', 'macromoleculeId', 'bufferId' ], + data : data + }); + store.sort([ { + property : 'name', + direction : 'ASC' + } ]); + + var grid = Ext.create('Ext.grid.Panel', { + title : title, + height : 400, + maxHeight : 400, + width : 900, + store : store, + margin : '10 0 50 10', + tbar : [ { + text : 'Go to Shipment', + icon : '../images/plane-small.gif', + handler : function() { + window.location = BUI.getCreateShipmentList(); + } + } ], + viewConfig : { + stripeRows : true, + listeners : { + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonCreate') { + var stockSolutionWindow = new StockSolutionWindow(); + /** On stock solution SAVED **/ + stockSolutionWindow.onSaved.attach(function(sender, stockSolution) { + BIOSAXS.proposal.onInitialized.attach(function(sender, data) { + _this.refresh(_this.experiment); + }); + BIOSAXS.proposal.init(); + }); + var acronym = "ST"; + if (record.raw.macromoleculeId != null) { + acronym = acronym + "_" + BIOSAXS.proposal.getMacromoleculeById(record.raw.macromoleculeId).acronym; + } + if (record.raw.bufferId != null) { + acronym = acronym + "_" + BIOSAXS.proposal.getBufferById(record.raw.bufferId).acronym; } + stockSolutionWindow.draw({ + concentration : record.raw.concentration, + macromoleculeId : record.raw.macromoleculeId, + bufferId : record.raw.bufferId, + name : acronym, + volume : record.raw.volume + }); } - }, { - "concentration" : "0.91", - "id" : "0.91000000000000003", - "bufferId" : "422.00", - "bufferAcronym" : "B1", - "rgGuinier" : [], - "frames" : [ { - "total" : null, - "bufferBeforeMeasurementId" : 15054, - "sampleMergeId" : 8182, - "averagedModelId" : null, - "I0" : "0.0", - "proposalCode" : "OPD", - "averagedModel" : null, - "bufferAfterMergeId" : 8183, - "framesCount" : "10", - "bufferBeforeMergeId" : 8181, - "averageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_071_ave.dat", - "bufferAfterMeasurementId" : 15057, - "rgGuinier" : null, - "subtractedFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_071_sub.dat", - "firstPointUsed" : "0", - "chi2RgFilePath" : null, - "abInitioModelId" : null, - "macromoleculeId" : 649, - "code" : "_4.0_.91", - "transmission" : "100.0", - "timeStart" : "2013-06-05 15:52:58.133705", - "bufferAcronym" : "B1", - "quality" : "0.0", - "shapeDeterminationModelId" : null, - "expermientComments" : "[BsxCube] Generated from BsxCube", - "bufferId" : 422, - "isagregated" : "False", - "dmax" : null, - "bufferBeforeAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_070_ave.dat", - "exposureTemperature" : "4.0", - "subtractionId" : 3380, - "conc" : "0.91000000000000003", - "rapidShapeDeterminationModel" : null, - "experimentCreationDate" : "Jun 5, 2013 3:30:30 PM", - "lastPointUsed" : "0", - "modelListId" : null, - "framesMerge" : "10", - "rapidShapeDeterminationModelId" : null, - "bufferAfterAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_072_ave.dat", - "nsdFilePath" : null, - "bufferAfterFramesMerged" : "10", - "experimentId" : 700, - "macromoleculeAcronym" : "L9", - "i0stdev" : "0.0", - "sampleMeasurementId" : 15056, - "measurementComments" : "[8]", - "priorityLevelId" : 16, - "bufferBeforeFramesMerged" : "10", - "substractionCreationTime" : "Jun 5, 2013 3:55:35 PM", - "proposalNumber" : "29", - "rgGnom" : null, - "volume" : null, - "shapeDeterminationModel" : null, - "comments" : null, - "groupeField" : "L9 B1" - } ], - "frames_warning" : 1, - "calculation" : { - "rgGuinier" : { - "std" : null, - "sum" : 0, - "avg" : 0, - "validNumber" : 0, - "totalNumber" : 0, - "values" : [] - }, - "i0Guinier" : { - "std" : null, - "sum" : 0, - "avg" : 0, - "validNumber" : 0, - "totalNumber" : 0, - "values" : [] + + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonStockSolutions') { + var stockSolutionGrid = new StockSolutionGrid({ + btnAddVisible : false, + btnEditVisible : false, + btnRemoveVisible : false, + btnAddExisting : false, + isPackedVisible : true, + multiselect : false + }); + + var window = Ext.create('Ext.window.Window', { + title : 'Stock solutions by specimen', + height : 400, + width : 800, + layout : 'fit', + items : [ stockSolutionGrid.getPanel() ], + buttons : [ { + text : 'Close', + handler : function() { + window.close(); + } + } ] + + }).show(); + stockSolutionGrid.refresh(BIOSAXS.proposal.getStockSolutionsBySpecimen(record.raw.macromoleculeId, record.raw.bufferId)); + } + } + } + }, + columns : [ +// { +// text : '', +// dataIndex : 'macromoleculeId', +// width : 20, +// renderer : function(val, y, sample) { +// if (val != null) { +//// return BUI.getRectangleColorDIV(BIOSAXS.proposal.macromoleculeColors[val], 10, 10); +// return BUI.getRectangleColorDIV(_this.experiment.macromoleculeColors[val], 10, 10); +// } +// } +// }, +// { +// text : '', +// dataIndex : 'bufferId', +// width : 20, +// renderer : function(val, y, sample) { +// if (val != null) { +// return BUI.getRectangleColorDIV(_this.experiment.getSpecimenColorByBufferId(val), 10, 10); +// } +// } +// }, + { + text : 'Specimen', + dataIndex : 'name', + flex : 0.5 + }, + { + text : 'Estimated Volume', + dataIndex : 'volume', + tooltip : 'Estimation of the maximum volume needed for making this experiment', + flex : 0.5, + editor : { + allowBlank : true + }, + renderer : function(val, y, sample) { + return BUI.formatValuesUnits(sample.data.volume, 'µl', { + fontSize : 16, + decimals : 2, + unitsFontSize : this.unitsFontSize + }); + } + }, + { + text : 'Stock Solution', + id : _this.id + 'buttonStockSolutions', + dataIndex : 'name', + flex : 0.5, + tooltip : 'Stock Solutions containing this specimen in this proposal', + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + var macromoleculeId = record.raw.macromoleculeId; + var bufferId = record.raw.bufferId; + var stockSolutions = BIOSAXS.proposal.getStockSolutionsBySpecimen(macromoleculeId, bufferId); + if (stockSolutions.length > 0) { + return "
" + stockSolutions.length + " x
"; + } + + } + }, { + id : _this.id + 'buttonCreate', + text : '', + tooltip : 'Create a new stock solution for shipping', + width : 170, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + return BUI.getGreenButton('NEW STOCK SOLUTION', { + width : 160 + }); + } + } ] + }); + return grid; + +}; + +VolumeGrid.prototype._prepareData = function(experiment) { + var keys = {}; + for ( var i = 0; i < experiment.getSamples().length; i++) { + var sample = experiment.getSamples()[i]; + var key = ""; + if (sample.macromoleculeId == null) { + key = experiment.getBufferById(sample.bufferId).acronym; + if (keys[key] == null) { + keys[key] = { + macromoleculeId : sample.macromoleculeId, + name : key, + bufferId : sample.bufferId, + volume : 0 + }; + } + keys[key].volume = Number(sample.volume) + Number(keys[key].volume); + } + + if ((sample.macromolecule3VO != null) || (sample.macromoleculeId != null)) { + macromoleculeId = sample.macromoleculeId; + if (sample.macromoleculeId == null) { + sample.macromoleculeId = sample.macromolecule3VO.macromoleculeId; + } + key = BIOSAXS.proposal.getMacromoleculeById(sample.macromoleculeId).acronym + " + " + experiment.getBufferById(sample.bufferId).acronym; + if (keys[key] == null) { + keys[key] = { + macromoleculeId : sample.macromoleculeId, + name : key, + bufferId : sample.bufferId, + volume : 0 + }; + } + keys[key].volume = Number(sample.volume) + Number(keys[key].volume); + } + } + var data = []; + for (var keyId in keys) { + data.push(keys[keyId]); + } + + return data; +}; + +VolumeGrid.prototype.refresh = function(experiment) { + this.experiment = experiment; + this.macromoleculeGrid.getStore().loadData(this._prepareData(this.experiment), false); +}; + +VolumeGrid.prototype.render = function() { + this.macromoleculeGrid = this.getVolumesPanel(this._prepareData(this.experiment), "Estimation of required Volume"); + + return { + xtype : 'container', + layout : 'vbox', + margin : "0, 0, 0, 5", + items : [ { + xtype : 'container', + layout : 'hbox', + margin : "0, 0, 0, 0", + items : [ this.macromoleculeGrid ] + } ] + }; +}; + +VolumeGrid.prototype.input = function(experiment) { + return { + experiment : DATADOC.getExperiment_10() + }; +}; + +VolumeGrid.prototype.test = function(targetId) { + var volumeGrid = new VolumeGrid(); + BIOSAXS.proposal = new Proposal(new MeasurementGrid().input().proposal); + var panel = volumeGrid.getPanel(new Experiment(new VolumeGrid().input().experiment)); + Ext.create('Ext.panel.Panel', { + height : 500, + width : 1000, + renderTo : targetId, + items : [ panel ] + }); +}; + +/** + * Example of a tab panel to be populated with widgets + * + * @width width in pixels + * @height height in pixels + * + * #myEvent event that this class is supposed to throw + * + **/ +function ExampleTabs(args) { + this.width = 500; + this.height = 500; + + if (args != null){ + if (args.width != null){ + this.width= args.width; + } + if (args.height != null){ + this.height= args.height; + } + } + + /** Events **/ + this.myEvent = new Event(); +} + +/** Populate the widget **/ +ExampleTabs.prototype.refresh = function(macromolecule) { + +}; + +/** It creates a tab panel with the specified with and height **/ +ExampleTabs.prototype.getPanel = function() { + this.panel = Ext.createWidget('tabpanel', { + height : this.height, + width : this.width, + style : { + padding : 2 + }, + items : [ { + tabConfig : { + title : 'Test', + icon : '/ispyb/images/plane-small.gif' + }, + items : [ { + xtype : 'container', + margin : '5 5 5 5', + items : [ ] + } ] + } ] + }); + return this.panel; +}; + + +/** + * Shows an experiments with the specimens, measurements, analysis tabs where + * results are shown and the frames widget + * + * @targetId + */ +function ExperimentTabs(targetId) { + this.height = 900; + this.targetId = targetId; + + this.id = BUI.id(); + var _this = this; + + this.INTERVAL_UPDATE = BUI.getUpdateInterval(); + + this.gridHeight = 1000; + /** data * */ + this.experiment = null; + + + /** Specimen Widget contains a specimenGrid and a sampleChangerWidget than can be displayed with are vertical or horizontal layout **/ + this.specimenWidget = new SpecimenWidget({ + height : 600 + }); + + + /** For Overview * */ + /*this.samplePlateGroupWidget = new SamplePlateGroupWidget({ + showTitle : false, + height : 250, + margin : 5, + border : 0 + + });*/ + + /** For Measurements * */ + /*this.measurementSamplePlateGroupWidget = new SamplePlateGroupWidget({ + showTitle : false, + height : 250, + margin : '5 0 0 0', + border : 0 + });*/ + + this.measurementGridDone = new MeasurementGrid({ + height : 600, + minHeight : 400, + maxHeight : 800, + positionColumnsHidden : true, + showTitle : false, + estimateTime : true, + width : 900, + maxWidth : 1500, + addBtnEnable : false, + markDone : true, + removeBtnEnabled : false + }); + this.measurementGridDone.onSelected.attach(function(sender, measurements) { + var specimens = []; + for ( var i = 0; i < measurements.length; i++) { + specimens.push(_this.experiment.getSampleById(measurements[i].specimenId)); + } + //_this.measurementSamplePlateGroupWidget.selectSpecimens(specimens); + }); + + /** AnalysisGrid * */ + this.analysisGrid = new AnalysisGrid({ + height : Ext.getBody().getViewSize().height * 0.9 - 300, + positionColumnsHidden : true, + sorters : [ { + property : 'priorityLevelId', + direction : 'ASC' + } ] + }); + + + /** Queue * */ + this.queueGrid = new QueueGrid({ + url : BUI.getQueueUrlByExperiment(), + height : Ext.getBody().getViewSize().height * 0.9 - 300, + width : Ext.getBody().getViewSize().width * 0.9 - 300, + isGrouped : true, + tbar : false, + bbar : false, + sorter : [{ + property: 'measurementId', + direction: 'DESC' + }] + }); + +} + +ExperimentTabs.prototype.error = function(error) { + var e = JSON.parse(error); + showError(e); + this.panel.setLoading(false); +}; + +ExperimentTabs.prototype.draw = function(experiment) { + this.renderDataAcquisition(experiment); +}; + +ExperimentTabs.prototype.refreshAnalysisData = function() { + var _this = this; + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + _this.analysisGrid.refresh(data, {experiment : _this.experiment}); + }); + adapter.getAnalysisInformationByExperimentId(this.experiment.experimentId); + + /** Auto load **/ + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + _this.queueGrid.refresh(data); + }); + adapter.getCompactAnalysisByExperimentId(this.experiment.experimentId); + this.queueGrid.store.proxy.url = BUI.getQueueUrlByExperiment(this.experiment.experimentId); + this.queueGrid.refresh(); +}; + +ExperimentTabs.prototype.getSpecimenContainerHeight = function(experiment) { + var maxItems = 0; + if (maxItems < experiment.getSamples().length + 1) { + maxItems = experiment.getSamples().length + 1; + } + + var height = (maxItems + 1) * 40 + 40; + if (height > 400) { + height = 400; + } + return height; +}; + +ExperimentTabs.prototype.getExperimentTitle = function() { + var experimentHeaderForm = new ExperimentHeaderForm(); + return experimentHeaderForm.getPanel(this.experiment); +}; + +ExperimentTabs.prototype.renderDataAcquisition = function(experiment) { + var _this = this; + this.experiment = experiment; + + var specimenGrid = new SpecimenGrid({ + height : 400, + maxHeight : 500, + width : 890 + }); + + specimenGrid.onClick.attach(function(sender, args) { + }); + + specimenGrid.onSelected.attach(function(sender, specimens) { + //_this.samplePlateGroupWidget.selectSpecimens(specimens); + }); + var specimenContainer = this.specimenWidget.getPanel(); + this.specimenWidget.refresh(experiment); + /* + var specimenContainer = Ext.create('Ext.container.Container', { + layout : 'hbox', + width : 900, + padding : '10 0 0 2', + items : [ specimenGrid.getPanel() ] + }); + + specimenGrid.refresh(experiment);*/ + + var experimentList = new ExperimentList([ _this.experiment ]); + var measurementContainer = Ext.create('Ext.container.Container', { + layout : 'vbox', + padding : '5px 0px 0px 10px', + items : [] + }); + measurementContainer.insert(0, _this.measurementGridDone.getPanel(this.experiment.getMeasurements(), experimentList)); +// measurementContainer.insert(1, _this.measurementSamplePlateGroupWidget.getPanel(experiment)); + + // this.dataCollectionCurveVisualizer = new DataCollectionCurveVisualizer(); + // this.dataCollectionCurveVisualizer.experiments = [experiment]; + // this.dataCollectionCurveVisualizer.dataCollectionFrameTree.experiments = + // [experiment]; + // this.dataCollectionCurveVisualizer.dataCollections = + // experiment.getDataCollections(); + + this.panel = Ext.createWidget('tabpanel', { + plain : true, + style : { + padding : 2 + }, + items : [ { + tabConfig : { + id : 'genralTabl', + title : "Overview" + }, + items : [ specimenContainer ] + }, { + tabConfig : { + title : 'Measurements' + }, + items : [ measurementContainer] + }, { + tabConfig : { + id : 'SpecimenTab', + title : 'Analysis', + hidden : this.isTemplate() + }, + items : [ { + xtype : 'container', + layout : 'vbox', + padding : '5px 0px 10px 10px', + items : [ _this.analysisGrid.getPanel([]) ] + } ] + }, + { + tabConfig : { + id : 'newAnalysisTab', + title : 'Analysis BETA', + hidden : this.isTemplate() + }, + items : [ { + xtype : 'container', + layout : 'vbox', + padding : '5px 0px 10px 10px', + items : [ _this.queueGrid.getPanel([]) ] + } ] + } + ] + }); + + return this.getPanel(this.panel); +}; + +ExperimentTabs.prototype.isTemplate = function() { + if (this.experiment.json.type == "TEMPLATE") { + return true; + } + return false; +}; + +ExperimentTabs.prototype.update = function() { + var _this = this; + var inter; + if (!_this.isTemplate()) { + function updateExperiments() { + _this.refreshAnalysisData(); + window.clearInterval(inter); + inter = setInterval(function() { + updateExperiments(); + }, _this.INTERVAL_UPDATE); + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + var experiment = new Experiment(data); + _this.measurementGridDone.refresh(experiment.getMeasurements(), new ExperimentList([ experiment ])); + }); + adapter.getExperimentById(_this.experiment.json.experimentId, "MEDIUM"); + } + inter = setInterval(function() { + updateExperiments(); + }, _this.INTERVAL_UPDATE); + } +}; + +ExperimentTabs.prototype.getPanel = function(panel) { + var _this = this; + if (this.experimentPanel == null) { + this.experimentPanel = Ext.create('Ext.container.Container', { + bodyPadding : 2, + width : Ext.getBody().getViewSize().width * 0.9, + renderTo : this.targetId, + style : { + padding : 2 + }, + items : [ this.getExperimentTitle(), this.panel ], + listeners : { + afterrender : function() { + _this.refreshAnalysisData(); + _this.update(); + } + } + }); + } + + return this.experimentPanel; +}; + +ExperimentTabs.prototype.input = function() { + return { + experiment : DATADOC.getExperiment_10(), + proposal : DATADOC.getProposal_10() + }; +}; + +ExperimentTabs.prototype.test = function(targetId) { + var experimentTabs = new ExperimentTabs(targetId); + BIOSAXS.proposal = new Proposal(experimentTabs.input().proposal); + experimentTabs.draw(new Experiment(experimentTabs.input().experiment)); +}; + + + +/** + * Shows an experiments with the specimens, measurements, analysis tabs where results are shown and the frames widget + * + * @targetId + */ +function HPLCTabs(targetId) { + this.height = 1400; + this.targetId = targetId; + + this.id = BUI.id(); + + this.gridHeight = 600; + this.pointsCount = 1036; + this.plotHeight = 350; + this.plotWidth = 800; + this.plotPanelPadding = 5; + + var _this = this; + + this.analysisGrid = new HPLCAnalysisGrid({ + height : Ext.getBody().getViewSize().height * 0.9 - 300, + positionColumnsHidden : true, + sorters : [ { + property : 'priorityLevelId', + direction : 'ASC' + } ] + }); + + this.frameGrid = new FrameGrid({ + width : 600, + height : 60, + collapsed : false, + tbar : false + }); + + this.peakGrid = new PeakGrid({ + width : 550, + height : 500, + collapsed : false, + tbar : false + }); + + this.peakGrid2 = new PeakGrid({ + width : 102, + height : this.plotHeight, + collapsed : false, + tbar : false, + showExtendedColumns : true + }); + + this.mainPlotPanel = new HPLCGraph({ + title : 'I0', + width : this.plotWidth - 110, + height : this.plotHeight, + bbar : true, + plots : { + "I0" : true, + "Rg" : true + }, + xlabel : "HPLC Frames", + scaled : true, + interactionModel : { + 'dblclick' : function(event, g, context) { + _this._selectFrame(g.lastx_); + var annotations = []; + annotations.push({ + series : g.selPoints_[0].name, + x : g.lastx_, + width : 100, + height : 23, + tickHeight : 4, + shortText : g.lastx_, + text : g.lastx_, + attachAtBottom : true + }); + g.setAnnotations(annotations); + + } + } + }); + + this.intensityPlotPanel = new MergesHPLCGraph({ + title : 'Scattering', + width : this.plotWidth, + height : 500, + showRangeSelector : false, + xParam : 0, + xlabel : "scattering_I", + plots : { + "scattering_I" : true, + "subtracted_I" : true, + "buffer_I" : true + } + }); + +} + +HPLCTabs.prototype._selectFrame = function(frameNumber) { + try{ + this._renderScatteringCurve(frameNumber); + this.frameGrid.refresh([this.mainPlotPanel.getDataByFrameNumber(frameNumber)], this.experiment.experimentId); + } + catch(e){ + console.log(e); + } +}; + +HPLCTabs.prototype.error = function(error) { + var e = JSON.parse(error); + showError(e); + this.panel.setLoading(false); +}; + +HPLCTabs.prototype.loadDataMainPlot = function(data) { + var zeroArray = []; + for ( var i = 0; i < data.I0.length; i++) { + zeroArray.push(0); + } + data = [ { + param : "I0", + data : data.I0, + std : data.I0_Stdev, + color : '#0066CC', + label : "I0" + }, + { + param : "sum_I", + label : "sum_I", + color : "#00FF00", + data : data.sum_I, + std : zeroArray + }, + { + param : "Rg", + label : "Rg", + color : "#21610B", + data : data.Rg, + std : data.Rg_Stdev + }, { + param : "Mass", + data : data.mass, + std : data.mass_Stdev, + color : '#FF9900', + label : "Mass" + }, { + param : "Vc", + data : data.Vc, + std : data.Vc_Stdev, + color : '#990099', + label : "Vc" + }, { + param : "Qr", + data : data.Qr, + std : data.Qr_Stdev, + color : '#FF0066', + label : "Qr" + }, { + param : "quality", + label : "quality", + color : "#FF00FF", + data : data.quality, + std : zeroArray + } ]; + this.data = data; + this.mainPlotPanel.loadData(data); +}; + +HPLCTabs.prototype._loadIntensityPlotByFrameNumber = function(frameNumber) { + var _this = this; + + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + var array = []; + data = [ { + param : "q", + data : data[frameNumber].q, + std : data[frameNumber].q, + fstd : function(a) { + return parseFloat(a); + }, + color : '#green', + label : "q", + showOnMenu : false + }, + { + param : "scattering_I", + data : data[frameNumber].scattering_I, + fdata : function(a) { + return Math.log(parseFloat(a)); + }, + std : data[frameNumber].scattering_Stdev, + fstd : function(a) { + return Math.log(Math.abs(parseFloat(a))); + }, + color : 'green', + label : "Log(I) Sample" + }, + { + param : "buffer_I", + data : data[frameNumber].buffer_I, + fdata : function(a) { + return Math.log(parseFloat(a)); + }, + fstd : function(a) { + return Math.log(Math.abs(parseFloat(a))); + }, + std : data[frameNumber].subtracted_Stdev, + color : '#0000FF', + label : "Log(I) Avg Buf." + }, + { + param : "subtracted_I", + data : data[frameNumber].subtracted_I, + fdata : function(a) { + var value = (Math.log(parseFloat(a))); + if (isNumber(value)) + return value; + }, + fstd : function(a) { + var value = Math.log(Math.abs(parseFloat(a))); + if (isNumber(value)) + return value; + }, + std : data[frameNumber].subtracted_Stdev, + color : 'red', + label : "Log(I) Sub." + } + ]; + + _this.intensityPlotPanel.xlabel = "Frame " + frameNumber + " (q, nm-1)"; + + if (_this.intensityPlotPanel.hplcData == null) { + /** It creates also top bar **/ + _this.intensityPlotPanel.loadData(data); + } else { + _this.intensityPlotPanel.reloadData(data); + + } + _this.intensityPlotPanel.panel.setLoading(false); + }); + adapter.onError.attach(function(sender, data) { + _this.intensityPlotPanel.panel.setLoading(false); + }); + this.intensityPlotPanel.panel.setLoading("Retrieving Frame " + frameNumber); + adapter.getH5FrameScattering(this.experiment.json.experimentId, frameNumber); +}; + +HPLCTabs.prototype._renderScatteringCurve = function(frameNumber) { + var _this = this; + + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + _this.intensityPlotPanel.setPeaks(data); + _this._loadIntensityPlotByFrameNumber(frameNumber); + try{ + var peaks = []; + for(key in data){ + peaks.push({ + start : key.split("-")[0], + end : key.split("-")[1], + experimentId : _this.experiment.json.experimentId + }); + } + _this.peakGrid2.refresh(JSON.parse(JSON.stringify(peaks))); + _this.peakGrid.refresh(peaks); +// console.log(peaks); + } + catch(e){ + showError(e); + } + }); + adapter.onError.attach(function(sender, data) { + _this.intensityPlotPanel.setLoading(false); + }); + this.intensityPlotPanel.panel.setLoading("Reading HDF5 File "); + adapter.getH5FramesMerge(this.experiment.json.experimentId); +}; + +HPLCTabs.prototype._postRenderOverviewPanel = function() { + var _this = this; + var adapter = new BiosaxsDataAdapter(); + adapter.onError.attach(function(sender, data) { + data = data.replace(/NaN/g, '0'); + _this.loadDataMainPlot(JSON.parse(data)); + + + }); + adapter.onSuccess.attach(function(sender, data) { + _this.loadDataMainPlot(data); + _this._renderScatteringCurve(0); + }); + adapter.getH5fileParameters(this.experiment.json.experimentId, [ + "I0", "I0_Stdev", "sum_I","Rg", "Rg_Stdev", "Vc", "Vc_Stdev", "Qr", "Qr_Stdev", "mass", "mass_Stdev", "quality" ]); + +}; + +HPLCTabs.prototype._postRenderDetailsPanel = function() { + if (this.data != null) { + this.I0PlotPanel.loadData(this.data); + this.RgPlotPanel.loadData(this.data); + this.MassPlotPanel.loadData(this.data); + this.VcPlotPanel.loadData(this.data); + } + +}; + +HPLCTabs.prototype.draw = function(experiment) { + var _this = this; + this.renderDataAcquisition(experiment); +}; + +HPLCTabs.prototype.getExperimentTitle = function() { + var experimentHeaderForm = new ExperimentHeaderForm(); + return experimentHeaderForm.getPanel(this.experiment); +}; + +HPLCTabs.prototype.renderDataAcquisition = function(experiment) { + var _this = this; + this.experiment = experiment; + if (this.experimentPanel == null) { + this.experimentPanel = Ext.create('Ext.container.Container', { + bodyPadding : 2, + height : this.height, + width : Ext.getBody().getViewSize().width * 0.9, + renderTo : this.targetId, + style : { + padding : 2 + }, + items : [ this.getExperimentTitle(), this.getPanel() ], + listeners : { + afterrender : function() { + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + _this.analysisGrid.refresh(data); + }); + adapter.getAnalysisInformationByExperimentId(_this.experiment.experimentId); + } + } + }); + } + return this.experimentPanel; +}; + +HPLCTabs.prototype.getPanel = function() { + var _this = this; + this.panel = Ext.createWidget('tabpanel', + { + plain : true, + height : this.height, +// width : 900, + style : { + padding : 2 + }, + items : [ + { + tabConfig : { + title : "Overview" + }, - "quality" : { - "std" : null, - "sum" : 0, - "avg" : 0, - "validNumber" : 0, - "totalNumber" : 0, - "values" : [] + items : [ { + xtype : 'container', + layout : 'hbox', + border : 1, + flex : 1, + items : [ { + xtype : 'container', + layout : 'vbox', + border : 1, + items : [ { + xtype : 'container', + margin : '10px', + border : 1, + items : [ + { + xtype : 'container', + margin : '0px', + layout : 'hbox', + border : 1, + items : [ + this.peakGrid2.getPanel([]), + this.mainPlotPanel.getPanel() + ] + }, + { + xtype : 'container', + layout : 'vbox', + border : 1, + items : [ + { + html: '
Select a frame by double-clicking on the HPLC Frames plot
', + margin: 5, + border : 0 + }, + this.frameGrid.getPanel([]), + this.intensityPlotPanel.getPanel() + ] + } + + ] + }], + listeners : { + afterrender : function() { + _this._postRenderOverviewPanel(); + } + } + } ] + } ] + }, +// { +// tabConfig : { +// title : "Details" +// }, +// items : [ { +// xtype : 'container', +// layout : 'hbox', +// border : 1, +// flex : 1, +// items : [ { +// xtype : 'container', +// layout : 'vbox', +// border : 1, +// items : [ { +// xtype : 'container', +// padding : '1px', +// items : [ +// this.I0PlotPanel.getPanel(), this.RgPlotPanel.getPanel(), this.MassPlotPanel.getPanel(), +// this.VcPlotPanel.getPanel() ] +// } ], +// listeners : { +// afterrender : function() { +// _this._postRenderDetailsPanel(); +// } +// } +// } ] +// } ] +// }, + { + tabConfig : { + title : "Analysis" }, - "rgGnom" : { - "std" : null, - "sum" : 0, - "avg" : 0, - "validNumber" : 0, - "totalNumber" : 0, - "values" : [] + items : [ { + xtype : 'container', + layout : 'vbox', + padding : '5px 0px 10px 10px', + items : [ _this.analysisGrid.getPanel([]) ] + } ] + }, + { + tabConfig : { + title : "File Manager" }, - "dMax" : { - "std" : null, - "sum" : 0, - "avg" : 0, - "validNumber" : 0, - "totalNumber" : 0, - "values" : [] + items : [ { + xtype : 'container', + layout : 'vbox', + padding : '5px 0px 10px 10px', + items : [ + { + html: '
Custom Download
', + margin : '10 0 10 5', + border : 0 + }, + { + html: '
Download has been temporary disabled. Contact your labcontact if you want to extract the frames from the HDF5 file
', + margin : '10 0 10 5', + hidden : _this.experiment.experimentId == 2602, + border : 0 + }, + { + xtype : 'container', + layout : 'hbox', + margin : '0 0 0 20', + flex : 1, + items :[ + { + xtype: 'numberfield', + id: 'field_start', + fieldLabel: 'Frames from', + value: 0, + minValue: 0 + }, + { + xtype: 'numberfield', + id: 'field_end', + fieldLabel: 'to', + labelWidth : 20, + margin : '0 0 0 10', + minValue: 0 + }, + { + xtype: 'button', + /** allowing test account to download frames **/ + disabled : _this.experiment.experimentId != 2602, + text : 'Download', + margin : '0 0 0 10', + handler : function() { + var experimentId = _this.experiment.experimentId; + var start = Ext.getCmp("field_start").getValue(); + var end = Ext.getCmp("field_end").getValue(); + /** Checking if start is bigger than end **/ + if (start > end){ + var aux = end; + end = start; + start = aux; + } + var url = BUI.getZipFrameHPLCUrl(experimentId, start, end); + window.open(url) + } + } + ] + }, + _this.peakGrid.getPanel([]) + + ] + } + ] + } + ] + }); + + return this.panel; +}; + +/** + * Main form tab for macromolecule + * + * @width + * @height + * + * #onClose when user clicks on close button in the MacromoleculeForm + * #onSave when macromole is saved by macromoleculeForm + */ +function MacromoleculeTabs(args) { + this.width = 500; + this.height = 500; + + if (args != null) { + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + } + + var _this = this; + + /** Widgets **/ + + /** Macromolecule Form **/ + this.macromoleculeForm = new MacromoleculeForm({ + width : this.width - 30, + height : this.height - 50, + }); + + this.macromoleculeForm.onClose.attach(function(sender) { + _this.onClose.notify(); + }); + + this.macromoleculeForm.onSave.attach(function(sender, macromolecule) { + _this.onSave.notify(macromolecule); + }); + + this.assemblyForm = new AssemblyForm({ + width : this.width - 30, + height : this.height - 50, + }); + + this.rigibBodyModelingForm = new RigibBodyModelingForm({ + width : this.width - 30, + height : this.height - 50, + }); + + this.rigibBodyModelingForm.onSave.attach(function(sender, macromolecule) { + _this.onSave.notify(macromolecule); + }); + + + /** Events **/ + this.onClose = new Event(this); + this.onSave = new Event(this); +} + +/** Populate the widget **/ +MacromoleculeTabs.prototype.refresh = function(macromolecule) { + this.macromoleculeForm.refresh(macromolecule); + this.assemblyForm.refresh(macromolecule); + this.rigibBodyModelingForm.refresh(macromolecule); + + if (macromolecule != null){ + if (macromolecule.macromoleculeId == null){ + Ext.getCmp(this.id + "_advancedTab").disable(); + Ext.getCmp(this.id + "_assemblyTab").disable(); + } + else{ + Ext.getCmp(this.id + "_advancedTab").enable(); + Ext.getCmp(this.id + "_assemblyTab").enable(); + } + } + else{ + Ext.getCmp(this.id + "_advancedTab").disable(); + Ext.getCmp(this.id + "_assemblyTab").disable(); + } +}; + +MacromoleculeTabs.prototype.getItems = function() { + return [ { + tabConfig : { + title : 'General' + }, + items : [ { + xtype : 'container', + items : [ this.macromoleculeForm.getPanel() ] + } ] + }, { + id : this.id + "_assemblyTab", + tabConfig : { + title : 'Assembly' + }, + items : [ { + xtype : 'container', + items : [ this.assemblyForm.getPanel() ] + } ] + },{ + id : this.id + "_advancedTab", + tabConfig : { + title : 'Advanced' + }, + items : [ this.rigibBodyModelingForm.getPanel() ] + } ]; +}; + +MacromoleculeTabs.prototype.getPanel = function() { + this.panel = Ext.createWidget('tabpanel', { + height : this.height, + width : this.width, + plain : true, + margin : 5, + border : 0, + items : this.getItems() + }); + return this.panel; +}; + +function ResultTabs() { +} + +ResultTabs.prototype.draw = function(targetId, data, macromoleculeId) { + var panel = this.getPanel(targetId, data, macromoleculeId); + return Ext.create('Ext.container.Container', { + renderTo : targetId, + items : [ BUI.getMacromoleculeHeader(macromoleculeId), panel ] + }); + +}; + +ResultTabs.prototype._splitBySpecimen = function(data) { + var splitted = {}; + + for ( var i = 0; i < data.length; i++) { + var row = data[i]; + if (splitted[row.macromoleculeId + "_" + row.bufferId] == null) { + splitted[row.macromoleculeId + "_" + row.bufferId] = []; + } + splitted[row.macromoleculeId + "_" + row.bufferId].push(row); + } + return splitted; + +}; + +ResultTabs.prototype._getTabTitle = function(key, data) { + var macromoleculeId = key.split("_")[0]; + var bufferId = key.split("_")[1]; + + return BIOSAXS.proposal.getMacromoleculeById(macromoleculeId).acronym + " + " + BIOSAXS.proposal.getBufferById(bufferId).acronym + "(" + data.length + ")"; +}; + +ResultTabs.prototype.getPanel = function(targetId, data, macromoleculeId) { + + var dataFiltered = new AnalysisGrid({ + hideNulls : true, + grouped : true, + sorters : [ { + property : 'quality', + direction : 'DESC' + } ] + })._prepareData(data); + + var items = [ { + tabConfig : { + title : 'Analysis (' + dataFiltered.length + ')' + }, + items : [ { + xtype : 'container', + layout : 'vbox', + padding : 10, + items : [ new AnalysisGrid({ + isScatteringPlotVisible : false + }).getPanel(dataFiltered) ] + } ] + }, { + tabConfig : { + title : 'Concentration Effects' + }, + items : [ new ResultSummaryForm().getPanel(data) ] + } ]; + + var splitted = this._splitBySpecimen(dataFiltered); + for ( var key in splitted) { + items.push({ + tabConfig : { + title : this._getTabTitle(key, splitted[key]) + }, + items : [ new ResultSummaryForm().getPanel(splitted[key]) ] + }); + } + + this.panel = Ext.createWidget('tabpanel', { + style : { + padding : 2 + }, + items : items + }); + return this.panel; + +}; + + +function ShipmentTabs(targetId) { + this.targetId = targetId; + + var _this = this; + this.gridHeight = 500; + /** data **/ + this.shipment = null; + + /** Shipment Form **/ + this.shipmentForm = new ShipmentForm({ + creationMode : false, + showTitle : false + }); + this.shipmentForm.onSaved.attach(function(sender, data) { + _this.refresh(data); + + }); + + + /** Cases grid **/ + this.caseGrid = new CaseGrid({ + height : this.gridHeight + }); + + this.caseGrid.onAddButtonClicked.attach(function(sender, dewar) { + _this.caseGrid.grid.setLoading("ISPyB: Creating a new case"); + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, shipment) { + /** updateing shipment on proposal **/ + for ( var i = 0; i < BIOSAXS.proposal.shippings.length; i++) { + if (BIOSAXS.proposal.shippings[i].shippingId == shipment.shippingId) { + BIOSAXS.proposal.shippings[i] = shipment; + } + } + _this.refresh(shipment); + }); + adapter.onError.attach(function(sender, shipment) { + _this.caseGrid.grid.setLoading(false); + }); + adapter.addCase(_this.shipment.json.shippingId); + }); + + this.caseGrid.onRemoveButtonClicked.attach(function(sender, dewarId) { + _this.panel.setLoading("ISPyB: removing case"); + _this.shipment.onSaved.attach(function(sender, shipment) { + _this.refresh(shipment); + + }); + _this.shipment.removeCase(dewarId); + }); +} + +ShipmentTabs.prototype.refresh = function(shipment) { + + var _this = this; + this.shipment = shipment; + var proposal = new Proposal(); + proposal.onDataRetrieved.attach(function(sender, plates) { + + _this.refreshWithPlates(shipment, plates); + _this.caseGrid.grid.setLoading(false); + }); + proposal.getPlatesByProposal(); +}; + +ShipmentTabs.prototype.refreshWithPlates = function(shipment, plates) { + this.shipment = new Shipment(shipment); + + this.caseGrid.refresh(this.shipment.getDewars(), plates); + this.panel.setLoading(false); +}; + +ShipmentTabs.prototype.error = function(error) { + var e = JSON.parse(error); + showError(e); + this.panel.setLoading(false); +}; + +//ShipmentTabs.prototype.refreshTabTitles = function() { +/*Ext.getCmp("MacromoleculeTab").setText(this.getMacromoleculeTitle()); +Ext.getCmp("BufferTab").setText(this.getBuffersTitle()); +Ext.getCmp("SpecimenTab").setText(this.getSpecimenTitle()); +Ext.getCmp("PlatesTab").setText(this.getPlatesTitle()); +Ext.getCmp("AssembliesTab").setText(this.getShipmentTitle()); +Ext.getCmp("PlateGroupsTab").setText(this.getPlateGroupsTitle());*/ +//}; +ShipmentTabs.prototype.draw = function(shipment) { + var _this = this; + _this.plates = []; + _this.shipment = shipment; + _this.render(shipment); + + // var proposal = new Proposal(); + // proposal.onDataRetrieved.attach(function(sender, plates){ + // _this.plates = plates; + // _this.shipment = shipment; + // _this.render(shipment); + // + // }); + // proposal.getPlatesByProposal(); +}; + +//ShipmentTabs.prototype.getShipmentTitle = function() { +// return 'Shipment'; +//}; + +//ShipmentTabs.prototype.getMacromoleculeTitle = function() { +// return 'Macromolecules (' + this.experiment.getMacromolecules().length + ')'; +//}; + +//ShipmentTabs.prototype.getBuffersTitle = function() { +// return 'Buffers (' + this.experiment.getBuffers().length + ')'; +//}; + +//ShipmentTabs.prototype.getPlateGroupsTitle = function() { +// return 'Plate Groups (' + this.experiment.getPlateGroups().length + ')'; +//}; + +//ShipmentTabs.prototype.getSampleChangerTitle = function() { +// return 'Sample Changer'; +//}; + +//ShipmentTabs.prototype.getSpecimenTitle = function() { +// return 'Specimens(' + this.experiment.getSpecimenCount() + ')'; +//}; + +//ShipmentTabs.prototype.getPlatesTitle = function() { +// return 'Plates(' + this.experiment.getSamplePlates().length + ')'; +//}; + +//ShipmentTabs.prototype.getBuffersTip = function() { +/*if (this.experiment.getBuffers().length == 0){ + return BUI.getWarningHTML("There are no buffers. Click on add to create new ones. Click on edit button or double click to edit them"); + +} +else{ + return BUI.getTipHTML("Click on edit button or double click to edit them. Click on duplicate to create an identical buffer including its additives") +}*/ +//}; + +//ShipmentTabs.prototype.refreshTips = function() { +/*Ext.getCmp("BufferTabTip").update(this.getBuffersTip()); +Ext.getCmp("SpecimenTabTip").update(this.getSpecimensTip());*/ +//}; + +ShipmentTabs.prototype.render = function(shipment) { + return this.getPanel(shipment); +}; + +ShipmentTabs.prototype.getShipmentHeader = function(shipment) { + var _this = this; + function getHTMLSource() { + var name = shipment.json.shippingName; + var status = shipment.json.shippingStatus; + var creationDate = shipment.json.creationDate; + var html = BUI.createFormLabel("Name :", name, 75, 400); + html = html + BUI.createFormLabel("Status :", status, 75, 400); + html = html + BUI.createFormLabel("Date :", creationDate, 75, 400); + return html; + } + + return Ext.create('Ext.container.Container', { + frame : false, + layout : 'hbox', + title : 'General', + padding : 5, + bodyPadding : '5 5 0 0', + width : 890, + margin : '0 0 10 0', + height : 100, + style : { + borderColor : '#BDBDBD', + borderStyle : 'solid', + borderWidth : '1px' + }, + fieldDefaults : { + msgTarget : 'side', + labelWidth : 100 + }, + items : [ { + margin : "0 0 0 0", + width : 475, + border : 0, + html : getHTMLSource() + } + ] + }); +}; + +ShipmentTabs.prototype.getTabPanel = function(shipment) { + this.panel = Ext.createWidget('tabpanel', { + height : 600, + style : { + padding : 2 + }, + items : [ { + tabConfig : { + id : 'Shipment', + title : 'Shipment', + icon : '/ispyb/images/plane-small.gif' + }, + items : [ { + xtype : 'container', + margin : '5 5 5 5', + items : [ this.shipmentForm.getPanel(shipment) ] + } ] + }, { + tabConfig : { + id : 'Cases', + title : 'Cases', + icon : '../images/box-icon-very-small.png' + }, + items : [ { + xtype : 'container', + margin : '5 5 5 5', + items : [ this.caseGrid.getPanel(shipment.getDewars(), this.plates) ] + } ] + } ] + }); + return this.panel; +}; + +ShipmentTabs.prototype.getPanel = function(shipment) { + var _this = this; + this.shipment = shipment; + if (this.plates == null) { + this.plates = []; + } + + if (this.shipPanel == null) { + this.shipPanel = Ext.create('Ext.container.Container', { + bodyPadding : 2, + width : Ext.getBody().getViewSize().width * 0.9, + renderTo : this.targetId, + style : { + padding : 2 + }, + items : [ this.getShipmentHeader(shipment), this.getTabPanel(shipment) ] + }); + } + + return this.shipPanel; +}; + +/** + * Shows an template with the specimens, measurements and the experiment's + * requirement + * + * @targetId + */ +function TemplateTabs(targetId) { + this.height = 600; + this.targetId = targetId; + + this.id = BUI.id(); + var _this = this; + + this.gridHeight = 1000; + /** data * */ + this.experiment = null; + + this.specimenSelected = null; + + /** Specimen Widget contains a specimenGrid and a sampleChangerWidget than can be displayed with are vertical or horizontal layout **/ + this.specimenWidget = new SpecimenWidget({ + height : this.height + }); + + this.samplePlateGroupWidget = new SamplePlateGroupWidget({ + showTitle : false, + height : 250, + margin : 5, + bbar : true + }); + + this.samplePlateGroupWidget.onExperimentChanged.attach(function(sender, experiment) { + _this.refresh(experiment); + }); + + this.samplePlateGroupWidget.onClick.attach(function(sender, args) { + }); + + this.volumePlanificator = new VolumeGrid(); + + /** For Measurements * */ + var storeViscosity = Ext.create('Ext.data.Store', { + fields : [ 'name' ], + data : [ { + "name" : "low" + }, { + "name" : "medium" + }, { + "name" : "high" + } ] + }); + + // Create the combo box, attached to the states data store + var viscosityEditor = Ext.create('Ext.form.ComboBox', { + fieldLabel : '', + store : storeViscosity, + queryMode : 'local', + displayField : 'name', + valueField : 'name' + }); + + this.measurementGrid = new MeasurementGrid({ + maxWidth : 1500, + estimateTime : false, + positionColumnsHidden : true, + isPriorityColumnHidden : true, + isStatusColumnHidden : true, + isTimeColumnHidden : true, + updateRowEnabled : true, + collapsed : true, + removeBtnEnabled : true, + showTitle : false, + collapseBtnEnable : false, + addBtnMultipleEdit : true, + sortingBtnEnable : true, + editor : { + exposureTemperature : { + xtype : 'textfield', + allowBlank : true + }, + comments : { + xtype : 'textfield', + allowBlank : true + }, + volumeToLoad : { + xtype : 'numberfield', + allowBlank : true + }, + transmission : { + xtype : 'numberfield', + allowBlank : true + }, + viscosity : viscosityEditor, + waitTime : { + xtype : 'numberfield', + allowBlank : true + }, + flow : { + xtype : 'checkbox', + allowBlank : true + } + } + }); + + this.measurementGrid.onSelected.attach(function(sender, measurements) { + var specimens = []; + for ( var i = 0; i < measurements.length; i++) { + specimens.push(_this.experiment.getSampleById(measurements[i].specimenId)); + } + }); + + this.measurementGrid.onMeasurementChanged.attach(function(sender, measurement) { + _this.experiment.setMeasurement(measurement); + _this.refresh(_this.experiment); + }); + + this.measurementGrid.onExperimentChanged.attach(function(sender, json) { + _this.refresh(new Experiment(json)); + }); + + this.measurementGrid.onRemoved.attach(function(sender, experiment) { + _this.refreshSpecimen(new Experiment(experiment)); + }); + + this.measurementGrid.onUpdateTime.attach(function(sender, args) { + document.getElementById(_this.id + "_counter").innerHTML = args.hours + 'h, ' + args.minutes + 'min and ' + args.seconds + ' seconds'; + }); + +} + +TemplateTabs.prototype.refreshMeasurement = function(experiment) { + this.experiment = experiment; + this.experiment.onSaved = new Event(this); + this.experiment.onSpecimenSaved = new Event(this); + var experimentList = new ExperimentList([ this.experiment ]); + this.measurementGrid.refresh(experimentList.getMeasurementsNotCollected(), experimentList); +}; + +TemplateTabs.prototype.refreshSpecimen = function(experiment) { + this.experiment = experiment; + this.experiment.onSaved = new Event(this); + this.experiment.onSpecimenSaved = new Event(this); + this.samplePlateGroupWidget.refresh(this.experiment); + this.specimenWidget.refresh(this.experiment); + this.volumePlanificator.refresh(this.experiment); +}; + +TemplateTabs.prototype.refresh = function(experiment) { + // var start = new Date().getTime(); + this.experiment = experiment; + this.experiment.onSaved = new Event(this); + this.experiment.onSpecimenSaved = new Event(this); + + // var experimentList = new ExperimentList([this.experiment]); + this.refreshMeasurement(experiment); + this.refreshSpecimen(experiment); + /** Refreshing grids * */ + this.panel.setLoading(false); + +}; + +TemplateTabs.prototype.error = function(error) { + var e = JSON.parse(error); + showError(e); + this.panel.setLoading(false); + +}; + +TemplateTabs.prototype.draw = function(experiment) { + this.render(experiment); +}; + + +TemplateTabs.prototype.getExperimentTitle = function() { + var _this = this; + var experimentHeaderForm = new ExperimentHeaderForm(); + return experimentHeaderForm.getPanel(this.experiment); +}; + +TemplateTabs.prototype.render = function(experiment) { + var _this = this; + this.experiment = experiment; + + /** + * + * Depending on the sample Changer configuration we want to display the plates vertically or horizontally + * Default is vertical + * + * */ + + var specimenContainer = this.specimenWidget.getPanel(); + this.specimenWidget.refresh(experiment); + + var experimentList = new ExperimentList([ _this.experiment ]); + var measurementContainer = Ext.create('Ext.container.Container', { + layout : { + type : 'vbox' + }, + defaults : { + style : { + padding : '5px 0px 0px 10px' + } + }, + items : [ _this.measurementGrid.getPanel(experimentList.getMeasurementsNotCollected(), experimentList) ] + }); + + this.panel = Ext + .createWidget( + 'tabpanel', + { + plain : true, + items : [ + { + tabConfig : { + title : 'Measurements' + }, + items : [ { + xtype : 'container', + layout : 'vbox', + border : 1, +// height : _this.gridHeight, + margin : "0 0 10 0", + items : [ measurementContainer ] + } + + ] + }, + { + tabConfig : { + id : 'genralTabl', + title : "Specimens" + // width : 900, + // border : 3 + + }, + items : [ specimenContainer ] + }, + { + tabConfig : { + title : "Requirements" + + }, + items : [ + { + html : BUI.getTipHTML("Estimated volume is the maximum volume required. Depending on the order of your measurements you may use less. Click on create stock solutions if you plan to ship these stock solutions"), + margin : "10 10 10 10", + border : 0 + }, this.volumePlanificator.getPanel(experiment) ] + } ] + }); + // ); + return this.getPanel(this.panel); +}; + +TemplateTabs.prototype.isTemplate = function() { + if (this.experiment.json.type == "TEMPLATE") { + return true; + } + return false; +}; + + +TemplateTabs.prototype.getPanel = function(panel) { + var _this = this; + if (this.experimentPanel == null) { + this.experimentPanel = Ext.create('Ext.container.Container', { + bodyPadding : 2, + width : 1000,//Ext.getBody().getViewSize().width * 0.9, + renderTo : this.targetId, + height : 500, +// style : { +// padding : 2 +// }, + items : [ + this.getExperimentTitle(), + this.panel + ], + listeners : { + afterrender : function(thisCmp) { + $("#SchemeReport" + _this.experiment.experimentId).click(function() { + $(this).target = "_blank"; + window.open('viewProjectList.do?reqCode=display&menu=platescheme&experimentId=' + _this.experiment.experimentId); + return false; + }); + + } + } + }); + } + return this.experimentPanel; +}; + +TemplateTabs.prototype.input = function(targetId) { + return new ExperimentTabs().input(); +}; + +TemplateTabs.prototype.test = function(targetId) { + var experimentTabs = new TemplateTabs(targetId); + BIOSAXS.proposal = new Proposal(experimentTabs.input().proposal); + experimentTabs.draw(new Experiment(experimentTabs.input().experiment)); +}; + +var BUI = { + //interval : 60000, + interval : 40000, + rainbow : function(numOfSteps, step) { + // This function generates vibrant, "evenly spaced" colours (i.e. no clustering). This is ideal for creating easily distinguishable vibrant markers in Google Maps and other apps. + // Adam Cole, 2011-Sept-14 + // HSV to RBG adapted from: http://mjijackson.com/2008/02/rgb-to-hsl-and-rgb-to-hsv-color-model-conversion-algorithms-in-javascript + var r, g, b; + var h = step / numOfSteps; + var i = ~~(h * 6); + var f = h * 6 - i; + var q = 1 - f; + switch (i % 6) { + case 0: + r = 1, g = f, b = 0; + break; + case 1: + r = q, g = 1, b = 0; + break; + case 2: + r = 0, g = 1, b = f; + break; + case 3: + r = 0, g = q, b = 1; + break; + case 4: + r = f, g = 0, b = 1; + break; + case 5: + r = 1, g = 0, b = q; + break; + } + var c = "#" + ("00" + (~~(r * 255)).toString(16)).slice(-2) + ("00" + (~~(g * 255)).toString(16)).slice(-2) + + ("00" + (~~(b * 255)).toString(16)).slice(-2); + return (c); + }, + getFileNameByPath : function(filePath) { + if (filePath != null){ + var split = filePath.split("/"); + if (split.length > 0){ + return split[split.length - 1]; + } + } + return "Not file"; + }, + getUpdateInterval : function() { + this.interval = this.interval + 2000; + return this.interval; + }, + getRadiationDamageThreshold : function() { + return 0.7; + }, + getQualityThreshold : function() { + return 0.7; + }, + getCreateShipmentURL : function() { + return '/ispyb/user/viewProjectList.do?reqCode=display&menu=create_shipment'; + }, + getCreateShipmentList : function() { + return '/ispyb/user/viewProjectList.do?reqCode=display&menu=list_shipment'; + }, + getShippingURL : function(shippingId) { + return '/ispyb/user/viewProjectList.do?reqCode=display&menu=shipment&shippingId=' + shippingId; + }, + + getMacromoleculeResultsURLByMultipleSearch : function(array) { + return '/ispyb/user/viewProjectList.do?reqCode=display&menu=macromolecule&search=' + + JSON.stringify(array).replace(new RegExp("\"", 'g'), "'"); + }, + getMacromoleculeResultsURL : function(macromoleculeId) { + return '/ispyb/user/viewProjectList.do?reqCode=display&menu=macromolecule¯omoleculeId=' + macromoleculeId; + }, + getMacromoleculeBufferResultsURL : function(macromoleculeId, bufferId) { + return '/ispyb/user/viewProjectList.do?reqCode=display&menu=macromolecule&bufferId=' + bufferId + '¯omoleculeId=' + macromoleculeId; + }, + + getMacromoleculeHeader : function(macromoleculeId) { + + function getHTMLSource(macromoleculeId) { + if (macromoleculeId != null) { + var html = BUI.createFormLabel("Name :", BIOSAXS.proposal.getMacromoleculeById(macromoleculeId).name, 75, 400); + html = html + BUI.createFormLabel("Acronym :", BIOSAXS.proposal.getMacromoleculeById(macromoleculeId).acronym, 75, 400); + if (BIOSAXS.proposal.getMacromoleculeById(macromoleculeId).comments != null) { + html = html + BUI.createFormLabel("Comments :", BIOSAXS.proposal.getMacromoleculeById(macromoleculeId).comments, 75, 400); + } + return html; + } + } + + return Ext.create('Ext.container.Container', { + frame : false, + layout : 'hbox', + title : 'Macromolecule', + bodyPadding : '5', + width : 890, + margin : '0 0 10 0', + height : 100, + style : { + borderColor : '#BDBDBD', + borderStyle : 'solid', + borderWidth : '1px' + }, + fieldDefaults : { + msgTarget : 'side', + labelWidth : 100 + }, + items : [ { + margin : "10 0 0 10", + width : 475, + border : 0, + html : getHTMLSource(macromoleculeId) + }, { + margin : "10 0 0 10", + width : 475, + border : 0, + html : BUI.getZipHTMLByMacromoleculeId(macromoleculeId) + } + ] + }); + }, + + getZipHTMLByMacromoleculeId : function(macromoleculeId) { + if (macromoleculeId != null) { + var fileName = BIOSAXS.proposal.getMacromoleculeById(macromoleculeId).acronym; + return ""; + } + }, + getZipHTMLByExperimentId : function(experimentId, filename) { + if (filename == null){ + filename = "experiment"; + } + return ""; + }, + + getZipURLByAverageId : function(averageId, filename) { + if (filename == null){ + filename = "experiment"; + } + return "/ispyb/user/dataadapter.do?reqCode=getZipFileByAverageListId&f&mergeIdsList=" + averageId + "&fileName=" + filename; + }, + getZipURLBySubtractionId : function(subtractionId, filename) { + if (filename == null){ + filename = "experiment"; + } + return "/ispyb/user/dataadapter.do?reqCode=getZipFileByAverageListId&f&subtractionIdList=" + subtractionId + "&fileName=" + filename; + }, + + + getZipHTMLByFrameRangeId : function(experimentId, start, end) { + var fileName = "experiment"; + return ""; + }, + getZipFrameHPLCUrl : function(experimentId, start, end) { + return "/ispyb/user/dataadapter.do?reqCode=getZipFileH5ByFramesRange&f&experimentId=" + experimentId + "&start=" + Number(start) +"&end="+ Number(end); + }, + + getQueueUrl : function() { + return "/ispyb/user/dataadapter.do?reqCode=getPagingCompactAnalysisByProposalId"; + }, + + getQueueUrlByExperiment: function(experimentId) { + return "/ispyb/user/dataadapter.do?reqCode=getPagingCompactAnalysisByExperimentId&f&experimentId=" + experimentId; + }, + getStandardDeviation : function(values) { + var sum = 0; + var count = 0; + var avg = null; + + var curatedValues = new Array(); + for ( var i = 0; i < values.length; i++) { + var value = values[i]; + if (value != null) { + if (!isNaN(value)) { + count = count + 1; + sum = sum + Number(value); + curatedValues.push(Number(value)); + } + } + } + + if (count > 0) { + avg = sum / count; + } else { + avg = sum; + } + var aux = 0; + for ( var i = 0; i < curatedValues.length; i++) { + var value = curatedValues[i]; + aux = aux + Math.pow(value - avg, 2); + } + /** std **/ + var std = Math.sqrt(aux / count); + return { + std : (std), + sum : (sum), + avg : (avg), + validNumber : count, + totalNumber : values.length, + values : values + }; + }, + + getHTMLTableForFrameAveraged : function(bufferAcronym, macromoleculeAcronym, bbmerges, molmerges, bamerges, totalframes, bufferId,macromoleculeId, macromoleculeColor) { + + function getFrameSpan(framesMerged, total) { + return "(" + framesMerged + " of " + total + ")"; + } + + function getColorFrame(framesMerged, total) { + if (framesMerged / total < 0.5) { + return "#FA5858"; + } + if ((framesMerged / total >= 0.5) && (framesMerged / total < 0.8)) { + return "#FF9900"; + } + return "white"; + } + + function getRow(color, acroynm, framesMerged, totalframes) { + return " " + + BUI.getRectangleColorDIV(color, 10, 10) + + " " + acroynm + "" + + getFrameSpan(framesMerged, totalframes) + ""; + } + + var html = ""; + + /** Buffer Before **/ + if (bufferAcronym != null) { + if (bbmerges != null) { + color = BIOSAXS.proposal.bufferColors[bufferId]; + html = html + getRow(color, bufferAcronym, bbmerges, totalframes); + } + } + + /** Molecule **/ + if (macromoleculeAcronym != null) { + if (molmerges != null) { + if (macromoleculeColor == null){ + color = BIOSAXS.proposal.macromoleculeColors[macromoleculeId]; + } + else{ + color = macromoleculeColor; //BIOSAXS.proposal.macromoleculeColors[macromoleculeId]; + } + html = html + getRow(color, macromoleculeAcronym, molmerges, totalframes); + } + } + + /** Buffer After **/ + if (bufferAcronym != null) { + if (bamerges != null) { + color = BIOSAXS.proposal.bufferColors[bufferId]; + html = html + getRow(color, bufferAcronym, bamerges, totalframes); + } + } + return html + "
"; + }, + isWebGLEnabled : function(return_context) { + if (!!window.WebGLRenderingContext) { + var canvas = document.createElement("canvas"); + names = [ "webgl", "experimental-webgl", "moz-webgl", "webkit-3d" ]; + context = false; + for ( var i = 0; i < 4; i++) { + try { + context = canvas.getContext(names[i]); + if (context && typeof context.getParameter == "function") { + // WebGL is enabled + if (return_context) { + // return WebGL object if the function's argument is present + return { + name : names[i], + gl : context + }; } + // else, return just true + return true; } - } ] - }, - "concentrationLabel" : "7.17 mg/ml ,3.53 mg/ml ,1.75 mg/ml ,0.91 mg/ml " + } catch (e) { + } + } + // WebGL is supported, but disabled + return false; + } + // WebGL not supported28. + return false; + }, + getHTMLTableForPrefixes : function(bufferBeforeaverageFilePath, averageFilePath, bufferAfterAverageFilePath) { + + function getRow(bufferBeforeaverageFilePath) { + file = bufferBeforeaverageFilePath; + try { + file = bufferBeforeaverageFilePath.split("/")[bufferBeforeaverageFilePath.split("/").length - 1]; + } catch (e) { + file = "NA"; + } + return "" + file + ""; + } + var html = ""; + + /** Buffer Before **/ + if (bufferBeforeaverageFilePath != null) { + html = html + getRow(bufferBeforeaverageFilePath); + } + + /** Molecule **/ + if (averageFilePath != null) { + html = html + getRow(averageFilePath); + } + + /** Buffer After **/ + if (bufferAfterAverageFilePath != null) { + html = html + getRow(bufferAfterAverageFilePath); + } + return html + "
"; + }, + + getBaseURL : function() { + return '/ispyb/user/dataadapter.do'; + }, + + getPrintcomponentURL : function(dewarId) { + return '/ispyb/user/viewDewarAction.do?reqCode=generateLabels&dewarId=' + dewarId; + + }, + getPDBVisualizerURL : function(modelId, subtractionId, experimentId) { + return '/ispyb/user/viewProjectList.do?reqCode=display&menu=PDBVisualizer&modelId=' + modelId + '&experimentId=' + experimentId + + '&subtractionId=' + subtractionId; + }, + + getURL : function() { + return this.getBaseURL() + '?reqCode=getImage'; + + }, + getAbinitioImageURL : function() { + return this.getBaseURL() + '?reqCode=getAbinitioImage'; + }, + getNSDImageURL : function(modelListId) { + return BUI.getAbinitioImageURL() + '&type=NSD&modelListId=' + modelListId; + }, + getCHI2ImageURL : function(modelListId) { + return BUI.getAbinitioImageURL() + '&type=CHI2&modelListId=' + modelListId; + }, + getModelFile : function(type, modelId, format) { + return this.getBaseURL() + '?reqCode=getModelFile' + "&type=" + type + "&modelId=" + modelId + "&format=" + format; + }, + getPdbURL : function() { + return this.getBaseURL() + '?reqCode=getPdbFiles'; + }, + getStvArray : function(value, error) { + value = Number(value); + error = Number(error); + return [ value - error, value, value + error ]; + }, + getPointArrayForDygraph : function(x, y, error) { + return [ x, BUI.getStvArray(y, error) ]; + }, + createDIV : function(text, width, className, backgroundColor) { + var nameContainer = document.createElement("div"); + var nameSpan = document.createElement("span"); + if (className != null) { + nameSpan.setAttribute("class", className); + } + if (backgroundColor != null) { + nameSpan.setAttribute("style", "float:left;width:" + width + "px;height:18px;background-color:" + backgroundColor); + } else { + nameSpan.setAttribute("style", "float:left;width:" + width + "px;height:18px;"); + } + nameSpan.appendChild(document.createTextNode(text)); + nameContainer.appendChild(nameSpan); + return nameContainer; + }, + + createFormLabel : function(labelText, text, labelWidth, textWidth, backgroundColor) { + var div = document.createElement("div"); + + div.appendChild(BUI.createDIV(labelText, labelWidth, "bLabel", backgroundColor)); + div.appendChild(BUI.createDIV(text, textWidth, "btext", backgroundColor)); + return div.innerHTML; + }, + + createTextArea : function(labelText, text, labelWidth, rows, cols) { + var div = document.createElement("div"); + div.appendChild(BUI.createDIV(labelText, labelWidth, "bLabel")); + var textArea = document.createElement("textarea"); + textArea.setAttribute("rows", rows); + textArea.setAttribute("cols", cols); + textArea.appendChild(document.createTextNode(text)); + div.appendChild(textArea); + return div.innerHTML; + }, + + showBetaWarning : function() { + alert("ISPyB for Biosaxs version Beta has not this functionality enabled"); + }, + + formatValuesErrorUnitsScientificFormat : function(val, error, unit, args) { + var fontSize = 14; + var decimals = 2; + var errorFontSize = 10; + /** line break **/ + var lineBreak = true; + if (args != null) { + if (args.fontSize != null) { + fontSize = args.fontSize; + } + if (args.decimals != null) { + decimals = args.decimals; + } + if (args.errorFontSize != null) { + errorFontSize = args.errorFontSize; + } + if (args.lineBreak != null) { + lineBreak = args.lineBreak; + } + + } + + if (val == "") { + return ""; + } + if (error == null) { + return "" + Number(val).toFixed(decimals) + ""; + } + var html = "" + Number(val).toFixed(decimals) + " " + unit + ""; + if (lineBreak) { + html = html + "
"; + } + return html + " ± " + Number(Number(error).toFixed(3)).toExponential() + + ""; + }, + + formatValuesErrorUnits : function(val, error, unit, args) { + var fontSize = 16; + var decimals = 2; + var errorFontSize = 10; + /** line break **/ + var lineBreak = true; + if (args != null) { + if (args.fontSize != null) { + fontSize = args.fontSize; + } + if (args.decimals != null) { + decimals = args.decimals; + } + if (args.errorFontSize != null) { + errorFontSize = args.errorFontSize; + } + if (args.lineBreak != null) { + lineBreak = args.lineBreak; + } + + } + + if (val == "") { + return ""; + } + if (error == null) { + return "" + Number(val).toFixed(decimals) + ""; + } + var html = "" + Number(val).toFixed(decimals) + " " + unit + ""; + if (lineBreak) { + html = html + "
"; + } + return html + " ± " + Number(Number(error).toFixed(8)).toExponential() + + ""; + }, + + formatValuesUnits : function(val, unit, args) { + var fontSize = 12; + var decimals = 2; + var unitsFontSize = 10; + if (args != null) { + if (args.fontSize != null) { + fontSize = args.fontSize; + } + if (args.decimals != null) { + decimals = args.decimals; + } + if (args.unitsFontSize != null) { + unitsFontSize = args.unitsFontSize; + } + + } + + if (val === "") { + return ""; + } + if (unit == null) { + return "" + Number(val).toFixed(decimals) + ""; + } + return "" + Number(val).toFixed(decimals) + " " + unit + ""; + }, + + getGreenButton : function(text, args) { + var width = 70; + var height = 20; + if (args != null) { + if (args.width != null) { + width = args.width; + } + if (args.height != null) { + height = args.height; + } + } + + return ''; + }, +// getBlueButton : function(text, args) { +// var width = 70; +// var height = 20; +// if (args != null) { +// if (args.width != null) { +// width = args.width; +// } +// if (args.height != null) { +// height = args.height; +// } +// } +// +// return ''; +// }, + + getBlueButton : function(text, args) { + var width = 70; + var height = 20; + var href = null; + if (args != null) { + if (args.width != null) { + width = args.width; + } + if (args.height != null) { + height = args.height; + } + if (args.href != null) { + href = args.href; + } + } + if (href != null) { + return ''; + } else { + return ''; +// return ''; + } + }, + + getSubmitGreenButton : function(text) { + return ''; + }, + + getRedButton : function(text) { + return ''; + + }, + getRectangleColorDIV : function(color, height, width) { + return '
'; + }, + + openBufferWindow : function(bufferId) { + var window = new BufferWindow(); + window.draw(tabs.experiment.getBufferById(bufferId), tabs.experiment); + }, + + /** Render for safety levels on grids **/ + safetyRenderer : function(val, y, specimen) { + var color = val; + if (val == "YELLOW") { + color = "#E9AB17"; + } + return '' + val + ''; + }, + + getSampleColor : function() { + return '#CB181D'; + }, + + getLightSampleColor : function() { + return '#FCBBA1'; + }, + + getBufferColor : function() { + return '#6A51A3'; + }, + getLightBufferColor : function() { + return '#BCBDDC'; + }, + + formatConcentration : function(val) { + if (val != null) { + return "" + Number(val).toFixed(2) + " mg/ml "; + } + return val; + }, + + formatVolume : function(sample, volume) { + if (Number(sample.data.volumeToLoad) > Number(sample.data.volume)) { + return "" + volume + " �l"; + } + if (Number(sample.data.volumeToLoad) == Number(sample.data.volume)) { + return "" + volume + " �l"; + } + return "" + volume + " �l"; + }, + + getProposal : function() { + return new Proposal(); + }, + + getSampleNameRenderer : function(val, y, record) { + var sample = record.data; + if (record.raw.macromolecule3VO == null) { + return '' + sample.code + ''; + } else { + return '' + sample.code + ''; + } + }, + + getSafetyLevels : function() { + var safetyLevels = new Array(); + safetyLevels.push({ + safetyLevelId : "", + name : "UNKNOWN" + }); + safetyLevels.push({ + safetyLevelId : 1, + name : "GREEN" + }); + safetyLevels.push({ + safetyLevelId : 2, + name : "YELLOW" + }); + safetyLevels.push({ + safetyLevelId : 3, + name : "RED" + }); + return safetyLevels; + }, + + getErrorColor : function() { + return '#F6CED8'; + }, + getWarningColor : function() { + return '#F5DA81'; + }, + getValidColor : function() { + return '#E0F8E0'; + }, + getSamplePlateLetters : function() { + return [ "A", "B", "C", "D", "E", "F", "G", "H" ]; + }, + getSamplePositionHTML : function(sample, experiment) { + var plate = ""; + var row = ""; + var column = ""; + var rows = this.getSamplePlateLetters(); + if (sample.sampleplateposition3VO != null) { + var samplePlate = experiment.getSamplePlateById(sample.sampleplateposition3VO.samplePlateId); + if (samplePlate != null) { + plate = (samplePlate.slotPositionColumn); + row = (sample.sampleplateposition3VO.rowNumber); + column = (sample.sampleplateposition3VO.columnNumber); + // var html = "Plate: " + "" + plate + ""; + // html = html + ", Row: " + "" + rows[row - 1] + ""; + // html = html + ", Column: " + "" + column + ""; + var html = "Plate: " + plate + + "-" + rows[row - 1] + "" + column + ""; + return html; + } + } + return ""; + }, + + getSafetyLabelName : function(safetyLevelId) { + var safetyLevels = BUI.getSafetyLevels(); + for ( var i = 0; i < safetyLevels.length; i++) { + if (safetyLevels[i].safetyLevelId == safetyLevelId) { + return safetyLevels[i].name; + } + } + return "UNKNOWN"; + }, + /** generate random id **/ + id : function() { + var text = ""; + var possible = "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789"; + + for ( var i = 0; i < 5; i++) + text += possible.charAt(Math.floor(Math.random() * possible.length)); + + return text; + }, + showWarning : function(message) { + Ext.Msg.show({ + title : 'Warning', + msg : message, + icon : Ext.Msg.WARNING, + animEl : 'elId' + }); + }, + showError : function(message) { + Ext.Msg.show({ + title : 'Warning', + msg : message, + icon : Ext.Msg.ERROR, + animEl : 'elId' + }); + }, + getTipHTML : function(message) { + //return "
Tip
" + // + message + "
"; + return "
Tip
" + + message + "
"; + }, + + getWarningHTML : function(message) { + return "
Warning
" + + message + "
"; + }, + + getErrorHTML : function(message) { + return "
Error
" + + message + "
"; + }, + + getProgessBar : function(percentage, text) { + /** percentage 100% green **/ + var color = "#0a0"; + + color = "#99CC00"; + if (percentage > 100) { + color = "yellow"; + percentage = 100; + } + if (isNaN(percentage)) { + color = "white"; + percentage = 0; + } + + var defaultText = percentage + "%"; + if (text != null) { + defaultText = text; + } + + return "
" + defaultText + "
"; + }, + getFileName : function(filePath){ + if (filePath != null){ + return filePath.split("/")[filePath.split("/").length - 1] + } + return ""; + } + +}; + +Ext.ux.form.RequiredCombo = Ext.extend(Ext.form.ComboBox, { + config : { + cls : 'custom-field-text-required' + }, + initComponent : function() { + Ext.ux.form.RequiredCombo.superclass.initComponent.apply(this, arguments); + }, + checkChange : function() { + if ((this.getValue() == null) || String(this.getValue()).length == 0) { + this.addCls('custom-field-text-required'); + } else { + this.removeCls('custom-field-text-required'); + } + } +}); + +Ext.define('Ext.form.field.RequiredNumber', { + extend : 'Ext.form.field.Number', + alias : 'widget.requirednumberfield', + alternateClassName : [ 'Ext.form.RequiredNumberField', 'Ext.form.RequiredNumber' ], + config : { + cls : 'custom-field-text-required' + }, + + initComponent : function() { + var me = this; + me.callParent(); + me.setMinValue(me.minValue); + me.setMaxValue(me.maxValue); + }, + + onChange : function() { + if ((this.getValue() == null) || String(this.getValue()).length == 0) { + this.addCls('custom-field-text-required'); + } else { + this.removeCls('custom-field-text-required'); + } + this.toggleSpinners(); + this.callParent(arguments); + } +}); + +Ext.define('Ext.form.field.RequiredText', { + extend : 'Ext.form.field.Text', + alias : 'widget.requiredtext', + requires : [ 'Ext.form.field.VTypes', 'Ext.layout.component.field.Text' ], + alternateClassName : [ 'Ext.form.RequiredTextField', 'Ext.form.RequiredText' ], + config : { + cls : 'custom-field-text-required' + }, + initComponent : function() { + var me = this; + if (me.allowOnlyWhitespace === false) { + me.allowBlank = false; } - }; -}; + me.callParent(); + me.addEvents( + /** + * @event autosize + * Fires when the **{@link #autoSize}** function is triggered and the field is resized according to the + * {@link #grow}/{@link #growMin}/{@link #growMax} configs as a result. This event provides a hook for the + * developer to apply additional logic at runtime to resize the field if needed. + * @param {Ext.form.field.Text} this This text field + * @param {Number} width The new field width + */ + 'autosize', -ConcentrationHTMLTableWidget.prototype.test = function(targetId) { - var concentrationHTMLTableWidget = new ConcentrationHTMLTableWidget(); - document.getElementById(targetId).innerHTML = concentrationHTMLTableWidget.getPanel(concentrationHTMLTableWidget.input().data); -}; - -function DataCollectionWidget() { + /** + * @event keydown + * Keydown input field event. This event only fires if **{@link #enableKeyEvents}** is set to true. + * @param {Ext.form.field.Text} this This text field + * @param {Ext.EventObject} e + */ + 'keydown', + /** + * @event keyup + * Keyup input field event. This event only fires if **{@link #enableKeyEvents}** is set to true. + * @param {Ext.form.field.Text} this This text field + * @param {Ext.EventObject} e + */ + 'keyup', + /** + * @event keypress + * Keypress input field event. This event only fires if **{@link #enableKeyEvents}** is set to true. + * @param {Ext.form.field.Text} this This text field + * @param {Ext.EventObject} e + */ + 'keypress'); + me.addStateEvents('change'); + me.setGrowSizePolicy(); + }, + checkChange : function() { + if ((this.getValue() == null) || String(this.getValue()).length == 0) { + this.addCls('custom-field-text-required'); + } else { + this.removeCls('custom-field-text-required'); + } + } +}); -}; +var BIOSAXS_COMBOMANAGER = { -DataCollectionWidget.prototype.refresh = function(subtractionId) { + getComboMacromoleculeByMacromolecules : function(macromolecules, args) { + var labelWidth = 150; + var margin = "0 0 5 0"; + var width = 300; -}; + if (args != null) { + if (args.labelWidth != null) { + labelWidth = args.labelWidth; + } + if (args.margin != null) { + margin = args.margin; + } + if (args.width != null) { + width = args.width; + } + } -DataCollectionWidget.prototype.getMacromolecule = function(data) { - for (var i = 0; i < data.length; i++) { - if (data[i].macromoleculeId != null) { - return BIOSAXS.proposal.getMacromoleculeById(data[i].macromoleculeId); + var store = Ext.create('Ext.data.Store', { + fields : [ 'macromoleculeId', 'acronym' ], + data : macromolecules, + sorters : [ 'acronym' ] + }); + + return Ext.create('Ext.form.ComboBox', { + fieldLabel : 'Macromolecules', + labelWidth : labelWidth, + width : width, + margin : margin, + store : store, + editable: false, + queryMode : 'local', + displayField : 'acronym', + valueField : 'macromoleculeId' + }); + }, + getComboBuffers : function(buffers, args) { + var labelWidth = 150; + var margin = "0 0 5 0"; + var width = 300; + var fieldLabel = 'Buffer'; + + if (args != null) { + if (args.labelWidth != null) { + labelWidth = args.labelWidth; + } + if (args.margin != null) { + margin = args.margin; + } + if (args.width != null) { + width = args.width; + } + if (args.noLabel != null) { + fieldLabel = null; + } } - } - return null; -}; -DataCollectionWidget.prototype.getMacromoleculeContainer = function(data) { - var macromolecule = this.getMacromolecule(data); + var store = Ext.create('Ext.data.Store', { + fields : [ 'bufferId', 'acronym' ], + data : buffers, + sorters : [ 'acronym' ] + }); - var disabled = false; - if (macromolecule == null) { - disabled = true; - } + return Ext.create('Ext.form.ComboBox', { + fieldLabel : fieldLabel, + labelWidth : labelWidth, + width : width, + margin : margin, + editable: false, + store : store, + queryMode : 'local', + displayField : 'acronym', + valueField : 'bufferId' + }); + }, + getComboSessions : function(sessions, args) { + var labelWidth = 150; + var margin = "0 0 5 0"; + var width = 300; - var acronym = (macromolecule == null ? "" : macromolecule.acronym); - var mm = (macromolecule == null ? "" : macromolecule.molecularMass); - var comments = (macromolecule == null ? "" : macromolecule.comments); + if (args != null) { + if (args.labelWidth != null) { + labelWidth = args.labelWidth; + } + if (args.margin != null) { + margin = args.margin; + } + if (args.width != null) { + width = args.width; + } + } - return Ext.create('Ext.Panel', { - width : 500, - height : 200, - disabled : disabled, - title : "Macromolecule", - layout : 'form', - bodyPadding : 5, - defaultType : 'textfield', - tbar : { - defaultButtonUI : 'default', - items : [ { - xtype : 'button', - text : 'Edit', - cls : 'btn-with-border', - handler : function() { - var macromoleculeWindow = new MacromoleculeWindow(); - macromoleculeWindow.draw(macromolecule); - /** TODO: update when save **/ - } - } ] - }, - items : [ { - fieldLabel : 'Acronym', - name : 'first', - readOnly : true, - value : acronym - }, { - fieldLabel : 'Molecular Mass', - name : 'last', - readOnly : true, - value : mm - }, { - xtype : 'textareafield', - fieldLabel : 'Comments', - value : '', - name : 'last', - readOnly : true, - value : comments - } ] - }); -}; + for ( var i = 0; i < sessions.length; i++) { + sessions[i]["startDateFormatted"] = moment(sessions[i].startDate).format("MMM Do YY"); + sessions[i]["sorter"] = moment(sessions[i].startDate).format("YYYYMMDD"); + } -DataCollectionWidget.prototype.getBufferContainer = function(data) { - var _this = this; - var buffer = BIOSAXS.proposal.getBufferById(data[0].bufferId); + var store = Ext.create('Ext.data.Store', { + fields : [ 'sessionId', 'startDateFormatted', 'beamlineName', 'startDate', 'endDate', 'beamlineOperator' ], + data : sessions, + sorters : [ 'sorter' ] + }); - return Ext.create('Ext.Panel', { - width : 500, - height : 200, - title : "Buffer", - layout : 'form', - // collapsed : true, - // collapsible : true, - bodyPadding : 5, - defaultType : 'textfield', - style : { - padding : '0px 0px 0px 2px' - }, - tbar : { - defaultButtonUI : 'default', - items : [ { - xtype : 'button', - text : 'Edit', - cls : 'btn-with-border', - handler : function() { - var bufferWindow = new BufferWindow(); - bufferWindow.draw(BIOSAXS.proposal.getBufferById(data[0].bufferId)); - /** TODO: update when save **/ - } + return Ext.create('Ext.form.ComboBox', { + fieldLabel : 'Sessions', + labelWidth : labelWidth, + width : width, + margin : margin, + store : store, + queryMode : 'local', + // displayField : 'startDate', + valueField : 'sessionId', + // Template for the dropdown menu. + // Note the use of "x-boundlist-item" class, + // this is required to make the items selectable. + tpl : Ext.create('Ext.XTemplate', '', + '
{startDateFormatted} {beamlineName}
', ''), + // template for the content inside text field + displayTpl : Ext.create('Ext.XTemplate', '', '{startDateFormatted}', '') - } ] - }, - items : [ { - fieldLabel : 'Buffer', - name : 'acronym', - readOnly : true, - value : buffer.acronym - }, { - fieldLabel : 'Composition', - name : 'last', - readOnly : true, - value : buffer.composition + }); + } +}; + + function GenericWindow(args){ + this.title = "title"; + this.width = 700; + this.height = 500; + this.id = BUI.id(); + + this.close = false; + this.draggable = true; + this.modal = true; + + if (args != null){ + if (args.actions != null){ + this.actions = args.actions; + } + if (args.form != null){ + this.form = args.form; + } + if (args.width != null){ + this.width = args.width; + } + if (args.modal != null){ + this.modal = args.modal; + } + + if (args.height != null){ + this.height = args.height; + } + if (args.title != null){ + this.title = args.title; + } + if (args.form != null){ + this.form = args.form; + } + if (args.close != null){ + this.close = args.close; + } + if (args.draggable != null){ + this.draggable = args.draggable; + } + + } + /** Events **/ + this.onSaved = new Event(this); + }; + + + +GenericWindow.prototype.getButtons = function() { + var _this = this; + + if (this.close){ + return [ { + text : 'Close', + handler : function() { + _this.panel.close(); + } + } ]; + } + else{ + return [ { + text : 'Save', + handler : function() { + _this.save(); + + } }, { - xtype : 'textareafield', - fieldLabel : 'Comments', - value : buffer.comments, - name : 'last', - readOnly : true - - } ] - }); + text : 'Cancel', + handler : function() { + _this.panel.close(); + } + } ]; + } }; -DataCollectionWidget.prototype.getSpecimenContainer = function(data) { - return Ext.create('Ext.container.Container', { - layout : { - type : 'hbox' - }, - style : { - margin : '10px 10px 10px 10px' - }, - border : 0, - style : { - borderColor : '#000000', - borderStyle : 'solid', - borderWidth : '1px' - }, - defaults : { - labelWidth : 80, - // implicitly create Container by specifying xtype - xtype : 'datefield', - flex : 1, - - }, - items : [ this.getMacromoleculeContainer(data), this.getBufferContainer(data) ] - }); +GenericWindow.prototype.save = function (){ + alert("Method save of GenerciWindow class is abstract"); }; -DataCollectionWidget.prototype.getSeparator = function() { - return { - html : "
", - border : 0 - } +GenericWindow.prototype._postRender = function(data, experiment){ + }; -DataCollectionWidget.prototype.getFitStructurePanel = function(data) { - var _this = this; - - return Ext.create('Ext.container.Container', { - layout : { - type : 'hbox' - }, - style : { - margin : '10px 10px 10px 10px' - }, - border : 0, - style : { - borderColor : '#000000', - borderStyle : 'solid', - borderWidth : '1px' - }, - defaults : { - labelWidth : 80, - xtype : 'datefield', - flex : 1 - }, - items : [ - ] - }); +GenericWindow.prototype.draw = function (data, experiment){ + this._render(data, experiment); }; -DataCollectionWidget.prototype.getFitStructurePanelWorkflow = function(data) { - var _this = this; - var macromolecule = this.getMacromolecule(data); - - var items = []; +GenericWindow.prototype.refresh = function(data, experiment){ + this.data = data; + this.experiment = experiment; + this.form.refresh(data, experiment); +}; - /** Adding all the pdb files linked to the macromolecule **/ - // if (macromolecule.structure3VOs != null) { - // if (macromolecule.structure3VOs.length > 0) { - // - // items.push(); - // } - // } else { - // items.push({ - // html : "No apriori information added to this macromolecule. Apriori information needed for further analysis", - // margin : "5 5 5 5" - // }); - // } - var fitStructureToExperimentDataGrid = new FitStructureToExperimentDataGrid(); - - fitStructureToExperimentDataGrid.refresh(_this.data[0].subtractionId, _this.getMacromolecule(data)); - return Ext.create('Ext.container.Container', { - style : { - margin : '10px 10px 10px 10px' - }, - border : 0, +GenericWindow.prototype._render = function(data, experiment){ + this.data = data; + var _this = this; + if (this.panel == null){ + this.panel = Ext.create('Ext.Window', { + id : this.id, + title : this.title, + resizable : true, + constrain : true, + border : 1, + modal : this.modal, + frame : false, + draggable : this.draggable, + closable : true, + autoscroll : true, + layout : { type: 'vbox',align: 'stretch'}, + width : this.width, + height : this.form.height, + buttonAlign :'right', + buttons : this.getButtons(), + items : this.form.getPanel(data, experiment), + listeners: { + scope : this, + minimize : function(){ + this.panel.hide(); + }, + destroy : function(){ + delete this.panel; + } + } + }); + this.panel.setLoading(); + } + + this.panel.show(); + this._postRender(); +}; +function CalendarWidget(args) { + this.height = 740; - style : { - borderColor : '#000000', - borderStyle : 'solid', - borderWidth : '1px' - }, - defaults : { - labelWidth : 80, - xtype : 'datefield', - flex : 1 - }, - items : [ fitStructureToExperimentDataGrid.getPanel() ], - listeners : { - afterrender : function() { - } + if (args != null) { + if (args.height != null) { + this.height = args.height; } - }); -}; -/** Static method **/ -DataCollectionWidget.prototype.RUNFitScattering = function(subtractionId, structureId) { - var _this = this; - /** Add to Workflow **/ - var adapter = new BiosaxsDataAdapter(); - var workflow = { - 'workflowTitle' : 'FitExperimentalDatatoStructure', - 'comments' : 'FitExperimentalDatatoStructure run from ISPyB for subtractionId: ' + subtractionId + ' and structureId ' + structureId } - var inputs = [ { - name : 'subtractionId', - value : subtractionId - }, { - name : 'structureId', - value : structureId - } ]; + this.onClick = new Event(); +} - adapter.onSuccess.attach(function(sender, data) { - /** Add to Fit **/ - var adapter2 = new BiosaxsDataAdapter(); - var fit = { - 'workflowId' : data.workflowId, - 'subtractionId' : subtractionId, - 'structureId' : structureId, - 'comments' : 'Sent to workflow engine' - } - adapter2.onSuccess.attach(function(sender, fit) { +CalendarWidget.prototype.loadData = function(data) { + this.events = []; - }); - adapter2.addFitStructureData(fit); + for ( var i = 0; i < data.length; i++) { + var date = moment(data[i].creationDate); + var textColor = 'black'; - }); - adapter.addWorkflow(workflow, inputs); + if (data[i].status == "FINISHED") { + textColor = 'green'; + } + if (data[i].status == "ABORTED") { + textColor = 'red'; + } + this.events.push({ + title : data[i].name, + start : date.format("YYYY-MM-DD HH:mm:ss"), + end : date.format("YYYY-MM-DD HH:mm:ss"), + date : date, + allDay : false, + color : textColor, + className : date.format("YYYY-MM-DD") + }); + } }; -DataCollectionWidget.prototype.getSuperpositionTab = function(data) { +CalendarWidget.prototype.draw = function(targetId) { var _this = this; + $('#' + targetId).fullCalendar({ + eventClick : function(calEvent, jsEvent, view) { + _this.onClick.notify(calEvent.className[0]); - this.superpositionGrid = new SuperpositionGrid(); - - return Ext.create('Ext.container.Container', { - style : { - margin : '10px 10px 10px 10px' - }, - border : 0, - style : { - borderColor : '#000000', - borderStyle : 'solid', - borderWidth : '1px' - }, - items : [ _this.superpositionGrid.getPanel() ], - listeners : { - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - - }, - afterrender : function() { - /** Getting Rigid bodies **/ - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, result) { - _this.superpositionGrid.refresh(result); - }); - adapter.getSuperpositionBySubtractionId(data[1].subtractionId); - } - } - }); -}; - -DataCollectionWidget.prototype.getAdvancedTab = function(data) { - var _this = this; - return Ext.create('Ext.container.Container', { - style : { - margin : '10px 10px 10px 10px' }, - border : 0, - style : { - borderColor : '#000000', - borderStyle : 'solid', - borderWidth : '1px' + contentHeight : _this.height, + header : { + left : 'prev,next today', + center : 'title', + right : 'month,basicWeek,basicDay' }, - items : [ _this.getFitStructurePanel(data), _this.getFitStructurePanelWorkflow(data) ] + editable : false, + events : this.events }); -}; - -DataCollectionWidget.prototype.getRigiBodyForm = function(data) { - var _this = this; - _this.rigiBodyGrid = new RigidModelGrid(); - return _this.rigiBodyGrid.getPanel(); }; + +/** + * It shows a table with the guinier and gnom data as well as passed and + * discarded measurements + * + * @height + * @showBufferColumns + */ +function ConcentrationHTMLTableWidget(args) { + this.id = BUI.id(); -DataCollectionWidget.prototype.getRigidBodyModelingTab = function(data) { - var _this = this; - return Ext.create('Ext.container.Container', { - style : { - margin : '10px 10px 10px 10px' - }, - border : 0, - style : { - borderColor : '#000000', - borderStyle : 'solid', - borderWidth : '1px' - }, - items : [ _this.getRigiBodyForm(data) ], - listeners : { - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + this.showBufferColumns = true; - }, - afterrender : function() { - /** Getting Rigid bodies **/ - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, result) { - _this.rigiBodyGrid.refresh(result); - }); - adapter.getRigidBodyModelingBySubtractionId(data[1].subtractionId); - } + if (args != null) { + if (args.height != null) { + this.height = args.height; } - }); -}; - -DataCollectionWidget.prototype.getTabs = function(data) { - var _this = this; - - this.subtractionCurveVisualizer = new SubtractionCurveVisualizer(); - - this.tabs = Ext.createWidget('tabpanel', { - activeTab : 1, - plain : true, - defaults : { - autoScroll : true, - bodyPadding : 10 - }, - items : [ { - title : 'Solution', - items : [ _this.getSpecimenContainer(data) ] - }, { - title : 'Primary Data Reduction', - active : true, - tabConfig : { - xtype : 'tab', - margins : '0 0 0 20', - }, - items : [ _this.subtractionCurveVisualizer.getPanel() ] - }, { - title : 'Abinitio', - items : [ _this.getAbinitioModellingContainer(data), _this.getSeparator(), _this.getModelViz(data) ] - }, { - title : 'Mixtures', - items : [ _this.getAdvancedTab(data) ] - }, { - title : 'Superpositions', - items : [ _this.getSuperpositionTab(data) ] - }, { - title : 'Rigid Body Modeling', - items : [ _this.getRigidBodyModelingTab(data) ] - } ] - }); - return this.tabs; -}; + if (args.showBufferColumns != null) { + this.showBufferColumns = args.showBufferColumns; + } + } +} -DataCollectionWidget.prototype.getPanel = function(data) { - var _this = this; - _this.data = data; - this.panel = Ext.create('Ext.container.Container', { - width : 1000, - layout : { - type : 'vbox', - align : 'stretch', - padding : 5 - }, - items : [ _this.getTabs(data) +ConcentrationHTMLTableWidget.prototype.refresh = function(parsedData) { + document.getElementById(this.id).innerHTML = this.getPanel(parsedData); +}; - ] - }); +ConcentrationHTMLTableWidget.prototype.getPanel = function(parsedData) { + var html = "
"; + html = html + ""; - this.panel.on("afterrender", function() { - _this.subtractionCurveVisualizer.refresh([ _this.data[1].mergeId ], [ _this.data[1].subtractionId ]); - }); - return this.panel; -}; + /** Title * */ + html = html + ""; + html = html + ""; + if (this.showBufferColumns) { + html = html + ""; + } + html = html + ""; + html = html + ""; + html = html + ""; + html = html + ""; -DataCollectionWidget.prototype.getModelViz = function(data) { - this.modelViz = new ModelVisualizerForm({ - height : 800, - width : 1000 - }); - return this.modelViz.getPanel(); -}; + html = html + ""; + html = html + ""; + html = html + ""; + html = html + ""; + html = html + ""; + html = html + ""; + html = html + ""; + html = html + ""; + html = html + ""; -/** - * PRIMARY DATA PROCESSING - */ -DataCollectionWidget.prototype.getPrimaryDataProcessingContainer = function(data) { - var _this = this; - this.primaryDataProcessingGrid = new PrimaryDataProcessingGrid({ - height : 250, - width : 1000, - title : 'Primary Data Processing' + parsedData.concentration.concentrations.sort(function(a, b) { + return a.concentration - b.concentration; }); + /** Row * */ + for ( var i = 0; i < parsedData.concentration.concentrations.length; i++) { + var row = parsedData[i]; - this.primaryDataProcessingGrid.onSelected.attach(function(sender, selected) { - /** Refresh tabs **/ - var averagesId = []; - var subtractionIds = []; - - var subtractionKeys = {}; - for (var i = 0; i < selected.length; i++) { - if (selected[i].mergeId != null) { - averagesId.push(selected[i].mergeId); - } + var tr = ""; + if (i % 2 == 1) { + tr = ""; + } + var goodMeasurements = (parsedData.concentration.concentrations[i].frames.length - parsedData.concentration.concentrations[i].frames_warning); + if (goodMeasurements == 0) { + tr = ""; + } + html = html + tr; + html = html + ""; + if (this.showBufferColumns) { + html = html + ""; + } + html = html + ""; + html = html + ""; + html = html + ""; + html = html + ""; + html = html + ""; + html = html + ""; + html = html + ""; + html = html + ""; + } + return html + "
ConcentrationBufferMeasurementsGuinierGnom
PassedDiscardedRgI0QualityRgdMax
" + parsedData.concentration.concentrations[i].concentration + "" + parsedData.concentration.concentrations[i].bufferAcronym + "" + goodMeasurements + " of " + parsedData.concentration.concentrations[i].frames.length + "" + parsedData.concentration.concentrations[i].frames_warning + "" + BUI.formatValuesErrorUnits(parsedData.concentration.concentrations[i].calculation.rgGuinier.avg, parsedData.concentration.concentrations[i].calculation.rgGuinier.std, "nm", { + lineBreak : false + }) + "" + BUI.formatValuesErrorUnits(parsedData.concentration.concentrations[i].calculation.i0Guinier.avg, parsedData.concentration.concentrations[i].calculation.i0Guinier.std, " ", { + lineBreak : false + }) + "" + BUI.formatValuesErrorUnits(parsedData.concentration.concentrations[i].calculation.quality.avg, parsedData.concentration.concentrations[i].calculation.quality.std, " ", { + lineBreak : false + }) + "" + BUI.formatValuesErrorUnits(parsedData.concentration.concentrations[i].calculation.rgGnom.avg, parsedData.concentration.concentrations[i].calculation.rgGnom.std, " ", { + lineBreak : false + }) + "" + BUI.formatValuesErrorUnits(parsedData.concentration.concentrations[i].calculation.dMax.avg, parsedData.concentration.concentrations[i].calculation.dMax.std, " ", { + lineBreak : false + }) + "
"; +}; - if (selected[i].subtractionId != null) { - if (selected[i].macromoleculeId != null) { - if (subtractionKeys[selected[i].subtractionId] == null) { - subtractionIds.push(selected[i].subtractionId); +ConcentrationHTMLTableWidget.prototype.input = function() { + return { + data : { + "dataCollectionCount" : 4, + "buffers" : [ { + "bufferId" : "422" + } ], + "concentration" : { + "concentrations" : [ { + "concentration" : "7.17", + "id" : "7.1699999999999999", + "bufferId" : "422.00", + "bufferAcronym" : "B1", + "rgGuinier" : [ "5.12723" ], + "frames" : [ { + "total" : "0.515705406286", + "bufferBeforeMeasurementId" : 15045, + "sampleMergeId" : 8176, + "averagedModelId" : null, + "I0" : "183.457461646", + "proposalCode" : "OPD", + "averagedModel" : null, + "bufferAfterMergeId" : 8177, + "framesCount" : "10", + "bufferBeforeMergeId" : 8175, + "averageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_065_ave.dat", + "bufferAfterMeasurementId" : 15048, + "rgGuinier" : "5.12723", + "subtractedFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_065_sub.dat", + "firstPointUsed" : "17", + "chi2RgFilePath" : null, + "abInitioModelId" : null, + "macromoleculeId" : 649, + "code" : "_4.0_7.17", + "transmission" : "100.0", + "timeStart" : "2013-06-05 15:43:54.348723", + "bufferAcronym" : "B1", + "quality" : "0.853011", + "shapeDeterminationModelId" : null, + "expermientComments" : "[BsxCube] Generated from BsxCube", + "bufferId" : 422, + "isagregated" : "False", + "dmax" : "25.63615", + "bufferBeforeAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_064_ave.dat", + "exposureTemperature" : "4.0", + "subtractionId" : 3377, + "conc" : "7.1699999999999999", + "rapidShapeDeterminationModel" : null, + "experimentCreationDate" : "Jun 5, 2013 3:30:30 PM", + "lastPointUsed" : "36", + "modelListId" : null, + "framesMerge" : "9", + "rapidShapeDeterminationModelId" : null, + "bufferAfterAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_066_ave.dat", + "nsdFilePath" : null, + "bufferAfterFramesMerged" : "10", + "experimentId" : 700, + "macromoleculeAcronym" : "L9", + "i0stdev" : "0.139364435146", + "sampleMeasurementId" : 15047, + "measurementComments" : "[5]", + "priorityLevelId" : 10, + "bufferBeforeFramesMerged" : "10", + "substractionCreationTime" : "Jun 5, 2013 3:46:31 PM", + "proposalNumber" : "29", + "rgGnom" : "5.40297914939", + "volume" : "475.302", + "shapeDeterminationModel" : null, + "comments" : null, + "groupeField" : "L9 B1" + } ], + "frames_warning" : 0, + "calculation" : { + "rgGuinier" : { + "std" : 0, + "sum" : 5.12723, + "avg" : 5.12723, + "validNumber" : 1, + "totalNumber" : 1, + "values" : [ "5.12723" ] + }, + "i0Guinier" : { + "std" : 0, + "sum" : 183.457461646, + "avg" : 183.457461646, + "validNumber" : 1, + "totalNumber" : 1, + "values" : [ "183.457461646" ] + }, + "quality" : { + "std" : 0, + "sum" : 0.853011, + "avg" : 0.853011, + "validNumber" : 1, + "totalNumber" : 1, + "values" : [ "0.853011" ] + }, + "rgGnom" : { + "std" : 0, + "sum" : 5.40297914939, + "avg" : 5.40297914939, + "validNumber" : 1, + "totalNumber" : 1, + "values" : [ "5.40297914939" ] + }, + "dMax" : { + "std" : 0, + "sum" : 25.63615, + "avg" : 25.63615, + "validNumber" : 1, + "totalNumber" : 1, + "values" : [ "25.63615" ] + } + } + }, { + "concentration" : "3.53", + "id" : "3.5299999999999998", + "bufferId" : "422.00", + "bufferAcronym" : "B1", + "rgGuinier" : [ "4.38278" ], + "frames" : [ { + "total" : "0.497164741078", + "bufferBeforeMeasurementId" : 15048, + "sampleMergeId" : 8178, + "averagedModelId" : null, + "I0" : "160.023229462", + "proposalCode" : "OPD", + "averagedModel" : null, + "bufferAfterMergeId" : 8179, + "framesCount" : "10", + "bufferBeforeMergeId" : 8177, + "averageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_067_ave.dat", + "bufferAfterMeasurementId" : 15051, + "rgGuinier" : "4.38278", + "subtractedFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_067_sub.dat", + "firstPointUsed" : "36", + "chi2RgFilePath" : null, + "abInitioModelId" : null, + "macromoleculeId" : 649, + "code" : "_4.0_3.53", + "transmission" : "100.0", + "timeStart" : "2013-06-05 15:47:04.630129", + "bufferAcronym" : "B1", + "quality" : "0.742825", + "shapeDeterminationModelId" : null, + "expermientComments" : "[BsxCube] Generated from BsxCube", + "bufferId" : 422, + "isagregated" : "False", + "dmax" : "15.33973", + "bufferBeforeAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_066_ave.dat", + "exposureTemperature" : "4.0", + "subtractionId" : 3378, + "conc" : "3.5299999999999998", + "rapidShapeDeterminationModel" : null, + "experimentCreationDate" : "Jun 5, 2013 3:30:30 PM", + "lastPointUsed" : "61", + "modelListId" : null, + "framesMerge" : "10", + "rapidShapeDeterminationModelId" : null, + "bufferAfterAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_068_ave.dat", + "nsdFilePath" : null, + "bufferAfterFramesMerged" : "10", + "experimentId" : 700, + "macromoleculeAcronym" : "L9", + "i0stdev" : "0.1499898017", + "sampleMeasurementId" : 15050, + "measurementComments" : "[6]", + "priorityLevelId" : 12, + "bufferBeforeFramesMerged" : "10", + "substractionCreationTime" : "Jun 5, 2013 3:49:42 PM", + "proposalNumber" : "29", + "rgGnom" : "4.40615474861", + "volume" : "372.656", + "shapeDeterminationModel" : null, + "comments" : null, + "groupeField" : "L9 B1" + } ], + "frames_warning" : 0, + "calculation" : { + "rgGuinier" : { + "std" : 0, + "sum" : 4.38278, + "avg" : 4.38278, + "validNumber" : 1, + "totalNumber" : 1, + "values" : [ "4.38278" ] + }, + "i0Guinier" : { + "std" : 0, + "sum" : 160.023229462, + "avg" : 160.023229462, + "validNumber" : 1, + "totalNumber" : 1, + "values" : [ "160.023229462" ] + }, + "quality" : { + "std" : 0, + "sum" : 0.742825, + "avg" : 0.742825, + "validNumber" : 1, + "totalNumber" : 1, + "values" : [ "0.742825" ] + }, + "rgGnom" : { + "std" : 0, + "sum" : 4.40615474861, + "avg" : 4.40615474861, + "validNumber" : 1, + "totalNumber" : 1, + "values" : [ "4.40615474861" ] + }, + "dMax" : { + "std" : 0, + "sum" : 15.33973, + "avg" : 15.33973, + "validNumber" : 1, + "totalNumber" : 1, + "values" : [ "15.33973" ] + } + } + }, { + "concentration" : "1.75", + "id" : "1.75", + "bufferId" : "422.00", + "bufferAcronym" : "B1", + "rgGuinier" : [], + "frames" : [ { + "total" : "0.5538035065", + "bufferBeforeMeasurementId" : 15051, + "sampleMergeId" : 8180, + "averagedModelId" : null, + "I0" : "146.927428571", + "proposalCode" : "OPD", + "averagedModel" : null, + "bufferAfterMergeId" : 8181, + "framesCount" : "10", + "bufferBeforeMergeId" : 8179, + "averageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_069_ave.dat", + "bufferAfterMeasurementId" : 15054, + "rgGuinier" : "4.27139", + "subtractedFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_069_sub.dat", + "firstPointUsed" : "33", + "chi2RgFilePath" : null, + "abInitioModelId" : null, + "macromoleculeId" : 649, + "code" : "_4.0_1.75", + "transmission" : "100.0", + "timeStart" : "2013-06-05 15:50:09.395824", + "bufferAcronym" : "B1", + "quality" : "0.765999", + "shapeDeterminationModelId" : null, + "expermientComments" : "[BsxCube] Generated from BsxCube", + "bufferId" : 422, + "isagregated" : "False", + "dmax" : "14.949865", + "bufferBeforeAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_068_ave.dat", + "exposureTemperature" : "4.0", + "subtractionId" : 3379, + "conc" : "1.75", + "rapidShapeDeterminationModel" : null, + "experimentCreationDate" : "Jun 5, 2013 3:30:30 PM", + "lastPointUsed" : "62", + "modelListId" : null, + "framesMerge" : "6", + "rapidShapeDeterminationModelId" : null, + "bufferAfterAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_070_ave.dat", + "nsdFilePath" : null, + "bufferAfterFramesMerged" : "10", + "experimentId" : 700, + "macromoleculeAcronym" : "L9", + "i0stdev" : "0.191914285714", + "sampleMeasurementId" : 15053, + "measurementComments" : "[7]", + "priorityLevelId" : 14, + "bufferBeforeFramesMerged" : "10", + "substractionCreationTime" : "Jun 5, 2013 3:52:31 PM", + "proposalNumber" : "29", + "rgGnom" : "4.28379338749", + "volume" : "356.326", + "shapeDeterminationModel" : null, + "comments" : null, + "groupeField" : "L9 B1" + } ], + "frames_warning" : 1, + "calculation" : { + "rgGuinier" : { + "std" : null, + "sum" : 0, + "avg" : 0, + "validNumber" : 0, + "totalNumber" : 0, + "values" : [] + }, + "i0Guinier" : { + "std" : null, + "sum" : 0, + "avg" : 0, + "validNumber" : 0, + "totalNumber" : 0, + "values" : [] + }, + "quality" : { + "std" : null, + "sum" : 0, + "avg" : 0, + "validNumber" : 0, + "totalNumber" : 0, + "values" : [] + }, + "rgGnom" : { + "std" : null, + "sum" : 0, + "avg" : 0, + "validNumber" : 0, + "totalNumber" : 0, + "values" : [] + }, + "dMax" : { + "std" : null, + "sum" : 0, + "avg" : 0, + "validNumber" : 0, + "totalNumber" : 0, + "values" : [] + } + } + }, { + "concentration" : "0.91", + "id" : "0.91000000000000003", + "bufferId" : "422.00", + "bufferAcronym" : "B1", + "rgGuinier" : [], + "frames" : [ { + "total" : null, + "bufferBeforeMeasurementId" : 15054, + "sampleMergeId" : 8182, + "averagedModelId" : null, + "I0" : "0.0", + "proposalCode" : "OPD", + "averagedModel" : null, + "bufferAfterMergeId" : 8183, + "framesCount" : "10", + "bufferBeforeMergeId" : 8181, + "averageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_071_ave.dat", + "bufferAfterMeasurementId" : 15057, + "rgGuinier" : null, + "subtractedFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_071_sub.dat", + "firstPointUsed" : "0", + "chi2RgFilePath" : null, + "abInitioModelId" : null, + "macromoleculeId" : 649, + "code" : "_4.0_.91", + "transmission" : "100.0", + "timeStart" : "2013-06-05 15:52:58.133705", + "bufferAcronym" : "B1", + "quality" : "0.0", + "shapeDeterminationModelId" : null, + "expermientComments" : "[BsxCube] Generated from BsxCube", + "bufferId" : 422, + "isagregated" : "False", + "dmax" : null, + "bufferBeforeAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_070_ave.dat", + "exposureTemperature" : "4.0", + "subtractionId" : 3380, + "conc" : "0.91000000000000003", + "rapidShapeDeterminationModel" : null, + "experimentCreationDate" : "Jun 5, 2013 3:30:30 PM", + "lastPointUsed" : "0", + "modelListId" : null, + "framesMerge" : "10", + "rapidShapeDeterminationModelId" : null, + "bufferAfterAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_072_ave.dat", + "nsdFilePath" : null, + "bufferAfterFramesMerged" : "10", + "experimentId" : 700, + "macromoleculeAcronym" : "L9", + "i0stdev" : "0.0", + "sampleMeasurementId" : 15056, + "measurementComments" : "[8]", + "priorityLevelId" : 16, + "bufferBeforeFramesMerged" : "10", + "substractionCreationTime" : "Jun 5, 2013 3:55:35 PM", + "proposalNumber" : "29", + "rgGnom" : null, + "volume" : null, + "shapeDeterminationModel" : null, + "comments" : null, + "groupeField" : "L9 B1" + } ], + "frames_warning" : 1, + "calculation" : { + "rgGuinier" : { + "std" : null, + "sum" : 0, + "avg" : 0, + "validNumber" : 0, + "totalNumber" : 0, + "values" : [] + }, + "i0Guinier" : { + "std" : null, + "sum" : 0, + "avg" : 0, + "validNumber" : 0, + "totalNumber" : 0, + "values" : [] + }, + "quality" : { + "std" : null, + "sum" : 0, + "avg" : 0, + "validNumber" : 0, + "totalNumber" : 0, + "values" : [] + }, + "rgGnom" : { + "std" : null, + "sum" : 0, + "avg" : 0, + "validNumber" : 0, + "totalNumber" : 0, + "values" : [] + }, + "dMax" : { + "std" : null, + "sum" : 0, + "avg" : 0, + "validNumber" : 0, + "totalNumber" : 0, + "values" : [] + } } - subtractionKeys[selected[i].subtractionId] = true; - } - } + } ] + }, + "concentrationLabel" : "7.17 mg/ml ,3.53 mg/ml ,1.75 mg/ml ,0.91 mg/ml " } - - /** Refreshing Primary Data Reduction **/ - _this.subtractionCurveVisualizer.refresh(averagesId, subtractionIds); - - }); - return this.primaryDataProcessingGrid.getPanel(data); + }; }; -/** - * getAbinitioModellingContainer - */ -DataCollectionWidget.prototype.getAbinitioModellingContainer = function(data) { - var _this = this; - - this.abinitioGrid = new AbinitioGrid(); - this.abinitioGrid.onSelected.attach(function(sender, models) { - _this.modelViz.refresh(models); - - }); - /** It may be abinitio models linked to the buffers **/ - var abinitioIdList = []; - for (var i = 0; i < data.length; i++) { - abinitioIdList.push(data[i].abInitioId); - } - - var uniqueIds = []; - $.each(abinitioIdList, function(i, el) { - if ($.inArray(el, uniqueIds) === -1) - uniqueIds.push(el); - }); - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - _this.abinitioGrid.refresh(data); - }); - adapter.getAbinitioByIdsList(uniqueIds); - return this.abinitioGrid.getPanel([]); +ConcentrationHTMLTableWidget.prototype.test = function(targetId) { + var concentrationHTMLTableWidget = new ConcentrationHTMLTableWidget(); + document.getElementById(targetId).innerHTML = concentrationHTMLTableWidget.getPanel(concentrationHTMLTableWidget.input().data); }; +function DataCollectionWidget() { + +}; + +DataCollectionWidget.prototype.refresh = function(subtractionId) { + +}; + +DataCollectionWidget.prototype.getMacromolecule = function(data) { + for (var i = 0; i < data.length; i++) { + if (data[i].macromoleculeId != null) { + return BIOSAXS.proposal.getMacromoleculeById(data[i].macromoleculeId); + } + } + return null; +}; + +DataCollectionWidget.prototype.getMacromoleculeContainer = function(data) { + var macromolecule = this.getMacromolecule(data); + + var disabled = false; + if (macromolecule == null) { + disabled = true; + } + + var acronym = (macromolecule == null ? "" : macromolecule.acronym); + var mm = (macromolecule == null ? "" : macromolecule.molecularMass); + var comments = (macromolecule == null ? "" : macromolecule.comments); + + return Ext.create('Ext.Panel', { + width : 500, + height : 200, + disabled : disabled, + title : "Macromolecule", + layout : 'form', + bodyPadding : 5, + defaultType : 'textfield', + tbar : { + defaultButtonUI : 'default', + items : [ { + xtype : 'button', + text : 'Edit', + cls : 'btn-with-border', + handler : function() { + var macromoleculeWindow = new MacromoleculeWindow(); + macromoleculeWindow.draw(macromolecule); + /** TODO: update when save **/ + } + } ] + }, + items : [ { + fieldLabel : 'Acronym', + name : 'first', + readOnly : true, + value : acronym + }, { + fieldLabel : 'Molecular Mass', + name : 'last', + readOnly : true, + value : mm + }, { + xtype : 'textareafield', + fieldLabel : 'Comments', + value : '', + name : 'last', + readOnly : true, + value : comments + } ] + }); +}; + +DataCollectionWidget.prototype.getBufferContainer = function(data) { + var _this = this; + var buffer = BIOSAXS.proposal.getBufferById(data[0].bufferId); + + return Ext.create('Ext.Panel', { + width : 500, + height : 200, + title : "Buffer", + layout : 'form', + // collapsed : true, + // collapsible : true, + bodyPadding : 5, + defaultType : 'textfield', + style : { + padding : '0px 0px 0px 2px' + }, + tbar : { + defaultButtonUI : 'default', + items : [ { + xtype : 'button', + text : 'Edit', + cls : 'btn-with-border', + handler : function() { + var bufferWindow = new BufferWindow(); + bufferWindow.draw(BIOSAXS.proposal.getBufferById(data[0].bufferId)); + /** TODO: update when save **/ + } + + } ] + }, + items : [ { + fieldLabel : 'Buffer', + name : 'acronym', + readOnly : true, + value : buffer.acronym + }, { + fieldLabel : 'Composition', + name : 'last', + readOnly : true, + value : buffer.composition + }, { + xtype : 'textareafield', + fieldLabel : 'Comments', + value : buffer.comments, + name : 'last', + readOnly : true + + } ] + }); +}; + +DataCollectionWidget.prototype.getSpecimenContainer = function(data) { + return Ext.create('Ext.container.Container', { + layout : { + type : 'hbox' + }, + style : { + margin : '10px 10px 10px 10px' + }, + border : 0, + style : { + borderColor : '#000000', + borderStyle : 'solid', + borderWidth : '1px' + }, + defaults : { + labelWidth : 80, + // implicitly create Container by specifying xtype + xtype : 'datefield', + flex : 1, + + }, + items : [ this.getMacromoleculeContainer(data), this.getBufferContainer(data) ] + }); +}; + +DataCollectionWidget.prototype.getSeparator = function() { + return { + html : "
", + border : 0 + } +}; + +DataCollectionWidget.prototype.getFitStructurePanel = function(data) { + var _this = this; + + return Ext.create('Ext.container.Container', { + layout : { + type : 'hbox' + }, + style : { + margin : '10px 10px 10px 10px' + }, + border : 0, + style : { + borderColor : '#000000', + borderStyle : 'solid', + borderWidth : '1px' + }, + defaults : { + labelWidth : 80, + xtype : 'datefield', + flex : 1 + }, + items : [ + + ] + }); +}; + +DataCollectionWidget.prototype.getFitStructurePanelWorkflow = function(data) { + var _this = this; + var macromolecule = this.getMacromolecule(data); + + var items = []; + + /** Adding all the pdb files linked to the macromolecule **/ + // if (macromolecule.structure3VOs != null) { + // if (macromolecule.structure3VOs.length > 0) { + // + // items.push(); + // } + // } else { + // items.push({ + // html : "No apriori information added to this macromolecule. Apriori information needed for further analysis", + // margin : "5 5 5 5" + // }); + // } + var fitStructureToExperimentDataGrid = new FitStructureToExperimentDataGrid(); + + fitStructureToExperimentDataGrid.refresh(_this.data[0].subtractionId, _this.getMacromolecule(data)); + return Ext.create('Ext.container.Container', { + style : { + margin : '10px 10px 10px 10px' + }, + border : 0, + + style : { + borderColor : '#000000', + borderStyle : 'solid', + borderWidth : '1px' + }, + defaults : { + labelWidth : 80, + xtype : 'datefield', + flex : 1 + }, + items : [ fitStructureToExperimentDataGrid.getPanel() ], + listeners : { + afterrender : function() { + } + } + }); +}; +/** Static method **/ +DataCollectionWidget.prototype.RUNFitScattering = function(subtractionId, structureId) { + var _this = this; + /** Add to Workflow **/ + var adapter = new BiosaxsDataAdapter(); + var workflow = { + 'workflowTitle' : 'FitExperimentalDatatoStructure', + 'comments' : 'FitExperimentalDatatoStructure run from ISPyB for subtractionId: ' + subtractionId + ' and structureId ' + structureId + } + + var inputs = [ { + name : 'subtractionId', + value : subtractionId + }, { + name : 'structureId', + value : structureId + } ]; + + adapter.onSuccess.attach(function(sender, data) { + /** Add to Fit **/ + var adapter2 = new BiosaxsDataAdapter(); + var fit = { + 'workflowId' : data.workflowId, + 'subtractionId' : subtractionId, + 'structureId' : structureId, + 'comments' : 'Sent to workflow engine' + } + adapter2.onSuccess.attach(function(sender, fit) { + + }); + adapter2.addFitStructureData(fit); + + }); + adapter.addWorkflow(workflow, inputs); + +}; + +DataCollectionWidget.prototype.getSuperpositionTab = function(data) { + var _this = this; + + this.superpositionGrid = new SuperpositionGrid(); + + return Ext.create('Ext.container.Container', { + style : { + margin : '10px 10px 10px 10px' + }, + border : 0, + style : { + borderColor : '#000000', + borderStyle : 'solid', + borderWidth : '1px' + }, + items : [ _this.superpositionGrid.getPanel() ], + listeners : { + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + + }, + afterrender : function() { + /** Getting Rigid bodies **/ + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, result) { + _this.superpositionGrid.refresh(result); + }); + adapter.getSuperpositionBySubtractionId(data[1].subtractionId); + } + } + }); +}; + +DataCollectionWidget.prototype.getAdvancedTab = function(data) { + var _this = this; + return Ext.create('Ext.container.Container', { + style : { + margin : '10px 10px 10px 10px' + }, + border : 0, + style : { + borderColor : '#000000', + borderStyle : 'solid', + borderWidth : '1px' + }, + items : [ _this.getFitStructurePanel(data), _this.getFitStructurePanelWorkflow(data) ] + }); +}; + +DataCollectionWidget.prototype.getRigiBodyForm = function(data) { + var _this = this; + _this.rigiBodyGrid = new RigidModelGrid(); + return _this.rigiBodyGrid.getPanel(); + +}; + +DataCollectionWidget.prototype.getRigidBodyModelingTab = function(data) { + var _this = this; + return Ext.create('Ext.container.Container', { + style : { + margin : '10px 10px 10px 10px' + }, + border : 0, + style : { + borderColor : '#000000', + borderStyle : 'solid', + borderWidth : '1px' + }, + items : [ _this.getRigiBodyForm(data) ], + listeners : { + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + + }, + afterrender : function() { + /** Getting Rigid bodies **/ + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, result) { + _this.rigiBodyGrid.refresh(result); + }); + adapter.getRigidBodyModelingBySubtractionId(data[1].subtractionId); + } + } + }); +}; + +DataCollectionWidget.prototype.getTabs = function(data) { + var _this = this; + + this.subtractionCurveVisualizer = new SubtractionCurveVisualizer(); + + this.tabs = Ext.createWidget('tabpanel', { + activeTab : 1, + plain : true, + defaults : { + autoScroll : true, + bodyPadding : 10 + }, + items : [ { + title : 'Solution', + items : [ _this.getSpecimenContainer(data) ] + }, { + title : 'Primary Data Reduction', + active : true, + tabConfig : { + xtype : 'tab', + margins : '0 0 0 20', + }, + items : [ _this.subtractionCurveVisualizer.getPanel() ] + }, { + title : 'Abinitio', + items : [ _this.getAbinitioModellingContainer(data), _this.getSeparator(), _this.getModelViz(data) ] + }, { + title : 'Mixtures', + items : [ _this.getAdvancedTab(data) ] + }, { + title : 'Superpositions', + items : [ _this.getSuperpositionTab(data) ] + }, { + title : 'Rigid Body Modeling', + items : [ _this.getRigidBodyModelingTab(data) ] + } ] + }); + return this.tabs; +}; + +DataCollectionWidget.prototype.getPanel = function(data) { + var _this = this; + _this.data = data; + this.panel = Ext.create('Ext.container.Container', { + width : 1000, + layout : { + type : 'vbox', + align : 'stretch', + padding : 5 + }, + items : [ _this.getTabs(data) + + ] + }); + + this.panel.on("afterrender", function() { + _this.subtractionCurveVisualizer.refresh([ _this.data[1].mergeId ], [ _this.data[1].subtractionId ]); + }); + return this.panel; +}; + +DataCollectionWidget.prototype.getModelViz = function(data) { + this.modelViz = new ModelVisualizerForm({ + height : 800, + width : 1000 + }); + return this.modelViz.getPanel(); +}; + +/** + * PRIMARY DATA PROCESSING + */ +DataCollectionWidget.prototype.getPrimaryDataProcessingContainer = function(data) { + var _this = this; + this.primaryDataProcessingGrid = new PrimaryDataProcessingGrid({ + height : 250, + width : 1000, + title : 'Primary Data Processing' + }); + + this.primaryDataProcessingGrid.onSelected.attach(function(sender, selected) { + /** Refresh tabs **/ + var averagesId = []; + var subtractionIds = []; + + var subtractionKeys = {}; + for (var i = 0; i < selected.length; i++) { + if (selected[i].mergeId != null) { + averagesId.push(selected[i].mergeId); + } + + if (selected[i].subtractionId != null) { + if (selected[i].macromoleculeId != null) { + if (subtractionKeys[selected[i].subtractionId] == null) { + subtractionIds.push(selected[i].subtractionId); + } + subtractionKeys[selected[i].subtractionId] = true; + } + } + } + + /** Refreshing Primary Data Reduction **/ + _this.subtractionCurveVisualizer.refresh(averagesId, subtractionIds); + + }); + return this.primaryDataProcessingGrid.getPanel(data); +}; +/** + * getAbinitioModellingContainer + */ +DataCollectionWidget.prototype.getAbinitioModellingContainer = function(data) { + var _this = this; + + this.abinitioGrid = new AbinitioGrid(); + this.abinitioGrid.onSelected.attach(function(sender, models) { + _this.modelViz.refresh(models); + + }); + /** It may be abinitio models linked to the buffers **/ + var abinitioIdList = []; + for (var i = 0; i < data.length; i++) { + abinitioIdList.push(data[i].abInitioId); + } + + var uniqueIds = []; + $.each(abinitioIdList, function(i, el) { + if ($.inArray(el, uniqueIds) === -1) + uniqueIds.push(el); + }); + + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + _this.abinitioGrid.refresh(data); + }); + adapter.getAbinitioByIdsList(uniqueIds); + return this.abinitioGrid.getPanel([]); +}; + /** * Edit the information of a buffer * @@ -29163,258 +29163,258 @@ ShippingWidget.prototype.refresh = function() { }; -/** - * Widget container of Specimen grid and samplePlate widget - * Depending of the sample changer layout it may be displayed vertically or horizontally - * - * @param args - * - * #onExperimentChanged It happens when specimen are modified - */ -function SpecimenWidget(args){ - - this.width = 1000; - this.height = 600; - - if (args != null){ - if (args.width != null){ - this.width = args.width; - } - if (args.height != null){ - this.height = args.height; - } - } - - var _this = this; - - /** Specimen Grid **/ - this.specimenGrid = new SpecimenGrid({ - minHeight : 425, - selectionMode : "SINGLE", - editEnabled : false, - updateRowEnabled : true, - width : 900, - showTitle : false - }); - - - this.specimenGrid.onSpecimenChanged.attach(function(sender, specimen) { - _this.experiment.setSpecimenById(specimen); - _this.refresh(_this.experiment); - }); - - this.specimenGrid.onSelected.attach(function(sender, specimens) { - if (specimens.length > 0) { - _this.specimenSelected = specimens[0]; - } else { - _this.specimenSelected = null; - } - _this.samplePlateGroupWidget.selectSpecimens(specimens); - }); - - - /** Sample plate Widget **/ - this.samplePlateGroupWidget = new SamplePlateGroupWidget({ - showTitle : false, - height : 250, - margin : 5, - bbar : true - }); - - - this.samplePlateGroupWidget.onExperimentChanged.attach(function(sender, json) { - _this.refresh(new Experiment(json)); - }); - - this.samplePlateGroupWidget.onClick.attach(function(sender, args) { - /** Clicking on a plate * */ - var row = args.row; - var column = args.column; - var samplePlateId = args.samplePlate.samplePlateId; - - /** is specimen selected on the grid? * */ - if (_this.specimenSelected != null) { - /** Is position target empty * */ - if (_this.experiment.getSampleByPosition(args.samplePlate.samplePlateId, args.row, args.column).length == 0) { - var specimen = _this.experiment.getSampleById(_this.specimenSelected.specimenId); - if (specimen.sampleplateposition3VO == null) { - specimen.sampleplateposition3VO = {}; - } - - specimen.sampleplateposition3VO = { - columnNumber : column, - rowNumber : row, - samplePlateId : samplePlateId - }; - - _this.samplePlateGroupWidget.panel.setLoading("ISPyB: Saving specimen"); - var adapter = new BiosaxsDataAdapter(); - /** If success * */ - adapter.onSuccess.attach(function(sender, experiment) { - _this.samplePlateGroupWidget.panel.setLoading(false); - }); - - adapter.onError.attach(function(sender, error) { - _this.samplePlateGroupWidget.panel.setLoading(false); - showError(error); - }); - - adapter.saveSpecimen(specimen, _this.experiment); - - _this.samplePlateGroupWidget.refresh(_this.experiment); - _this.specimenGrid.refresh(_this.experiment); - //_this.refresh(_this.experiment); - _this.specimenGrid.deselectAll(); - - } else { - /** - * Can we merge? We can merge when specimen are the - * same. So, same buffer, macromolecule, concentration * - */ - var target = _this.experiment.getSampleByPosition(args.samplePlate.samplePlateId, args.row, args.column)[0]; - var specimen = _this.experiment.getSampleById(_this.specimenSelected.specimenId); - - if ((specimen.bufferId == target.bufferId) && (specimen.concentration == target.concentration)) { - if (((specimen.macromolecule3VO != null) && (target.macromolecule3VO != null) && (specimen.macromolecule3VO.macromoleculeId == target.macromolecule3VO.macromoleculeId)) || - ((specimen.macromolecule3VO == null) && (target.macromolecule3VO == null))) { - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - _this.refresh(new Experiment(data)); - _this.samplePlateGroupWidget.panel.setLoading(false); - - _this.onExperimentChanged.notify(experiment); - }); - adapter.onError.attach(function(sender, error) { - _this.samplePlateGroupWidget.panel.setLoading(false); - showError(error); - }); - _this.samplePlateGroupWidget.panel.setLoading("ISPyB: Merging specimens"); - adapter.mergeSpecimens(specimen.specimenId, target.specimenId); - } - } else { - alert("Well is not empty. Select another well!"); - } - } - } else { - var specimen = _this.experiment.getSampleByPosition(args.samplePlate.samplePlateId, args.row, args.column)[0]; - if (specimen != null) { - _this.specimenGrid.selectById(specimen.specimenId); - } - } - }); - - /** Events **/ - this.onExperimentChanged = new Event(this); -}; - -/** - * Return vbox or hbox depending on the slot positions of the plates - */ -SpecimenWidget.prototype.getContainerLayoutConfiguration = function(experiment){ - var dimensions = this.samplePlateGroupWidget.getDimensions(experiment.getSamplePlates()); - if (dimensions.maxSlotPositionRow < dimensions.maxSlotPositionColumn){ - return { - layout : "vbox", - specimenGridWidth : this.width - 10, - specimenGridHeight : this.height - 260, - samplePlateGroupWidth : this.width - 10, - samplePlateGroupHeight : 250 - }; - } - return { - layout : "hbox", - samplePlateGroupWidth : this.width*1/3 -10, - samplePlateGroupHeight : this.height - 10, - specimenGridWidth : this.width*2/3, - specimenGridHeight : this.height - 10 - }; - -}; - - -SpecimenWidget.prototype.refresh = function(experiment){ - this.experiment = experiment; - - /** Removing all components **/ - this.panel.removeAll(); - - var layoutConfiguration = this.getContainerLayoutConfiguration(experiment); - - /** Setting new width and height for layout vbox and hbox **/ - this.specimenGrid.width = layoutConfiguration.specimenGridWidth; - this.specimenGrid.height = layoutConfiguration.specimenGridHeight; - - this.samplePlateGroupWidget.width = layoutConfiguration.samplePlateGroupWidth; - this.samplePlateGroupWidget.height = layoutConfiguration.samplePlateGroupHeight; - - if (layoutConfiguration.layout == "hbox"){ - this.specimenGrid.margin = "0 0 0 5"; - this.specimenGrid.width =this.specimenGrid.width - 5; - } - /** Insert container depending on layout [vertical|horizontal] */ - var container = Ext.create('Ext.container.Container', { - layout : layoutConfiguration.layout, - height : this.height, - width : this.width, - padding : '2px', - items : [ ] - }); - if (layoutConfiguration.layout == "vbox"){ - container.insert(this.specimenGrid.getPanel()); - container.insert(this.samplePlateGroupWidget.getPanel()); - } - else{ - container.insert(this.samplePlateGroupWidget.getPanel()); - container.insert(this.specimenGrid.getPanel()); - } - - /** Insert Widget **/ - this.panel.insert(container); - - /** Load data **/ - this.specimenGrid.refresh(experiment); - this.samplePlateGroupWidget.refresh(experiment); - - -}; - -/** It creates a dummy container to be inserted the plates once the method refresh has been called - * This is necessay because we can not know the sample changer layout before hand - * **/ -SpecimenWidget.prototype.getPanel = function(){ - this.panel = Ext.create('Ext.container.Container', { - layout : 'vbox', - height : this.height, - border : 0, - margin : 5, - width : this.width, - items : [] - }); - return this.panel; -}; - - -SpecimenWidget.prototype.input = function() { - return { - experiment : DATADOC.getExperiment_10(), - proposal : DATADOC.getProposal_10() - }; -}; - -SpecimenWidget.prototype.test = function(targetId) { - var specimenWidget = new SpecimenWidget({ - height : 500, - width : 1000 - }); - BIOSAXS.proposal = new Proposal(specimenWidget.input().proposal); - var experiment = new Experiment(specimenWidget.input().experiment); - var panel = specimenWidget.getPanel(); - panel.render(targetId); - specimenWidget.refresh(experiment); - -}; - - +/** + * Widget container of Specimen grid and samplePlate widget + * Depending of the sample changer layout it may be displayed vertically or horizontally + * + * @param args + * + * #onExperimentChanged It happens when specimen are modified + */ +function SpecimenWidget(args){ + + this.width = 1000; + this.height = 600; + + if (args != null){ + if (args.width != null){ + this.width = args.width; + } + if (args.height != null){ + this.height = args.height; + } + } + + var _this = this; + + /** Specimen Grid **/ + this.specimenGrid = new SpecimenGrid({ + minHeight : 425, + selectionMode : "SINGLE", + editEnabled : false, + updateRowEnabled : true, + width : 900, + showTitle : false + }); + + + this.specimenGrid.onSpecimenChanged.attach(function(sender, specimen) { + _this.experiment.setSpecimenById(specimen); + _this.refresh(_this.experiment); + }); + + this.specimenGrid.onSelected.attach(function(sender, specimens) { + if (specimens.length > 0) { + _this.specimenSelected = specimens[0]; + } else { + _this.specimenSelected = null; + } + _this.samplePlateGroupWidget.selectSpecimens(specimens); + }); + + + /** Sample plate Widget **/ + this.samplePlateGroupWidget = new SamplePlateGroupWidget({ + showTitle : false, + height : 250, + margin : 5, + bbar : true + }); + + + this.samplePlateGroupWidget.onExperimentChanged.attach(function(sender, json) { + _this.refresh(new Experiment(json)); + }); + + this.samplePlateGroupWidget.onClick.attach(function(sender, args) { + /** Clicking on a plate * */ + var row = args.row; + var column = args.column; + var samplePlateId = args.samplePlate.samplePlateId; + + /** is specimen selected on the grid? * */ + if (_this.specimenSelected != null) { + /** Is position target empty * */ + if (_this.experiment.getSampleByPosition(args.samplePlate.samplePlateId, args.row, args.column).length == 0) { + var specimen = _this.experiment.getSampleById(_this.specimenSelected.specimenId); + if (specimen.sampleplateposition3VO == null) { + specimen.sampleplateposition3VO = {}; + } + + specimen.sampleplateposition3VO = { + columnNumber : column, + rowNumber : row, + samplePlateId : samplePlateId + }; + + _this.samplePlateGroupWidget.panel.setLoading("ISPyB: Saving specimen"); + var adapter = new BiosaxsDataAdapter(); + /** If success * */ + adapter.onSuccess.attach(function(sender, experiment) { + _this.samplePlateGroupWidget.panel.setLoading(false); + }); + + adapter.onError.attach(function(sender, error) { + _this.samplePlateGroupWidget.panel.setLoading(false); + showError(error); + }); + + adapter.saveSpecimen(specimen, _this.experiment); + + _this.samplePlateGroupWidget.refresh(_this.experiment); + _this.specimenGrid.refresh(_this.experiment); + //_this.refresh(_this.experiment); + _this.specimenGrid.deselectAll(); + + } else { + /** + * Can we merge? We can merge when specimen are the + * same. So, same buffer, macromolecule, concentration * + */ + var target = _this.experiment.getSampleByPosition(args.samplePlate.samplePlateId, args.row, args.column)[0]; + var specimen = _this.experiment.getSampleById(_this.specimenSelected.specimenId); + + if ((specimen.bufferId == target.bufferId) && (specimen.concentration == target.concentration)) { + if (((specimen.macromolecule3VO != null) && (target.macromolecule3VO != null) && (specimen.macromolecule3VO.macromoleculeId == target.macromolecule3VO.macromoleculeId)) || + ((specimen.macromolecule3VO == null) && (target.macromolecule3VO == null))) { + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + _this.refresh(new Experiment(data)); + _this.samplePlateGroupWidget.panel.setLoading(false); + + _this.onExperimentChanged.notify(experiment); + }); + adapter.onError.attach(function(sender, error) { + _this.samplePlateGroupWidget.panel.setLoading(false); + showError(error); + }); + _this.samplePlateGroupWidget.panel.setLoading("ISPyB: Merging specimens"); + adapter.mergeSpecimens(specimen.specimenId, target.specimenId); + } + } else { + alert("Well is not empty. Select another well!"); + } + } + } else { + var specimen = _this.experiment.getSampleByPosition(args.samplePlate.samplePlateId, args.row, args.column)[0]; + if (specimen != null) { + _this.specimenGrid.selectById(specimen.specimenId); + } + } + }); + + /** Events **/ + this.onExperimentChanged = new Event(this); +}; + +/** + * Return vbox or hbox depending on the slot positions of the plates + */ +SpecimenWidget.prototype.getContainerLayoutConfiguration = function(experiment){ + var dimensions = this.samplePlateGroupWidget.getDimensions(experiment.getSamplePlates()); + if (dimensions.maxSlotPositionRow < dimensions.maxSlotPositionColumn){ + return { + layout : "vbox", + specimenGridWidth : this.width - 10, + specimenGridHeight : this.height - 260, + samplePlateGroupWidth : this.width - 10, + samplePlateGroupHeight : 250 + }; + } + return { + layout : "hbox", + samplePlateGroupWidth : this.width*1/3 -10, + samplePlateGroupHeight : this.height - 10, + specimenGridWidth : this.width*2/3, + specimenGridHeight : this.height - 10 + }; + +}; + + +SpecimenWidget.prototype.refresh = function(experiment){ + this.experiment = experiment; + + /** Removing all components **/ + this.panel.removeAll(); + + var layoutConfiguration = this.getContainerLayoutConfiguration(experiment); + + /** Setting new width and height for layout vbox and hbox **/ + this.specimenGrid.width = layoutConfiguration.specimenGridWidth; + this.specimenGrid.height = layoutConfiguration.specimenGridHeight; + + this.samplePlateGroupWidget.width = layoutConfiguration.samplePlateGroupWidth; + this.samplePlateGroupWidget.height = layoutConfiguration.samplePlateGroupHeight; + + if (layoutConfiguration.layout == "hbox"){ + this.specimenGrid.margin = "0 0 0 5"; + this.specimenGrid.width =this.specimenGrid.width - 5; + } + /** Insert container depending on layout [vertical|horizontal] */ + var container = Ext.create('Ext.container.Container', { + layout : layoutConfiguration.layout, + height : this.height, + width : this.width, + padding : '2px', + items : [ ] + }); + if (layoutConfiguration.layout == "vbox"){ + container.insert(this.specimenGrid.getPanel()); + container.insert(this.samplePlateGroupWidget.getPanel()); + } + else{ + container.insert(this.samplePlateGroupWidget.getPanel()); + container.insert(this.specimenGrid.getPanel()); + } + + /** Insert Widget **/ + this.panel.insert(container); + + /** Load data **/ + this.specimenGrid.refresh(experiment); + this.samplePlateGroupWidget.refresh(experiment); + + +}; + +/** It creates a dummy container to be inserted the plates once the method refresh has been called + * This is necessay because we can not know the sample changer layout before hand + * **/ +SpecimenWidget.prototype.getPanel = function(){ + this.panel = Ext.create('Ext.container.Container', { + layout : 'vbox', + height : this.height, + border : 0, + margin : 5, + width : this.width, + items : [] + }); + return this.panel; +}; + + +SpecimenWidget.prototype.input = function() { + return { + experiment : DATADOC.getExperiment_10(), + proposal : DATADOC.getProposal_10() + }; +}; + +SpecimenWidget.prototype.test = function(targetId) { + var specimenWidget = new SpecimenWidget({ + height : 500, + width : 1000 + }); + BIOSAXS.proposal = new Proposal(specimenWidget.input().proposal); + var experiment = new Experiment(specimenWidget.input().experiment); + var panel = specimenWidget.getPanel(); + panel.render(targetId); + specimenWidget.refresh(experiment); + +}; + + function WarningWidget(args) { this.actions = []; diff --git a/ispyb-ws/pom.xml b/ispyb-ws/pom.xml index ffe75402e..e3f4f6072 100644 --- a/ispyb-ws/pom.xml +++ b/ispyb-ws/pom.xml @@ -38,7 +38,6 @@ javax.ejb javax.ejb-api 3.2 - provided @@ -136,4 +135,4 @@ - + \ No newline at end of file From a6663f27e0ab4c6ce248dbd4cf9dca86690b58c4 Mon Sep 17 00:00:00 2001 From: Olof Svensson Date: Fri, 22 Sep 2017 09:43:44 +0200 Subject: [PATCH 02/38] Issue #174: Added MXPressP_SAD to LIST_EXPERIMENT_KIND_ESRF --- ispyb-ejb/src/main/java/ispyb/common/util/Constants.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ispyb-ejb/src/main/java/ispyb/common/util/Constants.java b/ispyb-ejb/src/main/java/ispyb/common/util/Constants.java index 5f9495e1f..f7be66d07 100644 --- a/ispyb-ejb/src/main/java/ispyb/common/util/Constants.java +++ b/ispyb-ejb/src/main/java/ispyb/common/util/Constants.java @@ -875,7 +875,7 @@ public static String getSAXSBeamline() { // public static final String[] LIST_EXPERIMENT_KIND_ESRF = { "Default", "MXPressE", "MXPressO", "MXPressE_SAD", "MXScore", "MXPressM","OSC", "SAD", // "MAD", "Fixed", "Ligand binding", "Refinement", "MAD - Inverse Beam", "SAD - Inverse Beam" }; - public static final String[] LIST_EXPERIMENT_KIND_ESRF = { "Default", "MXPressE", "MXPressO", "MXPressI", "MXPressE_SAD", "MXScore", "MXPressM", "MXPressP" }; + public static final String[] LIST_EXPERIMENT_KIND_ESRF = { "Default", "MXPressE", "MXPressO", "MXPressI", "MXPressE_SAD", "MXScore", "MXPressM", "MXPressP", "MXPressP_SAD" }; public static final String[] LIST_EXPERIMENT_KIND = (SITE_IS_ESRF()) ? LIST_EXPERIMENT_KIND_ESRF : LIST_EXPERIMENT_KIND_MAXIV; From 4e7a78716593738a5058d99fbc327614e6e0738a Mon Sep 17 00:00:00 2001 From: Olof Svensson Date: Fri, 22 Sep 2017 09:45:27 +0200 Subject: [PATCH 03/38] Update of release notes for issue #174 --- ispyb-ui/src/main/webapp/help/release_notes.txt | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/ispyb-ui/src/main/webapp/help/release_notes.txt b/ispyb-ui/src/main/webapp/help/release_notes.txt index ca4a293d1..fd87424b4 100644 --- a/ispyb-ui/src/main/webapp/help/release_notes.txt +++ b/ispyb-ui/src/main/webapp/help/release_notes.txt @@ -1,3 +1,9 @@ +************** +* 22.09.2017 * +************** + +- fixes: #174 + ************** * 12.09.2017 * ************** From fcb77f682b02b38c730bde03ba076bac3f236068 Mon Sep 17 00:00:00 2001 From: Alejandro De Maria Antolinos Date: Fri, 6 Oct 2017 12:11:42 +0200 Subject: [PATCH 04/38] Added index to README --- README.md | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/README.md b/README.md index 3631d405f..ca45cc71a 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,11 @@ # ISPyB Project [![Build Status](https://travis-ci.org/antolinos/ispyb.png)](https://travis-ci.org/antolinos/ispyb) +- [Installing](#Installing) +- [Versioning](#Versioning) +- [Database creation and update](#Database creation and update) +- [Database schema](#Database schema) + ## Installing 1. Clone or fork the ISPyB repository and then clone it by typing: From 140fab907fa05028474d758c8d4e3d7d1d73549b Mon Sep 17 00:00:00 2001 From: Alejandro De Maria Antolinos Date: Fri, 6 Oct 2017 12:12:35 +0200 Subject: [PATCH 05/38] Added index to README --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index ca45cc71a..df0655767 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ -# ISPyB Project [![Build Status](https://travis-ci.org/antolinos/ispyb.png)](https://travis-ci.org/antolinos/ispyb) +ISPyB Project [![Build Status](https://travis-ci.org/antolinos/ispyb.png)](https://travis-ci.org/antolinos/ispyb) - [Installing](#Installing) @@ -6,7 +6,7 @@ - [Database creation and update](#Database creation and update) - [Database schema](#Database schema) -## Installing +# Installing 1. Clone or fork the ISPyB repository and then clone it by typing: ``` From cd9c6eee33f86e050baee79c563654d6797e9d66 Mon Sep 17 00:00:00 2001 From: Alejandro De Maria Antolinos Date: Fri, 6 Oct 2017 12:13:45 +0200 Subject: [PATCH 06/38] Added index to README --- README.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index df0655767..3649a9ca2 100644 --- a/README.md +++ b/README.md @@ -1,10 +1,10 @@ -ISPyB Project [![Build Status](https://travis-ci.org/antolinos/ispyb.png)](https://travis-ci.org/antolinos/ispyb) +# ISPyB Project [![Build Status](https://travis-ci.org/antolinos/ispyb.png)](https://travis-ci.org/antolinos/ispyb) -- [Installing](#Installing) -- [Versioning](#Versioning) -- [Database creation and update](#Database creation and update) -- [Database schema](#Database schema) +1. [Installing](#Installing) +2. [Versioning](#Versioning) +3. [Database creation and update](#Database creation and update) +4. [Database schema](#Database schema) # Installing From fdedb062cfe0d9de600115ccac60b4948a96c3d9 Mon Sep 17 00:00:00 2001 From: Alejandro De Maria Antolinos Date: Fri, 6 Oct 2017 12:15:01 +0200 Subject: [PATCH 07/38] Added index to README --- README.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 3649a9ca2..a8cb48fcc 100644 --- a/README.md +++ b/README.md @@ -1,10 +1,10 @@ # ISPyB Project [![Build Status](https://travis-ci.org/antolinos/ispyb.png)](https://travis-ci.org/antolinos/ispyb) -1. [Installing](#Installing) -2. [Versioning](#Versioning) -3. [Database creation and update](#Database creation and update) -4. [Database schema](#Database schema) +1. [Installing](#installing) +2. [Versioning](#versioning) +3. [Database creation and update](#database-creation-and-update) +4. [Database schema](#database-schema) # Installing From 76f9e775b224f2f6905bba2fed9ee2747171228d Mon Sep 17 00:00:00 2001 From: Alejandro De Maria Antolinos Date: Fri, 6 Oct 2017 16:19:28 +0200 Subject: [PATCH 08/38] Added index to README --- README.md | 39 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) diff --git a/README.md b/README.md index a8cb48fcc..b65360ba2 100644 --- a/README.md +++ b/README.md @@ -5,6 +5,7 @@ 2. [Versioning](#versioning) 3. [Database creation and update](#database-creation-and-update) 4. [Database schema](#database-schema) +5. [Graylog on Widlfly 8.2](#graylog) # Installing @@ -152,3 +153,41 @@ Please do not forget to update the database schema : https://github.com/ispyb/ISPyB/blob/master/documentation/database/ISPyB_DataModel_5.mwb This schema can be updated using MySQLWorkbench (free tool from MySQL). + + +### Graylog on wildfly 8.2 + +Download [biz.paluch.logging](http://logging.paluch.biz) that provides logging to logstash using the Graylog Extended Logging Format (GELF) 1.0 and 1.1. + +Then create a custom handler on standalone.xml +``` + + + ... + + + + + + + + + + + ... + + + + + + + +``` + +I had some problems with the unvalid messages because of timestapPatter. It was fixed by using: +``` + +``` + + + From 8a29d10f2548ec22af84f895d4b6b0f6c300d1e8 Mon Sep 17 00:00:00 2001 From: Alejandro De Maria Antolinos Date: Fri, 6 Oct 2017 16:20:21 +0200 Subject: [PATCH 09/38] Added index to README --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index b65360ba2..7d8bdd6cd 100644 --- a/README.md +++ b/README.md @@ -155,7 +155,7 @@ Please do not forget to update the database schema : This schema can be updated using MySQLWorkbench (free tool from MySQL). -### Graylog on wildfly 8.2 +### Graylog Download [biz.paluch.logging](http://logging.paluch.biz) that provides logging to logstash using the Graylog Extended Logging Format (GELF) 1.0 and 1.1. From 4a4b6b566fd96263c36630f528f112d37d39d0a5 Mon Sep 17 00:00:00 2001 From: Alejandro De Maria Antolinos Date: Mon, 9 Oct 2017 09:54:40 +0200 Subject: [PATCH 10/38] Organizing imports --- .../java/ispyb/ws/soap/mx/ToolsForAutoprocessingWebService.java | 1 - 1 file changed, 1 deletion(-) diff --git a/ispyb-ws/src/main/java/ispyb/ws/soap/mx/ToolsForAutoprocessingWebService.java b/ispyb-ws/src/main/java/ispyb/ws/soap/mx/ToolsForAutoprocessingWebService.java index c37fd0ab0..3d5a9c407 100644 --- a/ispyb-ws/src/main/java/ispyb/ws/soap/mx/ToolsForAutoprocessingWebService.java +++ b/ispyb-ws/src/main/java/ispyb/ws/soap/mx/ToolsForAutoprocessingWebService.java @@ -102,7 +102,6 @@ import javax.jws.soap.SOAPBinding; import javax.jws.soap.SOAPBinding.Style; import javax.naming.NamingException; -import javax.ws.rs.core.Response; import org.apache.log4j.Logger; import org.jboss.ejb3.annotation.SecurityDomain; From 4e8c9e5ee8e49f3914544b43acb2c488206b7a2b Mon Sep 17 00:00:00 2001 From: delageniere Date: Mon, 9 Oct 2017 11:05:46 +0200 Subject: [PATCH 11/38] min file updated --- .../src/main/webapp/js/ispyb/min/ispyb-bx.js | 42726 ++++++++-------- 1 file changed, 21363 insertions(+), 21363 deletions(-) diff --git a/ispyb-ui/src/main/webapp/js/ispyb/min/ispyb-bx.js b/ispyb-ui/src/main/webapp/js/ispyb/min/ispyb-bx.js index a98a06520..23e07209a 100644 --- a/ispyb-ui/src/main/webapp/js/ispyb/min/ispyb-bx.js +++ b/ispyb-ui/src/main/webapp/js/ispyb/min/ispyb-bx.js @@ -38,321 +38,321 @@ Event.prototype = { } }; -function GenericGraph(args) { - this.width = 600; - this.height = 400; - - this.targetId = null; - /** Free spaces in the borders * */ - this.top = 10; - this.left = 10; - this.bottom = 50; - this.right = 40; - - /** Ruler * */ - this.rulerHeight = 50; - this.rulerWidth = 50; - this.rulerStroke = 2; - this.rulerVerticalMarksNumber = 5; - - this.rulerMaxValue = null; - this.rulerMinValue = null; - - /** plot options * */ - this.plotPoints = true; - this.pointRadius = 2; - this.fillOpacityPoint = 0.2; - this.strokeOpacityPoint = 0.2; - - /** Cluster titles * */ - this.clusterTitleHeight = 20; - this.interClassesSpace = 2; - this.interClustersSpace = 4; - this.fontSize = 7; - - /** - * If true classes and title will be rendender in the rule otherwise will be - * integer values - */ - this.plotHorizontalByCluster = true; - - if (args != null) { - if (args.targetId != null) { - this.targetId = args.targetId; - } - if (args.plotHorizontalByCluster != null) { - this.plotHorizontalByCluster = args.plotHorizontalByCluster; - } - if (args.height != null) { - this.height = args.height; - } - if (args.width != null) { - this.width = args.width; - } - if (args.rulerMinValue != null) { - this.rulerMinValue = args.rulerMinValue; - } - if (args.rulerMaxValue != null) { - this.rulerMaxValue = args.rulerMaxValue; - } - if (args.rulerHeight != null) { - this.rulerHeight = args.rulerHeight; - } - - } -} - -GenericGraph.prototype.calculate = function(data) { - var result = {}; - - var checked = this.cleanArray(data); - - /** sorting array * */ - checked.sort(function(a, b) { - return a - b; - }); - - var median = this.getMedian(checked); - - result.median = median; - result.Q1 = Number(this.getQ1(checked)); - result.Q2 = Number(this.getQ2(checked)); - result.Q3 = Number(this.getQ3(checked)); - result.population = checked; - - result.IQR = Number(result.Q3 - result.Q1); - result.outlier_below_limit = result.Q1 - (1.5 * result.IQR); - result.outlier_above_limit = result.Q3 + (1.5 * result.IQR); - result.below_outliers = this.getBelowOutliers(result.outlier_below_limit, checked); - result.above_outliers = this.getAboveOutliers(result.outlier_above_limit, checked); - - result.min_whisker = this.minValueWhisker(result.outlier_below_limit, result.Q1, checked); - result.max_whisker = this.maxValueWhisker(result.outlier_above_limit, result.Q3, checked); - - return result; -}; - -GenericGraph.prototype.drawSVGVerticalText = function(x, y, text, properties) { - var transform = [ "transform", "translate(" + x + ", " + y + "), rotate(-90) " ]; - properties.push(transform); - SVG.drawText(0, 0, text, this.svg, properties); -}; - -/** Plot the numbers on the axis * */ -GenericGraph.prototype.plotRuler = function(rulerProperties) { - - SVG.drawRectangle(rulerProperties.vertical.x, rulerProperties.vertical.y, rulerProperties.vertical.width, rulerProperties.vertical.height, - this.svg, [ [ "fill", "black" ] ]); - var distance = rulerProperties.vertical.height / (this.rulerVerticalMarksNumber + 1); - for ( var i = 0; i <= this.rulerVerticalMarksNumber + 1; i++) { - var deltaHeight = distance * i; - var aux = rulerProperties.vertical.height - deltaHeight; - - var text = Number((aux / rulerProperties.vertical.height) * (rulerProperties.maxPoint - rulerProperties.minPoint) + rulerProperties.minPoint) - .toFixed(3); - - SVG.drawLine(rulerProperties.horizontal.x, this.top + deltaHeight, rulerProperties.horizontal.x - rulerProperties.markWidth, - this.top + deltaHeight, this.svg, [ [ "stroke", "black" ] ]); - SVG.drawText(this.left, this.top + distance * i + 5, text, this.svg, [ [ "style", "font-size:xx-small" ] ]); - /** Drawing the mark up to the end * */ - SVG.drawLine(rulerProperties.horizontal.x, this.top + deltaHeight, this.width - this.right, this.top + deltaHeight, this.svg, [ - [ "stroke", rulerProperties.markColor ], [ "stroke-width", "0.3" ] ]); - - if (i == this.rulerVerticalMarksNumber + 1) { - SVG.drawLine(rulerProperties.horizontal.x, this.top + deltaHeight, this.width - this.right, this.top + deltaHeight, this.svg, [ [ - "stroke", rulerProperties.markColor ] ]); - } - } - - /** Drawing horizontal rulers * */ - if (!this.plotHorizontalByCluster) { - var width = rulerProperties.horizontal.width; - var ratio = width / (rulerProperties.horizontal.xValues.range); - for ( i = 0; i < rulerProperties.horizontal.xValues.values.length; i++) { - var coorX = rulerProperties.horizontal.xValues.values[i] - rulerProperties.horizontal.xValues.min; - SVG.drawText(rulerProperties.horizontal.x + coorX * ratio, this.height - (this.bottom + (this.clusterTitleHeight)), - rulerProperties.horizontal.xValues.values[i], this.svg, [ [ "style", "font-size:small" ] ]); - } - } -}; - -GenericGraph.prototype.plotAxes = function(properties) { - /** - * Drawing canvas plot-free spaces SVG.drawRectangle(0, this.top, this.left, - * this.height, this.svg, [["fill", "pink"]]); SVG.drawRectangle(this.width - - * this.right, this.top, plot.width, plot.height, this.svg, [["fill", - * "pink"]]); SVG.drawRectangle(0, 0, this.width, this.top, this.svg, - * [["fill", "red"]]); SVG.drawRectangle(0, this.height - this.bottom, - * this.width, this.bottom, this.svg, [["fill", "red"]]); - */ - - /** Drawing ruler Space * */ - this.plotRuler({ - minPoint : Number(properties.minPoint), - maxPoint : Number(properties.maxPoint), - markColor : "black", - markWidth : 20, - vertical : { - x : this.left + this.rulerWidth - this.rulerStroke, - y : this.top, - width : this.rulerStroke, - height : this.height - (this.top + this.bottom + this.clusterTitleHeight) - this.rulerHeight - }, - horizontal : { - x : this.left + this.rulerWidth - this.rulerStroke, - y : this.height - (this.bottom + this.clusterTitleHeight + this.rulerHeight), - width : properties.width, - height : this.rulerStroke, - xValues : properties.xValues - } - }); - -}; - -/** Remove nulls and NaN elements in the array * */ -GenericGraph.prototype.cleanArray = function(data) { - var checked = []; - - /** checking data are numbers * */ - for ( var i = 0; i < data.length; i++) { - if (data[i] != null) { - if (!isNaN(data[i])) { - checked.push(data[i]); - } - } - } - return checked; -}; - -GenericGraph.prototype.refresh = function(data) { - document.getElementById(this.targetId).innerHTML = ""; - this.draw(this.targetId, data); -}; - -GenericGraph.prototype.getClassColor = function(className) { - for ( var i = 0; i < this.data.clusters.length; i++) { - var cluster = this.data.clusters[i]; - for ( var j = 0; j < cluster.classes.length; j++) { - var classes = cluster.classes[j]; - if (classes.name == className) { - if (classes.color != null) { - return classes.color; - } - } - } - } - return "black"; -}; - -GenericGraph.prototype.getDimensions = function(data) { - var results = {}; - var points = []; - - this.data = data; - var classesNumber = 0; - var xValues = []; - - for ( var i = 0; i < data.clusters.length; i++) { - var cluster = data.clusters[i]; - if (!this.plotHorizontalByCluster) { - xValues.push(data.clusters[i].x); - } - for ( var j = 0; j < cluster.classes.length; j++) { - var classes = cluster.classes[j]; - points = points.concat(classes.values); - classesNumber = classesNumber + 1; - } - } - - var checked = this.cleanArray(points); - - checked.sort(function(a, b) { - return a - b; - }); - - results.minPoint = checked[0]; - if (this.rulerMinValue != null) { - results.minPoint = this.rulerMinValue; - } - results.maxPoint = checked[checked.length - 1]; - if (this.rulerMaxValue != null) { - results.maxPoint = this.rulerMaxValue; - } - - results.classesNumber = classesNumber; - results.clusterNumber = data.clusters.length; - - var totalInterClassesFreeSpace = (classesNumber - data.clusters.length) * this.interClassesSpace; - var totalInterClusterFreeSpace = (data.clusters.length) * this.interClustersSpace; - results.classWidth = (this.width - (this.rulerWidth + this.left + this.right + totalInterClassesFreeSpace + totalInterClusterFreeSpace))/ classesNumber; - results.width = this.width - (this.right + this.left) - this.rulerWidth + this.rulerStroke; - - results.xValues = {}; - - xValues.sort(function(a, b) { - return a - b; - }); - results.xValues.values = xValues; - if (xValues.length > 0) { - results.xValues.min = xValues[0]; - results.xValues.max = xValues[xValues.length - 1]; - results.xValues.range = results.xValues.max - results.xValues.min; - } - return results; - -}; - -GenericGraph.prototype.draw = function(targetId, data) { - this.targetId = targetId; - var properties = (this.getDimensions(data)); - this.svg = SVG.createSVGCanvas(document.getElementById(this.targetId), [ [ "width", this.width ], [ "height", this.height ] ]); - this.plotAxes(properties); -}; - -GenericGraph.prototype.getMedian = function(checked) { - /** Calculating median * */ - if (checked.length % 2 == 1) { - return checked[Math.floor(checked.length / 2)]; - } else { - return (Number(checked[(checked.length / 2) - 1]) + Number(checked[checked.length / 2])) / 2; - } -}; - -GenericGraph.prototype.pointToPixel = function(value, boxProperties) { - var ratio = (value - boxProperties.minPoint) / (boxProperties.maxPoint - boxProperties.minPoint); - var pixelLength = boxProperties.height - boxProperties.y + this.top; - return (-1 * ratio) * (pixelLength) + (boxProperties.y + boxProperties.height); -}; - -GenericGraph.prototype.maxValueWhisker = function(aboveLimit, q3, array) { - var points = []; - for ( var i = 0; i < array.length; i++) { - if ((array[i] > q3) && (array[i]) <= aboveLimit) { - points.push(array[i]); - } - } - if (points.length > 0) { - points.sort(function(a, b) { - return a - b; - }); - return points[points.length - 1]; - } - return null; -}; - -GenericGraph.prototype.input = function() { - return DATADOC.getBoxWhikerData(); -}; - -GenericGraph.prototype.test = function(targetId) { - var plot = new GenericGraph({ - targetId : targetId, - height : 350, - width : 450, - maxBoxWidth : 25 - }); - plot.refresh(this.input()); -}; +function GenericGraph(args) { + this.width = 600; + this.height = 400; + + this.targetId = null; + /** Free spaces in the borders * */ + this.top = 10; + this.left = 10; + this.bottom = 50; + this.right = 40; + + /** Ruler * */ + this.rulerHeight = 50; + this.rulerWidth = 50; + this.rulerStroke = 2; + this.rulerVerticalMarksNumber = 5; + + this.rulerMaxValue = null; + this.rulerMinValue = null; + + /** plot options * */ + this.plotPoints = true; + this.pointRadius = 2; + this.fillOpacityPoint = 0.2; + this.strokeOpacityPoint = 0.2; + + /** Cluster titles * */ + this.clusterTitleHeight = 20; + this.interClassesSpace = 2; + this.interClustersSpace = 4; + this.fontSize = 7; + + /** + * If true classes and title will be rendender in the rule otherwise will be + * integer values + */ + this.plotHorizontalByCluster = true; + + if (args != null) { + if (args.targetId != null) { + this.targetId = args.targetId; + } + if (args.plotHorizontalByCluster != null) { + this.plotHorizontalByCluster = args.plotHorizontalByCluster; + } + if (args.height != null) { + this.height = args.height; + } + if (args.width != null) { + this.width = args.width; + } + if (args.rulerMinValue != null) { + this.rulerMinValue = args.rulerMinValue; + } + if (args.rulerMaxValue != null) { + this.rulerMaxValue = args.rulerMaxValue; + } + if (args.rulerHeight != null) { + this.rulerHeight = args.rulerHeight; + } + + } +} + +GenericGraph.prototype.calculate = function(data) { + var result = {}; + + var checked = this.cleanArray(data); + + /** sorting array * */ + checked.sort(function(a, b) { + return a - b; + }); + + var median = this.getMedian(checked); + + result.median = median; + result.Q1 = Number(this.getQ1(checked)); + result.Q2 = Number(this.getQ2(checked)); + result.Q3 = Number(this.getQ3(checked)); + result.population = checked; + + result.IQR = Number(result.Q3 - result.Q1); + result.outlier_below_limit = result.Q1 - (1.5 * result.IQR); + result.outlier_above_limit = result.Q3 + (1.5 * result.IQR); + result.below_outliers = this.getBelowOutliers(result.outlier_below_limit, checked); + result.above_outliers = this.getAboveOutliers(result.outlier_above_limit, checked); + + result.min_whisker = this.minValueWhisker(result.outlier_below_limit, result.Q1, checked); + result.max_whisker = this.maxValueWhisker(result.outlier_above_limit, result.Q3, checked); + + return result; +}; + +GenericGraph.prototype.drawSVGVerticalText = function(x, y, text, properties) { + var transform = [ "transform", "translate(" + x + ", " + y + "), rotate(-90) " ]; + properties.push(transform); + SVG.drawText(0, 0, text, this.svg, properties); +}; + +/** Plot the numbers on the axis * */ +GenericGraph.prototype.plotRuler = function(rulerProperties) { + + SVG.drawRectangle(rulerProperties.vertical.x, rulerProperties.vertical.y, rulerProperties.vertical.width, rulerProperties.vertical.height, + this.svg, [ [ "fill", "black" ] ]); + var distance = rulerProperties.vertical.height / (this.rulerVerticalMarksNumber + 1); + for ( var i = 0; i <= this.rulerVerticalMarksNumber + 1; i++) { + var deltaHeight = distance * i; + var aux = rulerProperties.vertical.height - deltaHeight; + + var text = Number((aux / rulerProperties.vertical.height) * (rulerProperties.maxPoint - rulerProperties.minPoint) + rulerProperties.minPoint) + .toFixed(3); + + SVG.drawLine(rulerProperties.horizontal.x, this.top + deltaHeight, rulerProperties.horizontal.x - rulerProperties.markWidth, + this.top + deltaHeight, this.svg, [ [ "stroke", "black" ] ]); + SVG.drawText(this.left, this.top + distance * i + 5, text, this.svg, [ [ "style", "font-size:xx-small" ] ]); + /** Drawing the mark up to the end * */ + SVG.drawLine(rulerProperties.horizontal.x, this.top + deltaHeight, this.width - this.right, this.top + deltaHeight, this.svg, [ + [ "stroke", rulerProperties.markColor ], [ "stroke-width", "0.3" ] ]); + + if (i == this.rulerVerticalMarksNumber + 1) { + SVG.drawLine(rulerProperties.horizontal.x, this.top + deltaHeight, this.width - this.right, this.top + deltaHeight, this.svg, [ [ + "stroke", rulerProperties.markColor ] ]); + } + } + + /** Drawing horizontal rulers * */ + if (!this.plotHorizontalByCluster) { + var width = rulerProperties.horizontal.width; + var ratio = width / (rulerProperties.horizontal.xValues.range); + for ( i = 0; i < rulerProperties.horizontal.xValues.values.length; i++) { + var coorX = rulerProperties.horizontal.xValues.values[i] - rulerProperties.horizontal.xValues.min; + SVG.drawText(rulerProperties.horizontal.x + coorX * ratio, this.height - (this.bottom + (this.clusterTitleHeight)), + rulerProperties.horizontal.xValues.values[i], this.svg, [ [ "style", "font-size:small" ] ]); + } + } +}; + +GenericGraph.prototype.plotAxes = function(properties) { + /** + * Drawing canvas plot-free spaces SVG.drawRectangle(0, this.top, this.left, + * this.height, this.svg, [["fill", "pink"]]); SVG.drawRectangle(this.width - + * this.right, this.top, plot.width, plot.height, this.svg, [["fill", + * "pink"]]); SVG.drawRectangle(0, 0, this.width, this.top, this.svg, + * [["fill", "red"]]); SVG.drawRectangle(0, this.height - this.bottom, + * this.width, this.bottom, this.svg, [["fill", "red"]]); + */ + + /** Drawing ruler Space * */ + this.plotRuler({ + minPoint : Number(properties.minPoint), + maxPoint : Number(properties.maxPoint), + markColor : "black", + markWidth : 20, + vertical : { + x : this.left + this.rulerWidth - this.rulerStroke, + y : this.top, + width : this.rulerStroke, + height : this.height - (this.top + this.bottom + this.clusterTitleHeight) - this.rulerHeight + }, + horizontal : { + x : this.left + this.rulerWidth - this.rulerStroke, + y : this.height - (this.bottom + this.clusterTitleHeight + this.rulerHeight), + width : properties.width, + height : this.rulerStroke, + xValues : properties.xValues + } + }); + +}; + +/** Remove nulls and NaN elements in the array * */ +GenericGraph.prototype.cleanArray = function(data) { + var checked = []; + + /** checking data are numbers * */ + for ( var i = 0; i < data.length; i++) { + if (data[i] != null) { + if (!isNaN(data[i])) { + checked.push(data[i]); + } + } + } + return checked; +}; + +GenericGraph.prototype.refresh = function(data) { + document.getElementById(this.targetId).innerHTML = ""; + this.draw(this.targetId, data); +}; + +GenericGraph.prototype.getClassColor = function(className) { + for ( var i = 0; i < this.data.clusters.length; i++) { + var cluster = this.data.clusters[i]; + for ( var j = 0; j < cluster.classes.length; j++) { + var classes = cluster.classes[j]; + if (classes.name == className) { + if (classes.color != null) { + return classes.color; + } + } + } + } + return "black"; +}; + +GenericGraph.prototype.getDimensions = function(data) { + var results = {}; + var points = []; + + this.data = data; + var classesNumber = 0; + var xValues = []; + + for ( var i = 0; i < data.clusters.length; i++) { + var cluster = data.clusters[i]; + if (!this.plotHorizontalByCluster) { + xValues.push(data.clusters[i].x); + } + for ( var j = 0; j < cluster.classes.length; j++) { + var classes = cluster.classes[j]; + points = points.concat(classes.values); + classesNumber = classesNumber + 1; + } + } + + var checked = this.cleanArray(points); + + checked.sort(function(a, b) { + return a - b; + }); + + results.minPoint = checked[0]; + if (this.rulerMinValue != null) { + results.minPoint = this.rulerMinValue; + } + results.maxPoint = checked[checked.length - 1]; + if (this.rulerMaxValue != null) { + results.maxPoint = this.rulerMaxValue; + } + + results.classesNumber = classesNumber; + results.clusterNumber = data.clusters.length; + + var totalInterClassesFreeSpace = (classesNumber - data.clusters.length) * this.interClassesSpace; + var totalInterClusterFreeSpace = (data.clusters.length) * this.interClustersSpace; + results.classWidth = (this.width - (this.rulerWidth + this.left + this.right + totalInterClassesFreeSpace + totalInterClusterFreeSpace))/ classesNumber; + results.width = this.width - (this.right + this.left) - this.rulerWidth + this.rulerStroke; + + results.xValues = {}; + + xValues.sort(function(a, b) { + return a - b; + }); + results.xValues.values = xValues; + if (xValues.length > 0) { + results.xValues.min = xValues[0]; + results.xValues.max = xValues[xValues.length - 1]; + results.xValues.range = results.xValues.max - results.xValues.min; + } + return results; + +}; + +GenericGraph.prototype.draw = function(targetId, data) { + this.targetId = targetId; + var properties = (this.getDimensions(data)); + this.svg = SVG.createSVGCanvas(document.getElementById(this.targetId), [ [ "width", this.width ], [ "height", this.height ] ]); + this.plotAxes(properties); +}; + +GenericGraph.prototype.getMedian = function(checked) { + /** Calculating median * */ + if (checked.length % 2 == 1) { + return checked[Math.floor(checked.length / 2)]; + } else { + return (Number(checked[(checked.length / 2) - 1]) + Number(checked[checked.length / 2])) / 2; + } +}; + +GenericGraph.prototype.pointToPixel = function(value, boxProperties) { + var ratio = (value - boxProperties.minPoint) / (boxProperties.maxPoint - boxProperties.minPoint); + var pixelLength = boxProperties.height - boxProperties.y + this.top; + return (-1 * ratio) * (pixelLength) + (boxProperties.y + boxProperties.height); +}; + +GenericGraph.prototype.maxValueWhisker = function(aboveLimit, q3, array) { + var points = []; + for ( var i = 0; i < array.length; i++) { + if ((array[i] > q3) && (array[i]) <= aboveLimit) { + points.push(array[i]); + } + } + if (points.length > 0) { + points.sort(function(a, b) { + return a - b; + }); + return points[points.length - 1]; + } + return null; +}; + +GenericGraph.prototype.input = function() { + return DATADOC.getBoxWhikerData(); +}; + +GenericGraph.prototype.test = function(targetId) { + var plot = new GenericGraph({ + targetId : targetId, + height : 350, + width : 450, + maxBoxWidth : 25 + }); + plot.refresh(this.input()); +}; /** * Using dygraph it plots a chart. Params: targetId, labelsContainerId, args @@ -2087,338 +2087,338 @@ MacromoleculeConditionGrid.prototype.test = function(targetId) { panel.render(targetId); }; - -function ItemGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ - this.id = id; - this.args = new Object(); - - this.defaultFormat = new ItemFormat(defaultFormat); - - if(selectedFormat != null){ - this.selected = new ItemFormat(selectedFormat); - } - else{ - this.selected = new ItemFormat(defaultFormat); - } - - if(overFormat != null){ - this.over = new ItemFormat(overFormat); - } - else{ - this.over = new ItemFormat(defaultFormat); - } - - if(draggingFormat != null){ - this.dragging = new ItemFormat(draggingFormat); - } - else{ - this.dragging = new ItemFormat(defaultFormat); - } - - //Events - this.stateChanged = new Event(this); - - - //Attaching events - var _this = this; - this._setEvents(); -}; - -ItemGraphFormatter.prototype.getType = function(){ - return this.args.type; -}; - - -ItemGraphFormatter.prototype.toJSON = function(){ - var json = this.args; - json.defaultFormat = this.getDefault().toJSON(); - json.over = this.getOver().toJSON(); - json.selected = this.getSelected().toJSON(); - json.dragging = this.getDragging().toJSON(); - json.id = this.id; - return json; -}; - -ItemGraphFormatter.prototype.loadFromJSON = function(json){ - this.args = json; - this.defaultFormat = new ItemFormat(json.defaultFormat); - this.over = new ItemFormat(json.over); - this.selected = new ItemFormat(json.selected); - this.dragging = new ItemFormat(json.dragging); - this._setEvents(); -}; - -ItemGraphFormatter.prototype._setEvents = function(){ - //Attaching events - var _this = this; - - this.defaultFormat.changed.attach(function (sender, item){ - _this.over.setSize(_this.defaultFormat.getSize()); - _this.selected.setSize(_this.defaultFormat.getSize()); - _this.dragging.setSize(_this.defaultFormat.getSize()); - _this.stateChanged.notify(_this); - }); - - this.selected.changed.attach(function (sender, item){ - _this.stateChanged.notify(_this); - }); - - this.over.changed.attach(function (sender, item){ - _this.stateChanged.notify(_this); - }); - - this.dragging.changed.attach(function (sender, item){ - _this.stateChanged.notify(_this); - }); -}; - -/** Getters **/ -ItemGraphFormatter.prototype.getId = function(){return this.id;}; -ItemGraphFormatter.prototype.getDefault = function(){return this.defaultFormat;}; -ItemGraphFormatter.prototype.getSelected = function(){return this.selected;}; -ItemGraphFormatter.prototype.getOver = function(){return this.over;}; -ItemGraphFormatter.prototype.getDragging = function(){return this.dragging;}; - -function ItemFormat(args){ - this.defaultFormat = new Object(); - this.args = new Object(); - this.args.title = new Object(); - //Defult properties - this.args.visible = true; - this.args.hidden = false; - this.args.stroke = "#000000"; - this.args.strokeOpacity = 0.8; - this.args["stroke-width"] = 1; - this.args.fill = "#000000"; - this.args["fill-opacity"] = 1; - this.args.size = 1; - this.args.opacity = 1; - this.args.fontSize = "8"; - this.args.fontColor = "#000000"; - - /** For directed edge with arrow **/ - //this.args.arrowSize = 1; - - - if (args != null){ - if (args.visible != null){ - this.args.visible = args.visible; - } - if (args.opacity != null){ - this.args.opacity = args.opacity; - } - if (args.size != null){ - this.args.size = args.size; - } - if (args.hidden != null){ - this.args.hidden = args.hidden; - } - if (args.stroke != null){ - this.args.stroke = this._fixColor(args.stroke); - } - if (args.strokeOpacity != null){ - this.args.strokeOpacity = args.strokeOpacity; - } - if (args["stroke-width"]!=null){ - this.args["stroke-width"] = args["stroke-width"]; - } - if (args["fill-opacity"]!=null){ - this.args["fill-opacity"] = args["fill-opacity"]; - } - if (args.shape!=null){ - this.args.shape = args.shape; - } - if (args.fill!=null){ - this.args.fill = this._fixColor(args.fill); - } - - - if (args.title!=null){ - if (args.title.fontSize!=null){ - this.args.title.fontSize = args.title.fontSize; - } - if (args.title.fill!=null){ - this.args.title.fill = this._fixColor(args.title.fill); - } - } - - /** For directed edge with arrow **/ - /*if (args.arrowSize!=null){ - this.args.arrowSize = args.arrowSize; - }*/ - - } - - this.changed = new Event(); -}; - -ItemFormat.prototype._fixColor = function(color){ - var fixed = color; - if (color.indexOf("green") != -1){ - fixed = '#04B431'; - } - - if (color.indexOf("blue") != -1){ - fixed = '#045FB4'; - } - - if (color.indexOf("red") != -1){ - fixed = '#DF0101'; - } - - if (color.indexOf("black") != -1){ - fixed = '#000000'; - } - - if (color.indexOf("white") != -1){ - fixed = '#FFFFFF'; - } - - if (color.indexOf("#") == -1){ - fixed = "#" + color; - } - return fixed; -}; - -ItemFormat.prototype.toJSON = function(){ - if(this.args.strokeOpacity != null){ - this.args["stroke-opacity"] = this.args.strokeOpacity; - delete this.args.strokeOpacity; - } - -// if(this.args.strokeWidth != null){ -// this.args["stroke-width"] = this.args.strokeWidth; -// delete this.args["stroke-width"]; -// } - - if(this.args.title.fontColor != null){ - this.args.title["font-color"] = this.args.title.fontColor; - } - else{ - this.args.title["font-color"] = this.args.fontColor;//;this.args.title.fontColor; - } - - if(this.args.title.fontSize != null){ - this.args.title["font-size"] = this.args.title.fontSize;//;this.args.title.fontColor; - } - else{ - this.args.title["font-size"] = this.args.fontSize;//;this.args.title.fontColor; - } - //return this.args; - return this.args; -}; - -ItemFormat.prototype.getAttribute = function(name){return this.args[name];}; - -//Getters and Setters -ItemFormat.prototype.setVisible = function(visible){ - if (this.args.visible != visible){ - this.args.visible = visible; - this.changed.notify(this); - } -}; - -ItemFormat.prototype.getVisible = function(){return this.args.visible;}; - -ItemFormat.prototype.setHidden = function(hidden){ - if (this.args.hidden != hidden){ - this.args.hidden = hidden; - this.changed.notify(this); - } -}; - -ItemFormat.prototype.getHidden = function(){return this.args.hidden;}; - - -ItemFormat.prototype.setStroke = function(stroke){ - if (this.args.stroke != stroke){ - this.args.stroke = stroke; - this.changed.notify(this); - } -}; - -ItemFormat.prototype.getStroke = function(){return this.args.stroke;}; - -ItemFormat.prototype.setStrokeOpacity = function(strokeOpacity){ - if (this.args.strokeOpacity != strokeOpacity){ - this.args.strokeOpacity = strokeOpacity; - this.changed.notify(this); - } -}; - -ItemFormat.prototype.getStrokeOpacity = function(){return this.args["stroke-opacity"];}; - -ItemFormat.prototype.setStrokeWidth = function(strokeWidth){ - if (this.args["stroke-width"] != strokeWidth){ - this.args["stroke-width"] = strokeWidth; - this.changed.notify(this); - } -}; - - -ItemFormat.prototype.getFillOpacity = function(){return this.args["fill-opacity"];}; - -ItemFormat.prototype.setfillOpacity = function(strokeWidth){ - if (this.args["fill-opacity"] != strokeWidth){ - this.args["fill-opacity"] = strokeWidth; - this.changed.notify(this); - } -}; - - -ItemFormat.prototype.getStrokeWidth = function(){ - return this.args["stroke-width"]; -}; - -ItemFormat.prototype.setFill = function(fill){ - if (this.args.fill != fill){ - this.args.fill = fill; - this.changed.notify(this); - } -}; - -ItemFormat.prototype.getFill = function(){return this.args.fill;}; - -ItemFormat.prototype.setSize = function(size){ - if (this.args.size != size){ - this.args.size = size; - this.changed.notify(this); - } -}; - -ItemFormat.prototype.getSize = function(){return this.args.size;}; - -ItemFormat.prototype.setOpacity = function(opacity){ - if (this.args.opacity != opacity){ - this.args.opacity = opacity; - this.changed.notify(this); - } -}; - -ItemFormat.prototype.getOpacity = function(){return this.args.opacity;}; - -ItemFormat.prototype.getArrowSize = function(){return this.args.arrowSize;}; - -ItemFormat.prototype.setArrowSize = function(arrowSize){ - if (this.args.arrowSize != arrowSize){ - this.args.arrowSize = arrowSize; - this.changed.notify(this); - } -}; - -ItemFormat.prototype.getFontSize = function(){return this.args.title.fontSize;}; - -ItemFormat.prototype.setFontSize = function(fontSize){ - - if (this.args.title.fontSize != fontSize){ - this.args.title.fontSize = fontSize; - this.changed.notify(this); - } -}; - - - - + +function ItemGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ + this.id = id; + this.args = new Object(); + + this.defaultFormat = new ItemFormat(defaultFormat); + + if(selectedFormat != null){ + this.selected = new ItemFormat(selectedFormat); + } + else{ + this.selected = new ItemFormat(defaultFormat); + } + + if(overFormat != null){ + this.over = new ItemFormat(overFormat); + } + else{ + this.over = new ItemFormat(defaultFormat); + } + + if(draggingFormat != null){ + this.dragging = new ItemFormat(draggingFormat); + } + else{ + this.dragging = new ItemFormat(defaultFormat); + } + + //Events + this.stateChanged = new Event(this); + + + //Attaching events + var _this = this; + this._setEvents(); +}; + +ItemGraphFormatter.prototype.getType = function(){ + return this.args.type; +}; + + +ItemGraphFormatter.prototype.toJSON = function(){ + var json = this.args; + json.defaultFormat = this.getDefault().toJSON(); + json.over = this.getOver().toJSON(); + json.selected = this.getSelected().toJSON(); + json.dragging = this.getDragging().toJSON(); + json.id = this.id; + return json; +}; + +ItemGraphFormatter.prototype.loadFromJSON = function(json){ + this.args = json; + this.defaultFormat = new ItemFormat(json.defaultFormat); + this.over = new ItemFormat(json.over); + this.selected = new ItemFormat(json.selected); + this.dragging = new ItemFormat(json.dragging); + this._setEvents(); +}; + +ItemGraphFormatter.prototype._setEvents = function(){ + //Attaching events + var _this = this; + + this.defaultFormat.changed.attach(function (sender, item){ + _this.over.setSize(_this.defaultFormat.getSize()); + _this.selected.setSize(_this.defaultFormat.getSize()); + _this.dragging.setSize(_this.defaultFormat.getSize()); + _this.stateChanged.notify(_this); + }); + + this.selected.changed.attach(function (sender, item){ + _this.stateChanged.notify(_this); + }); + + this.over.changed.attach(function (sender, item){ + _this.stateChanged.notify(_this); + }); + + this.dragging.changed.attach(function (sender, item){ + _this.stateChanged.notify(_this); + }); +}; + +/** Getters **/ +ItemGraphFormatter.prototype.getId = function(){return this.id;}; +ItemGraphFormatter.prototype.getDefault = function(){return this.defaultFormat;}; +ItemGraphFormatter.prototype.getSelected = function(){return this.selected;}; +ItemGraphFormatter.prototype.getOver = function(){return this.over;}; +ItemGraphFormatter.prototype.getDragging = function(){return this.dragging;}; + +function ItemFormat(args){ + this.defaultFormat = new Object(); + this.args = new Object(); + this.args.title = new Object(); + //Defult properties + this.args.visible = true; + this.args.hidden = false; + this.args.stroke = "#000000"; + this.args.strokeOpacity = 0.8; + this.args["stroke-width"] = 1; + this.args.fill = "#000000"; + this.args["fill-opacity"] = 1; + this.args.size = 1; + this.args.opacity = 1; + this.args.fontSize = "8"; + this.args.fontColor = "#000000"; + + /** For directed edge with arrow **/ + //this.args.arrowSize = 1; + + + if (args != null){ + if (args.visible != null){ + this.args.visible = args.visible; + } + if (args.opacity != null){ + this.args.opacity = args.opacity; + } + if (args.size != null){ + this.args.size = args.size; + } + if (args.hidden != null){ + this.args.hidden = args.hidden; + } + if (args.stroke != null){ + this.args.stroke = this._fixColor(args.stroke); + } + if (args.strokeOpacity != null){ + this.args.strokeOpacity = args.strokeOpacity; + } + if (args["stroke-width"]!=null){ + this.args["stroke-width"] = args["stroke-width"]; + } + if (args["fill-opacity"]!=null){ + this.args["fill-opacity"] = args["fill-opacity"]; + } + if (args.shape!=null){ + this.args.shape = args.shape; + } + if (args.fill!=null){ + this.args.fill = this._fixColor(args.fill); + } + + + if (args.title!=null){ + if (args.title.fontSize!=null){ + this.args.title.fontSize = args.title.fontSize; + } + if (args.title.fill!=null){ + this.args.title.fill = this._fixColor(args.title.fill); + } + } + + /** For directed edge with arrow **/ + /*if (args.arrowSize!=null){ + this.args.arrowSize = args.arrowSize; + }*/ + + } + + this.changed = new Event(); +}; + +ItemFormat.prototype._fixColor = function(color){ + var fixed = color; + if (color.indexOf("green") != -1){ + fixed = '#04B431'; + } + + if (color.indexOf("blue") != -1){ + fixed = '#045FB4'; + } + + if (color.indexOf("red") != -1){ + fixed = '#DF0101'; + } + + if (color.indexOf("black") != -1){ + fixed = '#000000'; + } + + if (color.indexOf("white") != -1){ + fixed = '#FFFFFF'; + } + + if (color.indexOf("#") == -1){ + fixed = "#" + color; + } + return fixed; +}; + +ItemFormat.prototype.toJSON = function(){ + if(this.args.strokeOpacity != null){ + this.args["stroke-opacity"] = this.args.strokeOpacity; + delete this.args.strokeOpacity; + } + +// if(this.args.strokeWidth != null){ +// this.args["stroke-width"] = this.args.strokeWidth; +// delete this.args["stroke-width"]; +// } + + if(this.args.title.fontColor != null){ + this.args.title["font-color"] = this.args.title.fontColor; + } + else{ + this.args.title["font-color"] = this.args.fontColor;//;this.args.title.fontColor; + } + + if(this.args.title.fontSize != null){ + this.args.title["font-size"] = this.args.title.fontSize;//;this.args.title.fontColor; + } + else{ + this.args.title["font-size"] = this.args.fontSize;//;this.args.title.fontColor; + } + //return this.args; + return this.args; +}; + +ItemFormat.prototype.getAttribute = function(name){return this.args[name];}; + +//Getters and Setters +ItemFormat.prototype.setVisible = function(visible){ + if (this.args.visible != visible){ + this.args.visible = visible; + this.changed.notify(this); + } +}; + +ItemFormat.prototype.getVisible = function(){return this.args.visible;}; + +ItemFormat.prototype.setHidden = function(hidden){ + if (this.args.hidden != hidden){ + this.args.hidden = hidden; + this.changed.notify(this); + } +}; + +ItemFormat.prototype.getHidden = function(){return this.args.hidden;}; + + +ItemFormat.prototype.setStroke = function(stroke){ + if (this.args.stroke != stroke){ + this.args.stroke = stroke; + this.changed.notify(this); + } +}; + +ItemFormat.prototype.getStroke = function(){return this.args.stroke;}; + +ItemFormat.prototype.setStrokeOpacity = function(strokeOpacity){ + if (this.args.strokeOpacity != strokeOpacity){ + this.args.strokeOpacity = strokeOpacity; + this.changed.notify(this); + } +}; + +ItemFormat.prototype.getStrokeOpacity = function(){return this.args["stroke-opacity"];}; + +ItemFormat.prototype.setStrokeWidth = function(strokeWidth){ + if (this.args["stroke-width"] != strokeWidth){ + this.args["stroke-width"] = strokeWidth; + this.changed.notify(this); + } +}; + + +ItemFormat.prototype.getFillOpacity = function(){return this.args["fill-opacity"];}; + +ItemFormat.prototype.setfillOpacity = function(strokeWidth){ + if (this.args["fill-opacity"] != strokeWidth){ + this.args["fill-opacity"] = strokeWidth; + this.changed.notify(this); + } +}; + + +ItemFormat.prototype.getStrokeWidth = function(){ + return this.args["stroke-width"]; +}; + +ItemFormat.prototype.setFill = function(fill){ + if (this.args.fill != fill){ + this.args.fill = fill; + this.changed.notify(this); + } +}; + +ItemFormat.prototype.getFill = function(){return this.args.fill;}; + +ItemFormat.prototype.setSize = function(size){ + if (this.args.size != size){ + this.args.size = size; + this.changed.notify(this); + } +}; + +ItemFormat.prototype.getSize = function(){return this.args.size;}; + +ItemFormat.prototype.setOpacity = function(opacity){ + if (this.args.opacity != opacity){ + this.args.opacity = opacity; + this.changed.notify(this); + } +}; + +ItemFormat.prototype.getOpacity = function(){return this.args.opacity;}; + +ItemFormat.prototype.getArrowSize = function(){return this.args.arrowSize;}; + +ItemFormat.prototype.setArrowSize = function(arrowSize){ + if (this.args.arrowSize != arrowSize){ + this.args.arrowSize = arrowSize; + this.changed.notify(this); + } +}; + +ItemFormat.prototype.getFontSize = function(){return this.args.title.fontSize;}; + +ItemFormat.prototype.setFontSize = function(fontSize){ + + if (this.args.title.fontSize != fontSize){ + this.args.title.fontSize = fontSize; + this.changed.notify(this); + } +}; + + + + /** * This class executes the actions @@ -4952,1101 +4952,2095 @@ function openExperiment(experimentId) { BIOSAXS.openExperiment(experimentId); } -var SITE_CONF = { - SAMPLE_CHANGER_CONFIGURATION : { - "3":{ - "platetype3VO": {"plateTypeId":4,"name":"96 Well plate","rowCount":8,"columnCount":12,"shape":"REC"}, - "name":"96 Well plate", - "slotPositionRow":"1", - "slotPositionColumn":"3", - "storageTemperature":"0", - "sampleplateposition3VOs":[], - "experimentId":0 - }, - "2":{ - "platetype3VO":{"plateTypeId":2,"name":" 4 x ( 8 + 3 ) Block","rowCount":4,"columnCount":11,"shape":"REC"}, - "name":" 4 x ( 8 + 3 ) Block", - "slotPositionRow":"1", - "slotPositionColumn":"2", - "storageTemperature":"0", - "sampleplateposition3VOs":[],"experimentId":0 - }, - "1":{ - "platetype3VO":{"plateTypeId":1,"name":"Deep Well","rowCount":8,"columnCount":12,"shape":"REC"}, - "name":"Deep Well", - "slotPositionRow":"1", - "slotPositionColumn":"1", - "storageTemperature":"0", - "sampleplateposition3VOs":[], - "experimentId":0 - } - } +var SITE_CONF = { + SAMPLE_CHANGER_CONFIGURATION : { + "3":{ + "platetype3VO": {"plateTypeId":4,"name":"96 Well plate","rowCount":8,"columnCount":12,"shape":"REC"}, + "name":"96 Well plate", + "slotPositionRow":"1", + "slotPositionColumn":"3", + "storageTemperature":"0", + "sampleplateposition3VOs":[], + "experimentId":0 + }, + "2":{ + "platetype3VO":{"plateTypeId":2,"name":" 4 x ( 8 + 3 ) Block","rowCount":4,"columnCount":11,"shape":"REC"}, + "name":" 4 x ( 8 + 3 ) Block", + "slotPositionRow":"1", + "slotPositionColumn":"2", + "storageTemperature":"0", + "sampleplateposition3VOs":[],"experimentId":0 + }, + "1":{ + "platetype3VO":{"plateTypeId":1,"name":"Deep Well","rowCount":8,"columnCount":12,"shape":"REC"}, + "name":"Deep Well", + "slotPositionRow":"1", + "slotPositionColumn":"1", + "storageTemperature":"0", + "sampleplateposition3VOs":[], + "experimentId":0 + } + } }; - -var ISPYB_CONF = { - load : function(config) { - for (var key in config) { - ISPYB_CONF[key] = config[key]; - } - }, - SAMPLE_CHANGER_CONFIGURATION : { - "1": { - "platetype3VO": {"plateTypeId": 1, "name": "Deep Well", "rowCount": 8, "columnCount": 12, "shape": "REC"}, - "name": "Deep Well", - "slotPositionRow": "1", - "slotPositionColumn": "1", - "storageTemperature": "0", - "sampleplateposition3VOs": [], - "experimentId": 0 - } - } + +var ISPYB_CONF = { + load : function(config) { + for (var key in config) { + ISPYB_CONF[key] = config[key]; + } + }, + SAMPLE_CHANGER_CONFIGURATION : { + "1": { + "platetype3VO": {"plateTypeId": 1, "name": "Deep Well", "rowCount": 8, "columnCount": 12, "shape": "REC"}, + "name": "Deep Well", + "slotPositionRow": "1", + "slotPositionColumn": "1", + "storageTemperature": "0", + "sampleplateposition3VOs": [], + "experimentId": 0 + } + } }; -var SITE_CONF = { - -}; +var SITE_CONF = { + +}; -/** - * Example form - * - * @witdh - * @height - */ -function AbinitioForm(args) { - this.id = BUI.id(); - this.width = null; - this.height = null; - - if (args != null) { - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; - } - } - - var _this = this; - /** Widgets **/ - this.abinitioGrid = new AbinitioGrid({ - width : null, - height : 200 - }); - - this.abinitioGrid.onSelected.attach(function(sender, models) { - var modelsIdList = []; - for ( var i in models) { - modelsIdList.push(models[i].modelId); - } - _this._renderPlot(_this.subtractions[0].subtractionId, modelsIdList); - _this._renderPDB(modelsIdList); - }); - - /** Dygraph Widget that plots fir files**/ - this.plotWidget = new PlotWidget({ - width : 745 / 2, - height : 300, - margin : "10 0 5 10" - }); - - /** PDB viewer **/ - this.viewer = new PDBViewer({ - width : 745 / 2, - height : 300 - }); - -} - -AbinitioForm.prototype._renderPlot = function(subtractionId, modelsIdList) { - /** Trying to plot tje subtraction and the models **/ - try { - var colors = [ "#669900", "#0000FF" ]; - this.plotWidget.refresh([], [ ], modelsIdList, [], [], colors); - } catch (e) { - console.log(e); - } -}; - -AbinitioForm.prototype._renderPDB = function(modelsIdList) { - /** Trying to plot the PDB file **/ - try { - var viz = []; - for (var i = 0; i < modelsIdList.length; i++) { - viz.push({ - modelId : modelsIdList[i], - color : "0xFF6600", - opacity : 0.8 - }); - } - this.viewer.refresh(viz); - } catch (e) { - console.log(e); - } -}; - -AbinitioForm.prototype._getItems = function() { - var _this = this; - return [ { - xtype : 'label', - forId : 'myFieldId', - text : 'INLINE HELP: To be updated', - margin : '15 0 20 10', - cls : "inline-help" - }, this.abinitioGrid.getPanel(), { - xtype : 'container', - layout : 'hbox', - items : [ this.plotWidget.getPanel(), this.viewer.getPanel() ] - } ] -}; - -AbinitioForm.prototype._getButtons = function() { - return []; -}; - -AbinitioForm.prototype.getPanel = function() { - var _this = this; - this.panel = Ext.create('Ext.form.Panel', { - width : this.width, - height : this.height, - margin : 10, - border : 1, - defaultType : 'textfield', - items : this._getItems(), - buttons : this._getButtons(), - listeners : { - afterrender : function() { - _this._populate(); - - } - } - }); - return this.panel; -}; - -/** Populates could be call when the DOM is not filled yet **/ -AbinitioForm.prototype._populate = function() { -}; - -/** It populates the form * */ -AbinitioForm.prototype.refresh = function(subtractions) { - this.subtractions = subtractions; - this.abinitioGrid.refresh(subtractions); -}; - -AbinitioForm.prototype.input = function() { - return {}; -}; - -/** It populates the form **/ -AbinitioForm.prototype.test = function(targetId) { - var macromoleculeForm = new AbinitioForm(); - var panel = macromoleculeForm.getPanel(); - panel.render(targetId); -}; +/** + * Example form + * + * @witdh + * @height + */ +function AbinitioForm(args) { + this.id = BUI.id(); + this.width = null; + this.height = null; -/** - * Example form - * - * @witdh - * @height - */ -function DataReductionForm(args) { - this.id = BUI.id(); - this.width = null; - this.height = null; - - if (args != null) { - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; - } - } - + if (args != null) { + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + } + + var _this = this; + /** Widgets **/ + this.abinitioGrid = new AbinitioGrid({ + width : null, + height : 200 + }); + + this.abinitioGrid.onSelected.attach(function(sender, models) { + var modelsIdList = []; + for ( var i in models) { + modelsIdList.push(models[i].modelId); + } + _this._renderPlot(_this.subtractions[0].subtractionId, modelsIdList); + _this._renderPDB(modelsIdList); + }); + + /** Dygraph Widget that plots fir files**/ + this.plotWidget = new PlotWidget({ + width : 745 / 2, + height : 300, + margin : "10 0 5 10" + }); + + /** PDB viewer **/ + this.viewer = new PDBViewer({ + width : 745 / 2, + height : 300 + }); + +} + +AbinitioForm.prototype._renderPlot = function(subtractionId, modelsIdList) { + /** Trying to plot tje subtraction and the models **/ + try { + var colors = [ "#669900", "#0000FF" ]; + this.plotWidget.refresh([], [ ], modelsIdList, [], [], colors); + } catch (e) { + console.log(e); + } +}; + +AbinitioForm.prototype._renderPDB = function(modelsIdList) { + /** Trying to plot the PDB file **/ + try { + var viz = []; + for (var i = 0; i < modelsIdList.length; i++) { + viz.push({ + modelId : modelsIdList[i], + color : "0xFF6600", + opacity : 0.8 + }); + } + this.viewer.refresh(viz); + } catch (e) { + console.log(e); + } +}; + +AbinitioForm.prototype._getItems = function() { + var _this = this; + return [ { + xtype : 'label', + forId : 'myFieldId', + text : 'INLINE HELP: To be updated', + margin : '15 0 20 10', + cls : "inline-help" + }, this.abinitioGrid.getPanel(), { + xtype : 'container', + layout : 'hbox', + items : [ this.plotWidget.getPanel(), this.viewer.getPanel() ] + } ] +}; + +AbinitioForm.prototype._getButtons = function() { + return []; +}; + +AbinitioForm.prototype.getPanel = function() { + var _this = this; + this.panel = Ext.create('Ext.form.Panel', { + width : this.width, + height : this.height, + margin : 10, + border : 1, + defaultType : 'textfield', + items : this._getItems(), + buttons : this._getButtons(), + listeners : { + afterrender : function() { + _this._populate(); + + } + } + }); + return this.panel; +}; + +/** Populates could be call when the DOM is not filled yet **/ +AbinitioForm.prototype._populate = function() { +}; + +/** It populates the form * */ +AbinitioForm.prototype.refresh = function(subtractions) { + this.subtractions = subtractions; + this.abinitioGrid.refresh(subtractions); +}; + +AbinitioForm.prototype.input = function() { + return {}; +}; + +/** It populates the form **/ +AbinitioForm.prototype.test = function(targetId) { + var macromoleculeForm = new AbinitioForm(); + var panel = macromoleculeForm.getPanel(); + panel.render(targetId); +}; + +/** + * Example form + * + * @witdh + * @height + */ +function DataReductionForm(args) { + this.id = BUI.id(); + this.width = null; + this.height = null; + + if (args != null) { + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + } + + var _this = this; + + /** Widgets **/ + this.plotWidget = new PlotWidget({ + width : 650, + height : 490 + }); + + /** Selected frames to be displayed **/ + this.selectedItems = { + frames : [], + averages : [], + subtractions : [] + }; + +} + +DataReductionForm.prototype._parseSelectedItemsToIds = function(selectedArray) { + var ids = []; + if (selectedArray != null) { + for (var i = 0; i < selectedArray.length; i++) { + ids.push(selectedArray[i].id); + } + } + return ids; +}; + +DataReductionForm.prototype.onSelectionChanged = function(columnName, selected) { + if (selected != null) { + if (columnName == "Frames") { + this.selectedItems.frames = selected; + this.selectedItems.subtractions = []; + } + if (columnName == "Averages") { + this.selectedItems.averages = selected; + } + if (columnName == "Subtractions") { + this.selectedItems.frames = []; + this.selectedItems.subtractions = selected; + } + } + this.plotWidget.refresh(this._parseSelectedItemsToIds(this.selectedItems.frames), this._parseSelectedItemsToIds(this.selectedItems.subtractions)); +}; + +DataReductionForm.prototype._getFramesExtPanel = function(store, columnName, height) { + var _this = this; + + var selModel = Ext.create('Ext.selection.RowModel', { + allowDeselect : true, + mode : 'MULTI', + listeners : { + selectionchange : function(sm, selections) { + var selected = []; + for (var i = 0; i < selections.length; i++) { + selected.push(selections[i].raw); + } + _this.onSelectionChanged(columnName, selected); + } + } + }); + + return Ext.create('Ext.grid.Panel', { + store : store, + margin : 10, + height : height, + width : 200, + selModel : selModel, + columns : [ { + text : columnName, + dataIndex : 'fileName', + flex : 1 + } ], + viewConfig : { + } + }); +}; + +DataReductionForm.prototype._getFramesPanel = function() { + var fields = [ 'fileName', 'type', 'id' ]; + + this.framesStore = Ext.create('Ext.data.Store', { + fields : fields, + sorters : 'fileName' + }); + + this.averagesStore = Ext.create('Ext.data.Store', { + fields : fields + }); + + this.subtractionStore = Ext.create('Ext.data.Store', { + fields : fields + }); + + var gridFrames = this._getFramesExtPanel(this.framesStore, "Frames", 375); + var gridAvgs = this._getFramesExtPanel(this.averagesStore, "Averages", 125); + var subtractionAvgs = this._getFramesExtPanel(this.subtractionStore, "Subtractions", 75); + + return { + xtype : 'container', + layout : 'vbox', + items : [ gridFrames, subtractionAvgs ] + }; +}; + +DataReductionForm.prototype._getImageContainer = function(name, help) { + var html = "
" + name + "
" + return { + xtype : 'container', + layout : 'vbox', + items : [ { + html : html, + margin : "5 0 0 0", + height : 95, + width : 100 + }, { + xtype : 'label', + forId : 'myFieldId', + text : help, + margin : '5 0 0 0', + cls : "inline-help" + } ] + } +}; + +DataReductionForm.prototype._getItems = function() { + var _this = this; + return [ { + xtype : 'container', + layout : 'hbox', + items : [ + this._getFramesPanel(), + this.plotWidget.getPanel(), + { + xtype : 'panel', + width : 110, + frame : true, + margin : "10 5 5 5", + border : 0, + layout : 'vbox', + items : [ this._getImageContainer("scattering", "Scattering"), this._getImageContainer("guinier", "Guinier Region"), + this._getImageContainer("kratky", "Kratky Plot"), this._getImageContainer("gnom", "P(r) distribution") ] + } ] + } ] +}; + +DataReductionForm.prototype._getButtons = function() { + return []; +}; + +DataReductionForm.prototype.getPanel = function() { + var _this = this; + this.panel = Ext.create('Ext.form.Panel', { + width : this.width, + height : this.height, + border : 0, + items : this._getItems(), + buttons : this._getButtons(), + listeners : { + afterrender : function() { + _this._populate(); + } + } + }); + return this.panel; +}; + +/** Populates could be call when the DOM is not filled yet **/ +DataReductionForm.prototype._populate = function() { +}; + +/** It populates the form * */ +DataReductionForm.prototype.refresh = function(subtractions) { + if (subtractions != null) { + for (var i = 0; i < subtractions.length; i++) { + /** Loading frame grids **/ + var subtraction = subtractions[i]; + var averages = [ { + fileName : BUI.getFileName(subtraction.bufferAverageFilePath), + type : 'bufferAvg', + id : subtraction.subtractionId + }, { + fileName : BUI.getFileName(subtraction.sampleAverageFilePath), + type : 'sampleAvg', + id : subtraction.subtractionId + } + + ]; + this.averagesStore.loadData(averages, true); + this.subtractionStore.loadData([ { + fileName : BUI.getFileName(subtraction.substractedFilePath), + type : 'SUBTRACTION', + id : subtraction.subtractionId + } ], true); + + var frames = []; + /** Buffers **/ + if (subtraction.bufferOneDimensionalFiles != null) { + if (subtraction.bufferOneDimensionalFiles.frametolist3VOs != null) { + for (var j = 0; j < subtraction.bufferOneDimensionalFiles.frametolist3VOs.length; j++) { + var frametolist3VO = subtraction.bufferOneDimensionalFiles.frametolist3VOs[j]; + if (frametolist3VO.frame3VO != null) { + frames.push({ + fileName : BUI.getFileName(frametolist3VO.frame3VO.filePath), + type : 'BUFFER', + id : frametolist3VO.frame3VO.frameId + }); + } + } + } + } + /** Samples **/ + if (subtraction.sampleOneDimensionalFiles != null) { + if (subtraction.sampleOneDimensionalFiles.frametolist3VOs != null) { + for (var j = 0; j < subtraction.sampleOneDimensionalFiles.frametolist3VOs.length; j++) { + var frametolist3VO = subtraction.sampleOneDimensionalFiles.frametolist3VOs[j]; + if (frametolist3VO.frame3VO != null) { + frames.push({ + fileName : BUI.getFileName(frametolist3VO.frame3VO.filePath), + type : 'SAMPLE', + id : frametolist3VO.frame3VO.frameId + }); + } + } + } + } + + this.framesStore.loadData(frames, true); + + /** Loading images **/ + this._displayImage("scattering", subtraction.subtractionId); + this._displayImage("kratky", subtraction.subtractionId); + this._displayImage("guinier", subtraction.subtractionId); + this._displayImage("gnom", subtraction.subtractionId); + } + } +}; + +DataReductionForm.prototype._displayImage = function(name, subtractionId) { + var url = BUI.getURL() + '&type=' + name + '&subtractionId=' + subtractionId; + var event = "OnClick= window.open('" + url + "')"; + document.getElementById(this.id + "_" + name).innerHTML = ''; +}; + +DataReductionForm.prototype.input = function() { + return {}; +}; + +/** It populates the form **/ +DataReductionForm.prototype.test = function(targetId) { + var macromoleculeForm = new DataReductionForm(); + var panel = macromoleculeForm.getPanel(); + panel.render(targetId); +}; + +function PlotWidget(args) { + this.width = 600; + this.height = 600; + this.id = BUI.id(); + + this.linear = false; + + this.margin = "10 0 0 0"; + /** for each stat the max and minimum value when it is scaled in order to show correctly in the legend **/ + this.ranges = {}; + if (args != null) { + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + if (args.margin != null) { + this.margin = args.margin; + } + } + +} + +PlotWidget.prototype.getMenu = function() { + var _this = this; + /** Actions buttons **/ + var actions = []; + actions.push("->"); + actions.push({ + text : "Export as Image", + scope : this, + icon : '../images/save.gif', + handler : function(item, pressed) { + var largeImage = document.createElement("img"); + largeImage.style.display = 'block'; + largeImage.style.width = 200 + "px"; + largeImage.style.height = 200 + "px"; + largeImage.setAttribute('src', Dygraph.Export.asCanvas(this.dygraphObject.dygraph).toDataURL()); + window.open(Dygraph.Export.asCanvas(this.dygraphObject.dygraph).toDataURL(), 'Image', ''); + } + }); + + return actions; +}; + +/** Looks for the maximum value and then divide everything but that value **/ +PlotWidget.prototype.scaledData = function(data) { + for (var i = 0; i < data.length; i++) { + var values = this.getMaxAndMinValue(data[i]); + data[i] = this.divideValuesByMax(data[i], values.max); + this.ranges[data[i].label] = values; + } + return data; +}; + +/** Given a stat float[] and a max number it will divide each value by max **/ +PlotWidget.prototype.divideValuesByMax = function(stat, max) { + for (var j = 0; j < stat.data.length; j++) { + if (max != 0) { + stat.data[j] = Number(stat.data[j]) / max; + stat.std[j] = Number(stat.std[j]) / max; + } + } + return stat; +}; + +/** returns max value of a stat **/ +PlotWidget.prototype.getMaxAndMinValue = function(stat) { + var max = 0; + var min = stat.data[0]; + for (var j = 0; j < stat.data.length; j++) { + if (Number(stat.data[j]) > max) { + max = Number(stat.data[j]); + } + if (Number(stat.std[j]) > max) { + max = Number(stat.std[j]); + } + if (Number(stat.data[j]) < min) { + min = Number(stat.data[j]); + } + } + return { + max : Number(max), + min : Number(min) + }; +}; + +PlotWidget.prototype._renderDygraph = function(parsed, colors, labels) { + this.dygraphObject = new StdDevDyGraph(this.id, { + width : this.width - 20, + height : this.height - 40, + xlabel : "", + }); + + this.dygraphObject.draw(parsed, colors, labels); + +}; + +PlotWidget.prototype.getPanel = function() { + this.panel = Ext.create('Ext.panel.Panel', { + width : this.width, + height : this.height, + margin : this.margin, + tbar : this.getMenu(), + items : [ { + html : "", + id : this.id, + width : this.width, + height : this.height, + padding : 10, + margin : "0 0 0 -30", + border : 0 + } ] + }); + + return this.panel; +}; + +PlotWidget.prototype.getPoint = function(y, error) { + var minus = y - error; + var max = y + error; + + if (this.linear) { + return [ Math.abs(minus), y, Math.abs(max) ]; + } + if ((minus != 0) && (max != 0)) { + return [ Math.log(Math.abs(minus)), Math.log(y), Math.log(Math.abs(max)) ]; + } else { + return [ Math.log(y), Math.log(y), Math.log(y) ]; + } + +}; + +PlotWidget.prototype.getDataPlot = function(frames, subtractions, models, fits, rbms) { + var files = []; + var labels = [ "Intensity" ]; + if (frames != null) { + for (var i = 0; i < frames.length; i++) { + files.push(frames[i].data); + labels.push(frames[i].fileName); + } + } + function splitData(data, column, errorColumn, name){ + var result = [] + for (var j = 0; j < data.length; j++) { + console.log(data[j][column]); + result.push([j,data[j][column],data[j][errorColumn]]);//[0, data[i][column],0]]); + } + files.push(result); + labels.push(name); + } + + if (subtractions != null) { + for (var i = 0; i < subtractions.length; i++) { + /** For subtraction **/ + files.push(subtractions[i].subtraction.data); + labels.push(subtractions[i].subtraction.fileName); + /** For sample average **/ +// files.push(subtractions[i].sampleAvg.data); +// labels.push(subtractions[i].sampleAvg.fileName); + /** For buffer average **/ +// files.push(subtractions[i].bufferAvg.data); +// labels.push(subtractions[i].bufferAvg.fileName); + } + } + + if (models != null) { + for (var i = 0; i < models.length; i++) { + for ( var key in models[i]) { + splitData(models[i][key].fir.data, 1, 2, "Intensity"); + splitData(models[i][key].fir.data, 3, 3, "Fit"); + } + } + } + + if (fits != null) { + for (var i = 0; i < fits.length; i++) { + for ( var key in fits[i]) { + + /** adding fit file to be plotted **/ + if (fits[i][key].fit.data[0].length == 3){ + splitData(fits[i][key].fit.data, 1, 1, "Intensity"); + splitData(fits[i][key].fit.data, 2, 2, "Fit"); + } + + /** s, Iexp(s), err, Ifit(s). **/ + if (fits[i][key].fit.data[0].length == 4){ + splitData(fits[i][key].fit.data, 1, 2, "Intensity"); + splitData(fits[i][key].fit.data, 3, 3, "Fit"); + } + + if (fits[i][key].fit.data[0].length == 5){ + /** X Intensity Fit Error Residues **/ + + splitData(fits[i][key].fit.data, 1, 3, "Intensity"); + splitData(fits[i][key].fit.data, 2, 2, "Fit"); + } + } + } + } + + var dataPoints = []; + if (files.length > 0) { + for (var i = 0; i < files[0].length; i++) { + dataPoints.push([ files[0][i][0], this.getPoint(files[0][i][1], files[0][i][2]) ]); + } + if (files.length > 1) { + for (var i = 1; i < files.length; i++) { + for (var j = 0; j < dataPoints.length; j++) { + if (files[i][j] != null){ + dataPoints[j].push(this.getPoint(files[i][j][1], files[i][j][2])); + } + else{ + dataPoints[j].push([0,0,0]); + } + } + } + } + } + + return { + dataPoints : dataPoints, + labels : labels + } +}; + +PlotWidget.prototype.refresh = function(frames, subtractions, models, fits, rbms, colors) { + + var _this = this; + this.panel.setLoading("Reading Files"); + + var dataAdapter = new BiosaxsDataAdapter(); + dataAdapter.onSuccess.attach(function(sender, data) { + _this.panel.setLoading("Rendering"); + var parsed = _this.getDataPlot(data.frames, data.subtractions, data.models, data.fits, rbms); + _this._renderDygraph(parsed.dataPoints, colors, parsed.labels); + _this.panel.setLoading(false); + }); + dataAdapter.onError.attach(function(sender, data) { + _this.panel.setLoading(false); + }); + dataAdapter.getDataPlot(frames, subtractions, models, fits, rbms); +}; + +PlotWidget.prototype.input = function() { + return DATADOC.getHPLCData(); +}; + + +/** + * Fit form + * + * @witdh + * @height + */ +function FitForm(args) { + this.id = BUI.id(); + this.width = null; + this.height = null; + + if (args != null) { + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + } + + var _this = this; + + /** Widgets **/ + this.fitGrid = new FitStructureToExperimentDataGrid({ + width : null, + height : 200 + }); + + this.fitGrid.onSelected.attach(function(sender, fits) { + var modelsIdList = []; + for ( var i in fits) { + modelsIdList.push(fits[i].fitStructureToExperimentalDataId); + } + _this._renderPlot(_this.subtractions[0].subtractionId, modelsIdList); +// var adapter = new BiosaxsDataAdapter(); +// adapter.onSuccess.attach(function(sender, data) { +// +// }); +// adapter.getScatteringCurveByFrameIdsList([], [], [], ids); + }); + + + /** Dygraph Widget that plots fir files**/ + this.plotWidget = new PlotWidget({ + width : 745, + height : 300, + margin : "10 0 10 10" + }); +} + +FitForm.prototype._renderPlot = function(subtractionId, modelsIdList) { + /** Trying to plot tje subtraction and the models **/ + try { + var colors = [ "#669900", "#0000FF" ]; + + this.plotWidget.refresh([], [ ], [], modelsIdList, [], colors); + } catch (e) { + console.log(e); + } +}; + +FitForm.prototype._getItems = function() { + var _this = this; + return [ { + xtype : 'label', + forId : 'myFieldId', + text : 'INLINE HELP: To be updated', + margin : '15 0 20 10', + cls : "inline-help" + }, this.fitGrid.getPanel(), this.plotWidget.getPanel() ] + +}; + +FitForm.prototype._getButtons = function() { + return []; +}; + +FitForm.prototype.getPanel = function() { + var _this = this; + this.panel = Ext.create('Ext.form.Panel', { + width : this.width, + height : this.height, + margin : 10, + border : 1, + defaultType : 'textfield', + items : this._getItems(), + buttons : this._getButtons(), + listeners : { + afterrender : function() { + _this._populate(); + + } + } + }); + return this.panel; +}; + +/** Populates could be call when the DOM is not filled yet **/ +FitForm.prototype._populate = function() { +}; + +/** It populates the form * */ +FitForm.prototype.refresh = function(subtractions) { + this.subtractions = subtractions; + this.fitGrid.refresh(subtractions); +}; + +FitForm.prototype.input = function() { + return {}; +}; + +/** It populates the form **/ +FitForm.prototype.test = function(targetId) { + var macromoleculeForm = new FitForm(); + var panel = macromoleculeForm.getPanel(); + panel.render(targetId); +}; + +/** + * Example form + * + * @witdh + * @height + */ +function RigidBodyModelingResultForm(args) { + this.id = BUI.id(); + this.width = null; + this.height = null; + + if (args != null) { + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + } + + var _this = this; + /** Widgets **/ + this.rigidModelGrid = new RigidModelGrid({ + width : null, + height : 200 + }); + + this.rigidModelGrid.onSelected.attach(function(sender, fits){ + var ids = []; + for ( var i in fits) { + ids.push(fits[i].fitStructureToExperimentalDataId); + } + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data){ +// debugger + + }); + + adapter.getScatteringCurveByFrameIdsList([], [], [], ids); + }); + +} + +RigidBodyModelingResultForm.prototype._getItems = function() { + var _this = this; + return [ { + xtype : 'label', + forId : 'myFieldId', + text : 'INLINE HELP: To be updated', + margin : '15 0 20 10', + cls : "inline-help" + }, this.rigidModelGrid.getPanel() ] + +}; + +RigidBodyModelingResultForm.prototype._getButtons = function() { + return []; +}; + +RigidBodyModelingResultForm.prototype.getPanel = function() { + var _this = this; + this.panel = Ext.create('Ext.form.Panel', { + width : this.width, + height : this.height, + margin : 10, + border : 1, + defaultType : 'textfield', + items : this._getItems(), + buttons : this._getButtons(), + listeners : { + afterrender : function() { + _this._populate(); + + } + } + }); + return this.panel; +}; + +/** Populates could be call when the DOM is not filled yet **/ +RigidBodyModelingResultForm.prototype._populate = function() { +}; + +/** It populates the form * */ +RigidBodyModelingResultForm.prototype.refresh = function(subtractions) { + this.rigidModelGrid.refresh(subtractions); +}; + +RigidBodyModelingResultForm.prototype.input = function() { + return {}; +}; + +/** It populates the form **/ +RigidBodyModelingResultForm.prototype.test = function(targetId) { + var macromoleculeForm = new RigidBodyModelingResultForm(); + var panel = macromoleculeForm.getPanel(); + panel.render(targetId); +}; + +/** + * Example form + * + * @witdh + * @height + */ +function SuperpositionForm(args) { + this.id = BUI.id(); + this.width = null; + this.height = null; + + if (args != null) { + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + } + + var _this = this; + + /** Widgets **/ + this.superpositionGrid = new SuperpositionGrid({ + width : null, + height : 200 + }); + + this.superpositionGrid.onSelected.attach(function(sender, superpositions) { + var ids = []; + for ( var i in superpositions) { + ids.push(superpositions[i].superpositionId); + } +// _this._renderAbinitio(ids); +// _this.aprioriPDBViewer.refresh(); + _this._renderAligned(ids); + // getAlignedPDBContentBySuperpositionList + }); + + /** PDB viewer **/ +// this.abinitioPDBViewer = new PDBViewer({ +// width : 860 / 2, +// height : 300 / 2, +// margin : 0 +// }); +// +// /** PDB viewer **/ +// this.aprioriPDBViewer = new StructurePDBViewer({ +// width : 860 / 2, +// height : 300 / 2, +// margin : 0 +// }); + + this.alignedPDBViewer = new AlignedSuperpositionPDBViewer({ + width : 860 , + height : 300 + }); + +} + +SuperpositionForm.prototype._renderAligned = function(modelsIdList) { + /** Trying to plot the PDB file **/ + try { + this.alignedPDBViewer.refresh(modelsIdList); + } catch (e) { + console.log(e); + } +}; + +SuperpositionForm.prototype._renderAbinitio = function(modelsIdList) { + /** Trying to plot the PDB file **/ + try { + var viz = []; + for (var i = 0; i < modelsIdList.length; i++) { + viz.push({ + modelId : modelsIdList[i], + color : "0xFF6600", + opacity : 0.8 + }); + } + this.abinitioPDBViewer.refresh(viz); + } catch (e) { + console.log(e); + } +}; + +SuperpositionForm.prototype._getItems = function() { + var _this = this; + return [ { + xtype : 'label', + forId : 'myFieldId', + text : 'INLINE HELP: To be updated', + margin : '15 0 20 10', + cls : "inline-help" + }, this.superpositionGrid.getPanel(), { + xtype : 'container', + layout : 'hbox', + items : [ +// { +// xtype : 'container', +// layout : 'vbox', +// items : [ this.abinitioPDBViewer.getPanel(), this.aprioriPDBViewer.getPanel() +// +// ] +// }, + + this.alignedPDBViewer.getPanel() ] + } ] + +}; + +SuperpositionForm.prototype._getButtons = function() { + return []; +}; + +SuperpositionForm.prototype.getPanel = function() { + var _this = this; + this.panel = Ext.create('Ext.form.Panel', { + width : this.width, + height : this.height, + margin : 10, + border : 1, + defaultType : 'textfield', + items : this._getItems(), + buttons : this._getButtons(), + listeners : { + afterrender : function() { + _this._populate(); + + } + } + }); + return this.panel; +}; + +/** Populates could be call when the DOM is not filled yet **/ +SuperpositionForm.prototype._populate = function() { +}; + +/** It populates the form * */ +SuperpositionForm.prototype.refresh = function(subtractions) { + this.subtractions = subtractions; + this.superpositionGrid.refresh(subtractions); +}; + +SuperpositionForm.prototype.input = function() { + return {}; +}; + +/** It populates the form **/ +SuperpositionForm.prototype.test = function(targetId) { + var macromoleculeForm = new SuperpositionForm(); + var panel = macromoleculeForm.getPanel(); + panel.render(targetId); +}; + +/** + * Example form + * + * @witdh + * @height + */ +function AssemblyForm(args) { + this.id = BUI.id(); + this.width = 700; + this.height = 500; + + if (args != null) { + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + } + + this.molarityGrid = new MolarityGrid({height : this.height - 50}); +} + +AssemblyForm.prototype._getItems = function() { + return [ { + xtype : 'label', + forId : 'myFieldId', + text : 'List of previously defined macromolecules present in the assembly. This information will be used for additional cross-checks where possible', + margin : '15 0 20 10', + cls : "inline-help" + }, this.molarityGrid.getPanel() ]; +}; + +AssemblyForm.prototype._getButtons = function() { + return []; +}; + +AssemblyForm.prototype.getPanel = function() { + this.panel = Ext.create('Ext.form.Panel', { + width : this.width, + height : this.height, + margin : 10, + border : 0, + defaultType : 'textfield', + items : this._getItems(), + buttons : this._getButtons() + }); + return this.panel; +}; + + +/** It populates the form **/ +AssemblyForm.prototype.refresh = function(macromolecule) { + this.macromolecule = macromolecule; + this.molarityGrid.refresh(macromolecule); +}; + +AssemblyForm.prototype.input = function() { + return {}; +}; + + +AssemblyForm.prototype.test = function(targetId) { + var assemblyForm = new AssemblyForm(); + + var panel = assemblyForm.getPanel(); + panel.render(targetId); +}; +/** + * Edit the information of a buffer + * + * #onSaved + * #onRemoveAdditive + */ +function BufferForm() { var _this = this; - /** Widgets **/ - this.plotWidget = new PlotWidget({ - width : 650, - height : 490 + this.additiveGrid = new AdditiveGrid(); + this.additiveGrid.onRemoveButtonClicked.attach(function(sender, args) { + _this.onRemoveAdditive.notify(args); }); - /** Selected frames to be displayed **/ - this.selectedItems = { - frames : [], - averages : [], - subtractions : [] - }; - + this.onSaved = new Event(this); + this.onRemoveAdditive = new Event(this); } -DataReductionForm.prototype._parseSelectedItemsToIds = function(selectedArray) { - var ids = []; - if (selectedArray != null) { - for (var i = 0; i < selectedArray.length; i++) { - ids.push(selectedArray[i].id); - } - } - return ids; -}; - -DataReductionForm.prototype.onSelectionChanged = function(columnName, selected) { - if (selected != null) { - if (columnName == "Frames") { - this.selectedItems.frames = selected; - this.selectedItems.subtractions = []; - } - if (columnName == "Averages") { - this.selectedItems.averages = selected; - } - if (columnName == "Subtractions") { - this.selectedItems.frames = []; - this.selectedItems.subtractions = selected; - } - } - this.plotWidget.refresh(this._parseSelectedItemsToIds(this.selectedItems.frames), this._parseSelectedItemsToIds(this.selectedItems.subtractions)); -}; - -DataReductionForm.prototype._getFramesExtPanel = function(store, columnName, height) { - var _this = this; - - var selModel = Ext.create('Ext.selection.RowModel', { - allowDeselect : true, - mode : 'MULTI', - listeners : { - selectionchange : function(sm, selections) { - var selected = []; - for (var i = 0; i < selections.length; i++) { - selected.push(selections[i].raw); - } - _this.onSelectionChanged(columnName, selected); - } - } - }); - - return Ext.create('Ext.grid.Panel', { - store : store, - margin : 10, - height : height, - width : 200, - selModel : selModel, - columns : [ { - text : columnName, - dataIndex : 'fileName', - flex : 1 - } ], - viewConfig : { - } - }); +BufferForm.prototype.getBuffer = function() { + this.buffer.name = Ext.getCmp("buffer_name").getValue(); + this.buffer.acronym = Ext.getCmp("buffer_acronym").getValue(); + this.buffer.comments = Ext.getCmp("buffer_comments").getValue(); + this.buffer.ph = Ext.getCmp("buffer_ph").getValue(); + this.buffer.composition = Ext.getCmp("buffer_composition").getValue(); + this.buffer.bufferhasadditive3VOs = this.additiveGrid.getAdditives(); + return this.buffer; }; -DataReductionForm.prototype._getFramesPanel = function() { - var fields = [ 'fileName', 'type', 'id' ]; - - this.framesStore = Ext.create('Ext.data.Store', { - fields : fields, - sorters : 'fileName' - }); - - this.averagesStore = Ext.create('Ext.data.Store', { - fields : fields - }); - - this.subtractionStore = Ext.create('Ext.data.Store', { - fields : fields - }); - - var gridFrames = this._getFramesExtPanel(this.framesStore, "Frames", 375); - var gridAvgs = this._getFramesExtPanel(this.averagesStore, "Averages", 125); - var subtractionAvgs = this._getFramesExtPanel(this.subtractionStore, "Subtractions", 75); - - return { - xtype : 'container', - layout : 'vbox', - items : [ gridFrames, subtractionAvgs ] - }; -}; - -DataReductionForm.prototype._getImageContainer = function(name, help) { - var html = "
" + name + "
" +BufferForm.prototype._getTopPanel = function() { return { xtype : 'container', - layout : 'vbox', + layout : 'hbox', + border : 0, + frame : true, items : [ { - html : html, - margin : "5 0 0 0", - height : 95, - width : 100 + xtype : 'container', + layout : 'hbox', + items : [ { + xtype : 'container', + flex : 1, + border : false, + layout : 'anchor', + defaultType : 'textfield', + items : [ { + xtype : 'requiredtext', + id : 'buffer_name', + fieldLabel : 'Name', + name : 'name', + width : '200px', + value : this.buffer.name + }, { + xtype : 'requiredtext', + id : 'buffer_acronym', + fieldLabel : 'Acronym', + name : 'acronym', + width : '200px', + value : this.buffer.acronym + } ] + } ] }, { - xtype : 'label', - forId : 'myFieldId', - text : help, - margin : '5 0 0 0', - cls : "inline-help" + xtype : 'container', + flex : 1, + layout : 'anchor', + defaultType : 'textfield', + margin : '0 0 0 10', + items : [ { + id : 'buffer_ph', + fieldLabel : 'pH', + name : 'ph', + value : this.buffer.ph, + xtype : 'numberfield', + width : 200, + minValue : 0, + maxValue : 15 + }, { + xtype : 'requiredtext', + id : 'buffer_composition', + fieldLabel : 'Composition', + name : 'composition', + width : 200, + value : this.buffer.composition + } ] } ] - } + }; }; -DataReductionForm.prototype._getItems = function() { - var _this = this; - return [ { +BufferForm.prototype.getPanel = function(buffer) { + this.buffer = buffer; + this.panel = Ext.createWidget({ xtype : 'container', - layout : 'hbox', - items : [ - this._getFramesPanel(), - this.plotWidget.getPanel(), - { - xtype : 'panel', - width : 110, - frame : true, - margin : "10 5 5 5", - border : 0, - layout : 'vbox', - items : [ this._getImageContainer("scattering", "Scattering"), this._getImageContainer("guinier", "Guinier Region"), - this._getImageContainer("kratky", "Kratky Plot"), this._getImageContainer("gnom", "P(r) distribution") ] - } ] - } ] -}; - -DataReductionForm.prototype._getButtons = function() { - return []; -}; + layout : 'vbox', + style : { + padding : '10px' + }, + fieldDefaults : { + labelAlign : 'left', + labelWidth : 50 -DataReductionForm.prototype.getPanel = function() { - var _this = this; - this.panel = Ext.create('Ext.form.Panel', { - width : this.width, - height : this.height, - border : 0, - items : this._getItems(), - buttons : this._getButtons(), - listeners : { - afterrender : function() { - _this._populate(); - } - } + }, + items : [ this._getTopPanel(), { + id : 'buffer_comments', + xtype : 'textareafield', + name : 'comments', + fieldLabel : 'Comments', + width : '100%', + value : buffer.comments + }, this.additiveGrid.getPanel(buffer) ] }); return this.panel; }; -/** Populates could be call when the DOM is not filled yet **/ -DataReductionForm.prototype._populate = function() { -}; - -/** It populates the form * */ -DataReductionForm.prototype.refresh = function(subtractions) { - if (subtractions != null) { - for (var i = 0; i < subtractions.length; i++) { - /** Loading frame grids **/ - var subtraction = subtractions[i]; - var averages = [ { - fileName : BUI.getFileName(subtraction.bufferAverageFilePath), - type : 'bufferAvg', - id : subtraction.subtractionId - }, { - fileName : BUI.getFileName(subtraction.sampleAverageFilePath), - type : 'sampleAvg', - id : subtraction.subtractionId - } - - ]; - this.averagesStore.loadData(averages, true); - this.subtractionStore.loadData([ { - fileName : BUI.getFileName(subtraction.substractedFilePath), - type : 'SUBTRACTION', - id : subtraction.subtractionId - } ], true); - - var frames = []; - /** Buffers **/ - if (subtraction.bufferOneDimensionalFiles != null) { - if (subtraction.bufferOneDimensionalFiles.frametolist3VOs != null) { - for (var j = 0; j < subtraction.bufferOneDimensionalFiles.frametolist3VOs.length; j++) { - var frametolist3VO = subtraction.bufferOneDimensionalFiles.frametolist3VOs[j]; - if (frametolist3VO.frame3VO != null) { - frames.push({ - fileName : BUI.getFileName(frametolist3VO.frame3VO.filePath), - type : 'BUFFER', - id : frametolist3VO.frame3VO.frameId - }); - } - } - } - } - /** Samples **/ - if (subtraction.sampleOneDimensionalFiles != null) { - if (subtraction.sampleOneDimensionalFiles.frametolist3VOs != null) { - for (var j = 0; j < subtraction.sampleOneDimensionalFiles.frametolist3VOs.length; j++) { - var frametolist3VO = subtraction.sampleOneDimensionalFiles.frametolist3VOs[j]; - if (frametolist3VO.frame3VO != null) { - frames.push({ - fileName : BUI.getFileName(frametolist3VO.frame3VO.filePath), - type : 'SAMPLE', - id : frametolist3VO.frame3VO.frameId - }); - } - } - } - } - - this.framesStore.loadData(frames, true); - - /** Loading images **/ - this._displayImage("scattering", subtraction.subtractionId); - this._displayImage("kratky", subtraction.subtractionId); - this._displayImage("guinier", subtraction.subtractionId); - this._displayImage("gnom", subtraction.subtractionId); +BufferForm.prototype.input = function() { + return { + buffer : { + "bufferId" : 422, + "proposalId" : 10, + "safetyLevelId" : null, + "name" : "B1", + "acronym" : "B1", + "ph" : null, + "composition" : null, + "bufferhasadditive3VOs" : [], + "comments" : null } - } -}; - -DataReductionForm.prototype._displayImage = function(name, subtractionId) { - var url = BUI.getURL() + '&type=' + name + '&subtractionId=' + subtractionId; - var event = "OnClick= window.open('" + url + "')"; - document.getElementById(this.id + "_" + name).innerHTML = ''; -}; - -DataReductionForm.prototype.input = function() { - return {}; + }; }; -/** It populates the form **/ -DataReductionForm.prototype.test = function(targetId) { - var macromoleculeForm = new DataReductionForm(); - var panel = macromoleculeForm.getPanel(); +BufferForm.prototype.test = function(targetId) { + var bufferForm = new BufferForm(); + var panel = bufferForm.getPanel(bufferForm.input().buffer); panel.render(targetId); }; - -function PlotWidget(args) { - this.width = 600; - this.height = 600; - this.id = BUI.id(); - - this.linear = false; - - this.margin = "10 0 0 0"; - /** for each stat the max and minimum value when it is scaled in order to show correctly in the legend **/ - this.ranges = {}; + +/** + * @showTitle + * + * #onSaved + * #onAddPlates + * #onRemovePlates + **/ +function CaseForm(args) { + this.width = 700; + this.showTitle = true; if (args != null) { - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; - } - if (args.margin != null) { - this.margin = args.margin; + if (args.showTitle != null) { + this.showTitle = args.showTitle; } } -} - -PlotWidget.prototype.getMenu = function() { var _this = this; - /** Actions buttons **/ - var actions = []; - actions.push("->"); - actions.push({ - text : "Export as Image", - scope : this, - icon : '../images/save.gif', - handler : function(item, pressed) { - var largeImage = document.createElement("img"); - largeImage.style.display = 'block'; - largeImage.style.width = 200 + "px"; - largeImage.style.height = 200 + "px"; - largeImage.setAttribute('src', Dygraph.Export.asCanvas(this.dygraphObject.dygraph).toDataURL()); - window.open(Dygraph.Export.asCanvas(this.dygraphObject.dygraph).toDataURL(), 'Image', ''); + this.stockSolutionGrid = new StockSolutionGrid({ + width : this.width - 10, + minHeight : 300, + height : 300, + tbar : true, + showTitle : true, + isPackedVisible : false, + btnAddExisting : true, + btnRemoveVisible : false, + btnUnpackVisible : true + }); + + /** When selecting existing stock solutions **/ + this.stockSolutionGrid.onStockSolutionSelected.attach(function(sender, stockSolutions) { + if (stockSolutions != null) { + for ( var i = 0; i < stockSolutions.length; i++) { + _this.saveStockSolution(stockSolutions[i]); + } } }); - return actions; -}; + /** it can be because it has been added a new one or removed **/ + this.stockSolutionGrid.onProposalChanged.attach(function(sender, stockSolution) { + if (stockSolution != null) { + _this.saveStockSolution(stockSolution); + } else { + BIOSAXS.proposal.onInitialized.attach(function() { + _this.stockSolutionGrid.refresh(BIOSAXS.proposal.getStockSolutionsByDewarId(_this.dewar.dewarId)); -/** Looks for the maximum value and then divide everything but that value **/ -PlotWidget.prototype.scaledData = function(data) { - for (var i = 0; i < data.length; i++) { - var values = this.getMaxAndMinValue(data[i]); - data[i] = this.divideValuesByMax(data[i], values.max); - this.ranges[data[i].label] = values; - } - return data; -}; + _this.stockSolutionGrid.grid.setLoading(false); + }); + BIOSAXS.proposal.init(); -/** Given a stat float[] and a max number it will divide each value by max **/ -PlotWidget.prototype.divideValuesByMax = function(stat, max) { - for (var j = 0; j < stat.data.length; j++) { - if (max != 0) { - stat.data[j] = Number(stat.data[j]) / max; - stat.std[j] = Number(stat.std[j]) / max; } - } - return stat; -}; -/** returns max value of a stat **/ -PlotWidget.prototype.getMaxAndMinValue = function(stat) { - var max = 0; - var min = stat.data[0]; - for (var j = 0; j < stat.data.length; j++) { - if (Number(stat.data[j]) > max) { - max = Number(stat.data[j]); - } - if (Number(stat.std[j]) > max) { - max = Number(stat.std[j]); - } - if (Number(stat.data[j]) < min) { - min = Number(stat.data[j]); - } - } - return { - max : Number(max), - min : Number(min) - }; -}; - -PlotWidget.prototype._renderDygraph = function(parsed, colors, labels) { - this.dygraphObject = new StdDevDyGraph(this.id, { - width : this.width - 20, - height : this.height - 40, - xlabel : "", }); - this.dygraphObject.draw(parsed, colors, labels); + this.onSaved = new Event(this); + this.onAddPlates = new Event(this); + this.onRemovePlates = new Event(this); +} +CaseForm.prototype.saveStockSolution = function(stockSolution) { + var _this = this; + var adapter = new BiosaxsDataAdapter(); + this.stockSolutionGrid.grid.setLoading("ISPyB: setting case to Stock solution"); + adapter.onSuccess.attach(function(sender, stockSolution) { + BIOSAXS.proposal.onInitialized.attach(function() { + _this.stockSolutionGrid.refresh(BIOSAXS.proposal.getStockSolutionsByDewarId(_this.dewar.dewarId)); + _this.stockSolutionGrid.grid.setLoading(false); + }); + BIOSAXS.proposal.init(); + }); + adapter.onError.attach(function(sender, data) { + _this.stockSolutionGrid.grid.setLoading(false); + BUI.showError(data); + }); + stockSolution.boxId = _this.dewar.dewarId; + adapter.saveStockSolution(stockSolution); }; -PlotWidget.prototype.getPanel = function() { - this.panel = Ext.create('Ext.panel.Panel', { - width : this.width, - height : this.height, - margin : this.margin, - tbar : this.getMenu(), - items : [ { - html : "", - id : this.id, - width : this.width, - height : this.height, - padding : 10, - margin : "0 0 0 -30", - border : 0 - } ] +CaseForm.prototype.fillStores = function() { + var _this = this; + this.panel.setLoading("Loading Labcontacts from database"); + + var proposal = BUI.getProposal(); + proposal.onDataRetrieved.attach(function(sender, data) { + _this.labContactForSendingStore.loadData(data, false); + _this.labContactForReturnStore.loadData(data, false); + _this.panel.setLoading(false); }); + proposal.getLabContactsByProposalId(); - return this.panel; }; -PlotWidget.prototype.getPoint = function(y, error) { - var minus = y - error; - var max = y + error; - - if (this.linear) { - return [ Math.abs(minus), y, Math.abs(max) ]; - } - if ((minus != 0) && (max != 0)) { - return [ Math.log(Math.abs(minus)), Math.log(y), Math.log(Math.abs(max)) ]; - } else { - return [ Math.log(y), Math.log(y), Math.log(y) ]; - } - +CaseForm.prototype.refresh = function(dewar) { + this.setDewar(dewar); + this.stockSolutionGrid.refresh(BIOSAXS.proposal.getStockSolutionsByDewarId(dewar.dewarId)); }; -PlotWidget.prototype.getDataPlot = function(frames, subtractions, models, fits, rbms) { - var files = []; - var labels = [ "Intensity" ]; - if (frames != null) { - for (var i = 0; i < frames.length; i++) { - files.push(frames[i].data); - labels.push(frames[i].fileName); - } - } - function splitData(data, column, errorColumn, name){ - var result = [] - for (var j = 0; j < data.length; j++) { - console.log(data[j][column]); - result.push([j,data[j][column],data[j][errorColumn]]);//[0, data[i][column],0]]); - } - files.push(result); - labels.push(name); - } - - if (subtractions != null) { - for (var i = 0; i < subtractions.length; i++) { - /** For subtraction **/ - files.push(subtractions[i].subtraction.data); - labels.push(subtractions[i].subtraction.fileName); - /** For sample average **/ -// files.push(subtractions[i].sampleAvg.data); -// labels.push(subtractions[i].sampleAvg.fileName); - /** For buffer average **/ -// files.push(subtractions[i].bufferAvg.data); -// labels.push(subtractions[i].bufferAvg.fileName); - } - } - - if (models != null) { - for (var i = 0; i < models.length; i++) { - for ( var key in models[i]) { - splitData(models[i][key].fir.data, 1, 2, "Intensity"); - splitData(models[i][key].fir.data, 3, 3, "Fit"); - } - } - } - - if (fits != null) { - for (var i = 0; i < fits.length; i++) { - for ( var key in fits[i]) { - - /** adding fit file to be plotted **/ - if (fits[i][key].fit.data[0].length == 3){ - splitData(fits[i][key].fit.data, 1, 1, "Intensity"); - splitData(fits[i][key].fit.data, 2, 2, "Fit"); - } - - /** s, Iexp(s), err, Ifit(s). **/ - if (fits[i][key].fit.data[0].length == 4){ - splitData(fits[i][key].fit.data, 1, 2, "Intensity"); - splitData(fits[i][key].fit.data, 3, 3, "Fit"); - } - - if (fits[i][key].fit.data[0].length == 5){ - /** X Intensity Fit Error Residues **/ - - splitData(fits[i][key].fit.data, 1, 3, "Intensity"); - splitData(fits[i][key].fit.data, 2, 2, "Fit"); - } - } - } - } - - var dataPoints = []; - if (files.length > 0) { - for (var i = 0; i < files[0].length; i++) { - dataPoints.push([ files[0][i][0], this.getPoint(files[0][i][1], files[0][i][2]) ]); - } - if (files.length > 1) { - for (var i = 1; i < files.length; i++) { - for (var j = 0; j < dataPoints.length; j++) { - if (files[i][j] != null){ - dataPoints[j].push(this.getPoint(files[i][j][1], files[i][j][2])); - } - else{ - dataPoints[j].push([0,0,0]); - } - } - } - } - } +CaseForm.prototype.getDewar = function() { + this.dewar.code = Ext.getCmp("dewar_code").getValue(); + this.dewar.comments = Ext.getCmp("dewar_comments").getValue(); + this.dewar.trackingNumberFromSynchrotron = Ext.getCmp("dewar_trackingNumberFromSynchrotron").getValue(); + this.dewar.trackingNumberToSynchrotron = Ext.getCmp("dewar_trackingNumberToSynchrotron").getValue(); + this.dewar.transportValue = Ext.getCmp("dewar_transportValue").getValue(); + this.dewar.storageLocation = Ext.getCmp("dewar_storageLocation").getValue(); + this.dewar.firstExperimentId = this.macromoleculeCombo.getValue(); + return this.dewar; +}; - return { - dataPoints : dataPoints, - labels : labels +CaseForm.prototype.setDewar = function(dewar) { + this.dewar = dewar; + Ext.getCmp("dewar_code").setValue(this.dewar.code); + Ext.getCmp("dewar_dewarStatus").setText(new String(this.dewar.dewarStatus).toUpperCase()); + Ext.getCmp("dewar_comments").setValue(this.dewar.comments); + Ext.getCmp("dewar_trackingNumberFromSynchrotron").setValue(this.dewar.trackingNumberFromSynchrotron); + Ext.getCmp("dewar_trackingNumberToSynchrotron").setValue(this.dewar.trackingNumberToSynchrotron); + Ext.getCmp("dewar_transportValue").setValue(this.dewar.transportValue); + Ext.getCmp("dewar_storageLocation").setValue(this.dewar.storageLocation); + if (dewar.sessionVO != null) { + this.macromoleculeCombo.setValue(dewar.sessionVO.sessionId); } }; -PlotWidget.prototype.refresh = function(frames, subtractions, models, fits, rbms, colors) { - - var _this = this; - this.panel.setLoading("Reading Files"); - - var dataAdapter = new BiosaxsDataAdapter(); - dataAdapter.onSuccess.attach(function(sender, data) { - _this.panel.setLoading("Rendering"); - var parsed = _this.getDataPlot(data.frames, data.subtractions, data.models, data.fits, rbms); - _this._renderDygraph(parsed.dataPoints, colors, parsed.labels); - _this.panel.setLoading(false); - }); - dataAdapter.onError.attach(function(sender, data) { - _this.panel.setLoading(false); +CaseForm.prototype.getSessionCombo = function() { + this.macromoleculeCombo = BIOSAXS_COMBOMANAGER.getComboSessions(BIOSAXS.proposal.getSessions(), { + labelWidth : 100, + margin : '5 0 00 0', + width : 250 }); - dataAdapter.getDataPlot(frames, subtractions, models, fits, rbms); -}; - -PlotWidget.prototype.input = function() { - return DATADOC.getHPLCData(); + return this.macromoleculeCombo; }; - -/** - * Fit form - * - * @witdh - * @height - */ -function FitForm(args) { - this.id = BUI.id(); - this.width = null; - this.height = null; - - if (args != null) { - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; - } - } +CaseForm.prototype.getInformationPanel = function() { + if (this.panel == null) { + this.informationPanel = Ext.create('Ext.form.Panel', { + width : this.width - 10, + border : 0, + items : [ { + xtype : 'container', + margin : "2 2 2 2", + collapsible : false, + defaultType : 'textfield', + layout : 'anchor', + items : [ { + xtype : 'container', + layout : 'hbox', + items : [ { + xtype : 'requiredtext', + fieldLabel : 'Code', + allowBlank : false, + name : 'code', + id : 'dewar_code', + anchor : '50%' + }, { + xtype : 'label', + margin : '0 0 0 20', + readOnly : true, + id : 'dewar_dewarStatus', + anchor : '50%' + } ] + }, this.getSessionCombo(), { + margin : '5 0 0 0', + xtype : 'textareafield', + name : 'comments', + id : 'dewar_comments', + width : this.width - 50, + fieldLabel : 'Comments' + } ] + }, { + xtype : 'fieldset', + title : 'Courier Accounts Details for Return', + collapsible : false, + layout : 'anchor', + defaults : { + anchor : '100%' + }, + items : [ { + xtype : 'container', + layout : 'hbox', + items : [ { + xtype : 'textfield', + labelWidth : 200, + width : 280, + fieldLabel : 'Track Number From Synchrotron', + id : 'dewar_trackingNumberFromSynchrotron' + }, { + xtype : 'numberfield', + width : 190, + labelWidth : 110, + margin : '0 0 0 30', + fieldLabel : 'Transport Value', + id : 'dewar_transportValue' + } - var _this = this; - - /** Widgets **/ - this.fitGrid = new FitStructureToExperimentDataGrid({ - width : null, - height : 200 - }); + ] + }, { + xtype : 'container', + layout : 'hbox', + margin : '10 0 0 0', + items : [ - this.fitGrid.onSelected.attach(function(sender, fits) { - var modelsIdList = []; - for ( var i in fits) { - modelsIdList.push(fits[i].fitStructureToExperimentalDataId); - } - _this._renderPlot(_this.subtractions[0].subtractionId, modelsIdList); -// var adapter = new BiosaxsDataAdapter(); -// adapter.onSuccess.attach(function(sender, data) { -// -// }); -// adapter.getScatteringCurveByFrameIdsList([], [], [], ids); - }); - - - /** Dygraph Widget that plots fir files**/ - this.plotWidget = new PlotWidget({ - width : 745, - height : 300, - margin : "10 0 10 10" - }); -} + { + xtype : 'textfield', + labelWidth : 200, + width : 280, + fieldLabel : 'Track Number To Synchrotron', + id : 'dewar_trackingNumberToSynchrotron' + }, { + xtype : 'textfield', + margin : '0 0 0 30', + width : 190, + labelWidth : 110, + fieldLabel : 'Storage Location', + id : 'dewar_storageLocation' + } -FitForm.prototype._renderPlot = function(subtractionId, modelsIdList) { - /** Trying to plot tje subtraction and the models **/ - try { - var colors = [ "#669900", "#0000FF" ]; - - this.plotWidget.refresh([], [ ], [], modelsIdList, [], colors); - } catch (e) { - console.log(e); + ] + } ] + } ] + }); } -}; - -FitForm.prototype._getItems = function() { - var _this = this; - return [ { - xtype : 'label', - forId : 'myFieldId', - text : 'INLINE HELP: To be updated', - margin : '15 0 20 10', - cls : "inline-help" - }, this.fitGrid.getPanel(), this.plotWidget.getPanel() ] - -}; -FitForm.prototype._getButtons = function() { - return []; + return this.informationPanel; }; -FitForm.prototype.getPanel = function() { - var _this = this; - this.panel = Ext.create('Ext.form.Panel', { +CaseForm.prototype.getPanel = function(dewar) { + this.dewar = dewar; + this.panel = Ext.createWidget({ + xtype : 'container', + layout : 'vbox', width : this.width, - height : this.height, - margin : 10, - border : 1, - defaultType : 'textfield', - items : this._getItems(), - buttons : this._getButtons(), - listeners : { - afterrender : function() { - _this._populate(); + border : 0, + items : [ { + items : { + xtype : "container", + layout : "vbox", + margin : "5 5 5 5", + items : [ this.getInformationPanel(dewar), this.stockSolutionGrid.getPanel() ] } - } + } ] }); + + this.refresh(dewar); return this.panel; -}; -/** Populates could be call when the DOM is not filled yet **/ -FitForm.prototype._populate = function() { }; -/** It populates the form * */ -FitForm.prototype.refresh = function(subtractions) { - this.subtractions = subtractions; - this.fitGrid.refresh(subtractions); -}; +CaseForm.prototype.input = function() { + return { + dewar : { + "dewarId" : 305861, + "code" : "ESRF-TEST", + "comments" : "comments", + "storageLocation" : "FRIDGE", + "dewarStatus" : "opened", + "timeStamp" : null, + "isStorageDewar" : null, + "barCode" : "ESRF305861", + "customsValue" : null, + "transportValue" : null, + "trackingNumberToSynchrotron" : "3333", + "trackingNumberFromSynchrotron" : "224466", + "type" : "Dewar", + "sessionVO" : { + "sessionId" : 31697, + "expSessionPk" : null, + "projectCode" : null, + "startDate" : "2012 07 21", + "endDate" : "2012 07 23", + "beamlineName" : "BM29", + "scheduled" : 1, + "nbShifts" : 2, + "comments" : null, + "beamlineOperator" : "PERNOT P", + "usedFlag" : null, + "sessionTitle" : null, + "structureDeterminations" : null, + "dewarTransport" : null, + "databackupFrance" : null, + "databackupEurope" : null, + "visit_number" : null, + "operatorSiteNumber" : "14061", + "timeStamp" : "2012 04 25" + } + }, + proposal : { + "assemblies" : [], + "sessions" : [ { + "sessionId" : 31697, + "expSessionPk" : null, + "projectCode" : null, + "startDate" : "2012 07 21", + "endDate" : "2012 07 23", + "beamlineName" : "BM29", + "scheduled" : 1, + "nbShifts" : 2, + "comments" : null, + "beamlineOperator" : "PERNOT P", + "usedFlag" : null, + "sessionTitle" : null, + "structureDeterminations" : null, + "dewarTransport" : null, + "databackupFrance" : null, + "databackupEurope" : null, + "visit_number" : null, + "operatorSiteNumber" : "14061", + "timeStamp" : "2012 04 25" + } ], + "labcontacts" : [ { + "labContactId" : 787, + "personVO" : { + "personId" : 304252, + "personUUID" : null, + "familyName" : "KIM", + "givenName" : "Henry", + "title" : null, + "emailAddress" : "henry-sung.kim@ibs.fr", + "phoneNumber" : "", + "login" : "", + "passwd" : "", + "faxNumber" : "" + }, + "cardName" : "KIM-Institut de Bio", + "defaultCourrierCompany" : "22", + "courierAccount" : "", + "billingReference" : "", + "dewarAvgCustomsValue" : 0, + "dewarAvgTransportValue" : 0 + } ], + "buffers" : [ { + "bufferId" : 811, + "proposalId" : 3124, + "safetyLevelId" : null, + "name" : "EDTA", + "acronym" : "EDTA", + "ph" : null, + "composition" : "", + "bufferhasadditive3VOs" : [], + "comments" : "" + }, { + "bufferId" : 810, + "proposalId" : 3124, + "safetyLevelId" : null, + "name" : "HEPES", + "acronym" : "HEPES", + "ph" : null, + "composition" : "", + "bufferhasadditive3VOs" : [], + "comments" : "" + } ], + "shippings" : [ { + "shippingId" : 304107, + "shippingName" : "TEST", + "deliveryAgentAgentName" : null, + "deliveryAgentShippingDate" : null, + "deliveryAgentDeliveryDate" : null, + "deliveryAgentAgentCode" : null, + "deliveryAgentFlightCode" : null, + "shippingStatus" : "opened", + "timeStamp" : "2013 09 25", + "laboratoryId" : null, + "isStorageShipping" : null, + "creationDate" : "2013 09 25", + "comments" : "test", + "sendingLabContactVO" : { + "labContactId" : 787, + "personVO" : { + "personId" : 304252, + "personUUID" : null, + "familyName" : "KIM", + "givenName" : "Henry", + "title" : null, + "emailAddress" : "henry-sung.kim@ibs.fr", + "phoneNumber" : "", + "login" : "", + "passwd" : "", + "faxNumber" : "" + }, + "cardName" : "KIM-Institut de Bio", + "defaultCourrierCompany" : "22", + "courierAccount" : "", + "billingReference" : "", + "dewarAvgCustomsValue" : 0, + "dewarAvgTransportValue" : 0 + }, + "returnLabContactVO" : { + "labContactId" : 787, + "personVO" : { + "personId" : 304252, + "personUUID" : null, + "familyName" : "KIM", + "givenName" : "Henry", + "title" : null, + "emailAddress" : "henry-sung.kim@ibs.fr", + "phoneNumber" : "", + "login" : "", + "passwd" : "", + "faxNumber" : "" + }, + "cardName" : "KIM-Institut de Bio", + "defaultCourrierCompany" : "22", + "courierAccount" : "", + "billingReference" : "", + "dewarAvgCustomsValue" : 0, + "dewarAvgTransportValue" : 0 + }, + "returnCourier" : null, + "dateOfShippingToUser" : null, + "shippingType" : "DewarTracking", + "dewarVOs" : [ { + "dewarId" : 305861, + "code" : "ESRF-TEST", + "comments" : "comments", + "storageLocation" : "FRIDGE", + "dewarStatus" : "opened", + "timeStamp" : null, + "isStorageDewar" : null, + "barCode" : "ESRF305861", + "customsValue" : null, + "transportValue" : null, + "trackingNumberToSynchrotron" : "3333", + "trackingNumberFromSynchrotron" : "224466", + "type" : "Dewar", + "sessionVO" : { + "sessionId" : 31697, + "expSessionPk" : null, + "projectCode" : null, + "startDate" : "2012 07 21", + "endDate" : "2012 07 23", + "beamlineName" : "BM29", + "scheduled" : 1, + "nbShifts" : 2, + "comments" : null, + "beamlineOperator" : "PERNOT P", + "usedFlag" : null, + "sessionTitle" : null, + "structureDeterminations" : null, + "dewarTransport" : null, + "databackupFrance" : null, + "databackupEurope" : null, + "visit_number" : null, + "operatorSiteNumber" : "14061", + "timeStamp" : "2012 04 25" + } + } ] + } ], + "macromolecules" : [ { + "macromoleculeId" : 5933, + "safetylevelId" : null, + "proposalId" : 3124, + "name" : "A", + "acronym" : "A", + "molecularMass" : "", + "extintionCoefficient" : "", + "sequence" : null, + "creationDate" : null, + "comments" : "", + "macromoleculeregion3VOs" : [], + "stoichiometry3VOsForHostMacromoleculeId" : [], + "structure3VOs" : [] + } ], + "stockSolutions" : [ { + "stockSolutionId" : 6, + "proposalId" : 3124, + "macromoleculeId" : 5933, + "bufferId" : 811, + "instructionSet3VO" : null, + "boxId" : 305861, + "storageTemperature" : "20", + "volume" : "300", + "concentration" : "1.2", + "comments" : "Buffer EDTA with A", + "name" : "A_EDTA_1.2", + "samples" : [] + } ] + } -FitForm.prototype.input = function() { - return {}; + }; }; -/** It populates the form **/ -FitForm.prototype.test = function(targetId) { - var macromoleculeForm = new FitForm(); - var panel = macromoleculeForm.getPanel(); - panel.render(targetId); -}; - -/** - * Example form - * - * @witdh - * @height - */ -function RigidBodyModelingResultForm(args) { +CaseForm.prototype.test = function(targetId) { + var caseForm = new CaseForm(); + BIOSAXS.proposal = new Proposal(caseForm.input().proposal); + var panel = caseForm.getPanel(caseForm.input().dewar); + panel.render(targetId); +}; + +/** + * Example form + * + * @witdh + * @height + */ +function ExampleForm(args) { + this.id = BUI.id(); + this.width = 700; + this.height = 500; + + if (args != null) { + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + } +} + +ExampleForm.prototype._getItems = function() { + return [{ + fieldLabel : 'First Name', + name : 'first', + allowBlank : false + }, { + fieldLabel : 'Last Name', + name : 'last', + allowBlank : false + } ]; +}; + +ExampleForm.prototype._getItems = function() { + return [ ]; +}; + +ExampleForm.prototype._getButtons = function() { + return [ ]; +}; + +ExampleForm.prototype.getPanel = function() { + this.panel = Ext.create('Ext.form.Panel', { + width : this.width, + height : this.height, + margin : 10, + border : 1, + defaultType : 'textfield', + items : this._getItems(), + buttons : this._getButtons() + }); + return this.panel; +}; + +/** It populates the form **/ +ExampleForm.prototype.refresh = function(macromolecule) { +}; + +function ExperimentForm(args) { this.id = BUI.id(); - this.width = null; - this.height = null; if (args != null) { - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; - } } - var _this = this; - /** Widgets **/ - this.rigidModelGrid = new RigidModelGrid({ - width : null, - height : 200 + this.onSaved = new Event(this); +} + +ExperimentForm.prototype._getItems = function(experiment) { + this.experiment = experiment; + var typeCombo = Ext.create('Ext.form.ComboBox', { + id : this.id + 'type', + fieldLabel : 'Type', + store : [ "STATIC", "CALIBRATION", "HPLC" ], + queryMode : 'local', + labelWidth : 120, + displayField : 'name', + valueField : 'name', + value : experiment.json.type, + disabled : (experiment.json.type == 'TEMPLATE') }); - this.rigidModelGrid.onSelected.attach(function(sender, fits){ - var ids = []; - for ( var i in fits) { - ids.push(fits[i].fitStructureToExperimentalDataId); + var items = []; + + + if (experiment.json.type == "HPLC" ){ + var typeMacromolecule = BIOSAXS_COMBOMANAGER.getComboMacromoleculeByMacromolecules(BIOSAXS.proposal.getMacromolecules(), {labelWidth : 120, width: "120px"}); + if (experiment.getHPLCMacromolecule() != null){ + typeMacromolecule.setValue(experiment.getHPLCMacromolecule().macromoleculeId); + items.push(typeMacromolecule); } - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data){ -// debugger - - }); - - adapter.getScatteringCurveByFrameIdsList([], [], [], ids); + } + + + items.push(typeCombo, { + id : this.id + 'name', + xtype : 'textfield', + fieldLabel : 'Name', + labelWidth : 120, + width : '100%', + value : experiment.json.name + }, { + id : this.id + 'comments', + xtype : 'textareafield', + name : 'comments', + fieldLabel : 'Comments', + labelWidth : 120, + height : 120, + width : '100%', + value : experiment.json.comments }); - -} - -RigidBodyModelingResultForm.prototype._getItems = function() { - var _this = this; - return [ { - xtype : 'label', - forId : 'myFieldId', - text : 'INLINE HELP: To be updated', - margin : '15 0 20 10', - cls : "inline-help" - }, this.rigidModelGrid.getPanel() ] - -}; - -RigidBodyModelingResultForm.prototype._getButtons = function() { - return []; + return items; }; - -RigidBodyModelingResultForm.prototype.getPanel = function() { +ExperimentForm.prototype.getPanel = function(experiment) { var _this = this; - this.panel = Ext.create('Ext.form.Panel', { - width : this.width, - height : this.height, - margin : 10, - border : 1, - defaultType : 'textfield', - items : this._getItems(), - buttons : this._getButtons(), - listeners : { - afterrender : function() { - _this._populate(); - - } - } + + this.panel = Ext.createWidget({ + xtype : 'container', + layout : 'vbox', + border : 0, + style : { + padding : '10px' + }, + fieldDefaults : { + labelAlign : 'left', + labelWidth : 50 + }, + items : this._getItems(experiment) }); return this.panel; }; -/** Populates could be call when the DOM is not filled yet **/ -RigidBodyModelingResultForm.prototype._populate = function() { -}; - -/** It populates the form * */ -RigidBodyModelingResultForm.prototype.refresh = function(subtractions) { - this.rigidModelGrid.refresh(subtractions); -}; - -RigidBodyModelingResultForm.prototype.input = function() { - return {}; +ExperimentForm.prototype.input = function() { + return new ExperimentHeaderForm().input(); }; -/** It populates the form **/ -RigidBodyModelingResultForm.prototype.test = function(targetId) { - var macromoleculeForm = new RigidBodyModelingResultForm(); - var panel = macromoleculeForm.getPanel(); +ExperimentForm.prototype.test = function(targetId) { + var experimentForm = new ExperimentForm(); + var panel = experimentForm.getPanel(new Experiment(experimentForm.input().experiment)); panel.render(targetId); }; /** - * Example form + * Shows the header for the experiments changing the color and parameters depending on experiment type * - * @witdh - * @height */ -function SuperpositionForm(args) { +function ExperimentHeaderForm(args) { this.id = BUI.id(); - this.width = null; - this.height = null; + this.backgroundColor = '#FFFFFF'; +} - if (args != null) { - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; +ExperimentHeaderForm.prototype.getHTMLSource = function(experiment) { + var html = BUI.createFormLabel("Name :", experiment.json.name, 75, 400, this.backgroundColor); + if (experiment.json.type == "HPLC") { + if (experiment.getHPLCMacromolecule() != null){ + html = html + BUI.createFormLabel("Molecule :", experiment.getHPLCMacromolecule().acronym, 75, 400, this.backgroundColor); } } + else{ + html = html + BUI.createFormLabel("Type :", experiment.json.type, 75, 400, this.backgroundColor); + } + + html = html + BUI.createFormLabel("Date :", experiment.json.creationDate, 75, 400, this.backgroundColor); + return html; +}; - var _this = this; - - /** Widgets **/ - this.superpositionGrid = new SuperpositionGrid({ - width : null, - height : 200 - }); - - this.superpositionGrid.onSelected.attach(function(sender, superpositions) { - var ids = []; - for ( var i in superpositions) { - ids.push(superpositions[i].superpositionId); - } -// _this._renderAbinitio(ids); -// _this.aprioriPDBViewer.refresh(); - _this._renderAligned(ids); - // getAlignedPDBContentBySuperpositionList - }); - - /** PDB viewer **/ -// this.abinitioPDBViewer = new PDBViewer({ -// width : 860 / 2, -// height : 300 / 2, -// margin : 0 -// }); -// -// /** PDB viewer **/ -// this.aprioriPDBViewer = new StructurePDBViewer({ -// width : 860 / 2, -// height : 300 / 2, -// margin : 0 -// }); +ExperimentHeaderForm.prototype.getHTMLDownload = function(experiment) { + var bgcolor = "background-color:" + this.backgroundColor + ";"; + var html = "
"; + if ((experiment.json.type == "CALIBATION") || (experiment.json.type == "STATIC")) { + html = html + " Download Source File
"; + html = html + + ""; + } + if (experiment.json.type == "TEMPLATE") { + html = html + + " Download Source File
"; + } - this.alignedPDBViewer = new AlignedSuperpositionPDBViewer({ - width : 860 , - height : 300 - }); + if (experiment.json.type == "HPLC") { + html = html + " Download h5 File
"; + } -} + return html; +}; -SuperpositionForm.prototype._renderAligned = function(modelsIdList) { - /** Trying to plot the PDB file **/ - try { - this.alignedPDBViewer.refresh(modelsIdList); - } catch (e) { - console.log(e); - } +ExperimentHeaderForm.prototype.getTopPanel = function(experiment) { + return { + xtype : 'container', + layout : 'hbox', + items : [ { + margin : "0 0 0 0", + width : 475, + border : 0, + html : this.getHTMLSource(experiment) + }, { + margin : "0 0 0 0", + width : 475, + border : 0, + html : this.getHTMLDownload(experiment) + } ] + }; }; -SuperpositionForm.prototype._renderAbinitio = function(modelsIdList) { - /** Trying to plot the PDB file **/ - try { - var viz = []; - for (var i = 0; i < modelsIdList.length; i++) { - viz.push({ - modelId : modelsIdList[i], - color : "0xFF6600", - opacity : 0.8 +ExperimentHeaderForm.prototype.getButton = function(experiment) { + var _this = this; + return Ext.create('Ext.Button', { + text : 'EDIT', + minWidth : '100', + margin : '10 0 0 30', + handler : function() { + var experimentWindow = new ExperimentWindow(); + experimentWindow.onSaved.attach(function(sender, data) { + _this.experiment.json.name = data.name; + _this.experiment.json.type = data.type; + _this.experiment.json.comments = data.comments; + _this.panel.remove(_this.panel.items.items[0]); + _this.panel.remove(_this.panel.items.items[0]); + _this.panel.insert(_this.getTopPanel(_this.experiment)); + _this.panel.insert(_this.getBottomPanel(_this.experiment)); }); + experimentWindow.show(experiment); } - this.abinitioPDBViewer.refresh(viz); - } catch (e) { - console.log(e); - } + }); }; -SuperpositionForm.prototype._getItems = function() { - var _this = this; - return [ { - xtype : 'label', - forId : 'myFieldId', - text : 'INLINE HELP: To be updated', - margin : '15 0 20 10', - cls : "inline-help" - }, this.superpositionGrid.getPanel(), { +ExperimentHeaderForm.prototype.getBottomPanel = function(experiment) { + return { xtype : 'container', layout : 'hbox', - items : [ -// { -// xtype : 'container', -// layout : 'vbox', -// items : [ this.abinitioPDBViewer.getPanel(), this.aprioriPDBViewer.getPanel() -// -// ] -// }, - - this.alignedPDBViewer.getPanel() ] - } ] - -}; - -SuperpositionForm.prototype._getButtons = function() { - return []; + margin : '10 0 0 0', + items : [ this.getComments(experiment), this.getButton(experiment) ] + }; }; -SuperpositionForm.prototype.getPanel = function() { - var _this = this; - this.panel = Ext.create('Ext.form.Panel', { - width : this.width, - height : this.height, - margin : 10, - border : 1, - defaultType : 'textfield', - items : this._getItems(), - buttons : this._getButtons(), - listeners : { - afterrender : function() { - _this._populate(); - - } - } - }); - return this.panel; +ExperimentHeaderForm.prototype.getComments = function(experiment) { + return { + xtype : 'textareafield', + labelStyle : 'font-weight: bold;', + name : 'comments', + fieldLabel : 'Comments', + labelWidth : 70, + height : 40, + minWidth : '450', + readOnly : true, + value : experiment.json.comments + }; }; -/** Populates could be call when the DOM is not filled yet **/ -SuperpositionForm.prototype._populate = function() { -}; +ExperimentHeaderForm.prototype.getPanel = function(experiment) { + this.experiment = experiment; + + if (experiment.json.type == 'CALIBRATION') { + this.backgroundColor = '#EFFBFB'; + } + if (experiment.json.type == 'TEMPLATE') { + this.backgroundColor = '#E0F8E6'; + } -/** It populates the form * */ -SuperpositionForm.prototype.refresh = function(subtractions) { - this.subtractions = subtractions; - this.superpositionGrid.refresh(subtractions); + this.panel = Ext.create('Ext.container.Container', { + frame : false, + layout : 'vbox', + padding : 5, + bodyPadding : '5 5 0 0', + width : 890, + margin : '0 0 10 0', + height : 120, + style : { + borderColor : '#99bce8', + borderStyle : 'solid', + borderWidth : '1px', + 'background-color' : this.backgroundColor + }, + fieldDefaults : { + msgTarget : 'side', + labelWidth : 100 + }, + items : [ this.getTopPanel(experiment), this.getBottomPanel(experiment) ] + }); + return this.panel; }; -SuperpositionForm.prototype.input = function() { - return {}; +ExperimentHeaderForm.prototype.input = function() { + return { + experiment : DATADOC.getExperiment_10() + }; }; -/** It populates the form **/ -SuperpositionForm.prototype.test = function(targetId) { - var macromoleculeForm = new SuperpositionForm(); - var panel = macromoleculeForm.getPanel(); +ExperimentHeaderForm.prototype.test = function(targetId) { + var experimentHeaderForm = new ExperimentHeaderForm(); + var panel = experimentHeaderForm.getPanel(new Experiment(experimentHeaderForm.input().experiment)); panel.render(targetId); + }; /** - * Example form + * Macromolecule form with the general parameters of a macromolecule * * @witdh * @height + * + * #onSave button save has been clicked + * #onClose button close has been clicked */ -function AssemblyForm(args) { +function MacromoleculeForm(args) { this.id = BUI.id(); this.width = 700; this.height = 500; @@ -6059,15944 +7053,9793 @@ function AssemblyForm(args) { this.height = args.height; } } - - this.molarityGrid = new MolarityGrid({height : this.height - 50}); + + /** Events **/ + this.onSave = new Event(this); + this.onClose = new Event(this); } -AssemblyForm.prototype._getItems = function() { - return [ { - xtype : 'label', - forId : 'myFieldId', - text : 'List of previously defined macromolecules present in the assembly. This information will be used for additional cross-checks where possible', - margin : '15 0 20 10', - cls : "inline-help" - }, this.molarityGrid.getPanel() ]; -}; - -AssemblyForm.prototype._getButtons = function() { - return []; +/** Type : is the Ext type then requiredtext or textfield * */ +MacromoleculeForm.prototype._getFieldTextWithHelp = function(type, fieldLabel, fieldName, help) { + return Ext.create('Ext.container.Container', { + margin : "10 0 0 10", + items : [ { + xtype : type, + fieldLabel : fieldLabel, + name : fieldName, + id : this.id + fieldName + }, { + xtype : 'label', + forId : 'myFieldId', + text : help, + margin : "5 0 0 105", + cls : "inline-help" + } ] + }); }; -AssemblyForm.prototype.getPanel = function() { - this.panel = Ext.create('Ext.form.Panel', { - width : this.width, - height : this.height, - margin : 10, - border : 0, - defaultType : 'textfield', - items : this._getItems(), - buttons : this._getButtons() +MacromoleculeForm.prototype._getNumericWithHelp = function(type, fieldLabel, fieldName, help) { + return Ext.create('Ext.container.Container', { + margin : "0 0 0 10", + items : [ { + xtype : type, + fieldLabel : fieldLabel, + name : fieldName, + id : this.id + fieldName, + decimalPrecision : 6, + width : 220 + }, { + xtype : 'label', + forId : 'myFieldId', + text : help, + margin : "5 0 0 10", + cls : "inline-help" + } ] }); - return this.panel; }; - -/** It populates the form **/ -AssemblyForm.prototype.refresh = function(macromolecule) { - this.macromolecule = macromolecule; - this.molarityGrid.refresh(macromolecule); +MacromoleculeForm.prototype._getButtons = function() { + var _this = this; + return [ { + text : 'Save', + handler : function() { + _this._save(); + } + },{ + text : 'Close', + handler : function() { + _this.onClose.notify(); + + } + } ]; }; -AssemblyForm.prototype.input = function() { - return {}; +/** It persits the macromolecule in the database **/ +MacromoleculeForm.prototype._persist = function(macromoleculeId, acronym, name, molecularMass, extintionCoefficient, comments, refractiveIndex, solventViscosity) { + + /** Checking not duplicated acronym **/ + if (((macromoleculeId == null) && (BIOSAXS.proposal.getMacromoleculeByAcronym(acronym) != null))== true){ + BUI.showError("Duplicated acronym"); + return; + } + + + if (macromoleculeId == null){ + /** new macromolecule **/ + this.macromolecule = {}; + this.macromolecule.macromoleculeId = null; + } + else{ + this.macromolecule.macromoleculeId = macromoleculeId; + } + + this.macromolecule["acronym"] = acronym; + this.macromolecule["name"] = name; + this.macromolecule["molecularMass"] = molecularMass; + this.macromolecule["extintionCoefficient"] = extintionCoefficient; + this.macromolecule["comments"] = comments; + this.macromolecule["symmetry"] = Ext.getCmp(this.id + 'comboSym').getValue(); + this.macromolecule["refractiveIndex"] = refractiveIndex; + this.macromolecule["solventViscosity"] = solventViscosity; + + var _this = this; + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, proposal) { + /** Updating the proposal global object **/ + BIOSAXS.proposal.setItems(proposal); + _this.panel.setLoading(false); + + var saved = BIOSAXS.proposal.getMacromoleculeByAcronym(acronym); + /** Refreshing to check that everything is ok **/ + _this.refresh(saved); + _this.onSave.notify(saved); + }); + + this.panel.setLoading("Saving Macromolecule") + adapter.saveMacromolecule(this.macromolecule); }; - -AssemblyForm.prototype.test = function(targetId) { - var assemblyForm = new AssemblyForm(); +/** Save the macromolecule in the DB **/ +MacromoleculeForm.prototype._save = function() { - var panel = assemblyForm.getPanel(); - panel.render(targetId); -}; -/** - * Edit the information of a buffer - * - * #onSaved - * #onRemoveAdditive - */ -function BufferForm() { var _this = this; + + var acronym = this._getField("acronym"); + var name = this._getField("name"); + var molecularMass = this._getField("molecularMass"); + var extintionCoefficient = this._getField("extintionCoefficient"); + var comments = this._getField("comments"); + + var refractiveIndex = this._getField("refractiveIndex"); + var solventViscosity = this._getField("solventViscosity"); + + /** Checking required fields **/ + if (name == "") { + BUI.showError("Name field is mandatory"); + return; + } + if (acronym == "") { + BUI.showError("Acroynm field is mandatory"); + return; + } - this.additiveGrid = new AdditiveGrid(); - this.additiveGrid.onRemoveButtonClicked.attach(function(sender, args) { - _this.onRemoveAdditive.notify(args); - }); + if (this.macromolecule != null){ + /** Checking if it is a new macromolecule **/ + if (this.macromolecule.macromoleculeId == null){ + /** Check if the acronym exists already **/ + this._persist(null, acronym, name, molecularMass, extintionCoefficient, comments, refractiveIndex, solventViscosity); + } + else{ + /** It is an update **/ + this._persist(this.macromolecule.macromoleculeId, acronym, name, molecularMass, extintionCoefficient, comments, refractiveIndex, solventViscosity); + } + } + else{ + /** It is a new macromolecule **/ + this._persist(null, acronym, name, molecularMass, extintionCoefficient, comments, refractiveIndex, solventViscosity); + } +}; - this.onSaved = new Event(this); - this.onRemoveAdditive = new Event(this); -} -BufferForm.prototype.getBuffer = function() { - this.buffer.name = Ext.getCmp("buffer_name").getValue(); - this.buffer.acronym = Ext.getCmp("buffer_acronym").getValue(); - this.buffer.comments = Ext.getCmp("buffer_comments").getValue(); - this.buffer.ph = Ext.getCmp("buffer_ph").getValue(); - this.buffer.composition = Ext.getCmp("buffer_composition").getValue(); - this.buffer.bufferhasadditive3VOs = this.additiveGrid.getAdditives(); - return this.buffer; -}; -BufferForm.prototype._getTopPanel = function() { - return { - xtype : 'container', - layout : 'hbox', - border : 0, - frame : true, - items : [ { - xtype : 'container', - layout : 'hbox', - items : [ { +MacromoleculeForm.prototype._getItems = function() { + var _this = this; + /** Symmetry combo box **/ + var symmetry = Ext.create('Ext.data.Store', { + fields : [ 's' ], + data : this._getSymmetries() + }); + + this.symmetryComboBox = Ext.create('Ext.form.ComboBox', { + fieldLabel : 'Symmetry', + store : symmetry, + id : this.id + 'comboSym', + queryMode : 'local', + displayField : 's', + valueField : 's', + value : "P1", + margin : "0 0 0 30", + width : 220 + }); + + return [this._getFieldTextWithHelp("requiredtext", "Name", "name", "Long name. i.e: Bovine serum albumin"), + this._getFieldTextWithHelp("requiredtext", "Acronym", "acronym", "Acronym will be used in the files and analisys. i.e: BSA"), + this._getFieldTextWithHelp("textfield", "Mol. Mass (Da)", "molecularMass", "Atomic mass estimation measured in Da"), + { xtype : 'container', - flex : 1, - border : false, - layout : 'anchor', - defaultType : 'textfield', - items : [ { - xtype : 'requiredtext', - id : 'buffer_name', - fieldLabel : 'Name', - name : 'name', - width : '200px', - value : this.buffer.name - }, { - xtype : 'requiredtext', - id : 'buffer_acronym', - fieldLabel : 'Acronym', - name : 'acronym', - width : '200px', - value : this.buffer.acronym - } ] - } ] - }, { - xtype : 'container', - flex : 1, - layout : 'anchor', - defaultType : 'textfield', - margin : '0 0 0 10', - items : [ { - id : 'buffer_ph', - fieldLabel : 'pH', - name : 'ph', - value : this.buffer.ph, - xtype : 'numberfield', - width : 200, - minValue : 0, - maxValue : 15 - }, { - xtype : 'requiredtext', - id : 'buffer_composition', - fieldLabel : 'Composition', - name : 'composition', - width : 200, - value : this.buffer.composition - } ] - } ] - }; + layout : 'hbox', + margin : "10 0 0 0", + items :[ + this._getNumericWithHelp("numberfield", "Extinction coef.", "extintionCoefficient", ""), + this.symmetryComboBox + ] + }, + { + xtype : 'container', + layout : 'hbox', + margin : "5 0 0 0", + items :[ + this._getNumericWithHelp("numberfield", "Refractive Index", "refractiveIndex", "How radiation propagates through the medium"), + this._getNumericWithHelp("numberfield", "Solvent Viscosity", "solventViscosity", "") + ] + }, + { + id : this.id + "comments", + xtype : 'textareafield', + name : 'comments', + margin : '35 0 0 10', + fieldLabel : 'Comments', + width : this.width - 100 + } ]; }; -BufferForm.prototype.getPanel = function(buffer) { - this.buffer = buffer; - this.panel = Ext.createWidget({ - xtype : 'container', - layout : 'vbox', - style : { - padding : '10px' - }, - fieldDefaults : { - labelAlign : 'left', - labelWidth : 50 +MacromoleculeForm.prototype._getSymmetries = function() { + return [ { + "s" : "P1" + }, { + "s" : "P2" + }, { + "s" : "P3" + }, { + "s" : "P4" + }, { + "s" : "P5" + }, { + "s" : "P6" + }, { + "s" : "P32" + }, { + "s" : "P42" + }, { + "s" : "P52" + }, { + "s" : "P62" + }, { + "s" : "P222" + } ] +}; - }, - items : [ this._getTopPanel(), { - id : 'buffer_comments', - xtype : 'textareafield', - name : 'comments', - fieldLabel : 'Comments', - width : '100%', - value : buffer.comments - }, this.additiveGrid.getPanel(buffer) ] +MacromoleculeForm.prototype.getPanel = function() { + this.panel = Ext.create('Ext.form.Panel', { + width : this.width, + height : this.height, + margin : 10, + border : 1, + defaultType : 'textfield', + items : this._getItems(), + buttons : this._getButtons() }); return this.panel; }; -BufferForm.prototype.input = function() { - return { - buffer : { - "bufferId" : 422, - "proposalId" : 10, - "safetyLevelId" : null, - "name" : "B1", - "acronym" : "B1", - "ph" : null, - "composition" : null, - "bufferhasadditive3VOs" : [], - "comments" : null - } - }; + +/** Populates each text field by field name and value **/ +MacromoleculeForm.prototype._populateField = function(fieldName, value) { + if (value != null){ + Ext.getCmp(this.id + fieldName).setValue(value); + } }; -BufferForm.prototype.test = function(targetId) { - var bufferForm = new BufferForm(); - var panel = bufferForm.getPanel(bufferForm.input().buffer); - panel.render(targetId); +/** Gets the value of a textfield **/ +MacromoleculeForm.prototype._getField = function(fieldName) { + return Ext.getCmp(this.id + fieldName).getValue(); }; - -/** - * @showTitle - * - * #onSaved - * #onAddPlates - * #onRemovePlates - **/ -function CaseForm(args) { - this.width = 700; - this.showTitle = true; - if (args != null) { - if (args.showTitle != null) { - this.showTitle = args.showTitle; - } - } - var _this = this; - this.stockSolutionGrid = new StockSolutionGrid({ - width : this.width - 10, - minHeight : 300, - height : 300, - tbar : true, - showTitle : true, - isPackedVisible : false, - btnAddExisting : true, - btnRemoveVisible : false, - btnUnpackVisible : true - }); - /** When selecting existing stock solutions **/ - this.stockSolutionGrid.onStockSolutionSelected.attach(function(sender, stockSolutions) { - if (stockSolutions != null) { - for ( var i = 0; i < stockSolutions.length; i++) { - _this.saveStockSolution(stockSolutions[i]); - } +/** It populates the form **/ +MacromoleculeForm.prototype.refresh = function(macromolecule) { + this.macromolecule = macromolecule; + if (macromolecule != null){ + this._populateField("name", macromolecule.name); + this._populateField("acronym", macromolecule.acronym); + this._populateField("extintionCoefficient", macromolecule.extintionCoefficient); + this._populateField("molecularMass", macromolecule.molecularMass); + this._populateField("comments", macromolecule.comments); + this._populateField("refractiveIndex", macromolecule.refractiveIndex); + this._populateField("solventViscosity", macromolecule.solventViscosity); + if (macromolecule.symmetry != null){ + Ext.getCmp(this.id + 'comboSym').setValue(macromolecule.symmetry); } - }); + } +}; - /** it can be because it has been added a new one or removed **/ - this.stockSolutionGrid.onProposalChanged.attach(function(sender, stockSolution) { - if (stockSolution != null) { - _this.saveStockSolution(stockSolution); - } else { - BIOSAXS.proposal.onInitialized.attach(function() { - _this.stockSolutionGrid.refresh(BIOSAXS.proposal.getStockSolutionsByDewarId(_this.dewar.dewarId)); - _this.stockSolutionGrid.grid.setLoading(false); - }); - BIOSAXS.proposal.init(); +MacromoleculeForm.prototype.input = function() { + return {}; +}; - } +/** It populates the form **/ +MacromoleculeForm.prototype.test = function(targetId) { + var macromoleculeForm = new MacromoleculeForm(); + macromoleculeForm.onClose.attach(function(sender){ + alert("Click on close"); }); + var panel = macromoleculeForm.getPanel(); + panel.render(targetId); +}; - this.onSaved = new Event(this); - this.onAddPlates = new Event(this); - this.onRemovePlates = new Event(this); -} -CaseForm.prototype.saveStockSolution = function(stockSolution) { - var _this = this; - var adapter = new BiosaxsDataAdapter(); - this.stockSolutionGrid.grid.setLoading("ISPyB: setting case to Stock solution"); - adapter.onSuccess.attach(function(sender, stockSolution) { - BIOSAXS.proposal.onInitialized.attach(function() { - _this.stockSolutionGrid.refresh(BIOSAXS.proposal.getStockSolutionsByDewarId(_this.dewar.dewarId)); - _this.stockSolutionGrid.grid.setLoading(false); - }); - BIOSAXS.proposal.init(); - }); - adapter.onError.attach(function(sender, data) { - _this.stockSolutionGrid.grid.setLoading(false); - BUI.showError(data); - }); - stockSolution.boxId = _this.dewar.dewarId; - adapter.saveStockSolution(stockSolution); -}; - -CaseForm.prototype.fillStores = function() { - var _this = this; - this.panel.setLoading("Loading Labcontacts from database"); + - var proposal = BUI.getProposal(); - proposal.onDataRetrieved.attach(function(sender, data) { - _this.labContactForSendingStore.loadData(data, false); - _this.labContactForReturnStore.loadData(data, false); - _this.panel.setLoading(false); - }); - proposal.getLabContactsByProposalId(); +function ModelVisualizerForm(args){ + this.id =BUI.id(); + this.width = 600; + this.height = 400; + if (args!= null){ + if (args.width != null){ + this.width = args.width; + } + if (args.height != null){ + this.height = args.height; + } + } }; -CaseForm.prototype.refresh = function(dewar) { - this.setDewar(dewar); - this.stockSolutionGrid.refresh(BIOSAXS.proposal.getStockSolutionsByDewarId(dewar.dewarId)); +ModelVisualizerForm.prototype._getFirHTML = function(modelId, width, height, type, desc) { + var html = ""; + html = html + ''; + html = html + ''; + html = html + ''; + html = html + '
dammin.' + type + '
' + desc + '
'; + return html; }; -CaseForm.prototype.getDewar = function() { - this.dewar.code = Ext.getCmp("dewar_code").getValue(); - this.dewar.comments = Ext.getCmp("dewar_comments").getValue(); - this.dewar.trackingNumberFromSynchrotron = Ext.getCmp("dewar_trackingNumberFromSynchrotron").getValue(); - this.dewar.trackingNumberToSynchrotron = Ext.getCmp("dewar_trackingNumberToSynchrotron").getValue(); - this.dewar.transportValue = Ext.getCmp("dewar_transportValue").getValue(); - this.dewar.storageLocation = Ext.getCmp("dewar_storageLocation").getValue(); - this.dewar.firstExperimentId = this.macromoleculeCombo.getValue(); - return this.dewar; +ModelVisualizerForm.prototype.getItems = function(modelPanel){ + _this = this; + var height = _this.height/2 - 60; + var width = _this.width/2 - 10; + + return Ext.create('Ext.container.Container', { + layout: { + type: 'vbox', // Arrange child items vertically + }, + items: [ + modelPanel, + { + xtype : 'container', + layout: { + type: 'hbox', // Arrange child items vertically + }, + items : [{ + html : this._getFirHTML("id", width, height, "fir", "Fit of the simulated scattering curve versus a smoothed experimental data (spline interpolation)"), + height :height, + width : width, + padding: 2 + }, + { + html : this._getFirHTML("id", width, height, "fit", "Fit of the simulated scattering curve versus the experimental data."), + height : height, + width : width, + padding: 2 + }] + } + + ] + }); }; -CaseForm.prototype.setDewar = function(dewar) { - this.dewar = dewar; - Ext.getCmp("dewar_code").setValue(this.dewar.code); - Ext.getCmp("dewar_dewarStatus").setText(new String(this.dewar.dewarStatus).toUpperCase()); - Ext.getCmp("dewar_comments").setValue(this.dewar.comments); - Ext.getCmp("dewar_trackingNumberFromSynchrotron").setValue(this.dewar.trackingNumberFromSynchrotron); - Ext.getCmp("dewar_trackingNumberToSynchrotron").setValue(this.dewar.trackingNumberToSynchrotron); - Ext.getCmp("dewar_transportValue").setValue(this.dewar.transportValue); - Ext.getCmp("dewar_storageLocation").setValue(this.dewar.storageLocation); - if (dewar.sessionVO != null) { - this.macromoleculeCombo.setValue(dewar.sessionVO.sessionId); +ModelVisualizerForm.prototype.refresh = function(models){ + var input = []; +// var colors = ["008000", "F0A804", "0000FF", "800080", "C0C0C0"]; + for (var i = 0; i < models.length; i++) { + console.log(BUI.rainbow(models.length, i).replace("#", "0x")); + input.push({ + color: BUI.rainbow(models.length, i).replace("#", "0x"), + modelId: models[i].modelId, + opacity: 0.8, + radius: 3, + title: BUI.getFileNameByPath(models[i].pdbFile), + type: "SHAPEDETERMINATIONMODEL" + + }); } + + this.panel.removeAll(); + this.panel.add( + _this.getItems( + new PDBViewer({ + width : this.width - 10, + height : (this.height/2) - 10, + title : "" + }).draw(input) + ) + ); + + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + var splitted = data.toString().split("\n"); + var array = []; + for ( var i = 0; i < splitted.length; i++) { + var line = splitted[i].trim(); + var line_splited = line.split(/\s*[\s,]\s*/); + if (line_splited.length == 4) { + array.push([ Number(line_splited[0]), BUI.getStvArray(line_splited[1], line_splited[2]), BUI.getStvArray(line_splited[3], 0) ]); + } + } + + var id = (_this.id + "firid"); + var dygraphWidget = new StdDevDyGraph(id, { + width : (_this.width/2) - 10, + height :(_this.height/2) -110, + xlabel : 'q(nm-1)' + }); + dygraphWidget.draw(array, [ "#FF0000", "#0000FF", "#FF00FF" ], [ 's', 'I(exp)', 'I(sim)' ]); + }); + + adapter.getModelFile("FIR", models[0].modelId); + + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + var splitted = data.toString().split("\n"); + var array = []; + for ( var i = 0; i < splitted.length; i++) { + var line = splitted[i].trim(); + var line_splited = line.split(/\s*[\s,]\s*/); + if (line_splited.length == 3) { + array.push([ Number(line_splited[0]), BUI.getStvArray(line_splited[1], 0), BUI.getStvArray(line_splited[2], 0) ]); + } + } + + var id = (_this.id + "fitid"); + + var dygraphWidget = new StdDevDyGraph(id, { + width : (_this.width/2) - 10, + height : (_this.height/2) - 110, + xlabel : 'q(nm-1)' + }); + dygraphWidget.draw(array, [ "#FF0000", "#0000FF" ], [ "s", "I(exp)", "I(sim)" ]); + }); + adapter.getModelFile("FIT", models[0].modelId); }; -CaseForm.prototype.getSessionCombo = function() { - this.macromoleculeCombo = BIOSAXS_COMBOMANAGER.getComboSessions(BIOSAXS.proposal.getSessions(), { - labelWidth : 100, - margin : '5 0 00 0', - width : 250 +ModelVisualizerForm.prototype.getPanel = function(modelList){ + _this = this; + this.modelList = modelList; + this.panel = Ext.create('Ext.Panel', { + title: 'Results', + width: this.width, + height: this.height, + layout: { + type: 'vbox', // Arrange child items vertically +// align: 'stretch' // Each takes up full width + }, + items: [ + + ], + listeners : { + afterrender : function(grid, eOpts) { +// alert(_this.modelList) + } + } }); - return this.macromoleculeCombo; + + return this.panel; + }; -CaseForm.prototype.getInformationPanel = function() { - if (this.panel == null) { - this.informationPanel = Ext.create('Ext.form.Panel', { - width : this.width - 10, - border : 0, - items : [ { - xtype : 'container', - margin : "2 2 2 2", - collapsible : false, - defaultType : 'textfield', - layout : 'anchor', - items : [ { - xtype : 'container', - layout : 'hbox', - items : [ { - xtype : 'requiredtext', - fieldLabel : 'Code', - allowBlank : false, - name : 'code', - id : 'dewar_code', - anchor : '50%' - }, { - xtype : 'label', - margin : '0 0 0 20', - readOnly : true, - id : 'dewar_dewarStatus', - anchor : '50%' - } ] - }, this.getSessionCombo(), { - margin : '5 0 0 0', - xtype : 'textareafield', - name : 'comments', - id : 'dewar_comments', - width : this.width - 50, - fieldLabel : 'Comments' - } ] - }, { - xtype : 'fieldset', - title : 'Courier Accounts Details for Return', - collapsible : false, - layout : 'anchor', - defaults : { - anchor : '100%' - }, - items : [ { - xtype : 'container', - layout : 'hbox', - items : [ { - xtype : 'textfield', - labelWidth : 200, - width : 280, - fieldLabel : 'Track Number From Synchrotron', - id : 'dewar_trackingNumberFromSynchrotron' - }, { - xtype : 'numberfield', - width : 190, - labelWidth : 110, - margin : '0 0 0 30', - fieldLabel : 'Transport Value', - id : 'dewar_transportValue' - } - - ] - }, { - xtype : 'container', - layout : 'hbox', - margin : '10 0 0 0', - items : [ - - { - xtype : 'textfield', - labelWidth : 200, - width : 280, - fieldLabel : 'Track Number To Synchrotron', - id : 'dewar_trackingNumberToSynchrotron' - }, { - xtype : 'textfield', - margin : '0 0 0 30', - width : 190, - labelWidth : 110, - fieldLabel : 'Storage Location', - id : 'dewar_storageLocation' - } - - ] - } ] - } ] - }); - } - - return this.informationPanel; -}; - -CaseForm.prototype.getPanel = function(dewar) { - this.dewar = dewar; - this.panel = Ext.createWidget({ - xtype : 'container', - layout : 'vbox', - width : this.width, - border : 0, - items : [ { - items : { - xtype : "container", - layout : "vbox", - margin : "5 5 5 5", - items : [ this.getInformationPanel(dewar), this.stockSolutionGrid.getPanel() ] - - } - } ] - }); - - this.refresh(dewar); - return this.panel; - -}; - -CaseForm.prototype.input = function() { - return { - dewar : { - "dewarId" : 305861, - "code" : "ESRF-TEST", - "comments" : "comments", - "storageLocation" : "FRIDGE", - "dewarStatus" : "opened", - "timeStamp" : null, - "isStorageDewar" : null, - "barCode" : "ESRF305861", - "customsValue" : null, - "transportValue" : null, - "trackingNumberToSynchrotron" : "3333", - "trackingNumberFromSynchrotron" : "224466", - "type" : "Dewar", - "sessionVO" : { - "sessionId" : 31697, - "expSessionPk" : null, - "projectCode" : null, - "startDate" : "2012 07 21", - "endDate" : "2012 07 23", - "beamlineName" : "BM29", - "scheduled" : 1, - "nbShifts" : 2, - "comments" : null, - "beamlineOperator" : "PERNOT P", - "usedFlag" : null, - "sessionTitle" : null, - "structureDeterminations" : null, - "dewarTransport" : null, - "databackupFrance" : null, - "databackupEurope" : null, - "visit_number" : null, - "operatorSiteNumber" : "14061", - "timeStamp" : "2012 04 25" - } - }, - proposal : { - "assemblies" : [], - "sessions" : [ { - "sessionId" : 31697, - "expSessionPk" : null, - "projectCode" : null, - "startDate" : "2012 07 21", - "endDate" : "2012 07 23", - "beamlineName" : "BM29", - "scheduled" : 1, - "nbShifts" : 2, - "comments" : null, - "beamlineOperator" : "PERNOT P", - "usedFlag" : null, - "sessionTitle" : null, - "structureDeterminations" : null, - "dewarTransport" : null, - "databackupFrance" : null, - "databackupEurope" : null, - "visit_number" : null, - "operatorSiteNumber" : "14061", - "timeStamp" : "2012 04 25" - } ], - "labcontacts" : [ { - "labContactId" : 787, - "personVO" : { - "personId" : 304252, - "personUUID" : null, - "familyName" : "KIM", - "givenName" : "Henry", - "title" : null, - "emailAddress" : "henry-sung.kim@ibs.fr", - "phoneNumber" : "", - "login" : "", - "passwd" : "", - "faxNumber" : "" - }, - "cardName" : "KIM-Institut de Bio", - "defaultCourrierCompany" : "22", - "courierAccount" : "", - "billingReference" : "", - "dewarAvgCustomsValue" : 0, - "dewarAvgTransportValue" : 0 - } ], - "buffers" : [ { - "bufferId" : 811, - "proposalId" : 3124, - "safetyLevelId" : null, - "name" : "EDTA", - "acronym" : "EDTA", - "ph" : null, - "composition" : "", - "bufferhasadditive3VOs" : [], - "comments" : "" - }, { - "bufferId" : 810, - "proposalId" : 3124, - "safetyLevelId" : null, - "name" : "HEPES", - "acronym" : "HEPES", - "ph" : null, - "composition" : "", - "bufferhasadditive3VOs" : [], - "comments" : "" - } ], - "shippings" : [ { - "shippingId" : 304107, - "shippingName" : "TEST", - "deliveryAgentAgentName" : null, - "deliveryAgentShippingDate" : null, - "deliveryAgentDeliveryDate" : null, - "deliveryAgentAgentCode" : null, - "deliveryAgentFlightCode" : null, - "shippingStatus" : "opened", - "timeStamp" : "2013 09 25", - "laboratoryId" : null, - "isStorageShipping" : null, - "creationDate" : "2013 09 25", - "comments" : "test", - "sendingLabContactVO" : { - "labContactId" : 787, - "personVO" : { - "personId" : 304252, - "personUUID" : null, - "familyName" : "KIM", - "givenName" : "Henry", - "title" : null, - "emailAddress" : "henry-sung.kim@ibs.fr", - "phoneNumber" : "", - "login" : "", - "passwd" : "", - "faxNumber" : "" - }, - "cardName" : "KIM-Institut de Bio", - "defaultCourrierCompany" : "22", - "courierAccount" : "", - "billingReference" : "", - "dewarAvgCustomsValue" : 0, - "dewarAvgTransportValue" : 0 - }, - "returnLabContactVO" : { - "labContactId" : 787, - "personVO" : { - "personId" : 304252, - "personUUID" : null, - "familyName" : "KIM", - "givenName" : "Henry", - "title" : null, - "emailAddress" : "henry-sung.kim@ibs.fr", - "phoneNumber" : "", - "login" : "", - "passwd" : "", - "faxNumber" : "" - }, - "cardName" : "KIM-Institut de Bio", - "defaultCourrierCompany" : "22", - "courierAccount" : "", - "billingReference" : "", - "dewarAvgCustomsValue" : 0, - "dewarAvgTransportValue" : 0 - }, - "returnCourier" : null, - "dateOfShippingToUser" : null, - "shippingType" : "DewarTracking", - "dewarVOs" : [ { - "dewarId" : 305861, - "code" : "ESRF-TEST", - "comments" : "comments", - "storageLocation" : "FRIDGE", - "dewarStatus" : "opened", - "timeStamp" : null, - "isStorageDewar" : null, - "barCode" : "ESRF305861", - "customsValue" : null, - "transportValue" : null, - "trackingNumberToSynchrotron" : "3333", - "trackingNumberFromSynchrotron" : "224466", - "type" : "Dewar", - "sessionVO" : { - "sessionId" : 31697, - "expSessionPk" : null, - "projectCode" : null, - "startDate" : "2012 07 21", - "endDate" : "2012 07 23", - "beamlineName" : "BM29", - "scheduled" : 1, - "nbShifts" : 2, - "comments" : null, - "beamlineOperator" : "PERNOT P", - "usedFlag" : null, - "sessionTitle" : null, - "structureDeterminations" : null, - "dewarTransport" : null, - "databackupFrance" : null, - "databackupEurope" : null, - "visit_number" : null, - "operatorSiteNumber" : "14061", - "timeStamp" : "2012 04 25" - } - } ] - } ], - "macromolecules" : [ { - "macromoleculeId" : 5933, - "safetylevelId" : null, - "proposalId" : 3124, - "name" : "A", - "acronym" : "A", - "molecularMass" : "", - "extintionCoefficient" : "", - "sequence" : null, - "creationDate" : null, - "comments" : "", - "macromoleculeregion3VOs" : [], - "stoichiometry3VOsForHostMacromoleculeId" : [], - "structure3VOs" : [] - } ], - "stockSolutions" : [ { - "stockSolutionId" : 6, - "proposalId" : 3124, - "macromoleculeId" : 5933, - "bufferId" : 811, - "instructionSet3VO" : null, - "boxId" : 305861, - "storageTemperature" : "20", - "volume" : "300", - "concentration" : "1.2", - "comments" : "Buffer EDTA with A", - "name" : "A_EDTA_1.2", - "samples" : [] - } ] - } - - }; -}; - -CaseForm.prototype.test = function(targetId) { - var caseForm = new CaseForm(); - BIOSAXS.proposal = new Proposal(caseForm.input().proposal); - var panel = caseForm.getPanel(caseForm.input().dewar); - panel.render(targetId); -}; - -/** - * Example form - * - * @witdh - * @height - */ -function ExampleForm(args) { - this.id = BUI.id(); - this.width = 700; - this.height = 500; - - if (args != null) { - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; - } - } -} - -ExampleForm.prototype._getItems = function() { - return [{ - fieldLabel : 'First Name', - name : 'first', - allowBlank : false - }, { - fieldLabel : 'Last Name', - name : 'last', - allowBlank : false - } ]; -}; - -ExampleForm.prototype._getItems = function() { - return [ ]; -}; - -ExampleForm.prototype._getButtons = function() { - return [ ]; -}; - -ExampleForm.prototype.getPanel = function() { - this.panel = Ext.create('Ext.form.Panel', { - width : this.width, - height : this.height, - margin : 10, - border : 1, - defaultType : 'textfield', - items : this._getItems(), - buttons : this._getButtons() - }); - return this.panel; -}; - -/** It populates the form **/ -ExampleForm.prototype.refresh = function(macromolecule) { -}; - -function ExperimentForm(args) { - this.id = BUI.id(); - - if (args != null) { - } - - this.onSaved = new Event(this); -} - -ExperimentForm.prototype._getItems = function(experiment) { - this.experiment = experiment; - var typeCombo = Ext.create('Ext.form.ComboBox', { - id : this.id + 'type', - fieldLabel : 'Type', - store : [ "STATIC", "CALIBRATION", "HPLC" ], - queryMode : 'local', - labelWidth : 120, - displayField : 'name', - valueField : 'name', - value : experiment.json.type, - disabled : (experiment.json.type == 'TEMPLATE') - }); - - var items = []; - - - if (experiment.json.type == "HPLC" ){ - var typeMacromolecule = BIOSAXS_COMBOMANAGER.getComboMacromoleculeByMacromolecules(BIOSAXS.proposal.getMacromolecules(), {labelWidth : 120, width: "120px"}); - if (experiment.getHPLCMacromolecule() != null){ - typeMacromolecule.setValue(experiment.getHPLCMacromolecule().macromoleculeId); - items.push(typeMacromolecule); - } - } - - - items.push(typeCombo, { - id : this.id + 'name', - xtype : 'textfield', - fieldLabel : 'Name', - labelWidth : 120, - width : '100%', - value : experiment.json.name - }, { - id : this.id + 'comments', - xtype : 'textareafield', - name : 'comments', - fieldLabel : 'Comments', - labelWidth : 120, - height : 120, - width : '100%', - value : experiment.json.comments - }); - return items; -}; -ExperimentForm.prototype.getPanel = function(experiment) { - var _this = this; - - this.panel = Ext.createWidget({ - xtype : 'container', - layout : 'vbox', - border : 0, - style : { - padding : '10px' - }, - fieldDefaults : { - labelAlign : 'left', - labelWidth : 50 - }, - items : this._getItems(experiment) - }); - return this.panel; -}; - -ExperimentForm.prototype.input = function() { - return new ExperimentHeaderForm().input(); -}; - -ExperimentForm.prototype.test = function(targetId) { - var experimentForm = new ExperimentForm(); - var panel = experimentForm.getPanel(new Experiment(experimentForm.input().experiment)); - panel.render(targetId); -}; - -/** - * Shows the header for the experiments changing the color and parameters depending on experiment type - * - */ -function ExperimentHeaderForm(args) { - this.id = BUI.id(); - this.backgroundColor = '#FFFFFF'; -} - -ExperimentHeaderForm.prototype.getHTMLSource = function(experiment) { - var html = BUI.createFormLabel("Name :", experiment.json.name, 75, 400, this.backgroundColor); - if (experiment.json.type == "HPLC") { - if (experiment.getHPLCMacromolecule() != null){ - html = html + BUI.createFormLabel("Molecule :", experiment.getHPLCMacromolecule().acronym, 75, 400, this.backgroundColor); - } - } - else{ - html = html + BUI.createFormLabel("Type :", experiment.json.type, 75, 400, this.backgroundColor); - } - - html = html + BUI.createFormLabel("Date :", experiment.json.creationDate, 75, 400, this.backgroundColor); - return html; -}; - -ExperimentHeaderForm.prototype.getHTMLDownload = function(experiment) { - var bgcolor = "background-color:" + this.backgroundColor + ";"; - var html = "
"; - if ((experiment.json.type == "CALIBATION") || (experiment.json.type == "STATIC")) { - html = html + " Download Source File
"; - html = html - + ""; - } - if (experiment.json.type == "TEMPLATE") { - html = html - + " Download Source File"; - } - - if (experiment.json.type == "HPLC") { - html = html + " Download h5 File"; - } - - return html; -}; - -ExperimentHeaderForm.prototype.getTopPanel = function(experiment) { - return { - xtype : 'container', - layout : 'hbox', - items : [ { - margin : "0 0 0 0", - width : 475, - border : 0, - html : this.getHTMLSource(experiment) - }, { - margin : "0 0 0 0", - width : 475, - border : 0, - html : this.getHTMLDownload(experiment) - } ] - }; -}; - -ExperimentHeaderForm.prototype.getButton = function(experiment) { - var _this = this; - return Ext.create('Ext.Button', { - text : 'EDIT', - minWidth : '100', - margin : '10 0 0 30', - handler : function() { - var experimentWindow = new ExperimentWindow(); - experimentWindow.onSaved.attach(function(sender, data) { - _this.experiment.json.name = data.name; - _this.experiment.json.type = data.type; - _this.experiment.json.comments = data.comments; - _this.panel.remove(_this.panel.items.items[0]); - _this.panel.remove(_this.panel.items.items[0]); - _this.panel.insert(_this.getTopPanel(_this.experiment)); - _this.panel.insert(_this.getBottomPanel(_this.experiment)); - }); - experimentWindow.show(experiment); - } - }); -}; - -ExperimentHeaderForm.prototype.getBottomPanel = function(experiment) { - return { - xtype : 'container', - layout : 'hbox', - margin : '10 0 0 0', - items : [ this.getComments(experiment), this.getButton(experiment) ] - }; -}; - -ExperimentHeaderForm.prototype.getComments = function(experiment) { - return { - xtype : 'textareafield', - labelStyle : 'font-weight: bold;', - name : 'comments', - fieldLabel : 'Comments', - labelWidth : 70, - height : 40, - minWidth : '450', - readOnly : true, - value : experiment.json.comments - }; -}; - -ExperimentHeaderForm.prototype.getPanel = function(experiment) { - this.experiment = experiment; - - if (experiment.json.type == 'CALIBRATION') { - this.backgroundColor = '#EFFBFB'; - } - if (experiment.json.type == 'TEMPLATE') { - this.backgroundColor = '#E0F8E6'; - } - - this.panel = Ext.create('Ext.container.Container', { - frame : false, - layout : 'vbox', - padding : 5, - bodyPadding : '5 5 0 0', - width : 890, - margin : '0 0 10 0', - height : 120, - style : { - borderColor : '#99bce8', - borderStyle : 'solid', - borderWidth : '1px', - 'background-color' : this.backgroundColor - }, - fieldDefaults : { - msgTarget : 'side', - labelWidth : 100 - }, - items : [ this.getTopPanel(experiment), this.getBottomPanel(experiment) ] - }); - return this.panel; -}; - -ExperimentHeaderForm.prototype.input = function() { - return { - experiment : DATADOC.getExperiment_10() - }; -}; - -ExperimentHeaderForm.prototype.test = function(targetId) { - var experimentHeaderForm = new ExperimentHeaderForm(); - var panel = experimentHeaderForm.getPanel(new Experiment(experimentHeaderForm.input().experiment)); - panel.render(targetId); - -}; - -/** - * Macromolecule form with the general parameters of a macromolecule - * - * @witdh - * @height - * - * #onSave button save has been clicked - * #onClose button close has been clicked - */ -function MacromoleculeForm(args) { - this.id = BUI.id(); - this.width = 700; - this.height = 500; - - if (args != null) { - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; - } - } - - /** Events **/ - this.onSave = new Event(this); - this.onClose = new Event(this); -} - -/** Type : is the Ext type then requiredtext or textfield * */ -MacromoleculeForm.prototype._getFieldTextWithHelp = function(type, fieldLabel, fieldName, help) { - return Ext.create('Ext.container.Container', { - margin : "10 0 0 10", - items : [ { - xtype : type, - fieldLabel : fieldLabel, - name : fieldName, - id : this.id + fieldName - }, { - xtype : 'label', - forId : 'myFieldId', - text : help, - margin : "5 0 0 105", - cls : "inline-help" - } ] - }); -}; - -MacromoleculeForm.prototype._getNumericWithHelp = function(type, fieldLabel, fieldName, help) { - return Ext.create('Ext.container.Container', { - margin : "0 0 0 10", - items : [ { - xtype : type, - fieldLabel : fieldLabel, - name : fieldName, - id : this.id + fieldName, - decimalPrecision : 6, - width : 220 - }, { - xtype : 'label', - forId : 'myFieldId', - text : help, - margin : "5 0 0 10", - cls : "inline-help" - } ] - }); -}; - -MacromoleculeForm.prototype._getButtons = function() { - var _this = this; - return [ { - text : 'Save', - handler : function() { - _this._save(); - } - },{ - text : 'Close', - handler : function() { - _this.onClose.notify(); - - } - } ]; -}; - -/** It persits the macromolecule in the database **/ -MacromoleculeForm.prototype._persist = function(macromoleculeId, acronym, name, molecularMass, extintionCoefficient, comments, refractiveIndex, solventViscosity) { - - /** Checking not duplicated acronym **/ - if (((macromoleculeId == null) && (BIOSAXS.proposal.getMacromoleculeByAcronym(acronym) != null))== true){ - BUI.showError("Duplicated acronym"); - return; - } - - - if (macromoleculeId == null){ - /** new macromolecule **/ - this.macromolecule = {}; - this.macromolecule.macromoleculeId = null; - } - else{ - this.macromolecule.macromoleculeId = macromoleculeId; - } - - this.macromolecule["acronym"] = acronym; - this.macromolecule["name"] = name; - this.macromolecule["molecularMass"] = molecularMass; - this.macromolecule["extintionCoefficient"] = extintionCoefficient; - this.macromolecule["comments"] = comments; - this.macromolecule["symmetry"] = Ext.getCmp(this.id + 'comboSym').getValue(); - this.macromolecule["refractiveIndex"] = refractiveIndex; - this.macromolecule["solventViscosity"] = solventViscosity; - - var _this = this; - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, proposal) { - /** Updating the proposal global object **/ - BIOSAXS.proposal.setItems(proposal); - _this.panel.setLoading(false); - - var saved = BIOSAXS.proposal.getMacromoleculeByAcronym(acronym); - /** Refreshing to check that everything is ok **/ - _this.refresh(saved); - _this.onSave.notify(saved); - }); - - this.panel.setLoading("Saving Macromolecule") - adapter.saveMacromolecule(this.macromolecule); -}; - -/** Save the macromolecule in the DB **/ -MacromoleculeForm.prototype._save = function() { - - var _this = this; - - var acronym = this._getField("acronym"); - var name = this._getField("name"); - var molecularMass = this._getField("molecularMass"); - var extintionCoefficient = this._getField("extintionCoefficient"); - var comments = this._getField("comments"); - - var refractiveIndex = this._getField("refractiveIndex"); - var solventViscosity = this._getField("solventViscosity"); - - /** Checking required fields **/ - if (name == "") { - BUI.showError("Name field is mandatory"); - return; - } - if (acronym == "") { - BUI.showError("Acroynm field is mandatory"); - return; - } - - if (this.macromolecule != null){ - /** Checking if it is a new macromolecule **/ - if (this.macromolecule.macromoleculeId == null){ - /** Check if the acronym exists already **/ - this._persist(null, acronym, name, molecularMass, extintionCoefficient, comments, refractiveIndex, solventViscosity); - } - else{ - /** It is an update **/ - this._persist(this.macromolecule.macromoleculeId, acronym, name, molecularMass, extintionCoefficient, comments, refractiveIndex, solventViscosity); - } - } - else{ - /** It is a new macromolecule **/ - this._persist(null, acronym, name, molecularMass, extintionCoefficient, comments, refractiveIndex, solventViscosity); - } -}; - - - -MacromoleculeForm.prototype._getItems = function() { - var _this = this; - /** Symmetry combo box **/ - var symmetry = Ext.create('Ext.data.Store', { - fields : [ 's' ], - data : this._getSymmetries() - }); - - this.symmetryComboBox = Ext.create('Ext.form.ComboBox', { - fieldLabel : 'Symmetry', - store : symmetry, - id : this.id + 'comboSym', - queryMode : 'local', - displayField : 's', - valueField : 's', - value : "P1", - margin : "0 0 0 30", - width : 220 - }); - - return [this._getFieldTextWithHelp("requiredtext", "Name", "name", "Long name. i.e: Bovine serum albumin"), - this._getFieldTextWithHelp("requiredtext", "Acronym", "acronym", "Acronym will be used in the files and analisys. i.e: BSA"), - this._getFieldTextWithHelp("textfield", "Mol. Mass (Da)", "molecularMass", "Atomic mass estimation measured in Da"), - { - xtype : 'container', - layout : 'hbox', - margin : "10 0 0 0", - items :[ - this._getNumericWithHelp("numberfield", "Extinction coef.", "extintionCoefficient", ""), - this.symmetryComboBox - ] - }, - { - xtype : 'container', - layout : 'hbox', - margin : "5 0 0 0", - items :[ - this._getNumericWithHelp("numberfield", "Refractive Index", "refractiveIndex", "How radiation propagates through the medium"), - this._getNumericWithHelp("numberfield", "Solvent Viscosity", "solventViscosity", "") - ] - }, - { - id : this.id + "comments", - xtype : 'textareafield', - name : 'comments', - margin : '35 0 0 10', - fieldLabel : 'Comments', - width : this.width - 100 - } ]; -}; - -MacromoleculeForm.prototype._getSymmetries = function() { - return [ { - "s" : "P1" - }, { - "s" : "P2" - }, { - "s" : "P3" - }, { - "s" : "P4" - }, { - "s" : "P5" - }, { - "s" : "P6" - }, { - "s" : "P32" - }, { - "s" : "P42" - }, { - "s" : "P52" - }, { - "s" : "P62" - }, { - "s" : "P222" - } ] -}; - -MacromoleculeForm.prototype.getPanel = function() { - this.panel = Ext.create('Ext.form.Panel', { - width : this.width, - height : this.height, - margin : 10, - border : 1, - defaultType : 'textfield', - items : this._getItems(), - buttons : this._getButtons() - }); - return this.panel; -}; - - -/** Populates each text field by field name and value **/ -MacromoleculeForm.prototype._populateField = function(fieldName, value) { - if (value != null){ - Ext.getCmp(this.id + fieldName).setValue(value); - } -}; - -/** Gets the value of a textfield **/ -MacromoleculeForm.prototype._getField = function(fieldName) { - return Ext.getCmp(this.id + fieldName).getValue(); -}; - - -/** It populates the form **/ -MacromoleculeForm.prototype.refresh = function(macromolecule) { - this.macromolecule = macromolecule; - if (macromolecule != null){ - this._populateField("name", macromolecule.name); - this._populateField("acronym", macromolecule.acronym); - this._populateField("extintionCoefficient", macromolecule.extintionCoefficient); - this._populateField("molecularMass", macromolecule.molecularMass); - this._populateField("comments", macromolecule.comments); - this._populateField("refractiveIndex", macromolecule.refractiveIndex); - this._populateField("solventViscosity", macromolecule.solventViscosity); - if (macromolecule.symmetry != null){ - Ext.getCmp(this.id + 'comboSym').setValue(macromolecule.symmetry); - } - } -}; - - -MacromoleculeForm.prototype.input = function() { - return {}; -}; - - -/** It populates the form **/ -MacromoleculeForm.prototype.test = function(targetId) { - var macromoleculeForm = new MacromoleculeForm(); - macromoleculeForm.onClose.attach(function(sender){ - alert("Click on close"); - }); - var panel = macromoleculeForm.getPanel(); - panel.render(targetId); -}; - - - - - -function ModelVisualizerForm(args){ - this.id =BUI.id(); - this.width = 600; - this.height = 400; - if (args!= null){ - if (args.width != null){ - this.width = args.width; - } - if (args.height != null){ - this.height = args.height; - } - } -}; - -ModelVisualizerForm.prototype._getFirHTML = function(modelId, width, height, type, desc) { - var html = ""; - html = html + ''; - html = html + ''; - html = html + ''; - html = html + '
dammin.' + type + '
' + desc + '
'; - return html; -}; - -ModelVisualizerForm.prototype.getItems = function(modelPanel){ - _this = this; - var height = _this.height/2 - 60; - var width = _this.width/2 - 10; - - return Ext.create('Ext.container.Container', { - layout: { - type: 'vbox', // Arrange child items vertically - }, - items: [ - modelPanel, - { - xtype : 'container', - layout: { - type: 'hbox', // Arrange child items vertically - }, - items : [{ - html : this._getFirHTML("id", width, height, "fir", "Fit of the simulated scattering curve versus a smoothed experimental data (spline interpolation)"), - height :height, - width : width, - padding: 2 - }, - { - html : this._getFirHTML("id", width, height, "fit", "Fit of the simulated scattering curve versus the experimental data."), - height : height, - width : width, - padding: 2 - }] - } - - ] - }); -}; - -ModelVisualizerForm.prototype.refresh = function(models){ - var input = []; -// var colors = ["008000", "F0A804", "0000FF", "800080", "C0C0C0"]; - for (var i = 0; i < models.length; i++) { - console.log(BUI.rainbow(models.length, i).replace("#", "0x")); - input.push({ - color: BUI.rainbow(models.length, i).replace("#", "0x"), - modelId: models[i].modelId, - opacity: 0.8, - radius: 3, - title: BUI.getFileNameByPath(models[i].pdbFile), - type: "SHAPEDETERMINATIONMODEL" - - }); - } - - this.panel.removeAll(); - this.panel.add( - _this.getItems( - new PDBViewer({ - width : this.width - 10, - height : (this.height/2) - 10, - title : "" - }).draw(input) - ) - ); - - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - var splitted = data.toString().split("\n"); - var array = []; - for ( var i = 0; i < splitted.length; i++) { - var line = splitted[i].trim(); - var line_splited = line.split(/\s*[\s,]\s*/); - if (line_splited.length == 4) { - array.push([ Number(line_splited[0]), BUI.getStvArray(line_splited[1], line_splited[2]), BUI.getStvArray(line_splited[3], 0) ]); - } - } - - var id = (_this.id + "firid"); - var dygraphWidget = new StdDevDyGraph(id, { - width : (_this.width/2) - 10, - height :(_this.height/2) -110, - xlabel : 'q(nm-1)' - }); - dygraphWidget.draw(array, [ "#FF0000", "#0000FF", "#FF00FF" ], [ 's', 'I(exp)', 'I(sim)' ]); - }); - - adapter.getModelFile("FIR", models[0].modelId); - - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - var splitted = data.toString().split("\n"); - var array = []; - for ( var i = 0; i < splitted.length; i++) { - var line = splitted[i].trim(); - var line_splited = line.split(/\s*[\s,]\s*/); - if (line_splited.length == 3) { - array.push([ Number(line_splited[0]), BUI.getStvArray(line_splited[1], 0), BUI.getStvArray(line_splited[2], 0) ]); - } - } - - var id = (_this.id + "fitid"); - - var dygraphWidget = new StdDevDyGraph(id, { - width : (_this.width/2) - 10, - height : (_this.height/2) - 110, - xlabel : 'q(nm-1)' - }); - dygraphWidget.draw(array, [ "#FF0000", "#0000FF" ], [ "s", "I(exp)", "I(sim)" ]); - }); - adapter.getModelFile("FIT", models[0].modelId); -}; - -ModelVisualizerForm.prototype.getPanel = function(modelList){ - _this = this; - this.modelList = modelList; - this.panel = Ext.create('Ext.Panel', { - title: 'Results', - width: this.width, - height: this.height, - layout: { - type: 'vbox', // Arrange child items vertically -// align: 'stretch' // Each takes up full width - }, - items: [ - - ], - listeners : { - afterrender : function(grid, eOpts) { -// alert(_this.modelList) - } - } - }); - - return this.panel; - -}; - - -/** - * Example form - * - * @witdh - * @height - */ -function MolarityForm(args) { - this.id = BUI.id(); - this.width = 700; - this.height = 500; - - if (args != null) { - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; - } - } - - this.onSave = new Event(this); - this.onClose = new Event(this); -} - - -MolarityForm.prototype._getNumericWithHelp = function(type, fieldLabel, fieldName, help) { - return Ext.create('Ext.container.Container', { - margin : "10 0 0 10", - items : [ { - xtype : type, - fieldLabel : fieldLabel, - name : fieldName, - id : this.id + fieldName, - decimalPrecision : 6 - }, { - xtype : 'label', - forId : 'myFieldId', - text : help, - margin : "5 0 0 105", - cls : "inline-help" - } ] - }); -}; - - -MolarityForm.prototype._getItems = function() { - this.macromoleculeCombo = BIOSAXS_COMBOMANAGER.getComboMacromoleculeByMacromolecules(this.getMacromuleculesCandidates(this.macromolecule), { - width : 250, - labelWidth : 100, - margin : 10 - }); - - return [ { - xtype : 'container', - flex : 1, - margin : '10 0 0 10', - border : 0, - layout : 'anchor', - defaultType : 'requiredtext', - items : [ this.macromoleculeCombo, - this._getNumericWithHelp("textfield", "Ratio", "ratio", "Number in assymmetric units") - ] - } ]; -}; - -MolarityForm.prototype._persist = function() { - var _this = this; - var macromoleculeId = this.macromoleculeCombo.getValue(); - var ratio = Ext.getCmp(this.id + "ratio").getValue(); - var comments = "Not used yet"; - var dataAdapter = new BiosaxsDataAdapter(); - this.panel.setLoading("Saving"); - dataAdapter.onSuccess.attach(function(sender, args) { - _this.onSave.notify(); - }); - dataAdapter.saveStoichiometry(this.macromolecule.macromoleculeId, macromoleculeId, ratio, comments); -}; - -MolarityForm.prototype._getButtons = function() { - var _this = this; - - function onClose() { - _this.onClose.notify(); - } - - return [ { - text : 'Save', - handler : function() { - _this._persist(); - } - }, { - text : 'Cancel', - handler : function() { - onClose(); - } - } ]; -}; - -MolarityForm.prototype.getPanel = function() { - this.panel = Ext.create('Ext.form.Panel', { -// width : null, - height : this.height, - margin : 2, - border : 1, - defaultType : 'requiredtext', - items : this._getItems(), - buttons : this._getButtons() - }); - return this.panel; -}; - -/** macromolecules contains all macromolecules except this one **/ -MolarityForm.prototype.getMacromuleculesCandidates = function(macromolecule) { - var macromolecules = []; - if ( BIOSAXS.proposal.macromolecules){ - for (var i = 0; i < BIOSAXS.proposal.macromolecules.length; i++) { - var m = BIOSAXS.proposal.macromolecules[i]; - if (this.macromolecule != null){ - if (m.macromoleculeId != this.macromolecule.macromoleculeId) { - macromolecules.push(m); - } - } - } - } - return macromolecules; -}; - - -/** It populates the form **/ -MolarityForm.prototype.refresh = function(macromolecule) { - this.macromolecule = macromolecule; - -}; - - -MolarityForm.prototype.input = function() { - return {}; -}; - - -/** It populates the form **/ -MolarityForm.prototype.test = function(targetId) { - var macromoleculeForm = new MolarityForm(); - var panel = macromoleculeForm.getPanel(); - panel.render(targetId); -}; - -///** -// * -// * @witdh -// * @height -// */ -//function MacromoleculeForm(args) { -// this.id = BUI.id(); -// this.width = 700; -// this.height = 500; -// -// if (args != null) { -// if (args.width != null) { -// this.width = args.width; -// } -// if (args.height != null) { -// this.height = args.height; -// } -// } -// -// this.onClose = new Event(this); -//} -// -//MacromoleculeForm.prototype.getMacromolecule = function() { -// this.macromolecule.name = Ext.getCmp(this.panel.getItemId()).getValues().name; -// this.macromolecule.acronym = Ext.getCmp(this.panel.getItemId()).getValues().acronym; -// this.macromolecule.comments = Ext.getCmp(this.panel.getItemId()).getValues().comments; -// this.macromolecule.extintionCoefficient = Ext.getCmp(this.panel.getItemId()).getValues().extintionCoefficient; -// this.macromolecule.molecularMass = Ext.getCmp(this.panel.getItemId()).getValues().molecularMass; -// return this.macromolecule; -//}; -// -//MacromoleculeForm.prototype.setMacromolecule = function(macromolecule) { -// this.pdbStore.loadData(macromolecule.structure3VOs); -// -//}; -// -//MacromoleculeForm.prototype.getForm = function(macromolecule) { -// this.panel = Ext.createWidget('form', { -// frame : false, -// border : 0, -// padding : 15, -// width : 550, -// height : 350, -// items : [ { -// xtype : 'container', -// layout : 'hbox', -// items : [ { -// xtype : 'container', -// flex : 1, -// border : false, -// layout : 'anchor', -// defaultType : 'requiredtext', -// items : [ { -// fieldLabel : 'Name', -// name : 'name', -// anchor : '95%', -// tooltip : "Name of the macromolecule", -// value : macromolecule.name -// }, { -// fieldLabel : 'Acronym', -// name : 'acronym', -// anchor : '95%', -// value : macromolecule.acronym -// } ] -// }, { -// xtype : 'container', -// flex : 1, -// layout : 'anchor', -// defaultType : 'textfield', -// items : [ { -// xtype : 'numberfield', -// fieldLabel : 'Mol. Mass (Da)', -// name : 'molecularMass', -// value : macromolecule.molecularMass, -// decimalPrecision : 6 -// }, { -// xtype : 'numberfield', -// fieldLabel : 'Extinction coef.', -// name : 'extintionCoefficient', -// value : macromolecule.extintionCoefficient, -// decimalPrecision : 6 -// } ] -// } ] -// }, { -// xtype : 'textareafield', -// name : 'comments', -// fieldLabel : 'Comments', -// value : macromolecule.comments, -// width : this.width - 10 -// }, -// -// { -// html : BUI.getWarningHTML("The macromolecule is unsaved. Save the macromolecule to get access to other tabs"), -// margin : "150 10 10 10", -// id : this.id + "unsavedWarning", -// hidden : !(!macromolecule.macromoleculeId) -// } -// -// ] -// }); -// return this.panel; -//}; -// -//MacromoleculeForm.prototype.save = function() { -// var _this = this; -// -// var adapter = new BiosaxsDataAdapter(); -// adapter.onSuccess.attach(function(sender, proposal) { -// BIOSAXS.proposal.setItems(proposal); -// _this.panel.setLoading(false); -// -// Ext.getCmp(_this.id + "assembly").enable() -// Ext.getCmp(_this.id + "advanced").enable(); -// Ext.getCmp(_this.id + "unsavedWarning").hide(); -// }); -// -// if (this.getMacromolecule().name == "") { -// BUI.showError("Name field is mandatory"); -// return; -// } -// if (this.getMacromolecule().acronym == "") { -// BUI.showError("Acroynm field is mandatory"); -// return; -// } -// -// /** Check if acronym is unique * */ -// if (this.getMacromolecule().macromoleculeId == null) { -// if (BIOSAXS.proposal.getMacromoleculeByAcronym(this.getMacromolecule().acronym) == null) { -// this.panel.setLoading("ISPyB: Saving Macromolecule") -// adapter.saveMacromolecule(this.getMacromolecule()); -// } else { -// alert("There is already an existing macromolecule with the same acronym"); -// -// } -// } else { -// this.panel.setLoading("ISPyB: Saving Macromolecule") -// adapter.saveMacromolecule(this.getMacromolecule()); -// } -// -//}; -// -//MacromoleculeForm.prototype.getPanel = function(macromolecule) { -// var _this = this; -// this.macromolecule = macromolecule; -// return Ext.createWidget('tabpanel', { -// height : this.height, -// margin : 5, -// plain : true, -// style : { -// padding : 5 -// }, -// items : [ { -// tabConfig : { -// title : "General", -// disabled : false -// }, -// items : [ this.getForm(macromolecule) ], -// bbar : [ "->", { -// text : 'Save', -// cls : 'btn-with-border', -// style : { -// -// border : 1 -// }, -// handler : function() { -// _this.save(); -// } -// }, { -// text : 'Close', -// cls : 'btn-with-border', -// handler : function() { -// _this.onClose.notify(); -// } -// } ] -// }, { -// tabConfig : { -// id : this.id + "assembly", -// title : "Assembly", -// tooltip : 'Description of subunits present in the macromolecule', -// // hidden : (!macromolecule.macromoleculeId), -// disabled : (!macromolecule.macromoleculeId) -// }, -// items : [ this.getMolarityGrid(macromolecule) ] -// }, { -// tabConfig : { -// id : this.id + "advanced", -// title : "Advanced Modeling", -// // hidden : (!macromolecule.macromoleculeId), -// tooltip : 'Definition of the description contacts and symetries', -// disabled : (!macromolecule.macromoleculeId) -// }, -// items : [ this.getRigidBodyForm(macromolecule) ] -// } ] -// }); -//}; -// -//MacromoleculeForm.prototype.getRigidBodyForm = function(macromolecule) { -// var _this = this; -// -// // [P1, P2, P3, P4 ,P5 ,P6 ,32, P42, P52, P62] + P222 -// var symmetry = Ext.create('Ext.data.Store', { -// fields : [ 's' ], -// data : [ { -// "s" : "P1" -// }, { -// "s" : "P2" -// }, { -// "s" : "P3" -// }, { -// "s" : "P4" -// }, { -// "s" : "P5" -// }, { -// "s" : "P6" -// }, { -// "s" : "P32" -// }, { -// "s" : "P42" -// }, { -// "s" : "P52" -// }, { -// "s" : "P62" -// }, { -// "s" : "P222" -// } ] -// }); -// -// if (macromolecule.symmetry == null) { -// macromolecule.symmetry = "P1"; -// } -// var comboBox = Ext.create('Ext.form.ComboBox', { -// fieldLabel : 'Symmetry', -// store : symmetry, -// id : 'comboSym', -// queryMode : 'local', -// displayField : 's', -// valueField : 's', -// value : macromolecule.symmetry, -// margin : "10 0 0 0", -// listeners : { -// change : function(combo, newValue, oldValue, eOpts) { -// macromolecule.symmetry = newValue; -// } -// } -// }); -// -// this.rigidBodyPanel = Ext.createWidget('form', { -// frame : false, -// border : 0, -// padding : 10, -// width : 550, -// height : 400, -// items : [ { -// xtype : 'container', -// layout : 'hbox', -// items : [ { -// xtype : 'container', -// border : false, -// layout : 'hbox', -// items : [ { -// xtype : 'label', -// forId : 'myFieldId', -// text : 'Contact Desc:', -// width : 105, -// margin : '0 0 0 0' -// }, { -// xtype : 'textfield', -// hideLabel : true, -// id : "contactsDescriptionFilePath", -// margin : '0 0 0 0', -// width : 300, -// value : macromolecule.contactsDescriptionFilePath -// }, { -// text : 'Upload', -// xtype : 'button', -// margin : "0 0 0 20", -// width : 100, -// handler : function() { -// _this._openUploadDialog(macromolecule.macromoleculeId, "CONTACTS", "Upload Contact Description File"); -// } -// } ] -// } ] -// }, -// -// comboBox, { -// xtype : 'checkbox', -// margin : '10 0 0 5', -// boxLabel : "I want rigid body modeling run on this stuff", -// checked : true, -// width : 300 -// }, _this.getPDBGrid(macromolecule) ] -// }); -// return this.rigidBodyPanel; -//}; -// -//MacromoleculeForm.prototype.update = function() { -// var _this = this; -// BIOSAXS.proposal.onInitialized.attach(function() { -// if (BIOSAXS.proposal != null) { -// var macromolecules = BIOSAXS.proposal.macromolecules; -// for (var i = 0; i < macromolecules.length; i++) { -// if (macromolecules[i].macromoleculeId == _this.macromolecule.macromoleculeId) { -// _this.macromolecule = macromolecules[i]; -// _this.setMacromolecule(_this.macromolecule); -// _this.molarityStore.loadData(_this.parseMolarityData(_this.macromolecule)); -// _this.pdbGrid.setLoading(false); -// Ext.getCmp("contactsDescriptionFilePath").setValue(_this.macromolecule.contactsDescriptionFilePath) -// _this.molarityGrid.setLoading(false); -// -// } -// } -// } -// }); -// this.molarityGrid.setLoading("Updating"); -// this.pdbGrid.setLoading("Updating"); -// BIOSAXS.proposal.init(); -//}; -// -///******************************************************************************* -// * MOLARITY GRID -// ******************************************************************************/ -// -//MacromoleculeForm.prototype.parseMolarityData = function(macromolecule) { -// var data = []; -// if (macromolecule.stoichiometry != null) { -// for (var i = 0; i < macromolecule.stoichiometry.length; i++) { -// data.push({ -// ratio : macromolecule.stoichiometry[i].ratio, -// acronym : macromolecule.stoichiometry[i].macromolecule3VO.acronym, -// comments : macromolecule.stoichiometry[i].macromolecule3VO.comments, -// stoichiometryId : macromolecule.stoichiometry[i].stoichiometryId, -// name : macromolecule.stoichiometry[i].macromolecule3VO.name -// }); -// } -// } -// return data; -//}; -// -//MacromoleculeForm.prototype.getMolarityGrid = function(macromolecule) { -// var _this = this; -// -// this.molarityStore = Ext.create('Ext.data.Store', { -// fields : [ 'acronym', 'ratio', 'comments', 'stoichiometryId', 'name' ], -// data : this.parseMolarityData(macromolecule), -// sorters : { -// property : 'ratio', -// direction : 'DESC' -// } -// }); -// -// this.molarityGrid = Ext.create('Ext.grid.Panel', { -// store : this.molarityStore, -// height : 350, -// padding : 5, -// columns : [ -// -// { -// text : 'Subunit', -// columns : [ { -// text : "Acronym", -// width : 100, -// hidden : false, -// dataIndex : 'acronym', -// sortable : true -// }, { -// text : "Name", -// width : 100, -// hidden : false, -// dataIndex : 'name', -// sortable : true -// }, { -// text : "Comments", -// width : 100, -// dataIndex : 'comments', -// sortable : true -// } ] -// }, { -// text : "Number
in assymmetric units", -// width : 150, -// dataIndex : 'ratio', -// tooltip : 'Number of times this subunit is present in the macromolecule', -// sortable : true -// }, { -// id : this.id + 'MOLARITY_REMOVE', -// flex : 0.1, -// sortable : false, -// renderer : function(value, metaData, record, rowIndex, colIndex, store) { -// return BUI.getRedButton('REMOVE'); -// } -// } ], -// listeners : { -// cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { -// if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'MOLARITY_REMOVE') { -// var dataAdapter = new BiosaxsDataAdapter(); -// dataAdapter.onSuccess.attach(function() { -// _this.molarityGrid.setLoading(false); -// _this.update(); -// }); -// dataAdapter.removeStoichiometry(record.data.stoichiometryId); -// _this.molarityGrid.setLoading("Removing Structure"); -// } -// } -// }, -// buttons : [ { -// text : 'Add molarity', -// handler : function() { -// -// function onClose() { -// w.destroy(); -// _this.update(); -// } -// var w = Ext.create('Ext.window.Window', { -// title : 'Molarity', -// height : 300, -// width : 500, -// modal : true, -// buttons : [ { -// text : 'Save', -// handler : function() { -// var macromoleculeId = (_this.macromoleculeCombo.getValue()); -// var ratio = Ext.getCmp(_this.id + "ratio").getValue(); -// var comments = ""; -// var dataAdapter = new BiosaxsDataAdapter(); -// dataAdapter.onSuccess.attach(function(sender, args) { -// _this.update(); -// w.destroy(); -// }); -// dataAdapter.saveStoichiometry(_this.macromolecule.macromoleculeId, macromoleculeId, ratio, comments); -// } -// }, { -// text : 'Cancel', -// handler : function() { -// onClose(); -// } -// } ], -// items : [ _this.getMolarityForm(macromolecule) ], -// listeners : { -// onEsc : function() { -// onClose(); -// }, -// close : function() { -// onClose(); -// } -// } -// }).show(); -// } -// } ] -// }); -// return this.molarityGrid; -//}; -// -///******************************************************************************* -// * PDB GRID -// ******************************************************************************/ -// -//MacromoleculeForm.prototype._openUploadDialog = function(macromoleculeId, type, title) { -// var _this = this; -// function onClose() { -// w.destroy(); -// _this.update(); -// } -// -// var w = Ext.create('Ext.window.Window', { -// title : title, -// height : 200, -// width : 400, -// modal : true, -// buttons : [ { -// text : 'Close', -// handler : function() { -// onClose(); -// } -// } ], -// layout : 'fit', -// items : { -// html : "" -// }, -// listeners : { -// onEsc : function() { -// onClose(); -// }, -// close : function() { -// onClose(); -// } -// } -// }).show(); -//}; -// -//MacromoleculeForm.prototype._getPlugins = function() { -// var _this = this; -// var plugins = []; -// // if (this.updateRowEnabled) { -// plugins.push(Ext.create('Ext.grid.plugin.RowEditing', { -// clicksToEdit : 1, -// listeners : { -// validateedit : function(grid, e) { -// /** Comments are always updatable* */ -// e.record.raw.symmetry = e.newValues.symmetry; -// e.record.raw.multiplicity = e.newValues.multiplicity; -// -// var adapter = new BiosaxsDataAdapter(); -// adapter.onSuccess.attach(function(sender, measurement) { -// // _this.grid.setLoading(false); -// }); -// adapter.onError.attach(function() { -// alert("Error"); -// // _this.grid.setLoading(false); -// }); -// -// // _this.grid.setLoading(); -// adapter.saveStructure(e.record.raw); -// } -// } -// })); -// // } -// return plugins; -//}; -// -//MacromoleculeForm.prototype.getPDBGrid = function(macromolecule) { -// var _this = this; -// -// var data = macromolecule.structure3VOs; -// -// // /** Getting PDB from subunits **/ -// // if (macromolecule != null){ -// // if (macromolecule.stoichiometry != null){ -// // for (var i =0; i < macromolecule.stoichiometry.length; i++){ -// // var stoichiometry = macromolecule.stoichiometry[i]; -// // if (stoichiometry.macromolecule3VO != null){ -// // if (stoichiometry.macromolecule3VO.structure3VOs != null){ -// // for (var j = 0; j < stoichiometry.macromolecule3VO.structure3VOs.length; -// // j++) { -// // var structure = stoichiometry.macromolecule3VO.structure3VOs[j]; -// // structure["isSubunit"] = stoichiometry.macromolecule3VO.acronym; -// // data.push(structure) -// // } -// // } -// // } -// // } -// // } -// // } -// -// this.pdbStore = Ext.create('Ext.data.Store', { -// fields : [ 'filePath', 'structureId', 'structureType', 'symmetry', 'structureId', 'name', 'multiplicity' ], -// data : macromolecule.structure3VOs, -// groupField : 'structureType', -// sorters : { -// property : 'structureId', -// direction : 'DESC' -// } -// }); -// -// var groupingFeature = Ext.create('Ext.grid.feature.Grouping', { -// groupHeaderTpl : Ext.create('Ext.XTemplate', -// "
{name:this.formatName}
", { -// formatName : function(name) { -// return name; -// } -// }), -// hideGroupedHeader : true, -// startCollapsed : false -// }); -// -// this.pdbGrid = Ext.create('Ext.grid.Panel', { -// margin : "15 0 0 5", -// height : 250, -// store : this.pdbStore, -// plugins : _this._getPlugins(), -// buttons : [ { -// // text : 'Add PDB file', -// text : 'Add Modeling Option', -// handler : function() { -// _this._openUploadDialog(macromolecule.macromoleculeId, "PDB", 'Upload PDB File'); -// } -// } -// -// ], -// columns : [ -// { -// text : "structureId", -// flex : 0.2, -// hidden : true, -// dataIndex : 'structureId', -// sortable : true -// }, -// { -// text : "File", -// flex : 0.5, -// dataIndex : 'filePath', -// sortable : true, -// hidden : true -// }, -// { -// text : "PDB", -// flex : 0.4, -// dataIndex : 'name', -// sortable : true -// }, -// { -// text : "Symmetry", -// flex : 0.4, -// dataIndex : 'symmetry', -// sortable : true, -// editor : { -// xtype : 'combobox', -// typeAhead : true, -// triggerAction : 'all', -// selectOnTab : true, -// store : [ [ "P1", "P1" ], [ "P2", "P2" ], [ "P3", "P3" ], [ "P4", "P4" ], [ "P5", "P5" ], [ "P6", "P6" ], [ "P32", "P32" ], [ "P42", "P42" ], -// [ "P52", "P52" ], [ "P62", "P62" ], [ "P222", "P222" ] ], -// } -// }, { -// text : "Multiplicity", -// flex : 0.4, -// dataIndex : 'multiplicity', -// sortable : true, -// editor : { -// xtype : 'textfield' -// } -// -// }, { -// text : "Subunit", -// flex : 0.2, -// dataIndex : 'isSubunit', -// sortable : true, -// hidden : true -// }, { -// text : "Type", -// flex : 0.2, -// dataIndex : 'structureType', -// sortable : true, -// hidden : true -// }, -// -// { -// id : this.id + 'REMOVE', -// flex : 0.2, -// hidden : true, -// sortable : false, -// renderer : function(value, metaData, record, rowIndex, colIndex, store) { -// return BUI.getRedButton('REMOVE'); -// } -// }, ], -// -// listeners : { -// itemdblclick : function(dataview, record, item, e) { -// _this._editExperiment(record.raw.experimentId); -// }, -// cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { -// -// if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'REMOVE') { -// var dataAdapter = new BiosaxsDataAdapter(); -// dataAdapter.onSuccess.attach(function() { -// _this.pdbGrid.setLoading(false); -// _this.update(); -// }); -// dataAdapter.removeStructure(record.data.structureId); -// _this.pdbGrid.setLoading("Removing PDB file"); -// } -// -// } -// }, -// viewConfig : { -// getRowClass : function(record, rowIdx, params, store) { -// if (record.raw.isSubunit != null) { -// return "blue-row"; -// } -// } -// } -// }); -// -// return this.pdbGrid; -//}; -// -//MacromoleculeForm.prototype.getMolarityForm = function(macromolecule) { -// var _this = this; -// var data = []; -// for (var i = 0; i < BIOSAXS.proposal.macromolecules.length; i++) { -// var m = BIOSAXS.proposal.macromolecules[i]; -// if (m.macromoleculeId != macromolecule.macromoleculeId) { -// data.push(m); -// } -// -// } -// this.macromoleculeCombo = BIOSAXS_COMBOMANAGER.getComboMacromoleculeByMacromolecules(data, { -// width : 250, -// labelWidth : 100, -// margin : 10 -// }); -// -// return Ext.createWidget('form', { -// -// frame : false, -// border : 0, -// // padding : 15, -// width : 550, -// height : 350, -// items : [ { -// xtype : 'container', -// flex : 1, -// border : false, -// layout : 'anchor', -// defaultType : 'requiredtext', -// items : [ this.macromoleculeCombo, { -// xtype : 'numberfield', -// name : 'Ratio', -// id : _this.id + "ratio", -// fieldLabel : 'Number in assymmetric units', -// value : 1, -// decimalPrecision : 6, -// margin : 10 -// }, { -// xtype : 'textareafield', -// name : 'comments', -// fieldLabel : 'Comments', -// margin : 10, -// width : 400, -// value : "" -// -// } ] -// } ] -// }); -// -//}; -// -///******************************************************************************* -// * JAVASCRIPT DOC -// ******************************************************************************/ -//MacromoleculeForm.prototype.input = function() { -// return { -// macromolecule : DATADOC.getMacromolecule_10() -// }; -//}; -// -//MacromoleculeForm.prototype.test = function(targetId) { -// var macromoleculeForm = new MacromoleculeForm(); -// var panel = macromoleculeForm.getPanel(macromoleculeForm.input().macromolecule); -// panel.render(targetId); -//}; - -function ResultSummaryForm() { - this.radiationDamageThreshold = BUI.getRadiationDamageThreshold(); - this.qualityThreshold = BUI.getQualityThreshold(); - - /** Data clusters with bufers **/ - this.clusterByBuffers = false; - - /** Visualization are groupeb by concenttrations. Ex: 4.5mg/ml and 4.7mg/ml will be clusterized together **/ - this.collapseConcentrations = true; - - this.summaryHeight = 350; - this.id = BUI.id(); - - var _this = this; - - this.qualityControlResultsWidget = new QualityControlResultsWidget({ - qualityThreshold : this.radiationDamageThreshold, - radiationDamageThreshold : this.qualityThreshold - - }); - this.qualityControlResultsWidget.onQualityChanged.attach(function(sender, value) { - _this.qualityThreshold = value; - _this.thresholdsChanged(); - }); - - this.qualityControlResultsWidget.onRadiationDatamageChanged.attach(function(sender, value) { - _this.radiationDamageThreshold = value; - _this.thresholdsChanged(); - - }); - this.concentrationHTMLTableWidget = new ConcentrationHTMLTableWidget({ - height : 250, - showBufferColumns : this.clusterByBuffers - }); - - this.plot = new BoxWhiskerGraph({ - targetId : _this.id + '_boxPlot', - height : 350, - width : 450, - maxBoxWidth : 25 - }); - - this.rangePlot = new RangeWhiskerGraph({ - targetId : _this.id + '_rangePlot', - height : 350, - width : 450, - maxBoxWidth : 25 - }); -} - -ResultSummaryForm.prototype.thresholdsChanged = function() { - var parsedData = this.prepareData(this.rawData); - - var filtered = JSON.parse(JSON.stringify(parsedData)); - filtered.concentration.concentrations = []; - for ( var conc in parsedData.concentration.concentrations) { - if (parsedData.concentration.concentrations[conc].calculation.rgGnom.validNumber > 0) { - filtered.concentration.concentrations.push(parsedData.concentration.concentrations[conc]); - } - } - - this.plotWhisker(filtered); - this.plotRange(filtered); - - this.concentrationHTMLTableWidget.refresh(parsedData); -}; - -/** Given a frame object (object returned by analyzeFrames()) and depending of the threshold indicates if a datacollection has radiation damage **/ -ResultSummaryForm.prototype.hasRadiationDamage = function(frameObject) { - var bb = frameObject.bufferBeforeFramesMerged / frameObject.framesCount; - var ba = frameObject.bufferAfterFramesMerged / frameObject.framesCount; - var mol = frameObject.framesMerge / frameObject.framesCount; - return !((bb >= this.radiationDamageThreshold) && (ba >= this.radiationDamageThreshold) && (mol >= this.radiationDamageThreshold)); -}; - -/** Return (frameObject) an object with the information about the frames for a data collection**/ -ResultSummaryForm.prototype.analyzeFrames = function(dataCollectionRow) { - return { - bufferAfterFramesMerged : dataCollectionRow.bufferAfterFramesMerged, - bufferBeforeFramesMerged : dataCollectionRow.bufferBeforeFramesMerged, - framesCount : dataCollectionRow.framesCount, - framesMerge : dataCollectionRow.framesMerge - }; -}; - -ResultSummaryForm.prototype.detectDataCollectionWarnings = function(dataCollectionRow) { - var frameObject = this.analyzeFrames(dataCollectionRow); - var warnings = { - count : 0, - type : [] - }; - - if (this.hasRadiationDamage(frameObject)) { - warnings.count = warnings.count + 1; - warnings.type.push("RADIATION DAMAGE"); - } - - if (Number(dataCollectionRow.quality) < this.qualityThreshold) { - warnings.count = 1;//warnings.count + 1; - warnings.type.push("Quality <" + this.qualityThreshold); - } - return warnings; -}; - -/** Return array composed by {concentration} objects **/ -ResultSummaryForm.prototype.getConcentrations = function(data) { - var concentrationsId = {}; - - for ( var i = 0; i < data.length; i++) { - var warning = this.detectDataCollectionWarnings(data[i]); - var id = data[i].conc;// + "_" + data[i].bufferId; - if (this.clusterByBuffers) { - id = data[i].conc + "_" + data[i].bufferId; - } - - if (concentrationsId[id] == null) { - concentrationsId[id] = { - id : id, - concentration : Number(data[i].conc).toFixed(2), - bufferId : data[i].bufferId, - bufferAcronym : data[i].bufferAcronym, - rgGuinier : [], - i0Guinier : [], - rgGnom : [], - dMax : [], - quality : [], - frames : [], - frames_warning : warning.count - }; - } else { - concentrationsId[id].frames_warning = concentrationsId[id].frames_warning + warning.count; - } - - concentrationsId[id].frames.push(data[i]); - - if (warning.count == 0) { - concentrationsId[id].rgGuinier.push(data[i].rgGuinier); - concentrationsId[id].i0Guinier.push(data[i].I0); - concentrationsId[id].quality.push(data[i].quality); - concentrationsId[id].rgGnom.push(data[i].rgGnom); - concentrationsId[id].dMax.push(data[i].dmax); - } - - } - var concentrations = []; - for ( var item in concentrationsId) { - if (concentrationsId.hasOwnProperty(item)) { - concentrations.push({ - concentration : concentrationsId[item].concentration, - id : item, - bufferId : Number(concentrationsId[item].bufferId).toFixed(2), - bufferAcronym : concentrationsId[item].bufferAcronym, - rgGuinier : concentrationsId[item].rgGuinier, - /** Frames **/ - frames : concentrationsId[item].frames, - frames_warning : concentrationsId[item].frames_warning, - /** Calculation **/ - calculation : { - rgGuinier : BUI.getStandardDeviation(concentrationsId[item].rgGuinier), - i0Guinier : BUI.getStandardDeviation(concentrationsId[item].i0Guinier), - quality : BUI.getStandardDeviation(concentrationsId[item].quality), - rgGnom : BUI.getStandardDeviation(concentrationsId[item].rgGnom), - dMax : BUI.getStandardDeviation(concentrationsId[item].dMax) - - } - }); - } - } - - return { - concentrations : concentrations - }; -}; - -ResultSummaryForm.prototype.prepareData = function(data) { - /** Return array composed by {acronym, bufferId} objects **/ - function getBuffers(data) { - var buffersId = {}; - for ( var i = 0; i < data.length; i++) { - buffersId[data[i].bufferId] = data[i].acronym; - } - var buffers = []; - for ( var id in buffersId) { - if (buffersId.hasOwnProperty(id)) { - buffers.push({ - acronym : buffersId[id], - bufferId : id - }); - } - } - return buffers; - } - - /** Get a string with all the concentrations **/ - function getConcentrationString(parseConcentrations) { - var concentrations = []; - for ( var i = 0; i < parseConcentrations.concentrations.length; i++) { - concentrations.push(parseConcentrations.concentrations[i].concentration + " mg/ml "); - } - return concentrations.toString(); - } - - var parseConcentrations = this.getConcentrations(data); - - return { - dataCollectionCount : data.length, - buffers : getBuffers(data), - concentration : parseConcentrations, - concentrationLabel : getConcentrationString(parseConcentrations) - }; -}; - -ResultSummaryForm.prototype.getDataForWhisker = function(data) { - var clusters = []; - - var concentrations = {}; - var i = 0; - var conc = 0; - if (this.collapseConcentrations) { - for (i = 0; i < data.concentration.concentrations.length; i++) { - conc = data.concentration.concentrations[i]; - var concentration = Number(conc.concentration).toFixed(0); - if (concentrations[concentration] == null) { - concentrations[concentration] = {}; - concentrations[concentration].concentration = concentration; - concentrations[concentration].calculation = {}; - concentrations[concentration].calculation.rgGuinier = {}; - concentrations[concentration].calculation.rgGuinier.values = []; - concentrations[concentration].calculation.rgGuinier.values = conc.calculation.rgGuinier.values; - concentrations[concentration].calculation.rgGnom = {}; - concentrations[concentration].calculation.rgGnom.values = []; - concentrations[concentration].calculation.rgGnom.values = conc.calculation.rgGnom.values; - } else { - concentrations[concentration].calculation.rgGuinier.values = concentrations[concentration].calculation.rgGuinier.values - .concat(conc.calculation.rgGuinier.values); - concentrations[concentration].calculation.rgGnom.values = concentrations[concentration].calculation.rgGnom.values - .concat(conc.calculation.rgGnom.values); - } - } - - /** From object to array **/ - var array = []; - for ( var key in concentrations) { - if (concentrations.hasOwnProperty(key)) { - array.push(concentrations[key]); - } - } - data.concentration.concentrations = array; - } - - for (i = 0; i < data.concentration.concentrations.length; i++) { - conc = data.concentration.concentrations[i]; - clusters.push({ - name : conc.concentration + "mg/ml", - concentration : Number(conc.concentration), - x : Number(conc.concentration), - classes : [] - }); - clusters[clusters.length - 1].classes.push({ - name : "Guinier", - color : '#9A2EFE', - values : conc.calculation.rgGuinier.values - - }); - clusters[clusters.length - 1].classes.push({ - name : "P(r)", - color : '#2E64FE', - values : conc.calculation.rgGnom.values - - }); - } - return { - clusters : clusters.sort(function(a, b) { - return a.concentration - b.concentration; - }) - }; -}; - -ResultSummaryForm.prototype.getDataForWhiskerQuality = function(data) { - var clusters = []; - - for ( var i = 0; i < data.concentration.concentrations.length; i++) { - var conc = data.concentration.concentrations[i]; - clusters.push({ - name : conc.concentration + "mg/ml", - classes : [] - }); - clusters[clusters.length - 1].classes.push({ - name : "Quality", - values : conc.calculation.quality.values - - }); - } - - return { - clusters : clusters - }; -}; - -ResultSummaryForm.prototype.plotQualityWhisker = function(parsedData) { - this.qualityPlot.refresh(this.getDataForWhiskerQuality(parsedData)); -}; - -ResultSummaryForm.prototype.plotWhisker = function(parsedData) { - this.plot.refresh(this.getDataForWhisker(parsedData)); -}; - -ResultSummaryForm.prototype.plotRange = function(parsedData) { - this.rangePlot.refresh(this.getDataForWhisker(parsedData)); -}; - -ResultSummaryForm.prototype.getPanel = function(data) { - var _this = this; - _this.rawData = data; - var parsedData = this.prepareData(data); - - this.panel = Ext - .createWidget( - 'form', - { - bodyPadding : 20, - frame : false, - border : 0, - width : this.width, - height : this.summaryHeight + 1000, - items : [ { - xtype : 'container', - layout : 'hbox', - items : [ { - xtype : 'container', - flex : 1, - border : false, - layout : 'anchor', - defaultType : 'textfield', - items : [ - _this.qualityControlResultsWidget.getPanel(), - { - xtype : 'fieldset', - width : 950, - margin : "20, 0 0 0", - height : this.summaryHeight + 500, - items : [ - { - html : "
Concentration Analysis
", - border : 0, - width : 900 - - }, - { - html : this.concentrationHTMLTableWidget.getPanel(parsedData), - border : 0, - width : 900, - margin : "10, 0 0 10" - - }, - { - xtype : 'container', - layout : 'vbox', - border : 5, - items : [ - { - html : "
Rg based on Guinier and Gnom
", - border : 8, - width : 900, - margin : "20 0 0 10" - - }, { - xtype : 'container', - layout : 'hbox', - items : [ { - xtype : 'container', - layout : 'vbox', - items : [ { - html : "
", - border : 0, - width : this.plot.width, - padding : "10 0 0 20", - listeners : { - afterrender : function() { - _this.plotWhisker(parsedData); - - } - } - }, { - html : "
Concentration (mg/ml)
", - width : 450, - border : 0, - margin : "-50 0 0 0" - - } ] - }, { - xtype : 'container', - layout : 'vbox', - items : [ { - html : "
", - border : 0, - width : this.rangePlot.width, - padding : "10 0 0 10", - listeners : { - afterrender : function() { - _this.plotRange(parsedData); - } - } - }, { - html : "
Concentration (mg/ml)
", - width : 450, - border : 0, - margin : "-50 0 0 0" - - } ] - } ] - } ] - } ] - } ] - } - - ] - } ] - }); - return this.panel; - -}; - -ResultSummaryForm.prototype.input = function() { - return { - data : DATADOC.getData_3367() - }; -}; - -ResultSummaryForm.prototype.test = function(targetId) { - var resultSummaryForm = new ResultSummaryForm(); - var panel = resultSummaryForm.getPanel(resultSummaryForm.input().data); - panel.render(targetId); - -}; - -/** - * Example form - * - * @witdh - * @height - */ -function RigibBodyModelingForm(args) { - this.id = BUI.id(); - this.width = 700; - this.height = 500; - - if (args != null) { - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; - } - } - - var _this = this; - this.rigidBodyGrid = new AprioriRigidBodyGrid(); - - this.rigidBodyGrid.onUploadFile.attach(function(sender, type, title){ - _this._openUploadDialog(_this.macromolecule.macromoleculeId, type, title); - }); - - this.rigidBodyGrid.onRemove.attach(function(sender, type, title){ - _this._update(); - }); - - this.onSave = new Event(this); - -} - -RigibBodyModelingForm.prototype._getItems = function() { - var _this = this; - - - return [ { - xtype : 'label', - forId : 'myFieldId', - text : 'Information for model fit, mixture analysis and rigid body modeling', - margin : '15 0 20 10', - cls : "inline-help" - }, - this.rigidBodyGrid.getPanel(), - { - xtype : 'label', - forId : 'myFieldId', - text : 'Distance restraints may be imposed on the model using contacts conditions file (OPTIONAL)', - margin : '25 0 5 10', - cls : "inline-help" - }, - { - xtype : 'container', - layout : 'hbox', - items : [ { - xtype : 'container', - border : false, - layout : 'hbox', - items : [ { - xtype : 'label', - forId : 'myFieldId', - text : 'Contact Description File: (Optional)', - width : 150, - margin : '10 0 0 10' - }, { - id : this.id + "contactsDescriptionFilePath", - xtype : 'textfield', - hideLabel : true, - margin : '10 0 0 0', - width : 200, - disabled: true - }, { - text : 'Upload', - xtype : 'button', - margin : "10 0 0 10", - width : 80, - handler : function() { - - _this._openUploadDialog(_this.macromolecule.macromoleculeId, "CONTACTS", "Upload Contact Description File"); - } - }, { - text : 'Remove', - id : _this.id + "_remove", - xtype : 'button', - margin : "10 0 0 10", - width : 80, - handler : function() { - _this.macromolecule.contactsDescriptionFilePath = null; - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, proposal) { - /** Updating the proposal global object **/ - BIOSAXS.proposal.setItems(proposal); - _this.panel.setLoading(false); - - var saved = BIOSAXS.proposal.getMacromoleculeByAcronym(_this.macromolecule.acronym); - /** Refreshing to check that everything is ok **/ - _this.refresh(saved); - _this.onSave.notify(saved); - }); - - _this.panel.setLoading("Saving Macromolecule") - adapter.saveMacromolecule(_this.macromolecule); - } - } ] - } ] - }, { - xtype : 'panel', - html : "Go to SASREF manual for further information", - margin : "10 0 0 160", - border : 0 - - }, - { - xtype : 'checkbox', - margin : '10 0 0 5', - boxLabel : "I want rigid body modeling run on this stuff", - checked : true, - width : 300 - } ] - -}; - -/** Because update is a jsp page we don't know if the user has uploaded a file or not then we need to refresh **/ -RigibBodyModelingForm.prototype._update = function(macromoleculeId, type, title) { - var _this = this; - BIOSAXS.proposal.onInitialized.attach(function() { - if (BIOSAXS.proposal != null) { - _this.refresh(BIOSAXS.proposal.getMacromoleculeById(_this.macromolecule.macromoleculeId)); - _this.panel.setLoading(false); - } - }); - this.panel.setLoading(); - BIOSAXS.proposal.init(); -}; - -RigibBodyModelingForm.prototype._openUploadDialog = function(macromoleculeId, type, title) { - var _this = this; - function onClose() { - w.destroy(); - _this._update(); - - } - - var w = Ext.create('Ext.window.Window', { - title : title, - height : 200, - width : 400, - modal : true, - buttons : [ { - text : 'Close', - handler : function() { - onClose(); - } - } ], - layout : 'fit', - items : { - html : "" - }, - listeners : { - onEsc : function() { - onClose(); - }, - close : function() { - onClose(); - } - } - }).show(); -}; - -RigibBodyModelingForm.prototype._getButtons = function() { - return []; -}; - -RigibBodyModelingForm.prototype.getPanel = function() { - var _this = this; - this.panel = Ext.create('Ext.form.Panel', { - width : this.width, - height : this.height, - margin : 10, - border : 1, - defaultType : 'textfield', - items : this._getItems(), - buttons : this._getButtons(), - listeners : { - afterrender : function(){ - _this._populate(); - - } - } - }); - return this.panel; -}; - -/** Populates could be call when the DOM is not filled yet **/ -RigibBodyModelingForm.prototype._populate = function() { - if (this.macromolecule != null){ - if (Ext.getCmp(this.id + "contactsDescriptionFilePath") != null){ - if (this.macromolecule.contactsDescriptionFilePath != null){ - Ext.getCmp(this.id + "contactsDescriptionFilePath").setValue(this.macromolecule.contactsDescriptionFilePath); - Ext.getCmp(this.id + "_remove").enable(); - } - else{ - Ext.getCmp(this.id + "_remove").disable(); - Ext.getCmp(this.id + "contactsDescriptionFilePath").setValue(""); - - } - } - } -}; - -/** It populates the form * */ -RigibBodyModelingForm.prototype.refresh = function(macromolecule) { - this.macromolecule = macromolecule; - this.rigidBodyGrid.refresh(macromolecule); - this._populate(); -}; - -RigibBodyModelingForm.prototype.input = function() { - return {}; -}; - - -/** It populates the form **/ -RigibBodyModelingForm.prototype.test = function(targetId) { - var macromoleculeForm = new RigibBodyModelingForm(); - var panel = macromoleculeForm.getPanel(); - panel.render(targetId); -}; - - -/** - * Same form as MX part - * - * @creationMode if true a create button appears instead of save - * @showTitle true or false - */ -function ShipmentForm(args) { - this.id = BUI.id(); - - this.creationMode = false; - this.showTitle = true; - if (args != null) { - if (args.creationMode != null) { - this.creationMode = args.creationMode; - } - if (args.showTitle != null) { - this.showTitle = args.showTitle; - } - } - - this.onSaved = new Event(this); -} - -ShipmentForm.prototype.fillStores = function() { - this.panel.setLoading("Loading Labcontacts from database"); - this.labContactForSendingStore.loadData(BIOSAXS.proposal.getLabcontacts(), false); - this.labContactForReturnStore.loadData(BIOSAXS.proposal.getLabcontacts(), false); - this.panel.setLoading(false); - if (this.shipment != null) { - this.setShipment(this.shipment); - } -}; - -ShipmentForm.prototype.draw = function(targetId) { - this.getPanel().render(targetId); -}; - -ShipmentForm.prototype.setShipment = function(shipment) { - this.shipment = shipment; - var _this = this; - Ext.getCmp(_this.id + "shippingName").setValue(shipment.json.shippingName); - Ext.getCmp(_this.id + "shippingStatus").setValue(shipment.json.shippingStatus); - Ext.getCmp(_this.id + "comments").setValue(shipment.json.comments); - if (shipment.json.sendingLabContactVO != null) { - this.labContactsSendingCombo.setValue(shipment.json.sendingLabContactVO.labContactId); - } - if (shipment.json.returnLabContactVO != null) { - this.labContactsReturnCombo.setValue(shipment.json.returnLabContactVO.labContactId); - } - -}; - -ShipmentForm.prototype._saveShipment = function() { - var _this = this; - var shippingId = null; - if (this.shipment != null) { - shippingId = this.shipment.json.shippingId; - } - var json = { - shippingId : shippingId, - name : Ext.getCmp(_this.id + "shippingName").getValue(), - status : Ext.getCmp(_this.id + "shippingStatus").getValue(), - sendingLabContactId : Ext.getCmp(_this.id + "shipmentform_sendingLabContactId").getValue(), - returnLabContactId : Ext.getCmp(_this.id + "returnLabContactId").getValue(), - returnCourier : Ext.getCmp(_this.id + "returnCourier").getValue(), - courierAccount : Ext.getCmp(_this.id + "courierAccount").getValue(), - BillingReference : Ext.getCmp(_this.id + "BillingReference").getValue(), - dewarAvgCustomsValue : Ext.getCmp(_this.id + "dewarAvgCustomsValue").getValue(), - dewarAvgTransportValue : Ext.getCmp(_this.id + "dewarAvgTransportValue").getValue(), - comments : Ext.getCmp(_this.id + "comments").getValue() - }; - - var dataAdapter = new BiosaxsDataAdapter(); - dataAdapter.onSuccess.attach(function(sender, shipment) { - window.location = BUI.getShippingURL(shipment.shippingId); - }); - - dataAdapter.onError.attach(function(sender, error) { - _this.onError.notify(error); - }); - - /** Cheking params **/ - if (json.name == "") { - BUI.showError("Name field is mandatory"); - return; - } - - if (json.sendingLabContactId == null) { - BUI.showError("Lab contact for sending field is mandatory"); - return; - } - - if (json.returnLabContactId == null) { - BUI.showError("Lab contact for return field is mandatory"); - return; - } - - dataAdapter.createShipment(json.shippingId, json.name, json.status, json.comments, json.sendingLabContactId, json.returnLabContactId, - json.returnCourier, json.courierAccount, json.BillingReference, json.dewarAvgCustomsValue, json.dewarAvgTransportValue); - -}; - -ShipmentForm.prototype.getPanel = function(shipment) { - var _this = this; - this.shipment = shipment; - var required = '*'; - var buttons = []; - - if (_this.creationMode) { - buttons.push({ - text : 'Create', - scope : this, - handler : function() { - _this._saveShipment(); - } - }); - } else { - buttons.push({ - text : 'Save', - scope : this, - handler : function() { - _this._saveShipment(); - } - }); - - } - - this.labContactForSendingStore = Ext.create('Ext.data.Store', { - fields : [ 'cardName', 'labContactId' ] - }); - - this.labContactForReturnStore = Ext.create('Ext.data.Store', { - fields : [ 'cardName', 'labContactId' ] - }); - - // Create the combo box, attached to the states data store - this.labContactsSendingCombo = Ext.create('Ext.form.ComboBox', { - id : _this.id + "shipmentform_sendingLabContactId", - fieldLabel : 'Lab contact for sending', - afterLabelTextTpl : required, - store : this.labContactForSendingStore, - queryMode : 'local', - labelWidth : 200, - displayField : 'cardName', - valueField : 'labContactId' - }); - - this.labContactsReturnCombo = Ext.create('Ext.form.ComboBox', { - id : _this.id + "returnLabContactId", - fieldLabel : 'If No, Lab-Contact for Return', - afterLabelTextTpl : required, - store : this.labContactForReturnStore, - queryMode : 'local', - labelWidth : 200, - displayField : 'cardName', - valueField : 'labContactId', - listeners : { - change : function(x, newValue) { - for ( var i = 0; i < x.getStore().data.items.length; i++) { - if (x.getStore().data.items[i].raw.labContactId == newValue) { - Ext.getCmp(_this.id + "returnCourier").setValue(x.getStore().data.items[i].raw.defaultCourrierCompany); - Ext.getCmp(_this.id + "courierAccount").setValue(x.getStore().data.items[i].raw.courierAccount); - Ext.getCmp(_this.id + "BillingReference").setValue(x.getStore().data.items[i].raw.billingReference); - Ext.getCmp(_this.id + "dewarAvgCustomsValue").setValue(x.getStore().data.items[i].raw.dewarAvgCustomsValue); - Ext.getCmp(_this.id + "dewarAvgTransportValue").setValue(x.getStore().data.items[i].raw.dewarAvgTransportValue); - } - } - } - } - }); - - if (this.panel == null) { - this.panel = Ext.create('Ext.form.Panel', { - bodyPadding : 5, - width : 600, - border : 1, - items : [ { - xtype : 'fieldset', - title : 'Details', - collapsible : false, - defaultType : 'textfield', - layout : 'anchor', - defaults : { - anchor : '100%' - }, - items : [ { - xtype : 'requiredtext', - fieldLabel : 'Shipment Label', - allowBlank : false, - name : 'shippingName', - id : _this.id + 'shippingName', - value : '', - anchor : '50%' - }, { - - xtype : 'textareafield', - name : 'comments', - id : _this.id + 'comments', - fieldLabel : 'Comments', - value : '' - }, { - fieldLabel : 'Status', - readOnly : true, - id : _this.id + 'shippingStatus', - value : 'Opened', - anchor : '50%' - } ] - }, { - xtype : 'fieldset', - title : 'Lab-Contacts', - collapsible : false, - defaultType : 'textfield', - layout : 'anchor', - defaults : { - anchor : '100%' - }, - items : [ this.labContactsSendingCombo, this.labContactsReturnCombo ] - }, { - border : 0, - html : BUI.getWarningHTML("These informations are relevant for all shipments") - }, { - xtype : 'fieldset', - title : 'Courier accounts details for return', - collapsible : false, - layout : 'anchor', - defaults : { - anchor : '100%' - }, - items : [ { - xtype : 'textfield', - labelWidth : 400, - fieldLabel : 'Courier company for return (if ESRF sends a dewar back)', - id : _this.id + 'returnCourier', - value : '' - }, { - xtype : 'textfield', - labelWidth : 400, - fieldLabel : 'Courier account', - id : _this.id + 'courierAccount', - value : '' - }, { - xtype : 'textfield', - labelWidth : 400, - fieldLabel : 'Billing reference', - id : _this.id + 'BillingReference', - value : '' - }, { - xtype : 'numberfield', - labelWidth : 400, - fieldLabel : 'Average Customs value of a dewar (Euro)', - id : _this.id + 'dewarAvgCustomsValue', - value : '' - }, { - xtype : 'numberfield', - labelWidth : 400, - fieldLabel : 'Average Transport value of a dewar (Euro)', - id : _this.id + 'dewarAvgTransportValue', - value : '' - } ] - } ], - buttons : buttons - }); - } - this.fillStores(); - if (this.showTitle) { - this.panel.setTitle('Create a new Shipment'); - } - return this.panel; -}; - -ShipmentForm.prototype.input = function() { - return { - proposal : DATADOC.getProposal_10() - - }; -}; - -ShipmentForm.prototype.test = function(targetId) { - var shipmentForm = new ShipmentForm({ - creationMode : true - - }); - BIOSAXS.proposal = new Proposal(shipmentForm.input().proposal); - shipmentForm.getPanel().render(targetId); -}; - -/** - * #onSaved - */ -function StockSolutionForm(args) { - this.id = BUI.id(); - this.actions = []; - - if (args != null) { - if (args.actions != null) { - this.actions = args.actions; - } - } - this.onSaved = new Event(this); -} - -StockSolutionForm.prototype.getStockSolution = function() { - if (this.stockSolution != null) { - this.stockSolution.concentration = Ext.getCmp(this.id + "stockSolution_concentration").getValue(); - this.stockSolution.storageTemperature = Ext.getCmp(this.id + "stockSolution_storageTemperature").getValue(); - this.stockSolution.volume = Ext.getCmp(this.id + "stockSolution_volume").getValue(); - this.stockSolution.comments = Ext.getCmp(this.id + "stockSolution_comments").getValue(); - this.stockSolution.name = Ext.getCmp(this.id + "stockSolution_name").getValue(); - this.stockSolution.bufferId = this.bufferCombo.getValue(); - - if (this.macromoleculeCombo.getValue() != null) { - this.stockSolution.macromoleculeId = this.macromoleculeCombo.getValue(); - } else { - this.stockSolution.macromolecule3VO = null; - } - - } else { - return { - concentration : Ext.getCmp(this.id + "stockSolution_concentration").getValue(), - storageTemperature : Ext.getCmp(this.id + "stockSolution_storageTemperature").getValue(), - volume : Ext.getCmp(this.id + "stockSolution_volume").getValue(), - comments : Ext.getCmp(this.id + "stockSolution_comments").getValue(), - name : Ext.getCmp(this.id + "stockSolution_name").getValue(), - bufferId : this.bufferCombo.getValue(), - macromoleculeId : this.macromoleculeCombo.getValue() - }; - } - return this.stockSolution; -}; - -StockSolutionForm.prototype.setStockSolution = function(stockSolution) { - if (stockSolution != null) { - if (stockSolution.macromoleculeId != null) { - this.macromoleculeCombo.setValue(stockSolution.macromoleculeId); - } - this.bufferCombo.setValue(stockSolution.bufferId); - Ext.getCmp(this.id + "stockSolution_concentration").setValue(this.stockSolution.concentration); - Ext.getCmp(this.id + "stockSolution_storageTemperature").setValue(this.stockSolution.storageTemperature); - Ext.getCmp(this.id + "stockSolution_volume").setValue(this.stockSolution.volume); - Ext.getCmp(this.id + "stockSolution_name").setValue(this.stockSolution.name); - Ext.getCmp(this.id + "stockSolution_comments").setValue(this.stockSolution.comments); - } -}; - -StockSolutionForm.prototype.getBufferCombo = function() { - this.bufferCombo = BIOSAXS_COMBOMANAGER.getComboBuffers(BIOSAXS.proposal.getBuffers(), { - labelWidth : 120, - margin : '0 0 10 0', - width : 220 - - }); - return this.bufferCombo; -}; - -StockSolutionForm.prototype.getMacromoleculeCombo = function() { - this.macromoleculeCombo = BIOSAXS_COMBOMANAGER.getComboMacromoleculeByMacromolecules(BIOSAXS.proposal.getMacromolecules(), { - labelWidth : 120, - margin : '0 0 10 0', - width : 220 - - }); - return this.macromoleculeCombo; -}; - -StockSolutionForm.prototype.refresh = function() { -}; - -StockSolutionForm.prototype._getTopPanel = function() { - return { - xtype : 'container', - layout : 'hbox', - border : 0, - items : [ { - xtype : 'container', - layout : 'hbox', - items : [ { - xtype : 'container', - flex : 1, - border : false, - layout : 'anchor', - defaultType : 'textfield', - items : [ - - this.getMacromoleculeCombo(), { - xtype : 'requiredtext', - id : this.id + 'stockSolution_name', - fieldLabel : 'Acronym', - labelWidth : 120, - width : 250 - }, { - xtype : 'requiredtext', - id : this.id + 'stockSolution_concentration', - fieldLabel : 'Conc. (mg/ml)', - labelWidth : 120, - width : 250 - }, - - { - id : this.id + 'stockSolution_storageTemperature', - fieldLabel : 'Storage Temp.(C)', - labelWidth : 120, - width : 250 - }, { - xtype : 'requiredtext', - id : this.id + 'stockSolution_volume', - fieldLabel : 'Volume in Well (µl)', - labelWidth : 120, - width : 250 - } ] - } ] - }, { - xtype : 'container', - flex : 1, - layout : 'anchor', - defaultType : 'textfield', - margin : '0 0 0 10', - items : [ this.getBufferCombo() ] - } ] - }; - -}; - -StockSolutionForm.prototype.getPanel = function(stockSolution) { - this.stockSolution = stockSolution; - this.panel = Ext.createWidget({ - xtype : 'container', - layout : 'vbox', - border : 0, - style : { - padding : '10px' - }, - fieldDefaults : { - labelAlign : 'left', - labelWidth : 50 - }, - items : [ this._getTopPanel(stockSolution), { - id : this.id + 'stockSolution_comments', - xtype : 'textareafield', - name : 'comments', - fieldLabel : 'Comments', - labelWidth : 120, - width : '100%' - } ] - }); - - this.setStockSolution(stockSolution); - return this.panel; -}; - -StockSolutionForm.prototype.input = function() { - return { - stock : { - "stockSolutionId" : 6, - "proposalId" : 3124, - "macromoleculeId" : 5933, - "bufferId" : 811, - "instructionSet3VO" : null, - "boxId" : 305861, - "storageTemperature" : "20", - "volume" : "300", - "concentration" : "1.2", - "comments" : "Buffer EDTA with A", - "name" : "A_EDTA_1.2", - "samples" : [], - "buffer" : "EDTA", - "macromolecule" : "A" - }, - proposal : new MeasurementGrid().input().proposal - }; -}; - -StockSolutionForm.prototype.test = function(targetId) { - var stockSolutionForm = new StockSolutionForm(); - BIOSAXS.proposal = new Proposal(stockSolutionForm.input().proposal); - var panel = stockSolutionForm.getPanel(new Shipment(stockSolutionForm.input().stock)); - panel.render(targetId); -}; - - -BoxWhiskerGraph.prototype.cleanArray = GenericGraph.prototype.cleanArray; -BoxWhiskerGraph.prototype.plotAxes = GenericGraph.prototype.plotAxes; -BoxWhiskerGraph.prototype.plotRuler = GenericGraph.prototype.plotRuler; -BoxWhiskerGraph.prototype.drawSVGVerticalText = GenericGraph.prototype.drawSVGVerticalText; -BoxWhiskerGraph.prototype.getClassColor = GenericGraph.prototype.getClassColor; -BoxWhiskerGraph.prototype.getDimensions = GenericGraph.prototype.getDimensions; -BoxWhiskerGraph.prototype.calculate = GenericGraph.prototype.calculate; -BoxWhiskerGraph.prototype.getMedian = GenericGraph.prototype.getMedian; -BoxWhiskerGraph.prototype.pointToPixel = GenericGraph.prototype.pointToPixel; -BoxWhiskerGraph.prototype.maxValueWhisker = GenericGraph.prototype.maxValueWhisker; -BoxWhiskerGraph.prototype.refresh = GenericGraph.prototype.refresh; - -/** - * Subclass of GenericGraph - * - * @maxBoxWidth - */ -function BoxWhiskerGraph(args){ - this.maxBoxWidth = 25; - - if (args == null){ - args = new Object(); - } - args["plotHorizontalByCluster"] = true; - - GenericGraph.call(this, args); - - if (args.maxBoxWidth != null){ - this.maxBoxWidth = args.maxBoxWidth; - } -}; - - - -/** -There are several different methods for calculating quartiles.[1] This calculator uses a method described by Moore and McCabe to find quartile values. -The same method also used by The TI-83 to calculate quartile values. -With this method, the first quartile is the median of the numbers below the median, the third quartile is the median of the numbers above the median. - -http://www.miniwebtool.com/quartile-calculator/ -http://www.alcula.com/calculators/statistics/box-plot/ -**/ -BoxWhiskerGraph.prototype.getQ1 = function(array){ - array = array.slice(0, array.length/2); - return this.getMedian(array); -}; - -BoxWhiskerGraph.prototype.getQ3 = function(array){ - array = array.slice((array.length + 1)/2); - return this.getMedian(array); - -}; - -BoxWhiskerGraph.prototype.getQ2 = function(array){ - return this.getMedian(array); -}; - -BoxWhiskerGraph.prototype.getBelowOutliers = function(belowLimit, array){ - var points = new Array(); - for (var i = 0; i < array.length; i++){ - if (array[i] <= belowLimit){ - points.push(array[i]); - } - } - return points; -}; - -BoxWhiskerGraph.prototype.getAboveOutliers = function(aboveLimit, array){ - var points = new Array(); - for (var i = 0; i < array.length; i++){ - if (array[i] >= aboveLimit){ - points.push(array[i]); - } - } - return points; -}; - - -BoxWhiskerGraph.prototype.minValueWhisker = function(belowLimit, q1, array){ - var points = new Array(); - - for (var i = 0; i < array.length; i++){ - if ((array[i] < q1) && (array[i]) > belowLimit){ - points.push(array[i]); - } - } - - if (points.length > 0){ - points.sort(function(a, b){return a - b;}); - return points[0]; - } - return null; -}; - -BoxWhiskerGraph.prototype.isNumber = function(value){ - if (value=="") return false; - - var d = parseInt(value); - if (!isNaN(d)) return true; else return false; - -}; - -BoxWhiskerGraph.prototype.plotBoxWhisker = function(boxProperties){ - if (this.maxBoxWidth != null){ - if (boxProperties.width > this.maxBoxWidth){ - boxProperties.x = boxProperties.x + (boxProperties.width/2) - (this.maxBoxWidth/2); - boxProperties.width = this.maxBoxWidth; - } - - } - - if (this.plotPoints){ - for(var i = 0; i < boxProperties.values.length; i++){ - var value = boxProperties.values[i]; - var toPixel = this.pointToPixel(value, boxProperties); - SVG.drawCircle(boxProperties.x + (boxProperties.width/2) + 2, toPixel, this.pointRadius, this.svg, [["fill", "green"], ["fill-opacity", this.fillOpacityPoint],['stroke-opacity', this.strokeOpacityPoint], ["stroke", "black"]]); - } - } - - - var boxColor = this.getClassColor(boxProperties.name); - var result = this.calculate(boxProperties.values); - /** Q1 **/ - - if (this.isNumber(result.Q1)){ - SVG.drawLine(boxProperties.x, this.pointToPixel(result.Q1, boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result.Q1, boxProperties), this.svg, [["stroke", boxColor]]); - } - /** Q2 **/ - if (this.isNumber(result.Q2)){ - SVG.drawLine(boxProperties.x, this.pointToPixel(result.Q2, boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result.Q2, boxProperties), this.svg, [["stroke", "blue"], ["stroke-width", "2"]]); - } - - /** Q3 **/ - if (this.isNumber(result.Q3)){ - SVG.drawLine(boxProperties.x, this.pointToPixel(result.Q3, boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result.Q3, boxProperties), this.svg, [["stroke", boxColor]]); - } - - /** Concenting Q1 and Q3 **/ - if (this.isNumber(result.Q1)&&this.isNumber(result.Q3)){ - SVG.drawLine(boxProperties.x, this.pointToPixel(result.Q1, boxProperties), boxProperties.x, this.pointToPixel(result.Q3, boxProperties), this.svg, [["stroke", boxColor]]); - SVG.drawLine(boxProperties.x + boxProperties.width, this.pointToPixel(result.Q1, boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result.Q3, boxProperties), this.svg, [["stroke", boxColor]]); - } - - /** min-whisker **/ - if (result["min-whisker"] != null){ - if (this.isNumber(result.Q1)){ - SVG.drawLine(boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result.Q1, boxProperties), boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result["min-whisker"], boxProperties), this.svg, [["stroke", boxColor]]); - } - SVG.drawLine(boxProperties.x,this.pointToPixel(result["min-whisker"], boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result["min-whisker"], boxProperties) , this.svg, [["stroke", boxColor]]); - - } - - /** max-whisker **/ - if (result["max-whisker"] != null){ - if (this.isNumber(result.Q3)){ - SVG.drawLine(boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result.Q3, boxProperties), boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result["max-whisker"], boxProperties), this.svg, [["stroke", boxColor]]); - } - SVG.drawLine(boxProperties.x , this.pointToPixel(result["max-whisker"], boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result["max-whisker"], boxProperties), this.svg, [["stroke", boxColor]]); - - } - - /** outliners **/ - if (result["above-outliers"] != null){ - for (var point in result["above-outliers"]){ - SVG.drawCircle(boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result["above-outliers"][point], boxProperties), this.pointRadius, this.svg, [["fill", "red"], ["fill-opacity", "1"]]); - //SVG.drawText(boxProperties.x + (boxProperties.width/2) - 2, this.pointToPixel(result["above-outliers"][point], boxProperties) + 2, "x",this.svg, [["fill", "black"], ["font-size", "x-small"]]); - } - } - if (result["below-outliers"] != null){ - for (var point in result["below-outliers"]){ - SVG.drawCircle(boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result["below-outliers"][point], boxProperties), this.pointRadius, this.svg, [["fill", "red"], ["fill-opacity", "1"]]); - //SVG.drawText(boxProperties.x + (boxProperties.width/2) - 2, this.pointToPixel(result["below-outliers"][point], boxProperties) + 2, "x",this.svg, [["fill", "black"], ["font-size", "x-small"]]); - } - } -}; - - - -BoxWhiskerGraph.prototype.plotClusterTitles = function(properties){ - /** Cluster Titles **/ - var posX = this.left + this.rulerWidth; - var data = this.data; - for(var i = 0; i < data.clusters.length; i++ ){ - /** title for the clusters **/ - posX = posX + this.interClustersSpace; - - /** Drawing title of classes **/ - var cluster = data.clusters[i]; - var posXClasses = posX; - for(var j = 0; j < cluster.classes.length; j++){ - //SVG.drawRectangle(posXClasses, this.height - (this.bottom + this.clusterTitleHeight + this.rulerHeight), properties.classWidth, this.rulerHeight, this.svg, [["fill", "green"]]); -// SVG.drawText(posXClasses + 1/6*properties.classWidth, this.height - (this.bottom + this.clusterTitleHeight + (this.rulerHeight*1/4)), cluster.classes[j].name, this.svg, [["style", "font-size:xx-small"]]); - var color = cluster.classes[j].color; - this.drawSVGVerticalText(posXClasses + 1/2*(properties.classWidth), this.height - (this.bottom - this.clusterTitleHeight + (this.rulerHeight)), cluster.classes[j].name , [["style", "font-size:x-small;"], ["fill", color]]); - - // SVG.drawRectangle(posXClasses, this.height - (this.bottom + this.clusterTitleHeight), properties.classWidth, 2, this.svg, [["fill", "black"]]); - posXClasses = posXClasses + properties.classWidth + this.interClassesSpace; - } - - var clusterTitleSpace = (data.clusters[i].classes.length * properties.classWidth) + ((data.clusters[i].classes.length - 1) * this.interClassesSpace); - //SVG.drawRectangle(posX, this.height - (this.bottom + this.clusterTitleHeight), clusterTitleSpace, this.clusterTitleHeight, this.svg, [["fill", "pink"]]); - SVG.drawRectangle(posX, this.height - (this.clusterTitleHeight+this.bottom), clusterTitleSpace, 1, this.svg, []); - -// var transform = ["translate", "(" + posX + 1/3*clusterTitleSpace +", " + this.height - (this.bottom + (this.clusterTitleHeight*1/4)) +")"], ["transform", "rotate(180)"]; -// var transform = ["transform", "translate(" + (posX + 1/3*clusterTitleSpace) +", " + (this.height - (this.bottom + (this.clusterTitleHeight*1/4))) + "), rotate(-90) "]; -// this.drawSVGVerticalText(posX + 1/3*clusterTitleSpace, this.height - (this.bottom + (this.clusterTitleHeight*1/4)),data.clusters[i].name, [["style", "font-size:x-small"]]); - SVG.drawText(posX , this.height - (this.bottom + (this.clusterTitleHeight*1/4)),data.clusters[i].name ,this.svg, [["style", "font-size:x-small"]]); - posX = posX + clusterTitleSpace; - } -}; - -BoxWhiskerGraph.prototype.plotWhisters = function(data, properties){ - var colors = ["yellow", "orange", "green"]; - var posX = this.left + this.rulerWidth; - for(var i = 0; i < data.clusters.length; i++ ){ - var cluster = data.clusters[i]; - /** inter cluster space **/ - //SVG.drawRectangle(posX, this.top, this.interClustersSpace, this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight, this.svg, [["fill", "black"]]); - posX = posX + this.interClustersSpace; - - for (var j = 0; j < cluster.classes.length; j ++){ - - //SVG.drawRectangle(posX, this.top, properties.classWidth, this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight, this.svg, [["fill", colors[j]]]); - this.plotBoxWhisker( - { - name : cluster.classes[j].name, - values : cluster.classes[j].values, - minPoint : properties.minPoint, - maxPoint : properties.maxPoint, - x : posX, - y : this.top, - width : properties.classWidth, - height : this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight - - - } - ); - posX = posX + properties.classWidth; - //SVG.drawRectangle(posX, this.top, this.interClassesSpace, this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight, this.svg, [["fill", "black"]]); - if (j < cluster.classes.length - 1){ - posX = posX + this.interClassesSpace; - } - } - } -}; - -BoxWhiskerGraph.prototype.draw = function(targetId, data){ - this.targetId = targetId; - var properties = (this.getDimensions(data)); - this.svg = SVG.createSVGCanvas(document.getElementById(this.targetId), [["width", this.width], ["height", this.height]]); - this.plotAxes(properties); - this.plotClusterTitles(properties); - this.plotWhisters(data,properties); -}; - -BoxWhiskerGraph.prototype.input = function(){ - return DATADOC.getBoxWhikerData(); -}; - -BoxWhiskerGraph.prototype.test = function(targetId){ - var plot = new BoxWhiskerGraph( - { - targetId : targetId, - height : 350, - width : 450, - maxBoxWidth : 25 - } - ); - plot.refresh(this.input()); -}; - - - - - - - -function DataSet(){ - this.json = null; - -}; - - -DataSet.prototype.loadFromJSON = function(json){ - if(json != null) { - if(this.validate(json)) { - this.json = json; - } - } -}; - - -DataSet.prototype.toJSON = function(json){ - return this.json; -}; - - -/** Abstract method to be override on childs classes **/ -DataSet.prototype.validate = function(json){ - if (true){ - return true; - } - /*else{ - throw "Data validation failed"; - }*/ -}; - - - - -Edge.prototype.getName = GraphItem.prototype.getName; -Edge.prototype.setName = GraphItem.prototype.setName; -Edge.prototype.getId = GraphItem.prototype.getId; - -function Edge(id, name, nodeSource, nodeTarget, args){ - GraphItem.prototype.constructor.call(this, id, name, args); - - this.sourceNode = nodeSource; - this.targetNode = nodeTarget; - -}; - -Edge.prototype.toJSON = function(){ - return {"index": this.id,"sourceIndex":this.sourceNode.getId(),"targetIndex":this.targetNode.getId(),"args":this.args}; -}; - -Edge.prototype.getNodeSource = function(){ - return this.sourceNode; -}; - -Edge.prototype.getNodeTarget = function(){ - return this.targetNode; -}; - -Edge.prototype.remove = function(){ - //Remove edge object in the nodes - this.getNodeSource().removeEdge(this); - this.getNodeTarget().removeEdge(this); - - this.deleted.notify(this); -}; - - -EdgeGraphFormatter.prototype.setProperties = ItemGraphFormatter.prototype.setProperties; -EdgeGraphFormatter.prototype.getDefault = ItemGraphFormatter.prototype.getDefault; -EdgeGraphFormatter.prototype.getSelected = ItemGraphFormatter.prototype.getSelected; -EdgeGraphFormatter.prototype.getOver = ItemGraphFormatter.prototype.getOver; -EdgeGraphFormatter.prototype.getDragging = ItemGraphFormatter.prototype.getDragging; -EdgeGraphFormatter.prototype.getId = ItemGraphFormatter.prototype.getId; -EdgeGraphFormatter.prototype.toJSON = ItemGraphFormatter.prototype.toJSON; -EdgeGraphFormatter.prototype.loadFromJSON = ItemGraphFormatter.prototype.loadFromJSON; -EdgeGraphFormatter.prototype._setEvents = ItemGraphFormatter.prototype._setEvents; - -function EdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ - ItemGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); - - this.getDefault().args.type = "EdgeGraphFormatter"; -}; - - - - -LineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; -LineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; -LineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; -LineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; -LineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; -LineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; -LineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; -LineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; -LineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; - -function LineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ - EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); - this.args.type = "LineEdgeGraphFormatter"; -}; - -/** DIRECTED **/ -DirectedLineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; -DirectedLineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; -DirectedLineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; -DirectedLineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; -DirectedLineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; -DirectedLineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; -DirectedLineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; -DirectedLineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; -DirectedLineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; - -function DirectedLineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ - EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); - this.args.type = "DirectedLineEdgeGraphFormatter"; - this.args.arrowSize = "3"; -}; -DirectedLineEdgeGraphFormatter.prototype.getArrowSize = function(){ - return this.args.arrowSize; -}; - -OdirectedLineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; -OdirectedLineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; -OdirectedLineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; -OdirectedLineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; -OdirectedLineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; -OdirectedLineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; -OdirectedLineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; -OdirectedLineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; -OdirectedLineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; - -function OdirectedLineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ - EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); - this.args.type = "DirectedLineEdgeGraphFormatter"; - this.args.arrowSize = "3"; -}; - -OdirectedLineEdgeGraphFormatter.prototype.getArrowSize = function(){ - return this.args.arrowSize; -}; - - -/** CUT (inhibition) **/ -CutDirectedLineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; -CutDirectedLineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; -CutDirectedLineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; -CutDirectedLineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; -CutDirectedLineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; -CutDirectedLineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; -CutDirectedLineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; -CutDirectedLineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; -CutDirectedLineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; - -function CutDirectedLineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ - EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); - this.args.type = "CutDirectedLineEdgeGraphFormatter"; -}; - - - - -BezierEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; -BezierEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; -BezierEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; -BezierEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; -BezierEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; -BezierEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; -BezierEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; -BezierEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; -BezierEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; -BezierEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; - -function BezierEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ - EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); - this.args.type = "BezierEdgeGraphFormatter"; -}; - - - -DotDirectedLineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; -DotDirectedLineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; -DotDirectedLineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; -DotDirectedLineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; -DotDirectedLineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; -DotDirectedLineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; -DotDirectedLineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; -DotDirectedLineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; -DotDirectedLineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; - -function DotDirectedLineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ - EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); - this.args.type = "DotDirectedLineEdgeGraphFormatter"; -}; - - -OdotDirectedLineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; -OdotDirectedLineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; -OdotDirectedLineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; -OdotDirectedLineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; -OdotDirectedLineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; -OdotDirectedLineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; -OdotDirectedLineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; -OdotDirectedLineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; -OdotDirectedLineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; - -function OdotDirectedLineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ - EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); - this.args.type = "OdotDirectedLineEdgeGraphFormatter"; -}; - - - -function GraphDataset(){ - DataSet.prototype.constructor.call(this); - this.edges = new Object(); - this.vertices = new Object(); - this.verticesIndex = new Object(); - - //Events - this.newVertex = new Event(this); - this.vertexNameChanged = new Event(this); - this.vertexDeleted = new Event(this); - - this.newEdge = new Event(this); - this.edgeNameChanged = new Event(this); - this.edgeDeleted = new Event(this); - - this.json = new Object(); - this.json.vertices = new Array(); - this.json.edges = new Array(); - this.json.relations = new Array(); -}; - -GraphDataset.prototype.loadFromJSON = DataSet.prototype.loadFromJSON; -GraphDataset.prototype.toJSON = DataSet.prototype.toJSON; -GraphDataset.prototype.validate = DataSet.prototype.validate; - -/** Devuelve el numero de edges incidentes sobre el nodo con mas edges **/ -GraphDataset.prototype.getMaxClass = function(){ - var maxClassNode = 0; - for ( var node in this.vertices) { - if (this.vertices[node].getEdgesCount() > maxClassNode){ - maxClassNode = this.vertices[node].getEdgesCount(); - } - } - return maxClassNode; -}; - -/** Devuelve el numero de edges incidentes sobre el nodo con mas edges **/ -GraphDataset.prototype.getMinClass = function(){ - var minClassNode = Math.min(); - for ( var node in this.vertices) { - if (this.vertices[node].getEdgesCount() < minClassNode){ - minClassNode = this.vertices[node].getEdgesCount(); - } - } - return minClassNode; -}; - -GraphDataset.prototype.getVertexByName = function(nodeName){ - var results = new Array(); - - for (var vertexId in this.verticesIndex[nodeName]){ - var vertexByid = this.getVertexById(this.verticesIndex[nodeName][vertexId]); - results.push(vertexByid); - //* añadido nuevo porque fallaba el anterior codigo - return vertexByid - } - - if (results <= 1){ - return this.getVertexById(this.verticesIndex[nodeName]); - } - else{ - return results; - } -}; - -GraphDataset.prototype.getVertexById = function(id){ - return this.vertices[id]; -}; - -GraphDataset.prototype.toSIF = function(){ - var sifDataAdapter = new SifFileDataAdapter(); - return sifDataAdapter.toSIF(this); -}; - -GraphDataset.prototype.toSIFID = function(){ - var sifDataAdapter = new SifFileDataAdapter(); - return sifDataAdapter.toSIFID(this); -}; - -GraphDataset.prototype.toDOT = function(){ - var dotFileDataAdapter = new DotFileDataAdapter(); - return dotFileDataAdapter.toDOT(this); -}; - -GraphDataset.prototype.toDOTID = function(){ - var dotFileDataAdapter = new DotFileDataAdapter(); - return dotFileDataAdapter.toDOTID(this); -}; - -GraphDataset.prototype._addNode = function(nodeName, args){ - return new Vertex(this._getVerticesCount()-1, nodeName, args); -}; - -GraphDataset.prototype.addNode = function(nodeName, args){ - this.json.vertices.push(nodeName); - this._addVerticesIndex(nodeName, this._getVerticesCount() - 1); - var vertex = this._addNode(nodeName, args); - this.vertices[this._getVerticesCount()-1] = vertex; - this._setNodeEvents(vertex); - this.newVertex.notify(vertex); -}; - -GraphDataset.prototype._addVerticesIndex = function(nodeName, id){ - if (this.verticesIndex[nodeName] == null){ - this.verticesIndex[nodeName] = new Array(); - } - this.verticesIndex[nodeName].push(id); -}; - -GraphDataset.prototype.addEdge = function(edgeName, nodeSourceId, nodeTargetId, args){ - this.json.edges.push(edgeName); - var nodeSource = this.getVertexById(nodeSourceId); - var nodeTarget = this.getVertexById(nodeTargetId); - var index = this.getEdgesCount() - 1; - this.edges[index] = new Edge(index, edgeName, nodeSource, nodeTarget, args); - this.json.relations.push({"index": index, "sourceIndex": nodeSourceId, "targetIndex": nodeTargetId, "args": args }); - - nodeSource.addEdge(this.edges[index]); - nodeTarget.addEdge(this.edges[index]); - this._setEdgeEvents(this.edges[index]); - this.newEdge.notify(this.edges[index]); -}; - -GraphDataset.prototype.getVertices = function(){ - return this.vertices; -}; - -GraphDataset.prototype.getEdges = function(){ - return this.edges; -}; - -GraphDataset.prototype.getEdgeById = function(edgeId){ - return this.edges[edgeId]; -}; - -GraphDataset.prototype._getVerticesCount = function(){ - return this.json.vertices.length; -}; - - -GraphDataset.prototype.getVerticesCount = function(){ - var count = 0; - for ( var vertex in this.getVertices()) { - count ++; - } - return count; -}; - - -GraphDataset.prototype.getEdgesCount = function(){ - return this.json.edges.length; -}; - -GraphDataset.prototype.init = function(){ - this.edges = new Object(); - this.vertices = new Object(); -}; - -GraphDataset.prototype._setNodeEvents = function(node){ - var _this = this; - //NODE EVENTS - node.deleted.attach(function (sender, node){ - _this._removeNode(node); - }); - - node.nameChanged.attach(function (sender, args){ - var item = args.item; - var newName = item.name; - var indexes = _this.verticesIndex[args.previousName]; - for(var i = 0; i < indexes.length; i++){ - if(indexes[i] == item.id) - indexes.splice(i,1); - } - if(indexes.length == 0){ - delete _this.verticesIndex[args.previousName]; - } - _this._addVerticesIndex(newName, item.id); - _this.json.vertices[item.id] = newName; - _this.vertexNameChanged.notify(args); - }); -}; - -GraphDataset.prototype._setEdgeEvents = function(edge){ - var _this = this; - //EDGE EVENTS - edge.nameChanged.attach(function (sender, edge){ - _this.edgeNameChanged.notify(edge); - - }); - - edge.deleted.attach(function (sender, edge){ - _this._removeEdge(edge); - }); -}; - -GraphDataset.prototype._connectVerticesByName = function(nodeNameSource, nodeNameTarget){ - var source = this.getVertexByName(nodeNameSource); - var target = this.getVertexByName(nodeNameTarget); - - if ((source != null)&&(target!=null)){ - this.addEdge(source.getName() +"_" + target.getName(), source.getId(), target.getId(), {}); - } - else{ - if (source == null){ - console.log("No encontrado: " + nodeNameSource) - } - if (target == null){ - console.log("No encontrado: " + nodeNameTarget) - } - } -}; - -GraphDataset.prototype.loadFromJSON = function(json){ - var json = json; - this.init(); - this.json = new Object(); - this.json.vertices = new Array(); - this.json.edges = new Array(); - this.json.relations = new Array(); - - for ( var i = 0; i < json.nodes.length; i++) { - if (json.nodes[i] != null){ - var name = json.nodes[i]; - this.addNode(name); - } - else{ - this.json.vertices.push(null); - } - } - - for ( var i = 0; i < json.edges.length; i++) { - if (json.edges[i] != null){ - if (json.relations[i] != null){ - var name = json.edges[i]; - this.addEdge(name, json.relations[i].sourceIndex, json.relations[i].targetIndex, json.relations[i].args); - } - } - else{ - this.json.edges.push(null); - this.json.relations.push(null); - } - } -}; - -GraphDataset.prototype.prettyPrint = function(){ - for ( var node in this.vertices) { - console.log(this.vertices[node].getName() ); - for ( var j = 0; j < this.vertices[node].getEdgesIn().length; j++) { - console.log(" --> " + this.vertices[node].getEdgesIn()[j].getNodeTarget().getName() ); - } - } -}; - -GraphDataset.prototype._removeEdge = function(edge){ - this.json.edges[edge.getId()] = null; - this.json.relations[edge.getId()] = null; - - delete this.edges[edge.getId()]; - this.edgeDeleted.notify(edge); - - -}; - -GraphDataset.prototype._removeNode = function(node){ - this.json.vertices[node.getId()] = null; - delete this.vertices[node.getId()]; - this.vertexDeleted.notify(node); -}; - -GraphDataset.prototype.toJSON = function(){ - var json = new Object(); - var nodes = new Array(); - json.nodes = this.json.vertices; //nodes; - json.edges = this.json.edges; //edges; - json.relations = this.json.relations; - return json; -}; - -GraphDataset.prototype.clone = function(){ - var dsDataset = new GraphDataset(); - dsDataset.loadFromJSON(this.toJSON()); - return dsDataset; -}; -//GraphDataset.prototype.test = function(){ -// this.loadFromJSON(this.toJSON()); -//}; - -function labels(){ - var names = new Array(); - - var dataset = interactomeViewer.graphEditorWidget.dataset; - var layout = interactomeViewer.graphEditorWidget.layout; - - for ( var vertexId in interactomeViewer.graphEditorWidget.dataset.getVertices()) { - names.push(interactomeViewer.graphEditorWidget.dataset.getVertexById(vertexId).getName()); - } - - var sorted = (names.sort()); - console.log(sorted) - var distance = 0.01; - var altura = 0.6; - for ( var i = 0; i < names.length; i++) { - var id =dataset.getVertexByName(names[i]).getId(); - - layout.getNodeById(id).setCoordenates(distance, altura); - - - distance = parseFloat(distance) + parseFloat(0.03); - - altura = parseFloat(altura) + parseFloat(0.02); - - if (parseFloat(altura) == 0.9800000000000003){ - - altura = 0.6; - distance = distance - 0.51; - } - - } - - -}; - -function GraphItem(id, name, args){ - this.id = id; - this.name = name; - this.type = "NONE"; - - this.args = new Object(); - - - if (args!=null){ - this.args = args; - if (args.type !=null){ - this.type = args.type; - } - } - - //Events - this.nameChanged = new Event(this); - this.deleted = new Event(this); -} - -GraphItem.prototype.getName = function(){ - return this.name; -}; - -GraphItem.prototype.getId = function(){ - return this.id; -}; - -GraphItem.prototype.setName = function(name){ - var oldName = this.getName(); - this.name = name; - this.nameChanged.notify({"item": this, "previousName" : oldName}); -}; - - - - - -function LayoutDataset(){ - this.dataset = null; - this.vertices = new Object(); - this.changed = new Event(this); - - - this.args = new Object(); - - //RANDOM, CIRCLE - this.args.type = "CIRCLE"; -}; - -LayoutDataset.prototype.loadFromJSON = function(dataset, json){ - var _this = this; - this.vertices = new Object(); - this.dataset = dataset; //new GraphDataset(); - for ( var vertex in json) { - this.vertices[vertex] = new NodeLayout(vertex, json[vertex].x, json[vertex].y); - this.vertices[vertex].changed.attach(function (sender, item){ - _this.changed.notify(item); - }); - } - this._attachDatasetEvents(); -}; - - -LayoutDataset.prototype.toJSON = function(){ - var serialize = new Object(); - for ( var vertex in this.vertices) { - serialize[vertex] = new Object(); - serialize[vertex].x = this.vertices[vertex].x; - serialize[vertex].y = this.vertices[vertex].y; - } - serialize.dataset = new Object(); - serialize.dataset =this.dataset.toJSON(); - return serialize; -}; - -LayoutDataset.prototype.dataBind = function(graphDataset){ - this.dataset = graphDataset; - this._attachDatasetEvents(); - this._calculateLayout(); -}; - -LayoutDataset.prototype._removeVertex = function(vertexId){ - delete this.vertices[vertexId]; -}; - -LayoutDataset.prototype._attachDatasetEvents = function(){ - var _this = this; - - this.dataset.vertexDeleted.attach(function (sender, item){ - _this._removeVertex(item.getId()); - }); - - this.dataset.newVertex.attach(function (sender, item){ - _this.vertices[item.getId()] = new NodeLayout(item.getId(), 0.5, 0.5); - _this.vertices[item.getId()].changed.attach(function (sender, item){ - _this.changed.notify(item); - }); - }); -}; - -LayoutDataset.prototype.getType = function(){ - return this.args.type; -}; - -LayoutDataset.prototype._calculateLayoutVertices = function(type, count){ - - if (type == "CIRCLE"){ - var radius = 0.4; - var centerX = 0.5; - var centerY = 0.5; - var verticesCoordinates = new Array(); - for(var i = 0; i < count; i++){ - x = centerX + radius * Math.sin(i * 2 * Math.PI/count); - y = centerY + radius * Math.cos(i * 2 * Math.PI/count); - verticesCoordinates.push({'x':x,'y':y}); - } - return verticesCoordinates; - } -}; - - -LayoutDataset.prototype._calculateLayout = function(){ - var _this = this; - if (this.getType() == "RANDOM"){ - for ( var vertex in this.dataset.getVertices()) { - if (this.vertices[vertex] == null){ - this.vertices[vertex] = new NodeLayout(vertex, 0, 0); - } - this.vertices[vertex].setCoordinates(Math.random(), Math.random()); - this.vertices[vertex].changed.attach(function (sender, item){ - _this.changed.notify(item); - }); - } - } - - if ( this.getType() == "CIRCLE"){ - - var count = this.dataset._getVerticesCount(); - var verticesCoordinates = this._calculateLayoutVertices(this.getType(), count); - - var aux = 0; - for ( var vertex in this.dataset.getVertices()) { - if (this.vertices[vertex] == null){ - this.vertices[vertex] = new NodeLayout(vertex, 0, 0); - } - this.vertices[vertex].setCoordinates(verticesCoordinates[aux].x, verticesCoordinates[aux].y);//{"x":, "y":}; - aux++; - this.vertices[vertex].changed.attach(function (sender, item){ - _this.changed.notify(item); - }); - } - } - - - if (this.getType() == "SQUARE"){ - - var count = this.dataset._getVerticesCount(); - var xMin = 0.1; - var xMax = 0.9; - var yMin = 0.1; - var yMax = 0.9; - - var rows = Math.sqrt(count); - var step = (xMax - xMin) / rows; - - var verticesCoordinates = new Array(); - for(var i = 0; i < rows; i ++){ - for ( var j = 0; j < rows; j++) { - x = i * step + xMin; - y = j * step + yMin; - verticesCoordinates.push({'x':x,'y':y}); - } - } - - var aux = 0; - for ( var vertex in this.dataset.getVertices()) { - if (this.vertices[vertex] == null){ - this.vertices[vertex] = new NodeLayout(vertex, 0, 0); - } - this.vertices[vertex].setCoordinates(verticesCoordinates[aux].x, verticesCoordinates[aux].y);//{"x":, "y":}; - aux++; - this.vertices[vertex].changed.attach(function (sender, item){ - _this.changed.notify(item); - }); - } - } - -}; - -LayoutDataset.prototype.getNodeById = function(id){ - return this.vertices[id]; -}; - -LayoutDataset.prototype.getVerticesByArea = function(x1, y1, x2, y2){ - var vertices = new Array(); - for ( var vertex in this.dataset.getVertices()) { - if ((this.vertices[vertex].x >= x1)&&(this.vertices[vertex].x <= x2)){ - if ((this.vertices[vertex].y >= y1)&&(this.vertices[vertex].y <= y2)){ - vertices.push(this.vertices[vertex]); - } - } - } - return vertices; -}; - - - - -LayoutDataset.prototype.getLayout = function(type){ - - if (type == "CIRCLE"){ - this.args.type = "CIRCLE"; - this._calculateLayout(); - return; - } - - if (type == "SQUARE"){ - this.args.type = "SQUARE"; - this._calculateLayout(); - return; - } - - if (type == "RANDOM"){ - this.args.type = "RANDOM"; - this._calculateLayout(); - return; - } - - - var dotText = this.dataset.toDOTID(); - var url = "http://bioinfo.cipf.es/utils/ws/rest/network/layout/"+type+".coords"; - var _this = this; - - $.ajax({ - async: true, - type: "POST", - url: url, - dataType: "text", - data: { - dot :dotText - }, - cache: false, - success: function(data){ - var response = JSON.parse(data); - for ( var vertexId in response) { - _this.vertices[vertexId].setCoordinates(response[vertexId].x, response[vertexId].y); - } - } - }); - -// $.ajax({ -// async: true, -// type: "POST", -// url: url, -// dataType: "script", -// data: { -// dot :dotText -// }, -// cache: false, -// success: function(data){ -// var response = JSON.parse(data); -// for ( var vertexId in response) { -// _this.vertices[vertexId].setCoordinates(response[vertexId].x, response[vertexId].y); -// } -// } -// }); - -}; - -function NodeLayout(id, x, y, args){ - this.id = id; - this.x = x; - this.y = y; - this.changed = new Event(this); -}; - -NodeLayout.prototype.getId = function(id){ - return this.id; -}; - -NodeLayout.prototype.setCoordinates = function(x, y){ - this.x = x; - this.y = y; - this.changed.notify(this); -}; - - - -function NetworkDataSetFormatter(vertexFormatProperties, defaultEdgeProperties, args){ - DataSet.prototype.constructor.call(this); - - this.args = new Object(); - - this.vertices = new Object(); - this.edges = new Object(); - this.dataset = null; - this.maxClass = 0; - this.minClass = 0; - - /** Coordenates with default Setting */ - this.args.width = 1100; - this.args.height = 500; - - /** Optional parameters */ - this.args.backgroundColor = "#FFFFFF"; - this.args.backgroundImage = null; - this.args.backgroundImageHeight = null; - this.args.backgroundImageWidth = null; - this.args.backgroundImageX = null; - this.args.backgroundImageY = null; - - - this.args.balanceNodes = false; - this.args.nodesMaxSize = 3; - this.args.nodesMinSize = 0.5; - - - /** Zoom **/ - this.args.zoomScale = 1; - this.args.zoomScaleStepFactor = 0.4; - - if (args != null){ - if (args.backgroundImage != null){ - this.args.backgroundImage = args.backgroundImage; - } - - if (args.width != null){ - this.args.width = args.width; - } - - if (args.height != null){ - this.args.height = args.height; - this.args.svgHeight = args.height; - } - - if (args.svgHeight != null){ - this.args.svgHeight = args.svgHeight; - } - - if (args.backgroundColor != null){ - this.args.backgroundColor = args.backgroundColor; - } - - if(args.balanceNodes != null){ - this.args.balanceNodes = args.balanceNodes; - } - - if(args.nodesMaxSize != null){ - this.args.nodesMaxSize = args.nodesMaxSize; - } - if(args.nodesMinSize != null){ - this.args.nodesMinSize = args.nodesMinSize; - } - } - - this.args.defaultEdgeProperties = {"fill":"#000000", "radius":"1", "stroke":"#000000", "size":1, "title":{"fontSize":10, "fontColor":"#000000"}}; - this.args.vertexFormatProperties = { "fill":"#000000", "stroke":"#000000", "stroke-opacity":"#000000"}; - - if (vertexFormatProperties!= null){ - this.args.vertexFormatProperties = vertexFormatProperties; - } - if (defaultEdgeProperties!= null){ - this.args.defaultEdgeProperties = defaultEdgeProperties; - } - - /** Events **/ - this.changed = new Event(this); - this.edgeChanged = new Event(this); - this.resized = new Event(this); - this.backgroundImageChanged= new Event(this); - this.backgroundColorChanged= new Event(this); -}; - -NetworkDataSetFormatter.prototype.loadFromJSON = function(dataset, json){ - this.args = new Object(); - this.vertices = new Object(); - this.args = json; - this._setDataset(dataset); - var _this = this; - - for ( var vertex in json.vertices) { - this.addVertex(vertex, json.vertices[vertex]); - } - - for ( var edgeId in json.edges) { - this.addEdge(edgeId, json.edges[edgeId]); - } -}; - - -NetworkDataSetFormatter.prototype.toJSON = function(){ - - -// this.args.vertices = new Object(); -// this.args.edges = new Object(); -// -// for ( var vertex in this.vertices) { -// this.args.vertices[vertex] = this.getVertexById(vertex).toJSON(); -// } -// for ( var edge in this.edges) { -// this.args.edges[edge] = this.getEdgeById(edge).toJSON(); -// } -// -// return (this.args); - - - var serialize = new Object(); - serialize = JSON.parse(JSON.stringify(this.args)); - serialize.vertices = new Object(); - serialize.edges = new Object(); - - for ( var vertex in this.vertices) { - serialize.vertices[vertex] = this.getVertexById(vertex).toJSON(); - } - for ( var edge in this.edges) { - serialize.edges[edge] = this.getEdgeById(edge).toJSON(); - } - - return (serialize); -}; - - - -NetworkDataSetFormatter.prototype._getNodeSize = function(nodeId){ - if (this.isVerticesBalanced()){ - var total = this.maxClass - this.minClass; - if (total == 0){ total = 1;} - var nodeConnection = this.dataset.getVertexById(nodeId).getEdges().length; - return ((nodeConnection*this.args.nodesMaxSize)/total) + this.args.nodesMinSize; - } - return this.getVertexById(nodeId).getDefault().getSize(); -}; - -NetworkDataSetFormatter.prototype._recalculateSize = function(){ - if (this.isVerticesBalanced()){ - this.maxClass = this.dataset.getMaxClass(); - this.minClass = this.dataset.getMinClass(); - for ( var vertexIdAll in this.vertices) { - var size = this._getNodeSize(vertexIdAll); - this.vertices[vertexIdAll].getDefault().setSize(size); - this.vertices[vertexIdAll].getSelected().setSize(size); - this.vertices[vertexIdAll].getOver().setSize(size); - } - } -}; - - -NetworkDataSetFormatter.prototype.addVertex = function(vertexId, json){ - - - if (json == null){ - this.vertices[vertexId] = new CircleVertexGraphFormatter(vertexId, this.args.vertexFormatProperties.defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); - } - else{ - - /** Cargo los attributos desde el json **/ - if (json.type == null){ - this.vertices[vertexId] = new CircleVertexGraphFormatter(vertexId, this.args.vertexFormatProperties.defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); - } - - if ((json.type == "SquareVertexGraphFormatter")||(json.type == "SquareVertexNetworkFormatter")){ - this.vertices[vertexId] = new SquareVertexGraphFormatter(vertexId); - this.vertices[vertexId].loadFromJSON(json); - } - - if ((json.type == "CircleVertexGraphFormatter")||(json.type == "CircleVertexNetworkFormatter")){ - this.vertices[vertexId] = new CircleVertexGraphFormatter(vertexId); - this.vertices[vertexId].loadFromJSON(json); - } - - if ((json.type == "EllipseVertexGraphFormatter")||(json.type == "EllipseVertexNetworkFormatter")){ - this.vertices[vertexId] = new EllipseVertexGraphFormatter(vertexId); - this.vertices[vertexId].loadFromJSON(json); - } - - if ((json.type == "RectangleVertexGraphFormatter")||(json.type == "RectangleVertexNetworkFormatter")){ - this.vertices[vertexId] = new RectangleVertexGraphFormatter(vertexId); - this.vertices[vertexId].loadFromJSON(json); - } - - if ((json.type == "RoundedVertexGraphFormatter")||(json.type == "RoundedVertexNetworkFormatter")){ - this.vertices[vertexId] = new RoundedVertexGraphFormatter(vertexId); - this.vertices[vertexId].loadFromJSON(json); - } - - } - - - var _this = this; - this.vertices[vertexId].stateChanged.attach(function (sender, item){ - _this.changed.notify(item); - }); - - var size = this._getNodeSize(vertexId); - this.vertices[vertexId].defaultFormat.args.size = size; - this.vertices[vertexId].selected.args.size = size; - this.vertices[vertexId].over.args.size = size; - -}; - -NetworkDataSetFormatter.prototype.addEdge = function(edgeId, json){ - - /** Es un edge nuevo que le doy los atributos por defecto **/ - if (json == null){ - if (this.dataset.getEdgeById(edgeId).getNodeSource().getId() == this.dataset.getEdgeById(edgeId).getNodeTarget().getId()){ - this.edges[edgeId] = new BezierEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); - }else{ - this.edges[edgeId] = new DirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); - } - } - else{ - /** Cargo los attributos desde el json **/ - if (json.type == null){ - this.edges[edgeId] = new LineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); - } - - if ((json.type == "LineEdgeGraphFormatter")||(json.type == "LineEdgeNetworkFormatter")){ - this.edges[edgeId] = new LineEdgeGraphFormatter(edgeId); - this.edges[edgeId].loadFromJSON(json); - } - if ((json.type == "DirectedLineEdgeGraphFormatter")||(json.type == "DirectedLineEdgeNetworkFormatter")){ - this.edges[edgeId] = new DirectedLineEdgeGraphFormatter(edgeId); - this.edges[edgeId].loadFromJSON(json); - } - - if ((json.type == "BezierEdgeGraphFormatter")||(json.type == "BezierEdgeNetworkFormatter")){ - this.edges[edgeId] = new BezierEdgeGraphFormatter(edgeId); - this.edges[edgeId].loadFromJSON(json); - } - - - if ((json.type == "CutDirectedLineEdgeGraphFormatter")||(json.type == "CutDirectedLineEdgeNetworkFormatter")){ - this.edges[edgeId] = new CutDirectedLineEdgeGraphFormatter(edgeId); - this.edges[edgeId].loadFromJSON(json); - } - - if ((json.type == "DotDirectedLineEdgeGraphFormatter")||(json.type == "DotDirectedLineEdgeNetworkFormatter")){ - this.edges[edgeId] = new DotDirectedLineEdgeGraphFormatter(edgeId); - this.edges[edgeId].loadFromJSON(json); - } - if ((json.type == "OdotDirectedLineEdgeGraphFormatter")||(json.type == "OdotDirectedLineEdgeNetworkFormatter")){ - this.edges[edgeId] = new OdotDirectedLineEdgeGraphFormatter(edgeId); - this.edges[edgeId].loadFromJSON(json); - } - - if ((json.type == "OdirectedLineEdgeGraphFormatter")||(json.type == "OdirectedLineEdgeNetworkFormatter")){ - this.edges[edgeId] = new OdirectedLineEdgeGraphFormatter(edgeId); - this.edges[edgeId].loadFromJSON(json); - } - } - - var _this = this; - this.edges[edgeId].stateChanged.attach(function (sender, item){ - _this.edgeChanged.notify(item); - }); - - this._recalculateSize(); -}; - -NetworkDataSetFormatter.prototype._setDataset = function(dataset){ - this.dataset = dataset; - this.maxClass = dataset.getMaxClass(); - this.minClass = dataset.getMinClass(); - this._attachDatasetEvents(); -}; - -NetworkDataSetFormatter.prototype.changeEdgeType = function(edgeId, type){ - if ((type == "LineEdgeGraphFormatter")||(type == "LineEdgeNetworkFormatter")){ - this.edges[edgeId] = new LineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); - - } - if ((type == "DirectedLineEdgeGraphFormatter")||(type == "DirectedLineEdgeNetworkFormatter")){ - this.edges[edgeId] = new DirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); - } - - if ((type == "CutDirectedLineEdgeGraphFormatter")||(type == "CutDirectedLineEdgeNetworkFormatter")){ - this.edges[edgeId] = new CutDirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); - } - - if ((type == "DotDirectedLineEdgeGraphFormatter")||(type == "DotDirectedLineEdgeNetworkFormatter")){ - this.edges[edgeId] = new DotDirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); - } - - if ((type == "OdotDirectedLineEdgeGraphFormatter")||(type == "OdotDirectedLineEdgeNetworkFormatter")){ - this.edges[edgeId] = new OdotDirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); - } - - if ((type == "OdirectedLineEdgeGraphFormatter")||(type == "OdirectedLineEdgeNetworkFormatter")){ - this.edges[edgeId] = new OdirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); - } - - - - var _this = this; - this.edges[edgeId].stateChanged.attach(function (sender, item){ - _this.edgeChanged.notify(item); - }); - _this.edgeChanged.notify(this.edges[edgeId]); -}; -/* -classe = "SquareNetworkNodeFormatter"; -} -if (value == "circle"){ - classe = "CircleNetworkNodeFormatter"; - **/ -NetworkDataSetFormatter.prototype.changeNodeType = function(vertexId, type){ - var defaultFormat = JSON.parse(JSON.stringify(this.vertices[vertexId].getDefault())); - var selectedFormat = JSON.parse(JSON.stringify(this.vertices[vertexId].getSelected())); - var defaultFormat = JSON.parse(JSON.stringify(this.vertices[vertexId].getDefault())); - var defaultFormat = JSON.parse(JSON.stringify(this.vertices[vertexId].getDefault())); - - if ((type == "SquareVertexGraphFormatter")||(type == "SquareVertexNetworkFormatter")){ - this.vertices[vertexId] = new SquareVertexGraphFormatter(vertexId,defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); - } - - if ((type == "CircleVertexGraphFormatter")||(type == "CircleVertexNetworkFormatter")){ - this.vertices[vertexId] = new CircleVertexGraphFormatter(vertexId, defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); - } - - if ((type == "EllipseVertexGraphFormatter")||(type == "EllipseVertexNetworkFormatter")){ - this.vertices[vertexId] = new EllipseVertexGraphFormatter(vertexId, defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); - } - - if ((type == "RectangleVertexGraphFormatter")||(type == "RectangleVertexNetworkFormatter")){ - this.vertices[vertexId] = new RectangleVertexGraphFormatter(vertexId, defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); - } - - if ((type == "RoundedVertexGraphFormatter")||(type == "RoundedVertexNetworkFormatter")){ - this.vertices[vertexId] = new RoundedVertexGraphFormatter(vertexId, defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); - } - - if ((type == "OctagonVertexGraphFormatter")||(type == "OctagonVertexNetworkhFormatter")){ - this.vertices[vertexId] = new OctagonVertexGraphFormatter(vertexId, defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); - } - - - var _this = this; - this.vertices[vertexId].stateChanged.attach(function (sender, item){ - _this.changed.notify(item); - }); - _this.changed.notify(this.vertices[vertexId]); -}; - - - -NetworkDataSetFormatter.prototype.dataBind = function(networkDataSet){ - var _this = this; - this._setDataset(networkDataSet); - - for ( var vertex in this.dataset.getVertices()) { - this.addVertex(vertex); - } - - for ( var edge in this.dataset.getEdges()) { - this.addEdge(edge); - } -}; - -NetworkDataSetFormatter.prototype._removeEdge = function(edgeId){ - delete this.edges[edgeId]; -}; - -NetworkDataSetFormatter.prototype._removeVertex = function(vertexId){ - delete this.vertices[vertexId]; -}; - -NetworkDataSetFormatter.prototype._attachDatasetEvents = function(id){ - var _this = this; - this.dataset.vertexDeleted.attach(function (sender, item){ - _this._removeVertex(item.getId()); - }); - - this.dataset.edgeDeleted.attach(function (sender, item){ - _this._removeEdge(item.getId()); - }); - - this.dataset.newVertex.attach(function (sender, item){ - _this.addVertex(item.getId()); - }); - - this.dataset.newEdge.attach(function (sender, item){ - _this.addEdge(item.getId()); - }); -}; - - -NetworkDataSetFormatter.prototype.getVertexById = function(id){ - return this.vertices[id]; -}; - -NetworkDataSetFormatter.prototype.getEdgeById = function(id){ - return this.edges[id]; -}; - -NetworkDataSetFormatter.prototype.makeLabelsBigger = function(){ -for ( var vertexId in this.vertices) { - var fontSize = this.vertices[vertexId].getDefault().getFontSize() + 2; - this.vertices[vertexId].getDefault().setFontSize(fontSize); - } -}; - -NetworkDataSetFormatter.prototype.makeLabelsSmaller = function(){ - for ( var vertexId in this.vertices) { - var fontSize = this.vertices[vertexId].getDefault().getFontSize() - 2; - this.vertices[vertexId].getDefault().setFontSize(fontSize); - } -}; - - -NetworkDataSetFormatter.prototype.resize = function(width, height){ - this.args.width = width; - this.args.height = height; - this.resized.notify(); -}; - -/** ZOOM GETTERS **/ -NetworkDataSetFormatter.prototype.getZoomScaleStepFactor = function(){return this.args.zoomScaleStepFactor;}; -NetworkDataSetFormatter.prototype.setZoomScaleStepFactor = function(scaleFactor){this.args.zoomScaleStepFactor = scaleFactor;}; -NetworkDataSetFormatter.prototype.getZoomScale = function(){return this.args.zoomScale;}; -NetworkDataSetFormatter.prototype.setZoomScale = function(scale){this.args.zoomScale = scale;}; - -NetworkDataSetFormatter.prototype.getNodesMaxSize = function(){return this.args.nodesMaxSize;}; -NetworkDataSetFormatter.prototype.getNodesMinSize = function(){return this.args.nodesMinSize;}; - -/** SIZE SETTERS AND GETTERS **/ -NetworkDataSetFormatter.prototype.isVerticesBalanced = function(){return this.args.balanceNodes;}; -NetworkDataSetFormatter.prototype.getWidth = function(){return this.args.width;}; -NetworkDataSetFormatter.prototype.getHeight = function(){return this.args.height;}; - -/** OPTIONAL PARAMETERS GETTERS AND SETTERS **/ -NetworkDataSetFormatter.prototype.getBackgroundImage = function(){return this.args.backgroundImage;}; -NetworkDataSetFormatter.prototype.setBackgroundImage = function(value){this.args.backgroundImage = value; this.backgroundImageChanged.notify(this);}; - - -NetworkDataSetFormatter.prototype.getBackgroundImageWidth = function(){return this.args.backgroundImageWidth;}; -NetworkDataSetFormatter.prototype.setBackgroundImageWidth = function(value){this.args.backgroundImageWidth = value; this.backgroundImageChanged.notify(this);}; - -NetworkDataSetFormatter.prototype.getBackgroundImageHeight = function(){return this.args.backgroundImageHeight;}; -NetworkDataSetFormatter.prototype.setBackgroundImageHeight = function(value){this.args.backgroundImageHeight = value; this.backgroundImageChanged.notify(this);}; - -NetworkDataSetFormatter.prototype.getBackgroundImageX = function(){return this.args.backgroundImageX;}; -NetworkDataSetFormatter.prototype.setBackgroundImageX = function(value){this.args.backgroundImageX = value; this.backgroundImageChanged.notify(this);}; - -NetworkDataSetFormatter.prototype.getBackgroundImageY = function(){return this.args.backgroundImageX;}; -NetworkDataSetFormatter.prototype.setBackgroundImageY = function(value){this.args.backgroundImageY = value; this.backgroundImageChanged.notify(this);}; - - - -NetworkDataSetFormatter.prototype.getBackgroundColor = function(){return this.args.backgroundColor;}; -NetworkDataSetFormatter.prototype.setBackgroundColor = function(value){this.args.backgroundColor = value; this.backgroundColorChanged.notify(this);}; - -NetworkDataSetFormatter.prototype.getWidth = function(){return this.args.width;}; -NetworkDataSetFormatter.prototype.setWidth = function(value){this.args.width = value;}; - -NetworkDataSetFormatter.prototype.getHeight = function(){return this.args.height;}; -NetworkDataSetFormatter.prototype.setHeight = function(value){this.args.height = value;}; - - - - -Vertex.prototype.getName = GraphItem.prototype.getName; -Vertex.prototype.setName = GraphItem.prototype.setName; -Vertex.prototype.getId = GraphItem.prototype.getId; - -function Vertex(id, name, args){ - GraphItem.prototype.constructor.call(this, id, name, args); - this.edgesIn= new Array(); - this.edgesOut= new Array(); -}; - -Vertex.prototype.getEdges = function(){ - return this.edgesIn.concat(this.edgesOut); -}; - -Vertex.prototype.getEdgesCount = function(){ - return this.getEdges().length; -}; - -Vertex.prototype.getEdgesIn = function(){ - return this.edgesIn; -}; - -Vertex.prototype.getEdgesOut = function(){ - return this.edgesOut; -}; - -Vertex.prototype.addEdge = function(edge){ - if (edge.getNodeSource().getId() == this.id){ - this.edgesIn.push(edge); - } - else{ - this.edgesOut.push(edge); - } -}; - -Vertex.prototype.removeEdge = function(edge){ - for ( var i = 0; i < this.getEdgesIn().length; i++) { - var edgeIn = this.edgesIn[i]; - if (edgeIn.getId() == edge.getId()){ - this.edgesIn.splice(i, 1); - } - } - for ( var i = 0; i < this.getEdgesOut().length; i++) { - var edgeIn = this.edgesOut[i]; - if (edgeIn.getId() == edge.getId()){ - this.edgesOut.splice(i, 1); - } - } -}; - -Vertex.prototype.remove = function(){ - var edges = this.getEdges(); - for ( var i = 0; i < edges.length; i++) { - var edge = edges[i]; - edge.remove(); - } - this.deleted.notify(this); -}; - - - - - -VertexGraphFormatter.prototype.getDefault = ItemGraphFormatter.prototype.getDefault; -VertexGraphFormatter.prototype.getSelected = ItemGraphFormatter.prototype.getSelected; -VertexGraphFormatter.prototype.getOver = ItemGraphFormatter.prototype.getOver; -VertexGraphFormatter.prototype.getDragging = ItemGraphFormatter.prototype.getDragging; -VertexGraphFormatter.prototype.getId = ItemGraphFormatter.prototype.getId; -VertexGraphFormatter.prototype.toJSON = ItemGraphFormatter.prototype.toJSON; -VertexGraphFormatter.prototype.loadFromJSON = ItemGraphFormatter.prototype.loadFromJSON; -VertexGraphFormatter.prototype._setEvents = ItemGraphFormatter.prototype._setEvents; - - -function VertexGraphFormatter(defaultFormat, selectedFormat, overFormat, draggingFormat){ - ItemGraphFormatter.prototype.constructor.call(this, defaultFormat, selectedFormat, overFormat, draggingFormat); -}; - - -CircleVertexGraphFormatter.prototype.getDefault = VertexGraphFormatter.prototype.getDefault; -CircleVertexGraphFormatter.prototype.getSelected = VertexGraphFormatter.prototype.getSelected; -CircleVertexGraphFormatter.prototype.getOver = VertexGraphFormatter.prototype.getOver; -CircleVertexGraphFormatter.prototype.getDragging = VertexGraphFormatter.prototype.getDragging; -CircleVertexGraphFormatter.prototype.getId = VertexGraphFormatter.prototype.getId; -CircleVertexGraphFormatter.prototype.toJSON = VertexGraphFormatter.prototype.toJSON; -CircleVertexGraphFormatter.prototype.loadFromJSON = VertexGraphFormatter.prototype.loadFromJSON; -CircleVertexGraphFormatter.prototype._setEvents = VertexGraphFormatter.prototype._setEvents; - -function CircleVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ - VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); - this.args.type = "CircleVertexGraphFormatter"; - if (defaultFormat != null){ - if (defaultFormat.radius != null){ - this.defaultFormat.args.radius = defaultFormat.radius; - } - } - - if (selectedFormat != null){ - if (selectedFormat.radius != null){ - this.selected.args.radius = selectedFormat.radius; - } - } - - if (overFormat != null){ - if (overFormat.radius != null){ - this.over.args.radius = overFormat.radius; - } - } - - if (draggingFormat != null){ - if (draggingFormat.radius != null){ - this.dragging.args.draggingFormat = draggingFormat.radius; - } - } -}; - - - -SquareVertexGraphFormatter.prototype.getDefault = VertexGraphFormatter.prototype.getDefault; -SquareVertexGraphFormatter.prototype.getSelected = VertexGraphFormatter.prototype.getSelected; -SquareVertexGraphFormatter.prototype.getOver = VertexGraphFormatter.prototype.getOver; -SquareVertexGraphFormatter.prototype.getDragging = VertexGraphFormatter.prototype.getDragging; -SquareVertexGraphFormatter.prototype.getId = VertexGraphFormatter.prototype.getId; -SquareVertexGraphFormatter.prototype.toJSON = VertexGraphFormatter.prototype.toJSON; -SquareVertexGraphFormatter.prototype.loadFromJSON = VertexGraphFormatter.prototype.loadFromJSON; -SquareVertexGraphFormatter.prototype._setEvents = VertexGraphFormatter.prototype._setEvents; - -function SquareVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ - VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); - this.args.type = "SquareVertexGraphFormatter"; - if (defaultFormat != null){ - if (defaultFormat.radius != null){ - this.defaultFormat.args.radius = defaultFormat.radius; - } - } - - if (selectedFormat != null){ - if (selectedFormat.radius != null){ - this.selected.args.radius = selectedFormat.radius; - } - } - - if (overFormat != null){ - if (overFormat.radius != null){ - this.over.args.radius = overFormat.radius; - } - } - - if (draggingFormat != null){ - if (draggingFormat.radius != null){ - this.dragging.args.draggingFormat = draggingFormat.radius; - } - } -}; - - -EllipseVertexGraphFormatter.prototype.getDefault = VertexGraphFormatter.prototype.getDefault; -EllipseVertexGraphFormatter.prototype.getSelected = VertexGraphFormatter.prototype.getSelected; -EllipseVertexGraphFormatter.prototype.getOver = VertexGraphFormatter.prototype.getOver; -EllipseVertexGraphFormatter.prototype.getDragging = VertexGraphFormatter.prototype.getDragging; -EllipseVertexGraphFormatter.prototype.getId = VertexGraphFormatter.prototype.getId; -EllipseVertexGraphFormatter.prototype.toJSON = VertexGraphFormatter.prototype.toJSON; -EllipseVertexGraphFormatter.prototype.loadFromJSON = VertexGraphFormatter.prototype.loadFromJSON; -EllipseVertexGraphFormatter.prototype._setEvents = VertexGraphFormatter.prototype._setEvents; - -function EllipseVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ - VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); - this.args.type = "EllipseVertexGraphFormatter"; - if (defaultFormat != null){ - if (defaultFormat.radius != null){ - this.defaultFormat.args.radius = defaultFormat.radius; - } - } - - if (selectedFormat != null){ - if (selectedFormat.radius != null){ - this.selected.args.radius = selectedFormat.radius; - } - } - - if (overFormat != null){ - if (overFormat.radius != null){ - this.over.args.radius = overFormat.radius; - } - } - - if (draggingFormat != null){ - if (draggingFormat.radius != null){ - this.dragging.args.draggingFormat = draggingFormat.radius; - } - } -}; - - - -RectangleVertexGraphFormatter.prototype.getDefault = ItemGraphFormatter.prototype.getDefault; -RectangleVertexGraphFormatter.prototype.getSelected = ItemGraphFormatter.prototype.getSelected; -RectangleVertexGraphFormatter.prototype.getOver = ItemGraphFormatter.prototype.getOver; -RectangleVertexGraphFormatter.prototype.getDragging = ItemGraphFormatter.prototype.getDragging; -RectangleVertexGraphFormatter.prototype.getId = ItemGraphFormatter.prototype.getId; -RectangleVertexGraphFormatter.prototype.toJSON = ItemGraphFormatter.prototype.toJSON; -RectangleVertexGraphFormatter.prototype.loadFromJSON = ItemGraphFormatter.prototype.loadFromJSON; -RectangleVertexGraphFormatter.prototype._setEvents = ItemGraphFormatter.prototype._setEvents; - -function RectangleVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ - VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); - this.args.type = "RectangleVertexGraphFormatter"; - if (defaultFormat != null){ - if (defaultFormat.radius != null){ - this.defaultFormat.args.radius = defaultFormat.radius; - } - } - - if (selectedFormat != null){ - if (selectedFormat.radius != null){ - this.selected.args.radius = selectedFormat.radius; - } - } - - if (overFormat != null){ - if (overFormat.radius != null){ - this.over.args.radius = overFormat.radius; - } - } - - if (draggingFormat != null){ - if (draggingFormat.radius != null){ - this.dragging.args.draggingFormat = draggingFormat.radius; - } - } -}; - - - -RoundedVertexGraphFormatter.prototype.getDefault = ItemGraphFormatter.prototype.getDefault; -RoundedVertexGraphFormatter.prototype.getSelected = ItemGraphFormatter.prototype.getSelected; -RoundedVertexGraphFormatter.prototype.getOver = ItemGraphFormatter.prototype.getOver; -RoundedVertexGraphFormatter.prototype.getDragging = ItemGraphFormatter.prototype.getDragging; -RoundedVertexGraphFormatter.prototype.getId = ItemGraphFormatter.prototype.getId; -RoundedVertexGraphFormatter.prototype.toJSON = ItemGraphFormatter.prototype.toJSON; -RoundedVertexGraphFormatter.prototype.loadFromJSON = ItemGraphFormatter.prototype.loadFromJSON; -RoundedVertexGraphFormatter.prototype._setEvents = ItemGraphFormatter.prototype._setEvents; - -function RoundedVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ - VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); - this.args.type = "RoundedVertexGraphFormatter"; - if (defaultFormat != null){ - if (defaultFormat.radius != null){ - this.defaultFormat.args.radius = defaultFormat.radius; - } - } - - if (selectedFormat != null){ - if (selectedFormat.radius != null){ - this.selected.args.radius = selectedFormat.radius; - } - } - - if (overFormat != null){ - if (overFormat.radius != null){ - this.over.args.radius = overFormat.radius; - } - } - - if (draggingFormat != null){ - if (draggingFormat.radius != null){ - this.dragging.args.draggingFormat = draggingFormat.radius; - } - } -}; - - - -OctagonVertexGraphFormatter.prototype.getDefault = ItemGraphFormatter.prototype.getDefault; -OctagonVertexGraphFormatter.prototype.getSelected = ItemGraphFormatter.prototype.getSelected; -OctagonVertexGraphFormatter.prototype.getOver = ItemGraphFormatter.prototype.getOver; -OctagonVertexGraphFormatter.prototype.getDragging = ItemGraphFormatter.prototype.getDragging; -OctagonVertexGraphFormatter.prototype.getId = ItemGraphFormatter.prototype.getId; -OctagonVertexGraphFormatter.prototype.toJSON = ItemGraphFormatter.prototype.toJSON; -OctagonVertexGraphFormatter.prototype.loadFromJSON = ItemGraphFormatter.prototype.loadFromJSON; -OctagonVertexGraphFormatter.prototype._setEvents = ItemGraphFormatter.prototype._setEvents; - -function OctagonVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ - VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); - this.args.type = "OctagonVertexGraphFormatter"; - if (defaultFormat != null){ - if (defaultFormat.radius != null){ - this.defaultFormat.args.radius = defaultFormat.radius; - } - } - - if (selectedFormat != null){ - if (selectedFormat.radius != null){ - this.selected.args.radius = selectedFormat.radius; - } - } - - if (overFormat != null){ - if (overFormat.radius != null){ - this.over.args.radius = overFormat.radius; - } - } - - if (draggingFormat != null){ - if (draggingFormat.radius != null){ - this.dragging.args.draggingFormat = draggingFormat.radius; - } - } -}; - - - -var Colors = new function() -{ - this.hashColor = []; - this.getColorByScoreArrayValue = function (arrayScore) - { - var array = new Array(); - - for (var i = 0; i< arrayScore.length; i++) - { - - var color = this.getColorByScoreValue(arrayScore[i]) - array.push( color); - - } - return array; - }; - - this.getHexStringByScoreArrayValue = function (arrayScore) - { - var arrayColor = this.getColorByScoreArrayValue(arrayScore); - var arrayHex = new Array(); - for (var i = 0; i< arrayColor.length; i++) - { - arrayHex.push( arrayColor[i].HexString()); - } - return arrayHex; - }; - - this.getColorByScoreValue = function (score) - { - - var truncate = score.toString().substr(0,4); - if (this.hashColor[truncate]!=null) - { - return this.hashColor[truncate]; - } - - - if(isNaN(score)) { - return Colors.ColorFromRGB(0,0,0); - } - var value; - - var from, to; - if(score < 0.5) { - from = Colors.ColorFromRGB(0,0,255); - to = Colors.ColorFromRGB(255,255,255); - value = (score * 2); - } else { - from = Colors.ColorFromRGB(255,255,255); - to = Colors.ColorFromRGB(255,0,0); - value = (score * 2) - 1; - } - - var x = value; - var y = 1.0 - value; - var color = Colors.ColorFromRGB(y * from.Red() + x * to.Red(), y * from.Green() + x * to.Green(), y * from.Blue() + x * to.Blue()); - - this.hashColor[truncate] = color; - - return color; - }; - - this.ColorFromHSV = function(hue, sat, val) - { - var color = new Color(); - color.SetHSV(hue,sat,val); - return color; - }; - - this.ColorFromRGB = function(r, g, b) - { - var color = new Color(); - color.SetRGB(r,g,b); - return color; - }; - - this.ColorFromHex = function(hexStr) - { - var color = new Color(); - color.SetHexString(hexStr); - return color; - }; - - function Color() { - //Stored as values between 0 and 1 - var red = 0; - var green = 0; - var blue = 0; - - //Stored as values between 0 and 360 - var hue = 0; - - //Strored as values between 0 and 1 - var saturation = 0; - var value = 0; - - this.SetRGB = function(r, g, b) - { - red = r/255.0; - green = g/255.0; - blue = b/255.0; - calculateHSV(); - }; - - this.Red = function() { return Math.round(red*255); }; - - this.Green = function() { return Math.round(green*255); }; - - this.Blue = function() { return Math.round(blue*255); }; - - this.SetHSV = function(h, s, v) - { - hue = h; - saturation = s; - value = v; - calculateRGB(); - }; - - this.Hue = function() - { return hue; }; - - this.Saturation = function() - { return saturation; }; - - this.Value = function() - { return value; }; - - this.SetHexString = function(hexString) - { - if(hexString == null || typeof(hexString) != "string") - { - this.SetRGB(0,0,0); - return; - } - - if (hexString.substr(0, 1) == '#') - hexString = hexString.substr(1); - - if(hexString.length != 6) - { - this.SetRGB(0,0,0); - return; - } - - var r = parseInt(hexString.substr(0, 2), 16); - var g = parseInt(hexString.substr(2, 2), 16); - var b = parseInt(hexString.substr(4, 2), 16); - if (isNaN(r) || isNaN(g) || isNaN(b)) - { - this.SetRGB(0,0,0); - return; - } - - this.SetRGB(r,g,b); - }; - - this.HexString = function() - { - - var rStr = this.Red().toString(16); - if (rStr.length == 1) - rStr = '0' + rStr; - var gStr = this.Green().toString(16); - if (gStr.length == 1) - gStr = '0' + gStr; - var bStr = this.Blue().toString(16); - if (bStr.length == 1) - bStr = '0' + bStr; - return ('#' + rStr + gStr + bStr).toUpperCase(); - }; - - this.Complement = function() - { - var newHue = (hue >= 180) ? hue - 180 : hue + 180; - var newVal = (value * (saturation - 1) + 1); - var newSat = (value*saturation) / newVal; - var newColor = new Color(); - newColor.SetHSV(newHue, newSat, newVal); - return newColor; - } ; - - function calculateHSV() - { - var max = Math.max(Math.max(red, green), blue); - var min = Math.min(Math.min(red, green), blue); - - value = max; - - saturation = 0; - if(max != 0) - saturation = 1 - min/max; - - hue = 0; - if(min == max) - return; - - var delta = (max - min); - if (red == max) - hue = (green - blue) / delta; - else if (green == max) - hue = 2 + ((blue - red) / delta); - else - hue = 4 + ((red - green) / delta); - hue = hue * 60; - if(hue < 0) - hue += 360; - } - - function calculateRGB() - { - red = value; - green = value; - blue = value; - - if(value == 0 || saturation == 0) - return; - - var tHue = (hue / 60); - var i = Math.floor(tHue); - var f = tHue - i; - var p = value * (1 - saturation); - var q = value * (1 - saturation * f); - var t = value * (1 - saturation * (1 - f)); - switch(i) - { - case 0: - red = value; green = t; blue = p; - break; - case 1: - red = q; green = value; blue = p; - break; - case 2: - red = p; green = value; blue = t; - break; - case 3: - red = p; green = q; blue = value; - break; - case 4: - red = t; green = p; blue = value; - break; - default: - red = value; green = p; blue = q; - break; - } - } - } -} -(); -/* - * Clase gestiona la insercción, eliminación de los elementos en el DOM - * - * Vital hacerla SIEMPRE compatible hacia atrás - * - * Last update: 28-10-2010 - * - */ - - -var DOM = {}; - -DOM.createNewElement = function(type, nodeParent, attributes) -{ - - var node = document.createElement(type); - for (var i=0; i0) - { - parent.removeChild(parent.childNodes[0]); - - } -}; - -DOM.select = function(targetID) -{ - return document.getElementById(targetID); -// return $("#"+targetID); -}; -var Geometry = -{ - - /** From tow points obtains the angles formed with the cartesian side **/ - getAngleBetweenTwoPoints : function(x1, y1, x2, y2){ - //var m = (y1 - y2)/ (x1 - x2); - return Math.atan2(y2-y1, x2-x1); - }, - - getAdjacentSideOfRectangleRight : function(angle, hypotenuse){ - return Math.abs(Math.cos(angle)*hypotenuse); - }, - - getOppositeSideOfRectangleRight : function(angle, hypotenuse){ - return Math.abs(Math.sin(angle)*hypotenuse); - }, - - toDegree: function(radian){ - return radian*180/Math.PI; - - } - - -}; - -var SVG = -{ - svgns : 'http://www.w3.org/2000/svg', - xlinkns : "http://www.w3.org/1999/xlink", - - createSVGCanvas: function(parentNode, attributes) - { - - attributes.push( ['xmlns', SVG.svgns], ['xmlns:xlink', 'http://www.w3.org/1999/xlink']); - var svg = document.createElementNS("http://www.w3.org/2000/svg", "svg"); - this._setProperties(svg, attributes); - parentNode.appendChild( svg); - return svg; - - }, - - createRectangle : function (x, y, width, height, attributes){ - var rect = document.createElementNS(this.svgns, "rect"); - rect.setAttribute("x",x); - rect.setAttribute("y",y); - rect.setAttribute("width",width); - rect.setAttribute("height",height); - SVG._setProperties(rect, attributes); - return rect; - }, - - drawImage64 : function (x, y, width, height, base64, svgNode, attributes) { - var node = SVG.createImage64(x, y, width, height, base64, attributes); - svgNode.appendChild(node); - return node; - }, - - createImage64 : function (x, y, width, height, base64, attributes) { - var img = document.createElementNS(this.svgns, "image"); - img.setAttribute("x",x); - img.setAttribute("y",y); - img.setAttribute("width",width); - img.setAttribute("height",height); - img.setAttribute("xlink:href",base64); - SVG._setProperties(img, attributes); - return img; - }, - - createLine: function (x1, y1, x2, y2, attributes){ - var line = document.createElementNS(this.svgns,"line"); - line.setAttribute("x1",x1); - line.setAttribute("y1",y1); - line.setAttribute("x2", x2); - line.setAttribute("y2", y2); - SVG._setProperties(line, attributes); - return line; - }, - - createClip: function (id, nodeToClip, attributes){ - var clip = document.createElementNS(this.svgns,"clipPath"); - clip.setAttribute("id",id); - clip.appendChild(nodeToClip); - return clip; - }, - - drawClip : function (id, nodeToClip, svgNode) { - var node = SVG.createClip(id, nodeToClip); - svgNode.appendChild(node); - return node; - }, - - drawRectangle : function (cx, cy, width, height, svgNode, attributes) { - try{ - var node = SVG.createRectangle(cx, cy, width, height, attributes); - svgNode.appendChild(node); - } - catch(e){ - - console.log("-------------------- "); - console.log("Error on drawRectangle " + e); - console.log(attributes); - console.log("-------------------- "); - } - return node; - }, - - createEllipse : function (x, y, rx, ry, attributes){ - var rect = document.createElementNS(this.svgns, "ellipse"); - rect.setAttribute("cx",x); - rect.setAttribute("cy",y); - rect.setAttribute("rx",rx); - rect.setAttribute("ry",ry); - SVG._setProperties(rect, attributes); - return rect; - }, - - drawEllipse : function (cx, cy, rx, ry, svgNode, attributes) { - var node = SVG.createEllipse(cx, cy, rx, ry, attributes); - svgNode.appendChild(node); - return node; - }, - - drawImage : function (x, y, canvasSVG, attributes) { - var image = document.createElementNS(this.svgns, "image"); - image.setAttribute("x",x); - image.setAttribute("y",y); - canvasSVG.appendChild(image); - SVG._setProperties(image, attributes); - }, - - drawLine : function (x1, y1, x2, y2, nodeSVG, attributes) { - try{ - var line = SVG.createLine(x1, y1, x2, y2, attributes); - nodeSVG.appendChild(line); - }catch(e){ - } - return line; - }, - - - drawPath: function (d, nodeSVG, attributes) { - var path = SVG.createPath(d, attributes); - nodeSVG.appendChild(path); - return path; - }, - - createPoligon : function (points, attributes){ - var poligon = document.createElementNS(this.svgns, "polygon"); - poligon.setAttribute("points",points); - SVG._setProperties(poligon, attributes); - return poligon; - }, - - drawPoligon : function (points, canvasSVG, attributes){ - var poligon = SVG.createPoligon(points, attributes); - canvasSVG.appendChild(poligon); - return poligon; - }, - // - - createPath : function (d, attributes){ - var path = document.createElementNS(this.svgns, "path"); - path.setAttribute("d",d); - SVG._setProperties(path, attributes); - return path; - }, - - drawCircle : function (x, y, radio, canvasSVG, attributes) { - - var newText = document.createElementNS(this.svgns,"circle"); - newText.setAttribute("cx",x); - newText.setAttribute("cy",y); - newText.setAttribute("r",radio); - - canvasSVG.appendChild(newText); - attributes["cursor"] = "pointer"; - this._setProperties(newText, attributes); - return newText; - }, - - - _setProperties: function(node, attributes) - { - if (attributes instanceof Array){ - for (var i=0; i< attributes.length; i++) - { - node.setAttribute(attributes[i][0], attributes[i][1]); - } - } - else{ - for ( var key in attributes){ - node.setAttribute(key, attributes[key]); - } - } - }, - -/* drawPath: function(pointsArray, canvasSVG, attributes){ - var path = document.createElementNS(this.svgns,"polyline"); - path.setAttribute ('id', id); - - var d= pointsArray[0].x+ " "+ pointsArray[0].y; - for (var i=1; i< pointsArray.length; i++) - { - d=d+" "+pointsArray[i].x+" "+pointsArray[i].y; - } - path.setAttribute ('points', d); - canvasSVG.appendChild(path); - },*/ - - createText : function (x, y, text, attributes) { - var node = document.createElementNS(this.svgns,"text"); - node.setAttributeNS(null , "x",x); - node.setAttributeNS(null, "y",y); - - var textNode = document.createTextNode(text); - node.appendChild(textNode); - - this._setProperties(node, attributes); - return node; - }, - - drawText : function (x, y, text, canvasSVG, attributes) { - var text = SVG.createText(x, y, text, attributes); - canvasSVG.appendChild(text); - return text; - }, - - - - drawGroup: function(svgNode, attributes) - { - var group = SVG.createGroup(attributes); - svgNode.appendChild(group); - return group; - }, - - createGroup: function(attributes){ - var group = document.createElementNS(this.svgns,"g"); - this._setProperties(group, attributes); - return group; - } - -}; - - - -var CanvasToSVG = { - - convert: function(sourceCanvas, targetSVG, x, y, id, attributes) { - - var img = this._convert(sourceCanvas, targetSVG, x, y, id); - - for (var i=0; i< attributes.length; i++) - { - img.setAttribute(attributes[i][0], attributes[i][1]); - } - }, - - _convert: function(sourceCanvas, targetSVG, x, y, id) { - var svgNS = "http://www.w3.org/2000/svg"; - var xlinkNS = "http://www.w3.org/1999/xlink"; - // get base64 encoded png from Canvas - var image = sourceCanvas.toDataURL(); - - // must be careful with the namespaces - var svgimg = document.createElementNS(svgNS, "image"); - - svgimg.setAttribute('id', id); - - //svgimg.setAttribute('class', class); - //svgimg.setAttribute('xlink:href', image); - svgimg.setAttributeNS(xlinkNS, 'xlink:href', image); - - - - - svgimg.setAttribute('x', x ? x : 0); - svgimg.setAttribute('y', y ? y : 0); - svgimg.setAttribute('width', sourceCanvas.width); - svgimg.setAttribute('height', sourceCanvas.height); - //svgimg.setAttribute('cursor', 'pointer'); - svgimg.imageData = image; - - targetSVG.appendChild(svgimg); - return svgimg; - }, - - importSVG: function(sourceSVG, targetCanvas) { - svg_xml = sourceSVG;//(new XMLSerializer()).serializeToString(sourceSVG); - var ctx = targetCanvas.getContext('2d'); - - var img = new Image(); - img.src = "data:image/svg+xml;base64," + btoa(svg_xml); -// img.onload = function() { - ctx.drawImage(img, 0, 0); -// }; - } - -}; -/* -Graph.prototype.importSVG = function(sourceSVG, targetCanvas) { - sourceSVG = this._svg; - targetCanvas = document.createElementNS('canvas'); - // https://developer.mozilla.org/en/XMLSerializer - svg_xml = (new XMLSerializer()).serializeToString(sourceSVG); - var ctx = targetCanvas.getContext('2d'); - // this is just a JavaScript (HTML) image - var img = new Image(); - // http://en.wikipedia.org/wiki/SVG#Native_support - // https://developer.mozilla.org/en/DOM/window.btoa - img.src = "data:image/svg+xml;base64," + btoa(svg_xml); - img.onload = function() { - // after this, Canvas’ origin-clean is DIRTY - ctx.drawImage(img, 0, 0); - } -}; -*/ - -/* - -Normalizacion de datos para dibujar colores -Issues: - No sé como debería llamarse esta libreria - No sé si ya existe una funciçon en javascript que lo haga - - -*/ - - -var Normalizer = new function() -{ - this.normalizeArray = function (arrayData) - { - - return this.standardizeArray(this.normal(arrayData)); - -// var result = this._getMaxAndMin(arrayData); -// var min =result[0]; -// var max = result[1]; -// -// -// //los hacemos todos positivos -// for (var i = 0; i< arrayData.length; i++) -// { -// arrayData[i]= Math.abs(min) + parseFloat(arrayData[i]); -// } -// -// var result = this._getMaxAndMin(arrayData); -// var min =result[0]; -// var max = result[1]; -// -// -// var resultArray = new Array(); -// for (var i = 0; i< arrayData.length; i++) -// { -// resultArray.push(arrayData[i]*1/max); -// } -// return resultArray; - }; - - this.normal = function(arrayData){ - var mean = this._getMean(arrayData); - var deviation = this._getStdDeviation(arrayData); - var result = this._getMaxAndMin(arrayData); - var min = result[0]; - var max = result[1]; - - var resultArray = new Array(); - for (var i = 0; i< arrayData.length; i++) { - if (deviation!=0){ - resultArray.push((arrayData[i]-mean)/deviation); - }else{ - resultArray.push(arrayData[i]); - } - } - return resultArray; - }; - - this.standardizeArray = function(arrayData) - { - var result = this._getMaxAndMin(arrayData); - var min = result[0]; - var max = result[1]; - - var offset = ( min <= 0 ) ? Math.abs(min) : (-1 * min); - var resultArray = new Array(); - for (var i = 0; i< arrayData.length; i++) { - if(max + offset!=0){ - resultArray.push((arrayData[i] + offset) / (max + offset)); - }else{ - resultArray.push(arrayData[i]+offset); - } - } - return resultArray; - }; - - - this._getMean = function(arrayData) { - var sum = 0; - for (var i = 0; i< arrayData.length; i++) { - sum = sum + parseFloat(arrayData[i]); - } - return sum/arrayData.length; - }; - - this._getStdDeviation = function(arrayData) { - var mean = this._getMean(arrayData); - var acum = 0.0; - for(var i=0; i max) max = parseFloat(arrayData[i]); - } - - return [min, max]; - }; -}; -function GraphCanvas(componentID, targetNode, args) { - this.args = {}; - /** target */ - this.targetID = targetNode.id; - - /** id manage */ - this.id = componentID; - this.args.idGraph = this.id + "main"; - this.args.idBackgroundNode = this.id + "background"; - - this.args.idEdgesGraph = this.id + "edges"; - this.args.idNodesGraph = this.id + "vertices"; - this.args.idLabelGraph = this.id + "label"; - this.args.idBackground = this.id + "background"; - - /** Objects Graph **/ - this.dataset = null; - this.formatter = null; - this.layout = null; - - /** Drawing **/ - this.circleDefaultRadius = 2; - this.squareDefaultSide = this.circleDefaultRadius * 1.5; - - /** Directed Arrow **/ - this.arrowDefaultSize = this.circleDefaultRadius; - - /** Groups **/ - this.GraphGroup = null; - this.GraphNodeGroup = null; - this.GraphLabelGroup = null; - this.GraphBackground = null; - - /** SETTINGS FLAGS **/ - this.args.draggingCanvasEnabled = false; //Flag to set if the canvas can be dragged - this.args.multipleSelectionEnabled = false; - this.args.interactive = false; - this.args.labeled = false; - this.args.linkEnabled = false; - - /** If numberEdge > maxNumberEdgesMoving then only it will move edges when mouse up **/ - this.args.maxNumberEdgesMoving = 3; - this.args.maxNumberEdgesFiringEvents = 50; - - /** Linking edges **/ - this.args.linking = false; - this.linkStartX = 0; - this.linkStartY = 0; - this.linkSVGNode = null; - this.linkNodeSource = null; - this.linkNodeTarget = null; - - /** Dragging Control **/ - this.draggingElement = null; - this.dragging = false; - this.nMouseOffsetX = 0; - this.nMouseOffsetY = 0; - this.dragStartX = 0; - this.dragStartY = 0; - this.desplazamientoX = 0; - this.desplazamientoY = 0; - - /** Selection Control **/ - this.selecting = false; - this.selectorX = null; - this.selectorY = null; - this.selectorSVGNode = null; - - /** Node status **/ - this.args.isVertexSelected = {}; - this.args.selectedVertices = []; - - /** Edges status **/ - this.args.isEdgeSelected = {}; - //this.args.selectedEdges = []; - - if (args != null) { - if (args.multipleSelectionEnabled != null) { - this.args.multipleSelectionEnabled = args.multipleSelectionEnabled; - this.args.draggingCanvasEnabled = !(this.args.multipleSelectionEnabled); - } - if (args.draggingCanvasEnabled != null) { - this.args.draggingCanvasEnabled = args.draggingCanvasEnabled; - this.args.multipleSelectionEnabled = !(this.args.draggingCanvasEnabled); - } - if (args.interactive != null) { - this.args.interactive = args.interactive; - } - if (args.labeled != null) { - this.args.labeled = args.labeled; - } - - } - - /** Hashmap with the svg node labels **/ - this.svgLabels = {}; - - /** EVENTS **/ - this.onVertexOut = new Event(this); - this.onVertexOver = new Event(this); - this.onVertexSelect = new Event(this); - this.onEdgeSelect = new Event(this); - this.onCanvasClicked = new Event(this); - this.onVertexUp = new Event(this); -} - -GraphCanvas.prototype.showLabels = function(value) { - this.args.labeled = value; - this.removeLabels(); - if (value) { - this.renderLabels(); - } -}; - -GraphCanvas.prototype.getSelectedVertices = function() { - return this.args.selectedVertices; -}; - -GraphCanvas.prototype.getSelectedEdges = function() { - var selected = []; - for ( var selectedEdge in this.args.isEdgeSelected) { - selected.push(selectedEdge); - } - return selected; -}; - -GraphCanvas.prototype.createSVGDom = function(targetID, id, width, height, backgroundColor) { - var container = document.getElementById(targetID); - this._svg = SVG.createSVGCanvas(container, [ - [ "style", "background-color:" + backgroundColor + ";" ], [ "id", id ], [ "dragx", 0 ], [ "dragy", 0 ], - [ "height", this.getFormatter().getHeight() ], [ "width", this.getFormatter().getWidth() ] ]); - return this._svg; -}; - -/** MULTIPLE SELECTION **/ -GraphCanvas.prototype.isMultipleSelectionEnabled = function() { - return this.args.multipleSelectionEnabled; -}; - -GraphCanvas.prototype.setMultipleSelection = function(value) { - this.args.multipleSelectionEnabled = value; - this.args.draggingCanvasEnabled = (!value); -}; - -GraphCanvas.prototype.setSelecting = function(value) { - this.selecting = value; -}; - -/** linking **/ -GraphCanvas.prototype.setLinking = function(value) { - this.args.linkEnabled = value; - this.selecting = !value; - this.dragging = !value; -}; - -/** CANVAS MOVING **/ -GraphCanvas.prototype.setDraggingCanvas = function(value) { - this.args.draggingCanvasEnabled = value; - this.args.multipleSelectionEnabled = !value; -}; - -GraphCanvas.prototype.isDraggingCanvasEnabled = function() { - return this.args.draggingCanvasEnabled; -}; -/** ZOOM **/ -GraphCanvas.prototype.getScale = function() { - return this.getFormatter().getZoomScale(); -}; - -GraphCanvas.prototype.setScale = function(scale) { - var graphNode = document.getElementById(this.args.idGraph); - graphNode.setAttribute("transform", graphNode.getAttribute("transform").replace("scale(" + this.getScale() + ")", "scale(" + scale + ")")); - this.getFormatter().setZoomScale(scale); -}; - -GraphCanvas.prototype.zoomIn = function() { - this.setScale(this.getScale() + this.getFormatter().getZoomScaleStepFactor()); -}; - -GraphCanvas.prototype.zoomOut = function() { - this.setScale(this.getScale() - this.getFormatter().getZoomScaleStepFactor()); - -}; - -/** SVG COORDENATES **/ -GraphCanvas.prototype.getSVGCoordenates = function(evt) { - var p = this._svg.createSVGPoint(); - p.x = evt.clientX; - p.y = evt.clientY; - - var m = this._svg.getScreenCTM(document.documentElement); - p = p.matrixTransform(m.inverse()); - return p; -}; - -/** SVG EVENTS **/ -GraphCanvas.prototype.mouseClick = function(event) { - if (event.button == 0) { - if (!this.args.interactive) { - return; - } - - if (this.isVertex(event.target)) { - this.clickNode(this.getVertexIdFromSVGId(event.target.id)); - } - /** Como el evento mouseClick viene despues del mouse up es aqui donde manejo el tema de deseccionar los elementos que estoy dragging **/ - if (this.dragging) { - this.dragging = false; - } - } -}; - -GraphCanvas.prototype.mouseMove = function(evt) { - if (this.selecting) { - this.clearLabels(); - - var width = (this.getSVGCoordenates(evt).x - this.selectorX); - var height = (this.getSVGCoordenates(evt).y - this.selectorY); - if ((width > 0) && (height > 0)) { - this.displaySelection(this.selectorX, this.selectorY, width, height); - } - if ((width > 0) && (height < 0)) { - this.displaySelection(this.selectorX, this.getSVGCoordenates(evt).y, width, Math.abs(height)); - } - if ((width < 0) && (height < 0)) { - this.displaySelection(this.getSVGCoordenates(evt).x, this.getSVGCoordenates(evt).y, Math.abs(width), Math.abs(height)); - } - if ((width < 0) && (height > 0)) { - this.displaySelection(this.selectorX + width, this.selectorY, Math.abs(width), Math.abs(height)); - } - - var x1 = (parseFloat(this.selectorSVGNode.getAttribute("x")) - DOM.select(this.id).getAttribute("dragx")) / this.getFormatter().getWidth(); - var y1 = (parseFloat(this.selectorSVGNode.getAttribute("y")) - DOM.select(this.id).getAttribute("dragy")) / this.getFormatter().getHeight(); - var x2 = (x1 + parseFloat(this.selectorSVGNode.getAttribute("width") / this.getFormatter().getWidth())); - var y2 = (y1 + parseFloat(this.selectorSVGNode.getAttribute("height") / this.getFormatter().getHeight())); - - this.deselectNodes(this.getLayout()); - var verticesSelected = this.getLayout().getVerticesByArea(x1 / this.getFormatter().getZoomScale(), y1 / this.getFormatter().getZoomScale(), - x2 / this.getFormatter().getZoomScale(), y2 / this.getFormatter().getZoomScale()); - for ( var i = 0; i < verticesSelected.length; i++) { - this.selectNode(verticesSelected[i].getId()); - this.renderLabel(verticesSelected[i].getId()); - } - - } - var p = null; - if (this.args.linking) { - p = this.getSVGCoordenates(evt); - if (this.linkSVGNode != null) { - this.linkSVGNode.setAttribute("x2", p.x - 2); - this.linkSVGNode.setAttribute("y2", p.y - 2); - } - } - - if (this.dragging) { - p = this.getSVGCoordenates(evt); - p.x -= this.nMouseOffsetX; - p.y -= this.nMouseOffsetY; - this.desplazamientoX = (this.getSVGCoordenates(evt).x - this.dragStartX);// + parseFloat(DOM.select(this.id).getAttribute("dragx")); - this.desplazamientoY = (this.getSVGCoordenates(evt).y - this.dragStartY);// + parseFloat(DOM.select(this.id).getAttribute("dragy")); - - if (this.draggingElement != null) { - /** Click sobre el recct del banground que provoca que mueva todo el canvas **/ - if (this.isNodeCanvas(this.draggingElement)) { - - p = this.getSVGCoordenates(evt); - p.x = this.desplazamientoX; - p.y = this.desplazamientoY; - - this.draggingElement.setAttribute("dragx", p.x); - this.draggingElement.setAttribute("dragy", p.y); - this.draggingElement = document.getElementById(this.args.idGraph); - this.draggingElement.setAttribute("transform", "translate(" + p.x + "," + p.y + "), scale(" + this.getScale() + ")"); - - DOM.select(this.id).setAttribute("dragx", p.x); - DOM.select(this.id).setAttribute("dragy", p.y); - - if (this.NodeSVGbackgroundImage != null) { - this.NodeSVGbackgroundImage.setAttribute("dragx", p.x); - this.NodeSVGbackgroundImage.setAttribute("dragy", p.y); - } - } else { - if (this.isVertex(this.draggingElement)) { - this.selectNode(this.getVertexIdFromSVGId(this.draggingElement.id)); - this.desplazamientoX = this.desplazamientoX / this.getFormatter().getZoomScale(); - this.desplazamientoY = this.desplazamientoY / this.getFormatter().getZoomScale(); - this.moveSelectedNodes(this.desplazamientoX, this.desplazamientoY); - - this.dragStartX = this.getSVGCoordenates(evt).x; - this.dragStartY = this.getSVGCoordenates(evt).y; - } else { - if (this.isNodeBackground(this.draggingElement)) { - - this.draggingElement.setAttribute("dragx", p.x); - this.draggingElement.setAttribute("dragy", p.y); - this.draggingElement = document.getElementById(this.args.idGraph); - this.draggingElement.setAttribute("transform", "translate(" + p.x + "," + p.y + "), scale(" + this.getScale() + ")"); - } else { - this.draggingElement.setAttribute("transform", "translate(" + p.x + "," + p.y + ")"); - } - } - } - } - } -}; - -GraphCanvas.prototype.moveSelectedNodes = function(offsetX, offsetY) { - for ( var i = 0; i < this.getSelectedVertices().length; i++) { - - var nodeId = this.getSelectedVertices()[i]; - var svgNodeId = this.getSVGNodeId(nodeId); - - var x = parseFloat(DOM.select(svgNodeId).getAttribute("dragx")) + parseFloat(offsetX);// - parseFloat(DOM.select(this.id).getAttribute("dragx")); - var y = parseFloat(DOM.select(svgNodeId).getAttribute("dragy")) + parseFloat(offsetY);// + parseFloat(DOM.select(this.id).getAttribute("dragy")); - - this._movingNode(DOM.select(svgNodeId), x, y); - } -}; - -GraphCanvas.prototype.mouseDown = function(evt) { - if (event.button == 0) { - - /** if !no interactive mouse events do anything **/ - if (!this.args.interactive) { - return; - } - - var p = this.getSVGCoordenates(evt); - - /** When click on canvas or background deselect all **/ - if (this.isNodeCanvas(evt.target) || this.isNodeBackground(evt.target)) { - this.deselectNodes(); - this.deselectEdges(); - this.onCanvasClicked.notify(); - } - - /** if I am linking vertices **/ - if (this.args.linkEnabled) { - - if (!this.args.linking) { - this.args.linking = true; - if (this.isVertex(evt.target)) { - this.linkStartX = p.x; - this.linkStartY = p.y; - this.linkSVGNode = SVG.drawLine(p.x, p.y, p.x, p.y, this._svg, { - "stroke" : "#FF0000" - }); - this.linkNodeSource = this.getVertexIdFromSVGId(evt.target.id); - } - } else { - this.linkNodeTarget = this.getVertexIdFromSVGId(evt.target.id); - this.args.linking = false; - this.args.linkEnabled = false; - if (this.isVertex(evt.target)) { - this.getDataset().addEdge(this.linkNodeSource + "_" + this.linkNodeTarget, this.linkNodeSource, this.linkNodeTarget, {}); - } - this.linkSVGNode.parentNode.removeChild(this.linkSVGNode); - } - return; - } - - /** Id is a vertex or the canvas **/ - if (this.isVertex(evt.target) || this.isNodeCanvas(evt.target) || this.isNodeBackground(evt.target)) { - this._startDragging(evt); - } - /** if i is edge **/ - if (this.isEdge(evt.target)) { - this.selectEdge(this.getEdgeIdFromSVGId(evt.target.getAttribute("id"))); - } - - if (this.args.multipleSelectionEnabled) { - if (!this.dragging) { - this.setSelecting(true); - this.selectorX = p.x; - this.selectorY = p.y; - this.displaySelection(p.x, p.y, 1, 1); - } - } - - } - if (event.button == 1) { - this.setLinking(false); - this.setMultipleSelection(false); - this.selecting = false; - - /** Id is a vertex or the canvas **/ - if (this.isVertex(evt.target) || this.isNodeCanvas(evt.target) || this.isNodeBackground(evt.target)) { - this._startDragging(evt); - } - } -}; - -GraphCanvas.prototype.mouseUp = function(event) { - if (!this.args.interactive) { - return; - } - - if (this.dragging) { - this._stopDragging(event); - if (this.isVertex(event.target)) { - var vertexId = this.getVertexIdFromSVGId(event.target.id); - if (this.getDataset().getVertexById(vertexId).getEdges().length >= this.args.maxNumberEdgesMoving) { - this.moveEdge(vertexId); - } - } - } - - if (this.selecting) { - this.setSelecting(false); - - var x1 = (parseFloat(this.selectorSVGNode.getAttribute("x")) - DOM.select(this.id).getAttribute("dragx")) / this.getFormatter().getWidth(); - var y1 = (parseFloat(this.selectorSVGNode.getAttribute("y")) - DOM.select(this.id).getAttribute("dragy")) / this.getFormatter().getHeight(); - var x2 = (x1 + parseFloat(this.selectorSVGNode.getAttribute("width") / this.formatter.getWidth())); - var y2 = (y1 + parseFloat(this.selectorSVGNode.getAttribute("height") / this.formatter.getHeight())); - - var verticesSelected = this.getLayout().getVerticesByArea(x1 / this.getFormatter().getZoomScale, y1 / this.getFormatter().getZoomScale, - x2 / this.getFormatter().getZoomScale, y2 / this.getFormatter().getZoomScale); - - for ( var i = 0; i < verticesSelected.length; i++) { - this.selectNode(verticesSelected[i].getId()); - } - - if (this.selectorSVGNode != null) { - this._svg.removeChild(this.selectorSVGNode); - } - - if (this.args.labeled) { - this.clearLabels(); - this.renderLabels(); - } - - this.selectorSVGNode = null; - // this.renderLabels(); - } -}; - -/** SELECTION **/ -GraphCanvas.prototype.displaySelection = function(x, y, width, height) { - if (this.selectorSVGNode != null) { - this.selectorSVGNode.setAttribute("x", x); - this.selectorSVGNode.setAttribute("y", y); - this.selectorSVGNode.setAttribute("width", width); - this.selectorSVGNode.setAttribute("height", height); - } else { - this.selectorSVGNode = SVG.drawRectangle(x, y, width, height, this._svg, { - "fill" : "red", - "stroke" : "black", - "opacity" : "0.2", - "stroke-opacity" : "1" - }); - } -}; - -/** DRAGGING **/ -GraphCanvas.prototype._startDragging = function(evt) { - if (!this.isDraggingCanvasEnabled()) { - if (this.isNodeCanvas(evt.target)) { - this.draggingElement = null; - } - } - - if (this.isVertex(evt.target) || (this.isNodeBackground(evt.target) && (this.isDraggingCanvasEnabled()))|| (this.isNodeCanvas(evt.target) && (this.isDraggingCanvasEnabled()))) { - this.clearLabels(); - this.draggingElement = evt.target; - this.dragging = true; - var p = this.getSVGCoordenates(evt); - - this.nMouseOffsetX = p.x - parseInt(evt.target.getAttribute("dragx")); - this.nMouseOffsetY = p.y - parseInt(evt.target.getAttribute("dragy")); - - if (this.isVertex(evt.target)) { - this.dragStartX = parseInt(this.draggingElement.getAttribute("dragx")) * this.getFormatter().getZoomScale() - + parseFloat(DOM.select(this.id).getAttribute("dragx")); - this.dragStartY = parseInt(this.draggingElement.getAttribute("dragy")) * this.getFormatter().getZoomScale() - + parseFloat(DOM.select(this.id).getAttribute("dragy")); - } else { - this.dragStartX = p.x - parseInt(this.draggingElement.getAttribute("dragx"));// + parseFloat(DOM.select(this.id).getAttribute("dragx")); - this.dragStartY = p.y - parseInt(this.draggingElement.getAttribute("dragy"));// + parseFloat(DOM.select(this.id).getAttribute("dragy")); - } - } -}; - -GraphCanvas.prototype._stopDragging = function(event) { - this.nMouseOffsetX = 0; - this.nMouseOffsetX = 0; - /** despues del evento up viene el evento click entonces acabo el dragging en el mouseclick **/ - this.dragging = false; - this.draggingElement = null; - this.renderLabels(); - - this.setLinking(false); - this.setMultipleSelection(true); - this.selecting = false; - -}; - -/** Move the edges of the vertex with the vertexId indicado **/ -GraphCanvas.prototype.moveEdge = function(vertexId) { - var x = this.getLayout().getNodeById(vertexId).x * this.getFormatter().getWidth(); - var y = this.getLayout().getNodeById(vertexId).y * this.getFormatter().getHeight(); - - /** Moving edges out **/ - for ( var i = 0; i < this.getDataset().getVertexById(vertexId).getEdgesOut().length; i++) { - var edgeId = this.getDataset().getVertexById(vertexId).getEdgesOut()[i].getId(); - var svgEdgeId = this.getSVGEdgeId(edgeId); - var edgeFormatter = this.getFormatter().getEdgeById(edgeId); - if (edgeFormatter instanceof LineEdgeGraphFormatter) { - DOM.select(svgEdgeId + "_shadow").setAttribute("x2", x); - DOM.select(svgEdgeId + "_shadow").setAttribute("y2", y); - DOM.select(svgEdgeId).setAttribute("x2", x); - DOM.select(svgEdgeId).setAttribute("y2", y); - } - - if ((edgeFormatter instanceof DirectedLineEdgeGraphFormatter) || (edgeFormatter instanceof OdirectedLineEdgeGraphFormatter) - || (edgeFormatter instanceof OdotDirectedLineEdgeGraphFormatter) || (edgeFormatter instanceof DotDirectedLineEdgeGraphFormatter) - || (edgeFormatter instanceof CutDirectedLineEdgeGraphFormatter)) { - this.removeEdge(edgeId); - this.renderEdge(edgeId); - } - } - - /** Moving edges in **/ - for ( var i = 0; i < this.getDataset().getVertexById(vertexId).getEdgesIn().length; i++) { - var edgeId = this.getDataset().getVertexById(vertexId).getEdgesIn()[i].getId(); - var svgEdgeId = this.getSVGEdgeId(edgeId); - var edgeFormatter = this.getFormatter().getEdgeById(edgeId); - if (edgeFormatter instanceof LineEdgeGraphFormatter) { - DOM.select(svgEdgeId).setAttribute("x1", x); - DOM.select(svgEdgeId).setAttribute("y1", y); - DOM.select(svgEdgeId + "_shadow").setAttribute("x1", x); - DOM.select(svgEdgeId + "_shadow").setAttribute("y1", y); - } - - if ((edgeFormatter instanceof DirectedLineEdgeGraphFormatter) || (edgeFormatter instanceof OdirectedLineEdgeGraphFormatter) - || (edgeFormatter instanceof OdotDirectedLineEdgeGraphFormatter) || (edgeFormatter instanceof DotDirectedLineEdgeGraphFormatter) - || (edgeFormatter instanceof CutDirectedLineEdgeGraphFormatter)) { - this.removeEdge(edgeId); - this.renderEdge(edgeId); - } - - if (edgeFormatter instanceof BezierEdgeGraphFormatter) { - var radius = this.getFormatter().getVertexById(vertexId).getDefault().getSize() * this.getFormatter().getNodesMaxSize(); - var d = this.calculateCoordenatesBezier(radius, x, y); - DOM.select(svgEdgeId).setAttribute("d", d); - } - } -}; - -GraphCanvas.prototype.moveNode = function(vertexId) { - var x = this.getLayout().getNodeById(vertexId).x * this.getFormatter().getWidth(); - var y = this.getLayout().getNodeById(vertexId).y * this.getFormatter().getHeight(); - var svgNodeElement = DOM.select(this.getSVGNodeId(vertexId)); - - svgNodeElement.setAttribute("dragx", x); - svgNodeElement.setAttribute("dragy", y); - svgNodeElement.setAttribute("transform", "translate(" + x + "," + y + ")"); - - if (this.getDataset().getVertexById(vertexId).getEdges().length < this.args.maxNumberEdgesMoving) { - this.moveEdge(vertexId); - } -}; - -GraphCanvas.prototype._movingNode = function(svgNodeElement, x, y) { - var vertexId = this.getVertexIdFromSVGId(svgNodeElement.getAttribute("id")); - this.getLayout().getNodeById(vertexId).setCoordinates(x / this.getFormatter().getWidth(), y / this.getFormatter().getHeight()); - this.desplazamientoX = 0; - this.desplazamientoY = 0; - this.removeLabel(vertexId); - this.renderLabel(vertexId); -}; - -/** INIT **/ -GraphCanvas.prototype.init = function() { - - this._svg = this.createSVGDom(this.targetID, this.id, this.getFormatter().getWidth(), this.getFormatter().getHeight(), this.getFormatter() - .getBackgroundColor()); - this.GraphGroup = SVG.drawGroup(this._svg, [ [ "id", this.args.idGraph ], [ "transform", "translate(0,0), scale(1)" ] ]); - this.GraphBackground = SVG.drawGroup(this.GraphGroup, [ [ "id", this.args.idBackground ] ]); - this.GraphEdgeGroup = SVG.drawGroup(this.GraphGroup, [ [ "id", this.args.idEdgesGraph ] ]); - this.GraphNodeGroup = SVG.drawGroup(this.GraphGroup, [ [ "id", this.args.idNodesGraph ] ]); - this.GraphLabelGroup = SVG.drawGroup(this.GraphGroup, [ [ "id", this.args.idLabelGraph ] ]); - - if ((this.getFormatter().getBackgroundImage() != null) && (this.getFormatter().getBackgroundImage() != "")) { - this.setBackgroundImage(this.getFormatter().getBackgroundImage()); - } - /** SVG Events listener */ - var _this = this; - this._svg.addEventListener("click", function(event) { - _this.mouseClick(event); - }, false); - this._svg.addEventListener("mousemove", function(event) { - _this.mouseMove(event, _this); - }, false); - this._svg.addEventListener("mousedown", function(event) { - _this.mouseDown(event, _this); - }, false); - this._svg.addEventListener("mouseup", function(event) { - _this.mouseUp(event, _this); - }, false); -}; - -/* - GraphCanvas.prototype.backgroungToSVG = function(){ - var _this = this; - var canvas = document.createElement('canvas'); - canvas.setAttribute("id", "canvas"); - canvas.width = this.formatter.getWidth(); - canvas.height = this.formatter.getHeight(); - - this._svg.parentNode.parentNode.appendChild(canvas); - var ctx = document.getElementById('canvas').getContext('2d'); - var img = new Image(); - - img.src = this.formatter.getBackgroundImage(); - ctx.drawImage(img,0,0 ,_this.formatter.getWidth(), _this.formatter.getHeight()); - - - img.onload = function() { - canvas.parentNode.removeChild(canvas); - } - - this.NodeSVGbackgroundImage.setAttribute("xlink:href", document.getElementById("canvas").toDataURL()); - this.NodeSVGbackgroundImage.removeAttribute("href"); - - // - - };*/ - -GraphCanvas.prototype.setBackgroundImage = function() { - if (this.NodeSVGbackgroundImage != null) { - this.NodeSVGbackgroundImage.parentNode.removeChild(this.NodeSVGbackgroundImage); - } - $('#' + this.targetID).svg(); - $('#' + this.targetID).svg("get"); - - $('#' + this.targetID).svg("get")._svg = document.getElementById(this.id); - - var svg = $('#' + this.targetID).svg("get"); - this.NodeSVGbackgroundImage = svg.image(0, 0, this.getFormatter().getWidth(), this.getFormatter().getHeight(), this.getFormatter() - .getBackgroundImage()); - this.NodeSVGbackgroundImage.setAttribute("id", this.args.idBackgroundNode); - - this.NodeSVGbackgroundImage.setAttribute("x", 0); - this.NodeSVGbackgroundImage.setAttribute("y", 0); - - this.NodeSVGbackgroundImage.setAttribute("dragx", 0); - this.NodeSVGbackgroundImage.setAttribute("dragy", 0); - - if (this.getFormatter().args.backgroundImageHeight != null) { - this.NodeSVGbackgroundImage.setAttribute("height", this.getFormatter().args.backgroundImageHeight); - } - if (this.getFormatter().args.backgroundImageWidth != null) { - this.NodeSVGbackgroundImage.setAttribute("width", this.getFormatter().args.backgroundImageWidth); - } - - if (this.getFormatter().args.backgroundImageX != null) { - this.NodeSVGbackgroundImage.setAttribute("x", this.getFormatter().args.backgroundImageX); - } - if (this.getFormatter().args.backgroundImageY != null) { - this.NodeSVGbackgroundImage.setAttribute("y", this.getFormatter().args.backgroundImageY); - } - - this.GraphBackground.appendChild(this.NodeSVGbackgroundImage); - this.NodeSVGbackgroundImage.removeAttribute("href"); - this.NodeSVGbackgroundImage.setAttribute("xlink:href", this.getFormatter().getBackgroundImage()); -}; - -GraphCanvas.prototype.removeBackgroundImage = function() { - if (this.NodeSVGbackgroundImage != null) { - this.NodeSVGbackgroundImage.parentNode.removeChild(this.NodeSVGbackgroundImage); - } -}; - -GraphCanvas.prototype._setBackgroundColor = function(color) { - var attributes = [ [ "fill", color ] ]; - SVG.drawRectangle(0, 0, this.getFormatter().getWidth(), this.getFormatter().getHeight(), this.GraphBackground, attributes); -}; - -/** Serialize **/ -GraphCanvas.prototype.toJSON = function() { - var json = {}; - json.dataset = {}; - json.formatter = {}; - json.layout = {}; - json.dataset = this.getDataset().toJSON(); - json.formatter = this.getFormatter().toJSON(); - json.layout = this.getLayout().toJSON(); - return json; -}; - -GraphCanvas.prototype.toHTML = function() { - //this.backgroungToSVG(); - var html = this._svg.parentElement.innerHTML; - - var start = html.indexOf("") + 6; - - return html.substr(start, end); -}; - -/** DRAW **/ -GraphCanvas.prototype.draw = function(graphdataset, graphformatter, graphlayout) { - this.setDataset(graphdataset); - this.setFormatter(graphformatter); - this.setLayout(graphlayout); - - var _this = this; - this.getFormatter().changed.attach(function(sender, item) { - _this.removeNode(item.getId()); - _this.renderNode(item.getId()); - if (_this.args.labeled) { - _this.removeLabel(item.getId()); - _this.renderLabel(item.getId()); - } - - }); - //TODO - this.getFormatter().edgeChanged.attach(function(sender, item) { - _this.removeEdge(item.getId()); - _this.renderEdge(item.getId()); - }); - - this.getFormatter().resized.attach(function(sender, item) { - _this.resize(_this.getFormatter().getWidth(), _this.getFormatter().getHeight()); - }); - - this.getFormatter().backgroundImageChanged.attach(function(sender, item) { - _this.setBackgroundImage(_this.getFormatter().getBackgroundImage()); - }); - - this.getFormatter().backgroundColorChanged.attach(function(sender, item) { - _this._setBackgroundColor(_this.getFormatter().getBackgroundColor()); - }); - - this.getLayout().changed.attach(function(sender, item) { - _this.moveNode(item.getId()); - _this.moveEdge(item.getId()); - if (_this.args.labeled) { - _this.removeLabel(item.getId()); - _this.renderLabel(item.getId()); - } - }); - - this.getDataset().newVertex.attach(function(sender, item) { - - _this.renderNode(item.getId()); - if (_this.args.labeled) { - _this.renderLabel(item.getId()); - } - }); - - this.getDataset().newEdge.attach(function(sender, item) { - _this.renderEdge(item.getId()); - }); - - this.getDataset().vertexDeleted.attach(function(sender, item) { - _this.removeNode(item.getId()); - if (_this.args.labeled) { - _this.removeLabel(item.getId()); - } - }); - - this.getDataset().edgeDeleted.attach(function(sender, item) { - _this.removeEdge(item.getId()); - }); - - this.getDataset().vertexNameChanged.attach(function(sender, args) { - if (_this.args.labeled) { - _this.removeLabel(args.item.getId()); - _this.removeLabel(args.item.getId()); - _this.renderLabel(args.item.getId()); - } - }); - this.init(); - this.render(); -}; - -GraphCanvas.prototype.render = function() { - for ( var id in this.getDataset().getVertices()) { - this.renderNode(id); - } - this.renderLabels(); - this.renderEdges(); -}; - -GraphCanvas.prototype.renderLabels = function() { - if (this.args.labeled) { - for ( var id in this.getDataset().getVertices()) { - this.renderLabel(id); - } - } -}; - -GraphCanvas.prototype.removeLabels = function() { - for ( var id in this.getDataset().getVertices()) { - this.removeLabel(id); - } -}; - -/** Utilities method for nodes **/ -GraphCanvas.prototype.isNodeCanvas = function(node) { - return ((node.id == this.args.idGraph) || (node.id == this.id)); -}; - -GraphCanvas.prototype.isNodeBackground = function(node) { - return ((node.id == this.args.idBackgroundNode)); -}; - -GraphCanvas.prototype.isVertex = function(node) { - if (node.getAttribute("id") != null) { - if (node.getAttribute("id").indexOf("_v_") != -1) { - return true; - } - } - return false; -}; - -GraphCanvas.prototype.isLabel = function(node) { - if (node.getAttribute("id") != null) { - if (node.getAttribute("id").indexOf("_l_") != -1) { - return true; - } - } - return false; -}; - -GraphCanvas.prototype.isEdge = function(node) { - if (node.getAttribute("id") != null) { - if (node.getAttribute("id").indexOf("_e_") != -1) { - return true; - } - } - return false; -}; - -/** Resize **/ -GraphCanvas.prototype.resize = function(width, height) { - // this._svg.setAttribute("width", width); - // this._svg.setAttribute("height", height); - if (this.NodeSVGbackgroundImage != null) { - this.NodeSVGbackgroundImage.setAttribute("width", width); - this.NodeSVGbackgroundImage.setAttribute("height", height); - } - - this._svg.setAttribute("width", width); - this._svg.setAttribute("height", height); - - this.clearCanvas(); - this.render(); -}; - -GraphCanvas.prototype.clearCanvas = function() { - DOM.removeChilds(this.GraphEdgeGroup.getAttribute("id")); - DOM.removeChilds(this.GraphNodeGroup.getAttribute("id")); - this.clearLabels(); -}; - -GraphCanvas.prototype.clearLabels = function() { - DOM.removeChilds(this.GraphLabelGroup.getAttribute("id")); -}; - -/** ID'S converter **/ -GraphCanvas.prototype.getSVGNodeId = function(nodeId) { - return this.id + "_v_" + nodeId; -}; - -GraphCanvas.prototype.getSVGEdgeId = function(edgeId) { - return this.id + "_e_" + edgeId; -}; - -GraphCanvas.prototype.getSVGArrowEdgeId = function(edgeId) { - return this.id + "_arrow_" + edgeId; -}; - -GraphCanvas.prototype.getSVGLabelId = function(edgeId) { - return this.id + "_l_" + edgeId; -}; - -GraphCanvas.prototype.blinkVertexById = function(vertexId) { - $("#" + this.getSVGNodeId(vertexId)).fadeIn().fadeOut().fadeIn().fadeOut().fadeIn().fadeOut(); -}; - -GraphCanvas.prototype.getVertexIdFromSVGId = function(svgVertexId) { - return svgVertexId.replace(this.id, "").replace("_v_", ""); -}; - -GraphCanvas.prototype.getEdgeIdFromSVGId = function(svgEdgeId) { - return svgEdgeId.replace(this.id, "").replace("_e_", ""); -}; - -/** VERTEX **/ -GraphCanvas.prototype.getVertexById = function(id) { - return document.getElementById(this.getSVGNodeId(id)); -}; - -GraphCanvas.prototype.renderNodes = function() { - for ( var id in this.getDataset().getVertices()) { - this.renderNode(id); - } -}; - -GraphCanvas.prototype.overNode = function(nodeId) { - if (!this.args.interactive) { - return; - } - /** If selected we don't change the format **/ - if (this.args.isVertexSelected[nodeId] == null) { - var args = this.getFormatter().getVertexById(nodeId).getOver(); - args.args["cursor"] = 'pointer'; - this.changeVertexFormat(nodeId, args); - } -}; - -GraphCanvas.prototype.outNode = function(nodeId) { - if (!this.args.interactive) { - return; - } - - /** If selected we don't change the format **/ - if (this.args.isVertexSelected[nodeId] == null) { - this.changeVertexFormat(nodeId, this.getFormatter().getVertexById(nodeId).getDefault()); - } -}; - -GraphCanvas.prototype.overLabel = function(nodeId) { - this.overNode(nodeId); - // this.svgLabels[nodeId].setAttribute("cursor", "pointer"); -}; - -GraphCanvas.prototype.outLabel = function(nodeId) { - this.outNode(nodeId); - // this.svgLabels[nodeId].setAttribute("cursor", ""); -}; - -GraphCanvas.prototype.clickNode = function(nodeId) { - if (!this.args.interactive) { - return; - } - - /** si el evento se dispara oprque estaba dragging entonces no activo nada **/ - if (this.args.isVertexSelected[nodeId] == null) { - this.selectNode(nodeId); - } else { - this.deselectNode(nodeId); - } -}; - -GraphCanvas.prototype.selectNode = function(nodeId) { - for ( var i = 0; i < this.args.selectedVertices.length; i++) { - var format = this.getFormatter().getVertexById(nodeId).getSelected(); - format.opacity = 0.2; - this.changeVertexFormat(nodeId, this.getFormatter().getVertexById(nodeId).getSelected()); - } - - if (this.args.isVertexSelected[nodeId] == null) { - var format = this.getFormatter().getVertexById(nodeId).getSelected(); - format.opacity = 1; - this.changeVertexFormat(nodeId, this.getFormatter().getVertexById(nodeId).getSelected()); - this.args.selectedVertices.push(nodeId); - this.args.isVertexSelected[nodeId] = this.args.selectedVertices.length - 1; - this.onVertexSelect.notify(nodeId); - } -}; - -GraphCanvas.prototype.selectAllEdges = function() { - this.deselectNodes(); - this.deselectEdges(); - - for ( var edgesId in this.getDataset().edges) { - this.selectEdge(edgesId); - } -}; - -GraphCanvas.prototype.selectAllNodes = function() { - this.deselectNodes(); - this.deselectEdges(); - - for ( var vertexId in this.getDataset().vertices) { - this.selectNode(vertexId); - } -}; - -GraphCanvas.prototype.selectAll = function() { - this.deselectNodes(); - this.deselectEdges(); - - for ( var vertexId in this.getDataset().vertices) { - this.selectNode(vertexId); - } - - for ( var edgesId in this.getDataset().edges) { - this.selectEdge(edgesId); - } -}; - -GraphCanvas.prototype.selectEdge = function(edgeId) { - if (this.args.isEdgeSelected[edgeId] == null) { - this.changeEdgeFormat(edgeId, this.getFormatter().getEdgeById(edgeId).getSelected()); - //this.args.selectedEdges.push(edgeId); - this.args.isEdgeSelected[edgeId] = true; //this.args.selectedEdges.length - 1; - this.onEdgeSelect.notify(edgeId); - } -}; - -GraphCanvas.prototype.selectEdges = function(edges) { - - for ( var i = 0; i < edges.length; i++) { - this.selectEdge(edges[i]); - } -}; - -GraphCanvas.prototype.deselectNode = function(nodeId) { - if (this.args.isVertexSelected[nodeId] != null) { - this.changeVertexFormat(nodeId, this.getFormatter().getVertexById(nodeId).getDefault()); - this.args.selectedVertices.splice(this.args.isVertexSelected[nodeId], 1); - var index = this.args.isVertexSelected[nodeId]; - delete this.args.isVertexSelected[nodeId]; - - for ( var vertex in this.args.isVertexSelected) { - if (this.args.isVertexSelected[vertex] > index) { - this.args.isVertexSelected[vertex] = this.args.isVertexSelected[vertex] - 1; - } - } - } -}; - -GraphCanvas.prototype.deselectNodes = function() { - var selected = JSON.parse(JSON.stringify(this.getSelectedVertices())); - for ( var i = 0; i < selected.length; i++) { - this.deselectNode(selected[i]); - } -}; -GraphCanvas.prototype.selectNodes = function(idNodes) { - - for ( var i = 0; i < idNodes.length; i++) { - this.selectNode(idNodes[i]); - } - - // for ( var vertex in this.args.isVertexSelected) { - // if (this.args.isVertexSelected[vertex] > index){ - // this.args.isVertexSelected[vertex] = this.args.isVertexSelected[vertex] - 1; - // } - // } - -}; - -GraphCanvas.prototype.changeVertexFormat = function(nodeId, format) { - var svgNode = DOM.select(this.getSVGNodeId(nodeId)); - if (svgNode != null) { - var properties = format.toJSON(); - for ( var item in properties) { - svgNode.setAttribute(item, properties[item]); - } - - if (this.getFormatter().getVertexById(nodeId) instanceof CircleVertexGraphFormatter) { - var transform = "translate(" + svgNode.getAttribute("dragx") + "," + svgNode.getAttribute("dragy") + "), scale(" + format.getSize() + ")"; - svgNode.setAttribute("transform", transform); - } - } -}; - -GraphCanvas.prototype.renderLabel = function(nodeId) { - var x = Math.ceil(this.getLayout().getNodeById(nodeId).x * this.getFormatter().getWidth()); - var y = Math.ceil(this.getLayout().getNodeById(nodeId).y * this.getFormatter().getHeight()); - - var svgAttributesNode = JSON.parse(JSON.stringify(this.getFormatter().getVertexById(nodeId).getDefault().toJSON().title)); - svgAttributesNode.id = this.getSVGLabelId(this.getDataset().getVertexById(nodeId).getId()); - svgAttributesNode.dx = (-1) * (this.getDataset().getVertexById(nodeId).getName().length * svgAttributesNode["font-size"]) / 4 - 4; - - svgAttributesNode.dy = parseFloat((this.getFormatter().getVertexById(nodeId).getDefault().getSize())) - + parseFloat(svgAttributesNode["font-size"]) + parseFloat(this.getFormatter().getVertexById(nodeId).getDefault().getStrokeWidth()) - 4; - svgAttributesNode.dragx = Math.ceil(this.getLayout().getNodeById(nodeId).x * this.getFormatter().getWidth()); - - var gragy = parseFloat(this.getFormatter().getVertexById(nodeId).getDefault().getSize()) - + Math.ceil(this.getLayout().getNodeById(nodeId).y * this.getFormatter().getHeight()); - svgAttributesNode.dragy = gragy; - svgAttributesNode.transform = "translate(" + svgAttributesNode.dragx + "," + svgAttributesNode.dragy + ")";//, scale("+this.formatter.getVertexById(nodeId).getDefault().getSize()+")"; - - var nodeSVG = SVG.drawText(0, 0, this.getDataset().getVertexById(nodeId).getName(), this.GraphLabelGroup, svgAttributesNode); - - this.svgLabels[nodeId] = nodeSVG; - - /** Events for the SVG node **/ - var _this = this; - if (nodeSVG != null) { - nodeSVG.addEventListener("mouseover", function() { - _this.overLabel(nodeId); - }, false); - nodeSVG.addEventListener("mouseout", function() { - _this.outLabel(nodeId); - }, false); - } - -}; - -GraphCanvas.prototype.removeLabel = function(labelId) { - if (DOM.select(this.getSVGLabelId(labelId)) != null) { - DOM.select(this.getSVGLabelId(labelId)).parentNode.removeChild(DOM.select(this.getSVGLabelId(labelId))); - } -}; - -GraphCanvas.prototype.renderNode = function(nodeId) { - var svgAttributesNode = JSON.parse(JSON.stringify(this.getFormatter().getVertexById(nodeId).getDefault().toJSON())); - svgAttributesNode.dragx = Math.ceil(this.getLayout().getNodeById(nodeId).x * this.getFormatter().getWidth()); - svgAttributesNode.dragy = Math.ceil(this.getLayout().getNodeById(nodeId).y * this.getFormatter().getHeight()); - svgAttributesNode.transform = "translate(" + svgAttributesNode.dragx + "," + svgAttributesNode.dragy + ")"; - svgAttributesNode.id = this.getSVGNodeId(nodeId); - /*svgAttributesNode["stroke-width"] = 3 ; - svgAttributesNode["stroke-opacity"] = 1 ; - svgAttributesNode["fill-opacity"] = svgAttributesNode["opacity"] ; - svgAttributesNode["opacity"] = 1 ;*/ - this.circleDefaultRadius = this.getFormatter().getVertexById(nodeId).getDefault().getSize(); - var nodeSVG; - - if (this.getFormatter().getVertexById(nodeId) instanceof CircleVertexGraphFormatter) { - nodeSVG = SVG.drawCircle(0, 0, this.circleDefaultRadius, this.GraphNodeGroup, svgAttributesNode); - } - - if (this.getFormatter().getVertexById(nodeId) instanceof SquareVertexGraphFormatter) { - //nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius) ,0 - (this.formatter.getVertexById(nodeId).getDefault().getSize()) , (this.getFormatter().getVertexById(nodeId).getDefault().getSize()*2), (this.getFormatter().getVertexById(nodeId).getDefault().getSize()*2), this.GraphNodeGroup, svgAttributesNode); - nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius), 0 - (this.circleDefaultRadius), (this.circleDefaultRadius * 2), - (this.circleDefaultRadius * 2), this.GraphNodeGroup, svgAttributesNode); - } - - if (this.getFormatter().getVertexById(nodeId) instanceof EllipseVertexGraphFormatter) { - nodeSVG = SVG.drawEllipse(0, 0, this.circleDefaultRadius * 1.5, this.circleDefaultRadius, this.GraphNodeGroup, svgAttributesNode); - } - - if (this.getFormatter().getVertexById(nodeId) instanceof RectangleVertexGraphFormatter) { - //nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius) ,0 - ((this.circleDefaultRadius*2)/2) , (this.circleDefaultRadius*2), (this.circleDefaultRadius), this.GraphNodeGroup, svgAttributesNode); - nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius * 1.5), 0 - (this.circleDefaultRadius), (this.circleDefaultRadius * 2 * 1.5), - (this.circleDefaultRadius * 2), this.GraphNodeGroup, svgAttributesNode); - - } - - if (this.getFormatter().getVertexById(nodeId) instanceof RoundedVertexGraphFormatter) { - svgAttributesNode.ry = 2;// this.formatter.getVertexById(nodeId).getDefault().getSize()/4; - svgAttributesNode.rx = 2;// this.formatter.getVertexById(nodeId).getDefault().getSize()/4; - nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius * 1.5), 0 - (this.circleDefaultRadius), (this.circleDefaultRadius * 2 * 1.5), - (this.circleDefaultRadius * 2), this.GraphNodeGroup, svgAttributesNode); - } - - // - - if (this.getFormatter().getVertexById(nodeId) instanceof OctagonVertexGraphFormatter) { - svgAttributesNode.ry = 2; - svgAttributesNode.rx = 2; - nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius * 1.5), 0 - (this.circleDefaultRadius), (this.circleDefaultRadius * 2 * 1.5), - (this.circleDefaultRadius * 2), this.GraphNodeGroup, svgAttributesNode); - } - - nodeSVG.internalId = nodeId; - // - var _this = this; - - /** Events for the SVG node **/ - if (nodeSVG != null) { - nodeSVG.addEventListener("mouseover", function() { - _this.onVertexOver.notify(nodeId); - _this.overNode(nodeId); - }, false); - nodeSVG.addEventListener("mouseout", function() { - _this.onVertexOut.notify(nodeId); - _this.outNode(nodeId); - }, false); - //nodeSVG.addEventListener("click", function(){_this.clickNode(nodeId);}, false); - // - nodeSVG.addEventListener("mouseup", function() { - _this.onVertexUp.notify(nodeId); - }, false); - } -}; - -GraphCanvas.prototype.removeNode = function(nodeId) { - DOM.select(this.getSVGNodeId(nodeId)).parentNode.removeChild(DOM.select(this.getSVGNodeId(nodeId))); - if (this.args.labeled) { - this.removeLabel(nodeId); - } -}; - -/** REMOVING **/ -GraphCanvas.prototype.removeSelected = function() { - /** El orden importa **/ - this.removeSelectedEdges(); - this.removeSelectedNode(); - -}; - -GraphCanvas.prototype.removeSelectedNode = function() { - var selected = JSON.parse(JSON.stringify(this.getSelectedVertices())); - this.deselectNodes(); - var sorted = selected.sort(function(a, b) { - return a - b - }); - for ( var i = 0; i < sorted.length; i++) { - if (this.getDataset().getVertexById(sorted[i]) != null) { - this.getDataset().getVertexById(sorted[i]).remove(); - } - } -}; - -/** EDGES **/ -GraphCanvas.prototype.removeEdge = function(edgeId) { - if (DOM.select(this.getSVGEdgeId(edgeId)) != null) { - DOM.select(this.getSVGEdgeId(edgeId)).parentNode.removeChild(DOM.select(this.getSVGEdgeId(edgeId))); - } - - if (DOM.select(this.getSVGEdgeId(edgeId) + "_shadow") != null) { - DOM.select(this.getSVGEdgeId(edgeId) + "_shadow").parentNode.removeChild(DOM.select(this.getSVGEdgeId(edgeId) + "_shadow")); - } - - if (DOM.select(this.getSVGArrowEdgeId(edgeId)) != null) { - DOM.select(this.getSVGArrowEdgeId(edgeId)).parentNode.removeChild(DOM.select(this.getSVGArrowEdgeId(edgeId))); - } -}; - -GraphCanvas.prototype.overEdge = function(edgeId) { - if ((!this.args.interactive) || this.dragging || this.selecting) { - return; - } - - /** If selected we don't change the format **/ - if (this.args.isEdgeSelected[edgeId] == null) { - var format = this.getFormatter().getEdgeById(edgeId).getOver(); - format.args["cursor"] = "pointer"; - this.changeEdgeFormat(edgeId, format); - } -}; - -GraphCanvas.prototype.outEdge = function(edgeId) { - if (!this.args.interactive) { - return; - } - - /** If selected we don't change the format **/ - if (this.args.isEdgeSelected[edgeId] == null) { - this.changeEdgeFormat(edgeId, this.getFormatter().getEdgeById(edgeId).getDefault()); - } -}; - -GraphCanvas.prototype.changeEdgeFormat = function(edgeId, format) { - var svgEdge = DOM.select(this.getSVGEdgeId(edgeId) + "_shadow"); - if (svgEdge != null) { - var properties = format.toJSON(); - for ( var item in properties) { - svgEdge.setAttribute(item, properties[item]); - } - } -}; - -GraphCanvas.prototype.deselectEdge = function(edgeID) { - if (this.args.isEdgeSelected[edgeID] != null) { - this.changeEdgeFormat(edgeID, this.getFormatter().getEdgeById(edgeID).getDefault()); - var index = this.args.isEdgeSelected[edgeID]; - delete this.args.isEdgeSelected[edgeID]; - } -}; - -GraphCanvas.prototype.deselectEdges = function() { - var selected = JSON.parse(JSON.stringify(this.getSelectedEdges())); - for ( var i = 0; i < selected.length; i++) { - this.deselectEdge(selected[i]); - } -}; - -GraphCanvas.prototype.removeSelectedEdges = function() { - var selected = JSON.parse(JSON.stringify(this.getSelectedEdges())); - this.deselectEdges(); - for ( var i = 0; i < selected.length; i++) { - if (this.getDataset().getEdgeById(selected[i]) != null) { - this.getDataset().getEdgeById(selected[i]).remove(); - } - } -}; - -GraphCanvas.prototype.renderEdge = function(edgeId) { - var svgAttributesEdge = this.getFormatter().getEdgeById(edgeId).getDefault().toJSON(); - var edge = this.getDataset().getEdgeById(edgeId); - - var svgNodeTarget = this.getVertexById(edge.getNodeTarget().getId()); - var svgNodeSource = this.getVertexById(edge.getNodeSource().getId()); - svgAttributesEdge.id = this.getSVGEdgeId(edge.getId()) + "_shadow"; - - var svgEdge = null; - - if (this.getFormatter().getEdgeById(edgeId) instanceof LineEdgeGraphFormatter) { - var coordenateSourceX = svgNodeSource.getAttribute("dragx"); - var coordenateSourceY = svgNodeSource.getAttribute("dragy"); - var coordenateTargetX = svgNodeTarget.getAttribute("dragx"); - var coordenateTargetY = svgNodeTarget.getAttribute("dragy"); - - SVG.drawLine(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, this.GraphEdgeGroup, svgAttributesEdge); - var attributesShadow = {}; - attributesShadow.id = this.getSVGEdgeId(edge.getId()); - attributesShadow["stroke-opacity"] = 0; - attributesShadow["stroke-width"] = 4; - attributesShadow["stroke"] = "black"; - svgEdge = SVG.drawLine(svgNodeSource.getAttribute("dragx"), svgNodeSource.getAttribute("dragy"), svgNodeTarget.getAttribute("dragx"), - svgNodeTarget.getAttribute("dragy"), this.GraphEdgeGroup, attributesShadow); - } - - if (this.getFormatter().getEdgeById(edgeId) instanceof BezierEdgeGraphFormatter) { - var nodeId = edge.getNodeTarget().getId(); - var nodeSize = this.formatter.getVertexById(nodeId).getDefault().getSize() * this.getFormatter().getNodesMaxSize(); - svgAttributesEdge.fill = "none"; - svgAttributesEdge.id = this.getSVGEdgeId(edgeId); - var d = this.calculateCoordenatesBezier(nodeSize, svgNodeSource.getAttribute("dragx"), svgNodeSource.getAttribute("dragy")); - svgEdge = SVG.drawPath(d, this.GraphEdgeGroup, svgAttributesEdge); - } - ; - - if ((this.getFormatter().getEdgeById(edgeId) instanceof DirectedLineEdgeGraphFormatter) - || (this.getFormatter().getEdgeById(edgeId) instanceof CutDirectedLineEdgeGraphFormatter) - || (this.getFormatter().getEdgeById(edgeId) instanceof DotDirectedLineEdgeGraphFormatter) - || (this.getFormatter().getEdgeById(edgeId) instanceof OdotDirectedLineEdgeGraphFormatter) - || (this.getFormatter().getEdgeById(edgeId) instanceof OdirectedLineEdgeGraphFormatter)) { - var coordenateSourceX = svgNodeSource.getAttribute("dragx"); - var coordenateSourceY = svgNodeSource.getAttribute("dragy"); - var coordenateTargetX = svgNodeTarget.getAttribute("dragx"); - var coordenateTargetY = svgNodeTarget.getAttribute("dragy"); - - var offset = parseFloat(this.getFormatter().getVertexById(this.getDataset().getEdgeById(edgeId).getNodeTarget().getId()).getDefault() - .getSize() - * this.circleDefaultRadius); - var point = this._calculateEdgePointerPosition(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, offset); - coordenateTargetX = point.x; - coordenateTargetY = point.y; - SVG.drawLine(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, this.GraphEdgeGroup, svgAttributesEdge); - - var attributesShadow = {}; - attributesShadow.id = this.getSVGEdgeId(edge.getId()); - attributesShadow["stroke-opacity"] = 0; - attributesShadow["stroke-width"] = 4; - attributesShadow["stroke"] = "black"; - svgEdge = SVG.drawLine(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, this.GraphEdgeGroup, attributesShadow); - } - - if (this.getFormatter().getEdgeById(edgeId) instanceof DirectedLineEdgeGraphFormatter - || (this.getFormatter().getEdgeById(edgeId) instanceof OdirectedLineEdgeGraphFormatter)) { - var coordenateSourceX = svgNodeSource.getAttribute("dragx"); - var coordenateSourceY = svgNodeSource.getAttribute("dragy"); - var coordenateTargetX = svgNodeTarget.getAttribute("dragx"); - var coordenateTargetY = svgNodeTarget.getAttribute("dragy"); - - var point = this._calculateEdgePointerPosition(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, offset); - coordenateTargetX = point.x; - coordenateTargetY = point.y; - - var angle = Geometry.toDegree(point.angle) + 90; - this.arrowDefaultSize = this.getFormatter().getEdgeById(edgeId).getArrowSize(); //getDefault().getArrowSize(); - var d = "-" + this.arrowDefaultSize + ",0 0,-" + parseFloat(this.arrowDefaultSize) * 2 + " " + this.arrowDefaultSize + ",0"; - - var attributes; - - if (this.getFormatter().getEdgeById(edgeId) instanceof DirectedLineEdgeGraphFormatter) { - attributes = [ - [ "fill", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], - [ "stroke", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], [ "id", this.getSVGArrowEdgeId(edgeId) ] ]; - } else { - attributes = [ - [ "fill", "#FFFFFF" ], [ "stroke", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], - [ "id", this.getSVGArrowEdgeId(edgeId) ] ]; - } - - var flechaSVGNode = SVG.drawPoligon(d, this.GraphEdgeGroup, attributes);//, ["transform", "rotate("+angle+"), translate(0,0)"]]); - flechaSVGNode.setAttribute("transform", " translate(" + coordenateTargetX + ", " + coordenateTargetY + "), rotate(" + angle + ")"); - } - ; - - if (this.getFormatter().getEdgeById(edgeId) instanceof CutDirectedLineEdgeGraphFormatter) { - var coordenateSourceX = svgNodeSource.getAttribute("dragx"); - var coordenateSourceY = svgNodeSource.getAttribute("dragy"); - var coordenateTargetX = svgNodeTarget.getAttribute("dragx"); - var coordenateTargetY = svgNodeTarget.getAttribute("dragy"); - - var point = this._calculateEdgePointerPosition(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, offset); - coordenateTargetX = point.x; - coordenateTargetY = point.y; - - var angle = Geometry.toDegree(point.angle) + 90; - - //this.arrowDefaultSize = 2; //getDefault().getArrowSize(); - var d = "-4,0 4,0 4,-2 -4,-2"; - - var flechaSVGNode = SVG.drawPoligon(d, this.GraphEdgeGroup, [ - [ "fill", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], - [ "stroke", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], [ "id", this.getSVGArrowEdgeId(edgeId) ] ]);//, ["transform", "rotate("+angle+"), translate(0,0)"]]); - flechaSVGNode.setAttribute("transform", " translate(" + coordenateTargetX + ", " + coordenateTargetY + "), rotate(" + angle + ")"); - } - ; - - if ((this.getFormatter().getEdgeById(edgeId) instanceof DotDirectedLineEdgeGraphFormatter) - || (this.getFormatter().getEdgeById(edgeId) instanceof OdotDirectedLineEdgeGraphFormatter)) { - var coordenateSourceX = svgNodeSource.getAttribute("dragx"); - var coordenateSourceY = svgNodeSource.getAttribute("dragy"); - var coordenateTargetX = svgNodeTarget.getAttribute("dragx"); - var coordenateTargetY = svgNodeTarget.getAttribute("dragy"); - var point = this._calculateEdgePointerPosition(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, offset); - coordenateTargetX = point.x; - coordenateTargetY = point.y; - var angle = Geometry.toDegree(point.angle) + 90; - // this.arrowDefaultSize = this.formatter.getEdgeById(edgeId).getArrowSize(); //getDefault().getArrowSize(); - var attributes = []; - if (this.getFormatter().getEdgeById(edgeId) instanceof OdotDirectedLineEdgeGraphFormatter) { - attributes = [ - [ "fill", "#FFFFFF" ], [ "stroke", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], - [ "id", this.getSVGArrowEdgeId(edgeId) ] ]; - } else { - attributes = [ - [ "fill", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], - [ "stroke", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], [ "id", this.getSVGArrowEdgeId(edgeId) ] ]; - } - var flechaSVGNode = SVG.drawCircle(0, 0, 4, this.GraphEdgeGroup, attributes); - flechaSVGNode.setAttribute("transform", " translate(" + coordenateTargetX + ", " + coordenateTargetY + "), rotate(" + angle + ")"); - } - ; - - var _this = this; - /** Events for the SVG edge **/ - if (svgEdge != null) { - if (this.getDataset().getEdgesCount() < this.args.maxNumberEdgesFiringEvents) { - svgEdge.addEventListener("mouseover", function() { - _this.overEdge(edgeId); - }, false); - svgEdge.addEventListener("mouseout", function() { - _this.outEdge(edgeId); - }, false); - } - } -}; - -GraphCanvas.prototype._calculateEdgePointerPosition = function(sourceX, sourceY, targetX, targetY, radius) { - var angle = Geometry.getAngleBetweenTwoPoints(sourceX, sourceY, targetX, targetY); - - /** Suponiendo el node source que este a la derecha **/ - if ((targetX - sourceX) < 0) { - var b = Geometry.getAdjacentSideOfRectangleRight(angle, radius); - targetX = parseFloat(targetX) + parseFloat(b); - arrowX = parseFloat(targetX) + parseFloat(b) + this.arrowDefaultSize / 2; - } else { - var b = Geometry.getAdjacentSideOfRectangleRight(angle, radius); - targetX = parseFloat(targetX) - parseFloat(b); - arrowX = parseFloat(targetX) - parseFloat(b) - this.arrowDefaultSize / 2; - } - - /** Suponiendo el node source que este a la arriba **/ - if ((targetY - sourceY) > 0) { - var a = Geometry.getOppositeSideOfRectangleRight(angle, radius); - targetY = parseFloat(targetY) - parseFloat(a); - arrowY = parseFloat(targetY) - parseFloat(a) - this.arrowDefaultSize / 2; - } else { - var a = Geometry.getOppositeSideOfRectangleRight(angle, radius); - targetY = parseFloat(targetY) + parseFloat(a); - arrowY = parseFloat(targetY) + parseFloat(a) - this.arrowDefaultSize / 2; - - } - - return { - "x" : arrowX, - "y" : arrowY, - "angle" : angle - }; -}; - -GraphCanvas.prototype.calculateCoordenatesBezier = function(nodeSize, x1, y1) { - var x11 = x1 - (nodeSize / 2); - var y11 = y1 - (nodeSize / 2); - - var x12 = parseFloat(x1) + parseFloat(nodeSize / 2); - var y12 = y1 - (nodeSize / 2); - - var curvePointX = (x12 - x11) / 2 + x11; - var curvePointY = y1 - (nodeSize * 2); - var d = "M" + x11 + "," + y11 + " T" + curvePointX + "," + curvePointY + " " + x12 + "," + y12; - return d; - -}; - -GraphCanvas.prototype.renderEdges = function() { - for ( var edge in this.getDataset().getEdges()) { - this.renderEdge(this.getDataset().getEdgeById(edge).getId()); - - } -}; - -GraphCanvas.prototype.getLastSelectedNode = function() { - var node = null; - if (this.getSelectedVertices().length > 0) { - var nodeId = this.getSelectedVertices()[this.getSelectedVertices().length - 1]; - node = this.getDataset().getVertexById(nodeId); - } - return node; -}; -/* - GraphCanvas.prototype.getNodeByNameAndIndex = function(node, index){ - var nodeId = this.getDataset().verticesIndex[node][index]; - var nodeItem = this.getDataset().getVertexById(nodeId); - return nodeItem; - }; - */ - -GraphCanvas.prototype.setDataset = function(dataset) { - this.dataset = dataset; -}; - -GraphCanvas.prototype.setFormatter = function(formatter) { - this.formatter = formatter; -}; - -GraphCanvas.prototype.setLayout = function(layout) { - this.layout = layout; -}; - -/** API **/ -GraphCanvas.prototype.getDataset = function() { - return this.dataset; -}; - -GraphCanvas.prototype.getFormatter = function() { - return this.formatter; -}; - -GraphCanvas.prototype.getLayout = function() { - return this.layout; -}; - -/** API DATASET **/ -GraphCanvas.prototype.addVertex = function(name, args) { - this.getDataset().addNode(name, args); -}; - -GraphCanvas.prototype.removeVertex = function(vertexId) { - this.getDataset().getVertexById(vertexId).remove(); -}; - -GraphCanvas.prototype.addEdge = function(edgeName, nodeSourceId, nodeTargetId, args) { - this.getDataset().addEdge(edgeName, nodeSourceId, nodeTargetId, args); -}; -/* - GraphCanvas.prototype.removeEdge = function(edgeId){ - this.getDataset().getEdgeById(edgeId).remove(); - }; - */ - -/** API FORMATTER **/ -GraphCanvas.prototype.getWidth = function() { - return this.getFormatter().getWidth(); -}; - -GraphCanvas.prototype.getHeight = function() { - return this.getFormatter().getHeight(); -}; - -GraphCanvas.prototype.getBackgroundImage = function() { - return this.getFormatter().getBackgroundImage(); -}; - -//GraphCanvas.prototype.setBackgroundImage = function(value){ -// this.getFormatter().setBackgroundImage(value); -//}; - -GraphCanvas.prototype.getBackgroundColor = function() { - return this.getFormatter().getBackgroundColor(); -}; - -GraphCanvas.prototype.setBackgroundColor = function() { - this.getFormatter().setBackgroundColor(value); -}; - -//GraphCanvas.prototype.setEdgeFill = function(edgeId, value){ -// this.getFormatter().getEdgeById(edgeId).getDefault().setFill(value); -//}; -// -//GraphCanvas.prototype.getEdgeFill = function(edgeId){ -// return this.getFormatter().getEdgeById(edgeId).getDefault().getFill(); -//}; - -/** VERTICES FORMATTER **/ -GraphCanvas.prototype.setVertexSize = function(vertexId, value) { - this.getFormatter().getVertexById(vertexId).getDefault().setSize(value); -}; - -GraphCanvas.prototype.getVertexSize = function(vertexId) { - return this.getFormatter().getVertexById(vertexId).getDefault().getSize(); -}; - -GraphCanvas.prototype.setVertexStroke = function(vertexId, value) { - this.getFormatter().getVertexById(vertexId).getDefault().setStroke(value); -}; - -GraphCanvas.prototype.getVertexStroke = function(vertexId) { - return this.getFormatter().getVertexById(vertexId).getDefault().getStroke(); -}; - -GraphCanvas.prototype.setVertexStrokeOpacity = function(vertexId, value) { - this.getFormatter().getVertexById(vertexId).getDefault().setStrokeOpacity(value); -}; - -GraphCanvas.prototype.getVertexStrokeOpacity = function(vertexId) { - return this.getFormatter().getVertexById(vertexId).getDefault().getStrokeOpacity(); -}; - -GraphCanvas.prototype.setVertexOpacity = function(vertexId, value) { - this.getFormatter().getVertexById(vertexId).getDefault().setOpacity(value); -}; - -GraphCanvas.prototype.getVertexOpacity = function(vertexId) { - return this.getFormatter().getVertexById(vertexId).getDefault().getOpacity(); -}; - -GraphCanvas.prototype.setVertexFill = function(vertexId, color) { - this.getFormatter().getVertexById(vertexId).getDefault().setFill(color); -}; - -GraphCanvas.prototype.getVertexFill = function(vertexId) { - return this.getFormatter().getVertexById(vertexId).getDefault().getFill(); -}; - -/** EDGES FORMATTER **/ -GraphCanvas.prototype.setEdgeSize = function(edgeId, value) { - this.getFormatter().getEdgeById(edgeId).getDefault().setSize(value); -}; - -GraphCanvas.prototype.getEdgeSize = function(edgeId) { - return this.getFormatter().getEdgeById(edgeId).getDefault().getSize(); -}; - -GraphCanvas.prototype.setEdgeStroke = function(edgeId, value) { - this.getFormatter().getEdgeById(edgeId).getDefault().setStroke(value); -}; - -GraphCanvas.prototype.getEdgeStroke = function(edgeId) { - return this.getFormatter().getEdgeById(edgeId).getDefault().getStroke(); -}; - -GraphCanvas.prototype.setEdgeStrokeOpacity = function(edgeId, value) { - this.getFormatter().getEdgeById(edgeId).getDefault().setStrokeOpacity(value); -}; - -GraphCanvas.prototype.getEdgeStrokeOpacity = function(edgeId) { - return this.getFormatter().getEdgeById(edgeId).getDefault().getStrokeOpacity(); -}; - -GraphCanvas.prototype.setEdgeFill = function(edgeId, color) { - this.getFormatter().getEdgeById(edgeId).getDefault().setFill(color); -}; - -GraphCanvas.prototype.getEdgeFill = function(edgeId) { - return this.getFormatter().getEdgeById(edgeId).getDefault().getFill(); -}; - -/** API LAYOUT **/ -GraphCanvas.prototype.setCoordinates = function(vertexId, x, y) { - return this.getLayout().getEdgeById(vertexId).setCoordinates(x, y); -}; - - - -function HPLCGraph(args) { - this.width = 600; - this.height = 600; - this.title = ''; - this.bbar = false; - this.plotInnerPanelPadding = 10; - this.plotPanelPadding = 5; - this.id = BUI.id(); - - this.hidePlots = null; - this.xlabel = ""; - this.scaled = false; - this.xParam = null; - this.showRangeSelector = true; - this.interactionModel = null; - - /** for each stat the max and minimum value when it is scaled in order to show correctly in the legend **/ - this.ranges = {}; - if (args != null) { - if (args.interactionModel != null) { - this.interactionModel = args.interactionModel; - } - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; - } - if (args.bbar != null) { - this.bbar = args.bbar; - } - if (args.title != null) { - this.title = args.title; - } - if (args.plots != null) { - this.plots = args.plots; - } - - if (args.scaled != null) { - this.scaled = args.scaled; - } - if (args.xlabel != null) { - this.xlabel = args.xlabel; - } - if (args.xParam != null) { - this.xParam = args.xParam; - } - if (args.showRangeSelector != null) { - this.showRangeSelector = args.showRangeSelector; - } - } - - this.onZoomX = new Event(this); - this.onResetZoom = new Event(this); - this.dblclick = new Event(this); -} - -HPLCGraph.prototype.getMenu = function () { - var _this = this; - /** Actions buttons **/ - var actions = []; - - function toggle(item, pressed) { - if (pressed) { - _this.plots[item.param] = true; - } else { - delete _this.plots[item.param]; - } - _this.reloadData(this.hplcData); - } - - for (var i = 0; i < this.hplcData.length; i++) { - if (this.hplcData[i].showOnMenu != false) { - var param = this.hplcData[i].param; - var style = "style='padding:0 0px 0 5px;'"; - actions.push({ - text : "
" + BUI.getRectangleColorDIV(this.hplcData[i].color, 10, 10) + " " + this.hplcData[i].label + "
", - id : _this.id + param, - param : param, - enableToggle : true, - scope : this, - toggleHandler : toggle, - pressed : (_this.plots[param] != null) - }); - } - } - actions.push("-"); - - actions.push({ - text : "Scale", - enableToggle : true, - scope : this, - pressed : this.scaled, - icon : '../images/icon_graph.png', - toggleHandler : function (item, pressed) { - _this.scaled = pressed; - _this.reloadData(this.hplcData); - } - }); - - actions.push("->"); - actions.push({ - text : "Save", - scope : this, - icon : '../images/save.gif', - handler : function (item, pressed) { - var largeImage = document.createElement("img"); - largeImage.style.display = 'block'; - largeImage.style.width = 200 + "px"; - largeImage.style.height = 200 + "px"; - largeImage.setAttribute('src', Dygraph.Export.asCanvas(this.dygraphObject.dygraph).toDataURL()); - window.open(Dygraph.Export.asCanvas(this.dygraphObject.dygraph).toDataURL(), 'Image', ''); - } - }); - - return actions; -}; - -/** Looks for the maximum value and then divide everything but that value **/ -HPLCGraph.prototype.scaledData = function (data) { - for (var i = 0; i < data.length; i++) { - var values = this.getMaxAndMinValue(data[i]); - data[i] = this.divideValuesByMax(data[i], values.max); - this.ranges[data[i].label] = values; - } - return data; -}; - - -/** Given a stat float[] and a max number it will divide each value by max **/ -HPLCGraph.prototype.divideValuesByMax = function (stat, max) { - for (var j = 0; j < stat.data.length; j++) { - if (max != 0) { - stat.data[j] = Number(stat.data[j]) / max; - stat.std[j] = Number(stat.std[j]) / max; - } - } - return stat; -}; - -/** returns max value of a stat **/ -HPLCGraph.prototype.getMaxAndMinValue = function (stat) { - var max = 0; - var min = stat.data[0]; - for (var j = 0; j < stat.data.length; j++) { - if (Number(stat.data[j]) > max) { - max = Number(stat.data[j]); - } - if (Number(stat.std[j]) > max) { - max = Number(stat.std[j]); - } - if (Number(stat.data[j]) < min) { - min = Number(stat.data[j]); - } - } - return { - max : Number(max), - min : Number(min) - }; -}; - -HPLCGraph.prototype.getPoint = function (data, i) { - var point = [ 10, 10, 10 ]; - var y = parseFloat(data.data[i]); - var error = parseFloat(data.std[i]); - if (data.fdata == null) { - return [ y - error, y, y + error ]; - } else { - if (data.fstd != null) { - return [ data.fstd(y - error), data.fdata(y), data.fstd(y + error) ]; - } - return [ data.fdata(y) - error, data.fdata(y), data.fdata(y) + error ]; - } - return point; -}; - -HPLCGraph.prototype.reloadData = function(hplcData) { - this.panel.setLoading(false); - this.hplcData = hplcData; - - var data = hplcData; - - - /** In case of having peaks **/ - if (this.peaks != null) { - for (var peak in this.peaks) { - var values = []; - var std = []; - for (var i = 0; i < this.peaks[peak].length; i++) { - values.push(this.peaks[peak][i][1]); - std.push(this.peaks[peak][i][2]); - } - data.push({ - param : peak, - data : values, - showOnMenu : false, - fdata : function (a) { - var value = (Math.log(parseFloat(a))); - if (isNumber(value)) { - return value; - } - }, - fstd : function (a) { - var value = Math.log(Math.abs(parseFloat(a))); - if (isNumber(value)) - return value; - }, - std : std, - color : this.colorPeak[peak], - label : peak - }); - - } - } - - - if (this.scaled) { - data = this.scaledData(JSON.parse(JSON.stringify(hplcData))); - } - - var paramIndex = {}; - var parsed = []; - var j = 0; - for (var i = 0; i < data[0].data.length - 1; i++) { - var aux = []; - for (j = 0; j < data.length; j++) { - if (this.plots != null) { - if (this.plots[data[j].param] != null) { - aux.push(this.getPoint(data[j], i)); - paramIndex[data[j].param] = aux.length - 1; - } - } else { - aux.push([ data[j].data[i] - data[j].std[i], data[j].data[i], data[j].data[i] + data[j].std[i] ]); - } - } - parsed.push([]); - - var index = i; - if (this.xParam != null) { - index = parseFloat(data[this.xParam].data[i]); - } - - parsed[parsed.length - 1].push(index); - - for (j = 0; j < data.length; j++) { - if (this.plots != null) { - if (this.plots[data[j].param] != null) { - parsed[parsed.length - 1].push(aux[paramIndex[data[j].param]]); - } - } else { - parsed[parsed.length - 1].push(aux[j]); - } - } - } - - var colors = []; - var labels = [ "" ]; - for (j = 0; j < data.length; j++) { - if (this.plots != null) { - if (this.plots[data[j].param] != null) { - colors.push(data[j].color); - labels.push(data[j].label); - } - } else { - parsed[parsed.length - 1].push(aux[j]); - } - } - - this._renderDygraph(parsed, colors, labels); -}; - -HPLCGraph.prototype._renderDygraph = function (parsed, colors, labels) { - this.dygraphObject = new StdDevDyGraph(this.id, { - width : this.width, - height : this.height - 10, - xlabel : this.xlabel, - showRangeSelector : this.showRangeSelector, - interactionModel : this.interactionModel, - scaled : this.scaled, - ranges : this.ranges - }); - this.dygraphObject.draw(parsed, colors, labels); - - var _this = this; - this.dygraphObject.onZoomX.attach(function (sender, args) { - try { - _this.onZoomX.notify(args); - } catch (e) { - } - }); - - this.dygraphObject.onResetZoom.attach(function (sender, args) { - try { - _this.onResetZoom.notify(args); - } catch (e) { - } - }); - - this.dygraphObject.dblclick.attach(function (sender, args) { - try { - _this.dblclick.notify(args); - } catch (e) { - } - }); - -}; - -HPLCGraph.prototype.loadData = function (data) { - var _this = this; - this.reloadData(data); - this.panel.addDocked({ - xtype : 'toolbar', - items : this.getMenu() - }); - - - if (this.bbar == true){ - this.panel.addDocked({ - xtype : 'toolbar', - dock: 'bottom', - items : [ - { - xtype: 'numberfield', - id: 'main_field_start', - fieldLabel: 'Range from', - width: 170, - labelWidth : 70, - value: 0, - minValue: 0 - }, - { - xtype: 'numberfield', - id: 'main_field_end', - fieldLabel: 'to', - width: 130, - labelWidth : 30, - value: 0, - minValue: 0 - }, - { - xtype: 'button', - text: 'Go', - handler: function () { - var start = parseFloat(Ext.getCmp("main_field_start").getValue()); - var end = parseFloat(Ext.getCmp("main_field_end").getValue()); - - if (start < 0) { - start = 0; - } - if (end < 0) { - end = 0; - } - if (start > end) { - var aux = end; - end = start; - start = aux; - } - - _this.dygraphObject.dygraph.updateOptions({ isZoomedIgnoreProgrammaticZoom: true, dateWindow: [start, end] }); - } - } - ] - }); - } -}; - -HPLCGraph.prototype.getPanel = function () { - this.panel = Ext.create('Ext.panel.Panel', { - padding : this.plotPanelPadding, - width : this.width + 4 * this.plotInnerPanelPadding, - height : this.height + 4 * this.plotInnerPanelPadding, - items : [ { - html : "", - id : this.id, - width : this.width, - height : this.height - } ] - }); - - return this.panel; -}; - -HPLCGraph.prototype.input = function () { - return DATADOC.getHPLCData(); -}; - -HPLCGraph.prototype.getDataByFrameNumber = function (frameNumber) { - var data = {}; - data.frameNumber = frameNumber; - for (var key in this.hplcData){ - data[this.hplcData[key].label] = this.hplcData[key].data[frameNumber]; - } - console.log(data); - return data; -}; - - -HPLCGraph.prototype.test = function (targetId) { - var mainPlotPanel = new HPLCGraph({ - title : 'I0', - width : 800, - height : 400, - plots : { - "I0" : true, - "Rg" : true, - "Mass" : true - }, - xlabel : "HPLC Frames", - scaled : this.scaled, - interactionModel : { - 'dblclick' : function (event, g, context) { - } - } - }); - mainPlotPanel.getPanel().render(targetId); - mainPlotPanel.loadData(mainPlotPanel.input()); - -}; - - -function MergesHPLCGraph(args) { - HPLCGraph.prototype.constructor.call(this, args); - -// this.peakColors = ["#00FB42", "#00BA31", "#007C21", "#003E10"]; - this.peakColors = ["#DEBD00", "#6D9100", "#872900", "#0092CC"]; -} - - -MergesHPLCGraph.prototype.scaledData = HPLCGraph.prototype.scaledData; -MergesHPLCGraph.prototype.divideValuesByMax = HPLCGraph.prototype.divideValuesByMax; -MergesHPLCGraph.prototype.getMaxAndMinValue = HPLCGraph.prototype.getMaxAndMinValue; -MergesHPLCGraph.prototype.getPoint = HPLCGraph.prototype.getPoint; -MergesHPLCGraph.prototype.reloadData = HPLCGraph.prototype.reloadData; -MergesHPLCGraph.prototype._renderDygraph = HPLCGraph.prototype._renderDygraph; -MergesHPLCGraph.prototype.loadData = HPLCGraph.prototype.loadData; -MergesHPLCGraph.prototype.getPanel = HPLCGraph.prototype.getPanel; -MergesHPLCGraph.prototype.getDataByFrameNumber = HPLCGraph.prototype.getDataByFrameNumber; - - -MergesHPLCGraph.prototype.setPeaks = function (data) { - this.peaks = data; - /** get size of peaks **/ - this.peakKeys = []; - this.colorPeak = {}; - var colorCount = 1; - for (var key in this.peaks) { - if (this.peaks.hasOwnProperty(key)) { - var color = this.peakColors[colorCount % this.peakColors.length]; - colorCount = colorCount + 1; - this.peakKeys.push(key); - this.colorPeak[key] = color; - } - } - this.peakKeys.sort(); -}; - - -MergesHPLCGraph.prototype.getMenu = function () { - var _this = this; - /** Actions buttons **/ - var actions = []; - - function toggle(item, pressed) { - if (pressed) { - _this.plots[item.param] = true; - } else { - delete _this.plots[item.param]; - } - _this.reloadData(_this.hplcData); - } - - - /** Toolbar for peaks Average **/ - if (this.peaks != null) { - var items = []; - for (var i = 0; i < this.peakKeys.length; i++) { - var color = this.colorPeak[this.peakKeys[i]]; - items.push({ - text: "Peak #" + i + " " + this.peakKeys[i].replace("- ", " to #").replace(".0", "").replace(".0", "") + "", - peakid : this.peakKeys[i], - checked: false, - checkHandler: function (sender, pressed) { - var item = new Object(); - item.param = sender.peakid; - toggle(item, pressed); - } - }); - } - - var menu = Ext.create('Ext.menu.Menu', { - id: 'mainMenu', - style: { - overflow: 'visible' - }, - items: items - }); - var tb = Ext.create('Ext.toolbar.Toolbar'); - tb.add({ - text: 'Peaks Avg.', - menu: menu - }); - actions.push(tb); - } - - - - for (var i = 0; i < this.hplcData.length; i++) { - if (this.hplcData[i].showOnMenu != false) { - var param = this.hplcData[i].param; - var style = "style='padding:0 0px 0 5px;'"; - actions.push({ - text : "
" + BUI.getRectangleColorDIV(this.hplcData[i].color, 10, 10) + " " + this.hplcData[i].label + "
", - id : _this.id + param, - param : param, - enableToggle : true, - scope : this, - margin : 5, - toggleHandler : toggle, - pressed : (_this.plots[param] != null) - }); - } - } - - actions.push("->"); - actions.push({ - text : "Save", - scope : this, - icon : '../images/save.gif', - handler : function (item, pressed) { - var largeImage = document.createElement("img"); - largeImage.style.display = 'block'; - largeImage.style.width = 200 + "px"; - largeImage.style.height = 200 + "px"; - largeImage.setAttribute('src', Dygraph.Export.asCanvas(this.dygraphObject.dygraph).toDataURL()); - window.open(Dygraph.Export.asCanvas(this.dygraphObject.dygraph).toDataURL(), 'Image', ''); - } - }); - - return actions; -}; - - -MergesHPLCGraph.prototype.input = function () { - return DATADOC.getScatteringHPLCFrameData(); -}; - -MergesHPLCGraph.prototype.test = function (targetId) { - var mainPlotPanel = new MergesHPLCGraph({ - title : 'Scattering', - width : this.plotWidth, - height : 500, - showRangeSelector : false, - xParam : 0, - xlabel : "scattering_I", - plots : { - "scattering_I" : true, - "subtracted_I" : true, - "buffer_I" : true - } - }); - mainPlotPanel.getPanel().render(targetId); - mainPlotPanel.loadData(mainPlotPanel.input()); -}; - - -function NetworkWidget(args) { - this.id = "NetworkViewer_" + Math.random().toString().replace(".", "_"); - - this.label = true; - if (args != null) { - if (args.targetId != null) { - this.targetId = args.targetId; - } - if (args.label != null) { - this.label = args.label; - } - } - - this.onVertexOver = new Event(this); - this.onVertexOut = new Event(this); -} - -NetworkWidget.prototype.draw = function(dataset, formatter, layout) { - - this.graphCanvas = new GraphCanvas(this.id, document.getElementById(this.targetId), { - "labeled" : this.label, - "multipleSelectionEnabled" : false, - "draggingCanvasEnabled" : false - }); - this.graphCanvas.draw(dataset, formatter, layout); - - var _this = this; - this.graphCanvas.onVertexOver.attach(function(sender, nodeId) { - _this.onVertexOver.notify(nodeId); - }); - - this.graphCanvas.onVertexOut.attach(function(sender, nodeId) { - _this.onVertexOut.notify(nodeId); - }); -}; - -/** SELECT VERTICES BY NAME * */ -NetworkWidget.prototype.selectVertexByName = function(vertexName) { - var vertices = this.getDataset().getVertexByName(vertexName); - if (vertices != null) { - for ( var nodeId in vertices) { - if (vertices.hasOwnProperty(nodeId)) { - var vertexId = vertices[nodeId].getId(); - this.selectVertexById(vertexId); - } - } - } -}; - -NetworkWidget.prototype.selectVerticesByName = function(verticesName) { - for ( var i = 0; i < verticesName.length; i++) { - this.selectVertexByName(verticesName[i]); - } -}; - -/** SELECT VERTICES BY ID * */ -NetworkWidget.prototype.selectVertexById = function(vertexId) { - this.graphCanvas.selectNode(vertexId); - this.blinkVertexById(vertexId); -}; - -NetworkWidget.prototype.selectVerticesById = function(verticesId) { - for ( var i = 0; i < verticesId.length; i++) { - this.selectVertexById(verticesId[i]); - } -}; - -/** VECINDARIO * */ -NetworkWidget.prototype.selectNeighbourhood = function() { - this.selectEdgesFromVertices(); - this.selectAdjacent(); -}; - -/** DESELECT * */ -NetworkWidget.prototype.deselectNodes = function() { - this.graphCanvas.deselectNodes(); -}; - -/** SELECT ALL NODES * */ -NetworkWidget.prototype.selectAllNodes = function() { - this.getGraphCanvas().selectAllNodes(); -}; - -/** SELECT EVERYTHING * */ -NetworkWidget.prototype.selectAll = function() { - this.getGraphCanvas().selectAll(); -}; - -/** SELECT ALL EDGES * */ -NetworkWidget.prototype.selectAllEdges = function() { - this.getGraphCanvas().selectAllEdges(); -}; - -/** ZOOM * */ -NetworkWidget.prototype.setScale = function(value) { - this.graphCanvas.setScale(value); -}; - -NetworkWidget.prototype.getScale = function() { - return this.graphCanvas.getScale(value); -}; - -/** SELECT ADJACENT VERTICES FROM SELECTED VERTICES * */ -NetworkWidget.prototype.selectAdjacent = function() { - var selectedVertices = this.getGraphCanvas().getSelectedVertices(); - var edges = []; - for ( var i = 0; i < selectedVertices.length; i++) { - edges = edges.concat(this.getGraphCanvas().getDataset().getVertexById(selectedVertices[i]).getEdges()); - } - var vertices = []; - for ( i = 0; i < edges.length; i++) { - vertices.push(edges[i].getNodeSource().getId()); - vertices.push(edges[i].getNodeTarget().getId()); - } - - this.selectVerticesById(vertices); -}; - -/** SELECT EDGES FROM SELECTED VERTICES * */ -NetworkWidget.prototype.selectEdgesFromVertices = function() { - var selectedVertices = this.getGraphCanvas().getSelectedVertices(); - var edges = []; - for ( var i = 0; i < selectedVertices.length; i++) { - edges = edges.concat(this.getGraphCanvas().getDataset().getVertexById(selectedVertices[i]).getEdges()); - } - var edgesId = []; - for ( i = 0; i < edges.length; i++) { - edgesId.push(edges[i].getId()); - } - this.getGraphCanvas().selectEdges(edgesId); -}; - -/** BLINKING * */ -NetworkWidget.prototype.blinkVertexById = function(vertexId) { - this.graphCanvas.blinkVertexById(vertexId); -}; - -/** COMPONENTE CONEXA DE LOS NODOS SELECCIONADOS * */ -NetworkWidget.prototype.selectConnectedComponent = function() { - var elements = this.getConnectedComponent(); - this.selectVerticesById(elements.nodes); - this.graphCanvas.selectEdges(elements.edges); -}; - -NetworkWidget.prototype.getConnectedComponent = function() { - var nodosVisitados = {}; - var aristasVisitadas = {}; - var arrNodos = []; - var arrAristas = []; - var selectedGraphNodesId = this.getGraphCanvas().getSelectedVertices(); - for ( var i = 0; i < selectedGraphNodesId.length; i++) { - this.visitNode(selectedGraphNodesId[i], nodosVisitados, aristasVisitadas, arrNodos, arrAristas); - } - return { - nodes : arrNodos, - edges : arrAristas - }; -}; - -NetworkWidget.prototype.visitNode = function(nodeId, nodosVisitados, aristasVisitadas, arrNodos, arrAristas) { - nodosVisitados[nodeId] = true; - arrNodos.push(nodeId); - var nodeEdges = this.getDataset().getVertexById(nodeId).getEdges(); - for ( var j = 0; j < nodeEdges.length; j++) { - var edge = nodeEdges[j]; - var edgeId = edge.getId(); - if (aristasVisitadas[edgeId] == null) { - aristasVisitadas[edgeId] = true; - arrAristas.push(edgeId); - var nodeTargetId = edge.getNodeTarget().getId(); - if (nodosVisitados[nodeTargetId] == null) { - this.visitNode(nodeTargetId, nodosVisitados, aristasVisitadas, arrNodos, arrAristas); - } - var nodeSourceId = edge.getNodeSource().getId(); - if (nodosVisitados[nodeSourceId] == null) { - this.visitNode(nodeSourceId, nodosVisitados, aristasVisitadas, arrNodos, arrAristas); - } - } - } -}; - -/** COLLAPSE SELECTED VERTICES * */ -NetworkWidget.prototype.collapse = function() { - var selectedVertices = this.getGraphCanvas().getSelectedVertices(); - var xMin = -Infinity; - var xMax = Infinity; - var yMin = -Infinity; - var yMax = Infinity; - - for ( var i = 0; i < selectedVertices.length; i++) { - var vertex = this.getGraphCanvas().getLayout().getNodeById(selectedVertices[i]); - if (xMin < vertex.x) { - xMin = vertex.x; - } - if (xMax > vertex.x) { - xMax = vertex.x; - } - if (yMin < vertex.y) { - yMin = vertex.y; - } - if (yMax > vertex.y) { - yMax = vertex.y; - } - } - - var centerX = xMin - xMax; - var centerY = yMin - yMax; - var radius = (xMax - xMin) / 4; - - var count = selectedVertices.length; - var verticesCoordinates = []; - - for ( i = 0; i < selectedVertices.length; i++) { - x = centerX + radius * Math.sin(i * 2 * Math.PI / count); - y = centerY + radius * Math.cos(i * 2 * Math.PI / count); - verticesCoordinates.push({ - 'x' : x, - 'y' : y - }); - } - - for ( i = 0; i < selectedVertices.length; i++) { - this.getGraphCanvas().getLayout().getNodeById(selectedVertices[i]).setCoordinates(verticesCoordinates[i].x, verticesCoordinates[i].y); - } -}; - -/** SETTER FONT SIZE * */ -NetworkWidget.prototype.setVerticesFontSize = function(value) { - for ( var nodeId in this.getDataset().getVertices()) { - if (this.getDataset().getVertices().hasOwnProperty(nodeId)) { - this.getFormatter().getVertexById(nodeId).getDefault().setFontSize(value); - } - } -}; - -/** GETTERS * */ -NetworkWidget.prototype.getFormatter = function() { - return this.getGraphCanvas().getFormatter(); -}; -NetworkWidget.prototype.getLayout = function() { - return this.getGraphCanvas().getLayout(); -}; - -NetworkWidget.prototype.getDataset = function() { - return this.getGraphCanvas().getDataset(); -}; - -NetworkWidget.prototype.getGraphCanvas = function() { - return this.graphCanvas; -}; - -RangeWhiskerGraph.prototype.cleanArray = GenericGraph.prototype.cleanArray; -RangeWhiskerGraph.prototype.plotAxes = GenericGraph.prototype.plotAxes; -RangeWhiskerGraph.prototype.plotRuler = GenericGraph.prototype.plotRuler; -RangeWhiskerGraph.prototype.drawSVGVerticalText = GenericGraph.prototype.drawSVGVerticalText; -RangeWhiskerGraph.prototype.getClassColor = GenericGraph.prototype.getClassColor; -RangeWhiskerGraph.prototype.getDimensions = GenericGraph.prototype.getDimensions; -RangeWhiskerGraph.prototype.calculate = GenericGraph.prototype.calculate; -RangeWhiskerGraph.prototype.getMedian = GenericGraph.prototype.getMedian; -RangeWhiskerGraph.prototype.pointToPixel = GenericGraph.prototype.pointToPixel; -RangeWhiskerGraph.prototype.maxValueWhisker = GenericGraph.prototype.maxValueWhisker; -RangeWhiskerGraph.prototype.refresh = GenericGraph.prototype.refresh; - -/** - * Subclass of GenericGraph - * - * @plotHorizontalByCluster - */ -function RangeWhiskerGraph(args) { - this.maxBoxWidth = 25; - - if (args == null) { - args = {}; - } - args.plotHorizontalByCluster = false; - - GenericGraph.call(this, args); - - if (args.maxBoxWidth != null) { - this.maxBoxWidth = args.maxBoxWidth; - } -} - -RangeWhiskerGraph.prototype.refresh = function(data) { - document.getElementById(this.targetId).innerHTML = ""; - this.draw(this.targetId, data); -}; - -RangeWhiskerGraph.prototype.isNumber = function(value) { - if (value == "") - return false; - - var d = parseInt(value); - if (!isNaN(d)) - return true; - else - return false; - -}; - -/** - There are several different methods for calculating quartiles.[1] This calculator uses a method described by Moore and McCabe to find quartile values. - The same method also used by The TI-83 to calculate quartile values. - With this method, the first quartile is the median of the numbers below the median, the third quartile is the median of the numbers above the median. - - http://www.miniwebtool.com/quartile-calculator/ - http://www.alcula.com/calculators/statistics/box-plot/ - - **/ -RangeWhiskerGraph.prototype.getQ1 = function(array) { - array = array.slice(0, array.length / 2); - return this.getMedian(array); -}; - -RangeWhiskerGraph.prototype.getQ3 = function(array) { - array = array.slice((array.length + 1) / 2); - return this.getMedian(array); - -}; - -RangeWhiskerGraph.prototype.getQ2 = function(array) { - return this.getMedian(array); -}; - -RangeWhiskerGraph.prototype.getBelowOutliers = function(belowLimit, array) { - var points = []; - for ( var i = 0; i < array.length; i++) { - if (array[i] <= belowLimit) { - points.push(array[i]); - } - } - return points; -}; - -RangeWhiskerGraph.prototype.getAboveOutliers = function(aboveLimit, array) { - var points = []; - for ( var i = 0; i < array.length; i++) { - if (array[i] >= aboveLimit) { - points.push(array[i]); - } - } - return points; -}; - -RangeWhiskerGraph.prototype.minValueWhisker = function(belowLimit, q1, array) { - var points = []; - - for ( var i = 0; i < array.length; i++) { - if ((array[i] < q1) && (array[i]) > belowLimit) { - points.push(array[i]); - } - } - - if (points.length > 0) { - points.sort(function(a, b) { - return a - b; - }); - return points[0]; - } - return null; -}; - -//RangeWhiskerGraph.prototype.maxValueWhisker = function(aboveLimit, q3, array){ -// var points = []; -// for (var i = 0; i < array.length; i++){ -// if ((array[i] > q3) && (array[i]) <= aboveLimit){ -// points.push(array[i]); -// } -// } -// if (points.length > 0){ -// points.sort(function(a, b){return a - b;}); -// return points[points.length - 1]; -// } -// return null; -//}; - -RangeWhiskerGraph.prototype.drawPoints = function(boxProperties) { - if (this.plotPoints) { - for ( var i = 0; i < boxProperties.values.length; i++) { - var value = boxProperties.values[i]; - var toPixel = this.pointToPixel(value, boxProperties); - SVG.drawCircle(boxProperties.x, toPixel, this.pointRadius, this.svg, - [ - [ "fill", "green" ], [ "fill-opacity", this.fillOpacityPoint ], [ 'stroke-opacity', this.strokeOpacityPoint ], - [ "stroke", "black" ] ]); - } - } -}; - -RangeWhiskerGraph.prototype.plotRangeQ1Q3 = function(data, properties) { - var posX = this.left + this.rulerWidth; - - var boxBordersPointsQ1 = []; - var boxBordersPointsQ3 = []; - var Q2 = []; - - for ( var i = 0; i < data.clusters.length; i++) { - var cluster = data.clusters[i]; - /** inter cluster space **/ - posX = posX + this.interClustersSpace; - - for ( var j = 0; j < cluster.classes.length; j++) { - var ratio = properties.width / (properties.xValues.range); - var coorX = (cluster.x - properties.xValues.min) * ratio + this.rulerWidth; - var boxProperties = { - name : cluster.classes[j].name, - values : cluster.classes[j].values, - minPoint : properties.minPoint, - maxPoint : properties.maxPoint, - x : coorX + this.left, - y : this.top, - width : properties.classWidth, - height : this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight - }; - - var result = this.calculate(boxProperties.values); - var boxColor = this.getClassColor(boxProperties.name); - - if (this.isNumber(result.Q1) && this.isNumber(result.Q3)) { - var x = boxProperties.x; - var y = this.pointToPixel(result.Q1, boxProperties); - if (boxBordersPointsQ1[cluster.classes[j].name] == null) { - boxBordersPointsQ1[cluster.classes[j].name] = []; - } - boxBordersPointsQ1[cluster.classes[j].name].push({ - x : x, - y : y - }); - - x = boxProperties.x; - y = this.pointToPixel(result.Q3, boxProperties); - if (boxBordersPointsQ3[cluster.classes[j].name] == null) { - boxBordersPointsQ3[cluster.classes[j].name] = []; - } - boxBordersPointsQ3[cluster.classes[j].name].push({ - x : x, - y : y - }); - } else { - - if (this.isNumber(result.Q2)) { - - if (boxBordersPointsQ1[cluster.classes[j].name] == null) { - boxBordersPointsQ1[cluster.classes[j].name] = []; - } - - if (boxBordersPointsQ3[cluster.classes[j].name] == null) { - boxBordersPointsQ3[cluster.classes[j].name] = []; - } - - boxBordersPointsQ1[cluster.classes[j].name].push({ - x : boxProperties.x, - y : this.pointToPixel(result.Q2, boxProperties) - }); - boxBordersPointsQ3[cluster.classes[j].name].push({ - x : boxProperties.x, - y : this.pointToPixel(result.Q2, boxProperties) - }); - } - } - } - } - for ( var classe in boxBordersPointsQ1) { - var points = boxBordersPointsQ1[classe]; - var pointsSVG = ""; - for (var k = 0; k < points.length; k++) { - pointsSVG = Number(points[k].x).toFixed(1) + "," + Number(points[k].y).toFixed(1) + " " + pointsSVG; - } - - points = boxBordersPointsQ3[classe]; - for (var z = points.length - 1; z >= 0; z--) { - pointsSVG = Number(points[z].x).toFixed(1) + "," + Number(points[z].y).toFixed(1) + " " + pointsSVG; - } - - SVG.drawPoligon(pointsSVG, this.svg, [ - [ "fill", this.getClassColor(classe) ], [ "opacity", "0.3" ], [ "stroke", "black" ], [ "stroke-width", 1 ] ]); - } -}; - -RangeWhiskerGraph.prototype.plotWhisters = function(data, properties) { - var colors = [ "yellow", "orange", "green" ]; - - this.plotRangeQ1Q3(data, properties); - var Q2 = {}; - - for ( var i = 0; i < data.clusters.length; i++) { - var cluster = data.clusters[i]; - for ( var j = 0; j < cluster.classes.length; j++) { - var ratio = properties.width / (properties.xValues.range); - var coorX = (cluster.x - properties.xValues.min) * ratio + this.left + this.rulerWidth - this.rulerStroke; - var boxProperties = { - name : cluster.classes[j].name, - values : cluster.classes[j].values, - minPoint : properties.minPoint, - maxPoint : properties.maxPoint, - x : coorX, - y : this.top, - width : properties.classWidth, - height : this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight - }; - - this.drawPoints(boxProperties); - - /** PLOTTING Q2 **/ - var result = this.calculate(boxProperties.values); - var boxColor = this.getClassColor(boxProperties.name); - if (this.isNumber(result.Q2)) { - if (Q2[boxProperties.name] != null) { - SVG.drawLine(boxProperties.x, this.pointToPixel(result.Q2, boxProperties), Q2[boxProperties.name].x, Q2[boxProperties.name].y, - this.svg, [ [ "stroke", boxColor ], [ "stroke-width", "2" ] ]); - } - Q2[boxProperties.name] = { - x : boxProperties.x, - y : this.pointToPixel(result.Q2, boxProperties) - } - } - } - } - -}; - -RangeWhiskerGraph.prototype.draw = function(targetId, data) { - //this.calculate(data); - this.targetId = targetId; - var properties = (this.getDimensions(data)); - this.svg = SVG.createSVGCanvas(document.getElementById(this.targetId), [ [ "width", this.width ], [ "height", this.height ] ]); - this.plotAxes(properties); - this.plotWhisters(data, properties); -}; - -RangeWhiskerGraph.prototype.input = function() { - return DATADOC.getBoxWhikerData(); -}; - -RangeWhiskerGraph.prototype.test = function(targetId) { - var plot = new RangeWhiskerGraph({ - targetId : targetId, - height : 350, - width : 450, - maxBoxWidth : 25 - }); - plot.refresh(this.input()); -}; - -StdDevDyGraph.prototype.dblclick = DygraphWidget.prototype.dblclick; -StdDevDyGraph.prototype._createHTLMWrapper = DygraphWidget.prototype._createHTLMWrapper; -StdDevDyGraph.prototype.draw = DygraphWidget.prototype.draw; - -function StdDevDyGraph(targetId, args) { - this.scaled = false; - if (args == null) { - args = {}; - } - args.customBars = true; - DygraphWidget.prototype.constructor.call(this, targetId, args); -} - -StdDevDyGraph.prototype.input = function () { - return { - data : [ [ 1, [ 2, 3, 3.5 ], [ 4, 4.2, 5 ] ], [ 2, [ 5, 5.5, 5.7 ], [ 4, 4.2, 5 ] ] ], - colors : [ "blue", "red" ], - labels : [ "", 'data1', 'data2' ] - }; -}; - -StdDevDyGraph.prototype.test = function (targetId) { - var dygraphObject = new StdDevDyGraph(targetId, { - width : 500, - height : 400, - xlabel : "xLabel", - showRangeSelector : false - }); - - dygraphObject.draw(dygraphObject.input().data, dygraphObject.input().colors, dygraphObject.input().labels); -}; - - - -function AbinitioGrid(args) { - this.height = null; - this.width = null; - this.id = BUI.id(); - - if (args != null) { - if (args.height != null) { - this.height = args.height; - - if (args.width != null) { - this.width = args.width; - } - } - } - - this.onSelected = new Event(this); -}; - - -AbinitioGrid.prototype.refresh = function(subtractions){ - this.store.loadData(this._prepareData(subtractions)); -}; - -AbinitioGrid.prototype._prepareData = function(subtractions){ - /** Parsing data * */ - var models = []; - for (var l = 0; l < subtractions.length; l++) { - var subtraction = subtractions[l]; - for (var k = 0; k < subtraction.substractionToAbInitioModel3VOs.length; k++) { - var data = subtraction.substractionToAbInitioModel3VOs[k].abinitiomodel3VO; - if (data.averagedModel != null) { - models.push(data.averagedModel); - models[models.length - 1].type = "Reference"; - } - - if (data.shapeDeterminationModel != null) { - models.push(data.shapeDeterminationModel); - models[models.length - 1].type = "Refined"; - } - - if (data.modelList3VO != null) { - if (data.modelList3VO.modeltolist3VOs != null) { - for (var i = 0; i < data.modelList3VO.modeltolist3VOs.length; i++) { - models.push(data.modelList3VO.modeltolist3VOs[i].model3VO); - models[models.length - 1].type = "Model"; - } - } - } - } - } - return models; -}; - -AbinitioGrid.prototype.getPanel = function(){ - var _this = this; - - - var modelFields = [ "modelId", "type", "chiSqrt", "dmax", "firFile", "logFile", "fitFile", "pdbFile", "rfactor", "rg", "volume" ]; - Ext.define('AbinitioModel', { - extend : 'Ext.data.Model', - fields : modelFields - - }); - - /** - * Store in Memory - */ - this.store = Ext.create('Ext.data.Store', { - model : 'AbinitioModel', - autoload : true, - groupField : 'type' - }); - - - var groupingFeature = Ext.create('Ext.grid.feature.Grouping',{ - groupHeaderTpl: '{name} ({rows.length} model{[values.rows.length > 1 ? "s" : ""]})', - startCollapsed: true, - collapsible : true - }); - - this.grid = Ext.create('Ext.grid.Panel', { - collapsible : false, - resizable : true, - features: [groupingFeature], - autoscroll : true, - multiSelect : true, - store : this.store, - height : this.height, - width : this.width, - margin : 10, - columns : [ { - text : "Type", - dataindex : "type", - hidden : true, - renderer : function(a, b, record) { - return record.data.type; - }, - flex : 1 - }, - { - text : "ModelId", - dataindex : "modelId", - hidden : true, - renderer : function(a, b, record) { - return record.data.modelId; - - }, - flex : 1 - }, - - { - text : "chiSqrt", - dataindex : "chiSqrt", - renderer : function(a, b, record) { - if (record.data.dmax != null) { - return BUI.formatValuesUnits(record.data.chiSqrt, "", 12, this.decimals); - } - - }, - flex : 1 - }, - { - text : "Dmax", - dataindex : "dmax", - renderer : function(a, b, record) { - if (record.data.dmax != null) { - return BUI.formatValuesUnits(record.data.dmax, "nm", 12, this.decimals); - } - - }, - flex : 1 - }, { - text : "rFactor", - dataindex : "rfactor", - hidden : true, - renderer : function(a, b, record) { - if (record.data.rfactor != null) { - return record.data.rfactor; - } - }, - flex : 1 - }, { - text : "Rg", - dataindex : "rg", - renderer : function(a, b, record) { - if (record.data.rg != null) { - return BUI.formatValuesUnits(record.data.rg, "nm", 12, this.decimals); - } - - }, - flex : 1 - }, - { - text : "Volume", - dataindex : "volume", - renderer : function(a, b, record) { - if (record.raw.volume != null){ - return BUI.formatValuesUnits(record.raw.volume, '') + " nm3"; - } - }, - flex : 1 - }, - { - text : "PDB", - dataindex : "pdbFile", - renderer : function(a, b, record) { - if (record.data.pdbFile != null){ - return record.data.pdbFile.split("/")[record.data.pdbFile.split("/").length - 1]; - } - }, - flex : 1 - }, { - text : "Fir", - dataindex : "firFile", - renderer : function(a, b, record) { - if (record.data.firFile != null){ - return record.data.firFile.split("/")[record.data.firFile.split("/").length - 1]; - } - }, - flex : 1 - }, { - text : "LOG", - dataindex : "logFile", - hidden : true, - renderer : function(a, b, record) { - if (record.data.logFile != null){ - return record.data.logFile.split("/")[record.data.logFile.split("/").length - 1]; - } - }, - flex : 1 - } - ], - viewConfig : { - enableTextSelection : true, - preserveScrollOnRefresh : true, - stripeRows : true, - listeners : { - 'celldblclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - }, - 'cellclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - var models = []; - for (var i = 0; i < grid.getSelectionModel().selected.items.length; i++) { - models.push(grid.getSelectionModel().selected.items[i].raw); - } - _this.onSelected.notify(models); - } - } - } - }); - return this.grid; - -}; - - -function AdditiveGrid(args) { - this.onRemoveButtonClicked = new Event(this); -} - -AdditiveGrid.prototype.getBuffer = function() { - return this.buffer; -}; - -AdditiveGrid.prototype._getActions = function() { - var _this = this; - /** Actions buttons **/ - var actions = []; - - actions.push(Ext.create('Ext.Action', { - icon : '../images/add.png', - text : 'Add', - disabled : true, - alwaysEnabled : true, - handler : function(widget, event) { - _this.buffer.bufferhasadditive3VOs.push(BIOSAXS_BEANS.getBufferhasAdditive3VO()); - _this.refresh(_this.buffer, _this.experiment); - } - })); - - return actions; -}; - -AdditiveGrid.prototype.refresh = function(buffer, experiment) { - this.buffer = buffer; - this.experiment = experiment; - if (buffer) { - if (buffer.bufferhasadditive3VOs) { - this.features = buffer.bufferhasadditive3VOs; - } - } - this.experiment = experiment; - this.store.loadData(this._prepareData(), false); -}; - -AdditiveGrid.prototype.getAdditives = function() { - var additives = []; - for ( var i = 0; i < this.store.getCount(); i++) { - var bufferHasAdditive = BIOSAXS_BEANS.getBufferhasAdditive3VO(); - var data = this.store.getAt(i).getData(); - - bufferHasAdditive.additive3VO.name = data.name; - bufferHasAdditive.additive3VO.comments = data.comments; - bufferHasAdditive.additive3VO.additiveType = data.additiveType; - - bufferHasAdditive.bufferId = this.buffer.bufferId; - bufferHasAdditive.bufferHasAdditiveId = data.bufferHasAdditiveId; - bufferHasAdditive.quantity = data.quantity; - additives.push(bufferHasAdditive); - } - - return additives; -}; - -AdditiveGrid.prototype._getFields = function(buffers) { - var columns = [ - - { - header : 'Name', - dataIndex : 'name', - type : 'string', - editor : { - allowBlank : true - }, - flex : 1 - }, - { - header : 'Type', - name : 'additiveType', - dataIndex : 'additiveType', - editor : { - xtype : 'combobox', - typeAhead : true, - triggerAction : 'all', - selectOnTab : true, - store : BIOSAXS.proposal.getAdditiveTypes(), - lazyRender : true, - listClass : 'x-combo-list-small' - }, - flex : 0.6 - }, - { - header : 'Quantity', - dataIndex : 'quantity', - name : 'quantity', - editor : { - allowBlank : true - }, - type : 'string', - flex : 1 - }, - { - xtype : 'actioncolumn', - items : [ { - icon : '../images/cancel.png', - tooltip : 'Delete additive', - scope : this, - handler : function(grid, rowIndex, colIndex) { - if ((grid.getStore().getAt(rowIndex).data.bufferHasAdditiveId == null)|| (grid.getStore().getAt(rowIndex).data.bufferHasAdditiveId == "")) { - grid.getStore().removeAt(rowIndex); - } else { - this.onRemoveButtonClicked.notify({ - 'bufferId' : this.buffer.bufferId, - 'bufferHasAdditiveId' : this.store.getAt(rowIndex).data.bufferHasAdditiveId - }); - } - } - } ] - } ]; - - return columns; -}; - -AdditiveGrid.prototype._prepareData = function() { - var data = []; - if (this.features == null) { - this.features = []; - } - for (var i = 0; i < this.features.length; i++) { - var object = this.features[i]; - object.name = this.features[i].additive3VO.name; - object.additiveType = this.features[i].additive3VO.additiveType; - object.comments = this.features[i].additive3VO.comments; - object.additiveId = this.features[i].additive3VO.additiveId; - data.push(object); - } - return data; -}; - -AdditiveGrid.prototype.getPanel = function(buffer, experiment) { - this.buffer = buffer; - this.features = buffer.bufferhasadditive3VOs; - this.experiment = experiment; - return this._renderGrid(); -}; - -AdditiveGrid.prototype.getStore = function() { - var _this = this; - var store = Ext.create('Ext.data.Store', { - fields : [ "name", "additiveType", "comments", "additiveId", "bufferHasAdditiveId", "quantity" ], - autoload : false, - data : this._prepareData(), - listeners : { - update : function(store, record) { - record.index = _this.grid.getSelectionModel().getCurrentPosition().row; - _this.buffer.bufferhasadditive3VOs[record.index].additive3VO.name = record.data.name; - _this.buffer.bufferhasadditive3VOs[record.index].additive3VO.additiveType = record.data.additiveType; - _this.buffer.bufferhasadditive3VOs[record.index].additive3VO.comments = record.data.comments; - _this.buffer.bufferhasadditive3VOs[record.index].quantity = record.data.quantity; - } - } - }); - - // store.sort('bufferHasAdditiveId', 'ASC'); - store.loadData(this._prepareData(), false); - return store; -}; - -AdditiveGrid.prototype._renderGrid = function() { - var _this = this; - this.store = this.getStore(); - - var cellEditing = Ext.create('Ext.grid.plugin.CellEditing', { - clicksToEdit : 1 - }); - - this.grid = Ext.create('Ext.grid.Panel', { - dockedItems : [ { - xtype : 'toolbar', - items : this._getActions() - } ], - store : this.store, - height : 230, - title : "Additives", - width : "100%", - columns : _this._getFields(), - plugins : [ cellEditing ], - viewConfig : { - stripeRows : true, - listeners : { - itemcontextmenu : function(view, rec, node, index, e) { - e.stopEvent(); - contextMenu.showAt(e.getXY()); - return false; - } - } - }, - selModel : { - mode : 'SINGLE' - } - }); - - return this.grid; -}; - -AdditiveGrid.prototype.input = function() { -}; - -AdditiveGrid.prototype.test = function(targetId) { - var grid = new AdditiveGrid(); - var panel = grid.getPanel([]); - panel.render(targetId); - -}; - -/** AnalysisGrid **/ -function AnalysisGrid(args) { - var _this = this; - - this.id = BUI.id(); - if (Ext.get("mainPanel")){ - this.width = Ext.get("mainPanel").getWidth(); - } - else{ - this.width = this.maxWidth; - } - this.maxWidth = 1500; - - /** Visibles **/ - this.isGuinierTabVisible = true; - this.isGnomTabVisible = true; - this.isPorodTabVisible = true; - this.isScatteringPlotVisible = true; - this.isAbinitioTabVisible = true; - this.showButtonsVisible = true; - this.isI0Visible = true; - - this.margin = null; - this.grouped = true; - - this.hideNulls = false; - this.decimals = 4; - this.height = null; - this.sorters = [ { - property : 'conc', - direction : 'ASC' - } ]; - - if (args != null) { - if (args.grouped != null) { - this.grouped = args.grouped; - } - - if (args.showButtonsVisible != null) { - this.showButtonsVisible = args.showButtonsVisible; - } - if (args.isI0Visible != null) { - this.isI0Visible = args.isI0Visible; - } - if (args.sorters != null) { - this.sorters = args.sorters; - } - if (args.isScatteringPlotVisible != null) { - this.isScatteringPlotVisible = args.isScatteringPlotVisible; - } - if (args.isGuinierTabVisible != null) { - this.isGuinierTabVisible = args.isGuinierTabVisible; - } - if (args.isGnomTabVisible != null) { - this.isGnomTabVisible = args.isGnomTabVisible; - } - if (args.isPorodTabVisible != null) { - this.isPorodTabVisible = args.isPorodTabVisible; - } - if (args.hideNulls != null) { - this.hideNulls = args.hideNulls; - } - if (args.height != null) { - this.height = args.height; - } - if (args.width != null) { - this.width = args.width; - } - if (args.maxWidth != null) { - this.maxWidth = args.maxWidth; - } - } -} - -AnalysisGrid.prototype.refresh = function(data, args) { - this.store.loadData(this._prepareData(data), false); - if (args != null){ - if (args.experiment != null){ - this.experiment = args.experiment; - } - } -}; - -AnalysisGrid.prototype._getPorod = function() { - return { - text : 'Porod', - name : 'Porod', - columns : [ - { - text : 'Volume', - dataIndex : 'volumeEdna', - width : 75, - sortable : true, - hidden : !this.isPorodTabVisible, - renderer : function(val, y, sample) { - if (sample.raw.volume != null) - return BUI.formatValuesUnits(sample.raw.volume, '') + " nm3"; - } - }, - { - text : 'MM Vol. est.', - dataIndex : 'volumeEdna', - tooltip : '[Volume/2 - Volume/1.5] (Guinier)', - sortable : true, - width : 95, - hidden : !this.isPorodTabVisible, - renderer : function(val, y, sample) { - if (sample.raw.volume != null) - return Number(sample.raw.volume / 2).toFixed(1) + " - " + Number(sample.raw.volume / 1.5).toFixed(1)+ "kD"; - } - } ] - }; -}; - - -AnalysisGrid.prototype._getFramesColumn = function() { - var _this = this; - return { - text : 'Frames (Averaged/Total)', - dataIndex : 'datacollection', - name : 'datacollection', - sortable : true, - width : 150, - renderer : function(dataCollections, y, data) { - /** Bug of Webservices: frames count were swapped with frames averages **/ - if (data.raw.bufferAfterFramesCount){ - if (data.raw.bufferAfterFramesMerged){ - if (parseInt(data.raw.bufferAfterFramesMerged) > parseInt(data.raw.bufferAfterFramesCount)){ - var aux = parseInt(data.raw.bufferAfterFramesCount); - data.raw.bufferAfterFramesCount= data.raw.bufferAfterFramesMerged; - data.raw.bufferAfterFramesMerged = aux; - } - } - } - - if (data.raw.bufferBeforeFramesCount){ - if (data.raw.bufferBeforeFramesMerged){ - if (parseInt(data.raw.bufferBeforeFramesMerged) > parseInt(data.raw.bufferBeforeFramesCount)){ - var aux = parseInt(data.raw.bufferBeforeFramesCount); - data.raw.bufferBeforeFramesCount= data.raw.bufferBeforeFramesMerged; - data.raw.bufferBeforeFramesMerged = aux; - } - } - - } - - var bufferAcronym = data.raw.bufferAcronym; - var macromoleculeAcronym = data.raw.macromoleculeAcronym; - var bbmerges = data.raw.bufferBeforeFramesMerged; - var molmerges = data.raw.framesMerge; - var bamerges = data.raw.bufferAfterFramesMerged; - var totalframes = data.raw.framesCount; - var bufferId = data.raw.bufferId; - var macromoleculeId = data.raw.macromoleculeId; - var macromoleculeColor = null; - if (_this.experiment != null){ - macromoleculeColor = _this.experiment.macromoleculeColors[data.raw.macromoleculeId]; - } - - /** BUG in the database to be fixed **/ - try{ - if (totalframes != null){ - if(molmerges != null){ - if (parseFloat(totalframes) < parseFloat(molmerges)){ - var aux = totalframes; - totalframes = molmerges; - molmerges = aux; - } - } - } - } - catch(e){ - - } - - return BUI.getHTMLTableForFrameAveraged(bufferAcronym, - macromoleculeAcronym, - bbmerges, - molmerges, - bamerges, - totalframes, - bufferId, - macromoleculeId, - macromoleculeColor); - } - }; -}; - -AnalysisGrid.prototype._getColumns = function() { - var _this = this; - return [ - { - name : 'groupeField', - dataIndex : 'groupeField', - hidden : true - - }, - { - "header" : "subtractionId", - hidden : true, - "dataIndex" : "subtractionId", - "name" : "subtractionId" - }, - { - header : "Macromolecule", - dataIndex : "macromoleculeAcronym", - name : "macromoleculeAcronym", - renderer : function(val, y, sample) { - return '
' + val + '
' + - BUI.formatValuesUnits(sample.raw.conc, "mg/ml", 10, this.decimals) + '
' + - BUI.formatValuesUnits(sample.raw.exposureTemperature, "C", 10, this.decimals) + '
' - } - }, - { - header : "Order", - dataIndex : "priorityLevelId", - name : "priorityLevelId", - hidden : true - }, - { - header : "Code", - dataIndex : "code", - name : "code", - hidden : true - }, - { - header : "Conc.", - dataIndex : "conc", - width : 80, - name : "conc", - type : "number", - hidden : true, - renderer : function(val, y, sample) { - return BUI.formatValuesUnits(val, "mg/ml", 10, this.decimals); - } - }, - { - text : 'Scattering', - width : 100, - dataIndex : 'subtractionId', - name : 'subtractionId', - hidden : !this.isScatteringPlotVisible, - renderer : function(val, y, sample) { - var url = BUI.getURL() + '&type=scattering&subtractionId=' + sample.raw.subtractionId; - var event = "OnClick= window.open('" + url + "')"; - return ''; - } - }, - { - text : 'Kratky', - width : 100, - dataIndex : 'subtractionId', - hidden : true, - name : 'subtractionId', - renderer : function(val, y, sample) { - var url = BUI.getURL() + '&type=kratky&subtractionId=' + sample.raw.subtractionId; - var event = "OnClick= window.open('" + url + "')"; - return ''; - } - }, - this._getFramesColumn(), - { - text : 'File Name', - dataIndex : 'averageFilePath', - name : 'averageFilePath', - sortable : true, - width : 150, - hidden : true, - renderer : function(dataCollections, y, data) { - return BUI.getHTMLTableForPrefixes(data.raw.bufferBeforeAverageFilePath, data.raw.averageFilePath, - data.raw.bufferAfterAverageFilePath); - } - }, - - { - text : 'Guinier', - name : 'Guinier', - columns : [ - { - text : 'Rg', - dataIndex : 'rgGuinier', - name : 'rgGuinier', - hidden : !this.isGuinierTabVisible, - width : 75, - tooltip : 'In polymer physics, the radius of gyration is used to describe the dimensions of a polymer chain.', - sortable : true, - renderer : function(val, y, sample) { - if (sample.raw.rgGuinier != null) { - /** Show warning if rgGuinier and rgGnom differ more than 10% **/ - if (Math.abs(sample.raw.rgGuinier - sample.raw.rgGnom) > (sample.raw.rgGuinier * 0.1)) { - return "" + BUI.formatValuesUnits(sample.raw.rgGuinier, "") + ""; - - } - return BUI.formatValuesUnits(sample.raw.rgGuinier, "nm", 12, this.decimals); - } - } - }, - { - text : 'Points', - dataIndex : 'points', - sortable : true, - width : 100, - type : 'string', - hidden : !this.isGuinierTabVisible, - renderer : function(val, y, sample) { - if ((sample.raw.firstPointUsed == "") || (sample.raw.firstPointUsed == null)) - return; - return "" + sample.raw.firstPointUsed + " - " + sample.raw.lastPointUsed + " (" + - (sample.raw.lastPointUsed - sample.raw.firstPointUsed) + " )"; - } - }, - { - text : 'Quality', - dataIndex : 'quality', - hidden : !this.isGuinierTabVisible, - tooltip : 'Estimated data quality. 1.0 - means ideal quality, 0.0 - unusable data. In table format it is given in percent (100% - ideal quality, 0% - unusable data). Please note that this estimation is based only on the Guinier interval (very low angles).', - width : 60, - sortable : true, - renderer : function(val, y, sample) { - if (sample.raw.quality != null) { - val = sample.raw.quality; - if ((val != null) && (val != "")) { - return "" + (Number(val) * 100).toFixed(2) + " %"; - } - } - } - }, { - text : 'I(0)', - dataIndex : 'I0', - sortable : true, - hidden : !this.isI0Visible, - tooltip : 'Extrapolated scattering intensity at zero angle I(0) (forward scattering)', - width : 75, - type : 'string', - renderer : function(val, y, sample) { - if (sample.raw.I0 != null) { - return BUI.formatValuesErrorUnitsScientificFormat(sample.raw.I0, sample.raw.i0stdev, ""); - } - } - }, { - text : 'Aggregated', - tooltip : "If aggregation was detected from the slope of the data curve at low angles the value is '1', otherwise '0'.", - dataIndex : 'isagregated', - hidden : true, - width : 75, - renderer : function(val, y, sample) { - if ((sample.raw.isagregated != null)) { - if (val == true) { - return "Yes"; - } else { - return "No"; - } - } - } - }, { - text : 'Guinier', - sortable : true, - dataIndex : 'subtractionId', - type : 'string', - width : 100, - hidden : true, - renderer : function(val, y, sample) { - - if (sample.raw.subtractionId != null) { - var url = BUI.getURL() + '&type=guinier&subtractionId=' + sample.raw.subtractionId; - var event = "OnClick= window.open('" + url + "')"; - return ''; - } - } - } ] - }, - { - text : 'Gnom', - name : 'Gnom', - - columns : [ { - text : 'Rg', - dataIndex : 'rgGnom', - type : 'string', - width : 65, - hidden : !this.isGnomTabVisible, - sortable : true, - renderer : function(val, y, sample) { - /** Show warning if rgGuinier and rgGnom differ more than 10% **/ - if (sample.raw.rgGnom != null) { - if (Math.abs(sample.raw.rgGuinier - sample.raw.rgGnom) > (sample.raw.rgGuinier * 0.1)) { - return "" + BUI.formatValuesUnits(sample.raw.rgGnom, "") + ""; - - } - return BUI.formatValuesUnits(sample.raw.rgGnom, "nm"); - } - } - }, { - text : 'Total', - dataIndex : 'total', - width : 65, - hidden : !this.isGnomTabVisible, - sortable : true, - renderer : function(val, y, sample) { - if (sample.raw.total != null) - return BUI.formatValuesUnits(sample.raw.total, ''); - } - }, { - text : 'Dmax', - dataIndex : 'dmax', - sortable : true, - width : 75, - hidden : !this.isGnomTabVisible, - renderer : function(val, y, sample) { - if (sample.raw.dmax != null) - return BUI.formatValuesUnits(sample.raw.dmax, "") + " nm"; - } - }, { - text : 'P(r)', - sortable : true, - hidden : true, - width : 100, - dataIndex : 'subtractionId', - type : 'string', - renderer : function(val, y, sample) { - var url = BUI.getURL() + '&type=gnom&subtractionId=' + sample.raw.subtractionId; - var event = "OnClick= window.open('" + url + "')"; - return ''; - } - } ] - }, - this._getPorod(), - { - text : 'AbInitio Modeling', - name : 'AbInitio_modeling', - - columns : [ - { - text : 'NSD', - dataIndex : 'volumeEdna', - width : 100, - sortable : true, - hidden : true, - renderer : function(val, y, sample) { - var url = BUI.getNSDImageURL(sample.raw.modelListId); - var event = "OnClick= window.open('" + url + "')"; - return ''; - } - }, - { - text : 'Chi2', - dataIndex : 'volumeEdna', - sortable : true, - hidden : true, - width : 100, - renderer : function(val, y, sample) { - var url = BUI.getCHI2ImageURL(sample.raw.modelListId); - var event = "OnClick= window.open('" + url + "')"; - return ''; - } - }, - { - text : 'Pdb', - dataIndex : 'volumeEdna', - tooltip : 'Damaver: The program suite DAMAVER is a set of programs to align ab initio models, select the most typical one and build an averaged model. Dammif : Rapid ab initio shape determination by simulated annealing using a single phase dummy atom model. Dammin :Ab initio shape determination by simulated annealing using a single phase dummy atom model', - sortable : true, - width : 125, - hidden : !this.isAbinitioTabVisible, - renderer : function(val, y, sample) { - var html = new String(); - var split = null; - var url = null; - var file = sample.raw.averagedModel; - if (file != null) { - split = file.split("/"); - if (split.length > 0) { - url = BUI.getPdbURL() + '&type=AVERAGED&abInitioModelId=' + sample.raw.abInitioModelId; - html = html + ''+ split[split.length - 1] + '

'; - - } - } - - file = sample.raw.rapidShapeDeterminationModel; - if (file != null) { - split = file.split("/"); - if (split.length > 0) { - url = BUI.getPdbURL() + '&type=RAPIDSHAPEDETERMINATIONMODEL&abInitioModelId=' + sample.raw.abInitioModelId; - html = html + '' + split[split.length - 1] + '

'; - } - } - - file = sample.raw.shapeDeterminationModel; - if (file != null) { - split = file.split("/"); - if (split.length > 0) { - url = BUI.getPdbURL() + '&type=SHAPEDETERMINATIONMODEL&abInitioModelId=' + sample.raw.abInitioModelId; - html = html + ''+ split[split.length - 1] + ''; - } - } - return html; - } - }, - { - text : 'Damaver', - dataIndex : 'volumeEdna', - hidden : true, - tooltip : 'Damaver: The program suite DAMAVER is a set of programs to align ab initio models, select the most typical one and build an averaged model. ', - sortable : true, - width : 125, - renderer : function(val, y, sample) { - var file = sample.raw.averagedModel; - if (file != null) { - var split = file.split("/"); - if (split.length > 0) { - var url = BUI.getPdbURL() + '&type=AVERAGED&abInitioModelId=' + sample.raw.abInitioModelId; - return '' + split[split.length - 1]+ ''; - } - } - return sample.raw.averagedModel; - } - }, - { - text : 'Dammif', - dataIndex : 'volumeEdna', - hidden : true, - tooltip : 'Dammif : Rapid ab initio shape determination by simulated annealing using a single phase dummy atom model', - sortable : true, - width : 125, - renderer : function(val, y, sample) { - var file = sample.raw.rapidShapeDeterminationModel; - if (file != null) { - var split = file.split("/"); - if (split.length > 0) { - var url = BUI.getPdbURL() + '&type=RAPIDSHAPEDETERMINATIONMODEL&abInitioModelId=' + sample.raw.abInitioModelId; - return '' + split[split.length - 1] + ''; - } - } - return sample.raw.averagedModel; - } - }, - { - text : 'Dammin', - dataIndex : 'volumeEdna', - hidden : true, - tooltip : 'Dammin :Ab initio shape determination by simulated annealing using a single phase dummy atom model', - sortable : true, - width : 125, - renderer : function(val, y, sample) { - var file = sample.raw.shapeDeterminationModel; - if (file != null) { - var split = file.split("/"); - if (split.length > 0) { - var url = BUI.getPdbURL() + '&type=SHAPEDETERMINATIONMODEL&abInitioModelId=' + sample.raw.abInitioModelId; - return '' + split[split.length - 1]+ ''; - } - } - return sample.raw.averagedModel; - } - } ] - }, { - text : 'Time', - dataIndex : 'substractionCreationTime', - name : 'substractionCreationTime', - hidden : true, - width : 80, - sortable : true, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - try { - if (record.raw.substractionCreationTime != null) { - return moment(record.raw.substractionCreationTime).format('h:mm:ss a'); - } - } catch (e) { - return "NA"; - } - } - }, { - text : 'Date', - dataIndex : 'substractionCreationTime', - name : 'substractionCreationTime', - hidden : true, - width : 80, - sortable : true, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - try { - if (record.raw.substractionCreationTime != null) { - return moment(record.raw.substractionCreationTime).format("LL"); - } - } catch (e) { - return "NA"; - } - } - }, - this._getButtons()]; -}; - -AnalysisGrid.prototype._getButtons = function() { - return { - id : this.id + 'buttonPlot', - name : 'buttonPlot', - hidden : !this.showButtonsVisible, - width : 110, - sortable : false, - renderer : function(value, metaData, sample, rowIndex, colIndex, store) { - var html = ""; - - if (sample.raw.subtractionId) { - html = html + ""; - if (sample.raw.rapidShapeDeterminationModelId != null) { - html = html + ""; - } - } - return html + "
" + BUI.getGreenButton('Calibration', { - height : 20, - width : 100 - }) + "
" + BUI.getGreenButton('Primary Data Proc.', { - height : 20, - width : 100 - }) + "
" + BUI.getGreenButton('AbInitio Modeling', { - height : 20, - width : 100 - }) + "
"; - } - }; -}; -AnalysisGrid.prototype._prepareData = function(data) { - if (this.hideNulls) { - var result = []; - for ( var i = 0; i < data.length; i++) { - if (data[i].subtractionId != null) { - data[i].groupeField = data[i].macromoleculeAcronym + " " + data[i].bufferAcronym; - result.push(data[i]); - } - } - return result; - } else { - return data; - } -}; - -AnalysisGrid.prototype.getPanel = function(data) { - var _this = this; - var columns = this._getColumns(); - - var fields = JSON.parse(JSON.stringify(columns)); - fields.push({ - name : 'experimentId', - dataIndex : 'experimentId' - - }); - this.store = Ext.create('Ext.data.Store', { - fields : fields, - autoload : true, - data : this._prepareData(data), - groupField : 'groupeField' - }); - - this.store.sort(this.sorters); - - var features = []; - - if (this.grouped) { - features.push({ - ftype : 'grouping', - groupHeaderTpl : '{name}', - hideGroupedHeader : false, - startCollapsed : false - }); - } - - this.grid = Ext.create('Ext.grid.Panel', { - style : { - padding : 5 - }, - maxWidth : this.maxWidth, - width : this.width, - height : this.height, - store : this.store, - columns : columns, - resizable : true, - features : features, - viewConfig : { - preserveScrollOnRefresh : true, - stripeRows : true, - listeners : { - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonPlot') { - if (e.target.defaultValue == 'AbInitio Modeling') { - var url = BUI.getPDBVisualizerURL(record.raw.averagedModelId, record.raw.subtractionId, record.raw.experimentId); - window.open(url, "_blank"); - } - - if (e.target.defaultValue == 'Primary Data Proc.') { - _this._edit(record.raw); - } - - if (e.target.defaultValue == 'Calibration') { - _this._showCalibration(record.raw); - } - } - } - } - }, - selModel : { - mode : 'SINGLE' - } - }); - - return this.grid; - -}; - -AnalysisGrid.prototype._openVisualizarBySubstractionId = function(record) { - //experimentId, subtractionId) { - var experimentId = record.experimentId; - var subtractionId = record.subtractionId; - - var _this = this; - var adapter = new BiosaxsDataAdapter(); - this.subtractionId = subtractionId; - - adapter.onSuccess.attach(function(sender, data) { - var experiment = new Experiment(data); - var experimentList = new ExperimentList([ experiment ]); - var subtraction = experiment.getSubtractionById(_this.subtractionId); - _this.grid.setLoading(false); - _this._openVisualizer(experimentList, subtraction, record); - }); - this.grid.setLoading("ISPyB: Fetching experiment"); - adapter.getExperimentById(experimentId, "MEDIUM"); -}; - -AnalysisGrid.prototype._edit = function(record) { - var experimentId = record.experimentId; - var _this = this; - - if (BIOSAXS.proposal.macromolecules == null) { - this.grid.setLoading("ISPyB: Fetching proposal"); - BIOSAXS.proposal.onInitialized.attach(function(sender, data) { - _this._openVisualizarBySubstractionId(record); - }); - BIOSAXS.proposal.init(); - } else { - this._openVisualizarBySubstractionId(record); - } -}; - - -AnalysisGrid.prototype._showCalibration = function(row) { - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - Ext.create('Ext.window.Window', { - title : 'Calibration', - width : 900, - resizable : true, - height : 400, - modal : true, - frame : false, - draggable : true, - closable : true, - autoscroll : true, - paddin : 5, - layout : { - type : 'vbox', - align : 'stretch' - }, - items : [ new AnalysisGrid({ - isGuinierTabVisible : false, - isGnomTabVisible : false, - isPorodTabVisible : false, - isAbinitioTabVisible : false, - isI0Visible : true, - showButtonsVisible : false, - height : 350, - sorters : [ { - property : 'experimentId', - direction : 'DESC' - } ] - }).getPanel(data) ] - }).show(); - }); - adapter.getAnalysisCalibrationByProposalId(); -}; - -AnalysisGrid.prototype._openVisualizer = function(experimentList, subtraction, record) { - var merges = experimentList.getMergesByDataCollectionId(subtraction.dataCollectionId); - var mergeIdList = []; - for ( var i = 0; i < merges.length; i++) { - mergeIdList.push(merges[i].mergeId); - } - - var dataAdapter = new BiosaxsDataAdapter(); - dataAdapter.onSuccess.attach(function(sender, merges) { - var dataCollectionCurveVisualizer = new DataCollectionCurveVisualizer(); - dataCollectionCurveVisualizer.draw(); - dataCollectionCurveVisualizer.refresh(merges, experimentList, subtraction.dataCollectionId, record); - }); - - dataAdapter.onError.attach(function(sender, error) { - }); - - dataAdapter.getMergesByIdsList(mergeIdList); -}; - -AnalysisGrid.prototype.input = function() { - return { - data : DATADOC.getData_3367().slice(20, 30),//[{"total":"0.447505552082","bufferBeforeMeasurementId":22150,"sampleMergeId":12373,"averagedModelId":43636,"I0":"32.50776","proposalCode":"OPD","averagedModel":"/data/pyarch/bm29/opd29/1137/1d/damaver.pdb","bufferAfterMergeId":12374,"framesCount":"10","bufferBeforeMergeId":12372,"averageFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_016_ave.dat","bufferAfterMeasurementId":22152,"rgGuinier":"2.96883","subtractedFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_016_sub.dat","firstPointUsed":"30","chi2RgFilePath":"/data/pyarch/bm29/opd29/1137/1d/chi2_R.png","abInitioModelId":272,"macromoleculeId":112,"code":"_20.0_1.25","transmission":"100.0","timeStart":"2013-07-17 17:10:25.743734","bufferAcronym":"MES","quality":"0.87091","shapeDeterminationModelId":43638,"expermientComments":"[BsxCube] Generated from BsxCube","bufferId":707,"isagregated":"False","dmax":"10.390905","bufferBeforeAverageFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_015_ave.dat","exposureTemperature":"20.0","subtractionId":5165,"conc":"1.25","rapidShapeDeterminationModel":"/data/pyarch/bm29/opd29/1137/1d/damfilt.pdb","experimentCreationDate":"Jul 17, 2013 5:08:37 PM","lastPointUsed":"92","modelListId":272,"framesMerge":"10","rapidShapeDeterminationModelId":43637,"bufferAfterAverageFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_017_ave.dat","nsdFilePath":"/data/pyarch/bm29/opd29/1137/1d/nsd.png","bufferAfterFramesMerged":"10","experimentId":1137,"macromoleculeAcronym":"MG386","i0stdev":"0.05726128","sampleMeasurementId":22151,"measurementComments":"[1] MES","priorityLevelId":2,"bufferBeforeFramesMerged":"10","substractionCreationTime":"Jul 17, 2013 5:12:32 PM","proposalNumber":"29","rgGnom":"3.05242714339","volume":"44.1406","shapeDeterminationModel":"/data/pyarch/bm29/opd29/1137/1d/dammin.pdb","comments":null},{"total":"0.582641941147","bufferBeforeMeasurementId":22152,"sampleMergeId":12375,"averagedModelId":43809,"I0":"31.4366153846","proposalCode":"OPD","averagedModel":"/data/pyarch/bm29/opd29/1137/1d/damaver.pdb","bufferAfterMergeId":12376,"framesCount":"10","bufferBeforeMergeId":12374,"averageFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_018_ave.dat","bufferAfterMeasurementId":22155,"rgGuinier":"2.95541","subtractedFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_018_sub.dat","firstPointUsed":"21","chi2RgFilePath":"/data/pyarch/bm29/opd29/1137/1d/chi2_R.png","abInitioModelId":273,"macromoleculeId":112,"code":"_20.0_0.65000000000000002","transmission":"100.0","timeStart":"2013-07-17 17:12:55.837462","bufferAcronym":"MES","quality":"0.870164","shapeDeterminationModelId":43811,"expermientComments":"[BsxCube] Generated from BsxCube","bufferId":707,"isagregated":"False","dmax":"10.343935","bufferBeforeAverageFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_017_ave.dat","exposureTemperature":"20.0","subtractionId":5166,"conc":"0.65000000000000002","rapidShapeDeterminationModel":"/data/pyarch/bm29/opd29/1137/1d/damfilt.pdb","experimentCreationDate":"Jul 17, 2013 5:08:37 PM","lastPointUsed":"80","modelListId":273,"framesMerge":"10","rapidShapeDeterminationModelId":43810,"bufferAfterAverageFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_019_ave.dat","nsdFilePath":"/data/pyarch/bm29/opd29/1137/1d/nsd.png","bufferAfterFramesMerged":"10","experimentId":1137,"macromoleculeAcronym":"MG386","i0stdev":"0.100250461538","sampleMeasurementId":22154,"measurementComments":"[2] MES","priorityLevelId":4,"bufferBeforeFramesMerged":"10","substractionCreationTime":"Jul 17, 2013 5:15:02 PM","proposalNumber":"29","rgGnom":"2.9963404542","volume":"42.2255","shapeDeterminationModel":"/data/pyarch/bm29/opd29/1137/1d/dammin.pdb","comments":null}], - proposal : new ResultsAssemblyGrid().input().proposal - }; -}; - -AnalysisGrid.prototype.test = function(targetId) { - var analysisGrid = new AnalysisGrid(); - BIOSAXS.proposal = new Proposal(analysisGrid.input().proposal); - var panel = analysisGrid.getPanel(analysisGrid.input().data); - panel.render(targetId); -}; - - -function HPLCAnalysisGrid(args) { - AnalysisGrid.prototype.constructor.call(this, args); -} - -HPLCAnalysisGrid.prototype._edit = AnalysisGrid.prototype._edit; -HPLCAnalysisGrid.prototype._getColumns = AnalysisGrid.prototype._getColumns; -HPLCAnalysisGrid.prototype._openVisualizarBySubstractionId = AnalysisGrid.prototype._openVisualizarBySubstractionId; -HPLCAnalysisGrid.prototype._openVisualizer = AnalysisGrid.prototype._openVisualizer; -HPLCAnalysisGrid.prototype._prepareData = AnalysisGrid.prototype._prepareData; -HPLCAnalysisGrid.prototype._showCalibration = AnalysisGrid.prototype._showCalibration; -HPLCAnalysisGrid.prototype.getPanel = AnalysisGrid.prototype.getPanel; -HPLCAnalysisGrid.prototype.input = AnalysisGrid.prototype.input; -HPLCAnalysisGrid.prototype.test = AnalysisGrid.prototype.test; -HPLCAnalysisGrid.prototype.refresh = AnalysisGrid.prototype.refresh; -HPLCAnalysisGrid.prototype._getPorod = AnalysisGrid.prototype._getPorod; - -HPLCAnalysisGrid.prototype._getButtons = function() { - return { - id : this.id + 'buttonPlot', - name : 'buttonPlot', - hidden : !this.showButtonsVisible, - width : 110, - sortable : false, - renderer : function(value, metaData, sample, rowIndex, colIndex, store) { - var html = ""; - - if (sample.raw.subtractionId) { - if (sample.raw.rapidShapeDeterminationModelId != null) { - html = html + ""; - } - } - return html + "
" + BUI.getGreenButton('AbInitio Modeling', { - height : 20, - width : 100 - }) + "
"; - } - }; -}; - -HPLCAnalysisGrid.prototype._getFramesColumn = function() { - return { - text : 'Frames', - dataIndex : 'datacollection', - name : 'datacollection', - sortable : true, - width : 150, - renderer : function(dataCollections, y, data) { - molmerges = data.raw.framesMerge; - totalframes = data.raw.framesCount; - return molmerges +" - "+ totalframes; - } - }; -}; - - - - -/** - * Rigid body grid to show PDB, symmetry and multiplicity - * - * - * #onUploadFile click on upload file - */ -function AprioriRigidBodyGrid(args) { - - this.height = 250; - this.btnEditVisible = true; - this.btnRemoveVisible = true; - - if (args != null) { - if (args.height != null) { - this.height = args.height; - } - if (args.btnEditVisible != null) { - this.btnEditVisible = args.btnEditVisible; - } - if (args.btnRemoveVisible != null) { - this.btnRemoveVisible = args.btnRemoveVisible; - } - } - - /** Events **/ - this.onUploadFile = new Event(this); - this.onRemove = new Event(this); -} - -AprioriRigidBodyGrid.prototype._getColumns = function() { -}; - -AprioriRigidBodyGrid.prototype._getTopButtons = function() { - var _this = this; - /** Actions buttons **/ - var actions = []; - - /** ADD BUTTON **/ - actions.push(Ext.create('Ext.Action', { - icon : '../images/add.png', - text : 'Add', - disabled : false, - handler : function(widget, event) { - _this.onAddButtonClicked.notify(); - } - })); - - return actions; -}; - -AprioriRigidBodyGrid.prototype.refresh = function(macromolecule) { - this.macromolecule = macromolecule; - if (macromolecule != null){ - this.pdbStore.loadData(macromolecule.structure3VOs); - } -}; - -AprioriRigidBodyGrid.prototype._prepareData = function() { - var data = []; - for ( var i = 0; i < this.features.length; i++) { - data.push(this.features[i]); - } - return data; -}; - -AprioriRigidBodyGrid.prototype._getPlugins = function() { - var _this = this; - var plugins = []; - plugins.push(Ext.create('Ext.grid.plugin.RowEditing', { - clicksToEdit : 1, - listeners : { - validateedit : function(grid, e) { - /** Comments are always updatable* */ - e.record.raw.symmetry = e.newValues.symmetry; - e.record.raw.multiplicity = e.newValues.multiplicity; - - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, proposal) { - BIOSAXS.proposal.setItems(proposal); - _this.refresh(BIOSAXS.proposal.getMacromoleculeById(_this.macromolecule.macromoleculeId)); - _this.panel.setLoading(false); - }); - adapter.onError.attach(function() { - alert("Error"); - }); - - _this.panel.setLoading(); - adapter.saveStructure(e.record.raw); - } - } - })); - return plugins; -}; - -AprioriRigidBodyGrid.prototype.getPanel = function() { - var _this = this; - - this.pdbStore = Ext.create('Ext.data.Store', { - fields : [ 'filePath', 'structureId', 'structureType', 'symmetry', 'structureId', 'name', 'multiplicity' ], - groupField : 'structureType', - sorters : { - property : 'structureId', - direction : 'DESC' - } - }); - - var groupingFeature = Ext.create('Ext.grid.feature.Grouping', { - groupHeaderTpl : Ext.create('Ext.XTemplate', - "
{name:this.formatName}
", { - formatName : function(name) { - return name; - } - }), - hideGroupedHeader : true, - startCollapsed : false - }); - - this.panel = Ext.create('Ext.grid.Panel', { - margin : "15 10 0 10", - height : this.height, - store : this.pdbStore, - plugins : _this._getPlugins(), - tbar : [ { - text : 'Add Modeling Option (PDB)', - icon : '../images/add.png', - handler : function() { - _this.onUploadFile.notify('PDB', 'Upload PDB File'); - } - } - - ], - columns : [ - { - text : "structureId", - flex : 0.2, - hidden : true, - dataIndex : 'structureId', - sortable : true - }, - { - text : "File", - flex : 0.5, - dataIndex : 'filePath', - sortable : true, - hidden : true - }, - { - text : "PDB", - flex : 0.4, - dataIndex : 'name', - sortable : true - }, - { - text : "Symmetry", - flex : 0.2, - dataIndex : 'symmetry', - sortable : true, - editor : { - xtype : 'combobox', - typeAhead : true, - triggerAction : 'all', - selectOnTab : true, - store : [ [ "P1", "P1" ], [ "P2", "P2" ], [ "P3", "P3" ], [ "P4", "P4" ], [ "P5", "P5" ], [ "P6", "P6" ], [ "P32", "P32" ], [ "P42", "P42" ], - [ "P52", "P52" ], [ "P62", "P62" ], [ "P222", "P222" ] ], - } - }, { - text : "Multiplicity", - flex : 0.2, - dataIndex : 'multiplicity', - sortable : true, - editor : { - xtype : 'textfield' - } - - }, { - text : "Subunit", - flex : 0.2, - dataIndex : 'isSubunit', - sortable : true, - hidden : true - }, { - text : "Type", - flex : 0.2, - dataIndex : 'structureType', - sortable : true, - hidden : true - }, - - { - id : this.id + 'REMOVE', - flex : 0.2, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - return BUI.getRedButton('REMOVE'); - } - }, ], - - listeners : { - itemdblclick : function(dataview, record, item, e) { - _this._editExperiment(record.raw.experimentId); - }, - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'REMOVE') { - var dataAdapter = new BiosaxsDataAdapter(); - dataAdapter.onSuccess.attach(function() { - _this.panel.setLoading(false); - _this.onRemove.notify(); - }); - _this.panel.setLoading("Removing PDB file"); - dataAdapter.removeStructure(record.data.structureId); - } - - } - }, - viewConfig : { - getRowClass : function(record, rowIdx, params, store) { - if (record.raw.isSubunit != null) { - return "blue-row"; - } - } - } - }); - - return this.panel; -}; - - - - -AprioriRigidBodyGrid.prototype.input = function() { - return { - proposal : DATADOC.getProposal_10(), - dewars : DATADOC.getDewars_10() - - }; -}; - -AprioriRigidBodyGrid.prototype.test = function(targetId) { - var AprioriRigidBodyGrid = new AprioriRigidBodyGrid({ - height : 150 - }); - BIOSAXS.proposal = new Proposal(AprioriRigidBodyGrid.input().proposal); - var panel = AprioriRigidBodyGrid.getPanel(AprioriRigidBodyGrid.input().dewars); - panel.render(targetId); - -}; - -/** - * It shows buffer grid with a top bar with "Add" button - * - * @height - * @searchBar - * @collapsed - * @width - */ -function BufferGrid(args) { - this.height = 500; - this.searchBar = false; - this.tbar = false; - this.collapsed = false; - this.id = BUI.id(); - - if (args != null) { - if (args.height != null) { - this.height = args.height; - } - if (args.searchBar != null) { - this.searchBar = args.searchBar; - } - - if (args.tbar != null) { - this.tbar = args.tbar; - } - - if (args.collapsed != null) { - this.collapsed = args.collapsed; - } - - if (args.width != null) { - this.width = args.width; - } - } -} - -BufferGrid.prototype._edit = function(bufferId) { - var _this = this; - var window = new BufferWindow(); - window.onSuccess.attach(function(sender, proposal) { - _this.store.loadData(BIOSAXS.proposal.getBuffers()); - }); - window.draw(BIOSAXS.proposal.getBufferById(bufferId)); -}; - -BufferGrid.prototype.refresh = function(buffers) { - this.store.loadData(this._prepareData(buffers), false); -}; - -BufferGrid.prototype._prepareData = function(buffers) { - return buffers; -}; - -BufferGrid.prototype._getTbar = function() { - var _this = this; - var actions = []; - - actions.push(Ext.create('Ext.Action', { - icon : '../images/add.png', - text : 'Add buffer', - disabled : false, - handler : function(widget, event) { - var window = new BufferWindow(); - window.onSuccess.attach(function(sender) { - _this.store.loadData(BIOSAXS.proposal.getBuffers()); - }); - window.draw({}); - } - })); - return actions; -}; - -BufferGrid.prototype.getPanel = function(buffers) { - var _this = this; - - this.store = Ext.create('Ext.data.Store', { - fields : [ 'bufferId', 'acronym', 'name', 'composition' ], - data : buffers - }); - - this.store.sort('acronym'); - - var type = 'Ext.grid.Panel'; - if (this.searchBar == true) { - type = 'Ext.ux.LiveSearchGridPanel'; - } - - this.grid = Ext.create(type, { - title : 'Buffers', - collapsible : true, - collapsed : this.collapsed, - store : this.store, - height : this.height, - width : this.width, - columns : [ - /*{ - text : '', - dataIndex : 'bufferId', - width : 20, - renderer : function(val, y, sample) { - return BUI.getRectangleColorDIV(BIOSAXS.proposal.bufferColors[val], 10, 10); - } - },*/ - { - text : 'Acronym', - dataIndex : 'acronym', - flex : 1 - }, { - text : 'Name', - dataIndex : 'name', - flex : 1, - hidden : true - }, { - text : 'Composition', - dataIndex : 'composition', - flex : 1, - hidden : true - }, { - id : _this.id + 'buttonEditBuffer', - width : 80, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - return BUI.getGreenButton('EDIT'); - } - }, { - id : _this.id + 'buttonRemoveBuffer', - width : 85, - hidden : true, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - return BUI.getRedButton('REMOVE'); - } - } ], - flex : 1, - viewConfig : { - stripeRows : true, - listeners : { - 'celldblclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - _this._edit(record.data.bufferId); - }, - 'cellclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEditBuffer') { - _this._edit(record.data.bufferId); - } - - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemoveBuffer') { - BUI.showBetaWarning(); - } - } - - } - } - }); - - /** Adding the tbar **/ - if (this.tbar) { - this.grid.addDocked({ - xtype : 'toolbar', - items : this._getTbar() - }); - } - return this.grid; -}; - -BufferGrid.prototype.input = function() { - return new MacromoleculeGrid().input(); -}; - -BufferGrid.prototype.test = function(targetId) { - var bufferGrid = new BufferGrid({ - width : 800, - height : 350, - collapsed : false, - tbar : true - }); - - BIOSAXS.proposal = new Proposal(bufferGrid.input().proposal); - var panel = bufferGrid.getPanel(BIOSAXS.proposal.macromolecules); - panel.render(targetId); -}; - -/** - * A shipment may contains one or more cases where stock solutions and sample plates are stored - * - * @height - * @btnEditVisible - * @btnRemoveVisible - * - * #onEditButtonClicked - * #onAddButtonClicked - * #onRemoveButtonClicked - * #onDuplicateButtonClicked - */ -function CaseGrid(args) { - - this.height = 100; - this.btnEditVisible = true; - this.btnRemoveVisible = true; - - if (args != null) { - if (args.height != null) { - this.height = args.height; - } - if (args.btnEditVisible != null) { - this.btnEditVisible = args.btnEditVisible; - } - if (args.btnRemoveVisible != null) { - this.btnRemoveVisible = args.btnRemoveVisible; - } - } - - /** Events **/ - this.onEditButtonClicked = new Event(this); - this.onAddButtonClicked = new Event(this); - this.onRemoveButtonClicked = new Event(this); - this.onDuplicateButtonClicked = new Event(this); -} - -CaseGrid.prototype._getColumns = function() { - var _this = this; - - function actionItemRenderer(value, meta, record, rowIx, ColIx, store) { - /*if (record.raw.specimen3VOs.length > 0){ - return 'x-hide-display'; - }*/ - } - - var columns = [ - { - header : 'Code', - dataIndex : 'code', - name : 'code', - type : 'string', - flex : 1 - }, - { - header : 'Bar Code', - dataIndex : 'barCode', - name : 'barCode', - type : 'string', - flex : 1, - hidden : true - }, - { - header : 'BeamLine', - dataIndex : 'barCode', - type : 'string', - flex : 1, - renderer : function(comp, val, record) { - if (record.raw.sessionVO != null) { - return "" + record.raw.sessionVO.beamlineName + ""; - } - } - }, - { - header : 'Session', - dataIndex : 'barCode', - type : 'string', - flex : 1, - renderer : function(comp, val, record) { - if (record.raw.sessionVO != null) { - return "" + moment(record.raw.sessionVO.startDate).format("MMM Do YY") + ""; - } - } - }, - { - header : 'Status', - dataIndex : 'dewarStatus', - name : 'dewarStatus', - type : 'string', - flex : 1, - renderer : function(comp, val, record) { - if (new String(record.raw.dewarStatus).toUpperCase() == 'OPENED') { - return "" + new String(record.raw.dewarStatus).toUpperCase() + ""; - } - return "" + new String(record.raw.dewarStatus).toUpperCase() + ""; - } - }, - { - header : 'Type', - dataIndex : 'type', - name : 'type', - type : 'string', - flex : 1, - hidden : true - }, - { - header : 'Sample Plates', - dataIndex : 'plates', - name : 'plates', - type : 'string', - flex : 1, - hidden : true - }, - { - header : 'Stock Solutions', - dataIndex : 'plates', - name : 'plates', - type : 'string', - width : 100, - renderer : function(comp, val, record) { - var html = "
"; - var stockSolutions = BIOSAXS.proposal.getStockSolutionsByDewarId(record.raw.dewarId); - html = html + "" + stockSolutions.length + " x"; - return html + "
"; - } - }, { - header : 'isStorageDewar', - dataIndex : 'isStorageDewar', - name : 'isStorageDewar', - type : 'string', - flex : 1, - hidden : true - }, { - header : 'Tracking Number From Synchrotron', - dataIndex : 'trackingNumberFromSynchrotron', - name : 'trackingNumberFromSynchrotron', - type : 'string', - flex : 1, - hidden : true - }, { - header : 'Tracking Number To Synchrotron', - dataIndex : 'trackingNumberToSynchrotron', - name : 'trackingNumberToSynchrotron', - type : 'string', - flex : 1, - hidden : true - }, { - header : 'Storage Location', - dataIndex : 'storageLocation', - name : 'storageLocation', - type : 'string', - flex : 1, - hidden : false - }, { - header : 'Comments', - dataIndex : 'comments', - name : 'comments', - type : 'string', - flex : 1, - hidden : false - } - ]; - - if (this.btnEditVisible) { - columns.push({ - id : _this.id + 'buttonEdit', - text : '', - hidden : !_this.btnEditVisible, - width : 85, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - return BUI.getGreenButton('EDIT'); - } - }); - } - - if (this.btnRemoveVisible) { - columns.push({ - id : _this.id + 'buttonRemove', - width : 85, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - if (_this.btnRemoveVisible) { - return BUI.getRedButton('REMOVE'); - } - } - }); - } - - columns.push({ - dataIndex : 'comments', - type : 'string', - width : 85, - hidden : false, - renderer : function(comp, val, record) { - return BUI.getBlueButton("LABELS", { - href : BUI.getPrintcomponentURL(record.raw.dewarId) - }); - } - }); - - return columns; -}; - -CaseGrid.prototype._getTopButtons = function() { - var _this = this; - /** Actions buttons **/ - var actions = []; - - /** ADD BUTTON **/ - actions.push(Ext.create('Ext.Action', { - icon : '../images/add.png', - text : 'Add', - disabled : false, - handler : function(widget, event) { - _this.onAddButtonClicked.notify(); - } - })); - - return actions; -}; - -CaseGrid.prototype.refresh = function(dewars) { - this.features = dewars; - this.store.loadData(this._prepareData(dewars), false); -}; - -CaseGrid.prototype._sort = function(store) { - store.sort('dewarId', 'DESC'); -}; - -CaseGrid.prototype._prepareData = function() { - var data = []; - for ( var i = 0; i < this.features.length; i++) { - data.push(this.features[i]); - } - return data; -}; - -CaseGrid.prototype.getPanel = function(dewars, plates) { - this.features = dewars; - this.plates = plates; - return this._renderGrid(); -}; - -CaseGrid.prototype._edit = function(dewar) { - var _this = this; - var caseWindow = new CaseWindow(); - /**SAVED **/ - caseWindow.onSaved.attach(function(sender, dewar) { - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, shipment) { - _this.refresh(shipment.dewarVOs); - }); - adapter.saveCase(BIOSAXS.proposal.getShipmentByDewarId(dewar.dewarId).shippingId, dewar); - }); - caseWindow.draw(dewar); -}; - -CaseGrid.prototype._getStoreFields = function(data) { - return [ { - name : 'dewarId', - type : 'string' - }, { - name : 'barCode', - type : 'string' - }, { - name : 'code', - type : 'string' - }, { - name : 'comments', - type : 'string' - }, { - name : 'dewarStatus', - type : 'string' - }, { - name : 'isStorageDewar', - type : 'string' - }, { - name : 'plates', - type : 'string' - }, { - name : 'transportValue', - type : 'string' - }, { - name : 'trackingNumberFromSynchrotron', - type : 'string' - }, { - name : 'trackingNumberToSynchrotron', - type : 'string' - }, { - name : 'timeStamp', - type : 'string' - }, { - name : 'storageLocation', - type : 'string' - }, { - name : 'type', - type : 'string' - } - - ]; -}; - -CaseGrid.prototype._renderGrid = function() { - var _this = this; - - /** Store **/ - var data = this._prepareData(); - this.store = Ext.create('Ext.data.Store', { - fields : this._getStoreFields(data), - autoload : true, - data : data - }); - this._sort(this.store); - - this.store.loadData(data, false); - - this.grid = Ext.create('Ext.grid.Panel', { - style : { - padding : 5 - }, - height : this.height, - store : this.store, - columns : this._getColumns(), - viewConfig : { - stripeRows : true, - listeners : { - itemdblclick : function(dataview, record, item, e) { - _this._edit(record.raw); - }, - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEdit') { - _this._edit(record.raw); - } - - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemove') { - _this.onRemoveButtonClicked.notify(_this.store.getAt(rowIndex).raw.dewarId); - } - } - } - }, - selModel : { - mode : 'SINGLE' - } - }); - - var actions = _this._getTopButtons(); - this.grid.addDocked({ - xtype : 'toolbar', - items : actions - }); - - this.grid.getSelectionModel().on({ - selectionchange : function(sm, selections) { - if (selections.length) { - for ( var i = 0; i < actions.length; i++) { - if (actions[i].enable) { - actions[i].enable(); - } - } - } else { - for ( var i = 0; i < actions.length; i++) { - if (actions[i].alwaysEnabled == false) { - if (actions[i].disable) { - actions[i].disable(); - } - } - } - } - } - }); - return this.grid; -}; - -CaseGrid.prototype.input = function() { - return { - proposal : DATADOC.getProposal_10(), - dewars : DATADOC.getDewars_10() - - }; -}; - -CaseGrid.prototype.test = function(targetId) { - var CaseGrid = new CaseGrid({ - height : 150 - }); - BIOSAXS.proposal = new Proposal(CaseGrid.input().proposal); - var panel = CaseGrid.getPanel(CaseGrid.input().dewars); - panel.render(targetId); - -}; - -/** - * A shipment may contains one or more cases where stock solutions and sample plates are stored - * - * @height - * @btnEditVisible - * @btnRemoveVisible - * - * #onEditButtonClicked - * #onAddButtonClicked - * #onRemoveButtonClicked - * #onDuplicateButtonClicked - */ -function ExampleGrid(args) { - - this.height = 100; - this.btnEditVisible = true; - this.btnRemoveVisible = true; - - if (args != null) { - if (args.height != null) { - this.height = args.height; - } - if (args.btnEditVisible != null) { - this.btnEditVisible = args.btnEditVisible; - } - if (args.btnRemoveVisible != null) { - this.btnRemoveVisible = args.btnRemoveVisible; - } - } - - /** Events **/ - this.onEditButtonClicked = new Event(this); - this.onAddButtonClicked = new Event(this); - this.onRemoveButtonClicked = new Event(this); - this.onDuplicateButtonClicked = new Event(this); -} - -ExampleGrid.prototype._getColumns = function() { - var _this = this; - - function actionItemRenderer(value, meta, record, rowIx, ColIx, store) { - /*if (record.raw.specimen3VOs.length > 0){ - return 'x-hide-display'; - }*/ - } - - var columns = [ - { - header : 'Code', - dataIndex : 'code', - name : 'code', - type : 'string', - flex : 1 - }, - { - header : 'Bar Code', - dataIndex : 'barCode', - name : 'barCode', - type : 'string', - flex : 1, - hidden : true - }, - { - header : 'BeamLine', - dataIndex : 'barCode', - type : 'string', - flex : 1, - renderer : function(comp, val, record) { - if (record.raw.sessionVO != null) { - return "" + record.raw.sessionVO.beamlineName + ""; - } - } - }, - { - header : 'Session', - dataIndex : 'barCode', - type : 'string', - flex : 1, - renderer : function(comp, val, record) { - if (record.raw.sessionVO != null) { - return "" + moment(record.raw.sessionVO.startDate).format("MMM Do YY") + ""; - } - } - }, - { - header : 'Status', - dataIndex : 'dewarStatus', - name : 'dewarStatus', - type : 'string', - flex : 1, - renderer : function(comp, val, record) { - if (new String(record.raw.dewarStatus).toUpperCase() == 'OPENED') { - return "" + new String(record.raw.dewarStatus).toUpperCase() + ""; - } - return "" + new String(record.raw.dewarStatus).toUpperCase() + ""; - } - }, - { - header : 'Type', - dataIndex : 'type', - name : 'type', - type : 'string', - flex : 1, - hidden : true - }, - { - header : 'Sample Plates', - dataIndex : 'plates', - name : 'plates', - type : 'string', - flex : 1, - hidden : true - }, - { - header : 'Stock Solutions', - dataIndex : 'plates', - name : 'plates', - type : 'string', - width : 100, - renderer : function(comp, val, record) { - var html = "
"; - var stockSolutions = BIOSAXS.proposal.getStockSolutionsByDewarId(record.raw.dewarId); - html = html + "" + stockSolutions.length + " x"; - return html + "
"; - } - }, { - header : 'isStorageDewar', - dataIndex : 'isStorageDewar', - name : 'isStorageDewar', - type : 'string', - flex : 1, - hidden : true - }, { - header : 'Tracking Number From Synchrotron', - dataIndex : 'trackingNumberFromSynchrotron', - name : 'trackingNumberFromSynchrotron', - type : 'string', - flex : 1, - hidden : true - }, { - header : 'Tracking Number To Synchrotron', - dataIndex : 'trackingNumberToSynchrotron', - name : 'trackingNumberToSynchrotron', - type : 'string', - flex : 1, - hidden : true - }, { - header : 'Storage Location', - dataIndex : 'storageLocation', - name : 'storageLocation', - type : 'string', - flex : 1, - hidden : false - }, { - header : 'Comments', - dataIndex : 'comments', - name : 'comments', - type : 'string', - flex : 1, - hidden : false - } - ]; - - if (this.btnEditVisible) { - columns.push({ - id : _this.id + 'buttonEdit', - text : '', - hidden : !_this.btnEditVisible, - width : 85, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - return BUI.getGreenButton('EDIT'); - } - }); - } - - if (this.btnRemoveVisible) { - columns.push({ - id : _this.id + 'buttonRemove', - width : 85, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - if (_this.btnRemoveVisible) { - return BUI.getRedButton('REMOVE'); - } - } - }); - } - - columns.push({ - dataIndex : 'comments', - type : 'string', - width : 85, - hidden : false, - renderer : function(comp, val, record) { - return BUI.getBlueButton("LABELS", { - href : BUI.getPrintcomponentURL(record.raw.dewarId) - }); - } - }); - - return columns; -}; - -ExampleGrid.prototype._getTopButtons = function() { - var _this = this; - /** Actions buttons **/ - var actions = []; - - /** ADD BUTTON **/ - actions.push(Ext.create('Ext.Action', { - icon : '../images/add.png', - text : 'Add', - disabled : false, - handler : function(widget, event) { - _this.onAddButtonClicked.notify(); - } - })); - - return actions; -}; - -ExampleGrid.prototype.refresh = function(dewars) { - this.features = dewars; - this.store.loadData(this._prepareData(dewars), false); -}; - -ExampleGrid.prototype._sort = function(store) { - store.sort('dewarId', 'DESC'); -}; - -ExampleGrid.prototype._prepareData = function() { - var data = []; - for ( var i = 0; i < this.features.length; i++) { - data.push(this.features[i]); - } - return data; -}; - -ExampleGrid.prototype.getPanel = function() { - this.grid = Ext.create('Ext.grid.Panel', { - style : { - padding : 5 - }, - height : this.height, - store : this.store, - columns : this._getColumns(), - viewConfig : { - stripeRows : true, - listeners : { - itemdblclick : function(dataview, record, item, e) { - _this._edit(record.raw); - }, - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEdit') { - _this._edit(record.raw); - } - - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemove') { - _this.onRemoveButtonClicked.notify(_this.store.getAt(rowIndex).raw.dewarId); - } - } - } - }, - selModel : { - mode : 'SINGLE' - } - }); - - var actions = _this._getTopButtons(); - this.grid.addDocked({ - xtype : 'toolbar', - items : actions - }); - - this.grid.getSelectionModel().on({ - selectionchange : function(sm, selections) { - if (selections.length) { - for ( var i = 0; i < actions.length; i++) { - if (actions[i].enable) { - actions[i].enable(); - } - } - } else { - for ( var i = 0; i < actions.length; i++) { - if (actions[i].alwaysEnabled == false) { - if (actions[i].disable) { - actions[i].disable(); - } - } - } - } - } - }); - return this.grid; -}; - - -ExampleGrid.prototype._getStoreFields = function(data) { - return [ { - name : 'dewarId', - type : 'string' - }, { - name : 'barCode', - type : 'string' - }, { - name : 'code', - type : 'string' - }, { - name : 'comments', - type : 'string' - }, { - name : 'dewarStatus', - type : 'string' - }, { - name : 'isStorageDewar', - type : 'string' - }, { - name : 'plates', - type : 'string' - }, { - name : 'transportValue', - type : 'string' - }, { - name : 'trackingNumberFromSynchrotron', - type : 'string' - }, { - name : 'trackingNumberToSynchrotron', - type : 'string' - }, { - name : 'timeStamp', - type : 'string' - }, { - name : 'storageLocation', - type : 'string' - }, { - name : 'type', - type : 'string' - } - - ]; -}; - -ExampleGrid.prototype._renderGrid = function() { - var _this = this; - - /** Store **/ - var data = this._prepareData(); - this.store = Ext.create('Ext.data.Store', { - fields : this._getStoreFields(data), - autoload : true, - data : data - }); - this._sort(this.store); - - this.store.loadData(data, false); - - this.grid = Ext.create('Ext.grid.Panel', { - style : { - padding : 5 - }, - height : this.height, - store : this.store, - columns : this._getColumns(), - viewConfig : { - stripeRows : true, - listeners : { - itemdblclick : function(dataview, record, item, e) { - _this._edit(record.raw); - }, - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEdit') { - _this._edit(record.raw); - } - - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemove') { - _this.onRemoveButtonClicked.notify(_this.store.getAt(rowIndex).raw.dewarId); - } - } - } - }, - selModel : { - mode : 'SINGLE' - } - }); - - var actions = _this._getTopButtons(); - this.grid.addDocked({ - xtype : 'toolbar', - items : actions - }); - - this.grid.getSelectionModel().on({ - selectionchange : function(sm, selections) { - if (selections.length) { - for ( var i = 0; i < actions.length; i++) { - if (actions[i].enable) { - actions[i].enable(); - } - } - } else { - for ( var i = 0; i < actions.length; i++) { - if (actions[i].alwaysEnabled == false) { - if (actions[i].disable) { - actions[i].disable(); - } - } - } - } - } - }); - return this.grid; -}; - -ExampleGrid.prototype.input = function() { - return { - proposal : DATADOC.getProposal_10(), - dewars : DATADOC.getDewars_10() - - }; -}; - -ExampleGrid.prototype.test = function(targetId) { - var ExampleGrid = new ExampleGrid({ - height : 150 - }); - BIOSAXS.proposal = new Proposal(ExampleGrid.input().proposal); - var panel = ExampleGrid.getPanel(ExampleGrid.input().dewars); - panel.render(targetId); - -}; - - -/** - * Shows a list of experiment AKA data acquisitions - * @height - * @sorters - * @minHeight - * @gridType: Ext.ux.LiveSearchGridPanel or Ext.grid.Panel - * @tbar true or false - * @grouping true or false - * @width - * @title - * #onEditButtonClicked - */ -function ExperimentGrid(args) { - this.width = "100%"; - this.height = 700; - this.minHeight = 500; - - this.id = BUI.id(); - this.gridType = 'Ext.grid.Panel'; //'Ext.ux.LiveSearchGridPanel'; - this.tbar = false; - this.hideHeaders = false; - this.grouping = true; - this.title = null; - - this.filtered = null; - - /** maximum row count **/ - this.limit = 100; - - this.sessionIdFilter = null; - - /** if not null filtered by date **/ - this.date = null; - - this.sorters = [ { - property : 'date', - direction : 'DESC' - }, { - property : 'time', - direction : 'DESC' - } ]; - - this.dates = {}; - if (args != null) { - if (args.height != null) { - this.height = args.height; - } - if (args.limit != null) { - this.limit = args.limit; - } - if (args.sorters != null) { - this.sorters = args.sorters; - } - if (args.sessionId != null){ - this.sessionIdFilter = args.sessionId; - } - if (args.filtered != null) { - this.filtered = args.filtered; - } - if (args.minHeight != null) { - this.minHeight = args.minHeight; - } - if (args.gridType != null) { - this.gridType = args.gridType; - } - if (args.tbar != null) { - this.tbar = args.tbar; - } - if (args.grouping != null) { - this.grouping = args.grouping; - } - if (args.width != null) { - this.width = args.width; - } - if (args.title != null) { - this.title = args.title; - } - - } - /** Events **/ - this.onEditButtonClicked = new Event(this); -} - -ExperimentGrid.prototype._getFilterTypes = function() { - return []; -}; - -ExperimentGrid.prototype._prepareData = function(rows) { - var data = []; - var count = 0; - - rows.sort(function(a,b){return b.experimentId - a.experimentId;}); - for ( var i = 0; i < rows.length; i++) { - var row = rows[i]; - this.dates[moment(row.creationDate).format("YYYYMMDD")] = moment(row.creationDate).format("MMM Do YY"); - if ( - ( this.filtered == null || row.experimentType == this.filtered ) && (count < this.limit || this.limit == null ) && (this.sessionIdFilter == null || this.date != null || (this.date == null && this.sessionIdFilter == row.sessionId)) - ){ - - data.push({ - experimentId : row.experimentId, - status : row.status, - dataAcquisitionFilePath : row.dataAcquisitionFilePath, - type : row.experimentType, - name : row.name, - macromolecules_names : row.macromolecules, - percentageAnalysed : { - value : (row.dataCollectionDoneCount / row.dataCollectionCount) * 100, - text : row.dataCollectionDoneCount + " of " + row.dataCollectionCount - }, - percentageCollected : { - value : (row.measurementDoneCount / row.measurementCount) * 100, - text : row.measurementDoneCount + " of " + row.measurementCount - }, - percentageMerged : { - value : (row.measurementAveragedCount / row.measurementCount) * 100, - text : row.measurementAveragedCount + " of " + row.measurementCount - }, - date : moment(row.creationDate).format("YYYYMMDD"), - time : moment(row.creationDate).format("YYYYMMDDHHmmss"), - creationDate : row.creationDate - }); - count ++; - } - } - return data; -}; - -ExperimentGrid.prototype.getPanel = function(experiments) { - this.features = experiments; - return this._renderGrid(experiments); -}; - -ExperimentGrid.prototype.refresh = function(experiments) { - this.experiments = experiments; - var filtered = []; - for ( var i = 0; i < experiments.length; i++) { - if (experiments[i].experimentType != "TEMPLATE") { - filtered.push(experiments[i]); - } - } - - this.parsedData = this._prepareData(filtered); - - var day = {}; - var dates = []; - for ( var i = 0; i < this.experiments.length; i++) { - var date = moment(this.experiments[i].creationDate).format("MMM Do YYYY"); - if (day[date] == null){ - dates.push({ - date : date, - value : moment(this.experiments[i].creationDate) - }); - day[date] = true; - } - } - - this.storeDate.loadData(dates, false); - this.store.loadData(this.parsedData, false); - - /** If it has already been filtered by date we keep the filter **/ - if (this.date != null){ - this._filterByDate(this.date); - } -}; - -ExperimentGrid.prototype._getTopButtons = function() { - var _this = this; - /** Actions buttons **/ - var actions = []; - - actions.push(Ext.create('Ext.Action', { - icon : '../images/calendar_icon.png', - text : 'Show Calendar', - disabled : false, - handler : function(widget, event) { - var window = Ext.create('Ext.window.Window', { - title : 'Calendar', - width : 600, - height : 600, - modal : true, - closable : true, - layout : { - type : 'vbox', - align : 'stretch' - }, - items : [ { - xtype : 'label', - html : 'Click on a data acquisition to select:', - margin : '5 5 5 5' - }, { - html : '
', - margin : '5 5 5 5' - } - - ] - }).show(); - - var calendarWidget = new CalendarWidget({ - height : 450 - }); - var aux = _this.limit; - /** we remove the limit temporarily **/ - _this.limit = null; - _this.sessionIdFilter = null; - calendarWidget.loadData(_this._prepareData(_this.experiments)); - _this.limit = aux; - calendarWidget.draw('calendar'); - calendarWidget.onClick.attach(function(sender, date) { - date = moment(date, "YYYY-MM-DD"); - _this._filterByDate(date); - window.close(); - - }); - - } - })); - this.storeDate = Ext.create('Ext.data.ArrayStore', { - fields: ['date', 'value'], - data : [] - }); - - this.dateMenu = Ext.create('Ext.form.field.ComboBox', { - hideLabel: true, - store: this.storeDate, - displayField: 'date', - typeAhead: true, - queryMode: 'local', - margin : '0 0 0 30', - triggerAction: 'all', - emptyText:'Select a date...', - selectOnFocus:true, - width:135, - listeners:{ - scope: this, - 'select': function (a,b,c){ - _this.limit = null; - _this._filterByDate(moment(b[0].raw.value, "YYYY-MM-DD")); - } - } - }); - - actions.push(this.dateMenu); - - actions.push("->"); - if (_this.filtered != null){ - actions.push({ - html : "Experiment Type: " + _this.filtered +"" - }); - } - else{ - actions.push({ - html : "Experiment Type: ALL" - }); - } - return actions; -}; - -/** - * Date format: "YYYY-MM-DD" - */ -ExperimentGrid.prototype._filterByDate = function(date) { - var experimentsFiltered = []; - /** Getting all the experiments of date**/ - for ( var i = 0; i < this.experiments.length; i++) { - var experiment = this.experiments[i]; - if (experiment.creationDate != null) { - var experimentDate = moment(experiment.creationDate); - if (experimentDate.year() == date.year()) { - if (experimentDate.month() == date.month()) { - if (experimentDate.date() == date.date()) { - experimentsFiltered.push(experiment); - } - } - } - } - } - var parsedData = this._prepareData(experimentsFiltered); - this.store.loadData(parsedData); - this.date = date; -}; - -/** Only for templates **/ -ExperimentGrid.prototype._removeExperimentById = function(experimentId) { - var _this = this; - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(evt, args) { - _this.grid.setLoading(false); - document.getElementById(BIOSAXS.targetId).innerHTML = ""; - BIOSAXS.start(BIOSAXS.targetId); - }); - this.grid.setLoading("Removing experiment "); - adapter.removeExperimentById(experimentId); -}; - -ExperimentGrid.prototype._renderGrid = function() { - var _this = this; - - /** Store **/ - this.store = Ext.create('Ext.data.Store', { - fields : this._getColumns(), - groupField : 'date', - autoload : true, - data : [], - remoteSort: false, - sorters : this.sorters - }); - - - - - var groupingFeature = Ext.create('Ext.grid.feature.Grouping', { - groupHeaderTpl : Ext.create('Ext.XTemplate', - "
{name:this.formatName}
", { - formatName : function(name) { - return _this.dates[name]; - } - }), - hideGroupedHeader : true, - startCollapsed : false - }); - - this.features = []; - if (this.grouping) { - this.features.push(groupingFeature); - } - - /** Grid **/ - this.grid = Ext.create(this.gridType, { - hideHeaders : this.hideHeaders, - resizable : true, - title : this.title, - width : this.width, - minHeight : this.minHeight, - height : this.height, - features : this.features, - store : this.store, - columns : this._getColumns(), - selModel : { - mode : 'SINGLE' - }, - viewConfig : { - stripeRows : true, - getRowClass : function(record, rowIdx, params, store) { - if (record.raw.type == "TEMPLATE") { - return "template-color-row"; - } - if ((record.raw.type == "CALIBRATION") && (record.raw.status == "FINISHED")) { - return "blue-row"; - } - }, - listeners : { - itemdblclick : function(dataview, record, item, e) { - _this._editExperiment(record.raw.experimentId); - }, - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'GO') { - _this._editExperiment(record.raw.experimentId); - } - - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'REMOVE') { - _this._removeExperimentById(record.raw.experimentId); - } - - } - } - } - }); - - var actions = _this._getTopButtons(); - - if (this.tbar) { - this.grid.addDocked({ - xtype : 'toolbar', - items : actions - }); - this.grid.getSelectionModel().on({ - selectionchange : function(sm, selections) { - if (selections.length) { - for ( var i = 0; i < actions.length; i++) { - if (actions[i].enable) { - actions[i].enable(); - } - } - } else { - for ( var i = 0; i < actions.length; i++) { - if (actions[i].alwaysEnabled == false) { - if (actions[i].disable) { - actions[i].disable(); - } - } - } - } - } - }); - } - - return this.grid; -}; - -ExperimentGrid.prototype._getColumns = function() { - var _this = this; - function actionItemRenderer(value, meta, record, rowIx, ColIx, store) { - if (record.raw.buffer3VOs != null) { - if (record.raw.buffer3VOs.length > 0) { - return 'x-hide-display'; - } - } - - if (record.data.platesCount > 0) { - return 'x-hide-display'; - } - } - - return [ - { - text : 'experimentId', - dataIndex : 'experimentId', - name : 'experimentId', - type : 'string', - hidden : true - }, - { - xtype : 'rownumberer', - width : 40 - }, - { - text : 'Name', - dataIndex : 'name', - name : 'name', - type : 'string', - flex : 1 - }, - - { - text : 'Type', - dataIndex : 'type', - name : 'type', - type : 'string', - flex : 1, - renderer : function(val) { - if (val == "CALIBRATION") { - return "" + val + ""; - } - - return val; - } - }, - { - text : 'Macromolecules', - name : 'macromolecules_names', - dataIndex : 'macromolecules_names', - flex : 1, - renderer : function(val) { - if (val != null) { - return " " + val + ""; - } - return " Information not available"; - } - }, - { - text : 'Buffers', - dataIndex : 'buffer_names', - name : 'buffer_names', - flex : 1, - hidden : true, - renderer : function(val) { - return "Buffer/s: " + val + ""; - } - }, - { - text : 'Status', - dataIndex : 'status', - name : 'status', - type : 'string', - flex : 1, - renderer : function(val, x, sample) { - if (sample.raw.type == "TEMPLATE") { - return "READY"; - } - if (sample.raw.status == "ABORTED") { - return "" + val + ""; - } - return "" + val + ""; - } - }, - { - text : 'Download', - dataIndex : 'creationDate', - name : 'creationDate', - renderer : function(val, x, sample) { - if (sample != null) { - if (sample.raw.type == "HPLC") { - return; - } - return BUI.getZipHTMLByExperimentId(sample.raw.experimentId, sample.raw.name); - } - }, - width : 100 - - }, - { - header : 'Measurements', - dataIndex : 'percentageCollected', - name : 'percentageCollected', - type : 'string', - renderer : function(val, y, sample) { - if ((sample.raw.type == "TEMPLATE") || (sample.raw.type == "HPLC")) { - return; - } - return "
" + BUI.getProgessBar(sample.raw.percentageCollected.value, sample.raw.percentageCollected.text) + "
"; - }, - width : 100 - }, - { - header : 'Averaged', - dataIndex : 'percentageMerged', - name : 'percentageMerged', - type : 'string', - renderer : function(val, y, sample) { - if ((sample.raw.type == "TEMPLATE") || (sample.raw.type == "HPLC")) { - return; - } - return "
" + BUI.getProgessBar(sample.raw.percentageMerged.value, sample.raw.percentageMerged.text) + "
"; - }, - width : 100 - }, - { - header : 'Subtractions', - dataIndex : 'percentageAnalysed', - name : 'percentageAnalysed', - type : 'string', - renderer : function(val, y, sample) { - if ((sample.raw.type == "TEMPLATE") || (sample.raw.type == "HPLC")) { - return; - } - return "
" + BUI.getProgessBar(sample.raw.percentageAnalysed.value, sample.raw.percentageAnalysed.text) + "
"; - }, - width : 100 - }, - - { - text : 'time', - dataIndex : 'time', - name : 'time', - hidden : true, - renderer : function(val) { - return val; - }, - width : 100 - - }, { - text : 'Date', - dataIndex : 'date', - name : 'date', - renderer : function(val) { - return val; - }, - width : 100 - - }, - - { - text : 'Time', - dataIndex : 'creationDate', - name : 'creationDate', - renderer : function(val) { - return moment(val).format(" HH:mm:ss"); - }, - width : 100 - - }, { - id : _this.id + 'GO', - width : 80, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - return BUI.getGreenButton('GO'); - } - } ]; -}; - -/** Changes location.href in order to edit the experiment **/ -ExperimentGrid.prototype._editExperiment = function(experimentId) { - if (Ext.urlDecode(window.location.href).sessionId != null) { - location.href = 'viewProjectList.do?reqCode=display&experimentId=' + experimentId + '&sessionId='+ Ext.urlDecode(window.location.href).sessionId; - } else { - location.href = 'viewProjectList.do?reqCode=display&experimentId=' + experimentId; - } -}; - -ExperimentGrid.prototype.input = function() { - var experiments = DATADOC.getExperimentList_10(); - return { - experiments : experiments, - proposal : new MeasurementGrid().input().proposal - - }; -}; - -ExperimentGrid.prototype.test = function(targetId) { - var experimentGrid = new ExperimentGrid({ - height : 350, - minHeight : 350, - width : 1000 - - }); - BIOSAXS.proposal = new Proposal(experimentGrid.input().proposal); - var panel = experimentGrid.getPanel(experimentGrid.input().experiments); - experimentGrid.refresh(experimentGrid.input().experiments); - panel.render(targetId); -}; - -function FitStructureToExperimentDataGrid(args) { - this.height = null; - this.width = null; - this.id = BUI.id(); - - if (args != null) { - if (args.height != null) { - this.height = args.height; - - if (args.width != null) { - this.width = args.width; - } - } - } - - this.onSelected = new Event(this); -} - -FitStructureToExperimentDataGrid.prototype.getStructuresByMacromolecule = function(macromolecule) { - var structures = []; - if (macromolecule.structure3VOs != null) { - if (macromolecule.structure3VOs.length > 0) { - for (var i = 0; i < macromolecule.structure3VOs.length; i++) { - structures.push(macromolecule.structure3VOs[i]); - } - } - } - return structures; -}; - -FitStructureToExperimentDataGrid.prototype._prepareData = function(subtractions) { - var data = []; - for (var i = 0; i < subtractions.length; i++) { - - for (var j = 0; j < subtractions[i].fitStructureToExperimentalData3VOs.length; j++) { - var fit = subtractions[i].fitStructureToExperimentalData3VOs[j]; - data.push({ - fit : fit.fitFilePath, - fitStructureToExperimentalDataId : fit.fitStructureToExperimentalDataId, - mixtureToStructure3VOs : fit.mixtureToStructure3VOs, - subtractedFile : subtractions[i].substractedFilePath - }); - } - } - return data; - -}; - -FitStructureToExperimentDataGrid.prototype.refresh = function(subtractions) { - this.store.loadData(this._prepareData(subtractions), false); -}; - -FitStructureToExperimentDataGrid.prototype.getPanel = function() { - var _this = this; - this.store = Ext.create('Ext.data.Store', { - fields : [ 'fit', 'subtractedFile', 'structureId', 'fitFilePath', 'mixtureToStructure3VOs' ], - data : [] - }); - - this.store.sort([ { - property : 'name', - direction : 'ASC' - } ]); - - this.selModel = Ext.create('Ext.selection.RowModel', { - allowDeselect : true, - mode : 'MULTI', - listeners : { - selectionchange : function(sm, selections) { - var selected = []; - for (var i = 0; i < selections.length; i++) { - selected.push(selections[i].raw); - } - _this.onSelected.notify(selected); - } - } - }); - - this.panel = Ext.create('Ext.grid.Panel', { - store : this.store, - deferredRender : false, - width : this.width, - height : this.height, - margin : 10, - selModel : this.selModel, - columns : [ { - text : 'Name', - dataIndex : 'fit', - flex : 1, - renderer : function(val, b, record) { - return BUI.getFileName(val); - } - }, { - text : 'PDB', - dataIndex : 'mixtureToStructure3VOs', - flex : 1, - renderer : function(values, b, record) { - var html = ""; - for (var i = 0; i < values.length; i++) { - var structure = BIOSAXS.proposal.getStructuresById(values[i].structureId); - html = html + ""; - if (structure != null){ - html = html + ""; - } - html = html + ""; - } - return html + "
" + structure.name + "
"; - } - }, { - text : 'Volume Fraction', - dataIndex : 'mixtureToStructure3VOs', - flex : 1, - renderer : function(values, b, record) { - var html = ""; - for (var i = 0; i < values.length; i++) { - html = html + ""; - html = html + ""; - html = html + ""; - } - - return html + "
" + values[i].volumeFraction + "
"; - } - },{ - text : 'Subtraction', - dataIndex : 'subtractedFile', - flex : 1, - renderer : function(values, b, record) { - return values.split("/")[values.split("/").length - 1]; - } - },], - - viewConfig : { - enableTextSelection : true, - preserveScrollOnRefresh : true - }, - listeners : { - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - }, - afterrender : function() { - } - } - }); - return this.panel; -}; - -/** Static method **/ -FitStructureToExperimentDataGrid.prototype.RUNFitScattering = function(subtractionId, structureId) { - var _this = this; - /** Add to Workflow **/ - var adapter = new BiosaxsDataAdapter(); - var workflow = { - 'workflowTitle' : 'FitExperimentalDatatoStructure', - 'comments' : 'FitExperimentalDatatoStructure run from ISPyB for subtractionId: ' + subtractionId + ' and structureId ' + structureId - } - - var inputs = [ { - name : 'subtractionId', - value : subtractionId - }, { - name : 'structureId', - value : structureId - } ]; - - adapter.onSuccess.attach(function(sender, data) { - /** Add to Fit **/ - var adapter2 = new BiosaxsDataAdapter(); - var fit = { - 'workflowId' : data.workflowId, - 'subtractionId' : subtractionId, - 'structureId' : structureId, - 'comments' : 'Sent to workflow engine' - } - adapter2.onSuccess.attach(function(sender, fit) { - _this.refresh(_this.subtractionId, _this.macromolecule); - }); - adapter2.addFitStructureData(fit); - - }); - adapter.addWorkflow(workflow, inputs); - -}; +/** + * Example form + * + * @witdh + * @height + */ +function MolarityForm(args) { + this.id = BUI.id(); + this.width = 700; + this.height = 500; + + if (args != null) { + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + } + + this.onSave = new Event(this); + this.onClose = new Event(this); +} + -/** - * It shows buffer grid with a top bar with "Add" button - * - * @height - * @searchBar - * @collapsed - * @width - */ -function FrameGrid(args) { - this.height = 500; - this.width = 500; - this.searchBar = false; - this.tbar = false; - this.collapsed = false; - - - if (args != null) { - if (args.height != null) { - this.height = args.height; - } - - if (args.searchBar != null) { - this.searchBar = args.searchBar; - } - - if (args.tbar != null) { - this.tbar = args.tbar; - } - - if (args.collapsed != null) { - this.collapsed = args.collapsed; - } - - if (args.width != null) { - this.width = args.width; - } - } -} - -FrameGrid.prototype._edit = function(bufferId) { - var _this = this; - var window = new BufferWindow(); - window.onSuccess.attach(function(sender, proposal) { - _this.store.loadData(BIOSAXS.proposal.getBuffers()); - }); - window.draw(BIOSAXS.proposal.getBufferById(bufferId)); -}; - -FrameGrid.prototype.refresh = function(buffers, experimentId) { - this.experimentId = experimentId; - this.store.loadData(this._prepareData(buffers), false); -}; - -FrameGrid.prototype._prepareData = function(buffers) { - return buffers; -}; - -FrameGrid.prototype._getTbar = function() { - var _this = this; - var actions = []; - - actions.push(Ext.create('Ext.Action', { - icon : '../images/add.png', - text : 'Add Buffer', - disabled : false, - handler : function(widget, event) { - var window = new BufferWindow(); - window.onSuccess.attach(function(sender) { - _this.store.loadData(BIOSAXS.proposal.getBuffers()); - }); - window.draw({}); - } - })); - return actions; -}; - -FrameGrid.prototype.getPanel = function(buffers) { - var _this = this; - - this.store = Ext.create('Ext.data.Store', { - fields : [ 'frameNumber', 'I0', 'Rg', 'Mass', 'Vc', 'Qr', 'quality'], - data : buffers - }); - - this.store.sort('frameNumber'); - - var type = 'Ext.grid.Panel'; - if (this.searchBar == true) { - type = 'Ext.ux.LiveSearchGridPanel'; - } - - this.grid = Ext.create(type, { - store : this.store, - height : this.height, - width : this.width, - margin : 5, - columns : [{ - text : 'Frame', - dataIndex : 'frameNumber', - flex : 1 - },{ - text : 'I0', - dataIndex : 'I0', - flex : 1, - renderer : function(val, y, sample) { - return BUI.formatValuesUnits(sample.data.I0, "", 12, 3); - } - },{ - text : 'Rg', - dataIndex : 'Rg', - flex : 1, - renderer : function(val, y, sample) { - return BUI.formatValuesUnits(sample.data.Rg, "nm", 12, 3); - } - },{ - text : 'Mass', - dataIndex : 'Mass', - flex : 1, - renderer : function(val, y, sample) { - return BUI.formatValuesUnits(sample.data.Mass, "", 12, 3); - } - },{ - text : 'Vc', - dataIndex : 'Vc', - flex : 1, - renderer : function(val, y, sample) { - return BUI.formatValuesUnits(sample.data.Vc, "", 12, 3); - } - },{ - text : 'Qr', - dataIndex : 'Qr', - flex : 1, - renderer : function(val, y, sample) { - return BUI.formatValuesUnits(sample.data.Qr, "", 12, 3); - } - },{ - text : 'Quality', - dataIndex : 'quality', - flex : 1, - renderer : function(val, y, sample) { - return (Number(sample.data.quality) * 100).toFixed(2) + "%"; - } - }, - { - text : '', - renderer : function(val, x, sample) { - if (sample != null) { - return BUI.getZipHTMLByFrameRangeId(_this.experimentId, sample.raw.frameNumber, sample.raw.frameNumber); - } - }, - width : 100 - }], - flex : 1, - viewConfig : { - stripeRows : true - } - }); - - /** Adding the tbar **/ - if (this.tbar) { - this.grid.addDocked({ - xtype : 'toolbar', - items : this._getTbar() - }); - } - return this.grid; -}; - -FrameGrid.prototype.input = function() { - return []; -}; - -FrameGrid.prototype.test = function(targetId) { - var frameGrid = new FrameGrid({ - width : 800, - height : 350, - collapsed : false, - tbar : true - }); - - var panel = frameGrid.getPanel([]); - panel.render(targetId); -}; - - -function PeakGrid(args) { - this.height = 500; - this.searchBar = false; - this.tbar = false; - this.collapsed = false; - this.width = 500; - this.showExtendedColumns = false; - - if (args != null) { - if (args.showExtendedColumns != null) { - this.showExtendedColumns = args.showExtendedColumns; - } - if (args.height != null) { - this.height = args.height; - } - if (args.searchBar != null) { - this.searchBar = args.searchBar; - } - - if (args.tbar != null) { - this.tbar = args.tbar; - } - - if (args.collapsed != null) { - this.collapsed = args.collapsed; - } - - if (args.width != null) { - this.width = args.width; - } - } -} - - -PeakGrid.prototype.refresh = function(buffers) { - this.store.loadData(this._prepareData(buffers), false); -}; - -PeakGrid.prototype._prepareData = function(buffers) { - -// for ( var i = 0; i < buffers.length; i++) { -// buffers[i].name = "Peak #" + (i+1); +MolarityForm.prototype._getNumericWithHelp = function(type, fieldLabel, fieldName, help) { + return Ext.create('Ext.container.Container', { + margin : "10 0 0 10", + items : [ { + xtype : type, + fieldLabel : fieldLabel, + name : fieldName, + id : this.id + fieldName, + decimalPrecision : 6 + }, { + xtype : 'label', + forId : 'myFieldId', + text : help, + margin : "5 0 0 105", + cls : "inline-help" + } ] + }); +}; + + +MolarityForm.prototype._getItems = function() { + this.macromoleculeCombo = BIOSAXS_COMBOMANAGER.getComboMacromoleculeByMacromolecules(this.getMacromuleculesCandidates(this.macromolecule), { + width : 250, + labelWidth : 100, + margin : 10 + }); + + return [ { + xtype : 'container', + flex : 1, + margin : '10 0 0 10', + border : 0, + layout : 'anchor', + defaultType : 'requiredtext', + items : [ this.macromoleculeCombo, + this._getNumericWithHelp("textfield", "Ratio", "ratio", "Number in assymmetric units") + ] + } ]; +}; + +MolarityForm.prototype._persist = function() { + var _this = this; + var macromoleculeId = this.macromoleculeCombo.getValue(); + var ratio = Ext.getCmp(this.id + "ratio").getValue(); + var comments = "Not used yet"; + var dataAdapter = new BiosaxsDataAdapter(); + this.panel.setLoading("Saving"); + dataAdapter.onSuccess.attach(function(sender, args) { + _this.onSave.notify(); + }); + dataAdapter.saveStoichiometry(this.macromolecule.macromoleculeId, macromoleculeId, ratio, comments); +}; + +MolarityForm.prototype._getButtons = function() { + var _this = this; + + function onClose() { + _this.onClose.notify(); + } + + return [ { + text : 'Save', + handler : function() { + _this._persist(); + } + }, { + text : 'Cancel', + handler : function() { + onClose(); + } + } ]; +}; + +MolarityForm.prototype.getPanel = function() { + this.panel = Ext.create('Ext.form.Panel', { +// width : null, + height : this.height, + margin : 2, + border : 1, + defaultType : 'requiredtext', + items : this._getItems(), + buttons : this._getButtons() + }); + return this.panel; +}; + +/** macromolecules contains all macromolecules except this one **/ +MolarityForm.prototype.getMacromuleculesCandidates = function(macromolecule) { + var macromolecules = []; + if ( BIOSAXS.proposal.macromolecules){ + for (var i = 0; i < BIOSAXS.proposal.macromolecules.length; i++) { + var m = BIOSAXS.proposal.macromolecules[i]; + if (this.macromolecule != null){ + if (m.macromoleculeId != this.macromolecule.macromoleculeId) { + macromolecules.push(m); + } + } + } + } + return macromolecules; +}; + + +/** It populates the form **/ +MolarityForm.prototype.refresh = function(macromolecule) { + this.macromolecule = macromolecule; + +}; + + +MolarityForm.prototype.input = function() { + return {}; +}; + + +/** It populates the form **/ +MolarityForm.prototype.test = function(targetId) { + var macromoleculeForm = new MolarityForm(); + var panel = macromoleculeForm.getPanel(); + panel.render(targetId); +}; + +///** +// * +// * @witdh +// * @height +// */ +//function MacromoleculeForm(args) { +// this.id = BUI.id(); +// this.width = 700; +// this.height = 500; +// +// if (args != null) { +// if (args.width != null) { +// this.width = args.width; +// } +// if (args.height != null) { +// this.height = args.height; +// } +// } +// +// this.onClose = new Event(this); +//} +// +//MacromoleculeForm.prototype.getMacromolecule = function() { +// this.macromolecule.name = Ext.getCmp(this.panel.getItemId()).getValues().name; +// this.macromolecule.acronym = Ext.getCmp(this.panel.getItemId()).getValues().acronym; +// this.macromolecule.comments = Ext.getCmp(this.panel.getItemId()).getValues().comments; +// this.macromolecule.extintionCoefficient = Ext.getCmp(this.panel.getItemId()).getValues().extintionCoefficient; +// this.macromolecule.molecularMass = Ext.getCmp(this.panel.getItemId()).getValues().molecularMass; +// return this.macromolecule; +//}; +// +//MacromoleculeForm.prototype.setMacromolecule = function(macromolecule) { +// this.pdbStore.loadData(macromolecule.structure3VOs); +// +//}; +// +//MacromoleculeForm.prototype.getForm = function(macromolecule) { +// this.panel = Ext.createWidget('form', { +// frame : false, +// border : 0, +// padding : 15, +// width : 550, +// height : 350, +// items : [ { +// xtype : 'container', +// layout : 'hbox', +// items : [ { +// xtype : 'container', +// flex : 1, +// border : false, +// layout : 'anchor', +// defaultType : 'requiredtext', +// items : [ { +// fieldLabel : 'Name', +// name : 'name', +// anchor : '95%', +// tooltip : "Name of the macromolecule", +// value : macromolecule.name +// }, { +// fieldLabel : 'Acronym', +// name : 'acronym', +// anchor : '95%', +// value : macromolecule.acronym +// } ] +// }, { +// xtype : 'container', +// flex : 1, +// layout : 'anchor', +// defaultType : 'textfield', +// items : [ { +// xtype : 'numberfield', +// fieldLabel : 'Mol. Mass (Da)', +// name : 'molecularMass', +// value : macromolecule.molecularMass, +// decimalPrecision : 6 +// }, { +// xtype : 'numberfield', +// fieldLabel : 'Extinction coef.', +// name : 'extintionCoefficient', +// value : macromolecule.extintionCoefficient, +// decimalPrecision : 6 +// } ] +// } ] +// }, { +// xtype : 'textareafield', +// name : 'comments', +// fieldLabel : 'Comments', +// value : macromolecule.comments, +// width : this.width - 10 +// }, +// +// { +// html : BUI.getWarningHTML("The macromolecule is unsaved. Save the macromolecule to get access to other tabs"), +// margin : "150 10 10 10", +// id : this.id + "unsavedWarning", +// hidden : !(!macromolecule.macromoleculeId) +// } +// +// ] +// }); +// return this.panel; +//}; +// +//MacromoleculeForm.prototype.save = function() { +// var _this = this; +// +// var adapter = new BiosaxsDataAdapter(); +// adapter.onSuccess.attach(function(sender, proposal) { +// BIOSAXS.proposal.setItems(proposal); +// _this.panel.setLoading(false); +// +// Ext.getCmp(_this.id + "assembly").enable() +// Ext.getCmp(_this.id + "advanced").enable(); +// Ext.getCmp(_this.id + "unsavedWarning").hide(); +// }); +// +// if (this.getMacromolecule().name == "") { +// BUI.showError("Name field is mandatory"); +// return; +// } +// if (this.getMacromolecule().acronym == "") { +// BUI.showError("Acroynm field is mandatory"); +// return; +// } +// +// /** Check if acronym is unique * */ +// if (this.getMacromolecule().macromoleculeId == null) { +// if (BIOSAXS.proposal.getMacromoleculeByAcronym(this.getMacromolecule().acronym) == null) { +// this.panel.setLoading("ISPyB: Saving Macromolecule") +// adapter.saveMacromolecule(this.getMacromolecule()); +// } else { +// alert("There is already an existing macromolecule with the same acronym"); +// +// } +// } else { +// this.panel.setLoading("ISPyB: Saving Macromolecule") +// adapter.saveMacromolecule(this.getMacromolecule()); +// } +// +//}; +// +//MacromoleculeForm.prototype.getPanel = function(macromolecule) { +// var _this = this; +// this.macromolecule = macromolecule; +// return Ext.createWidget('tabpanel', { +// height : this.height, +// margin : 5, +// plain : true, +// style : { +// padding : 5 +// }, +// items : [ { +// tabConfig : { +// title : "General", +// disabled : false +// }, +// items : [ this.getForm(macromolecule) ], +// bbar : [ "->", { +// text : 'Save', +// cls : 'btn-with-border', +// style : { +// +// border : 1 +// }, +// handler : function() { +// _this.save(); +// } +// }, { +// text : 'Close', +// cls : 'btn-with-border', +// handler : function() { +// _this.onClose.notify(); +// } +// } ] +// }, { +// tabConfig : { +// id : this.id + "assembly", +// title : "Assembly", +// tooltip : 'Description of subunits present in the macromolecule', +// // hidden : (!macromolecule.macromoleculeId), +// disabled : (!macromolecule.macromoleculeId) +// }, +// items : [ this.getMolarityGrid(macromolecule) ] +// }, { +// tabConfig : { +// id : this.id + "advanced", +// title : "Advanced Modeling", +// // hidden : (!macromolecule.macromoleculeId), +// tooltip : 'Definition of the description contacts and symetries', +// disabled : (!macromolecule.macromoleculeId) +// }, +// items : [ this.getRigidBodyForm(macromolecule) ] +// } ] +// }); +//}; +// +//MacromoleculeForm.prototype.getRigidBodyForm = function(macromolecule) { +// var _this = this; +// +// // [P1, P2, P3, P4 ,P5 ,P6 ,32, P42, P52, P62] + P222 +// var symmetry = Ext.create('Ext.data.Store', { +// fields : [ 's' ], +// data : [ { +// "s" : "P1" +// }, { +// "s" : "P2" +// }, { +// "s" : "P3" +// }, { +// "s" : "P4" +// }, { +// "s" : "P5" +// }, { +// "s" : "P6" +// }, { +// "s" : "P32" +// }, { +// "s" : "P42" +// }, { +// "s" : "P52" +// }, { +// "s" : "P62" +// }, { +// "s" : "P222" +// } ] +// }); +// +// if (macromolecule.symmetry == null) { +// macromolecule.symmetry = "P1"; +// } +// var comboBox = Ext.create('Ext.form.ComboBox', { +// fieldLabel : 'Symmetry', +// store : symmetry, +// id : 'comboSym', +// queryMode : 'local', +// displayField : 's', +// valueField : 's', +// value : macromolecule.symmetry, +// margin : "10 0 0 0", +// listeners : { +// change : function(combo, newValue, oldValue, eOpts) { +// macromolecule.symmetry = newValue; +// } +// } +// }); +// +// this.rigidBodyPanel = Ext.createWidget('form', { +// frame : false, +// border : 0, +// padding : 10, +// width : 550, +// height : 400, +// items : [ { +// xtype : 'container', +// layout : 'hbox', +// items : [ { +// xtype : 'container', +// border : false, +// layout : 'hbox', +// items : [ { +// xtype : 'label', +// forId : 'myFieldId', +// text : 'Contact Desc:', +// width : 105, +// margin : '0 0 0 0' +// }, { +// xtype : 'textfield', +// hideLabel : true, +// id : "contactsDescriptionFilePath", +// margin : '0 0 0 0', +// width : 300, +// value : macromolecule.contactsDescriptionFilePath +// }, { +// text : 'Upload', +// xtype : 'button', +// margin : "0 0 0 20", +// width : 100, +// handler : function() { +// _this._openUploadDialog(macromolecule.macromoleculeId, "CONTACTS", "Upload Contact Description File"); +// } +// } ] +// } ] +// }, +// +// comboBox, { +// xtype : 'checkbox', +// margin : '10 0 0 5', +// boxLabel : "I want rigid body modeling run on this stuff", +// checked : true, +// width : 300 +// }, _this.getPDBGrid(macromolecule) ] +// }); +// return this.rigidBodyPanel; +//}; +// +//MacromoleculeForm.prototype.update = function() { +// var _this = this; +// BIOSAXS.proposal.onInitialized.attach(function() { +// if (BIOSAXS.proposal != null) { +// var macromolecules = BIOSAXS.proposal.macromolecules; +// for (var i = 0; i < macromolecules.length; i++) { +// if (macromolecules[i].macromoleculeId == _this.macromolecule.macromoleculeId) { +// _this.macromolecule = macromolecules[i]; +// _this.setMacromolecule(_this.macromolecule); +// _this.molarityStore.loadData(_this.parseMolarityData(_this.macromolecule)); +// _this.pdbGrid.setLoading(false); +// Ext.getCmp("contactsDescriptionFilePath").setValue(_this.macromolecule.contactsDescriptionFilePath) +// _this.molarityGrid.setLoading(false); +// +// } +// } +// } +// }); +// this.molarityGrid.setLoading("Updating"); +// this.pdbGrid.setLoading("Updating"); +// BIOSAXS.proposal.init(); +//}; +// +///******************************************************************************* +// * MOLARITY GRID +// ******************************************************************************/ +// +//MacromoleculeForm.prototype.parseMolarityData = function(macromolecule) { +// var data = []; +// if (macromolecule.stoichiometry != null) { +// for (var i = 0; i < macromolecule.stoichiometry.length; i++) { +// data.push({ +// ratio : macromolecule.stoichiometry[i].ratio, +// acronym : macromolecule.stoichiometry[i].macromolecule3VO.acronym, +// comments : macromolecule.stoichiometry[i].macromolecule3VO.comments, +// stoichiometryId : macromolecule.stoichiometry[i].stoichiometryId, +// name : macromolecule.stoichiometry[i].macromolecule3VO.name +// }); +// } +// } +// return data; +//}; +// +//MacromoleculeForm.prototype.getMolarityGrid = function(macromolecule) { +// var _this = this; +// +// this.molarityStore = Ext.create('Ext.data.Store', { +// fields : [ 'acronym', 'ratio', 'comments', 'stoichiometryId', 'name' ], +// data : this.parseMolarityData(macromolecule), +// sorters : { +// property : 'ratio', +// direction : 'DESC' +// } +// }); +// +// this.molarityGrid = Ext.create('Ext.grid.Panel', { +// store : this.molarityStore, +// height : 350, +// padding : 5, +// columns : [ +// +// { +// text : 'Subunit', +// columns : [ { +// text : "Acronym", +// width : 100, +// hidden : false, +// dataIndex : 'acronym', +// sortable : true +// }, { +// text : "Name", +// width : 100, +// hidden : false, +// dataIndex : 'name', +// sortable : true +// }, { +// text : "Comments", +// width : 100, +// dataIndex : 'comments', +// sortable : true +// } ] +// }, { +// text : "Number
in assymmetric units", +// width : 150, +// dataIndex : 'ratio', +// tooltip : 'Number of times this subunit is present in the macromolecule', +// sortable : true +// }, { +// id : this.id + 'MOLARITY_REMOVE', +// flex : 0.1, +// sortable : false, +// renderer : function(value, metaData, record, rowIndex, colIndex, store) { +// return BUI.getRedButton('REMOVE'); +// } +// } ], +// listeners : { +// cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { +// if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'MOLARITY_REMOVE') { +// var dataAdapter = new BiosaxsDataAdapter(); +// dataAdapter.onSuccess.attach(function() { +// _this.molarityGrid.setLoading(false); +// _this.update(); +// }); +// dataAdapter.removeStoichiometry(record.data.stoichiometryId); +// _this.molarityGrid.setLoading("Removing Structure"); +// } +// } +// }, +// buttons : [ { +// text : 'Add molarity', +// handler : function() { +// +// function onClose() { +// w.destroy(); +// _this.update(); +// } +// var w = Ext.create('Ext.window.Window', { +// title : 'Molarity', +// height : 300, +// width : 500, +// modal : true, +// buttons : [ { +// text : 'Save', +// handler : function() { +// var macromoleculeId = (_this.macromoleculeCombo.getValue()); +// var ratio = Ext.getCmp(_this.id + "ratio").getValue(); +// var comments = ""; +// var dataAdapter = new BiosaxsDataAdapter(); +// dataAdapter.onSuccess.attach(function(sender, args) { +// _this.update(); +// w.destroy(); +// }); +// dataAdapter.saveStoichiometry(_this.macromolecule.macromoleculeId, macromoleculeId, ratio, comments); +// } +// }, { +// text : 'Cancel', +// handler : function() { +// onClose(); +// } +// } ], +// items : [ _this.getMolarityForm(macromolecule) ], +// listeners : { +// onEsc : function() { +// onClose(); +// }, +// close : function() { +// onClose(); +// } +// } +// }).show(); +// } +// } ] +// }); +// return this.molarityGrid; +//}; +// +///******************************************************************************* +// * PDB GRID +// ******************************************************************************/ +// +//MacromoleculeForm.prototype._openUploadDialog = function(macromoleculeId, type, title) { +// var _this = this; +// function onClose() { +// w.destroy(); +// _this.update(); +// } +// +// var w = Ext.create('Ext.window.Window', { +// title : title, +// height : 200, +// width : 400, +// modal : true, +// buttons : [ { +// text : 'Close', +// handler : function() { +// onClose(); +// } +// } ], +// layout : 'fit', +// items : { +// html : "" +// }, +// listeners : { +// onEsc : function() { +// onClose(); +// }, +// close : function() { +// onClose(); +// } +// } +// }).show(); +//}; +// +//MacromoleculeForm.prototype._getPlugins = function() { +// var _this = this; +// var plugins = []; +// // if (this.updateRowEnabled) { +// plugins.push(Ext.create('Ext.grid.plugin.RowEditing', { +// clicksToEdit : 1, +// listeners : { +// validateedit : function(grid, e) { +// /** Comments are always updatable* */ +// e.record.raw.symmetry = e.newValues.symmetry; +// e.record.raw.multiplicity = e.newValues.multiplicity; +// +// var adapter = new BiosaxsDataAdapter(); +// adapter.onSuccess.attach(function(sender, measurement) { +// // _this.grid.setLoading(false); +// }); +// adapter.onError.attach(function() { +// alert("Error"); +// // _this.grid.setLoading(false); +// }); +// +// // _this.grid.setLoading(); +// adapter.saveStructure(e.record.raw); +// } +// } +// })); +// // } +// return plugins; +//}; +// +//MacromoleculeForm.prototype.getPDBGrid = function(macromolecule) { +// var _this = this; +// +// var data = macromolecule.structure3VOs; +// +// // /** Getting PDB from subunits **/ +// // if (macromolecule != null){ +// // if (macromolecule.stoichiometry != null){ +// // for (var i =0; i < macromolecule.stoichiometry.length; i++){ +// // var stoichiometry = macromolecule.stoichiometry[i]; +// // if (stoichiometry.macromolecule3VO != null){ +// // if (stoichiometry.macromolecule3VO.structure3VOs != null){ +// // for (var j = 0; j < stoichiometry.macromolecule3VO.structure3VOs.length; +// // j++) { +// // var structure = stoichiometry.macromolecule3VO.structure3VOs[j]; +// // structure["isSubunit"] = stoichiometry.macromolecule3VO.acronym; +// // data.push(structure) +// // } +// // } +// // } +// // } +// // } +// // } +// +// this.pdbStore = Ext.create('Ext.data.Store', { +// fields : [ 'filePath', 'structureId', 'structureType', 'symmetry', 'structureId', 'name', 'multiplicity' ], +// data : macromolecule.structure3VOs, +// groupField : 'structureType', +// sorters : { +// property : 'structureId', +// direction : 'DESC' +// } +// }); +// +// var groupingFeature = Ext.create('Ext.grid.feature.Grouping', { +// groupHeaderTpl : Ext.create('Ext.XTemplate', +// "
{name:this.formatName}
", { +// formatName : function(name) { +// return name; +// } +// }), +// hideGroupedHeader : true, +// startCollapsed : false +// }); +// +// this.pdbGrid = Ext.create('Ext.grid.Panel', { +// margin : "15 0 0 5", +// height : 250, +// store : this.pdbStore, +// plugins : _this._getPlugins(), +// buttons : [ { +// // text : 'Add PDB file', +// text : 'Add Modeling Option', +// handler : function() { +// _this._openUploadDialog(macromolecule.macromoleculeId, "PDB", 'Upload PDB File'); +// } +// } +// +// ], +// columns : [ +// { +// text : "structureId", +// flex : 0.2, +// hidden : true, +// dataIndex : 'structureId', +// sortable : true +// }, +// { +// text : "File", +// flex : 0.5, +// dataIndex : 'filePath', +// sortable : true, +// hidden : true +// }, +// { +// text : "PDB", +// flex : 0.4, +// dataIndex : 'name', +// sortable : true +// }, +// { +// text : "Symmetry", +// flex : 0.4, +// dataIndex : 'symmetry', +// sortable : true, +// editor : { +// xtype : 'combobox', +// typeAhead : true, +// triggerAction : 'all', +// selectOnTab : true, +// store : [ [ "P1", "P1" ], [ "P2", "P2" ], [ "P3", "P3" ], [ "P4", "P4" ], [ "P5", "P5" ], [ "P6", "P6" ], [ "P32", "P32" ], [ "P42", "P42" ], +// [ "P52", "P52" ], [ "P62", "P62" ], [ "P222", "P222" ] ], +// } +// }, { +// text : "Multiplicity", +// flex : 0.4, +// dataIndex : 'multiplicity', +// sortable : true, +// editor : { +// xtype : 'textfield' +// } +// +// }, { +// text : "Subunit", +// flex : 0.2, +// dataIndex : 'isSubunit', +// sortable : true, +// hidden : true +// }, { +// text : "Type", +// flex : 0.2, +// dataIndex : 'structureType', +// sortable : true, +// hidden : true +// }, +// +// { +// id : this.id + 'REMOVE', +// flex : 0.2, +// hidden : true, +// sortable : false, +// renderer : function(value, metaData, record, rowIndex, colIndex, store) { +// return BUI.getRedButton('REMOVE'); +// } +// }, ], +// +// listeners : { +// itemdblclick : function(dataview, record, item, e) { +// _this._editExperiment(record.raw.experimentId); +// }, +// cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { +// +// if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'REMOVE') { +// var dataAdapter = new BiosaxsDataAdapter(); +// dataAdapter.onSuccess.attach(function() { +// _this.pdbGrid.setLoading(false); +// _this.update(); +// }); +// dataAdapter.removeStructure(record.data.structureId); +// _this.pdbGrid.setLoading("Removing PDB file"); +// } +// +// } +// }, +// viewConfig : { +// getRowClass : function(record, rowIdx, params, store) { +// if (record.raw.isSubunit != null) { +// return "blue-row"; +// } +// } +// } +// }); +// +// return this.pdbGrid; +//}; +// +//MacromoleculeForm.prototype.getMolarityForm = function(macromolecule) { +// var _this = this; +// var data = []; +// for (var i = 0; i < BIOSAXS.proposal.macromolecules.length; i++) { +// var m = BIOSAXS.proposal.macromolecules[i]; +// if (m.macromoleculeId != macromolecule.macromoleculeId) { +// data.push(m); +// } +// // } - /** Adding information of buffer **/ - if (buffers.length > 0){ - buffers.unshift({ - name : "BUFFER", - start : 0, - experimentId : buffers[0].experimentId, - end : buffers[0].start - 1 - }); - } - - - return buffers; -}; - -PeakGrid.prototype._getTbar = function() { - var _this = this; - var actions = []; +// this.macromoleculeCombo = BIOSAXS_COMBOMANAGER.getComboMacromoleculeByMacromolecules(data, { +// width : 250, +// labelWidth : 100, +// margin : 10 +// }); +// +// return Ext.createWidget('form', { +// +// frame : false, +// border : 0, +// // padding : 15, +// width : 550, +// height : 350, +// items : [ { +// xtype : 'container', +// flex : 1, +// border : false, +// layout : 'anchor', +// defaultType : 'requiredtext', +// items : [ this.macromoleculeCombo, { +// xtype : 'numberfield', +// name : 'Ratio', +// id : _this.id + "ratio", +// fieldLabel : 'Number in assymmetric units', +// value : 1, +// decimalPrecision : 6, +// margin : 10 +// }, { +// xtype : 'textareafield', +// name : 'comments', +// fieldLabel : 'Comments', +// margin : 10, +// width : 400, +// value : "" +// +// } ] +// } ] +// }); +// +//}; +// +///******************************************************************************* +// * JAVASCRIPT DOC +// ******************************************************************************/ +//MacromoleculeForm.prototype.input = function() { +// return { +// macromolecule : DATADOC.getMacromolecule_10() +// }; +//}; +// +//MacromoleculeForm.prototype.test = function(targetId) { +// var macromoleculeForm = new MacromoleculeForm(); +// var panel = macromoleculeForm.getPanel(macromoleculeForm.input().macromolecule); +// panel.render(targetId); +//}; + +function ResultSummaryForm() { + this.radiationDamageThreshold = BUI.getRadiationDamageThreshold(); + this.qualityThreshold = BUI.getQualityThreshold(); - actions.push(Ext.create('Ext.Action', { - icon : '../images/add.png', - text : 'Add Buffer', - disabled : false, - handler : function(widget, event) { - var window = new BufferWindow(); - window.onSuccess.attach(function(sender) { - _this.store.loadData(BIOSAXS.proposal.getBuffers()); - }); - window.draw({}); - } - })); - return actions; -}; + /** Data clusters with bufers **/ + this.clusterByBuffers = false; + + /** Visualization are groupeb by concenttrations. Ex: 4.5mg/ml and 4.7mg/ml will be clusterized together **/ + this.collapseConcentrations = true; + + this.summaryHeight = 350; + this.id = BUI.id(); -PeakGrid.prototype.getPanel = function(buffers) { var _this = this; - this.peakCount = 0; - this.store = Ext.create('Ext.data.Store', { - fields : ['name', {name:'start', type : 'int'}, {name:'end', type : 'int'}], - data : buffers - - }); - - this.store.sort('start'); - var type = 'Ext.grid.Panel'; - if (this.searchBar == true) { - type = 'Ext.ux.LiveSearchGridPanel'; - } - this.grid = Ext.create(type, { - store : this.store, - height : this.height, - width : this.width, - margin : 5, - columns : [ - { - text : '', - dataIndex : 'name', - width : 100, - hidden : _this.showExtendedColumns, - renderer : function(val, y, sample) { - if (sample.data.name == "BUFFER") - return "BUFFER"; - _this.peakCount++; - return "Peak #" + _this.peakCount; - } - - - }, - { - text : 'Peaks', - dataIndex : 'start', - sortable : true, - width : 100, - hidden: !_this.showExtendedColumns, - renderer : function(val, y, sample) { - return "From " + Number(sample.raw.start) + " to " + Number(sample.raw.end); - } - }, - { - text : 'Frames', - hidden : _this.showExtendedColumns, - columns : [ - { - text : 'Start', - dataIndex : 'start', - sortable : true, - hidden : _this.showExtendedColumns, - width : 100, - renderer : function(val, y, sample) { - return Number(val); - } - },{ - text : 'End', - dataIndex : 'end', - width : 100, - hidden : _this.showExtendedColumns, - renderer : function(val, y, sample) { - return Number(val); - } - },{ - text : 'Total', - dataIndex : 'end', - width : 100, - hidden : _this.showExtendedColumns, - renderer : function(val, y, sample) { - return "" + (sample.raw.end - sample.raw.start) + " frames"; - } - } - ] - } -// , -// { -// text : '', -// hidden : _this.showExtendedColumns, -// renderer : function(val, x, sample) { -// if (sample != null) { -// return BUI.getZipHTMLByFrameRangeId(sample.raw.experimentId, sample.raw.start, sample.raw.end); -// } -// }, -// width : 100 -// } - ], - flex : 1, - viewConfig : { - stripeRows : true, - getRowClass : function(record, rowIdx, params, store) { - if (record.raw.name == "BUFFER") { - return "blue-row"; - } - } - } + this.qualityControlResultsWidget = new QualityControlResultsWidget({ + qualityThreshold : this.radiationDamageThreshold, + radiationDamageThreshold : this.qualityThreshold + + }); + this.qualityControlResultsWidget.onQualityChanged.attach(function(sender, value) { + _this.qualityThreshold = value; + _this.thresholdsChanged(); }); - /** Adding the tbar **/ - if (this.tbar) { - this.grid.addDocked({ - xtype : 'toolbar', - items : this._getTbar() - }); - } - return this.grid; -}; + this.qualityControlResultsWidget.onRadiationDatamageChanged.attach(function(sender, value) { + _this.radiationDamageThreshold = value; + _this.thresholdsChanged(); -PeakGrid.prototype.input = function() { - return []; -}; + }); + this.concentrationHTMLTableWidget = new ConcentrationHTMLTableWidget({ + height : 250, + showBufferColumns : this.clusterByBuffers + }); -PeakGrid.prototype.test = function(targetId) { - var PeakGrid = new PeakGrid({ - width : 800, + this.plot = new BoxWhiskerGraph({ + targetId : _this.id + '_boxPlot', height : 350, - collapsed : false, - tbar : true + width : 450, + maxBoxWidth : 25 }); - var panel = PeakGrid.getPanel([]); - panel.render(targetId); -}; - -/** - * Macromolecule Grid showing macromolecules and adding anb updating buttons - * - * @height - * @maxHeight - * @width - * @cssFontStyle - * @searchBar makes this grid as Ext.ux.LiveSearchGridPanel - * @tbar top bar containing "Add" and "Update From SMIS" button - * @collapsed - * @collapsible - * @btnEditVisible - * @btnRemoveVisible - * @multiselect makes it multiselect using Ext.selection.CheckboxModel - * - * #onSelected - * #onMacromoleculesChanged - */ -function MacromoleculeGrid(args) { - this.height = 500; - this.width = 500; - this.id = BUI.id(); - this.maxHeight = this.height; + this.rangePlot = new RangeWhiskerGraph({ + targetId : _this.id + '_rangePlot', + height : 350, + width : 450, + maxBoxWidth : 25 + }); +} - this.searchBar = false; - this.tbar = false; +ResultSummaryForm.prototype.thresholdsChanged = function() { + var parsedData = this.prepareData(this.rawData); - this.collapsible = true; - this.collapsed = true; + var filtered = JSON.parse(JSON.stringify(parsedData)); + filtered.concentration.concentrations = []; + for ( var conc in parsedData.concentration.concentrations) { + if (parsedData.concentration.concentrations[conc].calculation.rgGnom.validNumber > 0) { + filtered.concentration.concentrations.push(parsedData.concentration.concentrations[conc]); + } + } - this.btnEditVisible = true; - this.btnRemoveVisible = false; - this.multiselect = false; + this.plotWhisker(filtered); + this.plotRange(filtered); - /** Font style applied to the acronym column **/ - this.cssFontStyle = null; + this.concentrationHTMLTableWidget.refresh(parsedData); +}; - if (args != null) { - if (args.height != null) { - this.height = args.height; - this.maxHeight = this.height; - } - if (args.maxHeight != null) { - this.maxHeight = args.maxHeight; - } - if (args.width != null) { - this.width = args.width; - } - if (args.cssFontStyle != null) { - this.cssFontStyle = args.cssFontStyle; - } +/** Given a frame object (object returned by analyzeFrames()) and depending of the threshold indicates if a datacollection has radiation damage **/ +ResultSummaryForm.prototype.hasRadiationDamage = function(frameObject) { + var bb = frameObject.bufferBeforeFramesMerged / frameObject.framesCount; + var ba = frameObject.bufferAfterFramesMerged / frameObject.framesCount; + var mol = frameObject.framesMerge / frameObject.framesCount; + return !((bb >= this.radiationDamageThreshold) && (ba >= this.radiationDamageThreshold) && (mol >= this.radiationDamageThreshold)); +}; - if (args.searchBar != null) { - this.searchBar = args.searchBar; - } - if (args.tbar != null) { - this.tbar = args.tbar; - } - if (args.collapsible != null) { - this.collapsible = args.collapsible; - } - if (args.collapsed != null) { - this.collapsed = args.collapsed; - } - if (args.btnEditVisible != null) { - this.btnEditVisible = args.btnEditVisible; - } - if (args.btnRemoveVisible != null) { - this.btnRemoveVisible = args.btnRemoveVisible; - } - if (args.multiselect != null) { - this.multiselect = args.multiselect; - } +/** Return (frameObject) an object with the information about the frames for a data collection**/ +ResultSummaryForm.prototype.analyzeFrames = function(dataCollectionRow) { + return { + bufferAfterFramesMerged : dataCollectionRow.bufferAfterFramesMerged, + bufferBeforeFramesMerged : dataCollectionRow.bufferBeforeFramesMerged, + framesCount : dataCollectionRow.framesCount, + framesMerge : dataCollectionRow.framesMerge + }; +}; + +ResultSummaryForm.prototype.detectDataCollectionWarnings = function(dataCollectionRow) { + var frameObject = this.analyzeFrames(dataCollectionRow); + var warnings = { + count : 0, + type : [] + }; + + if (this.hasRadiationDamage(frameObject)) { + warnings.count = warnings.count + 1; + warnings.type.push("RADIATION DAMAGE"); } - this.onSelected = new Event(); - - this.onMacromoleculesChanged = new Event(); -} + if (Number(dataCollectionRow.quality) < this.qualityThreshold) { + warnings.count = 1;//warnings.count + 1; + warnings.type.push("Quality <" + this.qualityThreshold); + } + return warnings; +}; +/** Return array composed by {concentration} objects **/ +ResultSummaryForm.prototype.getConcentrations = function(data) { + var concentrationsId = {}; + for ( var i = 0; i < data.length; i++) { + var warning = this.detectDataCollectionWarnings(data[i]); + var id = data[i].conc;// + "_" + data[i].bufferId; + if (this.clusterByBuffers) { + id = data[i].conc + "_" + data[i].bufferId; + } + if (concentrationsId[id] == null) { + concentrationsId[id] = { + id : id, + concentration : Number(data[i].conc).toFixed(2), + bufferId : data[i].bufferId, + bufferAcronym : data[i].bufferAcronym, + rgGuinier : [], + i0Guinier : [], + rgGnom : [], + dMax : [], + quality : [], + frames : [], + frames_warning : warning.count + }; + } else { + concentrationsId[id].frames_warning = concentrationsId[id].frames_warning + warning.count; + } + concentrationsId[id].frames.push(data[i]); -MacromoleculeGrid.prototype.edit = function(macromolecule) { - var _this = this; - var window = new MacromoleculeWindow(); - window.onSave.attach(function(sender) { - _this.store.loadData(BIOSAXS.proposal.getMacromolecules()); - _this.onMacromoleculesChanged.notify(); - }); - window.draw(macromolecule); -}; + if (warning.count == 0) { + concentrationsId[id].rgGuinier.push(data[i].rgGuinier); + concentrationsId[id].i0Guinier.push(data[i].I0); + concentrationsId[id].quality.push(data[i].quality); + concentrationsId[id].rgGnom.push(data[i].rgGnom); + concentrationsId[id].dMax.push(data[i].dmax); + } -MacromoleculeGrid.prototype.getTbar = function() { - var _this = this; - var actions = []; + } + var concentrations = []; + for ( var item in concentrationsId) { + if (concentrationsId.hasOwnProperty(item)) { + concentrations.push({ + concentration : concentrationsId[item].concentration, + id : item, + bufferId : Number(concentrationsId[item].bufferId).toFixed(2), + bufferAcronym : concentrationsId[item].bufferAcronym, + rgGuinier : concentrationsId[item].rgGuinier, + /** Frames **/ + frames : concentrationsId[item].frames, + frames_warning : concentrationsId[item].frames_warning, + /** Calculation **/ + calculation : { + rgGuinier : BUI.getStandardDeviation(concentrationsId[item].rgGuinier), + i0Guinier : BUI.getStandardDeviation(concentrationsId[item].i0Guinier), + quality : BUI.getStandardDeviation(concentrationsId[item].quality), + rgGnom : BUI.getStandardDeviation(concentrationsId[item].rgGnom), + dMax : BUI.getStandardDeviation(concentrationsId[item].dMax) - actions.push(Ext.create('Ext.Action', { - icon : '../images/add.png', - text : 'Add macromolecule', - disabled : false, - handler : function(widget, event) { - _this.edit(); - } - })); - actions.push("->"); - actions.push(Ext.create('Ext.Action', { - icon : '../images/folder_go.png', - text : 'Update From SMIS', - tooltip : "Retrieve all the macromolecules of your proposal from SMIS database", - disabled : false, - handler : function(widget, event) { - _this.grid.setLoading("Connecting to SMIS"); - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - BIOSAXS.proposal.setMacromolecules(data.macromolecules); - _this.refresh(BIOSAXS.proposal.macromolecules); - _this.grid.setLoading(false); - }); - adapter.onError.attach(function(sender, data) { - _this.grid.setLoading(false); + } }); - adapter.updateDataBaseFromSMIS(); } - })); - return actions; -}; + } -MacromoleculeGrid.prototype.deselectAll = function() { - this.grid.getSelectionModel().deselectAll(); + return { + concentrations : concentrations + }; }; -MacromoleculeGrid.prototype.selectById = function(macromoleculeId) { - this.grid.getSelectionModel().deselectAll(); - for ( var i = 0; i < this.grid.getStore().data.items.length; i++) { - var item = this.grid.getStore().data.items[i].raw; - if (item.macromoleculeId == macromoleculeId) { - this.grid.getSelectionModel().select(i); +ResultSummaryForm.prototype.prepareData = function(data) { + /** Return array composed by {acronym, bufferId} objects **/ + function getBuffers(data) { + var buffersId = {}; + for ( var i = 0; i < data.length; i++) { + buffersId[data[i].bufferId] = data[i].acronym; + } + var buffers = []; + for ( var id in buffersId) { + if (buffersId.hasOwnProperty(id)) { + buffers.push({ + acronym : buffersId[id], + bufferId : id + }); + } } + return buffers; } -}; -MacromoleculeGrid.prototype.refresh = function(macromolecules) { - this.store.loadData(macromolecules, false); + /** Get a string with all the concentrations **/ + function getConcentrationString(parseConcentrations) { + var concentrations = []; + for ( var i = 0; i < parseConcentrations.concentrations.length; i++) { + concentrations.push(parseConcentrations.concentrations[i].concentration + " mg/ml "); + } + return concentrations.toString(); + } + + var parseConcentrations = this.getConcentrations(data); + + return { + dataCollectionCount : data.length, + buffers : getBuffers(data), + concentration : parseConcentrations, + concentrationLabel : getConcentrationString(parseConcentrations) + }; }; -MacromoleculeGrid.prototype.getColumns = function() { - var _this = this; - var columns = [ - { - text : 'Acronym', - dataIndex : 'acronym', - id : this.id + "acronym", - flex : 1, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - if (_this.cssFontStyle != null) { - return "" + value + ""; +ResultSummaryForm.prototype.getDataForWhisker = function(data) { + var clusters = []; + + var concentrations = {}; + var i = 0; + var conc = 0; + if (this.collapseConcentrations) { + for (i = 0; i < data.concentration.concentrations.length; i++) { + conc = data.concentration.concentrations[i]; + var concentration = Number(conc.concentration).toFixed(0); + if (concentrations[concentration] == null) { + concentrations[concentration] = {}; + concentrations[concentration].concentration = concentration; + concentrations[concentration].calculation = {}; + concentrations[concentration].calculation.rgGuinier = {}; + concentrations[concentration].calculation.rgGuinier.values = []; + concentrations[concentration].calculation.rgGuinier.values = conc.calculation.rgGuinier.values; + concentrations[concentration].calculation.rgGnom = {}; + concentrations[concentration].calculation.rgGnom.values = []; + concentrations[concentration].calculation.rgGnom.values = conc.calculation.rgGnom.values; + } else { + concentrations[concentration].calculation.rgGuinier.values = concentrations[concentration].calculation.rgGuinier.values + .concat(conc.calculation.rgGuinier.values); + concentrations[concentration].calculation.rgGnom.values = concentrations[concentration].calculation.rgGnom.values + .concat(conc.calculation.rgGnom.values); } - return value; } - }, { - text : 'Name', - dataIndex : 'name', - id : this.id + "name", - flex : 1, - hidden : true - } ]; - if (this.btnEditVisible) { - columns.push({ - id : _this.id + 'buttonEditMacromolecule', - width : 85, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - if (_this.btnEditVisible) { - return BUI.getGreenButton('EDIT'); - } - return null; + /** From object to array **/ + var array = []; + for ( var key in concentrations) { + if (concentrations.hasOwnProperty(key)) { + array.push(concentrations[key]); } + } + data.concentration.concentrations = array; + } + + for (i = 0; i < data.concentration.concentrations.length; i++) { + conc = data.concentration.concentrations[i]; + clusters.push({ + name : conc.concentration + "mg/ml", + concentration : Number(conc.concentration), + x : Number(conc.concentration), + classes : [] + }); + clusters[clusters.length - 1].classes.push({ + name : "Guinier", + color : '#9A2EFE', + values : conc.calculation.rgGuinier.values + + }); + clusters[clusters.length - 1].classes.push({ + name : "P(r)", + color : '#2E64FE', + values : conc.calculation.rgGnom.values + }); } - if (this.btnRemoveVisible) { - columns.push({ - id : _this.id + 'buttonRemoveMacromolecule', - width : 85, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - if (_this.btnRemoveVisible) { - return BUI.getRedButton('REMOVE'); - } - return null; - } + return { + clusters : clusters.sort(function(a, b) { + return a.concentration - b.concentration; + }) + }; +}; + +ResultSummaryForm.prototype.getDataForWhiskerQuality = function(data) { + var clusters = []; + + for ( var i = 0; i < data.concentration.concentrations.length; i++) { + var conc = data.concentration.concentrations[i]; + clusters.push({ + name : conc.concentration + "mg/ml", + classes : [] + }); + clusters[clusters.length - 1].classes.push({ + name : "Quality", + values : conc.calculation.quality.values + }); } - return columns; + return { + clusters : clusters + }; +}; + +ResultSummaryForm.prototype.plotQualityWhisker = function(parsedData) { + this.qualityPlot.refresh(this.getDataForWhiskerQuality(parsedData)); }; +ResultSummaryForm.prototype.plotWhisker = function(parsedData) { + this.plot.refresh(this.getDataForWhisker(parsedData)); +}; -/** Returns the grid **/ -MacromoleculeGrid.prototype.getPanel = function() { +ResultSummaryForm.prototype.plotRange = function(parsedData) { + this.rangePlot.refresh(this.getDataForWhisker(parsedData)); +}; + +ResultSummaryForm.prototype.getPanel = function(data) { var _this = this; + _this.rawData = data; + var parsedData = this.prepareData(data); - this.store = Ext.create('Ext.data.Store', { - fields : [ 'macromoleculeId', 'name', 'acronym' ] - }); + this.panel = Ext + .createWidget( + 'form', + { + bodyPadding : 20, + frame : false, + border : 0, + width : this.width, + height : this.summaryHeight + 1000, + items : [ { + xtype : 'container', + layout : 'hbox', + items : [ { + xtype : 'container', + flex : 1, + border : false, + layout : 'anchor', + defaultType : 'textfield', + items : [ + _this.qualityControlResultsWidget.getPanel(), + { + xtype : 'fieldset', + width : 950, + margin : "20, 0 0 0", + height : this.summaryHeight + 500, + items : [ + { + html : "
Concentration Analysis
", + border : 0, + width : 900 - var type = 'Ext.grid.Panel'; - if (this.searchBar == true) { - type = 'Ext.ux.LiveSearchGridPanel'; - } + }, + { + html : this.concentrationHTMLTableWidget.getPanel(parsedData), + border : 0, + width : 900, + margin : "10, 0 0 10" - this.selModel = Ext.create('Ext.selection.RowModel', { -// allowDeselect : true, -// mode : 'MULTI', - listeners : { - selectionchange : function(sm, selections) { - var selected = []; - for (var i = 0; i < selections.length; i++) { - selected.push(selections[i].raw); - } - _this.onSelected.notify(selected); - } - } - }); + }, + { + xtype : 'container', + layout : 'vbox', + border : 5, + items : [ + { + html : "
Rg based on Guinier and Gnom
", + border : 8, + width : 900, + margin : "20 0 0 10" - this.grid = Ext.create(type, { - id : this.id, - title : 'Macromolecules', - collapsible : this.collapsible, - collapsed : this.collapsed, - store : this.store, - height : this.height, - maxHeight : this.maxHeight, - selModel : this.selModel, - columns : this.getColumns(), - width : this.width, - viewConfig : { - stripeRows : true, - listeners : { - 'celldblclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - _this.edit(BIOSAXS.proposal.getMacromoleculeById(record.data.macromoleculeId)); - }, - 'cellclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEditMacromolecule') { - _this.edit(BIOSAXS.proposal.getMacromoleculeById(record.data.macromoleculeId)); - } - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemoveMacromolecule') { - BUI.showBetaWarning(); - } - } + }, { + xtype : 'container', + layout : 'hbox', + items : [ { + xtype : 'container', + layout : 'vbox', + items : [ { + html : "
", + border : 0, + width : this.plot.width, + padding : "10 0 0 20", + listeners : { + afterrender : function() { + _this.plotWhisker(parsedData); - } - } - }); + } + } + }, { + html : "
Concentration (mg/ml)
", + width : 450, + border : 0, + margin : "-50 0 0 0" + + } ] + }, { + xtype : 'container', + layout : 'vbox', + items : [ { + html : "
", + border : 0, + width : this.rangePlot.width, + padding : "10 0 0 10", + listeners : { + afterrender : function() { + _this.plotRange(parsedData); + } + } + }, { + html : "
Concentration (mg/ml)
", + width : 450, + border : 0, + margin : "-50 0 0 0" + + } ] + } ] + } ] + } ] + } ] + } + + ] + } ] + }); + return this.panel; - /** Adding the tbar **/ - if (this.tbar) { - this.grid.addDocked({ - xtype : 'toolbar', - items : this.getTbar() - }); - } - return this.grid; }; -MacromoleculeGrid.prototype.input = function() { +ResultSummaryForm.prototype.input = function() { return { - proposal : DATADOC.getProposal_10() + data : DATADOC.getData_3367() }; }; -MacromoleculeGrid.prototype.test = function(targetId) { - var macromoleculeGrid = new MacromoleculeGrid({ - width : 800, - height : 350, - collapsed : false, - tbar : true - }); - - BIOSAXS.proposal = new Proposal(macromoleculeGrid.input().proposal); - var panel = macromoleculeGrid.getPanel(BIOSAXS.proposal.macromolecules); +ResultSummaryForm.prototype.test = function(targetId) { + var resultSummaryForm = new ResultSummaryForm(); + var panel = resultSummaryForm.getPanel(resultSummaryForm.input().data); panel.render(targetId); + }; -/** - * Shows measurements with their attributes as specimen, exposure temperature, - * volume to load, transmission etc... - * - * @addBtnMultipleEdit: if true add a button for changing measurements' - * parameters by choosing multiple measurements. It opens - * MultipleEditMeasurementGridWindow - * @collapsed: if true it doesn't show buffer's measurements - * @editor: hashmap containing columns to be edited. It is an array of a json - * like editor of Ext - * @selModel - * @collapseBtnEnable - * @removeBtnEnabled Ext.selection.RowModel - * @addBtnEnable - * @updateRowEnabled true/false if update plugin is set to the grid - * @showTitle - * @title - * @isStatusColumnHidden - * @isPriorityColumnHidden - * @isTimeColumnHidden - * @estimateTime - * @margin - * @tbar - * @height - * @maxHeight - * @minHeight - * @width - * @maxWidth - * @resizable - * @experimentColorBased when colors for buffers and macromolecules are not - * selected by the proposal but by experiment, so the - * number of colors is smaller +/** + * Example form + * + * @witdh + * @height + */ +function RigibBodyModelingForm(args) { + this.id = BUI.id(); + this.width = 700; + this.height = 500; + + if (args != null) { + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + } + + var _this = this; + this.rigidBodyGrid = new AprioriRigidBodyGrid(); + + this.rigidBodyGrid.onUploadFile.attach(function(sender, type, title){ + _this._openUploadDialog(_this.macromolecule.macromoleculeId, type, title); + }); + + this.rigidBodyGrid.onRemove.attach(function(sender, type, title){ + _this._update(); + }); + + this.onSave = new Event(this); + +} + +RigibBodyModelingForm.prototype._getItems = function() { + var _this = this; + + + return [ { + xtype : 'label', + forId : 'myFieldId', + text : 'Information for model fit, mixture analysis and rigid body modeling', + margin : '15 0 20 10', + cls : "inline-help" + }, + this.rigidBodyGrid.getPanel(), + { + xtype : 'label', + forId : 'myFieldId', + text : 'Distance restraints may be imposed on the model using contacts conditions file (OPTIONAL)', + margin : '25 0 5 10', + cls : "inline-help" + }, + { + xtype : 'container', + layout : 'hbox', + items : [ { + xtype : 'container', + border : false, + layout : 'hbox', + items : [ { + xtype : 'label', + forId : 'myFieldId', + text : 'Contact Description File: (Optional)', + width : 150, + margin : '10 0 0 10' + }, { + id : this.id + "contactsDescriptionFilePath", + xtype : 'textfield', + hideLabel : true, + margin : '10 0 0 0', + width : 200, + disabled: true + }, { + text : 'Upload', + xtype : 'button', + margin : "10 0 0 10", + width : 80, + handler : function() { + + _this._openUploadDialog(_this.macromolecule.macromoleculeId, "CONTACTS", "Upload Contact Description File"); + } + }, { + text : 'Remove', + id : _this.id + "_remove", + xtype : 'button', + margin : "10 0 0 10", + width : 80, + handler : function() { + _this.macromolecule.contactsDescriptionFilePath = null; + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, proposal) { + /** Updating the proposal global object **/ + BIOSAXS.proposal.setItems(proposal); + _this.panel.setLoading(false); + + var saved = BIOSAXS.proposal.getMacromoleculeByAcronym(_this.macromolecule.acronym); + /** Refreshing to check that everything is ok **/ + _this.refresh(saved); + _this.onSave.notify(saved); + }); + + _this.panel.setLoading("Saving Macromolecule") + adapter.saveMacromolecule(_this.macromolecule); + } + } ] + } ] + }, { + xtype : 'panel', + html : "Go to SASREF manual for further information", + margin : "10 0 0 160", + border : 0 + + }, + { + xtype : 'checkbox', + margin : '10 0 0 5', + boxLabel : "I want rigid body modeling run on this stuff", + checked : true, + width : 300 + } ] + +}; + +/** Because update is a jsp page we don't know if the user has uploaded a file or not then we need to refresh **/ +RigibBodyModelingForm.prototype._update = function(macromoleculeId, type, title) { + var _this = this; + BIOSAXS.proposal.onInitialized.attach(function() { + if (BIOSAXS.proposal != null) { + _this.refresh(BIOSAXS.proposal.getMacromoleculeById(_this.macromolecule.macromoleculeId)); + _this.panel.setLoading(false); + } + }); + this.panel.setLoading(); + BIOSAXS.proposal.init(); +}; + +RigibBodyModelingForm.prototype._openUploadDialog = function(macromoleculeId, type, title) { + var _this = this; + function onClose() { + w.destroy(); + _this._update(); + + } + + var w = Ext.create('Ext.window.Window', { + title : title, + height : 200, + width : 400, + modal : true, + buttons : [ { + text : 'Close', + handler : function() { + onClose(); + } + } ], + layout : 'fit', + items : { + html : "" + }, + listeners : { + onEsc : function() { + onClose(); + }, + close : function() { + onClose(); + } + } + }).show(); +}; + +RigibBodyModelingForm.prototype._getButtons = function() { + return []; +}; + +RigibBodyModelingForm.prototype.getPanel = function() { + var _this = this; + this.panel = Ext.create('Ext.form.Panel', { + width : this.width, + height : this.height, + margin : 10, + border : 1, + defaultType : 'textfield', + items : this._getItems(), + buttons : this._getButtons(), + listeners : { + afterrender : function(){ + _this._populate(); + + } + } + }); + return this.panel; +}; + +/** Populates could be call when the DOM is not filled yet **/ +RigibBodyModelingForm.prototype._populate = function() { + if (this.macromolecule != null){ + if (Ext.getCmp(this.id + "contactsDescriptionFilePath") != null){ + if (this.macromolecule.contactsDescriptionFilePath != null){ + Ext.getCmp(this.id + "contactsDescriptionFilePath").setValue(this.macromolecule.contactsDescriptionFilePath); + Ext.getCmp(this.id + "_remove").enable(); + } + else{ + Ext.getCmp(this.id + "_remove").disable(); + Ext.getCmp(this.id + "contactsDescriptionFilePath").setValue(""); + + } + } + } +}; + +/** It populates the form * */ +RigibBodyModelingForm.prototype.refresh = function(macromolecule) { + this.macromolecule = macromolecule; + this.rigidBodyGrid.refresh(macromolecule); + this._populate(); +}; + +RigibBodyModelingForm.prototype.input = function() { + return {}; +}; + + +/** It populates the form **/ +RigibBodyModelingForm.prototype.test = function(targetId) { + var macromoleculeForm = new RigibBodyModelingForm(); + var panel = macromoleculeForm.getPanel(); + panel.render(targetId); +}; + + +/** + * Same form as MX part * - * #onClick #onSelected #onRemoved #onUpdateTime #onMeasurementChanged - * #onExperimentChanged + * @creationMode if true a create button appears instead of save + * @showTitle true or false */ -function MeasurementGrid(args) { +function ShipmentForm(args) { this.id = BUI.id(); - this.height = 500; - this.width = 900; - - this.maxWidth = 1200; - this.maxHeight = 600; - this.minHeight = 500; - - this.unitsFontSize = 9; - this.title = "Measurements"; - this.estimateTime = false; - this.collapsed = true; - this.tbar = true; - + this.creationMode = false; this.showTitle = true; - this.resizable = true; - this.updateRowEnabled = true; - - /** - * Hash map containing the keys of the editable columns. Ex: - * 'exposureTemperature' * - */ - this.editor = { - comments : { - xtype : 'textfield', - allowBlank : true + if (args != null) { + if (args.creationMode != null) { + this.creationMode = args.creationMode; } - }; + if (args.showTitle != null) { + this.showTitle = args.showTitle; + } + } - this.isTimeColumnHidden = false; - this.isStatusColumnHidden = false; - this.isPriorityColumnHidden = true; - this.margin = "0 0 0 0"; + this.onSaved = new Event(this); +} - this.addBtnEnable = true; - this.sorter = [ { - property : 'priority', - direction : 'ASC' - } ]; +ShipmentForm.prototype.fillStores = function() { + this.panel.setLoading("Loading Labcontacts from database"); + this.labContactForSendingStore.loadData(BIOSAXS.proposal.getLabcontacts(), false); + this.labContactForReturnStore.loadData(BIOSAXS.proposal.getLabcontacts(), false); + this.panel.setLoading(false); + if (this.shipment != null) { + this.setShipment(this.shipment); + } +}; - this.removeBtnEnabled = false; - this.collapseBtnEnable = true; - this.addBtnMultipleEdit = false; - this.sortingBtnEnable = false; +ShipmentForm.prototype.draw = function(targetId) { + this.getPanel().render(targetId); +}; +ShipmentForm.prototype.setShipment = function(shipment) { + this.shipment = shipment; var _this = this; - this.selModel = Ext.create('Ext.selection.RowModel', { - allowDeselect : true, - mode : 'MULTI', - listeners : { - selectionchange : function(sm, selections) { - var selected = []; - for (var i = 0; i < selections.length; i++) { - selected.push(selections[i].raw); - } - _this.onSelected.notify(selected); - } - } - }); - - if (args != null) { - - if (args.selModel != null) { - this.selModel = args.selModel; - } + Ext.getCmp(_this.id + "shippingName").setValue(shipment.json.shippingName); + Ext.getCmp(_this.id + "shippingStatus").setValue(shipment.json.shippingStatus); + Ext.getCmp(_this.id + "comments").setValue(shipment.json.comments); + if (shipment.json.sendingLabContactVO != null) { + this.labContactsSendingCombo.setValue(shipment.json.sendingLabContactVO.labContactId); + } + if (shipment.json.returnLabContactVO != null) { + this.labContactsReturnCombo.setValue(shipment.json.returnLabContactVO.labContactId); + } - if (args.removeBtnEnabled != null) { - this.removeBtnEnabled = args.removeBtnEnabled; - } +}; - if (args.addBtnMultipleEdit != null) { - this.addBtnMultipleEdit = args.addBtnMultipleEdit; - } +ShipmentForm.prototype._saveShipment = function() { + var _this = this; + var shippingId = null; + if (this.shipment != null) { + shippingId = this.shipment.json.shippingId; + } + var json = { + shippingId : shippingId, + name : Ext.getCmp(_this.id + "shippingName").getValue(), + status : Ext.getCmp(_this.id + "shippingStatus").getValue(), + sendingLabContactId : Ext.getCmp(_this.id + "shipmentform_sendingLabContactId").getValue(), + returnLabContactId : Ext.getCmp(_this.id + "returnLabContactId").getValue(), + returnCourier : Ext.getCmp(_this.id + "returnCourier").getValue(), + courierAccount : Ext.getCmp(_this.id + "courierAccount").getValue(), + BillingReference : Ext.getCmp(_this.id + "BillingReference").getValue(), + dewarAvgCustomsValue : Ext.getCmp(_this.id + "dewarAvgCustomsValue").getValue(), + dewarAvgTransportValue : Ext.getCmp(_this.id + "dewarAvgTransportValue").getValue(), + comments : Ext.getCmp(_this.id + "comments").getValue() + }; - // if (args.experimentColorBased != null) { - // this.experimentColorBased = args.experimentColorBased; - // } + var dataAdapter = new BiosaxsDataAdapter(); + dataAdapter.onSuccess.attach(function(sender, shipment) { + window.location = BUI.getShippingURL(shipment.shippingId); + }); - if (args.collapsed != null) { - this.collapsed = args.collapsed; - } - if (args.resizable != null) { - this.resizable = args.resizable; - } + dataAdapter.onError.attach(function(sender, error) { + _this.onError.notify(error); + }); - if (args.editor != null) { - this.editor = args.editor; - } + /** Cheking params **/ + if (json.name == "") { + BUI.showError("Name field is mandatory"); + return; + } - if (args.collapseBtnEnable != null) { - this.collapseBtnEnable = args.collapseBtnEnable; - } + if (json.sendingLabContactId == null) { + BUI.showError("Lab contact for sending field is mandatory"); + return; + } - if (args.addBtnEnable != null) { - this.addBtnEnable = args.addBtnEnable; - } - if (args.sortingBtnEnable != null) { - this.sortingBtnEnable = args.sortingBtnEnable; - } + if (json.returnLabContactId == null) { + BUI.showError("Lab contact for return field is mandatory"); + return; + } - if (args.isPriorityColumnHidden != null) { - this.isPriorityColumnHidden = args.isPriorityColumnHidden; - } + dataAdapter.createShipment(json.shippingId, json.name, json.status, json.comments, json.sendingLabContactId, json.returnLabContactId, + json.returnCourier, json.courierAccount, json.BillingReference, json.dewarAvgCustomsValue, json.dewarAvgTransportValue); - if (args.width != null) { - this.width = args.width; - } +}; - if (args.updateRowEnabled != null) { - this.updateRowEnabled = args.updateRowEnabled; - } +ShipmentForm.prototype.getPanel = function(shipment) { + var _this = this; + this.shipment = shipment; + var required = '*'; + var buttons = []; - if (args.showTitle != null) { - this.showTitle = args.showTitle; - if (this.showTitle == false) { - this.title = null; + if (_this.creationMode) { + buttons.push({ + text : 'Create', + scope : this, + handler : function() { + _this._saveShipment(); } - } - - if (args.height != null) { - this.height = args.height; - } - - if (args.maxHeight != null) { - this.maxHeight = args.maxHeight; - } - - if (args.minHeight != null) { - this.minHeight = args.minHeight; - } + }); + } else { + buttons.push({ + text : 'Save', + scope : this, + handler : function() { + _this._saveShipment(); + } + }); - if (args.maxWidth != null) { - this.maxWidth = args.maxWidth; - } + } - if (args.isStatusColumnHidden != null) { - this.isStatusColumnHidden = args.isStatusColumnHidden; - } - if (args.isTimeColumnHidden != null) { - this.isTimeColumnHidden = args.isTimeColumnHidden; - } + this.labContactForSendingStore = Ext.create('Ext.data.Store', { + fields : [ 'cardName', 'labContactId' ] + }); - if (args.title != null) { - this.title = args.title; - } - if (args.estimateTime != null) { - this.estimateTime = args.estimateTime; - } + this.labContactForReturnStore = Ext.create('Ext.data.Store', { + fields : [ 'cardName', 'labContactId' ] + }); - if (args.margin != null) { - this.margin = args.margin; - } + // Create the combo box, attached to the states data store + this.labContactsSendingCombo = Ext.create('Ext.form.ComboBox', { + id : _this.id + "shipmentform_sendingLabContactId", + fieldLabel : 'Lab contact for sending', + afterLabelTextTpl : required, + store : this.labContactForSendingStore, + queryMode : 'local', + labelWidth : 200, + displayField : 'cardName', + valueField : 'labContactId' + }); - if (args.tbar != null) { - this.tbar = args.tbar; + this.labContactsReturnCombo = Ext.create('Ext.form.ComboBox', { + id : _this.id + "returnLabContactId", + fieldLabel : 'If No, Lab-Contact for Return', + afterLabelTextTpl : required, + store : this.labContactForReturnStore, + queryMode : 'local', + labelWidth : 200, + displayField : 'cardName', + valueField : 'labContactId', + listeners : { + change : function(x, newValue) { + for ( var i = 0; i < x.getStore().data.items.length; i++) { + if (x.getStore().data.items[i].raw.labContactId == newValue) { + Ext.getCmp(_this.id + "returnCourier").setValue(x.getStore().data.items[i].raw.defaultCourrierCompany); + Ext.getCmp(_this.id + "courierAccount").setValue(x.getStore().data.items[i].raw.courierAccount); + Ext.getCmp(_this.id + "BillingReference").setValue(x.getStore().data.items[i].raw.billingReference); + Ext.getCmp(_this.id + "dewarAvgCustomsValue").setValue(x.getStore().data.items[i].raw.dewarAvgCustomsValue); + Ext.getCmp(_this.id + "dewarAvgTransportValue").setValue(x.getStore().data.items[i].raw.dewarAvgTransportValue); + } + } + } } + }); - if (args.sorter != null) { - this.sorter = args.sorter; - } + if (this.panel == null) { + this.panel = Ext.create('Ext.form.Panel', { + bodyPadding : 5, + width : 600, + border : 1, + items : [ { + xtype : 'fieldset', + title : 'Details', + collapsible : false, + defaultType : 'textfield', + layout : 'anchor', + defaults : { + anchor : '100%' + }, + items : [ { + xtype : 'requiredtext', + fieldLabel : 'Shipment Label', + allowBlank : false, + name : 'shippingName', + id : _this.id + 'shippingName', + value : '', + anchor : '50%' + }, { + xtype : 'textareafield', + name : 'comments', + id : _this.id + 'comments', + fieldLabel : 'Comments', + value : '' + }, { + fieldLabel : 'Status', + readOnly : true, + id : _this.id + 'shippingStatus', + value : 'Opened', + anchor : '50%' + } ] + }, { + xtype : 'fieldset', + title : 'Lab-Contacts', + collapsible : false, + defaultType : 'textfield', + layout : 'anchor', + defaults : { + anchor : '100%' + }, + items : [ this.labContactsSendingCombo, this.labContactsReturnCombo ] + }, { + border : 0, + html : BUI.getWarningHTML("These informations are relevant for all shipments") + }, { + xtype : 'fieldset', + title : 'Courier accounts details for return', + collapsible : false, + layout : 'anchor', + defaults : { + anchor : '100%' + }, + items : [ { + xtype : 'textfield', + labelWidth : 400, + fieldLabel : 'Courier company for return (if ESRF sends a dewar back)', + id : _this.id + 'returnCourier', + value : '' + }, { + xtype : 'textfield', + labelWidth : 400, + fieldLabel : 'Courier account', + id : _this.id + 'courierAccount', + value : '' + }, { + xtype : 'textfield', + labelWidth : 400, + fieldLabel : 'Billing reference', + id : _this.id + 'BillingReference', + value : '' + }, { + xtype : 'numberfield', + labelWidth : 400, + fieldLabel : 'Average Customs value of a dewar (Euro)', + id : _this.id + 'dewarAvgCustomsValue', + value : '' + }, { + xtype : 'numberfield', + labelWidth : 400, + fieldLabel : 'Average Transport value of a dewar (Euro)', + id : _this.id + 'dewarAvgTransportValue', + value : '' + } ] + } ], + buttons : buttons + }); } - this.onClick = new Event(this); - this.onSelected = new Event(this); - this.onRemoved = new Event(this); - this.onUpdateTime = new Event(this); - this.onMeasurementChanged = new Event(this); - this.onExperimentChanged = new Event(this); -} - -MeasurementGrid.prototype._sortBy = function(sort) { - var _this = this; - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - _this.onExperimentChanged.notify(data); - _this.grid.setLoading(false); - // wizardWidget.window.close(); - }); - adapter.onError.attach(function(sender, data) { - _this.grid.setLoading(false); - alert("Oops, there was a problem"); - }); - _this.grid.setLoading("Sorting"); - adapter.sortMeasurements(this.experiments.experiments[0].experimentId, sort); + this.fillStores(); + if (this.showTitle) { + this.panel.setTitle('Create a new Shipment'); + } + return this.panel; }; -MeasurementGrid.prototype._getMenu = function() { - var _this = this; - if (this.tbar) { +ShipmentForm.prototype.input = function() { + return { + proposal : DATADOC.getProposal_10() - var items = []; - if (_this.addBtnEnable) { - items.push({ - icon : '../images/add.png', - text : 'Add measurements', - handler : function() { - _this._openAddMeasurementWindow(); - } - }); - } + }; +}; - if (_this.addBtnMultipleEdit) { - items.push({ - icon : '../images/Edit_16x16_01.png', - text : 'Multiple Edit', - handler : function() { - var multipleEditMeasurementGridWindow = new MultipleEditMeasurementGridWindow(); - multipleEditMeasurementGridWindow.onExperimentChanged.attach(function(sender, data) { - _this.onExperimentChanged.notify(data); - }); +ShipmentForm.prototype.test = function(targetId) { + var shipmentForm = new ShipmentForm({ + creationMode : true - multipleEditMeasurementGridWindow.draw(_this.measurements, _this.experiments); + }); + BIOSAXS.proposal = new Proposal(shipmentForm.input().proposal); + shipmentForm.getPanel().render(targetId); +}; + +/** + * #onSaved + */ +function StockSolutionForm(args) { + this.id = BUI.id(); + this.actions = []; - } - }); + if (args != null) { + if (args.actions != null) { + this.actions = args.actions; } + } + this.onSaved = new Event(this); +} - items.push("->"); +StockSolutionForm.prototype.getStockSolution = function() { + if (this.stockSolution != null) { + this.stockSolution.concentration = Ext.getCmp(this.id + "stockSolution_concentration").getValue(); + this.stockSolution.storageTemperature = Ext.getCmp(this.id + "stockSolution_storageTemperature").getValue(); + this.stockSolution.volume = Ext.getCmp(this.id + "stockSolution_volume").getValue(); + this.stockSolution.comments = Ext.getCmp(this.id + "stockSolution_comments").getValue(); + this.stockSolution.name = Ext.getCmp(this.id + "stockSolution_name").getValue(); + this.stockSolution.bufferId = this.bufferCombo.getValue(); - if (_this.sortingBtnEnable) { - var split = Ext.create('Ext.button.Split', { - text : 'Sort by', - // handle a click on the button itself - handler : function() { - // alert("The button was clicked"); - }, - menu : new Ext.menu.Menu({ - items : [ - { - text : 'First Created First Measured', - handler : function() { - _this._sortBy("FIFO"); - } - }, "-", { - text : 'Default', - handler : function() { - _this._sortBy("DEFAULT"); - } - } ] - }) - }); - items.push(split); + if (this.macromoleculeCombo.getValue() != null) { + this.stockSolution.macromoleculeId = this.macromoleculeCombo.getValue(); + } else { + this.stockSolution.macromolecule3VO = null; } - if (_this.collapseBtnEnable) { - items.push({ - text : 'Collapse buffers', - enableToggle : true, - scope : this, - toggleHandler : function(item, pressed) { - this.collapsed = pressed; - this.grid.getStore().loadData(this._prepareData(this.measurements, this.experiments), false); - }, - pressed : this.collapsed - }); + } else { + return { + concentration : Ext.getCmp(this.id + "stockSolution_concentration").getValue(), + storageTemperature : Ext.getCmp(this.id + "stockSolution_storageTemperature").getValue(), + volume : Ext.getCmp(this.id + "stockSolution_volume").getValue(), + comments : Ext.getCmp(this.id + "stockSolution_comments").getValue(), + name : Ext.getCmp(this.id + "stockSolution_name").getValue(), + bufferId : this.bufferCombo.getValue(), + macromoleculeId : this.macromoleculeCombo.getValue() + }; + } + return this.stockSolution; +}; + +StockSolutionForm.prototype.setStockSolution = function(stockSolution) { + if (stockSolution != null) { + if (stockSolution.macromoleculeId != null) { + this.macromoleculeCombo.setValue(stockSolution.macromoleculeId); } - var tb = Ext.create('Ext.toolbar.Toolbar', { - items : items - }); - return tb; + this.bufferCombo.setValue(stockSolution.bufferId); + Ext.getCmp(this.id + "stockSolution_concentration").setValue(this.stockSolution.concentration); + Ext.getCmp(this.id + "stockSolution_storageTemperature").setValue(this.stockSolution.storageTemperature); + Ext.getCmp(this.id + "stockSolution_volume").setValue(this.stockSolution.volume); + Ext.getCmp(this.id + "stockSolution_name").setValue(this.stockSolution.name); + Ext.getCmp(this.id + "stockSolution_comments").setValue(this.stockSolution.comments); } - return null; }; -/** Opens WizardWidget for adding new measurements * */ -MeasurementGrid.prototype._openAddMeasurementWindow = function(measurements, experiments) { - var _this = this; - var wizardWidget = new WizardWidget(); - wizardWidget.onFinished.attach(function(sender, result) { - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - _this.onExperimentChanged.notify(data); - _this.grid.setLoading(false); - wizardWidget.window.close(); - }); - wizardWidget.current.setLoading("ISPyB: Adding measurements"); - adapter.addMeasurements(result.name, "comments", result.data, _this.experiments.experiments[0].experimentId); +StockSolutionForm.prototype.getBufferCombo = function() { + this.bufferCombo = BIOSAXS_COMBOMANAGER.getComboBuffers(BIOSAXS.proposal.getBuffers(), { + labelWidth : 120, + margin : '0 0 10 0', + width : 220 + }); + return this.bufferCombo; +}; - wizardWidget.draw(null, new MeasurementCreatorStepWizardForm(BIOSAXS.proposal.getMacromolecules(), { - noNext : true - })); +StockSolutionForm.prototype.getMacromoleculeCombo = function() { + this.macromoleculeCombo = BIOSAXS_COMBOMANAGER.getComboMacromoleculeByMacromolecules(BIOSAXS.proposal.getMacromolecules(), { + labelWidth : 120, + margin : '0 0 10 0', + width : 220 + + }); + return this.macromoleculeCombo; }; -/******************************************************************************* - * Opens WizardWidget for adding new measurements - * - * @Measurements - * @Experiments experimentList Object - ******************************************************************************/ -MeasurementGrid.prototype._prepareData = function(measurements, experiments) { - var data = []; - for (var i = 0; i < measurements.length; i++) { - var measurement = measurements[i]; - var specimen = experiments.getSampleById(measurement.specimenId); - var buffer = experiments.getBufferById(specimen.bufferId); - measurement.buffer_acronym = buffer.acronym; - measurement.bufferId = buffer.bufferId; - measurement.volume = specimen.volume; - if (specimen.macromolecule3VO != null) { - measurement.acronym = specimen.macromolecule3VO.acronym; - measurement.macromoleculeId = specimen.macromolecule3VO.macromoleculeId; - } - measurement.concentration = specimen.concentration; - if (measurement.run3VO != null) { - measurement.energy = measurement.run3VO.energy; - measurement.expExposureTemperature = measurement.run3VO.exposureTemperature; - measurement.storageTemperature = measurement.run3VO.storageTemperature; - measurement.timePerFrame = measurement.run3VO.timePerFrame; - measurement.radiationAbsolute = measurement.run3VO.radiationAbsolute; - measurement.radiationRelative = measurement.run3VO.radiationRelative; - measurement.status = "DONE"; +StockSolutionForm.prototype.refresh = function() { +}; - try { - if (measurement.run3VO.timeStart != null) { - if (measurement.run3VO.timeStart != "") { - measurement.miliseconds = moment(measurement.run3VO.timeStart).format("X"); - } - } - } catch (E) { - console.log(E); - } - } +StockSolutionForm.prototype._getTopPanel = function() { + return { + xtype : 'container', + layout : 'hbox', + border : 0, + items : [ { + xtype : 'container', + layout : 'hbox', + items : [ { + xtype : 'container', + flex : 1, + border : false, + layout : 'anchor', + defaultType : 'textfield', + items : [ - if (experiments.getDataCollectionByMeasurementId(measurement.measurementId).length > 0) { - var measurementtodatacollection3VOs = experiments.getDataCollectionByMeasurementId(measurement.measurementId)[0].measurementtodatacollection3VOs; - for (var k = 0; k < measurementtodatacollection3VOs.length; k++) { - if (measurementtodatacollection3VOs[k].dataCollectionOrder == 1) { - var specimenBuffer = experiments.getSampleById(experiments.getMeasurementById(measurementtodatacollection3VOs[k].measurementId).specimenId); - if (specimenBuffer.sampleplateposition3VO != null) { - measurement.bufferSampleplateposition3VO = specimenBuffer.sampleplateposition3VO; - measurement.bufferSampleplate = (experiments.getSamplePlateById(specimenBuffer.sampleplateposition3VO.samplePlateId)); - } - } - } - } + this.getMacromoleculeCombo(), { + xtype : 'requiredtext', + id : this.id + 'stockSolution_name', + fieldLabel : 'Acronym', + labelWidth : 120, + width : 250 + }, { + xtype : 'requiredtext', + id : this.id + 'stockSolution_concentration', + fieldLabel : 'Conc. (mg/ml)', + labelWidth : 120, + width : 250 + }, - if (this.collapsed) { - /** If collapsed only the samples * */ - if (specimen.macromolecule3VO != null) { - data.push(measurement); - } - } else { - data.push(measurement); - } + { + id : this.id + 'stockSolution_storageTemperature', + fieldLabel : 'Storage Temp.(C)', + labelWidth : 120, + width : 250 + }, { + xtype : 'requiredtext', + id : this.id + 'stockSolution_volume', + fieldLabel : 'Volume in Well (µl)', + labelWidth : 120, + width : 250 + } ] + } ] + }, { + xtype : 'container', + flex : 1, + layout : 'anchor', + defaultType : 'textfield', + margin : '0 0 0 10', + items : [ this.getBufferCombo() ] + } ] + }; - } - return data; }; -/** - * Refresh data grid with the measurements and the experiments - * - * @measurements array with measurement3VO objects - * @experiments array with experiments objects - */ -MeasurementGrid.prototype.refresh = function(measurements, experiments) { - this.experiments = experiments; - this.measurements = measurements; - this.store.loadData(this._prepareData(measurements, experiments), false); +StockSolutionForm.prototype.getPanel = function(stockSolution) { + this.stockSolution = stockSolution; + this.panel = Ext.createWidget({ + xtype : 'container', + layout : 'vbox', + border : 0, + style : { + padding : '10px' + }, + fieldDefaults : { + labelAlign : 'left', + labelWidth : 50 + }, + items : [ this._getTopPanel(stockSolution), { + id : this.id + 'stockSolution_comments', + xtype : 'textareafield', + name : 'comments', + fieldLabel : 'Comments', + labelWidth : 120, + width : '100%' + } ] + }); + + this.setStockSolution(stockSolution); + return this.panel; +}; + +StockSolutionForm.prototype.input = function() { + return { + stock : { + "stockSolutionId" : 6, + "proposalId" : 3124, + "macromoleculeId" : 5933, + "bufferId" : 811, + "instructionSet3VO" : null, + "boxId" : 305861, + "storageTemperature" : "20", + "volume" : "300", + "concentration" : "1.2", + "comments" : "Buffer EDTA with A", + "name" : "A_EDTA_1.2", + "samples" : [], + "buffer" : "EDTA", + "macromolecule" : "A" + }, + proposal : new MeasurementGrid().input().proposal + }; +}; + +StockSolutionForm.prototype.test = function(targetId) { + var stockSolutionForm = new StockSolutionForm(); + BIOSAXS.proposal = new Proposal(stockSolutionForm.input().proposal); + var panel = stockSolutionForm.getPanel(new Shipment(stockSolutionForm.input().stock)); + panel.render(targetId); }; + + +BoxWhiskerGraph.prototype.cleanArray = GenericGraph.prototype.cleanArray; +BoxWhiskerGraph.prototype.plotAxes = GenericGraph.prototype.plotAxes; +BoxWhiskerGraph.prototype.plotRuler = GenericGraph.prototype.plotRuler; +BoxWhiskerGraph.prototype.drawSVGVerticalText = GenericGraph.prototype.drawSVGVerticalText; +BoxWhiskerGraph.prototype.getClassColor = GenericGraph.prototype.getClassColor; +BoxWhiskerGraph.prototype.getDimensions = GenericGraph.prototype.getDimensions; +BoxWhiskerGraph.prototype.calculate = GenericGraph.prototype.calculate; +BoxWhiskerGraph.prototype.getMedian = GenericGraph.prototype.getMedian; +BoxWhiskerGraph.prototype.pointToPixel = GenericGraph.prototype.pointToPixel; +BoxWhiskerGraph.prototype.maxValueWhisker = GenericGraph.prototype.maxValueWhisker; +BoxWhiskerGraph.prototype.refresh = GenericGraph.prototype.refresh; /** - * Set status bar to busy (refreshing icon) + * Subclass of GenericGraph * - * @msg message to be displayed on the bar + * @maxBoxWidth */ -MeasurementGrid.prototype._showStatusBarBusy = function(msg) { - var statusBar = Ext.getCmp(this.id + 'basic-statusbar'); - statusBar.setStatus({ - text : msg, - iconCls : 'x-status-busy', - clear : false - }); +function BoxWhiskerGraph(args){ + this.maxBoxWidth = 25; + + if (args == null){ + args = new Object(); + } + args["plotHorizontalByCluster"] = true; + + GenericGraph.call(this, args); + + if (args.maxBoxWidth != null){ + this.maxBoxWidth = args.maxBoxWidth; + } }; + + /** - * Set status bar to ready (ok icon) - * - * @msg message to be displayed on the bar - */ -MeasurementGrid.prototype._showStatusBarReady = function(msg) { - var statusBar = Ext.getCmp(this.id + 'basic-statusbar'); - statusBar.setStatus({ - text : msg, - iconCls : 'x-status-valid', - clear : false - }); +There are several different methods for calculating quartiles.[1] This calculator uses a method described by Moore and McCabe to find quartile values. +The same method also used by The TI-83 to calculate quartile values. +With this method, the first quartile is the median of the numbers below the median, the third quartile is the median of the numbers above the median. + +http://www.miniwebtool.com/quartile-calculator/ +http://www.alcula.com/calculators/statistics/box-plot/ +**/ +BoxWhiskerGraph.prototype.getQ1 = function(array){ + array = array.slice(0, array.length/2); + return this.getMedian(array); }; -/** - * If updateRowEnabled returns an array with Ext.grid.plugin.RowEditing - */ -MeasurementGrid.prototype._getPlugins = function() { - var _this = this; - var plugins = []; - if (this.updateRowEnabled) { - plugins.push(Ext.create('Ext.grid.plugin.RowEditing', { - clicksToEdit : 1, - listeners : { - validateedit : function(grid, e) { - /** Setting values * */ - for ( var key in _this.editor) { - e.record.raw[key] = e.newValues[key]; - } - /** Comments are always updatable* */ - e.record.raw.comments = e.newValues.comments; +BoxWhiskerGraph.prototype.getQ3 = function(array){ + array = array.slice((array.length + 1)/2); + return this.getMedian(array); + +}; - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, measurement) { - _this.onMeasurementChanged.notify(measurement); - _this.grid.setLoading(false); - }); - adapter.onError.attach(function() { - alert("Error"); - _this.grid.setLoading(false); - }); +BoxWhiskerGraph.prototype.getQ2 = function(array){ + return this.getMedian(array); +}; - _this.grid.setLoading(); - adapter.saveMeasurement(e.record.raw, _this.experiments.experiments[0]); - } - } - })); +BoxWhiskerGraph.prototype.getBelowOutliers = function(belowLimit, array){ + var points = new Array(); + for (var i = 0; i < array.length; i++){ + if (array[i] <= belowLimit){ + points.push(array[i]); + } } - return plugins; + return points; }; -/** - * @key name of the columns mathing the this.editor[key] - */ -MeasurementGrid.prototype._getEditor = function(key) { - if (this.editor[key] != null) { - return this.editor[key]; +BoxWhiskerGraph.prototype.getAboveOutliers = function(aboveLimit, array){ + var points = new Array(); + for (var i = 0; i < array.length; i++){ + if (array[i] >= aboveLimit){ + points.push(array[i]); + } } - return null; + return points; }; -MeasurementGrid.prototype.getPanel = function(measurements, experiments) { - this.experiments = experiments; - this.measurements = measurements; - var _this = this; - this.store = Ext.create('Ext.data.Store', { - fields : [ { - name : 'miliseconds', - type : 'int' - }, 'priority', 'bufferId', { - name : 'exposureTemperature', - type : 'numeric' - }, 'volumeToLoad','code', 'transmission', 'viscosity', 'waitTime', 'flow', 'buffer_acronym', 'macromoleculeId', 'acronym', 'concentration', 'extraFlowTime', 'volume', 'energy', - 'expExposureTemperature', 'storageTemperature', 'timePerFrame', 'radiationAbsolute', 'radiationRelative', 'status', 'comments' ], - data : this._prepareData(measurements, experiments) - }); - this.store.sort(this.sorter); - var bbar = {}; - try { - bbar = Ext.create('Ext.ux.StatusBar', { - id : _this.id + 'basic-statusbar', - defaultText : 'Ready', - text : 'Ready', - iconCls : 'x-status-valid', - items : [] - }); - } catch (exp) { - console.log("bbar error"); + +BoxWhiskerGraph.prototype.minValueWhisker = function(belowLimit, q1, array){ + var points = new Array(); + + for (var i = 0; i < array.length; i++){ + if ((array[i] < q1) && (array[i]) > belowLimit){ + points.push(array[i]); + } + } + + if (points.length > 0){ + points.sort(function(a, b){return a - b;}); + return points[0]; } + return null; +}; - this.grid = Ext - .create( - 'Ext.grid.Panel', - { - id : this.id, - title : this.title, - store : this.store, - selModel : this.selModel, - plugins : this._getPlugins(), - resizable : this.resizable, - margin : this.margin, - maxHeight : this.maxHeight, - minHeight : this.minHeight, - maxWidth : this.maxWidth, - width : this.width, - tbar : this._getMenu(), - columns : [ - { - text : 'Order', - dataIndex : 'priority', - width : 50, - hidden : _this.isPriorityColumnHidden, - sortable : true +BoxWhiskerGraph.prototype.isNumber = function(value){ + if (value=="") return false; - }, - { - text : 'Run Number', - dataIndex : 'code', - width : 50, - hidden : true, - sortable : true + var d = parseInt(value); + if (!isNaN(d)) return true; else return false; - }, +}; - { - text : 'Specimen', - columns : [ +BoxWhiskerGraph.prototype.plotBoxWhisker = function(boxProperties){ + if (this.maxBoxWidth != null){ + if (boxProperties.width > this.maxBoxWidth){ + boxProperties.x = boxProperties.x + (boxProperties.width/2) - (this.maxBoxWidth/2); + boxProperties.width = this.maxBoxWidth; + } + + } - { - text : '', - dataIndex : 'macromoleculeId', - width : 30, - renderer : function(val, y, sample) { - if (val != null) { - if (_this.experiments == null) { - return BUI.getRectangleColorDIV(BIOSAXS.proposal.macromoleculeColors[val], 10, 10); - } else { - return BUI.getRectangleColorDIV(_this.experiments.macromoleculeColors[val], 10, 10); - } - } - }, - sortable : true - }, - { - text : 'Macromo.', - dataIndex : 'acronym', - width : 80, - renderer : function(val, y, sample) { - return val; - }, - sortable : true - }, - { - text : 'Conc. ', - dataIndex : 'concentration', - width : 80, - renderer : function(val, y, sample) { - if (sample.raw.macromoleculeId == null) { - return ""; - } - if (isNaN(val)) - return val; + if (this.plotPoints){ + for(var i = 0; i < boxProperties.values.length; i++){ + var value = boxProperties.values[i]; + var toPixel = this.pointToPixel(value, boxProperties); + SVG.drawCircle(boxProperties.x + (boxProperties.width/2) + 2, toPixel, this.pointRadius, this.svg, [["fill", "green"], ["fill-opacity", this.fillOpacityPoint],['stroke-opacity', this.strokeOpacityPoint], ["stroke", "black"]]); + } + } + - if (val != 0) { - return BUI.formatValuesUnits(val, '', { - fontSize : 16, - decimals : 3, - unitsFontSize : this.unitsFontSize - }); - } else { - return; - } + var boxColor = this.getClassColor(boxProperties.name); + var result = this.calculate(boxProperties.values); + /** Q1 **/ + + if (this.isNumber(result.Q1)){ + SVG.drawLine(boxProperties.x, this.pointToPixel(result.Q1, boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result.Q1, boxProperties), this.svg, [["stroke", boxColor]]); + } + /** Q2 **/ + if (this.isNumber(result.Q2)){ + SVG.drawLine(boxProperties.x, this.pointToPixel(result.Q2, boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result.Q2, boxProperties), this.svg, [["stroke", "blue"], ["stroke-width", "2"]]); + } + + /** Q3 **/ + if (this.isNumber(result.Q3)){ + SVG.drawLine(boxProperties.x, this.pointToPixel(result.Q3, boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result.Q3, boxProperties), this.svg, [["stroke", boxColor]]); + } + + /** Concenting Q1 and Q3 **/ + if (this.isNumber(result.Q1)&&this.isNumber(result.Q3)){ + SVG.drawLine(boxProperties.x, this.pointToPixel(result.Q1, boxProperties), boxProperties.x, this.pointToPixel(result.Q3, boxProperties), this.svg, [["stroke", boxColor]]); + SVG.drawLine(boxProperties.x + boxProperties.width, this.pointToPixel(result.Q1, boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result.Q3, boxProperties), this.svg, [["stroke", boxColor]]); + } + + /** min-whisker **/ + if (result["min-whisker"] != null){ + if (this.isNumber(result.Q1)){ + SVG.drawLine(boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result.Q1, boxProperties), boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result["min-whisker"], boxProperties), this.svg, [["stroke", boxColor]]); + } + SVG.drawLine(boxProperties.x,this.pointToPixel(result["min-whisker"], boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result["min-whisker"], boxProperties) , this.svg, [["stroke", boxColor]]); + + } + + /** max-whisker **/ + if (result["max-whisker"] != null){ + if (this.isNumber(result.Q3)){ + SVG.drawLine(boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result.Q3, boxProperties), boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result["max-whisker"], boxProperties), this.svg, [["stroke", boxColor]]); + } + SVG.drawLine(boxProperties.x , this.pointToPixel(result["max-whisker"], boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result["max-whisker"], boxProperties), this.svg, [["stroke", boxColor]]); + + } + + /** outliners **/ + if (result["above-outliers"] != null){ + for (var point in result["above-outliers"]){ + SVG.drawCircle(boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result["above-outliers"][point], boxProperties), this.pointRadius, this.svg, [["fill", "red"], ["fill-opacity", "1"]]); + //SVG.drawText(boxProperties.x + (boxProperties.width/2) - 2, this.pointToPixel(result["above-outliers"][point], boxProperties) + 2, "x",this.svg, [["fill", "black"], ["font-size", "x-small"]]); + } + } + if (result["below-outliers"] != null){ + for (var point in result["below-outliers"]){ + SVG.drawCircle(boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result["below-outliers"][point], boxProperties), this.pointRadius, this.svg, [["fill", "red"], ["fill-opacity", "1"]]); + //SVG.drawText(boxProperties.x + (boxProperties.width/2) - 2, this.pointToPixel(result["below-outliers"][point], boxProperties) + 2, "x",this.svg, [["fill", "black"], ["font-size", "x-small"]]); + } + } +}; - }, - sortable : true - }, - { - text : '', - dataIndex : 'bufferId', - width : 30, - hidden : false, - renderer : function(val, y, sample) { - if (val != null) { - var color = '#FFCCFF'; - if (_this.experiments != null) { - var dc = _this.experiments.getDataCollectionByMeasurementId(sample.raw.measurementId); - if (dc != null) { - if (dc.length > 0) { - color = _this.experiments.getSpecimenColorByBufferId(_this.experiments - .getMeasurementById(dc[0].measurementtodatacollection3VOs[0].measurementId).specimenId); - } - } - } else { - color = BIOSAXS.proposal.bufferColors[val]; - } - return BUI.getRectangleColorDIV(color, 10, 10); - } - }, - sortable : true - }, - { - text : 'Buffer', - dataIndex : 'buffer_acronym', - width : 120, - renderer : function(val, y, sample) { - if (sample.raw.bufferSampleplateposition3VO != null) { - return BIOSAXS.proposal.getBufferById(sample.raw.bufferId).acronym + " Plate: [" - + sample.raw.bufferSampleplate.slotPositionColumn + ", " - + BUI.getSamplePlateLetters()[sample.raw.bufferSampleplateposition3VO.rowNumber - 1] + "-" - + sample.raw.bufferSampleplateposition3VO.columnNumber + "]"; - } - return val; - }, - sortable : true - }, { - text : 'Position', - width : 100, - hidden : true, - renderer : function(val, y, sample) { - if (_this.experiments != null) { - return BUI.getSamplePositionHTML(_this.experiments.getSampleById(sample.raw.specimenId), _this.experiments.experiments[0]); - } - } - } ] - }, - { - text : 'Parameters', - columns : [ - { - text : 'Ex. Flow. time (s)', - dataIndex : 'extraFlowTime', - width : 100, - hidden : true, - renderer : function(val, y, sample) { - return BUI.formatValuesUnits(val, 's', { - fontSize : 12, - decimals : 0, - unitsFontSize : this.unitsFontSize - }); - } - }, - { - text : 'Exp. Temp.', - dataIndex : 'exposureTemperature', - width : 70, - renderer : function(val, y, sample) { - if (Number(val)) { - return BUI.formatValuesUnits(val, 'C', { - fontSize : 12, - decimals : 2, - unitsFontSize : this.unitsFontSize - }); - } - return null; - }, - sortable : true, - editor : this._getEditor("exposureTemperature") - }, - { - text : 'Vol. Load', - dataIndex : 'volumeToLoad', - width : 60, - hidden : false, - editor : this._getEditor("volumeToLoad"), - renderer : function(val, y, sample) { - // return val+ " µl"; - return BUI.formatValuesUnits(val, 'µl', { - fontSize : 12, - decimals : 2, - unitsFontSize : this.unitsFontSize - }); - } - }, - { - text : 'Volume in Well', - dataIndex : 'volume', - hidden : true, - editor : this._getEditor("volume"), - width : 80, - renderer : function(val, y, sample) { - // return val + "(µl)"; - return BUI.formatValuesUnits(val, 'µl', { - fontSize : 12, - decimals : 2, - unitsFontSize : this.unitsFontSize - }); - } - }, - { - text : 'Trans.', - dataIndex : 'transmission', - width : 60, - editor : this._getEditor("transmission"), - renderer : function(val, y, sample) { - return BUI.formatValuesUnits(val, '%', { - fontSize : 12, - decimals : 0, - unitsFontSize : this.unitsFontSize - }); - } - }, - { - text : 'Wait T.', - dataIndex : 'waitTime', - editor : this._getEditor("waitTime"), - width : 50, - renderer : function(val, y, sample) { - // if (val != 0) { - return BUI.formatValuesUnits(val, 's', { - fontSize : 12, - decimals : 0, - unitsFontSize : this.unitsFontSize - }); - // } - } - }, - { - text : 'Flow', - dataIndex : 'flow', - editor : this._getEditor("flow"), - width : 50, - renderer : function(val, y, sample) { - if (val == true) { - return "yes"; - } - return null; - } - }, - { - text : 'Viscosity', - dataIndex : 'viscosity', - tooltip : 'The viscosity of a fluid is a measure of its resistance to gradual deformation by shear stress or tensile stress. For liquids, it corresponds to the informal notion of "thickness"', - editor : this._getEditor("viscosity"), - width : 50, - renderer : function(val, y, sample) { - return val; - } - } ] - }, { - text : 'Status', - dataIndex : 'status', - width : 50, - hidden : _this.isStatusColumnHidden, - renderer : function(val, y, sample) { - if (val != null) { - if (val == 'DONE') { - return "" + val + " "; - } - } - } - }, { - text : 'Time', - dataIndex : 'time', - width : 80, - hidden : _this.isTimeColumnHidden, - renderer : function(val, y, sample) { - if (sample.raw.run3VO != null) { - if (sample.raw.run3VO.timeStart != null) { - if (sample.raw.run3VO.timeStart != "") { - var m = moment(sample.raw.run3VO.timeStart); - return m.format("hh:mm:ss a"); - } - } - } - } - }, { - text : 'Energy', - dataIndex : 'energy', - width : 100, - hidden : true - }, { - text : 'Real Exp. Temp.(C)', - width : 100, - dataIndex : 'expExposureTemperature', - hidden : true - }, { - text : 'Storage Temp.(C)', - width : 100, - dataIndex : 'storageTemperature', - hidden : true - }, { - text : 'Time/Frame (s)', - width : 100, - dataIndex : 'timePerFrame', - hidden : true - }, { - text : 'Radiation Relative', - dataIndex : 'radiationRelative', - width : 100, - hidden : true - }, { - text : 'Radiation Absolute', - dataIndex : 'radiationAbsolute', - width : 100, - hidden : true - }, { - text : 'Comments', - dataIndex : 'comments', - flex : 1, - hidden : false, - editor : this._getEditor("comments") - }, { - id : _this.id + 'buttonRemoveSample', - text : '', - hidden : !_this.removeBtnEnabled, - width : 100, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - if (record.raw.macromoleculeId != null) { - if (_this.removeBtnEnabled) { - return BUI.getRedButton('REMOVE'); - } - } - } - } ], - bbar : bbar, - viewConfig : { - stripeRows : true, - getRowClass : function(record, index, rowParams, store) { - if (record.data.status == "DONE") { - return 'green-row'; - } - }, - listeners : { - 'itemclick' : function(grid, record, item, index, e, eOpts) { - _this.onClick.notify({ - specimen : record.raw - }); - }, - 'cellclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemoveSample') { - grid.getStore().removeAt(rowIndex); +BoxWhiskerGraph.prototype.plotClusterTitles = function(properties){ + /** Cluster Titles **/ + var posX = this.left + this.rulerWidth; + var data = this.data; + for(var i = 0; i < data.clusters.length; i++ ){ + /** title for the clusters **/ + posX = posX + this.interClustersSpace; + + /** Drawing title of classes **/ + var cluster = data.clusters[i]; + var posXClasses = posX; + for(var j = 0; j < cluster.classes.length; j++){ + //SVG.drawRectangle(posXClasses, this.height - (this.bottom + this.clusterTitleHeight + this.rulerHeight), properties.classWidth, this.rulerHeight, this.svg, [["fill", "green"]]); +// SVG.drawText(posXClasses + 1/6*properties.classWidth, this.height - (this.bottom + this.clusterTitleHeight + (this.rulerHeight*1/4)), cluster.classes[j].name, this.svg, [["style", "font-size:xx-small"]]); + var color = cluster.classes[j].color; + this.drawSVGVerticalText(posXClasses + 1/2*(properties.classWidth), this.height - (this.bottom - this.clusterTitleHeight + (this.rulerHeight)), cluster.classes[j].name , [["style", "font-size:x-small;"], ["fill", color]]); + + // SVG.drawRectangle(posXClasses, this.height - (this.bottom + this.clusterTitleHeight), properties.classWidth, 2, this.svg, [["fill", "black"]]); + posXClasses = posXClasses + properties.classWidth + this.interClassesSpace; + } + + var clusterTitleSpace = (data.clusters[i].classes.length * properties.classWidth) + ((data.clusters[i].classes.length - 1) * this.interClassesSpace); + //SVG.drawRectangle(posX, this.height - (this.bottom + this.clusterTitleHeight), clusterTitleSpace, this.clusterTitleHeight, this.svg, [["fill", "pink"]]); + SVG.drawRectangle(posX, this.height - (this.clusterTitleHeight+this.bottom), clusterTitleSpace, 1, this.svg, []); + +// var transform = ["translate", "(" + posX + 1/3*clusterTitleSpace +", " + this.height - (this.bottom + (this.clusterTitleHeight*1/4)) +")"], ["transform", "rotate(180)"]; +// var transform = ["transform", "translate(" + (posX + 1/3*clusterTitleSpace) +", " + (this.height - (this.bottom + (this.clusterTitleHeight*1/4))) + "), rotate(-90) "]; +// this.drawSVGVerticalText(posX + 1/3*clusterTitleSpace, this.height - (this.bottom + (this.clusterTitleHeight*1/4)),data.clusters[i].name, [["style", "font-size:x-small"]]); + SVG.drawText(posX , this.height - (this.bottom + (this.clusterTitleHeight*1/4)),data.clusters[i].name ,this.svg, [["style", "font-size:x-small"]]); + posX = posX + clusterTitleSpace; + } +}; + +BoxWhiskerGraph.prototype.plotWhisters = function(data, properties){ + var colors = ["yellow", "orange", "green"]; + var posX = this.left + this.rulerWidth; + for(var i = 0; i < data.clusters.length; i++ ){ + var cluster = data.clusters[i]; + /** inter cluster space **/ + //SVG.drawRectangle(posX, this.top, this.interClustersSpace, this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight, this.svg, [["fill", "black"]]); + posX = posX + this.interClustersSpace; + + for (var j = 0; j < cluster.classes.length; j ++){ + + //SVG.drawRectangle(posX, this.top, properties.classWidth, this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight, this.svg, [["fill", colors[j]]]); + this.plotBoxWhisker( + { + name : cluster.classes[j].name, + values : cluster.classes[j].values, + minPoint : properties.minPoint, + maxPoint : properties.maxPoint, + x : posX, + y : this.top, + width : properties.classWidth, + height : this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight + + + } + ); + posX = posX + properties.classWidth; + //SVG.drawRectangle(posX, this.top, this.interClassesSpace, this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight, this.svg, [["fill", "black"]]); + if (j < cluster.classes.length - 1){ + posX = posX + this.interClassesSpace; + } + } + } +}; + +BoxWhiskerGraph.prototype.draw = function(targetId, data){ + this.targetId = targetId; + var properties = (this.getDimensions(data)); + this.svg = SVG.createSVGCanvas(document.getElementById(this.targetId), [["width", this.width], ["height", this.height]]); + this.plotAxes(properties); + this.plotClusterTitles(properties); + this.plotWhisters(data,properties); +}; + +BoxWhiskerGraph.prototype.input = function(){ + return DATADOC.getBoxWhikerData(); +}; + +BoxWhiskerGraph.prototype.test = function(targetId){ + var plot = new BoxWhiskerGraph( + { + targetId : targetId, + height : 350, + width : 450, + maxBoxWidth : 25 + } + ); + plot.refresh(this.input()); +}; + + + + + + + +function DataSet(){ + this.json = null; + +}; + + +DataSet.prototype.loadFromJSON = function(json){ + if(json != null) { + if(this.validate(json)) { + this.json = json; + } + } +}; + + +DataSet.prototype.toJSON = function(json){ + return this.json; +}; + + +/** Abstract method to be override on childs classes **/ +DataSet.prototype.validate = function(json){ + if (true){ + return true; + } + /*else{ + throw "Data validation failed"; + }*/ +}; + + + + +Edge.prototype.getName = GraphItem.prototype.getName; +Edge.prototype.setName = GraphItem.prototype.setName; +Edge.prototype.getId = GraphItem.prototype.getId; + +function Edge(id, name, nodeSource, nodeTarget, args){ + GraphItem.prototype.constructor.call(this, id, name, args); + + this.sourceNode = nodeSource; + this.targetNode = nodeTarget; + +}; + +Edge.prototype.toJSON = function(){ + return {"index": this.id,"sourceIndex":this.sourceNode.getId(),"targetIndex":this.targetNode.getId(),"args":this.args}; +}; + +Edge.prototype.getNodeSource = function(){ + return this.sourceNode; +}; + +Edge.prototype.getNodeTarget = function(){ + return this.targetNode; +}; + +Edge.prototype.remove = function(){ + //Remove edge object in the nodes + this.getNodeSource().removeEdge(this); + this.getNodeTarget().removeEdge(this); + + this.deleted.notify(this); +}; + + +EdgeGraphFormatter.prototype.setProperties = ItemGraphFormatter.prototype.setProperties; +EdgeGraphFormatter.prototype.getDefault = ItemGraphFormatter.prototype.getDefault; +EdgeGraphFormatter.prototype.getSelected = ItemGraphFormatter.prototype.getSelected; +EdgeGraphFormatter.prototype.getOver = ItemGraphFormatter.prototype.getOver; +EdgeGraphFormatter.prototype.getDragging = ItemGraphFormatter.prototype.getDragging; +EdgeGraphFormatter.prototype.getId = ItemGraphFormatter.prototype.getId; +EdgeGraphFormatter.prototype.toJSON = ItemGraphFormatter.prototype.toJSON; +EdgeGraphFormatter.prototype.loadFromJSON = ItemGraphFormatter.prototype.loadFromJSON; +EdgeGraphFormatter.prototype._setEvents = ItemGraphFormatter.prototype._setEvents; + +function EdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ + ItemGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); + + this.getDefault().args.type = "EdgeGraphFormatter"; +}; + + + + +LineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; +LineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; +LineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; +LineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; +LineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; +LineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; +LineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; +LineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; +LineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; + +function LineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ + EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); + this.args.type = "LineEdgeGraphFormatter"; +}; + +/** DIRECTED **/ +DirectedLineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; +DirectedLineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; +DirectedLineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; +DirectedLineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; +DirectedLineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; +DirectedLineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; +DirectedLineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; +DirectedLineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; +DirectedLineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; + +function DirectedLineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ + EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); + this.args.type = "DirectedLineEdgeGraphFormatter"; + this.args.arrowSize = "3"; +}; +DirectedLineEdgeGraphFormatter.prototype.getArrowSize = function(){ + return this.args.arrowSize; +}; + +OdirectedLineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; +OdirectedLineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; +OdirectedLineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; +OdirectedLineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; +OdirectedLineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; +OdirectedLineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; +OdirectedLineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; +OdirectedLineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; +OdirectedLineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; + +function OdirectedLineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ + EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); + this.args.type = "DirectedLineEdgeGraphFormatter"; + this.args.arrowSize = "3"; +}; + +OdirectedLineEdgeGraphFormatter.prototype.getArrowSize = function(){ + return this.args.arrowSize; +}; + + +/** CUT (inhibition) **/ +CutDirectedLineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; +CutDirectedLineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; +CutDirectedLineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; +CutDirectedLineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; +CutDirectedLineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; +CutDirectedLineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; +CutDirectedLineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; +CutDirectedLineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; +CutDirectedLineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; + +function CutDirectedLineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ + EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); + this.args.type = "CutDirectedLineEdgeGraphFormatter"; +}; + + + + +BezierEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; +BezierEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; +BezierEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; +BezierEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; +BezierEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; +BezierEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; +BezierEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; +BezierEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; +BezierEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; +BezierEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; + +function BezierEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ + EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); + this.args.type = "BezierEdgeGraphFormatter"; +}; + + + +DotDirectedLineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; +DotDirectedLineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; +DotDirectedLineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; +DotDirectedLineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; +DotDirectedLineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; +DotDirectedLineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; +DotDirectedLineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; +DotDirectedLineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; +DotDirectedLineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; + +function DotDirectedLineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ + EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); + this.args.type = "DotDirectedLineEdgeGraphFormatter"; +}; + + +OdotDirectedLineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; +OdotDirectedLineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; +OdotDirectedLineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; +OdotDirectedLineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; +OdotDirectedLineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; +OdotDirectedLineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; +OdotDirectedLineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; +OdotDirectedLineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; +OdotDirectedLineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; + +function OdotDirectedLineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ + EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); + this.args.type = "OdotDirectedLineEdgeGraphFormatter"; +}; + + + +function GraphDataset(){ + DataSet.prototype.constructor.call(this); + this.edges = new Object(); + this.vertices = new Object(); + this.verticesIndex = new Object(); + + //Events + this.newVertex = new Event(this); + this.vertexNameChanged = new Event(this); + this.vertexDeleted = new Event(this); + + this.newEdge = new Event(this); + this.edgeNameChanged = new Event(this); + this.edgeDeleted = new Event(this); + + this.json = new Object(); + this.json.vertices = new Array(); + this.json.edges = new Array(); + this.json.relations = new Array(); +}; + +GraphDataset.prototype.loadFromJSON = DataSet.prototype.loadFromJSON; +GraphDataset.prototype.toJSON = DataSet.prototype.toJSON; +GraphDataset.prototype.validate = DataSet.prototype.validate; + +/** Devuelve el numero de edges incidentes sobre el nodo con mas edges **/ +GraphDataset.prototype.getMaxClass = function(){ + var maxClassNode = 0; + for ( var node in this.vertices) { + if (this.vertices[node].getEdgesCount() > maxClassNode){ + maxClassNode = this.vertices[node].getEdgesCount(); + } + } + return maxClassNode; +}; + +/** Devuelve el numero de edges incidentes sobre el nodo con mas edges **/ +GraphDataset.prototype.getMinClass = function(){ + var minClassNode = Math.min(); + for ( var node in this.vertices) { + if (this.vertices[node].getEdgesCount() < minClassNode){ + minClassNode = this.vertices[node].getEdgesCount(); + } + } + return minClassNode; +}; + +GraphDataset.prototype.getVertexByName = function(nodeName){ + var results = new Array(); + + for (var vertexId in this.verticesIndex[nodeName]){ + var vertexByid = this.getVertexById(this.verticesIndex[nodeName][vertexId]); + results.push(vertexByid); + //* añadido nuevo porque fallaba el anterior codigo + return vertexByid + } + + if (results <= 1){ + return this.getVertexById(this.verticesIndex[nodeName]); + } + else{ + return results; + } +}; + +GraphDataset.prototype.getVertexById = function(id){ + return this.vertices[id]; +}; + +GraphDataset.prototype.toSIF = function(){ + var sifDataAdapter = new SifFileDataAdapter(); + return sifDataAdapter.toSIF(this); +}; + +GraphDataset.prototype.toSIFID = function(){ + var sifDataAdapter = new SifFileDataAdapter(); + return sifDataAdapter.toSIFID(this); +}; + +GraphDataset.prototype.toDOT = function(){ + var dotFileDataAdapter = new DotFileDataAdapter(); + return dotFileDataAdapter.toDOT(this); +}; + +GraphDataset.prototype.toDOTID = function(){ + var dotFileDataAdapter = new DotFileDataAdapter(); + return dotFileDataAdapter.toDOTID(this); +}; + +GraphDataset.prototype._addNode = function(nodeName, args){ + return new Vertex(this._getVerticesCount()-1, nodeName, args); +}; + +GraphDataset.prototype.addNode = function(nodeName, args){ + this.json.vertices.push(nodeName); + this._addVerticesIndex(nodeName, this._getVerticesCount() - 1); + var vertex = this._addNode(nodeName, args); + this.vertices[this._getVerticesCount()-1] = vertex; + this._setNodeEvents(vertex); + this.newVertex.notify(vertex); +}; + +GraphDataset.prototype._addVerticesIndex = function(nodeName, id){ + if (this.verticesIndex[nodeName] == null){ + this.verticesIndex[nodeName] = new Array(); + } + this.verticesIndex[nodeName].push(id); +}; + +GraphDataset.prototype.addEdge = function(edgeName, nodeSourceId, nodeTargetId, args){ + this.json.edges.push(edgeName); + var nodeSource = this.getVertexById(nodeSourceId); + var nodeTarget = this.getVertexById(nodeTargetId); + var index = this.getEdgesCount() - 1; + this.edges[index] = new Edge(index, edgeName, nodeSource, nodeTarget, args); + this.json.relations.push({"index": index, "sourceIndex": nodeSourceId, "targetIndex": nodeTargetId, "args": args }); + + nodeSource.addEdge(this.edges[index]); + nodeTarget.addEdge(this.edges[index]); + this._setEdgeEvents(this.edges[index]); + this.newEdge.notify(this.edges[index]); +}; + +GraphDataset.prototype.getVertices = function(){ + return this.vertices; +}; + +GraphDataset.prototype.getEdges = function(){ + return this.edges; +}; + +GraphDataset.prototype.getEdgeById = function(edgeId){ + return this.edges[edgeId]; +}; + +GraphDataset.prototype._getVerticesCount = function(){ + return this.json.vertices.length; +}; + + +GraphDataset.prototype.getVerticesCount = function(){ + var count = 0; + for ( var vertex in this.getVertices()) { + count ++; + } + return count; +}; + + +GraphDataset.prototype.getEdgesCount = function(){ + return this.json.edges.length; +}; + +GraphDataset.prototype.init = function(){ + this.edges = new Object(); + this.vertices = new Object(); +}; + +GraphDataset.prototype._setNodeEvents = function(node){ + var _this = this; + //NODE EVENTS + node.deleted.attach(function (sender, node){ + _this._removeNode(node); + }); + + node.nameChanged.attach(function (sender, args){ + var item = args.item; + var newName = item.name; + var indexes = _this.verticesIndex[args.previousName]; + for(var i = 0; i < indexes.length; i++){ + if(indexes[i] == item.id) + indexes.splice(i,1); + } + if(indexes.length == 0){ + delete _this.verticesIndex[args.previousName]; + } + _this._addVerticesIndex(newName, item.id); + _this.json.vertices[item.id] = newName; + _this.vertexNameChanged.notify(args); + }); +}; + +GraphDataset.prototype._setEdgeEvents = function(edge){ + var _this = this; + //EDGE EVENTS + edge.nameChanged.attach(function (sender, edge){ + _this.edgeNameChanged.notify(edge); + + }); + + edge.deleted.attach(function (sender, edge){ + _this._removeEdge(edge); + }); +}; + +GraphDataset.prototype._connectVerticesByName = function(nodeNameSource, nodeNameTarget){ + var source = this.getVertexByName(nodeNameSource); + var target = this.getVertexByName(nodeNameTarget); + + if ((source != null)&&(target!=null)){ + this.addEdge(source.getName() +"_" + target.getName(), source.getId(), target.getId(), {}); + } + else{ + if (source == null){ + console.log("No encontrado: " + nodeNameSource) + } + if (target == null){ + console.log("No encontrado: " + nodeNameTarget) + } + } +}; + +GraphDataset.prototype.loadFromJSON = function(json){ + var json = json; + this.init(); + this.json = new Object(); + this.json.vertices = new Array(); + this.json.edges = new Array(); + this.json.relations = new Array(); + + for ( var i = 0; i < json.nodes.length; i++) { + if (json.nodes[i] != null){ + var name = json.nodes[i]; + this.addNode(name); + } + else{ + this.json.vertices.push(null); + } + } + + for ( var i = 0; i < json.edges.length; i++) { + if (json.edges[i] != null){ + if (json.relations[i] != null){ + var name = json.edges[i]; + this.addEdge(name, json.relations[i].sourceIndex, json.relations[i].targetIndex, json.relations[i].args); + } + } + else{ + this.json.edges.push(null); + this.json.relations.push(null); + } + } +}; + +GraphDataset.prototype.prettyPrint = function(){ + for ( var node in this.vertices) { + console.log(this.vertices[node].getName() ); + for ( var j = 0; j < this.vertices[node].getEdgesIn().length; j++) { + console.log(" --> " + this.vertices[node].getEdgesIn()[j].getNodeTarget().getName() ); + } + } +}; + +GraphDataset.prototype._removeEdge = function(edge){ + this.json.edges[edge.getId()] = null; + this.json.relations[edge.getId()] = null; + + delete this.edges[edge.getId()]; + this.edgeDeleted.notify(edge); + + +}; + +GraphDataset.prototype._removeNode = function(node){ + this.json.vertices[node.getId()] = null; + delete this.vertices[node.getId()]; + this.vertexDeleted.notify(node); +}; + +GraphDataset.prototype.toJSON = function(){ + var json = new Object(); + var nodes = new Array(); + json.nodes = this.json.vertices; //nodes; + json.edges = this.json.edges; //edges; + json.relations = this.json.relations; + return json; +}; + +GraphDataset.prototype.clone = function(){ + var dsDataset = new GraphDataset(); + dsDataset.loadFromJSON(this.toJSON()); + return dsDataset; +}; +//GraphDataset.prototype.test = function(){ +// this.loadFromJSON(this.toJSON()); +//}; + +function labels(){ + var names = new Array(); + + var dataset = interactomeViewer.graphEditorWidget.dataset; + var layout = interactomeViewer.graphEditorWidget.layout; + + for ( var vertexId in interactomeViewer.graphEditorWidget.dataset.getVertices()) { + names.push(interactomeViewer.graphEditorWidget.dataset.getVertexById(vertexId).getName()); + } + + var sorted = (names.sort()); + console.log(sorted) + var distance = 0.01; + var altura = 0.6; + for ( var i = 0; i < names.length; i++) { + var id =dataset.getVertexByName(names[i]).getId(); + + layout.getNodeById(id).setCoordenates(distance, altura); + + + distance = parseFloat(distance) + parseFloat(0.03); + + altura = parseFloat(altura) + parseFloat(0.02); + + if (parseFloat(altura) == 0.9800000000000003){ + + altura = 0.6; + distance = distance - 0.51; + } + + } + + +}; + +function GraphItem(id, name, args){ + this.id = id; + this.name = name; + this.type = "NONE"; + + this.args = new Object(); + + + if (args!=null){ + this.args = args; + if (args.type !=null){ + this.type = args.type; + } + } + + //Events + this.nameChanged = new Event(this); + this.deleted = new Event(this); +} + +GraphItem.prototype.getName = function(){ + return this.name; +}; + +GraphItem.prototype.getId = function(){ + return this.id; +}; + +GraphItem.prototype.setName = function(name){ + var oldName = this.getName(); + this.name = name; + this.nameChanged.notify({"item": this, "previousName" : oldName}); +}; + + + + + +function LayoutDataset(){ + this.dataset = null; + this.vertices = new Object(); + this.changed = new Event(this); + + + this.args = new Object(); + + //RANDOM, CIRCLE + this.args.type = "CIRCLE"; +}; + +LayoutDataset.prototype.loadFromJSON = function(dataset, json){ + var _this = this; + this.vertices = new Object(); + this.dataset = dataset; //new GraphDataset(); + for ( var vertex in json) { + this.vertices[vertex] = new NodeLayout(vertex, json[vertex].x, json[vertex].y); + this.vertices[vertex].changed.attach(function (sender, item){ + _this.changed.notify(item); + }); + } + this._attachDatasetEvents(); +}; + + +LayoutDataset.prototype.toJSON = function(){ + var serialize = new Object(); + for ( var vertex in this.vertices) { + serialize[vertex] = new Object(); + serialize[vertex].x = this.vertices[vertex].x; + serialize[vertex].y = this.vertices[vertex].y; + } + serialize.dataset = new Object(); + serialize.dataset =this.dataset.toJSON(); + return serialize; +}; + +LayoutDataset.prototype.dataBind = function(graphDataset){ + this.dataset = graphDataset; + this._attachDatasetEvents(); + this._calculateLayout(); +}; + +LayoutDataset.prototype._removeVertex = function(vertexId){ + delete this.vertices[vertexId]; +}; + +LayoutDataset.prototype._attachDatasetEvents = function(){ + var _this = this; + + this.dataset.vertexDeleted.attach(function (sender, item){ + _this._removeVertex(item.getId()); + }); + + this.dataset.newVertex.attach(function (sender, item){ + _this.vertices[item.getId()] = new NodeLayout(item.getId(), 0.5, 0.5); + _this.vertices[item.getId()].changed.attach(function (sender, item){ + _this.changed.notify(item); + }); + }); +}; + +LayoutDataset.prototype.getType = function(){ + return this.args.type; +}; + +LayoutDataset.prototype._calculateLayoutVertices = function(type, count){ + + if (type == "CIRCLE"){ + var radius = 0.4; + var centerX = 0.5; + var centerY = 0.5; + var verticesCoordinates = new Array(); + for(var i = 0; i < count; i++){ + x = centerX + radius * Math.sin(i * 2 * Math.PI/count); + y = centerY + radius * Math.cos(i * 2 * Math.PI/count); + verticesCoordinates.push({'x':x,'y':y}); + } + return verticesCoordinates; + } +}; + + +LayoutDataset.prototype._calculateLayout = function(){ + var _this = this; + if (this.getType() == "RANDOM"){ + for ( var vertex in this.dataset.getVertices()) { + if (this.vertices[vertex] == null){ + this.vertices[vertex] = new NodeLayout(vertex, 0, 0); + } + this.vertices[vertex].setCoordinates(Math.random(), Math.random()); + this.vertices[vertex].changed.attach(function (sender, item){ + _this.changed.notify(item); + }); + } + } + + if ( this.getType() == "CIRCLE"){ + + var count = this.dataset._getVerticesCount(); + var verticesCoordinates = this._calculateLayoutVertices(this.getType(), count); + + var aux = 0; + for ( var vertex in this.dataset.getVertices()) { + if (this.vertices[vertex] == null){ + this.vertices[vertex] = new NodeLayout(vertex, 0, 0); + } + this.vertices[vertex].setCoordinates(verticesCoordinates[aux].x, verticesCoordinates[aux].y);//{"x":, "y":}; + aux++; + this.vertices[vertex].changed.attach(function (sender, item){ + _this.changed.notify(item); + }); + } + } + + + if (this.getType() == "SQUARE"){ + + var count = this.dataset._getVerticesCount(); + var xMin = 0.1; + var xMax = 0.9; + var yMin = 0.1; + var yMax = 0.9; + + var rows = Math.sqrt(count); + var step = (xMax - xMin) / rows; + + var verticesCoordinates = new Array(); + for(var i = 0; i < rows; i ++){ + for ( var j = 0; j < rows; j++) { + x = i * step + xMin; + y = j * step + yMin; + verticesCoordinates.push({'x':x,'y':y}); + } + } + + var aux = 0; + for ( var vertex in this.dataset.getVertices()) { + if (this.vertices[vertex] == null){ + this.vertices[vertex] = new NodeLayout(vertex, 0, 0); + } + this.vertices[vertex].setCoordinates(verticesCoordinates[aux].x, verticesCoordinates[aux].y);//{"x":, "y":}; + aux++; + this.vertices[vertex].changed.attach(function (sender, item){ + _this.changed.notify(item); + }); + } + } + +}; + +LayoutDataset.prototype.getNodeById = function(id){ + return this.vertices[id]; +}; + +LayoutDataset.prototype.getVerticesByArea = function(x1, y1, x2, y2){ + var vertices = new Array(); + for ( var vertex in this.dataset.getVertices()) { + if ((this.vertices[vertex].x >= x1)&&(this.vertices[vertex].x <= x2)){ + if ((this.vertices[vertex].y >= y1)&&(this.vertices[vertex].y <= y2)){ + vertices.push(this.vertices[vertex]); + } + } + } + return vertices; +}; + + + + +LayoutDataset.prototype.getLayout = function(type){ + + if (type == "CIRCLE"){ + this.args.type = "CIRCLE"; + this._calculateLayout(); + return; + } + + if (type == "SQUARE"){ + this.args.type = "SQUARE"; + this._calculateLayout(); + return; + } + + if (type == "RANDOM"){ + this.args.type = "RANDOM"; + this._calculateLayout(); + return; + } + + + var dotText = this.dataset.toDOTID(); + var url = "http://bioinfo.cipf.es/utils/ws/rest/network/layout/"+type+".coords"; + var _this = this; + + $.ajax({ + async: true, + type: "POST", + url: url, + dataType: "text", + data: { + dot :dotText + }, + cache: false, + success: function(data){ + var response = JSON.parse(data); + for ( var vertexId in response) { + _this.vertices[vertexId].setCoordinates(response[vertexId].x, response[vertexId].y); + } + } + }); + +// $.ajax({ +// async: true, +// type: "POST", +// url: url, +// dataType: "script", +// data: { +// dot :dotText +// }, +// cache: false, +// success: function(data){ +// var response = JSON.parse(data); +// for ( var vertexId in response) { +// _this.vertices[vertexId].setCoordinates(response[vertexId].x, response[vertexId].y); +// } +// } +// }); + +}; + +function NodeLayout(id, x, y, args){ + this.id = id; + this.x = x; + this.y = y; + this.changed = new Event(this); +}; + +NodeLayout.prototype.getId = function(id){ + return this.id; +}; + +NodeLayout.prototype.setCoordinates = function(x, y){ + this.x = x; + this.y = y; + this.changed.notify(this); +}; + + + +function NetworkDataSetFormatter(vertexFormatProperties, defaultEdgeProperties, args){ + DataSet.prototype.constructor.call(this); + + this.args = new Object(); + + this.vertices = new Object(); + this.edges = new Object(); + this.dataset = null; + this.maxClass = 0; + this.minClass = 0; + + /** Coordenates with default Setting */ + this.args.width = 1100; + this.args.height = 500; + + /** Optional parameters */ + this.args.backgroundColor = "#FFFFFF"; + this.args.backgroundImage = null; + this.args.backgroundImageHeight = null; + this.args.backgroundImageWidth = null; + this.args.backgroundImageX = null; + this.args.backgroundImageY = null; + + + this.args.balanceNodes = false; + this.args.nodesMaxSize = 3; + this.args.nodesMinSize = 0.5; + + + /** Zoom **/ + this.args.zoomScale = 1; + this.args.zoomScaleStepFactor = 0.4; + + if (args != null){ + if (args.backgroundImage != null){ + this.args.backgroundImage = args.backgroundImage; + } + + if (args.width != null){ + this.args.width = args.width; + } + + if (args.height != null){ + this.args.height = args.height; + this.args.svgHeight = args.height; + } + + if (args.svgHeight != null){ + this.args.svgHeight = args.svgHeight; + } + + if (args.backgroundColor != null){ + this.args.backgroundColor = args.backgroundColor; + } + + if(args.balanceNodes != null){ + this.args.balanceNodes = args.balanceNodes; + } + + if(args.nodesMaxSize != null){ + this.args.nodesMaxSize = args.nodesMaxSize; + } + if(args.nodesMinSize != null){ + this.args.nodesMinSize = args.nodesMinSize; + } + } + + this.args.defaultEdgeProperties = {"fill":"#000000", "radius":"1", "stroke":"#000000", "size":1, "title":{"fontSize":10, "fontColor":"#000000"}}; + this.args.vertexFormatProperties = { "fill":"#000000", "stroke":"#000000", "stroke-opacity":"#000000"}; + + if (vertexFormatProperties!= null){ + this.args.vertexFormatProperties = vertexFormatProperties; + } + if (defaultEdgeProperties!= null){ + this.args.defaultEdgeProperties = defaultEdgeProperties; + } + + /** Events **/ + this.changed = new Event(this); + this.edgeChanged = new Event(this); + this.resized = new Event(this); + this.backgroundImageChanged= new Event(this); + this.backgroundColorChanged= new Event(this); +}; + +NetworkDataSetFormatter.prototype.loadFromJSON = function(dataset, json){ + this.args = new Object(); + this.vertices = new Object(); + this.args = json; + this._setDataset(dataset); + var _this = this; + + for ( var vertex in json.vertices) { + this.addVertex(vertex, json.vertices[vertex]); + } + + for ( var edgeId in json.edges) { + this.addEdge(edgeId, json.edges[edgeId]); + } +}; + + +NetworkDataSetFormatter.prototype.toJSON = function(){ + + +// this.args.vertices = new Object(); +// this.args.edges = new Object(); +// +// for ( var vertex in this.vertices) { +// this.args.vertices[vertex] = this.getVertexById(vertex).toJSON(); +// } +// for ( var edge in this.edges) { +// this.args.edges[edge] = this.getEdgeById(edge).toJSON(); +// } +// +// return (this.args); + + + var serialize = new Object(); + serialize = JSON.parse(JSON.stringify(this.args)); + serialize.vertices = new Object(); + serialize.edges = new Object(); + + for ( var vertex in this.vertices) { + serialize.vertices[vertex] = this.getVertexById(vertex).toJSON(); + } + for ( var edge in this.edges) { + serialize.edges[edge] = this.getEdgeById(edge).toJSON(); + } + + return (serialize); +}; + + + +NetworkDataSetFormatter.prototype._getNodeSize = function(nodeId){ + if (this.isVerticesBalanced()){ + var total = this.maxClass - this.minClass; + if (total == 0){ total = 1;} + var nodeConnection = this.dataset.getVertexById(nodeId).getEdges().length; + return ((nodeConnection*this.args.nodesMaxSize)/total) + this.args.nodesMinSize; + } + return this.getVertexById(nodeId).getDefault().getSize(); +}; + +NetworkDataSetFormatter.prototype._recalculateSize = function(){ + if (this.isVerticesBalanced()){ + this.maxClass = this.dataset.getMaxClass(); + this.minClass = this.dataset.getMinClass(); + for ( var vertexIdAll in this.vertices) { + var size = this._getNodeSize(vertexIdAll); + this.vertices[vertexIdAll].getDefault().setSize(size); + this.vertices[vertexIdAll].getSelected().setSize(size); + this.vertices[vertexIdAll].getOver().setSize(size); + } + } +}; + + +NetworkDataSetFormatter.prototype.addVertex = function(vertexId, json){ + + + if (json == null){ + this.vertices[vertexId] = new CircleVertexGraphFormatter(vertexId, this.args.vertexFormatProperties.defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); + } + else{ + + /** Cargo los attributos desde el json **/ + if (json.type == null){ + this.vertices[vertexId] = new CircleVertexGraphFormatter(vertexId, this.args.vertexFormatProperties.defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); + } + + if ((json.type == "SquareVertexGraphFormatter")||(json.type == "SquareVertexNetworkFormatter")){ + this.vertices[vertexId] = new SquareVertexGraphFormatter(vertexId); + this.vertices[vertexId].loadFromJSON(json); + } + + if ((json.type == "CircleVertexGraphFormatter")||(json.type == "CircleVertexNetworkFormatter")){ + this.vertices[vertexId] = new CircleVertexGraphFormatter(vertexId); + this.vertices[vertexId].loadFromJSON(json); + } + + if ((json.type == "EllipseVertexGraphFormatter")||(json.type == "EllipseVertexNetworkFormatter")){ + this.vertices[vertexId] = new EllipseVertexGraphFormatter(vertexId); + this.vertices[vertexId].loadFromJSON(json); + } + + if ((json.type == "RectangleVertexGraphFormatter")||(json.type == "RectangleVertexNetworkFormatter")){ + this.vertices[vertexId] = new RectangleVertexGraphFormatter(vertexId); + this.vertices[vertexId].loadFromJSON(json); + } + + if ((json.type == "RoundedVertexGraphFormatter")||(json.type == "RoundedVertexNetworkFormatter")){ + this.vertices[vertexId] = new RoundedVertexGraphFormatter(vertexId); + this.vertices[vertexId].loadFromJSON(json); + } + + } + + + var _this = this; + this.vertices[vertexId].stateChanged.attach(function (sender, item){ + _this.changed.notify(item); + }); + + var size = this._getNodeSize(vertexId); + this.vertices[vertexId].defaultFormat.args.size = size; + this.vertices[vertexId].selected.args.size = size; + this.vertices[vertexId].over.args.size = size; + +}; + +NetworkDataSetFormatter.prototype.addEdge = function(edgeId, json){ + + /** Es un edge nuevo que le doy los atributos por defecto **/ + if (json == null){ + if (this.dataset.getEdgeById(edgeId).getNodeSource().getId() == this.dataset.getEdgeById(edgeId).getNodeTarget().getId()){ + this.edges[edgeId] = new BezierEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); + }else{ + this.edges[edgeId] = new DirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); + } + } + else{ + /** Cargo los attributos desde el json **/ + if (json.type == null){ + this.edges[edgeId] = new LineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); + } + + if ((json.type == "LineEdgeGraphFormatter")||(json.type == "LineEdgeNetworkFormatter")){ + this.edges[edgeId] = new LineEdgeGraphFormatter(edgeId); + this.edges[edgeId].loadFromJSON(json); + } + if ((json.type == "DirectedLineEdgeGraphFormatter")||(json.type == "DirectedLineEdgeNetworkFormatter")){ + this.edges[edgeId] = new DirectedLineEdgeGraphFormatter(edgeId); + this.edges[edgeId].loadFromJSON(json); + } + + if ((json.type == "BezierEdgeGraphFormatter")||(json.type == "BezierEdgeNetworkFormatter")){ + this.edges[edgeId] = new BezierEdgeGraphFormatter(edgeId); + this.edges[edgeId].loadFromJSON(json); + } + + + if ((json.type == "CutDirectedLineEdgeGraphFormatter")||(json.type == "CutDirectedLineEdgeNetworkFormatter")){ + this.edges[edgeId] = new CutDirectedLineEdgeGraphFormatter(edgeId); + this.edges[edgeId].loadFromJSON(json); + } + + if ((json.type == "DotDirectedLineEdgeGraphFormatter")||(json.type == "DotDirectedLineEdgeNetworkFormatter")){ + this.edges[edgeId] = new DotDirectedLineEdgeGraphFormatter(edgeId); + this.edges[edgeId].loadFromJSON(json); + } + if ((json.type == "OdotDirectedLineEdgeGraphFormatter")||(json.type == "OdotDirectedLineEdgeNetworkFormatter")){ + this.edges[edgeId] = new OdotDirectedLineEdgeGraphFormatter(edgeId); + this.edges[edgeId].loadFromJSON(json); + } + + if ((json.type == "OdirectedLineEdgeGraphFormatter")||(json.type == "OdirectedLineEdgeNetworkFormatter")){ + this.edges[edgeId] = new OdirectedLineEdgeGraphFormatter(edgeId); + this.edges[edgeId].loadFromJSON(json); + } + } + + var _this = this; + this.edges[edgeId].stateChanged.attach(function (sender, item){ + _this.edgeChanged.notify(item); + }); + + this._recalculateSize(); +}; + +NetworkDataSetFormatter.prototype._setDataset = function(dataset){ + this.dataset = dataset; + this.maxClass = dataset.getMaxClass(); + this.minClass = dataset.getMinClass(); + this._attachDatasetEvents(); +}; + +NetworkDataSetFormatter.prototype.changeEdgeType = function(edgeId, type){ + if ((type == "LineEdgeGraphFormatter")||(type == "LineEdgeNetworkFormatter")){ + this.edges[edgeId] = new LineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); + + } + if ((type == "DirectedLineEdgeGraphFormatter")||(type == "DirectedLineEdgeNetworkFormatter")){ + this.edges[edgeId] = new DirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); + } + + if ((type == "CutDirectedLineEdgeGraphFormatter")||(type == "CutDirectedLineEdgeNetworkFormatter")){ + this.edges[edgeId] = new CutDirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); + } + + if ((type == "DotDirectedLineEdgeGraphFormatter")||(type == "DotDirectedLineEdgeNetworkFormatter")){ + this.edges[edgeId] = new DotDirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); + } + + if ((type == "OdotDirectedLineEdgeGraphFormatter")||(type == "OdotDirectedLineEdgeNetworkFormatter")){ + this.edges[edgeId] = new OdotDirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); + } + + if ((type == "OdirectedLineEdgeGraphFormatter")||(type == "OdirectedLineEdgeNetworkFormatter")){ + this.edges[edgeId] = new OdirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); + } + + + + var _this = this; + this.edges[edgeId].stateChanged.attach(function (sender, item){ + _this.edgeChanged.notify(item); + }); + _this.edgeChanged.notify(this.edges[edgeId]); +}; +/* +classe = "SquareNetworkNodeFormatter"; +} +if (value == "circle"){ + classe = "CircleNetworkNodeFormatter"; + **/ +NetworkDataSetFormatter.prototype.changeNodeType = function(vertexId, type){ + var defaultFormat = JSON.parse(JSON.stringify(this.vertices[vertexId].getDefault())); + var selectedFormat = JSON.parse(JSON.stringify(this.vertices[vertexId].getSelected())); + var defaultFormat = JSON.parse(JSON.stringify(this.vertices[vertexId].getDefault())); + var defaultFormat = JSON.parse(JSON.stringify(this.vertices[vertexId].getDefault())); + + if ((type == "SquareVertexGraphFormatter")||(type == "SquareVertexNetworkFormatter")){ + this.vertices[vertexId] = new SquareVertexGraphFormatter(vertexId,defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); + } + + if ((type == "CircleVertexGraphFormatter")||(type == "CircleVertexNetworkFormatter")){ + this.vertices[vertexId] = new CircleVertexGraphFormatter(vertexId, defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); + } + + if ((type == "EllipseVertexGraphFormatter")||(type == "EllipseVertexNetworkFormatter")){ + this.vertices[vertexId] = new EllipseVertexGraphFormatter(vertexId, defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); + } + + if ((type == "RectangleVertexGraphFormatter")||(type == "RectangleVertexNetworkFormatter")){ + this.vertices[vertexId] = new RectangleVertexGraphFormatter(vertexId, defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); + } + + if ((type == "RoundedVertexGraphFormatter")||(type == "RoundedVertexNetworkFormatter")){ + this.vertices[vertexId] = new RoundedVertexGraphFormatter(vertexId, defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); + } + + if ((type == "OctagonVertexGraphFormatter")||(type == "OctagonVertexNetworkhFormatter")){ + this.vertices[vertexId] = new OctagonVertexGraphFormatter(vertexId, defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); + } + + + var _this = this; + this.vertices[vertexId].stateChanged.attach(function (sender, item){ + _this.changed.notify(item); + }); + _this.changed.notify(this.vertices[vertexId]); +}; + + + +NetworkDataSetFormatter.prototype.dataBind = function(networkDataSet){ + var _this = this; + this._setDataset(networkDataSet); + + for ( var vertex in this.dataset.getVertices()) { + this.addVertex(vertex); + } + + for ( var edge in this.dataset.getEdges()) { + this.addEdge(edge); + } +}; + +NetworkDataSetFormatter.prototype._removeEdge = function(edgeId){ + delete this.edges[edgeId]; +}; + +NetworkDataSetFormatter.prototype._removeVertex = function(vertexId){ + delete this.vertices[vertexId]; +}; + +NetworkDataSetFormatter.prototype._attachDatasetEvents = function(id){ + var _this = this; + this.dataset.vertexDeleted.attach(function (sender, item){ + _this._removeVertex(item.getId()); + }); + + this.dataset.edgeDeleted.attach(function (sender, item){ + _this._removeEdge(item.getId()); + }); + + this.dataset.newVertex.attach(function (sender, item){ + _this.addVertex(item.getId()); + }); + + this.dataset.newEdge.attach(function (sender, item){ + _this.addEdge(item.getId()); + }); +}; + + +NetworkDataSetFormatter.prototype.getVertexById = function(id){ + return this.vertices[id]; +}; + +NetworkDataSetFormatter.prototype.getEdgeById = function(id){ + return this.edges[id]; +}; + +NetworkDataSetFormatter.prototype.makeLabelsBigger = function(){ +for ( var vertexId in this.vertices) { + var fontSize = this.vertices[vertexId].getDefault().getFontSize() + 2; + this.vertices[vertexId].getDefault().setFontSize(fontSize); + } +}; + +NetworkDataSetFormatter.prototype.makeLabelsSmaller = function(){ + for ( var vertexId in this.vertices) { + var fontSize = this.vertices[vertexId].getDefault().getFontSize() - 2; + this.vertices[vertexId].getDefault().setFontSize(fontSize); + } +}; + + +NetworkDataSetFormatter.prototype.resize = function(width, height){ + this.args.width = width; + this.args.height = height; + this.resized.notify(); +}; + +/** ZOOM GETTERS **/ +NetworkDataSetFormatter.prototype.getZoomScaleStepFactor = function(){return this.args.zoomScaleStepFactor;}; +NetworkDataSetFormatter.prototype.setZoomScaleStepFactor = function(scaleFactor){this.args.zoomScaleStepFactor = scaleFactor;}; +NetworkDataSetFormatter.prototype.getZoomScale = function(){return this.args.zoomScale;}; +NetworkDataSetFormatter.prototype.setZoomScale = function(scale){this.args.zoomScale = scale;}; + +NetworkDataSetFormatter.prototype.getNodesMaxSize = function(){return this.args.nodesMaxSize;}; +NetworkDataSetFormatter.prototype.getNodesMinSize = function(){return this.args.nodesMinSize;}; + +/** SIZE SETTERS AND GETTERS **/ +NetworkDataSetFormatter.prototype.isVerticesBalanced = function(){return this.args.balanceNodes;}; +NetworkDataSetFormatter.prototype.getWidth = function(){return this.args.width;}; +NetworkDataSetFormatter.prototype.getHeight = function(){return this.args.height;}; + +/** OPTIONAL PARAMETERS GETTERS AND SETTERS **/ +NetworkDataSetFormatter.prototype.getBackgroundImage = function(){return this.args.backgroundImage;}; +NetworkDataSetFormatter.prototype.setBackgroundImage = function(value){this.args.backgroundImage = value; this.backgroundImageChanged.notify(this);}; + + +NetworkDataSetFormatter.prototype.getBackgroundImageWidth = function(){return this.args.backgroundImageWidth;}; +NetworkDataSetFormatter.prototype.setBackgroundImageWidth = function(value){this.args.backgroundImageWidth = value; this.backgroundImageChanged.notify(this);}; + +NetworkDataSetFormatter.prototype.getBackgroundImageHeight = function(){return this.args.backgroundImageHeight;}; +NetworkDataSetFormatter.prototype.setBackgroundImageHeight = function(value){this.args.backgroundImageHeight = value; this.backgroundImageChanged.notify(this);}; + +NetworkDataSetFormatter.prototype.getBackgroundImageX = function(){return this.args.backgroundImageX;}; +NetworkDataSetFormatter.prototype.setBackgroundImageX = function(value){this.args.backgroundImageX = value; this.backgroundImageChanged.notify(this);}; + +NetworkDataSetFormatter.prototype.getBackgroundImageY = function(){return this.args.backgroundImageX;}; +NetworkDataSetFormatter.prototype.setBackgroundImageY = function(value){this.args.backgroundImageY = value; this.backgroundImageChanged.notify(this);}; + + + +NetworkDataSetFormatter.prototype.getBackgroundColor = function(){return this.args.backgroundColor;}; +NetworkDataSetFormatter.prototype.setBackgroundColor = function(value){this.args.backgroundColor = value; this.backgroundColorChanged.notify(this);}; + +NetworkDataSetFormatter.prototype.getWidth = function(){return this.args.width;}; +NetworkDataSetFormatter.prototype.setWidth = function(value){this.args.width = value;}; + +NetworkDataSetFormatter.prototype.getHeight = function(){return this.args.height;}; +NetworkDataSetFormatter.prototype.setHeight = function(value){this.args.height = value;}; + + + + +Vertex.prototype.getName = GraphItem.prototype.getName; +Vertex.prototype.setName = GraphItem.prototype.setName; +Vertex.prototype.getId = GraphItem.prototype.getId; + +function Vertex(id, name, args){ + GraphItem.prototype.constructor.call(this, id, name, args); + this.edgesIn= new Array(); + this.edgesOut= new Array(); +}; + +Vertex.prototype.getEdges = function(){ + return this.edgesIn.concat(this.edgesOut); +}; + +Vertex.prototype.getEdgesCount = function(){ + return this.getEdges().length; +}; + +Vertex.prototype.getEdgesIn = function(){ + return this.edgesIn; +}; + +Vertex.prototype.getEdgesOut = function(){ + return this.edgesOut; +}; + +Vertex.prototype.addEdge = function(edge){ + if (edge.getNodeSource().getId() == this.id){ + this.edgesIn.push(edge); + } + else{ + this.edgesOut.push(edge); + } +}; + +Vertex.prototype.removeEdge = function(edge){ + for ( var i = 0; i < this.getEdgesIn().length; i++) { + var edgeIn = this.edgesIn[i]; + if (edgeIn.getId() == edge.getId()){ + this.edgesIn.splice(i, 1); + } + } + for ( var i = 0; i < this.getEdgesOut().length; i++) { + var edgeIn = this.edgesOut[i]; + if (edgeIn.getId() == edge.getId()){ + this.edgesOut.splice(i, 1); + } + } +}; + +Vertex.prototype.remove = function(){ + var edges = this.getEdges(); + for ( var i = 0; i < edges.length; i++) { + var edge = edges[i]; + edge.remove(); + } + this.deleted.notify(this); +}; + + + + + +VertexGraphFormatter.prototype.getDefault = ItemGraphFormatter.prototype.getDefault; +VertexGraphFormatter.prototype.getSelected = ItemGraphFormatter.prototype.getSelected; +VertexGraphFormatter.prototype.getOver = ItemGraphFormatter.prototype.getOver; +VertexGraphFormatter.prototype.getDragging = ItemGraphFormatter.prototype.getDragging; +VertexGraphFormatter.prototype.getId = ItemGraphFormatter.prototype.getId; +VertexGraphFormatter.prototype.toJSON = ItemGraphFormatter.prototype.toJSON; +VertexGraphFormatter.prototype.loadFromJSON = ItemGraphFormatter.prototype.loadFromJSON; +VertexGraphFormatter.prototype._setEvents = ItemGraphFormatter.prototype._setEvents; + + +function VertexGraphFormatter(defaultFormat, selectedFormat, overFormat, draggingFormat){ + ItemGraphFormatter.prototype.constructor.call(this, defaultFormat, selectedFormat, overFormat, draggingFormat); +}; + + +CircleVertexGraphFormatter.prototype.getDefault = VertexGraphFormatter.prototype.getDefault; +CircleVertexGraphFormatter.prototype.getSelected = VertexGraphFormatter.prototype.getSelected; +CircleVertexGraphFormatter.prototype.getOver = VertexGraphFormatter.prototype.getOver; +CircleVertexGraphFormatter.prototype.getDragging = VertexGraphFormatter.prototype.getDragging; +CircleVertexGraphFormatter.prototype.getId = VertexGraphFormatter.prototype.getId; +CircleVertexGraphFormatter.prototype.toJSON = VertexGraphFormatter.prototype.toJSON; +CircleVertexGraphFormatter.prototype.loadFromJSON = VertexGraphFormatter.prototype.loadFromJSON; +CircleVertexGraphFormatter.prototype._setEvents = VertexGraphFormatter.prototype._setEvents; + +function CircleVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ + VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); + this.args.type = "CircleVertexGraphFormatter"; + if (defaultFormat != null){ + if (defaultFormat.radius != null){ + this.defaultFormat.args.radius = defaultFormat.radius; + } + } + + if (selectedFormat != null){ + if (selectedFormat.radius != null){ + this.selected.args.radius = selectedFormat.radius; + } + } + + if (overFormat != null){ + if (overFormat.radius != null){ + this.over.args.radius = overFormat.radius; + } + } + + if (draggingFormat != null){ + if (draggingFormat.radius != null){ + this.dragging.args.draggingFormat = draggingFormat.radius; + } + } +}; + + + +SquareVertexGraphFormatter.prototype.getDefault = VertexGraphFormatter.prototype.getDefault; +SquareVertexGraphFormatter.prototype.getSelected = VertexGraphFormatter.prototype.getSelected; +SquareVertexGraphFormatter.prototype.getOver = VertexGraphFormatter.prototype.getOver; +SquareVertexGraphFormatter.prototype.getDragging = VertexGraphFormatter.prototype.getDragging; +SquareVertexGraphFormatter.prototype.getId = VertexGraphFormatter.prototype.getId; +SquareVertexGraphFormatter.prototype.toJSON = VertexGraphFormatter.prototype.toJSON; +SquareVertexGraphFormatter.prototype.loadFromJSON = VertexGraphFormatter.prototype.loadFromJSON; +SquareVertexGraphFormatter.prototype._setEvents = VertexGraphFormatter.prototype._setEvents; + +function SquareVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ + VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); + this.args.type = "SquareVertexGraphFormatter"; + if (defaultFormat != null){ + if (defaultFormat.radius != null){ + this.defaultFormat.args.radius = defaultFormat.radius; + } + } + + if (selectedFormat != null){ + if (selectedFormat.radius != null){ + this.selected.args.radius = selectedFormat.radius; + } + } + + if (overFormat != null){ + if (overFormat.radius != null){ + this.over.args.radius = overFormat.radius; + } + } + + if (draggingFormat != null){ + if (draggingFormat.radius != null){ + this.dragging.args.draggingFormat = draggingFormat.radius; + } + } +}; + + +EllipseVertexGraphFormatter.prototype.getDefault = VertexGraphFormatter.prototype.getDefault; +EllipseVertexGraphFormatter.prototype.getSelected = VertexGraphFormatter.prototype.getSelected; +EllipseVertexGraphFormatter.prototype.getOver = VertexGraphFormatter.prototype.getOver; +EllipseVertexGraphFormatter.prototype.getDragging = VertexGraphFormatter.prototype.getDragging; +EllipseVertexGraphFormatter.prototype.getId = VertexGraphFormatter.prototype.getId; +EllipseVertexGraphFormatter.prototype.toJSON = VertexGraphFormatter.prototype.toJSON; +EllipseVertexGraphFormatter.prototype.loadFromJSON = VertexGraphFormatter.prototype.loadFromJSON; +EllipseVertexGraphFormatter.prototype._setEvents = VertexGraphFormatter.prototype._setEvents; + +function EllipseVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ + VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); + this.args.type = "EllipseVertexGraphFormatter"; + if (defaultFormat != null){ + if (defaultFormat.radius != null){ + this.defaultFormat.args.radius = defaultFormat.radius; + } + } + + if (selectedFormat != null){ + if (selectedFormat.radius != null){ + this.selected.args.radius = selectedFormat.radius; + } + } + + if (overFormat != null){ + if (overFormat.radius != null){ + this.over.args.radius = overFormat.radius; + } + } + + if (draggingFormat != null){ + if (draggingFormat.radius != null){ + this.dragging.args.draggingFormat = draggingFormat.radius; + } + } +}; + + + +RectangleVertexGraphFormatter.prototype.getDefault = ItemGraphFormatter.prototype.getDefault; +RectangleVertexGraphFormatter.prototype.getSelected = ItemGraphFormatter.prototype.getSelected; +RectangleVertexGraphFormatter.prototype.getOver = ItemGraphFormatter.prototype.getOver; +RectangleVertexGraphFormatter.prototype.getDragging = ItemGraphFormatter.prototype.getDragging; +RectangleVertexGraphFormatter.prototype.getId = ItemGraphFormatter.prototype.getId; +RectangleVertexGraphFormatter.prototype.toJSON = ItemGraphFormatter.prototype.toJSON; +RectangleVertexGraphFormatter.prototype.loadFromJSON = ItemGraphFormatter.prototype.loadFromJSON; +RectangleVertexGraphFormatter.prototype._setEvents = ItemGraphFormatter.prototype._setEvents; + +function RectangleVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ + VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); + this.args.type = "RectangleVertexGraphFormatter"; + if (defaultFormat != null){ + if (defaultFormat.radius != null){ + this.defaultFormat.args.radius = defaultFormat.radius; + } + } + + if (selectedFormat != null){ + if (selectedFormat.radius != null){ + this.selected.args.radius = selectedFormat.radius; + } + } + + if (overFormat != null){ + if (overFormat.radius != null){ + this.over.args.radius = overFormat.radius; + } + } + + if (draggingFormat != null){ + if (draggingFormat.radius != null){ + this.dragging.args.draggingFormat = draggingFormat.radius; + } + } +}; + + + +RoundedVertexGraphFormatter.prototype.getDefault = ItemGraphFormatter.prototype.getDefault; +RoundedVertexGraphFormatter.prototype.getSelected = ItemGraphFormatter.prototype.getSelected; +RoundedVertexGraphFormatter.prototype.getOver = ItemGraphFormatter.prototype.getOver; +RoundedVertexGraphFormatter.prototype.getDragging = ItemGraphFormatter.prototype.getDragging; +RoundedVertexGraphFormatter.prototype.getId = ItemGraphFormatter.prototype.getId; +RoundedVertexGraphFormatter.prototype.toJSON = ItemGraphFormatter.prototype.toJSON; +RoundedVertexGraphFormatter.prototype.loadFromJSON = ItemGraphFormatter.prototype.loadFromJSON; +RoundedVertexGraphFormatter.prototype._setEvents = ItemGraphFormatter.prototype._setEvents; + +function RoundedVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ + VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); + this.args.type = "RoundedVertexGraphFormatter"; + if (defaultFormat != null){ + if (defaultFormat.radius != null){ + this.defaultFormat.args.radius = defaultFormat.radius; + } + } + + if (selectedFormat != null){ + if (selectedFormat.radius != null){ + this.selected.args.radius = selectedFormat.radius; + } + } + + if (overFormat != null){ + if (overFormat.radius != null){ + this.over.args.radius = overFormat.radius; + } + } + + if (draggingFormat != null){ + if (draggingFormat.radius != null){ + this.dragging.args.draggingFormat = draggingFormat.radius; + } + } +}; + + + +OctagonVertexGraphFormatter.prototype.getDefault = ItemGraphFormatter.prototype.getDefault; +OctagonVertexGraphFormatter.prototype.getSelected = ItemGraphFormatter.prototype.getSelected; +OctagonVertexGraphFormatter.prototype.getOver = ItemGraphFormatter.prototype.getOver; +OctagonVertexGraphFormatter.prototype.getDragging = ItemGraphFormatter.prototype.getDragging; +OctagonVertexGraphFormatter.prototype.getId = ItemGraphFormatter.prototype.getId; +OctagonVertexGraphFormatter.prototype.toJSON = ItemGraphFormatter.prototype.toJSON; +OctagonVertexGraphFormatter.prototype.loadFromJSON = ItemGraphFormatter.prototype.loadFromJSON; +OctagonVertexGraphFormatter.prototype._setEvents = ItemGraphFormatter.prototype._setEvents; + +function OctagonVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ + VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); + this.args.type = "OctagonVertexGraphFormatter"; + if (defaultFormat != null){ + if (defaultFormat.radius != null){ + this.defaultFormat.args.radius = defaultFormat.radius; + } + } + + if (selectedFormat != null){ + if (selectedFormat.radius != null){ + this.selected.args.radius = selectedFormat.radius; + } + } + + if (overFormat != null){ + if (overFormat.radius != null){ + this.over.args.radius = overFormat.radius; + } + } + + if (draggingFormat != null){ + if (draggingFormat.radius != null){ + this.dragging.args.draggingFormat = draggingFormat.radius; + } + } +}; + + + +var Colors = new function() +{ + this.hashColor = []; + this.getColorByScoreArrayValue = function (arrayScore) + { + var array = new Array(); + + for (var i = 0; i< arrayScore.length; i++) + { + + var color = this.getColorByScoreValue(arrayScore[i]) + array.push( color); + + } + return array; + }; + + this.getHexStringByScoreArrayValue = function (arrayScore) + { + var arrayColor = this.getColorByScoreArrayValue(arrayScore); + var arrayHex = new Array(); + for (var i = 0; i< arrayColor.length; i++) + { + arrayHex.push( arrayColor[i].HexString()); + } + return arrayHex; + }; + + this.getColorByScoreValue = function (score) + { + + var truncate = score.toString().substr(0,4); + if (this.hashColor[truncate]!=null) + { + return this.hashColor[truncate]; + } + + + if(isNaN(score)) { + return Colors.ColorFromRGB(0,0,0); + } + var value; + + var from, to; + if(score < 0.5) { + from = Colors.ColorFromRGB(0,0,255); + to = Colors.ColorFromRGB(255,255,255); + value = (score * 2); + } else { + from = Colors.ColorFromRGB(255,255,255); + to = Colors.ColorFromRGB(255,0,0); + value = (score * 2) - 1; + } + + var x = value; + var y = 1.0 - value; + var color = Colors.ColorFromRGB(y * from.Red() + x * to.Red(), y * from.Green() + x * to.Green(), y * from.Blue() + x * to.Blue()); + + this.hashColor[truncate] = color; + + return color; + }; + + this.ColorFromHSV = function(hue, sat, val) + { + var color = new Color(); + color.SetHSV(hue,sat,val); + return color; + }; + + this.ColorFromRGB = function(r, g, b) + { + var color = new Color(); + color.SetRGB(r,g,b); + return color; + }; + + this.ColorFromHex = function(hexStr) + { + var color = new Color(); + color.SetHexString(hexStr); + return color; + }; + + function Color() { + //Stored as values between 0 and 1 + var red = 0; + var green = 0; + var blue = 0; + + //Stored as values between 0 and 360 + var hue = 0; + + //Strored as values between 0 and 1 + var saturation = 0; + var value = 0; + + this.SetRGB = function(r, g, b) + { + red = r/255.0; + green = g/255.0; + blue = b/255.0; + calculateHSV(); + }; + + this.Red = function() { return Math.round(red*255); }; + + this.Green = function() { return Math.round(green*255); }; + + this.Blue = function() { return Math.round(blue*255); }; + + this.SetHSV = function(h, s, v) + { + hue = h; + saturation = s; + value = v; + calculateRGB(); + }; + + this.Hue = function() + { return hue; }; + + this.Saturation = function() + { return saturation; }; + + this.Value = function() + { return value; }; + + this.SetHexString = function(hexString) + { + if(hexString == null || typeof(hexString) != "string") + { + this.SetRGB(0,0,0); + return; + } + + if (hexString.substr(0, 1) == '#') + hexString = hexString.substr(1); + + if(hexString.length != 6) + { + this.SetRGB(0,0,0); + return; + } + + var r = parseInt(hexString.substr(0, 2), 16); + var g = parseInt(hexString.substr(2, 2), 16); + var b = parseInt(hexString.substr(4, 2), 16); + if (isNaN(r) || isNaN(g) || isNaN(b)) + { + this.SetRGB(0,0,0); + return; + } + + this.SetRGB(r,g,b); + }; + + this.HexString = function() + { + + var rStr = this.Red().toString(16); + if (rStr.length == 1) + rStr = '0' + rStr; + var gStr = this.Green().toString(16); + if (gStr.length == 1) + gStr = '0' + gStr; + var bStr = this.Blue().toString(16); + if (bStr.length == 1) + bStr = '0' + bStr; + return ('#' + rStr + gStr + bStr).toUpperCase(); + }; + + this.Complement = function() + { + var newHue = (hue >= 180) ? hue - 180 : hue + 180; + var newVal = (value * (saturation - 1) + 1); + var newSat = (value*saturation) / newVal; + var newColor = new Color(); + newColor.SetHSV(newHue, newSat, newVal); + return newColor; + } ; + + function calculateHSV() + { + var max = Math.max(Math.max(red, green), blue); + var min = Math.min(Math.min(red, green), blue); + + value = max; + + saturation = 0; + if(max != 0) + saturation = 1 - min/max; + + hue = 0; + if(min == max) + return; + + var delta = (max - min); + if (red == max) + hue = (green - blue) / delta; + else if (green == max) + hue = 2 + ((blue - red) / delta); + else + hue = 4 + ((red - green) / delta); + hue = hue * 60; + if(hue < 0) + hue += 360; + } + + function calculateRGB() + { + red = value; + green = value; + blue = value; + + if(value == 0 || saturation == 0) + return; + + var tHue = (hue / 60); + var i = Math.floor(tHue); + var f = tHue - i; + var p = value * (1 - saturation); + var q = value * (1 - saturation * f); + var t = value * (1 - saturation * (1 - f)); + switch(i) + { + case 0: + red = value; green = t; blue = p; + break; + case 1: + red = q; green = value; blue = p; + break; + case 2: + red = p; green = value; blue = t; + break; + case 3: + red = p; green = q; blue = value; + break; + case 4: + red = t; green = p; blue = value; + break; + default: + red = value; green = p; blue = q; + break; + } + } + } +} +(); +/* + * Clase gestiona la insercción, eliminación de los elementos en el DOM + * + * Vital hacerla SIEMPRE compatible hacia atrás + * + * Last update: 28-10-2010 + * + */ + + +var DOM = {}; + +DOM.createNewElement = function(type, nodeParent, attributes) +{ + + var node = document.createElement(type); + for (var i=0; i0) + { + parent.removeChild(parent.childNodes[0]); + + } +}; + +DOM.select = function(targetID) +{ + return document.getElementById(targetID); +// return $("#"+targetID); +}; +var Geometry = +{ + + /** From tow points obtains the angles formed with the cartesian side **/ + getAngleBetweenTwoPoints : function(x1, y1, x2, y2){ + //var m = (y1 - y2)/ (x1 - x2); + return Math.atan2(y2-y1, x2-x1); + }, + + getAdjacentSideOfRectangleRight : function(angle, hypotenuse){ + return Math.abs(Math.cos(angle)*hypotenuse); + }, + + getOppositeSideOfRectangleRight : function(angle, hypotenuse){ + return Math.abs(Math.sin(angle)*hypotenuse); + }, + + toDegree: function(radian){ + return radian*180/Math.PI; + + } + + +}; + +var SVG = +{ + svgns : 'http://www.w3.org/2000/svg', + xlinkns : "http://www.w3.org/1999/xlink", + + createSVGCanvas: function(parentNode, attributes) + { + + attributes.push( ['xmlns', SVG.svgns], ['xmlns:xlink', 'http://www.w3.org/1999/xlink']); + var svg = document.createElementNS("http://www.w3.org/2000/svg", "svg"); + this._setProperties(svg, attributes); + parentNode.appendChild( svg); + return svg; + + }, + + createRectangle : function (x, y, width, height, attributes){ + var rect = document.createElementNS(this.svgns, "rect"); + rect.setAttribute("x",x); + rect.setAttribute("y",y); + rect.setAttribute("width",width); + rect.setAttribute("height",height); + SVG._setProperties(rect, attributes); + return rect; + }, + + drawImage64 : function (x, y, width, height, base64, svgNode, attributes) { + var node = SVG.createImage64(x, y, width, height, base64, attributes); + svgNode.appendChild(node); + return node; + }, + + createImage64 : function (x, y, width, height, base64, attributes) { + var img = document.createElementNS(this.svgns, "image"); + img.setAttribute("x",x); + img.setAttribute("y",y); + img.setAttribute("width",width); + img.setAttribute("height",height); + img.setAttribute("xlink:href",base64); + SVG._setProperties(img, attributes); + return img; + }, + + createLine: function (x1, y1, x2, y2, attributes){ + var line = document.createElementNS(this.svgns,"line"); + line.setAttribute("x1",x1); + line.setAttribute("y1",y1); + line.setAttribute("x2", x2); + line.setAttribute("y2", y2); + SVG._setProperties(line, attributes); + return line; + }, + + createClip: function (id, nodeToClip, attributes){ + var clip = document.createElementNS(this.svgns,"clipPath"); + clip.setAttribute("id",id); + clip.appendChild(nodeToClip); + return clip; + }, + + drawClip : function (id, nodeToClip, svgNode) { + var node = SVG.createClip(id, nodeToClip); + svgNode.appendChild(node); + return node; + }, + + drawRectangle : function (cx, cy, width, height, svgNode, attributes) { + try{ + var node = SVG.createRectangle(cx, cy, width, height, attributes); + svgNode.appendChild(node); + } + catch(e){ + + console.log("-------------------- "); + console.log("Error on drawRectangle " + e); + console.log(attributes); + console.log("-------------------- "); + } + return node; + }, + + createEllipse : function (x, y, rx, ry, attributes){ + var rect = document.createElementNS(this.svgns, "ellipse"); + rect.setAttribute("cx",x); + rect.setAttribute("cy",y); + rect.setAttribute("rx",rx); + rect.setAttribute("ry",ry); + SVG._setProperties(rect, attributes); + return rect; + }, + + drawEllipse : function (cx, cy, rx, ry, svgNode, attributes) { + var node = SVG.createEllipse(cx, cy, rx, ry, attributes); + svgNode.appendChild(node); + return node; + }, + + drawImage : function (x, y, canvasSVG, attributes) { + var image = document.createElementNS(this.svgns, "image"); + image.setAttribute("x",x); + image.setAttribute("y",y); + canvasSVG.appendChild(image); + SVG._setProperties(image, attributes); + }, + + drawLine : function (x1, y1, x2, y2, nodeSVG, attributes) { + try{ + var line = SVG.createLine(x1, y1, x2, y2, attributes); + nodeSVG.appendChild(line); + }catch(e){ + } + return line; + }, + + + drawPath: function (d, nodeSVG, attributes) { + var path = SVG.createPath(d, attributes); + nodeSVG.appendChild(path); + return path; + }, + + createPoligon : function (points, attributes){ + var poligon = document.createElementNS(this.svgns, "polygon"); + poligon.setAttribute("points",points); + SVG._setProperties(poligon, attributes); + return poligon; + }, + + drawPoligon : function (points, canvasSVG, attributes){ + var poligon = SVG.createPoligon(points, attributes); + canvasSVG.appendChild(poligon); + return poligon; + }, + // + + createPath : function (d, attributes){ + var path = document.createElementNS(this.svgns, "path"); + path.setAttribute("d",d); + SVG._setProperties(path, attributes); + return path; + }, + + drawCircle : function (x, y, radio, canvasSVG, attributes) { + + var newText = document.createElementNS(this.svgns,"circle"); + newText.setAttribute("cx",x); + newText.setAttribute("cy",y); + newText.setAttribute("r",radio); + + canvasSVG.appendChild(newText); + attributes["cursor"] = "pointer"; + this._setProperties(newText, attributes); + return newText; + }, + + + _setProperties: function(node, attributes) + { + if (attributes instanceof Array){ + for (var i=0; i< attributes.length; i++) + { + node.setAttribute(attributes[i][0], attributes[i][1]); + } + } + else{ + for ( var key in attributes){ + node.setAttribute(key, attributes[key]); + } + } + }, + +/* drawPath: function(pointsArray, canvasSVG, attributes){ + var path = document.createElementNS(this.svgns,"polyline"); + path.setAttribute ('id', id); + + var d= pointsArray[0].x+ " "+ pointsArray[0].y; + for (var i=1; i< pointsArray.length; i++) + { + d=d+" "+pointsArray[i].x+" "+pointsArray[i].y; + } + path.setAttribute ('points', d); + canvasSVG.appendChild(path); + },*/ + + createText : function (x, y, text, attributes) { + var node = document.createElementNS(this.svgns,"text"); + node.setAttributeNS(null , "x",x); + node.setAttributeNS(null, "y",y); + + var textNode = document.createTextNode(text); + node.appendChild(textNode); + + this._setProperties(node, attributes); + return node; + }, + + drawText : function (x, y, text, canvasSVG, attributes) { + var text = SVG.createText(x, y, text, attributes); + canvasSVG.appendChild(text); + return text; + }, + + + + drawGroup: function(svgNode, attributes) + { + var group = SVG.createGroup(attributes); + svgNode.appendChild(group); + return group; + }, + + createGroup: function(attributes){ + var group = document.createElementNS(this.svgns,"g"); + this._setProperties(group, attributes); + return group; + } + +}; + + + +var CanvasToSVG = { + + convert: function(sourceCanvas, targetSVG, x, y, id, attributes) { + + var img = this._convert(sourceCanvas, targetSVG, x, y, id); + + for (var i=0; i< attributes.length; i++) + { + img.setAttribute(attributes[i][0], attributes[i][1]); + } + }, + + _convert: function(sourceCanvas, targetSVG, x, y, id) { + var svgNS = "http://www.w3.org/2000/svg"; + var xlinkNS = "http://www.w3.org/1999/xlink"; + // get base64 encoded png from Canvas + var image = sourceCanvas.toDataURL(); + + // must be careful with the namespaces + var svgimg = document.createElementNS(svgNS, "image"); + + svgimg.setAttribute('id', id); + + //svgimg.setAttribute('class', class); + //svgimg.setAttribute('xlink:href', image); + svgimg.setAttributeNS(xlinkNS, 'xlink:href', image); + + + + + svgimg.setAttribute('x', x ? x : 0); + svgimg.setAttribute('y', y ? y : 0); + svgimg.setAttribute('width', sourceCanvas.width); + svgimg.setAttribute('height', sourceCanvas.height); + //svgimg.setAttribute('cursor', 'pointer'); + svgimg.imageData = image; + + targetSVG.appendChild(svgimg); + return svgimg; + }, + + importSVG: function(sourceSVG, targetCanvas) { + svg_xml = sourceSVG;//(new XMLSerializer()).serializeToString(sourceSVG); + var ctx = targetCanvas.getContext('2d'); + + var img = new Image(); + img.src = "data:image/svg+xml;base64," + btoa(svg_xml); +// img.onload = function() { + ctx.drawImage(img, 0, 0); +// }; + } + +}; +/* +Graph.prototype.importSVG = function(sourceSVG, targetCanvas) { + sourceSVG = this._svg; + targetCanvas = document.createElementNS('canvas'); + // https://developer.mozilla.org/en/XMLSerializer + svg_xml = (new XMLSerializer()).serializeToString(sourceSVG); + var ctx = targetCanvas.getContext('2d'); + // this is just a JavaScript (HTML) image + var img = new Image(); + // http://en.wikipedia.org/wiki/SVG#Native_support + // https://developer.mozilla.org/en/DOM/window.btoa + img.src = "data:image/svg+xml;base64," + btoa(svg_xml); + img.onload = function() { + // after this, Canvas’ origin-clean is DIRTY + ctx.drawImage(img, 0, 0); + } +}; +*/ + +/* + +Normalizacion de datos para dibujar colores +Issues: + No sé como debería llamarse esta libreria + No sé si ya existe una funciçon en javascript que lo haga + + +*/ + + +var Normalizer = new function() +{ + this.normalizeArray = function (arrayData) + { + + return this.standardizeArray(this.normal(arrayData)); + +// var result = this._getMaxAndMin(arrayData); +// var min =result[0]; +// var max = result[1]; +// +// +// //los hacemos todos positivos +// for (var i = 0; i< arrayData.length; i++) +// { +// arrayData[i]= Math.abs(min) + parseFloat(arrayData[i]); +// } +// +// var result = this._getMaxAndMin(arrayData); +// var min =result[0]; +// var max = result[1]; +// +// +// var resultArray = new Array(); +// for (var i = 0; i< arrayData.length; i++) +// { +// resultArray.push(arrayData[i]*1/max); +// } +// return resultArray; + }; + + this.normal = function(arrayData){ + var mean = this._getMean(arrayData); + var deviation = this._getStdDeviation(arrayData); + var result = this._getMaxAndMin(arrayData); + var min = result[0]; + var max = result[1]; + + var resultArray = new Array(); + for (var i = 0; i< arrayData.length; i++) { + if (deviation!=0){ + resultArray.push((arrayData[i]-mean)/deviation); + }else{ + resultArray.push(arrayData[i]); + } + } + return resultArray; + }; + + this.standardizeArray = function(arrayData) + { + var result = this._getMaxAndMin(arrayData); + var min = result[0]; + var max = result[1]; + + var offset = ( min <= 0 ) ? Math.abs(min) : (-1 * min); + var resultArray = new Array(); + for (var i = 0; i< arrayData.length; i++) { + if(max + offset!=0){ + resultArray.push((arrayData[i] + offset) / (max + offset)); + }else{ + resultArray.push(arrayData[i]+offset); + } + } + return resultArray; + }; + + + this._getMean = function(arrayData) { + var sum = 0; + for (var i = 0; i< arrayData.length; i++) { + sum = sum + parseFloat(arrayData[i]); + } + return sum/arrayData.length; + }; + + this._getStdDeviation = function(arrayData) { + var mean = this._getMean(arrayData); + var acum = 0.0; + for(var i=0; i max) max = parseFloat(arrayData[i]); + } + + return [min, max]; + }; +}; +function GraphCanvas(componentID, targetNode, args) { + this.args = {}; + /** target */ + this.targetID = targetNode.id; + + /** id manage */ + this.id = componentID; + this.args.idGraph = this.id + "main"; + this.args.idBackgroundNode = this.id + "background"; + + this.args.idEdgesGraph = this.id + "edges"; + this.args.idNodesGraph = this.id + "vertices"; + this.args.idLabelGraph = this.id + "label"; + this.args.idBackground = this.id + "background"; + + /** Objects Graph **/ + this.dataset = null; + this.formatter = null; + this.layout = null; + + /** Drawing **/ + this.circleDefaultRadius = 2; + this.squareDefaultSide = this.circleDefaultRadius * 1.5; + + /** Directed Arrow **/ + this.arrowDefaultSize = this.circleDefaultRadius; + + /** Groups **/ + this.GraphGroup = null; + this.GraphNodeGroup = null; + this.GraphLabelGroup = null; + this.GraphBackground = null; + + /** SETTINGS FLAGS **/ + this.args.draggingCanvasEnabled = false; //Flag to set if the canvas can be dragged + this.args.multipleSelectionEnabled = false; + this.args.interactive = false; + this.args.labeled = false; + this.args.linkEnabled = false; + + /** If numberEdge > maxNumberEdgesMoving then only it will move edges when mouse up **/ + this.args.maxNumberEdgesMoving = 3; + this.args.maxNumberEdgesFiringEvents = 50; + + /** Linking edges **/ + this.args.linking = false; + this.linkStartX = 0; + this.linkStartY = 0; + this.linkSVGNode = null; + this.linkNodeSource = null; + this.linkNodeTarget = null; + + /** Dragging Control **/ + this.draggingElement = null; + this.dragging = false; + this.nMouseOffsetX = 0; + this.nMouseOffsetY = 0; + this.dragStartX = 0; + this.dragStartY = 0; + this.desplazamientoX = 0; + this.desplazamientoY = 0; + + /** Selection Control **/ + this.selecting = false; + this.selectorX = null; + this.selectorY = null; + this.selectorSVGNode = null; + + /** Node status **/ + this.args.isVertexSelected = {}; + this.args.selectedVertices = []; + + /** Edges status **/ + this.args.isEdgeSelected = {}; + //this.args.selectedEdges = []; + + if (args != null) { + if (args.multipleSelectionEnabled != null) { + this.args.multipleSelectionEnabled = args.multipleSelectionEnabled; + this.args.draggingCanvasEnabled = !(this.args.multipleSelectionEnabled); + } + if (args.draggingCanvasEnabled != null) { + this.args.draggingCanvasEnabled = args.draggingCanvasEnabled; + this.args.multipleSelectionEnabled = !(this.args.draggingCanvasEnabled); + } + if (args.interactive != null) { + this.args.interactive = args.interactive; + } + if (args.labeled != null) { + this.args.labeled = args.labeled; + } + + } + + /** Hashmap with the svg node labels **/ + this.svgLabels = {}; + + /** EVENTS **/ + this.onVertexOut = new Event(this); + this.onVertexOver = new Event(this); + this.onVertexSelect = new Event(this); + this.onEdgeSelect = new Event(this); + this.onCanvasClicked = new Event(this); + this.onVertexUp = new Event(this); +} + +GraphCanvas.prototype.showLabels = function(value) { + this.args.labeled = value; + this.removeLabels(); + if (value) { + this.renderLabels(); + } +}; + +GraphCanvas.prototype.getSelectedVertices = function() { + return this.args.selectedVertices; +}; + +GraphCanvas.prototype.getSelectedEdges = function() { + var selected = []; + for ( var selectedEdge in this.args.isEdgeSelected) { + selected.push(selectedEdge); + } + return selected; +}; + +GraphCanvas.prototype.createSVGDom = function(targetID, id, width, height, backgroundColor) { + var container = document.getElementById(targetID); + this._svg = SVG.createSVGCanvas(container, [ + [ "style", "background-color:" + backgroundColor + ";" ], [ "id", id ], [ "dragx", 0 ], [ "dragy", 0 ], + [ "height", this.getFormatter().getHeight() ], [ "width", this.getFormatter().getWidth() ] ]); + return this._svg; +}; + +/** MULTIPLE SELECTION **/ +GraphCanvas.prototype.isMultipleSelectionEnabled = function() { + return this.args.multipleSelectionEnabled; +}; + +GraphCanvas.prototype.setMultipleSelection = function(value) { + this.args.multipleSelectionEnabled = value; + this.args.draggingCanvasEnabled = (!value); +}; + +GraphCanvas.prototype.setSelecting = function(value) { + this.selecting = value; +}; + +/** linking **/ +GraphCanvas.prototype.setLinking = function(value) { + this.args.linkEnabled = value; + this.selecting = !value; + this.dragging = !value; +}; + +/** CANVAS MOVING **/ +GraphCanvas.prototype.setDraggingCanvas = function(value) { + this.args.draggingCanvasEnabled = value; + this.args.multipleSelectionEnabled = !value; +}; + +GraphCanvas.prototype.isDraggingCanvasEnabled = function() { + return this.args.draggingCanvasEnabled; +}; +/** ZOOM **/ +GraphCanvas.prototype.getScale = function() { + return this.getFormatter().getZoomScale(); +}; + +GraphCanvas.prototype.setScale = function(scale) { + var graphNode = document.getElementById(this.args.idGraph); + graphNode.setAttribute("transform", graphNode.getAttribute("transform").replace("scale(" + this.getScale() + ")", "scale(" + scale + ")")); + this.getFormatter().setZoomScale(scale); +}; + +GraphCanvas.prototype.zoomIn = function() { + this.setScale(this.getScale() + this.getFormatter().getZoomScaleStepFactor()); +}; + +GraphCanvas.prototype.zoomOut = function() { + this.setScale(this.getScale() - this.getFormatter().getZoomScaleStepFactor()); + +}; + +/** SVG COORDENATES **/ +GraphCanvas.prototype.getSVGCoordenates = function(evt) { + var p = this._svg.createSVGPoint(); + p.x = evt.clientX; + p.y = evt.clientY; + + var m = this._svg.getScreenCTM(document.documentElement); + p = p.matrixTransform(m.inverse()); + return p; +}; + +/** SVG EVENTS **/ +GraphCanvas.prototype.mouseClick = function(event) { + if (event.button == 0) { + if (!this.args.interactive) { + return; + } + + if (this.isVertex(event.target)) { + this.clickNode(this.getVertexIdFromSVGId(event.target.id)); + } + /** Como el evento mouseClick viene despues del mouse up es aqui donde manejo el tema de deseccionar los elementos que estoy dragging **/ + if (this.dragging) { + this.dragging = false; + } + } +}; + +GraphCanvas.prototype.mouseMove = function(evt) { + if (this.selecting) { + this.clearLabels(); + + var width = (this.getSVGCoordenates(evt).x - this.selectorX); + var height = (this.getSVGCoordenates(evt).y - this.selectorY); + if ((width > 0) && (height > 0)) { + this.displaySelection(this.selectorX, this.selectorY, width, height); + } + if ((width > 0) && (height < 0)) { + this.displaySelection(this.selectorX, this.getSVGCoordenates(evt).y, width, Math.abs(height)); + } + if ((width < 0) && (height < 0)) { + this.displaySelection(this.getSVGCoordenates(evt).x, this.getSVGCoordenates(evt).y, Math.abs(width), Math.abs(height)); + } + if ((width < 0) && (height > 0)) { + this.displaySelection(this.selectorX + width, this.selectorY, Math.abs(width), Math.abs(height)); + } + + var x1 = (parseFloat(this.selectorSVGNode.getAttribute("x")) - DOM.select(this.id).getAttribute("dragx")) / this.getFormatter().getWidth(); + var y1 = (parseFloat(this.selectorSVGNode.getAttribute("y")) - DOM.select(this.id).getAttribute("dragy")) / this.getFormatter().getHeight(); + var x2 = (x1 + parseFloat(this.selectorSVGNode.getAttribute("width") / this.getFormatter().getWidth())); + var y2 = (y1 + parseFloat(this.selectorSVGNode.getAttribute("height") / this.getFormatter().getHeight())); + + this.deselectNodes(this.getLayout()); + var verticesSelected = this.getLayout().getVerticesByArea(x1 / this.getFormatter().getZoomScale(), y1 / this.getFormatter().getZoomScale(), + x2 / this.getFormatter().getZoomScale(), y2 / this.getFormatter().getZoomScale()); + for ( var i = 0; i < verticesSelected.length; i++) { + this.selectNode(verticesSelected[i].getId()); + this.renderLabel(verticesSelected[i].getId()); + } + + } + var p = null; + if (this.args.linking) { + p = this.getSVGCoordenates(evt); + if (this.linkSVGNode != null) { + this.linkSVGNode.setAttribute("x2", p.x - 2); + this.linkSVGNode.setAttribute("y2", p.y - 2); + } + } + + if (this.dragging) { + p = this.getSVGCoordenates(evt); + p.x -= this.nMouseOffsetX; + p.y -= this.nMouseOffsetY; + this.desplazamientoX = (this.getSVGCoordenates(evt).x - this.dragStartX);// + parseFloat(DOM.select(this.id).getAttribute("dragx")); + this.desplazamientoY = (this.getSVGCoordenates(evt).y - this.dragStartY);// + parseFloat(DOM.select(this.id).getAttribute("dragy")); + + if (this.draggingElement != null) { + /** Click sobre el recct del banground que provoca que mueva todo el canvas **/ + if (this.isNodeCanvas(this.draggingElement)) { + + p = this.getSVGCoordenates(evt); + p.x = this.desplazamientoX; + p.y = this.desplazamientoY; + + this.draggingElement.setAttribute("dragx", p.x); + this.draggingElement.setAttribute("dragy", p.y); + this.draggingElement = document.getElementById(this.args.idGraph); + this.draggingElement.setAttribute("transform", "translate(" + p.x + "," + p.y + "), scale(" + this.getScale() + ")"); + + DOM.select(this.id).setAttribute("dragx", p.x); + DOM.select(this.id).setAttribute("dragy", p.y); + + if (this.NodeSVGbackgroundImage != null) { + this.NodeSVGbackgroundImage.setAttribute("dragx", p.x); + this.NodeSVGbackgroundImage.setAttribute("dragy", p.y); + } + } else { + if (this.isVertex(this.draggingElement)) { + this.selectNode(this.getVertexIdFromSVGId(this.draggingElement.id)); + this.desplazamientoX = this.desplazamientoX / this.getFormatter().getZoomScale(); + this.desplazamientoY = this.desplazamientoY / this.getFormatter().getZoomScale(); + this.moveSelectedNodes(this.desplazamientoX, this.desplazamientoY); + + this.dragStartX = this.getSVGCoordenates(evt).x; + this.dragStartY = this.getSVGCoordenates(evt).y; + } else { + if (this.isNodeBackground(this.draggingElement)) { + + this.draggingElement.setAttribute("dragx", p.x); + this.draggingElement.setAttribute("dragy", p.y); + this.draggingElement = document.getElementById(this.args.idGraph); + this.draggingElement.setAttribute("transform", "translate(" + p.x + "," + p.y + "), scale(" + this.getScale() + ")"); + } else { + this.draggingElement.setAttribute("transform", "translate(" + p.x + "," + p.y + ")"); + } + } + } + } + } +}; + +GraphCanvas.prototype.moveSelectedNodes = function(offsetX, offsetY) { + for ( var i = 0; i < this.getSelectedVertices().length; i++) { + + var nodeId = this.getSelectedVertices()[i]; + var svgNodeId = this.getSVGNodeId(nodeId); + + var x = parseFloat(DOM.select(svgNodeId).getAttribute("dragx")) + parseFloat(offsetX);// - parseFloat(DOM.select(this.id).getAttribute("dragx")); + var y = parseFloat(DOM.select(svgNodeId).getAttribute("dragy")) + parseFloat(offsetY);// + parseFloat(DOM.select(this.id).getAttribute("dragy")); + + this._movingNode(DOM.select(svgNodeId), x, y); + } +}; + +GraphCanvas.prototype.mouseDown = function(evt) { + if (event.button == 0) { + + /** if !no interactive mouse events do anything **/ + if (!this.args.interactive) { + return; + } + + var p = this.getSVGCoordenates(evt); + + /** When click on canvas or background deselect all **/ + if (this.isNodeCanvas(evt.target) || this.isNodeBackground(evt.target)) { + this.deselectNodes(); + this.deselectEdges(); + this.onCanvasClicked.notify(); + } + + /** if I am linking vertices **/ + if (this.args.linkEnabled) { + + if (!this.args.linking) { + this.args.linking = true; + if (this.isVertex(evt.target)) { + this.linkStartX = p.x; + this.linkStartY = p.y; + this.linkSVGNode = SVG.drawLine(p.x, p.y, p.x, p.y, this._svg, { + "stroke" : "#FF0000" + }); + this.linkNodeSource = this.getVertexIdFromSVGId(evt.target.id); + } + } else { + this.linkNodeTarget = this.getVertexIdFromSVGId(evt.target.id); + this.args.linking = false; + this.args.linkEnabled = false; + if (this.isVertex(evt.target)) { + this.getDataset().addEdge(this.linkNodeSource + "_" + this.linkNodeTarget, this.linkNodeSource, this.linkNodeTarget, {}); + } + this.linkSVGNode.parentNode.removeChild(this.linkSVGNode); + } + return; + } + + /** Id is a vertex or the canvas **/ + if (this.isVertex(evt.target) || this.isNodeCanvas(evt.target) || this.isNodeBackground(evt.target)) { + this._startDragging(evt); + } + /** if i is edge **/ + if (this.isEdge(evt.target)) { + this.selectEdge(this.getEdgeIdFromSVGId(evt.target.getAttribute("id"))); + } + + if (this.args.multipleSelectionEnabled) { + if (!this.dragging) { + this.setSelecting(true); + this.selectorX = p.x; + this.selectorY = p.y; + this.displaySelection(p.x, p.y, 1, 1); + } + } + + } + if (event.button == 1) { + this.setLinking(false); + this.setMultipleSelection(false); + this.selecting = false; + + /** Id is a vertex or the canvas **/ + if (this.isVertex(evt.target) || this.isNodeCanvas(evt.target) || this.isNodeBackground(evt.target)) { + this._startDragging(evt); + } + } +}; + +GraphCanvas.prototype.mouseUp = function(event) { + if (!this.args.interactive) { + return; + } + + if (this.dragging) { + this._stopDragging(event); + if (this.isVertex(event.target)) { + var vertexId = this.getVertexIdFromSVGId(event.target.id); + if (this.getDataset().getVertexById(vertexId).getEdges().length >= this.args.maxNumberEdgesMoving) { + this.moveEdge(vertexId); + } + } + } + + if (this.selecting) { + this.setSelecting(false); + + var x1 = (parseFloat(this.selectorSVGNode.getAttribute("x")) - DOM.select(this.id).getAttribute("dragx")) / this.getFormatter().getWidth(); + var y1 = (parseFloat(this.selectorSVGNode.getAttribute("y")) - DOM.select(this.id).getAttribute("dragy")) / this.getFormatter().getHeight(); + var x2 = (x1 + parseFloat(this.selectorSVGNode.getAttribute("width") / this.formatter.getWidth())); + var y2 = (y1 + parseFloat(this.selectorSVGNode.getAttribute("height") / this.formatter.getHeight())); + + var verticesSelected = this.getLayout().getVerticesByArea(x1 / this.getFormatter().getZoomScale, y1 / this.getFormatter().getZoomScale, + x2 / this.getFormatter().getZoomScale, y2 / this.getFormatter().getZoomScale); + + for ( var i = 0; i < verticesSelected.length; i++) { + this.selectNode(verticesSelected[i].getId()); + } + + if (this.selectorSVGNode != null) { + this._svg.removeChild(this.selectorSVGNode); + } + + if (this.args.labeled) { + this.clearLabels(); + this.renderLabels(); + } + + this.selectorSVGNode = null; + // this.renderLabels(); + } +}; + +/** SELECTION **/ +GraphCanvas.prototype.displaySelection = function(x, y, width, height) { + if (this.selectorSVGNode != null) { + this.selectorSVGNode.setAttribute("x", x); + this.selectorSVGNode.setAttribute("y", y); + this.selectorSVGNode.setAttribute("width", width); + this.selectorSVGNode.setAttribute("height", height); + } else { + this.selectorSVGNode = SVG.drawRectangle(x, y, width, height, this._svg, { + "fill" : "red", + "stroke" : "black", + "opacity" : "0.2", + "stroke-opacity" : "1" + }); + } +}; + +/** DRAGGING **/ +GraphCanvas.prototype._startDragging = function(evt) { + if (!this.isDraggingCanvasEnabled()) { + if (this.isNodeCanvas(evt.target)) { + this.draggingElement = null; + } + } + + if (this.isVertex(evt.target) || (this.isNodeBackground(evt.target) && (this.isDraggingCanvasEnabled()))|| (this.isNodeCanvas(evt.target) && (this.isDraggingCanvasEnabled()))) { + this.clearLabels(); + this.draggingElement = evt.target; + this.dragging = true; + var p = this.getSVGCoordenates(evt); + + this.nMouseOffsetX = p.x - parseInt(evt.target.getAttribute("dragx")); + this.nMouseOffsetY = p.y - parseInt(evt.target.getAttribute("dragy")); + + if (this.isVertex(evt.target)) { + this.dragStartX = parseInt(this.draggingElement.getAttribute("dragx")) * this.getFormatter().getZoomScale() + + parseFloat(DOM.select(this.id).getAttribute("dragx")); + this.dragStartY = parseInt(this.draggingElement.getAttribute("dragy")) * this.getFormatter().getZoomScale() + + parseFloat(DOM.select(this.id).getAttribute("dragy")); + } else { + this.dragStartX = p.x - parseInt(this.draggingElement.getAttribute("dragx"));// + parseFloat(DOM.select(this.id).getAttribute("dragx")); + this.dragStartY = p.y - parseInt(this.draggingElement.getAttribute("dragy"));// + parseFloat(DOM.select(this.id).getAttribute("dragy")); + } + } +}; + +GraphCanvas.prototype._stopDragging = function(event) { + this.nMouseOffsetX = 0; + this.nMouseOffsetX = 0; + /** despues del evento up viene el evento click entonces acabo el dragging en el mouseclick **/ + this.dragging = false; + this.draggingElement = null; + this.renderLabels(); + + this.setLinking(false); + this.setMultipleSelection(true); + this.selecting = false; + +}; + +/** Move the edges of the vertex with the vertexId indicado **/ +GraphCanvas.prototype.moveEdge = function(vertexId) { + var x = this.getLayout().getNodeById(vertexId).x * this.getFormatter().getWidth(); + var y = this.getLayout().getNodeById(vertexId).y * this.getFormatter().getHeight(); + + /** Moving edges out **/ + for ( var i = 0; i < this.getDataset().getVertexById(vertexId).getEdgesOut().length; i++) { + var edgeId = this.getDataset().getVertexById(vertexId).getEdgesOut()[i].getId(); + var svgEdgeId = this.getSVGEdgeId(edgeId); + var edgeFormatter = this.getFormatter().getEdgeById(edgeId); + if (edgeFormatter instanceof LineEdgeGraphFormatter) { + DOM.select(svgEdgeId + "_shadow").setAttribute("x2", x); + DOM.select(svgEdgeId + "_shadow").setAttribute("y2", y); + DOM.select(svgEdgeId).setAttribute("x2", x); + DOM.select(svgEdgeId).setAttribute("y2", y); + } + + if ((edgeFormatter instanceof DirectedLineEdgeGraphFormatter) || (edgeFormatter instanceof OdirectedLineEdgeGraphFormatter) + || (edgeFormatter instanceof OdotDirectedLineEdgeGraphFormatter) || (edgeFormatter instanceof DotDirectedLineEdgeGraphFormatter) + || (edgeFormatter instanceof CutDirectedLineEdgeGraphFormatter)) { + this.removeEdge(edgeId); + this.renderEdge(edgeId); + } + } + + /** Moving edges in **/ + for ( var i = 0; i < this.getDataset().getVertexById(vertexId).getEdgesIn().length; i++) { + var edgeId = this.getDataset().getVertexById(vertexId).getEdgesIn()[i].getId(); + var svgEdgeId = this.getSVGEdgeId(edgeId); + var edgeFormatter = this.getFormatter().getEdgeById(edgeId); + if (edgeFormatter instanceof LineEdgeGraphFormatter) { + DOM.select(svgEdgeId).setAttribute("x1", x); + DOM.select(svgEdgeId).setAttribute("y1", y); + DOM.select(svgEdgeId + "_shadow").setAttribute("x1", x); + DOM.select(svgEdgeId + "_shadow").setAttribute("y1", y); + } + + if ((edgeFormatter instanceof DirectedLineEdgeGraphFormatter) || (edgeFormatter instanceof OdirectedLineEdgeGraphFormatter) + || (edgeFormatter instanceof OdotDirectedLineEdgeGraphFormatter) || (edgeFormatter instanceof DotDirectedLineEdgeGraphFormatter) + || (edgeFormatter instanceof CutDirectedLineEdgeGraphFormatter)) { + this.removeEdge(edgeId); + this.renderEdge(edgeId); + } + + if (edgeFormatter instanceof BezierEdgeGraphFormatter) { + var radius = this.getFormatter().getVertexById(vertexId).getDefault().getSize() * this.getFormatter().getNodesMaxSize(); + var d = this.calculateCoordenatesBezier(radius, x, y); + DOM.select(svgEdgeId).setAttribute("d", d); + } + } +}; + +GraphCanvas.prototype.moveNode = function(vertexId) { + var x = this.getLayout().getNodeById(vertexId).x * this.getFormatter().getWidth(); + var y = this.getLayout().getNodeById(vertexId).y * this.getFormatter().getHeight(); + var svgNodeElement = DOM.select(this.getSVGNodeId(vertexId)); + + svgNodeElement.setAttribute("dragx", x); + svgNodeElement.setAttribute("dragy", y); + svgNodeElement.setAttribute("transform", "translate(" + x + "," + y + ")"); + + if (this.getDataset().getVertexById(vertexId).getEdges().length < this.args.maxNumberEdgesMoving) { + this.moveEdge(vertexId); + } +}; + +GraphCanvas.prototype._movingNode = function(svgNodeElement, x, y) { + var vertexId = this.getVertexIdFromSVGId(svgNodeElement.getAttribute("id")); + this.getLayout().getNodeById(vertexId).setCoordinates(x / this.getFormatter().getWidth(), y / this.getFormatter().getHeight()); + this.desplazamientoX = 0; + this.desplazamientoY = 0; + this.removeLabel(vertexId); + this.renderLabel(vertexId); +}; + +/** INIT **/ +GraphCanvas.prototype.init = function() { + + this._svg = this.createSVGDom(this.targetID, this.id, this.getFormatter().getWidth(), this.getFormatter().getHeight(), this.getFormatter() + .getBackgroundColor()); + this.GraphGroup = SVG.drawGroup(this._svg, [ [ "id", this.args.idGraph ], [ "transform", "translate(0,0), scale(1)" ] ]); + this.GraphBackground = SVG.drawGroup(this.GraphGroup, [ [ "id", this.args.idBackground ] ]); + this.GraphEdgeGroup = SVG.drawGroup(this.GraphGroup, [ [ "id", this.args.idEdgesGraph ] ]); + this.GraphNodeGroup = SVG.drawGroup(this.GraphGroup, [ [ "id", this.args.idNodesGraph ] ]); + this.GraphLabelGroup = SVG.drawGroup(this.GraphGroup, [ [ "id", this.args.idLabelGraph ] ]); + + if ((this.getFormatter().getBackgroundImage() != null) && (this.getFormatter().getBackgroundImage() != "")) { + this.setBackgroundImage(this.getFormatter().getBackgroundImage()); + } + /** SVG Events listener */ + var _this = this; + this._svg.addEventListener("click", function(event) { + _this.mouseClick(event); + }, false); + this._svg.addEventListener("mousemove", function(event) { + _this.mouseMove(event, _this); + }, false); + this._svg.addEventListener("mousedown", function(event) { + _this.mouseDown(event, _this); + }, false); + this._svg.addEventListener("mouseup", function(event) { + _this.mouseUp(event, _this); + }, false); +}; + +/* + GraphCanvas.prototype.backgroungToSVG = function(){ + var _this = this; + var canvas = document.createElement('canvas'); + canvas.setAttribute("id", "canvas"); + canvas.width = this.formatter.getWidth(); + canvas.height = this.formatter.getHeight(); + + this._svg.parentNode.parentNode.appendChild(canvas); + var ctx = document.getElementById('canvas').getContext('2d'); + var img = new Image(); + + img.src = this.formatter.getBackgroundImage(); + ctx.drawImage(img,0,0 ,_this.formatter.getWidth(), _this.formatter.getHeight()); + + + img.onload = function() { + canvas.parentNode.removeChild(canvas); + } + + this.NodeSVGbackgroundImage.setAttribute("xlink:href", document.getElementById("canvas").toDataURL()); + this.NodeSVGbackgroundImage.removeAttribute("href"); + + // + + };*/ + +GraphCanvas.prototype.setBackgroundImage = function() { + if (this.NodeSVGbackgroundImage != null) { + this.NodeSVGbackgroundImage.parentNode.removeChild(this.NodeSVGbackgroundImage); + } + $('#' + this.targetID).svg(); + $('#' + this.targetID).svg("get"); + + $('#' + this.targetID).svg("get")._svg = document.getElementById(this.id); + + var svg = $('#' + this.targetID).svg("get"); + this.NodeSVGbackgroundImage = svg.image(0, 0, this.getFormatter().getWidth(), this.getFormatter().getHeight(), this.getFormatter() + .getBackgroundImage()); + this.NodeSVGbackgroundImage.setAttribute("id", this.args.idBackgroundNode); + + this.NodeSVGbackgroundImage.setAttribute("x", 0); + this.NodeSVGbackgroundImage.setAttribute("y", 0); + + this.NodeSVGbackgroundImage.setAttribute("dragx", 0); + this.NodeSVGbackgroundImage.setAttribute("dragy", 0); + + if (this.getFormatter().args.backgroundImageHeight != null) { + this.NodeSVGbackgroundImage.setAttribute("height", this.getFormatter().args.backgroundImageHeight); + } + if (this.getFormatter().args.backgroundImageWidth != null) { + this.NodeSVGbackgroundImage.setAttribute("width", this.getFormatter().args.backgroundImageWidth); + } + + if (this.getFormatter().args.backgroundImageX != null) { + this.NodeSVGbackgroundImage.setAttribute("x", this.getFormatter().args.backgroundImageX); + } + if (this.getFormatter().args.backgroundImageY != null) { + this.NodeSVGbackgroundImage.setAttribute("y", this.getFormatter().args.backgroundImageY); + } + + this.GraphBackground.appendChild(this.NodeSVGbackgroundImage); + this.NodeSVGbackgroundImage.removeAttribute("href"); + this.NodeSVGbackgroundImage.setAttribute("xlink:href", this.getFormatter().getBackgroundImage()); +}; + +GraphCanvas.prototype.removeBackgroundImage = function() { + if (this.NodeSVGbackgroundImage != null) { + this.NodeSVGbackgroundImage.parentNode.removeChild(this.NodeSVGbackgroundImage); + } +}; + +GraphCanvas.prototype._setBackgroundColor = function(color) { + var attributes = [ [ "fill", color ] ]; + SVG.drawRectangle(0, 0, this.getFormatter().getWidth(), this.getFormatter().getHeight(), this.GraphBackground, attributes); +}; + +/** Serialize **/ +GraphCanvas.prototype.toJSON = function() { + var json = {}; + json.dataset = {}; + json.formatter = {}; + json.layout = {}; + json.dataset = this.getDataset().toJSON(); + json.formatter = this.getFormatter().toJSON(); + json.layout = this.getLayout().toJSON(); + return json; +}; + +GraphCanvas.prototype.toHTML = function() { + //this.backgroungToSVG(); + var html = this._svg.parentElement.innerHTML; + + var start = html.indexOf("") + 6; + + return html.substr(start, end); +}; + +/** DRAW **/ +GraphCanvas.prototype.draw = function(graphdataset, graphformatter, graphlayout) { + this.setDataset(graphdataset); + this.setFormatter(graphformatter); + this.setLayout(graphlayout); + + var _this = this; + this.getFormatter().changed.attach(function(sender, item) { + _this.removeNode(item.getId()); + _this.renderNode(item.getId()); + if (_this.args.labeled) { + _this.removeLabel(item.getId()); + _this.renderLabel(item.getId()); + } + + }); + //TODO + this.getFormatter().edgeChanged.attach(function(sender, item) { + _this.removeEdge(item.getId()); + _this.renderEdge(item.getId()); + }); + + this.getFormatter().resized.attach(function(sender, item) { + _this.resize(_this.getFormatter().getWidth(), _this.getFormatter().getHeight()); + }); + + this.getFormatter().backgroundImageChanged.attach(function(sender, item) { + _this.setBackgroundImage(_this.getFormatter().getBackgroundImage()); + }); + + this.getFormatter().backgroundColorChanged.attach(function(sender, item) { + _this._setBackgroundColor(_this.getFormatter().getBackgroundColor()); + }); + + this.getLayout().changed.attach(function(sender, item) { + _this.moveNode(item.getId()); + _this.moveEdge(item.getId()); + if (_this.args.labeled) { + _this.removeLabel(item.getId()); + _this.renderLabel(item.getId()); + } + }); + + this.getDataset().newVertex.attach(function(sender, item) { + + _this.renderNode(item.getId()); + if (_this.args.labeled) { + _this.renderLabel(item.getId()); + } + }); + + this.getDataset().newEdge.attach(function(sender, item) { + _this.renderEdge(item.getId()); + }); + + this.getDataset().vertexDeleted.attach(function(sender, item) { + _this.removeNode(item.getId()); + if (_this.args.labeled) { + _this.removeLabel(item.getId()); + } + }); + + this.getDataset().edgeDeleted.attach(function(sender, item) { + _this.removeEdge(item.getId()); + }); + + this.getDataset().vertexNameChanged.attach(function(sender, args) { + if (_this.args.labeled) { + _this.removeLabel(args.item.getId()); + _this.removeLabel(args.item.getId()); + _this.renderLabel(args.item.getId()); + } + }); + this.init(); + this.render(); +}; + +GraphCanvas.prototype.render = function() { + for ( var id in this.getDataset().getVertices()) { + this.renderNode(id); + } + this.renderLabels(); + this.renderEdges(); +}; + +GraphCanvas.prototype.renderLabels = function() { + if (this.args.labeled) { + for ( var id in this.getDataset().getVertices()) { + this.renderLabel(id); + } + } +}; + +GraphCanvas.prototype.removeLabels = function() { + for ( var id in this.getDataset().getVertices()) { + this.removeLabel(id); + } +}; + +/** Utilities method for nodes **/ +GraphCanvas.prototype.isNodeCanvas = function(node) { + return ((node.id == this.args.idGraph) || (node.id == this.id)); +}; + +GraphCanvas.prototype.isNodeBackground = function(node) { + return ((node.id == this.args.idBackgroundNode)); +}; + +GraphCanvas.prototype.isVertex = function(node) { + if (node.getAttribute("id") != null) { + if (node.getAttribute("id").indexOf("_v_") != -1) { + return true; + } + } + return false; +}; + +GraphCanvas.prototype.isLabel = function(node) { + if (node.getAttribute("id") != null) { + if (node.getAttribute("id").indexOf("_l_") != -1) { + return true; + } + } + return false; +}; + +GraphCanvas.prototype.isEdge = function(node) { + if (node.getAttribute("id") != null) { + if (node.getAttribute("id").indexOf("_e_") != -1) { + return true; + } + } + return false; +}; + +/** Resize **/ +GraphCanvas.prototype.resize = function(width, height) { + // this._svg.setAttribute("width", width); + // this._svg.setAttribute("height", height); + if (this.NodeSVGbackgroundImage != null) { + this.NodeSVGbackgroundImage.setAttribute("width", width); + this.NodeSVGbackgroundImage.setAttribute("height", height); + } + + this._svg.setAttribute("width", width); + this._svg.setAttribute("height", height); + + this.clearCanvas(); + this.render(); +}; + +GraphCanvas.prototype.clearCanvas = function() { + DOM.removeChilds(this.GraphEdgeGroup.getAttribute("id")); + DOM.removeChilds(this.GraphNodeGroup.getAttribute("id")); + this.clearLabels(); +}; + +GraphCanvas.prototype.clearLabels = function() { + DOM.removeChilds(this.GraphLabelGroup.getAttribute("id")); +}; + +/** ID'S converter **/ +GraphCanvas.prototype.getSVGNodeId = function(nodeId) { + return this.id + "_v_" + nodeId; +}; + +GraphCanvas.prototype.getSVGEdgeId = function(edgeId) { + return this.id + "_e_" + edgeId; +}; + +GraphCanvas.prototype.getSVGArrowEdgeId = function(edgeId) { + return this.id + "_arrow_" + edgeId; +}; + +GraphCanvas.prototype.getSVGLabelId = function(edgeId) { + return this.id + "_l_" + edgeId; +}; + +GraphCanvas.prototype.blinkVertexById = function(vertexId) { + $("#" + this.getSVGNodeId(vertexId)).fadeIn().fadeOut().fadeIn().fadeOut().fadeIn().fadeOut(); +}; + +GraphCanvas.prototype.getVertexIdFromSVGId = function(svgVertexId) { + return svgVertexId.replace(this.id, "").replace("_v_", ""); +}; + +GraphCanvas.prototype.getEdgeIdFromSVGId = function(svgEdgeId) { + return svgEdgeId.replace(this.id, "").replace("_e_", ""); +}; + +/** VERTEX **/ +GraphCanvas.prototype.getVertexById = function(id) { + return document.getElementById(this.getSVGNodeId(id)); +}; + +GraphCanvas.prototype.renderNodes = function() { + for ( var id in this.getDataset().getVertices()) { + this.renderNode(id); + } +}; + +GraphCanvas.prototype.overNode = function(nodeId) { + if (!this.args.interactive) { + return; + } + /** If selected we don't change the format **/ + if (this.args.isVertexSelected[nodeId] == null) { + var args = this.getFormatter().getVertexById(nodeId).getOver(); + args.args["cursor"] = 'pointer'; + this.changeVertexFormat(nodeId, args); + } +}; + +GraphCanvas.prototype.outNode = function(nodeId) { + if (!this.args.interactive) { + return; + } + + /** If selected we don't change the format **/ + if (this.args.isVertexSelected[nodeId] == null) { + this.changeVertexFormat(nodeId, this.getFormatter().getVertexById(nodeId).getDefault()); + } +}; + +GraphCanvas.prototype.overLabel = function(nodeId) { + this.overNode(nodeId); + // this.svgLabels[nodeId].setAttribute("cursor", "pointer"); +}; + +GraphCanvas.prototype.outLabel = function(nodeId) { + this.outNode(nodeId); + // this.svgLabels[nodeId].setAttribute("cursor", ""); +}; + +GraphCanvas.prototype.clickNode = function(nodeId) { + if (!this.args.interactive) { + return; + } + + /** si el evento se dispara oprque estaba dragging entonces no activo nada **/ + if (this.args.isVertexSelected[nodeId] == null) { + this.selectNode(nodeId); + } else { + this.deselectNode(nodeId); + } +}; + +GraphCanvas.prototype.selectNode = function(nodeId) { + for ( var i = 0; i < this.args.selectedVertices.length; i++) { + var format = this.getFormatter().getVertexById(nodeId).getSelected(); + format.opacity = 0.2; + this.changeVertexFormat(nodeId, this.getFormatter().getVertexById(nodeId).getSelected()); + } + + if (this.args.isVertexSelected[nodeId] == null) { + var format = this.getFormatter().getVertexById(nodeId).getSelected(); + format.opacity = 1; + this.changeVertexFormat(nodeId, this.getFormatter().getVertexById(nodeId).getSelected()); + this.args.selectedVertices.push(nodeId); + this.args.isVertexSelected[nodeId] = this.args.selectedVertices.length - 1; + this.onVertexSelect.notify(nodeId); + } +}; + +GraphCanvas.prototype.selectAllEdges = function() { + this.deselectNodes(); + this.deselectEdges(); + + for ( var edgesId in this.getDataset().edges) { + this.selectEdge(edgesId); + } +}; + +GraphCanvas.prototype.selectAllNodes = function() { + this.deselectNodes(); + this.deselectEdges(); + + for ( var vertexId in this.getDataset().vertices) { + this.selectNode(vertexId); + } +}; + +GraphCanvas.prototype.selectAll = function() { + this.deselectNodes(); + this.deselectEdges(); + + for ( var vertexId in this.getDataset().vertices) { + this.selectNode(vertexId); + } + + for ( var edgesId in this.getDataset().edges) { + this.selectEdge(edgesId); + } +}; + +GraphCanvas.prototype.selectEdge = function(edgeId) { + if (this.args.isEdgeSelected[edgeId] == null) { + this.changeEdgeFormat(edgeId, this.getFormatter().getEdgeById(edgeId).getSelected()); + //this.args.selectedEdges.push(edgeId); + this.args.isEdgeSelected[edgeId] = true; //this.args.selectedEdges.length - 1; + this.onEdgeSelect.notify(edgeId); + } +}; + +GraphCanvas.prototype.selectEdges = function(edges) { + + for ( var i = 0; i < edges.length; i++) { + this.selectEdge(edges[i]); + } +}; + +GraphCanvas.prototype.deselectNode = function(nodeId) { + if (this.args.isVertexSelected[nodeId] != null) { + this.changeVertexFormat(nodeId, this.getFormatter().getVertexById(nodeId).getDefault()); + this.args.selectedVertices.splice(this.args.isVertexSelected[nodeId], 1); + var index = this.args.isVertexSelected[nodeId]; + delete this.args.isVertexSelected[nodeId]; + + for ( var vertex in this.args.isVertexSelected) { + if (this.args.isVertexSelected[vertex] > index) { + this.args.isVertexSelected[vertex] = this.args.isVertexSelected[vertex] - 1; + } + } + } +}; + +GraphCanvas.prototype.deselectNodes = function() { + var selected = JSON.parse(JSON.stringify(this.getSelectedVertices())); + for ( var i = 0; i < selected.length; i++) { + this.deselectNode(selected[i]); + } +}; +GraphCanvas.prototype.selectNodes = function(idNodes) { + + for ( var i = 0; i < idNodes.length; i++) { + this.selectNode(idNodes[i]); + } + + // for ( var vertex in this.args.isVertexSelected) { + // if (this.args.isVertexSelected[vertex] > index){ + // this.args.isVertexSelected[vertex] = this.args.isVertexSelected[vertex] - 1; + // } + // } + +}; + +GraphCanvas.prototype.changeVertexFormat = function(nodeId, format) { + var svgNode = DOM.select(this.getSVGNodeId(nodeId)); + if (svgNode != null) { + var properties = format.toJSON(); + for ( var item in properties) { + svgNode.setAttribute(item, properties[item]); + } + + if (this.getFormatter().getVertexById(nodeId) instanceof CircleVertexGraphFormatter) { + var transform = "translate(" + svgNode.getAttribute("dragx") + "," + svgNode.getAttribute("dragy") + "), scale(" + format.getSize() + ")"; + svgNode.setAttribute("transform", transform); + } + } +}; + +GraphCanvas.prototype.renderLabel = function(nodeId) { + var x = Math.ceil(this.getLayout().getNodeById(nodeId).x * this.getFormatter().getWidth()); + var y = Math.ceil(this.getLayout().getNodeById(nodeId).y * this.getFormatter().getHeight()); + + var svgAttributesNode = JSON.parse(JSON.stringify(this.getFormatter().getVertexById(nodeId).getDefault().toJSON().title)); + svgAttributesNode.id = this.getSVGLabelId(this.getDataset().getVertexById(nodeId).getId()); + svgAttributesNode.dx = (-1) * (this.getDataset().getVertexById(nodeId).getName().length * svgAttributesNode["font-size"]) / 4 - 4; + + svgAttributesNode.dy = parseFloat((this.getFormatter().getVertexById(nodeId).getDefault().getSize())) + + parseFloat(svgAttributesNode["font-size"]) + parseFloat(this.getFormatter().getVertexById(nodeId).getDefault().getStrokeWidth()) - 4; + svgAttributesNode.dragx = Math.ceil(this.getLayout().getNodeById(nodeId).x * this.getFormatter().getWidth()); + + var gragy = parseFloat(this.getFormatter().getVertexById(nodeId).getDefault().getSize()) + + Math.ceil(this.getLayout().getNodeById(nodeId).y * this.getFormatter().getHeight()); + svgAttributesNode.dragy = gragy; + svgAttributesNode.transform = "translate(" + svgAttributesNode.dragx + "," + svgAttributesNode.dragy + ")";//, scale("+this.formatter.getVertexById(nodeId).getDefault().getSize()+")"; + + var nodeSVG = SVG.drawText(0, 0, this.getDataset().getVertexById(nodeId).getName(), this.GraphLabelGroup, svgAttributesNode); + + this.svgLabels[nodeId] = nodeSVG; + + /** Events for the SVG node **/ + var _this = this; + if (nodeSVG != null) { + nodeSVG.addEventListener("mouseover", function() { + _this.overLabel(nodeId); + }, false); + nodeSVG.addEventListener("mouseout", function() { + _this.outLabel(nodeId); + }, false); + } + +}; + +GraphCanvas.prototype.removeLabel = function(labelId) { + if (DOM.select(this.getSVGLabelId(labelId)) != null) { + DOM.select(this.getSVGLabelId(labelId)).parentNode.removeChild(DOM.select(this.getSVGLabelId(labelId))); + } +}; + +GraphCanvas.prototype.renderNode = function(nodeId) { + var svgAttributesNode = JSON.parse(JSON.stringify(this.getFormatter().getVertexById(nodeId).getDefault().toJSON())); + svgAttributesNode.dragx = Math.ceil(this.getLayout().getNodeById(nodeId).x * this.getFormatter().getWidth()); + svgAttributesNode.dragy = Math.ceil(this.getLayout().getNodeById(nodeId).y * this.getFormatter().getHeight()); + svgAttributesNode.transform = "translate(" + svgAttributesNode.dragx + "," + svgAttributesNode.dragy + ")"; + svgAttributesNode.id = this.getSVGNodeId(nodeId); + /*svgAttributesNode["stroke-width"] = 3 ; + svgAttributesNode["stroke-opacity"] = 1 ; + svgAttributesNode["fill-opacity"] = svgAttributesNode["opacity"] ; + svgAttributesNode["opacity"] = 1 ;*/ + this.circleDefaultRadius = this.getFormatter().getVertexById(nodeId).getDefault().getSize(); + var nodeSVG; + + if (this.getFormatter().getVertexById(nodeId) instanceof CircleVertexGraphFormatter) { + nodeSVG = SVG.drawCircle(0, 0, this.circleDefaultRadius, this.GraphNodeGroup, svgAttributesNode); + } + + if (this.getFormatter().getVertexById(nodeId) instanceof SquareVertexGraphFormatter) { + //nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius) ,0 - (this.formatter.getVertexById(nodeId).getDefault().getSize()) , (this.getFormatter().getVertexById(nodeId).getDefault().getSize()*2), (this.getFormatter().getVertexById(nodeId).getDefault().getSize()*2), this.GraphNodeGroup, svgAttributesNode); + nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius), 0 - (this.circleDefaultRadius), (this.circleDefaultRadius * 2), + (this.circleDefaultRadius * 2), this.GraphNodeGroup, svgAttributesNode); + } + + if (this.getFormatter().getVertexById(nodeId) instanceof EllipseVertexGraphFormatter) { + nodeSVG = SVG.drawEllipse(0, 0, this.circleDefaultRadius * 1.5, this.circleDefaultRadius, this.GraphNodeGroup, svgAttributesNode); + } + + if (this.getFormatter().getVertexById(nodeId) instanceof RectangleVertexGraphFormatter) { + //nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius) ,0 - ((this.circleDefaultRadius*2)/2) , (this.circleDefaultRadius*2), (this.circleDefaultRadius), this.GraphNodeGroup, svgAttributesNode); + nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius * 1.5), 0 - (this.circleDefaultRadius), (this.circleDefaultRadius * 2 * 1.5), + (this.circleDefaultRadius * 2), this.GraphNodeGroup, svgAttributesNode); + + } + + if (this.getFormatter().getVertexById(nodeId) instanceof RoundedVertexGraphFormatter) { + svgAttributesNode.ry = 2;// this.formatter.getVertexById(nodeId).getDefault().getSize()/4; + svgAttributesNode.rx = 2;// this.formatter.getVertexById(nodeId).getDefault().getSize()/4; + nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius * 1.5), 0 - (this.circleDefaultRadius), (this.circleDefaultRadius * 2 * 1.5), + (this.circleDefaultRadius * 2), this.GraphNodeGroup, svgAttributesNode); + } + + // + + if (this.getFormatter().getVertexById(nodeId) instanceof OctagonVertexGraphFormatter) { + svgAttributesNode.ry = 2; + svgAttributesNode.rx = 2; + nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius * 1.5), 0 - (this.circleDefaultRadius), (this.circleDefaultRadius * 2 * 1.5), + (this.circleDefaultRadius * 2), this.GraphNodeGroup, svgAttributesNode); + } + + nodeSVG.internalId = nodeId; + // + var _this = this; + + /** Events for the SVG node **/ + if (nodeSVG != null) { + nodeSVG.addEventListener("mouseover", function() { + _this.onVertexOver.notify(nodeId); + _this.overNode(nodeId); + }, false); + nodeSVG.addEventListener("mouseout", function() { + _this.onVertexOut.notify(nodeId); + _this.outNode(nodeId); + }, false); + //nodeSVG.addEventListener("click", function(){_this.clickNode(nodeId);}, false); + // + nodeSVG.addEventListener("mouseup", function() { + _this.onVertexUp.notify(nodeId); + }, false); + } +}; + +GraphCanvas.prototype.removeNode = function(nodeId) { + DOM.select(this.getSVGNodeId(nodeId)).parentNode.removeChild(DOM.select(this.getSVGNodeId(nodeId))); + if (this.args.labeled) { + this.removeLabel(nodeId); + } +}; + +/** REMOVING **/ +GraphCanvas.prototype.removeSelected = function() { + /** El orden importa **/ + this.removeSelectedEdges(); + this.removeSelectedNode(); + +}; + +GraphCanvas.prototype.removeSelectedNode = function() { + var selected = JSON.parse(JSON.stringify(this.getSelectedVertices())); + this.deselectNodes(); + var sorted = selected.sort(function(a, b) { + return a - b + }); + for ( var i = 0; i < sorted.length; i++) { + if (this.getDataset().getVertexById(sorted[i]) != null) { + this.getDataset().getVertexById(sorted[i]).remove(); + } + } +}; + +/** EDGES **/ +GraphCanvas.prototype.removeEdge = function(edgeId) { + if (DOM.select(this.getSVGEdgeId(edgeId)) != null) { + DOM.select(this.getSVGEdgeId(edgeId)).parentNode.removeChild(DOM.select(this.getSVGEdgeId(edgeId))); + } + + if (DOM.select(this.getSVGEdgeId(edgeId) + "_shadow") != null) { + DOM.select(this.getSVGEdgeId(edgeId) + "_shadow").parentNode.removeChild(DOM.select(this.getSVGEdgeId(edgeId) + "_shadow")); + } + + if (DOM.select(this.getSVGArrowEdgeId(edgeId)) != null) { + DOM.select(this.getSVGArrowEdgeId(edgeId)).parentNode.removeChild(DOM.select(this.getSVGArrowEdgeId(edgeId))); + } +}; + +GraphCanvas.prototype.overEdge = function(edgeId) { + if ((!this.args.interactive) || this.dragging || this.selecting) { + return; + } + + /** If selected we don't change the format **/ + if (this.args.isEdgeSelected[edgeId] == null) { + var format = this.getFormatter().getEdgeById(edgeId).getOver(); + format.args["cursor"] = "pointer"; + this.changeEdgeFormat(edgeId, format); + } +}; + +GraphCanvas.prototype.outEdge = function(edgeId) { + if (!this.args.interactive) { + return; + } + + /** If selected we don't change the format **/ + if (this.args.isEdgeSelected[edgeId] == null) { + this.changeEdgeFormat(edgeId, this.getFormatter().getEdgeById(edgeId).getDefault()); + } +}; + +GraphCanvas.prototype.changeEdgeFormat = function(edgeId, format) { + var svgEdge = DOM.select(this.getSVGEdgeId(edgeId) + "_shadow"); + if (svgEdge != null) { + var properties = format.toJSON(); + for ( var item in properties) { + svgEdge.setAttribute(item, properties[item]); + } + } +}; + +GraphCanvas.prototype.deselectEdge = function(edgeID) { + if (this.args.isEdgeSelected[edgeID] != null) { + this.changeEdgeFormat(edgeID, this.getFormatter().getEdgeById(edgeID).getDefault()); + var index = this.args.isEdgeSelected[edgeID]; + delete this.args.isEdgeSelected[edgeID]; + } +}; + +GraphCanvas.prototype.deselectEdges = function() { + var selected = JSON.parse(JSON.stringify(this.getSelectedEdges())); + for ( var i = 0; i < selected.length; i++) { + this.deselectEdge(selected[i]); + } +}; + +GraphCanvas.prototype.removeSelectedEdges = function() { + var selected = JSON.parse(JSON.stringify(this.getSelectedEdges())); + this.deselectEdges(); + for ( var i = 0; i < selected.length; i++) { + if (this.getDataset().getEdgeById(selected[i]) != null) { + this.getDataset().getEdgeById(selected[i]).remove(); + } + } +}; + +GraphCanvas.prototype.renderEdge = function(edgeId) { + var svgAttributesEdge = this.getFormatter().getEdgeById(edgeId).getDefault().toJSON(); + var edge = this.getDataset().getEdgeById(edgeId); + + var svgNodeTarget = this.getVertexById(edge.getNodeTarget().getId()); + var svgNodeSource = this.getVertexById(edge.getNodeSource().getId()); + svgAttributesEdge.id = this.getSVGEdgeId(edge.getId()) + "_shadow"; + + var svgEdge = null; + + if (this.getFormatter().getEdgeById(edgeId) instanceof LineEdgeGraphFormatter) { + var coordenateSourceX = svgNodeSource.getAttribute("dragx"); + var coordenateSourceY = svgNodeSource.getAttribute("dragy"); + var coordenateTargetX = svgNodeTarget.getAttribute("dragx"); + var coordenateTargetY = svgNodeTarget.getAttribute("dragy"); + + SVG.drawLine(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, this.GraphEdgeGroup, svgAttributesEdge); + var attributesShadow = {}; + attributesShadow.id = this.getSVGEdgeId(edge.getId()); + attributesShadow["stroke-opacity"] = 0; + attributesShadow["stroke-width"] = 4; + attributesShadow["stroke"] = "black"; + svgEdge = SVG.drawLine(svgNodeSource.getAttribute("dragx"), svgNodeSource.getAttribute("dragy"), svgNodeTarget.getAttribute("dragx"), + svgNodeTarget.getAttribute("dragy"), this.GraphEdgeGroup, attributesShadow); + } + + if (this.getFormatter().getEdgeById(edgeId) instanceof BezierEdgeGraphFormatter) { + var nodeId = edge.getNodeTarget().getId(); + var nodeSize = this.formatter.getVertexById(nodeId).getDefault().getSize() * this.getFormatter().getNodesMaxSize(); + svgAttributesEdge.fill = "none"; + svgAttributesEdge.id = this.getSVGEdgeId(edgeId); + var d = this.calculateCoordenatesBezier(nodeSize, svgNodeSource.getAttribute("dragx"), svgNodeSource.getAttribute("dragy")); + svgEdge = SVG.drawPath(d, this.GraphEdgeGroup, svgAttributesEdge); + } + ; + + if ((this.getFormatter().getEdgeById(edgeId) instanceof DirectedLineEdgeGraphFormatter) + || (this.getFormatter().getEdgeById(edgeId) instanceof CutDirectedLineEdgeGraphFormatter) + || (this.getFormatter().getEdgeById(edgeId) instanceof DotDirectedLineEdgeGraphFormatter) + || (this.getFormatter().getEdgeById(edgeId) instanceof OdotDirectedLineEdgeGraphFormatter) + || (this.getFormatter().getEdgeById(edgeId) instanceof OdirectedLineEdgeGraphFormatter)) { + var coordenateSourceX = svgNodeSource.getAttribute("dragx"); + var coordenateSourceY = svgNodeSource.getAttribute("dragy"); + var coordenateTargetX = svgNodeTarget.getAttribute("dragx"); + var coordenateTargetY = svgNodeTarget.getAttribute("dragy"); + + var offset = parseFloat(this.getFormatter().getVertexById(this.getDataset().getEdgeById(edgeId).getNodeTarget().getId()).getDefault() + .getSize() + * this.circleDefaultRadius); + var point = this._calculateEdgePointerPosition(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, offset); + coordenateTargetX = point.x; + coordenateTargetY = point.y; + SVG.drawLine(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, this.GraphEdgeGroup, svgAttributesEdge); + + var attributesShadow = {}; + attributesShadow.id = this.getSVGEdgeId(edge.getId()); + attributesShadow["stroke-opacity"] = 0; + attributesShadow["stroke-width"] = 4; + attributesShadow["stroke"] = "black"; + svgEdge = SVG.drawLine(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, this.GraphEdgeGroup, attributesShadow); + } + + if (this.getFormatter().getEdgeById(edgeId) instanceof DirectedLineEdgeGraphFormatter + || (this.getFormatter().getEdgeById(edgeId) instanceof OdirectedLineEdgeGraphFormatter)) { + var coordenateSourceX = svgNodeSource.getAttribute("dragx"); + var coordenateSourceY = svgNodeSource.getAttribute("dragy"); + var coordenateTargetX = svgNodeTarget.getAttribute("dragx"); + var coordenateTargetY = svgNodeTarget.getAttribute("dragy"); + + var point = this._calculateEdgePointerPosition(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, offset); + coordenateTargetX = point.x; + coordenateTargetY = point.y; + + var angle = Geometry.toDegree(point.angle) + 90; + this.arrowDefaultSize = this.getFormatter().getEdgeById(edgeId).getArrowSize(); //getDefault().getArrowSize(); + var d = "-" + this.arrowDefaultSize + ",0 0,-" + parseFloat(this.arrowDefaultSize) * 2 + " " + this.arrowDefaultSize + ",0"; + + var attributes; + + if (this.getFormatter().getEdgeById(edgeId) instanceof DirectedLineEdgeGraphFormatter) { + attributes = [ + [ "fill", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], + [ "stroke", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], [ "id", this.getSVGArrowEdgeId(edgeId) ] ]; + } else { + attributes = [ + [ "fill", "#FFFFFF" ], [ "stroke", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], + [ "id", this.getSVGArrowEdgeId(edgeId) ] ]; + } + + var flechaSVGNode = SVG.drawPoligon(d, this.GraphEdgeGroup, attributes);//, ["transform", "rotate("+angle+"), translate(0,0)"]]); + flechaSVGNode.setAttribute("transform", " translate(" + coordenateTargetX + ", " + coordenateTargetY + "), rotate(" + angle + ")"); + } + ; + + if (this.getFormatter().getEdgeById(edgeId) instanceof CutDirectedLineEdgeGraphFormatter) { + var coordenateSourceX = svgNodeSource.getAttribute("dragx"); + var coordenateSourceY = svgNodeSource.getAttribute("dragy"); + var coordenateTargetX = svgNodeTarget.getAttribute("dragx"); + var coordenateTargetY = svgNodeTarget.getAttribute("dragy"); + + var point = this._calculateEdgePointerPosition(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, offset); + coordenateTargetX = point.x; + coordenateTargetY = point.y; + + var angle = Geometry.toDegree(point.angle) + 90; + + //this.arrowDefaultSize = 2; //getDefault().getArrowSize(); + var d = "-4,0 4,0 4,-2 -4,-2"; + + var flechaSVGNode = SVG.drawPoligon(d, this.GraphEdgeGroup, [ + [ "fill", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], + [ "stroke", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], [ "id", this.getSVGArrowEdgeId(edgeId) ] ]);//, ["transform", "rotate("+angle+"), translate(0,0)"]]); + flechaSVGNode.setAttribute("transform", " translate(" + coordenateTargetX + ", " + coordenateTargetY + "), rotate(" + angle + ")"); + } + ; + + if ((this.getFormatter().getEdgeById(edgeId) instanceof DotDirectedLineEdgeGraphFormatter) + || (this.getFormatter().getEdgeById(edgeId) instanceof OdotDirectedLineEdgeGraphFormatter)) { + var coordenateSourceX = svgNodeSource.getAttribute("dragx"); + var coordenateSourceY = svgNodeSource.getAttribute("dragy"); + var coordenateTargetX = svgNodeTarget.getAttribute("dragx"); + var coordenateTargetY = svgNodeTarget.getAttribute("dragy"); + var point = this._calculateEdgePointerPosition(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, offset); + coordenateTargetX = point.x; + coordenateTargetY = point.y; + var angle = Geometry.toDegree(point.angle) + 90; + // this.arrowDefaultSize = this.formatter.getEdgeById(edgeId).getArrowSize(); //getDefault().getArrowSize(); + var attributes = []; + if (this.getFormatter().getEdgeById(edgeId) instanceof OdotDirectedLineEdgeGraphFormatter) { + attributes = [ + [ "fill", "#FFFFFF" ], [ "stroke", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], + [ "id", this.getSVGArrowEdgeId(edgeId) ] ]; + } else { + attributes = [ + [ "fill", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], + [ "stroke", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], [ "id", this.getSVGArrowEdgeId(edgeId) ] ]; + } + var flechaSVGNode = SVG.drawCircle(0, 0, 4, this.GraphEdgeGroup, attributes); + flechaSVGNode.setAttribute("transform", " translate(" + coordenateTargetX + ", " + coordenateTargetY + "), rotate(" + angle + ")"); + } + ; + + var _this = this; + /** Events for the SVG edge **/ + if (svgEdge != null) { + if (this.getDataset().getEdgesCount() < this.args.maxNumberEdgesFiringEvents) { + svgEdge.addEventListener("mouseover", function() { + _this.overEdge(edgeId); + }, false); + svgEdge.addEventListener("mouseout", function() { + _this.outEdge(edgeId); + }, false); + } + } +}; + +GraphCanvas.prototype._calculateEdgePointerPosition = function(sourceX, sourceY, targetX, targetY, radius) { + var angle = Geometry.getAngleBetweenTwoPoints(sourceX, sourceY, targetX, targetY); + + /** Suponiendo el node source que este a la derecha **/ + if ((targetX - sourceX) < 0) { + var b = Geometry.getAdjacentSideOfRectangleRight(angle, radius); + targetX = parseFloat(targetX) + parseFloat(b); + arrowX = parseFloat(targetX) + parseFloat(b) + this.arrowDefaultSize / 2; + } else { + var b = Geometry.getAdjacentSideOfRectangleRight(angle, radius); + targetX = parseFloat(targetX) - parseFloat(b); + arrowX = parseFloat(targetX) - parseFloat(b) - this.arrowDefaultSize / 2; + } + + /** Suponiendo el node source que este a la arriba **/ + if ((targetY - sourceY) > 0) { + var a = Geometry.getOppositeSideOfRectangleRight(angle, radius); + targetY = parseFloat(targetY) - parseFloat(a); + arrowY = parseFloat(targetY) - parseFloat(a) - this.arrowDefaultSize / 2; + } else { + var a = Geometry.getOppositeSideOfRectangleRight(angle, radius); + targetY = parseFloat(targetY) + parseFloat(a); + arrowY = parseFloat(targetY) + parseFloat(a) - this.arrowDefaultSize / 2; + + } + + return { + "x" : arrowX, + "y" : arrowY, + "angle" : angle + }; +}; + +GraphCanvas.prototype.calculateCoordenatesBezier = function(nodeSize, x1, y1) { + var x11 = x1 - (nodeSize / 2); + var y11 = y1 - (nodeSize / 2); + + var x12 = parseFloat(x1) + parseFloat(nodeSize / 2); + var y12 = y1 - (nodeSize / 2); + + var curvePointX = (x12 - x11) / 2 + x11; + var curvePointY = y1 - (nodeSize * 2); + var d = "M" + x11 + "," + y11 + " T" + curvePointX + "," + curvePointY + " " + x12 + "," + y12; + return d; + +}; + +GraphCanvas.prototype.renderEdges = function() { + for ( var edge in this.getDataset().getEdges()) { + this.renderEdge(this.getDataset().getEdgeById(edge).getId()); + + } +}; + +GraphCanvas.prototype.getLastSelectedNode = function() { + var node = null; + if (this.getSelectedVertices().length > 0) { + var nodeId = this.getSelectedVertices()[this.getSelectedVertices().length - 1]; + node = this.getDataset().getVertexById(nodeId); + } + return node; +}; +/* + GraphCanvas.prototype.getNodeByNameAndIndex = function(node, index){ + var nodeId = this.getDataset().verticesIndex[node][index]; + var nodeItem = this.getDataset().getVertexById(nodeId); + return nodeItem; + }; + */ + +GraphCanvas.prototype.setDataset = function(dataset) { + this.dataset = dataset; +}; + +GraphCanvas.prototype.setFormatter = function(formatter) { + this.formatter = formatter; +}; + +GraphCanvas.prototype.setLayout = function(layout) { + this.layout = layout; +}; + +/** API **/ +GraphCanvas.prototype.getDataset = function() { + return this.dataset; +}; + +GraphCanvas.prototype.getFormatter = function() { + return this.formatter; +}; + +GraphCanvas.prototype.getLayout = function() { + return this.layout; +}; + +/** API DATASET **/ +GraphCanvas.prototype.addVertex = function(name, args) { + this.getDataset().addNode(name, args); +}; + +GraphCanvas.prototype.removeVertex = function(vertexId) { + this.getDataset().getVertexById(vertexId).remove(); +}; + +GraphCanvas.prototype.addEdge = function(edgeName, nodeSourceId, nodeTargetId, args) { + this.getDataset().addEdge(edgeName, nodeSourceId, nodeTargetId, args); +}; +/* + GraphCanvas.prototype.removeEdge = function(edgeId){ + this.getDataset().getEdgeById(edgeId).remove(); + }; + */ + +/** API FORMATTER **/ +GraphCanvas.prototype.getWidth = function() { + return this.getFormatter().getWidth(); +}; + +GraphCanvas.prototype.getHeight = function() { + return this.getFormatter().getHeight(); +}; + +GraphCanvas.prototype.getBackgroundImage = function() { + return this.getFormatter().getBackgroundImage(); +}; + +//GraphCanvas.prototype.setBackgroundImage = function(value){ +// this.getFormatter().setBackgroundImage(value); +//}; + +GraphCanvas.prototype.getBackgroundColor = function() { + return this.getFormatter().getBackgroundColor(); +}; + +GraphCanvas.prototype.setBackgroundColor = function() { + this.getFormatter().setBackgroundColor(value); +}; + +//GraphCanvas.prototype.setEdgeFill = function(edgeId, value){ +// this.getFormatter().getEdgeById(edgeId).getDefault().setFill(value); +//}; +// +//GraphCanvas.prototype.getEdgeFill = function(edgeId){ +// return this.getFormatter().getEdgeById(edgeId).getDefault().getFill(); +//}; + +/** VERTICES FORMATTER **/ +GraphCanvas.prototype.setVertexSize = function(vertexId, value) { + this.getFormatter().getVertexById(vertexId).getDefault().setSize(value); +}; + +GraphCanvas.prototype.getVertexSize = function(vertexId) { + return this.getFormatter().getVertexById(vertexId).getDefault().getSize(); +}; + +GraphCanvas.prototype.setVertexStroke = function(vertexId, value) { + this.getFormatter().getVertexById(vertexId).getDefault().setStroke(value); +}; + +GraphCanvas.prototype.getVertexStroke = function(vertexId) { + return this.getFormatter().getVertexById(vertexId).getDefault().getStroke(); +}; + +GraphCanvas.prototype.setVertexStrokeOpacity = function(vertexId, value) { + this.getFormatter().getVertexById(vertexId).getDefault().setStrokeOpacity(value); +}; + +GraphCanvas.prototype.getVertexStrokeOpacity = function(vertexId) { + return this.getFormatter().getVertexById(vertexId).getDefault().getStrokeOpacity(); +}; + +GraphCanvas.prototype.setVertexOpacity = function(vertexId, value) { + this.getFormatter().getVertexById(vertexId).getDefault().setOpacity(value); +}; + +GraphCanvas.prototype.getVertexOpacity = function(vertexId) { + return this.getFormatter().getVertexById(vertexId).getDefault().getOpacity(); +}; + +GraphCanvas.prototype.setVertexFill = function(vertexId, color) { + this.getFormatter().getVertexById(vertexId).getDefault().setFill(color); +}; + +GraphCanvas.prototype.getVertexFill = function(vertexId) { + return this.getFormatter().getVertexById(vertexId).getDefault().getFill(); +}; + +/** EDGES FORMATTER **/ +GraphCanvas.prototype.setEdgeSize = function(edgeId, value) { + this.getFormatter().getEdgeById(edgeId).getDefault().setSize(value); +}; + +GraphCanvas.prototype.getEdgeSize = function(edgeId) { + return this.getFormatter().getEdgeById(edgeId).getDefault().getSize(); +}; + +GraphCanvas.prototype.setEdgeStroke = function(edgeId, value) { + this.getFormatter().getEdgeById(edgeId).getDefault().setStroke(value); +}; + +GraphCanvas.prototype.getEdgeStroke = function(edgeId) { + return this.getFormatter().getEdgeById(edgeId).getDefault().getStroke(); +}; + +GraphCanvas.prototype.setEdgeStrokeOpacity = function(edgeId, value) { + this.getFormatter().getEdgeById(edgeId).getDefault().setStrokeOpacity(value); +}; + +GraphCanvas.prototype.getEdgeStrokeOpacity = function(edgeId) { + return this.getFormatter().getEdgeById(edgeId).getDefault().getStrokeOpacity(); +}; + +GraphCanvas.prototype.setEdgeFill = function(edgeId, color) { + this.getFormatter().getEdgeById(edgeId).getDefault().setFill(color); +}; + +GraphCanvas.prototype.getEdgeFill = function(edgeId) { + return this.getFormatter().getEdgeById(edgeId).getDefault().getFill(); +}; + +/** API LAYOUT **/ +GraphCanvas.prototype.setCoordinates = function(vertexId, x, y) { + return this.getLayout().getEdgeById(vertexId).setCoordinates(x, y); +}; + + + +function HPLCGraph(args) { + this.width = 600; + this.height = 600; + this.title = ''; + this.bbar = false; + this.plotInnerPanelPadding = 10; + this.plotPanelPadding = 5; + this.id = BUI.id(); - if (record.raw.measurementId != null) { - /** For testing * */ - grid.setLoading("ISPyB: Removing measurement"); - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - grid.setLoading(false); - /** - * We get and refresh experiment - * because specimens has changed * - */ - var adapter2 = new BiosaxsDataAdapter(); - adapter2.onSuccess.attach(function(sender, experiment) { - _this.onRemoved.notify(experiment); - _this._showStatusBarReady('Ready'); - }); - if (_this.experiments.experiments[0].experimentId != null) { - adapter2.getExperimentById(_this.experiments.experiments[0].experimentId, "MEDIUM"); - _this._showStatusBarBusy("ISPyB: Removing Unused Specimens"); - } - }); + this.hidePlots = null; + this.xlabel = ""; + this.scaled = false; + this.xParam = null; + this.showRangeSelector = true; + this.interactionModel = null; + + /** for each stat the max and minimum value when it is scaled in order to show correctly in the legend **/ + this.ranges = {}; + if (args != null) { + if (args.interactionModel != null) { + this.interactionModel = args.interactionModel; + } + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + if (args.bbar != null) { + this.bbar = args.bbar; + } + if (args.title != null) { + this.title = args.title; + } + if (args.plots != null) { + this.plots = args.plots; + } + + if (args.scaled != null) { + this.scaled = args.scaled; + } + if (args.xlabel != null) { + this.xlabel = args.xlabel; + } + if (args.xParam != null) { + this.xParam = args.xParam; + } + if (args.showRangeSelector != null) { + this.showRangeSelector = args.showRangeSelector; + } + } + + this.onZoomX = new Event(this); + this.onResetZoom = new Event(this); + this.dblclick = new Event(this); +} + +HPLCGraph.prototype.getMenu = function () { + var _this = this; + /** Actions buttons **/ + var actions = []; + + function toggle(item, pressed) { + if (pressed) { + _this.plots[item.param] = true; + } else { + delete _this.plots[item.param]; + } + _this.reloadData(this.hplcData); + } + + for (var i = 0; i < this.hplcData.length; i++) { + if (this.hplcData[i].showOnMenu != false) { + var param = this.hplcData[i].param; + var style = "style='padding:0 0px 0 5px;'"; + actions.push({ + text : "
" + BUI.getRectangleColorDIV(this.hplcData[i].color, 10, 10) + " " + this.hplcData[i].label + "
", + id : _this.id + param, + param : param, + enableToggle : true, + scope : this, + toggleHandler : toggle, + pressed : (_this.plots[param] != null) + }); + } + } + actions.push("-"); + + actions.push({ + text : "Scale", + enableToggle : true, + scope : this, + pressed : this.scaled, + icon : '../images/icon_graph.png', + toggleHandler : function (item, pressed) { + _this.scaled = pressed; + _this.reloadData(this.hplcData); + } + }); + + actions.push("->"); + actions.push({ + text : "Save", + scope : this, + icon : '../images/save.gif', + handler : function (item, pressed) { + var largeImage = document.createElement("img"); + largeImage.style.display = 'block'; + largeImage.style.width = 200 + "px"; + largeImage.style.height = 200 + "px"; + largeImage.setAttribute('src', Dygraph.Export.asCanvas(this.dygraphObject.dygraph).toDataURL()); + window.open(Dygraph.Export.asCanvas(this.dygraphObject.dygraph).toDataURL(), 'Image', ''); + } + }); + + return actions; +}; - adapter.onError.attach(function(sender, data) { - alert("Error: " + data); - grid.setLoading(false); - }); +/** Looks for the maximum value and then divide everything but that value **/ +HPLCGraph.prototype.scaledData = function (data) { + for (var i = 0; i < data.length; i++) { + var values = this.getMaxAndMinValue(data[i]); + data[i] = this.divideValuesByMax(data[i], values.max); + this.ranges[data[i].label] = values; + } + return data; +}; - adapter.removeMeasurement(record.raw); - } - } - } +/** Given a stat float[] and a max number it will divide each value by max **/ +HPLCGraph.prototype.divideValuesByMax = function (stat, max) { + for (var j = 0; j < stat.data.length; j++) { + if (max != 0) { + stat.data[j] = Number(stat.data[j]) / max; + stat.std[j] = Number(stat.std[j]) / max; + } + } + return stat; +}; - } - } - }); +/** returns max value of a stat **/ +HPLCGraph.prototype.getMaxAndMinValue = function (stat) { + var max = 0; + var min = stat.data[0]; + for (var j = 0; j < stat.data.length; j++) { + if (Number(stat.data[j]) > max) { + max = Number(stat.data[j]); + } + if (Number(stat.std[j]) > max) { + max = Number(stat.std[j]); + } + if (Number(stat.data[j]) < min) { + min = Number(stat.data[j]); + } + } + return { + max : Number(max), + min : Number(min) + }; +}; - this.grid.on("afterrender", function() { +HPLCGraph.prototype.getPoint = function (data, i) { + var point = [ 10, 10, 10 ]; + var y = parseFloat(data.data[i]); + var error = parseFloat(data.std[i]); + if (data.fdata == null) { + return [ y - error, y, y + error ]; + } else { + if (data.fstd != null) { + return [ data.fstd(y - error), data.fdata(y), data.fstd(y + error) ]; + } + return [ data.fdata(y) - error, data.fdata(y), data.fdata(y) + error ]; + } + return point; +}; - function updateTime() { - try { - _this.estimatedTime = _this.estimatedTime - 1; +HPLCGraph.prototype.reloadData = function(hplcData) { + this.panel.setLoading(false); + this.hplcData = hplcData; - _this.onUpdateTime.notify({ - hours : (Number(_this.estimatedTime / 3600).toFixed()), - minutes : (Number((_this.estimatedTime / 60) % 60).toFixed()), - seconds : (Number(_this.estimatedTime % 60).toFixed()) + var data = hplcData; + - }); + /** In case of having peaks **/ + if (this.peaks != null) { + for (var peak in this.peaks) { + var values = []; + var std = []; + for (var i = 0; i < this.peaks[peak].length; i++) { + values.push(this.peaks[peak][i][1]); + std.push(this.peaks[peak][i][2]); + } + data.push({ + param : peak, + data : values, + showOnMenu : false, + fdata : function (a) { + var value = (Math.log(parseFloat(a))); + if (isNumber(value)) { + return value; + } + }, + fstd : function (a) { + var value = Math.log(Math.abs(parseFloat(a))); + if (isNumber(value)) + return value; + }, + std : std, + color : this.colorPeak[peak], + label : peak + }); + + } + } + + + if (this.scaled) { + data = this.scaledData(JSON.parse(JSON.stringify(hplcData))); + } - if (Number(_this.estimatedTime) < 0) { - _this.timer = null; - grid.setTitle(_this.title); + var paramIndex = {}; + var parsed = []; + var j = 0; + for (var i = 0; i < data[0].data.length - 1; i++) { + var aux = []; + for (j = 0; j < data.length; j++) { + if (this.plots != null) { + if (this.plots[data[j].param] != null) { + aux.push(this.getPoint(data[j], i)); + paramIndex[data[j].param] = aux.length - 1; } + } else { + aux.push([ data[j].data[i] - data[j].std[i], data[j].data[i], data[j].data[i] + data[j].std[i] ]); + } + } + parsed.push([]); - } catch (e) { - console.log(e); - _this.timer = null; + var index = i; + if (this.xParam != null) { + index = parseFloat(data[this.xParam].data[i]); + } + + parsed[parsed.length - 1].push(index); + + for (j = 0; j < data.length; j++) { + if (this.plots != null) { + if (this.plots[data[j].param] != null) { + parsed[parsed.length - 1].push(aux[paramIndex[data[j].param]]); + } + } else { + parsed[parsed.length - 1].push(aux[j]); } } + } - if (_this.estimateTime) { - var experimentList = _this.experiments; - var collected = experimentList.getMeasurementsCollected(); - if (collected.length > 0) { - if (collected[0].run3VO != null) { - try { - var end = collected[0].run3VO.timeEnd; - var start = collected[0].run3VO.timeStart; - var dstart = moment(start); - var dend = moment(end); - var seconds = Number(dend.diff(dstart) / 1000).toFixed(); + var colors = []; + var labels = [ "" ]; + for (j = 0; j < data.length; j++) { + if (this.plots != null) { + if (this.plots[data[j].param] != null) { + colors.push(data[j].color); + labels.push(data[j].label); + } + } else { + parsed[parsed.length - 1].push(aux[j]); + } + } - _this.estimatedTime = (seconds * experimentList.getMeasurementsNotCollected().length); + this._renderDygraph(parsed, colors, labels); +}; - if (_this.estimatedTime > 0) { - updateTime(); - _this.timer = setInterval(function() { - updateTime(); - }, 1000); +HPLCGraph.prototype._renderDygraph = function (parsed, colors, labels) { + this.dygraphObject = new StdDevDyGraph(this.id, { + width : this.width, + height : this.height - 10, + xlabel : this.xlabel, + showRangeSelector : this.showRangeSelector, + interactionModel : this.interactionModel, + scaled : this.scaled, + ranges : this.ranges + }); + this.dygraphObject.draw(parsed, colors, labels); + + var _this = this; + this.dygraphObject.onZoomX.attach(function (sender, args) { + try { + _this.onZoomX.notify(args); + } catch (e) { + } + }); + + this.dygraphObject.onResetZoom.attach(function (sender, args) { + try { + _this.onResetZoom.notify(args); + } catch (e) { + } + }); + + this.dygraphObject.dblclick.attach(function (sender, args) { + try { + _this.dblclick.notify(args); + } catch (e) { + } + }); + +}; + +HPLCGraph.prototype.loadData = function (data) { + var _this = this; + this.reloadData(data); + this.panel.addDocked({ + xtype : 'toolbar', + items : this.getMenu() + }); + + + if (this.bbar == true){ + this.panel.addDocked({ + xtype : 'toolbar', + dock: 'bottom', + items : [ + { + xtype: 'numberfield', + id: 'main_field_start', + fieldLabel: 'Range from', + width: 170, + labelWidth : 70, + value: 0, + minValue: 0 + }, + { + xtype: 'numberfield', + id: 'main_field_end', + fieldLabel: 'to', + width: 130, + labelWidth : 30, + value: 0, + minValue: 0 + }, + { + xtype: 'button', + text: 'Go', + handler: function () { + var start = parseFloat(Ext.getCmp("main_field_start").getValue()); + var end = parseFloat(Ext.getCmp("main_field_end").getValue()); + + if (start < 0) { + start = 0; + } + if (end < 0) { + end = 0; + } + if (start > end) { + var aux = end; + end = start; + start = aux; + } + + _this.dygraphObject.dygraph.updateOptions({ isZoomedIgnoreProgrammaticZoom: true, dateWindow: [start, end] }); + } } + ] + }); + } +}; - } catch (e) { - } - } - } - } +HPLCGraph.prototype.getPanel = function () { + this.panel = Ext.create('Ext.panel.Panel', { + padding : this.plotPanelPadding, + width : this.width + 4 * this.plotInnerPanelPadding, + height : this.height + 4 * this.plotInnerPanelPadding, + items : [ { + html : "", + id : this.id, + width : this.width, + height : this.height + } ] }); - return this.grid; + return this.panel; }; -/** Method for testing * */ -MeasurementGrid.prototype.input = function() { - var experiment = DATADOC.getExperiment_10(); - var measurements = DATADOC.getMeasurements_10(); - var proposal = DATADOC.getProposal_10(); - return { - experiment : experiment, - measurements : measurements, - proposal : proposal - }; +HPLCGraph.prototype.input = function () { + return DATADOC.getHPLCData(); }; -MeasurementGrid.prototype.test = function(targetId) { - var measurementGrid = new MeasurementGrid({ - tbar : true - - }); - BIOSAXS.proposal = new Proposal(measurementGrid.input().proposal); - var panel = measurementGrid.getPanel(measurementGrid.input().measurements, new ExperimentList([ new Experiment(measurementGrid.input().experiment) ])); - panel.render(targetId); +HPLCGraph.prototype.getDataByFrameNumber = function (frameNumber) { + var data = {}; + data.frameNumber = frameNumber; + for (var key in this.hplcData){ + data[this.hplcData[key].label] = this.hplcData[key].data[frameNumber]; + } + console.log(data); + return data; }; - -/** - * A shipment may contains one or more cases where stock solutions and sample - * plates are stored - * - * @height - * @btnEditVisible - * @btnRemoveVisible - * - * #onEditButtonClicked - */ -function MolarityGrid(args) { - this.height = 100; - this.width = 100; - if (args != null) { - if (args.height != null) { - this.height = args.height; - } - if (args.width != null) { - this.width = args.width; + +HPLCGraph.prototype.test = function (targetId) { + var mainPlotPanel = new HPLCGraph({ + title : 'I0', + width : 800, + height : 400, + plots : { + "I0" : true, + "Rg" : true, + "Mass" : true + }, + xlabel : "HPLC Frames", + scaled : this.scaled, + interactionModel : { + 'dblclick' : function (event, g, context) { + } } - } + }); + mainPlotPanel.getPanel().render(targetId); + mainPlotPanel.loadData(mainPlotPanel.input()); - var _this = this; - - this.molarityForm = new MolarityForm({height : 180, width : 455}); +}; - this.molarityForm.onSave.attach(function(sender){ - _this.molarityWindow.destroy(); - _this.updateProposal(); - - }); - - this.molarityForm.onClose.attach(function(sender){ - _this.molarityWindow.destroy(); - - }); + +function MergesHPLCGraph(args) { + HPLCGraph.prototype.constructor.call(this, args); - /** Events * */ - this.onEditButtonClicked = new Event(this); +// this.peakColors = ["#00FB42", "#00BA31", "#007C21", "#003E10"]; + this.peakColors = ["#DEBD00", "#6D9100", "#872900", "#0092CC"]; } -MolarityGrid.prototype._getColumns = function() { - return [ { - text : 'Subunit', - columns : [ { - text : "Acronym", - width : 100, - hidden : false, - dataIndex : 'acronym', - sortable : true - }, { - text : "Name", - width : 125, - hidden : false, - dataIndex : 'name', - sortable : true - }, { - text : "MM Est.", - width : 100, - dataIndex : 'molecularMass', - sortable : true, - renderer : function(grid, cls, record){ - return BUI.formatValuesUnits(record.data.molecularMass , "Da", 10, 2); - - } - } ] - }, { -// text : "Number
in assymmetric units", - text : "Ratio", - width : 100, - dataIndex : 'ratio', - tooltip : 'Number of times the subunit is present in the macromolecule', - sortable : true - }, { - id : this.id + 'MOLARITY_REMOVE', - flex : 0.1, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - return BUI.getRedButton('REMOVE'); - } - } ]; -}; -MolarityGrid.prototype._openMolarityWindow = function() { - this.molarityWindow = Ext.create('Ext.window.Window', { - title : 'Molarity', - height : 220, - width : 500, - modal : true, - items : [this.molarityForm.getPanel() ] - }).show(); -}; +MergesHPLCGraph.prototype.scaledData = HPLCGraph.prototype.scaledData; +MergesHPLCGraph.prototype.divideValuesByMax = HPLCGraph.prototype.divideValuesByMax; +MergesHPLCGraph.prototype.getMaxAndMinValue = HPLCGraph.prototype.getMaxAndMinValue; +MergesHPLCGraph.prototype.getPoint = HPLCGraph.prototype.getPoint; +MergesHPLCGraph.prototype.reloadData = HPLCGraph.prototype.reloadData; +MergesHPLCGraph.prototype._renderDygraph = HPLCGraph.prototype._renderDygraph; +MergesHPLCGraph.prototype.loadData = HPLCGraph.prototype.loadData; +MergesHPLCGraph.prototype.getPanel = HPLCGraph.prototype.getPanel; +MergesHPLCGraph.prototype.getDataByFrameNumber = HPLCGraph.prototype.getDataByFrameNumber; -MolarityGrid.prototype._getButtons = function() { - var _this = this; - return [ { - text : 'Add subunit', - icon : '../images/add.png', - handler : function() { - _this._openMolarityWindow(); + +MergesHPLCGraph.prototype.setPeaks = function (data) { + this.peaks = data; + /** get size of peaks **/ + this.peakKeys = []; + this.colorPeak = {}; + var colorCount = 1; + for (var key in this.peaks) { + if (this.peaks.hasOwnProperty(key)) { + var color = this.peakColors[colorCount % this.peakColors.length]; + colorCount = colorCount + 1; + this.peakKeys.push(key); + this.colorPeak[key] = color; } - }]; + } + this.peakKeys.sort(); }; -MolarityGrid.prototype.updateProposal = function() { +MergesHPLCGraph.prototype.getMenu = function () { var _this = this; - this.panel.setLoading(); - BIOSAXS.proposal.onInitialized.attach(function() { - if (BIOSAXS.proposal != null) { - var macromolecules = BIOSAXS.proposal.macromolecules; - for (var i = 0; i < macromolecules.length; i++) { - - if (macromolecules[i].macromoleculeId == _this.macromolecule.macromoleculeId) { - _this.refresh(macromolecules[i]); - _this.panel.setLoading(false); + /** Actions buttons **/ + var actions = []; + + function toggle(item, pressed) { + if (pressed) { + _this.plots[item.param] = true; + } else { + delete _this.plots[item.param]; + } + _this.reloadData(_this.hplcData); + } + + + /** Toolbar for peaks Average **/ + if (this.peaks != null) { + var items = []; + for (var i = 0; i < this.peakKeys.length; i++) { + var color = this.colorPeak[this.peakKeys[i]]; + items.push({ + text: "Peak #" + i + " " + this.peakKeys[i].replace("- ", " to #").replace(".0", "").replace(".0", "") + "", + peakid : this.peakKeys[i], + checked: false, + checkHandler: function (sender, pressed) { + var item = new Object(); + item.param = sender.peakid; + toggle(item, pressed); } - } + }); } - }); - BIOSAXS.proposal.init(); -}; - + + var menu = Ext.create('Ext.menu.Menu', { + id: 'mainMenu', + style: { + overflow: 'visible' + }, + items: items + }); + var tb = Ext.create('Ext.toolbar.Toolbar'); + tb.add({ + text: 'Peaks Avg.', + menu: menu + }); + actions.push(tb); + } -MolarityGrid.prototype.getPanel = function() { - var _this = this; + - this.molarityStore = Ext.create('Ext.data.Store', { - fields : [ 'acronym', 'ratio', 'comments', 'stoichiometryId', 'name', 'molecularMass' ], - sorters : { - property : 'ratio', - direction : 'DESC' + for (var i = 0; i < this.hplcData.length; i++) { + if (this.hplcData[i].showOnMenu != false) { + var param = this.hplcData[i].param; + var style = "style='padding:0 0px 0 5px;'"; + actions.push({ + text : "
" + BUI.getRectangleColorDIV(this.hplcData[i].color, 10, 10) + " " + this.hplcData[i].label + "
", + id : _this.id + param, + param : param, + enableToggle : true, + scope : this, + margin : 5, + toggleHandler : toggle, + pressed : (_this.plots[param] != null) + }); } - }); - - this.panel = Ext.create('Ext.grid.Panel', { - store : this.molarityStore, - height : this.height, - padding : 5, - columns : this._getColumns(), - listeners : { - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - - /** Remove entry * */ - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'MOLARITY_REMOVE') { - var dataAdapter = new BiosaxsDataAdapter(); - dataAdapter.onSuccess.attach(function(sender) { - _this.updateProposal(); - - }); - dataAdapter.removeStoichiometry(record.data.stoichiometryId); - _this.panel.setLoading("Removing Structure"); - } - } - }, - tbar : this._getButtons() - }); - return this.panel; -}; + } -MolarityGrid.prototype._prepareData = function(macromolecule) { - /** Return an array of [{ratio,acronym, stoichiometryId, name}] **/ - var data = []; - if (macromolecule.stoichiometry != null) { - for (var i = 0; i < macromolecule.stoichiometry.length; i++) { - var hostMacromolecule = BIOSAXS.proposal.getMacromoleculeById(macromolecule.stoichiometry[i].macromoleculeId); - data.push({ - ratio : macromolecule.stoichiometry[i].ratio, - acronym : hostMacromolecule.acronym, - comments : hostMacromolecule.comments, - molecularMass : hostMacromolecule.molecularMass, - stoichiometryId : macromolecule.stoichiometry[i].stoichiometryId, - name : hostMacromolecule.name - }); - } + actions.push("->"); + actions.push({ + text : "Save", + scope : this, + icon : '../images/save.gif', + handler : function (item, pressed) { + var largeImage = document.createElement("img"); + largeImage.style.display = 'block'; + largeImage.style.width = 200 + "px"; + largeImage.style.height = 200 + "px"; + largeImage.setAttribute('src', Dygraph.Export.asCanvas(this.dygraphObject.dygraph).toDataURL()); + window.open(Dygraph.Export.asCanvas(this.dygraphObject.dygraph).toDataURL(), 'Image', ''); } - return data; -}; + }); -MolarityGrid.prototype.refresh = function(macromolecule) { - if (macromolecule != null){ - this.molarityStore.loadData(this._prepareData(macromolecule)); - this.molarityForm.refresh(macromolecule); - this.macromolecule = macromolecule; - } + return actions; }; -MolarityGrid.prototype.input = function() { - return { - proposal : DATADOC.getProposal_10(), - dewars : DATADOC.getDewars_10() - }; +MergesHPLCGraph.prototype.input = function () { + return DATADOC.getScatteringHPLCFrameData(); }; -MolarityGrid.prototype.test = function(targetId) { - var MolarityGrid = new MolarityGrid({ - height : 150 +MergesHPLCGraph.prototype.test = function (targetId) { + var mainPlotPanel = new MergesHPLCGraph({ + title : 'Scattering', + width : this.plotWidth, + height : 500, + showRangeSelector : false, + xParam : 0, + xlabel : "scattering_I", + plots : { + "scattering_I" : true, + "subtracted_I" : true, + "buffer_I" : true + } }); - BIOSAXS.proposal = new Proposal(MolarityGrid.input().proposal); - var panel = MolarityGrid.getPanel(MolarityGrid.input().dewars); - panel.render(targetId); - + mainPlotPanel.getPanel().render(targetId); + mainPlotPanel.loadData(mainPlotPanel.input()); }; + + +function NetworkWidget(args) { + this.id = "NetworkViewer_" + Math.random().toString().replace(".", "_"); + + this.label = true; + if (args != null) { + if (args.targetId != null) { + this.targetId = args.targetId; + } + if (args.label != null) { + this.label = args.label; + } + } + + this.onVertexOver = new Event(this); + this.onVertexOut = new Event(this); +} + +NetworkWidget.prototype.draw = function(dataset, formatter, layout) { + + this.graphCanvas = new GraphCanvas(this.id, document.getElementById(this.targetId), { + "labeled" : this.label, + "multipleSelectionEnabled" : false, + "draggingCanvasEnabled" : false + }); + this.graphCanvas.draw(dataset, formatter, layout); + + var _this = this; + this.graphCanvas.onVertexOver.attach(function(sender, nodeId) { + _this.onVertexOver.notify(nodeId); + }); + + this.graphCanvas.onVertexOut.attach(function(sender, nodeId) { + _this.onVertexOut.notify(nodeId); + }); +}; + +/** SELECT VERTICES BY NAME * */ +NetworkWidget.prototype.selectVertexByName = function(vertexName) { + var vertices = this.getDataset().getVertexByName(vertexName); + if (vertices != null) { + for ( var nodeId in vertices) { + if (vertices.hasOwnProperty(nodeId)) { + var vertexId = vertices[nodeId].getId(); + this.selectVertexById(vertexId); + } + } + } +}; + +NetworkWidget.prototype.selectVerticesByName = function(verticesName) { + for ( var i = 0; i < verticesName.length; i++) { + this.selectVertexByName(verticesName[i]); + } +}; + +/** SELECT VERTICES BY ID * */ +NetworkWidget.prototype.selectVertexById = function(vertexId) { + this.graphCanvas.selectNode(vertexId); + this.blinkVertexById(vertexId); +}; + +NetworkWidget.prototype.selectVerticesById = function(verticesId) { + for ( var i = 0; i < verticesId.length; i++) { + this.selectVertexById(verticesId[i]); + } +}; + +/** VECINDARIO * */ +NetworkWidget.prototype.selectNeighbourhood = function() { + this.selectEdgesFromVertices(); + this.selectAdjacent(); +}; +/** DESELECT * */ +NetworkWidget.prototype.deselectNodes = function() { + this.graphCanvas.deselectNodes(); +}; + +/** SELECT ALL NODES * */ +NetworkWidget.prototype.selectAllNodes = function() { + this.getGraphCanvas().selectAllNodes(); +}; + +/** SELECT EVERYTHING * */ +NetworkWidget.prototype.selectAll = function() { + this.getGraphCanvas().selectAll(); +}; + +/** SELECT ALL EDGES * */ +NetworkWidget.prototype.selectAllEdges = function() { + this.getGraphCanvas().selectAllEdges(); +}; + +/** ZOOM * */ +NetworkWidget.prototype.setScale = function(value) { + this.graphCanvas.setScale(value); +}; + +NetworkWidget.prototype.getScale = function() { + return this.graphCanvas.getScale(value); +}; + +/** SELECT ADJACENT VERTICES FROM SELECTED VERTICES * */ +NetworkWidget.prototype.selectAdjacent = function() { + var selectedVertices = this.getGraphCanvas().getSelectedVertices(); + var edges = []; + for ( var i = 0; i < selectedVertices.length; i++) { + edges = edges.concat(this.getGraphCanvas().getDataset().getVertexById(selectedVertices[i]).getEdges()); + } + var vertices = []; + for ( i = 0; i < edges.length; i++) { + vertices.push(edges[i].getNodeSource().getId()); + vertices.push(edges[i].getNodeTarget().getId()); + } + + this.selectVerticesById(vertices); +}; + +/** SELECT EDGES FROM SELECTED VERTICES * */ +NetworkWidget.prototype.selectEdgesFromVertices = function() { + var selectedVertices = this.getGraphCanvas().getSelectedVertices(); + var edges = []; + for ( var i = 0; i < selectedVertices.length; i++) { + edges = edges.concat(this.getGraphCanvas().getDataset().getVertexById(selectedVertices[i]).getEdges()); + } + var edgesId = []; + for ( i = 0; i < edges.length; i++) { + edgesId.push(edges[i].getId()); + } + this.getGraphCanvas().selectEdges(edgesId); +}; + +/** BLINKING * */ +NetworkWidget.prototype.blinkVertexById = function(vertexId) { + this.graphCanvas.blinkVertexById(vertexId); +}; + +/** COMPONENTE CONEXA DE LOS NODOS SELECCIONADOS * */ +NetworkWidget.prototype.selectConnectedComponent = function() { + var elements = this.getConnectedComponent(); + this.selectVerticesById(elements.nodes); + this.graphCanvas.selectEdges(elements.edges); +}; + +NetworkWidget.prototype.getConnectedComponent = function() { + var nodosVisitados = {}; + var aristasVisitadas = {}; + var arrNodos = []; + var arrAristas = []; + var selectedGraphNodesId = this.getGraphCanvas().getSelectedVertices(); + for ( var i = 0; i < selectedGraphNodesId.length; i++) { + this.visitNode(selectedGraphNodesId[i], nodosVisitados, aristasVisitadas, arrNodos, arrAristas); + } + return { + nodes : arrNodos, + edges : arrAristas + }; +}; + +NetworkWidget.prototype.visitNode = function(nodeId, nodosVisitados, aristasVisitadas, arrNodos, arrAristas) { + nodosVisitados[nodeId] = true; + arrNodos.push(nodeId); + var nodeEdges = this.getDataset().getVertexById(nodeId).getEdges(); + for ( var j = 0; j < nodeEdges.length; j++) { + var edge = nodeEdges[j]; + var edgeId = edge.getId(); + if (aristasVisitadas[edgeId] == null) { + aristasVisitadas[edgeId] = true; + arrAristas.push(edgeId); + var nodeTargetId = edge.getNodeTarget().getId(); + if (nodosVisitados[nodeTargetId] == null) { + this.visitNode(nodeTargetId, nodosVisitados, aristasVisitadas, arrNodos, arrAristas); + } + var nodeSourceId = edge.getNodeSource().getId(); + if (nodosVisitados[nodeSourceId] == null) { + this.visitNode(nodeSourceId, nodosVisitados, aristasVisitadas, arrNodos, arrAristas); + } + } + } +}; + +/** COLLAPSE SELECTED VERTICES * */ +NetworkWidget.prototype.collapse = function() { + var selectedVertices = this.getGraphCanvas().getSelectedVertices(); + var xMin = -Infinity; + var xMax = Infinity; + var yMin = -Infinity; + var yMax = Infinity; + + for ( var i = 0; i < selectedVertices.length; i++) { + var vertex = this.getGraphCanvas().getLayout().getNodeById(selectedVertices[i]); + if (xMin < vertex.x) { + xMin = vertex.x; + } + if (xMax > vertex.x) { + xMax = vertex.x; + } + if (yMin < vertex.y) { + yMin = vertex.y; + } + if (yMax > vertex.y) { + yMax = vertex.y; + } + } + + var centerX = xMin - xMax; + var centerY = yMin - yMax; + var radius = (xMax - xMin) / 4; + + var count = selectedVertices.length; + var verticesCoordinates = []; + + for ( i = 0; i < selectedVertices.length; i++) { + x = centerX + radius * Math.sin(i * 2 * Math.PI / count); + y = centerY + radius * Math.cos(i * 2 * Math.PI / count); + verticesCoordinates.push({ + 'x' : x, + 'y' : y + }); + } + + for ( i = 0; i < selectedVertices.length; i++) { + this.getGraphCanvas().getLayout().getNodeById(selectedVertices[i]).setCoordinates(verticesCoordinates[i].x, verticesCoordinates[i].y); + } +}; +/** SETTER FONT SIZE * */ +NetworkWidget.prototype.setVerticesFontSize = function(value) { + for ( var nodeId in this.getDataset().getVertices()) { + if (this.getDataset().getVertices().hasOwnProperty(nodeId)) { + this.getFormatter().getVertexById(nodeId).getDefault().setFontSize(value); + } + } +}; + +/** GETTERS * */ +NetworkWidget.prototype.getFormatter = function() { + return this.getGraphCanvas().getFormatter(); +}; +NetworkWidget.prototype.getLayout = function() { + return this.getGraphCanvas().getLayout(); +}; + +NetworkWidget.prototype.getDataset = function() { + return this.getGraphCanvas().getDataset(); +}; + +NetworkWidget.prototype.getGraphCanvas = function() { + return this.graphCanvas; +}; + +RangeWhiskerGraph.prototype.cleanArray = GenericGraph.prototype.cleanArray; +RangeWhiskerGraph.prototype.plotAxes = GenericGraph.prototype.plotAxes; +RangeWhiskerGraph.prototype.plotRuler = GenericGraph.prototype.plotRuler; +RangeWhiskerGraph.prototype.drawSVGVerticalText = GenericGraph.prototype.drawSVGVerticalText; +RangeWhiskerGraph.prototype.getClassColor = GenericGraph.prototype.getClassColor; +RangeWhiskerGraph.prototype.getDimensions = GenericGraph.prototype.getDimensions; +RangeWhiskerGraph.prototype.calculate = GenericGraph.prototype.calculate; +RangeWhiskerGraph.prototype.getMedian = GenericGraph.prototype.getMedian; +RangeWhiskerGraph.prototype.pointToPixel = GenericGraph.prototype.pointToPixel; +RangeWhiskerGraph.prototype.maxValueWhisker = GenericGraph.prototype.maxValueWhisker; +RangeWhiskerGraph.prototype.refresh = GenericGraph.prototype.refresh; + /** - * Given data analysis parsed with ResultsAssemblyWidget makes a selector grid with buffer/protein - **/ -function SpecimenSelectorResultGrid() { - this.id = BUI.id(); -} + * Subclass of GenericGraph + * + * @plotHorizontalByCluster + */ +function RangeWhiskerGraph(args) { + this.maxBoxWidth = 25; -SpecimenSelectorResultGrid.prototype._prepareData = function(data) { - var parsed = []; - for ( var i = 0; i < data.length; i++) { - var row = data[i]; - for ( var j = 0; j < row.conditions.length; j++) { - parsed.push({ - bufferId : row.conditions[j].bufferId, - macromoleculeId : row.macromoleculeId, - macromoleculeAcronym : BIOSAXS.proposal.getMacromoleculeById(row.macromoleculeId).acronym, - bufferAcronym : BIOSAXS.proposal.getBufferById(row.conditions[j].bufferId).acronym - }); - } + if (args == null) { + args = {}; } - return parsed; -}; - -SpecimenSelectorResultGrid.prototype.refresh = function(data) { - this.store.loadData(this._prepareData(data)); -}; - -SpecimenSelectorResultGrid.prototype.getPanel = function(data) { - var _this = this; - this.store = Ext.create('Ext.data.Store', { - fields : [ 'macromoleculeId', 'bufferId', 'macromoleculeAcronym', 'bufferAcronym', 'concentration' ], - data : this._prepareData(data), - groupField : 'macromoleculeAcronym' - }); + args.plotHorizontalByCluster = false; - this.store.sort('concentration'); - this.grid = Ext.create('Ext.grid.Panel', { - id : this.id, - store : this.store, - width : this.width, - height : this.height, - maxHeight : this.maxHeight, - border : 1, - features : [ { - ftype : 'grouping', - groupHeaderTpl : '{name}', - hideGroupedHeader : true, - startCollapsed : false - } ], - selModel : Ext.create('Ext.selection.CheckboxModel', { - allowDeselect : true, - mode : 'MULTI', - listeners : { - selectionchange : function(sm, selections) { - _this.selected = []; - for ( var i = 0; i < selections.length; i++) { - _this.selected.push(selections[i].raw); - } - } - } - }), - margin : 10, - sortableColumns : true, - columns : [ { - text : 'Macromolecule', - dataIndex : 'macromoleculeAcronym', - flex : 1 - }, { - text : '', - dataIndex : 'bufferId', - width : 20, - hidden : false, - renderer : function(val, y, sample) { - return BUI.getRectangleColorDIV(BIOSAXS.proposal.bufferColors[val], 10, 10); - } - }, { - text : 'Buffer', - dataIndex : 'bufferAcronym', - flex : 1 - }, { - text : 'Concentration', - dataIndex : 'concentration', - flex : 1, - renderer : function(val, y, sample) { - return val + " mg/ml"; - } - } ] - }); + GenericGraph.call(this, args); - /** Adding the tbar **/ - if (this.tbar) { - this.grid.addDocked({ - xtype : 'toolbar', - items : this.getTbar() - }); + if (args.maxBoxWidth != null) { + this.maxBoxWidth = args.maxBoxWidth; } - return this.grid; -}; +} -SpecimenSelectorResultGrid.prototype.input = function() { - return { - data : new ResultsAssemblyGrid()._prepareData(new ResultsAssemblyGrid().input().data), - proposal : new ResultsAssemblyGrid().input().proposal - }; +RangeWhiskerGraph.prototype.refresh = function(data) { + document.getElementById(this.targetId).innerHTML = ""; + this.draw(this.targetId, data); }; -SpecimenSelectorResultGrid.prototype.test = function(targetId) { - var specimenSelectorResultGrid = new SpecimenSelectorResultGrid(); - BIOSAXS.proposal = new Proposal(specimenSelectorResultGrid.input().proposal); - var panel = specimenSelectorResultGrid.getPanel(specimenSelectorResultGrid.input().data); - panel.render(targetId); -}; +RangeWhiskerGraph.prototype.isNumber = function(value) { + if (value == "") + return false; -/** - * Show all buffer conditions for each macromolecules pointing out the measurements quality - * - * @height - * @maxHeight - * @width - * @searchBar - * @tbar - * @btnResultVisible - * - * #onClick - */ -function ResultsAssemblyGrid(args) { - this.height = 500; - this.id = BUI.id(); - this.maxHeight = this.height; + var d = parseInt(value); + if (!isNaN(d)) + return true; + else + return false; - this.width = 900; - this.searchBar = false; - this.tbar = false; - this.btnResultVisible = false; +}; - /** For processing **/ - this.processed = {}; - this.renderedPlotIndex = 0; +/** + There are several different methods for calculating quartiles.[1] This calculator uses a method described by Moore and McCabe to find quartile values. + The same method also used by The TI-83 to calculate quartile values. + With this method, the first quartile is the median of the numbers below the median, the third quartile is the median of the numbers above the median. - this.plotWidth = 210; - this.plotHeight = 80; + http://www.miniwebtool.com/quartile-calculator/ + http://www.alcula.com/calculators/statistics/box-plot/ - /** Colors **/ - this.validColor = BUI.getValidColor(); - this.warningColor = BUI.getWarningColor(); - this.notValidColor = BUI.getErrorColor(); + **/ +RangeWhiskerGraph.prototype.getQ1 = function(array) { + array = array.slice(0, array.length / 2); + return this.getMedian(array); +}; - /** Show warning if guinier quality less than **/ - this.guinierQuality = BUI.getQualityThreshold(); - this.framePercentageThreshold = BUI.getRadiationDamageThreshold(); +RangeWhiskerGraph.prototype.getQ3 = function(array) { + array = array.slice((array.length + 1) / 2); + return this.getMedian(array); - if (args != null) { - if (args.height != null) { - this.height = args.height; - this.maxHeight = this.height; - } - if (args.maxHeight != null) { - this.maxHeight = args.maxHeight; - } - if (args.width != null) { - this.width = args.width; - } - if (args.searchBar != null) { - this.searchBar = args.searchBar; +}; + +RangeWhiskerGraph.prototype.getQ2 = function(array) { + return this.getMedian(array); +}; + +RangeWhiskerGraph.prototype.getBelowOutliers = function(belowLimit, array) { + var points = []; + for ( var i = 0; i < array.length; i++) { + if (array[i] <= belowLimit) { + points.push(array[i]); } + } + return points; +}; - if (args.tbar != null) { - this.tbar = args.tbar; +RangeWhiskerGraph.prototype.getAboveOutliers = function(aboveLimit, array) { + var points = []; + for ( var i = 0; i < array.length; i++) { + if (array[i] >= aboveLimit) { + points.push(array[i]); } - if (args.btnResultVisible != null) { - this.btnResultVisible = args.btnResultVisible; + } + return points; +}; + +RangeWhiskerGraph.prototype.minValueWhisker = function(belowLimit, q1, array) { + var points = []; + + for ( var i = 0; i < array.length; i++) { + if ((array[i] < q1) && (array[i]) > belowLimit) { + points.push(array[i]); } + } + if (points.length > 0) { + points.sort(function(a, b) { + return a - b; + }); + return points[0]; } + return null; +}; - this.onClick = new Event(); -} +//RangeWhiskerGraph.prototype.maxValueWhisker = function(aboveLimit, q3, array){ +// var points = []; +// for (var i = 0; i < array.length; i++){ +// if ((array[i] > q3) && (array[i]) <= aboveLimit){ +// points.push(array[i]); +// } +// } +// if (points.length > 0){ +// points.sort(function(a, b){return a - b;}); +// return points[points.length - 1]; +// } +// return null; +//}; -ResultsAssemblyGrid.prototype.edit = function(macromoleculeId) { - var _this = this; - var window = new MacromoleculeWindow(); - window.onSuccess.attach(function(sender, proposal) { - _this.store.loadData(_this._prepareData(BIOSAXS.proposal.getMacromolecules())); - }); - window.draw(BIOSAXS.proposal.getMacromoleculeById(macromoleculeId)); +RangeWhiskerGraph.prototype.drawPoints = function(boxProperties) { + if (this.plotPoints) { + for ( var i = 0; i < boxProperties.values.length; i++) { + var value = boxProperties.values[i]; + var toPixel = this.pointToPixel(value, boxProperties); + SVG.drawCircle(boxProperties.x, toPixel, this.pointRadius, this.svg, + [ + [ "fill", "green" ], [ "fill-opacity", this.fillOpacityPoint ], [ 'stroke-opacity', this.strokeOpacityPoint ], + [ "stroke", "black" ] ]); + } + } }; -ResultsAssemblyGrid.prototype.getTbar = function() { - var _this = this; - var actions = []; +RangeWhiskerGraph.prototype.plotRangeQ1Q3 = function(data, properties) { + var posX = this.left + this.rulerWidth; - actions.push(Ext.create('Ext.Action', { - icon : '../images/add.png', - text : 'Add Macromolecule', - disabled : false, - handler : function(widget, event) { - var window = new MacromoleculeWindow(); - window.onSuccess.attach(function(sender) { - _this.refresh(); - }); - window.draw({}); - } - })); + var boxBordersPointsQ1 = []; + var boxBordersPointsQ3 = []; + var Q2 = []; - actions.push(Ext.create('Ext.Action', { - icon : '../images/add.png', - text : 'Define an Assembly', - disabled : false, - handler : function(widget, event) { - var createAssemblywindow = new CreateAssemblyWindow(); - createAssemblywindow.onSaved.attach(function(evt, args) { - if (args.macromoleculeIds.length > 0) { - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, proposal) { - _this.refresh(); - }); - adapter.saveAssembly(args.assemblyId, args.macromoleculeIds); + for ( var i = 0; i < data.clusters.length; i++) { + var cluster = data.clusters[i]; + /** inter cluster space **/ + posX = posX + this.interClustersSpace; - } + for ( var j = 0; j < cluster.classes.length; j++) { + var ratio = properties.width / (properties.xValues.range); + var coorX = (cluster.x - properties.xValues.min) * ratio + this.rulerWidth; + var boxProperties = { + name : cluster.classes[j].name, + values : cluster.classes[j].values, + minPoint : properties.minPoint, + maxPoint : properties.maxPoint, + x : coorX + this.left, + y : this.top, + width : properties.classWidth, + height : this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight + }; - }); - createAssemblywindow.draw(_this.experiment); - } - })); + var result = this.calculate(boxProperties.values); + var boxColor = this.getClassColor(boxProperties.name); - return actions; -}; + if (this.isNumber(result.Q1) && this.isNumber(result.Q3)) { + var x = boxProperties.x; + var y = this.pointToPixel(result.Q1, boxProperties); + if (boxBordersPointsQ1[cluster.classes[j].name] == null) { + boxBordersPointsQ1[cluster.classes[j].name] = []; + } + boxBordersPointsQ1[cluster.classes[j].name].push({ + x : x, + y : y + }); -ResultsAssemblyGrid.prototype.refresh = function() { - this.store.loadData(this._prepareData()); -}; + x = boxProperties.x; + y = this.pointToPixel(result.Q3, boxProperties); + if (boxBordersPointsQ3[cluster.classes[j].name] == null) { + boxBordersPointsQ3[cluster.classes[j].name] = []; + } + boxBordersPointsQ3[cluster.classes[j].name].push({ + x : x, + y : y + }); + } else { -ResultsAssemblyGrid.prototype.addCondition = function(record, data_parsed, i) { - function getCondition(record) { - return { - concentration : record.conc, - quality : record.quality, - bufferBeforeFramesMerged : record.bufferBeforeFramesMerged, - bufferAfterFramesMerged : record.bufferAfterFramesMerged, - framesCount : record.framesCount, - framesMerge : record.framesMerge - }; - } + if (this.isNumber(result.Q2)) { - if (data_parsed[i].conditions != null) { - var bufferFound = false; - for ( var index in data_parsed[i].conditions) { - condition = data_parsed[i].conditions[index]; + if (boxBordersPointsQ1[cluster.classes[j].name] == null) { + boxBordersPointsQ1[cluster.classes[j].name] = []; + } - if ((condition.macromoleculeId == record.macromoleculeId) && (condition.bufferId == record.bufferId)) { - data_parsed[i].conditions[index].concentrations.push(getCondition(record)); - bufferFound = true; + if (boxBordersPointsQ3[cluster.classes[j].name] == null) { + boxBordersPointsQ3[cluster.classes[j].name] = []; + } + + boxBordersPointsQ1[cluster.classes[j].name].push({ + x : boxProperties.x, + y : this.pointToPixel(result.Q2, boxProperties) + }); + boxBordersPointsQ3[cluster.classes[j].name].push({ + x : boxProperties.x, + y : this.pointToPixel(result.Q2, boxProperties) + }); + } } } - if (!bufferFound) { - data_parsed[i].conditions.push({ - macromoleculeId : record.macromoleculeId, - bufferId : record.bufferId, - concentrations : [ getCondition(record) ] - }); + } + for ( var classe in boxBordersPointsQ1) { + var points = boxBordersPointsQ1[classe]; + var pointsSVG = ""; + for (var k = 0; k < points.length; k++) { + pointsSVG = Number(points[k].x).toFixed(1) + "," + Number(points[k].y).toFixed(1) + " " + pointsSVG; + } + + points = boxBordersPointsQ3[classe]; + for (var z = points.length - 1; z >= 0; z--) { + pointsSVG = Number(points[z].x).toFixed(1) + "," + Number(points[z].y).toFixed(1) + " " + pointsSVG; } + + SVG.drawPoligon(pointsSVG, this.svg, [ + [ "fill", this.getClassColor(classe) ], [ "opacity", "0.3" ], [ "stroke", "black" ], [ "stroke-width", 1 ] ]); } }; -ResultsAssemblyGrid.prototype.process = function(record, data_parsed) { - if (this.processed[record.macromoleculeId] == null) { - this.processed[record.macromoleculeId] = true; - record.measurementCount = 1; - record.subtractionCount = 1; - record.averageCount = 1; - record.conditions = []; - data_parsed.push(record); - } +RangeWhiskerGraph.prototype.plotWhisters = function(data, properties) { + var colors = [ "yellow", "orange", "green" ]; - for ( var i = 0; i < data_parsed.length; i++) { - if (data_parsed[i].macromoleculeId == record.macromoleculeId) { - data_parsed[i].measurementCount = data_parsed[i].measurementCount + 1; + this.plotRangeQ1Q3(data, properties); + var Q2 = {}; - if (record.subtractionId != null) { - data_parsed[i].subtractionCount = data_parsed[i].subtractionCount + 1; - this.addCondition(record, data_parsed, i); - } + for ( var i = 0; i < data.clusters.length; i++) { + var cluster = data.clusters[i]; + for ( var j = 0; j < cluster.classes.length; j++) { + var ratio = properties.width / (properties.xValues.range); + var coorX = (cluster.x - properties.xValues.min) * ratio + this.left + this.rulerWidth - this.rulerStroke; + var boxProperties = { + name : cluster.classes[j].name, + values : cluster.classes[j].values, + minPoint : properties.minPoint, + maxPoint : properties.maxPoint, + x : coorX, + y : this.top, + width : properties.classWidth, + height : this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight + }; - if (record.framesMerge != null) { - data_parsed[i].averageCount = data_parsed[i].averageCount + 1; - } + this.drawPoints(boxProperties); - if (record.timeStart != null) { - if (data_parsed[i].timeStart != null) { - if (moment(data_parsed[i].timeStart).format("X") > moment(record.timeStart).format("X")) { - data_parsed[i].timeStart = record.timeStart; - } + /** PLOTTING Q2 **/ + var result = this.calculate(boxProperties.values); + var boxColor = this.getClassColor(boxProperties.name); + if (this.isNumber(result.Q2)) { + if (Q2[boxProperties.name] != null) { + SVG.drawLine(boxProperties.x, this.pointToPixel(result.Q2, boxProperties), Q2[boxProperties.name].x, Q2[boxProperties.name].y, + this.svg, [ [ "stroke", boxColor ], [ "stroke-width", "2" ] ]); + } + Q2[boxProperties.name] = { + x : boxProperties.x, + y : this.pointToPixel(result.Q2, boxProperties) } } } } - return data_parsed; - }; -ResultsAssemblyGrid.prototype._prepareData = function(data) { - var data_parsed = []; - for ( var i = 0; i < data.length; i++) { - data_parsed = this.process(data[i], data_parsed); - } - this.data = data_parsed; - return data_parsed; +RangeWhiskerGraph.prototype.draw = function(targetId, data) { + //this.calculate(data); + this.targetId = targetId; + var properties = (this.getDimensions(data)); + this.svg = SVG.createSVGCanvas(document.getElementById(this.targetId), [ [ "width", this.width ], [ "height", this.height ] ]); + this.plotAxes(properties); + this.plotWhisters(data, properties); }; -/** Given an array of conditions it returns distinct(concentrations) order by concentration and hash map with number of ocurrences**/ -ResultsAssemblyGrid.prototype.parseConcentrations = function(val, conditions, differentConcentration, quality) { - var conditions = []; - var differentConcentration = {}; - var quality = []; - for ( var i = 0; i < val.length; i++) { - var conc = Number(val[i].concentration).toFixed(1); - var quality = Number(val[i].quality).toFixed(2); - if (differentConcentration[conc] == null) { - differentConcentration[conc] = 0; - conditions.push({ - concentration : conc, - quality : [ quality ], - frames : [ { - bufferAfterFramesMerged : val[i].bufferAfterFramesMerged, - bufferBeforeFramesMerged : val[i].bufferBeforeFramesMerged, - framesMerge : val[i].framesMerge, - framesCount : val[i].framesCount - } ] - }); - } else { - /** Add quality **/ - for ( var j = 0; j < conditions.length; j++) { - if (conditions[j].concentration == conc) { - conditions[j].quality.push(quality); - conditions[j].frames.push({ - bufferAfterFramesMerged : val[i].bufferAfterFramesMerged, - bufferBeforeFramesMerged : val[i].bufferBeforeFramesMerged, - framesMerge : val[i].framesMerge, - framesCount : val[i].framesCount - }); - } - } - } +RangeWhiskerGraph.prototype.input = function() { + return DATADOC.getBoxWhikerData(); +}; - differentConcentration[conc] = differentConcentration[conc] + 1; - } - /** sorting concentrations **/ - conditions.sort(function(a, b) { - return a.concentration - b.concentration; +RangeWhiskerGraph.prototype.test = function(targetId) { + var plot = new RangeWhiskerGraph({ + targetId : targetId, + height : 350, + width : 450, + maxBoxWidth : 25 }); - return { - concentrations : conditions, - differentConcentration : differentConcentration - }; + plot.refresh(this.input()); }; + +StdDevDyGraph.prototype.dblclick = DygraphWidget.prototype.dblclick; +StdDevDyGraph.prototype._createHTLMWrapper = DygraphWidget.prototype._createHTLMWrapper; +StdDevDyGraph.prototype.draw = DygraphWidget.prototype.draw; -ResultsAssemblyGrid.prototype.getConditionWarnings = function(condition) { - - var withWarnings = 0; - - for ( var i = 0; i < condition.frames.length; i++) { - if (condition.quality[i] == null) { - withWarnings = withWarnings + 1; - continue; - } else { - if (Number(condition.quality[i]) < this.guinierQuality) { - withWarnings = withWarnings + 1; - continue; - } - } - - if (condition.frames[i].bufferBeforeFramesMerged / condition.frames[i].framesCount < this.framePercentageThreshold|| condition.frames[i].framesMerged / condition.frames[i].framesCount < this.framePercentageThreshold|| condition.frames[i].bufferAfterFramesMerged / condition.frames[i].framesCount < this.framePercentageThreshold) { - withWarnings = withWarnings + 1; - continue; - } +function StdDevDyGraph(targetId, args) { + this.scaled = false; + if (args == null) { + args = {}; } + args.customBars = true; + DygraphWidget.prototype.constructor.call(this, targetId, args); +} +StdDevDyGraph.prototype.input = function () { return { - withWarnings : withWarnings, - withoutWarnings : condition.frames.length - withWarnings + data : [ [ 1, [ 2, 3, 3.5 ], [ 4, 4.2, 5 ] ], [ 2, [ 5, 5.5, 5.7 ], [ 4, 4.2, 5 ] ] ], + colors : [ "blue", "red" ], + labels : [ "", 'data1', 'data2' ] }; }; -ResultsAssemblyGrid.prototype.getFrameHTMLTable = function(warnings) { - var html = ""; - if (warnings.withWarnings > 0) { - html = html + "
" + warnings.withWarnings + - "x
"; - } - - if (warnings.withoutWarnings > 0) { - html = html + "
" + warnings.withoutWarnings + - "x
"; - } - return html; -}; +StdDevDyGraph.prototype.test = function (targetId) { + var dygraphObject = new StdDevDyGraph(targetId, { + width : 500, + height : 400, + xlabel : "xLabel", + showRangeSelector : false + }); -ResultsAssemblyGrid.prototype.createConcentrationRow = function(numberOcu, condition, warnings){ - var html = ""; - if (numberOcu > 1){ - html = html + "" +numberOcu + "x " + BUI.formatConcentration(condition.concentration); - } - else{ - html = html + BUI.formatConcentration(condition.concentration); - } - html = html + ""; - html = html + this.getFrameHTMLTable(warnings); + ""; - html = html + ""; - return html; + dygraphObject.draw(dygraphObject.input().data, dygraphObject.input().colors, dygraphObject.input().labels); }; + + + +function AbinitioGrid(args) { + this.height = null; + this.width = null; + this.id = BUI.id(); + + if (args != null) { + if (args.height != null) { + this.height = args.height; + + if (args.width != null) { + this.width = args.width; + } + } + } + + this.onSelected = new Event(this); +}; + + +AbinitioGrid.prototype.refresh = function(subtractions){ + this.store.loadData(this._prepareData(subtractions)); +}; + +AbinitioGrid.prototype._prepareData = function(subtractions){ + /** Parsing data * */ + var models = []; + for (var l = 0; l < subtractions.length; l++) { + var subtraction = subtractions[l]; + for (var k = 0; k < subtraction.substractionToAbInitioModel3VOs.length; k++) { + var data = subtraction.substractionToAbInitioModel3VOs[k].abinitiomodel3VO; + if (data.averagedModel != null) { + models.push(data.averagedModel); + models[models.length - 1].type = "Reference"; + } + + if (data.shapeDeterminationModel != null) { + models.push(data.shapeDeterminationModel); + models[models.length - 1].type = "Refined"; + } + + if (data.modelList3VO != null) { + if (data.modelList3VO.modeltolist3VOs != null) { + for (var i = 0; i < data.modelList3VO.modeltolist3VOs.length; i++) { + models.push(data.modelList3VO.modeltolist3VOs[i].model3VO); + models[models.length - 1].type = "Model"; + } + } + } + } + } + return models; +}; + +AbinitioGrid.prototype.getPanel = function(){ + var _this = this; + + + var modelFields = [ "modelId", "type", "chiSqrt", "dmax", "firFile", "logFile", "fitFile", "pdbFile", "rfactor", "rg", "volume" ]; + Ext.define('AbinitioModel', { + extend : 'Ext.data.Model', + fields : modelFields + + }); + + /** + * Store in Memory + */ + this.store = Ext.create('Ext.data.Store', { + model : 'AbinitioModel', + autoload : true, + groupField : 'type' + }); + + + var groupingFeature = Ext.create('Ext.grid.feature.Grouping',{ + groupHeaderTpl: '{name} ({rows.length} model{[values.rows.length > 1 ? "s" : ""]})', + startCollapsed: true, + collapsible : true + }); + + this.grid = Ext.create('Ext.grid.Panel', { + collapsible : false, + resizable : true, + features: [groupingFeature], + autoscroll : true, + multiSelect : true, + store : this.store, + height : this.height, + width : this.width, + margin : 10, + columns : [ { + text : "Type", + dataindex : "type", + hidden : true, + renderer : function(a, b, record) { + return record.data.type; + }, + flex : 1 + }, + { + text : "ModelId", + dataindex : "modelId", + hidden : true, + renderer : function(a, b, record) { + return record.data.modelId; + + }, + flex : 1 + }, + + { + text : "chiSqrt", + dataindex : "chiSqrt", + renderer : function(a, b, record) { + if (record.data.dmax != null) { + return BUI.formatValuesUnits(record.data.chiSqrt, "", 12, this.decimals); + } + + }, + flex : 1 + }, + { + text : "Dmax", + dataindex : "dmax", + renderer : function(a, b, record) { + if (record.data.dmax != null) { + return BUI.formatValuesUnits(record.data.dmax, "nm", 12, this.decimals); + } + + }, + flex : 1 + }, { + text : "rFactor", + dataindex : "rfactor", + hidden : true, + renderer : function(a, b, record) { + if (record.data.rfactor != null) { + return record.data.rfactor; + } + }, + flex : 1 + }, { + text : "Rg", + dataindex : "rg", + renderer : function(a, b, record) { + if (record.data.rg != null) { + return BUI.formatValuesUnits(record.data.rg, "nm", 12, this.decimals); + } + + }, + flex : 1 + }, + { + text : "Volume", + dataindex : "volume", + renderer : function(a, b, record) { + if (record.raw.volume != null){ + return BUI.formatValuesUnits(record.raw.volume, '') + " nm3"; + } + }, + flex : 1 + }, + { + text : "PDB", + dataindex : "pdbFile", + renderer : function(a, b, record) { + if (record.data.pdbFile != null){ + return record.data.pdbFile.split("/")[record.data.pdbFile.split("/").length - 1]; + } + }, + flex : 1 + }, { + text : "Fir", + dataindex : "firFile", + renderer : function(a, b, record) { + if (record.data.firFile != null){ + return record.data.firFile.split("/")[record.data.firFile.split("/").length - 1]; + } + }, + flex : 1 + }, { + text : "LOG", + dataindex : "logFile", + hidden : true, + renderer : function(a, b, record) { + if (record.data.logFile != null){ + return record.data.logFile.split("/")[record.data.logFile.split("/").length - 1]; + } + }, + flex : 1 + } + ], + viewConfig : { + enableTextSelection : true, + preserveScrollOnRefresh : true, + stripeRows : true, + listeners : { + 'celldblclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + }, + 'cellclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + var models = []; + for (var i = 0; i < grid.getSelectionModel().selected.items.length; i++) { + models.push(grid.getSelectionModel().selected.items[i].raw); + } + _this.onSelected.notify(models); + } + } + } + }); + return this.grid; + +}; + +function AdditiveGrid(args) { + this.onRemoveButtonClicked = new Event(this); +} -ResultsAssemblyGrid.prototype.getConditionHTMLTable = function(val, style, record) { - var maxNumberColumns = 2; - var html = "
"; - var nColumns = 0; - for ( var r = 0; r < val.length; r++) { - if (nColumns == maxNumberColumns) { - nColumns = 0; - html = html + ""; - } - html = html + ""; - nColumns = nColumns + 1; - } - html = html + "
"; - var value = val[r]; - - var bufferAcronym = (BIOSAXS.proposal.getBufferById(value.bufferId).acronym); - - var parsed = (this.parseConcentrations(value.concentrations)); - var conditions = parsed.concentrations; - var differentConcentration = parsed.differentConcentration; - - /** Checking warnings **/ - var warnings = []; - var concentrationValidPerconcentration = 0; - var measurements = 0; - for ( var i = 0; i < conditions.length; i++) { - measurements = measurements + conditions[i].frames.length; - var warning = this.getConditionWarnings(conditions[i]); - warnings.push(warning); - if (warning.withoutWarnings > 0) { - concentrationValidPerconcentration = concentrationValidPerconcentration + 1; - } - } - - this.validColor = '#E0F8E0'; - this.warningColor = '#F5DA81'; - this.notValidColor = '#F6CED8'; - - var color = this.warningColor; - if (concentrationValidPerconcentration > 2) { - color = this.validColor; - } - /** More measurement need to be done **/ - if (measurements < 3) { - color = this.notValidColor; - } - - html = html + ""; - html = html + ""; - for ( var i = 0; i < conditions.length; i++) { - html = html + this.createConcentrationRow(differentConcentration[conditions[i].concentration], conditions[i], warnings[i]); - } - - html = html + ""; - html = html + "
" + bufferAcronym.toUpperCase() + - "
"; - - html = html + "
"; - return html; +AdditiveGrid.prototype.getBuffer = function() { + return this.buffer; }; -ResultsAssemblyGrid.prototype._getTbar = function() { - function goTo(url) { - window.location = url; - } - +AdditiveGrid.prototype._getActions = function() { var _this = this; - return [ { - icon : '../images/application_view_list.png', - text : 'Multiple Select', - handler : function() { - var specimenSelectorResultGrid = new SpecimenSelectorResultGrid(); - var window = Ext.create('Ext.window.Window', { - title : 'Multiple select', - height : 600, - width : 600, - layout : 'fit', - items : [ specimenSelectorResultGrid.getPanel(_this.data) ], - buttons : [ { - text : 'Go', - handler : function() { - var array = []; - for ( var i = 0; i < specimenSelectorResultGrid.selected.length; i++) { - var row = specimenSelectorResultGrid.selected[i]; - array.push({ - macromoleculeId : row.macromoleculeId, - bufferId : row.bufferId - }); - } - goTo(BUI.getMacromoleculeResultsURLByMultipleSearch(array)); + /** Actions buttons **/ + var actions = []; - } - }, { - text : 'Cancel', - handler : function() { - window.close(); - } - } ] + actions.push(Ext.create('Ext.Action', { + icon : '../images/add.png', + text : 'Add', + disabled : true, + alwaysEnabled : true, + handler : function(widget, event) { + _this.buffer.bufferhasadditive3VOs.push(BIOSAXS_BEANS.getBufferhasAdditive3VO()); + _this.refresh(_this.buffer, _this.experiment); + } + })); - }).show(); + return actions; +}; +AdditiveGrid.prototype.refresh = function(buffer, experiment) { + this.buffer = buffer; + this.experiment = experiment; + if (buffer) { + if (buffer.bufferhasadditive3VOs) { + this.features = buffer.bufferhasadditive3VOs; } - } ]; + } + this.experiment = experiment; + this.store.loadData(this._prepareData(), false); }; -ResultsAssemblyGrid.prototype.getLegendPanel = function() { - return { - html : '
' + BUI.getRectangleColorDIV(this.validColor, 10, 10) + - 'Good quality measurements' + - BUI.getRectangleColorDIV(this.warningColor, 10, 10) + - 'Probably valid with manual processing' + - BUI.getRectangleColorDIV(this.notValidColor, 10, 10) + - 'More measurements need to be done
' - }; -}; -/** Returns the grid **/ -ResultsAssemblyGrid.prototype.getPanel = function(macromolecules) { - var _this = this; +AdditiveGrid.prototype.getAdditives = function() { + var additives = []; + for ( var i = 0; i < this.store.getCount(); i++) { + var bufferHasAdditive = BIOSAXS_BEANS.getBufferhasAdditive3VO(); + var data = this.store.getAt(i).getData(); - this.store = Ext.create('Ext.data.Store', { - fields : [ - 'macromoleculeId', 'macromoleculeAcronym', 'measurementCount', 'subtractionCount', 'averageCount', 'timeStart', 'concentrationArray', - 'bufferConditions', 'conditions' ], - data : this._prepareData(macromolecules) - }); + bufferHasAdditive.additive3VO.name = data.name; + bufferHasAdditive.additive3VO.comments = data.comments; + bufferHasAdditive.additive3VO.additiveType = data.additiveType; - this.store.sort('macromoleculeAcronym'); + bufferHasAdditive.bufferId = this.buffer.bufferId; + bufferHasAdditive.bufferHasAdditiveId = data.bufferHasAdditiveId; + bufferHasAdditive.quantity = data.quantity; + additives.push(bufferHasAdditive); + } - this.grid = Ext.create('Ext.grid.Panel', { - id : this.id, - title : 'Macromolecules', - store : this.store, - tbar : this._getTbar(), - bbar : [ this.getLegendPanel() ], - width : this.width, - height : this.height, - maxHeight : this.maxHeight, - sortableColumns : true, - columns : [ - { - text : '', - dataIndex : 'macromoleculeId', - width : 20, - hidden : false, - renderer : function(val, y, sample) { - return BUI.getRectangleColorDIV(BIOSAXS.proposal.macromoleculeColors[val], 10, 10); - } - }, - { - text : 'Macromolecule', - dataIndex : 'macromoleculeAcronym', - width : 200 + return additives; +}; + +AdditiveGrid.prototype._getFields = function(buffers) { + var columns = [ + + { + header : 'Name', + dataIndex : 'name', + type : 'string', + editor : { + allowBlank : true }, - { - text : 'Buffer Conditions', - dataIndex : 'conditions', - flex : 1, - renderer : function(val, style, record) { - return _this.getConditionHTMLTable(val, style, record); - } + flex : 1 + }, + { + header : 'Type', + name : 'additiveType', + dataIndex : 'additiveType', + editor : { + xtype : 'combobox', + typeAhead : true, + triggerAction : 'all', + selectOnTab : true, + store : BIOSAXS.proposal.getAdditiveTypes(), + lazyRender : true, + listClass : 'x-combo-list-small' }, - { - header : 'Average', - dataIndex : 'percentageCollected', - name : 'percentageCollected', - type : 'string', - hidden : true, - renderer : function(val, y, sample) { - return "
" + - BUI.getProgessBar((sample.raw.averageCount / sample.raw.measurementCount) * 100, sample.raw.averageCount + "/" + - sample.raw.measurementCount) + "
"; - }, - width : 100, - sorter : false + flex : 0.6 + }, + { + header : 'Quantity', + dataIndex : 'quantity', + name : 'quantity', + editor : { + allowBlank : true }, - { - header : 'Subtractions', - dataIndex : 'percentageCollected', - name : 'percentageCollected', - type : 'string', - hidden : true, - renderer : function(val, y, sample) { - return "
"+ BUI.getProgessBar((sample.raw.subtractionCount / sample.raw.measurementCount) * 100, sample.raw.subtractionCount + "/" + - sample.raw.measurementCount) + "
"; - }, - width : 100 - }, { - header : 'Date', - dataIndex : 'timeStart', - name : 'timeStart', - type : 'string', - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - if (record.raw.timeStart != null) { - return moment(record.raw.timeStart).format("MMM Do YY"); + type : 'string', + flex : 1 + }, + { + xtype : 'actioncolumn', + items : [ { + icon : '../images/cancel.png', + tooltip : 'Delete additive', + scope : this, + handler : function(grid, rowIndex, colIndex) { + if ((grid.getStore().getAt(rowIndex).data.bufferHasAdditiveId == null)|| (grid.getStore().getAt(rowIndex).data.bufferHasAdditiveId == "")) { + grid.getStore().removeAt(rowIndex); + } else { + this.onRemoveButtonClicked.notify({ + 'bufferId' : this.buffer.bufferId, + 'bufferHasAdditiveId' : this.store.getAt(rowIndex).data.bufferHasAdditiveId + }); } } - }, { - header : 'Download', - dataIndex : 'percentageCollected', - name : 'percentageCollected', - type : 'string', - renderer : function(val, y, sample) { - return BUI.getZipHTMLByMacromoleculeId(sample.raw.macromoleculeId); - }, - width : 100 - }, + } ] + } ]; + + return columns; +}; + +AdditiveGrid.prototype._prepareData = function() { + var data = []; + if (this.features == null) { + this.features = []; + } + for (var i = 0; i < this.features.length; i++) { + var object = this.features[i]; + object.name = this.features[i].additive3VO.name; + object.additiveType = this.features[i].additive3VO.additiveType; + object.comments = this.features[i].additive3VO.comments; + object.additiveId = this.features[i].additive3VO.additiveId; + data.push(object); + } + return data; +}; - { - id : 'btnResultVisible', - width : 85, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - return BUI.getGreenButton('GO'); - } - } ], +AdditiveGrid.prototype.getPanel = function(buffer, experiment) { + this.buffer = buffer; + this.features = buffer.bufferhasadditive3VOs; + this.experiment = experiment; + return this._renderGrid(); +}; + +AdditiveGrid.prototype.getStore = function() { + var _this = this; + var store = Ext.create('Ext.data.Store', { + fields : [ "name", "additiveType", "comments", "additiveId", "bufferHasAdditiveId", "quantity" ], + autoload : false, + data : this._prepareData(), + listeners : { + update : function(store, record) { + record.index = _this.grid.getSelectionModel().getCurrentPosition().row; + _this.buffer.bufferhasadditive3VOs[record.index].additive3VO.name = record.data.name; + _this.buffer.bufferhasadditive3VOs[record.index].additive3VO.additiveType = record.data.additiveType; + _this.buffer.bufferhasadditive3VOs[record.index].additive3VO.comments = record.data.comments; + _this.buffer.bufferhasadditive3VOs[record.index].quantity = record.data.quantity; + } + } + }); + + // store.sort('bufferHasAdditiveId', 'ASC'); + store.loadData(this._prepareData(), false); + return store; +}; + +AdditiveGrid.prototype._renderGrid = function() { + var _this = this; + this.store = this.getStore(); + + var cellEditing = Ext.create('Ext.grid.plugin.CellEditing', { + clicksToEdit : 1 + }); + + this.grid = Ext.create('Ext.grid.Panel', { + dockedItems : [ { + xtype : 'toolbar', + items : this._getActions() + } ], + store : this.store, + height : 230, + title : "Additives", + width : "100%", + columns : _this._getFields(), + plugins : [ cellEditing ], viewConfig : { stripeRows : true, listeners : { - afterrender : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - }, - celldblclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - _this.edit(record.data.macromoleculeId); - }, - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - if (grid.getGridColumns()[cellIndex].getId() == 'buttonEditMacromolecule') { - _this.edit(record.data.macromoleculeId); - } - if (grid.getGridColumns()[cellIndex].getId() == 'buttonRemoveMacromolecule') { - BUI.showBetaWarning(); - } - if (grid.getGridColumns()[cellIndex].getId() == 'btnResultVisible') { - window.location = BUI.getMacromoleculeResultsURL(record.data.macromoleculeId); - } + itemcontextmenu : function(view, rec, node, index, e) { + e.stopEvent(); + contextMenu.showAt(e.getXY()); + return false; } } + }, + selModel : { + mode : 'SINGLE' } }); - /** Adding the tbar **/ - if (this.tbar) { - this.grid.addDocked({ - xtype : 'toolbar', - items : this.getTbar() - }); - } return this.grid; }; -ResultsAssemblyGrid.prototype.input = function(targetId) { - return { - data : DATADOC.getData_3367(), - proposal : DATADOC.getProposal_3367() - }; +AdditiveGrid.prototype.input = function() { }; -ResultsAssemblyGrid.prototype.test = function(targetId) { - var grid = new ResultsAssemblyGrid({ - height : 600, - searchBar : false, - tbar : false, - btnResultVisible : true, - width : 1000 - }); - BIOSAXS.proposal = new Proposal(grid.input().proposal); - var panel = grid.getPanel(grid.input().data); +AdditiveGrid.prototype.test = function(targetId) { + var grid = new AdditiveGrid(); + var panel = grid.getPanel([]); panel.render(targetId); }; +/** AnalysisGrid **/ +function AnalysisGrid(args) { + var _this = this; -function RigidModelGrid(args) { - this.height = null; - this.width = null; this.id = BUI.id(); + if (Ext.get("mainPanel")){ + this.width = Ext.get("mainPanel").getWidth(); + } + else{ + this.width = this.maxWidth; + } + this.maxWidth = 1500; + + /** Visibles **/ + this.isGuinierTabVisible = true; + this.isGnomTabVisible = true; + this.isPorodTabVisible = true; + this.isScatteringPlotVisible = true; + this.isAbinitioTabVisible = true; + this.showButtonsVisible = true; + this.isI0Visible = true; + + this.margin = null; + this.grouped = true; + + this.hideNulls = false; + this.decimals = 4; + this.height = null; + this.sorters = [ { + property : 'conc', + direction : 'ASC' + } ]; if (args != null) { + if (args.grouped != null) { + this.grouped = args.grouped; + } + + if (args.showButtonsVisible != null) { + this.showButtonsVisible = args.showButtonsVisible; + } + if (args.isI0Visible != null) { + this.isI0Visible = args.isI0Visible; + } + if (args.sorters != null) { + this.sorters = args.sorters; + } + if (args.isScatteringPlotVisible != null) { + this.isScatteringPlotVisible = args.isScatteringPlotVisible; + } + if (args.isGuinierTabVisible != null) { + this.isGuinierTabVisible = args.isGuinierTabVisible; + } + if (args.isGnomTabVisible != null) { + this.isGnomTabVisible = args.isGnomTabVisible; + } + if (args.isPorodTabVisible != null) { + this.isPorodTabVisible = args.isPorodTabVisible; + } + if (args.hideNulls != null) { + this.hideNulls = args.hideNulls; + } if (args.height != null) { this.height = args.height; + } + if (args.width != null) { + this.width = args.width; + } + if (args.maxWidth != null) { + this.maxWidth = args.maxWidth; + } + } +} - if (args.width != null) { - this.width = args.width; +AnalysisGrid.prototype.refresh = function(data, args) { + this.store.loadData(this._prepareData(data), false); + if (args != null){ + if (args.experiment != null){ + this.experiment = args.experiment; + } + } +}; + +AnalysisGrid.prototype._getPorod = function() { + return { + text : 'Porod', + name : 'Porod', + columns : [ + { + text : 'Volume', + dataIndex : 'volumeEdna', + width : 75, + sortable : true, + hidden : !this.isPorodTabVisible, + renderer : function(val, y, sample) { + if (sample.raw.volume != null) + return BUI.formatValuesUnits(sample.raw.volume, '') + " nm3"; + } + }, + { + text : 'MM Vol. est.', + dataIndex : 'volumeEdna', + tooltip : '[Volume/2 - Volume/1.5] (Guinier)', + sortable : true, + width : 95, + hidden : !this.isPorodTabVisible, + renderer : function(val, y, sample) { + if (sample.raw.volume != null) + return Number(sample.raw.volume / 2).toFixed(1) + " - " + Number(sample.raw.volume / 1.5).toFixed(1)+ "kD"; + } + } ] + }; +}; + + +AnalysisGrid.prototype._getFramesColumn = function() { + var _this = this; + return { + text : 'Frames (Averaged/Total)', + dataIndex : 'datacollection', + name : 'datacollection', + sortable : true, + width : 150, + renderer : function(dataCollections, y, data) { + /** Bug of Webservices: frames count were swapped with frames averages **/ + if (data.raw.bufferAfterFramesCount){ + if (data.raw.bufferAfterFramesMerged){ + if (parseInt(data.raw.bufferAfterFramesMerged) > parseInt(data.raw.bufferAfterFramesCount)){ + var aux = parseInt(data.raw.bufferAfterFramesCount); + data.raw.bufferAfterFramesCount= data.raw.bufferAfterFramesMerged; + data.raw.bufferAfterFramesMerged = aux; + } + } + } + + if (data.raw.bufferBeforeFramesCount){ + if (data.raw.bufferBeforeFramesMerged){ + if (parseInt(data.raw.bufferBeforeFramesMerged) > parseInt(data.raw.bufferBeforeFramesCount)){ + var aux = parseInt(data.raw.bufferBeforeFramesCount); + data.raw.bufferBeforeFramesCount= data.raw.bufferBeforeFramesMerged; + data.raw.bufferBeforeFramesMerged = aux; + } + } + + } + + var bufferAcronym = data.raw.bufferAcronym; + var macromoleculeAcronym = data.raw.macromoleculeAcronym; + var bbmerges = data.raw.bufferBeforeFramesMerged; + var molmerges = data.raw.framesMerge; + var bamerges = data.raw.bufferAfterFramesMerged; + var totalframes = data.raw.framesCount; + var bufferId = data.raw.bufferId; + var macromoleculeId = data.raw.macromoleculeId; + var macromoleculeColor = null; + if (_this.experiment != null){ + macromoleculeColor = _this.experiment.macromoleculeColors[data.raw.macromoleculeId]; } - } - } - - this.onSelected = new Event(this); -} - - -RigidModelGrid.prototype.refresh = function(subtractions) { - var data = []; - if (subtractions != null){ - if (subtractions.length > 0){ - for (j in subtractions){ - var subtraction = subtractions[j]; - if (subtraction.rigidBodyModeling3VOs != null){ - for (i in subtraction.rigidBodyModeling3VOs){ - data.push(subtraction.rigidBodyModeling3VOs[i]); + + /** BUG in the database to be fixed **/ + try{ + if (totalframes != null){ + if(molmerges != null){ + if (parseFloat(totalframes) < parseFloat(molmerges)){ + var aux = totalframes; + totalframes = molmerges; + molmerges = aux; + } } } } + catch(e){ + + } + + return BUI.getHTMLTableForFrameAveraged(bufferAcronym, + macromoleculeAcronym, + bbmerges, + molmerges, + bamerges, + totalframes, + bufferId, + macromoleculeId, + macromoleculeColor); } - } - this.store.loadData(data); + }; }; -RigidModelGrid.prototype.getPanel = function() { +AnalysisGrid.prototype._getColumns = function() { var _this = this; - this.store = Ext.create('Ext.data.Store', { - fields : [ 'symmetry', 'subtractionId', 'subUnitConfigFilePath', 'rigidBodyModelingId', 'rigidBodyModelFilePath', 'logFilePath', 'fitFilePath', 'curveConfigFilePath', - 'crossCorrConfigFilePath', 'contactDescriptionFilePath' ], - data : [] - }); - - this.store.sort([ { - property : 'name', - direction : 'ASC' - } ]); + return [ + { + name : 'groupeField', + dataIndex : 'groupeField', + hidden : true - this.panel = Ext.create('Ext.grid.Panel', { - store : this.store, - width : this.width, - height : this.height, - margin : 10, - deferredRender : false, - columns : [ { - text : 'RBM', - dataIndex : 'rigidBodyModelFilePath', - hidden : false, - flex : 1, - renderer : function(val){ - return BUI.getFileName(val); - } - }, { - text : 'Sub Unit Conf.', - dataIndex : 'subUnitConfigFilePath', + }, + { + "header" : "subtractionId", hidden : true, - flex : 1, - renderer : function(val){ - return BUI.getFileName(val); + "dataIndex" : "subtractionId", + "name" : "subtractionId" + }, + { + header : "Macromolecule", + dataIndex : "macromoleculeAcronym", + name : "macromoleculeAcronym", + renderer : function(val, y, sample) { + return '
' + val + '
' + + BUI.formatValuesUnits(sample.raw.conc, "mg/ml", 10, this.decimals) + '
' + + BUI.formatValuesUnits(sample.raw.exposureTemperature, "C", 10, this.decimals) + '
' } - }, { - text : 'Log', - dataIndex : 'logFilePath', + }, + { + header : "Order", + dataIndex : "priorityLevelId", + name : "priorityLevelId", + hidden : true + }, + { + header : "Code", + dataIndex : "code", + name : "code", + hidden : true + }, + { + header : "Conc.", + dataIndex : "conc", + width : 80, + name : "conc", + type : "number", hidden : true, - flex : 1, - renderer : function(val){ - return BUI.getFileName(val); - } - }, { - text : 'Fit', - dataIndex : 'fitFilePath', - hidden : false, - flex : 1, - renderer : function(val){ - return BUI.getFileName(val); - } - }, { - text : 'Curve Conf.', - dataIndex : 'curveConfigFilePath', - hidden : false, - flex : 1, - renderer : function(val){ - return BUI.getFileName(val); + renderer : function(val, y, sample) { + return BUI.formatValuesUnits(val, "mg/ml", 10, this.decimals); } - }, { - text : 'Cross Corr.', - dataIndex : 'crossCorrConfigFilePath', - hidden : false, - flex : 1, - renderer : function(val){ - return BUI.getFileName(val); + }, + { + text : 'Scattering', + width : 100, + dataIndex : 'subtractionId', + name : 'subtractionId', + hidden : !this.isScatteringPlotVisible, + renderer : function(val, y, sample) { + var url = BUI.getURL() + '&type=scattering&subtractionId=' + sample.raw.subtractionId; + var event = "OnClick= window.open('" + url + "')"; + return ''; } - }, { - text : 'Contact Desc.', - dataIndex : 'contactDescriptionFilePath', + }, + { + text : 'Kratky', + width : 100, + dataIndex : 'subtractionId', hidden : true, - flex : 1, - renderer : function(val){ - return BUI.getFileName(val); + name : 'subtractionId', + renderer : function(val, y, sample) { + var url = BUI.getURL() + '&type=kratky&subtractionId=' + sample.raw.subtractionId; + var event = "OnClick= window.open('" + url + "')"; + return ''; } - } ], - - viewConfig : { - enableTextSelection : true, - preserveScrollOnRefresh : true }, - listeners : { - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - - }, - afterrender : function() { + this._getFramesColumn(), + { + text : 'File Name', + dataIndex : 'averageFilePath', + name : 'averageFilePath', + sortable : true, + width : 150, + hidden : true, + renderer : function(dataCollections, y, data) { + return BUI.getHTMLTableForPrefixes(data.raw.bufferBeforeAverageFilePath, data.raw.averageFilePath, + data.raw.bufferAfterAverageFilePath); } - } - }); - return this.panel; -}; + }, - -/** - * shows shipments - * - * @height - * @width - * @minHeight - * @btnEditVisible - */ -function ShipmentGrid(args) { - this.id = BUI.id(); - this.height = 100; - this.width = null; - this.minHeight = null; - this.btnEditVisible = true; + { + text : 'Guinier', + name : 'Guinier', + columns : [ + { + text : 'Rg', + dataIndex : 'rgGuinier', + name : 'rgGuinier', + hidden : !this.isGuinierTabVisible, + width : 75, + tooltip : 'In polymer physics, the radius of gyration is used to describe the dimensions of a polymer chain.', + sortable : true, + renderer : function(val, y, sample) { + if (sample.raw.rgGuinier != null) { + /** Show warning if rgGuinier and rgGnom differ more than 10% **/ + if (Math.abs(sample.raw.rgGuinier - sample.raw.rgGnom) > (sample.raw.rgGuinier * 0.1)) { + return "" + BUI.formatValuesUnits(sample.raw.rgGuinier, "") + ""; - if (args != null) { - if (args.height != null) { - this.height = args.height; - } - if (args.width != null) { - this.width = args.width; - } - if (args.minHeight != null) { - this.minHeight = args.minHeight; - } - if (args.btnEditVisible != null) { - this.btnEditVisible = args.btnEditVisible; - } - } -} + } + return BUI.formatValuesUnits(sample.raw.rgGuinier, "nm", 12, this.decimals); + } + } + }, + { + text : 'Points', + dataIndex : 'points', + sortable : true, + width : 100, + type : 'string', + hidden : !this.isGuinierTabVisible, + renderer : function(val, y, sample) { + if ((sample.raw.firstPointUsed == "") || (sample.raw.firstPointUsed == null)) + return; + return "" + sample.raw.firstPointUsed + " - " + sample.raw.lastPointUsed + " (" + + (sample.raw.lastPointUsed - sample.raw.firstPointUsed) + " )"; + } + }, + { + text : 'Quality', + dataIndex : 'quality', + hidden : !this.isGuinierTabVisible, + tooltip : 'Estimated data quality. 1.0 - means ideal quality, 0.0 - unusable data. In table format it is given in percent (100% - ideal quality, 0% - unusable data). Please note that this estimation is based only on the Guinier interval (very low angles).', + width : 60, + sortable : true, + renderer : function(val, y, sample) { + if (sample.raw.quality != null) { + val = sample.raw.quality; + if ((val != null) && (val != "")) { + return "" + (Number(val) * 100).toFixed(2) + " %"; + } + } + } + }, { + text : 'I(0)', + dataIndex : 'I0', + sortable : true, + hidden : !this.isI0Visible, + tooltip : 'Extrapolated scattering intensity at zero angle I(0) (forward scattering)', + width : 75, + type : 'string', + renderer : function(val, y, sample) { + if (sample.raw.I0 != null) { + return BUI.formatValuesErrorUnitsScientificFormat(sample.raw.I0, sample.raw.i0stdev, ""); + } + } + }, { + text : 'Aggregated', + tooltip : "If aggregation was detected from the slope of the data curve at low angles the value is '1', otherwise '0'.", + dataIndex : 'isagregated', + hidden : true, + width : 75, + renderer : function(val, y, sample) { + if ((sample.raw.isagregated != null)) { + if (val == true) { + return "Yes"; + } else { + return "No"; + } + } + } + }, { + text : 'Guinier', + sortable : true, + dataIndex : 'subtractionId', + type : 'string', + width : 100, + hidden : true, + renderer : function(val, y, sample) { -ShipmentGrid.prototype._getColumns = function() { - var _this = this; - var columns = [ - { - text : 'Name', - dataIndex : 'shippingName', - flex : 1 + if (sample.raw.subtractionId != null) { + var url = BUI.getURL() + '&type=guinier&subtractionId=' + sample.raw.subtractionId; + var event = "OnClick= window.open('" + url + "')"; + return ''; + } + } + } ] }, { - header : 'Type', - dataIndex : 'shippingType', - flex : 1, - hidden : true, - renderer : function(val, comp, record) { - if (val != null) { - return val.toUpperCase(); - } + text : 'Gnom', + name : 'Gnom', - } - }, - { - header : 'Status', - type : 'string', - flex : 1, - hidden : false, - renderer : function(comp, val, record) { - if (record.raw.shippingStatus != null) { - if (new String(record.raw.shippingStatus).toUpperCase() == 'OPENED') { - return "" + new String(record.raw.shippingStatus).toUpperCase() + ""; + columns : [ { + text : 'Rg', + dataIndex : 'rgGnom', + type : 'string', + width : 65, + hidden : !this.isGnomTabVisible, + sortable : true, + renderer : function(val, y, sample) { + /** Show warning if rgGuinier and rgGnom differ more than 10% **/ + if (sample.raw.rgGnom != null) { + if (Math.abs(sample.raw.rgGuinier - sample.raw.rgGnom) > (sample.raw.rgGuinier * 0.1)) { + return "" + BUI.formatValuesUnits(sample.raw.rgGnom, "") + ""; + + } + return BUI.formatValuesUnits(sample.raw.rgGnom, "nm"); } - return "" + new String(record.raw.shippingStatus).toUpperCase() + ""; } - } + }, { + text : 'Total', + dataIndex : 'total', + width : 65, + hidden : !this.isGnomTabVisible, + sortable : true, + renderer : function(val, y, sample) { + if (sample.raw.total != null) + return BUI.formatValuesUnits(sample.raw.total, ''); + } + }, { + text : 'Dmax', + dataIndex : 'dmax', + sortable : true, + width : 75, + hidden : !this.isGnomTabVisible, + renderer : function(val, y, sample) { + if (sample.raw.dmax != null) + return BUI.formatValuesUnits(sample.raw.dmax, "") + " nm"; + } + }, { + text : 'P(r)', + sortable : true, + hidden : true, + width : 100, + dataIndex : 'subtractionId', + type : 'string', + renderer : function(val, y, sample) { + var url = BUI.getURL() + '&type=gnom&subtractionId=' + sample.raw.subtractionId; + var event = "OnClick= window.open('" + url + "')"; + return ''; + } + } ] }, + this._getPorod(), { - text : 'Cases', - flex : 1, - hidden : false, - renderer : function(comp, val, record) { - var shipment = BIOSAXS.proposal.getShipmentById(record.data.shippingId); - var container = ""; - if (shipment.dewarVOs.length > 0) { - container = container + ""; - } else { - return "Empty"; - } - return container + "
" + shipment.dewarVOs.length + "x
"; - } - }, { - header : 'Comments', - dataIndex : 'comments', - flex : 1, - hidden : false - }, { - header : 'Creation Date', - dataIndex : 'creationDate', - hidden : true - } ]; - - if (this.btnEditVisible) { - columns.push({ - id : _this.id + 'buttonEdit', - text : '', - hidden : !_this.btnEditVisible, - width : 100, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - return BUI.getGreenButton('EDIT'); - } - }); - } - - columns.push({ - id : _this.id + 'buttonRemove', - text : '', - width : 100, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - var shipment = BIOSAXS.proposal.getShipmentById(record.data.shippingId); - if (shipment.dewarVOs.length == 0) { - return BUI.getRedButton('REMOVE'); - } - - } - }); - - return columns; -}; - -ShipmentGrid.prototype._getTopButtons = function() { - var _this = this; - /** Actions buttons **/ - var actions = []; - actions.push(Ext.create('Ext.Action', { - icon : '../images/add.png', - text : 'Add Shipment', - handler : function(widget, event) { - //window.location = BUI.getCreateShipmentURL(); - var _this = this; - - var shipmentForm = new ShipmentForm({ - creationMode : true, - showTitle : false - }); - shipmentForm.onSaved.attach(function(sender, shipment) { - _this.showShipmentTabs(shipment, targetId); - }); - - var window = Ext.create('Ext.window.Window', { - title : 'New Shipment', - height : 600, - width : 800, - layout : 'fit', - items : [ shipmentForm.getPanel() ] - }).show(); - - } - })); - return actions; -}; - -ShipmentGrid.prototype.refresh = function(shippings) { - this.features = shippings; - this.store.loadData(this._prepareData(), false); -}; - -ShipmentGrid.prototype._prepareData = function() { - var data = []; - for ( var i = 0; i < this.features.length; i++) { - data.push(this.features[i]); - } - return data; -}; - -ShipmentGrid.prototype.getPanel = function(shipments) { - this.features = shipments; - return this._renderGrid(); -}; - -ShipmentGrid.prototype.edit = function(shippingId) { - window.location = BUI.getShippingURL(shippingId); -}; - -ShipmentGrid.prototype._getStoreFields = function(data) { - var _this = this; - return [ { - name : 'shippingId' - }, { - name : 'shippingName' - }, { - name : 'shippingStatus' - }, { - name : 'shippingType' - }, { - name : 'creationDate' - }, { - name : 'comments' - } ]; -}; - -ShipmentGrid.prototype._renderGrid = function() { - var _this = this; - - /** Store **/ - var data = this._prepareData(); - this.store = Ext.create('Ext.data.Store', { - fields : this._getStoreFields(data), - autoload : true, - data : data - }); - - this.store.loadData(data, false); + text : 'AbInitio Modeling', + name : 'AbInitio_modeling', - this.grid = Ext.create('Ext.grid.Panel', { - title : "Shipping", - icon : '/ispyb/images/plane.gif', - width : this.width, - minWidth : this.minWidth, - height : this.height, - store : this.store, - columns : this._getColumns(), - viewConfig : { - stripeRows : true, - listeners : { - itemdblclick : function(dataview, record, item, e) { - _this.edit(record.raw.shippingId); + columns : [ + { + text : 'NSD', + dataIndex : 'volumeEdna', + width : 100, + sortable : true, + hidden : true, + renderer : function(val, y, sample) { + var url = BUI.getNSDImageURL(sample.raw.modelListId); + var event = "OnClick= window.open('" + url + "')"; + return ''; + } }, - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEdit') { - _this.edit(record.data.shippingId); + { + text : 'Chi2', + dataIndex : 'volumeEdna', + sortable : true, + hidden : true, + width : 100, + renderer : function(val, y, sample) { + var url = BUI.getCHI2ImageURL(sample.raw.modelListId); + var event = "OnClick= window.open('" + url + "')"; + return ''; } + }, + { + text : 'Pdb', + dataIndex : 'volumeEdna', + tooltip : 'Damaver: The program suite DAMAVER is a set of programs to align ab initio models, select the most typical one and build an averaged model. Dammif : Rapid ab initio shape determination by simulated annealing using a single phase dummy atom model. Dammin :Ab initio shape determination by simulated annealing using a single phase dummy atom model', + sortable : true, + width : 125, + hidden : !this.isAbinitioTabVisible, + renderer : function(val, y, sample) { + var html = new String(); + var split = null; + var url = null; + var file = sample.raw.averagedModel; + if (file != null) { + split = file.split("/"); + if (split.length > 0) { + url = BUI.getPdbURL() + '&type=AVERAGED&abInitioModelId=' + sample.raw.abInitioModelId; + html = html + ''+ split[split.length - 1] + '

'; - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemove') { - var shipment = BIOSAXS.proposal.getShipmentById(record.data.shippingId); - if (shipment.dewarVOs.length == 0) { + } + } - var adapter = new BiosaxsDataAdapter(); - _this.grid.setLoading("ISPyB: Removing shipment"); - adapter.onSuccess.attach(function(sender) { - BIOSAXS.proposal.onInitialized.attach(function(sender) { - _this.refresh(BIOSAXS.proposal.getShipments()); - _this.grid.setLoading(false); - }); - BIOSAXS.proposal.init(); - }); + file = sample.raw.rapidShapeDeterminationModel; + if (file != null) { + split = file.split("/"); + if (split.length > 0) { + url = BUI.getPdbURL() + '&type=RAPIDSHAPEDETERMINATIONMODEL&abInitioModelId=' + sample.raw.abInitioModelId; + html = html + '' + split[split.length - 1] + '

'; + } + } - adapter.onError.attach(function(sender) { - alert("Error"); - _this.grid.setLoading(false); - }); - adapter.removeShipment(record.data.shippingId); + file = sample.raw.shapeDeterminationModel; + if (file != null) { + split = file.split("/"); + if (split.length > 0) { + url = BUI.getPdbURL() + '&type=SHAPEDETERMINATIONMODEL&abInitioModelId=' + sample.raw.abInitioModelId; + html = html + ''+ split[split.length - 1] + ''; + } } + return html; } - } - } - }, - selModel : { - mode : 'SINGLE' - } - }); - - var actions = _this._getTopButtons(); - this.grid.addDocked({ - xtype : 'toolbar', - items : actions - }); - - this.grid.getSelectionModel().on({ - selectionchange : function(sm, selections) { - if (selections.length) { - for ( var i = 0; i < actions.length; i++) { - if (actions[i].enable) { - actions[i].enable(); + }, + { + text : 'Damaver', + dataIndex : 'volumeEdna', + hidden : true, + tooltip : 'Damaver: The program suite DAMAVER is a set of programs to align ab initio models, select the most typical one and build an averaged model. ', + sortable : true, + width : 125, + renderer : function(val, y, sample) { + var file = sample.raw.averagedModel; + if (file != null) { + var split = file.split("/"); + if (split.length > 0) { + var url = BUI.getPdbURL() + '&type=AVERAGED&abInitioModelId=' + sample.raw.abInitioModelId; + return '' + split[split.length - 1]+ ''; + } + } + return sample.raw.averagedModel; } - } - } else { - for ( var i = 0; i < actions.length; i++) { - if (actions[i].alwaysEnabled == false) { - if (actions[i].disable) { - actions[i].disable(); + }, + { + text : 'Dammif', + dataIndex : 'volumeEdna', + hidden : true, + tooltip : 'Dammif : Rapid ab initio shape determination by simulated annealing using a single phase dummy atom model', + sortable : true, + width : 125, + renderer : function(val, y, sample) { + var file = sample.raw.rapidShapeDeterminationModel; + if (file != null) { + var split = file.split("/"); + if (split.length > 0) { + var url = BUI.getPdbURL() + '&type=RAPIDSHAPEDETERMINATIONMODEL&abInitioModelId=' + sample.raw.abInitioModelId; + return '' + split[split.length - 1] + ''; + } } + return sample.raw.averagedModel; } - } - } - } - }); - return this.grid; -}; - -ShipmentGrid.prototype.input = function() { - return { - proposal : new MeasurementGrid().input().proposal, - shippings : DATADOC.getShippings_10() - }; -}; - -ShipmentGrid.prototype.test = function(targetId) { - var shipmentGrid = new ShipmentGrid({ - minHeight : 300, - height : 440 - }); - BIOSAXS.proposal = new Proposal(shipmentGrid.input().proposal); - var panel = shipmentGrid.getPanel(targetId); - panel.render(targetId); - shipmentGrid.refresh(shipmentGrid.input().shippings); -}; - -function SpecimenGrid(args) { - this.id = BUI.id(); - this.height = 500; - this.unitsFontSize = 9; - this.editEnabled = false; - this.isPositionColumnHidden = false; - this.removeBtnEnabled = false; - - this.selectionMode = "MULTI"; - this.updateRowEnabled = false; - this.grouped = true; - this.width = 900; - this.title = 'Specimens'; - - this.margin = "0 0 0 0"; -// this.experimentColorBased = false; - - if (args != null) { - if (args.height != null) { - this.height = args.height; - } - - if (args.showTitle == false) { - this.title = null; - } - - if (args.margin == false) { - this.margin = args.margin; - } - - if (args.grouped == false) { - this.grouped = null; - } - - if (args.width != null) { - this.width = args.width; - } - - - if (args.editEnabled != null) { - this.editEnabled = args.editEnabled; - } - if (args.removeBtnEnabled != null) { - this.removeBtnEnabled = args.removeBtnEnabled; - } - if (args.isPositionColumnHidden != null) { - this.isPositionColumnHidden = args.isPositionColumnHidden; - } - if (args.selectionMode != null) { - this.selectionMode = args.selectionMode; - } - if (args.updateRowEnabled != null) { - this.updateRowEnabled = args.updateRowEnabled; - } - - } - this.onClick = new Event(this); - this.onSelected = new Event(this); - this.onRemoved = new Event(this); - this.onSpecimenChanged = new Event(); -} - -SpecimenGrid.prototype._prepareData = function(experiment) { - var data = []; - - var samples = experiment.getSamples(); - for ( var i = 0; i < samples.length; i++) { - var sample = samples[i]; - if (sample.macromolecule3VO != null) { - sample.macromolecule = sample.macromolecule3VO.acronym; - sample.exposureTemperature = []; - sample.macromoleculeId = sample.macromolecule3VO.macromoleculeId; - } + }, + { + text : 'Dammin', + dataIndex : 'volumeEdna', + hidden : true, + tooltip : 'Dammin :Ab initio shape determination by simulated annealing using a single phase dummy atom model', + sortable : true, + width : 125, + renderer : function(val, y, sample) { + var file = sample.raw.shapeDeterminationModel; + if (file != null) { + var split = file.split("/"); + if (split.length > 0) { + var url = BUI.getPdbURL() + '&type=SHAPEDETERMINATIONMODEL&abInitioModelId=' + sample.raw.abInitioModelId; + return '' + split[split.length - 1]+ ''; + } + } + return sample.raw.averagedModel; + } + } ] + }, { + text : 'Time', + dataIndex : 'substractionCreationTime', + name : 'substractionCreationTime', + hidden : true, + width : 80, + sortable : true, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + try { + if (record.raw.substractionCreationTime != null) { + return moment(record.raw.substractionCreationTime).format('h:mm:ss a'); + } + } catch (e) { + return "NA"; + } + } + }, { + text : 'Date', + dataIndex : 'substractionCreationTime', + name : 'substractionCreationTime', + hidden : true, + width : 80, + sortable : true, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + try { + if (record.raw.substractionCreationTime != null) { + return moment(record.raw.substractionCreationTime).format("LL"); + } + } catch (e) { + return "NA"; + } + } + }, + this._getButtons()]; +}; - if (sample.sampleplateposition3VO != null) { - if (sample.sampleplateposition3VO.samplePlateId != null) { - sample.samplePlateId = sample.sampleplateposition3VO.samplePlateId; - sample.rowNumber = sample.sampleplateposition3VO.rowNumber; - sample.columnNumber = sample.sampleplateposition3VO.columnNumber; - if (experiment.getSamplePlateById(sample.sampleplateposition3VO.samplePlateId).plategroup3VO != null) { - sample.plateGroupName = experiment.getSamplePlateById(sample.sampleplateposition3VO.samplePlateId).plategroup3VO.name; - sample.samplePlateName = experiment.getSamplePlateById(sample.sampleplateposition3VO.samplePlateId).name + " [" + sample.plateGroupName + "]"; - sample.slotPositionColumn = experiment.getSamplePlateById(sample.sampleplateposition3VO.samplePlateId).slotPositionColumn; +AnalysisGrid.prototype._getButtons = function() { + return { + id : this.id + 'buttonPlot', + name : 'buttonPlot', + hidden : !this.showButtonsVisible, + width : 110, + sortable : false, + renderer : function(value, metaData, sample, rowIndex, colIndex, store) { + var html = ""; + + if (sample.raw.subtractionId) { + html = html + ""; + if (sample.raw.rapidShapeDeterminationModelId != null) { + html = html + ""; } } - } else { - sample.samplePlateName = "Unallocated Specimens"; + return html + "
" + BUI.getGreenButton('Calibration', { + height : 20, + width : 100 + }) + "
" + BUI.getGreenButton('Primary Data Proc.', { + height : 20, + width : 100 + }) + "
" + BUI.getGreenButton('AbInitio Modeling', { + height : 20, + width : 100 + }) + "
"; } - - /** For grouping, because sencha has not option for multiple grouping I add a field to your store with a convert function that concatenates these two fields and then group by that field.**/ - sample.groupIndex = sample.bufferId + sample.macromoleculeId; - var macromolecule = BIOSAXS.proposal.getMacromoleculeById(sample.macromoleculeId); - - sample.acronym = "Buffers"; - if (macromolecule != null) { - sample.acronym = BIOSAXS.proposal.getMacromoleculeById(sample.macromoleculeId).acronym; + }; +}; +AnalysisGrid.prototype._prepareData = function(data) { + if (this.hideNulls) { + var result = []; + for ( var i = 0; i < data.length; i++) { + if (data[i].subtractionId != null) { + data[i].groupeField = data[i].macromoleculeAcronym + " " + data[i].bufferAcronym; + result.push(data[i]); + } } - - sample.buffer = experiment.getBufferById(sample.bufferId); - - sample.volumeToLoad = experiment.getVolumeToLoadBySampleId(sample.sampleId); - data.push(sample); + return result; + } else { + return data; } - return data; }; -SpecimenGrid.prototype.deselectAll = function() { - this.grid.getSelectionModel().deselectAll(); -}; +AnalysisGrid.prototype.getPanel = function(data) { + var _this = this; + var columns = this._getColumns(); -SpecimenGrid.prototype.selectById = function(specimenId) { - this.grid.getSelectionModel().deselectAll(); - for ( var i = 0; i < this.grid.getStore().data.items.length; i++) { - var item = this.grid.getStore().data.items[i].raw; - if (item.specimenId == specimenId) { - this.grid.getSelectionModel().select(i); - } - } -}; + var fields = JSON.parse(JSON.stringify(columns)); + fields.push({ + name : 'experimentId', + dataIndex : 'experimentId' -SpecimenGrid.prototype.getStore = function() { - return this.store; -}; + }); + this.store = Ext.create('Ext.data.Store', { + fields : fields, + autoload : true, + data : this._prepareData(data), + groupField : 'groupeField' + }); -SpecimenGrid.prototype.getPlugins = function() { - var _this = this; + this.store.sort(this.sorters); - var plugins = []; + var features = []; - if (this.updateRowEnabled) { - plugins.push(Ext.create('Ext.grid.plugin.RowEditing', { - clicksToEdit : 1, + if (this.grouped) { + features.push({ + ftype : 'grouping', + groupHeaderTpl : '{name}', + hideGroupedHeader : false, + startCollapsed : false + }); + } + + this.grid = Ext.create('Ext.grid.Panel', { + style : { + padding : 5 + }, + maxWidth : this.maxWidth, + width : this.width, + height : this.height, + store : this.store, + columns : columns, + resizable : true, + features : features, + viewConfig : { + preserveScrollOnRefresh : true, + stripeRows : true, listeners : { - validateedit : function(grid, e) { - var measurements = []; + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - if (e.newValues.bufferId != e.record.raw.bufferId) { - /** If buffer has changed we have to change all the specimens sharing same datacollection **/ - var dataCollections = []; - if (e.record.raw.macromoleculeId == null) { - dataCollections = dataCollections.concat(_this.experiment.getDataCollectionsBySpecimenId(e.record.raw.specimenId)); - } else { - var sampleDataCollections = _this.experiment.getDataCollectionsBySpecimenId(e.record.raw.specimenId); - for ( var i = 0; i < sampleDataCollections.length; i++) { - var sampleDataCollection = sampleDataCollections[i]; - if (sampleDataCollection != null) { - for ( var j = 0; j < sampleDataCollection.measurementtodatacollection3VOs.length; j++) { - var measurementTODc = sampleDataCollection.measurementtodatacollection3VOs[j]; - if (measurementTODc.dataCollectionOrder == 1) { - dataCollections = dataCollections.concat(_this.experiment.getDataCollectionsBySpecimenId(_this.experiment - .getMeasurementById(measurementTODc.measurementId).specimenId)); - } - } - } - } - } - var i = null; - for ( i = 0; i < dataCollections.length; i++) { - var dataCollection = dataCollections[i]; - var specimens = _this.experiment.getSpecimenByDataCollectionId(dataCollection.dataCollectionId); - measurements = measurements.concat(specimens); + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonPlot') { + if (e.target.defaultValue == 'AbInitio Modeling') { + var url = BUI.getPDBVisualizerURL(record.raw.averagedModelId, record.raw.subtractionId, record.raw.experimentId); + window.open(url, "_blank"); } - for ( i = 0; i < measurements.length; i++) { - var measurement = measurements[i]; - var specimen = _this.experiment.getSpecimenById(measurement.specimenId); - specimen.bufferId = e.newValues.bufferId; - new BiosaxsDataAdapter().saveSpecimen(specimen, _this.experiment); + if (e.target.defaultValue == 'Primary Data Proc.') { + _this._edit(record.raw); } - } - - /** Setting values **/ - e.record.raw.concentration = e.newValues.concentration; - e.record.raw.volume = e.newValues.volume; - /** Position **/ - if (e.record.raw.sampleplateposition3VO != null) { - var samplePlate = _this.experiment.getSamplePlateBySlotPositionColumn(e.newValues.slotPositionColumn); - if (samplePlate != null) { - e.record.raw.sampleplateposition3VO = { - columnNumber : e.newValues.columnNumber, - rowNumber : e.newValues.rowNumber, - samplePlateId : samplePlate.samplePlateId - }; - } - } else { - if (e.newValues.slotPositionColumn != null) { - var samplePlate = _this.experiment.getSamplePlateBySlotPositionColumn(e.newValues.slotPositionColumn); - if (samplePlate != null) { - e.record.raw.sampleplateposition3VO = { - columnNumber : e.newValues.columnNumber, - rowNumber : e.newValues.rowNumber, - samplePlateId : samplePlate.samplePlateId - }; - } + if (e.target.defaultValue == 'Calibration') { + _this._showCalibration(record.raw); } } - - var macromoleculeId = e.record.data.macromoleculeId; - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, specimen) { - /** Because macromolecule3VO is fecthed LAZY **/ - if (macromoleculeId != null) { - specimen.macromolecule3VO = BIOSAXS.proposal.getMacromoleculeById(macromoleculeId); - } - _this.onSpecimenChanged.notify(specimen); - _this.grid.setLoading(false); - }); - adapter.onError.attach(function() { - alert("Error"); - _this.grid.setLoading(false); - }); - _this.grid.setLoading(); - adapter.saveSpecimen(e.record.raw, _this.experiment); } } - })); - } - return plugins; + }, + selModel : { + mode : 'SINGLE' + } + }); + + return this.grid; + +}; + +AnalysisGrid.prototype._openVisualizarBySubstractionId = function(record) { + //experimentId, subtractionId) { + var experimentId = record.experimentId; + var subtractionId = record.subtractionId; + + var _this = this; + var adapter = new BiosaxsDataAdapter(); + this.subtractionId = subtractionId; + + adapter.onSuccess.attach(function(sender, data) { + var experiment = new Experiment(data); + var experimentList = new ExperimentList([ experiment ]); + var subtraction = experiment.getSubtractionById(_this.subtractionId); + _this.grid.setLoading(false); + _this._openVisualizer(experimentList, subtraction, record); + }); + this.grid.setLoading("ISPyB: Fetching experiment"); + adapter.getExperimentById(experimentId, "MEDIUM"); }; -SpecimenGrid.prototype._getRowCombo = function() { - var data = []; - for ( var i = 1; i <= 8; i++) { - data.push({ - rowNumber : i, - name : BUI.getSamplePlateLetters()[i - 1] +AnalysisGrid.prototype._edit = function(record) { + var experimentId = record.experimentId; + var _this = this; + + if (BIOSAXS.proposal.macromolecules == null) { + this.grid.setLoading("ISPyB: Fetching proposal"); + BIOSAXS.proposal.onInitialized.attach(function(sender, data) { + _this._openVisualizarBySubstractionId(record); }); + BIOSAXS.proposal.init(); + } else { + this._openVisualizarBySubstractionId(record); } +}; - var positionsStore = Ext.create('Ext.data.Store', { - fields : [ 'rowNumber', 'name' ], - data : data - }); - return Ext.create('Ext.form.ComboBox', { - store : positionsStore, - queryMode : 'local', - displayField : 'name', - valueField : 'rowNumber' +AnalysisGrid.prototype._showCalibration = function(row) { + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + Ext.create('Ext.window.Window', { + title : 'Calibration', + width : 900, + resizable : true, + height : 400, + modal : true, + frame : false, + draggable : true, + closable : true, + autoscroll : true, + paddin : 5, + layout : { + type : 'vbox', + align : 'stretch' + }, + items : [ new AnalysisGrid({ + isGuinierTabVisible : false, + isGnomTabVisible : false, + isPorodTabVisible : false, + isAbinitioTabVisible : false, + isI0Visible : true, + showButtonsVisible : false, + height : 350, + sorters : [ { + property : 'experimentId', + direction : 'DESC' + } ] + }).getPanel(data) ] + }).show(); }); + adapter.getAnalysisCalibrationByProposalId(); }; -SpecimenGrid.prototype._getColumnCombo = function() { - var data = []; - for ( var i = 1; i <= 12; i++) { - data.push({ - columnNumber : i - }); +AnalysisGrid.prototype._openVisualizer = function(experimentList, subtraction, record) { + var merges = experimentList.getMergesByDataCollectionId(subtraction.dataCollectionId); + var mergeIdList = []; + for ( var i = 0; i < merges.length; i++) { + mergeIdList.push(merges[i].mergeId); } - var positionsStore = Ext.create('Ext.data.Store', { - fields : [ 'columnNumber' ], - data : data + var dataAdapter = new BiosaxsDataAdapter(); + dataAdapter.onSuccess.attach(function(sender, merges) { + var dataCollectionCurveVisualizer = new DataCollectionCurveVisualizer(); + dataCollectionCurveVisualizer.draw(); + dataCollectionCurveVisualizer.refresh(merges, experimentList, subtraction.dataCollectionId, record); }); - return Ext.create('Ext.form.ComboBox', { - store : positionsStore, - queryMode : 'local', - displayField : 'columnNumber', - valueField : 'columnNumber' + dataAdapter.onError.attach(function(sender, error) { }); + + dataAdapter.getMergesByIdsList(mergeIdList); }; -SpecimenGrid.prototype._getSlotColumBombo = function() { - if (this.experiment){ - var length = this.experiment.getSamplePlates().length; - - var data = []; - for ( var i = 1; i <= length; i++) { - data.push({ - slotPositionColumn : i - }); - } +AnalysisGrid.prototype.input = function() { + return { + data : DATADOC.getData_3367().slice(20, 30),//[{"total":"0.447505552082","bufferBeforeMeasurementId":22150,"sampleMergeId":12373,"averagedModelId":43636,"I0":"32.50776","proposalCode":"OPD","averagedModel":"/data/pyarch/bm29/opd29/1137/1d/damaver.pdb","bufferAfterMergeId":12374,"framesCount":"10","bufferBeforeMergeId":12372,"averageFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_016_ave.dat","bufferAfterMeasurementId":22152,"rgGuinier":"2.96883","subtractedFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_016_sub.dat","firstPointUsed":"30","chi2RgFilePath":"/data/pyarch/bm29/opd29/1137/1d/chi2_R.png","abInitioModelId":272,"macromoleculeId":112,"code":"_20.0_1.25","transmission":"100.0","timeStart":"2013-07-17 17:10:25.743734","bufferAcronym":"MES","quality":"0.87091","shapeDeterminationModelId":43638,"expermientComments":"[BsxCube] Generated from BsxCube","bufferId":707,"isagregated":"False","dmax":"10.390905","bufferBeforeAverageFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_015_ave.dat","exposureTemperature":"20.0","subtractionId":5165,"conc":"1.25","rapidShapeDeterminationModel":"/data/pyarch/bm29/opd29/1137/1d/damfilt.pdb","experimentCreationDate":"Jul 17, 2013 5:08:37 PM","lastPointUsed":"92","modelListId":272,"framesMerge":"10","rapidShapeDeterminationModelId":43637,"bufferAfterAverageFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_017_ave.dat","nsdFilePath":"/data/pyarch/bm29/opd29/1137/1d/nsd.png","bufferAfterFramesMerged":"10","experimentId":1137,"macromoleculeAcronym":"MG386","i0stdev":"0.05726128","sampleMeasurementId":22151,"measurementComments":"[1] MES","priorityLevelId":2,"bufferBeforeFramesMerged":"10","substractionCreationTime":"Jul 17, 2013 5:12:32 PM","proposalNumber":"29","rgGnom":"3.05242714339","volume":"44.1406","shapeDeterminationModel":"/data/pyarch/bm29/opd29/1137/1d/dammin.pdb","comments":null},{"total":"0.582641941147","bufferBeforeMeasurementId":22152,"sampleMergeId":12375,"averagedModelId":43809,"I0":"31.4366153846","proposalCode":"OPD","averagedModel":"/data/pyarch/bm29/opd29/1137/1d/damaver.pdb","bufferAfterMergeId":12376,"framesCount":"10","bufferBeforeMergeId":12374,"averageFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_018_ave.dat","bufferAfterMeasurementId":22155,"rgGuinier":"2.95541","subtractedFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_018_sub.dat","firstPointUsed":"21","chi2RgFilePath":"/data/pyarch/bm29/opd29/1137/1d/chi2_R.png","abInitioModelId":273,"macromoleculeId":112,"code":"_20.0_0.65000000000000002","transmission":"100.0","timeStart":"2013-07-17 17:12:55.837462","bufferAcronym":"MES","quality":"0.870164","shapeDeterminationModelId":43811,"expermientComments":"[BsxCube] Generated from BsxCube","bufferId":707,"isagregated":"False","dmax":"10.343935","bufferBeforeAverageFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_017_ave.dat","exposureTemperature":"20.0","subtractionId":5166,"conc":"0.65000000000000002","rapidShapeDeterminationModel":"/data/pyarch/bm29/opd29/1137/1d/damfilt.pdb","experimentCreationDate":"Jul 17, 2013 5:08:37 PM","lastPointUsed":"80","modelListId":273,"framesMerge":"10","rapidShapeDeterminationModelId":43810,"bufferAfterAverageFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_019_ave.dat","nsdFilePath":"/data/pyarch/bm29/opd29/1137/1d/nsd.png","bufferAfterFramesMerged":"10","experimentId":1137,"macromoleculeAcronym":"MG386","i0stdev":"0.100250461538","sampleMeasurementId":22154,"measurementComments":"[2] MES","priorityLevelId":4,"bufferBeforeFramesMerged":"10","substractionCreationTime":"Jul 17, 2013 5:15:02 PM","proposalNumber":"29","rgGnom":"2.9963404542","volume":"42.2255","shapeDeterminationModel":"/data/pyarch/bm29/opd29/1137/1d/dammin.pdb","comments":null}], + proposal : new ResultsAssemblyGrid().input().proposal + }; +}; + +AnalysisGrid.prototype.test = function(targetId) { + var analysisGrid = new AnalysisGrid(); + BIOSAXS.proposal = new Proposal(analysisGrid.input().proposal); + var panel = analysisGrid.getPanel(analysisGrid.input().data); + panel.render(targetId); +}; + + +function HPLCAnalysisGrid(args) { + AnalysisGrid.prototype.constructor.call(this, args); +} - var positionsStore = Ext.create('Ext.data.Store', { - fields : [ 'slotPositionColumn' ], - data : data - }); +HPLCAnalysisGrid.prototype._edit = AnalysisGrid.prototype._edit; +HPLCAnalysisGrid.prototype._getColumns = AnalysisGrid.prototype._getColumns; +HPLCAnalysisGrid.prototype._openVisualizarBySubstractionId = AnalysisGrid.prototype._openVisualizarBySubstractionId; +HPLCAnalysisGrid.prototype._openVisualizer = AnalysisGrid.prototype._openVisualizer; +HPLCAnalysisGrid.prototype._prepareData = AnalysisGrid.prototype._prepareData; +HPLCAnalysisGrid.prototype._showCalibration = AnalysisGrid.prototype._showCalibration; +HPLCAnalysisGrid.prototype.getPanel = AnalysisGrid.prototype.getPanel; +HPLCAnalysisGrid.prototype.input = AnalysisGrid.prototype.input; +HPLCAnalysisGrid.prototype.test = AnalysisGrid.prototype.test; +HPLCAnalysisGrid.prototype.refresh = AnalysisGrid.prototype.refresh; +HPLCAnalysisGrid.prototype._getPorod = AnalysisGrid.prototype._getPorod; + +HPLCAnalysisGrid.prototype._getButtons = function() { + return { + id : this.id + 'buttonPlot', + name : 'buttonPlot', + hidden : !this.showButtonsVisible, + width : 110, + sortable : false, + renderer : function(value, metaData, sample, rowIndex, colIndex, store) { + var html = ""; - return Ext.create('Ext.form.ComboBox', { - store : positionsStore, - queryMode : 'local', - displayField : 'slotPositionColumn', - valueField : 'slotPositionColumn' - }); + if (sample.raw.subtractionId) { + if (sample.raw.rapidShapeDeterminationModelId != null) { + html = html + ""; + } + } + return html + "
" + BUI.getGreenButton('AbInitio Modeling', { + height : 20, + width : 100 + }) + "
"; + } + }; +}; + +HPLCAnalysisGrid.prototype._getFramesColumn = function() { + return { + text : 'Frames', + dataIndex : 'datacollection', + name : 'datacollection', + sortable : true, + width : 150, + renderer : function(dataCollections, y, data) { + molmerges = data.raw.framesMerge; + totalframes = data.raw.framesCount; + return molmerges +" - "+ totalframes; + } + }; +}; + + + + +/** + * Rigid body grid to show PDB, symmetry and multiplicity + * + * + * #onUploadFile click on upload file + */ +function AprioriRigidBodyGrid(args) { + + this.height = 250; + this.btnEditVisible = true; + this.btnRemoveVisible = true; + + if (args != null) { + if (args.height != null) { + this.height = args.height; + } + if (args.btnEditVisible != null) { + this.btnEditVisible = args.btnEditVisible; + } + if (args.btnRemoveVisible != null) { + this.btnRemoveVisible = args.btnRemoveVisible; + } + } + + /** Events **/ + this.onUploadFile = new Event(this); + this.onRemove = new Event(this); +} + +AprioriRigidBodyGrid.prototype._getColumns = function() { +}; + +AprioriRigidBodyGrid.prototype._getTopButtons = function() { + var _this = this; + /** Actions buttons **/ + var actions = []; + + /** ADD BUTTON **/ + actions.push(Ext.create('Ext.Action', { + icon : '../images/add.png', + text : 'Add', + disabled : false, + handler : function(widget, event) { + _this.onAddButtonClicked.notify(); + } + })); + + return actions; +}; + +AprioriRigidBodyGrid.prototype.refresh = function(macromolecule) { + this.macromolecule = macromolecule; + if (macromolecule != null){ + this.pdbStore.loadData(macromolecule.structure3VOs); + } +}; + +AprioriRigidBodyGrid.prototype._prepareData = function() { + var data = []; + for ( var i = 0; i < this.features.length; i++) { + data.push(this.features[i]); + } + return data; +}; + +AprioriRigidBodyGrid.prototype._getPlugins = function() { + var _this = this; + var plugins = []; + plugins.push(Ext.create('Ext.grid.plugin.RowEditing', { + clicksToEdit : 1, + listeners : { + validateedit : function(grid, e) { + /** Comments are always updatable* */ + e.record.raw.symmetry = e.newValues.symmetry; + e.record.raw.multiplicity = e.newValues.multiplicity; + + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, proposal) { + BIOSAXS.proposal.setItems(proposal); + _this.refresh(BIOSAXS.proposal.getMacromoleculeById(_this.macromolecule.macromoleculeId)); + _this.panel.setLoading(false); + }); + adapter.onError.attach(function() { + alert("Error"); + }); + + _this.panel.setLoading(); + adapter.saveStructure(e.record.raw); + } + } + })); + return plugins; +}; + +AprioriRigidBodyGrid.prototype.getPanel = function() { + var _this = this; + + this.pdbStore = Ext.create('Ext.data.Store', { + fields : [ 'filePath', 'structureId', 'structureType', 'symmetry', 'structureId', 'name', 'multiplicity' ], + groupField : 'structureType', + sorters : { + property : 'structureId', + direction : 'DESC' + } + }); + + var groupingFeature = Ext.create('Ext.grid.feature.Grouping', { + groupHeaderTpl : Ext.create('Ext.XTemplate', + "
{name:this.formatName}
", { + formatName : function(name) { + return name; + } + }), + hideGroupedHeader : true, + startCollapsed : false + }); + + this.panel = Ext.create('Ext.grid.Panel', { + margin : "15 10 0 10", + height : this.height, + store : this.pdbStore, + plugins : _this._getPlugins(), + tbar : [ { + text : 'Add Modeling Option (PDB)', + icon : '../images/add.png', + handler : function() { + _this.onUploadFile.notify('PDB', 'Upload PDB File'); + } + } + + ], + columns : [ + { + text : "structureId", + flex : 0.2, + hidden : true, + dataIndex : 'structureId', + sortable : true + }, + { + text : "File", + flex : 0.5, + dataIndex : 'filePath', + sortable : true, + hidden : true + }, + { + text : "PDB", + flex : 0.4, + dataIndex : 'name', + sortable : true + }, + { + text : "Symmetry", + flex : 0.2, + dataIndex : 'symmetry', + sortable : true, + editor : { + xtype : 'combobox', + typeAhead : true, + triggerAction : 'all', + selectOnTab : true, + store : [ [ "P1", "P1" ], [ "P2", "P2" ], [ "P3", "P3" ], [ "P4", "P4" ], [ "P5", "P5" ], [ "P6", "P6" ], [ "P32", "P32" ], [ "P42", "P42" ], + [ "P52", "P52" ], [ "P62", "P62" ], [ "P222", "P222" ] ], + } + }, { + text : "Multiplicity", + flex : 0.2, + dataIndex : 'multiplicity', + sortable : true, + editor : { + xtype : 'textfield' + } + + }, { + text : "Subunit", + flex : 0.2, + dataIndex : 'isSubunit', + sortable : true, + hidden : true + }, { + text : "Type", + flex : 0.2, + dataIndex : 'structureType', + sortable : true, + hidden : true + }, + + { + id : this.id + 'REMOVE', + flex : 0.2, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + return BUI.getRedButton('REMOVE'); + } + }, ], + + listeners : { + itemdblclick : function(dataview, record, item, e) { + _this._editExperiment(record.raw.experimentId); + }, + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'REMOVE') { + var dataAdapter = new BiosaxsDataAdapter(); + dataAdapter.onSuccess.attach(function() { + _this.panel.setLoading(false); + _this.onRemove.notify(); + }); + _this.panel.setLoading("Removing PDB file"); + dataAdapter.removeStructure(record.data.structureId); + } + + } + }, + viewConfig : { + getRowClass : function(record, rowIdx, params, store) { + if (record.raw.isSubunit != null) { + return "blue-row"; + } + } + } + }); + + return this.panel; +}; + + + + +AprioriRigidBodyGrid.prototype.input = function() { + return { + proposal : DATADOC.getProposal_10(), + dewars : DATADOC.getDewars_10() + + }; +}; + +AprioriRigidBodyGrid.prototype.test = function(targetId) { + var AprioriRigidBodyGrid = new AprioriRigidBodyGrid({ + height : 150 + }); + BIOSAXS.proposal = new Proposal(AprioriRigidBodyGrid.input().proposal); + var panel = AprioriRigidBodyGrid.getPanel(AprioriRigidBodyGrid.input().dewars); + panel.render(targetId); + +}; + +/** + * It shows buffer grid with a top bar with "Add" button + * + * @height + * @searchBar + * @collapsed + * @width + */ +function BufferGrid(args) { + this.height = 500; + this.searchBar = false; + this.tbar = false; + this.collapsed = false; + this.id = BUI.id(); + + if (args != null) { + if (args.height != null) { + this.height = args.height; + } + if (args.searchBar != null) { + this.searchBar = args.searchBar; + } + + if (args.tbar != null) { + this.tbar = args.tbar; + } + + if (args.collapsed != null) { + this.collapsed = args.collapsed; + } + + if (args.width != null) { + this.width = args.width; + } } +} + +BufferGrid.prototype._edit = function(bufferId) { + var _this = this; + var window = new BufferWindow(); + window.onSuccess.attach(function(sender, proposal) { + _this.store.loadData(BIOSAXS.proposal.getBuffers()); + }); + window.draw(BIOSAXS.proposal.getBufferById(bufferId)); }; -SpecimenGrid.prototype.getPanelByExperiment = function(experiment) { - this.experiment = experiment; - var data = this._prepareData(experiment); - return this.getPanel(data); +BufferGrid.prototype.refresh = function(buffers) { + this.store.loadData(this._prepareData(buffers), false); }; -SpecimenGrid.prototype.refresh = function(experiment) { - this.experiment = experiment; - var data = this._prepareData(experiment); - this.store.loadData(data); +BufferGrid.prototype._prepareData = function(buffers) { + return buffers; }; -SpecimenGrid.prototype.getPanel = function() { +BufferGrid.prototype._getTbar = function() { var _this = this; - this.store = Ext.create('Ext.data.Store', { - fields : [ - 'buffer', 'bufferId', 'code', 'macromolecule', 'acronym', 'macromoleculeId', 'concentration', 'volume', 'samplePlateId', - 'slotPositionColumn', 'rowNumber', 'columnNumber', 'groupIndex' ], - data : [], - groupField : 'acronym' - }); - this.store.sort([ { - property : 'concentration', - direction : 'ASC' - }, { - property : 'buffer', - direction : 'ASC' - } ]); + var actions = []; - var selModel = Ext.create('Ext.selection.RowModel', { - allowDeselect : true, - mode : this.selectionMode, - listeners : { - selectionchange : function(sm, selections) { - var selected = []; - for ( var i = 0; i < selections.length; i++) { - selected.push(selections[i].raw); - } - _this.onSelected.notify(selected); - } + actions.push(Ext.create('Ext.Action', { + icon : '../images/add.png', + text : 'Add buffer', + disabled : false, + handler : function(widget, event) { + var window = new BufferWindow(); + window.onSuccess.attach(function(sender) { + _this.store.loadData(BIOSAXS.proposal.getBuffers()); + }); + window.draw({}); } - }); - - var features = []; - - if (this.grouped) { - features.push({ - ftype : 'grouping', - groupHeaderTpl : '{name}', - hideGroupedHeader : false, - startCollapsed : false, - id : 'myGroupedStore' - }); - } + })); + return actions; +}; - this.grid = Ext.create( - 'Ext.grid.Panel', - { - title : this.title, - height : this.height, - width : this.width, - selModel : selModel, - store : this.store, - features : features, - margin : this.margin, - plugins : this.getPlugins(), - columns : [ - { - text : '', - dataIndex : 'macromolecule', - width : 20, - renderer : function(val, y, sample) { - var macromoleculeId = null; - if (sample.raw.macromolecule3VO != null) { - macromoleculeId = sample.raw.macromolecule3VO.macromoleculeId; - } - else{ - macromoleculeId = sample.raw.macromoleculeId; - } - - if (macromoleculeId == null) return; - return BUI.getRectangleColorDIV(_this.experiment.macromoleculeColors[macromoleculeId], 10, 10); - } - }, - { - text : 'Macromolecule', - dataIndex : 'macromolecule', - width : 100 - }, - { - text : '', - dataIndex : 'buffer', - width : 20, - renderer : function(val, y, sample) { - var color = "black"; - if (sample.raw.bufferId != null) { - if (_this.experiment.getDataCollectionsBySpecimenId(sample.raw.specimenId)[0] != null){ - color = _this.experiment.getSpecimenColorByBufferId(_this.experiment.getMeasurementById(_this.experiment.getDataCollectionsBySpecimenId(sample.raw.specimenId)[0].measurementtodatacollection3VOs[0].measurementId).specimenId); - } - return BUI.getRectangleColorDIV(color, 10, 10); - } - } - }, { - text : 'Buffer', - dataIndex : 'bufferId', - width : 140, - renderer : function(val, y, sample) { - if (sample.raw.bufferId != null) { - return BIOSAXS.proposal.getBufferById(val).acronym; - } - }, - editor : BIOSAXS_COMBOMANAGER.getComboBuffers(BIOSAXS.proposal.getBuffers(), { - noLabel : true, - width : 300 - }) - }, { - text : 'Conc.', - dataIndex : 'concentration', - width : 100, - editor : { - allowBlank : false - }, - renderer : function(val, meta, sample) { - if (isNaN(val)) { - meta.tdCls = 'yellow-cell'; - return val; - } else { - if (val != 0) { - return BUI.formatValuesUnits(val, 'mg/ml', { - fontSize : 16, - decimals : 3, - unitsFontSize : this.unitsFontSize - }); - } else { - return; - } - } - } - }, { - text : 'Vol. Well', - dataIndex : 'volume', - width : 70, - editor : { - allowBlank : true - }, - renderer : function(val, y, sample) { - return BUI.formatValuesUnits(sample.data.volume, 'µl', { - fontSize : 12, - decimals : 2, - unitsFontSize : this.unitsFontSize - }); - } - }, { - text : 'Position', - hidden : true, - flex : 1, - renderer : function(val, y, sample) { - return BUI.getSamplePositionHTML(sample.raw, _this.experiment); - } - }, { - text : 'samplePlateId', - dataIndex : 'samplePlateId', - hidden : true - }, { - text : 'Plate', - hidden : this.isPositionColumnHidden, - dataIndex : 'slotPositionColumn', - editor : _this._getSlotColumBombo(), - flex : 1, - renderer : function(val, meta, sample) { - if ((val != null) & (val != "")) { - return val; - } else { - meta.tdCls = 'yellow-cell'; - } - } - }, { - text : 'Row', - hidden : this.isPositionColumnHidden, - dataIndex : 'rowNumber', - editor : this._getRowCombo(), - flex : 1, - renderer : function(val, meta, sample) { - if ((val != null) && (val != "")) { - return BUI.getSamplePlateLetters()[val - 1]; - } else { - meta.tdCls = 'yellow-cell'; - } - } - }, { - text : 'Well', - hidden : this.isPositionColumnHidden, - dataIndex : 'columnNumber', - editor : this._getColumnCombo(), - flex : 1, - renderer : function(val, meta, sample) { - if ((val != null) && (val != "")) { - return val; - } else { - meta.tdCls = 'yellow-cell'; - } - } - }, { - id : _this.id + 'buttonEditSample', - text : 'Edit', - width : 80, - sortable : false, - hidden : !_this.editEnabled, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - if (_this.editEnabled) { - return BUI.getGreenButton('EDIT'); - } - } - }, { - id : _this.id + 'buttonRemoveSample', - text : '', - hidden : !_this.removeBtnEnabled, - width : 100, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - if (_this.removeBtnEnabled) { - return BUI.getRedButton('REMOVE'); - } - } - } +BufferGrid.prototype.getPanel = function(buffers) { + var _this = this; - ], - viewConfig : { - preserveScrollOnRefresh : true, - stripeRows : true, - getRowClass : function(record) { - var specimens = _this.experiment.getSampleByPosition(record.data.samplePlateId, record.data.rowNumber, - record.data.columnNumber); - if (specimens.length > 1) { - return 'red-row'; + this.store = Ext.create('Ext.data.Store', { + fields : [ 'bufferId', 'acronym', 'name', 'composition' ], + data : buffers + }); - } - }, - listeners : { - selectionchange : function(grid, selected) { - _this.onClick.notify(record.raw); - }, - cellclick : function(grid, td, cellIndex, record, tr) { - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEditSample') { - } - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemoveSample') { - grid.getStore().removeAt(rowIndex); - _this.onRemoved.notify(); - } + this.store.sort('acronym'); - } + var type = 'Ext.grid.Panel'; + if (this.searchBar == true) { + type = 'Ext.ux.LiveSearchGridPanel'; + } - } - } - }); + this.grid = Ext.create(type, { + title : 'Buffers', + collapsible : true, + collapsed : this.collapsed, + store : this.store, + height : this.height, + width : this.width, + columns : [ + /*{ + text : '', + dataIndex : 'bufferId', + width : 20, + renderer : function(val, y, sample) { + return BUI.getRectangleColorDIV(BIOSAXS.proposal.bufferColors[val], 10, 10); + } + },*/ + { + text : 'Acronym', + dataIndex : 'acronym', + flex : 1 + }, { + text : 'Name', + dataIndex : 'name', + flex : 1, + hidden : true + }, { + text : 'Composition', + dataIndex : 'composition', + flex : 1, + hidden : true + }, { + id : _this.id + 'buttonEditBuffer', + width : 80, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + return BUI.getGreenButton('EDIT'); + } + }, { + id : _this.id + 'buttonRemoveBuffer', + width : 85, + hidden : true, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + return BUI.getRedButton('REMOVE'); + } + } ], + flex : 1, + viewConfig : { + stripeRows : true, + listeners : { + 'celldblclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + _this._edit(record.data.bufferId); + }, + 'cellclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEditBuffer') { + _this._edit(record.data.bufferId); + } + + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemoveBuffer') { + BUI.showBetaWarning(); + } + } + + } + } + }); + + /** Adding the tbar **/ + if (this.tbar) { + this.grid.addDocked({ + xtype : 'toolbar', + items : this._getTbar() + }); + } return this.grid; }; -SpecimenGrid.prototype.input = function() { - return { - experiment : DATADOC.getExperiment_10(), - proposal : DATADOC.getProposal_10() - }; +BufferGrid.prototype.input = function() { + return new MacromoleculeGrid().input(); }; -SpecimenGrid.prototype.test = function(targetId) { - var specimenGrid = new SpecimenGrid({ - height : 400, - maxHeight : 400, - width : 1000 +BufferGrid.prototype.test = function(targetId) { + var bufferGrid = new BufferGrid({ + width : 800, + height : 350, + collapsed : false, + tbar : true }); - BIOSAXS.proposal = new Proposal(specimenGrid.input().proposal); - var experiment = new Experiment(specimenGrid.input().experiment); - var panel = specimenGrid.getPanelByExperiment(experiment); + BIOSAXS.proposal = new Proposal(bufferGrid.input().proposal); + var panel = bufferGrid.getPanel(BIOSAXS.proposal.macromolecules); panel.render(targetId); - }; /** - * Shows a list of stock solutions with macromolecule, buffer, storage temperature, concentration, shipment and comments + * A shipment may contains one or more cases where stock solutions and sample plates are stored * - * @multiselect allows multiple selection - * @height - * @minHeight - * @width - * @tbar - * @showTitle - * @isPackedVisible shows is stock solution is in a box - * @btnEditVisible shows edit button - * @btnAddVisible - * @btnAddExisting - * @btnUnpackVisible allows to unpack a stock solution - * @btnRemoveVisible allow to remove a stock solution + * @height + * @btnEditVisible + * @btnRemoveVisible + * + * #onEditButtonClicked + * #onAddButtonClicked + * #onRemoveButtonClicked + * #onDuplicateButtonClicked */ +function CaseGrid(args) { -function StockSolutionGrid(args) { - this.id = BUI.id(); this.height = 100; - this.width = null; - this.minHeight = null; - this.tbar = true; - - this.title = "Stock Solutions"; - - /** Visible buttons and actions **/ this.btnEditVisible = true; this.btnRemoveVisible = true; - this.btnAddVisible = true; - this.btnAddExisting = false; - this.isPackedVisible = true; - this.btnUnpackVisible = false; - - /** Selectors **/ - this.multiselect = false; - this.selectedStockSolutions = []; if (args != null) { - if (args.btnUnpackVisible != null) { - this.btnUnpackVisible = args.btnUnpackVisible; - } - if (args.multiselect != null) { - this.multiselect = args.multiselect; - } if (args.height != null) { this.height = args.height; } if (args.btnEditVisible != null) { this.btnEditVisible = args.btnEditVisible; } - if (args.btnAddVisible != null) { - this.btnAddVisible = args.btnAddVisible; - } - if (args.btnAddExisting != null) { - this.btnAddExisting = args.btnAddExisting; - } - if (args.width != null) { - this.width = args.width; - } - if (args.minHeight != null) { - this.minHeight = args.minHeight; - } - if (args.tbar != null) { - this.tbar = args.tbar; - } if (args.btnRemoveVisible != null) { this.btnRemoveVisible = args.btnRemoveVisible; } - if (args.isPackedVisible != null) { - this.isPackedVisible = args.isPackedVisible; - } - if (args.showTitle != null) { - this.showTitle = args.showTitle; - if (this.showTitle == false) { - this.title = null; + } + + /** Events **/ + this.onEditButtonClicked = new Event(this); + this.onAddButtonClicked = new Event(this); + this.onRemoveButtonClicked = new Event(this); + this.onDuplicateButtonClicked = new Event(this); +} + +CaseGrid.prototype._getColumns = function() { + var _this = this; + + function actionItemRenderer(value, meta, record, rowIx, ColIx, store) { + /*if (record.raw.specimen3VOs.length > 0){ + return 'x-hide-display'; + }*/ + } + + var columns = [ + { + header : 'Code', + dataIndex : 'code', + name : 'code', + type : 'string', + flex : 1 + }, + { + header : 'Bar Code', + dataIndex : 'barCode', + name : 'barCode', + type : 'string', + flex : 1, + hidden : true + }, + { + header : 'BeamLine', + dataIndex : 'barCode', + type : 'string', + flex : 1, + renderer : function(comp, val, record) { + if (record.raw.sessionVO != null) { + return "" + record.raw.sessionVO.beamlineName + ""; + } + } + }, + { + header : 'Session', + dataIndex : 'barCode', + type : 'string', + flex : 1, + renderer : function(comp, val, record) { + if (record.raw.sessionVO != null) { + return "" + moment(record.raw.sessionVO.startDate).format("MMM Do YY") + ""; + } } - } - - } - - /** Events **/ - this.onProposalChanged = new Event(this); - this.onStockSolutionSelected = new Event(this); -} - -StockSolutionGrid.prototype._getColumns = function() { - var _this = this; - var columns = [ - - { - header : 'Macromolecule', - dataIndex : 'macromolecule', - id : _this.id + 'macromolecule', - type : 'string', - renderer : function(val, y, specimen) { - return '' + val + ''; }, - hidden : false, - flex : 1 - }, { - header : 'Buffer', - dataIndex : 'buffer', - name : 'buffer', - hidden : false, - renderer : function(val, y, specimen) { - return '' + val + ''; + { + header : 'Status', + dataIndex : 'dewarStatus', + name : 'dewarStatus', + type : 'string', + flex : 1, + renderer : function(comp, val, record) { + if (new String(record.raw.dewarStatus).toUpperCase() == 'OPENED') { + return "" + new String(record.raw.dewarStatus).toUpperCase() + ""; + } + return "" + new String(record.raw.dewarStatus).toUpperCase() + ""; + } }, - type : 'string', - flex : 1 - }, { - header : 'Acronym', - dataIndex : 'name', - name : 'name', - type : 'string', - flex : 1, - hidden : true - }, { - header : 'Storage Temp.', - dataIndex : 'storageTemperature', - name : 'storageTemperature', - type : 'string', - flex : 1, - hidden : false, - renderer : function(val) { - return BUI.formatValuesUnits(val, 'C', { - fontSize : 12, - decimals : 2, - unitsFontSize : 10 - }); - } - }, { - header : 'Volume', - dataIndex : 'volume', - type : 'string', - flex : 1, - hidden : false, - renderer : function(val) { - return BUI.formatValuesUnits(val, 'µl', { - fontSize : 12, - decimals : 2, - unitsFontSize : 10 - }); - } - }, { - header : 'Concentration', - dataIndex : 'concentration', - name : 'concentration', - type : 'string', - flex : 1, - renderer : function(val) { - return BUI.formatValuesUnits(val, 'mg/ml', { - fontSize : 12, - decimals : 2, - unitsFontSize : 10 - }); - } - }, { - header : 'Packed', - dataIndex : 'comments', - id : _this.id + "box", - type : 'string', - width : 50, - hidden : !this.isPackedVisible, - renderer : function(val, cmp, a) { - if (a.raw.boxId != null) { - return "
"; + { + header : 'Type', + dataIndex : 'type', + name : 'type', + type : 'string', + flex : 1, + hidden : true + }, + { + header : 'Sample Plates', + dataIndex : 'plates', + name : 'plates', + type : 'string', + flex : 1, + hidden : true + }, + { + header : 'Stock Solutions', + dataIndex : 'plates', + name : 'plates', + type : 'string', + width : 100, + renderer : function(comp, val, record) { + var html = "
"; + var stockSolutions = BIOSAXS.proposal.getStockSolutionsByDewarId(record.raw.dewarId); + html = html + "" + stockSolutions.length + " x"; + return html + "
"; } - + }, { + header : 'isStorageDewar', + dataIndex : 'isStorageDewar', + name : 'isStorageDewar', + type : 'string', + flex : 1, + hidden : true + }, { + header : 'Tracking Number From Synchrotron', + dataIndex : 'trackingNumberFromSynchrotron', + name : 'trackingNumberFromSynchrotron', + type : 'string', + flex : 1, + hidden : true + }, { + header : 'Tracking Number To Synchrotron', + dataIndex : 'trackingNumberToSynchrotron', + name : 'trackingNumberToSynchrotron', + type : 'string', + flex : 1, + hidden : true + }, { + header : 'Storage Location', + dataIndex : 'storageLocation', + name : 'storageLocation', + type : 'string', + flex : 1, + hidden : false + }, { + header : 'Comments', + dataIndex : 'comments', + name : 'comments', + type : 'string', + flex : 1, + hidden : false } - }, { - header : 'Comments', - dataIndex : 'comments', - type : 'string', - flex : 1 - } ]; + ]; if (this.btnEditVisible) { columns.push({ id : _this.id + 'buttonEdit', + text : '', + hidden : !_this.btnEditVisible, width : 85, sortable : false, renderer : function(value, metaData, record, rowIndex, colIndex, store) { - if (_this.btnEditVisible) { - return BUI.getGreenButton('EDIT'); - } + return BUI.getGreenButton('EDIT'); } }); } @@ -22014,4646 +16857,9803 @@ StockSolutionGrid.prototype._getColumns = function() { }); } - if (this.btnUnpackVisible) { - columns.push({ - id : _this.id + 'buttonUnpack', - width : 85, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - if (_this.btnUnpackVisible) { - return BUI.getBlueButton('UNPACK'); - } - } - }); - } + columns.push({ + dataIndex : 'comments', + type : 'string', + width : 85, + hidden : false, + renderer : function(comp, val, record) { + return BUI.getBlueButton("LABELS", { + href : BUI.getPrintcomponentURL(record.raw.dewarId) + }); + } + }); + return columns; }; -StockSolutionGrid.prototype._getTopButtons = function() { - var _this = this; - /** Actions buttons **/ - var actions = []; - - /** ADD BUTTON **/ - if (this.btnAddVisible) { - actions.push(Ext.create('Ext.Action', { - icon : '../images/add.png', - text : 'Add Stock Solution', - tooltip : 'Will create a new stock solution', - disabled : false, - alwaysEnabled : true, - handler : function(widget, event) { - _this.edit(); - } - })); - } - - if (this.btnAddExisting) { - actions.push(Ext.create('Ext.Action', { - icon : '../images/add.png', - text : 'Add Existing', - tooltip : 'Allows to select upacked stock solutions', - disabled : false, - alwaysEnabled : true, - handler : function(widget, event) { - var stockSolutionGrid = new StockSolutionGrid({ - btnAddVisible : false, - btnEditVisible : false, - btnRemoveVisible : false, - btnAddExisting : false, - isPackedVisible : true, - multiselect : true - }); - - var window = Ext.create('Ext.window.Window', { - title : 'Select', - height : 400, - width : 800, - layout : 'fit', - items : [ stockSolutionGrid.getPanel() ], - buttons : [ { - text : 'Pack', - handler : function() { - _this.onStockSolutionSelected.notify(stockSolutionGrid.selectedStockSolutions); - window.close(); - } - }, { - text : 'Cancel', - handler : function() { - window.close(); - } - } ] - - }).show(); +CaseGrid.prototype._getTopButtons = function() { + var _this = this; + /** Actions buttons **/ + var actions = []; - stockSolutionGrid.refresh(BIOSAXS.proposal.getUnpackedStockSolutions()); - } - })); - } + /** ADD BUTTON **/ + actions.push(Ext.create('Ext.Action', { + icon : '../images/add.png', + text : 'Add', + disabled : false, + handler : function(widget, event) { + _this.onAddButtonClicked.notify(); + } + })); return actions; }; -StockSolutionGrid.prototype.refresh = function(stockSolutions) { - this.features = stockSolutions; - this.store.loadData(this._prepareData(), false); +CaseGrid.prototype.refresh = function(dewars) { + this.features = dewars; + this.store.loadData(this._prepareData(dewars), false); }; -StockSolutionGrid.prototype._prepareData = function() { +CaseGrid.prototype._sort = function(store) { + store.sort('dewarId', 'DESC'); +}; + +CaseGrid.prototype._prepareData = function() { var data = []; for ( var i = 0; i < this.features.length; i++) { - var stockSolution = this.features[i]; - stockSolution.buffer = BIOSAXS.proposal.getBufferById(stockSolution.bufferId).acronym; - if (stockSolution.macromoleculeId != null) { - stockSolution.macromolecule = BIOSAXS.proposal.getMacromoleculeById(stockSolution.macromoleculeId).acronym; - } - data.push(stockSolution); + data.push(this.features[i]); } return data; }; -StockSolutionGrid.prototype.getPanel = function() { +CaseGrid.prototype.getPanel = function(dewars, plates) { + this.features = dewars; + this.plates = plates; return this._renderGrid(); }; -StockSolutionGrid.prototype.edit = function(stockSolutionId) { +CaseGrid.prototype._edit = function(dewar) { var _this = this; - var stockSolutionWindow = new StockSolutionWindow(); - /** On stock solution SAVED **/ - stockSolutionWindow.onSaved.attach(function(sender, stockSolution) { - _this.onProposalChanged.notify(stockSolution); + var caseWindow = new CaseWindow(); + /**SAVED **/ + caseWindow.onSaved.attach(function(sender, dewar) { + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, shipment) { + _this.refresh(shipment.dewarVOs); + }); + adapter.saveCase(BIOSAXS.proposal.getShipmentByDewarId(dewar.dewarId).shippingId, dewar); }); - stockSolutionWindow.draw(BIOSAXS.proposal.getStockSolutionById(stockSolutionId)); + caseWindow.draw(dewar); }; -StockSolutionGrid.prototype._getStoreFields = function() { +CaseGrid.prototype._getStoreFields = function(data) { return [ { - name : 'name', + name : 'dewarId', type : 'string' }, { - name : 'stockSolutionId', + name : 'barCode', type : 'string' }, { - name : 'macromolecule', + name : 'code', type : 'string' }, { - name : 'buffer', + name : 'comments', type : 'string' }, { - name : 'storageTemperature', - type : 'numeric' + name : 'dewarStatus', + type : 'string' }, { - name : 'volume', + name : 'isStorageDewar', type : 'string' }, { - name : 'concentration', + name : 'plates', type : 'string' }, { - name : 'buffer', + name : 'transportValue', type : 'string' }, { - name : 'comments', + name : 'trackingNumberFromSynchrotron', type : 'string' - } ]; -}; + }, { + name : 'trackingNumberToSynchrotron', + type : 'string' + }, { + name : 'timeStamp', + type : 'string' + }, { + name : 'storageLocation', + type : 'string' + }, { + name : 'type', + type : 'string' + } -//StockSolutionGrid.prototype.refresh = function() { -// this.proposal.onInitialized.attach(function(sender){ -// -// }); -// this.proposal.init(Ext.urlDecode(window.location.href).sessionId); -//}; + ]; +}; -StockSolutionGrid.prototype._renderGrid = function() { +CaseGrid.prototype._renderGrid = function() { var _this = this; /** Store **/ + var data = this._prepareData(); this.store = Ext.create('Ext.data.Store', { - fields : this._getStoreFields(), //columns, - autoload : true + fields : this._getStoreFields(data), + autoload : true, + data : data }); + this._sort(this.store); - var filters = { - ftype : 'filters', - local : true, - filters : this.filters - }; - - var selModel = null; - - if (this.multiselect) { - selModel = Ext.create('Ext.selection.CheckboxModel', { - //multiSelect : false,//this.multiselect, - mode : 'SINGLE', - listeners : { - selectionchange : function(sm, selections) { - _this.selectedStockSolutions = []; - for ( var i = 0; i < selections.length; i++) { - _this.selectedStockSolutions.push(selections[i].raw); - } - } - } - }); - } else { - selModel = { - mode : 'SINGLE' - }; - } - - this.store.sort("stockSolutionId", "desc"); + this.store.loadData(data, false); this.grid = Ext.create('Ext.grid.Panel', { style : { padding : 5 }, - icon : '/ispyb/images/SampleHolder_24x24_01.png', - title : this.title, height : this.height, - width : this.width, - minWidth : this.minWidth, - selModel : selModel, store : this.store, columns : this._getColumns(), viewConfig : { stripeRows : true, listeners : { itemdblclick : function(dataview, record, item, e) { - _this.edit(record.raw.stockSolutionId); - }, - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - var adapter = null; - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonUnpack') { - _this.grid.setLoading("ISPyB: Unpacking stock solution"); - adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender) { - _this.onProposalChanged.notify(); - _this.grid.setLoading(false); - }); - adapter.onError.attach(function(sender) { - _this.onProposalChanged.notify(); - _this.grid.setLoading(false); - }); - record.raw.boxId = null; - adapter.saveStockSolution(record.raw); - } - - if (grid.getGridColumns()[cellIndex].getId() == _this.id + "box") { - window.location = BUI.getShippingURL(BIOSAXS.proposal.getShipmentByDewarId(record.raw.boxId).shippingId); - } - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEdit') { - _this.edit(record.data.stockSolutionId); - } - - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemove') { - _this.grid.setLoading("ISPyB: Removing stock solution"); - adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender) { - _this.onProposalChanged.notify(); - _this.grid.setLoading(false); - }); - adapter.onError.attach(function(sender) { - _this.onProposalChanged.notify(); - _this.grid.setLoading(false); - }); - adapter.removeStockSolution(record.data.stockSolutionId); - } - } - } - } - - }); - - var actions = _this._getTopButtons(); - this.grid.addDocked({ - xtype : 'toolbar', - items : actions - }); - - var i = null; - this.grid.getSelectionModel().on({ - selectionchange : function(sm, selections) { - if (selections.length) { - for ( i = 0; i < actions.length; i++) { - if (actions[i].enable) { - actions[i].enable(); - } - } - } else { - for ( i = 0; i < actions.length; i++) { - if (actions[i].alwaysEnabled == false) { - if (actions[i].disable) { - actions[i].disable(); - } - } - } - } - } - }); - return this.grid; -}; - -StockSolutionGrid.prototype.input = function() { - return { - proposal : DATADOC.getProposal_10() - }; -}; - -StockSolutionGrid.prototype.test = function(targetId) { - var stockSolutionGrid = new StockSolutionGrid({ - height : 300, - width : 900 - }); - BIOSAXS.proposal = new Proposal(stockSolutionGrid.input().proposal); - var panel = stockSolutionGrid.getPanel(); - stockSolutionGrid.refresh(BIOSAXS.proposal.getStockSolutions()); - panel.render(targetId); -}; - - -function SuperpositionGrid(args) { - this.height = null; - this.width = null; - this.id = BUI.id(); - - if (args != null) { - if (args.height != null) { - this.height = args.height; - - if (args.width != null) { - this.width = args.width; - } - } - } - - this.onSelected = new Event(this); -} - -SuperpositionGrid.prototype._prepareData = function(data) { - return data; -}; + _this._edit(record.raw); + }, + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEdit') { + _this._edit(record.raw); + } -SuperpositionGrid.prototype.refresh = function(subtractions) { - var data = []; - if (subtractions != null){ - if (subtractions.length > 0){ - for (j in subtractions){ - var subtraction = subtractions[j]; - if (subtraction.superposition3VOs != null){ - for (i in subtraction.superposition3VOs){ - data.push(subtraction.superposition3VOs[i]); + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemove') { + _this.onRemoveButtonClicked.notify(_this.store.getAt(rowIndex).raw.dewarId); } } } + }, + selModel : { + mode : 'SINGLE' } - } - this.store.loadData(data); -}; + }); -SuperpositionGrid.prototype.getPanel = function() { - var _this = this; - this.store = Ext.create('Ext.data.Store', { - fields : [ 'abinitioModelPdbFilePath', 'aprioriPdbFilePath', 'alignedPdbFilePath' ], - data : [] + var actions = _this._getTopButtons(); + this.grid.addDocked({ + xtype : 'toolbar', + items : actions }); - this.selModel = Ext.create('Ext.selection.RowModel', { - allowDeselect : true, - mode : 'MULTI', - listeners : { - selectionchange : function(sm, selections) { - var selected = []; - for (var i = 0; i < selections.length; i++) { - selected.push(selections[i].raw); + this.grid.getSelectionModel().on({ + selectionchange : function(sm, selections) { + if (selections.length) { + for ( var i = 0; i < actions.length; i++) { + if (actions[i].enable) { + actions[i].enable(); + } + } + } else { + for ( var i = 0; i < actions.length; i++) { + if (actions[i].alwaysEnabled == false) { + if (actions[i].disable) { + actions[i].disable(); + } + } } - _this.onSelected.notify(selected); } } }); - - this.store.sort([ { - property : 'name', - direction : 'ASC' - } ]); + return this.grid; +}; - this.panel = Ext.create('Ext.grid.Panel', { - store : this.store, - selModel : this.selModel, - width : this.width, - height : this.height, - margin : 10, - deferredRender : false, - columns : [ { - text : 'Abinitio', - dataIndex : 'abinitioModelPdbFilePath', - hidden : false, - flex : 1, - renderer : function(val){ - return BUI.getFileName(val); - } - }, { - text : 'Apriori', - dataIndex : 'aprioriPdbFilePath', - hidden : false, - flex : 1, - renderer : function(val){ - return BUI.getFileName(val); - } - }, { - text : 'Aligned', - dataIndex : 'alignedPdbFilePath', - hidden : false, - flex : 1, - renderer : function(val){ - return BUI.getFileName(val); - } - } ], +CaseGrid.prototype.input = function() { + return { + proposal : DATADOC.getProposal_10(), + dewars : DATADOC.getDewars_10() - viewConfig : { - enableTextSelection : true, - preserveScrollOnRefresh : true - }, - listeners : { - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + }; +}; - }, - afterrender : function() { - } - } +CaseGrid.prototype.test = function(targetId) { + var CaseGrid = new CaseGrid({ + height : 150 }); - return this.panel; + BIOSAXS.proposal = new Proposal(CaseGrid.input().proposal); + var panel = CaseGrid.getPanel(CaseGrid.input().dewars); + panel.render(targetId); + }; +/** + * A shipment may contains one or more cases where stock solutions and sample plates are stored + * + * @height + * @btnEditVisible + * @btnRemoveVisible + * + * #onEditButtonClicked + * #onAddButtonClicked + * #onRemoveButtonClicked + * #onDuplicateButtonClicked + */ +function ExampleGrid(args) { + + this.height = 100; + this.btnEditVisible = true; + this.btnRemoveVisible = true; + + if (args != null) { + if (args.height != null) { + this.height = args.height; + } + if (args.btnEditVisible != null) { + this.btnEditVisible = args.btnEditVisible; + } + if (args.btnRemoveVisible != null) { + this.btnRemoveVisible = args.btnRemoveVisible; + } + } + + /** Events **/ + this.onEditButtonClicked = new Event(this); + this.onAddButtonClicked = new Event(this); + this.onRemoveButtonClicked = new Event(this); + this.onDuplicateButtonClicked = new Event(this); +} + +ExampleGrid.prototype._getColumns = function() { + var _this = this; + + function actionItemRenderer(value, meta, record, rowIx, ColIx, store) { + /*if (record.raw.specimen3VOs.length > 0){ + return 'x-hide-display'; + }*/ + } + + var columns = [ + { + header : 'Code', + dataIndex : 'code', + name : 'code', + type : 'string', + flex : 1 + }, + { + header : 'Bar Code', + dataIndex : 'barCode', + name : 'barCode', + type : 'string', + flex : 1, + hidden : true + }, + { + header : 'BeamLine', + dataIndex : 'barCode', + type : 'string', + flex : 1, + renderer : function(comp, val, record) { + if (record.raw.sessionVO != null) { + return "" + record.raw.sessionVO.beamlineName + ""; + } + } + }, + { + header : 'Session', + dataIndex : 'barCode', + type : 'string', + flex : 1, + renderer : function(comp, val, record) { + if (record.raw.sessionVO != null) { + return "" + moment(record.raw.sessionVO.startDate).format("MMM Do YY") + ""; + } + } + }, + { + header : 'Status', + dataIndex : 'dewarStatus', + name : 'dewarStatus', + type : 'string', + flex : 1, + renderer : function(comp, val, record) { + if (new String(record.raw.dewarStatus).toUpperCase() == 'OPENED') { + return "" + new String(record.raw.dewarStatus).toUpperCase() + ""; + } + return "" + new String(record.raw.dewarStatus).toUpperCase() + ""; + } + }, + { + header : 'Type', + dataIndex : 'type', + name : 'type', + type : 'string', + flex : 1, + hidden : true + }, + { + header : 'Sample Plates', + dataIndex : 'plates', + name : 'plates', + type : 'string', + flex : 1, + hidden : true + }, + { + header : 'Stock Solutions', + dataIndex : 'plates', + name : 'plates', + type : 'string', + width : 100, + renderer : function(comp, val, record) { + var html = "
"; + var stockSolutions = BIOSAXS.proposal.getStockSolutionsByDewarId(record.raw.dewarId); + html = html + "" + stockSolutions.length + " x"; + return html + "
"; + } + }, { + header : 'isStorageDewar', + dataIndex : 'isStorageDewar', + name : 'isStorageDewar', + type : 'string', + flex : 1, + hidden : true + }, { + header : 'Tracking Number From Synchrotron', + dataIndex : 'trackingNumberFromSynchrotron', + name : 'trackingNumberFromSynchrotron', + type : 'string', + flex : 1, + hidden : true + }, { + header : 'Tracking Number To Synchrotron', + dataIndex : 'trackingNumberToSynchrotron', + name : 'trackingNumberToSynchrotron', + type : 'string', + flex : 1, + hidden : true + }, { + header : 'Storage Location', + dataIndex : 'storageLocation', + name : 'storageLocation', + type : 'string', + flex : 1, + hidden : false + }, { + header : 'Comments', + dataIndex : 'comments', + name : 'comments', + type : 'string', + flex : 1, + hidden : false + } + ]; + + if (this.btnEditVisible) { + columns.push({ + id : _this.id + 'buttonEdit', + text : '', + hidden : !_this.btnEditVisible, + width : 85, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + return BUI.getGreenButton('EDIT'); + } + }); + } + + if (this.btnRemoveVisible) { + columns.push({ + id : _this.id + 'buttonRemove', + width : 85, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + if (_this.btnRemoveVisible) { + return BUI.getRedButton('REMOVE'); + } + } + }); + } + + columns.push({ + dataIndex : 'comments', + type : 'string', + width : 85, + hidden : false, + renderer : function(comp, val, record) { + return BUI.getBlueButton("LABELS", { + href : BUI.getPrintcomponentURL(record.raw.dewarId) + }); + } + }); + + return columns; +}; + +ExampleGrid.prototype._getTopButtons = function() { + var _this = this; + /** Actions buttons **/ + var actions = []; + + /** ADD BUTTON **/ + actions.push(Ext.create('Ext.Action', { + icon : '../images/add.png', + text : 'Add', + disabled : false, + handler : function(widget, event) { + _this.onAddButtonClicked.notify(); + } + })); + + return actions; +}; + +ExampleGrid.prototype.refresh = function(dewars) { + this.features = dewars; + this.store.loadData(this._prepareData(dewars), false); +}; + +ExampleGrid.prototype._sort = function(store) { + store.sort('dewarId', 'DESC'); +}; + +ExampleGrid.prototype._prepareData = function() { + var data = []; + for ( var i = 0; i < this.features.length; i++) { + data.push(this.features[i]); + } + return data; +}; + +ExampleGrid.prototype.getPanel = function() { + this.grid = Ext.create('Ext.grid.Panel', { + style : { + padding : 5 + }, + height : this.height, + store : this.store, + columns : this._getColumns(), + viewConfig : { + stripeRows : true, + listeners : { + itemdblclick : function(dataview, record, item, e) { + _this._edit(record.raw); + }, + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEdit') { + _this._edit(record.raw); + } + + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemove') { + _this.onRemoveButtonClicked.notify(_this.store.getAt(rowIndex).raw.dewarId); + } + } + } + }, + selModel : { + mode : 'SINGLE' + } + }); + + var actions = _this._getTopButtons(); + this.grid.addDocked({ + xtype : 'toolbar', + items : actions + }); + + this.grid.getSelectionModel().on({ + selectionchange : function(sm, selections) { + if (selections.length) { + for ( var i = 0; i < actions.length; i++) { + if (actions[i].enable) { + actions[i].enable(); + } + } + } else { + for ( var i = 0; i < actions.length; i++) { + if (actions[i].alwaysEnabled == false) { + if (actions[i].disable) { + actions[i].disable(); + } + } + } + } + } + }); + return this.grid; +}; + + +ExampleGrid.prototype._getStoreFields = function(data) { + return [ { + name : 'dewarId', + type : 'string' + }, { + name : 'barCode', + type : 'string' + }, { + name : 'code', + type : 'string' + }, { + name : 'comments', + type : 'string' + }, { + name : 'dewarStatus', + type : 'string' + }, { + name : 'isStorageDewar', + type : 'string' + }, { + name : 'plates', + type : 'string' + }, { + name : 'transportValue', + type : 'string' + }, { + name : 'trackingNumberFromSynchrotron', + type : 'string' + }, { + name : 'trackingNumberToSynchrotron', + type : 'string' + }, { + name : 'timeStamp', + type : 'string' + }, { + name : 'storageLocation', + type : 'string' + }, { + name : 'type', + type : 'string' + } + + ]; +}; + +ExampleGrid.prototype._renderGrid = function() { + var _this = this; + + /** Store **/ + var data = this._prepareData(); + this.store = Ext.create('Ext.data.Store', { + fields : this._getStoreFields(data), + autoload : true, + data : data + }); + this._sort(this.store); + + this.store.loadData(data, false); + + this.grid = Ext.create('Ext.grid.Panel', { + style : { + padding : 5 + }, + height : this.height, + store : this.store, + columns : this._getColumns(), + viewConfig : { + stripeRows : true, + listeners : { + itemdblclick : function(dataview, record, item, e) { + _this._edit(record.raw); + }, + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEdit') { + _this._edit(record.raw); + } + + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemove') { + _this.onRemoveButtonClicked.notify(_this.store.getAt(rowIndex).raw.dewarId); + } + } + } + }, + selModel : { + mode : 'SINGLE' + } + }); + + var actions = _this._getTopButtons(); + this.grid.addDocked({ + xtype : 'toolbar', + items : actions + }); + + this.grid.getSelectionModel().on({ + selectionchange : function(sm, selections) { + if (selections.length) { + for ( var i = 0; i < actions.length; i++) { + if (actions[i].enable) { + actions[i].enable(); + } + } + } else { + for ( var i = 0; i < actions.length; i++) { + if (actions[i].alwaysEnabled == false) { + if (actions[i].disable) { + actions[i].disable(); + } + } + } + } + } + }); + return this.grid; +}; + +ExampleGrid.prototype.input = function() { + return { + proposal : DATADOC.getProposal_10(), + dewars : DATADOC.getDewars_10() + + }; +}; + +ExampleGrid.prototype.test = function(targetId) { + var ExampleGrid = new ExampleGrid({ + height : 150 + }); + BIOSAXS.proposal = new Proposal(ExampleGrid.input().proposal); + var panel = ExampleGrid.getPanel(ExampleGrid.input().dewars); + panel.render(targetId); + +}; + + /** - * See ExperimentGrid - * + * Shows a list of experiment AKA data acquisitions + * @height + * @sorters + * @minHeight + * @gridType: Ext.ux.LiveSearchGridPanel or Ext.grid.Panel + * @tbar true or false + * @grouping true or false + * @width + * @title + * #onEditButtonClicked */ -function TemplateGrid(args) { - - if (args == null) { - args = {}; - } - args.sorters = [ { - property : 'experimentId', - direction : 'DESC' - } ]; - - ExperimentGrid.prototype.constructor.call(this, args); -} - -TemplateGrid.prototype._getFilterTypes = ExperimentGrid.prototype._getFilterTypes; -TemplateGrid.prototype._prettyPrintMacromolecules = ExperimentGrid.prototype._prettyPrintMacromolecules; -TemplateGrid.prototype._getPercentage = ExperimentGrid.prototype._getPercentage; -TemplateGrid.prototype._getPercentageCollected = ExperimentGrid.prototype._getPercentageCollected; -TemplateGrid.prototype.getPercentageMerged = ExperimentGrid.prototype.getPercentageMerged; -TemplateGrid.prototype._prepareData = ExperimentGrid.prototype._prepareData; -TemplateGrid.prototype.getPanel = ExperimentGrid.prototype.getPanel; -TemplateGrid.prototype._renderGrid = ExperimentGrid.prototype._renderGrid; -TemplateGrid.prototype._editExperiment = ExperimentGrid.prototype._editExperiment; -TemplateGrid.prototype._removeExperimentById = ExperimentGrid.prototype._removeExperimentById; - -TemplateGrid.prototype._getTopButtons = function() { - /** Actions buttons * */ - var actions = []; - - actions.push(Ext.create('Ext.Action', { - icon : '../images/add.png', - text : 'Add experiment', - handler : function(widget, event) { - var wizardWidget = new WizardWidget({ - windowMode : true - }); - - wizardWidget.onFinished.attach(function(sender, result) { - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - var experiment = new Experiment(data); - BIOSAXS.openExperimentByExperiment(experiment); - wizardWidget.window.close(); - }); - wizardWidget.current.setLoading("ISPyB: Creating experiment"); - adapter.createTemplate(result.name, "comments", result.data); - }); - -// wizardWidget.draw(this.targetId, new ExperimentTypeWizardForm()); - wizardWidget.draw(this.targetId, new MeasurementCreatorStepWizardForm(BIOSAXS.proposal.getMacromolecules())); - } - })); - return actions; -}; - -TemplateGrid.prototype.refresh = function(data) { - var filtered = []; - for ( var i = 0; i < data.length; i++) { - if (data[i].experimentType == "TEMPLATE") { - filtered.push(data[i]); - } - } - this.store.loadData(this._prepareData(filtered), false); -}; - -TemplateGrid.prototype._getColumns = function() { - var _this = this; - function actionItemRenderer(value, meta, record, rowIx, ColIx, store) { - if (record.raw.buffer3VOs != null) { - if (record.raw.buffer3VOs.length > 0) { - return 'x-hide-display'; - } - } +function ExperimentGrid(args) { + this.width = "100%"; + this.height = 700; + this.minHeight = 500; - if (record.data.platesCount > 0) { - return 'x-hide-display'; - } - } + this.id = BUI.id(); + this.gridType = 'Ext.grid.Panel'; //'Ext.ux.LiveSearchGridPanel'; + this.tbar = false; + this.hideHeaders = false; + this.grouping = true; + this.title = null; - return [ { - xtype : 'rownumberer', - width : 40 - }, { - text : 'experimentId', - dataIndex : 'experimentId', - name : 'experimentId', - type : 'string', - hidden : true + this.filtered = null; + + /** maximum row count **/ + this.limit = 100; + + this.sessionIdFilter = null; + + /** if not null filtered by date **/ + this.date = null; + + this.sorters = [ { + property : 'date', + direction : 'DESC' }, { - text : 'Name', - dataIndex : 'name', - name : 'name', - type : 'string', - flex : 1 - }, + property : 'time', + direction : 'DESC' + } ]; - { - text : 'Type', - dataIndex : 'type', - name : 'type', - type : 'string', - hidden : true, - flex : 1, - renderer : function(val) { - return val; + this.dates = {}; + if (args != null) { + if (args.height != null) { + this.height = args.height; } - }, { - text : 'Macromolecules', - name : 'macromolecules_names', - dataIndex : 'macromolecules_names', - flex : 1, - renderer : function(val) { - return " " + val + ""; + if (args.limit != null) { + this.limit = args.limit; } - }, { - id : _this.id + 'GO', - width : 80, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - return BUI.getGreenButton('EDIT'); + if (args.sorters != null) { + this.sorters = args.sorters; } - }, { - id : _this.id + 'REMOVE', - width : 100, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - return BUI.getRedButton('REMOVE'); + if (args.sessionId != null){ + this.sessionIdFilter = args.sessionId; + } + if (args.filtered != null) { + this.filtered = args.filtered; + } + if (args.minHeight != null) { + this.minHeight = args.minHeight; + } + if (args.gridType != null) { + this.gridType = args.gridType; + } + if (args.tbar != null) { + this.tbar = args.tbar; + } + if (args.grouping != null) { + this.grouping = args.grouping; + } + if (args.width != null) { + this.width = args.width; + } + if (args.title != null) { + this.title = args.title; } - } ]; -}; - -TemplateGrid.prototype.input = function() { - var experiments = DATADOC.getExperimentList_10(); - return { - experiments : experiments, - proposal : new MeasurementGrid().input().proposal - - }; -}; - -TemplateGrid.prototype.test = function(targetId) { - var experimentGrid = new TemplateGrid({ - height : 350, - minHeight : 350, - width : 1000, - gridType : 'Ext.grid.Panel', - title : 'Experiments', - grouping : false, - tbar : true - }); - BIOSAXS.proposal = new Proposal(experimentGrid.input().proposal); - var panel = experimentGrid.getPanel(experimentGrid.input().experiments); - experimentGrid.refresh(experimentGrid.input().experiments); - panel.render(targetId); -}; - -function VolumeGrid() { - this.id = BUI.id(); + } + /** Events **/ + this.onEditButtonClicked = new Event(this); } -VolumeGrid.prototype.getPanel = function(experiment) { - this.experiment = experiment; - return this.render(); +ExperimentGrid.prototype._getFilterTypes = function() { + return []; }; -VolumeGrid.prototype.getVolumesPanel = function(data, title) { - var _this = this; - var store = Ext.create('Ext.data.Store', { - fields : [ 'name', 'volume', 'macromoleculeId', 'bufferId' ], - data : data - }); - store.sort([ { - property : 'name', - direction : 'ASC' - } ]); - - var grid = Ext.create('Ext.grid.Panel', { - title : title, - height : 400, - maxHeight : 400, - width : 900, - store : store, - margin : '10 0 50 10', - tbar : [ { - text : 'Go to Shipment', - icon : '../images/plane-small.gif', - handler : function() { - window.location = BUI.getCreateShipmentList(); - } - } ], - viewConfig : { - stripeRows : true, - listeners : { - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonCreate') { - var stockSolutionWindow = new StockSolutionWindow(); - /** On stock solution SAVED **/ - stockSolutionWindow.onSaved.attach(function(sender, stockSolution) { - BIOSAXS.proposal.onInitialized.attach(function(sender, data) { - _this.refresh(_this.experiment); - }); - BIOSAXS.proposal.init(); - }); - var acronym = "ST"; - if (record.raw.macromoleculeId != null) { - acronym = acronym + "_" + BIOSAXS.proposal.getMacromoleculeById(record.raw.macromoleculeId).acronym; - } - if (record.raw.bufferId != null) { - acronym = acronym + "_" + BIOSAXS.proposal.getBufferById(record.raw.bufferId).acronym; - } - stockSolutionWindow.draw({ - concentration : record.raw.concentration, - macromoleculeId : record.raw.macromoleculeId, - bufferId : record.raw.bufferId, - name : acronym, - volume : record.raw.volume - }); - } - - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonStockSolutions') { - var stockSolutionGrid = new StockSolutionGrid({ - btnAddVisible : false, - btnEditVisible : false, - btnRemoveVisible : false, - btnAddExisting : false, - isPackedVisible : true, - multiselect : false - }); - - var window = Ext.create('Ext.window.Window', { - title : 'Stock solutions by specimen', - height : 400, - width : 800, - layout : 'fit', - items : [ stockSolutionGrid.getPanel() ], - buttons : [ { - text : 'Close', - handler : function() { - window.close(); - } - } ] - - }).show(); - stockSolutionGrid.refresh(BIOSAXS.proposal.getStockSolutionsBySpecimen(record.raw.macromoleculeId, record.raw.bufferId)); - } - } - } - }, - columns : [ -// { -// text : '', -// dataIndex : 'macromoleculeId', -// width : 20, -// renderer : function(val, y, sample) { -// if (val != null) { -//// return BUI.getRectangleColorDIV(BIOSAXS.proposal.macromoleculeColors[val], 10, 10); -// return BUI.getRectangleColorDIV(_this.experiment.macromoleculeColors[val], 10, 10); -// } -// } -// }, -// { -// text : '', -// dataIndex : 'bufferId', -// width : 20, -// renderer : function(val, y, sample) { -// if (val != null) { -// return BUI.getRectangleColorDIV(_this.experiment.getSpecimenColorByBufferId(val), 10, 10); -// } -// } -// }, - { - text : 'Specimen', - dataIndex : 'name', - flex : 0.5 - }, - { - text : 'Estimated Volume', - dataIndex : 'volume', - tooltip : 'Estimation of the maximum volume needed for making this experiment', - flex : 0.5, - editor : { - allowBlank : true - }, - renderer : function(val, y, sample) { - return BUI.formatValuesUnits(sample.data.volume, 'µl', { - fontSize : 16, - decimals : 2, - unitsFontSize : this.unitsFontSize - }); - } - }, - { - text : 'Stock Solution', - id : _this.id + 'buttonStockSolutions', - dataIndex : 'name', - flex : 0.5, - tooltip : 'Stock Solutions containing this specimen in this proposal', - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - var macromoleculeId = record.raw.macromoleculeId; - var bufferId = record.raw.bufferId; - var stockSolutions = BIOSAXS.proposal.getStockSolutionsBySpecimen(macromoleculeId, bufferId); - if (stockSolutions.length > 0) { - return "
" + stockSolutions.length + " x
"; - } +ExperimentGrid.prototype._prepareData = function(rows) { + var data = []; + var count = 0; + + rows.sort(function(a,b){return b.experimentId - a.experimentId;}); + for ( var i = 0; i < rows.length; i++) { + var row = rows[i]; + this.dates[moment(row.creationDate).format("YYYYMMDD")] = moment(row.creationDate).format("MMM Do YY"); + if ( + ( this.filtered == null || row.experimentType == this.filtered ) && (count < this.limit || this.limit == null ) && (this.sessionIdFilter == null || this.date != null || (this.date == null && this.sessionIdFilter == row.sessionId)) + ){ - } - }, { - id : _this.id + 'buttonCreate', - text : '', - tooltip : 'Create a new stock solution for shipping', - width : 170, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - return BUI.getGreenButton('NEW STOCK SOLUTION', { - width : 160 + data.push({ + experimentId : row.experimentId, + status : row.status, + dataAcquisitionFilePath : row.dataAcquisitionFilePath, + type : row.experimentType, + name : row.name, + macromolecules_names : row.macromolecules, + percentageAnalysed : { + value : (row.dataCollectionDoneCount / row.dataCollectionCount) * 100, + text : row.dataCollectionDoneCount + " of " + row.dataCollectionCount + }, + percentageCollected : { + value : (row.measurementDoneCount / row.measurementCount) * 100, + text : row.measurementDoneCount + " of " + row.measurementCount + }, + percentageMerged : { + value : (row.measurementAveragedCount / row.measurementCount) * 100, + text : row.measurementAveragedCount + " of " + row.measurementCount + }, + date : moment(row.creationDate).format("YYYYMMDD"), + time : moment(row.creationDate).format("YYYYMMDDHHmmss"), + creationDate : row.creationDate }); - } - } ] - }); - return grid; + count ++; + } + } + return data; +}; +ExperimentGrid.prototype.getPanel = function(experiments) { + this.features = experiments; + return this._renderGrid(experiments); }; -VolumeGrid.prototype._prepareData = function(experiment) { - var keys = {}; - for ( var i = 0; i < experiment.getSamples().length; i++) { - var sample = experiment.getSamples()[i]; - var key = ""; - if (sample.macromoleculeId == null) { - key = experiment.getBufferById(sample.bufferId).acronym; - if (keys[key] == null) { - keys[key] = { - macromoleculeId : sample.macromoleculeId, - name : key, - bufferId : sample.bufferId, - volume : 0 - }; - } - keys[key].volume = Number(sample.volume) + Number(keys[key].volume); +ExperimentGrid.prototype.refresh = function(experiments) { + this.experiments = experiments; + var filtered = []; + for ( var i = 0; i < experiments.length; i++) { + if (experiments[i].experimentType != "TEMPLATE") { + filtered.push(experiments[i]); } + } - if ((sample.macromolecule3VO != null) || (sample.macromoleculeId != null)) { - macromoleculeId = sample.macromoleculeId; - if (sample.macromoleculeId == null) { - sample.macromoleculeId = sample.macromolecule3VO.macromoleculeId; - } - key = BIOSAXS.proposal.getMacromoleculeById(sample.macromoleculeId).acronym + " + " + experiment.getBufferById(sample.bufferId).acronym; - if (keys[key] == null) { - keys[key] = { - macromoleculeId : sample.macromoleculeId, - name : key, - bufferId : sample.bufferId, - volume : 0 - }; - } - keys[key].volume = Number(sample.volume) + Number(keys[key].volume); + this.parsedData = this._prepareData(filtered); + + var day = {}; + var dates = []; + for ( var i = 0; i < this.experiments.length; i++) { + var date = moment(this.experiments[i].creationDate).format("MMM Do YYYY"); + if (day[date] == null){ + dates.push({ + date : date, + value : moment(this.experiments[i].creationDate) + }); + day[date] = true; } } - var data = []; - for (var keyId in keys) { - data.push(keys[keyId]); + + this.storeDate.loadData(dates, false); + this.store.loadData(this.parsedData, false); + + /** If it has already been filtered by date we keep the filter **/ + if (this.date != null){ + this._filterByDate(this.date); } - - return data; }; -VolumeGrid.prototype.refresh = function(experiment) { - this.experiment = experiment; - this.macromoleculeGrid.getStore().loadData(this._prepareData(this.experiment), false); -}; +ExperimentGrid.prototype._getTopButtons = function() { + var _this = this; + /** Actions buttons **/ + var actions = []; -VolumeGrid.prototype.render = function() { - this.macromoleculeGrid = this.getVolumesPanel(this._prepareData(this.experiment), "Estimation of required Volume"); + actions.push(Ext.create('Ext.Action', { + icon : '../images/calendar_icon.png', + text : 'Show Calendar', + disabled : false, + handler : function(widget, event) { + var window = Ext.create('Ext.window.Window', { + title : 'Calendar', + width : 600, + height : 600, + modal : true, + closable : true, + layout : { + type : 'vbox', + align : 'stretch' + }, + items : [ { + xtype : 'label', + html : 'Click on a data acquisition to select:', + margin : '5 5 5 5' + }, { + html : '
', + margin : '5 5 5 5' + } - return { - xtype : 'container', - layout : 'vbox', - margin : "0, 0, 0, 5", - items : [ { - xtype : 'container', - layout : 'hbox', - margin : "0, 0, 0, 0", - items : [ this.macromoleculeGrid ] - } ] - }; + ] + }).show(); + + var calendarWidget = new CalendarWidget({ + height : 450 + }); + var aux = _this.limit; + /** we remove the limit temporarily **/ + _this.limit = null; + _this.sessionIdFilter = null; + calendarWidget.loadData(_this._prepareData(_this.experiments)); + _this.limit = aux; + calendarWidget.draw('calendar'); + calendarWidget.onClick.attach(function(sender, date) { + date = moment(date, "YYYY-MM-DD"); + _this._filterByDate(date); + window.close(); + + }); + + } + })); + this.storeDate = Ext.create('Ext.data.ArrayStore', { + fields: ['date', 'value'], + data : [] + }); + + this.dateMenu = Ext.create('Ext.form.field.ComboBox', { + hideLabel: true, + store: this.storeDate, + displayField: 'date', + typeAhead: true, + queryMode: 'local', + margin : '0 0 0 30', + triggerAction: 'all', + emptyText:'Select a date...', + selectOnFocus:true, + width:135, + listeners:{ + scope: this, + 'select': function (a,b,c){ + _this.limit = null; + _this._filterByDate(moment(b[0].raw.value, "YYYY-MM-DD")); + } + } + }); + + actions.push(this.dateMenu); + + actions.push("->"); + if (_this.filtered != null){ + actions.push({ + html : "Experiment Type: " + _this.filtered +"" + }); + } + else{ + actions.push({ + html : "Experiment Type: ALL" + }); + } + return actions; }; -VolumeGrid.prototype.input = function(experiment) { - return { - experiment : DATADOC.getExperiment_10() - }; +/** + * Date format: "YYYY-MM-DD" + */ +ExperimentGrid.prototype._filterByDate = function(date) { + var experimentsFiltered = []; + /** Getting all the experiments of date**/ + for ( var i = 0; i < this.experiments.length; i++) { + var experiment = this.experiments[i]; + if (experiment.creationDate != null) { + var experimentDate = moment(experiment.creationDate); + if (experimentDate.year() == date.year()) { + if (experimentDate.month() == date.month()) { + if (experimentDate.date() == date.date()) { + experimentsFiltered.push(experiment); + } + } + } + } + } + var parsedData = this._prepareData(experimentsFiltered); + this.store.loadData(parsedData); + this.date = date; }; -VolumeGrid.prototype.test = function(targetId) { - var volumeGrid = new VolumeGrid(); - BIOSAXS.proposal = new Proposal(new MeasurementGrid().input().proposal); - var panel = volumeGrid.getPanel(new Experiment(new VolumeGrid().input().experiment)); - Ext.create('Ext.panel.Panel', { - height : 500, - width : 1000, - renderTo : targetId, - items : [ panel ] +/** Only for templates **/ +ExperimentGrid.prototype._removeExperimentById = function(experimentId) { + var _this = this; + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(evt, args) { + _this.grid.setLoading(false); + document.getElementById(BIOSAXS.targetId).innerHTML = ""; + BIOSAXS.start(BIOSAXS.targetId); }); + this.grid.setLoading("Removing experiment "); + adapter.removeExperimentById(experimentId); }; - -/** - * Example of a tab panel to be populated with widgets - * - * @width width in pixels - * @height height in pixels - * - * #myEvent event that this class is supposed to throw - * - **/ -function ExampleTabs(args) { - this.width = 500; - this.height = 500; + +ExperimentGrid.prototype._renderGrid = function() { + var _this = this; + + /** Store **/ + this.store = Ext.create('Ext.data.Store', { + fields : this._getColumns(), + groupField : 'date', + autoload : true, + data : [], + remoteSort: false, + sorters : this.sorters + }); + - if (args != null){ - if (args.width != null){ - this.width= args.width; - } - if (args.height != null){ - this.height= args.height; - } - } - /** Events **/ - this.myEvent = new Event(); -} - -/** Populate the widget **/ -ExampleTabs.prototype.refresh = function(macromolecule) { -}; + var groupingFeature = Ext.create('Ext.grid.feature.Grouping', { + groupHeaderTpl : Ext.create('Ext.XTemplate', + "
{name:this.formatName}
", { + formatName : function(name) { + return _this.dates[name]; + } + }), + hideGroupedHeader : true, + startCollapsed : false + }); -/** It creates a tab panel with the specified with and height **/ -ExampleTabs.prototype.getPanel = function() { - this.panel = Ext.createWidget('tabpanel', { - height : this.height, - width : this.width, - style : { - padding : 2 + this.features = []; + if (this.grouping) { + this.features.push(groupingFeature); + } + + /** Grid **/ + this.grid = Ext.create(this.gridType, { + hideHeaders : this.hideHeaders, + resizable : true, + title : this.title, + width : this.width, + minHeight : this.minHeight, + height : this.height, + features : this.features, + store : this.store, + columns : this._getColumns(), + selModel : { + mode : 'SINGLE' }, - items : [ { - tabConfig : { - title : 'Test', - icon : '/ispyb/images/plane-small.gif' + viewConfig : { + stripeRows : true, + getRowClass : function(record, rowIdx, params, store) { + if (record.raw.type == "TEMPLATE") { + return "template-color-row"; + } + if ((record.raw.type == "CALIBRATION") && (record.raw.status == "FINISHED")) { + return "blue-row"; + } }, - items : [ { - xtype : 'container', - margin : '5 5 5 5', - items : [ ] - } ] - } ] + listeners : { + itemdblclick : function(dataview, record, item, e) { + _this._editExperiment(record.raw.experimentId); + }, + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'GO') { + _this._editExperiment(record.raw.experimentId); + } + + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'REMOVE') { + _this._removeExperimentById(record.raw.experimentId); + } + + } + } + } }); - return this.panel; -}; - -/** - * Shows an experiments with the specimens, measurements, analysis tabs where - * results are shown and the frames widget - * - * @targetId - */ -function ExperimentTabs(targetId) { - this.height = 900; - this.targetId = targetId; + var actions = _this._getTopButtons(); - this.id = BUI.id(); - var _this = this; + if (this.tbar) { + this.grid.addDocked({ + xtype : 'toolbar', + items : actions + }); + this.grid.getSelectionModel().on({ + selectionchange : function(sm, selections) { + if (selections.length) { + for ( var i = 0; i < actions.length; i++) { + if (actions[i].enable) { + actions[i].enable(); + } + } + } else { + for ( var i = 0; i < actions.length; i++) { + if (actions[i].alwaysEnabled == false) { + if (actions[i].disable) { + actions[i].disable(); + } + } + } + } + } + }); + } - this.INTERVAL_UPDATE = BUI.getUpdateInterval(); + return this.grid; +}; - this.gridHeight = 1000; - /** data * */ - this.experiment = null; +ExperimentGrid.prototype._getColumns = function() { + var _this = this; + function actionItemRenderer(value, meta, record, rowIx, ColIx, store) { + if (record.raw.buffer3VOs != null) { + if (record.raw.buffer3VOs.length > 0) { + return 'x-hide-display'; + } + } - - /** Specimen Widget contains a specimenGrid and a sampleChangerWidget than can be displayed with are vertical or horizontal layout **/ - this.specimenWidget = new SpecimenWidget({ - height : 600 - }); - - - /** For Overview * */ - /*this.samplePlateGroupWidget = new SamplePlateGroupWidget({ - showTitle : false, - height : 250, - margin : 5, - border : 0 + if (record.data.platesCount > 0) { + return 'x-hide-display'; + } + } - });*/ + return [ + { + text : 'experimentId', + dataIndex : 'experimentId', + name : 'experimentId', + type : 'string', + hidden : true + }, + { + xtype : 'rownumberer', + width : 40 + }, + { + text : 'Name', + dataIndex : 'name', + name : 'name', + type : 'string', + flex : 1 + }, - /** For Measurements * */ - /*this.measurementSamplePlateGroupWidget = new SamplePlateGroupWidget({ - showTitle : false, - height : 250, - margin : '5 0 0 0', - border : 0 - });*/ + { + text : 'Type', + dataIndex : 'type', + name : 'type', + type : 'string', + flex : 1, + renderer : function(val) { + if (val == "CALIBRATION") { + return "" + val + ""; + } + + return val; + } + }, + { + text : 'Macromolecules', + name : 'macromolecules_names', + dataIndex : 'macromolecules_names', + flex : 1, + renderer : function(val) { + if (val != null) { + return " " + val + ""; + } + return " Information not available"; + } + }, + { + text : 'Buffers', + dataIndex : 'buffer_names', + name : 'buffer_names', + flex : 1, + hidden : true, + renderer : function(val) { + return "Buffer/s: " + val + ""; + } + }, + { + text : 'Status', + dataIndex : 'status', + name : 'status', + type : 'string', + flex : 1, + renderer : function(val, x, sample) { + if (sample.raw.type == "TEMPLATE") { + return "READY"; + } + if (sample.raw.status == "ABORTED") { + return "" + val + ""; + } + return "" + val + ""; + } + }, + { + text : 'Download', + dataIndex : 'creationDate', + name : 'creationDate', + renderer : function(val, x, sample) { + if (sample != null) { + if (sample.raw.type == "HPLC") { + return; + } + return BUI.getZipHTMLByExperimentId(sample.raw.experimentId, sample.raw.name); + } + }, + width : 100 - this.measurementGridDone = new MeasurementGrid({ - height : 600, - minHeight : 400, - maxHeight : 800, - positionColumnsHidden : true, - showTitle : false, - estimateTime : true, - width : 900, - maxWidth : 1500, - addBtnEnable : false, - markDone : true, - removeBtnEnabled : false - }); - this.measurementGridDone.onSelected.attach(function(sender, measurements) { - var specimens = []; - for ( var i = 0; i < measurements.length; i++) { - specimens.push(_this.experiment.getSampleById(measurements[i].specimenId)); - } - //_this.measurementSamplePlateGroupWidget.selectSpecimens(specimens); - }); + }, + { + header : 'Measurements', + dataIndex : 'percentageCollected', + name : 'percentageCollected', + type : 'string', + renderer : function(val, y, sample) { + if ((sample.raw.type == "TEMPLATE") || (sample.raw.type == "HPLC")) { + return; + } + return "
" + BUI.getProgessBar(sample.raw.percentageCollected.value, sample.raw.percentageCollected.text) + "
"; + }, + width : 100 + }, + { + header : 'Averaged', + dataIndex : 'percentageMerged', + name : 'percentageMerged', + type : 'string', + renderer : function(val, y, sample) { + if ((sample.raw.type == "TEMPLATE") || (sample.raw.type == "HPLC")) { + return; + } + return "
" + BUI.getProgessBar(sample.raw.percentageMerged.value, sample.raw.percentageMerged.text) + "
"; + }, + width : 100 + }, + { + header : 'Subtractions', + dataIndex : 'percentageAnalysed', + name : 'percentageAnalysed', + type : 'string', + renderer : function(val, y, sample) { + if ((sample.raw.type == "TEMPLATE") || (sample.raw.type == "HPLC")) { + return; + } + return "
" + BUI.getProgessBar(sample.raw.percentageAnalysed.value, sample.raw.percentageAnalysed.text) + "
"; + }, + width : 100 + }, - /** AnalysisGrid * */ - this.analysisGrid = new AnalysisGrid({ - height : Ext.getBody().getViewSize().height * 0.9 - 300, - positionColumnsHidden : true, - sorters : [ { - property : 'priorityLevelId', - direction : 'ASC' - } ] - }); - - - /** Queue * */ - this.queueGrid = new QueueGrid({ - url : BUI.getQueueUrlByExperiment(), - height : Ext.getBody().getViewSize().height * 0.9 - 300, - width : Ext.getBody().getViewSize().width * 0.9 - 300, - isGrouped : true, - tbar : false, - bbar : false, - sorter : [{ - property: 'measurementId', - direction: 'DESC' - }] - }); + { + text : 'time', + dataIndex : 'time', + name : 'time', + hidden : true, + renderer : function(val) { + return val; + }, + width : 100 -} + }, { + text : 'Date', + dataIndex : 'date', + name : 'date', + renderer : function(val) { + return val; + }, + width : 100 -ExperimentTabs.prototype.error = function(error) { - var e = JSON.parse(error); - showError(e); - this.panel.setLoading(false); -}; + }, -ExperimentTabs.prototype.draw = function(experiment) { - this.renderDataAcquisition(experiment); -}; + { + text : 'Time', + dataIndex : 'creationDate', + name : 'creationDate', + renderer : function(val) { + return moment(val).format(" HH:mm:ss"); + }, + width : 100 -ExperimentTabs.prototype.refreshAnalysisData = function() { - var _this = this; - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - _this.analysisGrid.refresh(data, {experiment : _this.experiment}); - }); - adapter.getAnalysisInformationByExperimentId(this.experiment.experimentId); - - /** Auto load **/ - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - _this.queueGrid.refresh(data); - }); - adapter.getCompactAnalysisByExperimentId(this.experiment.experimentId); - this.queueGrid.store.proxy.url = BUI.getQueueUrlByExperiment(this.experiment.experimentId); - this.queueGrid.refresh(); + }, { + id : _this.id + 'GO', + width : 80, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + return BUI.getGreenButton('GO'); + } + } ]; }; -ExperimentTabs.prototype.getSpecimenContainerHeight = function(experiment) { - var maxItems = 0; - if (maxItems < experiment.getSamples().length + 1) { - maxItems = experiment.getSamples().length + 1; - } - - var height = (maxItems + 1) * 40 + 40; - if (height > 400) { - height = 400; +/** Changes location.href in order to edit the experiment **/ +ExperimentGrid.prototype._editExperiment = function(experimentId) { + if (Ext.urlDecode(window.location.href).sessionId != null) { + location.href = 'viewProjectList.do?reqCode=display&experimentId=' + experimentId + '&sessionId='+ Ext.urlDecode(window.location.href).sessionId; + } else { + location.href = 'viewProjectList.do?reqCode=display&experimentId=' + experimentId; } - return height; -}; - -ExperimentTabs.prototype.getExperimentTitle = function() { - var experimentHeaderForm = new ExperimentHeaderForm(); - return experimentHeaderForm.getPanel(this.experiment); }; -ExperimentTabs.prototype.renderDataAcquisition = function(experiment) { - var _this = this; - this.experiment = experiment; +ExperimentGrid.prototype.input = function() { + var experiments = DATADOC.getExperimentList_10(); + return { + experiments : experiments, + proposal : new MeasurementGrid().input().proposal - var specimenGrid = new SpecimenGrid({ - height : 400, - maxHeight : 500, - width : 890 - }); + }; +}; - specimenGrid.onClick.attach(function(sender, args) { - }); +ExperimentGrid.prototype.test = function(targetId) { + var experimentGrid = new ExperimentGrid({ + height : 350, + minHeight : 350, + width : 1000 - specimenGrid.onSelected.attach(function(sender, specimens) { - //_this.samplePlateGroupWidget.selectSpecimens(specimens); - }); - var specimenContainer = this.specimenWidget.getPanel(); - this.specimenWidget.refresh(experiment); - /* - var specimenContainer = Ext.create('Ext.container.Container', { - layout : 'hbox', - width : 900, - padding : '10 0 0 2', - items : [ specimenGrid.getPanel() ] }); + BIOSAXS.proposal = new Proposal(experimentGrid.input().proposal); + var panel = experimentGrid.getPanel(experimentGrid.input().experiments); + experimentGrid.refresh(experimentGrid.input().experiments); + panel.render(targetId); +}; + + +function FitStructureToExperimentDataGrid(args) { + this.height = null; + this.width = null; + this.id = BUI.id(); + + if (args != null) { + if (args.height != null) { + this.height = args.height; + + if (args.width != null) { + this.width = args.width; + } + } + } + + this.onSelected = new Event(this); +} + +FitStructureToExperimentDataGrid.prototype.getStructuresByMacromolecule = function(macromolecule) { + var structures = []; + if (macromolecule.structure3VOs != null) { + if (macromolecule.structure3VOs.length > 0) { + for (var i = 0; i < macromolecule.structure3VOs.length; i++) { + structures.push(macromolecule.structure3VOs[i]); + } + } + } + return structures; +}; + +FitStructureToExperimentDataGrid.prototype._prepareData = function(subtractions) { + var data = []; + for (var i = 0; i < subtractions.length; i++) { + + for (var j = 0; j < subtractions[i].fitStructureToExperimentalData3VOs.length; j++) { + var fit = subtractions[i].fitStructureToExperimentalData3VOs[j]; + data.push({ + fit : fit.fitFilePath, + fitStructureToExperimentalDataId : fit.fitStructureToExperimentalDataId, + mixtureToStructure3VOs : fit.mixtureToStructure3VOs, + subtractedFile : subtractions[i].substractedFilePath + }); + } + } + return data; + +}; + +FitStructureToExperimentDataGrid.prototype.refresh = function(subtractions) { + this.store.loadData(this._prepareData(subtractions), false); +}; + +FitStructureToExperimentDataGrid.prototype.getPanel = function() { + var _this = this; + this.store = Ext.create('Ext.data.Store', { + fields : [ 'fit', 'subtractedFile', 'structureId', 'fitFilePath', 'mixtureToStructure3VOs' ], + data : [] + }); + + this.store.sort([ { + property : 'name', + direction : 'ASC' + } ]); + + this.selModel = Ext.create('Ext.selection.RowModel', { + allowDeselect : true, + mode : 'MULTI', + listeners : { + selectionchange : function(sm, selections) { + var selected = []; + for (var i = 0; i < selections.length; i++) { + selected.push(selections[i].raw); + } + _this.onSelected.notify(selected); + } + } + }); + + this.panel = Ext.create('Ext.grid.Panel', { + store : this.store, + deferredRender : false, + width : this.width, + height : this.height, + margin : 10, + selModel : this.selModel, + columns : [ { + text : 'Name', + dataIndex : 'fit', + flex : 1, + renderer : function(val, b, record) { + return BUI.getFileName(val); + } + }, { + text : 'PDB', + dataIndex : 'mixtureToStructure3VOs', + flex : 1, + renderer : function(values, b, record) { + var html = ""; + for (var i = 0; i < values.length; i++) { + var structure = BIOSAXS.proposal.getStructuresById(values[i].structureId); + html = html + ""; + if (structure != null){ + html = html + ""; + } + html = html + ""; + } + return html + "
" + structure.name + "
"; + } + }, { + text : 'Volume Fraction', + dataIndex : 'mixtureToStructure3VOs', + flex : 1, + renderer : function(values, b, record) { + var html = ""; + for (var i = 0; i < values.length; i++) { + html = html + ""; + html = html + ""; + html = html + ""; + } + + return html + "
" + values[i].volumeFraction + "
"; + } + },{ + text : 'Subtraction', + dataIndex : 'subtractedFile', + flex : 1, + renderer : function(values, b, record) { + return values.split("/")[values.split("/").length - 1]; + } + },], + + viewConfig : { + enableTextSelection : true, + preserveScrollOnRefresh : true + }, + listeners : { + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + }, + afterrender : function() { + } + } + }); + return this.panel; +}; + +/** Static method **/ +FitStructureToExperimentDataGrid.prototype.RUNFitScattering = function(subtractionId, structureId) { + var _this = this; + /** Add to Workflow **/ + var adapter = new BiosaxsDataAdapter(); + var workflow = { + 'workflowTitle' : 'FitExperimentalDatatoStructure', + 'comments' : 'FitExperimentalDatatoStructure run from ISPyB for subtractionId: ' + subtractionId + ' and structureId ' + structureId + } + + var inputs = [ { + name : 'subtractionId', + value : subtractionId + }, { + name : 'structureId', + value : structureId + } ]; + + adapter.onSuccess.attach(function(sender, data) { + /** Add to Fit **/ + var adapter2 = new BiosaxsDataAdapter(); + var fit = { + 'workflowId' : data.workflowId, + 'subtractionId' : subtractionId, + 'structureId' : structureId, + 'comments' : 'Sent to workflow engine' + } + adapter2.onSuccess.attach(function(sender, fit) { + _this.refresh(_this.subtractionId, _this.macromolecule); + }); + adapter2.addFitStructureData(fit); + + }); + adapter.addWorkflow(workflow, inputs); + +}; + +/** + * It shows buffer grid with a top bar with "Add" button + * + * @height + * @searchBar + * @collapsed + * @width + */ +function FrameGrid(args) { + this.height = 500; + this.width = 500; + this.searchBar = false; + this.tbar = false; + this.collapsed = false; - specimenGrid.refresh(experiment);*/ - var experimentList = new ExperimentList([ _this.experiment ]); - var measurementContainer = Ext.create('Ext.container.Container', { - layout : 'vbox', - padding : '5px 0px 0px 10px', - items : [] - }); - measurementContainer.insert(0, _this.measurementGridDone.getPanel(this.experiment.getMeasurements(), experimentList)); -// measurementContainer.insert(1, _this.measurementSamplePlateGroupWidget.getPanel(experiment)); + if (args != null) { + if (args.height != null) { + this.height = args.height; + } + + if (args.searchBar != null) { + this.searchBar = args.searchBar; + } - // this.dataCollectionCurveVisualizer = new DataCollectionCurveVisualizer(); - // this.dataCollectionCurveVisualizer.experiments = [experiment]; - // this.dataCollectionCurveVisualizer.dataCollectionFrameTree.experiments = - // [experiment]; - // this.dataCollectionCurveVisualizer.dataCollections = - // experiment.getDataCollections(); + if (args.tbar != null) { + this.tbar = args.tbar; + } - this.panel = Ext.createWidget('tabpanel', { - plain : true, - style : { - padding : 2 - }, - items : [ { - tabConfig : { - id : 'genralTabl', - title : "Overview" - }, - items : [ specimenContainer ] - }, { - tabConfig : { - title : 'Measurements' - }, - items : [ measurementContainer] - }, { - tabConfig : { - id : 'SpecimenTab', - title : 'Analysis', - hidden : this.isTemplate() - }, - items : [ { - xtype : 'container', - layout : 'vbox', - padding : '5px 0px 10px 10px', - items : [ _this.analysisGrid.getPanel([]) ] - } ] - }, - { - tabConfig : { - id : 'newAnalysisTab', - title : 'Analysis BETA', - hidden : this.isTemplate() - }, - items : [ { - xtype : 'container', - layout : 'vbox', - padding : '5px 0px 10px 10px', - items : [ _this.queueGrid.getPanel([]) ] - } ] + if (args.collapsed != null) { + this.collapsed = args.collapsed; } - ] + + if (args.width != null) { + this.width = args.width; + } + } +} + +FrameGrid.prototype._edit = function(bufferId) { + var _this = this; + var window = new BufferWindow(); + window.onSuccess.attach(function(sender, proposal) { + _this.store.loadData(BIOSAXS.proposal.getBuffers()); }); + window.draw(BIOSAXS.proposal.getBufferById(bufferId)); +}; - return this.getPanel(this.panel); +FrameGrid.prototype.refresh = function(buffers, experimentId) { + this.experimentId = experimentId; + this.store.loadData(this._prepareData(buffers), false); }; -ExperimentTabs.prototype.isTemplate = function() { - if (this.experiment.json.type == "TEMPLATE") { - return true; - } - return false; +FrameGrid.prototype._prepareData = function(buffers) { + return buffers; }; -ExperimentTabs.prototype.update = function() { +FrameGrid.prototype._getTbar = function() { var _this = this; - var inter; - if (!_this.isTemplate()) { - function updateExperiments() { - _this.refreshAnalysisData(); - window.clearInterval(inter); - inter = setInterval(function() { - updateExperiments(); - }, _this.INTERVAL_UPDATE); - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - var experiment = new Experiment(data); - _this.measurementGridDone.refresh(experiment.getMeasurements(), new ExperimentList([ experiment ])); + var actions = []; + + actions.push(Ext.create('Ext.Action', { + icon : '../images/add.png', + text : 'Add Buffer', + disabled : false, + handler : function(widget, event) { + var window = new BufferWindow(); + window.onSuccess.attach(function(sender) { + _this.store.loadData(BIOSAXS.proposal.getBuffers()); }); - adapter.getExperimentById(_this.experiment.json.experimentId, "MEDIUM"); + window.draw({}); } - inter = setInterval(function() { - updateExperiments(); - }, _this.INTERVAL_UPDATE); - } + })); + return actions; }; -ExperimentTabs.prototype.getPanel = function(panel) { +FrameGrid.prototype.getPanel = function(buffers) { var _this = this; - if (this.experimentPanel == null) { - this.experimentPanel = Ext.create('Ext.container.Container', { - bodyPadding : 2, - width : Ext.getBody().getViewSize().width * 0.9, - renderTo : this.targetId, - style : { - padding : 2 - }, - items : [ this.getExperimentTitle(), this.panel ], - listeners : { - afterrender : function() { - _this.refreshAnalysisData(); - _this.update(); - } - } - }); - } - - return this.experimentPanel; -}; - -ExperimentTabs.prototype.input = function() { - return { - experiment : DATADOC.getExperiment_10(), - proposal : DATADOC.getProposal_10() - }; -}; - -ExperimentTabs.prototype.test = function(targetId) { - var experimentTabs = new ExperimentTabs(targetId); - BIOSAXS.proposal = new Proposal(experimentTabs.input().proposal); - experimentTabs.draw(new Experiment(experimentTabs.input().experiment)); -}; + this.store = Ext.create('Ext.data.Store', { + fields : [ 'frameNumber', 'I0', 'Rg', 'Mass', 'Vc', 'Qr', 'quality'], + data : buffers + }); - -/** - * Shows an experiments with the specimens, measurements, analysis tabs where results are shown and the frames widget - * - * @targetId - */ -function HPLCTabs(targetId) { - this.height = 1400; - this.targetId = targetId; + this.store.sort('frameNumber'); - this.id = BUI.id(); + var type = 'Ext.grid.Panel'; + if (this.searchBar == true) { + type = 'Ext.ux.LiveSearchGridPanel'; + } - this.gridHeight = 600; - this.pointsCount = 1036; - this.plotHeight = 350; - this.plotWidth = 800; - this.plotPanelPadding = 5; + this.grid = Ext.create(type, { + store : this.store, + height : this.height, + width : this.width, + margin : 5, + columns : [{ + text : 'Frame', + dataIndex : 'frameNumber', + flex : 1 + },{ + text : 'I0', + dataIndex : 'I0', + flex : 1, + renderer : function(val, y, sample) { + return BUI.formatValuesUnits(sample.data.I0, "", 12, 3); + } + },{ + text : 'Rg', + dataIndex : 'Rg', + flex : 1, + renderer : function(val, y, sample) { + return BUI.formatValuesUnits(sample.data.Rg, "nm", 12, 3); + } + },{ + text : 'Mass', + dataIndex : 'Mass', + flex : 1, + renderer : function(val, y, sample) { + return BUI.formatValuesUnits(sample.data.Mass, "", 12, 3); + } + },{ + text : 'Vc', + dataIndex : 'Vc', + flex : 1, + renderer : function(val, y, sample) { + return BUI.formatValuesUnits(sample.data.Vc, "", 12, 3); + } + },{ + text : 'Qr', + dataIndex : 'Qr', + flex : 1, + renderer : function(val, y, sample) { + return BUI.formatValuesUnits(sample.data.Qr, "", 12, 3); + } + },{ + text : 'Quality', + dataIndex : 'quality', + flex : 1, + renderer : function(val, y, sample) { + return (Number(sample.data.quality) * 100).toFixed(2) + "%"; + } + }, + { + text : '', + renderer : function(val, x, sample) { + if (sample != null) { + return BUI.getZipHTMLByFrameRangeId(_this.experimentId, sample.raw.frameNumber, sample.raw.frameNumber); + } + }, + width : 100 + }], + flex : 1, + viewConfig : { + stripeRows : true + } + }); - var _this = this; + /** Adding the tbar **/ + if (this.tbar) { + this.grid.addDocked({ + xtype : 'toolbar', + items : this._getTbar() + }); + } + return this.grid; +}; - this.analysisGrid = new HPLCAnalysisGrid({ - height : Ext.getBody().getViewSize().height * 0.9 - 300, - positionColumnsHidden : true, - sorters : [ { - property : 'priorityLevelId', - direction : 'ASC' - } ] - }); +FrameGrid.prototype.input = function() { + return []; +}; - this.frameGrid = new FrameGrid({ - width : 600, - height : 60, - collapsed : false, - tbar : false - }); - - this.peakGrid = new PeakGrid({ - width : 550, - height : 500, - collapsed : false, - tbar : false - }); - - this.peakGrid2 = new PeakGrid({ - width : 102, - height : this.plotHeight, +FrameGrid.prototype.test = function(targetId) { + var frameGrid = new FrameGrid({ + width : 800, + height : 350, collapsed : false, - tbar : false, - showExtendedColumns : true + tbar : true }); - - this.mainPlotPanel = new HPLCGraph({ - title : 'I0', - width : this.plotWidth - 110, - height : this.plotHeight, - bbar : true, - plots : { - "I0" : true, - "Rg" : true - }, - xlabel : "HPLC Frames", - scaled : true, - interactionModel : { - 'dblclick' : function(event, g, context) { - _this._selectFrame(g.lastx_); - var annotations = []; - annotations.push({ - series : g.selPoints_[0].name, - x : g.lastx_, - width : 100, - height : 23, - tickHeight : 4, - shortText : g.lastx_, - text : g.lastx_, - attachAtBottom : true - }); - g.setAnnotations(annotations); - } + var panel = frameGrid.getPanel([]); + panel.render(targetId); +}; + + +function PeakGrid(args) { + this.height = 500; + this.searchBar = false; + this.tbar = false; + this.collapsed = false; + this.width = 500; + this.showExtendedColumns = false; + + if (args != null) { + if (args.showExtendedColumns != null) { + this.showExtendedColumns = args.showExtendedColumns; + } + if (args.height != null) { + this.height = args.height; + } + if (args.searchBar != null) { + this.searchBar = args.searchBar; } - }); - this.intensityPlotPanel = new MergesHPLCGraph({ - title : 'Scattering', - width : this.plotWidth, - height : 500, - showRangeSelector : false, - xParam : 0, - xlabel : "scattering_I", - plots : { - "scattering_I" : true, - "subtracted_I" : true, - "buffer_I" : true + if (args.tbar != null) { + this.tbar = args.tbar; } - }); -} + if (args.collapsed != null) { + this.collapsed = args.collapsed; + } -HPLCTabs.prototype._selectFrame = function(frameNumber) { - try{ - this._renderScatteringCurve(frameNumber); - this.frameGrid.refresh([this.mainPlotPanel.getDataByFrameNumber(frameNumber)], this.experiment.experimentId); - } - catch(e){ - console.log(e); + if (args.width != null) { + this.width = args.width; + } } -}; +} -HPLCTabs.prototype.error = function(error) { - var e = JSON.parse(error); - showError(e); - this.panel.setLoading(false); -}; -HPLCTabs.prototype.loadDataMainPlot = function(data) { - var zeroArray = []; - for ( var i = 0; i < data.I0.length; i++) { - zeroArray.push(0); - } - data = [ { - param : "I0", - data : data.I0, - std : data.I0_Stdev, - color : '#0066CC', - label : "I0" - }, - { - param : "sum_I", - label : "sum_I", - color : "#00FF00", - data : data.sum_I, - std : zeroArray - }, - { - param : "Rg", - label : "Rg", - color : "#21610B", - data : data.Rg, - std : data.Rg_Stdev - }, { - param : "Mass", - data : data.mass, - std : data.mass_Stdev, - color : '#FF9900', - label : "Mass" - }, { - param : "Vc", - data : data.Vc, - std : data.Vc_Stdev, - color : '#990099', - label : "Vc" - }, { - param : "Qr", - data : data.Qr, - std : data.Qr_Stdev, - color : '#FF0066', - label : "Qr" - }, { - param : "quality", - label : "quality", - color : "#FF00FF", - data : data.quality, - std : zeroArray - } ]; - this.data = data; - this.mainPlotPanel.loadData(data); +PeakGrid.prototype.refresh = function(buffers) { + this.store.loadData(this._prepareData(buffers), false); }; -HPLCTabs.prototype._loadIntensityPlotByFrameNumber = function(frameNumber) { - var _this = this; +PeakGrid.prototype._prepareData = function(buffers) { - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - var array = []; - data = [ { - param : "q", - data : data[frameNumber].q, - std : data[frameNumber].q, - fstd : function(a) { - return parseFloat(a); - }, - color : '#green', - label : "q", - showOnMenu : false - }, - { - param : "scattering_I", - data : data[frameNumber].scattering_I, - fdata : function(a) { - return Math.log(parseFloat(a)); - }, - std : data[frameNumber].scattering_Stdev, - fstd : function(a) { - return Math.log(Math.abs(parseFloat(a))); - }, - color : 'green', - label : "Log(I) Sample" - }, - { - param : "buffer_I", - data : data[frameNumber].buffer_I, - fdata : function(a) { - return Math.log(parseFloat(a)); - }, - fstd : function(a) { - return Math.log(Math.abs(parseFloat(a))); - }, - std : data[frameNumber].subtracted_Stdev, - color : '#0000FF', - label : "Log(I) Avg Buf." - }, - { - param : "subtracted_I", - data : data[frameNumber].subtracted_I, - fdata : function(a) { - var value = (Math.log(parseFloat(a))); - if (isNumber(value)) - return value; - }, - fstd : function(a) { - var value = Math.log(Math.abs(parseFloat(a))); - if (isNumber(value)) - return value; - }, - std : data[frameNumber].subtracted_Stdev, - color : 'red', - label : "Log(I) Sub." - } - ]; +// for ( var i = 0; i < buffers.length; i++) { +// buffers[i].name = "Peak #" + (i+1); +// } + /** Adding information of buffer **/ + if (buffers.length > 0){ + buffers.unshift({ + name : "BUFFER", + start : 0, + experimentId : buffers[0].experimentId, + end : buffers[0].start - 1 + }); + } + + + return buffers; +}; - _this.intensityPlotPanel.xlabel = "Frame " + frameNumber + " (q, nm-1)"; +PeakGrid.prototype._getTbar = function() { + var _this = this; + var actions = []; - if (_this.intensityPlotPanel.hplcData == null) { - /** It creates also top bar **/ - _this.intensityPlotPanel.loadData(data); - } else { - _this.intensityPlotPanel.reloadData(data); - + actions.push(Ext.create('Ext.Action', { + icon : '../images/add.png', + text : 'Add Buffer', + disabled : false, + handler : function(widget, event) { + var window = new BufferWindow(); + window.onSuccess.attach(function(sender) { + _this.store.loadData(BIOSAXS.proposal.getBuffers()); + }); + window.draw({}); } - _this.intensityPlotPanel.panel.setLoading(false); - }); - adapter.onError.attach(function(sender, data) { - _this.intensityPlotPanel.panel.setLoading(false); - }); - this.intensityPlotPanel.panel.setLoading("Retrieving Frame " + frameNumber); - adapter.getH5FrameScattering(this.experiment.json.experimentId, frameNumber); + })); + return actions; }; -HPLCTabs.prototype._renderScatteringCurve = function(frameNumber) { +PeakGrid.prototype.getPanel = function(buffers) { var _this = this; + this.peakCount = 0; + this.store = Ext.create('Ext.data.Store', { + fields : ['name', {name:'start', type : 'int'}, {name:'end', type : 'int'}], + data : buffers + + }); - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - _this.intensityPlotPanel.setPeaks(data); - _this._loadIntensityPlotByFrameNumber(frameNumber); - try{ - var peaks = []; - for(key in data){ - peaks.push({ - start : key.split("-")[0], - end : key.split("-")[1], - experimentId : _this.experiment.json.experimentId - }); + this.store.sort('start'); + + var type = 'Ext.grid.Panel'; + if (this.searchBar == true) { + type = 'Ext.ux.LiveSearchGridPanel'; + } + this.grid = Ext.create(type, { + store : this.store, + height : this.height, + width : this.width, + margin : 5, + columns : [ + { + text : '', + dataIndex : 'name', + width : 100, + hidden : _this.showExtendedColumns, + renderer : function(val, y, sample) { + if (sample.data.name == "BUFFER") + return "BUFFER"; + _this.peakCount++; + return "Peak #" + _this.peakCount; + } + + + }, + { + text : 'Peaks', + dataIndex : 'start', + sortable : true, + width : 100, + hidden: !_this.showExtendedColumns, + renderer : function(val, y, sample) { + return "From " + Number(sample.raw.start) + " to " + Number(sample.raw.end); + } + }, + { + text : 'Frames', + hidden : _this.showExtendedColumns, + columns : [ + { + text : 'Start', + dataIndex : 'start', + sortable : true, + hidden : _this.showExtendedColumns, + width : 100, + renderer : function(val, y, sample) { + return Number(val); + } + },{ + text : 'End', + dataIndex : 'end', + width : 100, + hidden : _this.showExtendedColumns, + renderer : function(val, y, sample) { + return Number(val); + } + },{ + text : 'Total', + dataIndex : 'end', + width : 100, + hidden : _this.showExtendedColumns, + renderer : function(val, y, sample) { + return "" + (sample.raw.end - sample.raw.start) + " frames"; + } + } + ] + } +// , +// { +// text : '', +// hidden : _this.showExtendedColumns, +// renderer : function(val, x, sample) { +// if (sample != null) { +// return BUI.getZipHTMLByFrameRangeId(sample.raw.experimentId, sample.raw.start, sample.raw.end); +// } +// }, +// width : 100 +// } + ], + flex : 1, + viewConfig : { + stripeRows : true, + getRowClass : function(record, rowIdx, params, store) { + if (record.raw.name == "BUFFER") { + return "blue-row"; + } } - _this.peakGrid2.refresh(JSON.parse(JSON.stringify(peaks))); - _this.peakGrid.refresh(peaks); -// console.log(peaks); - } - catch(e){ - showError(e); } }); - adapter.onError.attach(function(sender, data) { - _this.intensityPlotPanel.setLoading(false); + + /** Adding the tbar **/ + if (this.tbar) { + this.grid.addDocked({ + xtype : 'toolbar', + items : this._getTbar() + }); + } + return this.grid; +}; + +PeakGrid.prototype.input = function() { + return []; +}; + +PeakGrid.prototype.test = function(targetId) { + var PeakGrid = new PeakGrid({ + width : 800, + height : 350, + collapsed : false, + tbar : true }); - this.intensityPlotPanel.panel.setLoading("Reading HDF5 File "); - adapter.getH5FramesMerge(this.experiment.json.experimentId); + + var panel = PeakGrid.getPanel([]); + panel.render(targetId); }; + +/** + * Macromolecule Grid showing macromolecules and adding anb updating buttons + * + * @height + * @maxHeight + * @width + * @cssFontStyle + * @searchBar makes this grid as Ext.ux.LiveSearchGridPanel + * @tbar top bar containing "Add" and "Update From SMIS" button + * @collapsed + * @collapsible + * @btnEditVisible + * @btnRemoveVisible + * @multiselect makes it multiselect using Ext.selection.CheckboxModel + * + * #onSelected + * #onMacromoleculesChanged + */ +function MacromoleculeGrid(args) { + this.height = 500; + this.width = 500; + this.id = BUI.id(); + this.maxHeight = this.height; -HPLCTabs.prototype._postRenderOverviewPanel = function() { - var _this = this; - var adapter = new BiosaxsDataAdapter(); - adapter.onError.attach(function(sender, data) { - data = data.replace(/NaN/g, '0'); - _this.loadDataMainPlot(JSON.parse(data)); - + this.searchBar = false; + this.tbar = false; + + this.collapsible = true; + this.collapsed = true; + + this.btnEditVisible = true; + this.btnRemoveVisible = false; + this.multiselect = false; + + /** Font style applied to the acronym column **/ + this.cssFontStyle = null; + + if (args != null) { + if (args.height != null) { + this.height = args.height; + this.maxHeight = this.height; + } + if (args.maxHeight != null) { + this.maxHeight = args.maxHeight; + } + if (args.width != null) { + this.width = args.width; + } + if (args.cssFontStyle != null) { + this.cssFontStyle = args.cssFontStyle; + } + + if (args.searchBar != null) { + this.searchBar = args.searchBar; + } + if (args.tbar != null) { + this.tbar = args.tbar; + } + if (args.collapsible != null) { + this.collapsible = args.collapsible; + } + if (args.collapsed != null) { + this.collapsed = args.collapsed; + } + if (args.btnEditVisible != null) { + this.btnEditVisible = args.btnEditVisible; + } + if (args.btnRemoveVisible != null) { + this.btnRemoveVisible = args.btnRemoveVisible; + } + if (args.multiselect != null) { + this.multiselect = args.multiselect; + } + } - }); - adapter.onSuccess.attach(function(sender, data) { - _this.loadDataMainPlot(data); - _this._renderScatteringCurve(0); - }); - adapter.getH5fileParameters(this.experiment.json.experimentId, [ - "I0", "I0_Stdev", "sum_I","Rg", "Rg_Stdev", "Vc", "Vc_Stdev", "Qr", "Qr_Stdev", "mass", "mass_Stdev", "quality" ]); + this.onSelected = new Event(); -}; + this.onMacromoleculesChanged = new Event(); +} -HPLCTabs.prototype._postRenderDetailsPanel = function() { - if (this.data != null) { - this.I0PlotPanel.loadData(this.data); - this.RgPlotPanel.loadData(this.data); - this.MassPlotPanel.loadData(this.data); - this.VcPlotPanel.loadData(this.data); - } -}; -HPLCTabs.prototype.draw = function(experiment) { - var _this = this; - this.renderDataAcquisition(experiment); -}; -HPLCTabs.prototype.getExperimentTitle = function() { - var experimentHeaderForm = new ExperimentHeaderForm(); - return experimentHeaderForm.getPanel(this.experiment); -}; -HPLCTabs.prototype.renderDataAcquisition = function(experiment) { +MacromoleculeGrid.prototype.edit = function(macromolecule) { var _this = this; - this.experiment = experiment; - if (this.experimentPanel == null) { - this.experimentPanel = Ext.create('Ext.container.Container', { - bodyPadding : 2, - height : this.height, - width : Ext.getBody().getViewSize().width * 0.9, - renderTo : this.targetId, - style : { - padding : 2 - }, - items : [ this.getExperimentTitle(), this.getPanel() ], - listeners : { - afterrender : function() { - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - _this.analysisGrid.refresh(data); - }); - adapter.getAnalysisInformationByExperimentId(_this.experiment.experimentId); - } - } - }); - } - return this.experimentPanel; + var window = new MacromoleculeWindow(); + window.onSave.attach(function(sender) { + _this.store.loadData(BIOSAXS.proposal.getMacromolecules()); + _this.onMacromoleculesChanged.notify(); + }); + window.draw(macromolecule); }; -HPLCTabs.prototype.getPanel = function() { +MacromoleculeGrid.prototype.getTbar = function() { var _this = this; - this.panel = Ext.createWidget('tabpanel', - { - plain : true, - height : this.height, -// width : 900, - style : { - padding : 2 - }, - items : [ - { - tabConfig : { - title : "Overview" + var actions = []; - }, - items : [ { - xtype : 'container', - layout : 'hbox', - border : 1, - flex : 1, - items : [ { - xtype : 'container', - layout : 'vbox', - border : 1, - items : [ { - xtype : 'container', - margin : '10px', - border : 1, - items : [ - { - xtype : 'container', - margin : '0px', - layout : 'hbox', - border : 1, - items : [ - this.peakGrid2.getPanel([]), - this.mainPlotPanel.getPanel() - ] - }, - { - xtype : 'container', - layout : 'vbox', - border : 1, - items : [ - { - html: '
Select a frame by double-clicking on the HPLC Frames plot
', - margin: 5, - border : 0 - }, - this.frameGrid.getPanel([]), - this.intensityPlotPanel.getPanel() - ] - } - - ] - }], - listeners : { - afterrender : function() { - _this._postRenderOverviewPanel(); - } - } - } ] - } ] - }, -// { -// tabConfig : { -// title : "Details" -// }, -// items : [ { -// xtype : 'container', -// layout : 'hbox', -// border : 1, -// flex : 1, -// items : [ { -// xtype : 'container', -// layout : 'vbox', -// border : 1, -// items : [ { -// xtype : 'container', -// padding : '1px', -// items : [ -// this.I0PlotPanel.getPanel(), this.RgPlotPanel.getPanel(), this.MassPlotPanel.getPanel(), -// this.VcPlotPanel.getPanel() ] -// } ], -// listeners : { -// afterrender : function() { -// _this._postRenderDetailsPanel(); -// } -// } -// } ] -// } ] -// }, - { - tabConfig : { - title : "Analysis" - }, - items : [ { - xtype : 'container', - layout : 'vbox', - padding : '5px 0px 10px 10px', - items : [ _this.analysisGrid.getPanel([]) ] - } ] - }, - { - tabConfig : { - title : "File Manager" - }, - items : [ { - xtype : 'container', - layout : 'vbox', - padding : '5px 0px 10px 10px', - items : [ - { - html: '
Custom Download
', - margin : '10 0 10 5', - border : 0 - }, - { - html: '
Download has been temporary disabled. Contact your labcontact if you want to extract the frames from the HDF5 file
', - margin : '10 0 10 5', - hidden : _this.experiment.experimentId == 2602, - border : 0 - }, - { - xtype : 'container', - layout : 'hbox', - margin : '0 0 0 20', - flex : 1, - items :[ - { - xtype: 'numberfield', - id: 'field_start', - fieldLabel: 'Frames from', - value: 0, - minValue: 0 - }, - { - xtype: 'numberfield', - id: 'field_end', - fieldLabel: 'to', - labelWidth : 20, - margin : '0 0 0 10', - minValue: 0 - }, - { - xtype: 'button', - /** allowing test account to download frames **/ - disabled : _this.experiment.experimentId != 2602, - text : 'Download', - margin : '0 0 0 10', - handler : function() { - var experimentId = _this.experiment.experimentId; - var start = Ext.getCmp("field_start").getValue(); - var end = Ext.getCmp("field_end").getValue(); - /** Checking if start is bigger than end **/ - if (start > end){ - var aux = end; - end = start; - start = aux; - } - var url = BUI.getZipFrameHPLCUrl(experimentId, start, end); - window.open(url) - } - } - ] - }, - _this.peakGrid.getPanel([]) - - ] - } - ] - } - ] + actions.push(Ext.create('Ext.Action', { + icon : '../images/add.png', + text : 'Add macromolecule', + disabled : false, + handler : function(widget, event) { + _this.edit(); + } + })); + actions.push("->"); + actions.push(Ext.create('Ext.Action', { + icon : '../images/folder_go.png', + text : 'Update From SMIS', + tooltip : "Retrieve all the macromolecules of your proposal from SMIS database", + disabled : false, + handler : function(widget, event) { + _this.grid.setLoading("Connecting to SMIS"); + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + BIOSAXS.proposal.setMacromolecules(data.macromolecules); + _this.refresh(BIOSAXS.proposal.macromolecules); + _this.grid.setLoading(false); + }); + adapter.onError.attach(function(sender, data) { + _this.grid.setLoading(false); }); + adapter.updateDataBaseFromSMIS(); + } + })); + return actions; +}; - return this.panel; +MacromoleculeGrid.prototype.deselectAll = function() { + this.grid.getSelectionModel().deselectAll(); +}; + +MacromoleculeGrid.prototype.selectById = function(macromoleculeId) { + this.grid.getSelectionModel().deselectAll(); + for ( var i = 0; i < this.grid.getStore().data.items.length; i++) { + var item = this.grid.getStore().data.items[i].raw; + if (item.macromoleculeId == macromoleculeId) { + this.grid.getSelectionModel().select(i); + } + } +}; + +MacromoleculeGrid.prototype.refresh = function(macromolecules) { + this.store.loadData(macromolecules, false); +}; + +MacromoleculeGrid.prototype.getColumns = function() { + var _this = this; + var columns = [ + { + text : 'Acronym', + dataIndex : 'acronym', + id : this.id + "acronym", + flex : 1, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + if (_this.cssFontStyle != null) { + return "" + value + ""; + } + return value; + } + }, { + text : 'Name', + dataIndex : 'name', + id : this.id + "name", + flex : 1, + hidden : true + } ]; + + if (this.btnEditVisible) { + columns.push({ + id : _this.id + 'buttonEditMacromolecule', + width : 85, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + if (_this.btnEditVisible) { + return BUI.getGreenButton('EDIT'); + } + return null; + } + }); + } + if (this.btnRemoveVisible) { + columns.push({ + id : _this.id + 'buttonRemoveMacromolecule', + width : 85, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + if (_this.btnRemoveVisible) { + return BUI.getRedButton('REMOVE'); + } + return null; + } + }); + } + + return columns; +}; + + +/** Returns the grid **/ +MacromoleculeGrid.prototype.getPanel = function() { + var _this = this; + + this.store = Ext.create('Ext.data.Store', { + fields : [ 'macromoleculeId', 'name', 'acronym' ] + }); + + var type = 'Ext.grid.Panel'; + if (this.searchBar == true) { + type = 'Ext.ux.LiveSearchGridPanel'; + } + + this.selModel = Ext.create('Ext.selection.RowModel', { +// allowDeselect : true, +// mode : 'MULTI', + listeners : { + selectionchange : function(sm, selections) { + var selected = []; + for (var i = 0; i < selections.length; i++) { + selected.push(selections[i].raw); + } + _this.onSelected.notify(selected); + } + } + }); + + this.grid = Ext.create(type, { + id : this.id, + title : 'Macromolecules', + collapsible : this.collapsible, + collapsed : this.collapsed, + store : this.store, + height : this.height, + maxHeight : this.maxHeight, + selModel : this.selModel, + columns : this.getColumns(), + width : this.width, + viewConfig : { + stripeRows : true, + listeners : { + 'celldblclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + _this.edit(BIOSAXS.proposal.getMacromoleculeById(record.data.macromoleculeId)); + }, + 'cellclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEditMacromolecule') { + _this.edit(BIOSAXS.proposal.getMacromoleculeById(record.data.macromoleculeId)); + } + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemoveMacromolecule') { + BUI.showBetaWarning(); + } + } + + } + } + }); + + /** Adding the tbar **/ + if (this.tbar) { + this.grid.addDocked({ + xtype : 'toolbar', + items : this.getTbar() + }); + } + return this.grid; +}; + +MacromoleculeGrid.prototype.input = function() { + return { + proposal : DATADOC.getProposal_10() + }; +}; + +MacromoleculeGrid.prototype.test = function(targetId) { + var macromoleculeGrid = new MacromoleculeGrid({ + width : 800, + height : 350, + collapsed : false, + tbar : true + }); + + BIOSAXS.proposal = new Proposal(macromoleculeGrid.input().proposal); + var panel = macromoleculeGrid.getPanel(BIOSAXS.proposal.macromolecules); + panel.render(targetId); }; /** - * Main form tab for macromolecule + * Shows measurements with their attributes as specimen, exposure temperature, + * volume to load, transmission etc... * - * @width + * @addBtnMultipleEdit: if true add a button for changing measurements' + * parameters by choosing multiple measurements. It opens + * MultipleEditMeasurementGridWindow + * @collapsed: if true it doesn't show buffer's measurements + * @editor: hashmap containing columns to be edited. It is an array of a json + * like editor of Ext + * @selModel + * @collapseBtnEnable + * @removeBtnEnabled Ext.selection.RowModel + * @addBtnEnable + * @updateRowEnabled true/false if update plugin is set to the grid + * @showTitle + * @title + * @isStatusColumnHidden + * @isPriorityColumnHidden + * @isTimeColumnHidden + * @estimateTime + * @margin + * @tbar * @height + * @maxHeight + * @minHeight + * @width + * @maxWidth + * @resizable + * @experimentColorBased when colors for buffers and macromolecules are not + * selected by the proposal but by experiment, so the + * number of colors is smaller * - * #onClose when user clicks on close button in the MacromoleculeForm - * #onSave when macromole is saved by macromoleculeForm + * #onClick #onSelected #onRemoved #onUpdateTime #onMeasurementChanged + * #onExperimentChanged */ -function MacromoleculeTabs(args) { - this.width = 500; +function MeasurementGrid(args) { + this.id = BUI.id(); + this.height = 500; + this.width = 900; - if (args != null) { - if (args.width != null) { - this.width = args.width; + this.maxWidth = 1200; + this.maxHeight = 600; + this.minHeight = 500; + + this.unitsFontSize = 9; + this.title = "Measurements"; + this.estimateTime = false; + this.collapsed = true; + this.tbar = true; + + this.showTitle = true; + this.resizable = true; + this.updateRowEnabled = true; + + /** + * Hash map containing the keys of the editable columns. Ex: + * 'exposureTemperature' * + */ + this.editor = { + comments : { + xtype : 'textfield', + allowBlank : true } - if (args.height != null) { - this.height = args.height; + }; + + this.isTimeColumnHidden = false; + this.isStatusColumnHidden = false; + this.isPriorityColumnHidden = true; + this.margin = "0 0 0 0"; + + this.addBtnEnable = true; + this.sorter = [ { + property : 'priority', + direction : 'ASC' + } ]; + + this.removeBtnEnabled = false; + this.collapseBtnEnable = true; + this.addBtnMultipleEdit = false; + this.sortingBtnEnable = false; + + var _this = this; + this.selModel = Ext.create('Ext.selection.RowModel', { + allowDeselect : true, + mode : 'MULTI', + listeners : { + selectionchange : function(sm, selections) { + var selected = []; + for (var i = 0; i < selections.length; i++) { + selected.push(selections[i].raw); + } + _this.onSelected.notify(selected); + } } - } + }); - var _this = this; + if (args != null) { - /** Widgets **/ + if (args.selModel != null) { + this.selModel = args.selModel; + } - /** Macromolecule Form **/ - this.macromoleculeForm = new MacromoleculeForm({ - width : this.width - 30, - height : this.height - 50, - }); + if (args.removeBtnEnabled != null) { + this.removeBtnEnabled = args.removeBtnEnabled; + } - this.macromoleculeForm.onClose.attach(function(sender) { - _this.onClose.notify(); - }); + if (args.addBtnMultipleEdit != null) { + this.addBtnMultipleEdit = args.addBtnMultipleEdit; + } - this.macromoleculeForm.onSave.attach(function(sender, macromolecule) { - _this.onSave.notify(macromolecule); - }); + // if (args.experimentColorBased != null) { + // this.experimentColorBased = args.experimentColorBased; + // } - this.assemblyForm = new AssemblyForm({ - width : this.width - 30, - height : this.height - 50, - }); - - this.rigibBodyModelingForm = new RigibBodyModelingForm({ - width : this.width - 30, - height : this.height - 50, - }); - - this.rigibBodyModelingForm.onSave.attach(function(sender, macromolecule) { - _this.onSave.notify(macromolecule); - }); - + if (args.collapsed != null) { + this.collapsed = args.collapsed; + } + if (args.resizable != null) { + this.resizable = args.resizable; + } - /** Events **/ - this.onClose = new Event(this); - this.onSave = new Event(this); -} + if (args.editor != null) { + this.editor = args.editor; + } -/** Populate the widget **/ -MacromoleculeTabs.prototype.refresh = function(macromolecule) { - this.macromoleculeForm.refresh(macromolecule); - this.assemblyForm.refresh(macromolecule); - this.rigibBodyModelingForm.refresh(macromolecule); + if (args.collapseBtnEnable != null) { + this.collapseBtnEnable = args.collapseBtnEnable; + } - if (macromolecule != null){ - if (macromolecule.macromoleculeId == null){ - Ext.getCmp(this.id + "_advancedTab").disable(); - Ext.getCmp(this.id + "_assemblyTab").disable(); + if (args.addBtnEnable != null) { + this.addBtnEnable = args.addBtnEnable; } - else{ - Ext.getCmp(this.id + "_advancedTab").enable(); - Ext.getCmp(this.id + "_assemblyTab").enable(); + if (args.sortingBtnEnable != null) { + this.sortingBtnEnable = args.sortingBtnEnable; } - } - else{ - Ext.getCmp(this.id + "_advancedTab").disable(); - Ext.getCmp(this.id + "_assemblyTab").disable(); - } -}; -MacromoleculeTabs.prototype.getItems = function() { - return [ { - tabConfig : { - title : 'General' - }, - items : [ { - xtype : 'container', - items : [ this.macromoleculeForm.getPanel() ] - } ] - }, { - id : this.id + "_assemblyTab", - tabConfig : { - title : 'Assembly' - }, - items : [ { - xtype : 'container', - items : [ this.assemblyForm.getPanel() ] - } ] - },{ - id : this.id + "_advancedTab", - tabConfig : { - title : 'Advanced' - }, - items : [ this.rigibBodyModelingForm.getPanel() ] - } ]; -}; + if (args.isPriorityColumnHidden != null) { + this.isPriorityColumnHidden = args.isPriorityColumnHidden; + } -MacromoleculeTabs.prototype.getPanel = function() { - this.panel = Ext.createWidget('tabpanel', { - height : this.height, - width : this.width, - plain : true, - margin : 5, - border : 0, - items : this.getItems() - }); - return this.panel; -}; - -function ResultTabs() { -} + if (args.width != null) { + this.width = args.width; + } -ResultTabs.prototype.draw = function(targetId, data, macromoleculeId) { - var panel = this.getPanel(targetId, data, macromoleculeId); - return Ext.create('Ext.container.Container', { - renderTo : targetId, - items : [ BUI.getMacromoleculeHeader(macromoleculeId), panel ] - }); + if (args.updateRowEnabled != null) { + this.updateRowEnabled = args.updateRowEnabled; + } -}; + if (args.showTitle != null) { + this.showTitle = args.showTitle; + if (this.showTitle == false) { + this.title = null; + } + } -ResultTabs.prototype._splitBySpecimen = function(data) { - var splitted = {}; + if (args.height != null) { + this.height = args.height; + } - for ( var i = 0; i < data.length; i++) { - var row = data[i]; - if (splitted[row.macromoleculeId + "_" + row.bufferId] == null) { - splitted[row.macromoleculeId + "_" + row.bufferId] = []; + if (args.maxHeight != null) { + this.maxHeight = args.maxHeight; } - splitted[row.macromoleculeId + "_" + row.bufferId].push(row); - } - return splitted; -}; + if (args.minHeight != null) { + this.minHeight = args.minHeight; + } -ResultTabs.prototype._getTabTitle = function(key, data) { - var macromoleculeId = key.split("_")[0]; - var bufferId = key.split("_")[1]; + if (args.maxWidth != null) { + this.maxWidth = args.maxWidth; + } - return BIOSAXS.proposal.getMacromoleculeById(macromoleculeId).acronym + " + " + BIOSAXS.proposal.getBufferById(bufferId).acronym + "(" + data.length + ")"; -}; + if (args.isStatusColumnHidden != null) { + this.isStatusColumnHidden = args.isStatusColumnHidden; + } + if (args.isTimeColumnHidden != null) { + this.isTimeColumnHidden = args.isTimeColumnHidden; + } -ResultTabs.prototype.getPanel = function(targetId, data, macromoleculeId) { + if (args.title != null) { + this.title = args.title; + } + if (args.estimateTime != null) { + this.estimateTime = args.estimateTime; + } - var dataFiltered = new AnalysisGrid({ - hideNulls : true, - grouped : true, - sorters : [ { - property : 'quality', - direction : 'DESC' - } ] - })._prepareData(data); + if (args.margin != null) { + this.margin = args.margin; + } - var items = [ { - tabConfig : { - title : 'Analysis (' + dataFiltered.length + ')' - }, - items : [ { - xtype : 'container', - layout : 'vbox', - padding : 10, - items : [ new AnalysisGrid({ - isScatteringPlotVisible : false - }).getPanel(dataFiltered) ] - } ] - }, { - tabConfig : { - title : 'Concentration Effects' - }, - items : [ new ResultSummaryForm().getPanel(data) ] - } ]; + if (args.tbar != null) { + this.tbar = args.tbar; + } + + if (args.sorter != null) { + this.sorter = args.sorter; + } - var splitted = this._splitBySpecimen(dataFiltered); - for ( var key in splitted) { - items.push({ - tabConfig : { - title : this._getTabTitle(key, splitted[key]) - }, - items : [ new ResultSummaryForm().getPanel(splitted[key]) ] - }); } + this.onClick = new Event(this); + this.onSelected = new Event(this); + this.onRemoved = new Event(this); + this.onUpdateTime = new Event(this); + this.onMeasurementChanged = new Event(this); + this.onExperimentChanged = new Event(this); +} - this.panel = Ext.createWidget('tabpanel', { - style : { - padding : 2 - }, - items : items +MeasurementGrid.prototype._sortBy = function(sort) { + var _this = this; + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + _this.onExperimentChanged.notify(data); + _this.grid.setLoading(false); + // wizardWidget.window.close(); }); - return this.panel; - + adapter.onError.attach(function(sender, data) { + _this.grid.setLoading(false); + alert("Oops, there was a problem"); + }); + _this.grid.setLoading("Sorting"); + adapter.sortMeasurements(this.experiments.experiments[0].experimentId, sort); }; - - -function ShipmentTabs(targetId) { - this.targetId = targetId; +MeasurementGrid.prototype._getMenu = function() { var _this = this; - this.gridHeight = 500; - /** data **/ - this.shipment = null; - - /** Shipment Form **/ - this.shipmentForm = new ShipmentForm({ - creationMode : false, - showTitle : false - }); - this.shipmentForm.onSaved.attach(function(sender, data) { - _this.refresh(data); + if (this.tbar) { - }); + var items = []; + if (_this.addBtnEnable) { + items.push({ + icon : '../images/add.png', + text : 'Add measurements', + handler : function() { + _this._openAddMeasurementWindow(); + } + }); + } + if (_this.addBtnMultipleEdit) { + items.push({ + icon : '../images/Edit_16x16_01.png', + text : 'Multiple Edit', + handler : function() { + var multipleEditMeasurementGridWindow = new MultipleEditMeasurementGridWindow(); + multipleEditMeasurementGridWindow.onExperimentChanged.attach(function(sender, data) { + _this.onExperimentChanged.notify(data); + }); - /** Cases grid **/ - this.caseGrid = new CaseGrid({ - height : this.gridHeight - }); + multipleEditMeasurementGridWindow.draw(_this.measurements, _this.experiments); - this.caseGrid.onAddButtonClicked.attach(function(sender, dewar) { - _this.caseGrid.grid.setLoading("ISPyB: Creating a new case"); - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, shipment) { - /** updateing shipment on proposal **/ - for ( var i = 0; i < BIOSAXS.proposal.shippings.length; i++) { - if (BIOSAXS.proposal.shippings[i].shippingId == shipment.shippingId) { - BIOSAXS.proposal.shippings[i] = shipment; } - } - _this.refresh(shipment); - }); - adapter.onError.attach(function(sender, shipment) { - _this.caseGrid.grid.setLoading(false); - }); - adapter.addCase(_this.shipment.json.shippingId); - }); + }); + } - this.caseGrid.onRemoveButtonClicked.attach(function(sender, dewarId) { - _this.panel.setLoading("ISPyB: removing case"); - _this.shipment.onSaved.attach(function(sender, shipment) { - _this.refresh(shipment); + items.push("->"); - }); - _this.shipment.removeCase(dewarId); - }); -} + if (_this.sortingBtnEnable) { + var split = Ext.create('Ext.button.Split', { + text : 'Sort by', + // handle a click on the button itself + handler : function() { + // alert("The button was clicked"); + }, + menu : new Ext.menu.Menu({ + items : [ + { + text : 'First Created First Measured', + handler : function() { + _this._sortBy("FIFO"); + } + }, "-", { + text : 'Default', + handler : function() { + _this._sortBy("DEFAULT"); + } + } ] + }) + }); + items.push(split); + } -ShipmentTabs.prototype.refresh = function(shipment) { + if (_this.collapseBtnEnable) { + items.push({ + text : 'Collapse buffers', + enableToggle : true, + scope : this, + toggleHandler : function(item, pressed) { + this.collapsed = pressed; + this.grid.getStore().loadData(this._prepareData(this.measurements, this.experiments), false); + }, + pressed : this.collapsed + }); + } + var tb = Ext.create('Ext.toolbar.Toolbar', { + items : items + }); + return tb; + } + return null; +}; +/** Opens WizardWidget for adding new measurements * */ +MeasurementGrid.prototype._openAddMeasurementWindow = function(measurements, experiments) { var _this = this; - this.shipment = shipment; - var proposal = new Proposal(); - proposal.onDataRetrieved.attach(function(sender, plates) { - - _this.refreshWithPlates(shipment, plates); - _this.caseGrid.grid.setLoading(false); + var wizardWidget = new WizardWidget(); + wizardWidget.onFinished.attach(function(sender, result) { + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + _this.onExperimentChanged.notify(data); + _this.grid.setLoading(false); + wizardWidget.window.close(); + }); + wizardWidget.current.setLoading("ISPyB: Adding measurements"); + adapter.addMeasurements(result.name, "comments", result.data, _this.experiments.experiments[0].experimentId); }); - proposal.getPlatesByProposal(); + + wizardWidget.draw(null, new MeasurementCreatorStepWizardForm(BIOSAXS.proposal.getMacromolecules(), { + noNext : true + })); }; -ShipmentTabs.prototype.refreshWithPlates = function(shipment, plates) { - this.shipment = new Shipment(shipment); +/******************************************************************************* + * Opens WizardWidget for adding new measurements + * + * @Measurements + * @Experiments experimentList Object + ******************************************************************************/ +MeasurementGrid.prototype._prepareData = function(measurements, experiments) { + var data = []; + for (var i = 0; i < measurements.length; i++) { + var measurement = measurements[i]; + var specimen = experiments.getSampleById(measurement.specimenId); + var buffer = experiments.getBufferById(specimen.bufferId); + measurement.buffer_acronym = buffer.acronym; + measurement.bufferId = buffer.bufferId; + measurement.volume = specimen.volume; + if (specimen.macromolecule3VO != null) { + measurement.acronym = specimen.macromolecule3VO.acronym; + measurement.macromoleculeId = specimen.macromolecule3VO.macromoleculeId; + } + measurement.concentration = specimen.concentration; + if (measurement.run3VO != null) { + measurement.energy = measurement.run3VO.energy; + measurement.expExposureTemperature = measurement.run3VO.exposureTemperature; + measurement.storageTemperature = measurement.run3VO.storageTemperature; + measurement.timePerFrame = measurement.run3VO.timePerFrame; + measurement.radiationAbsolute = measurement.run3VO.radiationAbsolute; + measurement.radiationRelative = measurement.run3VO.radiationRelative; + measurement.status = "DONE"; - this.caseGrid.refresh(this.shipment.getDewars(), plates); - this.panel.setLoading(false); + try { + if (measurement.run3VO.timeStart != null) { + if (measurement.run3VO.timeStart != "") { + measurement.miliseconds = moment(measurement.run3VO.timeStart).format("X"); + } + } + } catch (E) { + console.log(E); + } + } + + if (experiments.getDataCollectionByMeasurementId(measurement.measurementId).length > 0) { + var measurementtodatacollection3VOs = experiments.getDataCollectionByMeasurementId(measurement.measurementId)[0].measurementtodatacollection3VOs; + for (var k = 0; k < measurementtodatacollection3VOs.length; k++) { + if (measurementtodatacollection3VOs[k].dataCollectionOrder == 1) { + var specimenBuffer = experiments.getSampleById(experiments.getMeasurementById(measurementtodatacollection3VOs[k].measurementId).specimenId); + if (specimenBuffer.sampleplateposition3VO != null) { + measurement.bufferSampleplateposition3VO = specimenBuffer.sampleplateposition3VO; + measurement.bufferSampleplate = (experiments.getSamplePlateById(specimenBuffer.sampleplateposition3VO.samplePlateId)); + } + } + } + } + + if (this.collapsed) { + /** If collapsed only the samples * */ + if (specimen.macromolecule3VO != null) { + data.push(measurement); + } + } else { + data.push(measurement); + } + + } + return data; }; -ShipmentTabs.prototype.error = function(error) { - var e = JSON.parse(error); - showError(e); - this.panel.setLoading(false); +/** + * Refresh data grid with the measurements and the experiments + * + * @measurements array with measurement3VO objects + * @experiments array with experiments objects + */ +MeasurementGrid.prototype.refresh = function(measurements, experiments) { + this.experiments = experiments; + this.measurements = measurements; + this.store.loadData(this._prepareData(measurements, experiments), false); }; -//ShipmentTabs.prototype.refreshTabTitles = function() { -/*Ext.getCmp("MacromoleculeTab").setText(this.getMacromoleculeTitle()); -Ext.getCmp("BufferTab").setText(this.getBuffersTitle()); -Ext.getCmp("SpecimenTab").setText(this.getSpecimenTitle()); -Ext.getCmp("PlatesTab").setText(this.getPlatesTitle()); -Ext.getCmp("AssembliesTab").setText(this.getShipmentTitle()); -Ext.getCmp("PlateGroupsTab").setText(this.getPlateGroupsTitle());*/ -//}; -ShipmentTabs.prototype.draw = function(shipment) { - var _this = this; - _this.plates = []; - _this.shipment = shipment; - _this.render(shipment); +/** + * Set status bar to busy (refreshing icon) + * + * @msg message to be displayed on the bar + */ +MeasurementGrid.prototype._showStatusBarBusy = function(msg) { + var statusBar = Ext.getCmp(this.id + 'basic-statusbar'); + statusBar.setStatus({ + text : msg, + iconCls : 'x-status-busy', + clear : false + }); +}; - // var proposal = new Proposal(); - // proposal.onDataRetrieved.attach(function(sender, plates){ - // _this.plates = plates; - // _this.shipment = shipment; - // _this.render(shipment); - // - // }); - // proposal.getPlatesByProposal(); +/** + * Set status bar to ready (ok icon) + * + * @msg message to be displayed on the bar + */ +MeasurementGrid.prototype._showStatusBarReady = function(msg) { + var statusBar = Ext.getCmp(this.id + 'basic-statusbar'); + statusBar.setStatus({ + text : msg, + iconCls : 'x-status-valid', + clear : false + }); }; -//ShipmentTabs.prototype.getShipmentTitle = function() { -// return 'Shipment'; -//}; +/** + * If updateRowEnabled returns an array with Ext.grid.plugin.RowEditing + */ +MeasurementGrid.prototype._getPlugins = function() { + var _this = this; + var plugins = []; + if (this.updateRowEnabled) { + plugins.push(Ext.create('Ext.grid.plugin.RowEditing', { + clicksToEdit : 1, + listeners : { + validateedit : function(grid, e) { + /** Setting values * */ + for ( var key in _this.editor) { + e.record.raw[key] = e.newValues[key]; + } + /** Comments are always updatable* */ + e.record.raw.comments = e.newValues.comments; -//ShipmentTabs.prototype.getMacromoleculeTitle = function() { -// return 'Macromolecules (' + this.experiment.getMacromolecules().length + ')'; -//}; + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, measurement) { + _this.onMeasurementChanged.notify(measurement); + _this.grid.setLoading(false); + }); + adapter.onError.attach(function() { + alert("Error"); + _this.grid.setLoading(false); + }); -//ShipmentTabs.prototype.getBuffersTitle = function() { -// return 'Buffers (' + this.experiment.getBuffers().length + ')'; -//}; + _this.grid.setLoading(); + adapter.saveMeasurement(e.record.raw, _this.experiments.experiments[0]); + } + } + })); + } + return plugins; +}; -//ShipmentTabs.prototype.getPlateGroupsTitle = function() { -// return 'Plate Groups (' + this.experiment.getPlateGroups().length + ')'; -//}; +/** + * @key name of the columns mathing the this.editor[key] + */ +MeasurementGrid.prototype._getEditor = function(key) { + if (this.editor[key] != null) { + return this.editor[key]; + } + return null; +}; -//ShipmentTabs.prototype.getSampleChangerTitle = function() { -// return 'Sample Changer'; -//}; +MeasurementGrid.prototype.getPanel = function(measurements, experiments) { + this.experiments = experiments; + this.measurements = measurements; + var _this = this; + this.store = Ext.create('Ext.data.Store', { + fields : [ { + name : 'miliseconds', + type : 'int' + }, 'priority', 'bufferId', { + name : 'exposureTemperature', + type : 'numeric' + }, 'volumeToLoad','code', 'transmission', 'viscosity', 'waitTime', 'flow', 'buffer_acronym', 'macromoleculeId', 'acronym', 'concentration', 'extraFlowTime', 'volume', 'energy', + 'expExposureTemperature', 'storageTemperature', 'timePerFrame', 'radiationAbsolute', 'radiationRelative', 'status', 'comments' ], + data : this._prepareData(measurements, experiments) + }); + this.store.sort(this.sorter); + var bbar = {}; + try { + bbar = Ext.create('Ext.ux.StatusBar', { + id : _this.id + 'basic-statusbar', + defaultText : 'Ready', + text : 'Ready', + iconCls : 'x-status-valid', + items : [] + }); + } catch (exp) { + console.log("bbar error"); + } -//ShipmentTabs.prototype.getSpecimenTitle = function() { -// return 'Specimens(' + this.experiment.getSpecimenCount() + ')'; -//}; + this.grid = Ext + .create( + 'Ext.grid.Panel', + { + id : this.id, + title : this.title, + store : this.store, + selModel : this.selModel, + plugins : this._getPlugins(), + resizable : this.resizable, + margin : this.margin, + maxHeight : this.maxHeight, + minHeight : this.minHeight, + maxWidth : this.maxWidth, + width : this.width, + tbar : this._getMenu(), + columns : [ + { + text : 'Order', + dataIndex : 'priority', + width : 50, + hidden : _this.isPriorityColumnHidden, + sortable : true -//ShipmentTabs.prototype.getPlatesTitle = function() { -// return 'Plates(' + this.experiment.getSamplePlates().length + ')'; -//}; + }, + { + text : 'Run Number', + dataIndex : 'code', + width : 50, + hidden : true, + sortable : true -//ShipmentTabs.prototype.getBuffersTip = function() { -/*if (this.experiment.getBuffers().length == 0){ - return BUI.getWarningHTML("There are no buffers. Click on add to create new ones. Click on edit button or double click to edit them"); - -} -else{ - return BUI.getTipHTML("Click on edit button or double click to edit them. Click on duplicate to create an identical buffer including its additives") -}*/ -//}; + }, -//ShipmentTabs.prototype.refreshTips = function() { -/*Ext.getCmp("BufferTabTip").update(this.getBuffersTip()); -Ext.getCmp("SpecimenTabTip").update(this.getSpecimensTip());*/ -//}; + { + text : 'Specimen', + columns : [ -ShipmentTabs.prototype.render = function(shipment) { - return this.getPanel(shipment); -}; + { + text : '', + dataIndex : 'macromoleculeId', + width : 30, + renderer : function(val, y, sample) { + if (val != null) { + if (_this.experiments == null) { + return BUI.getRectangleColorDIV(BIOSAXS.proposal.macromoleculeColors[val], 10, 10); + } else { + return BUI.getRectangleColorDIV(_this.experiments.macromoleculeColors[val], 10, 10); + } + } + }, + sortable : true + }, + { + text : 'Macromo.', + dataIndex : 'acronym', + width : 80, + renderer : function(val, y, sample) { + return val; + }, + sortable : true + }, + { + text : 'Conc. ', + dataIndex : 'concentration', + width : 80, + renderer : function(val, y, sample) { + if (sample.raw.macromoleculeId == null) { + return ""; + } + if (isNaN(val)) + return val; -ShipmentTabs.prototype.getShipmentHeader = function(shipment) { - var _this = this; - function getHTMLSource() { - var name = shipment.json.shippingName; - var status = shipment.json.shippingStatus; - var creationDate = shipment.json.creationDate; - var html = BUI.createFormLabel("Name :", name, 75, 400); - html = html + BUI.createFormLabel("Status :", status, 75, 400); - html = html + BUI.createFormLabel("Date :", creationDate, 75, 400); - return html; - } + if (val != 0) { + return BUI.formatValuesUnits(val, '', { + fontSize : 16, + decimals : 3, + unitsFontSize : this.unitsFontSize + }); + } else { + return; + } - return Ext.create('Ext.container.Container', { - frame : false, - layout : 'hbox', - title : 'General', - padding : 5, - bodyPadding : '5 5 0 0', - width : 890, - margin : '0 0 10 0', - height : 100, - style : { - borderColor : '#BDBDBD', - borderStyle : 'solid', - borderWidth : '1px' - }, - fieldDefaults : { - msgTarget : 'side', - labelWidth : 100 - }, - items : [ { - margin : "0 0 0 0", - width : 475, - border : 0, - html : getHTMLSource() - } - ] - }); -}; + }, + sortable : true + }, + { + text : '', + dataIndex : 'bufferId', + width : 30, + hidden : false, + renderer : function(val, y, sample) { + if (val != null) { + var color = '#FFCCFF'; + if (_this.experiments != null) { + var dc = _this.experiments.getDataCollectionByMeasurementId(sample.raw.measurementId); + if (dc != null) { + if (dc.length > 0) { + color = _this.experiments.getSpecimenColorByBufferId(_this.experiments + .getMeasurementById(dc[0].measurementtodatacollection3VOs[0].measurementId).specimenId); + } + } + } else { + color = BIOSAXS.proposal.bufferColors[val]; + } + return BUI.getRectangleColorDIV(color, 10, 10); + } + }, + sortable : true + }, + { + text : 'Buffer', + dataIndex : 'buffer_acronym', + width : 120, + renderer : function(val, y, sample) { + if (sample.raw.bufferSampleplateposition3VO != null) { + return BIOSAXS.proposal.getBufferById(sample.raw.bufferId).acronym + " Plate: [" + + sample.raw.bufferSampleplate.slotPositionColumn + ", " + + BUI.getSamplePlateLetters()[sample.raw.bufferSampleplateposition3VO.rowNumber - 1] + "-" + + sample.raw.bufferSampleplateposition3VO.columnNumber + "]"; + } + return val; + }, + sortable : true + }, { + text : 'Position', + width : 100, + hidden : true, + renderer : function(val, y, sample) { + if (_this.experiments != null) { + return BUI.getSamplePositionHTML(_this.experiments.getSampleById(sample.raw.specimenId), _this.experiments.experiments[0]); + } + } + } ] + }, + { + text : 'Parameters', + columns : [ + { + text : 'Ex. Flow. time (s)', + dataIndex : 'extraFlowTime', + width : 100, + hidden : true, + renderer : function(val, y, sample) { + return BUI.formatValuesUnits(val, 's', { + fontSize : 12, + decimals : 0, + unitsFontSize : this.unitsFontSize + }); + } + }, + { + text : 'Exp. Temp.', + dataIndex : 'exposureTemperature', + width : 70, + renderer : function(val, y, sample) { + if (Number(val)) { + return BUI.formatValuesUnits(val, 'C', { + fontSize : 12, + decimals : 2, + unitsFontSize : this.unitsFontSize + }); + } + return null; + }, + sortable : true, + editor : this._getEditor("exposureTemperature") + }, + { + text : 'Vol. Load', + dataIndex : 'volumeToLoad', + width : 60, + hidden : false, + editor : this._getEditor("volumeToLoad"), + renderer : function(val, y, sample) { + // return val+ " µl"; + return BUI.formatValuesUnits(val, 'µl', { + fontSize : 12, + decimals : 2, + unitsFontSize : this.unitsFontSize + }); + } + }, + { + text : 'Volume in Well', + dataIndex : 'volume', + hidden : true, + editor : this._getEditor("volume"), + width : 80, + renderer : function(val, y, sample) { + // return val + "(µl)"; + return BUI.formatValuesUnits(val, 'µl', { + fontSize : 12, + decimals : 2, + unitsFontSize : this.unitsFontSize + }); + } + }, + { + text : 'Trans.', + dataIndex : 'transmission', + width : 60, + editor : this._getEditor("transmission"), + renderer : function(val, y, sample) { + return BUI.formatValuesUnits(val, '%', { + fontSize : 12, + decimals : 0, + unitsFontSize : this.unitsFontSize + }); + } + }, + { + text : 'Wait T.', + dataIndex : 'waitTime', + editor : this._getEditor("waitTime"), + width : 50, + renderer : function(val, y, sample) { + // if (val != 0) { + return BUI.formatValuesUnits(val, 's', { + fontSize : 12, + decimals : 0, + unitsFontSize : this.unitsFontSize + }); + // } + } + }, + { + text : 'Flow', + dataIndex : 'flow', + editor : this._getEditor("flow"), + width : 50, + renderer : function(val, y, sample) { + if (val == true) { + return "yes"; + } + return null; + } + }, + { + text : 'Viscosity', + dataIndex : 'viscosity', + tooltip : 'The viscosity of a fluid is a measure of its resistance to gradual deformation by shear stress or tensile stress. For liquids, it corresponds to the informal notion of "thickness"', + editor : this._getEditor("viscosity"), + width : 50, + renderer : function(val, y, sample) { + return val; + } + } ] + }, { + text : 'Status', + dataIndex : 'status', + width : 50, + hidden : _this.isStatusColumnHidden, + renderer : function(val, y, sample) { + if (val != null) { + if (val == 'DONE') { + return "" + val + " "; + } + } + } + }, { + text : 'Time', + dataIndex : 'time', + width : 80, + hidden : _this.isTimeColumnHidden, + renderer : function(val, y, sample) { + if (sample.raw.run3VO != null) { + if (sample.raw.run3VO.timeStart != null) { + if (sample.raw.run3VO.timeStart != "") { + var m = moment(sample.raw.run3VO.timeStart); + return m.format("hh:mm:ss a"); + } + } + } + } + }, { + text : 'Energy', + dataIndex : 'energy', + width : 100, + hidden : true + }, { + text : 'Real Exp. Temp.(C)', + width : 100, + dataIndex : 'expExposureTemperature', + hidden : true + }, { + text : 'Storage Temp.(C)', + width : 100, + dataIndex : 'storageTemperature', + hidden : true + }, { + text : 'Time/Frame (s)', + width : 100, + dataIndex : 'timePerFrame', + hidden : true + }, { + text : 'Radiation Relative', + dataIndex : 'radiationRelative', + width : 100, + hidden : true + }, { + text : 'Radiation Absolute', + dataIndex : 'radiationAbsolute', + width : 100, + hidden : true + }, { + text : 'Comments', + dataIndex : 'comments', + flex : 1, + hidden : false, + editor : this._getEditor("comments") -ShipmentTabs.prototype.getTabPanel = function(shipment) { - this.panel = Ext.createWidget('tabpanel', { - height : 600, - style : { - padding : 2 - }, - items : [ { - tabConfig : { - id : 'Shipment', - title : 'Shipment', - icon : '/ispyb/images/plane-small.gif' - }, - items : [ { - xtype : 'container', - margin : '5 5 5 5', - items : [ this.shipmentForm.getPanel(shipment) ] - } ] - }, { - tabConfig : { - id : 'Cases', - title : 'Cases', - icon : '../images/box-icon-very-small.png' - }, - items : [ { - xtype : 'container', - margin : '5 5 5 5', - items : [ this.caseGrid.getPanel(shipment.getDewars(), this.plates) ] - } ] - } ] - }); - return this.panel; -}; + }, { + id : _this.id + 'buttonRemoveSample', + text : '', + hidden : !_this.removeBtnEnabled, + width : 100, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + if (record.raw.macromoleculeId != null) { + if (_this.removeBtnEnabled) { + return BUI.getRedButton('REMOVE'); + } + } + } + } ], + bbar : bbar, + viewConfig : { + stripeRows : true, + getRowClass : function(record, index, rowParams, store) { + if (record.data.status == "DONE") { + return 'green-row'; + } -ShipmentTabs.prototype.getPanel = function(shipment) { - var _this = this; - this.shipment = shipment; - if (this.plates == null) { - this.plates = []; - } + }, + listeners : { + 'itemclick' : function(grid, record, item, index, e, eOpts) { + _this.onClick.notify({ + specimen : record.raw + }); + }, + 'cellclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemoveSample') { + grid.getStore().removeAt(rowIndex); - if (this.shipPanel == null) { - this.shipPanel = Ext.create('Ext.container.Container', { - bodyPadding : 2, - width : Ext.getBody().getViewSize().width * 0.9, - renderTo : this.targetId, - style : { - padding : 2 - }, - items : [ this.getShipmentHeader(shipment), this.getTabPanel(shipment) ] - }); - } + if (record.raw.measurementId != null) { + /** For testing * */ + grid.setLoading("ISPyB: Removing measurement"); + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + grid.setLoading(false); + /** + * We get and refresh experiment + * because specimens has changed * + */ + var adapter2 = new BiosaxsDataAdapter(); + adapter2.onSuccess.attach(function(sender, experiment) { + _this.onRemoved.notify(experiment); + _this._showStatusBarReady('Ready'); + }); + if (_this.experiments.experiments[0].experimentId != null) { + adapter2.getExperimentById(_this.experiments.experiments[0].experimentId, "MEDIUM"); + _this._showStatusBarBusy("ISPyB: Removing Unused Specimens"); + } + }); - return this.shipPanel; -}; - -/** - * Shows an template with the specimens, measurements and the experiment's - * requirement - * - * @targetId - */ -function TemplateTabs(targetId) { - this.height = 600; - this.targetId = targetId; + adapter.onError.attach(function(sender, data) { + alert("Error: " + data); + grid.setLoading(false); + }); - this.id = BUI.id(); - var _this = this; + adapter.removeMeasurement(record.raw); + } + } - this.gridHeight = 1000; - /** data * */ - this.experiment = null; + } - this.specimenSelected = null; + } + } + }); - /** Specimen Widget contains a specimenGrid and a sampleChangerWidget than can be displayed with are vertical or horizontal layout **/ - this.specimenWidget = new SpecimenWidget({ - height : this.height - }); - - this.samplePlateGroupWidget = new SamplePlateGroupWidget({ - showTitle : false, - height : 250, - margin : 5, - bbar : true - }); - - this.samplePlateGroupWidget.onExperimentChanged.attach(function(sender, experiment) { - _this.refresh(experiment); - }); + this.grid.on("afterrender", function() { - this.samplePlateGroupWidget.onClick.attach(function(sender, args) { - }); + function updateTime() { + try { + _this.estimatedTime = _this.estimatedTime - 1; - this.volumePlanificator = new VolumeGrid(); + _this.onUpdateTime.notify({ + hours : (Number(_this.estimatedTime / 3600).toFixed()), + minutes : (Number((_this.estimatedTime / 60) % 60).toFixed()), + seconds : (Number(_this.estimatedTime % 60).toFixed()) - /** For Measurements * */ - var storeViscosity = Ext.create('Ext.data.Store', { - fields : [ 'name' ], - data : [ { - "name" : "low" - }, { - "name" : "medium" - }, { - "name" : "high" - } ] - }); + }); - // Create the combo box, attached to the states data store - var viscosityEditor = Ext.create('Ext.form.ComboBox', { - fieldLabel : '', - store : storeViscosity, - queryMode : 'local', - displayField : 'name', - valueField : 'name' - }); + if (Number(_this.estimatedTime) < 0) { + _this.timer = null; + grid.setTitle(_this.title); + } - this.measurementGrid = new MeasurementGrid({ - maxWidth : 1500, - estimateTime : false, - positionColumnsHidden : true, - isPriorityColumnHidden : true, - isStatusColumnHidden : true, - isTimeColumnHidden : true, - updateRowEnabled : true, - collapsed : true, - removeBtnEnabled : true, - showTitle : false, - collapseBtnEnable : false, - addBtnMultipleEdit : true, - sortingBtnEnable : true, - editor : { - exposureTemperature : { - xtype : 'textfield', - allowBlank : true - }, - comments : { - xtype : 'textfield', - allowBlank : true - }, - volumeToLoad : { - xtype : 'numberfield', - allowBlank : true - }, - transmission : { - xtype : 'numberfield', - allowBlank : true - }, - viscosity : viscosityEditor, - waitTime : { - xtype : 'numberfield', - allowBlank : true - }, - flow : { - xtype : 'checkbox', - allowBlank : true + } catch (e) { + console.log(e); + _this.timer = null; } } - }); - - this.measurementGrid.onSelected.attach(function(sender, measurements) { - var specimens = []; - for ( var i = 0; i < measurements.length; i++) { - specimens.push(_this.experiment.getSampleById(measurements[i].specimenId)); - } - }); - this.measurementGrid.onMeasurementChanged.attach(function(sender, measurement) { - _this.experiment.setMeasurement(measurement); - _this.refresh(_this.experiment); - }); + if (_this.estimateTime) { + var experimentList = _this.experiments; + var collected = experimentList.getMeasurementsCollected(); + if (collected.length > 0) { + if (collected[0].run3VO != null) { + try { + var end = collected[0].run3VO.timeEnd; + var start = collected[0].run3VO.timeStart; + var dstart = moment(start); + var dend = moment(end); + var seconds = Number(dend.diff(dstart) / 1000).toFixed(); - this.measurementGrid.onExperimentChanged.attach(function(sender, json) { - _this.refresh(new Experiment(json)); - }); + _this.estimatedTime = (seconds * experimentList.getMeasurementsNotCollected().length); - this.measurementGrid.onRemoved.attach(function(sender, experiment) { - _this.refreshSpecimen(new Experiment(experiment)); - }); + if (_this.estimatedTime > 0) { + updateTime(); + _this.timer = setInterval(function() { + updateTime(); + }, 1000); + } - this.measurementGrid.onUpdateTime.attach(function(sender, args) { - document.getElementById(_this.id + "_counter").innerHTML = args.hours + 'h, ' + args.minutes + 'min and ' + args.seconds + ' seconds'; + } catch (e) { + } + } + } + } }); - -} - -TemplateTabs.prototype.refreshMeasurement = function(experiment) { - this.experiment = experiment; - this.experiment.onSaved = new Event(this); - this.experiment.onSpecimenSaved = new Event(this); - var experimentList = new ExperimentList([ this.experiment ]); - this.measurementGrid.refresh(experimentList.getMeasurementsNotCollected(), experimentList); -}; -TemplateTabs.prototype.refreshSpecimen = function(experiment) { - this.experiment = experiment; - this.experiment.onSaved = new Event(this); - this.experiment.onSpecimenSaved = new Event(this); - this.samplePlateGroupWidget.refresh(this.experiment); - this.specimenWidget.refresh(this.experiment); - this.volumePlanificator.refresh(this.experiment); + return this.grid; }; -TemplateTabs.prototype.refresh = function(experiment) { - // var start = new Date().getTime(); - this.experiment = experiment; - this.experiment.onSaved = new Event(this); - this.experiment.onSpecimenSaved = new Event(this); - - // var experimentList = new ExperimentList([this.experiment]); - this.refreshMeasurement(experiment); - this.refreshSpecimen(experiment); - /** Refreshing grids * */ - this.panel.setLoading(false); - +/** Method for testing * */ +MeasurementGrid.prototype.input = function() { + var experiment = DATADOC.getExperiment_10(); + var measurements = DATADOC.getMeasurements_10(); + var proposal = DATADOC.getProposal_10(); + return { + experiment : experiment, + measurements : measurements, + proposal : proposal + }; }; -TemplateTabs.prototype.error = function(error) { - var e = JSON.parse(error); - showError(e); - this.panel.setLoading(false); +MeasurementGrid.prototype.test = function(targetId) { + var measurementGrid = new MeasurementGrid({ + tbar : true + }); + BIOSAXS.proposal = new Proposal(measurementGrid.input().proposal); + var panel = measurementGrid.getPanel(measurementGrid.input().measurements, new ExperimentList([ new Experiment(measurementGrid.input().experiment) ])); + panel.render(targetId); }; + +/** + * A shipment may contains one or more cases where stock solutions and sample + * plates are stored + * + * @height + * @btnEditVisible + * @btnRemoveVisible + * + * #onEditButtonClicked + */ +function MolarityGrid(args) { + this.height = 100; + this.width = 100; + + if (args != null) { + if (args.height != null) { + this.height = args.height; + } + if (args.width != null) { + this.width = args.width; + } + } + + var _this = this; + + this.molarityForm = new MolarityForm({height : 180, width : 455}); + + this.molarityForm.onSave.attach(function(sender){ + _this.molarityWindow.destroy(); + _this.updateProposal(); + + }); + + this.molarityForm.onClose.attach(function(sender){ + _this.molarityWindow.destroy(); + + }); + + /** Events * */ + this.onEditButtonClicked = new Event(this); +} + +MolarityGrid.prototype._getColumns = function() { + return [ { + text : 'Subunit', + columns : [ { + text : "Acronym", + width : 100, + hidden : false, + dataIndex : 'acronym', + sortable : true + }, { + text : "Name", + width : 125, + hidden : false, + dataIndex : 'name', + sortable : true + }, { + text : "MM Est.", + width : 100, + dataIndex : 'molecularMass', + sortable : true, + renderer : function(grid, cls, record){ + return BUI.formatValuesUnits(record.data.molecularMass , "Da", 10, 2); + + } + } ] + }, { +// text : "Number
in assymmetric units", + text : "Ratio", + width : 100, + dataIndex : 'ratio', + tooltip : 'Number of times the subunit is present in the macromolecule', + sortable : true + }, { + id : this.id + 'MOLARITY_REMOVE', + flex : 0.1, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + return BUI.getRedButton('REMOVE'); + } + } ]; +}; + +MolarityGrid.prototype._openMolarityWindow = function() { + this.molarityWindow = Ext.create('Ext.window.Window', { + title : 'Molarity', + height : 220, + width : 500, + modal : true, + items : [this.molarityForm.getPanel() ] + }).show(); +}; + +MolarityGrid.prototype._getButtons = function() { + var _this = this; + return [ { + text : 'Add subunit', + icon : '../images/add.png', + handler : function() { + _this._openMolarityWindow(); + } + }]; +}; + + +MolarityGrid.prototype.updateProposal = function() { + var _this = this; + this.panel.setLoading(); + BIOSAXS.proposal.onInitialized.attach(function() { + if (BIOSAXS.proposal != null) { + var macromolecules = BIOSAXS.proposal.macromolecules; + for (var i = 0; i < macromolecules.length; i++) { + + if (macromolecules[i].macromoleculeId == _this.macromolecule.macromoleculeId) { + _this.refresh(macromolecules[i]); + _this.panel.setLoading(false); + } + } + } + }); + BIOSAXS.proposal.init(); +}; + + +MolarityGrid.prototype.getPanel = function() { + var _this = this; + + this.molarityStore = Ext.create('Ext.data.Store', { + fields : [ 'acronym', 'ratio', 'comments', 'stoichiometryId', 'name', 'molecularMass' ], + sorters : { + property : 'ratio', + direction : 'DESC' + } + }); + + this.panel = Ext.create('Ext.grid.Panel', { + store : this.molarityStore, + height : this.height, + padding : 5, + columns : this._getColumns(), + listeners : { + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + + /** Remove entry * */ + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'MOLARITY_REMOVE') { + var dataAdapter = new BiosaxsDataAdapter(); + dataAdapter.onSuccess.attach(function(sender) { + _this.updateProposal(); + + }); + dataAdapter.removeStoichiometry(record.data.stoichiometryId); + _this.panel.setLoading("Removing Structure"); + } + } + }, + tbar : this._getButtons() + }); + return this.panel; +}; + +MolarityGrid.prototype._prepareData = function(macromolecule) { + /** Return an array of [{ratio,acronym, stoichiometryId, name}] **/ + var data = []; + if (macromolecule.stoichiometry != null) { + for (var i = 0; i < macromolecule.stoichiometry.length; i++) { + var hostMacromolecule = BIOSAXS.proposal.getMacromoleculeById(macromolecule.stoichiometry[i].macromoleculeId); + data.push({ + ratio : macromolecule.stoichiometry[i].ratio, + acronym : hostMacromolecule.acronym, + comments : hostMacromolecule.comments, + molecularMass : hostMacromolecule.molecularMass, + stoichiometryId : macromolecule.stoichiometry[i].stoichiometryId, + name : hostMacromolecule.name + }); + } + } + return data; +}; + +MolarityGrid.prototype.refresh = function(macromolecule) { + if (macromolecule != null){ + this.molarityStore.loadData(this._prepareData(macromolecule)); + this.molarityForm.refresh(macromolecule); + this.macromolecule = macromolecule; + } +}; + +MolarityGrid.prototype.input = function() { + return { + proposal : DATADOC.getProposal_10(), + dewars : DATADOC.getDewars_10() + + }; +}; + +MolarityGrid.prototype.test = function(targetId) { + var MolarityGrid = new MolarityGrid({ + height : 150 + }); + BIOSAXS.proposal = new Proposal(MolarityGrid.input().proposal); + var panel = MolarityGrid.getPanel(MolarityGrid.input().dewars); + panel.render(targetId); + +}; + + +/** + * Given data analysis parsed with ResultsAssemblyWidget makes a selector grid with buffer/protein + **/ +function SpecimenSelectorResultGrid() { + this.id = BUI.id(); +} -TemplateTabs.prototype.draw = function(experiment) { - this.render(experiment); +SpecimenSelectorResultGrid.prototype._prepareData = function(data) { + var parsed = []; + for ( var i = 0; i < data.length; i++) { + var row = data[i]; + for ( var j = 0; j < row.conditions.length; j++) { + parsed.push({ + bufferId : row.conditions[j].bufferId, + macromoleculeId : row.macromoleculeId, + macromoleculeAcronym : BIOSAXS.proposal.getMacromoleculeById(row.macromoleculeId).acronym, + bufferAcronym : BIOSAXS.proposal.getBufferById(row.conditions[j].bufferId).acronym + }); + } + } + return parsed; }; - -TemplateTabs.prototype.getExperimentTitle = function() { - var _this = this; - var experimentHeaderForm = new ExperimentHeaderForm(); - return experimentHeaderForm.getPanel(this.experiment); +SpecimenSelectorResultGrid.prototype.refresh = function(data) { + this.store.loadData(this._prepareData(data)); }; -TemplateTabs.prototype.render = function(experiment) { +SpecimenSelectorResultGrid.prototype.getPanel = function(data) { var _this = this; - this.experiment = experiment; + this.store = Ext.create('Ext.data.Store', { + fields : [ 'macromoleculeId', 'bufferId', 'macromoleculeAcronym', 'bufferAcronym', 'concentration' ], + data : this._prepareData(data), + groupField : 'macromoleculeAcronym' + }); - /** - * - * Depending on the sample Changer configuration we want to display the plates vertically or horizontally - * Default is vertical - * - * */ - - var specimenContainer = this.specimenWidget.getPanel(); - this.specimenWidget.refresh(experiment); - - var experimentList = new ExperimentList([ _this.experiment ]); - var measurementContainer = Ext.create('Ext.container.Container', { - layout : { - type : 'vbox' - }, - defaults : { - style : { - padding : '5px 0px 0px 10px' + this.store.sort('concentration'); + this.grid = Ext.create('Ext.grid.Panel', { + id : this.id, + store : this.store, + width : this.width, + height : this.height, + maxHeight : this.maxHeight, + border : 1, + features : [ { + ftype : 'grouping', + groupHeaderTpl : '{name}', + hideGroupedHeader : true, + startCollapsed : false + } ], + selModel : Ext.create('Ext.selection.CheckboxModel', { + allowDeselect : true, + mode : 'MULTI', + listeners : { + selectionchange : function(sm, selections) { + _this.selected = []; + for ( var i = 0; i < selections.length; i++) { + _this.selected.push(selections[i].raw); + } + } } - }, - items : [ _this.measurementGrid.getPanel(experimentList.getMeasurementsNotCollected(), experimentList) ] + }), + margin : 10, + sortableColumns : true, + columns : [ { + text : 'Macromolecule', + dataIndex : 'macromoleculeAcronym', + flex : 1 + }, { + text : '', + dataIndex : 'bufferId', + width : 20, + hidden : false, + renderer : function(val, y, sample) { + return BUI.getRectangleColorDIV(BIOSAXS.proposal.bufferColors[val], 10, 10); + } + }, { + text : 'Buffer', + dataIndex : 'bufferAcronym', + flex : 1 + }, { + text : 'Concentration', + dataIndex : 'concentration', + flex : 1, + renderer : function(val, y, sample) { + return val + " mg/ml"; + } + } ] }); - this.panel = Ext - .createWidget( - 'tabpanel', - { - plain : true, - items : [ - { - tabConfig : { - title : 'Measurements' - }, - items : [ { - xtype : 'container', - layout : 'vbox', - border : 1, -// height : _this.gridHeight, - margin : "0 0 10 0", - items : [ measurementContainer ] - } - - ] - }, - { - tabConfig : { - id : 'genralTabl', - title : "Specimens" - // width : 900, - // border : 3 - - }, - items : [ specimenContainer ] - }, - { - tabConfig : { - title : "Requirements" + /** Adding the tbar **/ + if (this.tbar) { + this.grid.addDocked({ + xtype : 'toolbar', + items : this.getTbar() + }); + } + return this.grid; +}; - }, - items : [ - { - html : BUI.getTipHTML("Estimated volume is the maximum volume required. Depending on the order of your measurements you may use less. Click on create stock solutions if you plan to ship these stock solutions"), - margin : "10 10 10 10", - border : 0 - }, this.volumePlanificator.getPanel(experiment) ] - } ] - }); - // ); - return this.getPanel(this.panel); +SpecimenSelectorResultGrid.prototype.input = function() { + return { + data : new ResultsAssemblyGrid()._prepareData(new ResultsAssemblyGrid().input().data), + proposal : new ResultsAssemblyGrid().input().proposal + }; }; -TemplateTabs.prototype.isTemplate = function() { - if (this.experiment.json.type == "TEMPLATE") { - return true; - } - return false; +SpecimenSelectorResultGrid.prototype.test = function(targetId) { + var specimenSelectorResultGrid = new SpecimenSelectorResultGrid(); + BIOSAXS.proposal = new Proposal(specimenSelectorResultGrid.input().proposal); + var panel = specimenSelectorResultGrid.getPanel(specimenSelectorResultGrid.input().data); + panel.render(targetId); }; +/** + * Show all buffer conditions for each macromolecules pointing out the measurements quality + * + * @height + * @maxHeight + * @width + * @searchBar + * @tbar + * @btnResultVisible + * + * #onClick + */ +function ResultsAssemblyGrid(args) { + this.height = 500; + this.id = BUI.id(); + this.maxHeight = this.height; -TemplateTabs.prototype.getPanel = function(panel) { - var _this = this; - if (this.experimentPanel == null) { - this.experimentPanel = Ext.create('Ext.container.Container', { - bodyPadding : 2, - width : 1000,//Ext.getBody().getViewSize().width * 0.9, - renderTo : this.targetId, - height : 500, -// style : { -// padding : 2 -// }, - items : [ - this.getExperimentTitle(), - this.panel - ], - listeners : { - afterrender : function(thisCmp) { - $("#SchemeReport" + _this.experiment.experimentId).click(function() { - $(this).target = "_blank"; - window.open('viewProjectList.do?reqCode=display&menu=platescheme&experimentId=' + _this.experiment.experimentId); - return false; - }); + this.width = 900; + this.searchBar = false; + this.tbar = false; + this.btnResultVisible = false; - } - } - }); - } - return this.experimentPanel; -}; + /** For processing **/ + this.processed = {}; + this.renderedPlotIndex = 0; -TemplateTabs.prototype.input = function(targetId) { - return new ExperimentTabs().input(); -}; + this.plotWidth = 210; + this.plotHeight = 80; -TemplateTabs.prototype.test = function(targetId) { - var experimentTabs = new TemplateTabs(targetId); - BIOSAXS.proposal = new Proposal(experimentTabs.input().proposal); - experimentTabs.draw(new Experiment(experimentTabs.input().experiment)); -}; - -var BUI = { - //interval : 60000, - interval : 40000, - rainbow : function(numOfSteps, step) { - // This function generates vibrant, "evenly spaced" colours (i.e. no clustering). This is ideal for creating easily distinguishable vibrant markers in Google Maps and other apps. - // Adam Cole, 2011-Sept-14 - // HSV to RBG adapted from: http://mjijackson.com/2008/02/rgb-to-hsl-and-rgb-to-hsv-color-model-conversion-algorithms-in-javascript - var r, g, b; - var h = step / numOfSteps; - var i = ~~(h * 6); - var f = h * 6 - i; - var q = 1 - f; - switch (i % 6) { - case 0: - r = 1, g = f, b = 0; - break; - case 1: - r = q, g = 1, b = 0; - break; - case 2: - r = 0, g = 1, b = f; - break; - case 3: - r = 0, g = q, b = 1; - break; - case 4: - r = f, g = 0, b = 1; - break; - case 5: - r = 1, g = 0, b = q; - break; + /** Colors **/ + this.validColor = BUI.getValidColor(); + this.warningColor = BUI.getWarningColor(); + this.notValidColor = BUI.getErrorColor(); + + /** Show warning if guinier quality less than **/ + this.guinierQuality = BUI.getQualityThreshold(); + this.framePercentageThreshold = BUI.getRadiationDamageThreshold(); + + if (args != null) { + if (args.height != null) { + this.height = args.height; + this.maxHeight = this.height; } - var c = "#" + ("00" + (~~(r * 255)).toString(16)).slice(-2) + ("00" + (~~(g * 255)).toString(16)).slice(-2) - + ("00" + (~~(b * 255)).toString(16)).slice(-2); - return (c); - }, - getFileNameByPath : function(filePath) { - if (filePath != null){ - var split = filePath.split("/"); - if (split.length > 0){ - return split[split.length - 1]; - } + if (args.maxHeight != null) { + this.maxHeight = args.maxHeight; + } + if (args.width != null) { + this.width = args.width; + } + if (args.searchBar != null) { + this.searchBar = args.searchBar; } - return "Not file"; - }, - getUpdateInterval : function() { - this.interval = this.interval + 2000; - return this.interval; - }, - getRadiationDamageThreshold : function() { - return 0.7; - }, - getQualityThreshold : function() { - return 0.7; - }, - getCreateShipmentURL : function() { - return '/ispyb/user/viewProjectList.do?reqCode=display&menu=create_shipment'; - }, - getCreateShipmentList : function() { - return '/ispyb/user/viewProjectList.do?reqCode=display&menu=list_shipment'; - }, - getShippingURL : function(shippingId) { - return '/ispyb/user/viewProjectList.do?reqCode=display&menu=shipment&shippingId=' + shippingId; - }, - getMacromoleculeResultsURLByMultipleSearch : function(array) { - return '/ispyb/user/viewProjectList.do?reqCode=display&menu=macromolecule&search=' - + JSON.stringify(array).replace(new RegExp("\"", 'g'), "'"); - }, - getMacromoleculeResultsURL : function(macromoleculeId) { - return '/ispyb/user/viewProjectList.do?reqCode=display&menu=macromolecule¯omoleculeId=' + macromoleculeId; - }, - getMacromoleculeBufferResultsURL : function(macromoleculeId, bufferId) { - return '/ispyb/user/viewProjectList.do?reqCode=display&menu=macromolecule&bufferId=' + bufferId + '¯omoleculeId=' + macromoleculeId; - }, + if (args.tbar != null) { + this.tbar = args.tbar; + } + if (args.btnResultVisible != null) { + this.btnResultVisible = args.btnResultVisible; + } - getMacromoleculeHeader : function(macromoleculeId) { + } - function getHTMLSource(macromoleculeId) { - if (macromoleculeId != null) { - var html = BUI.createFormLabel("Name :", BIOSAXS.proposal.getMacromoleculeById(macromoleculeId).name, 75, 400); - html = html + BUI.createFormLabel("Acronym :", BIOSAXS.proposal.getMacromoleculeById(macromoleculeId).acronym, 75, 400); - if (BIOSAXS.proposal.getMacromoleculeById(macromoleculeId).comments != null) { - html = html + BUI.createFormLabel("Comments :", BIOSAXS.proposal.getMacromoleculeById(macromoleculeId).comments, 75, 400); - } - return html; - } - } + this.onClick = new Event(); +} - return Ext.create('Ext.container.Container', { - frame : false, - layout : 'hbox', - title : 'Macromolecule', - bodyPadding : '5', - width : 890, - margin : '0 0 10 0', - height : 100, - style : { - borderColor : '#BDBDBD', - borderStyle : 'solid', - borderWidth : '1px' - }, - fieldDefaults : { - msgTarget : 'side', - labelWidth : 100 - }, - items : [ { - margin : "10 0 0 10", - width : 475, - border : 0, - html : getHTMLSource(macromoleculeId) - }, { - margin : "10 0 0 10", - width : 475, - border : 0, - html : BUI.getZipHTMLByMacromoleculeId(macromoleculeId) - } - ] - }); - }, +ResultsAssemblyGrid.prototype.edit = function(macromoleculeId) { + var _this = this; + var window = new MacromoleculeWindow(); + window.onSuccess.attach(function(sender, proposal) { + _this.store.loadData(_this._prepareData(BIOSAXS.proposal.getMacromolecules())); + }); + window.draw(BIOSAXS.proposal.getMacromoleculeById(macromoleculeId)); +}; - getZipHTMLByMacromoleculeId : function(macromoleculeId) { - if (macromoleculeId != null) { - var fileName = BIOSAXS.proposal.getMacromoleculeById(macromoleculeId).acronym; - return ""; - } - }, - getZipHTMLByExperimentId : function(experimentId, filename) { - if (filename == null){ - filename = "experiment"; - } - return ""; - }, - - getZipURLByAverageId : function(averageId, filename) { - if (filename == null){ - filename = "experiment"; - } - return "/ispyb/user/dataadapter.do?reqCode=getZipFileByAverageListId&f&mergeIdsList=" + averageId + "&fileName=" + filename; - }, - getZipURLBySubtractionId : function(subtractionId, filename) { - if (filename == null){ - filename = "experiment"; +ResultsAssemblyGrid.prototype.getTbar = function() { + var _this = this; + var actions = []; + + actions.push(Ext.create('Ext.Action', { + icon : '../images/add.png', + text : 'Add Macromolecule', + disabled : false, + handler : function(widget, event) { + var window = new MacromoleculeWindow(); + window.onSuccess.attach(function(sender) { + _this.refresh(); + }); + window.draw({}); } - return "/ispyb/user/dataadapter.do?reqCode=getZipFileByAverageListId&f&subtractionIdList=" + subtractionId + "&fileName=" + filename; - }, - - - getZipHTMLByFrameRangeId : function(experimentId, start, end) { - var fileName = "experiment"; - return ""; - }, - getZipFrameHPLCUrl : function(experimentId, start, end) { - return "/ispyb/user/dataadapter.do?reqCode=getZipFileH5ByFramesRange&f&experimentId=" + experimentId + "&start=" + Number(start) +"&end="+ Number(end); - }, - - getQueueUrl : function() { - return "/ispyb/user/dataadapter.do?reqCode=getPagingCompactAnalysisByProposalId"; - }, - - getQueueUrlByExperiment: function(experimentId) { - return "/ispyb/user/dataadapter.do?reqCode=getPagingCompactAnalysisByExperimentId&f&experimentId=" + experimentId; - }, - getStandardDeviation : function(values) { - var sum = 0; - var count = 0; - var avg = null; + })); + + actions.push(Ext.create('Ext.Action', { + icon : '../images/add.png', + text : 'Define an Assembly', + disabled : false, + handler : function(widget, event) { + var createAssemblywindow = new CreateAssemblyWindow(); + createAssemblywindow.onSaved.attach(function(evt, args) { + if (args.macromoleculeIds.length > 0) { + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, proposal) { + _this.refresh(); + }); + adapter.saveAssembly(args.assemblyId, args.macromoleculeIds); - var curatedValues = new Array(); - for ( var i = 0; i < values.length; i++) { - var value = values[i]; - if (value != null) { - if (!isNaN(value)) { - count = count + 1; - sum = sum + Number(value); - curatedValues.push(Number(value)); } - } - } - if (count > 0) { - avg = sum / count; - } else { - avg = sum; - } - var aux = 0; - for ( var i = 0; i < curatedValues.length; i++) { - var value = curatedValues[i]; - aux = aux + Math.pow(value - avg, 2); + }); + createAssemblywindow.draw(_this.experiment); } - /** std **/ - var std = Math.sqrt(aux / count); + })); + + return actions; +}; + +ResultsAssemblyGrid.prototype.refresh = function() { + this.store.loadData(this._prepareData()); +}; + +ResultsAssemblyGrid.prototype.addCondition = function(record, data_parsed, i) { + function getCondition(record) { return { - std : (std), - sum : (sum), - avg : (avg), - validNumber : count, - totalNumber : values.length, - values : values + concentration : record.conc, + quality : record.quality, + bufferBeforeFramesMerged : record.bufferBeforeFramesMerged, + bufferAfterFramesMerged : record.bufferAfterFramesMerged, + framesCount : record.framesCount, + framesMerge : record.framesMerge }; - }, - - getHTMLTableForFrameAveraged : function(bufferAcronym, macromoleculeAcronym, bbmerges, molmerges, bamerges, totalframes, bufferId,macromoleculeId, macromoleculeColor) { - - function getFrameSpan(framesMerged, total) { - return "(" + framesMerged + " of " + total + ")"; - } + } - function getColorFrame(framesMerged, total) { - if (framesMerged / total < 0.5) { - return "#FA5858"; - } - if ((framesMerged / total >= 0.5) && (framesMerged / total < 0.8)) { - return "#FF9900"; + if (data_parsed[i].conditions != null) { + var bufferFound = false; + for ( var index in data_parsed[i].conditions) { + condition = data_parsed[i].conditions[index]; + + if ((condition.macromoleculeId == record.macromoleculeId) && (condition.bufferId == record.bufferId)) { + data_parsed[i].conditions[index].concentrations.push(getCondition(record)); + bufferFound = true; } - return "white"; } - - function getRow(color, acroynm, framesMerged, totalframes) { - return " " - + BUI.getRectangleColorDIV(color, 10, 10) - + " " + acroynm + "" - + getFrameSpan(framesMerged, totalframes) + ""; + if (!bufferFound) { + data_parsed[i].conditions.push({ + macromoleculeId : record.macromoleculeId, + bufferId : record.bufferId, + concentrations : [ getCondition(record) ] + }); } + } +}; - var html = ""; +ResultsAssemblyGrid.prototype.process = function(record, data_parsed) { + if (this.processed[record.macromoleculeId] == null) { + this.processed[record.macromoleculeId] = true; + record.measurementCount = 1; + record.subtractionCount = 1; + record.averageCount = 1; + record.conditions = []; + data_parsed.push(record); + } - /** Buffer Before **/ - if (bufferAcronym != null) { - if (bbmerges != null) { - color = BIOSAXS.proposal.bufferColors[bufferId]; - html = html + getRow(color, bufferAcronym, bbmerges, totalframes); + for ( var i = 0; i < data_parsed.length; i++) { + if (data_parsed[i].macromoleculeId == record.macromoleculeId) { + data_parsed[i].measurementCount = data_parsed[i].measurementCount + 1; + + if (record.subtractionId != null) { + data_parsed[i].subtractionCount = data_parsed[i].subtractionCount + 1; + this.addCondition(record, data_parsed, i); } - } - /** Molecule **/ - if (macromoleculeAcronym != null) { - if (molmerges != null) { - if (macromoleculeColor == null){ - color = BIOSAXS.proposal.macromoleculeColors[macromoleculeId]; - } - else{ - color = macromoleculeColor; //BIOSAXS.proposal.macromoleculeColors[macromoleculeId]; + if (record.framesMerge != null) { + data_parsed[i].averageCount = data_parsed[i].averageCount + 1; + } + + if (record.timeStart != null) { + if (data_parsed[i].timeStart != null) { + if (moment(data_parsed[i].timeStart).format("X") > moment(record.timeStart).format("X")) { + data_parsed[i].timeStart = record.timeStart; + } } - html = html + getRow(color, macromoleculeAcronym, molmerges, totalframes); } } + } - /** Buffer After **/ - if (bufferAcronym != null) { - if (bamerges != null) { - color = BIOSAXS.proposal.bufferColors[bufferId]; - html = html + getRow(color, bufferAcronym, bamerges, totalframes); + return data_parsed; + +}; + +ResultsAssemblyGrid.prototype._prepareData = function(data) { + var data_parsed = []; + for ( var i = 0; i < data.length; i++) { + data_parsed = this.process(data[i], data_parsed); + } + this.data = data_parsed; + return data_parsed; +}; + +/** Given an array of conditions it returns distinct(concentrations) order by concentration and hash map with number of ocurrences**/ +ResultsAssemblyGrid.prototype.parseConcentrations = function(val, conditions, differentConcentration, quality) { + var conditions = []; + var differentConcentration = {}; + var quality = []; + for ( var i = 0; i < val.length; i++) { + var conc = Number(val[i].concentration).toFixed(1); + var quality = Number(val[i].quality).toFixed(2); + if (differentConcentration[conc] == null) { + differentConcentration[conc] = 0; + conditions.push({ + concentration : conc, + quality : [ quality ], + frames : [ { + bufferAfterFramesMerged : val[i].bufferAfterFramesMerged, + bufferBeforeFramesMerged : val[i].bufferBeforeFramesMerged, + framesMerge : val[i].framesMerge, + framesCount : val[i].framesCount + } ] + }); + } else { + /** Add quality **/ + for ( var j = 0; j < conditions.length; j++) { + if (conditions[j].concentration == conc) { + conditions[j].quality.push(quality); + conditions[j].frames.push({ + bufferAfterFramesMerged : val[i].bufferAfterFramesMerged, + bufferBeforeFramesMerged : val[i].bufferBeforeFramesMerged, + framesMerge : val[i].framesMerge, + framesCount : val[i].framesCount + }); + } } } - return html + "
"; - }, - isWebGLEnabled : function(return_context) { - if (!!window.WebGLRenderingContext) { - var canvas = document.createElement("canvas"); - names = [ "webgl", "experimental-webgl", "moz-webgl", "webkit-3d" ]; - context = false; - for ( var i = 0; i < 4; i++) { - try { - context = canvas.getContext(names[i]); - if (context && typeof context.getParameter == "function") { - // WebGL is enabled - if (return_context) { - // return WebGL object if the function's argument is present - return { - name : names[i], - gl : context - }; - } - // else, return just true - return true; - } - } catch (e) { - } + + differentConcentration[conc] = differentConcentration[conc] + 1; + } + /** sorting concentrations **/ + conditions.sort(function(a, b) { + return a.concentration - b.concentration; + }); + return { + concentrations : conditions, + differentConcentration : differentConcentration + }; +}; + +ResultsAssemblyGrid.prototype.getConditionWarnings = function(condition) { + + var withWarnings = 0; + + for ( var i = 0; i < condition.frames.length; i++) { + if (condition.quality[i] == null) { + withWarnings = withWarnings + 1; + continue; + } else { + if (Number(condition.quality[i]) < this.guinierQuality) { + withWarnings = withWarnings + 1; + continue; } - // WebGL is supported, but disabled - return false; } - // WebGL not supported28. - return false; - }, - getHTMLTableForPrefixes : function(bufferBeforeaverageFilePath, averageFilePath, bufferAfterAverageFilePath) { - function getRow(bufferBeforeaverageFilePath) { - file = bufferBeforeaverageFilePath; - try { - file = bufferBeforeaverageFilePath.split("/")[bufferBeforeaverageFilePath.split("/").length - 1]; - } catch (e) { - file = "NA"; + if (condition.frames[i].bufferBeforeFramesMerged / condition.frames[i].framesCount < this.framePercentageThreshold|| condition.frames[i].framesMerged / condition.frames[i].framesCount < this.framePercentageThreshold|| condition.frames[i].bufferAfterFramesMerged / condition.frames[i].framesCount < this.framePercentageThreshold) { + withWarnings = withWarnings + 1; + continue; + } + } + + return { + withWarnings : withWarnings, + withoutWarnings : condition.frames.length - withWarnings + }; +}; + +ResultsAssemblyGrid.prototype.getFrameHTMLTable = function(warnings) { + var html = ""; + if (warnings.withWarnings > 0) { + html = html + "
" + warnings.withWarnings + + "x
"; + } + + if (warnings.withoutWarnings > 0) { + html = html + "
" + warnings.withoutWarnings + + "x
"; + } + return html; +}; + +ResultsAssemblyGrid.prototype.createConcentrationRow = function(numberOcu, condition, warnings){ + var html = ""; + if (numberOcu > 1){ + html = html + "" +numberOcu + "x " + BUI.formatConcentration(condition.concentration); + } + else{ + html = html + BUI.formatConcentration(condition.concentration); + } + html = html + ""; + html = html + this.getFrameHTMLTable(warnings); + ""; + html = html + ""; + return html; +}; + + +ResultsAssemblyGrid.prototype.getConditionHTMLTable = function(val, style, record) { + var maxNumberColumns = 2; + var html = "
"; + var nColumns = 0; + for ( var r = 0; r < val.length; r++) { + if (nColumns == maxNumberColumns) { + nColumns = 0; + html = html + ""; + } + html = html + ""; } - var html = "
"; + var value = val[r]; + + var bufferAcronym = (BIOSAXS.proposal.getBufferById(value.bufferId).acronym); + + var parsed = (this.parseConcentrations(value.concentrations)); + var conditions = parsed.concentrations; + var differentConcentration = parsed.differentConcentration; + + /** Checking warnings **/ + var warnings = []; + var concentrationValidPerconcentration = 0; + var measurements = 0; + for ( var i = 0; i < conditions.length; i++) { + measurements = measurements + conditions[i].frames.length; + var warning = this.getConditionWarnings(conditions[i]); + warnings.push(warning); + if (warning.withoutWarnings > 0) { + concentrationValidPerconcentration = concentrationValidPerconcentration + 1; } - return "
" + file + "
"; - /** Buffer Before **/ - if (bufferBeforeaverageFilePath != null) { - html = html + getRow(bufferBeforeaverageFilePath); - } + this.validColor = '#E0F8E0'; + this.warningColor = '#F5DA81'; + this.notValidColor = '#F6CED8'; - /** Molecule **/ - if (averageFilePath != null) { - html = html + getRow(averageFilePath); + var color = this.warningColor; + if (concentrationValidPerconcentration > 2) { + color = this.validColor; + } + /** More measurement need to be done **/ + if (measurements < 3) { + color = this.notValidColor; } - /** Buffer After **/ - if (bufferAfterAverageFilePath != null) { - html = html + getRow(bufferAfterAverageFilePath); + html = html + "
"; + html = html + ""; + for ( var i = 0; i < conditions.length; i++) { + html = html + this.createConcentrationRow(differentConcentration[conditions[i].concentration], conditions[i], warnings[i]); } - return html + "
" + bufferAcronym.toUpperCase() + + "
"; - }, - getBaseURL : function() { - return '/ispyb/user/dataadapter.do'; - }, + html = html + ""; + html = html + ""; - getPrintcomponentURL : function(dewarId) { - return '/ispyb/user/viewDewarAction.do?reqCode=generateLabels&dewarId=' + dewarId; + html = html + ""; + nColumns = nColumns + 1; + } + html = html + "
"; + return html; +}; - }, - getPDBVisualizerURL : function(modelId, subtractionId, experimentId) { - return '/ispyb/user/viewProjectList.do?reqCode=display&menu=PDBVisualizer&modelId=' + modelId + '&experimentId=' + experimentId - + '&subtractionId=' + subtractionId; - }, +ResultsAssemblyGrid.prototype._getTbar = function() { + function goTo(url) { + window.location = url; + } - getURL : function() { - return this.getBaseURL() + '?reqCode=getImage'; + var _this = this; + return [ { + icon : '../images/application_view_list.png', + text : 'Multiple Select', + handler : function() { + var specimenSelectorResultGrid = new SpecimenSelectorResultGrid(); + var window = Ext.create('Ext.window.Window', { + title : 'Multiple select', + height : 600, + width : 600, + layout : 'fit', + items : [ specimenSelectorResultGrid.getPanel(_this.data) ], + buttons : [ { + text : 'Go', + handler : function() { + var array = []; + for ( var i = 0; i < specimenSelectorResultGrid.selected.length; i++) { + var row = specimenSelectorResultGrid.selected[i]; + array.push({ + macromoleculeId : row.macromoleculeId, + bufferId : row.bufferId + }); + } + goTo(BUI.getMacromoleculeResultsURLByMultipleSearch(array)); + + } + }, { + text : 'Cancel', + handler : function() { + window.close(); + } + } ] + + }).show(); - }, - getAbinitioImageURL : function() { - return this.getBaseURL() + '?reqCode=getAbinitioImage'; - }, - getNSDImageURL : function(modelListId) { - return BUI.getAbinitioImageURL() + '&type=NSD&modelListId=' + modelListId; - }, - getCHI2ImageURL : function(modelListId) { - return BUI.getAbinitioImageURL() + '&type=CHI2&modelListId=' + modelListId; - }, - getModelFile : function(type, modelId, format) { - return this.getBaseURL() + '?reqCode=getModelFile' + "&type=" + type + "&modelId=" + modelId + "&format=" + format; - }, - getPdbURL : function() { - return this.getBaseURL() + '?reqCode=getPdbFiles'; - }, - getStvArray : function(value, error) { - value = Number(value); - error = Number(error); - return [ value - error, value, value + error ]; - }, - getPointArrayForDygraph : function(x, y, error) { - return [ x, BUI.getStvArray(y, error) ]; - }, - createDIV : function(text, width, className, backgroundColor) { - var nameContainer = document.createElement("div"); - var nameSpan = document.createElement("span"); - if (className != null) { - nameSpan.setAttribute("class", className); - } - if (backgroundColor != null) { - nameSpan.setAttribute("style", "float:left;width:" + width + "px;height:18px;background-color:" + backgroundColor); - } else { - nameSpan.setAttribute("style", "float:left;width:" + width + "px;height:18px;"); } - nameSpan.appendChild(document.createTextNode(text)); - nameContainer.appendChild(nameSpan); - return nameContainer; - }, + } ]; +}; - createFormLabel : function(labelText, text, labelWidth, textWidth, backgroundColor) { - var div = document.createElement("div"); +ResultsAssemblyGrid.prototype.getLegendPanel = function() { + return { + html : '
' + BUI.getRectangleColorDIV(this.validColor, 10, 10) + + 'Good quality measurements' + + BUI.getRectangleColorDIV(this.warningColor, 10, 10) + + 'Probably valid with manual processing' + + BUI.getRectangleColorDIV(this.notValidColor, 10, 10) + + 'More measurements need to be done
' + }; +}; +/** Returns the grid **/ +ResultsAssemblyGrid.prototype.getPanel = function(macromolecules) { + var _this = this; - div.appendChild(BUI.createDIV(labelText, labelWidth, "bLabel", backgroundColor)); - div.appendChild(BUI.createDIV(text, textWidth, "btext", backgroundColor)); - return div.innerHTML; - }, + this.store = Ext.create('Ext.data.Store', { + fields : [ + 'macromoleculeId', 'macromoleculeAcronym', 'measurementCount', 'subtractionCount', 'averageCount', 'timeStart', 'concentrationArray', + 'bufferConditions', 'conditions' ], + data : this._prepareData(macromolecules) + }); - createTextArea : function(labelText, text, labelWidth, rows, cols) { - var div = document.createElement("div"); - div.appendChild(BUI.createDIV(labelText, labelWidth, "bLabel")); - var textArea = document.createElement("textarea"); - textArea.setAttribute("rows", rows); - textArea.setAttribute("cols", cols); - textArea.appendChild(document.createTextNode(text)); - div.appendChild(textArea); - return div.innerHTML; - }, + this.store.sort('macromoleculeAcronym'); - showBetaWarning : function() { - alert("ISPyB for Biosaxs version Beta has not this functionality enabled"); - }, + this.grid = Ext.create('Ext.grid.Panel', { + id : this.id, + title : 'Macromolecules', + store : this.store, + tbar : this._getTbar(), + bbar : [ this.getLegendPanel() ], + width : this.width, + height : this.height, + maxHeight : this.maxHeight, + sortableColumns : true, + columns : [ + { + text : '', + dataIndex : 'macromoleculeId', + width : 20, + hidden : false, + renderer : function(val, y, sample) { + return BUI.getRectangleColorDIV(BIOSAXS.proposal.macromoleculeColors[val], 10, 10); + } + }, + { + text : 'Macromolecule', + dataIndex : 'macromoleculeAcronym', + width : 200 + }, + { + text : 'Buffer Conditions', + dataIndex : 'conditions', + flex : 1, + renderer : function(val, style, record) { + return _this.getConditionHTMLTable(val, style, record); + } + }, + { + header : 'Average', + dataIndex : 'percentageCollected', + name : 'percentageCollected', + type : 'string', + hidden : true, + renderer : function(val, y, sample) { + return "
" + + BUI.getProgessBar((sample.raw.averageCount / sample.raw.measurementCount) * 100, sample.raw.averageCount + "/" + + sample.raw.measurementCount) + "
"; + }, + width : 100, + sorter : false + }, + { + header : 'Subtractions', + dataIndex : 'percentageCollected', + name : 'percentageCollected', + type : 'string', + hidden : true, + renderer : function(val, y, sample) { + return "
"+ BUI.getProgessBar((sample.raw.subtractionCount / sample.raw.measurementCount) * 100, sample.raw.subtractionCount + "/" + + sample.raw.measurementCount) + "
"; + }, + width : 100 + }, { + header : 'Date', + dataIndex : 'timeStart', + name : 'timeStart', + type : 'string', + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + if (record.raw.timeStart != null) { + return moment(record.raw.timeStart).format("MMM Do YY"); + } + } + }, { + header : 'Download', + dataIndex : 'percentageCollected', + name : 'percentageCollected', + type : 'string', + renderer : function(val, y, sample) { + return BUI.getZipHTMLByMacromoleculeId(sample.raw.macromoleculeId); + }, + width : 100 + }, - formatValuesErrorUnitsScientificFormat : function(val, error, unit, args) { - var fontSize = 14; - var decimals = 2; - var errorFontSize = 10; - /** line break **/ - var lineBreak = true; - if (args != null) { - if (args.fontSize != null) { - fontSize = args.fontSize; - } - if (args.decimals != null) { - decimals = args.decimals; - } - if (args.errorFontSize != null) { - errorFontSize = args.errorFontSize; - } - if (args.lineBreak != null) { - lineBreak = args.lineBreak; + { + id : 'btnResultVisible', + width : 85, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + return BUI.getGreenButton('GO'); + } + } ], + viewConfig : { + stripeRows : true, + listeners : { + afterrender : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + }, + celldblclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + _this.edit(record.data.macromoleculeId); + }, + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + if (grid.getGridColumns()[cellIndex].getId() == 'buttonEditMacromolecule') { + _this.edit(record.data.macromoleculeId); + } + if (grid.getGridColumns()[cellIndex].getId() == 'buttonRemoveMacromolecule') { + BUI.showBetaWarning(); + } + if (grid.getGridColumns()[cellIndex].getId() == 'btnResultVisible') { + window.location = BUI.getMacromoleculeResultsURL(record.data.macromoleculeId); + } + } } - } + }); - if (val == "") { - return ""; - } - if (error == null) { - return "" + Number(val).toFixed(decimals) + ""; - } - var html = "" + Number(val).toFixed(decimals) + " " + unit + ""; - if (lineBreak) { - html = html + "
"; - } - return html + " ± " + Number(Number(error).toFixed(3)).toExponential() - + ""; - }, + /** Adding the tbar **/ + if (this.tbar) { + this.grid.addDocked({ + xtype : 'toolbar', + items : this.getTbar() + }); + } + return this.grid; +}; - formatValuesErrorUnits : function(val, error, unit, args) { - var fontSize = 16; - var decimals = 2; - var errorFontSize = 10; - /** line break **/ - var lineBreak = true; - if (args != null) { - if (args.fontSize != null) { - fontSize = args.fontSize; - } - if (args.decimals != null) { - decimals = args.decimals; - } - if (args.errorFontSize != null) { - errorFontSize = args.errorFontSize; - } - if (args.lineBreak != null) { - lineBreak = args.lineBreak; - } +ResultsAssemblyGrid.prototype.input = function(targetId) { + return { + data : DATADOC.getData_3367(), + proposal : DATADOC.getProposal_3367() + }; +}; - } +ResultsAssemblyGrid.prototype.test = function(targetId) { + var grid = new ResultsAssemblyGrid({ + height : 600, + searchBar : false, + tbar : false, + btnResultVisible : true, + width : 1000 + }); + BIOSAXS.proposal = new Proposal(grid.input().proposal); + var panel = grid.getPanel(grid.input().data); + panel.render(targetId); - if (val == "") { - return ""; +}; + + +function RigidModelGrid(args) { + this.height = null; + this.width = null; + this.id = BUI.id(); + + if (args != null) { + if (args.height != null) { + this.height = args.height; + + if (args.width != null) { + this.width = args.width; + } + } + } + + this.onSelected = new Event(this); +} + + +RigidModelGrid.prototype.refresh = function(subtractions) { + var data = []; + if (subtractions != null){ + if (subtractions.length > 0){ + for (j in subtractions){ + var subtraction = subtractions[j]; + if (subtraction.rigidBodyModeling3VOs != null){ + for (i in subtraction.rigidBodyModeling3VOs){ + data.push(subtraction.rigidBodyModeling3VOs[i]); + } + } + } + } + } + this.store.loadData(data); +}; + +RigidModelGrid.prototype.getPanel = function() { + var _this = this; + this.store = Ext.create('Ext.data.Store', { + fields : [ 'symmetry', 'subtractionId', 'subUnitConfigFilePath', 'rigidBodyModelingId', 'rigidBodyModelFilePath', 'logFilePath', 'fitFilePath', 'curveConfigFilePath', + 'crossCorrConfigFilePath', 'contactDescriptionFilePath' ], + data : [] + }); + + this.store.sort([ { + property : 'name', + direction : 'ASC' + } ]); + + this.panel = Ext.create('Ext.grid.Panel', { + store : this.store, + width : this.width, + height : this.height, + margin : 10, + deferredRender : false, + columns : [ { + text : 'RBM', + dataIndex : 'rigidBodyModelFilePath', + hidden : false, + flex : 1, + renderer : function(val){ + return BUI.getFileName(val); + } + }, { + text : 'Sub Unit Conf.', + dataIndex : 'subUnitConfigFilePath', + hidden : true, + flex : 1, + renderer : function(val){ + return BUI.getFileName(val); + } + }, { + text : 'Log', + dataIndex : 'logFilePath', + hidden : true, + flex : 1, + renderer : function(val){ + return BUI.getFileName(val); + } + }, { + text : 'Fit', + dataIndex : 'fitFilePath', + hidden : false, + flex : 1, + renderer : function(val){ + return BUI.getFileName(val); + } + }, { + text : 'Curve Conf.', + dataIndex : 'curveConfigFilePath', + hidden : false, + flex : 1, + renderer : function(val){ + return BUI.getFileName(val); + } + }, { + text : 'Cross Corr.', + dataIndex : 'crossCorrConfigFilePath', + hidden : false, + flex : 1, + renderer : function(val){ + return BUI.getFileName(val); + } + }, { + text : 'Contact Desc.', + dataIndex : 'contactDescriptionFilePath', + hidden : true, + flex : 1, + renderer : function(val){ + return BUI.getFileName(val); + } + } ], + + viewConfig : { + enableTextSelection : true, + preserveScrollOnRefresh : true + }, + listeners : { + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + + }, + afterrender : function() { + } + } + }); + return this.panel; +}; + + +/** + * shows shipments + * + * @height + * @width + * @minHeight + * @btnEditVisible + */ +function ShipmentGrid(args) { + this.id = BUI.id(); + this.height = 100; + this.width = null; + this.minHeight = null; + this.btnEditVisible = true; + + if (args != null) { + if (args.height != null) { + this.height = args.height; } - if (error == null) { - return "" + Number(val).toFixed(decimals) + ""; + if (args.width != null) { + this.width = args.width; } - var html = "" + Number(val).toFixed(decimals) + " " + unit + ""; - if (lineBreak) { - html = html + "
"; + if (args.minHeight != null) { + this.minHeight = args.minHeight; } - return html + " ± " + Number(Number(error).toFixed(8)).toExponential() - + ""; - }, - - formatValuesUnits : function(val, unit, args) { - var fontSize = 12; - var decimals = 2; - var unitsFontSize = 10; - if (args != null) { - if (args.fontSize != null) { - fontSize = args.fontSize; - } - if (args.decimals != null) { - decimals = args.decimals; - } - if (args.unitsFontSize != null) { - unitsFontSize = args.unitsFontSize; - } - + if (args.btnEditVisible != null) { + this.btnEditVisible = args.btnEditVisible; } + } +} - if (val === "") { - return ""; - } - if (unit == null) { - return "" + Number(val).toFixed(decimals) + ""; - } - return "" + Number(val).toFixed(decimals) + " " + unit + ""; - }, +ShipmentGrid.prototype._getColumns = function() { + var _this = this; + var columns = [ + { + text : 'Name', + dataIndex : 'shippingName', + flex : 1 + }, + { + header : 'Type', + dataIndex : 'shippingType', + flex : 1, + hidden : true, + renderer : function(val, comp, record) { + if (val != null) { + return val.toUpperCase(); + } - getGreenButton : function(text, args) { - var width = 70; - var height = 20; - if (args != null) { - if (args.width != null) { - width = args.width; } - if (args.height != null) { - height = args.height; + }, + { + header : 'Status', + type : 'string', + flex : 1, + hidden : false, + renderer : function(comp, val, record) { + if (record.raw.shippingStatus != null) { + if (new String(record.raw.shippingStatus).toUpperCase() == 'OPENED') { + return "" + new String(record.raw.shippingStatus).toUpperCase() + ""; + } + return "" + new String(record.raw.shippingStatus).toUpperCase() + ""; + } + } + }, + { + text : 'Cases', + flex : 1, + hidden : false, + renderer : function(comp, val, record) { + var shipment = BIOSAXS.proposal.getShipmentById(record.data.shippingId); + var container = ""; + if (shipment.dewarVOs.length > 0) { + container = container + ""; + } else { + return "Empty"; + } + return container + "
" + shipment.dewarVOs.length + "x
"; } - } - - return ''; - }, -// getBlueButton : function(text, args) { -// var width = 70; -// var height = 20; -// if (args != null) { -// if (args.width != null) { -// width = args.width; -// } -// if (args.height != null) { -// height = args.height; -// } -// } -// -// return ''; -// }, + }, { + header : 'Comments', + dataIndex : 'comments', + flex : 1, + hidden : false + }, { + header : 'Creation Date', + dataIndex : 'creationDate', + hidden : true + } ]; - getBlueButton : function(text, args) { - var width = 70; - var height = 20; - var href = null; - if (args != null) { - if (args.width != null) { - width = args.width; - } - if (args.height != null) { - height = args.height; + if (this.btnEditVisible) { + columns.push({ + id : _this.id + 'buttonEdit', + text : '', + hidden : !_this.btnEditVisible, + width : 100, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + return BUI.getGreenButton('EDIT'); } - if (args.href != null) { - href = args.href; + }); + } + + columns.push({ + id : _this.id + 'buttonRemove', + text : '', + width : 100, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + var shipment = BIOSAXS.proposal.getShipmentById(record.data.shippingId); + if (shipment.dewarVOs.length == 0) { + return BUI.getRedButton('REMOVE'); } + } - if (href != null) { - return ''; - } else { - return ''; -// return ''; - } - }, - - getSubmitGreenButton : function(text) { - return ''; - }, + }); - getRedButton : function(text) { - return ''; + return columns; +}; - }, - getRectangleColorDIV : function(color, height, width) { - return '
'; - }, +ShipmentGrid.prototype._getTopButtons = function() { + var _this = this; + /** Actions buttons **/ + var actions = []; + actions.push(Ext.create('Ext.Action', { + icon : '../images/add.png', + text : 'Add Shipment', + handler : function(widget, event) { + //window.location = BUI.getCreateShipmentURL(); + var _this = this; - openBufferWindow : function(bufferId) { - var window = new BufferWindow(); - window.draw(tabs.experiment.getBufferById(bufferId), tabs.experiment); - }, + var shipmentForm = new ShipmentForm({ + creationMode : true, + showTitle : false + }); + shipmentForm.onSaved.attach(function(sender, shipment) { + _this.showShipmentTabs(shipment, targetId); + }); + + var window = Ext.create('Ext.window.Window', { + title : 'New Shipment', + height : 600, + width : 800, + layout : 'fit', + items : [ shipmentForm.getPanel() ] + }).show(); - /** Render for safety levels on grids **/ - safetyRenderer : function(val, y, specimen) { - var color = val; - if (val == "YELLOW") { - color = "#E9AB17"; } - return '' + val + ''; - }, + })); + return actions; +}; - getSampleColor : function() { - return '#CB181D'; - }, +ShipmentGrid.prototype.refresh = function(shippings) { + this.features = shippings; + this.store.loadData(this._prepareData(), false); +}; - getLightSampleColor : function() { - return '#FCBBA1'; - }, +ShipmentGrid.prototype._prepareData = function() { + var data = []; + for ( var i = 0; i < this.features.length; i++) { + data.push(this.features[i]); + } + return data; +}; - getBufferColor : function() { - return '#6A51A3'; - }, - getLightBufferColor : function() { - return '#BCBDDC'; - }, +ShipmentGrid.prototype.getPanel = function(shipments) { + this.features = shipments; + return this._renderGrid(); +}; - formatConcentration : function(val) { - if (val != null) { - return "" + Number(val).toFixed(2) + " mg/ml "; - } - return val; - }, +ShipmentGrid.prototype.edit = function(shippingId) { + window.location = BUI.getShippingURL(shippingId); +}; - formatVolume : function(sample, volume) { - if (Number(sample.data.volumeToLoad) > Number(sample.data.volume)) { - return "" + volume + " �l"; - } - if (Number(sample.data.volumeToLoad) == Number(sample.data.volume)) { - return "" + volume + " �l"; - } - return "" + volume + " �l"; - }, +ShipmentGrid.prototype._getStoreFields = function(data) { + var _this = this; + return [ { + name : 'shippingId' + }, { + name : 'shippingName' + }, { + name : 'shippingStatus' + }, { + name : 'shippingType' + }, { + name : 'creationDate' + }, { + name : 'comments' + } ]; +}; - getProposal : function() { - return new Proposal(); - }, +ShipmentGrid.prototype._renderGrid = function() { + var _this = this; - getSampleNameRenderer : function(val, y, record) { - var sample = record.data; - if (record.raw.macromolecule3VO == null) { - return '' + sample.code + ''; - } else { - return '' + sample.code + ''; - } - }, + /** Store **/ + var data = this._prepareData(); + this.store = Ext.create('Ext.data.Store', { + fields : this._getStoreFields(data), + autoload : true, + data : data + }); - getSafetyLevels : function() { - var safetyLevels = new Array(); - safetyLevels.push({ - safetyLevelId : "", - name : "UNKNOWN" - }); - safetyLevels.push({ - safetyLevelId : 1, - name : "GREEN" - }); - safetyLevels.push({ - safetyLevelId : 2, - name : "YELLOW" - }); - safetyLevels.push({ - safetyLevelId : 3, - name : "RED" - }); - return safetyLevels; - }, + this.store.loadData(data, false); + + this.grid = Ext.create('Ext.grid.Panel', { + title : "Shipping", + icon : '/ispyb/images/plane.gif', + width : this.width, + minWidth : this.minWidth, + height : this.height, + store : this.store, + columns : this._getColumns(), + viewConfig : { + stripeRows : true, + listeners : { + itemdblclick : function(dataview, record, item, e) { + _this.edit(record.raw.shippingId); + }, + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEdit') { + _this.edit(record.data.shippingId); + } - getErrorColor : function() { - return '#F6CED8'; - }, - getWarningColor : function() { - return '#F5DA81'; - }, - getValidColor : function() { - return '#E0F8E0'; - }, - getSamplePlateLetters : function() { - return [ "A", "B", "C", "D", "E", "F", "G", "H" ]; - }, - getSamplePositionHTML : function(sample, experiment) { - var plate = ""; - var row = ""; - var column = ""; - var rows = this.getSamplePlateLetters(); - if (sample.sampleplateposition3VO != null) { - var samplePlate = experiment.getSamplePlateById(sample.sampleplateposition3VO.samplePlateId); - if (samplePlate != null) { - plate = (samplePlate.slotPositionColumn); - row = (sample.sampleplateposition3VO.rowNumber); - column = (sample.sampleplateposition3VO.columnNumber); - // var html = "Plate: " + "" + plate + ""; - // html = html + ", Row: " + "" + rows[row - 1] + ""; - // html = html + ", Column: " + "" + column + ""; - var html = "Plate: " + plate - + "-" + rows[row - 1] + "" + column + ""; - return html; + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemove') { + var shipment = BIOSAXS.proposal.getShipmentById(record.data.shippingId); + if (shipment.dewarVOs.length == 0) { + + var adapter = new BiosaxsDataAdapter(); + _this.grid.setLoading("ISPyB: Removing shipment"); + adapter.onSuccess.attach(function(sender) { + BIOSAXS.proposal.onInitialized.attach(function(sender) { + _this.refresh(BIOSAXS.proposal.getShipments()); + _this.grid.setLoading(false); + }); + BIOSAXS.proposal.init(); + }); + + adapter.onError.attach(function(sender) { + alert("Error"); + _this.grid.setLoading(false); + }); + adapter.removeShipment(record.data.shippingId); + } + } + } } + }, + selModel : { + mode : 'SINGLE' } - return ""; - }, + }); - getSafetyLabelName : function(safetyLevelId) { - var safetyLevels = BUI.getSafetyLevels(); - for ( var i = 0; i < safetyLevels.length; i++) { - if (safetyLevels[i].safetyLevelId == safetyLevelId) { - return safetyLevels[i].name; + var actions = _this._getTopButtons(); + this.grid.addDocked({ + xtype : 'toolbar', + items : actions + }); + + this.grid.getSelectionModel().on({ + selectionchange : function(sm, selections) { + if (selections.length) { + for ( var i = 0; i < actions.length; i++) { + if (actions[i].enable) { + actions[i].enable(); + } + } + } else { + for ( var i = 0; i < actions.length; i++) { + if (actions[i].alwaysEnabled == false) { + if (actions[i].disable) { + actions[i].disable(); + } + } + } } } - return "UNKNOWN"; - }, - /** generate random id **/ - id : function() { - var text = ""; - var possible = "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789"; - - for ( var i = 0; i < 5; i++) - text += possible.charAt(Math.floor(Math.random() * possible.length)); + }); + return this.grid; +}; - return text; - }, - showWarning : function(message) { - Ext.Msg.show({ - title : 'Warning', - msg : message, - icon : Ext.Msg.WARNING, - animEl : 'elId' - }); - }, - showError : function(message) { - Ext.Msg.show({ - title : 'Warning', - msg : message, - icon : Ext.Msg.ERROR, - animEl : 'elId' - }); - }, - getTipHTML : function(message) { - //return "
Tip
" - // + message + "
"; - return "
Tip
" - + message + "
"; - }, +ShipmentGrid.prototype.input = function() { + return { + proposal : new MeasurementGrid().input().proposal, + shippings : DATADOC.getShippings_10() + }; +}; - getWarningHTML : function(message) { - return "
Warning
" - + message + "
"; - }, +ShipmentGrid.prototype.test = function(targetId) { + var shipmentGrid = new ShipmentGrid({ + minHeight : 300, + height : 440 + }); + BIOSAXS.proposal = new Proposal(shipmentGrid.input().proposal); + var panel = shipmentGrid.getPanel(targetId); + panel.render(targetId); + shipmentGrid.refresh(shipmentGrid.input().shippings); +}; + +function SpecimenGrid(args) { + this.id = BUI.id(); + this.height = 500; + this.unitsFontSize = 9; + this.editEnabled = false; + this.isPositionColumnHidden = false; + this.removeBtnEnabled = false; - getErrorHTML : function(message) { - return "
Error
" - + message + "
"; - }, + this.selectionMode = "MULTI"; + this.updateRowEnabled = false; + this.grouped = true; + this.width = 900; + this.title = 'Specimens'; + + this.margin = "0 0 0 0"; +// this.experimentColorBased = false; - getProgessBar : function(percentage, text) { - /** percentage 100% green **/ - var color = "#0a0"; + if (args != null) { + if (args.height != null) { + this.height = args.height; + } - color = "#99CC00"; - if (percentage > 100) { - color = "yellow"; - percentage = 100; + if (args.showTitle == false) { + this.title = null; } - if (isNaN(percentage)) { - color = "white"; - percentage = 0; + + if (args.margin == false) { + this.margin = args.margin; } - var defaultText = percentage + "%"; - if (text != null) { - defaultText = text; + if (args.grouped == false) { + this.grouped = null; } - return "
" + defaultText + "
"; - }, - getFileName : function(filePath){ - if (filePath != null){ - return filePath.split("/")[filePath.split("/").length - 1] + if (args.width != null) { + this.width = args.width; } - return ""; - } -}; -Ext.ux.form.RequiredCombo = Ext.extend(Ext.form.ComboBox, { - config : { - cls : 'custom-field-text-required' - }, - initComponent : function() { - Ext.ux.form.RequiredCombo.superclass.initComponent.apply(this, arguments); - }, - checkChange : function() { - if ((this.getValue() == null) || String(this.getValue()).length == 0) { - this.addCls('custom-field-text-required'); - } else { - this.removeCls('custom-field-text-required'); + if (args.editEnabled != null) { + this.editEnabled = args.editEnabled; + } + if (args.removeBtnEnabled != null) { + this.removeBtnEnabled = args.removeBtnEnabled; + } + if (args.isPositionColumnHidden != null) { + this.isPositionColumnHidden = args.isPositionColumnHidden; + } + if (args.selectionMode != null) { + this.selectionMode = args.selectionMode; + } + if (args.updateRowEnabled != null) { + this.updateRowEnabled = args.updateRowEnabled; } + } -}); + this.onClick = new Event(this); + this.onSelected = new Event(this); + this.onRemoved = new Event(this); + this.onSpecimenChanged = new Event(); +} -Ext.define('Ext.form.field.RequiredNumber', { - extend : 'Ext.form.field.Number', - alias : 'widget.requirednumberfield', - alternateClassName : [ 'Ext.form.RequiredNumberField', 'Ext.form.RequiredNumber' ], - config : { - cls : 'custom-field-text-required' - }, +SpecimenGrid.prototype._prepareData = function(experiment) { + var data = []; - initComponent : function() { - var me = this; - me.callParent(); - me.setMinValue(me.minValue); - me.setMaxValue(me.maxValue); - }, + var samples = experiment.getSamples(); + for ( var i = 0; i < samples.length; i++) { + var sample = samples[i]; + if (sample.macromolecule3VO != null) { + sample.macromolecule = sample.macromolecule3VO.acronym; + sample.exposureTemperature = []; + sample.macromoleculeId = sample.macromolecule3VO.macromoleculeId; + } - onChange : function() { - if ((this.getValue() == null) || String(this.getValue()).length == 0) { - this.addCls('custom-field-text-required'); + if (sample.sampleplateposition3VO != null) { + if (sample.sampleplateposition3VO.samplePlateId != null) { + sample.samplePlateId = sample.sampleplateposition3VO.samplePlateId; + sample.rowNumber = sample.sampleplateposition3VO.rowNumber; + sample.columnNumber = sample.sampleplateposition3VO.columnNumber; + if (experiment.getSamplePlateById(sample.sampleplateposition3VO.samplePlateId).plategroup3VO != null) { + sample.plateGroupName = experiment.getSamplePlateById(sample.sampleplateposition3VO.samplePlateId).plategroup3VO.name; + sample.samplePlateName = experiment.getSamplePlateById(sample.sampleplateposition3VO.samplePlateId).name + " [" + sample.plateGroupName + "]"; + sample.slotPositionColumn = experiment.getSamplePlateById(sample.sampleplateposition3VO.samplePlateId).slotPositionColumn; + } + } } else { - this.removeCls('custom-field-text-required'); + sample.samplePlateName = "Unallocated Specimens"; } - this.toggleSpinners(); - this.callParent(arguments); - } -}); -Ext.define('Ext.form.field.RequiredText', { - extend : 'Ext.form.field.Text', - alias : 'widget.requiredtext', - requires : [ 'Ext.form.field.VTypes', 'Ext.layout.component.field.Text' ], - alternateClassName : [ 'Ext.form.RequiredTextField', 'Ext.form.RequiredText' ], - config : { - cls : 'custom-field-text-required' - }, - initComponent : function() { - var me = this; - if (me.allowOnlyWhitespace === false) { - me.allowBlank = false; + /** For grouping, because sencha has not option for multiple grouping I add a field to your store with a convert function that concatenates these two fields and then group by that field.**/ + sample.groupIndex = sample.bufferId + sample.macromoleculeId; + var macromolecule = BIOSAXS.proposal.getMacromoleculeById(sample.macromoleculeId); + + sample.acronym = "Buffers"; + if (macromolecule != null) { + sample.acronym = BIOSAXS.proposal.getMacromoleculeById(sample.macromoleculeId).acronym; } - me.callParent(); - me.addEvents( - /** - * @event autosize - * Fires when the **{@link #autoSize}** function is triggered and the field is resized according to the - * {@link #grow}/{@link #growMin}/{@link #growMax} configs as a result. This event provides a hook for the - * developer to apply additional logic at runtime to resize the field if needed. - * @param {Ext.form.field.Text} this This text field - * @param {Number} width The new field width - */ - 'autosize', - /** - * @event keydown - * Keydown input field event. This event only fires if **{@link #enableKeyEvents}** is set to true. - * @param {Ext.form.field.Text} this This text field - * @param {Ext.EventObject} e - */ - 'keydown', - /** - * @event keyup - * Keyup input field event. This event only fires if **{@link #enableKeyEvents}** is set to true. - * @param {Ext.form.field.Text} this This text field - * @param {Ext.EventObject} e - */ - 'keyup', - /** - * @event keypress - * Keypress input field event. This event only fires if **{@link #enableKeyEvents}** is set to true. - * @param {Ext.form.field.Text} this This text field - * @param {Ext.EventObject} e - */ - 'keypress'); - me.addStateEvents('change'); - me.setGrowSizePolicy(); - }, - checkChange : function() { - if ((this.getValue() == null) || String(this.getValue()).length == 0) { - this.addCls('custom-field-text-required'); - } else { - this.removeCls('custom-field-text-required'); + sample.buffer = experiment.getBufferById(sample.bufferId); + + sample.volumeToLoad = experiment.getVolumeToLoadBySampleId(sample.sampleId); + data.push(sample); + } + return data; +}; + +SpecimenGrid.prototype.deselectAll = function() { + this.grid.getSelectionModel().deselectAll(); +}; + +SpecimenGrid.prototype.selectById = function(specimenId) { + this.grid.getSelectionModel().deselectAll(); + for ( var i = 0; i < this.grid.getStore().data.items.length; i++) { + var item = this.grid.getStore().data.items[i].raw; + if (item.specimenId == specimenId) { + this.grid.getSelectionModel().select(i); } } -}); +}; -var BIOSAXS_COMBOMANAGER = { +SpecimenGrid.prototype.getStore = function() { + return this.store; +}; - getComboMacromoleculeByMacromolecules : function(macromolecules, args) { - var labelWidth = 150; - var margin = "0 0 5 0"; - var width = 300; +SpecimenGrid.prototype.getPlugins = function() { + var _this = this; - if (args != null) { - if (args.labelWidth != null) { - labelWidth = args.labelWidth; - } - if (args.margin != null) { - margin = args.margin; - } - if (args.width != null) { - width = args.width; - } - } + var plugins = []; - var store = Ext.create('Ext.data.Store', { - fields : [ 'macromoleculeId', 'acronym' ], - data : macromolecules, - sorters : [ 'acronym' ] - }); + if (this.updateRowEnabled) { + plugins.push(Ext.create('Ext.grid.plugin.RowEditing', { + clicksToEdit : 1, + listeners : { + validateedit : function(grid, e) { + var measurements = []; - return Ext.create('Ext.form.ComboBox', { - fieldLabel : 'Macromolecules', - labelWidth : labelWidth, - width : width, - margin : margin, - store : store, - editable: false, - queryMode : 'local', - displayField : 'acronym', - valueField : 'macromoleculeId' - }); - }, - getComboBuffers : function(buffers, args) { - var labelWidth = 150; - var margin = "0 0 5 0"; - var width = 300; - var fieldLabel = 'Buffer'; + if (e.newValues.bufferId != e.record.raw.bufferId) { + /** If buffer has changed we have to change all the specimens sharing same datacollection **/ + var dataCollections = []; + if (e.record.raw.macromoleculeId == null) { + dataCollections = dataCollections.concat(_this.experiment.getDataCollectionsBySpecimenId(e.record.raw.specimenId)); + } else { + var sampleDataCollections = _this.experiment.getDataCollectionsBySpecimenId(e.record.raw.specimenId); + for ( var i = 0; i < sampleDataCollections.length; i++) { + var sampleDataCollection = sampleDataCollections[i]; + if (sampleDataCollection != null) { + for ( var j = 0; j < sampleDataCollection.measurementtodatacollection3VOs.length; j++) { + var measurementTODc = sampleDataCollection.measurementtodatacollection3VOs[j]; + if (measurementTODc.dataCollectionOrder == 1) { + dataCollections = dataCollections.concat(_this.experiment.getDataCollectionsBySpecimenId(_this.experiment + .getMeasurementById(measurementTODc.measurementId).specimenId)); + } + } + } + } + } + var i = null; + for ( i = 0; i < dataCollections.length; i++) { + var dataCollection = dataCollections[i]; + var specimens = _this.experiment.getSpecimenByDataCollectionId(dataCollection.dataCollectionId); + measurements = measurements.concat(specimens); + } - if (args != null) { - if (args.labelWidth != null) { - labelWidth = args.labelWidth; - } - if (args.margin != null) { - margin = args.margin; - } - if (args.width != null) { - width = args.width; - } - if (args.noLabel != null) { - fieldLabel = null; - } - } + for ( i = 0; i < measurements.length; i++) { + var measurement = measurements[i]; + var specimen = _this.experiment.getSpecimenById(measurement.specimenId); + specimen.bufferId = e.newValues.bufferId; + new BiosaxsDataAdapter().saveSpecimen(specimen, _this.experiment); + } + } - var store = Ext.create('Ext.data.Store', { - fields : [ 'bufferId', 'acronym' ], - data : buffers, - sorters : [ 'acronym' ] - }); + /** Setting values **/ + e.record.raw.concentration = e.newValues.concentration; + e.record.raw.volume = e.newValues.volume; - return Ext.create('Ext.form.ComboBox', { - fieldLabel : fieldLabel, - labelWidth : labelWidth, - width : width, - margin : margin, - editable: false, - store : store, - queryMode : 'local', - displayField : 'acronym', - valueField : 'bufferId' - }); - }, - getComboSessions : function(sessions, args) { - var labelWidth = 150; - var margin = "0 0 5 0"; - var width = 300; + /** Position **/ + if (e.record.raw.sampleplateposition3VO != null) { + var samplePlate = _this.experiment.getSamplePlateBySlotPositionColumn(e.newValues.slotPositionColumn); + if (samplePlate != null) { + e.record.raw.sampleplateposition3VO = { + columnNumber : e.newValues.columnNumber, + rowNumber : e.newValues.rowNumber, + samplePlateId : samplePlate.samplePlateId + }; + } + } else { + if (e.newValues.slotPositionColumn != null) { + var samplePlate = _this.experiment.getSamplePlateBySlotPositionColumn(e.newValues.slotPositionColumn); + if (samplePlate != null) { + e.record.raw.sampleplateposition3VO = { + columnNumber : e.newValues.columnNumber, + rowNumber : e.newValues.rowNumber, + samplePlateId : samplePlate.samplePlateId + }; + } + } + } - if (args != null) { - if (args.labelWidth != null) { - labelWidth = args.labelWidth; - } - if (args.margin != null) { - margin = args.margin; - } - if (args.width != null) { - width = args.width; + var macromoleculeId = e.record.data.macromoleculeId; + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, specimen) { + /** Because macromolecule3VO is fecthed LAZY **/ + if (macromoleculeId != null) { + specimen.macromolecule3VO = BIOSAXS.proposal.getMacromoleculeById(macromoleculeId); + } + _this.onSpecimenChanged.notify(specimen); + _this.grid.setLoading(false); + }); + adapter.onError.attach(function() { + alert("Error"); + _this.grid.setLoading(false); + }); + _this.grid.setLoading(); + adapter.saveSpecimen(e.record.raw, _this.experiment); + } } - } - - for ( var i = 0; i < sessions.length; i++) { - sessions[i]["startDateFormatted"] = moment(sessions[i].startDate).format("MMM Do YY"); - sessions[i]["sorter"] = moment(sessions[i].startDate).format("YYYYMMDD"); - } + })); + } + return plugins; +}; - var store = Ext.create('Ext.data.Store', { - fields : [ 'sessionId', 'startDateFormatted', 'beamlineName', 'startDate', 'endDate', 'beamlineOperator' ], - data : sessions, - sorters : [ 'sorter' ] +SpecimenGrid.prototype._getRowCombo = function() { + var data = []; + for ( var i = 1; i <= 8; i++) { + data.push({ + rowNumber : i, + name : BUI.getSamplePlateLetters()[i - 1] }); + } - return Ext.create('Ext.form.ComboBox', { - fieldLabel : 'Sessions', - labelWidth : labelWidth, - width : width, - margin : margin, - store : store, - queryMode : 'local', - // displayField : 'startDate', - valueField : 'sessionId', - // Template for the dropdown menu. - // Note the use of "x-boundlist-item" class, - // this is required to make the items selectable. - tpl : Ext.create('Ext.XTemplate', '', - '
{startDateFormatted} {beamlineName}
', ''), - // template for the content inside text field - displayTpl : Ext.create('Ext.XTemplate', '', '{startDateFormatted}', '') + var positionsStore = Ext.create('Ext.data.Store', { + fields : [ 'rowNumber', 'name' ], + data : data + }); - }); - } + return Ext.create('Ext.form.ComboBox', { + store : positionsStore, + queryMode : 'local', + displayField : 'name', + valueField : 'rowNumber' + }); }; - - function GenericWindow(args){ - this.title = "title"; - this.width = 700; - this.height = 500; - this.id = BUI.id(); - - this.close = false; - this.draggable = true; - this.modal = true; - - if (args != null){ - if (args.actions != null){ - this.actions = args.actions; - } - if (args.form != null){ - this.form = args.form; - } - if (args.width != null){ - this.width = args.width; - } - if (args.modal != null){ - this.modal = args.modal; - } - - if (args.height != null){ - this.height = args.height; - } - if (args.title != null){ - this.title = args.title; - } - if (args.form != null){ - this.form = args.form; - } - if (args.close != null){ - this.close = args.close; - } - if (args.draggable != null){ - this.draggable = args.draggable; - } - - } - /** Events **/ - this.onSaved = new Event(this); - }; - - -GenericWindow.prototype.getButtons = function() { - var _this = this; - - if (this.close){ - return [ { - text : 'Close', - handler : function() { - _this.panel.close(); - } - } ]; - } - else{ - return [ { - text : 'Save', - handler : function() { - _this.save(); - - } - }, { - text : 'Cancel', - handler : function() { - _this.panel.close(); - } - } ]; +SpecimenGrid.prototype._getColumnCombo = function() { + var data = []; + for ( var i = 1; i <= 12; i++) { + data.push({ + columnNumber : i + }); } -}; -GenericWindow.prototype.save = function (){ - alert("Method save of GenerciWindow class is abstract"); + var positionsStore = Ext.create('Ext.data.Store', { + fields : [ 'columnNumber' ], + data : data + }); + + return Ext.create('Ext.form.ComboBox', { + store : positionsStore, + queryMode : 'local', + displayField : 'columnNumber', + valueField : 'columnNumber' + }); }; -GenericWindow.prototype._postRender = function(data, experiment){ +SpecimenGrid.prototype._getSlotColumBombo = function() { + if (this.experiment){ + var length = this.experiment.getSamplePlates().length; + + var data = []; + for ( var i = 1; i <= length; i++) { + data.push({ + slotPositionColumn : i + }); + } + + var positionsStore = Ext.create('Ext.data.Store', { + fields : [ 'slotPositionColumn' ], + data : data + }); + return Ext.create('Ext.form.ComboBox', { + store : positionsStore, + queryMode : 'local', + displayField : 'slotPositionColumn', + valueField : 'slotPositionColumn' + }); + } }; - -GenericWindow.prototype.draw = function (data, experiment){ - this._render(data, experiment); +SpecimenGrid.prototype.getPanelByExperiment = function(experiment) { + this.experiment = experiment; + var data = this._prepareData(experiment); + return this.getPanel(data); }; -GenericWindow.prototype.refresh = function(data, experiment){ - this.data = data; - this.experiment = experiment; - this.form.refresh(data, experiment); +SpecimenGrid.prototype.refresh = function(experiment) { + this.experiment = experiment; + var data = this._prepareData(experiment); + this.store.loadData(data); }; -GenericWindow.prototype._render = function(data, experiment){ - this.data = data; - var _this = this; - if (this.panel == null){ - this.panel = Ext.create('Ext.Window', { - id : this.id, - title : this.title, - resizable : true, - constrain : true, - border : 1, - modal : this.modal, - frame : false, - draggable : this.draggable, - closable : true, - autoscroll : true, - layout : { type: 'vbox',align: 'stretch'}, - width : this.width, - height : this.form.height, - buttonAlign :'right', - buttons : this.getButtons(), - items : this.form.getPanel(data, experiment), - listeners: { - scope : this, - minimize : function(){ - this.panel.hide(); - }, - destroy : function(){ - delete this.panel; - } - } - }); - this.panel.setLoading(); - } - - this.panel.show(); - this._postRender(); -}; -function CalendarWidget(args) { - this.height = 740; +SpecimenGrid.prototype.getPanel = function() { + var _this = this; + this.store = Ext.create('Ext.data.Store', { + fields : [ + 'buffer', 'bufferId', 'code', 'macromolecule', 'acronym', 'macromoleculeId', 'concentration', 'volume', 'samplePlateId', + 'slotPositionColumn', 'rowNumber', 'columnNumber', 'groupIndex' ], + data : [], + groupField : 'acronym' + }); + this.store.sort([ { + property : 'concentration', + direction : 'ASC' + }, { + property : 'buffer', + direction : 'ASC' + } ]); - if (args != null) { - if (args.height != null) { - this.height = args.height; + var selModel = Ext.create('Ext.selection.RowModel', { + allowDeselect : true, + mode : this.selectionMode, + listeners : { + selectionchange : function(sm, selections) { + var selected = []; + for ( var i = 0; i < selections.length; i++) { + selected.push(selections[i].raw); + } + _this.onSelected.notify(selected); + } } + }); + + var features = []; + + if (this.grouped) { + features.push({ + ftype : 'grouping', + groupHeaderTpl : '{name}', + hideGroupedHeader : false, + startCollapsed : false, + id : 'myGroupedStore' + }); } - this.onClick = new Event(); -} + this.grid = Ext.create( + 'Ext.grid.Panel', + { + title : this.title, + height : this.height, + width : this.width, + selModel : selModel, + store : this.store, + features : features, + margin : this.margin, + plugins : this.getPlugins(), + columns : [ + { + text : '', + dataIndex : 'macromolecule', + width : 20, + renderer : function(val, y, sample) { + var macromoleculeId = null; + if (sample.raw.macromolecule3VO != null) { + macromoleculeId = sample.raw.macromolecule3VO.macromoleculeId; + } + else{ + macromoleculeId = sample.raw.macromoleculeId; + } + + if (macromoleculeId == null) return; + return BUI.getRectangleColorDIV(_this.experiment.macromoleculeColors[macromoleculeId], 10, 10); + } + }, + { + text : 'Macromolecule', + dataIndex : 'macromolecule', + width : 100 + }, + { + text : '', + dataIndex : 'buffer', + width : 20, + renderer : function(val, y, sample) { + var color = "black"; + if (sample.raw.bufferId != null) { + if (_this.experiment.getDataCollectionsBySpecimenId(sample.raw.specimenId)[0] != null){ + color = _this.experiment.getSpecimenColorByBufferId(_this.experiment.getMeasurementById(_this.experiment.getDataCollectionsBySpecimenId(sample.raw.specimenId)[0].measurementtodatacollection3VOs[0].measurementId).specimenId); + } + return BUI.getRectangleColorDIV(color, 10, 10); + } + } + }, { + text : 'Buffer', + dataIndex : 'bufferId', + width : 140, + renderer : function(val, y, sample) { + if (sample.raw.bufferId != null) { + return BIOSAXS.proposal.getBufferById(val).acronym; + } + }, + editor : BIOSAXS_COMBOMANAGER.getComboBuffers(BIOSAXS.proposal.getBuffers(), { + noLabel : true, + width : 300 + }) + }, { + text : 'Conc.', + dataIndex : 'concentration', + width : 100, + editor : { + allowBlank : false + }, + renderer : function(val, meta, sample) { + if (isNaN(val)) { + meta.tdCls = 'yellow-cell'; + return val; + } else { + if (val != 0) { + return BUI.formatValuesUnits(val, 'mg/ml', { + fontSize : 16, + decimals : 3, + unitsFontSize : this.unitsFontSize + }); + } else { + return; + } + } + } + }, { + text : 'Vol. Well', + dataIndex : 'volume', + width : 70, + editor : { + allowBlank : true + }, + renderer : function(val, y, sample) { + return BUI.formatValuesUnits(sample.data.volume, 'µl', { + fontSize : 12, + decimals : 2, + unitsFontSize : this.unitsFontSize + }); + } + }, { + text : 'Position', + hidden : true, + flex : 1, + renderer : function(val, y, sample) { + return BUI.getSamplePositionHTML(sample.raw, _this.experiment); + } + }, { + text : 'samplePlateId', + dataIndex : 'samplePlateId', + hidden : true + }, { + text : 'Plate', + hidden : this.isPositionColumnHidden, + dataIndex : 'slotPositionColumn', + editor : _this._getSlotColumBombo(), + flex : 1, + renderer : function(val, meta, sample) { + if ((val != null) & (val != "")) { + return val; + } else { + meta.tdCls = 'yellow-cell'; + } + } + }, { + text : 'Row', + hidden : this.isPositionColumnHidden, + dataIndex : 'rowNumber', + editor : this._getRowCombo(), + flex : 1, + renderer : function(val, meta, sample) { + if ((val != null) && (val != "")) { + return BUI.getSamplePlateLetters()[val - 1]; + } else { + meta.tdCls = 'yellow-cell'; + } + } + }, { + text : 'Well', + hidden : this.isPositionColumnHidden, + dataIndex : 'columnNumber', + editor : this._getColumnCombo(), + flex : 1, + renderer : function(val, meta, sample) { + if ((val != null) && (val != "")) { + return val; + } else { + meta.tdCls = 'yellow-cell'; + } + } + }, { + id : _this.id + 'buttonEditSample', + text : 'Edit', + width : 80, + sortable : false, + hidden : !_this.editEnabled, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + if (_this.editEnabled) { + return BUI.getGreenButton('EDIT'); + } + } + }, { + id : _this.id + 'buttonRemoveSample', + text : '', + hidden : !_this.removeBtnEnabled, + width : 100, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + if (_this.removeBtnEnabled) { + return BUI.getRedButton('REMOVE'); + } + } + } -CalendarWidget.prototype.loadData = function(data) { - this.events = []; + ], + viewConfig : { + preserveScrollOnRefresh : true, + stripeRows : true, + getRowClass : function(record) { + var specimens = _this.experiment.getSampleByPosition(record.data.samplePlateId, record.data.rowNumber, + record.data.columnNumber); + if (specimens.length > 1) { + return 'red-row'; - for ( var i = 0; i < data.length; i++) { - var date = moment(data[i].creationDate); - var textColor = 'black'; + } + }, + listeners : { + selectionchange : function(grid, selected) { + _this.onClick.notify(record.raw); + }, + cellclick : function(grid, td, cellIndex, record, tr) { + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEditSample') { + } + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemoveSample') { + grid.getStore().removeAt(rowIndex); + _this.onRemoved.notify(); + } - if (data[i].status == "FINISHED") { - textColor = 'green'; - } - if (data[i].status == "ABORTED") { - textColor = 'red'; - } - this.events.push({ - title : data[i].name, - start : date.format("YYYY-MM-DD HH:mm:ss"), - end : date.format("YYYY-MM-DD HH:mm:ss"), - date : date, - allDay : false, - color : textColor, - className : date.format("YYYY-MM-DD") - }); - } + } + } + } + }); + return this.grid; }; -CalendarWidget.prototype.draw = function(targetId) { - var _this = this; - $('#' + targetId).fullCalendar({ - eventClick : function(calEvent, jsEvent, view) { - _this.onClick.notify(calEvent.className[0]); - - }, - contentHeight : _this.height, - header : { - left : 'prev,next today', - center : 'title', - right : 'month,basicWeek,basicDay' - }, - editable : false, - events : this.events +SpecimenGrid.prototype.input = function() { + return { + experiment : DATADOC.getExperiment_10(), + proposal : DATADOC.getProposal_10() + }; +}; + +SpecimenGrid.prototype.test = function(targetId) { + var specimenGrid = new SpecimenGrid({ + height : 400, + maxHeight : 400, + width : 1000 }); + BIOSAXS.proposal = new Proposal(specimenGrid.input().proposal); + + var experiment = new Experiment(specimenGrid.input().experiment); + var panel = specimenGrid.getPanelByExperiment(experiment); + panel.render(targetId); }; /** - * It shows a table with the guinier and gnom data as well as passed and - * discarded measurements + * Shows a list of stock solutions with macromolecule, buffer, storage temperature, concentration, shipment and comments * - * @height - * @showBufferColumns + * @multiselect allows multiple selection + * @height + * @minHeight + * @width + * @tbar + * @showTitle + * @isPackedVisible shows is stock solution is in a box + * @btnEditVisible shows edit button + * @btnAddVisible + * @btnAddExisting + * @btnUnpackVisible allows to unpack a stock solution + * @btnRemoveVisible allow to remove a stock solution */ -function ConcentrationHTMLTableWidget(args) { + +function StockSolutionGrid(args) { this.id = BUI.id(); + this.height = 100; + this.width = null; + this.minHeight = null; + this.tbar = true; - this.showBufferColumns = true; + this.title = "Stock Solutions"; + + /** Visible buttons and actions **/ + this.btnEditVisible = true; + this.btnRemoveVisible = true; + this.btnAddVisible = true; + this.btnAddExisting = false; + this.isPackedVisible = true; + this.btnUnpackVisible = false; + + /** Selectors **/ + this.multiselect = false; + this.selectedStockSolutions = []; if (args != null) { + if (args.btnUnpackVisible != null) { + this.btnUnpackVisible = args.btnUnpackVisible; + } + if (args.multiselect != null) { + this.multiselect = args.multiselect; + } if (args.height != null) { this.height = args.height; } - if (args.showBufferColumns != null) { - this.showBufferColumns = args.showBufferColumns; + if (args.btnEditVisible != null) { + this.btnEditVisible = args.btnEditVisible; + } + if (args.btnAddVisible != null) { + this.btnAddVisible = args.btnAddVisible; + } + if (args.btnAddExisting != null) { + this.btnAddExisting = args.btnAddExisting; + } + if (args.width != null) { + this.width = args.width; + } + if (args.minHeight != null) { + this.minHeight = args.minHeight; + } + if (args.tbar != null) { + this.tbar = args.tbar; + } + if (args.btnRemoveVisible != null) { + this.btnRemoveVisible = args.btnRemoveVisible; + } + if (args.isPackedVisible != null) { + this.isPackedVisible = args.isPackedVisible; + } + if (args.showTitle != null) { + this.showTitle = args.showTitle; + if (this.showTitle == false) { + this.title = null; + } } - } -} - -ConcentrationHTMLTableWidget.prototype.refresh = function(parsedData) { - document.getElementById(this.id).innerHTML = this.getPanel(parsedData); -}; - -ConcentrationHTMLTableWidget.prototype.getPanel = function(parsedData) { - var html = "
"; - html = html + ""; - /** Title * */ - html = html + ""; - html = html + ""; - if (this.showBufferColumns) { - html = html + ""; } - html = html + ""; - html = html + ""; - html = html + ""; - html = html + ""; - html = html + ""; - html = html + ""; - html = html + ""; - html = html + ""; - html = html + ""; - html = html + ""; - html = html + ""; - html = html + ""; - html = html + ""; + /** Events **/ + this.onProposalChanged = new Event(this); + this.onStockSolutionSelected = new Event(this); +} - parsedData.concentration.concentrations.sort(function(a, b) { - return a.concentration - b.concentration; - }); - /** Row * */ - for ( var i = 0; i < parsedData.concentration.concentrations.length; i++) { - var row = parsedData[i]; +StockSolutionGrid.prototype._getColumns = function() { + var _this = this; + var columns = [ - var tr = ""; - if (i % 2 == 1) { - tr = ""; + { + header : 'Macromolecule', + dataIndex : 'macromolecule', + id : _this.id + 'macromolecule', + type : 'string', + renderer : function(val, y, specimen) { + return '' + val + ''; + }, + hidden : false, + flex : 1 + }, { + header : 'Buffer', + dataIndex : 'buffer', + name : 'buffer', + hidden : false, + renderer : function(val, y, specimen) { + return '' + val + ''; + }, + type : 'string', + flex : 1 + }, { + header : 'Acronym', + dataIndex : 'name', + name : 'name', + type : 'string', + flex : 1, + hidden : true + }, { + header : 'Storage Temp.', + dataIndex : 'storageTemperature', + name : 'storageTemperature', + type : 'string', + flex : 1, + hidden : false, + renderer : function(val) { + return BUI.formatValuesUnits(val, 'C', { + fontSize : 12, + decimals : 2, + unitsFontSize : 10 + }); } - var goodMeasurements = (parsedData.concentration.concentrations[i].frames.length - parsedData.concentration.concentrations[i].frames_warning); - if (goodMeasurements == 0) { - tr = ""; + }, { + header : 'Volume', + dataIndex : 'volume', + type : 'string', + flex : 1, + hidden : false, + renderer : function(val) { + return BUI.formatValuesUnits(val, 'µl', { + fontSize : 12, + decimals : 2, + unitsFontSize : 10 + }); } - html = html + tr; - html = html + ""; - if (this.showBufferColumns) { - html = html + ""; + }, { + header : 'Concentration', + dataIndex : 'concentration', + name : 'concentration', + type : 'string', + flex : 1, + renderer : function(val) { + return BUI.formatValuesUnits(val, 'mg/ml', { + fontSize : 12, + decimals : 2, + unitsFontSize : 10 + }); } - html = html + ""; - html = html + ""; - html = html + ""; - html = html + ""; - html = html + ""; - html = html + ""; - html = html + ""; - html = html + ""; + }, { + header : 'Packed', + dataIndex : 'comments', + id : _this.id + "box", + type : 'string', + width : 50, + hidden : !this.isPackedVisible, + renderer : function(val, cmp, a) { + if (a.raw.boxId != null) { + return "
"; + } + + } + }, { + header : 'Comments', + dataIndex : 'comments', + type : 'string', + flex : 1 + } ]; + + if (this.btnEditVisible) { + columns.push({ + id : _this.id + 'buttonEdit', + width : 85, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + if (_this.btnEditVisible) { + return BUI.getGreenButton('EDIT'); + } + } + }); + } + + if (this.btnRemoveVisible) { + columns.push({ + id : _this.id + 'buttonRemove', + width : 85, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + if (_this.btnRemoveVisible) { + return BUI.getRedButton('REMOVE'); + } + } + }); } - return html + "
ConcentrationBufferMeasurementsGuinierGnom
PassedDiscardedRgI0QualityRgdMax
" + parsedData.concentration.concentrations[i].concentration + "" + parsedData.concentration.concentrations[i].bufferAcronym + "" + goodMeasurements + " of " + parsedData.concentration.concentrations[i].frames.length + "" + parsedData.concentration.concentrations[i].frames_warning + "" + BUI.formatValuesErrorUnits(parsedData.concentration.concentrations[i].calculation.rgGuinier.avg, parsedData.concentration.concentrations[i].calculation.rgGuinier.std, "nm", { - lineBreak : false - }) + "" + BUI.formatValuesErrorUnits(parsedData.concentration.concentrations[i].calculation.i0Guinier.avg, parsedData.concentration.concentrations[i].calculation.i0Guinier.std, " ", { - lineBreak : false - }) + "" + BUI.formatValuesErrorUnits(parsedData.concentration.concentrations[i].calculation.quality.avg, parsedData.concentration.concentrations[i].calculation.quality.std, " ", { - lineBreak : false - }) + "" + BUI.formatValuesErrorUnits(parsedData.concentration.concentrations[i].calculation.rgGnom.avg, parsedData.concentration.concentrations[i].calculation.rgGnom.std, " ", { - lineBreak : false - }) + "" + BUI.formatValuesErrorUnits(parsedData.concentration.concentrations[i].calculation.dMax.avg, parsedData.concentration.concentrations[i].calculation.dMax.std, " ", { - lineBreak : false - }) + "
"; + + if (this.btnUnpackVisible) { + columns.push({ + id : _this.id + 'buttonUnpack', + width : 85, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + if (_this.btnUnpackVisible) { + return BUI.getBlueButton('UNPACK'); + } + } + }); + } + return columns; }; -ConcentrationHTMLTableWidget.prototype.input = function() { - return { - data : { - "dataCollectionCount" : 4, - "buffers" : [ { - "bufferId" : "422" - } ], - "concentration" : { - "concentrations" : [ { - "concentration" : "7.17", - "id" : "7.1699999999999999", - "bufferId" : "422.00", - "bufferAcronym" : "B1", - "rgGuinier" : [ "5.12723" ], - "frames" : [ { - "total" : "0.515705406286", - "bufferBeforeMeasurementId" : 15045, - "sampleMergeId" : 8176, - "averagedModelId" : null, - "I0" : "183.457461646", - "proposalCode" : "OPD", - "averagedModel" : null, - "bufferAfterMergeId" : 8177, - "framesCount" : "10", - "bufferBeforeMergeId" : 8175, - "averageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_065_ave.dat", - "bufferAfterMeasurementId" : 15048, - "rgGuinier" : "5.12723", - "subtractedFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_065_sub.dat", - "firstPointUsed" : "17", - "chi2RgFilePath" : null, - "abInitioModelId" : null, - "macromoleculeId" : 649, - "code" : "_4.0_7.17", - "transmission" : "100.0", - "timeStart" : "2013-06-05 15:43:54.348723", - "bufferAcronym" : "B1", - "quality" : "0.853011", - "shapeDeterminationModelId" : null, - "expermientComments" : "[BsxCube] Generated from BsxCube", - "bufferId" : 422, - "isagregated" : "False", - "dmax" : "25.63615", - "bufferBeforeAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_064_ave.dat", - "exposureTemperature" : "4.0", - "subtractionId" : 3377, - "conc" : "7.1699999999999999", - "rapidShapeDeterminationModel" : null, - "experimentCreationDate" : "Jun 5, 2013 3:30:30 PM", - "lastPointUsed" : "36", - "modelListId" : null, - "framesMerge" : "9", - "rapidShapeDeterminationModelId" : null, - "bufferAfterAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_066_ave.dat", - "nsdFilePath" : null, - "bufferAfterFramesMerged" : "10", - "experimentId" : 700, - "macromoleculeAcronym" : "L9", - "i0stdev" : "0.139364435146", - "sampleMeasurementId" : 15047, - "measurementComments" : "[5]", - "priorityLevelId" : 10, - "bufferBeforeFramesMerged" : "10", - "substractionCreationTime" : "Jun 5, 2013 3:46:31 PM", - "proposalNumber" : "29", - "rgGnom" : "5.40297914939", - "volume" : "475.302", - "shapeDeterminationModel" : null, - "comments" : null, - "groupeField" : "L9 B1" - } ], - "frames_warning" : 0, - "calculation" : { - "rgGuinier" : { - "std" : 0, - "sum" : 5.12723, - "avg" : 5.12723, - "validNumber" : 1, - "totalNumber" : 1, - "values" : [ "5.12723" ] - }, - "i0Guinier" : { - "std" : 0, - "sum" : 183.457461646, - "avg" : 183.457461646, - "validNumber" : 1, - "totalNumber" : 1, - "values" : [ "183.457461646" ] - }, - "quality" : { - "std" : 0, - "sum" : 0.853011, - "avg" : 0.853011, - "validNumber" : 1, - "totalNumber" : 1, - "values" : [ "0.853011" ] - }, - "rgGnom" : { - "std" : 0, - "sum" : 5.40297914939, - "avg" : 5.40297914939, - "validNumber" : 1, - "totalNumber" : 1, - "values" : [ "5.40297914939" ] - }, - "dMax" : { - "std" : 0, - "sum" : 25.63615, - "avg" : 25.63615, - "validNumber" : 1, - "totalNumber" : 1, - "values" : [ "25.63615" ] - } - } - }, { - "concentration" : "3.53", - "id" : "3.5299999999999998", - "bufferId" : "422.00", - "bufferAcronym" : "B1", - "rgGuinier" : [ "4.38278" ], - "frames" : [ { - "total" : "0.497164741078", - "bufferBeforeMeasurementId" : 15048, - "sampleMergeId" : 8178, - "averagedModelId" : null, - "I0" : "160.023229462", - "proposalCode" : "OPD", - "averagedModel" : null, - "bufferAfterMergeId" : 8179, - "framesCount" : "10", - "bufferBeforeMergeId" : 8177, - "averageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_067_ave.dat", - "bufferAfterMeasurementId" : 15051, - "rgGuinier" : "4.38278", - "subtractedFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_067_sub.dat", - "firstPointUsed" : "36", - "chi2RgFilePath" : null, - "abInitioModelId" : null, - "macromoleculeId" : 649, - "code" : "_4.0_3.53", - "transmission" : "100.0", - "timeStart" : "2013-06-05 15:47:04.630129", - "bufferAcronym" : "B1", - "quality" : "0.742825", - "shapeDeterminationModelId" : null, - "expermientComments" : "[BsxCube] Generated from BsxCube", - "bufferId" : 422, - "isagregated" : "False", - "dmax" : "15.33973", - "bufferBeforeAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_066_ave.dat", - "exposureTemperature" : "4.0", - "subtractionId" : 3378, - "conc" : "3.5299999999999998", - "rapidShapeDeterminationModel" : null, - "experimentCreationDate" : "Jun 5, 2013 3:30:30 PM", - "lastPointUsed" : "61", - "modelListId" : null, - "framesMerge" : "10", - "rapidShapeDeterminationModelId" : null, - "bufferAfterAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_068_ave.dat", - "nsdFilePath" : null, - "bufferAfterFramesMerged" : "10", - "experimentId" : 700, - "macromoleculeAcronym" : "L9", - "i0stdev" : "0.1499898017", - "sampleMeasurementId" : 15050, - "measurementComments" : "[6]", - "priorityLevelId" : 12, - "bufferBeforeFramesMerged" : "10", - "substractionCreationTime" : "Jun 5, 2013 3:49:42 PM", - "proposalNumber" : "29", - "rgGnom" : "4.40615474861", - "volume" : "372.656", - "shapeDeterminationModel" : null, - "comments" : null, - "groupeField" : "L9 B1" - } ], - "frames_warning" : 0, - "calculation" : { - "rgGuinier" : { - "std" : 0, - "sum" : 4.38278, - "avg" : 4.38278, - "validNumber" : 1, - "totalNumber" : 1, - "values" : [ "4.38278" ] - }, - "i0Guinier" : { - "std" : 0, - "sum" : 160.023229462, - "avg" : 160.023229462, - "validNumber" : 1, - "totalNumber" : 1, - "values" : [ "160.023229462" ] - }, - "quality" : { - "std" : 0, - "sum" : 0.742825, - "avg" : 0.742825, - "validNumber" : 1, - "totalNumber" : 1, - "values" : [ "0.742825" ] - }, - "rgGnom" : { - "std" : 0, - "sum" : 4.40615474861, - "avg" : 4.40615474861, - "validNumber" : 1, - "totalNumber" : 1, - "values" : [ "4.40615474861" ] - }, - "dMax" : { - "std" : 0, - "sum" : 15.33973, - "avg" : 15.33973, - "validNumber" : 1, - "totalNumber" : 1, - "values" : [ "15.33973" ] +StockSolutionGrid.prototype._getTopButtons = function() { + var _this = this; + /** Actions buttons **/ + var actions = []; + + /** ADD BUTTON **/ + if (this.btnAddVisible) { + actions.push(Ext.create('Ext.Action', { + icon : '../images/add.png', + text : 'Add Stock Solution', + tooltip : 'Will create a new stock solution', + disabled : false, + alwaysEnabled : true, + handler : function(widget, event) { + _this.edit(); + } + })); + } + + if (this.btnAddExisting) { + actions.push(Ext.create('Ext.Action', { + icon : '../images/add.png', + text : 'Add Existing', + tooltip : 'Allows to select upacked stock solutions', + disabled : false, + alwaysEnabled : true, + handler : function(widget, event) { + var stockSolutionGrid = new StockSolutionGrid({ + btnAddVisible : false, + btnEditVisible : false, + btnRemoveVisible : false, + btnAddExisting : false, + isPackedVisible : true, + multiselect : true + }); + + var window = Ext.create('Ext.window.Window', { + title : 'Select', + height : 400, + width : 800, + layout : 'fit', + items : [ stockSolutionGrid.getPanel() ], + buttons : [ { + text : 'Pack', + handler : function() { + _this.onStockSolutionSelected.notify(stockSolutionGrid.selectedStockSolutions); + window.close(); + } + }, { + text : 'Cancel', + handler : function() { + window.close(); } + } ] + + }).show(); + + stockSolutionGrid.refresh(BIOSAXS.proposal.getUnpackedStockSolutions()); + } + })); + } + + return actions; +}; + +StockSolutionGrid.prototype.refresh = function(stockSolutions) { + this.features = stockSolutions; + this.store.loadData(this._prepareData(), false); +}; + +StockSolutionGrid.prototype._prepareData = function() { + var data = []; + for ( var i = 0; i < this.features.length; i++) { + var stockSolution = this.features[i]; + stockSolution.buffer = BIOSAXS.proposal.getBufferById(stockSolution.bufferId).acronym; + if (stockSolution.macromoleculeId != null) { + stockSolution.macromolecule = BIOSAXS.proposal.getMacromoleculeById(stockSolution.macromoleculeId).acronym; + } + data.push(stockSolution); + } + return data; +}; + +StockSolutionGrid.prototype.getPanel = function() { + return this._renderGrid(); +}; + +StockSolutionGrid.prototype.edit = function(stockSolutionId) { + var _this = this; + var stockSolutionWindow = new StockSolutionWindow(); + /** On stock solution SAVED **/ + stockSolutionWindow.onSaved.attach(function(sender, stockSolution) { + _this.onProposalChanged.notify(stockSolution); + }); + stockSolutionWindow.draw(BIOSAXS.proposal.getStockSolutionById(stockSolutionId)); +}; + +StockSolutionGrid.prototype._getStoreFields = function() { + return [ { + name : 'name', + type : 'string' + }, { + name : 'stockSolutionId', + type : 'string' + }, { + name : 'macromolecule', + type : 'string' + }, { + name : 'buffer', + type : 'string' + }, { + name : 'storageTemperature', + type : 'numeric' + }, { + name : 'volume', + type : 'string' + }, { + name : 'concentration', + type : 'string' + }, { + name : 'buffer', + type : 'string' + }, { + name : 'comments', + type : 'string' + } ]; +}; + +//StockSolutionGrid.prototype.refresh = function() { +// this.proposal.onInitialized.attach(function(sender){ +// +// }); +// this.proposal.init(Ext.urlDecode(window.location.href).sessionId); +//}; + +StockSolutionGrid.prototype._renderGrid = function() { + var _this = this; + + /** Store **/ + this.store = Ext.create('Ext.data.Store', { + fields : this._getStoreFields(), //columns, + autoload : true + }); + + var filters = { + ftype : 'filters', + local : true, + filters : this.filters + }; + + var selModel = null; + + if (this.multiselect) { + selModel = Ext.create('Ext.selection.CheckboxModel', { + //multiSelect : false,//this.multiselect, + mode : 'SINGLE', + listeners : { + selectionchange : function(sm, selections) { + _this.selectedStockSolutions = []; + for ( var i = 0; i < selections.length; i++) { + _this.selectedStockSolutions.push(selections[i].raw); } - }, { - "concentration" : "1.75", - "id" : "1.75", - "bufferId" : "422.00", - "bufferAcronym" : "B1", - "rgGuinier" : [], - "frames" : [ { - "total" : "0.5538035065", - "bufferBeforeMeasurementId" : 15051, - "sampleMergeId" : 8180, - "averagedModelId" : null, - "I0" : "146.927428571", - "proposalCode" : "OPD", - "averagedModel" : null, - "bufferAfterMergeId" : 8181, - "framesCount" : "10", - "bufferBeforeMergeId" : 8179, - "averageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_069_ave.dat", - "bufferAfterMeasurementId" : 15054, - "rgGuinier" : "4.27139", - "subtractedFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_069_sub.dat", - "firstPointUsed" : "33", - "chi2RgFilePath" : null, - "abInitioModelId" : null, - "macromoleculeId" : 649, - "code" : "_4.0_1.75", - "transmission" : "100.0", - "timeStart" : "2013-06-05 15:50:09.395824", - "bufferAcronym" : "B1", - "quality" : "0.765999", - "shapeDeterminationModelId" : null, - "expermientComments" : "[BsxCube] Generated from BsxCube", - "bufferId" : 422, - "isagregated" : "False", - "dmax" : "14.949865", - "bufferBeforeAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_068_ave.dat", - "exposureTemperature" : "4.0", - "subtractionId" : 3379, - "conc" : "1.75", - "rapidShapeDeterminationModel" : null, - "experimentCreationDate" : "Jun 5, 2013 3:30:30 PM", - "lastPointUsed" : "62", - "modelListId" : null, - "framesMerge" : "6", - "rapidShapeDeterminationModelId" : null, - "bufferAfterAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_070_ave.dat", - "nsdFilePath" : null, - "bufferAfterFramesMerged" : "10", - "experimentId" : 700, - "macromoleculeAcronym" : "L9", - "i0stdev" : "0.191914285714", - "sampleMeasurementId" : 15053, - "measurementComments" : "[7]", - "priorityLevelId" : 14, - "bufferBeforeFramesMerged" : "10", - "substractionCreationTime" : "Jun 5, 2013 3:52:31 PM", - "proposalNumber" : "29", - "rgGnom" : "4.28379338749", - "volume" : "356.326", - "shapeDeterminationModel" : null, - "comments" : null, - "groupeField" : "L9 B1" - } ], - "frames_warning" : 1, - "calculation" : { - "rgGuinier" : { - "std" : null, - "sum" : 0, - "avg" : 0, - "validNumber" : 0, - "totalNumber" : 0, - "values" : [] - }, - "i0Guinier" : { - "std" : null, - "sum" : 0, - "avg" : 0, - "validNumber" : 0, - "totalNumber" : 0, - "values" : [] - }, - "quality" : { - "std" : null, - "sum" : 0, - "avg" : 0, - "validNumber" : 0, - "totalNumber" : 0, - "values" : [] - }, - "rgGnom" : { - "std" : null, - "sum" : 0, - "avg" : 0, - "validNumber" : 0, - "totalNumber" : 0, - "values" : [] - }, - "dMax" : { - "std" : null, - "sum" : 0, - "avg" : 0, - "validNumber" : 0, - "totalNumber" : 0, - "values" : [] + } + } + }); + } else { + selModel = { + mode : 'SINGLE' + }; + } + + this.store.sort("stockSolutionId", "desc"); + + this.grid = Ext.create('Ext.grid.Panel', { + style : { + padding : 5 + }, + icon : '/ispyb/images/SampleHolder_24x24_01.png', + title : this.title, + height : this.height, + width : this.width, + minWidth : this.minWidth, + selModel : selModel, + store : this.store, + columns : this._getColumns(), + viewConfig : { + stripeRows : true, + listeners : { + itemdblclick : function(dataview, record, item, e) { + _this.edit(record.raw.stockSolutionId); + }, + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + var adapter = null; + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonUnpack') { + _this.grid.setLoading("ISPyB: Unpacking stock solution"); + adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender) { + _this.onProposalChanged.notify(); + _this.grid.setLoading(false); + }); + adapter.onError.attach(function(sender) { + _this.onProposalChanged.notify(); + _this.grid.setLoading(false); + }); + record.raw.boxId = null; + adapter.saveStockSolution(record.raw); + } + + if (grid.getGridColumns()[cellIndex].getId() == _this.id + "box") { + window.location = BUI.getShippingURL(BIOSAXS.proposal.getShipmentByDewarId(record.raw.boxId).shippingId); + } + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEdit') { + _this.edit(record.data.stockSolutionId); + } + + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemove') { + _this.grid.setLoading("ISPyB: Removing stock solution"); + adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender) { + _this.onProposalChanged.notify(); + _this.grid.setLoading(false); + }); + adapter.onError.attach(function(sender) { + _this.onProposalChanged.notify(); + _this.grid.setLoading(false); + }); + adapter.removeStockSolution(record.data.stockSolutionId); + } + } + } + } + + }); + + var actions = _this._getTopButtons(); + this.grid.addDocked({ + xtype : 'toolbar', + items : actions + }); + + var i = null; + this.grid.getSelectionModel().on({ + selectionchange : function(sm, selections) { + if (selections.length) { + for ( i = 0; i < actions.length; i++) { + if (actions[i].enable) { + actions[i].enable(); + } + } + } else { + for ( i = 0; i < actions.length; i++) { + if (actions[i].alwaysEnabled == false) { + if (actions[i].disable) { + actions[i].disable(); + } + } + } + } + } + }); + return this.grid; +}; + +StockSolutionGrid.prototype.input = function() { + return { + proposal : DATADOC.getProposal_10() + }; +}; + +StockSolutionGrid.prototype.test = function(targetId) { + var stockSolutionGrid = new StockSolutionGrid({ + height : 300, + width : 900 + }); + BIOSAXS.proposal = new Proposal(stockSolutionGrid.input().proposal); + var panel = stockSolutionGrid.getPanel(); + stockSolutionGrid.refresh(BIOSAXS.proposal.getStockSolutions()); + panel.render(targetId); +}; + + +function SuperpositionGrid(args) { + this.height = null; + this.width = null; + this.id = BUI.id(); + + if (args != null) { + if (args.height != null) { + this.height = args.height; + + if (args.width != null) { + this.width = args.width; + } + } + } + + this.onSelected = new Event(this); +} + +SuperpositionGrid.prototype._prepareData = function(data) { + return data; +}; + +SuperpositionGrid.prototype.refresh = function(subtractions) { + var data = []; + if (subtractions != null){ + if (subtractions.length > 0){ + for (j in subtractions){ + var subtraction = subtractions[j]; + if (subtraction.superposition3VOs != null){ + for (i in subtraction.superposition3VOs){ + data.push(subtraction.superposition3VOs[i]); + } + } + } + } + } + this.store.loadData(data); +}; + +SuperpositionGrid.prototype.getPanel = function() { + var _this = this; + this.store = Ext.create('Ext.data.Store', { + fields : [ 'abinitioModelPdbFilePath', 'aprioriPdbFilePath', 'alignedPdbFilePath' ], + data : [] + }); + + this.selModel = Ext.create('Ext.selection.RowModel', { + allowDeselect : true, + mode : 'MULTI', + listeners : { + selectionchange : function(sm, selections) { + var selected = []; + for (var i = 0; i < selections.length; i++) { + selected.push(selections[i].raw); + } + _this.onSelected.notify(selected); + } + } + }); + + this.store.sort([ { + property : 'name', + direction : 'ASC' + } ]); + + this.panel = Ext.create('Ext.grid.Panel', { + store : this.store, + selModel : this.selModel, + width : this.width, + height : this.height, + margin : 10, + deferredRender : false, + columns : [ { + text : 'Abinitio', + dataIndex : 'abinitioModelPdbFilePath', + hidden : false, + flex : 1, + renderer : function(val){ + return BUI.getFileName(val); + } + }, { + text : 'Apriori', + dataIndex : 'aprioriPdbFilePath', + hidden : false, + flex : 1, + renderer : function(val){ + return BUI.getFileName(val); + } + }, { + text : 'Aligned', + dataIndex : 'alignedPdbFilePath', + hidden : false, + flex : 1, + renderer : function(val){ + return BUI.getFileName(val); + } + } ], + + viewConfig : { + enableTextSelection : true, + preserveScrollOnRefresh : true + }, + listeners : { + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + + }, + afterrender : function() { + } + } + }); + return this.panel; +}; + +/** + * See ExperimentGrid + * + */ +function TemplateGrid(args) { + + if (args == null) { + args = {}; + } + args.sorters = [ { + property : 'experimentId', + direction : 'DESC' + } ]; + + ExperimentGrid.prototype.constructor.call(this, args); +} + +TemplateGrid.prototype._getFilterTypes = ExperimentGrid.prototype._getFilterTypes; +TemplateGrid.prototype._prettyPrintMacromolecules = ExperimentGrid.prototype._prettyPrintMacromolecules; +TemplateGrid.prototype._getPercentage = ExperimentGrid.prototype._getPercentage; +TemplateGrid.prototype._getPercentageCollected = ExperimentGrid.prototype._getPercentageCollected; +TemplateGrid.prototype.getPercentageMerged = ExperimentGrid.prototype.getPercentageMerged; +TemplateGrid.prototype._prepareData = ExperimentGrid.prototype._prepareData; +TemplateGrid.prototype.getPanel = ExperimentGrid.prototype.getPanel; +TemplateGrid.prototype._renderGrid = ExperimentGrid.prototype._renderGrid; +TemplateGrid.prototype._editExperiment = ExperimentGrid.prototype._editExperiment; +TemplateGrid.prototype._removeExperimentById = ExperimentGrid.prototype._removeExperimentById; + +TemplateGrid.prototype._getTopButtons = function() { + /** Actions buttons * */ + var actions = []; + + actions.push(Ext.create('Ext.Action', { + icon : '../images/add.png', + text : 'Add experiment', + handler : function(widget, event) { + var wizardWidget = new WizardWidget({ + windowMode : true + }); + + wizardWidget.onFinished.attach(function(sender, result) { + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + var experiment = new Experiment(data); + BIOSAXS.openExperimentByExperiment(experiment); + wizardWidget.window.close(); + }); + wizardWidget.current.setLoading("ISPyB: Creating experiment"); + adapter.createTemplate(result.name, "comments", result.data); + }); + +// wizardWidget.draw(this.targetId, new ExperimentTypeWizardForm()); + wizardWidget.draw(this.targetId, new MeasurementCreatorStepWizardForm(BIOSAXS.proposal.getMacromolecules())); + } + })); + return actions; +}; + +TemplateGrid.prototype.refresh = function(data) { + var filtered = []; + for ( var i = 0; i < data.length; i++) { + if (data[i].experimentType == "TEMPLATE") { + filtered.push(data[i]); + } + } + this.store.loadData(this._prepareData(filtered), false); +}; + +TemplateGrid.prototype._getColumns = function() { + var _this = this; + function actionItemRenderer(value, meta, record, rowIx, ColIx, store) { + if (record.raw.buffer3VOs != null) { + if (record.raw.buffer3VOs.length > 0) { + return 'x-hide-display'; + } + } + + if (record.data.platesCount > 0) { + return 'x-hide-display'; + } + } + + return [ { + xtype : 'rownumberer', + width : 40 + }, { + text : 'experimentId', + dataIndex : 'experimentId', + name : 'experimentId', + type : 'string', + hidden : true + }, { + text : 'Name', + dataIndex : 'name', + name : 'name', + type : 'string', + flex : 1 + }, + + { + text : 'Type', + dataIndex : 'type', + name : 'type', + type : 'string', + hidden : true, + flex : 1, + renderer : function(val) { + return val; + } + }, { + text : 'Macromolecules', + name : 'macromolecules_names', + dataIndex : 'macromolecules_names', + flex : 1, + renderer : function(val) { + return " " + val + ""; + } + }, { + id : _this.id + 'GO', + width : 80, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + return BUI.getGreenButton('EDIT'); + } + }, { + id : _this.id + 'REMOVE', + width : 100, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + return BUI.getRedButton('REMOVE'); + } + } ]; +}; + +TemplateGrid.prototype.input = function() { + var experiments = DATADOC.getExperimentList_10(); + return { + experiments : experiments, + proposal : new MeasurementGrid().input().proposal + + }; +}; + +TemplateGrid.prototype.test = function(targetId) { + var experimentGrid = new TemplateGrid({ + height : 350, + minHeight : 350, + width : 1000, + gridType : 'Ext.grid.Panel', + title : 'Experiments', + grouping : false, + tbar : true + + }); + BIOSAXS.proposal = new Proposal(experimentGrid.input().proposal); + var panel = experimentGrid.getPanel(experimentGrid.input().experiments); + experimentGrid.refresh(experimentGrid.input().experiments); + panel.render(targetId); +}; + +function VolumeGrid() { + this.id = BUI.id(); +} + +VolumeGrid.prototype.getPanel = function(experiment) { + this.experiment = experiment; + return this.render(); +}; + +VolumeGrid.prototype.getVolumesPanel = function(data, title) { + var _this = this; + var store = Ext.create('Ext.data.Store', { + fields : [ 'name', 'volume', 'macromoleculeId', 'bufferId' ], + data : data + }); + store.sort([ { + property : 'name', + direction : 'ASC' + } ]); + + var grid = Ext.create('Ext.grid.Panel', { + title : title, + height : 400, + maxHeight : 400, + width : 900, + store : store, + margin : '10 0 50 10', + tbar : [ { + text : 'Go to Shipment', + icon : '../images/plane-small.gif', + handler : function() { + window.location = BUI.getCreateShipmentList(); + } + } ], + viewConfig : { + stripeRows : true, + listeners : { + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonCreate') { + var stockSolutionWindow = new StockSolutionWindow(); + /** On stock solution SAVED **/ + stockSolutionWindow.onSaved.attach(function(sender, stockSolution) { + BIOSAXS.proposal.onInitialized.attach(function(sender, data) { + _this.refresh(_this.experiment); + }); + BIOSAXS.proposal.init(); + }); + var acronym = "ST"; + if (record.raw.macromoleculeId != null) { + acronym = acronym + "_" + BIOSAXS.proposal.getMacromoleculeById(record.raw.macromoleculeId).acronym; + } + if (record.raw.bufferId != null) { + acronym = acronym + "_" + BIOSAXS.proposal.getBufferById(record.raw.bufferId).acronym; } + stockSolutionWindow.draw({ + concentration : record.raw.concentration, + macromoleculeId : record.raw.macromoleculeId, + bufferId : record.raw.bufferId, + name : acronym, + volume : record.raw.volume + }); } - }, { - "concentration" : "0.91", - "id" : "0.91000000000000003", - "bufferId" : "422.00", - "bufferAcronym" : "B1", - "rgGuinier" : [], - "frames" : [ { - "total" : null, - "bufferBeforeMeasurementId" : 15054, - "sampleMergeId" : 8182, - "averagedModelId" : null, - "I0" : "0.0", - "proposalCode" : "OPD", - "averagedModel" : null, - "bufferAfterMergeId" : 8183, - "framesCount" : "10", - "bufferBeforeMergeId" : 8181, - "averageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_071_ave.dat", - "bufferAfterMeasurementId" : 15057, - "rgGuinier" : null, - "subtractedFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_071_sub.dat", - "firstPointUsed" : "0", - "chi2RgFilePath" : null, - "abInitioModelId" : null, - "macromoleculeId" : 649, - "code" : "_4.0_.91", - "transmission" : "100.0", - "timeStart" : "2013-06-05 15:52:58.133705", - "bufferAcronym" : "B1", - "quality" : "0.0", - "shapeDeterminationModelId" : null, - "expermientComments" : "[BsxCube] Generated from BsxCube", - "bufferId" : 422, - "isagregated" : "False", - "dmax" : null, - "bufferBeforeAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_070_ave.dat", - "exposureTemperature" : "4.0", - "subtractionId" : 3380, - "conc" : "0.91000000000000003", - "rapidShapeDeterminationModel" : null, - "experimentCreationDate" : "Jun 5, 2013 3:30:30 PM", - "lastPointUsed" : "0", - "modelListId" : null, - "framesMerge" : "10", - "rapidShapeDeterminationModelId" : null, - "bufferAfterAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_072_ave.dat", - "nsdFilePath" : null, - "bufferAfterFramesMerged" : "10", - "experimentId" : 700, - "macromoleculeAcronym" : "L9", - "i0stdev" : "0.0", - "sampleMeasurementId" : 15056, - "measurementComments" : "[8]", - "priorityLevelId" : 16, - "bufferBeforeFramesMerged" : "10", - "substractionCreationTime" : "Jun 5, 2013 3:55:35 PM", - "proposalNumber" : "29", - "rgGnom" : null, - "volume" : null, - "shapeDeterminationModel" : null, - "comments" : null, - "groupeField" : "L9 B1" - } ], - "frames_warning" : 1, - "calculation" : { - "rgGuinier" : { - "std" : null, - "sum" : 0, - "avg" : 0, - "validNumber" : 0, - "totalNumber" : 0, - "values" : [] - }, - "i0Guinier" : { - "std" : null, - "sum" : 0, - "avg" : 0, - "validNumber" : 0, - "totalNumber" : 0, - "values" : [] + + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonStockSolutions') { + var stockSolutionGrid = new StockSolutionGrid({ + btnAddVisible : false, + btnEditVisible : false, + btnRemoveVisible : false, + btnAddExisting : false, + isPackedVisible : true, + multiselect : false + }); + + var window = Ext.create('Ext.window.Window', { + title : 'Stock solutions by specimen', + height : 400, + width : 800, + layout : 'fit', + items : [ stockSolutionGrid.getPanel() ], + buttons : [ { + text : 'Close', + handler : function() { + window.close(); + } + } ] + + }).show(); + stockSolutionGrid.refresh(BIOSAXS.proposal.getStockSolutionsBySpecimen(record.raw.macromoleculeId, record.raw.bufferId)); + } + } + } + }, + columns : [ +// { +// text : '', +// dataIndex : 'macromoleculeId', +// width : 20, +// renderer : function(val, y, sample) { +// if (val != null) { +//// return BUI.getRectangleColorDIV(BIOSAXS.proposal.macromoleculeColors[val], 10, 10); +// return BUI.getRectangleColorDIV(_this.experiment.macromoleculeColors[val], 10, 10); +// } +// } +// }, +// { +// text : '', +// dataIndex : 'bufferId', +// width : 20, +// renderer : function(val, y, sample) { +// if (val != null) { +// return BUI.getRectangleColorDIV(_this.experiment.getSpecimenColorByBufferId(val), 10, 10); +// } +// } +// }, + { + text : 'Specimen', + dataIndex : 'name', + flex : 0.5 + }, + { + text : 'Estimated Volume', + dataIndex : 'volume', + tooltip : 'Estimation of the maximum volume needed for making this experiment', + flex : 0.5, + editor : { + allowBlank : true + }, + renderer : function(val, y, sample) { + return BUI.formatValuesUnits(sample.data.volume, 'µl', { + fontSize : 16, + decimals : 2, + unitsFontSize : this.unitsFontSize + }); + } + }, + { + text : 'Stock Solution', + id : _this.id + 'buttonStockSolutions', + dataIndex : 'name', + flex : 0.5, + tooltip : 'Stock Solutions containing this specimen in this proposal', + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + var macromoleculeId = record.raw.macromoleculeId; + var bufferId = record.raw.bufferId; + var stockSolutions = BIOSAXS.proposal.getStockSolutionsBySpecimen(macromoleculeId, bufferId); + if (stockSolutions.length > 0) { + return "
" + stockSolutions.length + " x
"; + } + + } + }, { + id : _this.id + 'buttonCreate', + text : '', + tooltip : 'Create a new stock solution for shipping', + width : 170, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + return BUI.getGreenButton('NEW STOCK SOLUTION', { + width : 160 + }); + } + } ] + }); + return grid; + +}; + +VolumeGrid.prototype._prepareData = function(experiment) { + var keys = {}; + for ( var i = 0; i < experiment.getSamples().length; i++) { + var sample = experiment.getSamples()[i]; + var key = ""; + if (sample.macromoleculeId == null) { + key = experiment.getBufferById(sample.bufferId).acronym; + if (keys[key] == null) { + keys[key] = { + macromoleculeId : sample.macromoleculeId, + name : key, + bufferId : sample.bufferId, + volume : 0 + }; + } + keys[key].volume = Number(sample.volume) + Number(keys[key].volume); + } + + if ((sample.macromolecule3VO != null) || (sample.macromoleculeId != null)) { + macromoleculeId = sample.macromoleculeId; + if (sample.macromoleculeId == null) { + sample.macromoleculeId = sample.macromolecule3VO.macromoleculeId; + } + key = BIOSAXS.proposal.getMacromoleculeById(sample.macromoleculeId).acronym + " + " + experiment.getBufferById(sample.bufferId).acronym; + if (keys[key] == null) { + keys[key] = { + macromoleculeId : sample.macromoleculeId, + name : key, + bufferId : sample.bufferId, + volume : 0 + }; + } + keys[key].volume = Number(sample.volume) + Number(keys[key].volume); + } + } + var data = []; + for (var keyId in keys) { + data.push(keys[keyId]); + } + + return data; +}; + +VolumeGrid.prototype.refresh = function(experiment) { + this.experiment = experiment; + this.macromoleculeGrid.getStore().loadData(this._prepareData(this.experiment), false); +}; + +VolumeGrid.prototype.render = function() { + this.macromoleculeGrid = this.getVolumesPanel(this._prepareData(this.experiment), "Estimation of required Volume"); + + return { + xtype : 'container', + layout : 'vbox', + margin : "0, 0, 0, 5", + items : [ { + xtype : 'container', + layout : 'hbox', + margin : "0, 0, 0, 0", + items : [ this.macromoleculeGrid ] + } ] + }; +}; + +VolumeGrid.prototype.input = function(experiment) { + return { + experiment : DATADOC.getExperiment_10() + }; +}; + +VolumeGrid.prototype.test = function(targetId) { + var volumeGrid = new VolumeGrid(); + BIOSAXS.proposal = new Proposal(new MeasurementGrid().input().proposal); + var panel = volumeGrid.getPanel(new Experiment(new VolumeGrid().input().experiment)); + Ext.create('Ext.panel.Panel', { + height : 500, + width : 1000, + renderTo : targetId, + items : [ panel ] + }); +}; + +/** + * Example of a tab panel to be populated with widgets + * + * @width width in pixels + * @height height in pixels + * + * #myEvent event that this class is supposed to throw + * + **/ +function ExampleTabs(args) { + this.width = 500; + this.height = 500; + + if (args != null){ + if (args.width != null){ + this.width= args.width; + } + if (args.height != null){ + this.height= args.height; + } + } + + /** Events **/ + this.myEvent = new Event(); +} + +/** Populate the widget **/ +ExampleTabs.prototype.refresh = function(macromolecule) { + +}; + +/** It creates a tab panel with the specified with and height **/ +ExampleTabs.prototype.getPanel = function() { + this.panel = Ext.createWidget('tabpanel', { + height : this.height, + width : this.width, + style : { + padding : 2 + }, + items : [ { + tabConfig : { + title : 'Test', + icon : '/ispyb/images/plane-small.gif' + }, + items : [ { + xtype : 'container', + margin : '5 5 5 5', + items : [ ] + } ] + } ] + }); + return this.panel; +}; + + +/** + * Shows an experiments with the specimens, measurements, analysis tabs where + * results are shown and the frames widget + * + * @targetId + */ +function ExperimentTabs(targetId) { + this.height = 900; + this.targetId = targetId; + + this.id = BUI.id(); + var _this = this; + + this.INTERVAL_UPDATE = BUI.getUpdateInterval(); + + this.gridHeight = 1000; + /** data * */ + this.experiment = null; + + + /** Specimen Widget contains a specimenGrid and a sampleChangerWidget than can be displayed with are vertical or horizontal layout **/ + this.specimenWidget = new SpecimenWidget({ + height : 600 + }); + + + /** For Overview * */ + /*this.samplePlateGroupWidget = new SamplePlateGroupWidget({ + showTitle : false, + height : 250, + margin : 5, + border : 0 + + });*/ + + /** For Measurements * */ + /*this.measurementSamplePlateGroupWidget = new SamplePlateGroupWidget({ + showTitle : false, + height : 250, + margin : '5 0 0 0', + border : 0 + });*/ + + this.measurementGridDone = new MeasurementGrid({ + height : 600, + minHeight : 400, + maxHeight : 800, + positionColumnsHidden : true, + showTitle : false, + estimateTime : true, + width : 900, + maxWidth : 1500, + addBtnEnable : false, + markDone : true, + removeBtnEnabled : false + }); + this.measurementGridDone.onSelected.attach(function(sender, measurements) { + var specimens = []; + for ( var i = 0; i < measurements.length; i++) { + specimens.push(_this.experiment.getSampleById(measurements[i].specimenId)); + } + //_this.measurementSamplePlateGroupWidget.selectSpecimens(specimens); + }); + + /** AnalysisGrid * */ + this.analysisGrid = new AnalysisGrid({ + height : Ext.getBody().getViewSize().height * 0.9 - 300, + positionColumnsHidden : true, + sorters : [ { + property : 'priorityLevelId', + direction : 'ASC' + } ] + }); + + + /** Queue * */ + this.queueGrid = new QueueGrid({ + url : BUI.getQueueUrlByExperiment(), + height : Ext.getBody().getViewSize().height * 0.9 - 300, + width : Ext.getBody().getViewSize().width * 0.9 - 300, + isGrouped : true, + tbar : false, + bbar : false, + sorter : [{ + property: 'measurementId', + direction: 'DESC' + }] + }); + +} + +ExperimentTabs.prototype.error = function(error) { + var e = JSON.parse(error); + showError(e); + this.panel.setLoading(false); +}; + +ExperimentTabs.prototype.draw = function(experiment) { + this.renderDataAcquisition(experiment); +}; + +ExperimentTabs.prototype.refreshAnalysisData = function() { + var _this = this; + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + _this.analysisGrid.refresh(data, {experiment : _this.experiment}); + }); + adapter.getAnalysisInformationByExperimentId(this.experiment.experimentId); + + /** Auto load **/ + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + _this.queueGrid.refresh(data); + }); + adapter.getCompactAnalysisByExperimentId(this.experiment.experimentId); + this.queueGrid.store.proxy.url = BUI.getQueueUrlByExperiment(this.experiment.experimentId); + this.queueGrid.refresh(); +}; + +ExperimentTabs.prototype.getSpecimenContainerHeight = function(experiment) { + var maxItems = 0; + if (maxItems < experiment.getSamples().length + 1) { + maxItems = experiment.getSamples().length + 1; + } + + var height = (maxItems + 1) * 40 + 40; + if (height > 400) { + height = 400; + } + return height; +}; + +ExperimentTabs.prototype.getExperimentTitle = function() { + var experimentHeaderForm = new ExperimentHeaderForm(); + return experimentHeaderForm.getPanel(this.experiment); +}; + +ExperimentTabs.prototype.renderDataAcquisition = function(experiment) { + var _this = this; + this.experiment = experiment; + + var specimenGrid = new SpecimenGrid({ + height : 400, + maxHeight : 500, + width : 890 + }); + + specimenGrid.onClick.attach(function(sender, args) { + }); + + specimenGrid.onSelected.attach(function(sender, specimens) { + //_this.samplePlateGroupWidget.selectSpecimens(specimens); + }); + var specimenContainer = this.specimenWidget.getPanel(); + this.specimenWidget.refresh(experiment); + /* + var specimenContainer = Ext.create('Ext.container.Container', { + layout : 'hbox', + width : 900, + padding : '10 0 0 2', + items : [ specimenGrid.getPanel() ] + }); + + specimenGrid.refresh(experiment);*/ + + var experimentList = new ExperimentList([ _this.experiment ]); + var measurementContainer = Ext.create('Ext.container.Container', { + layout : 'vbox', + padding : '5px 0px 0px 10px', + items : [] + }); + measurementContainer.insert(0, _this.measurementGridDone.getPanel(this.experiment.getMeasurements(), experimentList)); +// measurementContainer.insert(1, _this.measurementSamplePlateGroupWidget.getPanel(experiment)); + + // this.dataCollectionCurveVisualizer = new DataCollectionCurveVisualizer(); + // this.dataCollectionCurveVisualizer.experiments = [experiment]; + // this.dataCollectionCurveVisualizer.dataCollectionFrameTree.experiments = + // [experiment]; + // this.dataCollectionCurveVisualizer.dataCollections = + // experiment.getDataCollections(); + + this.panel = Ext.createWidget('tabpanel', { + plain : true, + style : { + padding : 2 + }, + items : [ { + tabConfig : { + id : 'genralTabl', + title : "Overview" + }, + items : [ specimenContainer ] + }, { + tabConfig : { + title : 'Measurements' + }, + items : [ measurementContainer] + }, { + tabConfig : { + id : 'SpecimenTab', + title : 'Analysis', + hidden : this.isTemplate() + }, + items : [ { + xtype : 'container', + layout : 'vbox', + padding : '5px 0px 10px 10px', + items : [ _this.analysisGrid.getPanel([]) ] + } ] + }, + { + tabConfig : { + id : 'newAnalysisTab', + title : 'Analysis BETA', + hidden : this.isTemplate() + }, + items : [ { + xtype : 'container', + layout : 'vbox', + padding : '5px 0px 10px 10px', + items : [ _this.queueGrid.getPanel([]) ] + } ] + } + ] + }); + + return this.getPanel(this.panel); +}; + +ExperimentTabs.prototype.isTemplate = function() { + if (this.experiment.json.type == "TEMPLATE") { + return true; + } + return false; +}; + +ExperimentTabs.prototype.update = function() { + var _this = this; + var inter; + if (!_this.isTemplate()) { + function updateExperiments() { + _this.refreshAnalysisData(); + window.clearInterval(inter); + inter = setInterval(function() { + updateExperiments(); + }, _this.INTERVAL_UPDATE); + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + var experiment = new Experiment(data); + _this.measurementGridDone.refresh(experiment.getMeasurements(), new ExperimentList([ experiment ])); + }); + adapter.getExperimentById(_this.experiment.json.experimentId, "MEDIUM"); + } + inter = setInterval(function() { + updateExperiments(); + }, _this.INTERVAL_UPDATE); + } +}; + +ExperimentTabs.prototype.getPanel = function(panel) { + var _this = this; + if (this.experimentPanel == null) { + this.experimentPanel = Ext.create('Ext.container.Container', { + bodyPadding : 2, + width : Ext.getBody().getViewSize().width * 0.9, + renderTo : this.targetId, + style : { + padding : 2 + }, + items : [ this.getExperimentTitle(), this.panel ], + listeners : { + afterrender : function() { + _this.refreshAnalysisData(); + _this.update(); + } + } + }); + } + + return this.experimentPanel; +}; + +ExperimentTabs.prototype.input = function() { + return { + experiment : DATADOC.getExperiment_10(), + proposal : DATADOC.getProposal_10() + }; +}; + +ExperimentTabs.prototype.test = function(targetId) { + var experimentTabs = new ExperimentTabs(targetId); + BIOSAXS.proposal = new Proposal(experimentTabs.input().proposal); + experimentTabs.draw(new Experiment(experimentTabs.input().experiment)); +}; + + + +/** + * Shows an experiments with the specimens, measurements, analysis tabs where results are shown and the frames widget + * + * @targetId + */ +function HPLCTabs(targetId) { + this.height = 1400; + this.targetId = targetId; + + this.id = BUI.id(); + + this.gridHeight = 600; + this.pointsCount = 1036; + this.plotHeight = 350; + this.plotWidth = 800; + this.plotPanelPadding = 5; + + var _this = this; + + this.analysisGrid = new HPLCAnalysisGrid({ + height : Ext.getBody().getViewSize().height * 0.9 - 300, + positionColumnsHidden : true, + sorters : [ { + property : 'priorityLevelId', + direction : 'ASC' + } ] + }); + + this.frameGrid = new FrameGrid({ + width : 600, + height : 60, + collapsed : false, + tbar : false + }); + + this.peakGrid = new PeakGrid({ + width : 550, + height : 500, + collapsed : false, + tbar : false + }); + + this.peakGrid2 = new PeakGrid({ + width : 102, + height : this.plotHeight, + collapsed : false, + tbar : false, + showExtendedColumns : true + }); + + this.mainPlotPanel = new HPLCGraph({ + title : 'I0', + width : this.plotWidth - 110, + height : this.plotHeight, + bbar : true, + plots : { + "I0" : true, + "Rg" : true + }, + xlabel : "HPLC Frames", + scaled : true, + interactionModel : { + 'dblclick' : function(event, g, context) { + _this._selectFrame(g.lastx_); + var annotations = []; + annotations.push({ + series : g.selPoints_[0].name, + x : g.lastx_, + width : 100, + height : 23, + tickHeight : 4, + shortText : g.lastx_, + text : g.lastx_, + attachAtBottom : true + }); + g.setAnnotations(annotations); + + } + } + }); + + this.intensityPlotPanel = new MergesHPLCGraph({ + title : 'Scattering', + width : this.plotWidth, + height : 500, + showRangeSelector : false, + xParam : 0, + xlabel : "scattering_I", + plots : { + "scattering_I" : true, + "subtracted_I" : true, + "buffer_I" : true + } + }); + +} + +HPLCTabs.prototype._selectFrame = function(frameNumber) { + try{ + this._renderScatteringCurve(frameNumber); + this.frameGrid.refresh([this.mainPlotPanel.getDataByFrameNumber(frameNumber)], this.experiment.experimentId); + } + catch(e){ + console.log(e); + } +}; + +HPLCTabs.prototype.error = function(error) { + var e = JSON.parse(error); + showError(e); + this.panel.setLoading(false); +}; + +HPLCTabs.prototype.loadDataMainPlot = function(data) { + var zeroArray = []; + for ( var i = 0; i < data.I0.length; i++) { + zeroArray.push(0); + } + data = [ { + param : "I0", + data : data.I0, + std : data.I0_Stdev, + color : '#0066CC', + label : "I0" + }, + { + param : "sum_I", + label : "sum_I", + color : "#00FF00", + data : data.sum_I, + std : zeroArray + }, + { + param : "Rg", + label : "Rg", + color : "#21610B", + data : data.Rg, + std : data.Rg_Stdev + }, { + param : "Mass", + data : data.mass, + std : data.mass_Stdev, + color : '#FF9900', + label : "Mass" + }, { + param : "Vc", + data : data.Vc, + std : data.Vc_Stdev, + color : '#990099', + label : "Vc" + }, { + param : "Qr", + data : data.Qr, + std : data.Qr_Stdev, + color : '#FF0066', + label : "Qr" + }, { + param : "quality", + label : "quality", + color : "#FF00FF", + data : data.quality, + std : zeroArray + } ]; + this.data = data; + this.mainPlotPanel.loadData(data); +}; + +HPLCTabs.prototype._loadIntensityPlotByFrameNumber = function(frameNumber) { + var _this = this; + + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + var array = []; + data = [ { + param : "q", + data : data[frameNumber].q, + std : data[frameNumber].q, + fstd : function(a) { + return parseFloat(a); + }, + color : '#green', + label : "q", + showOnMenu : false + }, + { + param : "scattering_I", + data : data[frameNumber].scattering_I, + fdata : function(a) { + return Math.log(parseFloat(a)); + }, + std : data[frameNumber].scattering_Stdev, + fstd : function(a) { + return Math.log(Math.abs(parseFloat(a))); + }, + color : 'green', + label : "Log(I) Sample" + }, + { + param : "buffer_I", + data : data[frameNumber].buffer_I, + fdata : function(a) { + return Math.log(parseFloat(a)); + }, + fstd : function(a) { + return Math.log(Math.abs(parseFloat(a))); + }, + std : data[frameNumber].subtracted_Stdev, + color : '#0000FF', + label : "Log(I) Avg Buf." + }, + { + param : "subtracted_I", + data : data[frameNumber].subtracted_I, + fdata : function(a) { + var value = (Math.log(parseFloat(a))); + if (isNumber(value)) + return value; + }, + fstd : function(a) { + var value = Math.log(Math.abs(parseFloat(a))); + if (isNumber(value)) + return value; + }, + std : data[frameNumber].subtracted_Stdev, + color : 'red', + label : "Log(I) Sub." + } + ]; + + _this.intensityPlotPanel.xlabel = "Frame " + frameNumber + " (q, nm-1)"; + + if (_this.intensityPlotPanel.hplcData == null) { + /** It creates also top bar **/ + _this.intensityPlotPanel.loadData(data); + } else { + _this.intensityPlotPanel.reloadData(data); + + } + _this.intensityPlotPanel.panel.setLoading(false); + }); + adapter.onError.attach(function(sender, data) { + _this.intensityPlotPanel.panel.setLoading(false); + }); + this.intensityPlotPanel.panel.setLoading("Retrieving Frame " + frameNumber); + adapter.getH5FrameScattering(this.experiment.json.experimentId, frameNumber); +}; + +HPLCTabs.prototype._renderScatteringCurve = function(frameNumber) { + var _this = this; + + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + _this.intensityPlotPanel.setPeaks(data); + _this._loadIntensityPlotByFrameNumber(frameNumber); + try{ + var peaks = []; + for(key in data){ + peaks.push({ + start : key.split("-")[0], + end : key.split("-")[1], + experimentId : _this.experiment.json.experimentId + }); + } + _this.peakGrid2.refresh(JSON.parse(JSON.stringify(peaks))); + _this.peakGrid.refresh(peaks); +// console.log(peaks); + } + catch(e){ + showError(e); + } + }); + adapter.onError.attach(function(sender, data) { + _this.intensityPlotPanel.setLoading(false); + }); + this.intensityPlotPanel.panel.setLoading("Reading HDF5 File "); + adapter.getH5FramesMerge(this.experiment.json.experimentId); +}; + +HPLCTabs.prototype._postRenderOverviewPanel = function() { + var _this = this; + var adapter = new BiosaxsDataAdapter(); + adapter.onError.attach(function(sender, data) { + data = data.replace(/NaN/g, '0'); + _this.loadDataMainPlot(JSON.parse(data)); + + + }); + adapter.onSuccess.attach(function(sender, data) { + _this.loadDataMainPlot(data); + _this._renderScatteringCurve(0); + }); + adapter.getH5fileParameters(this.experiment.json.experimentId, [ + "I0", "I0_Stdev", "sum_I","Rg", "Rg_Stdev", "Vc", "Vc_Stdev", "Qr", "Qr_Stdev", "mass", "mass_Stdev", "quality" ]); + +}; + +HPLCTabs.prototype._postRenderDetailsPanel = function() { + if (this.data != null) { + this.I0PlotPanel.loadData(this.data); + this.RgPlotPanel.loadData(this.data); + this.MassPlotPanel.loadData(this.data); + this.VcPlotPanel.loadData(this.data); + } + +}; + +HPLCTabs.prototype.draw = function(experiment) { + var _this = this; + this.renderDataAcquisition(experiment); +}; + +HPLCTabs.prototype.getExperimentTitle = function() { + var experimentHeaderForm = new ExperimentHeaderForm(); + return experimentHeaderForm.getPanel(this.experiment); +}; + +HPLCTabs.prototype.renderDataAcquisition = function(experiment) { + var _this = this; + this.experiment = experiment; + if (this.experimentPanel == null) { + this.experimentPanel = Ext.create('Ext.container.Container', { + bodyPadding : 2, + height : this.height, + width : Ext.getBody().getViewSize().width * 0.9, + renderTo : this.targetId, + style : { + padding : 2 + }, + items : [ this.getExperimentTitle(), this.getPanel() ], + listeners : { + afterrender : function() { + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + _this.analysisGrid.refresh(data); + }); + adapter.getAnalysisInformationByExperimentId(_this.experiment.experimentId); + } + } + }); + } + return this.experimentPanel; +}; + +HPLCTabs.prototype.getPanel = function() { + var _this = this; + this.panel = Ext.createWidget('tabpanel', + { + plain : true, + height : this.height, +// width : 900, + style : { + padding : 2 + }, + items : [ + { + tabConfig : { + title : "Overview" + }, - "quality" : { - "std" : null, - "sum" : 0, - "avg" : 0, - "validNumber" : 0, - "totalNumber" : 0, - "values" : [] + items : [ { + xtype : 'container', + layout : 'hbox', + border : 1, + flex : 1, + items : [ { + xtype : 'container', + layout : 'vbox', + border : 1, + items : [ { + xtype : 'container', + margin : '10px', + border : 1, + items : [ + { + xtype : 'container', + margin : '0px', + layout : 'hbox', + border : 1, + items : [ + this.peakGrid2.getPanel([]), + this.mainPlotPanel.getPanel() + ] + }, + { + xtype : 'container', + layout : 'vbox', + border : 1, + items : [ + { + html: '
Select a frame by double-clicking on the HPLC Frames plot
', + margin: 5, + border : 0 + }, + this.frameGrid.getPanel([]), + this.intensityPlotPanel.getPanel() + ] + } + + ] + }], + listeners : { + afterrender : function() { + _this._postRenderOverviewPanel(); + } + } + } ] + } ] + }, +// { +// tabConfig : { +// title : "Details" +// }, +// items : [ { +// xtype : 'container', +// layout : 'hbox', +// border : 1, +// flex : 1, +// items : [ { +// xtype : 'container', +// layout : 'vbox', +// border : 1, +// items : [ { +// xtype : 'container', +// padding : '1px', +// items : [ +// this.I0PlotPanel.getPanel(), this.RgPlotPanel.getPanel(), this.MassPlotPanel.getPanel(), +// this.VcPlotPanel.getPanel() ] +// } ], +// listeners : { +// afterrender : function() { +// _this._postRenderDetailsPanel(); +// } +// } +// } ] +// } ] +// }, + { + tabConfig : { + title : "Analysis" }, - "rgGnom" : { - "std" : null, - "sum" : 0, - "avg" : 0, - "validNumber" : 0, - "totalNumber" : 0, - "values" : [] + items : [ { + xtype : 'container', + layout : 'vbox', + padding : '5px 0px 10px 10px', + items : [ _this.analysisGrid.getPanel([]) ] + } ] + }, + { + tabConfig : { + title : "File Manager" }, - "dMax" : { - "std" : null, - "sum" : 0, - "avg" : 0, - "validNumber" : 0, - "totalNumber" : 0, - "values" : [] + items : [ { + xtype : 'container', + layout : 'vbox', + padding : '5px 0px 10px 10px', + items : [ + { + html: '
Custom Download
', + margin : '10 0 10 5', + border : 0 + }, + { + html: '
Download has been temporary disabled. Contact your labcontact if you want to extract the frames from the HDF5 file
', + margin : '10 0 10 5', + hidden : _this.experiment.experimentId == 2602, + border : 0 + }, + { + xtype : 'container', + layout : 'hbox', + margin : '0 0 0 20', + flex : 1, + items :[ + { + xtype: 'numberfield', + id: 'field_start', + fieldLabel: 'Frames from', + value: 0, + minValue: 0 + }, + { + xtype: 'numberfield', + id: 'field_end', + fieldLabel: 'to', + labelWidth : 20, + margin : '0 0 0 10', + minValue: 0 + }, + { + xtype: 'button', + /** allowing test account to download frames **/ + disabled : _this.experiment.experimentId != 2602, + text : 'Download', + margin : '0 0 0 10', + handler : function() { + var experimentId = _this.experiment.experimentId; + var start = Ext.getCmp("field_start").getValue(); + var end = Ext.getCmp("field_end").getValue(); + /** Checking if start is bigger than end **/ + if (start > end){ + var aux = end; + end = start; + start = aux; + } + var url = BUI.getZipFrameHPLCUrl(experimentId, start, end); + window.open(url) + } + } + ] + }, + _this.peakGrid.getPanel([]) + + ] + } + ] + } + ] + }); + + return this.panel; +}; + +/** + * Main form tab for macromolecule + * + * @width + * @height + * + * #onClose when user clicks on close button in the MacromoleculeForm + * #onSave when macromole is saved by macromoleculeForm + */ +function MacromoleculeTabs(args) { + this.width = 500; + this.height = 500; + + if (args != null) { + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + } + + var _this = this; + + /** Widgets **/ + + /** Macromolecule Form **/ + this.macromoleculeForm = new MacromoleculeForm({ + width : this.width - 30, + height : this.height - 50, + }); + + this.macromoleculeForm.onClose.attach(function(sender) { + _this.onClose.notify(); + }); + + this.macromoleculeForm.onSave.attach(function(sender, macromolecule) { + _this.onSave.notify(macromolecule); + }); + + this.assemblyForm = new AssemblyForm({ + width : this.width - 30, + height : this.height - 50, + }); + + this.rigibBodyModelingForm = new RigibBodyModelingForm({ + width : this.width - 30, + height : this.height - 50, + }); + + this.rigibBodyModelingForm.onSave.attach(function(sender, macromolecule) { + _this.onSave.notify(macromolecule); + }); + + + /** Events **/ + this.onClose = new Event(this); + this.onSave = new Event(this); +} + +/** Populate the widget **/ +MacromoleculeTabs.prototype.refresh = function(macromolecule) { + this.macromoleculeForm.refresh(macromolecule); + this.assemblyForm.refresh(macromolecule); + this.rigibBodyModelingForm.refresh(macromolecule); + + if (macromolecule != null){ + if (macromolecule.macromoleculeId == null){ + Ext.getCmp(this.id + "_advancedTab").disable(); + Ext.getCmp(this.id + "_assemblyTab").disable(); + } + else{ + Ext.getCmp(this.id + "_advancedTab").enable(); + Ext.getCmp(this.id + "_assemblyTab").enable(); + } + } + else{ + Ext.getCmp(this.id + "_advancedTab").disable(); + Ext.getCmp(this.id + "_assemblyTab").disable(); + } +}; + +MacromoleculeTabs.prototype.getItems = function() { + return [ { + tabConfig : { + title : 'General' + }, + items : [ { + xtype : 'container', + items : [ this.macromoleculeForm.getPanel() ] + } ] + }, { + id : this.id + "_assemblyTab", + tabConfig : { + title : 'Assembly' + }, + items : [ { + xtype : 'container', + items : [ this.assemblyForm.getPanel() ] + } ] + },{ + id : this.id + "_advancedTab", + tabConfig : { + title : 'Advanced' + }, + items : [ this.rigibBodyModelingForm.getPanel() ] + } ]; +}; + +MacromoleculeTabs.prototype.getPanel = function() { + this.panel = Ext.createWidget('tabpanel', { + height : this.height, + width : this.width, + plain : true, + margin : 5, + border : 0, + items : this.getItems() + }); + return this.panel; +}; + +function ResultTabs() { +} + +ResultTabs.prototype.draw = function(targetId, data, macromoleculeId) { + var panel = this.getPanel(targetId, data, macromoleculeId); + return Ext.create('Ext.container.Container', { + renderTo : targetId, + items : [ BUI.getMacromoleculeHeader(macromoleculeId), panel ] + }); + +}; + +ResultTabs.prototype._splitBySpecimen = function(data) { + var splitted = {}; + + for ( var i = 0; i < data.length; i++) { + var row = data[i]; + if (splitted[row.macromoleculeId + "_" + row.bufferId] == null) { + splitted[row.macromoleculeId + "_" + row.bufferId] = []; + } + splitted[row.macromoleculeId + "_" + row.bufferId].push(row); + } + return splitted; + +}; + +ResultTabs.prototype._getTabTitle = function(key, data) { + var macromoleculeId = key.split("_")[0]; + var bufferId = key.split("_")[1]; + + return BIOSAXS.proposal.getMacromoleculeById(macromoleculeId).acronym + " + " + BIOSAXS.proposal.getBufferById(bufferId).acronym + "(" + data.length + ")"; +}; + +ResultTabs.prototype.getPanel = function(targetId, data, macromoleculeId) { + + var dataFiltered = new AnalysisGrid({ + hideNulls : true, + grouped : true, + sorters : [ { + property : 'quality', + direction : 'DESC' + } ] + })._prepareData(data); + + var items = [ { + tabConfig : { + title : 'Analysis (' + dataFiltered.length + ')' + }, + items : [ { + xtype : 'container', + layout : 'vbox', + padding : 10, + items : [ new AnalysisGrid({ + isScatteringPlotVisible : false + }).getPanel(dataFiltered) ] + } ] + }, { + tabConfig : { + title : 'Concentration Effects' + }, + items : [ new ResultSummaryForm().getPanel(data) ] + } ]; + + var splitted = this._splitBySpecimen(dataFiltered); + for ( var key in splitted) { + items.push({ + tabConfig : { + title : this._getTabTitle(key, splitted[key]) + }, + items : [ new ResultSummaryForm().getPanel(splitted[key]) ] + }); + } + + this.panel = Ext.createWidget('tabpanel', { + style : { + padding : 2 + }, + items : items + }); + return this.panel; + +}; + + +function ShipmentTabs(targetId) { + this.targetId = targetId; + + var _this = this; + this.gridHeight = 500; + /** data **/ + this.shipment = null; + + /** Shipment Form **/ + this.shipmentForm = new ShipmentForm({ + creationMode : false, + showTitle : false + }); + this.shipmentForm.onSaved.attach(function(sender, data) { + _this.refresh(data); + + }); + + + /** Cases grid **/ + this.caseGrid = new CaseGrid({ + height : this.gridHeight + }); + + this.caseGrid.onAddButtonClicked.attach(function(sender, dewar) { + _this.caseGrid.grid.setLoading("ISPyB: Creating a new case"); + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, shipment) { + /** updateing shipment on proposal **/ + for ( var i = 0; i < BIOSAXS.proposal.shippings.length; i++) { + if (BIOSAXS.proposal.shippings[i].shippingId == shipment.shippingId) { + BIOSAXS.proposal.shippings[i] = shipment; + } + } + _this.refresh(shipment); + }); + adapter.onError.attach(function(sender, shipment) { + _this.caseGrid.grid.setLoading(false); + }); + adapter.addCase(_this.shipment.json.shippingId); + }); + + this.caseGrid.onRemoveButtonClicked.attach(function(sender, dewarId) { + _this.panel.setLoading("ISPyB: removing case"); + _this.shipment.onSaved.attach(function(sender, shipment) { + _this.refresh(shipment); + + }); + _this.shipment.removeCase(dewarId); + }); +} + +ShipmentTabs.prototype.refresh = function(shipment) { + + var _this = this; + this.shipment = shipment; + var proposal = new Proposal(); + proposal.onDataRetrieved.attach(function(sender, plates) { + + _this.refreshWithPlates(shipment, plates); + _this.caseGrid.grid.setLoading(false); + }); + proposal.getPlatesByProposal(); +}; + +ShipmentTabs.prototype.refreshWithPlates = function(shipment, plates) { + this.shipment = new Shipment(shipment); + + this.caseGrid.refresh(this.shipment.getDewars(), plates); + this.panel.setLoading(false); +}; + +ShipmentTabs.prototype.error = function(error) { + var e = JSON.parse(error); + showError(e); + this.panel.setLoading(false); +}; + +//ShipmentTabs.prototype.refreshTabTitles = function() { +/*Ext.getCmp("MacromoleculeTab").setText(this.getMacromoleculeTitle()); +Ext.getCmp("BufferTab").setText(this.getBuffersTitle()); +Ext.getCmp("SpecimenTab").setText(this.getSpecimenTitle()); +Ext.getCmp("PlatesTab").setText(this.getPlatesTitle()); +Ext.getCmp("AssembliesTab").setText(this.getShipmentTitle()); +Ext.getCmp("PlateGroupsTab").setText(this.getPlateGroupsTitle());*/ +//}; +ShipmentTabs.prototype.draw = function(shipment) { + var _this = this; + _this.plates = []; + _this.shipment = shipment; + _this.render(shipment); + + // var proposal = new Proposal(); + // proposal.onDataRetrieved.attach(function(sender, plates){ + // _this.plates = plates; + // _this.shipment = shipment; + // _this.render(shipment); + // + // }); + // proposal.getPlatesByProposal(); +}; + +//ShipmentTabs.prototype.getShipmentTitle = function() { +// return 'Shipment'; +//}; + +//ShipmentTabs.prototype.getMacromoleculeTitle = function() { +// return 'Macromolecules (' + this.experiment.getMacromolecules().length + ')'; +//}; + +//ShipmentTabs.prototype.getBuffersTitle = function() { +// return 'Buffers (' + this.experiment.getBuffers().length + ')'; +//}; + +//ShipmentTabs.prototype.getPlateGroupsTitle = function() { +// return 'Plate Groups (' + this.experiment.getPlateGroups().length + ')'; +//}; + +//ShipmentTabs.prototype.getSampleChangerTitle = function() { +// return 'Sample Changer'; +//}; + +//ShipmentTabs.prototype.getSpecimenTitle = function() { +// return 'Specimens(' + this.experiment.getSpecimenCount() + ')'; +//}; + +//ShipmentTabs.prototype.getPlatesTitle = function() { +// return 'Plates(' + this.experiment.getSamplePlates().length + ')'; +//}; + +//ShipmentTabs.prototype.getBuffersTip = function() { +/*if (this.experiment.getBuffers().length == 0){ + return BUI.getWarningHTML("There are no buffers. Click on add to create new ones. Click on edit button or double click to edit them"); + +} +else{ + return BUI.getTipHTML("Click on edit button or double click to edit them. Click on duplicate to create an identical buffer including its additives") +}*/ +//}; + +//ShipmentTabs.prototype.refreshTips = function() { +/*Ext.getCmp("BufferTabTip").update(this.getBuffersTip()); +Ext.getCmp("SpecimenTabTip").update(this.getSpecimensTip());*/ +//}; + +ShipmentTabs.prototype.render = function(shipment) { + return this.getPanel(shipment); +}; + +ShipmentTabs.prototype.getShipmentHeader = function(shipment) { + var _this = this; + function getHTMLSource() { + var name = shipment.json.shippingName; + var status = shipment.json.shippingStatus; + var creationDate = shipment.json.creationDate; + var html = BUI.createFormLabel("Name :", name, 75, 400); + html = html + BUI.createFormLabel("Status :", status, 75, 400); + html = html + BUI.createFormLabel("Date :", creationDate, 75, 400); + return html; + } + + return Ext.create('Ext.container.Container', { + frame : false, + layout : 'hbox', + title : 'General', + padding : 5, + bodyPadding : '5 5 0 0', + width : 890, + margin : '0 0 10 0', + height : 100, + style : { + borderColor : '#BDBDBD', + borderStyle : 'solid', + borderWidth : '1px' + }, + fieldDefaults : { + msgTarget : 'side', + labelWidth : 100 + }, + items : [ { + margin : "0 0 0 0", + width : 475, + border : 0, + html : getHTMLSource() + } + ] + }); +}; + +ShipmentTabs.prototype.getTabPanel = function(shipment) { + this.panel = Ext.createWidget('tabpanel', { + height : 600, + style : { + padding : 2 + }, + items : [ { + tabConfig : { + id : 'Shipment', + title : 'Shipment', + icon : '/ispyb/images/plane-small.gif' + }, + items : [ { + xtype : 'container', + margin : '5 5 5 5', + items : [ this.shipmentForm.getPanel(shipment) ] + } ] + }, { + tabConfig : { + id : 'Cases', + title : 'Cases', + icon : '../images/box-icon-very-small.png' + }, + items : [ { + xtype : 'container', + margin : '5 5 5 5', + items : [ this.caseGrid.getPanel(shipment.getDewars(), this.plates) ] + } ] + } ] + }); + return this.panel; +}; + +ShipmentTabs.prototype.getPanel = function(shipment) { + var _this = this; + this.shipment = shipment; + if (this.plates == null) { + this.plates = []; + } + + if (this.shipPanel == null) { + this.shipPanel = Ext.create('Ext.container.Container', { + bodyPadding : 2, + width : Ext.getBody().getViewSize().width * 0.9, + renderTo : this.targetId, + style : { + padding : 2 + }, + items : [ this.getShipmentHeader(shipment), this.getTabPanel(shipment) ] + }); + } + + return this.shipPanel; +}; + +/** + * Shows an template with the specimens, measurements and the experiment's + * requirement + * + * @targetId + */ +function TemplateTabs(targetId) { + this.height = 600; + this.targetId = targetId; + + this.id = BUI.id(); + var _this = this; + + this.gridHeight = 1000; + /** data * */ + this.experiment = null; + + this.specimenSelected = null; + + /** Specimen Widget contains a specimenGrid and a sampleChangerWidget than can be displayed with are vertical or horizontal layout **/ + this.specimenWidget = new SpecimenWidget({ + height : this.height + }); + + this.samplePlateGroupWidget = new SamplePlateGroupWidget({ + showTitle : false, + height : 250, + margin : 5, + bbar : true + }); + + this.samplePlateGroupWidget.onExperimentChanged.attach(function(sender, experiment) { + _this.refresh(experiment); + }); + + this.samplePlateGroupWidget.onClick.attach(function(sender, args) { + }); + + this.volumePlanificator = new VolumeGrid(); + + /** For Measurements * */ + var storeViscosity = Ext.create('Ext.data.Store', { + fields : [ 'name' ], + data : [ { + "name" : "low" + }, { + "name" : "medium" + }, { + "name" : "high" + } ] + }); + + // Create the combo box, attached to the states data store + var viscosityEditor = Ext.create('Ext.form.ComboBox', { + fieldLabel : '', + store : storeViscosity, + queryMode : 'local', + displayField : 'name', + valueField : 'name' + }); + + this.measurementGrid = new MeasurementGrid({ + maxWidth : 1500, + estimateTime : false, + positionColumnsHidden : true, + isPriorityColumnHidden : true, + isStatusColumnHidden : true, + isTimeColumnHidden : true, + updateRowEnabled : true, + collapsed : true, + removeBtnEnabled : true, + showTitle : false, + collapseBtnEnable : false, + addBtnMultipleEdit : true, + sortingBtnEnable : true, + editor : { + exposureTemperature : { + xtype : 'textfield', + allowBlank : true + }, + comments : { + xtype : 'textfield', + allowBlank : true + }, + volumeToLoad : { + xtype : 'numberfield', + allowBlank : true + }, + transmission : { + xtype : 'numberfield', + allowBlank : true + }, + viscosity : viscosityEditor, + waitTime : { + xtype : 'numberfield', + allowBlank : true + }, + flow : { + xtype : 'checkbox', + allowBlank : true + } + } + }); + + this.measurementGrid.onSelected.attach(function(sender, measurements) { + var specimens = []; + for ( var i = 0; i < measurements.length; i++) { + specimens.push(_this.experiment.getSampleById(measurements[i].specimenId)); + } + }); + + this.measurementGrid.onMeasurementChanged.attach(function(sender, measurement) { + _this.experiment.setMeasurement(measurement); + _this.refresh(_this.experiment); + }); + + this.measurementGrid.onExperimentChanged.attach(function(sender, json) { + _this.refresh(new Experiment(json)); + }); + + this.measurementGrid.onRemoved.attach(function(sender, experiment) { + _this.refreshSpecimen(new Experiment(experiment)); + }); + + this.measurementGrid.onUpdateTime.attach(function(sender, args) { + document.getElementById(_this.id + "_counter").innerHTML = args.hours + 'h, ' + args.minutes + 'min and ' + args.seconds + ' seconds'; + }); + +} + +TemplateTabs.prototype.refreshMeasurement = function(experiment) { + this.experiment = experiment; + this.experiment.onSaved = new Event(this); + this.experiment.onSpecimenSaved = new Event(this); + var experimentList = new ExperimentList([ this.experiment ]); + this.measurementGrid.refresh(experimentList.getMeasurementsNotCollected(), experimentList); +}; + +TemplateTabs.prototype.refreshSpecimen = function(experiment) { + this.experiment = experiment; + this.experiment.onSaved = new Event(this); + this.experiment.onSpecimenSaved = new Event(this); + this.samplePlateGroupWidget.refresh(this.experiment); + this.specimenWidget.refresh(this.experiment); + this.volumePlanificator.refresh(this.experiment); +}; + +TemplateTabs.prototype.refresh = function(experiment) { + // var start = new Date().getTime(); + this.experiment = experiment; + this.experiment.onSaved = new Event(this); + this.experiment.onSpecimenSaved = new Event(this); + + // var experimentList = new ExperimentList([this.experiment]); + this.refreshMeasurement(experiment); + this.refreshSpecimen(experiment); + /** Refreshing grids * */ + this.panel.setLoading(false); + +}; + +TemplateTabs.prototype.error = function(error) { + var e = JSON.parse(error); + showError(e); + this.panel.setLoading(false); + +}; + +TemplateTabs.prototype.draw = function(experiment) { + this.render(experiment); +}; + + +TemplateTabs.prototype.getExperimentTitle = function() { + var _this = this; + var experimentHeaderForm = new ExperimentHeaderForm(); + return experimentHeaderForm.getPanel(this.experiment); +}; + +TemplateTabs.prototype.render = function(experiment) { + var _this = this; + this.experiment = experiment; + + /** + * + * Depending on the sample Changer configuration we want to display the plates vertically or horizontally + * Default is vertical + * + * */ + + var specimenContainer = this.specimenWidget.getPanel(); + this.specimenWidget.refresh(experiment); + + var experimentList = new ExperimentList([ _this.experiment ]); + var measurementContainer = Ext.create('Ext.container.Container', { + layout : { + type : 'vbox' + }, + defaults : { + style : { + padding : '5px 0px 0px 10px' + } + }, + items : [ _this.measurementGrid.getPanel(experimentList.getMeasurementsNotCollected(), experimentList) ] + }); + + this.panel = Ext + .createWidget( + 'tabpanel', + { + plain : true, + items : [ + { + tabConfig : { + title : 'Measurements' + }, + items : [ { + xtype : 'container', + layout : 'vbox', + border : 1, +// height : _this.gridHeight, + margin : "0 0 10 0", + items : [ measurementContainer ] + } + + ] + }, + { + tabConfig : { + id : 'genralTabl', + title : "Specimens" + // width : 900, + // border : 3 + + }, + items : [ specimenContainer ] + }, + { + tabConfig : { + title : "Requirements" + + }, + items : [ + { + html : BUI.getTipHTML("Estimated volume is the maximum volume required. Depending on the order of your measurements you may use less. Click on create stock solutions if you plan to ship these stock solutions"), + margin : "10 10 10 10", + border : 0 + }, this.volumePlanificator.getPanel(experiment) ] + } ] + }); + // ); + return this.getPanel(this.panel); +}; + +TemplateTabs.prototype.isTemplate = function() { + if (this.experiment.json.type == "TEMPLATE") { + return true; + } + return false; +}; + + +TemplateTabs.prototype.getPanel = function(panel) { + var _this = this; + if (this.experimentPanel == null) { + this.experimentPanel = Ext.create('Ext.container.Container', { + bodyPadding : 2, + width : 1000,//Ext.getBody().getViewSize().width * 0.9, + renderTo : this.targetId, + height : 500, +// style : { +// padding : 2 +// }, + items : [ + this.getExperimentTitle(), + this.panel + ], + listeners : { + afterrender : function(thisCmp) { + $("#SchemeReport" + _this.experiment.experimentId).click(function() { + $(this).target = "_blank"; + window.open('viewProjectList.do?reqCode=display&menu=platescheme&experimentId=' + _this.experiment.experimentId); + return false; + }); + + } + } + }); + } + return this.experimentPanel; +}; + +TemplateTabs.prototype.input = function(targetId) { + return new ExperimentTabs().input(); +}; + +TemplateTabs.prototype.test = function(targetId) { + var experimentTabs = new TemplateTabs(targetId); + BIOSAXS.proposal = new Proposal(experimentTabs.input().proposal); + experimentTabs.draw(new Experiment(experimentTabs.input().experiment)); +}; + +var BUI = { + //interval : 60000, + interval : 40000, + rainbow : function(numOfSteps, step) { + // This function generates vibrant, "evenly spaced" colours (i.e. no clustering). This is ideal for creating easily distinguishable vibrant markers in Google Maps and other apps. + // Adam Cole, 2011-Sept-14 + // HSV to RBG adapted from: http://mjijackson.com/2008/02/rgb-to-hsl-and-rgb-to-hsv-color-model-conversion-algorithms-in-javascript + var r, g, b; + var h = step / numOfSteps; + var i = ~~(h * 6); + var f = h * 6 - i; + var q = 1 - f; + switch (i % 6) { + case 0: + r = 1, g = f, b = 0; + break; + case 1: + r = q, g = 1, b = 0; + break; + case 2: + r = 0, g = 1, b = f; + break; + case 3: + r = 0, g = q, b = 1; + break; + case 4: + r = f, g = 0, b = 1; + break; + case 5: + r = 1, g = 0, b = q; + break; + } + var c = "#" + ("00" + (~~(r * 255)).toString(16)).slice(-2) + ("00" + (~~(g * 255)).toString(16)).slice(-2) + + ("00" + (~~(b * 255)).toString(16)).slice(-2); + return (c); + }, + getFileNameByPath : function(filePath) { + if (filePath != null){ + var split = filePath.split("/"); + if (split.length > 0){ + return split[split.length - 1]; + } + } + return "Not file"; + }, + getUpdateInterval : function() { + this.interval = this.interval + 2000; + return this.interval; + }, + getRadiationDamageThreshold : function() { + return 0.7; + }, + getQualityThreshold : function() { + return 0.7; + }, + getCreateShipmentURL : function() { + return '/ispyb/user/viewProjectList.do?reqCode=display&menu=create_shipment'; + }, + getCreateShipmentList : function() { + return '/ispyb/user/viewProjectList.do?reqCode=display&menu=list_shipment'; + }, + getShippingURL : function(shippingId) { + return '/ispyb/user/viewProjectList.do?reqCode=display&menu=shipment&shippingId=' + shippingId; + }, + + getMacromoleculeResultsURLByMultipleSearch : function(array) { + return '/ispyb/user/viewProjectList.do?reqCode=display&menu=macromolecule&search=' + + JSON.stringify(array).replace(new RegExp("\"", 'g'), "'"); + }, + getMacromoleculeResultsURL : function(macromoleculeId) { + return '/ispyb/user/viewProjectList.do?reqCode=display&menu=macromolecule¯omoleculeId=' + macromoleculeId; + }, + getMacromoleculeBufferResultsURL : function(macromoleculeId, bufferId) { + return '/ispyb/user/viewProjectList.do?reqCode=display&menu=macromolecule&bufferId=' + bufferId + '¯omoleculeId=' + macromoleculeId; + }, + + getMacromoleculeHeader : function(macromoleculeId) { + + function getHTMLSource(macromoleculeId) { + if (macromoleculeId != null) { + var html = BUI.createFormLabel("Name :", BIOSAXS.proposal.getMacromoleculeById(macromoleculeId).name, 75, 400); + html = html + BUI.createFormLabel("Acronym :", BIOSAXS.proposal.getMacromoleculeById(macromoleculeId).acronym, 75, 400); + if (BIOSAXS.proposal.getMacromoleculeById(macromoleculeId).comments != null) { + html = html + BUI.createFormLabel("Comments :", BIOSAXS.proposal.getMacromoleculeById(macromoleculeId).comments, 75, 400); + } + return html; + } + } + + return Ext.create('Ext.container.Container', { + frame : false, + layout : 'hbox', + title : 'Macromolecule', + bodyPadding : '5', + width : 890, + margin : '0 0 10 0', + height : 100, + style : { + borderColor : '#BDBDBD', + borderStyle : 'solid', + borderWidth : '1px' + }, + fieldDefaults : { + msgTarget : 'side', + labelWidth : 100 + }, + items : [ { + margin : "10 0 0 10", + width : 475, + border : 0, + html : getHTMLSource(macromoleculeId) + }, { + margin : "10 0 0 10", + width : 475, + border : 0, + html : BUI.getZipHTMLByMacromoleculeId(macromoleculeId) + } + ] + }); + }, + + getZipHTMLByMacromoleculeId : function(macromoleculeId) { + if (macromoleculeId != null) { + var fileName = BIOSAXS.proposal.getMacromoleculeById(macromoleculeId).acronym; + return ""; + } + }, + getZipHTMLByExperimentId : function(experimentId, filename) { + if (filename == null){ + filename = "experiment"; + } + return ""; + }, + + getZipURLByAverageId : function(averageId, filename) { + if (filename == null){ + filename = "experiment"; + } + return "/ispyb/user/dataadapter.do?reqCode=getZipFileByAverageListId&f&mergeIdsList=" + averageId + "&fileName=" + filename; + }, + getZipURLBySubtractionId : function(subtractionId, filename) { + if (filename == null){ + filename = "experiment"; + } + return "/ispyb/user/dataadapter.do?reqCode=getZipFileByAverageListId&f&subtractionIdList=" + subtractionId + "&fileName=" + filename; + }, + + + getZipHTMLByFrameRangeId : function(experimentId, start, end) { + var fileName = "experiment"; + return ""; + }, + getZipFrameHPLCUrl : function(experimentId, start, end) { + return "/ispyb/user/dataadapter.do?reqCode=getZipFileH5ByFramesRange&f&experimentId=" + experimentId + "&start=" + Number(start) +"&end="+ Number(end); + }, + + getQueueUrl : function() { + return "/ispyb/user/dataadapter.do?reqCode=getPagingCompactAnalysisByProposalId"; + }, + + getQueueUrlByExperiment: function(experimentId) { + return "/ispyb/user/dataadapter.do?reqCode=getPagingCompactAnalysisByExperimentId&f&experimentId=" + experimentId; + }, + getStandardDeviation : function(values) { + var sum = 0; + var count = 0; + var avg = null; + + var curatedValues = new Array(); + for ( var i = 0; i < values.length; i++) { + var value = values[i]; + if (value != null) { + if (!isNaN(value)) { + count = count + 1; + sum = sum + Number(value); + curatedValues.push(Number(value)); + } + } + } + + if (count > 0) { + avg = sum / count; + } else { + avg = sum; + } + var aux = 0; + for ( var i = 0; i < curatedValues.length; i++) { + var value = curatedValues[i]; + aux = aux + Math.pow(value - avg, 2); + } + /** std **/ + var std = Math.sqrt(aux / count); + return { + std : (std), + sum : (sum), + avg : (avg), + validNumber : count, + totalNumber : values.length, + values : values + }; + }, + + getHTMLTableForFrameAveraged : function(bufferAcronym, macromoleculeAcronym, bbmerges, molmerges, bamerges, totalframes, bufferId,macromoleculeId, macromoleculeColor) { + + function getFrameSpan(framesMerged, total) { + return "(" + framesMerged + " of " + total + ")"; + } + + function getColorFrame(framesMerged, total) { + if (framesMerged / total < 0.5) { + return "#FA5858"; + } + if ((framesMerged / total >= 0.5) && (framesMerged / total < 0.8)) { + return "#FF9900"; + } + return "white"; + } + + function getRow(color, acroynm, framesMerged, totalframes) { + return " " + + BUI.getRectangleColorDIV(color, 10, 10) + + " " + acroynm + "" + + getFrameSpan(framesMerged, totalframes) + ""; + } + + var html = ""; + + /** Buffer Before **/ + if (bufferAcronym != null) { + if (bbmerges != null) { + color = BIOSAXS.proposal.bufferColors[bufferId]; + html = html + getRow(color, bufferAcronym, bbmerges, totalframes); + } + } + + /** Molecule **/ + if (macromoleculeAcronym != null) { + if (molmerges != null) { + if (macromoleculeColor == null){ + color = BIOSAXS.proposal.macromoleculeColors[macromoleculeId]; + } + else{ + color = macromoleculeColor; //BIOSAXS.proposal.macromoleculeColors[macromoleculeId]; + } + html = html + getRow(color, macromoleculeAcronym, molmerges, totalframes); + } + } + + /** Buffer After **/ + if (bufferAcronym != null) { + if (bamerges != null) { + color = BIOSAXS.proposal.bufferColors[bufferId]; + html = html + getRow(color, bufferAcronym, bamerges, totalframes); + } + } + return html + "
"; + }, + isWebGLEnabled : function(return_context) { + if (!!window.WebGLRenderingContext) { + var canvas = document.createElement("canvas"); + names = [ "webgl", "experimental-webgl", "moz-webgl", "webkit-3d" ]; + context = false; + for ( var i = 0; i < 4; i++) { + try { + context = canvas.getContext(names[i]); + if (context && typeof context.getParameter == "function") { + // WebGL is enabled + if (return_context) { + // return WebGL object if the function's argument is present + return { + name : names[i], + gl : context + }; } + // else, return just true + return true; } - } ] - }, - "concentrationLabel" : "7.17 mg/ml ,3.53 mg/ml ,1.75 mg/ml ,0.91 mg/ml " + } catch (e) { + } + } + // WebGL is supported, but disabled + return false; + } + // WebGL not supported28. + return false; + }, + getHTMLTableForPrefixes : function(bufferBeforeaverageFilePath, averageFilePath, bufferAfterAverageFilePath) { + + function getRow(bufferBeforeaverageFilePath) { + file = bufferBeforeaverageFilePath; + try { + file = bufferBeforeaverageFilePath.split("/")[bufferBeforeaverageFilePath.split("/").length - 1]; + } catch (e) { + file = "NA"; + } + return "" + file + ""; + } + var html = ""; + + /** Buffer Before **/ + if (bufferBeforeaverageFilePath != null) { + html = html + getRow(bufferBeforeaverageFilePath); + } + + /** Molecule **/ + if (averageFilePath != null) { + html = html + getRow(averageFilePath); + } + + /** Buffer After **/ + if (bufferAfterAverageFilePath != null) { + html = html + getRow(bufferAfterAverageFilePath); + } + return html + "
"; + }, + + getBaseURL : function() { + return '/ispyb/user/dataadapter.do'; + }, + + getPrintcomponentURL : function(dewarId) { + return '/ispyb/user/viewDewarAction.do?reqCode=generateLabels&dewarId=' + dewarId; + + }, + getPDBVisualizerURL : function(modelId, subtractionId, experimentId) { + return '/ispyb/user/viewProjectList.do?reqCode=display&menu=PDBVisualizer&modelId=' + modelId + '&experimentId=' + experimentId + + '&subtractionId=' + subtractionId; + }, + + getURL : function() { + return this.getBaseURL() + '?reqCode=getImage'; + + }, + getAbinitioImageURL : function() { + return this.getBaseURL() + '?reqCode=getAbinitioImage'; + }, + getNSDImageURL : function(modelListId) { + return BUI.getAbinitioImageURL() + '&type=NSD&modelListId=' + modelListId; + }, + getCHI2ImageURL : function(modelListId) { + return BUI.getAbinitioImageURL() + '&type=CHI2&modelListId=' + modelListId; + }, + getModelFile : function(type, modelId, format) { + return this.getBaseURL() + '?reqCode=getModelFile' + "&type=" + type + "&modelId=" + modelId + "&format=" + format; + }, + getPdbURL : function() { + return this.getBaseURL() + '?reqCode=getPdbFiles'; + }, + getStvArray : function(value, error) { + value = Number(value); + error = Number(error); + return [ value - error, value, value + error ]; + }, + getPointArrayForDygraph : function(x, y, error) { + return [ x, BUI.getStvArray(y, error) ]; + }, + createDIV : function(text, width, className, backgroundColor) { + var nameContainer = document.createElement("div"); + var nameSpan = document.createElement("span"); + if (className != null) { + nameSpan.setAttribute("class", className); + } + if (backgroundColor != null) { + nameSpan.setAttribute("style", "float:left;width:" + width + "px;height:18px;background-color:" + backgroundColor); + } else { + nameSpan.setAttribute("style", "float:left;width:" + width + "px;height:18px;"); + } + nameSpan.appendChild(document.createTextNode(text)); + nameContainer.appendChild(nameSpan); + return nameContainer; + }, + + createFormLabel : function(labelText, text, labelWidth, textWidth, backgroundColor) { + var div = document.createElement("div"); + + div.appendChild(BUI.createDIV(labelText, labelWidth, "bLabel", backgroundColor)); + div.appendChild(BUI.createDIV(text, textWidth, "btext", backgroundColor)); + return div.innerHTML; + }, + + createTextArea : function(labelText, text, labelWidth, rows, cols) { + var div = document.createElement("div"); + div.appendChild(BUI.createDIV(labelText, labelWidth, "bLabel")); + var textArea = document.createElement("textarea"); + textArea.setAttribute("rows", rows); + textArea.setAttribute("cols", cols); + textArea.appendChild(document.createTextNode(text)); + div.appendChild(textArea); + return div.innerHTML; + }, + + showBetaWarning : function() { + alert("ISPyB for Biosaxs version Beta has not this functionality enabled"); + }, + + formatValuesErrorUnitsScientificFormat : function(val, error, unit, args) { + var fontSize = 14; + var decimals = 2; + var errorFontSize = 10; + /** line break **/ + var lineBreak = true; + if (args != null) { + if (args.fontSize != null) { + fontSize = args.fontSize; + } + if (args.decimals != null) { + decimals = args.decimals; + } + if (args.errorFontSize != null) { + errorFontSize = args.errorFontSize; + } + if (args.lineBreak != null) { + lineBreak = args.lineBreak; + } + + } + + if (val == "") { + return ""; + } + if (error == null) { + return "" + Number(val).toFixed(decimals) + ""; + } + var html = "" + Number(val).toFixed(decimals) + " " + unit + ""; + if (lineBreak) { + html = html + "
"; + } + return html + " ± " + Number(Number(error).toFixed(3)).toExponential() + + ""; + }, + + formatValuesErrorUnits : function(val, error, unit, args) { + var fontSize = 16; + var decimals = 2; + var errorFontSize = 10; + /** line break **/ + var lineBreak = true; + if (args != null) { + if (args.fontSize != null) { + fontSize = args.fontSize; + } + if (args.decimals != null) { + decimals = args.decimals; + } + if (args.errorFontSize != null) { + errorFontSize = args.errorFontSize; + } + if (args.lineBreak != null) { + lineBreak = args.lineBreak; + } + + } + + if (val == "") { + return ""; + } + if (error == null) { + return "" + Number(val).toFixed(decimals) + ""; + } + var html = "" + Number(val).toFixed(decimals) + " " + unit + ""; + if (lineBreak) { + html = html + "
"; + } + return html + " ± " + Number(Number(error).toFixed(8)).toExponential() + + ""; + }, + + formatValuesUnits : function(val, unit, args) { + var fontSize = 12; + var decimals = 2; + var unitsFontSize = 10; + if (args != null) { + if (args.fontSize != null) { + fontSize = args.fontSize; + } + if (args.decimals != null) { + decimals = args.decimals; + } + if (args.unitsFontSize != null) { + unitsFontSize = args.unitsFontSize; + } + + } + + if (val === "") { + return ""; + } + if (unit == null) { + return "" + Number(val).toFixed(decimals) + ""; + } + return "" + Number(val).toFixed(decimals) + " " + unit + ""; + }, + + getGreenButton : function(text, args) { + var width = 70; + var height = 20; + if (args != null) { + if (args.width != null) { + width = args.width; + } + if (args.height != null) { + height = args.height; + } + } + + return ''; + }, +// getBlueButton : function(text, args) { +// var width = 70; +// var height = 20; +// if (args != null) { +// if (args.width != null) { +// width = args.width; +// } +// if (args.height != null) { +// height = args.height; +// } +// } +// +// return ''; +// }, + + getBlueButton : function(text, args) { + var width = 70; + var height = 20; + var href = null; + if (args != null) { + if (args.width != null) { + width = args.width; + } + if (args.height != null) { + height = args.height; + } + if (args.href != null) { + href = args.href; + } + } + if (href != null) { + return ''; + } else { + return ''; +// return ''; + } + }, + + getSubmitGreenButton : function(text) { + return ''; + }, + + getRedButton : function(text) { + return ''; + + }, + getRectangleColorDIV : function(color, height, width) { + return '
'; + }, + + openBufferWindow : function(bufferId) { + var window = new BufferWindow(); + window.draw(tabs.experiment.getBufferById(bufferId), tabs.experiment); + }, + + /** Render for safety levels on grids **/ + safetyRenderer : function(val, y, specimen) { + var color = val; + if (val == "YELLOW") { + color = "#E9AB17"; + } + return '' + val + ''; + }, + + getSampleColor : function() { + return '#CB181D'; + }, + + getLightSampleColor : function() { + return '#FCBBA1'; + }, + + getBufferColor : function() { + return '#6A51A3'; + }, + getLightBufferColor : function() { + return '#BCBDDC'; + }, + + formatConcentration : function(val) { + if (val != null) { + return "" + Number(val).toFixed(2) + " mg/ml "; + } + return val; + }, + + formatVolume : function(sample, volume) { + if (Number(sample.data.volumeToLoad) > Number(sample.data.volume)) { + return "" + volume + " �l"; + } + if (Number(sample.data.volumeToLoad) == Number(sample.data.volume)) { + return "" + volume + " �l"; + } + return "" + volume + " �l"; + }, + + getProposal : function() { + return new Proposal(); + }, + + getSampleNameRenderer : function(val, y, record) { + var sample = record.data; + if (record.raw.macromolecule3VO == null) { + return '' + sample.code + ''; + } else { + return '' + sample.code + ''; + } + }, + + getSafetyLevels : function() { + var safetyLevels = new Array(); + safetyLevels.push({ + safetyLevelId : "", + name : "UNKNOWN" + }); + safetyLevels.push({ + safetyLevelId : 1, + name : "GREEN" + }); + safetyLevels.push({ + safetyLevelId : 2, + name : "YELLOW" + }); + safetyLevels.push({ + safetyLevelId : 3, + name : "RED" + }); + return safetyLevels; + }, + + getErrorColor : function() { + return '#F6CED8'; + }, + getWarningColor : function() { + return '#F5DA81'; + }, + getValidColor : function() { + return '#E0F8E0'; + }, + getSamplePlateLetters : function() { + return [ "A", "B", "C", "D", "E", "F", "G", "H" ]; + }, + getSamplePositionHTML : function(sample, experiment) { + var plate = ""; + var row = ""; + var column = ""; + var rows = this.getSamplePlateLetters(); + if (sample.sampleplateposition3VO != null) { + var samplePlate = experiment.getSamplePlateById(sample.sampleplateposition3VO.samplePlateId); + if (samplePlate != null) { + plate = (samplePlate.slotPositionColumn); + row = (sample.sampleplateposition3VO.rowNumber); + column = (sample.sampleplateposition3VO.columnNumber); + // var html = "Plate: " + "" + plate + ""; + // html = html + ", Row: " + "" + rows[row - 1] + ""; + // html = html + ", Column: " + "" + column + ""; + var html = "Plate: " + plate + + "-" + rows[row - 1] + "" + column + ""; + return html; + } + } + return ""; + }, + + getSafetyLabelName : function(safetyLevelId) { + var safetyLevels = BUI.getSafetyLevels(); + for ( var i = 0; i < safetyLevels.length; i++) { + if (safetyLevels[i].safetyLevelId == safetyLevelId) { + return safetyLevels[i].name; + } + } + return "UNKNOWN"; + }, + /** generate random id **/ + id : function() { + var text = ""; + var possible = "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789"; + + for ( var i = 0; i < 5; i++) + text += possible.charAt(Math.floor(Math.random() * possible.length)); + + return text; + }, + showWarning : function(message) { + Ext.Msg.show({ + title : 'Warning', + msg : message, + icon : Ext.Msg.WARNING, + animEl : 'elId' + }); + }, + showError : function(message) { + Ext.Msg.show({ + title : 'Warning', + msg : message, + icon : Ext.Msg.ERROR, + animEl : 'elId' + }); + }, + getTipHTML : function(message) { + //return "
Tip
" + // + message + "
"; + return "
Tip
" + + message + "
"; + }, + + getWarningHTML : function(message) { + return "
Warning
" + + message + "
"; + }, + + getErrorHTML : function(message) { + return "
Error
" + + message + "
"; + }, + + getProgessBar : function(percentage, text) { + /** percentage 100% green **/ + var color = "#0a0"; + + color = "#99CC00"; + if (percentage > 100) { + color = "yellow"; + percentage = 100; + } + if (isNaN(percentage)) { + color = "white"; + percentage = 0; + } + + var defaultText = percentage + "%"; + if (text != null) { + defaultText = text; + } + + return "
" + defaultText + "
"; + }, + getFileName : function(filePath){ + if (filePath != null){ + return filePath.split("/")[filePath.split("/").length - 1] + } + return ""; + } + +}; + +Ext.ux.form.RequiredCombo = Ext.extend(Ext.form.ComboBox, { + config : { + cls : 'custom-field-text-required' + }, + initComponent : function() { + Ext.ux.form.RequiredCombo.superclass.initComponent.apply(this, arguments); + }, + checkChange : function() { + if ((this.getValue() == null) || String(this.getValue()).length == 0) { + this.addCls('custom-field-text-required'); + } else { + this.removeCls('custom-field-text-required'); + } + } +}); + +Ext.define('Ext.form.field.RequiredNumber', { + extend : 'Ext.form.field.Number', + alias : 'widget.requirednumberfield', + alternateClassName : [ 'Ext.form.RequiredNumberField', 'Ext.form.RequiredNumber' ], + config : { + cls : 'custom-field-text-required' + }, + + initComponent : function() { + var me = this; + me.callParent(); + me.setMinValue(me.minValue); + me.setMaxValue(me.maxValue); + }, + + onChange : function() { + if ((this.getValue() == null) || String(this.getValue()).length == 0) { + this.addCls('custom-field-text-required'); + } else { + this.removeCls('custom-field-text-required'); + } + this.toggleSpinners(); + this.callParent(arguments); + } +}); + +Ext.define('Ext.form.field.RequiredText', { + extend : 'Ext.form.field.Text', + alias : 'widget.requiredtext', + requires : [ 'Ext.form.field.VTypes', 'Ext.layout.component.field.Text' ], + alternateClassName : [ 'Ext.form.RequiredTextField', 'Ext.form.RequiredText' ], + config : { + cls : 'custom-field-text-required' + }, + initComponent : function() { + var me = this; + if (me.allowOnlyWhitespace === false) { + me.allowBlank = false; } - }; -}; + me.callParent(); + me.addEvents( + /** + * @event autosize + * Fires when the **{@link #autoSize}** function is triggered and the field is resized according to the + * {@link #grow}/{@link #growMin}/{@link #growMax} configs as a result. This event provides a hook for the + * developer to apply additional logic at runtime to resize the field if needed. + * @param {Ext.form.field.Text} this This text field + * @param {Number} width The new field width + */ + 'autosize', -ConcentrationHTMLTableWidget.prototype.test = function(targetId) { - var concentrationHTMLTableWidget = new ConcentrationHTMLTableWidget(); - document.getElementById(targetId).innerHTML = concentrationHTMLTableWidget.getPanel(concentrationHTMLTableWidget.input().data); -}; - -function DataCollectionWidget() { + /** + * @event keydown + * Keydown input field event. This event only fires if **{@link #enableKeyEvents}** is set to true. + * @param {Ext.form.field.Text} this This text field + * @param {Ext.EventObject} e + */ + 'keydown', + /** + * @event keyup + * Keyup input field event. This event only fires if **{@link #enableKeyEvents}** is set to true. + * @param {Ext.form.field.Text} this This text field + * @param {Ext.EventObject} e + */ + 'keyup', + /** + * @event keypress + * Keypress input field event. This event only fires if **{@link #enableKeyEvents}** is set to true. + * @param {Ext.form.field.Text} this This text field + * @param {Ext.EventObject} e + */ + 'keypress'); + me.addStateEvents('change'); + me.setGrowSizePolicy(); + }, + checkChange : function() { + if ((this.getValue() == null) || String(this.getValue()).length == 0) { + this.addCls('custom-field-text-required'); + } else { + this.removeCls('custom-field-text-required'); + } + } +}); -}; +var BIOSAXS_COMBOMANAGER = { -DataCollectionWidget.prototype.refresh = function(subtractionId) { + getComboMacromoleculeByMacromolecules : function(macromolecules, args) { + var labelWidth = 150; + var margin = "0 0 5 0"; + var width = 300; -}; + if (args != null) { + if (args.labelWidth != null) { + labelWidth = args.labelWidth; + } + if (args.margin != null) { + margin = args.margin; + } + if (args.width != null) { + width = args.width; + } + } -DataCollectionWidget.prototype.getMacromolecule = function(data) { - for (var i = 0; i < data.length; i++) { - if (data[i].macromoleculeId != null) { - return BIOSAXS.proposal.getMacromoleculeById(data[i].macromoleculeId); + var store = Ext.create('Ext.data.Store', { + fields : [ 'macromoleculeId', 'acronym' ], + data : macromolecules, + sorters : [ 'acronym' ] + }); + + return Ext.create('Ext.form.ComboBox', { + fieldLabel : 'Macromolecules', + labelWidth : labelWidth, + width : width, + margin : margin, + store : store, + editable: false, + queryMode : 'local', + displayField : 'acronym', + valueField : 'macromoleculeId' + }); + }, + getComboBuffers : function(buffers, args) { + var labelWidth = 150; + var margin = "0 0 5 0"; + var width = 300; + var fieldLabel = 'Buffer'; + + if (args != null) { + if (args.labelWidth != null) { + labelWidth = args.labelWidth; + } + if (args.margin != null) { + margin = args.margin; + } + if (args.width != null) { + width = args.width; + } + if (args.noLabel != null) { + fieldLabel = null; + } } - } - return null; -}; -DataCollectionWidget.prototype.getMacromoleculeContainer = function(data) { - var macromolecule = this.getMacromolecule(data); + var store = Ext.create('Ext.data.Store', { + fields : [ 'bufferId', 'acronym' ], + data : buffers, + sorters : [ 'acronym' ] + }); - var disabled = false; - if (macromolecule == null) { - disabled = true; - } + return Ext.create('Ext.form.ComboBox', { + fieldLabel : fieldLabel, + labelWidth : labelWidth, + width : width, + margin : margin, + editable: false, + store : store, + queryMode : 'local', + displayField : 'acronym', + valueField : 'bufferId' + }); + }, + getComboSessions : function(sessions, args) { + var labelWidth = 150; + var margin = "0 0 5 0"; + var width = 300; - var acronym = (macromolecule == null ? "" : macromolecule.acronym); - var mm = (macromolecule == null ? "" : macromolecule.molecularMass); - var comments = (macromolecule == null ? "" : macromolecule.comments); + if (args != null) { + if (args.labelWidth != null) { + labelWidth = args.labelWidth; + } + if (args.margin != null) { + margin = args.margin; + } + if (args.width != null) { + width = args.width; + } + } - return Ext.create('Ext.Panel', { - width : 500, - height : 200, - disabled : disabled, - title : "Macromolecule", - layout : 'form', - bodyPadding : 5, - defaultType : 'textfield', - tbar : { - defaultButtonUI : 'default', - items : [ { - xtype : 'button', - text : 'Edit', - cls : 'btn-with-border', - handler : function() { - var macromoleculeWindow = new MacromoleculeWindow(); - macromoleculeWindow.draw(macromolecule); - /** TODO: update when save **/ - } - } ] - }, - items : [ { - fieldLabel : 'Acronym', - name : 'first', - readOnly : true, - value : acronym - }, { - fieldLabel : 'Molecular Mass', - name : 'last', - readOnly : true, - value : mm - }, { - xtype : 'textareafield', - fieldLabel : 'Comments', - value : '', - name : 'last', - readOnly : true, - value : comments - } ] - }); -}; + for ( var i = 0; i < sessions.length; i++) { + sessions[i]["startDateFormatted"] = moment(sessions[i].startDate).format("MMM Do YY"); + sessions[i]["sorter"] = moment(sessions[i].startDate).format("YYYYMMDD"); + } -DataCollectionWidget.prototype.getBufferContainer = function(data) { - var _this = this; - var buffer = BIOSAXS.proposal.getBufferById(data[0].bufferId); + var store = Ext.create('Ext.data.Store', { + fields : [ 'sessionId', 'startDateFormatted', 'beamlineName', 'startDate', 'endDate', 'beamlineOperator' ], + data : sessions, + sorters : [ 'sorter' ] + }); - return Ext.create('Ext.Panel', { - width : 500, - height : 200, - title : "Buffer", - layout : 'form', - // collapsed : true, - // collapsible : true, - bodyPadding : 5, - defaultType : 'textfield', - style : { - padding : '0px 0px 0px 2px' - }, - tbar : { - defaultButtonUI : 'default', - items : [ { - xtype : 'button', - text : 'Edit', - cls : 'btn-with-border', - handler : function() { - var bufferWindow = new BufferWindow(); - bufferWindow.draw(BIOSAXS.proposal.getBufferById(data[0].bufferId)); - /** TODO: update when save **/ - } + return Ext.create('Ext.form.ComboBox', { + fieldLabel : 'Sessions', + labelWidth : labelWidth, + width : width, + margin : margin, + store : store, + queryMode : 'local', + // displayField : 'startDate', + valueField : 'sessionId', + // Template for the dropdown menu. + // Note the use of "x-boundlist-item" class, + // this is required to make the items selectable. + tpl : Ext.create('Ext.XTemplate', '', + '
{startDateFormatted} {beamlineName}
', ''), + // template for the content inside text field + displayTpl : Ext.create('Ext.XTemplate', '', '{startDateFormatted}', '') - } ] - }, - items : [ { - fieldLabel : 'Buffer', - name : 'acronym', - readOnly : true, - value : buffer.acronym - }, { - fieldLabel : 'Composition', - name : 'last', - readOnly : true, - value : buffer.composition + }); + } +}; + + function GenericWindow(args){ + this.title = "title"; + this.width = 700; + this.height = 500; + this.id = BUI.id(); + + this.close = false; + this.draggable = true; + this.modal = true; + + if (args != null){ + if (args.actions != null){ + this.actions = args.actions; + } + if (args.form != null){ + this.form = args.form; + } + if (args.width != null){ + this.width = args.width; + } + if (args.modal != null){ + this.modal = args.modal; + } + + if (args.height != null){ + this.height = args.height; + } + if (args.title != null){ + this.title = args.title; + } + if (args.form != null){ + this.form = args.form; + } + if (args.close != null){ + this.close = args.close; + } + if (args.draggable != null){ + this.draggable = args.draggable; + } + + } + /** Events **/ + this.onSaved = new Event(this); + }; + + + +GenericWindow.prototype.getButtons = function() { + var _this = this; + + if (this.close){ + return [ { + text : 'Close', + handler : function() { + _this.panel.close(); + } + } ]; + } + else{ + return [ { + text : 'Save', + handler : function() { + _this.save(); + + } }, { - xtype : 'textareafield', - fieldLabel : 'Comments', - value : buffer.comments, - name : 'last', - readOnly : true - - } ] - }); + text : 'Cancel', + handler : function() { + _this.panel.close(); + } + } ]; + } }; -DataCollectionWidget.prototype.getSpecimenContainer = function(data) { - return Ext.create('Ext.container.Container', { - layout : { - type : 'hbox' - }, - style : { - margin : '10px 10px 10px 10px' - }, - border : 0, - style : { - borderColor : '#000000', - borderStyle : 'solid', - borderWidth : '1px' - }, - defaults : { - labelWidth : 80, - // implicitly create Container by specifying xtype - xtype : 'datefield', - flex : 1, - - }, - items : [ this.getMacromoleculeContainer(data), this.getBufferContainer(data) ] - }); +GenericWindow.prototype.save = function (){ + alert("Method save of GenerciWindow class is abstract"); }; -DataCollectionWidget.prototype.getSeparator = function() { - return { - html : "
", - border : 0 - } +GenericWindow.prototype._postRender = function(data, experiment){ + }; -DataCollectionWidget.prototype.getFitStructurePanel = function(data) { - var _this = this; - - return Ext.create('Ext.container.Container', { - layout : { - type : 'hbox' - }, - style : { - margin : '10px 10px 10px 10px' - }, - border : 0, - style : { - borderColor : '#000000', - borderStyle : 'solid', - borderWidth : '1px' - }, - defaults : { - labelWidth : 80, - xtype : 'datefield', - flex : 1 - }, - items : [ - ] - }); +GenericWindow.prototype.draw = function (data, experiment){ + this._render(data, experiment); }; -DataCollectionWidget.prototype.getFitStructurePanelWorkflow = function(data) { - var _this = this; - var macromolecule = this.getMacromolecule(data); - - var items = []; +GenericWindow.prototype.refresh = function(data, experiment){ + this.data = data; + this.experiment = experiment; + this.form.refresh(data, experiment); +}; - /** Adding all the pdb files linked to the macromolecule **/ - // if (macromolecule.structure3VOs != null) { - // if (macromolecule.structure3VOs.length > 0) { - // - // items.push(); - // } - // } else { - // items.push({ - // html : "No apriori information added to this macromolecule. Apriori information needed for further analysis", - // margin : "5 5 5 5" - // }); - // } - var fitStructureToExperimentDataGrid = new FitStructureToExperimentDataGrid(); - - fitStructureToExperimentDataGrid.refresh(_this.data[0].subtractionId, _this.getMacromolecule(data)); - return Ext.create('Ext.container.Container', { - style : { - margin : '10px 10px 10px 10px' - }, - border : 0, +GenericWindow.prototype._render = function(data, experiment){ + this.data = data; + var _this = this; + if (this.panel == null){ + this.panel = Ext.create('Ext.Window', { + id : this.id, + title : this.title, + resizable : true, + constrain : true, + border : 1, + modal : this.modal, + frame : false, + draggable : this.draggable, + closable : true, + autoscroll : true, + layout : { type: 'vbox',align: 'stretch'}, + width : this.width, + height : this.form.height, + buttonAlign :'right', + buttons : this.getButtons(), + items : this.form.getPanel(data, experiment), + listeners: { + scope : this, + minimize : function(){ + this.panel.hide(); + }, + destroy : function(){ + delete this.panel; + } + } + }); + this.panel.setLoading(); + } + + this.panel.show(); + this._postRender(); +}; +function CalendarWidget(args) { + this.height = 740; - style : { - borderColor : '#000000', - borderStyle : 'solid', - borderWidth : '1px' - }, - defaults : { - labelWidth : 80, - xtype : 'datefield', - flex : 1 - }, - items : [ fitStructureToExperimentDataGrid.getPanel() ], - listeners : { - afterrender : function() { - } + if (args != null) { + if (args.height != null) { + this.height = args.height; } - }); -}; -/** Static method **/ -DataCollectionWidget.prototype.RUNFitScattering = function(subtractionId, structureId) { - var _this = this; - /** Add to Workflow **/ - var adapter = new BiosaxsDataAdapter(); - var workflow = { - 'workflowTitle' : 'FitExperimentalDatatoStructure', - 'comments' : 'FitExperimentalDatatoStructure run from ISPyB for subtractionId: ' + subtractionId + ' and structureId ' + structureId } - var inputs = [ { - name : 'subtractionId', - value : subtractionId - }, { - name : 'structureId', - value : structureId - } ]; + this.onClick = new Event(); +} - adapter.onSuccess.attach(function(sender, data) { - /** Add to Fit **/ - var adapter2 = new BiosaxsDataAdapter(); - var fit = { - 'workflowId' : data.workflowId, - 'subtractionId' : subtractionId, - 'structureId' : structureId, - 'comments' : 'Sent to workflow engine' - } - adapter2.onSuccess.attach(function(sender, fit) { +CalendarWidget.prototype.loadData = function(data) { + this.events = []; - }); - adapter2.addFitStructureData(fit); + for ( var i = 0; i < data.length; i++) { + var date = moment(data[i].creationDate); + var textColor = 'black'; - }); - adapter.addWorkflow(workflow, inputs); + if (data[i].status == "FINISHED") { + textColor = 'green'; + } + if (data[i].status == "ABORTED") { + textColor = 'red'; + } + this.events.push({ + title : data[i].name, + start : date.format("YYYY-MM-DD HH:mm:ss"), + end : date.format("YYYY-MM-DD HH:mm:ss"), + date : date, + allDay : false, + color : textColor, + className : date.format("YYYY-MM-DD") + }); + } }; -DataCollectionWidget.prototype.getSuperpositionTab = function(data) { +CalendarWidget.prototype.draw = function(targetId) { var _this = this; + $('#' + targetId).fullCalendar({ + eventClick : function(calEvent, jsEvent, view) { + _this.onClick.notify(calEvent.className[0]); - this.superpositionGrid = new SuperpositionGrid(); - - return Ext.create('Ext.container.Container', { - style : { - margin : '10px 10px 10px 10px' - }, - border : 0, - style : { - borderColor : '#000000', - borderStyle : 'solid', - borderWidth : '1px' - }, - items : [ _this.superpositionGrid.getPanel() ], - listeners : { - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - - }, - afterrender : function() { - /** Getting Rigid bodies **/ - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, result) { - _this.superpositionGrid.refresh(result); - }); - adapter.getSuperpositionBySubtractionId(data[1].subtractionId); - } - } - }); -}; - -DataCollectionWidget.prototype.getAdvancedTab = function(data) { - var _this = this; - return Ext.create('Ext.container.Container', { - style : { - margin : '10px 10px 10px 10px' }, - border : 0, - style : { - borderColor : '#000000', - borderStyle : 'solid', - borderWidth : '1px' + contentHeight : _this.height, + header : { + left : 'prev,next today', + center : 'title', + right : 'month,basicWeek,basicDay' }, - items : [ _this.getFitStructurePanel(data), _this.getFitStructurePanelWorkflow(data) ] + editable : false, + events : this.events }); -}; - -DataCollectionWidget.prototype.getRigiBodyForm = function(data) { - var _this = this; - _this.rigiBodyGrid = new RigidModelGrid(); - return _this.rigiBodyGrid.getPanel(); }; + +/** + * It shows a table with the guinier and gnom data as well as passed and + * discarded measurements + * + * @height + * @showBufferColumns + */ +function ConcentrationHTMLTableWidget(args) { + this.id = BUI.id(); -DataCollectionWidget.prototype.getRigidBodyModelingTab = function(data) { - var _this = this; - return Ext.create('Ext.container.Container', { - style : { - margin : '10px 10px 10px 10px' - }, - border : 0, - style : { - borderColor : '#000000', - borderStyle : 'solid', - borderWidth : '1px' - }, - items : [ _this.getRigiBodyForm(data) ], - listeners : { - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + this.showBufferColumns = true; - }, - afterrender : function() { - /** Getting Rigid bodies **/ - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, result) { - _this.rigiBodyGrid.refresh(result); - }); - adapter.getRigidBodyModelingBySubtractionId(data[1].subtractionId); - } + if (args != null) { + if (args.height != null) { + this.height = args.height; } - }); -}; - -DataCollectionWidget.prototype.getTabs = function(data) { - var _this = this; - - this.subtractionCurveVisualizer = new SubtractionCurveVisualizer(); - - this.tabs = Ext.createWidget('tabpanel', { - activeTab : 1, - plain : true, - defaults : { - autoScroll : true, - bodyPadding : 10 - }, - items : [ { - title : 'Solution', - items : [ _this.getSpecimenContainer(data) ] - }, { - title : 'Primary Data Reduction', - active : true, - tabConfig : { - xtype : 'tab', - margins : '0 0 0 20', - }, - items : [ _this.subtractionCurveVisualizer.getPanel() ] - }, { - title : 'Abinitio', - items : [ _this.getAbinitioModellingContainer(data), _this.getSeparator(), _this.getModelViz(data) ] - }, { - title : 'Mixtures', - items : [ _this.getAdvancedTab(data) ] - }, { - title : 'Superpositions', - items : [ _this.getSuperpositionTab(data) ] - }, { - title : 'Rigid Body Modeling', - items : [ _this.getRigidBodyModelingTab(data) ] - } ] - }); - return this.tabs; -}; + if (args.showBufferColumns != null) { + this.showBufferColumns = args.showBufferColumns; + } + } +} -DataCollectionWidget.prototype.getPanel = function(data) { - var _this = this; - _this.data = data; - this.panel = Ext.create('Ext.container.Container', { - width : 1000, - layout : { - type : 'vbox', - align : 'stretch', - padding : 5 - }, - items : [ _this.getTabs(data) +ConcentrationHTMLTableWidget.prototype.refresh = function(parsedData) { + document.getElementById(this.id).innerHTML = this.getPanel(parsedData); +}; - ] - }); +ConcentrationHTMLTableWidget.prototype.getPanel = function(parsedData) { + var html = "
"; + html = html + ""; - this.panel.on("afterrender", function() { - _this.subtractionCurveVisualizer.refresh([ _this.data[1].mergeId ], [ _this.data[1].subtractionId ]); - }); - return this.panel; -}; + /** Title * */ + html = html + ""; + html = html + ""; + if (this.showBufferColumns) { + html = html + ""; + } + html = html + ""; + html = html + ""; + html = html + ""; + html = html + ""; -DataCollectionWidget.prototype.getModelViz = function(data) { - this.modelViz = new ModelVisualizerForm({ - height : 800, - width : 1000 - }); - return this.modelViz.getPanel(); -}; + html = html + ""; + html = html + ""; + html = html + ""; + html = html + ""; + html = html + ""; + html = html + ""; + html = html + ""; + html = html + ""; + html = html + ""; -/** - * PRIMARY DATA PROCESSING - */ -DataCollectionWidget.prototype.getPrimaryDataProcessingContainer = function(data) { - var _this = this; - this.primaryDataProcessingGrid = new PrimaryDataProcessingGrid({ - height : 250, - width : 1000, - title : 'Primary Data Processing' + parsedData.concentration.concentrations.sort(function(a, b) { + return a.concentration - b.concentration; }); + /** Row * */ + for ( var i = 0; i < parsedData.concentration.concentrations.length; i++) { + var row = parsedData[i]; - this.primaryDataProcessingGrid.onSelected.attach(function(sender, selected) { - /** Refresh tabs **/ - var averagesId = []; - var subtractionIds = []; - - var subtractionKeys = {}; - for (var i = 0; i < selected.length; i++) { - if (selected[i].mergeId != null) { - averagesId.push(selected[i].mergeId); - } + var tr = ""; + if (i % 2 == 1) { + tr = ""; + } + var goodMeasurements = (parsedData.concentration.concentrations[i].frames.length - parsedData.concentration.concentrations[i].frames_warning); + if (goodMeasurements == 0) { + tr = ""; + } + html = html + tr; + html = html + ""; + if (this.showBufferColumns) { + html = html + ""; + } + html = html + ""; + html = html + ""; + html = html + ""; + html = html + ""; + html = html + ""; + html = html + ""; + html = html + ""; + html = html + ""; + } + return html + "
ConcentrationBufferMeasurementsGuinierGnom
PassedDiscardedRgI0QualityRgdMax
" + parsedData.concentration.concentrations[i].concentration + "" + parsedData.concentration.concentrations[i].bufferAcronym + "" + goodMeasurements + " of " + parsedData.concentration.concentrations[i].frames.length + "" + parsedData.concentration.concentrations[i].frames_warning + "" + BUI.formatValuesErrorUnits(parsedData.concentration.concentrations[i].calculation.rgGuinier.avg, parsedData.concentration.concentrations[i].calculation.rgGuinier.std, "nm", { + lineBreak : false + }) + "" + BUI.formatValuesErrorUnits(parsedData.concentration.concentrations[i].calculation.i0Guinier.avg, parsedData.concentration.concentrations[i].calculation.i0Guinier.std, " ", { + lineBreak : false + }) + "" + BUI.formatValuesErrorUnits(parsedData.concentration.concentrations[i].calculation.quality.avg, parsedData.concentration.concentrations[i].calculation.quality.std, " ", { + lineBreak : false + }) + "" + BUI.formatValuesErrorUnits(parsedData.concentration.concentrations[i].calculation.rgGnom.avg, parsedData.concentration.concentrations[i].calculation.rgGnom.std, " ", { + lineBreak : false + }) + "" + BUI.formatValuesErrorUnits(parsedData.concentration.concentrations[i].calculation.dMax.avg, parsedData.concentration.concentrations[i].calculation.dMax.std, " ", { + lineBreak : false + }) + "
"; +}; - if (selected[i].subtractionId != null) { - if (selected[i].macromoleculeId != null) { - if (subtractionKeys[selected[i].subtractionId] == null) { - subtractionIds.push(selected[i].subtractionId); +ConcentrationHTMLTableWidget.prototype.input = function() { + return { + data : { + "dataCollectionCount" : 4, + "buffers" : [ { + "bufferId" : "422" + } ], + "concentration" : { + "concentrations" : [ { + "concentration" : "7.17", + "id" : "7.1699999999999999", + "bufferId" : "422.00", + "bufferAcronym" : "B1", + "rgGuinier" : [ "5.12723" ], + "frames" : [ { + "total" : "0.515705406286", + "bufferBeforeMeasurementId" : 15045, + "sampleMergeId" : 8176, + "averagedModelId" : null, + "I0" : "183.457461646", + "proposalCode" : "OPD", + "averagedModel" : null, + "bufferAfterMergeId" : 8177, + "framesCount" : "10", + "bufferBeforeMergeId" : 8175, + "averageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_065_ave.dat", + "bufferAfterMeasurementId" : 15048, + "rgGuinier" : "5.12723", + "subtractedFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_065_sub.dat", + "firstPointUsed" : "17", + "chi2RgFilePath" : null, + "abInitioModelId" : null, + "macromoleculeId" : 649, + "code" : "_4.0_7.17", + "transmission" : "100.0", + "timeStart" : "2013-06-05 15:43:54.348723", + "bufferAcronym" : "B1", + "quality" : "0.853011", + "shapeDeterminationModelId" : null, + "expermientComments" : "[BsxCube] Generated from BsxCube", + "bufferId" : 422, + "isagregated" : "False", + "dmax" : "25.63615", + "bufferBeforeAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_064_ave.dat", + "exposureTemperature" : "4.0", + "subtractionId" : 3377, + "conc" : "7.1699999999999999", + "rapidShapeDeterminationModel" : null, + "experimentCreationDate" : "Jun 5, 2013 3:30:30 PM", + "lastPointUsed" : "36", + "modelListId" : null, + "framesMerge" : "9", + "rapidShapeDeterminationModelId" : null, + "bufferAfterAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_066_ave.dat", + "nsdFilePath" : null, + "bufferAfterFramesMerged" : "10", + "experimentId" : 700, + "macromoleculeAcronym" : "L9", + "i0stdev" : "0.139364435146", + "sampleMeasurementId" : 15047, + "measurementComments" : "[5]", + "priorityLevelId" : 10, + "bufferBeforeFramesMerged" : "10", + "substractionCreationTime" : "Jun 5, 2013 3:46:31 PM", + "proposalNumber" : "29", + "rgGnom" : "5.40297914939", + "volume" : "475.302", + "shapeDeterminationModel" : null, + "comments" : null, + "groupeField" : "L9 B1" + } ], + "frames_warning" : 0, + "calculation" : { + "rgGuinier" : { + "std" : 0, + "sum" : 5.12723, + "avg" : 5.12723, + "validNumber" : 1, + "totalNumber" : 1, + "values" : [ "5.12723" ] + }, + "i0Guinier" : { + "std" : 0, + "sum" : 183.457461646, + "avg" : 183.457461646, + "validNumber" : 1, + "totalNumber" : 1, + "values" : [ "183.457461646" ] + }, + "quality" : { + "std" : 0, + "sum" : 0.853011, + "avg" : 0.853011, + "validNumber" : 1, + "totalNumber" : 1, + "values" : [ "0.853011" ] + }, + "rgGnom" : { + "std" : 0, + "sum" : 5.40297914939, + "avg" : 5.40297914939, + "validNumber" : 1, + "totalNumber" : 1, + "values" : [ "5.40297914939" ] + }, + "dMax" : { + "std" : 0, + "sum" : 25.63615, + "avg" : 25.63615, + "validNumber" : 1, + "totalNumber" : 1, + "values" : [ "25.63615" ] + } + } + }, { + "concentration" : "3.53", + "id" : "3.5299999999999998", + "bufferId" : "422.00", + "bufferAcronym" : "B1", + "rgGuinier" : [ "4.38278" ], + "frames" : [ { + "total" : "0.497164741078", + "bufferBeforeMeasurementId" : 15048, + "sampleMergeId" : 8178, + "averagedModelId" : null, + "I0" : "160.023229462", + "proposalCode" : "OPD", + "averagedModel" : null, + "bufferAfterMergeId" : 8179, + "framesCount" : "10", + "bufferBeforeMergeId" : 8177, + "averageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_067_ave.dat", + "bufferAfterMeasurementId" : 15051, + "rgGuinier" : "4.38278", + "subtractedFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_067_sub.dat", + "firstPointUsed" : "36", + "chi2RgFilePath" : null, + "abInitioModelId" : null, + "macromoleculeId" : 649, + "code" : "_4.0_3.53", + "transmission" : "100.0", + "timeStart" : "2013-06-05 15:47:04.630129", + "bufferAcronym" : "B1", + "quality" : "0.742825", + "shapeDeterminationModelId" : null, + "expermientComments" : "[BsxCube] Generated from BsxCube", + "bufferId" : 422, + "isagregated" : "False", + "dmax" : "15.33973", + "bufferBeforeAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_066_ave.dat", + "exposureTemperature" : "4.0", + "subtractionId" : 3378, + "conc" : "3.5299999999999998", + "rapidShapeDeterminationModel" : null, + "experimentCreationDate" : "Jun 5, 2013 3:30:30 PM", + "lastPointUsed" : "61", + "modelListId" : null, + "framesMerge" : "10", + "rapidShapeDeterminationModelId" : null, + "bufferAfterAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_068_ave.dat", + "nsdFilePath" : null, + "bufferAfterFramesMerged" : "10", + "experimentId" : 700, + "macromoleculeAcronym" : "L9", + "i0stdev" : "0.1499898017", + "sampleMeasurementId" : 15050, + "measurementComments" : "[6]", + "priorityLevelId" : 12, + "bufferBeforeFramesMerged" : "10", + "substractionCreationTime" : "Jun 5, 2013 3:49:42 PM", + "proposalNumber" : "29", + "rgGnom" : "4.40615474861", + "volume" : "372.656", + "shapeDeterminationModel" : null, + "comments" : null, + "groupeField" : "L9 B1" + } ], + "frames_warning" : 0, + "calculation" : { + "rgGuinier" : { + "std" : 0, + "sum" : 4.38278, + "avg" : 4.38278, + "validNumber" : 1, + "totalNumber" : 1, + "values" : [ "4.38278" ] + }, + "i0Guinier" : { + "std" : 0, + "sum" : 160.023229462, + "avg" : 160.023229462, + "validNumber" : 1, + "totalNumber" : 1, + "values" : [ "160.023229462" ] + }, + "quality" : { + "std" : 0, + "sum" : 0.742825, + "avg" : 0.742825, + "validNumber" : 1, + "totalNumber" : 1, + "values" : [ "0.742825" ] + }, + "rgGnom" : { + "std" : 0, + "sum" : 4.40615474861, + "avg" : 4.40615474861, + "validNumber" : 1, + "totalNumber" : 1, + "values" : [ "4.40615474861" ] + }, + "dMax" : { + "std" : 0, + "sum" : 15.33973, + "avg" : 15.33973, + "validNumber" : 1, + "totalNumber" : 1, + "values" : [ "15.33973" ] + } + } + }, { + "concentration" : "1.75", + "id" : "1.75", + "bufferId" : "422.00", + "bufferAcronym" : "B1", + "rgGuinier" : [], + "frames" : [ { + "total" : "0.5538035065", + "bufferBeforeMeasurementId" : 15051, + "sampleMergeId" : 8180, + "averagedModelId" : null, + "I0" : "146.927428571", + "proposalCode" : "OPD", + "averagedModel" : null, + "bufferAfterMergeId" : 8181, + "framesCount" : "10", + "bufferBeforeMergeId" : 8179, + "averageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_069_ave.dat", + "bufferAfterMeasurementId" : 15054, + "rgGuinier" : "4.27139", + "subtractedFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_069_sub.dat", + "firstPointUsed" : "33", + "chi2RgFilePath" : null, + "abInitioModelId" : null, + "macromoleculeId" : 649, + "code" : "_4.0_1.75", + "transmission" : "100.0", + "timeStart" : "2013-06-05 15:50:09.395824", + "bufferAcronym" : "B1", + "quality" : "0.765999", + "shapeDeterminationModelId" : null, + "expermientComments" : "[BsxCube] Generated from BsxCube", + "bufferId" : 422, + "isagregated" : "False", + "dmax" : "14.949865", + "bufferBeforeAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_068_ave.dat", + "exposureTemperature" : "4.0", + "subtractionId" : 3379, + "conc" : "1.75", + "rapidShapeDeterminationModel" : null, + "experimentCreationDate" : "Jun 5, 2013 3:30:30 PM", + "lastPointUsed" : "62", + "modelListId" : null, + "framesMerge" : "6", + "rapidShapeDeterminationModelId" : null, + "bufferAfterAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_070_ave.dat", + "nsdFilePath" : null, + "bufferAfterFramesMerged" : "10", + "experimentId" : 700, + "macromoleculeAcronym" : "L9", + "i0stdev" : "0.191914285714", + "sampleMeasurementId" : 15053, + "measurementComments" : "[7]", + "priorityLevelId" : 14, + "bufferBeforeFramesMerged" : "10", + "substractionCreationTime" : "Jun 5, 2013 3:52:31 PM", + "proposalNumber" : "29", + "rgGnom" : "4.28379338749", + "volume" : "356.326", + "shapeDeterminationModel" : null, + "comments" : null, + "groupeField" : "L9 B1" + } ], + "frames_warning" : 1, + "calculation" : { + "rgGuinier" : { + "std" : null, + "sum" : 0, + "avg" : 0, + "validNumber" : 0, + "totalNumber" : 0, + "values" : [] + }, + "i0Guinier" : { + "std" : null, + "sum" : 0, + "avg" : 0, + "validNumber" : 0, + "totalNumber" : 0, + "values" : [] + }, + "quality" : { + "std" : null, + "sum" : 0, + "avg" : 0, + "validNumber" : 0, + "totalNumber" : 0, + "values" : [] + }, + "rgGnom" : { + "std" : null, + "sum" : 0, + "avg" : 0, + "validNumber" : 0, + "totalNumber" : 0, + "values" : [] + }, + "dMax" : { + "std" : null, + "sum" : 0, + "avg" : 0, + "validNumber" : 0, + "totalNumber" : 0, + "values" : [] + } + } + }, { + "concentration" : "0.91", + "id" : "0.91000000000000003", + "bufferId" : "422.00", + "bufferAcronym" : "B1", + "rgGuinier" : [], + "frames" : [ { + "total" : null, + "bufferBeforeMeasurementId" : 15054, + "sampleMergeId" : 8182, + "averagedModelId" : null, + "I0" : "0.0", + "proposalCode" : "OPD", + "averagedModel" : null, + "bufferAfterMergeId" : 8183, + "framesCount" : "10", + "bufferBeforeMergeId" : 8181, + "averageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_071_ave.dat", + "bufferAfterMeasurementId" : 15057, + "rgGuinier" : null, + "subtractedFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_071_sub.dat", + "firstPointUsed" : "0", + "chi2RgFilePath" : null, + "abInitioModelId" : null, + "macromoleculeId" : 649, + "code" : "_4.0_.91", + "transmission" : "100.0", + "timeStart" : "2013-06-05 15:52:58.133705", + "bufferAcronym" : "B1", + "quality" : "0.0", + "shapeDeterminationModelId" : null, + "expermientComments" : "[BsxCube] Generated from BsxCube", + "bufferId" : 422, + "isagregated" : "False", + "dmax" : null, + "bufferBeforeAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_070_ave.dat", + "exposureTemperature" : "4.0", + "subtractionId" : 3380, + "conc" : "0.91000000000000003", + "rapidShapeDeterminationModel" : null, + "experimentCreationDate" : "Jun 5, 2013 3:30:30 PM", + "lastPointUsed" : "0", + "modelListId" : null, + "framesMerge" : "10", + "rapidShapeDeterminationModelId" : null, + "bufferAfterAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_072_ave.dat", + "nsdFilePath" : null, + "bufferAfterFramesMerged" : "10", + "experimentId" : 700, + "macromoleculeAcronym" : "L9", + "i0stdev" : "0.0", + "sampleMeasurementId" : 15056, + "measurementComments" : "[8]", + "priorityLevelId" : 16, + "bufferBeforeFramesMerged" : "10", + "substractionCreationTime" : "Jun 5, 2013 3:55:35 PM", + "proposalNumber" : "29", + "rgGnom" : null, + "volume" : null, + "shapeDeterminationModel" : null, + "comments" : null, + "groupeField" : "L9 B1" + } ], + "frames_warning" : 1, + "calculation" : { + "rgGuinier" : { + "std" : null, + "sum" : 0, + "avg" : 0, + "validNumber" : 0, + "totalNumber" : 0, + "values" : [] + }, + "i0Guinier" : { + "std" : null, + "sum" : 0, + "avg" : 0, + "validNumber" : 0, + "totalNumber" : 0, + "values" : [] + }, + "quality" : { + "std" : null, + "sum" : 0, + "avg" : 0, + "validNumber" : 0, + "totalNumber" : 0, + "values" : [] + }, + "rgGnom" : { + "std" : null, + "sum" : 0, + "avg" : 0, + "validNumber" : 0, + "totalNumber" : 0, + "values" : [] + }, + "dMax" : { + "std" : null, + "sum" : 0, + "avg" : 0, + "validNumber" : 0, + "totalNumber" : 0, + "values" : [] + } } - subtractionKeys[selected[i].subtractionId] = true; - } - } + } ] + }, + "concentrationLabel" : "7.17 mg/ml ,3.53 mg/ml ,1.75 mg/ml ,0.91 mg/ml " } - - /** Refreshing Primary Data Reduction **/ - _this.subtractionCurveVisualizer.refresh(averagesId, subtractionIds); - - }); - return this.primaryDataProcessingGrid.getPanel(data); + }; }; -/** - * getAbinitioModellingContainer - */ -DataCollectionWidget.prototype.getAbinitioModellingContainer = function(data) { - var _this = this; - - this.abinitioGrid = new AbinitioGrid(); - this.abinitioGrid.onSelected.attach(function(sender, models) { - _this.modelViz.refresh(models); - - }); - /** It may be abinitio models linked to the buffers **/ - var abinitioIdList = []; - for (var i = 0; i < data.length; i++) { - abinitioIdList.push(data[i].abInitioId); - } - - var uniqueIds = []; - $.each(abinitioIdList, function(i, el) { - if ($.inArray(el, uniqueIds) === -1) - uniqueIds.push(el); - }); - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - _this.abinitioGrid.refresh(data); - }); - adapter.getAbinitioByIdsList(uniqueIds); - return this.abinitioGrid.getPanel([]); +ConcentrationHTMLTableWidget.prototype.test = function(targetId) { + var concentrationHTMLTableWidget = new ConcentrationHTMLTableWidget(); + document.getElementById(targetId).innerHTML = concentrationHTMLTableWidget.getPanel(concentrationHTMLTableWidget.input().data); }; +function DataCollectionWidget() { + +}; + +DataCollectionWidget.prototype.refresh = function(subtractionId) { + +}; + +DataCollectionWidget.prototype.getMacromolecule = function(data) { + for (var i = 0; i < data.length; i++) { + if (data[i].macromoleculeId != null) { + return BIOSAXS.proposal.getMacromoleculeById(data[i].macromoleculeId); + } + } + return null; +}; + +DataCollectionWidget.prototype.getMacromoleculeContainer = function(data) { + var macromolecule = this.getMacromolecule(data); + + var disabled = false; + if (macromolecule == null) { + disabled = true; + } + + var acronym = (macromolecule == null ? "" : macromolecule.acronym); + var mm = (macromolecule == null ? "" : macromolecule.molecularMass); + var comments = (macromolecule == null ? "" : macromolecule.comments); + + return Ext.create('Ext.Panel', { + width : 500, + height : 200, + disabled : disabled, + title : "Macromolecule", + layout : 'form', + bodyPadding : 5, + defaultType : 'textfield', + tbar : { + defaultButtonUI : 'default', + items : [ { + xtype : 'button', + text : 'Edit', + cls : 'btn-with-border', + handler : function() { + var macromoleculeWindow = new MacromoleculeWindow(); + macromoleculeWindow.draw(macromolecule); + /** TODO: update when save **/ + } + } ] + }, + items : [ { + fieldLabel : 'Acronym', + name : 'first', + readOnly : true, + value : acronym + }, { + fieldLabel : 'Molecular Mass', + name : 'last', + readOnly : true, + value : mm + }, { + xtype : 'textareafield', + fieldLabel : 'Comments', + value : '', + name : 'last', + readOnly : true, + value : comments + } ] + }); +}; + +DataCollectionWidget.prototype.getBufferContainer = function(data) { + var _this = this; + var buffer = BIOSAXS.proposal.getBufferById(data[0].bufferId); + + return Ext.create('Ext.Panel', { + width : 500, + height : 200, + title : "Buffer", + layout : 'form', + // collapsed : true, + // collapsible : true, + bodyPadding : 5, + defaultType : 'textfield', + style : { + padding : '0px 0px 0px 2px' + }, + tbar : { + defaultButtonUI : 'default', + items : [ { + xtype : 'button', + text : 'Edit', + cls : 'btn-with-border', + handler : function() { + var bufferWindow = new BufferWindow(); + bufferWindow.draw(BIOSAXS.proposal.getBufferById(data[0].bufferId)); + /** TODO: update when save **/ + } + + } ] + }, + items : [ { + fieldLabel : 'Buffer', + name : 'acronym', + readOnly : true, + value : buffer.acronym + }, { + fieldLabel : 'Composition', + name : 'last', + readOnly : true, + value : buffer.composition + }, { + xtype : 'textareafield', + fieldLabel : 'Comments', + value : buffer.comments, + name : 'last', + readOnly : true + + } ] + }); +}; + +DataCollectionWidget.prototype.getSpecimenContainer = function(data) { + return Ext.create('Ext.container.Container', { + layout : { + type : 'hbox' + }, + style : { + margin : '10px 10px 10px 10px' + }, + border : 0, + style : { + borderColor : '#000000', + borderStyle : 'solid', + borderWidth : '1px' + }, + defaults : { + labelWidth : 80, + // implicitly create Container by specifying xtype + xtype : 'datefield', + flex : 1, + + }, + items : [ this.getMacromoleculeContainer(data), this.getBufferContainer(data) ] + }); +}; + +DataCollectionWidget.prototype.getSeparator = function() { + return { + html : "
", + border : 0 + } +}; + +DataCollectionWidget.prototype.getFitStructurePanel = function(data) { + var _this = this; + + return Ext.create('Ext.container.Container', { + layout : { + type : 'hbox' + }, + style : { + margin : '10px 10px 10px 10px' + }, + border : 0, + style : { + borderColor : '#000000', + borderStyle : 'solid', + borderWidth : '1px' + }, + defaults : { + labelWidth : 80, + xtype : 'datefield', + flex : 1 + }, + items : [ + + ] + }); +}; + +DataCollectionWidget.prototype.getFitStructurePanelWorkflow = function(data) { + var _this = this; + var macromolecule = this.getMacromolecule(data); + + var items = []; + + /** Adding all the pdb files linked to the macromolecule **/ + // if (macromolecule.structure3VOs != null) { + // if (macromolecule.structure3VOs.length > 0) { + // + // items.push(); + // } + // } else { + // items.push({ + // html : "No apriori information added to this macromolecule. Apriori information needed for further analysis", + // margin : "5 5 5 5" + // }); + // } + var fitStructureToExperimentDataGrid = new FitStructureToExperimentDataGrid(); + + fitStructureToExperimentDataGrid.refresh(_this.data[0].subtractionId, _this.getMacromolecule(data)); + return Ext.create('Ext.container.Container', { + style : { + margin : '10px 10px 10px 10px' + }, + border : 0, + + style : { + borderColor : '#000000', + borderStyle : 'solid', + borderWidth : '1px' + }, + defaults : { + labelWidth : 80, + xtype : 'datefield', + flex : 1 + }, + items : [ fitStructureToExperimentDataGrid.getPanel() ], + listeners : { + afterrender : function() { + } + } + }); +}; +/** Static method **/ +DataCollectionWidget.prototype.RUNFitScattering = function(subtractionId, structureId) { + var _this = this; + /** Add to Workflow **/ + var adapter = new BiosaxsDataAdapter(); + var workflow = { + 'workflowTitle' : 'FitExperimentalDatatoStructure', + 'comments' : 'FitExperimentalDatatoStructure run from ISPyB for subtractionId: ' + subtractionId + ' and structureId ' + structureId + } + + var inputs = [ { + name : 'subtractionId', + value : subtractionId + }, { + name : 'structureId', + value : structureId + } ]; + + adapter.onSuccess.attach(function(sender, data) { + /** Add to Fit **/ + var adapter2 = new BiosaxsDataAdapter(); + var fit = { + 'workflowId' : data.workflowId, + 'subtractionId' : subtractionId, + 'structureId' : structureId, + 'comments' : 'Sent to workflow engine' + } + adapter2.onSuccess.attach(function(sender, fit) { + + }); + adapter2.addFitStructureData(fit); + + }); + adapter.addWorkflow(workflow, inputs); + +}; + +DataCollectionWidget.prototype.getSuperpositionTab = function(data) { + var _this = this; + + this.superpositionGrid = new SuperpositionGrid(); + + return Ext.create('Ext.container.Container', { + style : { + margin : '10px 10px 10px 10px' + }, + border : 0, + style : { + borderColor : '#000000', + borderStyle : 'solid', + borderWidth : '1px' + }, + items : [ _this.superpositionGrid.getPanel() ], + listeners : { + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + + }, + afterrender : function() { + /** Getting Rigid bodies **/ + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, result) { + _this.superpositionGrid.refresh(result); + }); + adapter.getSuperpositionBySubtractionId(data[1].subtractionId); + } + } + }); +}; + +DataCollectionWidget.prototype.getAdvancedTab = function(data) { + var _this = this; + return Ext.create('Ext.container.Container', { + style : { + margin : '10px 10px 10px 10px' + }, + border : 0, + style : { + borderColor : '#000000', + borderStyle : 'solid', + borderWidth : '1px' + }, + items : [ _this.getFitStructurePanel(data), _this.getFitStructurePanelWorkflow(data) ] + }); +}; + +DataCollectionWidget.prototype.getRigiBodyForm = function(data) { + var _this = this; + _this.rigiBodyGrid = new RigidModelGrid(); + return _this.rigiBodyGrid.getPanel(); + +}; + +DataCollectionWidget.prototype.getRigidBodyModelingTab = function(data) { + var _this = this; + return Ext.create('Ext.container.Container', { + style : { + margin : '10px 10px 10px 10px' + }, + border : 0, + style : { + borderColor : '#000000', + borderStyle : 'solid', + borderWidth : '1px' + }, + items : [ _this.getRigiBodyForm(data) ], + listeners : { + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + + }, + afterrender : function() { + /** Getting Rigid bodies **/ + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, result) { + _this.rigiBodyGrid.refresh(result); + }); + adapter.getRigidBodyModelingBySubtractionId(data[1].subtractionId); + } + } + }); +}; + +DataCollectionWidget.prototype.getTabs = function(data) { + var _this = this; + + this.subtractionCurveVisualizer = new SubtractionCurveVisualizer(); + + this.tabs = Ext.createWidget('tabpanel', { + activeTab : 1, + plain : true, + defaults : { + autoScroll : true, + bodyPadding : 10 + }, + items : [ { + title : 'Solution', + items : [ _this.getSpecimenContainer(data) ] + }, { + title : 'Primary Data Reduction', + active : true, + tabConfig : { + xtype : 'tab', + margins : '0 0 0 20', + }, + items : [ _this.subtractionCurveVisualizer.getPanel() ] + }, { + title : 'Abinitio', + items : [ _this.getAbinitioModellingContainer(data), _this.getSeparator(), _this.getModelViz(data) ] + }, { + title : 'Mixtures', + items : [ _this.getAdvancedTab(data) ] + }, { + title : 'Superpositions', + items : [ _this.getSuperpositionTab(data) ] + }, { + title : 'Rigid Body Modeling', + items : [ _this.getRigidBodyModelingTab(data) ] + } ] + }); + return this.tabs; +}; + +DataCollectionWidget.prototype.getPanel = function(data) { + var _this = this; + _this.data = data; + this.panel = Ext.create('Ext.container.Container', { + width : 1000, + layout : { + type : 'vbox', + align : 'stretch', + padding : 5 + }, + items : [ _this.getTabs(data) + + ] + }); + + this.panel.on("afterrender", function() { + _this.subtractionCurveVisualizer.refresh([ _this.data[1].mergeId ], [ _this.data[1].subtractionId ]); + }); + return this.panel; +}; + +DataCollectionWidget.prototype.getModelViz = function(data) { + this.modelViz = new ModelVisualizerForm({ + height : 800, + width : 1000 + }); + return this.modelViz.getPanel(); +}; + +/** + * PRIMARY DATA PROCESSING + */ +DataCollectionWidget.prototype.getPrimaryDataProcessingContainer = function(data) { + var _this = this; + this.primaryDataProcessingGrid = new PrimaryDataProcessingGrid({ + height : 250, + width : 1000, + title : 'Primary Data Processing' + }); + + this.primaryDataProcessingGrid.onSelected.attach(function(sender, selected) { + /** Refresh tabs **/ + var averagesId = []; + var subtractionIds = []; + + var subtractionKeys = {}; + for (var i = 0; i < selected.length; i++) { + if (selected[i].mergeId != null) { + averagesId.push(selected[i].mergeId); + } + + if (selected[i].subtractionId != null) { + if (selected[i].macromoleculeId != null) { + if (subtractionKeys[selected[i].subtractionId] == null) { + subtractionIds.push(selected[i].subtractionId); + } + subtractionKeys[selected[i].subtractionId] = true; + } + } + } + + /** Refreshing Primary Data Reduction **/ + _this.subtractionCurveVisualizer.refresh(averagesId, subtractionIds); + + }); + return this.primaryDataProcessingGrid.getPanel(data); +}; +/** + * getAbinitioModellingContainer + */ +DataCollectionWidget.prototype.getAbinitioModellingContainer = function(data) { + var _this = this; + + this.abinitioGrid = new AbinitioGrid(); + this.abinitioGrid.onSelected.attach(function(sender, models) { + _this.modelViz.refresh(models); + + }); + /** It may be abinitio models linked to the buffers **/ + var abinitioIdList = []; + for (var i = 0; i < data.length; i++) { + abinitioIdList.push(data[i].abInitioId); + } + + var uniqueIds = []; + $.each(abinitioIdList, function(i, el) { + if ($.inArray(el, uniqueIds) === -1) + uniqueIds.push(el); + }); + + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + _this.abinitioGrid.refresh(data); + }); + adapter.getAbinitioByIdsList(uniqueIds); + return this.abinitioGrid.getPanel([]); +}; + /** * Edit the information of a buffer * @@ -29163,258 +29163,258 @@ ShippingWidget.prototype.refresh = function() { }; -/** - * Widget container of Specimen grid and samplePlate widget - * Depending of the sample changer layout it may be displayed vertically or horizontally - * - * @param args - * - * #onExperimentChanged It happens when specimen are modified - */ -function SpecimenWidget(args){ - - this.width = 1000; - this.height = 600; - - if (args != null){ - if (args.width != null){ - this.width = args.width; - } - if (args.height != null){ - this.height = args.height; - } - } - - var _this = this; - - /** Specimen Grid **/ - this.specimenGrid = new SpecimenGrid({ - minHeight : 425, - selectionMode : "SINGLE", - editEnabled : false, - updateRowEnabled : true, - width : 900, - showTitle : false - }); - - - this.specimenGrid.onSpecimenChanged.attach(function(sender, specimen) { - _this.experiment.setSpecimenById(specimen); - _this.refresh(_this.experiment); - }); - - this.specimenGrid.onSelected.attach(function(sender, specimens) { - if (specimens.length > 0) { - _this.specimenSelected = specimens[0]; - } else { - _this.specimenSelected = null; - } - _this.samplePlateGroupWidget.selectSpecimens(specimens); - }); - - - /** Sample plate Widget **/ - this.samplePlateGroupWidget = new SamplePlateGroupWidget({ - showTitle : false, - height : 250, - margin : 5, - bbar : true - }); - - - this.samplePlateGroupWidget.onExperimentChanged.attach(function(sender, json) { - _this.refresh(new Experiment(json)); - }); - - this.samplePlateGroupWidget.onClick.attach(function(sender, args) { - /** Clicking on a plate * */ - var row = args.row; - var column = args.column; - var samplePlateId = args.samplePlate.samplePlateId; - - /** is specimen selected on the grid? * */ - if (_this.specimenSelected != null) { - /** Is position target empty * */ - if (_this.experiment.getSampleByPosition(args.samplePlate.samplePlateId, args.row, args.column).length == 0) { - var specimen = _this.experiment.getSampleById(_this.specimenSelected.specimenId); - if (specimen.sampleplateposition3VO == null) { - specimen.sampleplateposition3VO = {}; - } - - specimen.sampleplateposition3VO = { - columnNumber : column, - rowNumber : row, - samplePlateId : samplePlateId - }; - - _this.samplePlateGroupWidget.panel.setLoading("ISPyB: Saving specimen"); - var adapter = new BiosaxsDataAdapter(); - /** If success * */ - adapter.onSuccess.attach(function(sender, experiment) { - _this.samplePlateGroupWidget.panel.setLoading(false); - }); - - adapter.onError.attach(function(sender, error) { - _this.samplePlateGroupWidget.panel.setLoading(false); - showError(error); - }); - - adapter.saveSpecimen(specimen, _this.experiment); - - _this.samplePlateGroupWidget.refresh(_this.experiment); - _this.specimenGrid.refresh(_this.experiment); - //_this.refresh(_this.experiment); - _this.specimenGrid.deselectAll(); - - } else { - /** - * Can we merge? We can merge when specimen are the - * same. So, same buffer, macromolecule, concentration * - */ - var target = _this.experiment.getSampleByPosition(args.samplePlate.samplePlateId, args.row, args.column)[0]; - var specimen = _this.experiment.getSampleById(_this.specimenSelected.specimenId); - - if ((specimen.bufferId == target.bufferId) && (specimen.concentration == target.concentration)) { - if (((specimen.macromolecule3VO != null) && (target.macromolecule3VO != null) && (specimen.macromolecule3VO.macromoleculeId == target.macromolecule3VO.macromoleculeId)) || - ((specimen.macromolecule3VO == null) && (target.macromolecule3VO == null))) { - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - _this.refresh(new Experiment(data)); - _this.samplePlateGroupWidget.panel.setLoading(false); - - _this.onExperimentChanged.notify(experiment); - }); - adapter.onError.attach(function(sender, error) { - _this.samplePlateGroupWidget.panel.setLoading(false); - showError(error); - }); - _this.samplePlateGroupWidget.panel.setLoading("ISPyB: Merging specimens"); - adapter.mergeSpecimens(specimen.specimenId, target.specimenId); - } - } else { - alert("Well is not empty. Select another well!"); - } - } - } else { - var specimen = _this.experiment.getSampleByPosition(args.samplePlate.samplePlateId, args.row, args.column)[0]; - if (specimen != null) { - _this.specimenGrid.selectById(specimen.specimenId); - } - } - }); - - /** Events **/ - this.onExperimentChanged = new Event(this); -}; - -/** - * Return vbox or hbox depending on the slot positions of the plates - */ -SpecimenWidget.prototype.getContainerLayoutConfiguration = function(experiment){ - var dimensions = this.samplePlateGroupWidget.getDimensions(experiment.getSamplePlates()); - if (dimensions.maxSlotPositionRow < dimensions.maxSlotPositionColumn){ - return { - layout : "vbox", - specimenGridWidth : this.width - 10, - specimenGridHeight : this.height - 260, - samplePlateGroupWidth : this.width - 10, - samplePlateGroupHeight : 250 - }; - } - return { - layout : "hbox", - samplePlateGroupWidth : this.width*1/3 -10, - samplePlateGroupHeight : this.height - 10, - specimenGridWidth : this.width*2/3, - specimenGridHeight : this.height - 10 - }; - -}; - - -SpecimenWidget.prototype.refresh = function(experiment){ - this.experiment = experiment; - - /** Removing all components **/ - this.panel.removeAll(); - - var layoutConfiguration = this.getContainerLayoutConfiguration(experiment); - - /** Setting new width and height for layout vbox and hbox **/ - this.specimenGrid.width = layoutConfiguration.specimenGridWidth; - this.specimenGrid.height = layoutConfiguration.specimenGridHeight; - - this.samplePlateGroupWidget.width = layoutConfiguration.samplePlateGroupWidth; - this.samplePlateGroupWidget.height = layoutConfiguration.samplePlateGroupHeight; - - if (layoutConfiguration.layout == "hbox"){ - this.specimenGrid.margin = "0 0 0 5"; - this.specimenGrid.width =this.specimenGrid.width - 5; - } - /** Insert container depending on layout [vertical|horizontal] */ - var container = Ext.create('Ext.container.Container', { - layout : layoutConfiguration.layout, - height : this.height, - width : this.width, - padding : '2px', - items : [ ] - }); - if (layoutConfiguration.layout == "vbox"){ - container.insert(this.specimenGrid.getPanel()); - container.insert(this.samplePlateGroupWidget.getPanel()); - } - else{ - container.insert(this.samplePlateGroupWidget.getPanel()); - container.insert(this.specimenGrid.getPanel()); - } - - /** Insert Widget **/ - this.panel.insert(container); - - /** Load data **/ - this.specimenGrid.refresh(experiment); - this.samplePlateGroupWidget.refresh(experiment); - - -}; - -/** It creates a dummy container to be inserted the plates once the method refresh has been called - * This is necessay because we can not know the sample changer layout before hand - * **/ -SpecimenWidget.prototype.getPanel = function(){ - this.panel = Ext.create('Ext.container.Container', { - layout : 'vbox', - height : this.height, - border : 0, - margin : 5, - width : this.width, - items : [] - }); - return this.panel; -}; - - -SpecimenWidget.prototype.input = function() { - return { - experiment : DATADOC.getExperiment_10(), - proposal : DATADOC.getProposal_10() - }; -}; - -SpecimenWidget.prototype.test = function(targetId) { - var specimenWidget = new SpecimenWidget({ - height : 500, - width : 1000 - }); - BIOSAXS.proposal = new Proposal(specimenWidget.input().proposal); - var experiment = new Experiment(specimenWidget.input().experiment); - var panel = specimenWidget.getPanel(); - panel.render(targetId); - specimenWidget.refresh(experiment); - -}; - - +/** + * Widget container of Specimen grid and samplePlate widget + * Depending of the sample changer layout it may be displayed vertically or horizontally + * + * @param args + * + * #onExperimentChanged It happens when specimen are modified + */ +function SpecimenWidget(args){ + + this.width = 1000; + this.height = 600; + + if (args != null){ + if (args.width != null){ + this.width = args.width; + } + if (args.height != null){ + this.height = args.height; + } + } + + var _this = this; + + /** Specimen Grid **/ + this.specimenGrid = new SpecimenGrid({ + minHeight : 425, + selectionMode : "SINGLE", + editEnabled : false, + updateRowEnabled : true, + width : 900, + showTitle : false + }); + + + this.specimenGrid.onSpecimenChanged.attach(function(sender, specimen) { + _this.experiment.setSpecimenById(specimen); + _this.refresh(_this.experiment); + }); + + this.specimenGrid.onSelected.attach(function(sender, specimens) { + if (specimens.length > 0) { + _this.specimenSelected = specimens[0]; + } else { + _this.specimenSelected = null; + } + _this.samplePlateGroupWidget.selectSpecimens(specimens); + }); + + + /** Sample plate Widget **/ + this.samplePlateGroupWidget = new SamplePlateGroupWidget({ + showTitle : false, + height : 250, + margin : 5, + bbar : true + }); + + + this.samplePlateGroupWidget.onExperimentChanged.attach(function(sender, json) { + _this.refresh(new Experiment(json)); + }); + + this.samplePlateGroupWidget.onClick.attach(function(sender, args) { + /** Clicking on a plate * */ + var row = args.row; + var column = args.column; + var samplePlateId = args.samplePlate.samplePlateId; + + /** is specimen selected on the grid? * */ + if (_this.specimenSelected != null) { + /** Is position target empty * */ + if (_this.experiment.getSampleByPosition(args.samplePlate.samplePlateId, args.row, args.column).length == 0) { + var specimen = _this.experiment.getSampleById(_this.specimenSelected.specimenId); + if (specimen.sampleplateposition3VO == null) { + specimen.sampleplateposition3VO = {}; + } + + specimen.sampleplateposition3VO = { + columnNumber : column, + rowNumber : row, + samplePlateId : samplePlateId + }; + + _this.samplePlateGroupWidget.panel.setLoading("ISPyB: Saving specimen"); + var adapter = new BiosaxsDataAdapter(); + /** If success * */ + adapter.onSuccess.attach(function(sender, experiment) { + _this.samplePlateGroupWidget.panel.setLoading(false); + }); + + adapter.onError.attach(function(sender, error) { + _this.samplePlateGroupWidget.panel.setLoading(false); + showError(error); + }); + + adapter.saveSpecimen(specimen, _this.experiment); + + _this.samplePlateGroupWidget.refresh(_this.experiment); + _this.specimenGrid.refresh(_this.experiment); + //_this.refresh(_this.experiment); + _this.specimenGrid.deselectAll(); + + } else { + /** + * Can we merge? We can merge when specimen are the + * same. So, same buffer, macromolecule, concentration * + */ + var target = _this.experiment.getSampleByPosition(args.samplePlate.samplePlateId, args.row, args.column)[0]; + var specimen = _this.experiment.getSampleById(_this.specimenSelected.specimenId); + + if ((specimen.bufferId == target.bufferId) && (specimen.concentration == target.concentration)) { + if (((specimen.macromolecule3VO != null) && (target.macromolecule3VO != null) && (specimen.macromolecule3VO.macromoleculeId == target.macromolecule3VO.macromoleculeId)) || + ((specimen.macromolecule3VO == null) && (target.macromolecule3VO == null))) { + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + _this.refresh(new Experiment(data)); + _this.samplePlateGroupWidget.panel.setLoading(false); + + _this.onExperimentChanged.notify(experiment); + }); + adapter.onError.attach(function(sender, error) { + _this.samplePlateGroupWidget.panel.setLoading(false); + showError(error); + }); + _this.samplePlateGroupWidget.panel.setLoading("ISPyB: Merging specimens"); + adapter.mergeSpecimens(specimen.specimenId, target.specimenId); + } + } else { + alert("Well is not empty. Select another well!"); + } + } + } else { + var specimen = _this.experiment.getSampleByPosition(args.samplePlate.samplePlateId, args.row, args.column)[0]; + if (specimen != null) { + _this.specimenGrid.selectById(specimen.specimenId); + } + } + }); + + /** Events **/ + this.onExperimentChanged = new Event(this); +}; + +/** + * Return vbox or hbox depending on the slot positions of the plates + */ +SpecimenWidget.prototype.getContainerLayoutConfiguration = function(experiment){ + var dimensions = this.samplePlateGroupWidget.getDimensions(experiment.getSamplePlates()); + if (dimensions.maxSlotPositionRow < dimensions.maxSlotPositionColumn){ + return { + layout : "vbox", + specimenGridWidth : this.width - 10, + specimenGridHeight : this.height - 260, + samplePlateGroupWidth : this.width - 10, + samplePlateGroupHeight : 250 + }; + } + return { + layout : "hbox", + samplePlateGroupWidth : this.width*1/3 -10, + samplePlateGroupHeight : this.height - 10, + specimenGridWidth : this.width*2/3, + specimenGridHeight : this.height - 10 + }; + +}; + + +SpecimenWidget.prototype.refresh = function(experiment){ + this.experiment = experiment; + + /** Removing all components **/ + this.panel.removeAll(); + + var layoutConfiguration = this.getContainerLayoutConfiguration(experiment); + + /** Setting new width and height for layout vbox and hbox **/ + this.specimenGrid.width = layoutConfiguration.specimenGridWidth; + this.specimenGrid.height = layoutConfiguration.specimenGridHeight; + + this.samplePlateGroupWidget.width = layoutConfiguration.samplePlateGroupWidth; + this.samplePlateGroupWidget.height = layoutConfiguration.samplePlateGroupHeight; + + if (layoutConfiguration.layout == "hbox"){ + this.specimenGrid.margin = "0 0 0 5"; + this.specimenGrid.width =this.specimenGrid.width - 5; + } + /** Insert container depending on layout [vertical|horizontal] */ + var container = Ext.create('Ext.container.Container', { + layout : layoutConfiguration.layout, + height : this.height, + width : this.width, + padding : '2px', + items : [ ] + }); + if (layoutConfiguration.layout == "vbox"){ + container.insert(this.specimenGrid.getPanel()); + container.insert(this.samplePlateGroupWidget.getPanel()); + } + else{ + container.insert(this.samplePlateGroupWidget.getPanel()); + container.insert(this.specimenGrid.getPanel()); + } + + /** Insert Widget **/ + this.panel.insert(container); + + /** Load data **/ + this.specimenGrid.refresh(experiment); + this.samplePlateGroupWidget.refresh(experiment); + + +}; + +/** It creates a dummy container to be inserted the plates once the method refresh has been called + * This is necessay because we can not know the sample changer layout before hand + * **/ +SpecimenWidget.prototype.getPanel = function(){ + this.panel = Ext.create('Ext.container.Container', { + layout : 'vbox', + height : this.height, + border : 0, + margin : 5, + width : this.width, + items : [] + }); + return this.panel; +}; + + +SpecimenWidget.prototype.input = function() { + return { + experiment : DATADOC.getExperiment_10(), + proposal : DATADOC.getProposal_10() + }; +}; + +SpecimenWidget.prototype.test = function(targetId) { + var specimenWidget = new SpecimenWidget({ + height : 500, + width : 1000 + }); + BIOSAXS.proposal = new Proposal(specimenWidget.input().proposal); + var experiment = new Experiment(specimenWidget.input().experiment); + var panel = specimenWidget.getPanel(); + panel.render(targetId); + specimenWidget.refresh(experiment); + +}; + + function WarningWidget(args) { this.actions = []; From 27ef65ffe3f154ee26acc484bbd5d136ff88dc0b Mon Sep 17 00:00:00 2001 From: delageniere Date: Mon, 16 Oct 2017 15:13:02 +0200 Subject: [PATCH 12/38] rename parameter reportType to nbRows --- .../src/main/webapp/js/ispyb/min/ispyb-bx.js | 42726 ++++++++-------- .../rest/mx/DataCollectionRestWebService.java | 20 +- 2 files changed, 21371 insertions(+), 21375 deletions(-) diff --git a/ispyb-ui/src/main/webapp/js/ispyb/min/ispyb-bx.js b/ispyb-ui/src/main/webapp/js/ispyb/min/ispyb-bx.js index a98a06520..23e07209a 100644 --- a/ispyb-ui/src/main/webapp/js/ispyb/min/ispyb-bx.js +++ b/ispyb-ui/src/main/webapp/js/ispyb/min/ispyb-bx.js @@ -38,321 +38,321 @@ Event.prototype = { } }; -function GenericGraph(args) { - this.width = 600; - this.height = 400; - - this.targetId = null; - /** Free spaces in the borders * */ - this.top = 10; - this.left = 10; - this.bottom = 50; - this.right = 40; - - /** Ruler * */ - this.rulerHeight = 50; - this.rulerWidth = 50; - this.rulerStroke = 2; - this.rulerVerticalMarksNumber = 5; - - this.rulerMaxValue = null; - this.rulerMinValue = null; - - /** plot options * */ - this.plotPoints = true; - this.pointRadius = 2; - this.fillOpacityPoint = 0.2; - this.strokeOpacityPoint = 0.2; - - /** Cluster titles * */ - this.clusterTitleHeight = 20; - this.interClassesSpace = 2; - this.interClustersSpace = 4; - this.fontSize = 7; - - /** - * If true classes and title will be rendender in the rule otherwise will be - * integer values - */ - this.plotHorizontalByCluster = true; - - if (args != null) { - if (args.targetId != null) { - this.targetId = args.targetId; - } - if (args.plotHorizontalByCluster != null) { - this.plotHorizontalByCluster = args.plotHorizontalByCluster; - } - if (args.height != null) { - this.height = args.height; - } - if (args.width != null) { - this.width = args.width; - } - if (args.rulerMinValue != null) { - this.rulerMinValue = args.rulerMinValue; - } - if (args.rulerMaxValue != null) { - this.rulerMaxValue = args.rulerMaxValue; - } - if (args.rulerHeight != null) { - this.rulerHeight = args.rulerHeight; - } - - } -} - -GenericGraph.prototype.calculate = function(data) { - var result = {}; - - var checked = this.cleanArray(data); - - /** sorting array * */ - checked.sort(function(a, b) { - return a - b; - }); - - var median = this.getMedian(checked); - - result.median = median; - result.Q1 = Number(this.getQ1(checked)); - result.Q2 = Number(this.getQ2(checked)); - result.Q3 = Number(this.getQ3(checked)); - result.population = checked; - - result.IQR = Number(result.Q3 - result.Q1); - result.outlier_below_limit = result.Q1 - (1.5 * result.IQR); - result.outlier_above_limit = result.Q3 + (1.5 * result.IQR); - result.below_outliers = this.getBelowOutliers(result.outlier_below_limit, checked); - result.above_outliers = this.getAboveOutliers(result.outlier_above_limit, checked); - - result.min_whisker = this.minValueWhisker(result.outlier_below_limit, result.Q1, checked); - result.max_whisker = this.maxValueWhisker(result.outlier_above_limit, result.Q3, checked); - - return result; -}; - -GenericGraph.prototype.drawSVGVerticalText = function(x, y, text, properties) { - var transform = [ "transform", "translate(" + x + ", " + y + "), rotate(-90) " ]; - properties.push(transform); - SVG.drawText(0, 0, text, this.svg, properties); -}; - -/** Plot the numbers on the axis * */ -GenericGraph.prototype.plotRuler = function(rulerProperties) { - - SVG.drawRectangle(rulerProperties.vertical.x, rulerProperties.vertical.y, rulerProperties.vertical.width, rulerProperties.vertical.height, - this.svg, [ [ "fill", "black" ] ]); - var distance = rulerProperties.vertical.height / (this.rulerVerticalMarksNumber + 1); - for ( var i = 0; i <= this.rulerVerticalMarksNumber + 1; i++) { - var deltaHeight = distance * i; - var aux = rulerProperties.vertical.height - deltaHeight; - - var text = Number((aux / rulerProperties.vertical.height) * (rulerProperties.maxPoint - rulerProperties.minPoint) + rulerProperties.minPoint) - .toFixed(3); - - SVG.drawLine(rulerProperties.horizontal.x, this.top + deltaHeight, rulerProperties.horizontal.x - rulerProperties.markWidth, - this.top + deltaHeight, this.svg, [ [ "stroke", "black" ] ]); - SVG.drawText(this.left, this.top + distance * i + 5, text, this.svg, [ [ "style", "font-size:xx-small" ] ]); - /** Drawing the mark up to the end * */ - SVG.drawLine(rulerProperties.horizontal.x, this.top + deltaHeight, this.width - this.right, this.top + deltaHeight, this.svg, [ - [ "stroke", rulerProperties.markColor ], [ "stroke-width", "0.3" ] ]); - - if (i == this.rulerVerticalMarksNumber + 1) { - SVG.drawLine(rulerProperties.horizontal.x, this.top + deltaHeight, this.width - this.right, this.top + deltaHeight, this.svg, [ [ - "stroke", rulerProperties.markColor ] ]); - } - } - - /** Drawing horizontal rulers * */ - if (!this.plotHorizontalByCluster) { - var width = rulerProperties.horizontal.width; - var ratio = width / (rulerProperties.horizontal.xValues.range); - for ( i = 0; i < rulerProperties.horizontal.xValues.values.length; i++) { - var coorX = rulerProperties.horizontal.xValues.values[i] - rulerProperties.horizontal.xValues.min; - SVG.drawText(rulerProperties.horizontal.x + coorX * ratio, this.height - (this.bottom + (this.clusterTitleHeight)), - rulerProperties.horizontal.xValues.values[i], this.svg, [ [ "style", "font-size:small" ] ]); - } - } -}; - -GenericGraph.prototype.plotAxes = function(properties) { - /** - * Drawing canvas plot-free spaces SVG.drawRectangle(0, this.top, this.left, - * this.height, this.svg, [["fill", "pink"]]); SVG.drawRectangle(this.width - - * this.right, this.top, plot.width, plot.height, this.svg, [["fill", - * "pink"]]); SVG.drawRectangle(0, 0, this.width, this.top, this.svg, - * [["fill", "red"]]); SVG.drawRectangle(0, this.height - this.bottom, - * this.width, this.bottom, this.svg, [["fill", "red"]]); - */ - - /** Drawing ruler Space * */ - this.plotRuler({ - minPoint : Number(properties.minPoint), - maxPoint : Number(properties.maxPoint), - markColor : "black", - markWidth : 20, - vertical : { - x : this.left + this.rulerWidth - this.rulerStroke, - y : this.top, - width : this.rulerStroke, - height : this.height - (this.top + this.bottom + this.clusterTitleHeight) - this.rulerHeight - }, - horizontal : { - x : this.left + this.rulerWidth - this.rulerStroke, - y : this.height - (this.bottom + this.clusterTitleHeight + this.rulerHeight), - width : properties.width, - height : this.rulerStroke, - xValues : properties.xValues - } - }); - -}; - -/** Remove nulls and NaN elements in the array * */ -GenericGraph.prototype.cleanArray = function(data) { - var checked = []; - - /** checking data are numbers * */ - for ( var i = 0; i < data.length; i++) { - if (data[i] != null) { - if (!isNaN(data[i])) { - checked.push(data[i]); - } - } - } - return checked; -}; - -GenericGraph.prototype.refresh = function(data) { - document.getElementById(this.targetId).innerHTML = ""; - this.draw(this.targetId, data); -}; - -GenericGraph.prototype.getClassColor = function(className) { - for ( var i = 0; i < this.data.clusters.length; i++) { - var cluster = this.data.clusters[i]; - for ( var j = 0; j < cluster.classes.length; j++) { - var classes = cluster.classes[j]; - if (classes.name == className) { - if (classes.color != null) { - return classes.color; - } - } - } - } - return "black"; -}; - -GenericGraph.prototype.getDimensions = function(data) { - var results = {}; - var points = []; - - this.data = data; - var classesNumber = 0; - var xValues = []; - - for ( var i = 0; i < data.clusters.length; i++) { - var cluster = data.clusters[i]; - if (!this.plotHorizontalByCluster) { - xValues.push(data.clusters[i].x); - } - for ( var j = 0; j < cluster.classes.length; j++) { - var classes = cluster.classes[j]; - points = points.concat(classes.values); - classesNumber = classesNumber + 1; - } - } - - var checked = this.cleanArray(points); - - checked.sort(function(a, b) { - return a - b; - }); - - results.minPoint = checked[0]; - if (this.rulerMinValue != null) { - results.minPoint = this.rulerMinValue; - } - results.maxPoint = checked[checked.length - 1]; - if (this.rulerMaxValue != null) { - results.maxPoint = this.rulerMaxValue; - } - - results.classesNumber = classesNumber; - results.clusterNumber = data.clusters.length; - - var totalInterClassesFreeSpace = (classesNumber - data.clusters.length) * this.interClassesSpace; - var totalInterClusterFreeSpace = (data.clusters.length) * this.interClustersSpace; - results.classWidth = (this.width - (this.rulerWidth + this.left + this.right + totalInterClassesFreeSpace + totalInterClusterFreeSpace))/ classesNumber; - results.width = this.width - (this.right + this.left) - this.rulerWidth + this.rulerStroke; - - results.xValues = {}; - - xValues.sort(function(a, b) { - return a - b; - }); - results.xValues.values = xValues; - if (xValues.length > 0) { - results.xValues.min = xValues[0]; - results.xValues.max = xValues[xValues.length - 1]; - results.xValues.range = results.xValues.max - results.xValues.min; - } - return results; - -}; - -GenericGraph.prototype.draw = function(targetId, data) { - this.targetId = targetId; - var properties = (this.getDimensions(data)); - this.svg = SVG.createSVGCanvas(document.getElementById(this.targetId), [ [ "width", this.width ], [ "height", this.height ] ]); - this.plotAxes(properties); -}; - -GenericGraph.prototype.getMedian = function(checked) { - /** Calculating median * */ - if (checked.length % 2 == 1) { - return checked[Math.floor(checked.length / 2)]; - } else { - return (Number(checked[(checked.length / 2) - 1]) + Number(checked[checked.length / 2])) / 2; - } -}; - -GenericGraph.prototype.pointToPixel = function(value, boxProperties) { - var ratio = (value - boxProperties.minPoint) / (boxProperties.maxPoint - boxProperties.minPoint); - var pixelLength = boxProperties.height - boxProperties.y + this.top; - return (-1 * ratio) * (pixelLength) + (boxProperties.y + boxProperties.height); -}; - -GenericGraph.prototype.maxValueWhisker = function(aboveLimit, q3, array) { - var points = []; - for ( var i = 0; i < array.length; i++) { - if ((array[i] > q3) && (array[i]) <= aboveLimit) { - points.push(array[i]); - } - } - if (points.length > 0) { - points.sort(function(a, b) { - return a - b; - }); - return points[points.length - 1]; - } - return null; -}; - -GenericGraph.prototype.input = function() { - return DATADOC.getBoxWhikerData(); -}; - -GenericGraph.prototype.test = function(targetId) { - var plot = new GenericGraph({ - targetId : targetId, - height : 350, - width : 450, - maxBoxWidth : 25 - }); - plot.refresh(this.input()); -}; +function GenericGraph(args) { + this.width = 600; + this.height = 400; + + this.targetId = null; + /** Free spaces in the borders * */ + this.top = 10; + this.left = 10; + this.bottom = 50; + this.right = 40; + + /** Ruler * */ + this.rulerHeight = 50; + this.rulerWidth = 50; + this.rulerStroke = 2; + this.rulerVerticalMarksNumber = 5; + + this.rulerMaxValue = null; + this.rulerMinValue = null; + + /** plot options * */ + this.plotPoints = true; + this.pointRadius = 2; + this.fillOpacityPoint = 0.2; + this.strokeOpacityPoint = 0.2; + + /** Cluster titles * */ + this.clusterTitleHeight = 20; + this.interClassesSpace = 2; + this.interClustersSpace = 4; + this.fontSize = 7; + + /** + * If true classes and title will be rendender in the rule otherwise will be + * integer values + */ + this.plotHorizontalByCluster = true; + + if (args != null) { + if (args.targetId != null) { + this.targetId = args.targetId; + } + if (args.plotHorizontalByCluster != null) { + this.plotHorizontalByCluster = args.plotHorizontalByCluster; + } + if (args.height != null) { + this.height = args.height; + } + if (args.width != null) { + this.width = args.width; + } + if (args.rulerMinValue != null) { + this.rulerMinValue = args.rulerMinValue; + } + if (args.rulerMaxValue != null) { + this.rulerMaxValue = args.rulerMaxValue; + } + if (args.rulerHeight != null) { + this.rulerHeight = args.rulerHeight; + } + + } +} + +GenericGraph.prototype.calculate = function(data) { + var result = {}; + + var checked = this.cleanArray(data); + + /** sorting array * */ + checked.sort(function(a, b) { + return a - b; + }); + + var median = this.getMedian(checked); + + result.median = median; + result.Q1 = Number(this.getQ1(checked)); + result.Q2 = Number(this.getQ2(checked)); + result.Q3 = Number(this.getQ3(checked)); + result.population = checked; + + result.IQR = Number(result.Q3 - result.Q1); + result.outlier_below_limit = result.Q1 - (1.5 * result.IQR); + result.outlier_above_limit = result.Q3 + (1.5 * result.IQR); + result.below_outliers = this.getBelowOutliers(result.outlier_below_limit, checked); + result.above_outliers = this.getAboveOutliers(result.outlier_above_limit, checked); + + result.min_whisker = this.minValueWhisker(result.outlier_below_limit, result.Q1, checked); + result.max_whisker = this.maxValueWhisker(result.outlier_above_limit, result.Q3, checked); + + return result; +}; + +GenericGraph.prototype.drawSVGVerticalText = function(x, y, text, properties) { + var transform = [ "transform", "translate(" + x + ", " + y + "), rotate(-90) " ]; + properties.push(transform); + SVG.drawText(0, 0, text, this.svg, properties); +}; + +/** Plot the numbers on the axis * */ +GenericGraph.prototype.plotRuler = function(rulerProperties) { + + SVG.drawRectangle(rulerProperties.vertical.x, rulerProperties.vertical.y, rulerProperties.vertical.width, rulerProperties.vertical.height, + this.svg, [ [ "fill", "black" ] ]); + var distance = rulerProperties.vertical.height / (this.rulerVerticalMarksNumber + 1); + for ( var i = 0; i <= this.rulerVerticalMarksNumber + 1; i++) { + var deltaHeight = distance * i; + var aux = rulerProperties.vertical.height - deltaHeight; + + var text = Number((aux / rulerProperties.vertical.height) * (rulerProperties.maxPoint - rulerProperties.minPoint) + rulerProperties.minPoint) + .toFixed(3); + + SVG.drawLine(rulerProperties.horizontal.x, this.top + deltaHeight, rulerProperties.horizontal.x - rulerProperties.markWidth, + this.top + deltaHeight, this.svg, [ [ "stroke", "black" ] ]); + SVG.drawText(this.left, this.top + distance * i + 5, text, this.svg, [ [ "style", "font-size:xx-small" ] ]); + /** Drawing the mark up to the end * */ + SVG.drawLine(rulerProperties.horizontal.x, this.top + deltaHeight, this.width - this.right, this.top + deltaHeight, this.svg, [ + [ "stroke", rulerProperties.markColor ], [ "stroke-width", "0.3" ] ]); + + if (i == this.rulerVerticalMarksNumber + 1) { + SVG.drawLine(rulerProperties.horizontal.x, this.top + deltaHeight, this.width - this.right, this.top + deltaHeight, this.svg, [ [ + "stroke", rulerProperties.markColor ] ]); + } + } + + /** Drawing horizontal rulers * */ + if (!this.plotHorizontalByCluster) { + var width = rulerProperties.horizontal.width; + var ratio = width / (rulerProperties.horizontal.xValues.range); + for ( i = 0; i < rulerProperties.horizontal.xValues.values.length; i++) { + var coorX = rulerProperties.horizontal.xValues.values[i] - rulerProperties.horizontal.xValues.min; + SVG.drawText(rulerProperties.horizontal.x + coorX * ratio, this.height - (this.bottom + (this.clusterTitleHeight)), + rulerProperties.horizontal.xValues.values[i], this.svg, [ [ "style", "font-size:small" ] ]); + } + } +}; + +GenericGraph.prototype.plotAxes = function(properties) { + /** + * Drawing canvas plot-free spaces SVG.drawRectangle(0, this.top, this.left, + * this.height, this.svg, [["fill", "pink"]]); SVG.drawRectangle(this.width - + * this.right, this.top, plot.width, plot.height, this.svg, [["fill", + * "pink"]]); SVG.drawRectangle(0, 0, this.width, this.top, this.svg, + * [["fill", "red"]]); SVG.drawRectangle(0, this.height - this.bottom, + * this.width, this.bottom, this.svg, [["fill", "red"]]); + */ + + /** Drawing ruler Space * */ + this.plotRuler({ + minPoint : Number(properties.minPoint), + maxPoint : Number(properties.maxPoint), + markColor : "black", + markWidth : 20, + vertical : { + x : this.left + this.rulerWidth - this.rulerStroke, + y : this.top, + width : this.rulerStroke, + height : this.height - (this.top + this.bottom + this.clusterTitleHeight) - this.rulerHeight + }, + horizontal : { + x : this.left + this.rulerWidth - this.rulerStroke, + y : this.height - (this.bottom + this.clusterTitleHeight + this.rulerHeight), + width : properties.width, + height : this.rulerStroke, + xValues : properties.xValues + } + }); + +}; + +/** Remove nulls and NaN elements in the array * */ +GenericGraph.prototype.cleanArray = function(data) { + var checked = []; + + /** checking data are numbers * */ + for ( var i = 0; i < data.length; i++) { + if (data[i] != null) { + if (!isNaN(data[i])) { + checked.push(data[i]); + } + } + } + return checked; +}; + +GenericGraph.prototype.refresh = function(data) { + document.getElementById(this.targetId).innerHTML = ""; + this.draw(this.targetId, data); +}; + +GenericGraph.prototype.getClassColor = function(className) { + for ( var i = 0; i < this.data.clusters.length; i++) { + var cluster = this.data.clusters[i]; + for ( var j = 0; j < cluster.classes.length; j++) { + var classes = cluster.classes[j]; + if (classes.name == className) { + if (classes.color != null) { + return classes.color; + } + } + } + } + return "black"; +}; + +GenericGraph.prototype.getDimensions = function(data) { + var results = {}; + var points = []; + + this.data = data; + var classesNumber = 0; + var xValues = []; + + for ( var i = 0; i < data.clusters.length; i++) { + var cluster = data.clusters[i]; + if (!this.plotHorizontalByCluster) { + xValues.push(data.clusters[i].x); + } + for ( var j = 0; j < cluster.classes.length; j++) { + var classes = cluster.classes[j]; + points = points.concat(classes.values); + classesNumber = classesNumber + 1; + } + } + + var checked = this.cleanArray(points); + + checked.sort(function(a, b) { + return a - b; + }); + + results.minPoint = checked[0]; + if (this.rulerMinValue != null) { + results.minPoint = this.rulerMinValue; + } + results.maxPoint = checked[checked.length - 1]; + if (this.rulerMaxValue != null) { + results.maxPoint = this.rulerMaxValue; + } + + results.classesNumber = classesNumber; + results.clusterNumber = data.clusters.length; + + var totalInterClassesFreeSpace = (classesNumber - data.clusters.length) * this.interClassesSpace; + var totalInterClusterFreeSpace = (data.clusters.length) * this.interClustersSpace; + results.classWidth = (this.width - (this.rulerWidth + this.left + this.right + totalInterClassesFreeSpace + totalInterClusterFreeSpace))/ classesNumber; + results.width = this.width - (this.right + this.left) - this.rulerWidth + this.rulerStroke; + + results.xValues = {}; + + xValues.sort(function(a, b) { + return a - b; + }); + results.xValues.values = xValues; + if (xValues.length > 0) { + results.xValues.min = xValues[0]; + results.xValues.max = xValues[xValues.length - 1]; + results.xValues.range = results.xValues.max - results.xValues.min; + } + return results; + +}; + +GenericGraph.prototype.draw = function(targetId, data) { + this.targetId = targetId; + var properties = (this.getDimensions(data)); + this.svg = SVG.createSVGCanvas(document.getElementById(this.targetId), [ [ "width", this.width ], [ "height", this.height ] ]); + this.plotAxes(properties); +}; + +GenericGraph.prototype.getMedian = function(checked) { + /** Calculating median * */ + if (checked.length % 2 == 1) { + return checked[Math.floor(checked.length / 2)]; + } else { + return (Number(checked[(checked.length / 2) - 1]) + Number(checked[checked.length / 2])) / 2; + } +}; + +GenericGraph.prototype.pointToPixel = function(value, boxProperties) { + var ratio = (value - boxProperties.minPoint) / (boxProperties.maxPoint - boxProperties.minPoint); + var pixelLength = boxProperties.height - boxProperties.y + this.top; + return (-1 * ratio) * (pixelLength) + (boxProperties.y + boxProperties.height); +}; + +GenericGraph.prototype.maxValueWhisker = function(aboveLimit, q3, array) { + var points = []; + for ( var i = 0; i < array.length; i++) { + if ((array[i] > q3) && (array[i]) <= aboveLimit) { + points.push(array[i]); + } + } + if (points.length > 0) { + points.sort(function(a, b) { + return a - b; + }); + return points[points.length - 1]; + } + return null; +}; + +GenericGraph.prototype.input = function() { + return DATADOC.getBoxWhikerData(); +}; + +GenericGraph.prototype.test = function(targetId) { + var plot = new GenericGraph({ + targetId : targetId, + height : 350, + width : 450, + maxBoxWidth : 25 + }); + plot.refresh(this.input()); +}; /** * Using dygraph it plots a chart. Params: targetId, labelsContainerId, args @@ -2087,338 +2087,338 @@ MacromoleculeConditionGrid.prototype.test = function(targetId) { panel.render(targetId); }; - -function ItemGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ - this.id = id; - this.args = new Object(); - - this.defaultFormat = new ItemFormat(defaultFormat); - - if(selectedFormat != null){ - this.selected = new ItemFormat(selectedFormat); - } - else{ - this.selected = new ItemFormat(defaultFormat); - } - - if(overFormat != null){ - this.over = new ItemFormat(overFormat); - } - else{ - this.over = new ItemFormat(defaultFormat); - } - - if(draggingFormat != null){ - this.dragging = new ItemFormat(draggingFormat); - } - else{ - this.dragging = new ItemFormat(defaultFormat); - } - - //Events - this.stateChanged = new Event(this); - - - //Attaching events - var _this = this; - this._setEvents(); -}; - -ItemGraphFormatter.prototype.getType = function(){ - return this.args.type; -}; - - -ItemGraphFormatter.prototype.toJSON = function(){ - var json = this.args; - json.defaultFormat = this.getDefault().toJSON(); - json.over = this.getOver().toJSON(); - json.selected = this.getSelected().toJSON(); - json.dragging = this.getDragging().toJSON(); - json.id = this.id; - return json; -}; - -ItemGraphFormatter.prototype.loadFromJSON = function(json){ - this.args = json; - this.defaultFormat = new ItemFormat(json.defaultFormat); - this.over = new ItemFormat(json.over); - this.selected = new ItemFormat(json.selected); - this.dragging = new ItemFormat(json.dragging); - this._setEvents(); -}; - -ItemGraphFormatter.prototype._setEvents = function(){ - //Attaching events - var _this = this; - - this.defaultFormat.changed.attach(function (sender, item){ - _this.over.setSize(_this.defaultFormat.getSize()); - _this.selected.setSize(_this.defaultFormat.getSize()); - _this.dragging.setSize(_this.defaultFormat.getSize()); - _this.stateChanged.notify(_this); - }); - - this.selected.changed.attach(function (sender, item){ - _this.stateChanged.notify(_this); - }); - - this.over.changed.attach(function (sender, item){ - _this.stateChanged.notify(_this); - }); - - this.dragging.changed.attach(function (sender, item){ - _this.stateChanged.notify(_this); - }); -}; - -/** Getters **/ -ItemGraphFormatter.prototype.getId = function(){return this.id;}; -ItemGraphFormatter.prototype.getDefault = function(){return this.defaultFormat;}; -ItemGraphFormatter.prototype.getSelected = function(){return this.selected;}; -ItemGraphFormatter.prototype.getOver = function(){return this.over;}; -ItemGraphFormatter.prototype.getDragging = function(){return this.dragging;}; - -function ItemFormat(args){ - this.defaultFormat = new Object(); - this.args = new Object(); - this.args.title = new Object(); - //Defult properties - this.args.visible = true; - this.args.hidden = false; - this.args.stroke = "#000000"; - this.args.strokeOpacity = 0.8; - this.args["stroke-width"] = 1; - this.args.fill = "#000000"; - this.args["fill-opacity"] = 1; - this.args.size = 1; - this.args.opacity = 1; - this.args.fontSize = "8"; - this.args.fontColor = "#000000"; - - /** For directed edge with arrow **/ - //this.args.arrowSize = 1; - - - if (args != null){ - if (args.visible != null){ - this.args.visible = args.visible; - } - if (args.opacity != null){ - this.args.opacity = args.opacity; - } - if (args.size != null){ - this.args.size = args.size; - } - if (args.hidden != null){ - this.args.hidden = args.hidden; - } - if (args.stroke != null){ - this.args.stroke = this._fixColor(args.stroke); - } - if (args.strokeOpacity != null){ - this.args.strokeOpacity = args.strokeOpacity; - } - if (args["stroke-width"]!=null){ - this.args["stroke-width"] = args["stroke-width"]; - } - if (args["fill-opacity"]!=null){ - this.args["fill-opacity"] = args["fill-opacity"]; - } - if (args.shape!=null){ - this.args.shape = args.shape; - } - if (args.fill!=null){ - this.args.fill = this._fixColor(args.fill); - } - - - if (args.title!=null){ - if (args.title.fontSize!=null){ - this.args.title.fontSize = args.title.fontSize; - } - if (args.title.fill!=null){ - this.args.title.fill = this._fixColor(args.title.fill); - } - } - - /** For directed edge with arrow **/ - /*if (args.arrowSize!=null){ - this.args.arrowSize = args.arrowSize; - }*/ - - } - - this.changed = new Event(); -}; - -ItemFormat.prototype._fixColor = function(color){ - var fixed = color; - if (color.indexOf("green") != -1){ - fixed = '#04B431'; - } - - if (color.indexOf("blue") != -1){ - fixed = '#045FB4'; - } - - if (color.indexOf("red") != -1){ - fixed = '#DF0101'; - } - - if (color.indexOf("black") != -1){ - fixed = '#000000'; - } - - if (color.indexOf("white") != -1){ - fixed = '#FFFFFF'; - } - - if (color.indexOf("#") == -1){ - fixed = "#" + color; - } - return fixed; -}; - -ItemFormat.prototype.toJSON = function(){ - if(this.args.strokeOpacity != null){ - this.args["stroke-opacity"] = this.args.strokeOpacity; - delete this.args.strokeOpacity; - } - -// if(this.args.strokeWidth != null){ -// this.args["stroke-width"] = this.args.strokeWidth; -// delete this.args["stroke-width"]; -// } - - if(this.args.title.fontColor != null){ - this.args.title["font-color"] = this.args.title.fontColor; - } - else{ - this.args.title["font-color"] = this.args.fontColor;//;this.args.title.fontColor; - } - - if(this.args.title.fontSize != null){ - this.args.title["font-size"] = this.args.title.fontSize;//;this.args.title.fontColor; - } - else{ - this.args.title["font-size"] = this.args.fontSize;//;this.args.title.fontColor; - } - //return this.args; - return this.args; -}; - -ItemFormat.prototype.getAttribute = function(name){return this.args[name];}; - -//Getters and Setters -ItemFormat.prototype.setVisible = function(visible){ - if (this.args.visible != visible){ - this.args.visible = visible; - this.changed.notify(this); - } -}; - -ItemFormat.prototype.getVisible = function(){return this.args.visible;}; - -ItemFormat.prototype.setHidden = function(hidden){ - if (this.args.hidden != hidden){ - this.args.hidden = hidden; - this.changed.notify(this); - } -}; - -ItemFormat.prototype.getHidden = function(){return this.args.hidden;}; - - -ItemFormat.prototype.setStroke = function(stroke){ - if (this.args.stroke != stroke){ - this.args.stroke = stroke; - this.changed.notify(this); - } -}; - -ItemFormat.prototype.getStroke = function(){return this.args.stroke;}; - -ItemFormat.prototype.setStrokeOpacity = function(strokeOpacity){ - if (this.args.strokeOpacity != strokeOpacity){ - this.args.strokeOpacity = strokeOpacity; - this.changed.notify(this); - } -}; - -ItemFormat.prototype.getStrokeOpacity = function(){return this.args["stroke-opacity"];}; - -ItemFormat.prototype.setStrokeWidth = function(strokeWidth){ - if (this.args["stroke-width"] != strokeWidth){ - this.args["stroke-width"] = strokeWidth; - this.changed.notify(this); - } -}; - - -ItemFormat.prototype.getFillOpacity = function(){return this.args["fill-opacity"];}; - -ItemFormat.prototype.setfillOpacity = function(strokeWidth){ - if (this.args["fill-opacity"] != strokeWidth){ - this.args["fill-opacity"] = strokeWidth; - this.changed.notify(this); - } -}; - - -ItemFormat.prototype.getStrokeWidth = function(){ - return this.args["stroke-width"]; -}; - -ItemFormat.prototype.setFill = function(fill){ - if (this.args.fill != fill){ - this.args.fill = fill; - this.changed.notify(this); - } -}; - -ItemFormat.prototype.getFill = function(){return this.args.fill;}; - -ItemFormat.prototype.setSize = function(size){ - if (this.args.size != size){ - this.args.size = size; - this.changed.notify(this); - } -}; - -ItemFormat.prototype.getSize = function(){return this.args.size;}; - -ItemFormat.prototype.setOpacity = function(opacity){ - if (this.args.opacity != opacity){ - this.args.opacity = opacity; - this.changed.notify(this); - } -}; - -ItemFormat.prototype.getOpacity = function(){return this.args.opacity;}; - -ItemFormat.prototype.getArrowSize = function(){return this.args.arrowSize;}; - -ItemFormat.prototype.setArrowSize = function(arrowSize){ - if (this.args.arrowSize != arrowSize){ - this.args.arrowSize = arrowSize; - this.changed.notify(this); - } -}; - -ItemFormat.prototype.getFontSize = function(){return this.args.title.fontSize;}; - -ItemFormat.prototype.setFontSize = function(fontSize){ - - if (this.args.title.fontSize != fontSize){ - this.args.title.fontSize = fontSize; - this.changed.notify(this); - } -}; - - - - + +function ItemGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ + this.id = id; + this.args = new Object(); + + this.defaultFormat = new ItemFormat(defaultFormat); + + if(selectedFormat != null){ + this.selected = new ItemFormat(selectedFormat); + } + else{ + this.selected = new ItemFormat(defaultFormat); + } + + if(overFormat != null){ + this.over = new ItemFormat(overFormat); + } + else{ + this.over = new ItemFormat(defaultFormat); + } + + if(draggingFormat != null){ + this.dragging = new ItemFormat(draggingFormat); + } + else{ + this.dragging = new ItemFormat(defaultFormat); + } + + //Events + this.stateChanged = new Event(this); + + + //Attaching events + var _this = this; + this._setEvents(); +}; + +ItemGraphFormatter.prototype.getType = function(){ + return this.args.type; +}; + + +ItemGraphFormatter.prototype.toJSON = function(){ + var json = this.args; + json.defaultFormat = this.getDefault().toJSON(); + json.over = this.getOver().toJSON(); + json.selected = this.getSelected().toJSON(); + json.dragging = this.getDragging().toJSON(); + json.id = this.id; + return json; +}; + +ItemGraphFormatter.prototype.loadFromJSON = function(json){ + this.args = json; + this.defaultFormat = new ItemFormat(json.defaultFormat); + this.over = new ItemFormat(json.over); + this.selected = new ItemFormat(json.selected); + this.dragging = new ItemFormat(json.dragging); + this._setEvents(); +}; + +ItemGraphFormatter.prototype._setEvents = function(){ + //Attaching events + var _this = this; + + this.defaultFormat.changed.attach(function (sender, item){ + _this.over.setSize(_this.defaultFormat.getSize()); + _this.selected.setSize(_this.defaultFormat.getSize()); + _this.dragging.setSize(_this.defaultFormat.getSize()); + _this.stateChanged.notify(_this); + }); + + this.selected.changed.attach(function (sender, item){ + _this.stateChanged.notify(_this); + }); + + this.over.changed.attach(function (sender, item){ + _this.stateChanged.notify(_this); + }); + + this.dragging.changed.attach(function (sender, item){ + _this.stateChanged.notify(_this); + }); +}; + +/** Getters **/ +ItemGraphFormatter.prototype.getId = function(){return this.id;}; +ItemGraphFormatter.prototype.getDefault = function(){return this.defaultFormat;}; +ItemGraphFormatter.prototype.getSelected = function(){return this.selected;}; +ItemGraphFormatter.prototype.getOver = function(){return this.over;}; +ItemGraphFormatter.prototype.getDragging = function(){return this.dragging;}; + +function ItemFormat(args){ + this.defaultFormat = new Object(); + this.args = new Object(); + this.args.title = new Object(); + //Defult properties + this.args.visible = true; + this.args.hidden = false; + this.args.stroke = "#000000"; + this.args.strokeOpacity = 0.8; + this.args["stroke-width"] = 1; + this.args.fill = "#000000"; + this.args["fill-opacity"] = 1; + this.args.size = 1; + this.args.opacity = 1; + this.args.fontSize = "8"; + this.args.fontColor = "#000000"; + + /** For directed edge with arrow **/ + //this.args.arrowSize = 1; + + + if (args != null){ + if (args.visible != null){ + this.args.visible = args.visible; + } + if (args.opacity != null){ + this.args.opacity = args.opacity; + } + if (args.size != null){ + this.args.size = args.size; + } + if (args.hidden != null){ + this.args.hidden = args.hidden; + } + if (args.stroke != null){ + this.args.stroke = this._fixColor(args.stroke); + } + if (args.strokeOpacity != null){ + this.args.strokeOpacity = args.strokeOpacity; + } + if (args["stroke-width"]!=null){ + this.args["stroke-width"] = args["stroke-width"]; + } + if (args["fill-opacity"]!=null){ + this.args["fill-opacity"] = args["fill-opacity"]; + } + if (args.shape!=null){ + this.args.shape = args.shape; + } + if (args.fill!=null){ + this.args.fill = this._fixColor(args.fill); + } + + + if (args.title!=null){ + if (args.title.fontSize!=null){ + this.args.title.fontSize = args.title.fontSize; + } + if (args.title.fill!=null){ + this.args.title.fill = this._fixColor(args.title.fill); + } + } + + /** For directed edge with arrow **/ + /*if (args.arrowSize!=null){ + this.args.arrowSize = args.arrowSize; + }*/ + + } + + this.changed = new Event(); +}; + +ItemFormat.prototype._fixColor = function(color){ + var fixed = color; + if (color.indexOf("green") != -1){ + fixed = '#04B431'; + } + + if (color.indexOf("blue") != -1){ + fixed = '#045FB4'; + } + + if (color.indexOf("red") != -1){ + fixed = '#DF0101'; + } + + if (color.indexOf("black") != -1){ + fixed = '#000000'; + } + + if (color.indexOf("white") != -1){ + fixed = '#FFFFFF'; + } + + if (color.indexOf("#") == -1){ + fixed = "#" + color; + } + return fixed; +}; + +ItemFormat.prototype.toJSON = function(){ + if(this.args.strokeOpacity != null){ + this.args["stroke-opacity"] = this.args.strokeOpacity; + delete this.args.strokeOpacity; + } + +// if(this.args.strokeWidth != null){ +// this.args["stroke-width"] = this.args.strokeWidth; +// delete this.args["stroke-width"]; +// } + + if(this.args.title.fontColor != null){ + this.args.title["font-color"] = this.args.title.fontColor; + } + else{ + this.args.title["font-color"] = this.args.fontColor;//;this.args.title.fontColor; + } + + if(this.args.title.fontSize != null){ + this.args.title["font-size"] = this.args.title.fontSize;//;this.args.title.fontColor; + } + else{ + this.args.title["font-size"] = this.args.fontSize;//;this.args.title.fontColor; + } + //return this.args; + return this.args; +}; + +ItemFormat.prototype.getAttribute = function(name){return this.args[name];}; + +//Getters and Setters +ItemFormat.prototype.setVisible = function(visible){ + if (this.args.visible != visible){ + this.args.visible = visible; + this.changed.notify(this); + } +}; + +ItemFormat.prototype.getVisible = function(){return this.args.visible;}; + +ItemFormat.prototype.setHidden = function(hidden){ + if (this.args.hidden != hidden){ + this.args.hidden = hidden; + this.changed.notify(this); + } +}; + +ItemFormat.prototype.getHidden = function(){return this.args.hidden;}; + + +ItemFormat.prototype.setStroke = function(stroke){ + if (this.args.stroke != stroke){ + this.args.stroke = stroke; + this.changed.notify(this); + } +}; + +ItemFormat.prototype.getStroke = function(){return this.args.stroke;}; + +ItemFormat.prototype.setStrokeOpacity = function(strokeOpacity){ + if (this.args.strokeOpacity != strokeOpacity){ + this.args.strokeOpacity = strokeOpacity; + this.changed.notify(this); + } +}; + +ItemFormat.prototype.getStrokeOpacity = function(){return this.args["stroke-opacity"];}; + +ItemFormat.prototype.setStrokeWidth = function(strokeWidth){ + if (this.args["stroke-width"] != strokeWidth){ + this.args["stroke-width"] = strokeWidth; + this.changed.notify(this); + } +}; + + +ItemFormat.prototype.getFillOpacity = function(){return this.args["fill-opacity"];}; + +ItemFormat.prototype.setfillOpacity = function(strokeWidth){ + if (this.args["fill-opacity"] != strokeWidth){ + this.args["fill-opacity"] = strokeWidth; + this.changed.notify(this); + } +}; + + +ItemFormat.prototype.getStrokeWidth = function(){ + return this.args["stroke-width"]; +}; + +ItemFormat.prototype.setFill = function(fill){ + if (this.args.fill != fill){ + this.args.fill = fill; + this.changed.notify(this); + } +}; + +ItemFormat.prototype.getFill = function(){return this.args.fill;}; + +ItemFormat.prototype.setSize = function(size){ + if (this.args.size != size){ + this.args.size = size; + this.changed.notify(this); + } +}; + +ItemFormat.prototype.getSize = function(){return this.args.size;}; + +ItemFormat.prototype.setOpacity = function(opacity){ + if (this.args.opacity != opacity){ + this.args.opacity = opacity; + this.changed.notify(this); + } +}; + +ItemFormat.prototype.getOpacity = function(){return this.args.opacity;}; + +ItemFormat.prototype.getArrowSize = function(){return this.args.arrowSize;}; + +ItemFormat.prototype.setArrowSize = function(arrowSize){ + if (this.args.arrowSize != arrowSize){ + this.args.arrowSize = arrowSize; + this.changed.notify(this); + } +}; + +ItemFormat.prototype.getFontSize = function(){return this.args.title.fontSize;}; + +ItemFormat.prototype.setFontSize = function(fontSize){ + + if (this.args.title.fontSize != fontSize){ + this.args.title.fontSize = fontSize; + this.changed.notify(this); + } +}; + + + + /** * This class executes the actions @@ -4952,1101 +4952,2095 @@ function openExperiment(experimentId) { BIOSAXS.openExperiment(experimentId); } -var SITE_CONF = { - SAMPLE_CHANGER_CONFIGURATION : { - "3":{ - "platetype3VO": {"plateTypeId":4,"name":"96 Well plate","rowCount":8,"columnCount":12,"shape":"REC"}, - "name":"96 Well plate", - "slotPositionRow":"1", - "slotPositionColumn":"3", - "storageTemperature":"0", - "sampleplateposition3VOs":[], - "experimentId":0 - }, - "2":{ - "platetype3VO":{"plateTypeId":2,"name":" 4 x ( 8 + 3 ) Block","rowCount":4,"columnCount":11,"shape":"REC"}, - "name":" 4 x ( 8 + 3 ) Block", - "slotPositionRow":"1", - "slotPositionColumn":"2", - "storageTemperature":"0", - "sampleplateposition3VOs":[],"experimentId":0 - }, - "1":{ - "platetype3VO":{"plateTypeId":1,"name":"Deep Well","rowCount":8,"columnCount":12,"shape":"REC"}, - "name":"Deep Well", - "slotPositionRow":"1", - "slotPositionColumn":"1", - "storageTemperature":"0", - "sampleplateposition3VOs":[], - "experimentId":0 - } - } +var SITE_CONF = { + SAMPLE_CHANGER_CONFIGURATION : { + "3":{ + "platetype3VO": {"plateTypeId":4,"name":"96 Well plate","rowCount":8,"columnCount":12,"shape":"REC"}, + "name":"96 Well plate", + "slotPositionRow":"1", + "slotPositionColumn":"3", + "storageTemperature":"0", + "sampleplateposition3VOs":[], + "experimentId":0 + }, + "2":{ + "platetype3VO":{"plateTypeId":2,"name":" 4 x ( 8 + 3 ) Block","rowCount":4,"columnCount":11,"shape":"REC"}, + "name":" 4 x ( 8 + 3 ) Block", + "slotPositionRow":"1", + "slotPositionColumn":"2", + "storageTemperature":"0", + "sampleplateposition3VOs":[],"experimentId":0 + }, + "1":{ + "platetype3VO":{"plateTypeId":1,"name":"Deep Well","rowCount":8,"columnCount":12,"shape":"REC"}, + "name":"Deep Well", + "slotPositionRow":"1", + "slotPositionColumn":"1", + "storageTemperature":"0", + "sampleplateposition3VOs":[], + "experimentId":0 + } + } }; - -var ISPYB_CONF = { - load : function(config) { - for (var key in config) { - ISPYB_CONF[key] = config[key]; - } - }, - SAMPLE_CHANGER_CONFIGURATION : { - "1": { - "platetype3VO": {"plateTypeId": 1, "name": "Deep Well", "rowCount": 8, "columnCount": 12, "shape": "REC"}, - "name": "Deep Well", - "slotPositionRow": "1", - "slotPositionColumn": "1", - "storageTemperature": "0", - "sampleplateposition3VOs": [], - "experimentId": 0 - } - } + +var ISPYB_CONF = { + load : function(config) { + for (var key in config) { + ISPYB_CONF[key] = config[key]; + } + }, + SAMPLE_CHANGER_CONFIGURATION : { + "1": { + "platetype3VO": {"plateTypeId": 1, "name": "Deep Well", "rowCount": 8, "columnCount": 12, "shape": "REC"}, + "name": "Deep Well", + "slotPositionRow": "1", + "slotPositionColumn": "1", + "storageTemperature": "0", + "sampleplateposition3VOs": [], + "experimentId": 0 + } + } }; -var SITE_CONF = { - -}; +var SITE_CONF = { + +}; -/** - * Example form - * - * @witdh - * @height - */ -function AbinitioForm(args) { - this.id = BUI.id(); - this.width = null; - this.height = null; - - if (args != null) { - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; - } - } - - var _this = this; - /** Widgets **/ - this.abinitioGrid = new AbinitioGrid({ - width : null, - height : 200 - }); - - this.abinitioGrid.onSelected.attach(function(sender, models) { - var modelsIdList = []; - for ( var i in models) { - modelsIdList.push(models[i].modelId); - } - _this._renderPlot(_this.subtractions[0].subtractionId, modelsIdList); - _this._renderPDB(modelsIdList); - }); - - /** Dygraph Widget that plots fir files**/ - this.plotWidget = new PlotWidget({ - width : 745 / 2, - height : 300, - margin : "10 0 5 10" - }); - - /** PDB viewer **/ - this.viewer = new PDBViewer({ - width : 745 / 2, - height : 300 - }); - -} - -AbinitioForm.prototype._renderPlot = function(subtractionId, modelsIdList) { - /** Trying to plot tje subtraction and the models **/ - try { - var colors = [ "#669900", "#0000FF" ]; - this.plotWidget.refresh([], [ ], modelsIdList, [], [], colors); - } catch (e) { - console.log(e); - } -}; - -AbinitioForm.prototype._renderPDB = function(modelsIdList) { - /** Trying to plot the PDB file **/ - try { - var viz = []; - for (var i = 0; i < modelsIdList.length; i++) { - viz.push({ - modelId : modelsIdList[i], - color : "0xFF6600", - opacity : 0.8 - }); - } - this.viewer.refresh(viz); - } catch (e) { - console.log(e); - } -}; - -AbinitioForm.prototype._getItems = function() { - var _this = this; - return [ { - xtype : 'label', - forId : 'myFieldId', - text : 'INLINE HELP: To be updated', - margin : '15 0 20 10', - cls : "inline-help" - }, this.abinitioGrid.getPanel(), { - xtype : 'container', - layout : 'hbox', - items : [ this.plotWidget.getPanel(), this.viewer.getPanel() ] - } ] -}; - -AbinitioForm.prototype._getButtons = function() { - return []; -}; - -AbinitioForm.prototype.getPanel = function() { - var _this = this; - this.panel = Ext.create('Ext.form.Panel', { - width : this.width, - height : this.height, - margin : 10, - border : 1, - defaultType : 'textfield', - items : this._getItems(), - buttons : this._getButtons(), - listeners : { - afterrender : function() { - _this._populate(); - - } - } - }); - return this.panel; -}; - -/** Populates could be call when the DOM is not filled yet **/ -AbinitioForm.prototype._populate = function() { -}; - -/** It populates the form * */ -AbinitioForm.prototype.refresh = function(subtractions) { - this.subtractions = subtractions; - this.abinitioGrid.refresh(subtractions); -}; - -AbinitioForm.prototype.input = function() { - return {}; -}; - -/** It populates the form **/ -AbinitioForm.prototype.test = function(targetId) { - var macromoleculeForm = new AbinitioForm(); - var panel = macromoleculeForm.getPanel(); - panel.render(targetId); -}; +/** + * Example form + * + * @witdh + * @height + */ +function AbinitioForm(args) { + this.id = BUI.id(); + this.width = null; + this.height = null; -/** - * Example form - * - * @witdh - * @height - */ -function DataReductionForm(args) { - this.id = BUI.id(); - this.width = null; - this.height = null; - - if (args != null) { - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; - } - } - + if (args != null) { + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + } + + var _this = this; + /** Widgets **/ + this.abinitioGrid = new AbinitioGrid({ + width : null, + height : 200 + }); + + this.abinitioGrid.onSelected.attach(function(sender, models) { + var modelsIdList = []; + for ( var i in models) { + modelsIdList.push(models[i].modelId); + } + _this._renderPlot(_this.subtractions[0].subtractionId, modelsIdList); + _this._renderPDB(modelsIdList); + }); + + /** Dygraph Widget that plots fir files**/ + this.plotWidget = new PlotWidget({ + width : 745 / 2, + height : 300, + margin : "10 0 5 10" + }); + + /** PDB viewer **/ + this.viewer = new PDBViewer({ + width : 745 / 2, + height : 300 + }); + +} + +AbinitioForm.prototype._renderPlot = function(subtractionId, modelsIdList) { + /** Trying to plot tje subtraction and the models **/ + try { + var colors = [ "#669900", "#0000FF" ]; + this.plotWidget.refresh([], [ ], modelsIdList, [], [], colors); + } catch (e) { + console.log(e); + } +}; + +AbinitioForm.prototype._renderPDB = function(modelsIdList) { + /** Trying to plot the PDB file **/ + try { + var viz = []; + for (var i = 0; i < modelsIdList.length; i++) { + viz.push({ + modelId : modelsIdList[i], + color : "0xFF6600", + opacity : 0.8 + }); + } + this.viewer.refresh(viz); + } catch (e) { + console.log(e); + } +}; + +AbinitioForm.prototype._getItems = function() { + var _this = this; + return [ { + xtype : 'label', + forId : 'myFieldId', + text : 'INLINE HELP: To be updated', + margin : '15 0 20 10', + cls : "inline-help" + }, this.abinitioGrid.getPanel(), { + xtype : 'container', + layout : 'hbox', + items : [ this.plotWidget.getPanel(), this.viewer.getPanel() ] + } ] +}; + +AbinitioForm.prototype._getButtons = function() { + return []; +}; + +AbinitioForm.prototype.getPanel = function() { + var _this = this; + this.panel = Ext.create('Ext.form.Panel', { + width : this.width, + height : this.height, + margin : 10, + border : 1, + defaultType : 'textfield', + items : this._getItems(), + buttons : this._getButtons(), + listeners : { + afterrender : function() { + _this._populate(); + + } + } + }); + return this.panel; +}; + +/** Populates could be call when the DOM is not filled yet **/ +AbinitioForm.prototype._populate = function() { +}; + +/** It populates the form * */ +AbinitioForm.prototype.refresh = function(subtractions) { + this.subtractions = subtractions; + this.abinitioGrid.refresh(subtractions); +}; + +AbinitioForm.prototype.input = function() { + return {}; +}; + +/** It populates the form **/ +AbinitioForm.prototype.test = function(targetId) { + var macromoleculeForm = new AbinitioForm(); + var panel = macromoleculeForm.getPanel(); + panel.render(targetId); +}; + +/** + * Example form + * + * @witdh + * @height + */ +function DataReductionForm(args) { + this.id = BUI.id(); + this.width = null; + this.height = null; + + if (args != null) { + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + } + + var _this = this; + + /** Widgets **/ + this.plotWidget = new PlotWidget({ + width : 650, + height : 490 + }); + + /** Selected frames to be displayed **/ + this.selectedItems = { + frames : [], + averages : [], + subtractions : [] + }; + +} + +DataReductionForm.prototype._parseSelectedItemsToIds = function(selectedArray) { + var ids = []; + if (selectedArray != null) { + for (var i = 0; i < selectedArray.length; i++) { + ids.push(selectedArray[i].id); + } + } + return ids; +}; + +DataReductionForm.prototype.onSelectionChanged = function(columnName, selected) { + if (selected != null) { + if (columnName == "Frames") { + this.selectedItems.frames = selected; + this.selectedItems.subtractions = []; + } + if (columnName == "Averages") { + this.selectedItems.averages = selected; + } + if (columnName == "Subtractions") { + this.selectedItems.frames = []; + this.selectedItems.subtractions = selected; + } + } + this.plotWidget.refresh(this._parseSelectedItemsToIds(this.selectedItems.frames), this._parseSelectedItemsToIds(this.selectedItems.subtractions)); +}; + +DataReductionForm.prototype._getFramesExtPanel = function(store, columnName, height) { + var _this = this; + + var selModel = Ext.create('Ext.selection.RowModel', { + allowDeselect : true, + mode : 'MULTI', + listeners : { + selectionchange : function(sm, selections) { + var selected = []; + for (var i = 0; i < selections.length; i++) { + selected.push(selections[i].raw); + } + _this.onSelectionChanged(columnName, selected); + } + } + }); + + return Ext.create('Ext.grid.Panel', { + store : store, + margin : 10, + height : height, + width : 200, + selModel : selModel, + columns : [ { + text : columnName, + dataIndex : 'fileName', + flex : 1 + } ], + viewConfig : { + } + }); +}; + +DataReductionForm.prototype._getFramesPanel = function() { + var fields = [ 'fileName', 'type', 'id' ]; + + this.framesStore = Ext.create('Ext.data.Store', { + fields : fields, + sorters : 'fileName' + }); + + this.averagesStore = Ext.create('Ext.data.Store', { + fields : fields + }); + + this.subtractionStore = Ext.create('Ext.data.Store', { + fields : fields + }); + + var gridFrames = this._getFramesExtPanel(this.framesStore, "Frames", 375); + var gridAvgs = this._getFramesExtPanel(this.averagesStore, "Averages", 125); + var subtractionAvgs = this._getFramesExtPanel(this.subtractionStore, "Subtractions", 75); + + return { + xtype : 'container', + layout : 'vbox', + items : [ gridFrames, subtractionAvgs ] + }; +}; + +DataReductionForm.prototype._getImageContainer = function(name, help) { + var html = "
" + name + "
" + return { + xtype : 'container', + layout : 'vbox', + items : [ { + html : html, + margin : "5 0 0 0", + height : 95, + width : 100 + }, { + xtype : 'label', + forId : 'myFieldId', + text : help, + margin : '5 0 0 0', + cls : "inline-help" + } ] + } +}; + +DataReductionForm.prototype._getItems = function() { + var _this = this; + return [ { + xtype : 'container', + layout : 'hbox', + items : [ + this._getFramesPanel(), + this.plotWidget.getPanel(), + { + xtype : 'panel', + width : 110, + frame : true, + margin : "10 5 5 5", + border : 0, + layout : 'vbox', + items : [ this._getImageContainer("scattering", "Scattering"), this._getImageContainer("guinier", "Guinier Region"), + this._getImageContainer("kratky", "Kratky Plot"), this._getImageContainer("gnom", "P(r) distribution") ] + } ] + } ] +}; + +DataReductionForm.prototype._getButtons = function() { + return []; +}; + +DataReductionForm.prototype.getPanel = function() { + var _this = this; + this.panel = Ext.create('Ext.form.Panel', { + width : this.width, + height : this.height, + border : 0, + items : this._getItems(), + buttons : this._getButtons(), + listeners : { + afterrender : function() { + _this._populate(); + } + } + }); + return this.panel; +}; + +/** Populates could be call when the DOM is not filled yet **/ +DataReductionForm.prototype._populate = function() { +}; + +/** It populates the form * */ +DataReductionForm.prototype.refresh = function(subtractions) { + if (subtractions != null) { + for (var i = 0; i < subtractions.length; i++) { + /** Loading frame grids **/ + var subtraction = subtractions[i]; + var averages = [ { + fileName : BUI.getFileName(subtraction.bufferAverageFilePath), + type : 'bufferAvg', + id : subtraction.subtractionId + }, { + fileName : BUI.getFileName(subtraction.sampleAverageFilePath), + type : 'sampleAvg', + id : subtraction.subtractionId + } + + ]; + this.averagesStore.loadData(averages, true); + this.subtractionStore.loadData([ { + fileName : BUI.getFileName(subtraction.substractedFilePath), + type : 'SUBTRACTION', + id : subtraction.subtractionId + } ], true); + + var frames = []; + /** Buffers **/ + if (subtraction.bufferOneDimensionalFiles != null) { + if (subtraction.bufferOneDimensionalFiles.frametolist3VOs != null) { + for (var j = 0; j < subtraction.bufferOneDimensionalFiles.frametolist3VOs.length; j++) { + var frametolist3VO = subtraction.bufferOneDimensionalFiles.frametolist3VOs[j]; + if (frametolist3VO.frame3VO != null) { + frames.push({ + fileName : BUI.getFileName(frametolist3VO.frame3VO.filePath), + type : 'BUFFER', + id : frametolist3VO.frame3VO.frameId + }); + } + } + } + } + /** Samples **/ + if (subtraction.sampleOneDimensionalFiles != null) { + if (subtraction.sampleOneDimensionalFiles.frametolist3VOs != null) { + for (var j = 0; j < subtraction.sampleOneDimensionalFiles.frametolist3VOs.length; j++) { + var frametolist3VO = subtraction.sampleOneDimensionalFiles.frametolist3VOs[j]; + if (frametolist3VO.frame3VO != null) { + frames.push({ + fileName : BUI.getFileName(frametolist3VO.frame3VO.filePath), + type : 'SAMPLE', + id : frametolist3VO.frame3VO.frameId + }); + } + } + } + } + + this.framesStore.loadData(frames, true); + + /** Loading images **/ + this._displayImage("scattering", subtraction.subtractionId); + this._displayImage("kratky", subtraction.subtractionId); + this._displayImage("guinier", subtraction.subtractionId); + this._displayImage("gnom", subtraction.subtractionId); + } + } +}; + +DataReductionForm.prototype._displayImage = function(name, subtractionId) { + var url = BUI.getURL() + '&type=' + name + '&subtractionId=' + subtractionId; + var event = "OnClick= window.open('" + url + "')"; + document.getElementById(this.id + "_" + name).innerHTML = ''; +}; + +DataReductionForm.prototype.input = function() { + return {}; +}; + +/** It populates the form **/ +DataReductionForm.prototype.test = function(targetId) { + var macromoleculeForm = new DataReductionForm(); + var panel = macromoleculeForm.getPanel(); + panel.render(targetId); +}; + +function PlotWidget(args) { + this.width = 600; + this.height = 600; + this.id = BUI.id(); + + this.linear = false; + + this.margin = "10 0 0 0"; + /** for each stat the max and minimum value when it is scaled in order to show correctly in the legend **/ + this.ranges = {}; + if (args != null) { + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + if (args.margin != null) { + this.margin = args.margin; + } + } + +} + +PlotWidget.prototype.getMenu = function() { + var _this = this; + /** Actions buttons **/ + var actions = []; + actions.push("->"); + actions.push({ + text : "Export as Image", + scope : this, + icon : '../images/save.gif', + handler : function(item, pressed) { + var largeImage = document.createElement("img"); + largeImage.style.display = 'block'; + largeImage.style.width = 200 + "px"; + largeImage.style.height = 200 + "px"; + largeImage.setAttribute('src', Dygraph.Export.asCanvas(this.dygraphObject.dygraph).toDataURL()); + window.open(Dygraph.Export.asCanvas(this.dygraphObject.dygraph).toDataURL(), 'Image', ''); + } + }); + + return actions; +}; + +/** Looks for the maximum value and then divide everything but that value **/ +PlotWidget.prototype.scaledData = function(data) { + for (var i = 0; i < data.length; i++) { + var values = this.getMaxAndMinValue(data[i]); + data[i] = this.divideValuesByMax(data[i], values.max); + this.ranges[data[i].label] = values; + } + return data; +}; + +/** Given a stat float[] and a max number it will divide each value by max **/ +PlotWidget.prototype.divideValuesByMax = function(stat, max) { + for (var j = 0; j < stat.data.length; j++) { + if (max != 0) { + stat.data[j] = Number(stat.data[j]) / max; + stat.std[j] = Number(stat.std[j]) / max; + } + } + return stat; +}; + +/** returns max value of a stat **/ +PlotWidget.prototype.getMaxAndMinValue = function(stat) { + var max = 0; + var min = stat.data[0]; + for (var j = 0; j < stat.data.length; j++) { + if (Number(stat.data[j]) > max) { + max = Number(stat.data[j]); + } + if (Number(stat.std[j]) > max) { + max = Number(stat.std[j]); + } + if (Number(stat.data[j]) < min) { + min = Number(stat.data[j]); + } + } + return { + max : Number(max), + min : Number(min) + }; +}; + +PlotWidget.prototype._renderDygraph = function(parsed, colors, labels) { + this.dygraphObject = new StdDevDyGraph(this.id, { + width : this.width - 20, + height : this.height - 40, + xlabel : "", + }); + + this.dygraphObject.draw(parsed, colors, labels); + +}; + +PlotWidget.prototype.getPanel = function() { + this.panel = Ext.create('Ext.panel.Panel', { + width : this.width, + height : this.height, + margin : this.margin, + tbar : this.getMenu(), + items : [ { + html : "", + id : this.id, + width : this.width, + height : this.height, + padding : 10, + margin : "0 0 0 -30", + border : 0 + } ] + }); + + return this.panel; +}; + +PlotWidget.prototype.getPoint = function(y, error) { + var minus = y - error; + var max = y + error; + + if (this.linear) { + return [ Math.abs(minus), y, Math.abs(max) ]; + } + if ((minus != 0) && (max != 0)) { + return [ Math.log(Math.abs(minus)), Math.log(y), Math.log(Math.abs(max)) ]; + } else { + return [ Math.log(y), Math.log(y), Math.log(y) ]; + } + +}; + +PlotWidget.prototype.getDataPlot = function(frames, subtractions, models, fits, rbms) { + var files = []; + var labels = [ "Intensity" ]; + if (frames != null) { + for (var i = 0; i < frames.length; i++) { + files.push(frames[i].data); + labels.push(frames[i].fileName); + } + } + function splitData(data, column, errorColumn, name){ + var result = [] + for (var j = 0; j < data.length; j++) { + console.log(data[j][column]); + result.push([j,data[j][column],data[j][errorColumn]]);//[0, data[i][column],0]]); + } + files.push(result); + labels.push(name); + } + + if (subtractions != null) { + for (var i = 0; i < subtractions.length; i++) { + /** For subtraction **/ + files.push(subtractions[i].subtraction.data); + labels.push(subtractions[i].subtraction.fileName); + /** For sample average **/ +// files.push(subtractions[i].sampleAvg.data); +// labels.push(subtractions[i].sampleAvg.fileName); + /** For buffer average **/ +// files.push(subtractions[i].bufferAvg.data); +// labels.push(subtractions[i].bufferAvg.fileName); + } + } + + if (models != null) { + for (var i = 0; i < models.length; i++) { + for ( var key in models[i]) { + splitData(models[i][key].fir.data, 1, 2, "Intensity"); + splitData(models[i][key].fir.data, 3, 3, "Fit"); + } + } + } + + if (fits != null) { + for (var i = 0; i < fits.length; i++) { + for ( var key in fits[i]) { + + /** adding fit file to be plotted **/ + if (fits[i][key].fit.data[0].length == 3){ + splitData(fits[i][key].fit.data, 1, 1, "Intensity"); + splitData(fits[i][key].fit.data, 2, 2, "Fit"); + } + + /** s, Iexp(s), err, Ifit(s). **/ + if (fits[i][key].fit.data[0].length == 4){ + splitData(fits[i][key].fit.data, 1, 2, "Intensity"); + splitData(fits[i][key].fit.data, 3, 3, "Fit"); + } + + if (fits[i][key].fit.data[0].length == 5){ + /** X Intensity Fit Error Residues **/ + + splitData(fits[i][key].fit.data, 1, 3, "Intensity"); + splitData(fits[i][key].fit.data, 2, 2, "Fit"); + } + } + } + } + + var dataPoints = []; + if (files.length > 0) { + for (var i = 0; i < files[0].length; i++) { + dataPoints.push([ files[0][i][0], this.getPoint(files[0][i][1], files[0][i][2]) ]); + } + if (files.length > 1) { + for (var i = 1; i < files.length; i++) { + for (var j = 0; j < dataPoints.length; j++) { + if (files[i][j] != null){ + dataPoints[j].push(this.getPoint(files[i][j][1], files[i][j][2])); + } + else{ + dataPoints[j].push([0,0,0]); + } + } + } + } + } + + return { + dataPoints : dataPoints, + labels : labels + } +}; + +PlotWidget.prototype.refresh = function(frames, subtractions, models, fits, rbms, colors) { + + var _this = this; + this.panel.setLoading("Reading Files"); + + var dataAdapter = new BiosaxsDataAdapter(); + dataAdapter.onSuccess.attach(function(sender, data) { + _this.panel.setLoading("Rendering"); + var parsed = _this.getDataPlot(data.frames, data.subtractions, data.models, data.fits, rbms); + _this._renderDygraph(parsed.dataPoints, colors, parsed.labels); + _this.panel.setLoading(false); + }); + dataAdapter.onError.attach(function(sender, data) { + _this.panel.setLoading(false); + }); + dataAdapter.getDataPlot(frames, subtractions, models, fits, rbms); +}; + +PlotWidget.prototype.input = function() { + return DATADOC.getHPLCData(); +}; + + +/** + * Fit form + * + * @witdh + * @height + */ +function FitForm(args) { + this.id = BUI.id(); + this.width = null; + this.height = null; + + if (args != null) { + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + } + + var _this = this; + + /** Widgets **/ + this.fitGrid = new FitStructureToExperimentDataGrid({ + width : null, + height : 200 + }); + + this.fitGrid.onSelected.attach(function(sender, fits) { + var modelsIdList = []; + for ( var i in fits) { + modelsIdList.push(fits[i].fitStructureToExperimentalDataId); + } + _this._renderPlot(_this.subtractions[0].subtractionId, modelsIdList); +// var adapter = new BiosaxsDataAdapter(); +// adapter.onSuccess.attach(function(sender, data) { +// +// }); +// adapter.getScatteringCurveByFrameIdsList([], [], [], ids); + }); + + + /** Dygraph Widget that plots fir files**/ + this.plotWidget = new PlotWidget({ + width : 745, + height : 300, + margin : "10 0 10 10" + }); +} + +FitForm.prototype._renderPlot = function(subtractionId, modelsIdList) { + /** Trying to plot tje subtraction and the models **/ + try { + var colors = [ "#669900", "#0000FF" ]; + + this.plotWidget.refresh([], [ ], [], modelsIdList, [], colors); + } catch (e) { + console.log(e); + } +}; + +FitForm.prototype._getItems = function() { + var _this = this; + return [ { + xtype : 'label', + forId : 'myFieldId', + text : 'INLINE HELP: To be updated', + margin : '15 0 20 10', + cls : "inline-help" + }, this.fitGrid.getPanel(), this.plotWidget.getPanel() ] + +}; + +FitForm.prototype._getButtons = function() { + return []; +}; + +FitForm.prototype.getPanel = function() { + var _this = this; + this.panel = Ext.create('Ext.form.Panel', { + width : this.width, + height : this.height, + margin : 10, + border : 1, + defaultType : 'textfield', + items : this._getItems(), + buttons : this._getButtons(), + listeners : { + afterrender : function() { + _this._populate(); + + } + } + }); + return this.panel; +}; + +/** Populates could be call when the DOM is not filled yet **/ +FitForm.prototype._populate = function() { +}; + +/** It populates the form * */ +FitForm.prototype.refresh = function(subtractions) { + this.subtractions = subtractions; + this.fitGrid.refresh(subtractions); +}; + +FitForm.prototype.input = function() { + return {}; +}; + +/** It populates the form **/ +FitForm.prototype.test = function(targetId) { + var macromoleculeForm = new FitForm(); + var panel = macromoleculeForm.getPanel(); + panel.render(targetId); +}; + +/** + * Example form + * + * @witdh + * @height + */ +function RigidBodyModelingResultForm(args) { + this.id = BUI.id(); + this.width = null; + this.height = null; + + if (args != null) { + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + } + + var _this = this; + /** Widgets **/ + this.rigidModelGrid = new RigidModelGrid({ + width : null, + height : 200 + }); + + this.rigidModelGrid.onSelected.attach(function(sender, fits){ + var ids = []; + for ( var i in fits) { + ids.push(fits[i].fitStructureToExperimentalDataId); + } + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data){ +// debugger + + }); + + adapter.getScatteringCurveByFrameIdsList([], [], [], ids); + }); + +} + +RigidBodyModelingResultForm.prototype._getItems = function() { + var _this = this; + return [ { + xtype : 'label', + forId : 'myFieldId', + text : 'INLINE HELP: To be updated', + margin : '15 0 20 10', + cls : "inline-help" + }, this.rigidModelGrid.getPanel() ] + +}; + +RigidBodyModelingResultForm.prototype._getButtons = function() { + return []; +}; + +RigidBodyModelingResultForm.prototype.getPanel = function() { + var _this = this; + this.panel = Ext.create('Ext.form.Panel', { + width : this.width, + height : this.height, + margin : 10, + border : 1, + defaultType : 'textfield', + items : this._getItems(), + buttons : this._getButtons(), + listeners : { + afterrender : function() { + _this._populate(); + + } + } + }); + return this.panel; +}; + +/** Populates could be call when the DOM is not filled yet **/ +RigidBodyModelingResultForm.prototype._populate = function() { +}; + +/** It populates the form * */ +RigidBodyModelingResultForm.prototype.refresh = function(subtractions) { + this.rigidModelGrid.refresh(subtractions); +}; + +RigidBodyModelingResultForm.prototype.input = function() { + return {}; +}; + +/** It populates the form **/ +RigidBodyModelingResultForm.prototype.test = function(targetId) { + var macromoleculeForm = new RigidBodyModelingResultForm(); + var panel = macromoleculeForm.getPanel(); + panel.render(targetId); +}; + +/** + * Example form + * + * @witdh + * @height + */ +function SuperpositionForm(args) { + this.id = BUI.id(); + this.width = null; + this.height = null; + + if (args != null) { + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + } + + var _this = this; + + /** Widgets **/ + this.superpositionGrid = new SuperpositionGrid({ + width : null, + height : 200 + }); + + this.superpositionGrid.onSelected.attach(function(sender, superpositions) { + var ids = []; + for ( var i in superpositions) { + ids.push(superpositions[i].superpositionId); + } +// _this._renderAbinitio(ids); +// _this.aprioriPDBViewer.refresh(); + _this._renderAligned(ids); + // getAlignedPDBContentBySuperpositionList + }); + + /** PDB viewer **/ +// this.abinitioPDBViewer = new PDBViewer({ +// width : 860 / 2, +// height : 300 / 2, +// margin : 0 +// }); +// +// /** PDB viewer **/ +// this.aprioriPDBViewer = new StructurePDBViewer({ +// width : 860 / 2, +// height : 300 / 2, +// margin : 0 +// }); + + this.alignedPDBViewer = new AlignedSuperpositionPDBViewer({ + width : 860 , + height : 300 + }); + +} + +SuperpositionForm.prototype._renderAligned = function(modelsIdList) { + /** Trying to plot the PDB file **/ + try { + this.alignedPDBViewer.refresh(modelsIdList); + } catch (e) { + console.log(e); + } +}; + +SuperpositionForm.prototype._renderAbinitio = function(modelsIdList) { + /** Trying to plot the PDB file **/ + try { + var viz = []; + for (var i = 0; i < modelsIdList.length; i++) { + viz.push({ + modelId : modelsIdList[i], + color : "0xFF6600", + opacity : 0.8 + }); + } + this.abinitioPDBViewer.refresh(viz); + } catch (e) { + console.log(e); + } +}; + +SuperpositionForm.prototype._getItems = function() { + var _this = this; + return [ { + xtype : 'label', + forId : 'myFieldId', + text : 'INLINE HELP: To be updated', + margin : '15 0 20 10', + cls : "inline-help" + }, this.superpositionGrid.getPanel(), { + xtype : 'container', + layout : 'hbox', + items : [ +// { +// xtype : 'container', +// layout : 'vbox', +// items : [ this.abinitioPDBViewer.getPanel(), this.aprioriPDBViewer.getPanel() +// +// ] +// }, + + this.alignedPDBViewer.getPanel() ] + } ] + +}; + +SuperpositionForm.prototype._getButtons = function() { + return []; +}; + +SuperpositionForm.prototype.getPanel = function() { + var _this = this; + this.panel = Ext.create('Ext.form.Panel', { + width : this.width, + height : this.height, + margin : 10, + border : 1, + defaultType : 'textfield', + items : this._getItems(), + buttons : this._getButtons(), + listeners : { + afterrender : function() { + _this._populate(); + + } + } + }); + return this.panel; +}; + +/** Populates could be call when the DOM is not filled yet **/ +SuperpositionForm.prototype._populate = function() { +}; + +/** It populates the form * */ +SuperpositionForm.prototype.refresh = function(subtractions) { + this.subtractions = subtractions; + this.superpositionGrid.refresh(subtractions); +}; + +SuperpositionForm.prototype.input = function() { + return {}; +}; + +/** It populates the form **/ +SuperpositionForm.prototype.test = function(targetId) { + var macromoleculeForm = new SuperpositionForm(); + var panel = macromoleculeForm.getPanel(); + panel.render(targetId); +}; + +/** + * Example form + * + * @witdh + * @height + */ +function AssemblyForm(args) { + this.id = BUI.id(); + this.width = 700; + this.height = 500; + + if (args != null) { + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + } + + this.molarityGrid = new MolarityGrid({height : this.height - 50}); +} + +AssemblyForm.prototype._getItems = function() { + return [ { + xtype : 'label', + forId : 'myFieldId', + text : 'List of previously defined macromolecules present in the assembly. This information will be used for additional cross-checks where possible', + margin : '15 0 20 10', + cls : "inline-help" + }, this.molarityGrid.getPanel() ]; +}; + +AssemblyForm.prototype._getButtons = function() { + return []; +}; + +AssemblyForm.prototype.getPanel = function() { + this.panel = Ext.create('Ext.form.Panel', { + width : this.width, + height : this.height, + margin : 10, + border : 0, + defaultType : 'textfield', + items : this._getItems(), + buttons : this._getButtons() + }); + return this.panel; +}; + + +/** It populates the form **/ +AssemblyForm.prototype.refresh = function(macromolecule) { + this.macromolecule = macromolecule; + this.molarityGrid.refresh(macromolecule); +}; + +AssemblyForm.prototype.input = function() { + return {}; +}; + + +AssemblyForm.prototype.test = function(targetId) { + var assemblyForm = new AssemblyForm(); + + var panel = assemblyForm.getPanel(); + panel.render(targetId); +}; +/** + * Edit the information of a buffer + * + * #onSaved + * #onRemoveAdditive + */ +function BufferForm() { var _this = this; - /** Widgets **/ - this.plotWidget = new PlotWidget({ - width : 650, - height : 490 + this.additiveGrid = new AdditiveGrid(); + this.additiveGrid.onRemoveButtonClicked.attach(function(sender, args) { + _this.onRemoveAdditive.notify(args); }); - /** Selected frames to be displayed **/ - this.selectedItems = { - frames : [], - averages : [], - subtractions : [] - }; - + this.onSaved = new Event(this); + this.onRemoveAdditive = new Event(this); } -DataReductionForm.prototype._parseSelectedItemsToIds = function(selectedArray) { - var ids = []; - if (selectedArray != null) { - for (var i = 0; i < selectedArray.length; i++) { - ids.push(selectedArray[i].id); - } - } - return ids; -}; - -DataReductionForm.prototype.onSelectionChanged = function(columnName, selected) { - if (selected != null) { - if (columnName == "Frames") { - this.selectedItems.frames = selected; - this.selectedItems.subtractions = []; - } - if (columnName == "Averages") { - this.selectedItems.averages = selected; - } - if (columnName == "Subtractions") { - this.selectedItems.frames = []; - this.selectedItems.subtractions = selected; - } - } - this.plotWidget.refresh(this._parseSelectedItemsToIds(this.selectedItems.frames), this._parseSelectedItemsToIds(this.selectedItems.subtractions)); -}; - -DataReductionForm.prototype._getFramesExtPanel = function(store, columnName, height) { - var _this = this; - - var selModel = Ext.create('Ext.selection.RowModel', { - allowDeselect : true, - mode : 'MULTI', - listeners : { - selectionchange : function(sm, selections) { - var selected = []; - for (var i = 0; i < selections.length; i++) { - selected.push(selections[i].raw); - } - _this.onSelectionChanged(columnName, selected); - } - } - }); - - return Ext.create('Ext.grid.Panel', { - store : store, - margin : 10, - height : height, - width : 200, - selModel : selModel, - columns : [ { - text : columnName, - dataIndex : 'fileName', - flex : 1 - } ], - viewConfig : { - } - }); +BufferForm.prototype.getBuffer = function() { + this.buffer.name = Ext.getCmp("buffer_name").getValue(); + this.buffer.acronym = Ext.getCmp("buffer_acronym").getValue(); + this.buffer.comments = Ext.getCmp("buffer_comments").getValue(); + this.buffer.ph = Ext.getCmp("buffer_ph").getValue(); + this.buffer.composition = Ext.getCmp("buffer_composition").getValue(); + this.buffer.bufferhasadditive3VOs = this.additiveGrid.getAdditives(); + return this.buffer; }; -DataReductionForm.prototype._getFramesPanel = function() { - var fields = [ 'fileName', 'type', 'id' ]; - - this.framesStore = Ext.create('Ext.data.Store', { - fields : fields, - sorters : 'fileName' - }); - - this.averagesStore = Ext.create('Ext.data.Store', { - fields : fields - }); - - this.subtractionStore = Ext.create('Ext.data.Store', { - fields : fields - }); - - var gridFrames = this._getFramesExtPanel(this.framesStore, "Frames", 375); - var gridAvgs = this._getFramesExtPanel(this.averagesStore, "Averages", 125); - var subtractionAvgs = this._getFramesExtPanel(this.subtractionStore, "Subtractions", 75); - - return { - xtype : 'container', - layout : 'vbox', - items : [ gridFrames, subtractionAvgs ] - }; -}; - -DataReductionForm.prototype._getImageContainer = function(name, help) { - var html = "
" + name + "
" +BufferForm.prototype._getTopPanel = function() { return { xtype : 'container', - layout : 'vbox', + layout : 'hbox', + border : 0, + frame : true, items : [ { - html : html, - margin : "5 0 0 0", - height : 95, - width : 100 + xtype : 'container', + layout : 'hbox', + items : [ { + xtype : 'container', + flex : 1, + border : false, + layout : 'anchor', + defaultType : 'textfield', + items : [ { + xtype : 'requiredtext', + id : 'buffer_name', + fieldLabel : 'Name', + name : 'name', + width : '200px', + value : this.buffer.name + }, { + xtype : 'requiredtext', + id : 'buffer_acronym', + fieldLabel : 'Acronym', + name : 'acronym', + width : '200px', + value : this.buffer.acronym + } ] + } ] }, { - xtype : 'label', - forId : 'myFieldId', - text : help, - margin : '5 0 0 0', - cls : "inline-help" + xtype : 'container', + flex : 1, + layout : 'anchor', + defaultType : 'textfield', + margin : '0 0 0 10', + items : [ { + id : 'buffer_ph', + fieldLabel : 'pH', + name : 'ph', + value : this.buffer.ph, + xtype : 'numberfield', + width : 200, + minValue : 0, + maxValue : 15 + }, { + xtype : 'requiredtext', + id : 'buffer_composition', + fieldLabel : 'Composition', + name : 'composition', + width : 200, + value : this.buffer.composition + } ] } ] - } + }; }; -DataReductionForm.prototype._getItems = function() { - var _this = this; - return [ { +BufferForm.prototype.getPanel = function(buffer) { + this.buffer = buffer; + this.panel = Ext.createWidget({ xtype : 'container', - layout : 'hbox', - items : [ - this._getFramesPanel(), - this.plotWidget.getPanel(), - { - xtype : 'panel', - width : 110, - frame : true, - margin : "10 5 5 5", - border : 0, - layout : 'vbox', - items : [ this._getImageContainer("scattering", "Scattering"), this._getImageContainer("guinier", "Guinier Region"), - this._getImageContainer("kratky", "Kratky Plot"), this._getImageContainer("gnom", "P(r) distribution") ] - } ] - } ] -}; - -DataReductionForm.prototype._getButtons = function() { - return []; -}; + layout : 'vbox', + style : { + padding : '10px' + }, + fieldDefaults : { + labelAlign : 'left', + labelWidth : 50 -DataReductionForm.prototype.getPanel = function() { - var _this = this; - this.panel = Ext.create('Ext.form.Panel', { - width : this.width, - height : this.height, - border : 0, - items : this._getItems(), - buttons : this._getButtons(), - listeners : { - afterrender : function() { - _this._populate(); - } - } + }, + items : [ this._getTopPanel(), { + id : 'buffer_comments', + xtype : 'textareafield', + name : 'comments', + fieldLabel : 'Comments', + width : '100%', + value : buffer.comments + }, this.additiveGrid.getPanel(buffer) ] }); return this.panel; }; -/** Populates could be call when the DOM is not filled yet **/ -DataReductionForm.prototype._populate = function() { -}; - -/** It populates the form * */ -DataReductionForm.prototype.refresh = function(subtractions) { - if (subtractions != null) { - for (var i = 0; i < subtractions.length; i++) { - /** Loading frame grids **/ - var subtraction = subtractions[i]; - var averages = [ { - fileName : BUI.getFileName(subtraction.bufferAverageFilePath), - type : 'bufferAvg', - id : subtraction.subtractionId - }, { - fileName : BUI.getFileName(subtraction.sampleAverageFilePath), - type : 'sampleAvg', - id : subtraction.subtractionId - } - - ]; - this.averagesStore.loadData(averages, true); - this.subtractionStore.loadData([ { - fileName : BUI.getFileName(subtraction.substractedFilePath), - type : 'SUBTRACTION', - id : subtraction.subtractionId - } ], true); - - var frames = []; - /** Buffers **/ - if (subtraction.bufferOneDimensionalFiles != null) { - if (subtraction.bufferOneDimensionalFiles.frametolist3VOs != null) { - for (var j = 0; j < subtraction.bufferOneDimensionalFiles.frametolist3VOs.length; j++) { - var frametolist3VO = subtraction.bufferOneDimensionalFiles.frametolist3VOs[j]; - if (frametolist3VO.frame3VO != null) { - frames.push({ - fileName : BUI.getFileName(frametolist3VO.frame3VO.filePath), - type : 'BUFFER', - id : frametolist3VO.frame3VO.frameId - }); - } - } - } - } - /** Samples **/ - if (subtraction.sampleOneDimensionalFiles != null) { - if (subtraction.sampleOneDimensionalFiles.frametolist3VOs != null) { - for (var j = 0; j < subtraction.sampleOneDimensionalFiles.frametolist3VOs.length; j++) { - var frametolist3VO = subtraction.sampleOneDimensionalFiles.frametolist3VOs[j]; - if (frametolist3VO.frame3VO != null) { - frames.push({ - fileName : BUI.getFileName(frametolist3VO.frame3VO.filePath), - type : 'SAMPLE', - id : frametolist3VO.frame3VO.frameId - }); - } - } - } - } - - this.framesStore.loadData(frames, true); - - /** Loading images **/ - this._displayImage("scattering", subtraction.subtractionId); - this._displayImage("kratky", subtraction.subtractionId); - this._displayImage("guinier", subtraction.subtractionId); - this._displayImage("gnom", subtraction.subtractionId); +BufferForm.prototype.input = function() { + return { + buffer : { + "bufferId" : 422, + "proposalId" : 10, + "safetyLevelId" : null, + "name" : "B1", + "acronym" : "B1", + "ph" : null, + "composition" : null, + "bufferhasadditive3VOs" : [], + "comments" : null } - } -}; - -DataReductionForm.prototype._displayImage = function(name, subtractionId) { - var url = BUI.getURL() + '&type=' + name + '&subtractionId=' + subtractionId; - var event = "OnClick= window.open('" + url + "')"; - document.getElementById(this.id + "_" + name).innerHTML = ''; -}; - -DataReductionForm.prototype.input = function() { - return {}; + }; }; -/** It populates the form **/ -DataReductionForm.prototype.test = function(targetId) { - var macromoleculeForm = new DataReductionForm(); - var panel = macromoleculeForm.getPanel(); +BufferForm.prototype.test = function(targetId) { + var bufferForm = new BufferForm(); + var panel = bufferForm.getPanel(bufferForm.input().buffer); panel.render(targetId); }; - -function PlotWidget(args) { - this.width = 600; - this.height = 600; - this.id = BUI.id(); - - this.linear = false; - - this.margin = "10 0 0 0"; - /** for each stat the max and minimum value when it is scaled in order to show correctly in the legend **/ - this.ranges = {}; + +/** + * @showTitle + * + * #onSaved + * #onAddPlates + * #onRemovePlates + **/ +function CaseForm(args) { + this.width = 700; + this.showTitle = true; if (args != null) { - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; - } - if (args.margin != null) { - this.margin = args.margin; + if (args.showTitle != null) { + this.showTitle = args.showTitle; } } -} - -PlotWidget.prototype.getMenu = function() { var _this = this; - /** Actions buttons **/ - var actions = []; - actions.push("->"); - actions.push({ - text : "Export as Image", - scope : this, - icon : '../images/save.gif', - handler : function(item, pressed) { - var largeImage = document.createElement("img"); - largeImage.style.display = 'block'; - largeImage.style.width = 200 + "px"; - largeImage.style.height = 200 + "px"; - largeImage.setAttribute('src', Dygraph.Export.asCanvas(this.dygraphObject.dygraph).toDataURL()); - window.open(Dygraph.Export.asCanvas(this.dygraphObject.dygraph).toDataURL(), 'Image', ''); + this.stockSolutionGrid = new StockSolutionGrid({ + width : this.width - 10, + minHeight : 300, + height : 300, + tbar : true, + showTitle : true, + isPackedVisible : false, + btnAddExisting : true, + btnRemoveVisible : false, + btnUnpackVisible : true + }); + + /** When selecting existing stock solutions **/ + this.stockSolutionGrid.onStockSolutionSelected.attach(function(sender, stockSolutions) { + if (stockSolutions != null) { + for ( var i = 0; i < stockSolutions.length; i++) { + _this.saveStockSolution(stockSolutions[i]); + } } }); - return actions; -}; + /** it can be because it has been added a new one or removed **/ + this.stockSolutionGrid.onProposalChanged.attach(function(sender, stockSolution) { + if (stockSolution != null) { + _this.saveStockSolution(stockSolution); + } else { + BIOSAXS.proposal.onInitialized.attach(function() { + _this.stockSolutionGrid.refresh(BIOSAXS.proposal.getStockSolutionsByDewarId(_this.dewar.dewarId)); -/** Looks for the maximum value and then divide everything but that value **/ -PlotWidget.prototype.scaledData = function(data) { - for (var i = 0; i < data.length; i++) { - var values = this.getMaxAndMinValue(data[i]); - data[i] = this.divideValuesByMax(data[i], values.max); - this.ranges[data[i].label] = values; - } - return data; -}; + _this.stockSolutionGrid.grid.setLoading(false); + }); + BIOSAXS.proposal.init(); -/** Given a stat float[] and a max number it will divide each value by max **/ -PlotWidget.prototype.divideValuesByMax = function(stat, max) { - for (var j = 0; j < stat.data.length; j++) { - if (max != 0) { - stat.data[j] = Number(stat.data[j]) / max; - stat.std[j] = Number(stat.std[j]) / max; } - } - return stat; -}; -/** returns max value of a stat **/ -PlotWidget.prototype.getMaxAndMinValue = function(stat) { - var max = 0; - var min = stat.data[0]; - for (var j = 0; j < stat.data.length; j++) { - if (Number(stat.data[j]) > max) { - max = Number(stat.data[j]); - } - if (Number(stat.std[j]) > max) { - max = Number(stat.std[j]); - } - if (Number(stat.data[j]) < min) { - min = Number(stat.data[j]); - } - } - return { - max : Number(max), - min : Number(min) - }; -}; - -PlotWidget.prototype._renderDygraph = function(parsed, colors, labels) { - this.dygraphObject = new StdDevDyGraph(this.id, { - width : this.width - 20, - height : this.height - 40, - xlabel : "", }); - this.dygraphObject.draw(parsed, colors, labels); + this.onSaved = new Event(this); + this.onAddPlates = new Event(this); + this.onRemovePlates = new Event(this); +} +CaseForm.prototype.saveStockSolution = function(stockSolution) { + var _this = this; + var adapter = new BiosaxsDataAdapter(); + this.stockSolutionGrid.grid.setLoading("ISPyB: setting case to Stock solution"); + adapter.onSuccess.attach(function(sender, stockSolution) { + BIOSAXS.proposal.onInitialized.attach(function() { + _this.stockSolutionGrid.refresh(BIOSAXS.proposal.getStockSolutionsByDewarId(_this.dewar.dewarId)); + _this.stockSolutionGrid.grid.setLoading(false); + }); + BIOSAXS.proposal.init(); + }); + adapter.onError.attach(function(sender, data) { + _this.stockSolutionGrid.grid.setLoading(false); + BUI.showError(data); + }); + stockSolution.boxId = _this.dewar.dewarId; + adapter.saveStockSolution(stockSolution); }; -PlotWidget.prototype.getPanel = function() { - this.panel = Ext.create('Ext.panel.Panel', { - width : this.width, - height : this.height, - margin : this.margin, - tbar : this.getMenu(), - items : [ { - html : "", - id : this.id, - width : this.width, - height : this.height, - padding : 10, - margin : "0 0 0 -30", - border : 0 - } ] +CaseForm.prototype.fillStores = function() { + var _this = this; + this.panel.setLoading("Loading Labcontacts from database"); + + var proposal = BUI.getProposal(); + proposal.onDataRetrieved.attach(function(sender, data) { + _this.labContactForSendingStore.loadData(data, false); + _this.labContactForReturnStore.loadData(data, false); + _this.panel.setLoading(false); }); + proposal.getLabContactsByProposalId(); - return this.panel; }; -PlotWidget.prototype.getPoint = function(y, error) { - var minus = y - error; - var max = y + error; - - if (this.linear) { - return [ Math.abs(minus), y, Math.abs(max) ]; - } - if ((minus != 0) && (max != 0)) { - return [ Math.log(Math.abs(minus)), Math.log(y), Math.log(Math.abs(max)) ]; - } else { - return [ Math.log(y), Math.log(y), Math.log(y) ]; - } - +CaseForm.prototype.refresh = function(dewar) { + this.setDewar(dewar); + this.stockSolutionGrid.refresh(BIOSAXS.proposal.getStockSolutionsByDewarId(dewar.dewarId)); }; -PlotWidget.prototype.getDataPlot = function(frames, subtractions, models, fits, rbms) { - var files = []; - var labels = [ "Intensity" ]; - if (frames != null) { - for (var i = 0; i < frames.length; i++) { - files.push(frames[i].data); - labels.push(frames[i].fileName); - } - } - function splitData(data, column, errorColumn, name){ - var result = [] - for (var j = 0; j < data.length; j++) { - console.log(data[j][column]); - result.push([j,data[j][column],data[j][errorColumn]]);//[0, data[i][column],0]]); - } - files.push(result); - labels.push(name); - } - - if (subtractions != null) { - for (var i = 0; i < subtractions.length; i++) { - /** For subtraction **/ - files.push(subtractions[i].subtraction.data); - labels.push(subtractions[i].subtraction.fileName); - /** For sample average **/ -// files.push(subtractions[i].sampleAvg.data); -// labels.push(subtractions[i].sampleAvg.fileName); - /** For buffer average **/ -// files.push(subtractions[i].bufferAvg.data); -// labels.push(subtractions[i].bufferAvg.fileName); - } - } - - if (models != null) { - for (var i = 0; i < models.length; i++) { - for ( var key in models[i]) { - splitData(models[i][key].fir.data, 1, 2, "Intensity"); - splitData(models[i][key].fir.data, 3, 3, "Fit"); - } - } - } - - if (fits != null) { - for (var i = 0; i < fits.length; i++) { - for ( var key in fits[i]) { - - /** adding fit file to be plotted **/ - if (fits[i][key].fit.data[0].length == 3){ - splitData(fits[i][key].fit.data, 1, 1, "Intensity"); - splitData(fits[i][key].fit.data, 2, 2, "Fit"); - } - - /** s, Iexp(s), err, Ifit(s). **/ - if (fits[i][key].fit.data[0].length == 4){ - splitData(fits[i][key].fit.data, 1, 2, "Intensity"); - splitData(fits[i][key].fit.data, 3, 3, "Fit"); - } - - if (fits[i][key].fit.data[0].length == 5){ - /** X Intensity Fit Error Residues **/ - - splitData(fits[i][key].fit.data, 1, 3, "Intensity"); - splitData(fits[i][key].fit.data, 2, 2, "Fit"); - } - } - } - } - - var dataPoints = []; - if (files.length > 0) { - for (var i = 0; i < files[0].length; i++) { - dataPoints.push([ files[0][i][0], this.getPoint(files[0][i][1], files[0][i][2]) ]); - } - if (files.length > 1) { - for (var i = 1; i < files.length; i++) { - for (var j = 0; j < dataPoints.length; j++) { - if (files[i][j] != null){ - dataPoints[j].push(this.getPoint(files[i][j][1], files[i][j][2])); - } - else{ - dataPoints[j].push([0,0,0]); - } - } - } - } - } +CaseForm.prototype.getDewar = function() { + this.dewar.code = Ext.getCmp("dewar_code").getValue(); + this.dewar.comments = Ext.getCmp("dewar_comments").getValue(); + this.dewar.trackingNumberFromSynchrotron = Ext.getCmp("dewar_trackingNumberFromSynchrotron").getValue(); + this.dewar.trackingNumberToSynchrotron = Ext.getCmp("dewar_trackingNumberToSynchrotron").getValue(); + this.dewar.transportValue = Ext.getCmp("dewar_transportValue").getValue(); + this.dewar.storageLocation = Ext.getCmp("dewar_storageLocation").getValue(); + this.dewar.firstExperimentId = this.macromoleculeCombo.getValue(); + return this.dewar; +}; - return { - dataPoints : dataPoints, - labels : labels +CaseForm.prototype.setDewar = function(dewar) { + this.dewar = dewar; + Ext.getCmp("dewar_code").setValue(this.dewar.code); + Ext.getCmp("dewar_dewarStatus").setText(new String(this.dewar.dewarStatus).toUpperCase()); + Ext.getCmp("dewar_comments").setValue(this.dewar.comments); + Ext.getCmp("dewar_trackingNumberFromSynchrotron").setValue(this.dewar.trackingNumberFromSynchrotron); + Ext.getCmp("dewar_trackingNumberToSynchrotron").setValue(this.dewar.trackingNumberToSynchrotron); + Ext.getCmp("dewar_transportValue").setValue(this.dewar.transportValue); + Ext.getCmp("dewar_storageLocation").setValue(this.dewar.storageLocation); + if (dewar.sessionVO != null) { + this.macromoleculeCombo.setValue(dewar.sessionVO.sessionId); } }; -PlotWidget.prototype.refresh = function(frames, subtractions, models, fits, rbms, colors) { - - var _this = this; - this.panel.setLoading("Reading Files"); - - var dataAdapter = new BiosaxsDataAdapter(); - dataAdapter.onSuccess.attach(function(sender, data) { - _this.panel.setLoading("Rendering"); - var parsed = _this.getDataPlot(data.frames, data.subtractions, data.models, data.fits, rbms); - _this._renderDygraph(parsed.dataPoints, colors, parsed.labels); - _this.panel.setLoading(false); - }); - dataAdapter.onError.attach(function(sender, data) { - _this.panel.setLoading(false); +CaseForm.prototype.getSessionCombo = function() { + this.macromoleculeCombo = BIOSAXS_COMBOMANAGER.getComboSessions(BIOSAXS.proposal.getSessions(), { + labelWidth : 100, + margin : '5 0 00 0', + width : 250 }); - dataAdapter.getDataPlot(frames, subtractions, models, fits, rbms); -}; - -PlotWidget.prototype.input = function() { - return DATADOC.getHPLCData(); + return this.macromoleculeCombo; }; - -/** - * Fit form - * - * @witdh - * @height - */ -function FitForm(args) { - this.id = BUI.id(); - this.width = null; - this.height = null; - - if (args != null) { - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; - } - } +CaseForm.prototype.getInformationPanel = function() { + if (this.panel == null) { + this.informationPanel = Ext.create('Ext.form.Panel', { + width : this.width - 10, + border : 0, + items : [ { + xtype : 'container', + margin : "2 2 2 2", + collapsible : false, + defaultType : 'textfield', + layout : 'anchor', + items : [ { + xtype : 'container', + layout : 'hbox', + items : [ { + xtype : 'requiredtext', + fieldLabel : 'Code', + allowBlank : false, + name : 'code', + id : 'dewar_code', + anchor : '50%' + }, { + xtype : 'label', + margin : '0 0 0 20', + readOnly : true, + id : 'dewar_dewarStatus', + anchor : '50%' + } ] + }, this.getSessionCombo(), { + margin : '5 0 0 0', + xtype : 'textareafield', + name : 'comments', + id : 'dewar_comments', + width : this.width - 50, + fieldLabel : 'Comments' + } ] + }, { + xtype : 'fieldset', + title : 'Courier Accounts Details for Return', + collapsible : false, + layout : 'anchor', + defaults : { + anchor : '100%' + }, + items : [ { + xtype : 'container', + layout : 'hbox', + items : [ { + xtype : 'textfield', + labelWidth : 200, + width : 280, + fieldLabel : 'Track Number From Synchrotron', + id : 'dewar_trackingNumberFromSynchrotron' + }, { + xtype : 'numberfield', + width : 190, + labelWidth : 110, + margin : '0 0 0 30', + fieldLabel : 'Transport Value', + id : 'dewar_transportValue' + } - var _this = this; - - /** Widgets **/ - this.fitGrid = new FitStructureToExperimentDataGrid({ - width : null, - height : 200 - }); + ] + }, { + xtype : 'container', + layout : 'hbox', + margin : '10 0 0 0', + items : [ - this.fitGrid.onSelected.attach(function(sender, fits) { - var modelsIdList = []; - for ( var i in fits) { - modelsIdList.push(fits[i].fitStructureToExperimentalDataId); - } - _this._renderPlot(_this.subtractions[0].subtractionId, modelsIdList); -// var adapter = new BiosaxsDataAdapter(); -// adapter.onSuccess.attach(function(sender, data) { -// -// }); -// adapter.getScatteringCurveByFrameIdsList([], [], [], ids); - }); - - - /** Dygraph Widget that plots fir files**/ - this.plotWidget = new PlotWidget({ - width : 745, - height : 300, - margin : "10 0 10 10" - }); -} + { + xtype : 'textfield', + labelWidth : 200, + width : 280, + fieldLabel : 'Track Number To Synchrotron', + id : 'dewar_trackingNumberToSynchrotron' + }, { + xtype : 'textfield', + margin : '0 0 0 30', + width : 190, + labelWidth : 110, + fieldLabel : 'Storage Location', + id : 'dewar_storageLocation' + } -FitForm.prototype._renderPlot = function(subtractionId, modelsIdList) { - /** Trying to plot tje subtraction and the models **/ - try { - var colors = [ "#669900", "#0000FF" ]; - - this.plotWidget.refresh([], [ ], [], modelsIdList, [], colors); - } catch (e) { - console.log(e); + ] + } ] + } ] + }); } -}; - -FitForm.prototype._getItems = function() { - var _this = this; - return [ { - xtype : 'label', - forId : 'myFieldId', - text : 'INLINE HELP: To be updated', - margin : '15 0 20 10', - cls : "inline-help" - }, this.fitGrid.getPanel(), this.plotWidget.getPanel() ] - -}; -FitForm.prototype._getButtons = function() { - return []; + return this.informationPanel; }; -FitForm.prototype.getPanel = function() { - var _this = this; - this.panel = Ext.create('Ext.form.Panel', { +CaseForm.prototype.getPanel = function(dewar) { + this.dewar = dewar; + this.panel = Ext.createWidget({ + xtype : 'container', + layout : 'vbox', width : this.width, - height : this.height, - margin : 10, - border : 1, - defaultType : 'textfield', - items : this._getItems(), - buttons : this._getButtons(), - listeners : { - afterrender : function() { - _this._populate(); + border : 0, + items : [ { + items : { + xtype : "container", + layout : "vbox", + margin : "5 5 5 5", + items : [ this.getInformationPanel(dewar), this.stockSolutionGrid.getPanel() ] } - } + } ] }); + + this.refresh(dewar); return this.panel; -}; -/** Populates could be call when the DOM is not filled yet **/ -FitForm.prototype._populate = function() { }; -/** It populates the form * */ -FitForm.prototype.refresh = function(subtractions) { - this.subtractions = subtractions; - this.fitGrid.refresh(subtractions); -}; +CaseForm.prototype.input = function() { + return { + dewar : { + "dewarId" : 305861, + "code" : "ESRF-TEST", + "comments" : "comments", + "storageLocation" : "FRIDGE", + "dewarStatus" : "opened", + "timeStamp" : null, + "isStorageDewar" : null, + "barCode" : "ESRF305861", + "customsValue" : null, + "transportValue" : null, + "trackingNumberToSynchrotron" : "3333", + "trackingNumberFromSynchrotron" : "224466", + "type" : "Dewar", + "sessionVO" : { + "sessionId" : 31697, + "expSessionPk" : null, + "projectCode" : null, + "startDate" : "2012 07 21", + "endDate" : "2012 07 23", + "beamlineName" : "BM29", + "scheduled" : 1, + "nbShifts" : 2, + "comments" : null, + "beamlineOperator" : "PERNOT P", + "usedFlag" : null, + "sessionTitle" : null, + "structureDeterminations" : null, + "dewarTransport" : null, + "databackupFrance" : null, + "databackupEurope" : null, + "visit_number" : null, + "operatorSiteNumber" : "14061", + "timeStamp" : "2012 04 25" + } + }, + proposal : { + "assemblies" : [], + "sessions" : [ { + "sessionId" : 31697, + "expSessionPk" : null, + "projectCode" : null, + "startDate" : "2012 07 21", + "endDate" : "2012 07 23", + "beamlineName" : "BM29", + "scheduled" : 1, + "nbShifts" : 2, + "comments" : null, + "beamlineOperator" : "PERNOT P", + "usedFlag" : null, + "sessionTitle" : null, + "structureDeterminations" : null, + "dewarTransport" : null, + "databackupFrance" : null, + "databackupEurope" : null, + "visit_number" : null, + "operatorSiteNumber" : "14061", + "timeStamp" : "2012 04 25" + } ], + "labcontacts" : [ { + "labContactId" : 787, + "personVO" : { + "personId" : 304252, + "personUUID" : null, + "familyName" : "KIM", + "givenName" : "Henry", + "title" : null, + "emailAddress" : "henry-sung.kim@ibs.fr", + "phoneNumber" : "", + "login" : "", + "passwd" : "", + "faxNumber" : "" + }, + "cardName" : "KIM-Institut de Bio", + "defaultCourrierCompany" : "22", + "courierAccount" : "", + "billingReference" : "", + "dewarAvgCustomsValue" : 0, + "dewarAvgTransportValue" : 0 + } ], + "buffers" : [ { + "bufferId" : 811, + "proposalId" : 3124, + "safetyLevelId" : null, + "name" : "EDTA", + "acronym" : "EDTA", + "ph" : null, + "composition" : "", + "bufferhasadditive3VOs" : [], + "comments" : "" + }, { + "bufferId" : 810, + "proposalId" : 3124, + "safetyLevelId" : null, + "name" : "HEPES", + "acronym" : "HEPES", + "ph" : null, + "composition" : "", + "bufferhasadditive3VOs" : [], + "comments" : "" + } ], + "shippings" : [ { + "shippingId" : 304107, + "shippingName" : "TEST", + "deliveryAgentAgentName" : null, + "deliveryAgentShippingDate" : null, + "deliveryAgentDeliveryDate" : null, + "deliveryAgentAgentCode" : null, + "deliveryAgentFlightCode" : null, + "shippingStatus" : "opened", + "timeStamp" : "2013 09 25", + "laboratoryId" : null, + "isStorageShipping" : null, + "creationDate" : "2013 09 25", + "comments" : "test", + "sendingLabContactVO" : { + "labContactId" : 787, + "personVO" : { + "personId" : 304252, + "personUUID" : null, + "familyName" : "KIM", + "givenName" : "Henry", + "title" : null, + "emailAddress" : "henry-sung.kim@ibs.fr", + "phoneNumber" : "", + "login" : "", + "passwd" : "", + "faxNumber" : "" + }, + "cardName" : "KIM-Institut de Bio", + "defaultCourrierCompany" : "22", + "courierAccount" : "", + "billingReference" : "", + "dewarAvgCustomsValue" : 0, + "dewarAvgTransportValue" : 0 + }, + "returnLabContactVO" : { + "labContactId" : 787, + "personVO" : { + "personId" : 304252, + "personUUID" : null, + "familyName" : "KIM", + "givenName" : "Henry", + "title" : null, + "emailAddress" : "henry-sung.kim@ibs.fr", + "phoneNumber" : "", + "login" : "", + "passwd" : "", + "faxNumber" : "" + }, + "cardName" : "KIM-Institut de Bio", + "defaultCourrierCompany" : "22", + "courierAccount" : "", + "billingReference" : "", + "dewarAvgCustomsValue" : 0, + "dewarAvgTransportValue" : 0 + }, + "returnCourier" : null, + "dateOfShippingToUser" : null, + "shippingType" : "DewarTracking", + "dewarVOs" : [ { + "dewarId" : 305861, + "code" : "ESRF-TEST", + "comments" : "comments", + "storageLocation" : "FRIDGE", + "dewarStatus" : "opened", + "timeStamp" : null, + "isStorageDewar" : null, + "barCode" : "ESRF305861", + "customsValue" : null, + "transportValue" : null, + "trackingNumberToSynchrotron" : "3333", + "trackingNumberFromSynchrotron" : "224466", + "type" : "Dewar", + "sessionVO" : { + "sessionId" : 31697, + "expSessionPk" : null, + "projectCode" : null, + "startDate" : "2012 07 21", + "endDate" : "2012 07 23", + "beamlineName" : "BM29", + "scheduled" : 1, + "nbShifts" : 2, + "comments" : null, + "beamlineOperator" : "PERNOT P", + "usedFlag" : null, + "sessionTitle" : null, + "structureDeterminations" : null, + "dewarTransport" : null, + "databackupFrance" : null, + "databackupEurope" : null, + "visit_number" : null, + "operatorSiteNumber" : "14061", + "timeStamp" : "2012 04 25" + } + } ] + } ], + "macromolecules" : [ { + "macromoleculeId" : 5933, + "safetylevelId" : null, + "proposalId" : 3124, + "name" : "A", + "acronym" : "A", + "molecularMass" : "", + "extintionCoefficient" : "", + "sequence" : null, + "creationDate" : null, + "comments" : "", + "macromoleculeregion3VOs" : [], + "stoichiometry3VOsForHostMacromoleculeId" : [], + "structure3VOs" : [] + } ], + "stockSolutions" : [ { + "stockSolutionId" : 6, + "proposalId" : 3124, + "macromoleculeId" : 5933, + "bufferId" : 811, + "instructionSet3VO" : null, + "boxId" : 305861, + "storageTemperature" : "20", + "volume" : "300", + "concentration" : "1.2", + "comments" : "Buffer EDTA with A", + "name" : "A_EDTA_1.2", + "samples" : [] + } ] + } -FitForm.prototype.input = function() { - return {}; + }; }; -/** It populates the form **/ -FitForm.prototype.test = function(targetId) { - var macromoleculeForm = new FitForm(); - var panel = macromoleculeForm.getPanel(); - panel.render(targetId); -}; - -/** - * Example form - * - * @witdh - * @height - */ -function RigidBodyModelingResultForm(args) { +CaseForm.prototype.test = function(targetId) { + var caseForm = new CaseForm(); + BIOSAXS.proposal = new Proposal(caseForm.input().proposal); + var panel = caseForm.getPanel(caseForm.input().dewar); + panel.render(targetId); +}; + +/** + * Example form + * + * @witdh + * @height + */ +function ExampleForm(args) { + this.id = BUI.id(); + this.width = 700; + this.height = 500; + + if (args != null) { + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + } +} + +ExampleForm.prototype._getItems = function() { + return [{ + fieldLabel : 'First Name', + name : 'first', + allowBlank : false + }, { + fieldLabel : 'Last Name', + name : 'last', + allowBlank : false + } ]; +}; + +ExampleForm.prototype._getItems = function() { + return [ ]; +}; + +ExampleForm.prototype._getButtons = function() { + return [ ]; +}; + +ExampleForm.prototype.getPanel = function() { + this.panel = Ext.create('Ext.form.Panel', { + width : this.width, + height : this.height, + margin : 10, + border : 1, + defaultType : 'textfield', + items : this._getItems(), + buttons : this._getButtons() + }); + return this.panel; +}; + +/** It populates the form **/ +ExampleForm.prototype.refresh = function(macromolecule) { +}; + +function ExperimentForm(args) { this.id = BUI.id(); - this.width = null; - this.height = null; if (args != null) { - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; - } } - var _this = this; - /** Widgets **/ - this.rigidModelGrid = new RigidModelGrid({ - width : null, - height : 200 + this.onSaved = new Event(this); +} + +ExperimentForm.prototype._getItems = function(experiment) { + this.experiment = experiment; + var typeCombo = Ext.create('Ext.form.ComboBox', { + id : this.id + 'type', + fieldLabel : 'Type', + store : [ "STATIC", "CALIBRATION", "HPLC" ], + queryMode : 'local', + labelWidth : 120, + displayField : 'name', + valueField : 'name', + value : experiment.json.type, + disabled : (experiment.json.type == 'TEMPLATE') }); - this.rigidModelGrid.onSelected.attach(function(sender, fits){ - var ids = []; - for ( var i in fits) { - ids.push(fits[i].fitStructureToExperimentalDataId); + var items = []; + + + if (experiment.json.type == "HPLC" ){ + var typeMacromolecule = BIOSAXS_COMBOMANAGER.getComboMacromoleculeByMacromolecules(BIOSAXS.proposal.getMacromolecules(), {labelWidth : 120, width: "120px"}); + if (experiment.getHPLCMacromolecule() != null){ + typeMacromolecule.setValue(experiment.getHPLCMacromolecule().macromoleculeId); + items.push(typeMacromolecule); } - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data){ -// debugger - - }); - - adapter.getScatteringCurveByFrameIdsList([], [], [], ids); + } + + + items.push(typeCombo, { + id : this.id + 'name', + xtype : 'textfield', + fieldLabel : 'Name', + labelWidth : 120, + width : '100%', + value : experiment.json.name + }, { + id : this.id + 'comments', + xtype : 'textareafield', + name : 'comments', + fieldLabel : 'Comments', + labelWidth : 120, + height : 120, + width : '100%', + value : experiment.json.comments }); - -} - -RigidBodyModelingResultForm.prototype._getItems = function() { - var _this = this; - return [ { - xtype : 'label', - forId : 'myFieldId', - text : 'INLINE HELP: To be updated', - margin : '15 0 20 10', - cls : "inline-help" - }, this.rigidModelGrid.getPanel() ] - -}; - -RigidBodyModelingResultForm.prototype._getButtons = function() { - return []; + return items; }; - -RigidBodyModelingResultForm.prototype.getPanel = function() { +ExperimentForm.prototype.getPanel = function(experiment) { var _this = this; - this.panel = Ext.create('Ext.form.Panel', { - width : this.width, - height : this.height, - margin : 10, - border : 1, - defaultType : 'textfield', - items : this._getItems(), - buttons : this._getButtons(), - listeners : { - afterrender : function() { - _this._populate(); - - } - } + + this.panel = Ext.createWidget({ + xtype : 'container', + layout : 'vbox', + border : 0, + style : { + padding : '10px' + }, + fieldDefaults : { + labelAlign : 'left', + labelWidth : 50 + }, + items : this._getItems(experiment) }); return this.panel; }; -/** Populates could be call when the DOM is not filled yet **/ -RigidBodyModelingResultForm.prototype._populate = function() { -}; - -/** It populates the form * */ -RigidBodyModelingResultForm.prototype.refresh = function(subtractions) { - this.rigidModelGrid.refresh(subtractions); -}; - -RigidBodyModelingResultForm.prototype.input = function() { - return {}; +ExperimentForm.prototype.input = function() { + return new ExperimentHeaderForm().input(); }; -/** It populates the form **/ -RigidBodyModelingResultForm.prototype.test = function(targetId) { - var macromoleculeForm = new RigidBodyModelingResultForm(); - var panel = macromoleculeForm.getPanel(); +ExperimentForm.prototype.test = function(targetId) { + var experimentForm = new ExperimentForm(); + var panel = experimentForm.getPanel(new Experiment(experimentForm.input().experiment)); panel.render(targetId); }; /** - * Example form + * Shows the header for the experiments changing the color and parameters depending on experiment type * - * @witdh - * @height */ -function SuperpositionForm(args) { +function ExperimentHeaderForm(args) { this.id = BUI.id(); - this.width = null; - this.height = null; + this.backgroundColor = '#FFFFFF'; +} - if (args != null) { - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; +ExperimentHeaderForm.prototype.getHTMLSource = function(experiment) { + var html = BUI.createFormLabel("Name :", experiment.json.name, 75, 400, this.backgroundColor); + if (experiment.json.type == "HPLC") { + if (experiment.getHPLCMacromolecule() != null){ + html = html + BUI.createFormLabel("Molecule :", experiment.getHPLCMacromolecule().acronym, 75, 400, this.backgroundColor); } } + else{ + html = html + BUI.createFormLabel("Type :", experiment.json.type, 75, 400, this.backgroundColor); + } + + html = html + BUI.createFormLabel("Date :", experiment.json.creationDate, 75, 400, this.backgroundColor); + return html; +}; - var _this = this; - - /** Widgets **/ - this.superpositionGrid = new SuperpositionGrid({ - width : null, - height : 200 - }); - - this.superpositionGrid.onSelected.attach(function(sender, superpositions) { - var ids = []; - for ( var i in superpositions) { - ids.push(superpositions[i].superpositionId); - } -// _this._renderAbinitio(ids); -// _this.aprioriPDBViewer.refresh(); - _this._renderAligned(ids); - // getAlignedPDBContentBySuperpositionList - }); - - /** PDB viewer **/ -// this.abinitioPDBViewer = new PDBViewer({ -// width : 860 / 2, -// height : 300 / 2, -// margin : 0 -// }); -// -// /** PDB viewer **/ -// this.aprioriPDBViewer = new StructurePDBViewer({ -// width : 860 / 2, -// height : 300 / 2, -// margin : 0 -// }); +ExperimentHeaderForm.prototype.getHTMLDownload = function(experiment) { + var bgcolor = "background-color:" + this.backgroundColor + ";"; + var html = "
"; + if ((experiment.json.type == "CALIBATION") || (experiment.json.type == "STATIC")) { + html = html + " Download Source File
"; + html = html + + ""; + } + if (experiment.json.type == "TEMPLATE") { + html = html + + " Download Source File
"; + } - this.alignedPDBViewer = new AlignedSuperpositionPDBViewer({ - width : 860 , - height : 300 - }); + if (experiment.json.type == "HPLC") { + html = html + " Download h5 File
"; + } -} + return html; +}; -SuperpositionForm.prototype._renderAligned = function(modelsIdList) { - /** Trying to plot the PDB file **/ - try { - this.alignedPDBViewer.refresh(modelsIdList); - } catch (e) { - console.log(e); - } +ExperimentHeaderForm.prototype.getTopPanel = function(experiment) { + return { + xtype : 'container', + layout : 'hbox', + items : [ { + margin : "0 0 0 0", + width : 475, + border : 0, + html : this.getHTMLSource(experiment) + }, { + margin : "0 0 0 0", + width : 475, + border : 0, + html : this.getHTMLDownload(experiment) + } ] + }; }; -SuperpositionForm.prototype._renderAbinitio = function(modelsIdList) { - /** Trying to plot the PDB file **/ - try { - var viz = []; - for (var i = 0; i < modelsIdList.length; i++) { - viz.push({ - modelId : modelsIdList[i], - color : "0xFF6600", - opacity : 0.8 +ExperimentHeaderForm.prototype.getButton = function(experiment) { + var _this = this; + return Ext.create('Ext.Button', { + text : 'EDIT', + minWidth : '100', + margin : '10 0 0 30', + handler : function() { + var experimentWindow = new ExperimentWindow(); + experimentWindow.onSaved.attach(function(sender, data) { + _this.experiment.json.name = data.name; + _this.experiment.json.type = data.type; + _this.experiment.json.comments = data.comments; + _this.panel.remove(_this.panel.items.items[0]); + _this.panel.remove(_this.panel.items.items[0]); + _this.panel.insert(_this.getTopPanel(_this.experiment)); + _this.panel.insert(_this.getBottomPanel(_this.experiment)); }); + experimentWindow.show(experiment); } - this.abinitioPDBViewer.refresh(viz); - } catch (e) { - console.log(e); - } + }); }; -SuperpositionForm.prototype._getItems = function() { - var _this = this; - return [ { - xtype : 'label', - forId : 'myFieldId', - text : 'INLINE HELP: To be updated', - margin : '15 0 20 10', - cls : "inline-help" - }, this.superpositionGrid.getPanel(), { +ExperimentHeaderForm.prototype.getBottomPanel = function(experiment) { + return { xtype : 'container', layout : 'hbox', - items : [ -// { -// xtype : 'container', -// layout : 'vbox', -// items : [ this.abinitioPDBViewer.getPanel(), this.aprioriPDBViewer.getPanel() -// -// ] -// }, - - this.alignedPDBViewer.getPanel() ] - } ] - -}; - -SuperpositionForm.prototype._getButtons = function() { - return []; + margin : '10 0 0 0', + items : [ this.getComments(experiment), this.getButton(experiment) ] + }; }; -SuperpositionForm.prototype.getPanel = function() { - var _this = this; - this.panel = Ext.create('Ext.form.Panel', { - width : this.width, - height : this.height, - margin : 10, - border : 1, - defaultType : 'textfield', - items : this._getItems(), - buttons : this._getButtons(), - listeners : { - afterrender : function() { - _this._populate(); - - } - } - }); - return this.panel; +ExperimentHeaderForm.prototype.getComments = function(experiment) { + return { + xtype : 'textareafield', + labelStyle : 'font-weight: bold;', + name : 'comments', + fieldLabel : 'Comments', + labelWidth : 70, + height : 40, + minWidth : '450', + readOnly : true, + value : experiment.json.comments + }; }; -/** Populates could be call when the DOM is not filled yet **/ -SuperpositionForm.prototype._populate = function() { -}; +ExperimentHeaderForm.prototype.getPanel = function(experiment) { + this.experiment = experiment; + + if (experiment.json.type == 'CALIBRATION') { + this.backgroundColor = '#EFFBFB'; + } + if (experiment.json.type == 'TEMPLATE') { + this.backgroundColor = '#E0F8E6'; + } -/** It populates the form * */ -SuperpositionForm.prototype.refresh = function(subtractions) { - this.subtractions = subtractions; - this.superpositionGrid.refresh(subtractions); + this.panel = Ext.create('Ext.container.Container', { + frame : false, + layout : 'vbox', + padding : 5, + bodyPadding : '5 5 0 0', + width : 890, + margin : '0 0 10 0', + height : 120, + style : { + borderColor : '#99bce8', + borderStyle : 'solid', + borderWidth : '1px', + 'background-color' : this.backgroundColor + }, + fieldDefaults : { + msgTarget : 'side', + labelWidth : 100 + }, + items : [ this.getTopPanel(experiment), this.getBottomPanel(experiment) ] + }); + return this.panel; }; -SuperpositionForm.prototype.input = function() { - return {}; +ExperimentHeaderForm.prototype.input = function() { + return { + experiment : DATADOC.getExperiment_10() + }; }; -/** It populates the form **/ -SuperpositionForm.prototype.test = function(targetId) { - var macromoleculeForm = new SuperpositionForm(); - var panel = macromoleculeForm.getPanel(); +ExperimentHeaderForm.prototype.test = function(targetId) { + var experimentHeaderForm = new ExperimentHeaderForm(); + var panel = experimentHeaderForm.getPanel(new Experiment(experimentHeaderForm.input().experiment)); panel.render(targetId); + }; /** - * Example form + * Macromolecule form with the general parameters of a macromolecule * * @witdh * @height + * + * #onSave button save has been clicked + * #onClose button close has been clicked */ -function AssemblyForm(args) { +function MacromoleculeForm(args) { this.id = BUI.id(); this.width = 700; this.height = 500; @@ -6059,15944 +7053,9793 @@ function AssemblyForm(args) { this.height = args.height; } } - - this.molarityGrid = new MolarityGrid({height : this.height - 50}); + + /** Events **/ + this.onSave = new Event(this); + this.onClose = new Event(this); } -AssemblyForm.prototype._getItems = function() { - return [ { - xtype : 'label', - forId : 'myFieldId', - text : 'List of previously defined macromolecules present in the assembly. This information will be used for additional cross-checks where possible', - margin : '15 0 20 10', - cls : "inline-help" - }, this.molarityGrid.getPanel() ]; -}; - -AssemblyForm.prototype._getButtons = function() { - return []; +/** Type : is the Ext type then requiredtext or textfield * */ +MacromoleculeForm.prototype._getFieldTextWithHelp = function(type, fieldLabel, fieldName, help) { + return Ext.create('Ext.container.Container', { + margin : "10 0 0 10", + items : [ { + xtype : type, + fieldLabel : fieldLabel, + name : fieldName, + id : this.id + fieldName + }, { + xtype : 'label', + forId : 'myFieldId', + text : help, + margin : "5 0 0 105", + cls : "inline-help" + } ] + }); }; -AssemblyForm.prototype.getPanel = function() { - this.panel = Ext.create('Ext.form.Panel', { - width : this.width, - height : this.height, - margin : 10, - border : 0, - defaultType : 'textfield', - items : this._getItems(), - buttons : this._getButtons() +MacromoleculeForm.prototype._getNumericWithHelp = function(type, fieldLabel, fieldName, help) { + return Ext.create('Ext.container.Container', { + margin : "0 0 0 10", + items : [ { + xtype : type, + fieldLabel : fieldLabel, + name : fieldName, + id : this.id + fieldName, + decimalPrecision : 6, + width : 220 + }, { + xtype : 'label', + forId : 'myFieldId', + text : help, + margin : "5 0 0 10", + cls : "inline-help" + } ] }); - return this.panel; }; - -/** It populates the form **/ -AssemblyForm.prototype.refresh = function(macromolecule) { - this.macromolecule = macromolecule; - this.molarityGrid.refresh(macromolecule); +MacromoleculeForm.prototype._getButtons = function() { + var _this = this; + return [ { + text : 'Save', + handler : function() { + _this._save(); + } + },{ + text : 'Close', + handler : function() { + _this.onClose.notify(); + + } + } ]; }; -AssemblyForm.prototype.input = function() { - return {}; +/** It persits the macromolecule in the database **/ +MacromoleculeForm.prototype._persist = function(macromoleculeId, acronym, name, molecularMass, extintionCoefficient, comments, refractiveIndex, solventViscosity) { + + /** Checking not duplicated acronym **/ + if (((macromoleculeId == null) && (BIOSAXS.proposal.getMacromoleculeByAcronym(acronym) != null))== true){ + BUI.showError("Duplicated acronym"); + return; + } + + + if (macromoleculeId == null){ + /** new macromolecule **/ + this.macromolecule = {}; + this.macromolecule.macromoleculeId = null; + } + else{ + this.macromolecule.macromoleculeId = macromoleculeId; + } + + this.macromolecule["acronym"] = acronym; + this.macromolecule["name"] = name; + this.macromolecule["molecularMass"] = molecularMass; + this.macromolecule["extintionCoefficient"] = extintionCoefficient; + this.macromolecule["comments"] = comments; + this.macromolecule["symmetry"] = Ext.getCmp(this.id + 'comboSym').getValue(); + this.macromolecule["refractiveIndex"] = refractiveIndex; + this.macromolecule["solventViscosity"] = solventViscosity; + + var _this = this; + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, proposal) { + /** Updating the proposal global object **/ + BIOSAXS.proposal.setItems(proposal); + _this.panel.setLoading(false); + + var saved = BIOSAXS.proposal.getMacromoleculeByAcronym(acronym); + /** Refreshing to check that everything is ok **/ + _this.refresh(saved); + _this.onSave.notify(saved); + }); + + this.panel.setLoading("Saving Macromolecule") + adapter.saveMacromolecule(this.macromolecule); }; - -AssemblyForm.prototype.test = function(targetId) { - var assemblyForm = new AssemblyForm(); +/** Save the macromolecule in the DB **/ +MacromoleculeForm.prototype._save = function() { - var panel = assemblyForm.getPanel(); - panel.render(targetId); -}; -/** - * Edit the information of a buffer - * - * #onSaved - * #onRemoveAdditive - */ -function BufferForm() { var _this = this; + + var acronym = this._getField("acronym"); + var name = this._getField("name"); + var molecularMass = this._getField("molecularMass"); + var extintionCoefficient = this._getField("extintionCoefficient"); + var comments = this._getField("comments"); + + var refractiveIndex = this._getField("refractiveIndex"); + var solventViscosity = this._getField("solventViscosity"); + + /** Checking required fields **/ + if (name == "") { + BUI.showError("Name field is mandatory"); + return; + } + if (acronym == "") { + BUI.showError("Acroynm field is mandatory"); + return; + } - this.additiveGrid = new AdditiveGrid(); - this.additiveGrid.onRemoveButtonClicked.attach(function(sender, args) { - _this.onRemoveAdditive.notify(args); - }); + if (this.macromolecule != null){ + /** Checking if it is a new macromolecule **/ + if (this.macromolecule.macromoleculeId == null){ + /** Check if the acronym exists already **/ + this._persist(null, acronym, name, molecularMass, extintionCoefficient, comments, refractiveIndex, solventViscosity); + } + else{ + /** It is an update **/ + this._persist(this.macromolecule.macromoleculeId, acronym, name, molecularMass, extintionCoefficient, comments, refractiveIndex, solventViscosity); + } + } + else{ + /** It is a new macromolecule **/ + this._persist(null, acronym, name, molecularMass, extintionCoefficient, comments, refractiveIndex, solventViscosity); + } +}; - this.onSaved = new Event(this); - this.onRemoveAdditive = new Event(this); -} -BufferForm.prototype.getBuffer = function() { - this.buffer.name = Ext.getCmp("buffer_name").getValue(); - this.buffer.acronym = Ext.getCmp("buffer_acronym").getValue(); - this.buffer.comments = Ext.getCmp("buffer_comments").getValue(); - this.buffer.ph = Ext.getCmp("buffer_ph").getValue(); - this.buffer.composition = Ext.getCmp("buffer_composition").getValue(); - this.buffer.bufferhasadditive3VOs = this.additiveGrid.getAdditives(); - return this.buffer; -}; -BufferForm.prototype._getTopPanel = function() { - return { - xtype : 'container', - layout : 'hbox', - border : 0, - frame : true, - items : [ { - xtype : 'container', - layout : 'hbox', - items : [ { +MacromoleculeForm.prototype._getItems = function() { + var _this = this; + /** Symmetry combo box **/ + var symmetry = Ext.create('Ext.data.Store', { + fields : [ 's' ], + data : this._getSymmetries() + }); + + this.symmetryComboBox = Ext.create('Ext.form.ComboBox', { + fieldLabel : 'Symmetry', + store : symmetry, + id : this.id + 'comboSym', + queryMode : 'local', + displayField : 's', + valueField : 's', + value : "P1", + margin : "0 0 0 30", + width : 220 + }); + + return [this._getFieldTextWithHelp("requiredtext", "Name", "name", "Long name. i.e: Bovine serum albumin"), + this._getFieldTextWithHelp("requiredtext", "Acronym", "acronym", "Acronym will be used in the files and analisys. i.e: BSA"), + this._getFieldTextWithHelp("textfield", "Mol. Mass (Da)", "molecularMass", "Atomic mass estimation measured in Da"), + { xtype : 'container', - flex : 1, - border : false, - layout : 'anchor', - defaultType : 'textfield', - items : [ { - xtype : 'requiredtext', - id : 'buffer_name', - fieldLabel : 'Name', - name : 'name', - width : '200px', - value : this.buffer.name - }, { - xtype : 'requiredtext', - id : 'buffer_acronym', - fieldLabel : 'Acronym', - name : 'acronym', - width : '200px', - value : this.buffer.acronym - } ] - } ] - }, { - xtype : 'container', - flex : 1, - layout : 'anchor', - defaultType : 'textfield', - margin : '0 0 0 10', - items : [ { - id : 'buffer_ph', - fieldLabel : 'pH', - name : 'ph', - value : this.buffer.ph, - xtype : 'numberfield', - width : 200, - minValue : 0, - maxValue : 15 - }, { - xtype : 'requiredtext', - id : 'buffer_composition', - fieldLabel : 'Composition', - name : 'composition', - width : 200, - value : this.buffer.composition - } ] - } ] - }; + layout : 'hbox', + margin : "10 0 0 0", + items :[ + this._getNumericWithHelp("numberfield", "Extinction coef.", "extintionCoefficient", ""), + this.symmetryComboBox + ] + }, + { + xtype : 'container', + layout : 'hbox', + margin : "5 0 0 0", + items :[ + this._getNumericWithHelp("numberfield", "Refractive Index", "refractiveIndex", "How radiation propagates through the medium"), + this._getNumericWithHelp("numberfield", "Solvent Viscosity", "solventViscosity", "") + ] + }, + { + id : this.id + "comments", + xtype : 'textareafield', + name : 'comments', + margin : '35 0 0 10', + fieldLabel : 'Comments', + width : this.width - 100 + } ]; }; -BufferForm.prototype.getPanel = function(buffer) { - this.buffer = buffer; - this.panel = Ext.createWidget({ - xtype : 'container', - layout : 'vbox', - style : { - padding : '10px' - }, - fieldDefaults : { - labelAlign : 'left', - labelWidth : 50 +MacromoleculeForm.prototype._getSymmetries = function() { + return [ { + "s" : "P1" + }, { + "s" : "P2" + }, { + "s" : "P3" + }, { + "s" : "P4" + }, { + "s" : "P5" + }, { + "s" : "P6" + }, { + "s" : "P32" + }, { + "s" : "P42" + }, { + "s" : "P52" + }, { + "s" : "P62" + }, { + "s" : "P222" + } ] +}; - }, - items : [ this._getTopPanel(), { - id : 'buffer_comments', - xtype : 'textareafield', - name : 'comments', - fieldLabel : 'Comments', - width : '100%', - value : buffer.comments - }, this.additiveGrid.getPanel(buffer) ] +MacromoleculeForm.prototype.getPanel = function() { + this.panel = Ext.create('Ext.form.Panel', { + width : this.width, + height : this.height, + margin : 10, + border : 1, + defaultType : 'textfield', + items : this._getItems(), + buttons : this._getButtons() }); return this.panel; }; -BufferForm.prototype.input = function() { - return { - buffer : { - "bufferId" : 422, - "proposalId" : 10, - "safetyLevelId" : null, - "name" : "B1", - "acronym" : "B1", - "ph" : null, - "composition" : null, - "bufferhasadditive3VOs" : [], - "comments" : null - } - }; + +/** Populates each text field by field name and value **/ +MacromoleculeForm.prototype._populateField = function(fieldName, value) { + if (value != null){ + Ext.getCmp(this.id + fieldName).setValue(value); + } }; -BufferForm.prototype.test = function(targetId) { - var bufferForm = new BufferForm(); - var panel = bufferForm.getPanel(bufferForm.input().buffer); - panel.render(targetId); +/** Gets the value of a textfield **/ +MacromoleculeForm.prototype._getField = function(fieldName) { + return Ext.getCmp(this.id + fieldName).getValue(); }; - -/** - * @showTitle - * - * #onSaved - * #onAddPlates - * #onRemovePlates - **/ -function CaseForm(args) { - this.width = 700; - this.showTitle = true; - if (args != null) { - if (args.showTitle != null) { - this.showTitle = args.showTitle; - } - } - var _this = this; - this.stockSolutionGrid = new StockSolutionGrid({ - width : this.width - 10, - minHeight : 300, - height : 300, - tbar : true, - showTitle : true, - isPackedVisible : false, - btnAddExisting : true, - btnRemoveVisible : false, - btnUnpackVisible : true - }); - /** When selecting existing stock solutions **/ - this.stockSolutionGrid.onStockSolutionSelected.attach(function(sender, stockSolutions) { - if (stockSolutions != null) { - for ( var i = 0; i < stockSolutions.length; i++) { - _this.saveStockSolution(stockSolutions[i]); - } +/** It populates the form **/ +MacromoleculeForm.prototype.refresh = function(macromolecule) { + this.macromolecule = macromolecule; + if (macromolecule != null){ + this._populateField("name", macromolecule.name); + this._populateField("acronym", macromolecule.acronym); + this._populateField("extintionCoefficient", macromolecule.extintionCoefficient); + this._populateField("molecularMass", macromolecule.molecularMass); + this._populateField("comments", macromolecule.comments); + this._populateField("refractiveIndex", macromolecule.refractiveIndex); + this._populateField("solventViscosity", macromolecule.solventViscosity); + if (macromolecule.symmetry != null){ + Ext.getCmp(this.id + 'comboSym').setValue(macromolecule.symmetry); } - }); + } +}; - /** it can be because it has been added a new one or removed **/ - this.stockSolutionGrid.onProposalChanged.attach(function(sender, stockSolution) { - if (stockSolution != null) { - _this.saveStockSolution(stockSolution); - } else { - BIOSAXS.proposal.onInitialized.attach(function() { - _this.stockSolutionGrid.refresh(BIOSAXS.proposal.getStockSolutionsByDewarId(_this.dewar.dewarId)); - _this.stockSolutionGrid.grid.setLoading(false); - }); - BIOSAXS.proposal.init(); +MacromoleculeForm.prototype.input = function() { + return {}; +}; - } +/** It populates the form **/ +MacromoleculeForm.prototype.test = function(targetId) { + var macromoleculeForm = new MacromoleculeForm(); + macromoleculeForm.onClose.attach(function(sender){ + alert("Click on close"); }); + var panel = macromoleculeForm.getPanel(); + panel.render(targetId); +}; - this.onSaved = new Event(this); - this.onAddPlates = new Event(this); - this.onRemovePlates = new Event(this); -} -CaseForm.prototype.saveStockSolution = function(stockSolution) { - var _this = this; - var adapter = new BiosaxsDataAdapter(); - this.stockSolutionGrid.grid.setLoading("ISPyB: setting case to Stock solution"); - adapter.onSuccess.attach(function(sender, stockSolution) { - BIOSAXS.proposal.onInitialized.attach(function() { - _this.stockSolutionGrid.refresh(BIOSAXS.proposal.getStockSolutionsByDewarId(_this.dewar.dewarId)); - _this.stockSolutionGrid.grid.setLoading(false); - }); - BIOSAXS.proposal.init(); - }); - adapter.onError.attach(function(sender, data) { - _this.stockSolutionGrid.grid.setLoading(false); - BUI.showError(data); - }); - stockSolution.boxId = _this.dewar.dewarId; - adapter.saveStockSolution(stockSolution); -}; - -CaseForm.prototype.fillStores = function() { - var _this = this; - this.panel.setLoading("Loading Labcontacts from database"); + - var proposal = BUI.getProposal(); - proposal.onDataRetrieved.attach(function(sender, data) { - _this.labContactForSendingStore.loadData(data, false); - _this.labContactForReturnStore.loadData(data, false); - _this.panel.setLoading(false); - }); - proposal.getLabContactsByProposalId(); +function ModelVisualizerForm(args){ + this.id =BUI.id(); + this.width = 600; + this.height = 400; + if (args!= null){ + if (args.width != null){ + this.width = args.width; + } + if (args.height != null){ + this.height = args.height; + } + } }; -CaseForm.prototype.refresh = function(dewar) { - this.setDewar(dewar); - this.stockSolutionGrid.refresh(BIOSAXS.proposal.getStockSolutionsByDewarId(dewar.dewarId)); +ModelVisualizerForm.prototype._getFirHTML = function(modelId, width, height, type, desc) { + var html = ""; + html = html + ''; + html = html + ''; + html = html + ''; + html = html + '
dammin.' + type + '
' + desc + '
'; + return html; }; -CaseForm.prototype.getDewar = function() { - this.dewar.code = Ext.getCmp("dewar_code").getValue(); - this.dewar.comments = Ext.getCmp("dewar_comments").getValue(); - this.dewar.trackingNumberFromSynchrotron = Ext.getCmp("dewar_trackingNumberFromSynchrotron").getValue(); - this.dewar.trackingNumberToSynchrotron = Ext.getCmp("dewar_trackingNumberToSynchrotron").getValue(); - this.dewar.transportValue = Ext.getCmp("dewar_transportValue").getValue(); - this.dewar.storageLocation = Ext.getCmp("dewar_storageLocation").getValue(); - this.dewar.firstExperimentId = this.macromoleculeCombo.getValue(); - return this.dewar; +ModelVisualizerForm.prototype.getItems = function(modelPanel){ + _this = this; + var height = _this.height/2 - 60; + var width = _this.width/2 - 10; + + return Ext.create('Ext.container.Container', { + layout: { + type: 'vbox', // Arrange child items vertically + }, + items: [ + modelPanel, + { + xtype : 'container', + layout: { + type: 'hbox', // Arrange child items vertically + }, + items : [{ + html : this._getFirHTML("id", width, height, "fir", "Fit of the simulated scattering curve versus a smoothed experimental data (spline interpolation)"), + height :height, + width : width, + padding: 2 + }, + { + html : this._getFirHTML("id", width, height, "fit", "Fit of the simulated scattering curve versus the experimental data."), + height : height, + width : width, + padding: 2 + }] + } + + ] + }); }; -CaseForm.prototype.setDewar = function(dewar) { - this.dewar = dewar; - Ext.getCmp("dewar_code").setValue(this.dewar.code); - Ext.getCmp("dewar_dewarStatus").setText(new String(this.dewar.dewarStatus).toUpperCase()); - Ext.getCmp("dewar_comments").setValue(this.dewar.comments); - Ext.getCmp("dewar_trackingNumberFromSynchrotron").setValue(this.dewar.trackingNumberFromSynchrotron); - Ext.getCmp("dewar_trackingNumberToSynchrotron").setValue(this.dewar.trackingNumberToSynchrotron); - Ext.getCmp("dewar_transportValue").setValue(this.dewar.transportValue); - Ext.getCmp("dewar_storageLocation").setValue(this.dewar.storageLocation); - if (dewar.sessionVO != null) { - this.macromoleculeCombo.setValue(dewar.sessionVO.sessionId); +ModelVisualizerForm.prototype.refresh = function(models){ + var input = []; +// var colors = ["008000", "F0A804", "0000FF", "800080", "C0C0C0"]; + for (var i = 0; i < models.length; i++) { + console.log(BUI.rainbow(models.length, i).replace("#", "0x")); + input.push({ + color: BUI.rainbow(models.length, i).replace("#", "0x"), + modelId: models[i].modelId, + opacity: 0.8, + radius: 3, + title: BUI.getFileNameByPath(models[i].pdbFile), + type: "SHAPEDETERMINATIONMODEL" + + }); } + + this.panel.removeAll(); + this.panel.add( + _this.getItems( + new PDBViewer({ + width : this.width - 10, + height : (this.height/2) - 10, + title : "" + }).draw(input) + ) + ); + + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + var splitted = data.toString().split("\n"); + var array = []; + for ( var i = 0; i < splitted.length; i++) { + var line = splitted[i].trim(); + var line_splited = line.split(/\s*[\s,]\s*/); + if (line_splited.length == 4) { + array.push([ Number(line_splited[0]), BUI.getStvArray(line_splited[1], line_splited[2]), BUI.getStvArray(line_splited[3], 0) ]); + } + } + + var id = (_this.id + "firid"); + var dygraphWidget = new StdDevDyGraph(id, { + width : (_this.width/2) - 10, + height :(_this.height/2) -110, + xlabel : 'q(nm-1)' + }); + dygraphWidget.draw(array, [ "#FF0000", "#0000FF", "#FF00FF" ], [ 's', 'I(exp)', 'I(sim)' ]); + }); + + adapter.getModelFile("FIR", models[0].modelId); + + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + var splitted = data.toString().split("\n"); + var array = []; + for ( var i = 0; i < splitted.length; i++) { + var line = splitted[i].trim(); + var line_splited = line.split(/\s*[\s,]\s*/); + if (line_splited.length == 3) { + array.push([ Number(line_splited[0]), BUI.getStvArray(line_splited[1], 0), BUI.getStvArray(line_splited[2], 0) ]); + } + } + + var id = (_this.id + "fitid"); + + var dygraphWidget = new StdDevDyGraph(id, { + width : (_this.width/2) - 10, + height : (_this.height/2) - 110, + xlabel : 'q(nm-1)' + }); + dygraphWidget.draw(array, [ "#FF0000", "#0000FF" ], [ "s", "I(exp)", "I(sim)" ]); + }); + adapter.getModelFile("FIT", models[0].modelId); }; -CaseForm.prototype.getSessionCombo = function() { - this.macromoleculeCombo = BIOSAXS_COMBOMANAGER.getComboSessions(BIOSAXS.proposal.getSessions(), { - labelWidth : 100, - margin : '5 0 00 0', - width : 250 +ModelVisualizerForm.prototype.getPanel = function(modelList){ + _this = this; + this.modelList = modelList; + this.panel = Ext.create('Ext.Panel', { + title: 'Results', + width: this.width, + height: this.height, + layout: { + type: 'vbox', // Arrange child items vertically +// align: 'stretch' // Each takes up full width + }, + items: [ + + ], + listeners : { + afterrender : function(grid, eOpts) { +// alert(_this.modelList) + } + } }); - return this.macromoleculeCombo; + + return this.panel; + }; -CaseForm.prototype.getInformationPanel = function() { - if (this.panel == null) { - this.informationPanel = Ext.create('Ext.form.Panel', { - width : this.width - 10, - border : 0, - items : [ { - xtype : 'container', - margin : "2 2 2 2", - collapsible : false, - defaultType : 'textfield', - layout : 'anchor', - items : [ { - xtype : 'container', - layout : 'hbox', - items : [ { - xtype : 'requiredtext', - fieldLabel : 'Code', - allowBlank : false, - name : 'code', - id : 'dewar_code', - anchor : '50%' - }, { - xtype : 'label', - margin : '0 0 0 20', - readOnly : true, - id : 'dewar_dewarStatus', - anchor : '50%' - } ] - }, this.getSessionCombo(), { - margin : '5 0 0 0', - xtype : 'textareafield', - name : 'comments', - id : 'dewar_comments', - width : this.width - 50, - fieldLabel : 'Comments' - } ] - }, { - xtype : 'fieldset', - title : 'Courier Accounts Details for Return', - collapsible : false, - layout : 'anchor', - defaults : { - anchor : '100%' - }, - items : [ { - xtype : 'container', - layout : 'hbox', - items : [ { - xtype : 'textfield', - labelWidth : 200, - width : 280, - fieldLabel : 'Track Number From Synchrotron', - id : 'dewar_trackingNumberFromSynchrotron' - }, { - xtype : 'numberfield', - width : 190, - labelWidth : 110, - margin : '0 0 0 30', - fieldLabel : 'Transport Value', - id : 'dewar_transportValue' - } - - ] - }, { - xtype : 'container', - layout : 'hbox', - margin : '10 0 0 0', - items : [ - - { - xtype : 'textfield', - labelWidth : 200, - width : 280, - fieldLabel : 'Track Number To Synchrotron', - id : 'dewar_trackingNumberToSynchrotron' - }, { - xtype : 'textfield', - margin : '0 0 0 30', - width : 190, - labelWidth : 110, - fieldLabel : 'Storage Location', - id : 'dewar_storageLocation' - } - - ] - } ] - } ] - }); - } - - return this.informationPanel; -}; - -CaseForm.prototype.getPanel = function(dewar) { - this.dewar = dewar; - this.panel = Ext.createWidget({ - xtype : 'container', - layout : 'vbox', - width : this.width, - border : 0, - items : [ { - items : { - xtype : "container", - layout : "vbox", - margin : "5 5 5 5", - items : [ this.getInformationPanel(dewar), this.stockSolutionGrid.getPanel() ] - - } - } ] - }); - - this.refresh(dewar); - return this.panel; - -}; - -CaseForm.prototype.input = function() { - return { - dewar : { - "dewarId" : 305861, - "code" : "ESRF-TEST", - "comments" : "comments", - "storageLocation" : "FRIDGE", - "dewarStatus" : "opened", - "timeStamp" : null, - "isStorageDewar" : null, - "barCode" : "ESRF305861", - "customsValue" : null, - "transportValue" : null, - "trackingNumberToSynchrotron" : "3333", - "trackingNumberFromSynchrotron" : "224466", - "type" : "Dewar", - "sessionVO" : { - "sessionId" : 31697, - "expSessionPk" : null, - "projectCode" : null, - "startDate" : "2012 07 21", - "endDate" : "2012 07 23", - "beamlineName" : "BM29", - "scheduled" : 1, - "nbShifts" : 2, - "comments" : null, - "beamlineOperator" : "PERNOT P", - "usedFlag" : null, - "sessionTitle" : null, - "structureDeterminations" : null, - "dewarTransport" : null, - "databackupFrance" : null, - "databackupEurope" : null, - "visit_number" : null, - "operatorSiteNumber" : "14061", - "timeStamp" : "2012 04 25" - } - }, - proposal : { - "assemblies" : [], - "sessions" : [ { - "sessionId" : 31697, - "expSessionPk" : null, - "projectCode" : null, - "startDate" : "2012 07 21", - "endDate" : "2012 07 23", - "beamlineName" : "BM29", - "scheduled" : 1, - "nbShifts" : 2, - "comments" : null, - "beamlineOperator" : "PERNOT P", - "usedFlag" : null, - "sessionTitle" : null, - "structureDeterminations" : null, - "dewarTransport" : null, - "databackupFrance" : null, - "databackupEurope" : null, - "visit_number" : null, - "operatorSiteNumber" : "14061", - "timeStamp" : "2012 04 25" - } ], - "labcontacts" : [ { - "labContactId" : 787, - "personVO" : { - "personId" : 304252, - "personUUID" : null, - "familyName" : "KIM", - "givenName" : "Henry", - "title" : null, - "emailAddress" : "henry-sung.kim@ibs.fr", - "phoneNumber" : "", - "login" : "", - "passwd" : "", - "faxNumber" : "" - }, - "cardName" : "KIM-Institut de Bio", - "defaultCourrierCompany" : "22", - "courierAccount" : "", - "billingReference" : "", - "dewarAvgCustomsValue" : 0, - "dewarAvgTransportValue" : 0 - } ], - "buffers" : [ { - "bufferId" : 811, - "proposalId" : 3124, - "safetyLevelId" : null, - "name" : "EDTA", - "acronym" : "EDTA", - "ph" : null, - "composition" : "", - "bufferhasadditive3VOs" : [], - "comments" : "" - }, { - "bufferId" : 810, - "proposalId" : 3124, - "safetyLevelId" : null, - "name" : "HEPES", - "acronym" : "HEPES", - "ph" : null, - "composition" : "", - "bufferhasadditive3VOs" : [], - "comments" : "" - } ], - "shippings" : [ { - "shippingId" : 304107, - "shippingName" : "TEST", - "deliveryAgentAgentName" : null, - "deliveryAgentShippingDate" : null, - "deliveryAgentDeliveryDate" : null, - "deliveryAgentAgentCode" : null, - "deliveryAgentFlightCode" : null, - "shippingStatus" : "opened", - "timeStamp" : "2013 09 25", - "laboratoryId" : null, - "isStorageShipping" : null, - "creationDate" : "2013 09 25", - "comments" : "test", - "sendingLabContactVO" : { - "labContactId" : 787, - "personVO" : { - "personId" : 304252, - "personUUID" : null, - "familyName" : "KIM", - "givenName" : "Henry", - "title" : null, - "emailAddress" : "henry-sung.kim@ibs.fr", - "phoneNumber" : "", - "login" : "", - "passwd" : "", - "faxNumber" : "" - }, - "cardName" : "KIM-Institut de Bio", - "defaultCourrierCompany" : "22", - "courierAccount" : "", - "billingReference" : "", - "dewarAvgCustomsValue" : 0, - "dewarAvgTransportValue" : 0 - }, - "returnLabContactVO" : { - "labContactId" : 787, - "personVO" : { - "personId" : 304252, - "personUUID" : null, - "familyName" : "KIM", - "givenName" : "Henry", - "title" : null, - "emailAddress" : "henry-sung.kim@ibs.fr", - "phoneNumber" : "", - "login" : "", - "passwd" : "", - "faxNumber" : "" - }, - "cardName" : "KIM-Institut de Bio", - "defaultCourrierCompany" : "22", - "courierAccount" : "", - "billingReference" : "", - "dewarAvgCustomsValue" : 0, - "dewarAvgTransportValue" : 0 - }, - "returnCourier" : null, - "dateOfShippingToUser" : null, - "shippingType" : "DewarTracking", - "dewarVOs" : [ { - "dewarId" : 305861, - "code" : "ESRF-TEST", - "comments" : "comments", - "storageLocation" : "FRIDGE", - "dewarStatus" : "opened", - "timeStamp" : null, - "isStorageDewar" : null, - "barCode" : "ESRF305861", - "customsValue" : null, - "transportValue" : null, - "trackingNumberToSynchrotron" : "3333", - "trackingNumberFromSynchrotron" : "224466", - "type" : "Dewar", - "sessionVO" : { - "sessionId" : 31697, - "expSessionPk" : null, - "projectCode" : null, - "startDate" : "2012 07 21", - "endDate" : "2012 07 23", - "beamlineName" : "BM29", - "scheduled" : 1, - "nbShifts" : 2, - "comments" : null, - "beamlineOperator" : "PERNOT P", - "usedFlag" : null, - "sessionTitle" : null, - "structureDeterminations" : null, - "dewarTransport" : null, - "databackupFrance" : null, - "databackupEurope" : null, - "visit_number" : null, - "operatorSiteNumber" : "14061", - "timeStamp" : "2012 04 25" - } - } ] - } ], - "macromolecules" : [ { - "macromoleculeId" : 5933, - "safetylevelId" : null, - "proposalId" : 3124, - "name" : "A", - "acronym" : "A", - "molecularMass" : "", - "extintionCoefficient" : "", - "sequence" : null, - "creationDate" : null, - "comments" : "", - "macromoleculeregion3VOs" : [], - "stoichiometry3VOsForHostMacromoleculeId" : [], - "structure3VOs" : [] - } ], - "stockSolutions" : [ { - "stockSolutionId" : 6, - "proposalId" : 3124, - "macromoleculeId" : 5933, - "bufferId" : 811, - "instructionSet3VO" : null, - "boxId" : 305861, - "storageTemperature" : "20", - "volume" : "300", - "concentration" : "1.2", - "comments" : "Buffer EDTA with A", - "name" : "A_EDTA_1.2", - "samples" : [] - } ] - } - - }; -}; - -CaseForm.prototype.test = function(targetId) { - var caseForm = new CaseForm(); - BIOSAXS.proposal = new Proposal(caseForm.input().proposal); - var panel = caseForm.getPanel(caseForm.input().dewar); - panel.render(targetId); -}; - -/** - * Example form - * - * @witdh - * @height - */ -function ExampleForm(args) { - this.id = BUI.id(); - this.width = 700; - this.height = 500; - - if (args != null) { - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; - } - } -} - -ExampleForm.prototype._getItems = function() { - return [{ - fieldLabel : 'First Name', - name : 'first', - allowBlank : false - }, { - fieldLabel : 'Last Name', - name : 'last', - allowBlank : false - } ]; -}; - -ExampleForm.prototype._getItems = function() { - return [ ]; -}; - -ExampleForm.prototype._getButtons = function() { - return [ ]; -}; - -ExampleForm.prototype.getPanel = function() { - this.panel = Ext.create('Ext.form.Panel', { - width : this.width, - height : this.height, - margin : 10, - border : 1, - defaultType : 'textfield', - items : this._getItems(), - buttons : this._getButtons() - }); - return this.panel; -}; - -/** It populates the form **/ -ExampleForm.prototype.refresh = function(macromolecule) { -}; - -function ExperimentForm(args) { - this.id = BUI.id(); - - if (args != null) { - } - - this.onSaved = new Event(this); -} - -ExperimentForm.prototype._getItems = function(experiment) { - this.experiment = experiment; - var typeCombo = Ext.create('Ext.form.ComboBox', { - id : this.id + 'type', - fieldLabel : 'Type', - store : [ "STATIC", "CALIBRATION", "HPLC" ], - queryMode : 'local', - labelWidth : 120, - displayField : 'name', - valueField : 'name', - value : experiment.json.type, - disabled : (experiment.json.type == 'TEMPLATE') - }); - - var items = []; - - - if (experiment.json.type == "HPLC" ){ - var typeMacromolecule = BIOSAXS_COMBOMANAGER.getComboMacromoleculeByMacromolecules(BIOSAXS.proposal.getMacromolecules(), {labelWidth : 120, width: "120px"}); - if (experiment.getHPLCMacromolecule() != null){ - typeMacromolecule.setValue(experiment.getHPLCMacromolecule().macromoleculeId); - items.push(typeMacromolecule); - } - } - - - items.push(typeCombo, { - id : this.id + 'name', - xtype : 'textfield', - fieldLabel : 'Name', - labelWidth : 120, - width : '100%', - value : experiment.json.name - }, { - id : this.id + 'comments', - xtype : 'textareafield', - name : 'comments', - fieldLabel : 'Comments', - labelWidth : 120, - height : 120, - width : '100%', - value : experiment.json.comments - }); - return items; -}; -ExperimentForm.prototype.getPanel = function(experiment) { - var _this = this; - - this.panel = Ext.createWidget({ - xtype : 'container', - layout : 'vbox', - border : 0, - style : { - padding : '10px' - }, - fieldDefaults : { - labelAlign : 'left', - labelWidth : 50 - }, - items : this._getItems(experiment) - }); - return this.panel; -}; - -ExperimentForm.prototype.input = function() { - return new ExperimentHeaderForm().input(); -}; - -ExperimentForm.prototype.test = function(targetId) { - var experimentForm = new ExperimentForm(); - var panel = experimentForm.getPanel(new Experiment(experimentForm.input().experiment)); - panel.render(targetId); -}; - -/** - * Shows the header for the experiments changing the color and parameters depending on experiment type - * - */ -function ExperimentHeaderForm(args) { - this.id = BUI.id(); - this.backgroundColor = '#FFFFFF'; -} - -ExperimentHeaderForm.prototype.getHTMLSource = function(experiment) { - var html = BUI.createFormLabel("Name :", experiment.json.name, 75, 400, this.backgroundColor); - if (experiment.json.type == "HPLC") { - if (experiment.getHPLCMacromolecule() != null){ - html = html + BUI.createFormLabel("Molecule :", experiment.getHPLCMacromolecule().acronym, 75, 400, this.backgroundColor); - } - } - else{ - html = html + BUI.createFormLabel("Type :", experiment.json.type, 75, 400, this.backgroundColor); - } - - html = html + BUI.createFormLabel("Date :", experiment.json.creationDate, 75, 400, this.backgroundColor); - return html; -}; - -ExperimentHeaderForm.prototype.getHTMLDownload = function(experiment) { - var bgcolor = "background-color:" + this.backgroundColor + ";"; - var html = "
"; - if ((experiment.json.type == "CALIBATION") || (experiment.json.type == "STATIC")) { - html = html + " Download Source File
"; - html = html - + ""; - } - if (experiment.json.type == "TEMPLATE") { - html = html - + " Download Source File"; - } - - if (experiment.json.type == "HPLC") { - html = html + " Download h5 File"; - } - - return html; -}; - -ExperimentHeaderForm.prototype.getTopPanel = function(experiment) { - return { - xtype : 'container', - layout : 'hbox', - items : [ { - margin : "0 0 0 0", - width : 475, - border : 0, - html : this.getHTMLSource(experiment) - }, { - margin : "0 0 0 0", - width : 475, - border : 0, - html : this.getHTMLDownload(experiment) - } ] - }; -}; - -ExperimentHeaderForm.prototype.getButton = function(experiment) { - var _this = this; - return Ext.create('Ext.Button', { - text : 'EDIT', - minWidth : '100', - margin : '10 0 0 30', - handler : function() { - var experimentWindow = new ExperimentWindow(); - experimentWindow.onSaved.attach(function(sender, data) { - _this.experiment.json.name = data.name; - _this.experiment.json.type = data.type; - _this.experiment.json.comments = data.comments; - _this.panel.remove(_this.panel.items.items[0]); - _this.panel.remove(_this.panel.items.items[0]); - _this.panel.insert(_this.getTopPanel(_this.experiment)); - _this.panel.insert(_this.getBottomPanel(_this.experiment)); - }); - experimentWindow.show(experiment); - } - }); -}; - -ExperimentHeaderForm.prototype.getBottomPanel = function(experiment) { - return { - xtype : 'container', - layout : 'hbox', - margin : '10 0 0 0', - items : [ this.getComments(experiment), this.getButton(experiment) ] - }; -}; - -ExperimentHeaderForm.prototype.getComments = function(experiment) { - return { - xtype : 'textareafield', - labelStyle : 'font-weight: bold;', - name : 'comments', - fieldLabel : 'Comments', - labelWidth : 70, - height : 40, - minWidth : '450', - readOnly : true, - value : experiment.json.comments - }; -}; - -ExperimentHeaderForm.prototype.getPanel = function(experiment) { - this.experiment = experiment; - - if (experiment.json.type == 'CALIBRATION') { - this.backgroundColor = '#EFFBFB'; - } - if (experiment.json.type == 'TEMPLATE') { - this.backgroundColor = '#E0F8E6'; - } - - this.panel = Ext.create('Ext.container.Container', { - frame : false, - layout : 'vbox', - padding : 5, - bodyPadding : '5 5 0 0', - width : 890, - margin : '0 0 10 0', - height : 120, - style : { - borderColor : '#99bce8', - borderStyle : 'solid', - borderWidth : '1px', - 'background-color' : this.backgroundColor - }, - fieldDefaults : { - msgTarget : 'side', - labelWidth : 100 - }, - items : [ this.getTopPanel(experiment), this.getBottomPanel(experiment) ] - }); - return this.panel; -}; - -ExperimentHeaderForm.prototype.input = function() { - return { - experiment : DATADOC.getExperiment_10() - }; -}; - -ExperimentHeaderForm.prototype.test = function(targetId) { - var experimentHeaderForm = new ExperimentHeaderForm(); - var panel = experimentHeaderForm.getPanel(new Experiment(experimentHeaderForm.input().experiment)); - panel.render(targetId); - -}; - -/** - * Macromolecule form with the general parameters of a macromolecule - * - * @witdh - * @height - * - * #onSave button save has been clicked - * #onClose button close has been clicked - */ -function MacromoleculeForm(args) { - this.id = BUI.id(); - this.width = 700; - this.height = 500; - - if (args != null) { - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; - } - } - - /** Events **/ - this.onSave = new Event(this); - this.onClose = new Event(this); -} - -/** Type : is the Ext type then requiredtext or textfield * */ -MacromoleculeForm.prototype._getFieldTextWithHelp = function(type, fieldLabel, fieldName, help) { - return Ext.create('Ext.container.Container', { - margin : "10 0 0 10", - items : [ { - xtype : type, - fieldLabel : fieldLabel, - name : fieldName, - id : this.id + fieldName - }, { - xtype : 'label', - forId : 'myFieldId', - text : help, - margin : "5 0 0 105", - cls : "inline-help" - } ] - }); -}; - -MacromoleculeForm.prototype._getNumericWithHelp = function(type, fieldLabel, fieldName, help) { - return Ext.create('Ext.container.Container', { - margin : "0 0 0 10", - items : [ { - xtype : type, - fieldLabel : fieldLabel, - name : fieldName, - id : this.id + fieldName, - decimalPrecision : 6, - width : 220 - }, { - xtype : 'label', - forId : 'myFieldId', - text : help, - margin : "5 0 0 10", - cls : "inline-help" - } ] - }); -}; - -MacromoleculeForm.prototype._getButtons = function() { - var _this = this; - return [ { - text : 'Save', - handler : function() { - _this._save(); - } - },{ - text : 'Close', - handler : function() { - _this.onClose.notify(); - - } - } ]; -}; - -/** It persits the macromolecule in the database **/ -MacromoleculeForm.prototype._persist = function(macromoleculeId, acronym, name, molecularMass, extintionCoefficient, comments, refractiveIndex, solventViscosity) { - - /** Checking not duplicated acronym **/ - if (((macromoleculeId == null) && (BIOSAXS.proposal.getMacromoleculeByAcronym(acronym) != null))== true){ - BUI.showError("Duplicated acronym"); - return; - } - - - if (macromoleculeId == null){ - /** new macromolecule **/ - this.macromolecule = {}; - this.macromolecule.macromoleculeId = null; - } - else{ - this.macromolecule.macromoleculeId = macromoleculeId; - } - - this.macromolecule["acronym"] = acronym; - this.macromolecule["name"] = name; - this.macromolecule["molecularMass"] = molecularMass; - this.macromolecule["extintionCoefficient"] = extintionCoefficient; - this.macromolecule["comments"] = comments; - this.macromolecule["symmetry"] = Ext.getCmp(this.id + 'comboSym').getValue(); - this.macromolecule["refractiveIndex"] = refractiveIndex; - this.macromolecule["solventViscosity"] = solventViscosity; - - var _this = this; - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, proposal) { - /** Updating the proposal global object **/ - BIOSAXS.proposal.setItems(proposal); - _this.panel.setLoading(false); - - var saved = BIOSAXS.proposal.getMacromoleculeByAcronym(acronym); - /** Refreshing to check that everything is ok **/ - _this.refresh(saved); - _this.onSave.notify(saved); - }); - - this.panel.setLoading("Saving Macromolecule") - adapter.saveMacromolecule(this.macromolecule); -}; - -/** Save the macromolecule in the DB **/ -MacromoleculeForm.prototype._save = function() { - - var _this = this; - - var acronym = this._getField("acronym"); - var name = this._getField("name"); - var molecularMass = this._getField("molecularMass"); - var extintionCoefficient = this._getField("extintionCoefficient"); - var comments = this._getField("comments"); - - var refractiveIndex = this._getField("refractiveIndex"); - var solventViscosity = this._getField("solventViscosity"); - - /** Checking required fields **/ - if (name == "") { - BUI.showError("Name field is mandatory"); - return; - } - if (acronym == "") { - BUI.showError("Acroynm field is mandatory"); - return; - } - - if (this.macromolecule != null){ - /** Checking if it is a new macromolecule **/ - if (this.macromolecule.macromoleculeId == null){ - /** Check if the acronym exists already **/ - this._persist(null, acronym, name, molecularMass, extintionCoefficient, comments, refractiveIndex, solventViscosity); - } - else{ - /** It is an update **/ - this._persist(this.macromolecule.macromoleculeId, acronym, name, molecularMass, extintionCoefficient, comments, refractiveIndex, solventViscosity); - } - } - else{ - /** It is a new macromolecule **/ - this._persist(null, acronym, name, molecularMass, extintionCoefficient, comments, refractiveIndex, solventViscosity); - } -}; - - - -MacromoleculeForm.prototype._getItems = function() { - var _this = this; - /** Symmetry combo box **/ - var symmetry = Ext.create('Ext.data.Store', { - fields : [ 's' ], - data : this._getSymmetries() - }); - - this.symmetryComboBox = Ext.create('Ext.form.ComboBox', { - fieldLabel : 'Symmetry', - store : symmetry, - id : this.id + 'comboSym', - queryMode : 'local', - displayField : 's', - valueField : 's', - value : "P1", - margin : "0 0 0 30", - width : 220 - }); - - return [this._getFieldTextWithHelp("requiredtext", "Name", "name", "Long name. i.e: Bovine serum albumin"), - this._getFieldTextWithHelp("requiredtext", "Acronym", "acronym", "Acronym will be used in the files and analisys. i.e: BSA"), - this._getFieldTextWithHelp("textfield", "Mol. Mass (Da)", "molecularMass", "Atomic mass estimation measured in Da"), - { - xtype : 'container', - layout : 'hbox', - margin : "10 0 0 0", - items :[ - this._getNumericWithHelp("numberfield", "Extinction coef.", "extintionCoefficient", ""), - this.symmetryComboBox - ] - }, - { - xtype : 'container', - layout : 'hbox', - margin : "5 0 0 0", - items :[ - this._getNumericWithHelp("numberfield", "Refractive Index", "refractiveIndex", "How radiation propagates through the medium"), - this._getNumericWithHelp("numberfield", "Solvent Viscosity", "solventViscosity", "") - ] - }, - { - id : this.id + "comments", - xtype : 'textareafield', - name : 'comments', - margin : '35 0 0 10', - fieldLabel : 'Comments', - width : this.width - 100 - } ]; -}; - -MacromoleculeForm.prototype._getSymmetries = function() { - return [ { - "s" : "P1" - }, { - "s" : "P2" - }, { - "s" : "P3" - }, { - "s" : "P4" - }, { - "s" : "P5" - }, { - "s" : "P6" - }, { - "s" : "P32" - }, { - "s" : "P42" - }, { - "s" : "P52" - }, { - "s" : "P62" - }, { - "s" : "P222" - } ] -}; - -MacromoleculeForm.prototype.getPanel = function() { - this.panel = Ext.create('Ext.form.Panel', { - width : this.width, - height : this.height, - margin : 10, - border : 1, - defaultType : 'textfield', - items : this._getItems(), - buttons : this._getButtons() - }); - return this.panel; -}; - - -/** Populates each text field by field name and value **/ -MacromoleculeForm.prototype._populateField = function(fieldName, value) { - if (value != null){ - Ext.getCmp(this.id + fieldName).setValue(value); - } -}; - -/** Gets the value of a textfield **/ -MacromoleculeForm.prototype._getField = function(fieldName) { - return Ext.getCmp(this.id + fieldName).getValue(); -}; - - -/** It populates the form **/ -MacromoleculeForm.prototype.refresh = function(macromolecule) { - this.macromolecule = macromolecule; - if (macromolecule != null){ - this._populateField("name", macromolecule.name); - this._populateField("acronym", macromolecule.acronym); - this._populateField("extintionCoefficient", macromolecule.extintionCoefficient); - this._populateField("molecularMass", macromolecule.molecularMass); - this._populateField("comments", macromolecule.comments); - this._populateField("refractiveIndex", macromolecule.refractiveIndex); - this._populateField("solventViscosity", macromolecule.solventViscosity); - if (macromolecule.symmetry != null){ - Ext.getCmp(this.id + 'comboSym').setValue(macromolecule.symmetry); - } - } -}; - - -MacromoleculeForm.prototype.input = function() { - return {}; -}; - - -/** It populates the form **/ -MacromoleculeForm.prototype.test = function(targetId) { - var macromoleculeForm = new MacromoleculeForm(); - macromoleculeForm.onClose.attach(function(sender){ - alert("Click on close"); - }); - var panel = macromoleculeForm.getPanel(); - panel.render(targetId); -}; - - - - - -function ModelVisualizerForm(args){ - this.id =BUI.id(); - this.width = 600; - this.height = 400; - if (args!= null){ - if (args.width != null){ - this.width = args.width; - } - if (args.height != null){ - this.height = args.height; - } - } -}; - -ModelVisualizerForm.prototype._getFirHTML = function(modelId, width, height, type, desc) { - var html = ""; - html = html + ''; - html = html + ''; - html = html + ''; - html = html + '
dammin.' + type + '
' + desc + '
'; - return html; -}; - -ModelVisualizerForm.prototype.getItems = function(modelPanel){ - _this = this; - var height = _this.height/2 - 60; - var width = _this.width/2 - 10; - - return Ext.create('Ext.container.Container', { - layout: { - type: 'vbox', // Arrange child items vertically - }, - items: [ - modelPanel, - { - xtype : 'container', - layout: { - type: 'hbox', // Arrange child items vertically - }, - items : [{ - html : this._getFirHTML("id", width, height, "fir", "Fit of the simulated scattering curve versus a smoothed experimental data (spline interpolation)"), - height :height, - width : width, - padding: 2 - }, - { - html : this._getFirHTML("id", width, height, "fit", "Fit of the simulated scattering curve versus the experimental data."), - height : height, - width : width, - padding: 2 - }] - } - - ] - }); -}; - -ModelVisualizerForm.prototype.refresh = function(models){ - var input = []; -// var colors = ["008000", "F0A804", "0000FF", "800080", "C0C0C0"]; - for (var i = 0; i < models.length; i++) { - console.log(BUI.rainbow(models.length, i).replace("#", "0x")); - input.push({ - color: BUI.rainbow(models.length, i).replace("#", "0x"), - modelId: models[i].modelId, - opacity: 0.8, - radius: 3, - title: BUI.getFileNameByPath(models[i].pdbFile), - type: "SHAPEDETERMINATIONMODEL" - - }); - } - - this.panel.removeAll(); - this.panel.add( - _this.getItems( - new PDBViewer({ - width : this.width - 10, - height : (this.height/2) - 10, - title : "" - }).draw(input) - ) - ); - - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - var splitted = data.toString().split("\n"); - var array = []; - for ( var i = 0; i < splitted.length; i++) { - var line = splitted[i].trim(); - var line_splited = line.split(/\s*[\s,]\s*/); - if (line_splited.length == 4) { - array.push([ Number(line_splited[0]), BUI.getStvArray(line_splited[1], line_splited[2]), BUI.getStvArray(line_splited[3], 0) ]); - } - } - - var id = (_this.id + "firid"); - var dygraphWidget = new StdDevDyGraph(id, { - width : (_this.width/2) - 10, - height :(_this.height/2) -110, - xlabel : 'q(nm-1)' - }); - dygraphWidget.draw(array, [ "#FF0000", "#0000FF", "#FF00FF" ], [ 's', 'I(exp)', 'I(sim)' ]); - }); - - adapter.getModelFile("FIR", models[0].modelId); - - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - var splitted = data.toString().split("\n"); - var array = []; - for ( var i = 0; i < splitted.length; i++) { - var line = splitted[i].trim(); - var line_splited = line.split(/\s*[\s,]\s*/); - if (line_splited.length == 3) { - array.push([ Number(line_splited[0]), BUI.getStvArray(line_splited[1], 0), BUI.getStvArray(line_splited[2], 0) ]); - } - } - - var id = (_this.id + "fitid"); - - var dygraphWidget = new StdDevDyGraph(id, { - width : (_this.width/2) - 10, - height : (_this.height/2) - 110, - xlabel : 'q(nm-1)' - }); - dygraphWidget.draw(array, [ "#FF0000", "#0000FF" ], [ "s", "I(exp)", "I(sim)" ]); - }); - adapter.getModelFile("FIT", models[0].modelId); -}; - -ModelVisualizerForm.prototype.getPanel = function(modelList){ - _this = this; - this.modelList = modelList; - this.panel = Ext.create('Ext.Panel', { - title: 'Results', - width: this.width, - height: this.height, - layout: { - type: 'vbox', // Arrange child items vertically -// align: 'stretch' // Each takes up full width - }, - items: [ - - ], - listeners : { - afterrender : function(grid, eOpts) { -// alert(_this.modelList) - } - } - }); - - return this.panel; - -}; - - -/** - * Example form - * - * @witdh - * @height - */ -function MolarityForm(args) { - this.id = BUI.id(); - this.width = 700; - this.height = 500; - - if (args != null) { - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; - } - } - - this.onSave = new Event(this); - this.onClose = new Event(this); -} - - -MolarityForm.prototype._getNumericWithHelp = function(type, fieldLabel, fieldName, help) { - return Ext.create('Ext.container.Container', { - margin : "10 0 0 10", - items : [ { - xtype : type, - fieldLabel : fieldLabel, - name : fieldName, - id : this.id + fieldName, - decimalPrecision : 6 - }, { - xtype : 'label', - forId : 'myFieldId', - text : help, - margin : "5 0 0 105", - cls : "inline-help" - } ] - }); -}; - - -MolarityForm.prototype._getItems = function() { - this.macromoleculeCombo = BIOSAXS_COMBOMANAGER.getComboMacromoleculeByMacromolecules(this.getMacromuleculesCandidates(this.macromolecule), { - width : 250, - labelWidth : 100, - margin : 10 - }); - - return [ { - xtype : 'container', - flex : 1, - margin : '10 0 0 10', - border : 0, - layout : 'anchor', - defaultType : 'requiredtext', - items : [ this.macromoleculeCombo, - this._getNumericWithHelp("textfield", "Ratio", "ratio", "Number in assymmetric units") - ] - } ]; -}; - -MolarityForm.prototype._persist = function() { - var _this = this; - var macromoleculeId = this.macromoleculeCombo.getValue(); - var ratio = Ext.getCmp(this.id + "ratio").getValue(); - var comments = "Not used yet"; - var dataAdapter = new BiosaxsDataAdapter(); - this.panel.setLoading("Saving"); - dataAdapter.onSuccess.attach(function(sender, args) { - _this.onSave.notify(); - }); - dataAdapter.saveStoichiometry(this.macromolecule.macromoleculeId, macromoleculeId, ratio, comments); -}; - -MolarityForm.prototype._getButtons = function() { - var _this = this; - - function onClose() { - _this.onClose.notify(); - } - - return [ { - text : 'Save', - handler : function() { - _this._persist(); - } - }, { - text : 'Cancel', - handler : function() { - onClose(); - } - } ]; -}; - -MolarityForm.prototype.getPanel = function() { - this.panel = Ext.create('Ext.form.Panel', { -// width : null, - height : this.height, - margin : 2, - border : 1, - defaultType : 'requiredtext', - items : this._getItems(), - buttons : this._getButtons() - }); - return this.panel; -}; - -/** macromolecules contains all macromolecules except this one **/ -MolarityForm.prototype.getMacromuleculesCandidates = function(macromolecule) { - var macromolecules = []; - if ( BIOSAXS.proposal.macromolecules){ - for (var i = 0; i < BIOSAXS.proposal.macromolecules.length; i++) { - var m = BIOSAXS.proposal.macromolecules[i]; - if (this.macromolecule != null){ - if (m.macromoleculeId != this.macromolecule.macromoleculeId) { - macromolecules.push(m); - } - } - } - } - return macromolecules; -}; - - -/** It populates the form **/ -MolarityForm.prototype.refresh = function(macromolecule) { - this.macromolecule = macromolecule; - -}; - - -MolarityForm.prototype.input = function() { - return {}; -}; - - -/** It populates the form **/ -MolarityForm.prototype.test = function(targetId) { - var macromoleculeForm = new MolarityForm(); - var panel = macromoleculeForm.getPanel(); - panel.render(targetId); -}; - -///** -// * -// * @witdh -// * @height -// */ -//function MacromoleculeForm(args) { -// this.id = BUI.id(); -// this.width = 700; -// this.height = 500; -// -// if (args != null) { -// if (args.width != null) { -// this.width = args.width; -// } -// if (args.height != null) { -// this.height = args.height; -// } -// } -// -// this.onClose = new Event(this); -//} -// -//MacromoleculeForm.prototype.getMacromolecule = function() { -// this.macromolecule.name = Ext.getCmp(this.panel.getItemId()).getValues().name; -// this.macromolecule.acronym = Ext.getCmp(this.panel.getItemId()).getValues().acronym; -// this.macromolecule.comments = Ext.getCmp(this.panel.getItemId()).getValues().comments; -// this.macromolecule.extintionCoefficient = Ext.getCmp(this.panel.getItemId()).getValues().extintionCoefficient; -// this.macromolecule.molecularMass = Ext.getCmp(this.panel.getItemId()).getValues().molecularMass; -// return this.macromolecule; -//}; -// -//MacromoleculeForm.prototype.setMacromolecule = function(macromolecule) { -// this.pdbStore.loadData(macromolecule.structure3VOs); -// -//}; -// -//MacromoleculeForm.prototype.getForm = function(macromolecule) { -// this.panel = Ext.createWidget('form', { -// frame : false, -// border : 0, -// padding : 15, -// width : 550, -// height : 350, -// items : [ { -// xtype : 'container', -// layout : 'hbox', -// items : [ { -// xtype : 'container', -// flex : 1, -// border : false, -// layout : 'anchor', -// defaultType : 'requiredtext', -// items : [ { -// fieldLabel : 'Name', -// name : 'name', -// anchor : '95%', -// tooltip : "Name of the macromolecule", -// value : macromolecule.name -// }, { -// fieldLabel : 'Acronym', -// name : 'acronym', -// anchor : '95%', -// value : macromolecule.acronym -// } ] -// }, { -// xtype : 'container', -// flex : 1, -// layout : 'anchor', -// defaultType : 'textfield', -// items : [ { -// xtype : 'numberfield', -// fieldLabel : 'Mol. Mass (Da)', -// name : 'molecularMass', -// value : macromolecule.molecularMass, -// decimalPrecision : 6 -// }, { -// xtype : 'numberfield', -// fieldLabel : 'Extinction coef.', -// name : 'extintionCoefficient', -// value : macromolecule.extintionCoefficient, -// decimalPrecision : 6 -// } ] -// } ] -// }, { -// xtype : 'textareafield', -// name : 'comments', -// fieldLabel : 'Comments', -// value : macromolecule.comments, -// width : this.width - 10 -// }, -// -// { -// html : BUI.getWarningHTML("The macromolecule is unsaved. Save the macromolecule to get access to other tabs"), -// margin : "150 10 10 10", -// id : this.id + "unsavedWarning", -// hidden : !(!macromolecule.macromoleculeId) -// } -// -// ] -// }); -// return this.panel; -//}; -// -//MacromoleculeForm.prototype.save = function() { -// var _this = this; -// -// var adapter = new BiosaxsDataAdapter(); -// adapter.onSuccess.attach(function(sender, proposal) { -// BIOSAXS.proposal.setItems(proposal); -// _this.panel.setLoading(false); -// -// Ext.getCmp(_this.id + "assembly").enable() -// Ext.getCmp(_this.id + "advanced").enable(); -// Ext.getCmp(_this.id + "unsavedWarning").hide(); -// }); -// -// if (this.getMacromolecule().name == "") { -// BUI.showError("Name field is mandatory"); -// return; -// } -// if (this.getMacromolecule().acronym == "") { -// BUI.showError("Acroynm field is mandatory"); -// return; -// } -// -// /** Check if acronym is unique * */ -// if (this.getMacromolecule().macromoleculeId == null) { -// if (BIOSAXS.proposal.getMacromoleculeByAcronym(this.getMacromolecule().acronym) == null) { -// this.panel.setLoading("ISPyB: Saving Macromolecule") -// adapter.saveMacromolecule(this.getMacromolecule()); -// } else { -// alert("There is already an existing macromolecule with the same acronym"); -// -// } -// } else { -// this.panel.setLoading("ISPyB: Saving Macromolecule") -// adapter.saveMacromolecule(this.getMacromolecule()); -// } -// -//}; -// -//MacromoleculeForm.prototype.getPanel = function(macromolecule) { -// var _this = this; -// this.macromolecule = macromolecule; -// return Ext.createWidget('tabpanel', { -// height : this.height, -// margin : 5, -// plain : true, -// style : { -// padding : 5 -// }, -// items : [ { -// tabConfig : { -// title : "General", -// disabled : false -// }, -// items : [ this.getForm(macromolecule) ], -// bbar : [ "->", { -// text : 'Save', -// cls : 'btn-with-border', -// style : { -// -// border : 1 -// }, -// handler : function() { -// _this.save(); -// } -// }, { -// text : 'Close', -// cls : 'btn-with-border', -// handler : function() { -// _this.onClose.notify(); -// } -// } ] -// }, { -// tabConfig : { -// id : this.id + "assembly", -// title : "Assembly", -// tooltip : 'Description of subunits present in the macromolecule', -// // hidden : (!macromolecule.macromoleculeId), -// disabled : (!macromolecule.macromoleculeId) -// }, -// items : [ this.getMolarityGrid(macromolecule) ] -// }, { -// tabConfig : { -// id : this.id + "advanced", -// title : "Advanced Modeling", -// // hidden : (!macromolecule.macromoleculeId), -// tooltip : 'Definition of the description contacts and symetries', -// disabled : (!macromolecule.macromoleculeId) -// }, -// items : [ this.getRigidBodyForm(macromolecule) ] -// } ] -// }); -//}; -// -//MacromoleculeForm.prototype.getRigidBodyForm = function(macromolecule) { -// var _this = this; -// -// // [P1, P2, P3, P4 ,P5 ,P6 ,32, P42, P52, P62] + P222 -// var symmetry = Ext.create('Ext.data.Store', { -// fields : [ 's' ], -// data : [ { -// "s" : "P1" -// }, { -// "s" : "P2" -// }, { -// "s" : "P3" -// }, { -// "s" : "P4" -// }, { -// "s" : "P5" -// }, { -// "s" : "P6" -// }, { -// "s" : "P32" -// }, { -// "s" : "P42" -// }, { -// "s" : "P52" -// }, { -// "s" : "P62" -// }, { -// "s" : "P222" -// } ] -// }); -// -// if (macromolecule.symmetry == null) { -// macromolecule.symmetry = "P1"; -// } -// var comboBox = Ext.create('Ext.form.ComboBox', { -// fieldLabel : 'Symmetry', -// store : symmetry, -// id : 'comboSym', -// queryMode : 'local', -// displayField : 's', -// valueField : 's', -// value : macromolecule.symmetry, -// margin : "10 0 0 0", -// listeners : { -// change : function(combo, newValue, oldValue, eOpts) { -// macromolecule.symmetry = newValue; -// } -// } -// }); -// -// this.rigidBodyPanel = Ext.createWidget('form', { -// frame : false, -// border : 0, -// padding : 10, -// width : 550, -// height : 400, -// items : [ { -// xtype : 'container', -// layout : 'hbox', -// items : [ { -// xtype : 'container', -// border : false, -// layout : 'hbox', -// items : [ { -// xtype : 'label', -// forId : 'myFieldId', -// text : 'Contact Desc:', -// width : 105, -// margin : '0 0 0 0' -// }, { -// xtype : 'textfield', -// hideLabel : true, -// id : "contactsDescriptionFilePath", -// margin : '0 0 0 0', -// width : 300, -// value : macromolecule.contactsDescriptionFilePath -// }, { -// text : 'Upload', -// xtype : 'button', -// margin : "0 0 0 20", -// width : 100, -// handler : function() { -// _this._openUploadDialog(macromolecule.macromoleculeId, "CONTACTS", "Upload Contact Description File"); -// } -// } ] -// } ] -// }, -// -// comboBox, { -// xtype : 'checkbox', -// margin : '10 0 0 5', -// boxLabel : "I want rigid body modeling run on this stuff", -// checked : true, -// width : 300 -// }, _this.getPDBGrid(macromolecule) ] -// }); -// return this.rigidBodyPanel; -//}; -// -//MacromoleculeForm.prototype.update = function() { -// var _this = this; -// BIOSAXS.proposal.onInitialized.attach(function() { -// if (BIOSAXS.proposal != null) { -// var macromolecules = BIOSAXS.proposal.macromolecules; -// for (var i = 0; i < macromolecules.length; i++) { -// if (macromolecules[i].macromoleculeId == _this.macromolecule.macromoleculeId) { -// _this.macromolecule = macromolecules[i]; -// _this.setMacromolecule(_this.macromolecule); -// _this.molarityStore.loadData(_this.parseMolarityData(_this.macromolecule)); -// _this.pdbGrid.setLoading(false); -// Ext.getCmp("contactsDescriptionFilePath").setValue(_this.macromolecule.contactsDescriptionFilePath) -// _this.molarityGrid.setLoading(false); -// -// } -// } -// } -// }); -// this.molarityGrid.setLoading("Updating"); -// this.pdbGrid.setLoading("Updating"); -// BIOSAXS.proposal.init(); -//}; -// -///******************************************************************************* -// * MOLARITY GRID -// ******************************************************************************/ -// -//MacromoleculeForm.prototype.parseMolarityData = function(macromolecule) { -// var data = []; -// if (macromolecule.stoichiometry != null) { -// for (var i = 0; i < macromolecule.stoichiometry.length; i++) { -// data.push({ -// ratio : macromolecule.stoichiometry[i].ratio, -// acronym : macromolecule.stoichiometry[i].macromolecule3VO.acronym, -// comments : macromolecule.stoichiometry[i].macromolecule3VO.comments, -// stoichiometryId : macromolecule.stoichiometry[i].stoichiometryId, -// name : macromolecule.stoichiometry[i].macromolecule3VO.name -// }); -// } -// } -// return data; -//}; -// -//MacromoleculeForm.prototype.getMolarityGrid = function(macromolecule) { -// var _this = this; -// -// this.molarityStore = Ext.create('Ext.data.Store', { -// fields : [ 'acronym', 'ratio', 'comments', 'stoichiometryId', 'name' ], -// data : this.parseMolarityData(macromolecule), -// sorters : { -// property : 'ratio', -// direction : 'DESC' -// } -// }); -// -// this.molarityGrid = Ext.create('Ext.grid.Panel', { -// store : this.molarityStore, -// height : 350, -// padding : 5, -// columns : [ -// -// { -// text : 'Subunit', -// columns : [ { -// text : "Acronym", -// width : 100, -// hidden : false, -// dataIndex : 'acronym', -// sortable : true -// }, { -// text : "Name", -// width : 100, -// hidden : false, -// dataIndex : 'name', -// sortable : true -// }, { -// text : "Comments", -// width : 100, -// dataIndex : 'comments', -// sortable : true -// } ] -// }, { -// text : "Number
in assymmetric units", -// width : 150, -// dataIndex : 'ratio', -// tooltip : 'Number of times this subunit is present in the macromolecule', -// sortable : true -// }, { -// id : this.id + 'MOLARITY_REMOVE', -// flex : 0.1, -// sortable : false, -// renderer : function(value, metaData, record, rowIndex, colIndex, store) { -// return BUI.getRedButton('REMOVE'); -// } -// } ], -// listeners : { -// cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { -// if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'MOLARITY_REMOVE') { -// var dataAdapter = new BiosaxsDataAdapter(); -// dataAdapter.onSuccess.attach(function() { -// _this.molarityGrid.setLoading(false); -// _this.update(); -// }); -// dataAdapter.removeStoichiometry(record.data.stoichiometryId); -// _this.molarityGrid.setLoading("Removing Structure"); -// } -// } -// }, -// buttons : [ { -// text : 'Add molarity', -// handler : function() { -// -// function onClose() { -// w.destroy(); -// _this.update(); -// } -// var w = Ext.create('Ext.window.Window', { -// title : 'Molarity', -// height : 300, -// width : 500, -// modal : true, -// buttons : [ { -// text : 'Save', -// handler : function() { -// var macromoleculeId = (_this.macromoleculeCombo.getValue()); -// var ratio = Ext.getCmp(_this.id + "ratio").getValue(); -// var comments = ""; -// var dataAdapter = new BiosaxsDataAdapter(); -// dataAdapter.onSuccess.attach(function(sender, args) { -// _this.update(); -// w.destroy(); -// }); -// dataAdapter.saveStoichiometry(_this.macromolecule.macromoleculeId, macromoleculeId, ratio, comments); -// } -// }, { -// text : 'Cancel', -// handler : function() { -// onClose(); -// } -// } ], -// items : [ _this.getMolarityForm(macromolecule) ], -// listeners : { -// onEsc : function() { -// onClose(); -// }, -// close : function() { -// onClose(); -// } -// } -// }).show(); -// } -// } ] -// }); -// return this.molarityGrid; -//}; -// -///******************************************************************************* -// * PDB GRID -// ******************************************************************************/ -// -//MacromoleculeForm.prototype._openUploadDialog = function(macromoleculeId, type, title) { -// var _this = this; -// function onClose() { -// w.destroy(); -// _this.update(); -// } -// -// var w = Ext.create('Ext.window.Window', { -// title : title, -// height : 200, -// width : 400, -// modal : true, -// buttons : [ { -// text : 'Close', -// handler : function() { -// onClose(); -// } -// } ], -// layout : 'fit', -// items : { -// html : "" -// }, -// listeners : { -// onEsc : function() { -// onClose(); -// }, -// close : function() { -// onClose(); -// } -// } -// }).show(); -//}; -// -//MacromoleculeForm.prototype._getPlugins = function() { -// var _this = this; -// var plugins = []; -// // if (this.updateRowEnabled) { -// plugins.push(Ext.create('Ext.grid.plugin.RowEditing', { -// clicksToEdit : 1, -// listeners : { -// validateedit : function(grid, e) { -// /** Comments are always updatable* */ -// e.record.raw.symmetry = e.newValues.symmetry; -// e.record.raw.multiplicity = e.newValues.multiplicity; -// -// var adapter = new BiosaxsDataAdapter(); -// adapter.onSuccess.attach(function(sender, measurement) { -// // _this.grid.setLoading(false); -// }); -// adapter.onError.attach(function() { -// alert("Error"); -// // _this.grid.setLoading(false); -// }); -// -// // _this.grid.setLoading(); -// adapter.saveStructure(e.record.raw); -// } -// } -// })); -// // } -// return plugins; -//}; -// -//MacromoleculeForm.prototype.getPDBGrid = function(macromolecule) { -// var _this = this; -// -// var data = macromolecule.structure3VOs; -// -// // /** Getting PDB from subunits **/ -// // if (macromolecule != null){ -// // if (macromolecule.stoichiometry != null){ -// // for (var i =0; i < macromolecule.stoichiometry.length; i++){ -// // var stoichiometry = macromolecule.stoichiometry[i]; -// // if (stoichiometry.macromolecule3VO != null){ -// // if (stoichiometry.macromolecule3VO.structure3VOs != null){ -// // for (var j = 0; j < stoichiometry.macromolecule3VO.structure3VOs.length; -// // j++) { -// // var structure = stoichiometry.macromolecule3VO.structure3VOs[j]; -// // structure["isSubunit"] = stoichiometry.macromolecule3VO.acronym; -// // data.push(structure) -// // } -// // } -// // } -// // } -// // } -// // } -// -// this.pdbStore = Ext.create('Ext.data.Store', { -// fields : [ 'filePath', 'structureId', 'structureType', 'symmetry', 'structureId', 'name', 'multiplicity' ], -// data : macromolecule.structure3VOs, -// groupField : 'structureType', -// sorters : { -// property : 'structureId', -// direction : 'DESC' -// } -// }); -// -// var groupingFeature = Ext.create('Ext.grid.feature.Grouping', { -// groupHeaderTpl : Ext.create('Ext.XTemplate', -// "
{name:this.formatName}
", { -// formatName : function(name) { -// return name; -// } -// }), -// hideGroupedHeader : true, -// startCollapsed : false -// }); -// -// this.pdbGrid = Ext.create('Ext.grid.Panel', { -// margin : "15 0 0 5", -// height : 250, -// store : this.pdbStore, -// plugins : _this._getPlugins(), -// buttons : [ { -// // text : 'Add PDB file', -// text : 'Add Modeling Option', -// handler : function() { -// _this._openUploadDialog(macromolecule.macromoleculeId, "PDB", 'Upload PDB File'); -// } -// } -// -// ], -// columns : [ -// { -// text : "structureId", -// flex : 0.2, -// hidden : true, -// dataIndex : 'structureId', -// sortable : true -// }, -// { -// text : "File", -// flex : 0.5, -// dataIndex : 'filePath', -// sortable : true, -// hidden : true -// }, -// { -// text : "PDB", -// flex : 0.4, -// dataIndex : 'name', -// sortable : true -// }, -// { -// text : "Symmetry", -// flex : 0.4, -// dataIndex : 'symmetry', -// sortable : true, -// editor : { -// xtype : 'combobox', -// typeAhead : true, -// triggerAction : 'all', -// selectOnTab : true, -// store : [ [ "P1", "P1" ], [ "P2", "P2" ], [ "P3", "P3" ], [ "P4", "P4" ], [ "P5", "P5" ], [ "P6", "P6" ], [ "P32", "P32" ], [ "P42", "P42" ], -// [ "P52", "P52" ], [ "P62", "P62" ], [ "P222", "P222" ] ], -// } -// }, { -// text : "Multiplicity", -// flex : 0.4, -// dataIndex : 'multiplicity', -// sortable : true, -// editor : { -// xtype : 'textfield' -// } -// -// }, { -// text : "Subunit", -// flex : 0.2, -// dataIndex : 'isSubunit', -// sortable : true, -// hidden : true -// }, { -// text : "Type", -// flex : 0.2, -// dataIndex : 'structureType', -// sortable : true, -// hidden : true -// }, -// -// { -// id : this.id + 'REMOVE', -// flex : 0.2, -// hidden : true, -// sortable : false, -// renderer : function(value, metaData, record, rowIndex, colIndex, store) { -// return BUI.getRedButton('REMOVE'); -// } -// }, ], -// -// listeners : { -// itemdblclick : function(dataview, record, item, e) { -// _this._editExperiment(record.raw.experimentId); -// }, -// cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { -// -// if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'REMOVE') { -// var dataAdapter = new BiosaxsDataAdapter(); -// dataAdapter.onSuccess.attach(function() { -// _this.pdbGrid.setLoading(false); -// _this.update(); -// }); -// dataAdapter.removeStructure(record.data.structureId); -// _this.pdbGrid.setLoading("Removing PDB file"); -// } -// -// } -// }, -// viewConfig : { -// getRowClass : function(record, rowIdx, params, store) { -// if (record.raw.isSubunit != null) { -// return "blue-row"; -// } -// } -// } -// }); -// -// return this.pdbGrid; -//}; -// -//MacromoleculeForm.prototype.getMolarityForm = function(macromolecule) { -// var _this = this; -// var data = []; -// for (var i = 0; i < BIOSAXS.proposal.macromolecules.length; i++) { -// var m = BIOSAXS.proposal.macromolecules[i]; -// if (m.macromoleculeId != macromolecule.macromoleculeId) { -// data.push(m); -// } -// -// } -// this.macromoleculeCombo = BIOSAXS_COMBOMANAGER.getComboMacromoleculeByMacromolecules(data, { -// width : 250, -// labelWidth : 100, -// margin : 10 -// }); -// -// return Ext.createWidget('form', { -// -// frame : false, -// border : 0, -// // padding : 15, -// width : 550, -// height : 350, -// items : [ { -// xtype : 'container', -// flex : 1, -// border : false, -// layout : 'anchor', -// defaultType : 'requiredtext', -// items : [ this.macromoleculeCombo, { -// xtype : 'numberfield', -// name : 'Ratio', -// id : _this.id + "ratio", -// fieldLabel : 'Number in assymmetric units', -// value : 1, -// decimalPrecision : 6, -// margin : 10 -// }, { -// xtype : 'textareafield', -// name : 'comments', -// fieldLabel : 'Comments', -// margin : 10, -// width : 400, -// value : "" -// -// } ] -// } ] -// }); -// -//}; -// -///******************************************************************************* -// * JAVASCRIPT DOC -// ******************************************************************************/ -//MacromoleculeForm.prototype.input = function() { -// return { -// macromolecule : DATADOC.getMacromolecule_10() -// }; -//}; -// -//MacromoleculeForm.prototype.test = function(targetId) { -// var macromoleculeForm = new MacromoleculeForm(); -// var panel = macromoleculeForm.getPanel(macromoleculeForm.input().macromolecule); -// panel.render(targetId); -//}; - -function ResultSummaryForm() { - this.radiationDamageThreshold = BUI.getRadiationDamageThreshold(); - this.qualityThreshold = BUI.getQualityThreshold(); - - /** Data clusters with bufers **/ - this.clusterByBuffers = false; - - /** Visualization are groupeb by concenttrations. Ex: 4.5mg/ml and 4.7mg/ml will be clusterized together **/ - this.collapseConcentrations = true; - - this.summaryHeight = 350; - this.id = BUI.id(); - - var _this = this; - - this.qualityControlResultsWidget = new QualityControlResultsWidget({ - qualityThreshold : this.radiationDamageThreshold, - radiationDamageThreshold : this.qualityThreshold - - }); - this.qualityControlResultsWidget.onQualityChanged.attach(function(sender, value) { - _this.qualityThreshold = value; - _this.thresholdsChanged(); - }); - - this.qualityControlResultsWidget.onRadiationDatamageChanged.attach(function(sender, value) { - _this.radiationDamageThreshold = value; - _this.thresholdsChanged(); - - }); - this.concentrationHTMLTableWidget = new ConcentrationHTMLTableWidget({ - height : 250, - showBufferColumns : this.clusterByBuffers - }); - - this.plot = new BoxWhiskerGraph({ - targetId : _this.id + '_boxPlot', - height : 350, - width : 450, - maxBoxWidth : 25 - }); - - this.rangePlot = new RangeWhiskerGraph({ - targetId : _this.id + '_rangePlot', - height : 350, - width : 450, - maxBoxWidth : 25 - }); -} - -ResultSummaryForm.prototype.thresholdsChanged = function() { - var parsedData = this.prepareData(this.rawData); - - var filtered = JSON.parse(JSON.stringify(parsedData)); - filtered.concentration.concentrations = []; - for ( var conc in parsedData.concentration.concentrations) { - if (parsedData.concentration.concentrations[conc].calculation.rgGnom.validNumber > 0) { - filtered.concentration.concentrations.push(parsedData.concentration.concentrations[conc]); - } - } - - this.plotWhisker(filtered); - this.plotRange(filtered); - - this.concentrationHTMLTableWidget.refresh(parsedData); -}; - -/** Given a frame object (object returned by analyzeFrames()) and depending of the threshold indicates if a datacollection has radiation damage **/ -ResultSummaryForm.prototype.hasRadiationDamage = function(frameObject) { - var bb = frameObject.bufferBeforeFramesMerged / frameObject.framesCount; - var ba = frameObject.bufferAfterFramesMerged / frameObject.framesCount; - var mol = frameObject.framesMerge / frameObject.framesCount; - return !((bb >= this.radiationDamageThreshold) && (ba >= this.radiationDamageThreshold) && (mol >= this.radiationDamageThreshold)); -}; - -/** Return (frameObject) an object with the information about the frames for a data collection**/ -ResultSummaryForm.prototype.analyzeFrames = function(dataCollectionRow) { - return { - bufferAfterFramesMerged : dataCollectionRow.bufferAfterFramesMerged, - bufferBeforeFramesMerged : dataCollectionRow.bufferBeforeFramesMerged, - framesCount : dataCollectionRow.framesCount, - framesMerge : dataCollectionRow.framesMerge - }; -}; - -ResultSummaryForm.prototype.detectDataCollectionWarnings = function(dataCollectionRow) { - var frameObject = this.analyzeFrames(dataCollectionRow); - var warnings = { - count : 0, - type : [] - }; - - if (this.hasRadiationDamage(frameObject)) { - warnings.count = warnings.count + 1; - warnings.type.push("RADIATION DAMAGE"); - } - - if (Number(dataCollectionRow.quality) < this.qualityThreshold) { - warnings.count = 1;//warnings.count + 1; - warnings.type.push("Quality <" + this.qualityThreshold); - } - return warnings; -}; - -/** Return array composed by {concentration} objects **/ -ResultSummaryForm.prototype.getConcentrations = function(data) { - var concentrationsId = {}; - - for ( var i = 0; i < data.length; i++) { - var warning = this.detectDataCollectionWarnings(data[i]); - var id = data[i].conc;// + "_" + data[i].bufferId; - if (this.clusterByBuffers) { - id = data[i].conc + "_" + data[i].bufferId; - } - - if (concentrationsId[id] == null) { - concentrationsId[id] = { - id : id, - concentration : Number(data[i].conc).toFixed(2), - bufferId : data[i].bufferId, - bufferAcronym : data[i].bufferAcronym, - rgGuinier : [], - i0Guinier : [], - rgGnom : [], - dMax : [], - quality : [], - frames : [], - frames_warning : warning.count - }; - } else { - concentrationsId[id].frames_warning = concentrationsId[id].frames_warning + warning.count; - } - - concentrationsId[id].frames.push(data[i]); - - if (warning.count == 0) { - concentrationsId[id].rgGuinier.push(data[i].rgGuinier); - concentrationsId[id].i0Guinier.push(data[i].I0); - concentrationsId[id].quality.push(data[i].quality); - concentrationsId[id].rgGnom.push(data[i].rgGnom); - concentrationsId[id].dMax.push(data[i].dmax); - } - - } - var concentrations = []; - for ( var item in concentrationsId) { - if (concentrationsId.hasOwnProperty(item)) { - concentrations.push({ - concentration : concentrationsId[item].concentration, - id : item, - bufferId : Number(concentrationsId[item].bufferId).toFixed(2), - bufferAcronym : concentrationsId[item].bufferAcronym, - rgGuinier : concentrationsId[item].rgGuinier, - /** Frames **/ - frames : concentrationsId[item].frames, - frames_warning : concentrationsId[item].frames_warning, - /** Calculation **/ - calculation : { - rgGuinier : BUI.getStandardDeviation(concentrationsId[item].rgGuinier), - i0Guinier : BUI.getStandardDeviation(concentrationsId[item].i0Guinier), - quality : BUI.getStandardDeviation(concentrationsId[item].quality), - rgGnom : BUI.getStandardDeviation(concentrationsId[item].rgGnom), - dMax : BUI.getStandardDeviation(concentrationsId[item].dMax) - - } - }); - } - } - - return { - concentrations : concentrations - }; -}; - -ResultSummaryForm.prototype.prepareData = function(data) { - /** Return array composed by {acronym, bufferId} objects **/ - function getBuffers(data) { - var buffersId = {}; - for ( var i = 0; i < data.length; i++) { - buffersId[data[i].bufferId] = data[i].acronym; - } - var buffers = []; - for ( var id in buffersId) { - if (buffersId.hasOwnProperty(id)) { - buffers.push({ - acronym : buffersId[id], - bufferId : id - }); - } - } - return buffers; - } - - /** Get a string with all the concentrations **/ - function getConcentrationString(parseConcentrations) { - var concentrations = []; - for ( var i = 0; i < parseConcentrations.concentrations.length; i++) { - concentrations.push(parseConcentrations.concentrations[i].concentration + " mg/ml "); - } - return concentrations.toString(); - } - - var parseConcentrations = this.getConcentrations(data); - - return { - dataCollectionCount : data.length, - buffers : getBuffers(data), - concentration : parseConcentrations, - concentrationLabel : getConcentrationString(parseConcentrations) - }; -}; - -ResultSummaryForm.prototype.getDataForWhisker = function(data) { - var clusters = []; - - var concentrations = {}; - var i = 0; - var conc = 0; - if (this.collapseConcentrations) { - for (i = 0; i < data.concentration.concentrations.length; i++) { - conc = data.concentration.concentrations[i]; - var concentration = Number(conc.concentration).toFixed(0); - if (concentrations[concentration] == null) { - concentrations[concentration] = {}; - concentrations[concentration].concentration = concentration; - concentrations[concentration].calculation = {}; - concentrations[concentration].calculation.rgGuinier = {}; - concentrations[concentration].calculation.rgGuinier.values = []; - concentrations[concentration].calculation.rgGuinier.values = conc.calculation.rgGuinier.values; - concentrations[concentration].calculation.rgGnom = {}; - concentrations[concentration].calculation.rgGnom.values = []; - concentrations[concentration].calculation.rgGnom.values = conc.calculation.rgGnom.values; - } else { - concentrations[concentration].calculation.rgGuinier.values = concentrations[concentration].calculation.rgGuinier.values - .concat(conc.calculation.rgGuinier.values); - concentrations[concentration].calculation.rgGnom.values = concentrations[concentration].calculation.rgGnom.values - .concat(conc.calculation.rgGnom.values); - } - } - - /** From object to array **/ - var array = []; - for ( var key in concentrations) { - if (concentrations.hasOwnProperty(key)) { - array.push(concentrations[key]); - } - } - data.concentration.concentrations = array; - } - - for (i = 0; i < data.concentration.concentrations.length; i++) { - conc = data.concentration.concentrations[i]; - clusters.push({ - name : conc.concentration + "mg/ml", - concentration : Number(conc.concentration), - x : Number(conc.concentration), - classes : [] - }); - clusters[clusters.length - 1].classes.push({ - name : "Guinier", - color : '#9A2EFE', - values : conc.calculation.rgGuinier.values - - }); - clusters[clusters.length - 1].classes.push({ - name : "P(r)", - color : '#2E64FE', - values : conc.calculation.rgGnom.values - - }); - } - return { - clusters : clusters.sort(function(a, b) { - return a.concentration - b.concentration; - }) - }; -}; - -ResultSummaryForm.prototype.getDataForWhiskerQuality = function(data) { - var clusters = []; - - for ( var i = 0; i < data.concentration.concentrations.length; i++) { - var conc = data.concentration.concentrations[i]; - clusters.push({ - name : conc.concentration + "mg/ml", - classes : [] - }); - clusters[clusters.length - 1].classes.push({ - name : "Quality", - values : conc.calculation.quality.values - - }); - } - - return { - clusters : clusters - }; -}; - -ResultSummaryForm.prototype.plotQualityWhisker = function(parsedData) { - this.qualityPlot.refresh(this.getDataForWhiskerQuality(parsedData)); -}; - -ResultSummaryForm.prototype.plotWhisker = function(parsedData) { - this.plot.refresh(this.getDataForWhisker(parsedData)); -}; - -ResultSummaryForm.prototype.plotRange = function(parsedData) { - this.rangePlot.refresh(this.getDataForWhisker(parsedData)); -}; - -ResultSummaryForm.prototype.getPanel = function(data) { - var _this = this; - _this.rawData = data; - var parsedData = this.prepareData(data); - - this.panel = Ext - .createWidget( - 'form', - { - bodyPadding : 20, - frame : false, - border : 0, - width : this.width, - height : this.summaryHeight + 1000, - items : [ { - xtype : 'container', - layout : 'hbox', - items : [ { - xtype : 'container', - flex : 1, - border : false, - layout : 'anchor', - defaultType : 'textfield', - items : [ - _this.qualityControlResultsWidget.getPanel(), - { - xtype : 'fieldset', - width : 950, - margin : "20, 0 0 0", - height : this.summaryHeight + 500, - items : [ - { - html : "
Concentration Analysis
", - border : 0, - width : 900 - - }, - { - html : this.concentrationHTMLTableWidget.getPanel(parsedData), - border : 0, - width : 900, - margin : "10, 0 0 10" - - }, - { - xtype : 'container', - layout : 'vbox', - border : 5, - items : [ - { - html : "
Rg based on Guinier and Gnom
", - border : 8, - width : 900, - margin : "20 0 0 10" - - }, { - xtype : 'container', - layout : 'hbox', - items : [ { - xtype : 'container', - layout : 'vbox', - items : [ { - html : "
", - border : 0, - width : this.plot.width, - padding : "10 0 0 20", - listeners : { - afterrender : function() { - _this.plotWhisker(parsedData); - - } - } - }, { - html : "
Concentration (mg/ml)
", - width : 450, - border : 0, - margin : "-50 0 0 0" - - } ] - }, { - xtype : 'container', - layout : 'vbox', - items : [ { - html : "
", - border : 0, - width : this.rangePlot.width, - padding : "10 0 0 10", - listeners : { - afterrender : function() { - _this.plotRange(parsedData); - } - } - }, { - html : "
Concentration (mg/ml)
", - width : 450, - border : 0, - margin : "-50 0 0 0" - - } ] - } ] - } ] - } ] - } ] - } - - ] - } ] - }); - return this.panel; - -}; - -ResultSummaryForm.prototype.input = function() { - return { - data : DATADOC.getData_3367() - }; -}; - -ResultSummaryForm.prototype.test = function(targetId) { - var resultSummaryForm = new ResultSummaryForm(); - var panel = resultSummaryForm.getPanel(resultSummaryForm.input().data); - panel.render(targetId); - -}; - -/** - * Example form - * - * @witdh - * @height - */ -function RigibBodyModelingForm(args) { - this.id = BUI.id(); - this.width = 700; - this.height = 500; - - if (args != null) { - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; - } - } - - var _this = this; - this.rigidBodyGrid = new AprioriRigidBodyGrid(); - - this.rigidBodyGrid.onUploadFile.attach(function(sender, type, title){ - _this._openUploadDialog(_this.macromolecule.macromoleculeId, type, title); - }); - - this.rigidBodyGrid.onRemove.attach(function(sender, type, title){ - _this._update(); - }); - - this.onSave = new Event(this); - -} - -RigibBodyModelingForm.prototype._getItems = function() { - var _this = this; - - - return [ { - xtype : 'label', - forId : 'myFieldId', - text : 'Information for model fit, mixture analysis and rigid body modeling', - margin : '15 0 20 10', - cls : "inline-help" - }, - this.rigidBodyGrid.getPanel(), - { - xtype : 'label', - forId : 'myFieldId', - text : 'Distance restraints may be imposed on the model using contacts conditions file (OPTIONAL)', - margin : '25 0 5 10', - cls : "inline-help" - }, - { - xtype : 'container', - layout : 'hbox', - items : [ { - xtype : 'container', - border : false, - layout : 'hbox', - items : [ { - xtype : 'label', - forId : 'myFieldId', - text : 'Contact Description File: (Optional)', - width : 150, - margin : '10 0 0 10' - }, { - id : this.id + "contactsDescriptionFilePath", - xtype : 'textfield', - hideLabel : true, - margin : '10 0 0 0', - width : 200, - disabled: true - }, { - text : 'Upload', - xtype : 'button', - margin : "10 0 0 10", - width : 80, - handler : function() { - - _this._openUploadDialog(_this.macromolecule.macromoleculeId, "CONTACTS", "Upload Contact Description File"); - } - }, { - text : 'Remove', - id : _this.id + "_remove", - xtype : 'button', - margin : "10 0 0 10", - width : 80, - handler : function() { - _this.macromolecule.contactsDescriptionFilePath = null; - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, proposal) { - /** Updating the proposal global object **/ - BIOSAXS.proposal.setItems(proposal); - _this.panel.setLoading(false); - - var saved = BIOSAXS.proposal.getMacromoleculeByAcronym(_this.macromolecule.acronym); - /** Refreshing to check that everything is ok **/ - _this.refresh(saved); - _this.onSave.notify(saved); - }); - - _this.panel.setLoading("Saving Macromolecule") - adapter.saveMacromolecule(_this.macromolecule); - } - } ] - } ] - }, { - xtype : 'panel', - html : "Go to SASREF manual for further information", - margin : "10 0 0 160", - border : 0 - - }, - { - xtype : 'checkbox', - margin : '10 0 0 5', - boxLabel : "I want rigid body modeling run on this stuff", - checked : true, - width : 300 - } ] - -}; - -/** Because update is a jsp page we don't know if the user has uploaded a file or not then we need to refresh **/ -RigibBodyModelingForm.prototype._update = function(macromoleculeId, type, title) { - var _this = this; - BIOSAXS.proposal.onInitialized.attach(function() { - if (BIOSAXS.proposal != null) { - _this.refresh(BIOSAXS.proposal.getMacromoleculeById(_this.macromolecule.macromoleculeId)); - _this.panel.setLoading(false); - } - }); - this.panel.setLoading(); - BIOSAXS.proposal.init(); -}; - -RigibBodyModelingForm.prototype._openUploadDialog = function(macromoleculeId, type, title) { - var _this = this; - function onClose() { - w.destroy(); - _this._update(); - - } - - var w = Ext.create('Ext.window.Window', { - title : title, - height : 200, - width : 400, - modal : true, - buttons : [ { - text : 'Close', - handler : function() { - onClose(); - } - } ], - layout : 'fit', - items : { - html : "" - }, - listeners : { - onEsc : function() { - onClose(); - }, - close : function() { - onClose(); - } - } - }).show(); -}; - -RigibBodyModelingForm.prototype._getButtons = function() { - return []; -}; - -RigibBodyModelingForm.prototype.getPanel = function() { - var _this = this; - this.panel = Ext.create('Ext.form.Panel', { - width : this.width, - height : this.height, - margin : 10, - border : 1, - defaultType : 'textfield', - items : this._getItems(), - buttons : this._getButtons(), - listeners : { - afterrender : function(){ - _this._populate(); - - } - } - }); - return this.panel; -}; - -/** Populates could be call when the DOM is not filled yet **/ -RigibBodyModelingForm.prototype._populate = function() { - if (this.macromolecule != null){ - if (Ext.getCmp(this.id + "contactsDescriptionFilePath") != null){ - if (this.macromolecule.contactsDescriptionFilePath != null){ - Ext.getCmp(this.id + "contactsDescriptionFilePath").setValue(this.macromolecule.contactsDescriptionFilePath); - Ext.getCmp(this.id + "_remove").enable(); - } - else{ - Ext.getCmp(this.id + "_remove").disable(); - Ext.getCmp(this.id + "contactsDescriptionFilePath").setValue(""); - - } - } - } -}; - -/** It populates the form * */ -RigibBodyModelingForm.prototype.refresh = function(macromolecule) { - this.macromolecule = macromolecule; - this.rigidBodyGrid.refresh(macromolecule); - this._populate(); -}; - -RigibBodyModelingForm.prototype.input = function() { - return {}; -}; - - -/** It populates the form **/ -RigibBodyModelingForm.prototype.test = function(targetId) { - var macromoleculeForm = new RigibBodyModelingForm(); - var panel = macromoleculeForm.getPanel(); - panel.render(targetId); -}; - - -/** - * Same form as MX part - * - * @creationMode if true a create button appears instead of save - * @showTitle true or false - */ -function ShipmentForm(args) { - this.id = BUI.id(); - - this.creationMode = false; - this.showTitle = true; - if (args != null) { - if (args.creationMode != null) { - this.creationMode = args.creationMode; - } - if (args.showTitle != null) { - this.showTitle = args.showTitle; - } - } - - this.onSaved = new Event(this); -} - -ShipmentForm.prototype.fillStores = function() { - this.panel.setLoading("Loading Labcontacts from database"); - this.labContactForSendingStore.loadData(BIOSAXS.proposal.getLabcontacts(), false); - this.labContactForReturnStore.loadData(BIOSAXS.proposal.getLabcontacts(), false); - this.panel.setLoading(false); - if (this.shipment != null) { - this.setShipment(this.shipment); - } -}; - -ShipmentForm.prototype.draw = function(targetId) { - this.getPanel().render(targetId); -}; - -ShipmentForm.prototype.setShipment = function(shipment) { - this.shipment = shipment; - var _this = this; - Ext.getCmp(_this.id + "shippingName").setValue(shipment.json.shippingName); - Ext.getCmp(_this.id + "shippingStatus").setValue(shipment.json.shippingStatus); - Ext.getCmp(_this.id + "comments").setValue(shipment.json.comments); - if (shipment.json.sendingLabContactVO != null) { - this.labContactsSendingCombo.setValue(shipment.json.sendingLabContactVO.labContactId); - } - if (shipment.json.returnLabContactVO != null) { - this.labContactsReturnCombo.setValue(shipment.json.returnLabContactVO.labContactId); - } - -}; - -ShipmentForm.prototype._saveShipment = function() { - var _this = this; - var shippingId = null; - if (this.shipment != null) { - shippingId = this.shipment.json.shippingId; - } - var json = { - shippingId : shippingId, - name : Ext.getCmp(_this.id + "shippingName").getValue(), - status : Ext.getCmp(_this.id + "shippingStatus").getValue(), - sendingLabContactId : Ext.getCmp(_this.id + "shipmentform_sendingLabContactId").getValue(), - returnLabContactId : Ext.getCmp(_this.id + "returnLabContactId").getValue(), - returnCourier : Ext.getCmp(_this.id + "returnCourier").getValue(), - courierAccount : Ext.getCmp(_this.id + "courierAccount").getValue(), - BillingReference : Ext.getCmp(_this.id + "BillingReference").getValue(), - dewarAvgCustomsValue : Ext.getCmp(_this.id + "dewarAvgCustomsValue").getValue(), - dewarAvgTransportValue : Ext.getCmp(_this.id + "dewarAvgTransportValue").getValue(), - comments : Ext.getCmp(_this.id + "comments").getValue() - }; - - var dataAdapter = new BiosaxsDataAdapter(); - dataAdapter.onSuccess.attach(function(sender, shipment) { - window.location = BUI.getShippingURL(shipment.shippingId); - }); - - dataAdapter.onError.attach(function(sender, error) { - _this.onError.notify(error); - }); - - /** Cheking params **/ - if (json.name == "") { - BUI.showError("Name field is mandatory"); - return; - } - - if (json.sendingLabContactId == null) { - BUI.showError("Lab contact for sending field is mandatory"); - return; - } - - if (json.returnLabContactId == null) { - BUI.showError("Lab contact for return field is mandatory"); - return; - } - - dataAdapter.createShipment(json.shippingId, json.name, json.status, json.comments, json.sendingLabContactId, json.returnLabContactId, - json.returnCourier, json.courierAccount, json.BillingReference, json.dewarAvgCustomsValue, json.dewarAvgTransportValue); - -}; - -ShipmentForm.prototype.getPanel = function(shipment) { - var _this = this; - this.shipment = shipment; - var required = '*'; - var buttons = []; - - if (_this.creationMode) { - buttons.push({ - text : 'Create', - scope : this, - handler : function() { - _this._saveShipment(); - } - }); - } else { - buttons.push({ - text : 'Save', - scope : this, - handler : function() { - _this._saveShipment(); - } - }); - - } - - this.labContactForSendingStore = Ext.create('Ext.data.Store', { - fields : [ 'cardName', 'labContactId' ] - }); - - this.labContactForReturnStore = Ext.create('Ext.data.Store', { - fields : [ 'cardName', 'labContactId' ] - }); - - // Create the combo box, attached to the states data store - this.labContactsSendingCombo = Ext.create('Ext.form.ComboBox', { - id : _this.id + "shipmentform_sendingLabContactId", - fieldLabel : 'Lab contact for sending', - afterLabelTextTpl : required, - store : this.labContactForSendingStore, - queryMode : 'local', - labelWidth : 200, - displayField : 'cardName', - valueField : 'labContactId' - }); - - this.labContactsReturnCombo = Ext.create('Ext.form.ComboBox', { - id : _this.id + "returnLabContactId", - fieldLabel : 'If No, Lab-Contact for Return', - afterLabelTextTpl : required, - store : this.labContactForReturnStore, - queryMode : 'local', - labelWidth : 200, - displayField : 'cardName', - valueField : 'labContactId', - listeners : { - change : function(x, newValue) { - for ( var i = 0; i < x.getStore().data.items.length; i++) { - if (x.getStore().data.items[i].raw.labContactId == newValue) { - Ext.getCmp(_this.id + "returnCourier").setValue(x.getStore().data.items[i].raw.defaultCourrierCompany); - Ext.getCmp(_this.id + "courierAccount").setValue(x.getStore().data.items[i].raw.courierAccount); - Ext.getCmp(_this.id + "BillingReference").setValue(x.getStore().data.items[i].raw.billingReference); - Ext.getCmp(_this.id + "dewarAvgCustomsValue").setValue(x.getStore().data.items[i].raw.dewarAvgCustomsValue); - Ext.getCmp(_this.id + "dewarAvgTransportValue").setValue(x.getStore().data.items[i].raw.dewarAvgTransportValue); - } - } - } - } - }); - - if (this.panel == null) { - this.panel = Ext.create('Ext.form.Panel', { - bodyPadding : 5, - width : 600, - border : 1, - items : [ { - xtype : 'fieldset', - title : 'Details', - collapsible : false, - defaultType : 'textfield', - layout : 'anchor', - defaults : { - anchor : '100%' - }, - items : [ { - xtype : 'requiredtext', - fieldLabel : 'Shipment Label', - allowBlank : false, - name : 'shippingName', - id : _this.id + 'shippingName', - value : '', - anchor : '50%' - }, { - - xtype : 'textareafield', - name : 'comments', - id : _this.id + 'comments', - fieldLabel : 'Comments', - value : '' - }, { - fieldLabel : 'Status', - readOnly : true, - id : _this.id + 'shippingStatus', - value : 'Opened', - anchor : '50%' - } ] - }, { - xtype : 'fieldset', - title : 'Lab-Contacts', - collapsible : false, - defaultType : 'textfield', - layout : 'anchor', - defaults : { - anchor : '100%' - }, - items : [ this.labContactsSendingCombo, this.labContactsReturnCombo ] - }, { - border : 0, - html : BUI.getWarningHTML("These informations are relevant for all shipments") - }, { - xtype : 'fieldset', - title : 'Courier accounts details for return', - collapsible : false, - layout : 'anchor', - defaults : { - anchor : '100%' - }, - items : [ { - xtype : 'textfield', - labelWidth : 400, - fieldLabel : 'Courier company for return (if ESRF sends a dewar back)', - id : _this.id + 'returnCourier', - value : '' - }, { - xtype : 'textfield', - labelWidth : 400, - fieldLabel : 'Courier account', - id : _this.id + 'courierAccount', - value : '' - }, { - xtype : 'textfield', - labelWidth : 400, - fieldLabel : 'Billing reference', - id : _this.id + 'BillingReference', - value : '' - }, { - xtype : 'numberfield', - labelWidth : 400, - fieldLabel : 'Average Customs value of a dewar (Euro)', - id : _this.id + 'dewarAvgCustomsValue', - value : '' - }, { - xtype : 'numberfield', - labelWidth : 400, - fieldLabel : 'Average Transport value of a dewar (Euro)', - id : _this.id + 'dewarAvgTransportValue', - value : '' - } ] - } ], - buttons : buttons - }); - } - this.fillStores(); - if (this.showTitle) { - this.panel.setTitle('Create a new Shipment'); - } - return this.panel; -}; - -ShipmentForm.prototype.input = function() { - return { - proposal : DATADOC.getProposal_10() - - }; -}; - -ShipmentForm.prototype.test = function(targetId) { - var shipmentForm = new ShipmentForm({ - creationMode : true - - }); - BIOSAXS.proposal = new Proposal(shipmentForm.input().proposal); - shipmentForm.getPanel().render(targetId); -}; - -/** - * #onSaved - */ -function StockSolutionForm(args) { - this.id = BUI.id(); - this.actions = []; - - if (args != null) { - if (args.actions != null) { - this.actions = args.actions; - } - } - this.onSaved = new Event(this); -} - -StockSolutionForm.prototype.getStockSolution = function() { - if (this.stockSolution != null) { - this.stockSolution.concentration = Ext.getCmp(this.id + "stockSolution_concentration").getValue(); - this.stockSolution.storageTemperature = Ext.getCmp(this.id + "stockSolution_storageTemperature").getValue(); - this.stockSolution.volume = Ext.getCmp(this.id + "stockSolution_volume").getValue(); - this.stockSolution.comments = Ext.getCmp(this.id + "stockSolution_comments").getValue(); - this.stockSolution.name = Ext.getCmp(this.id + "stockSolution_name").getValue(); - this.stockSolution.bufferId = this.bufferCombo.getValue(); - - if (this.macromoleculeCombo.getValue() != null) { - this.stockSolution.macromoleculeId = this.macromoleculeCombo.getValue(); - } else { - this.stockSolution.macromolecule3VO = null; - } - - } else { - return { - concentration : Ext.getCmp(this.id + "stockSolution_concentration").getValue(), - storageTemperature : Ext.getCmp(this.id + "stockSolution_storageTemperature").getValue(), - volume : Ext.getCmp(this.id + "stockSolution_volume").getValue(), - comments : Ext.getCmp(this.id + "stockSolution_comments").getValue(), - name : Ext.getCmp(this.id + "stockSolution_name").getValue(), - bufferId : this.bufferCombo.getValue(), - macromoleculeId : this.macromoleculeCombo.getValue() - }; - } - return this.stockSolution; -}; - -StockSolutionForm.prototype.setStockSolution = function(stockSolution) { - if (stockSolution != null) { - if (stockSolution.macromoleculeId != null) { - this.macromoleculeCombo.setValue(stockSolution.macromoleculeId); - } - this.bufferCombo.setValue(stockSolution.bufferId); - Ext.getCmp(this.id + "stockSolution_concentration").setValue(this.stockSolution.concentration); - Ext.getCmp(this.id + "stockSolution_storageTemperature").setValue(this.stockSolution.storageTemperature); - Ext.getCmp(this.id + "stockSolution_volume").setValue(this.stockSolution.volume); - Ext.getCmp(this.id + "stockSolution_name").setValue(this.stockSolution.name); - Ext.getCmp(this.id + "stockSolution_comments").setValue(this.stockSolution.comments); - } -}; - -StockSolutionForm.prototype.getBufferCombo = function() { - this.bufferCombo = BIOSAXS_COMBOMANAGER.getComboBuffers(BIOSAXS.proposal.getBuffers(), { - labelWidth : 120, - margin : '0 0 10 0', - width : 220 - - }); - return this.bufferCombo; -}; - -StockSolutionForm.prototype.getMacromoleculeCombo = function() { - this.macromoleculeCombo = BIOSAXS_COMBOMANAGER.getComboMacromoleculeByMacromolecules(BIOSAXS.proposal.getMacromolecules(), { - labelWidth : 120, - margin : '0 0 10 0', - width : 220 - - }); - return this.macromoleculeCombo; -}; - -StockSolutionForm.prototype.refresh = function() { -}; - -StockSolutionForm.prototype._getTopPanel = function() { - return { - xtype : 'container', - layout : 'hbox', - border : 0, - items : [ { - xtype : 'container', - layout : 'hbox', - items : [ { - xtype : 'container', - flex : 1, - border : false, - layout : 'anchor', - defaultType : 'textfield', - items : [ - - this.getMacromoleculeCombo(), { - xtype : 'requiredtext', - id : this.id + 'stockSolution_name', - fieldLabel : 'Acronym', - labelWidth : 120, - width : 250 - }, { - xtype : 'requiredtext', - id : this.id + 'stockSolution_concentration', - fieldLabel : 'Conc. (mg/ml)', - labelWidth : 120, - width : 250 - }, - - { - id : this.id + 'stockSolution_storageTemperature', - fieldLabel : 'Storage Temp.(C)', - labelWidth : 120, - width : 250 - }, { - xtype : 'requiredtext', - id : this.id + 'stockSolution_volume', - fieldLabel : 'Volume in Well (µl)', - labelWidth : 120, - width : 250 - } ] - } ] - }, { - xtype : 'container', - flex : 1, - layout : 'anchor', - defaultType : 'textfield', - margin : '0 0 0 10', - items : [ this.getBufferCombo() ] - } ] - }; - -}; - -StockSolutionForm.prototype.getPanel = function(stockSolution) { - this.stockSolution = stockSolution; - this.panel = Ext.createWidget({ - xtype : 'container', - layout : 'vbox', - border : 0, - style : { - padding : '10px' - }, - fieldDefaults : { - labelAlign : 'left', - labelWidth : 50 - }, - items : [ this._getTopPanel(stockSolution), { - id : this.id + 'stockSolution_comments', - xtype : 'textareafield', - name : 'comments', - fieldLabel : 'Comments', - labelWidth : 120, - width : '100%' - } ] - }); - - this.setStockSolution(stockSolution); - return this.panel; -}; - -StockSolutionForm.prototype.input = function() { - return { - stock : { - "stockSolutionId" : 6, - "proposalId" : 3124, - "macromoleculeId" : 5933, - "bufferId" : 811, - "instructionSet3VO" : null, - "boxId" : 305861, - "storageTemperature" : "20", - "volume" : "300", - "concentration" : "1.2", - "comments" : "Buffer EDTA with A", - "name" : "A_EDTA_1.2", - "samples" : [], - "buffer" : "EDTA", - "macromolecule" : "A" - }, - proposal : new MeasurementGrid().input().proposal - }; -}; - -StockSolutionForm.prototype.test = function(targetId) { - var stockSolutionForm = new StockSolutionForm(); - BIOSAXS.proposal = new Proposal(stockSolutionForm.input().proposal); - var panel = stockSolutionForm.getPanel(new Shipment(stockSolutionForm.input().stock)); - panel.render(targetId); -}; - - -BoxWhiskerGraph.prototype.cleanArray = GenericGraph.prototype.cleanArray; -BoxWhiskerGraph.prototype.plotAxes = GenericGraph.prototype.plotAxes; -BoxWhiskerGraph.prototype.plotRuler = GenericGraph.prototype.plotRuler; -BoxWhiskerGraph.prototype.drawSVGVerticalText = GenericGraph.prototype.drawSVGVerticalText; -BoxWhiskerGraph.prototype.getClassColor = GenericGraph.prototype.getClassColor; -BoxWhiskerGraph.prototype.getDimensions = GenericGraph.prototype.getDimensions; -BoxWhiskerGraph.prototype.calculate = GenericGraph.prototype.calculate; -BoxWhiskerGraph.prototype.getMedian = GenericGraph.prototype.getMedian; -BoxWhiskerGraph.prototype.pointToPixel = GenericGraph.prototype.pointToPixel; -BoxWhiskerGraph.prototype.maxValueWhisker = GenericGraph.prototype.maxValueWhisker; -BoxWhiskerGraph.prototype.refresh = GenericGraph.prototype.refresh; - -/** - * Subclass of GenericGraph - * - * @maxBoxWidth - */ -function BoxWhiskerGraph(args){ - this.maxBoxWidth = 25; - - if (args == null){ - args = new Object(); - } - args["plotHorizontalByCluster"] = true; - - GenericGraph.call(this, args); - - if (args.maxBoxWidth != null){ - this.maxBoxWidth = args.maxBoxWidth; - } -}; - - - -/** -There are several different methods for calculating quartiles.[1] This calculator uses a method described by Moore and McCabe to find quartile values. -The same method also used by The TI-83 to calculate quartile values. -With this method, the first quartile is the median of the numbers below the median, the third quartile is the median of the numbers above the median. - -http://www.miniwebtool.com/quartile-calculator/ -http://www.alcula.com/calculators/statistics/box-plot/ -**/ -BoxWhiskerGraph.prototype.getQ1 = function(array){ - array = array.slice(0, array.length/2); - return this.getMedian(array); -}; - -BoxWhiskerGraph.prototype.getQ3 = function(array){ - array = array.slice((array.length + 1)/2); - return this.getMedian(array); - -}; - -BoxWhiskerGraph.prototype.getQ2 = function(array){ - return this.getMedian(array); -}; - -BoxWhiskerGraph.prototype.getBelowOutliers = function(belowLimit, array){ - var points = new Array(); - for (var i = 0; i < array.length; i++){ - if (array[i] <= belowLimit){ - points.push(array[i]); - } - } - return points; -}; - -BoxWhiskerGraph.prototype.getAboveOutliers = function(aboveLimit, array){ - var points = new Array(); - for (var i = 0; i < array.length; i++){ - if (array[i] >= aboveLimit){ - points.push(array[i]); - } - } - return points; -}; - - -BoxWhiskerGraph.prototype.minValueWhisker = function(belowLimit, q1, array){ - var points = new Array(); - - for (var i = 0; i < array.length; i++){ - if ((array[i] < q1) && (array[i]) > belowLimit){ - points.push(array[i]); - } - } - - if (points.length > 0){ - points.sort(function(a, b){return a - b;}); - return points[0]; - } - return null; -}; - -BoxWhiskerGraph.prototype.isNumber = function(value){ - if (value=="") return false; - - var d = parseInt(value); - if (!isNaN(d)) return true; else return false; - -}; - -BoxWhiskerGraph.prototype.plotBoxWhisker = function(boxProperties){ - if (this.maxBoxWidth != null){ - if (boxProperties.width > this.maxBoxWidth){ - boxProperties.x = boxProperties.x + (boxProperties.width/2) - (this.maxBoxWidth/2); - boxProperties.width = this.maxBoxWidth; - } - - } - - if (this.plotPoints){ - for(var i = 0; i < boxProperties.values.length; i++){ - var value = boxProperties.values[i]; - var toPixel = this.pointToPixel(value, boxProperties); - SVG.drawCircle(boxProperties.x + (boxProperties.width/2) + 2, toPixel, this.pointRadius, this.svg, [["fill", "green"], ["fill-opacity", this.fillOpacityPoint],['stroke-opacity', this.strokeOpacityPoint], ["stroke", "black"]]); - } - } - - - var boxColor = this.getClassColor(boxProperties.name); - var result = this.calculate(boxProperties.values); - /** Q1 **/ - - if (this.isNumber(result.Q1)){ - SVG.drawLine(boxProperties.x, this.pointToPixel(result.Q1, boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result.Q1, boxProperties), this.svg, [["stroke", boxColor]]); - } - /** Q2 **/ - if (this.isNumber(result.Q2)){ - SVG.drawLine(boxProperties.x, this.pointToPixel(result.Q2, boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result.Q2, boxProperties), this.svg, [["stroke", "blue"], ["stroke-width", "2"]]); - } - - /** Q3 **/ - if (this.isNumber(result.Q3)){ - SVG.drawLine(boxProperties.x, this.pointToPixel(result.Q3, boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result.Q3, boxProperties), this.svg, [["stroke", boxColor]]); - } - - /** Concenting Q1 and Q3 **/ - if (this.isNumber(result.Q1)&&this.isNumber(result.Q3)){ - SVG.drawLine(boxProperties.x, this.pointToPixel(result.Q1, boxProperties), boxProperties.x, this.pointToPixel(result.Q3, boxProperties), this.svg, [["stroke", boxColor]]); - SVG.drawLine(boxProperties.x + boxProperties.width, this.pointToPixel(result.Q1, boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result.Q3, boxProperties), this.svg, [["stroke", boxColor]]); - } - - /** min-whisker **/ - if (result["min-whisker"] != null){ - if (this.isNumber(result.Q1)){ - SVG.drawLine(boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result.Q1, boxProperties), boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result["min-whisker"], boxProperties), this.svg, [["stroke", boxColor]]); - } - SVG.drawLine(boxProperties.x,this.pointToPixel(result["min-whisker"], boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result["min-whisker"], boxProperties) , this.svg, [["stroke", boxColor]]); - - } - - /** max-whisker **/ - if (result["max-whisker"] != null){ - if (this.isNumber(result.Q3)){ - SVG.drawLine(boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result.Q3, boxProperties), boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result["max-whisker"], boxProperties), this.svg, [["stroke", boxColor]]); - } - SVG.drawLine(boxProperties.x , this.pointToPixel(result["max-whisker"], boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result["max-whisker"], boxProperties), this.svg, [["stroke", boxColor]]); - - } - - /** outliners **/ - if (result["above-outliers"] != null){ - for (var point in result["above-outliers"]){ - SVG.drawCircle(boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result["above-outliers"][point], boxProperties), this.pointRadius, this.svg, [["fill", "red"], ["fill-opacity", "1"]]); - //SVG.drawText(boxProperties.x + (boxProperties.width/2) - 2, this.pointToPixel(result["above-outliers"][point], boxProperties) + 2, "x",this.svg, [["fill", "black"], ["font-size", "x-small"]]); - } - } - if (result["below-outliers"] != null){ - for (var point in result["below-outliers"]){ - SVG.drawCircle(boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result["below-outliers"][point], boxProperties), this.pointRadius, this.svg, [["fill", "red"], ["fill-opacity", "1"]]); - //SVG.drawText(boxProperties.x + (boxProperties.width/2) - 2, this.pointToPixel(result["below-outliers"][point], boxProperties) + 2, "x",this.svg, [["fill", "black"], ["font-size", "x-small"]]); - } - } -}; - - - -BoxWhiskerGraph.prototype.plotClusterTitles = function(properties){ - /** Cluster Titles **/ - var posX = this.left + this.rulerWidth; - var data = this.data; - for(var i = 0; i < data.clusters.length; i++ ){ - /** title for the clusters **/ - posX = posX + this.interClustersSpace; - - /** Drawing title of classes **/ - var cluster = data.clusters[i]; - var posXClasses = posX; - for(var j = 0; j < cluster.classes.length; j++){ - //SVG.drawRectangle(posXClasses, this.height - (this.bottom + this.clusterTitleHeight + this.rulerHeight), properties.classWidth, this.rulerHeight, this.svg, [["fill", "green"]]); -// SVG.drawText(posXClasses + 1/6*properties.classWidth, this.height - (this.bottom + this.clusterTitleHeight + (this.rulerHeight*1/4)), cluster.classes[j].name, this.svg, [["style", "font-size:xx-small"]]); - var color = cluster.classes[j].color; - this.drawSVGVerticalText(posXClasses + 1/2*(properties.classWidth), this.height - (this.bottom - this.clusterTitleHeight + (this.rulerHeight)), cluster.classes[j].name , [["style", "font-size:x-small;"], ["fill", color]]); - - // SVG.drawRectangle(posXClasses, this.height - (this.bottom + this.clusterTitleHeight), properties.classWidth, 2, this.svg, [["fill", "black"]]); - posXClasses = posXClasses + properties.classWidth + this.interClassesSpace; - } - - var clusterTitleSpace = (data.clusters[i].classes.length * properties.classWidth) + ((data.clusters[i].classes.length - 1) * this.interClassesSpace); - //SVG.drawRectangle(posX, this.height - (this.bottom + this.clusterTitleHeight), clusterTitleSpace, this.clusterTitleHeight, this.svg, [["fill", "pink"]]); - SVG.drawRectangle(posX, this.height - (this.clusterTitleHeight+this.bottom), clusterTitleSpace, 1, this.svg, []); - -// var transform = ["translate", "(" + posX + 1/3*clusterTitleSpace +", " + this.height - (this.bottom + (this.clusterTitleHeight*1/4)) +")"], ["transform", "rotate(180)"]; -// var transform = ["transform", "translate(" + (posX + 1/3*clusterTitleSpace) +", " + (this.height - (this.bottom + (this.clusterTitleHeight*1/4))) + "), rotate(-90) "]; -// this.drawSVGVerticalText(posX + 1/3*clusterTitleSpace, this.height - (this.bottom + (this.clusterTitleHeight*1/4)),data.clusters[i].name, [["style", "font-size:x-small"]]); - SVG.drawText(posX , this.height - (this.bottom + (this.clusterTitleHeight*1/4)),data.clusters[i].name ,this.svg, [["style", "font-size:x-small"]]); - posX = posX + clusterTitleSpace; - } -}; - -BoxWhiskerGraph.prototype.plotWhisters = function(data, properties){ - var colors = ["yellow", "orange", "green"]; - var posX = this.left + this.rulerWidth; - for(var i = 0; i < data.clusters.length; i++ ){ - var cluster = data.clusters[i]; - /** inter cluster space **/ - //SVG.drawRectangle(posX, this.top, this.interClustersSpace, this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight, this.svg, [["fill", "black"]]); - posX = posX + this.interClustersSpace; - - for (var j = 0; j < cluster.classes.length; j ++){ - - //SVG.drawRectangle(posX, this.top, properties.classWidth, this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight, this.svg, [["fill", colors[j]]]); - this.plotBoxWhisker( - { - name : cluster.classes[j].name, - values : cluster.classes[j].values, - minPoint : properties.minPoint, - maxPoint : properties.maxPoint, - x : posX, - y : this.top, - width : properties.classWidth, - height : this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight - - - } - ); - posX = posX + properties.classWidth; - //SVG.drawRectangle(posX, this.top, this.interClassesSpace, this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight, this.svg, [["fill", "black"]]); - if (j < cluster.classes.length - 1){ - posX = posX + this.interClassesSpace; - } - } - } -}; - -BoxWhiskerGraph.prototype.draw = function(targetId, data){ - this.targetId = targetId; - var properties = (this.getDimensions(data)); - this.svg = SVG.createSVGCanvas(document.getElementById(this.targetId), [["width", this.width], ["height", this.height]]); - this.plotAxes(properties); - this.plotClusterTitles(properties); - this.plotWhisters(data,properties); -}; - -BoxWhiskerGraph.prototype.input = function(){ - return DATADOC.getBoxWhikerData(); -}; - -BoxWhiskerGraph.prototype.test = function(targetId){ - var plot = new BoxWhiskerGraph( - { - targetId : targetId, - height : 350, - width : 450, - maxBoxWidth : 25 - } - ); - plot.refresh(this.input()); -}; - - - - - - - -function DataSet(){ - this.json = null; - -}; - - -DataSet.prototype.loadFromJSON = function(json){ - if(json != null) { - if(this.validate(json)) { - this.json = json; - } - } -}; - - -DataSet.prototype.toJSON = function(json){ - return this.json; -}; - - -/** Abstract method to be override on childs classes **/ -DataSet.prototype.validate = function(json){ - if (true){ - return true; - } - /*else{ - throw "Data validation failed"; - }*/ -}; - - - - -Edge.prototype.getName = GraphItem.prototype.getName; -Edge.prototype.setName = GraphItem.prototype.setName; -Edge.prototype.getId = GraphItem.prototype.getId; - -function Edge(id, name, nodeSource, nodeTarget, args){ - GraphItem.prototype.constructor.call(this, id, name, args); - - this.sourceNode = nodeSource; - this.targetNode = nodeTarget; - -}; - -Edge.prototype.toJSON = function(){ - return {"index": this.id,"sourceIndex":this.sourceNode.getId(),"targetIndex":this.targetNode.getId(),"args":this.args}; -}; - -Edge.prototype.getNodeSource = function(){ - return this.sourceNode; -}; - -Edge.prototype.getNodeTarget = function(){ - return this.targetNode; -}; - -Edge.prototype.remove = function(){ - //Remove edge object in the nodes - this.getNodeSource().removeEdge(this); - this.getNodeTarget().removeEdge(this); - - this.deleted.notify(this); -}; - - -EdgeGraphFormatter.prototype.setProperties = ItemGraphFormatter.prototype.setProperties; -EdgeGraphFormatter.prototype.getDefault = ItemGraphFormatter.prototype.getDefault; -EdgeGraphFormatter.prototype.getSelected = ItemGraphFormatter.prototype.getSelected; -EdgeGraphFormatter.prototype.getOver = ItemGraphFormatter.prototype.getOver; -EdgeGraphFormatter.prototype.getDragging = ItemGraphFormatter.prototype.getDragging; -EdgeGraphFormatter.prototype.getId = ItemGraphFormatter.prototype.getId; -EdgeGraphFormatter.prototype.toJSON = ItemGraphFormatter.prototype.toJSON; -EdgeGraphFormatter.prototype.loadFromJSON = ItemGraphFormatter.prototype.loadFromJSON; -EdgeGraphFormatter.prototype._setEvents = ItemGraphFormatter.prototype._setEvents; - -function EdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ - ItemGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); - - this.getDefault().args.type = "EdgeGraphFormatter"; -}; - - - - -LineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; -LineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; -LineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; -LineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; -LineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; -LineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; -LineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; -LineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; -LineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; - -function LineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ - EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); - this.args.type = "LineEdgeGraphFormatter"; -}; - -/** DIRECTED **/ -DirectedLineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; -DirectedLineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; -DirectedLineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; -DirectedLineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; -DirectedLineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; -DirectedLineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; -DirectedLineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; -DirectedLineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; -DirectedLineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; - -function DirectedLineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ - EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); - this.args.type = "DirectedLineEdgeGraphFormatter"; - this.args.arrowSize = "3"; -}; -DirectedLineEdgeGraphFormatter.prototype.getArrowSize = function(){ - return this.args.arrowSize; -}; - -OdirectedLineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; -OdirectedLineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; -OdirectedLineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; -OdirectedLineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; -OdirectedLineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; -OdirectedLineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; -OdirectedLineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; -OdirectedLineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; -OdirectedLineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; - -function OdirectedLineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ - EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); - this.args.type = "DirectedLineEdgeGraphFormatter"; - this.args.arrowSize = "3"; -}; - -OdirectedLineEdgeGraphFormatter.prototype.getArrowSize = function(){ - return this.args.arrowSize; -}; - - -/** CUT (inhibition) **/ -CutDirectedLineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; -CutDirectedLineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; -CutDirectedLineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; -CutDirectedLineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; -CutDirectedLineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; -CutDirectedLineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; -CutDirectedLineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; -CutDirectedLineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; -CutDirectedLineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; - -function CutDirectedLineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ - EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); - this.args.type = "CutDirectedLineEdgeGraphFormatter"; -}; - - - - -BezierEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; -BezierEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; -BezierEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; -BezierEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; -BezierEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; -BezierEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; -BezierEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; -BezierEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; -BezierEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; -BezierEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; - -function BezierEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ - EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); - this.args.type = "BezierEdgeGraphFormatter"; -}; - - - -DotDirectedLineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; -DotDirectedLineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; -DotDirectedLineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; -DotDirectedLineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; -DotDirectedLineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; -DotDirectedLineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; -DotDirectedLineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; -DotDirectedLineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; -DotDirectedLineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; - -function DotDirectedLineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ - EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); - this.args.type = "DotDirectedLineEdgeGraphFormatter"; -}; - - -OdotDirectedLineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; -OdotDirectedLineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; -OdotDirectedLineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; -OdotDirectedLineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; -OdotDirectedLineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; -OdotDirectedLineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; -OdotDirectedLineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; -OdotDirectedLineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; -OdotDirectedLineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; - -function OdotDirectedLineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ - EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); - this.args.type = "OdotDirectedLineEdgeGraphFormatter"; -}; - - - -function GraphDataset(){ - DataSet.prototype.constructor.call(this); - this.edges = new Object(); - this.vertices = new Object(); - this.verticesIndex = new Object(); - - //Events - this.newVertex = new Event(this); - this.vertexNameChanged = new Event(this); - this.vertexDeleted = new Event(this); - - this.newEdge = new Event(this); - this.edgeNameChanged = new Event(this); - this.edgeDeleted = new Event(this); - - this.json = new Object(); - this.json.vertices = new Array(); - this.json.edges = new Array(); - this.json.relations = new Array(); -}; - -GraphDataset.prototype.loadFromJSON = DataSet.prototype.loadFromJSON; -GraphDataset.prototype.toJSON = DataSet.prototype.toJSON; -GraphDataset.prototype.validate = DataSet.prototype.validate; - -/** Devuelve el numero de edges incidentes sobre el nodo con mas edges **/ -GraphDataset.prototype.getMaxClass = function(){ - var maxClassNode = 0; - for ( var node in this.vertices) { - if (this.vertices[node].getEdgesCount() > maxClassNode){ - maxClassNode = this.vertices[node].getEdgesCount(); - } - } - return maxClassNode; -}; - -/** Devuelve el numero de edges incidentes sobre el nodo con mas edges **/ -GraphDataset.prototype.getMinClass = function(){ - var minClassNode = Math.min(); - for ( var node in this.vertices) { - if (this.vertices[node].getEdgesCount() < minClassNode){ - minClassNode = this.vertices[node].getEdgesCount(); - } - } - return minClassNode; -}; - -GraphDataset.prototype.getVertexByName = function(nodeName){ - var results = new Array(); - - for (var vertexId in this.verticesIndex[nodeName]){ - var vertexByid = this.getVertexById(this.verticesIndex[nodeName][vertexId]); - results.push(vertexByid); - //* añadido nuevo porque fallaba el anterior codigo - return vertexByid - } - - if (results <= 1){ - return this.getVertexById(this.verticesIndex[nodeName]); - } - else{ - return results; - } -}; - -GraphDataset.prototype.getVertexById = function(id){ - return this.vertices[id]; -}; - -GraphDataset.prototype.toSIF = function(){ - var sifDataAdapter = new SifFileDataAdapter(); - return sifDataAdapter.toSIF(this); -}; - -GraphDataset.prototype.toSIFID = function(){ - var sifDataAdapter = new SifFileDataAdapter(); - return sifDataAdapter.toSIFID(this); -}; - -GraphDataset.prototype.toDOT = function(){ - var dotFileDataAdapter = new DotFileDataAdapter(); - return dotFileDataAdapter.toDOT(this); -}; - -GraphDataset.prototype.toDOTID = function(){ - var dotFileDataAdapter = new DotFileDataAdapter(); - return dotFileDataAdapter.toDOTID(this); -}; - -GraphDataset.prototype._addNode = function(nodeName, args){ - return new Vertex(this._getVerticesCount()-1, nodeName, args); -}; - -GraphDataset.prototype.addNode = function(nodeName, args){ - this.json.vertices.push(nodeName); - this._addVerticesIndex(nodeName, this._getVerticesCount() - 1); - var vertex = this._addNode(nodeName, args); - this.vertices[this._getVerticesCount()-1] = vertex; - this._setNodeEvents(vertex); - this.newVertex.notify(vertex); -}; - -GraphDataset.prototype._addVerticesIndex = function(nodeName, id){ - if (this.verticesIndex[nodeName] == null){ - this.verticesIndex[nodeName] = new Array(); - } - this.verticesIndex[nodeName].push(id); -}; - -GraphDataset.prototype.addEdge = function(edgeName, nodeSourceId, nodeTargetId, args){ - this.json.edges.push(edgeName); - var nodeSource = this.getVertexById(nodeSourceId); - var nodeTarget = this.getVertexById(nodeTargetId); - var index = this.getEdgesCount() - 1; - this.edges[index] = new Edge(index, edgeName, nodeSource, nodeTarget, args); - this.json.relations.push({"index": index, "sourceIndex": nodeSourceId, "targetIndex": nodeTargetId, "args": args }); - - nodeSource.addEdge(this.edges[index]); - nodeTarget.addEdge(this.edges[index]); - this._setEdgeEvents(this.edges[index]); - this.newEdge.notify(this.edges[index]); -}; - -GraphDataset.prototype.getVertices = function(){ - return this.vertices; -}; - -GraphDataset.prototype.getEdges = function(){ - return this.edges; -}; - -GraphDataset.prototype.getEdgeById = function(edgeId){ - return this.edges[edgeId]; -}; - -GraphDataset.prototype._getVerticesCount = function(){ - return this.json.vertices.length; -}; - - -GraphDataset.prototype.getVerticesCount = function(){ - var count = 0; - for ( var vertex in this.getVertices()) { - count ++; - } - return count; -}; - - -GraphDataset.prototype.getEdgesCount = function(){ - return this.json.edges.length; -}; - -GraphDataset.prototype.init = function(){ - this.edges = new Object(); - this.vertices = new Object(); -}; - -GraphDataset.prototype._setNodeEvents = function(node){ - var _this = this; - //NODE EVENTS - node.deleted.attach(function (sender, node){ - _this._removeNode(node); - }); - - node.nameChanged.attach(function (sender, args){ - var item = args.item; - var newName = item.name; - var indexes = _this.verticesIndex[args.previousName]; - for(var i = 0; i < indexes.length; i++){ - if(indexes[i] == item.id) - indexes.splice(i,1); - } - if(indexes.length == 0){ - delete _this.verticesIndex[args.previousName]; - } - _this._addVerticesIndex(newName, item.id); - _this.json.vertices[item.id] = newName; - _this.vertexNameChanged.notify(args); - }); -}; - -GraphDataset.prototype._setEdgeEvents = function(edge){ - var _this = this; - //EDGE EVENTS - edge.nameChanged.attach(function (sender, edge){ - _this.edgeNameChanged.notify(edge); - - }); - - edge.deleted.attach(function (sender, edge){ - _this._removeEdge(edge); - }); -}; - -GraphDataset.prototype._connectVerticesByName = function(nodeNameSource, nodeNameTarget){ - var source = this.getVertexByName(nodeNameSource); - var target = this.getVertexByName(nodeNameTarget); - - if ((source != null)&&(target!=null)){ - this.addEdge(source.getName() +"_" + target.getName(), source.getId(), target.getId(), {}); - } - else{ - if (source == null){ - console.log("No encontrado: " + nodeNameSource) - } - if (target == null){ - console.log("No encontrado: " + nodeNameTarget) - } - } -}; - -GraphDataset.prototype.loadFromJSON = function(json){ - var json = json; - this.init(); - this.json = new Object(); - this.json.vertices = new Array(); - this.json.edges = new Array(); - this.json.relations = new Array(); - - for ( var i = 0; i < json.nodes.length; i++) { - if (json.nodes[i] != null){ - var name = json.nodes[i]; - this.addNode(name); - } - else{ - this.json.vertices.push(null); - } - } - - for ( var i = 0; i < json.edges.length; i++) { - if (json.edges[i] != null){ - if (json.relations[i] != null){ - var name = json.edges[i]; - this.addEdge(name, json.relations[i].sourceIndex, json.relations[i].targetIndex, json.relations[i].args); - } - } - else{ - this.json.edges.push(null); - this.json.relations.push(null); - } - } -}; - -GraphDataset.prototype.prettyPrint = function(){ - for ( var node in this.vertices) { - console.log(this.vertices[node].getName() ); - for ( var j = 0; j < this.vertices[node].getEdgesIn().length; j++) { - console.log(" --> " + this.vertices[node].getEdgesIn()[j].getNodeTarget().getName() ); - } - } -}; - -GraphDataset.prototype._removeEdge = function(edge){ - this.json.edges[edge.getId()] = null; - this.json.relations[edge.getId()] = null; - - delete this.edges[edge.getId()]; - this.edgeDeleted.notify(edge); - - -}; - -GraphDataset.prototype._removeNode = function(node){ - this.json.vertices[node.getId()] = null; - delete this.vertices[node.getId()]; - this.vertexDeleted.notify(node); -}; - -GraphDataset.prototype.toJSON = function(){ - var json = new Object(); - var nodes = new Array(); - json.nodes = this.json.vertices; //nodes; - json.edges = this.json.edges; //edges; - json.relations = this.json.relations; - return json; -}; - -GraphDataset.prototype.clone = function(){ - var dsDataset = new GraphDataset(); - dsDataset.loadFromJSON(this.toJSON()); - return dsDataset; -}; -//GraphDataset.prototype.test = function(){ -// this.loadFromJSON(this.toJSON()); -//}; - -function labels(){ - var names = new Array(); - - var dataset = interactomeViewer.graphEditorWidget.dataset; - var layout = interactomeViewer.graphEditorWidget.layout; - - for ( var vertexId in interactomeViewer.graphEditorWidget.dataset.getVertices()) { - names.push(interactomeViewer.graphEditorWidget.dataset.getVertexById(vertexId).getName()); - } - - var sorted = (names.sort()); - console.log(sorted) - var distance = 0.01; - var altura = 0.6; - for ( var i = 0; i < names.length; i++) { - var id =dataset.getVertexByName(names[i]).getId(); - - layout.getNodeById(id).setCoordenates(distance, altura); - - - distance = parseFloat(distance) + parseFloat(0.03); - - altura = parseFloat(altura) + parseFloat(0.02); - - if (parseFloat(altura) == 0.9800000000000003){ - - altura = 0.6; - distance = distance - 0.51; - } - - } - - -}; - -function GraphItem(id, name, args){ - this.id = id; - this.name = name; - this.type = "NONE"; - - this.args = new Object(); - - - if (args!=null){ - this.args = args; - if (args.type !=null){ - this.type = args.type; - } - } - - //Events - this.nameChanged = new Event(this); - this.deleted = new Event(this); -} - -GraphItem.prototype.getName = function(){ - return this.name; -}; - -GraphItem.prototype.getId = function(){ - return this.id; -}; - -GraphItem.prototype.setName = function(name){ - var oldName = this.getName(); - this.name = name; - this.nameChanged.notify({"item": this, "previousName" : oldName}); -}; - - - - - -function LayoutDataset(){ - this.dataset = null; - this.vertices = new Object(); - this.changed = new Event(this); - - - this.args = new Object(); - - //RANDOM, CIRCLE - this.args.type = "CIRCLE"; -}; - -LayoutDataset.prototype.loadFromJSON = function(dataset, json){ - var _this = this; - this.vertices = new Object(); - this.dataset = dataset; //new GraphDataset(); - for ( var vertex in json) { - this.vertices[vertex] = new NodeLayout(vertex, json[vertex].x, json[vertex].y); - this.vertices[vertex].changed.attach(function (sender, item){ - _this.changed.notify(item); - }); - } - this._attachDatasetEvents(); -}; - - -LayoutDataset.prototype.toJSON = function(){ - var serialize = new Object(); - for ( var vertex in this.vertices) { - serialize[vertex] = new Object(); - serialize[vertex].x = this.vertices[vertex].x; - serialize[vertex].y = this.vertices[vertex].y; - } - serialize.dataset = new Object(); - serialize.dataset =this.dataset.toJSON(); - return serialize; -}; - -LayoutDataset.prototype.dataBind = function(graphDataset){ - this.dataset = graphDataset; - this._attachDatasetEvents(); - this._calculateLayout(); -}; - -LayoutDataset.prototype._removeVertex = function(vertexId){ - delete this.vertices[vertexId]; -}; - -LayoutDataset.prototype._attachDatasetEvents = function(){ - var _this = this; - - this.dataset.vertexDeleted.attach(function (sender, item){ - _this._removeVertex(item.getId()); - }); - - this.dataset.newVertex.attach(function (sender, item){ - _this.vertices[item.getId()] = new NodeLayout(item.getId(), 0.5, 0.5); - _this.vertices[item.getId()].changed.attach(function (sender, item){ - _this.changed.notify(item); - }); - }); -}; - -LayoutDataset.prototype.getType = function(){ - return this.args.type; -}; - -LayoutDataset.prototype._calculateLayoutVertices = function(type, count){ - - if (type == "CIRCLE"){ - var radius = 0.4; - var centerX = 0.5; - var centerY = 0.5; - var verticesCoordinates = new Array(); - for(var i = 0; i < count; i++){ - x = centerX + radius * Math.sin(i * 2 * Math.PI/count); - y = centerY + radius * Math.cos(i * 2 * Math.PI/count); - verticesCoordinates.push({'x':x,'y':y}); - } - return verticesCoordinates; - } -}; - - -LayoutDataset.prototype._calculateLayout = function(){ - var _this = this; - if (this.getType() == "RANDOM"){ - for ( var vertex in this.dataset.getVertices()) { - if (this.vertices[vertex] == null){ - this.vertices[vertex] = new NodeLayout(vertex, 0, 0); - } - this.vertices[vertex].setCoordinates(Math.random(), Math.random()); - this.vertices[vertex].changed.attach(function (sender, item){ - _this.changed.notify(item); - }); - } - } - - if ( this.getType() == "CIRCLE"){ - - var count = this.dataset._getVerticesCount(); - var verticesCoordinates = this._calculateLayoutVertices(this.getType(), count); - - var aux = 0; - for ( var vertex in this.dataset.getVertices()) { - if (this.vertices[vertex] == null){ - this.vertices[vertex] = new NodeLayout(vertex, 0, 0); - } - this.vertices[vertex].setCoordinates(verticesCoordinates[aux].x, verticesCoordinates[aux].y);//{"x":, "y":}; - aux++; - this.vertices[vertex].changed.attach(function (sender, item){ - _this.changed.notify(item); - }); - } - } - - - if (this.getType() == "SQUARE"){ - - var count = this.dataset._getVerticesCount(); - var xMin = 0.1; - var xMax = 0.9; - var yMin = 0.1; - var yMax = 0.9; - - var rows = Math.sqrt(count); - var step = (xMax - xMin) / rows; - - var verticesCoordinates = new Array(); - for(var i = 0; i < rows; i ++){ - for ( var j = 0; j < rows; j++) { - x = i * step + xMin; - y = j * step + yMin; - verticesCoordinates.push({'x':x,'y':y}); - } - } - - var aux = 0; - for ( var vertex in this.dataset.getVertices()) { - if (this.vertices[vertex] == null){ - this.vertices[vertex] = new NodeLayout(vertex, 0, 0); - } - this.vertices[vertex].setCoordinates(verticesCoordinates[aux].x, verticesCoordinates[aux].y);//{"x":, "y":}; - aux++; - this.vertices[vertex].changed.attach(function (sender, item){ - _this.changed.notify(item); - }); - } - } - -}; - -LayoutDataset.prototype.getNodeById = function(id){ - return this.vertices[id]; -}; - -LayoutDataset.prototype.getVerticesByArea = function(x1, y1, x2, y2){ - var vertices = new Array(); - for ( var vertex in this.dataset.getVertices()) { - if ((this.vertices[vertex].x >= x1)&&(this.vertices[vertex].x <= x2)){ - if ((this.vertices[vertex].y >= y1)&&(this.vertices[vertex].y <= y2)){ - vertices.push(this.vertices[vertex]); - } - } - } - return vertices; -}; - - - - -LayoutDataset.prototype.getLayout = function(type){ - - if (type == "CIRCLE"){ - this.args.type = "CIRCLE"; - this._calculateLayout(); - return; - } - - if (type == "SQUARE"){ - this.args.type = "SQUARE"; - this._calculateLayout(); - return; - } - - if (type == "RANDOM"){ - this.args.type = "RANDOM"; - this._calculateLayout(); - return; - } - - - var dotText = this.dataset.toDOTID(); - var url = "http://bioinfo.cipf.es/utils/ws/rest/network/layout/"+type+".coords"; - var _this = this; - - $.ajax({ - async: true, - type: "POST", - url: url, - dataType: "text", - data: { - dot :dotText - }, - cache: false, - success: function(data){ - var response = JSON.parse(data); - for ( var vertexId in response) { - _this.vertices[vertexId].setCoordinates(response[vertexId].x, response[vertexId].y); - } - } - }); - -// $.ajax({ -// async: true, -// type: "POST", -// url: url, -// dataType: "script", -// data: { -// dot :dotText -// }, -// cache: false, -// success: function(data){ -// var response = JSON.parse(data); -// for ( var vertexId in response) { -// _this.vertices[vertexId].setCoordinates(response[vertexId].x, response[vertexId].y); -// } -// } -// }); - -}; - -function NodeLayout(id, x, y, args){ - this.id = id; - this.x = x; - this.y = y; - this.changed = new Event(this); -}; - -NodeLayout.prototype.getId = function(id){ - return this.id; -}; - -NodeLayout.prototype.setCoordinates = function(x, y){ - this.x = x; - this.y = y; - this.changed.notify(this); -}; - - - -function NetworkDataSetFormatter(vertexFormatProperties, defaultEdgeProperties, args){ - DataSet.prototype.constructor.call(this); - - this.args = new Object(); - - this.vertices = new Object(); - this.edges = new Object(); - this.dataset = null; - this.maxClass = 0; - this.minClass = 0; - - /** Coordenates with default Setting */ - this.args.width = 1100; - this.args.height = 500; - - /** Optional parameters */ - this.args.backgroundColor = "#FFFFFF"; - this.args.backgroundImage = null; - this.args.backgroundImageHeight = null; - this.args.backgroundImageWidth = null; - this.args.backgroundImageX = null; - this.args.backgroundImageY = null; - - - this.args.balanceNodes = false; - this.args.nodesMaxSize = 3; - this.args.nodesMinSize = 0.5; - - - /** Zoom **/ - this.args.zoomScale = 1; - this.args.zoomScaleStepFactor = 0.4; - - if (args != null){ - if (args.backgroundImage != null){ - this.args.backgroundImage = args.backgroundImage; - } - - if (args.width != null){ - this.args.width = args.width; - } - - if (args.height != null){ - this.args.height = args.height; - this.args.svgHeight = args.height; - } - - if (args.svgHeight != null){ - this.args.svgHeight = args.svgHeight; - } - - if (args.backgroundColor != null){ - this.args.backgroundColor = args.backgroundColor; - } - - if(args.balanceNodes != null){ - this.args.balanceNodes = args.balanceNodes; - } - - if(args.nodesMaxSize != null){ - this.args.nodesMaxSize = args.nodesMaxSize; - } - if(args.nodesMinSize != null){ - this.args.nodesMinSize = args.nodesMinSize; - } - } - - this.args.defaultEdgeProperties = {"fill":"#000000", "radius":"1", "stroke":"#000000", "size":1, "title":{"fontSize":10, "fontColor":"#000000"}}; - this.args.vertexFormatProperties = { "fill":"#000000", "stroke":"#000000", "stroke-opacity":"#000000"}; - - if (vertexFormatProperties!= null){ - this.args.vertexFormatProperties = vertexFormatProperties; - } - if (defaultEdgeProperties!= null){ - this.args.defaultEdgeProperties = defaultEdgeProperties; - } - - /** Events **/ - this.changed = new Event(this); - this.edgeChanged = new Event(this); - this.resized = new Event(this); - this.backgroundImageChanged= new Event(this); - this.backgroundColorChanged= new Event(this); -}; - -NetworkDataSetFormatter.prototype.loadFromJSON = function(dataset, json){ - this.args = new Object(); - this.vertices = new Object(); - this.args = json; - this._setDataset(dataset); - var _this = this; - - for ( var vertex in json.vertices) { - this.addVertex(vertex, json.vertices[vertex]); - } - - for ( var edgeId in json.edges) { - this.addEdge(edgeId, json.edges[edgeId]); - } -}; - - -NetworkDataSetFormatter.prototype.toJSON = function(){ - - -// this.args.vertices = new Object(); -// this.args.edges = new Object(); -// -// for ( var vertex in this.vertices) { -// this.args.vertices[vertex] = this.getVertexById(vertex).toJSON(); -// } -// for ( var edge in this.edges) { -// this.args.edges[edge] = this.getEdgeById(edge).toJSON(); -// } -// -// return (this.args); - - - var serialize = new Object(); - serialize = JSON.parse(JSON.stringify(this.args)); - serialize.vertices = new Object(); - serialize.edges = new Object(); - - for ( var vertex in this.vertices) { - serialize.vertices[vertex] = this.getVertexById(vertex).toJSON(); - } - for ( var edge in this.edges) { - serialize.edges[edge] = this.getEdgeById(edge).toJSON(); - } - - return (serialize); -}; - - - -NetworkDataSetFormatter.prototype._getNodeSize = function(nodeId){ - if (this.isVerticesBalanced()){ - var total = this.maxClass - this.minClass; - if (total == 0){ total = 1;} - var nodeConnection = this.dataset.getVertexById(nodeId).getEdges().length; - return ((nodeConnection*this.args.nodesMaxSize)/total) + this.args.nodesMinSize; - } - return this.getVertexById(nodeId).getDefault().getSize(); -}; - -NetworkDataSetFormatter.prototype._recalculateSize = function(){ - if (this.isVerticesBalanced()){ - this.maxClass = this.dataset.getMaxClass(); - this.minClass = this.dataset.getMinClass(); - for ( var vertexIdAll in this.vertices) { - var size = this._getNodeSize(vertexIdAll); - this.vertices[vertexIdAll].getDefault().setSize(size); - this.vertices[vertexIdAll].getSelected().setSize(size); - this.vertices[vertexIdAll].getOver().setSize(size); - } - } -}; - - -NetworkDataSetFormatter.prototype.addVertex = function(vertexId, json){ - - - if (json == null){ - this.vertices[vertexId] = new CircleVertexGraphFormatter(vertexId, this.args.vertexFormatProperties.defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); - } - else{ - - /** Cargo los attributos desde el json **/ - if (json.type == null){ - this.vertices[vertexId] = new CircleVertexGraphFormatter(vertexId, this.args.vertexFormatProperties.defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); - } - - if ((json.type == "SquareVertexGraphFormatter")||(json.type == "SquareVertexNetworkFormatter")){ - this.vertices[vertexId] = new SquareVertexGraphFormatter(vertexId); - this.vertices[vertexId].loadFromJSON(json); - } - - if ((json.type == "CircleVertexGraphFormatter")||(json.type == "CircleVertexNetworkFormatter")){ - this.vertices[vertexId] = new CircleVertexGraphFormatter(vertexId); - this.vertices[vertexId].loadFromJSON(json); - } - - if ((json.type == "EllipseVertexGraphFormatter")||(json.type == "EllipseVertexNetworkFormatter")){ - this.vertices[vertexId] = new EllipseVertexGraphFormatter(vertexId); - this.vertices[vertexId].loadFromJSON(json); - } - - if ((json.type == "RectangleVertexGraphFormatter")||(json.type == "RectangleVertexNetworkFormatter")){ - this.vertices[vertexId] = new RectangleVertexGraphFormatter(vertexId); - this.vertices[vertexId].loadFromJSON(json); - } - - if ((json.type == "RoundedVertexGraphFormatter")||(json.type == "RoundedVertexNetworkFormatter")){ - this.vertices[vertexId] = new RoundedVertexGraphFormatter(vertexId); - this.vertices[vertexId].loadFromJSON(json); - } - - } - - - var _this = this; - this.vertices[vertexId].stateChanged.attach(function (sender, item){ - _this.changed.notify(item); - }); - - var size = this._getNodeSize(vertexId); - this.vertices[vertexId].defaultFormat.args.size = size; - this.vertices[vertexId].selected.args.size = size; - this.vertices[vertexId].over.args.size = size; - -}; - -NetworkDataSetFormatter.prototype.addEdge = function(edgeId, json){ - - /** Es un edge nuevo que le doy los atributos por defecto **/ - if (json == null){ - if (this.dataset.getEdgeById(edgeId).getNodeSource().getId() == this.dataset.getEdgeById(edgeId).getNodeTarget().getId()){ - this.edges[edgeId] = new BezierEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); - }else{ - this.edges[edgeId] = new DirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); - } - } - else{ - /** Cargo los attributos desde el json **/ - if (json.type == null){ - this.edges[edgeId] = new LineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); - } - - if ((json.type == "LineEdgeGraphFormatter")||(json.type == "LineEdgeNetworkFormatter")){ - this.edges[edgeId] = new LineEdgeGraphFormatter(edgeId); - this.edges[edgeId].loadFromJSON(json); - } - if ((json.type == "DirectedLineEdgeGraphFormatter")||(json.type == "DirectedLineEdgeNetworkFormatter")){ - this.edges[edgeId] = new DirectedLineEdgeGraphFormatter(edgeId); - this.edges[edgeId].loadFromJSON(json); - } - - if ((json.type == "BezierEdgeGraphFormatter")||(json.type == "BezierEdgeNetworkFormatter")){ - this.edges[edgeId] = new BezierEdgeGraphFormatter(edgeId); - this.edges[edgeId].loadFromJSON(json); - } - - - if ((json.type == "CutDirectedLineEdgeGraphFormatter")||(json.type == "CutDirectedLineEdgeNetworkFormatter")){ - this.edges[edgeId] = new CutDirectedLineEdgeGraphFormatter(edgeId); - this.edges[edgeId].loadFromJSON(json); - } - - if ((json.type == "DotDirectedLineEdgeGraphFormatter")||(json.type == "DotDirectedLineEdgeNetworkFormatter")){ - this.edges[edgeId] = new DotDirectedLineEdgeGraphFormatter(edgeId); - this.edges[edgeId].loadFromJSON(json); - } - if ((json.type == "OdotDirectedLineEdgeGraphFormatter")||(json.type == "OdotDirectedLineEdgeNetworkFormatter")){ - this.edges[edgeId] = new OdotDirectedLineEdgeGraphFormatter(edgeId); - this.edges[edgeId].loadFromJSON(json); - } - - if ((json.type == "OdirectedLineEdgeGraphFormatter")||(json.type == "OdirectedLineEdgeNetworkFormatter")){ - this.edges[edgeId] = new OdirectedLineEdgeGraphFormatter(edgeId); - this.edges[edgeId].loadFromJSON(json); - } - } - - var _this = this; - this.edges[edgeId].stateChanged.attach(function (sender, item){ - _this.edgeChanged.notify(item); - }); - - this._recalculateSize(); -}; - -NetworkDataSetFormatter.prototype._setDataset = function(dataset){ - this.dataset = dataset; - this.maxClass = dataset.getMaxClass(); - this.minClass = dataset.getMinClass(); - this._attachDatasetEvents(); -}; - -NetworkDataSetFormatter.prototype.changeEdgeType = function(edgeId, type){ - if ((type == "LineEdgeGraphFormatter")||(type == "LineEdgeNetworkFormatter")){ - this.edges[edgeId] = new LineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); - - } - if ((type == "DirectedLineEdgeGraphFormatter")||(type == "DirectedLineEdgeNetworkFormatter")){ - this.edges[edgeId] = new DirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); - } - - if ((type == "CutDirectedLineEdgeGraphFormatter")||(type == "CutDirectedLineEdgeNetworkFormatter")){ - this.edges[edgeId] = new CutDirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); - } - - if ((type == "DotDirectedLineEdgeGraphFormatter")||(type == "DotDirectedLineEdgeNetworkFormatter")){ - this.edges[edgeId] = new DotDirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); - } - - if ((type == "OdotDirectedLineEdgeGraphFormatter")||(type == "OdotDirectedLineEdgeNetworkFormatter")){ - this.edges[edgeId] = new OdotDirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); - } - - if ((type == "OdirectedLineEdgeGraphFormatter")||(type == "OdirectedLineEdgeNetworkFormatter")){ - this.edges[edgeId] = new OdirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); - } - - - - var _this = this; - this.edges[edgeId].stateChanged.attach(function (sender, item){ - _this.edgeChanged.notify(item); - }); - _this.edgeChanged.notify(this.edges[edgeId]); -}; -/* -classe = "SquareNetworkNodeFormatter"; -} -if (value == "circle"){ - classe = "CircleNetworkNodeFormatter"; - **/ -NetworkDataSetFormatter.prototype.changeNodeType = function(vertexId, type){ - var defaultFormat = JSON.parse(JSON.stringify(this.vertices[vertexId].getDefault())); - var selectedFormat = JSON.parse(JSON.stringify(this.vertices[vertexId].getSelected())); - var defaultFormat = JSON.parse(JSON.stringify(this.vertices[vertexId].getDefault())); - var defaultFormat = JSON.parse(JSON.stringify(this.vertices[vertexId].getDefault())); - - if ((type == "SquareVertexGraphFormatter")||(type == "SquareVertexNetworkFormatter")){ - this.vertices[vertexId] = new SquareVertexGraphFormatter(vertexId,defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); - } - - if ((type == "CircleVertexGraphFormatter")||(type == "CircleVertexNetworkFormatter")){ - this.vertices[vertexId] = new CircleVertexGraphFormatter(vertexId, defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); - } - - if ((type == "EllipseVertexGraphFormatter")||(type == "EllipseVertexNetworkFormatter")){ - this.vertices[vertexId] = new EllipseVertexGraphFormatter(vertexId, defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); - } - - if ((type == "RectangleVertexGraphFormatter")||(type == "RectangleVertexNetworkFormatter")){ - this.vertices[vertexId] = new RectangleVertexGraphFormatter(vertexId, defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); - } - - if ((type == "RoundedVertexGraphFormatter")||(type == "RoundedVertexNetworkFormatter")){ - this.vertices[vertexId] = new RoundedVertexGraphFormatter(vertexId, defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); - } - - if ((type == "OctagonVertexGraphFormatter")||(type == "OctagonVertexNetworkhFormatter")){ - this.vertices[vertexId] = new OctagonVertexGraphFormatter(vertexId, defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); - } - - - var _this = this; - this.vertices[vertexId].stateChanged.attach(function (sender, item){ - _this.changed.notify(item); - }); - _this.changed.notify(this.vertices[vertexId]); -}; - - - -NetworkDataSetFormatter.prototype.dataBind = function(networkDataSet){ - var _this = this; - this._setDataset(networkDataSet); - - for ( var vertex in this.dataset.getVertices()) { - this.addVertex(vertex); - } - - for ( var edge in this.dataset.getEdges()) { - this.addEdge(edge); - } -}; - -NetworkDataSetFormatter.prototype._removeEdge = function(edgeId){ - delete this.edges[edgeId]; -}; - -NetworkDataSetFormatter.prototype._removeVertex = function(vertexId){ - delete this.vertices[vertexId]; -}; - -NetworkDataSetFormatter.prototype._attachDatasetEvents = function(id){ - var _this = this; - this.dataset.vertexDeleted.attach(function (sender, item){ - _this._removeVertex(item.getId()); - }); - - this.dataset.edgeDeleted.attach(function (sender, item){ - _this._removeEdge(item.getId()); - }); - - this.dataset.newVertex.attach(function (sender, item){ - _this.addVertex(item.getId()); - }); - - this.dataset.newEdge.attach(function (sender, item){ - _this.addEdge(item.getId()); - }); -}; - - -NetworkDataSetFormatter.prototype.getVertexById = function(id){ - return this.vertices[id]; -}; - -NetworkDataSetFormatter.prototype.getEdgeById = function(id){ - return this.edges[id]; -}; - -NetworkDataSetFormatter.prototype.makeLabelsBigger = function(){ -for ( var vertexId in this.vertices) { - var fontSize = this.vertices[vertexId].getDefault().getFontSize() + 2; - this.vertices[vertexId].getDefault().setFontSize(fontSize); - } -}; - -NetworkDataSetFormatter.prototype.makeLabelsSmaller = function(){ - for ( var vertexId in this.vertices) { - var fontSize = this.vertices[vertexId].getDefault().getFontSize() - 2; - this.vertices[vertexId].getDefault().setFontSize(fontSize); - } -}; - - -NetworkDataSetFormatter.prototype.resize = function(width, height){ - this.args.width = width; - this.args.height = height; - this.resized.notify(); -}; - -/** ZOOM GETTERS **/ -NetworkDataSetFormatter.prototype.getZoomScaleStepFactor = function(){return this.args.zoomScaleStepFactor;}; -NetworkDataSetFormatter.prototype.setZoomScaleStepFactor = function(scaleFactor){this.args.zoomScaleStepFactor = scaleFactor;}; -NetworkDataSetFormatter.prototype.getZoomScale = function(){return this.args.zoomScale;}; -NetworkDataSetFormatter.prototype.setZoomScale = function(scale){this.args.zoomScale = scale;}; - -NetworkDataSetFormatter.prototype.getNodesMaxSize = function(){return this.args.nodesMaxSize;}; -NetworkDataSetFormatter.prototype.getNodesMinSize = function(){return this.args.nodesMinSize;}; - -/** SIZE SETTERS AND GETTERS **/ -NetworkDataSetFormatter.prototype.isVerticesBalanced = function(){return this.args.balanceNodes;}; -NetworkDataSetFormatter.prototype.getWidth = function(){return this.args.width;}; -NetworkDataSetFormatter.prototype.getHeight = function(){return this.args.height;}; - -/** OPTIONAL PARAMETERS GETTERS AND SETTERS **/ -NetworkDataSetFormatter.prototype.getBackgroundImage = function(){return this.args.backgroundImage;}; -NetworkDataSetFormatter.prototype.setBackgroundImage = function(value){this.args.backgroundImage = value; this.backgroundImageChanged.notify(this);}; - - -NetworkDataSetFormatter.prototype.getBackgroundImageWidth = function(){return this.args.backgroundImageWidth;}; -NetworkDataSetFormatter.prototype.setBackgroundImageWidth = function(value){this.args.backgroundImageWidth = value; this.backgroundImageChanged.notify(this);}; - -NetworkDataSetFormatter.prototype.getBackgroundImageHeight = function(){return this.args.backgroundImageHeight;}; -NetworkDataSetFormatter.prototype.setBackgroundImageHeight = function(value){this.args.backgroundImageHeight = value; this.backgroundImageChanged.notify(this);}; - -NetworkDataSetFormatter.prototype.getBackgroundImageX = function(){return this.args.backgroundImageX;}; -NetworkDataSetFormatter.prototype.setBackgroundImageX = function(value){this.args.backgroundImageX = value; this.backgroundImageChanged.notify(this);}; - -NetworkDataSetFormatter.prototype.getBackgroundImageY = function(){return this.args.backgroundImageX;}; -NetworkDataSetFormatter.prototype.setBackgroundImageY = function(value){this.args.backgroundImageY = value; this.backgroundImageChanged.notify(this);}; - - - -NetworkDataSetFormatter.prototype.getBackgroundColor = function(){return this.args.backgroundColor;}; -NetworkDataSetFormatter.prototype.setBackgroundColor = function(value){this.args.backgroundColor = value; this.backgroundColorChanged.notify(this);}; - -NetworkDataSetFormatter.prototype.getWidth = function(){return this.args.width;}; -NetworkDataSetFormatter.prototype.setWidth = function(value){this.args.width = value;}; - -NetworkDataSetFormatter.prototype.getHeight = function(){return this.args.height;}; -NetworkDataSetFormatter.prototype.setHeight = function(value){this.args.height = value;}; - - - - -Vertex.prototype.getName = GraphItem.prototype.getName; -Vertex.prototype.setName = GraphItem.prototype.setName; -Vertex.prototype.getId = GraphItem.prototype.getId; - -function Vertex(id, name, args){ - GraphItem.prototype.constructor.call(this, id, name, args); - this.edgesIn= new Array(); - this.edgesOut= new Array(); -}; - -Vertex.prototype.getEdges = function(){ - return this.edgesIn.concat(this.edgesOut); -}; - -Vertex.prototype.getEdgesCount = function(){ - return this.getEdges().length; -}; - -Vertex.prototype.getEdgesIn = function(){ - return this.edgesIn; -}; - -Vertex.prototype.getEdgesOut = function(){ - return this.edgesOut; -}; - -Vertex.prototype.addEdge = function(edge){ - if (edge.getNodeSource().getId() == this.id){ - this.edgesIn.push(edge); - } - else{ - this.edgesOut.push(edge); - } -}; - -Vertex.prototype.removeEdge = function(edge){ - for ( var i = 0; i < this.getEdgesIn().length; i++) { - var edgeIn = this.edgesIn[i]; - if (edgeIn.getId() == edge.getId()){ - this.edgesIn.splice(i, 1); - } - } - for ( var i = 0; i < this.getEdgesOut().length; i++) { - var edgeIn = this.edgesOut[i]; - if (edgeIn.getId() == edge.getId()){ - this.edgesOut.splice(i, 1); - } - } -}; - -Vertex.prototype.remove = function(){ - var edges = this.getEdges(); - for ( var i = 0; i < edges.length; i++) { - var edge = edges[i]; - edge.remove(); - } - this.deleted.notify(this); -}; - - - - - -VertexGraphFormatter.prototype.getDefault = ItemGraphFormatter.prototype.getDefault; -VertexGraphFormatter.prototype.getSelected = ItemGraphFormatter.prototype.getSelected; -VertexGraphFormatter.prototype.getOver = ItemGraphFormatter.prototype.getOver; -VertexGraphFormatter.prototype.getDragging = ItemGraphFormatter.prototype.getDragging; -VertexGraphFormatter.prototype.getId = ItemGraphFormatter.prototype.getId; -VertexGraphFormatter.prototype.toJSON = ItemGraphFormatter.prototype.toJSON; -VertexGraphFormatter.prototype.loadFromJSON = ItemGraphFormatter.prototype.loadFromJSON; -VertexGraphFormatter.prototype._setEvents = ItemGraphFormatter.prototype._setEvents; - - -function VertexGraphFormatter(defaultFormat, selectedFormat, overFormat, draggingFormat){ - ItemGraphFormatter.prototype.constructor.call(this, defaultFormat, selectedFormat, overFormat, draggingFormat); -}; - - -CircleVertexGraphFormatter.prototype.getDefault = VertexGraphFormatter.prototype.getDefault; -CircleVertexGraphFormatter.prototype.getSelected = VertexGraphFormatter.prototype.getSelected; -CircleVertexGraphFormatter.prototype.getOver = VertexGraphFormatter.prototype.getOver; -CircleVertexGraphFormatter.prototype.getDragging = VertexGraphFormatter.prototype.getDragging; -CircleVertexGraphFormatter.prototype.getId = VertexGraphFormatter.prototype.getId; -CircleVertexGraphFormatter.prototype.toJSON = VertexGraphFormatter.prototype.toJSON; -CircleVertexGraphFormatter.prototype.loadFromJSON = VertexGraphFormatter.prototype.loadFromJSON; -CircleVertexGraphFormatter.prototype._setEvents = VertexGraphFormatter.prototype._setEvents; - -function CircleVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ - VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); - this.args.type = "CircleVertexGraphFormatter"; - if (defaultFormat != null){ - if (defaultFormat.radius != null){ - this.defaultFormat.args.radius = defaultFormat.radius; - } - } - - if (selectedFormat != null){ - if (selectedFormat.radius != null){ - this.selected.args.radius = selectedFormat.radius; - } - } - - if (overFormat != null){ - if (overFormat.radius != null){ - this.over.args.radius = overFormat.radius; - } - } - - if (draggingFormat != null){ - if (draggingFormat.radius != null){ - this.dragging.args.draggingFormat = draggingFormat.radius; - } - } -}; - - - -SquareVertexGraphFormatter.prototype.getDefault = VertexGraphFormatter.prototype.getDefault; -SquareVertexGraphFormatter.prototype.getSelected = VertexGraphFormatter.prototype.getSelected; -SquareVertexGraphFormatter.prototype.getOver = VertexGraphFormatter.prototype.getOver; -SquareVertexGraphFormatter.prototype.getDragging = VertexGraphFormatter.prototype.getDragging; -SquareVertexGraphFormatter.prototype.getId = VertexGraphFormatter.prototype.getId; -SquareVertexGraphFormatter.prototype.toJSON = VertexGraphFormatter.prototype.toJSON; -SquareVertexGraphFormatter.prototype.loadFromJSON = VertexGraphFormatter.prototype.loadFromJSON; -SquareVertexGraphFormatter.prototype._setEvents = VertexGraphFormatter.prototype._setEvents; - -function SquareVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ - VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); - this.args.type = "SquareVertexGraphFormatter"; - if (defaultFormat != null){ - if (defaultFormat.radius != null){ - this.defaultFormat.args.radius = defaultFormat.radius; - } - } - - if (selectedFormat != null){ - if (selectedFormat.radius != null){ - this.selected.args.radius = selectedFormat.radius; - } - } - - if (overFormat != null){ - if (overFormat.radius != null){ - this.over.args.radius = overFormat.radius; - } - } - - if (draggingFormat != null){ - if (draggingFormat.radius != null){ - this.dragging.args.draggingFormat = draggingFormat.radius; - } - } -}; - - -EllipseVertexGraphFormatter.prototype.getDefault = VertexGraphFormatter.prototype.getDefault; -EllipseVertexGraphFormatter.prototype.getSelected = VertexGraphFormatter.prototype.getSelected; -EllipseVertexGraphFormatter.prototype.getOver = VertexGraphFormatter.prototype.getOver; -EllipseVertexGraphFormatter.prototype.getDragging = VertexGraphFormatter.prototype.getDragging; -EllipseVertexGraphFormatter.prototype.getId = VertexGraphFormatter.prototype.getId; -EllipseVertexGraphFormatter.prototype.toJSON = VertexGraphFormatter.prototype.toJSON; -EllipseVertexGraphFormatter.prototype.loadFromJSON = VertexGraphFormatter.prototype.loadFromJSON; -EllipseVertexGraphFormatter.prototype._setEvents = VertexGraphFormatter.prototype._setEvents; - -function EllipseVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ - VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); - this.args.type = "EllipseVertexGraphFormatter"; - if (defaultFormat != null){ - if (defaultFormat.radius != null){ - this.defaultFormat.args.radius = defaultFormat.radius; - } - } - - if (selectedFormat != null){ - if (selectedFormat.radius != null){ - this.selected.args.radius = selectedFormat.radius; - } - } - - if (overFormat != null){ - if (overFormat.radius != null){ - this.over.args.radius = overFormat.radius; - } - } - - if (draggingFormat != null){ - if (draggingFormat.radius != null){ - this.dragging.args.draggingFormat = draggingFormat.radius; - } - } -}; - - - -RectangleVertexGraphFormatter.prototype.getDefault = ItemGraphFormatter.prototype.getDefault; -RectangleVertexGraphFormatter.prototype.getSelected = ItemGraphFormatter.prototype.getSelected; -RectangleVertexGraphFormatter.prototype.getOver = ItemGraphFormatter.prototype.getOver; -RectangleVertexGraphFormatter.prototype.getDragging = ItemGraphFormatter.prototype.getDragging; -RectangleVertexGraphFormatter.prototype.getId = ItemGraphFormatter.prototype.getId; -RectangleVertexGraphFormatter.prototype.toJSON = ItemGraphFormatter.prototype.toJSON; -RectangleVertexGraphFormatter.prototype.loadFromJSON = ItemGraphFormatter.prototype.loadFromJSON; -RectangleVertexGraphFormatter.prototype._setEvents = ItemGraphFormatter.prototype._setEvents; - -function RectangleVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ - VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); - this.args.type = "RectangleVertexGraphFormatter"; - if (defaultFormat != null){ - if (defaultFormat.radius != null){ - this.defaultFormat.args.radius = defaultFormat.radius; - } - } - - if (selectedFormat != null){ - if (selectedFormat.radius != null){ - this.selected.args.radius = selectedFormat.radius; - } - } - - if (overFormat != null){ - if (overFormat.radius != null){ - this.over.args.radius = overFormat.radius; - } - } - - if (draggingFormat != null){ - if (draggingFormat.radius != null){ - this.dragging.args.draggingFormat = draggingFormat.radius; - } - } -}; - - - -RoundedVertexGraphFormatter.prototype.getDefault = ItemGraphFormatter.prototype.getDefault; -RoundedVertexGraphFormatter.prototype.getSelected = ItemGraphFormatter.prototype.getSelected; -RoundedVertexGraphFormatter.prototype.getOver = ItemGraphFormatter.prototype.getOver; -RoundedVertexGraphFormatter.prototype.getDragging = ItemGraphFormatter.prototype.getDragging; -RoundedVertexGraphFormatter.prototype.getId = ItemGraphFormatter.prototype.getId; -RoundedVertexGraphFormatter.prototype.toJSON = ItemGraphFormatter.prototype.toJSON; -RoundedVertexGraphFormatter.prototype.loadFromJSON = ItemGraphFormatter.prototype.loadFromJSON; -RoundedVertexGraphFormatter.prototype._setEvents = ItemGraphFormatter.prototype._setEvents; - -function RoundedVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ - VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); - this.args.type = "RoundedVertexGraphFormatter"; - if (defaultFormat != null){ - if (defaultFormat.radius != null){ - this.defaultFormat.args.radius = defaultFormat.radius; - } - } - - if (selectedFormat != null){ - if (selectedFormat.radius != null){ - this.selected.args.radius = selectedFormat.radius; - } - } - - if (overFormat != null){ - if (overFormat.radius != null){ - this.over.args.radius = overFormat.radius; - } - } - - if (draggingFormat != null){ - if (draggingFormat.radius != null){ - this.dragging.args.draggingFormat = draggingFormat.radius; - } - } -}; - - - -OctagonVertexGraphFormatter.prototype.getDefault = ItemGraphFormatter.prototype.getDefault; -OctagonVertexGraphFormatter.prototype.getSelected = ItemGraphFormatter.prototype.getSelected; -OctagonVertexGraphFormatter.prototype.getOver = ItemGraphFormatter.prototype.getOver; -OctagonVertexGraphFormatter.prototype.getDragging = ItemGraphFormatter.prototype.getDragging; -OctagonVertexGraphFormatter.prototype.getId = ItemGraphFormatter.prototype.getId; -OctagonVertexGraphFormatter.prototype.toJSON = ItemGraphFormatter.prototype.toJSON; -OctagonVertexGraphFormatter.prototype.loadFromJSON = ItemGraphFormatter.prototype.loadFromJSON; -OctagonVertexGraphFormatter.prototype._setEvents = ItemGraphFormatter.prototype._setEvents; - -function OctagonVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ - VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); - this.args.type = "OctagonVertexGraphFormatter"; - if (defaultFormat != null){ - if (defaultFormat.radius != null){ - this.defaultFormat.args.radius = defaultFormat.radius; - } - } - - if (selectedFormat != null){ - if (selectedFormat.radius != null){ - this.selected.args.radius = selectedFormat.radius; - } - } - - if (overFormat != null){ - if (overFormat.radius != null){ - this.over.args.radius = overFormat.radius; - } - } - - if (draggingFormat != null){ - if (draggingFormat.radius != null){ - this.dragging.args.draggingFormat = draggingFormat.radius; - } - } -}; - - - -var Colors = new function() -{ - this.hashColor = []; - this.getColorByScoreArrayValue = function (arrayScore) - { - var array = new Array(); - - for (var i = 0; i< arrayScore.length; i++) - { - - var color = this.getColorByScoreValue(arrayScore[i]) - array.push( color); - - } - return array; - }; - - this.getHexStringByScoreArrayValue = function (arrayScore) - { - var arrayColor = this.getColorByScoreArrayValue(arrayScore); - var arrayHex = new Array(); - for (var i = 0; i< arrayColor.length; i++) - { - arrayHex.push( arrayColor[i].HexString()); - } - return arrayHex; - }; - - this.getColorByScoreValue = function (score) - { - - var truncate = score.toString().substr(0,4); - if (this.hashColor[truncate]!=null) - { - return this.hashColor[truncate]; - } - - - if(isNaN(score)) { - return Colors.ColorFromRGB(0,0,0); - } - var value; - - var from, to; - if(score < 0.5) { - from = Colors.ColorFromRGB(0,0,255); - to = Colors.ColorFromRGB(255,255,255); - value = (score * 2); - } else { - from = Colors.ColorFromRGB(255,255,255); - to = Colors.ColorFromRGB(255,0,0); - value = (score * 2) - 1; - } - - var x = value; - var y = 1.0 - value; - var color = Colors.ColorFromRGB(y * from.Red() + x * to.Red(), y * from.Green() + x * to.Green(), y * from.Blue() + x * to.Blue()); - - this.hashColor[truncate] = color; - - return color; - }; - - this.ColorFromHSV = function(hue, sat, val) - { - var color = new Color(); - color.SetHSV(hue,sat,val); - return color; - }; - - this.ColorFromRGB = function(r, g, b) - { - var color = new Color(); - color.SetRGB(r,g,b); - return color; - }; - - this.ColorFromHex = function(hexStr) - { - var color = new Color(); - color.SetHexString(hexStr); - return color; - }; - - function Color() { - //Stored as values between 0 and 1 - var red = 0; - var green = 0; - var blue = 0; - - //Stored as values between 0 and 360 - var hue = 0; - - //Strored as values between 0 and 1 - var saturation = 0; - var value = 0; - - this.SetRGB = function(r, g, b) - { - red = r/255.0; - green = g/255.0; - blue = b/255.0; - calculateHSV(); - }; - - this.Red = function() { return Math.round(red*255); }; - - this.Green = function() { return Math.round(green*255); }; - - this.Blue = function() { return Math.round(blue*255); }; - - this.SetHSV = function(h, s, v) - { - hue = h; - saturation = s; - value = v; - calculateRGB(); - }; - - this.Hue = function() - { return hue; }; - - this.Saturation = function() - { return saturation; }; - - this.Value = function() - { return value; }; - - this.SetHexString = function(hexString) - { - if(hexString == null || typeof(hexString) != "string") - { - this.SetRGB(0,0,0); - return; - } - - if (hexString.substr(0, 1) == '#') - hexString = hexString.substr(1); - - if(hexString.length != 6) - { - this.SetRGB(0,0,0); - return; - } - - var r = parseInt(hexString.substr(0, 2), 16); - var g = parseInt(hexString.substr(2, 2), 16); - var b = parseInt(hexString.substr(4, 2), 16); - if (isNaN(r) || isNaN(g) || isNaN(b)) - { - this.SetRGB(0,0,0); - return; - } - - this.SetRGB(r,g,b); - }; - - this.HexString = function() - { - - var rStr = this.Red().toString(16); - if (rStr.length == 1) - rStr = '0' + rStr; - var gStr = this.Green().toString(16); - if (gStr.length == 1) - gStr = '0' + gStr; - var bStr = this.Blue().toString(16); - if (bStr.length == 1) - bStr = '0' + bStr; - return ('#' + rStr + gStr + bStr).toUpperCase(); - }; - - this.Complement = function() - { - var newHue = (hue >= 180) ? hue - 180 : hue + 180; - var newVal = (value * (saturation - 1) + 1); - var newSat = (value*saturation) / newVal; - var newColor = new Color(); - newColor.SetHSV(newHue, newSat, newVal); - return newColor; - } ; - - function calculateHSV() - { - var max = Math.max(Math.max(red, green), blue); - var min = Math.min(Math.min(red, green), blue); - - value = max; - - saturation = 0; - if(max != 0) - saturation = 1 - min/max; - - hue = 0; - if(min == max) - return; - - var delta = (max - min); - if (red == max) - hue = (green - blue) / delta; - else if (green == max) - hue = 2 + ((blue - red) / delta); - else - hue = 4 + ((red - green) / delta); - hue = hue * 60; - if(hue < 0) - hue += 360; - } - - function calculateRGB() - { - red = value; - green = value; - blue = value; - - if(value == 0 || saturation == 0) - return; - - var tHue = (hue / 60); - var i = Math.floor(tHue); - var f = tHue - i; - var p = value * (1 - saturation); - var q = value * (1 - saturation * f); - var t = value * (1 - saturation * (1 - f)); - switch(i) - { - case 0: - red = value; green = t; blue = p; - break; - case 1: - red = q; green = value; blue = p; - break; - case 2: - red = p; green = value; blue = t; - break; - case 3: - red = p; green = q; blue = value; - break; - case 4: - red = t; green = p; blue = value; - break; - default: - red = value; green = p; blue = q; - break; - } - } - } -} -(); -/* - * Clase gestiona la insercción, eliminación de los elementos en el DOM - * - * Vital hacerla SIEMPRE compatible hacia atrás - * - * Last update: 28-10-2010 - * - */ - - -var DOM = {}; - -DOM.createNewElement = function(type, nodeParent, attributes) -{ - - var node = document.createElement(type); - for (var i=0; i0) - { - parent.removeChild(parent.childNodes[0]); - - } -}; - -DOM.select = function(targetID) -{ - return document.getElementById(targetID); -// return $("#"+targetID); -}; -var Geometry = -{ - - /** From tow points obtains the angles formed with the cartesian side **/ - getAngleBetweenTwoPoints : function(x1, y1, x2, y2){ - //var m = (y1 - y2)/ (x1 - x2); - return Math.atan2(y2-y1, x2-x1); - }, - - getAdjacentSideOfRectangleRight : function(angle, hypotenuse){ - return Math.abs(Math.cos(angle)*hypotenuse); - }, - - getOppositeSideOfRectangleRight : function(angle, hypotenuse){ - return Math.abs(Math.sin(angle)*hypotenuse); - }, - - toDegree: function(radian){ - return radian*180/Math.PI; - - } - - -}; - -var SVG = -{ - svgns : 'http://www.w3.org/2000/svg', - xlinkns : "http://www.w3.org/1999/xlink", - - createSVGCanvas: function(parentNode, attributes) - { - - attributes.push( ['xmlns', SVG.svgns], ['xmlns:xlink', 'http://www.w3.org/1999/xlink']); - var svg = document.createElementNS("http://www.w3.org/2000/svg", "svg"); - this._setProperties(svg, attributes); - parentNode.appendChild( svg); - return svg; - - }, - - createRectangle : function (x, y, width, height, attributes){ - var rect = document.createElementNS(this.svgns, "rect"); - rect.setAttribute("x",x); - rect.setAttribute("y",y); - rect.setAttribute("width",width); - rect.setAttribute("height",height); - SVG._setProperties(rect, attributes); - return rect; - }, - - drawImage64 : function (x, y, width, height, base64, svgNode, attributes) { - var node = SVG.createImage64(x, y, width, height, base64, attributes); - svgNode.appendChild(node); - return node; - }, - - createImage64 : function (x, y, width, height, base64, attributes) { - var img = document.createElementNS(this.svgns, "image"); - img.setAttribute("x",x); - img.setAttribute("y",y); - img.setAttribute("width",width); - img.setAttribute("height",height); - img.setAttribute("xlink:href",base64); - SVG._setProperties(img, attributes); - return img; - }, - - createLine: function (x1, y1, x2, y2, attributes){ - var line = document.createElementNS(this.svgns,"line"); - line.setAttribute("x1",x1); - line.setAttribute("y1",y1); - line.setAttribute("x2", x2); - line.setAttribute("y2", y2); - SVG._setProperties(line, attributes); - return line; - }, - - createClip: function (id, nodeToClip, attributes){ - var clip = document.createElementNS(this.svgns,"clipPath"); - clip.setAttribute("id",id); - clip.appendChild(nodeToClip); - return clip; - }, - - drawClip : function (id, nodeToClip, svgNode) { - var node = SVG.createClip(id, nodeToClip); - svgNode.appendChild(node); - return node; - }, - - drawRectangle : function (cx, cy, width, height, svgNode, attributes) { - try{ - var node = SVG.createRectangle(cx, cy, width, height, attributes); - svgNode.appendChild(node); - } - catch(e){ - - console.log("-------------------- "); - console.log("Error on drawRectangle " + e); - console.log(attributes); - console.log("-------------------- "); - } - return node; - }, - - createEllipse : function (x, y, rx, ry, attributes){ - var rect = document.createElementNS(this.svgns, "ellipse"); - rect.setAttribute("cx",x); - rect.setAttribute("cy",y); - rect.setAttribute("rx",rx); - rect.setAttribute("ry",ry); - SVG._setProperties(rect, attributes); - return rect; - }, - - drawEllipse : function (cx, cy, rx, ry, svgNode, attributes) { - var node = SVG.createEllipse(cx, cy, rx, ry, attributes); - svgNode.appendChild(node); - return node; - }, - - drawImage : function (x, y, canvasSVG, attributes) { - var image = document.createElementNS(this.svgns, "image"); - image.setAttribute("x",x); - image.setAttribute("y",y); - canvasSVG.appendChild(image); - SVG._setProperties(image, attributes); - }, - - drawLine : function (x1, y1, x2, y2, nodeSVG, attributes) { - try{ - var line = SVG.createLine(x1, y1, x2, y2, attributes); - nodeSVG.appendChild(line); - }catch(e){ - } - return line; - }, - - - drawPath: function (d, nodeSVG, attributes) { - var path = SVG.createPath(d, attributes); - nodeSVG.appendChild(path); - return path; - }, - - createPoligon : function (points, attributes){ - var poligon = document.createElementNS(this.svgns, "polygon"); - poligon.setAttribute("points",points); - SVG._setProperties(poligon, attributes); - return poligon; - }, - - drawPoligon : function (points, canvasSVG, attributes){ - var poligon = SVG.createPoligon(points, attributes); - canvasSVG.appendChild(poligon); - return poligon; - }, - // - - createPath : function (d, attributes){ - var path = document.createElementNS(this.svgns, "path"); - path.setAttribute("d",d); - SVG._setProperties(path, attributes); - return path; - }, - - drawCircle : function (x, y, radio, canvasSVG, attributes) { - - var newText = document.createElementNS(this.svgns,"circle"); - newText.setAttribute("cx",x); - newText.setAttribute("cy",y); - newText.setAttribute("r",radio); - - canvasSVG.appendChild(newText); - attributes["cursor"] = "pointer"; - this._setProperties(newText, attributes); - return newText; - }, - - - _setProperties: function(node, attributes) - { - if (attributes instanceof Array){ - for (var i=0; i< attributes.length; i++) - { - node.setAttribute(attributes[i][0], attributes[i][1]); - } - } - else{ - for ( var key in attributes){ - node.setAttribute(key, attributes[key]); - } - } - }, - -/* drawPath: function(pointsArray, canvasSVG, attributes){ - var path = document.createElementNS(this.svgns,"polyline"); - path.setAttribute ('id', id); - - var d= pointsArray[0].x+ " "+ pointsArray[0].y; - for (var i=1; i< pointsArray.length; i++) - { - d=d+" "+pointsArray[i].x+" "+pointsArray[i].y; - } - path.setAttribute ('points', d); - canvasSVG.appendChild(path); - },*/ - - createText : function (x, y, text, attributes) { - var node = document.createElementNS(this.svgns,"text"); - node.setAttributeNS(null , "x",x); - node.setAttributeNS(null, "y",y); - - var textNode = document.createTextNode(text); - node.appendChild(textNode); - - this._setProperties(node, attributes); - return node; - }, - - drawText : function (x, y, text, canvasSVG, attributes) { - var text = SVG.createText(x, y, text, attributes); - canvasSVG.appendChild(text); - return text; - }, - - - - drawGroup: function(svgNode, attributes) - { - var group = SVG.createGroup(attributes); - svgNode.appendChild(group); - return group; - }, - - createGroup: function(attributes){ - var group = document.createElementNS(this.svgns,"g"); - this._setProperties(group, attributes); - return group; - } - -}; - - - -var CanvasToSVG = { - - convert: function(sourceCanvas, targetSVG, x, y, id, attributes) { - - var img = this._convert(sourceCanvas, targetSVG, x, y, id); - - for (var i=0; i< attributes.length; i++) - { - img.setAttribute(attributes[i][0], attributes[i][1]); - } - }, - - _convert: function(sourceCanvas, targetSVG, x, y, id) { - var svgNS = "http://www.w3.org/2000/svg"; - var xlinkNS = "http://www.w3.org/1999/xlink"; - // get base64 encoded png from Canvas - var image = sourceCanvas.toDataURL(); - - // must be careful with the namespaces - var svgimg = document.createElementNS(svgNS, "image"); - - svgimg.setAttribute('id', id); - - //svgimg.setAttribute('class', class); - //svgimg.setAttribute('xlink:href', image); - svgimg.setAttributeNS(xlinkNS, 'xlink:href', image); - - - - - svgimg.setAttribute('x', x ? x : 0); - svgimg.setAttribute('y', y ? y : 0); - svgimg.setAttribute('width', sourceCanvas.width); - svgimg.setAttribute('height', sourceCanvas.height); - //svgimg.setAttribute('cursor', 'pointer'); - svgimg.imageData = image; - - targetSVG.appendChild(svgimg); - return svgimg; - }, - - importSVG: function(sourceSVG, targetCanvas) { - svg_xml = sourceSVG;//(new XMLSerializer()).serializeToString(sourceSVG); - var ctx = targetCanvas.getContext('2d'); - - var img = new Image(); - img.src = "data:image/svg+xml;base64," + btoa(svg_xml); -// img.onload = function() { - ctx.drawImage(img, 0, 0); -// }; - } - -}; -/* -Graph.prototype.importSVG = function(sourceSVG, targetCanvas) { - sourceSVG = this._svg; - targetCanvas = document.createElementNS('canvas'); - // https://developer.mozilla.org/en/XMLSerializer - svg_xml = (new XMLSerializer()).serializeToString(sourceSVG); - var ctx = targetCanvas.getContext('2d'); - // this is just a JavaScript (HTML) image - var img = new Image(); - // http://en.wikipedia.org/wiki/SVG#Native_support - // https://developer.mozilla.org/en/DOM/window.btoa - img.src = "data:image/svg+xml;base64," + btoa(svg_xml); - img.onload = function() { - // after this, Canvas’ origin-clean is DIRTY - ctx.drawImage(img, 0, 0); - } -}; -*/ - -/* - -Normalizacion de datos para dibujar colores -Issues: - No sé como debería llamarse esta libreria - No sé si ya existe una funciçon en javascript que lo haga - - -*/ - - -var Normalizer = new function() -{ - this.normalizeArray = function (arrayData) - { - - return this.standardizeArray(this.normal(arrayData)); - -// var result = this._getMaxAndMin(arrayData); -// var min =result[0]; -// var max = result[1]; -// -// -// //los hacemos todos positivos -// for (var i = 0; i< arrayData.length; i++) -// { -// arrayData[i]= Math.abs(min) + parseFloat(arrayData[i]); -// } -// -// var result = this._getMaxAndMin(arrayData); -// var min =result[0]; -// var max = result[1]; -// -// -// var resultArray = new Array(); -// for (var i = 0; i< arrayData.length; i++) -// { -// resultArray.push(arrayData[i]*1/max); -// } -// return resultArray; - }; - - this.normal = function(arrayData){ - var mean = this._getMean(arrayData); - var deviation = this._getStdDeviation(arrayData); - var result = this._getMaxAndMin(arrayData); - var min = result[0]; - var max = result[1]; - - var resultArray = new Array(); - for (var i = 0; i< arrayData.length; i++) { - if (deviation!=0){ - resultArray.push((arrayData[i]-mean)/deviation); - }else{ - resultArray.push(arrayData[i]); - } - } - return resultArray; - }; - - this.standardizeArray = function(arrayData) - { - var result = this._getMaxAndMin(arrayData); - var min = result[0]; - var max = result[1]; - - var offset = ( min <= 0 ) ? Math.abs(min) : (-1 * min); - var resultArray = new Array(); - for (var i = 0; i< arrayData.length; i++) { - if(max + offset!=0){ - resultArray.push((arrayData[i] + offset) / (max + offset)); - }else{ - resultArray.push(arrayData[i]+offset); - } - } - return resultArray; - }; - - - this._getMean = function(arrayData) { - var sum = 0; - for (var i = 0; i< arrayData.length; i++) { - sum = sum + parseFloat(arrayData[i]); - } - return sum/arrayData.length; - }; - - this._getStdDeviation = function(arrayData) { - var mean = this._getMean(arrayData); - var acum = 0.0; - for(var i=0; i max) max = parseFloat(arrayData[i]); - } - - return [min, max]; - }; -}; -function GraphCanvas(componentID, targetNode, args) { - this.args = {}; - /** target */ - this.targetID = targetNode.id; - - /** id manage */ - this.id = componentID; - this.args.idGraph = this.id + "main"; - this.args.idBackgroundNode = this.id + "background"; - - this.args.idEdgesGraph = this.id + "edges"; - this.args.idNodesGraph = this.id + "vertices"; - this.args.idLabelGraph = this.id + "label"; - this.args.idBackground = this.id + "background"; - - /** Objects Graph **/ - this.dataset = null; - this.formatter = null; - this.layout = null; - - /** Drawing **/ - this.circleDefaultRadius = 2; - this.squareDefaultSide = this.circleDefaultRadius * 1.5; - - /** Directed Arrow **/ - this.arrowDefaultSize = this.circleDefaultRadius; - - /** Groups **/ - this.GraphGroup = null; - this.GraphNodeGroup = null; - this.GraphLabelGroup = null; - this.GraphBackground = null; - - /** SETTINGS FLAGS **/ - this.args.draggingCanvasEnabled = false; //Flag to set if the canvas can be dragged - this.args.multipleSelectionEnabled = false; - this.args.interactive = false; - this.args.labeled = false; - this.args.linkEnabled = false; - - /** If numberEdge > maxNumberEdgesMoving then only it will move edges when mouse up **/ - this.args.maxNumberEdgesMoving = 3; - this.args.maxNumberEdgesFiringEvents = 50; - - /** Linking edges **/ - this.args.linking = false; - this.linkStartX = 0; - this.linkStartY = 0; - this.linkSVGNode = null; - this.linkNodeSource = null; - this.linkNodeTarget = null; - - /** Dragging Control **/ - this.draggingElement = null; - this.dragging = false; - this.nMouseOffsetX = 0; - this.nMouseOffsetY = 0; - this.dragStartX = 0; - this.dragStartY = 0; - this.desplazamientoX = 0; - this.desplazamientoY = 0; - - /** Selection Control **/ - this.selecting = false; - this.selectorX = null; - this.selectorY = null; - this.selectorSVGNode = null; - - /** Node status **/ - this.args.isVertexSelected = {}; - this.args.selectedVertices = []; - - /** Edges status **/ - this.args.isEdgeSelected = {}; - //this.args.selectedEdges = []; - - if (args != null) { - if (args.multipleSelectionEnabled != null) { - this.args.multipleSelectionEnabled = args.multipleSelectionEnabled; - this.args.draggingCanvasEnabled = !(this.args.multipleSelectionEnabled); - } - if (args.draggingCanvasEnabled != null) { - this.args.draggingCanvasEnabled = args.draggingCanvasEnabled; - this.args.multipleSelectionEnabled = !(this.args.draggingCanvasEnabled); - } - if (args.interactive != null) { - this.args.interactive = args.interactive; - } - if (args.labeled != null) { - this.args.labeled = args.labeled; - } - - } - - /** Hashmap with the svg node labels **/ - this.svgLabels = {}; - - /** EVENTS **/ - this.onVertexOut = new Event(this); - this.onVertexOver = new Event(this); - this.onVertexSelect = new Event(this); - this.onEdgeSelect = new Event(this); - this.onCanvasClicked = new Event(this); - this.onVertexUp = new Event(this); -} - -GraphCanvas.prototype.showLabels = function(value) { - this.args.labeled = value; - this.removeLabels(); - if (value) { - this.renderLabels(); - } -}; - -GraphCanvas.prototype.getSelectedVertices = function() { - return this.args.selectedVertices; -}; - -GraphCanvas.prototype.getSelectedEdges = function() { - var selected = []; - for ( var selectedEdge in this.args.isEdgeSelected) { - selected.push(selectedEdge); - } - return selected; -}; - -GraphCanvas.prototype.createSVGDom = function(targetID, id, width, height, backgroundColor) { - var container = document.getElementById(targetID); - this._svg = SVG.createSVGCanvas(container, [ - [ "style", "background-color:" + backgroundColor + ";" ], [ "id", id ], [ "dragx", 0 ], [ "dragy", 0 ], - [ "height", this.getFormatter().getHeight() ], [ "width", this.getFormatter().getWidth() ] ]); - return this._svg; -}; - -/** MULTIPLE SELECTION **/ -GraphCanvas.prototype.isMultipleSelectionEnabled = function() { - return this.args.multipleSelectionEnabled; -}; - -GraphCanvas.prototype.setMultipleSelection = function(value) { - this.args.multipleSelectionEnabled = value; - this.args.draggingCanvasEnabled = (!value); -}; - -GraphCanvas.prototype.setSelecting = function(value) { - this.selecting = value; -}; - -/** linking **/ -GraphCanvas.prototype.setLinking = function(value) { - this.args.linkEnabled = value; - this.selecting = !value; - this.dragging = !value; -}; - -/** CANVAS MOVING **/ -GraphCanvas.prototype.setDraggingCanvas = function(value) { - this.args.draggingCanvasEnabled = value; - this.args.multipleSelectionEnabled = !value; -}; - -GraphCanvas.prototype.isDraggingCanvasEnabled = function() { - return this.args.draggingCanvasEnabled; -}; -/** ZOOM **/ -GraphCanvas.prototype.getScale = function() { - return this.getFormatter().getZoomScale(); -}; - -GraphCanvas.prototype.setScale = function(scale) { - var graphNode = document.getElementById(this.args.idGraph); - graphNode.setAttribute("transform", graphNode.getAttribute("transform").replace("scale(" + this.getScale() + ")", "scale(" + scale + ")")); - this.getFormatter().setZoomScale(scale); -}; - -GraphCanvas.prototype.zoomIn = function() { - this.setScale(this.getScale() + this.getFormatter().getZoomScaleStepFactor()); -}; - -GraphCanvas.prototype.zoomOut = function() { - this.setScale(this.getScale() - this.getFormatter().getZoomScaleStepFactor()); - -}; - -/** SVG COORDENATES **/ -GraphCanvas.prototype.getSVGCoordenates = function(evt) { - var p = this._svg.createSVGPoint(); - p.x = evt.clientX; - p.y = evt.clientY; - - var m = this._svg.getScreenCTM(document.documentElement); - p = p.matrixTransform(m.inverse()); - return p; -}; - -/** SVG EVENTS **/ -GraphCanvas.prototype.mouseClick = function(event) { - if (event.button == 0) { - if (!this.args.interactive) { - return; - } - - if (this.isVertex(event.target)) { - this.clickNode(this.getVertexIdFromSVGId(event.target.id)); - } - /** Como el evento mouseClick viene despues del mouse up es aqui donde manejo el tema de deseccionar los elementos que estoy dragging **/ - if (this.dragging) { - this.dragging = false; - } - } -}; - -GraphCanvas.prototype.mouseMove = function(evt) { - if (this.selecting) { - this.clearLabels(); - - var width = (this.getSVGCoordenates(evt).x - this.selectorX); - var height = (this.getSVGCoordenates(evt).y - this.selectorY); - if ((width > 0) && (height > 0)) { - this.displaySelection(this.selectorX, this.selectorY, width, height); - } - if ((width > 0) && (height < 0)) { - this.displaySelection(this.selectorX, this.getSVGCoordenates(evt).y, width, Math.abs(height)); - } - if ((width < 0) && (height < 0)) { - this.displaySelection(this.getSVGCoordenates(evt).x, this.getSVGCoordenates(evt).y, Math.abs(width), Math.abs(height)); - } - if ((width < 0) && (height > 0)) { - this.displaySelection(this.selectorX + width, this.selectorY, Math.abs(width), Math.abs(height)); - } - - var x1 = (parseFloat(this.selectorSVGNode.getAttribute("x")) - DOM.select(this.id).getAttribute("dragx")) / this.getFormatter().getWidth(); - var y1 = (parseFloat(this.selectorSVGNode.getAttribute("y")) - DOM.select(this.id).getAttribute("dragy")) / this.getFormatter().getHeight(); - var x2 = (x1 + parseFloat(this.selectorSVGNode.getAttribute("width") / this.getFormatter().getWidth())); - var y2 = (y1 + parseFloat(this.selectorSVGNode.getAttribute("height") / this.getFormatter().getHeight())); - - this.deselectNodes(this.getLayout()); - var verticesSelected = this.getLayout().getVerticesByArea(x1 / this.getFormatter().getZoomScale(), y1 / this.getFormatter().getZoomScale(), - x2 / this.getFormatter().getZoomScale(), y2 / this.getFormatter().getZoomScale()); - for ( var i = 0; i < verticesSelected.length; i++) { - this.selectNode(verticesSelected[i].getId()); - this.renderLabel(verticesSelected[i].getId()); - } - - } - var p = null; - if (this.args.linking) { - p = this.getSVGCoordenates(evt); - if (this.linkSVGNode != null) { - this.linkSVGNode.setAttribute("x2", p.x - 2); - this.linkSVGNode.setAttribute("y2", p.y - 2); - } - } - - if (this.dragging) { - p = this.getSVGCoordenates(evt); - p.x -= this.nMouseOffsetX; - p.y -= this.nMouseOffsetY; - this.desplazamientoX = (this.getSVGCoordenates(evt).x - this.dragStartX);// + parseFloat(DOM.select(this.id).getAttribute("dragx")); - this.desplazamientoY = (this.getSVGCoordenates(evt).y - this.dragStartY);// + parseFloat(DOM.select(this.id).getAttribute("dragy")); - - if (this.draggingElement != null) { - /** Click sobre el recct del banground que provoca que mueva todo el canvas **/ - if (this.isNodeCanvas(this.draggingElement)) { - - p = this.getSVGCoordenates(evt); - p.x = this.desplazamientoX; - p.y = this.desplazamientoY; - - this.draggingElement.setAttribute("dragx", p.x); - this.draggingElement.setAttribute("dragy", p.y); - this.draggingElement = document.getElementById(this.args.idGraph); - this.draggingElement.setAttribute("transform", "translate(" + p.x + "," + p.y + "), scale(" + this.getScale() + ")"); - - DOM.select(this.id).setAttribute("dragx", p.x); - DOM.select(this.id).setAttribute("dragy", p.y); - - if (this.NodeSVGbackgroundImage != null) { - this.NodeSVGbackgroundImage.setAttribute("dragx", p.x); - this.NodeSVGbackgroundImage.setAttribute("dragy", p.y); - } - } else { - if (this.isVertex(this.draggingElement)) { - this.selectNode(this.getVertexIdFromSVGId(this.draggingElement.id)); - this.desplazamientoX = this.desplazamientoX / this.getFormatter().getZoomScale(); - this.desplazamientoY = this.desplazamientoY / this.getFormatter().getZoomScale(); - this.moveSelectedNodes(this.desplazamientoX, this.desplazamientoY); - - this.dragStartX = this.getSVGCoordenates(evt).x; - this.dragStartY = this.getSVGCoordenates(evt).y; - } else { - if (this.isNodeBackground(this.draggingElement)) { - - this.draggingElement.setAttribute("dragx", p.x); - this.draggingElement.setAttribute("dragy", p.y); - this.draggingElement = document.getElementById(this.args.idGraph); - this.draggingElement.setAttribute("transform", "translate(" + p.x + "," + p.y + "), scale(" + this.getScale() + ")"); - } else { - this.draggingElement.setAttribute("transform", "translate(" + p.x + "," + p.y + ")"); - } - } - } - } - } -}; - -GraphCanvas.prototype.moveSelectedNodes = function(offsetX, offsetY) { - for ( var i = 0; i < this.getSelectedVertices().length; i++) { - - var nodeId = this.getSelectedVertices()[i]; - var svgNodeId = this.getSVGNodeId(nodeId); - - var x = parseFloat(DOM.select(svgNodeId).getAttribute("dragx")) + parseFloat(offsetX);// - parseFloat(DOM.select(this.id).getAttribute("dragx")); - var y = parseFloat(DOM.select(svgNodeId).getAttribute("dragy")) + parseFloat(offsetY);// + parseFloat(DOM.select(this.id).getAttribute("dragy")); - - this._movingNode(DOM.select(svgNodeId), x, y); - } -}; - -GraphCanvas.prototype.mouseDown = function(evt) { - if (event.button == 0) { - - /** if !no interactive mouse events do anything **/ - if (!this.args.interactive) { - return; - } - - var p = this.getSVGCoordenates(evt); - - /** When click on canvas or background deselect all **/ - if (this.isNodeCanvas(evt.target) || this.isNodeBackground(evt.target)) { - this.deselectNodes(); - this.deselectEdges(); - this.onCanvasClicked.notify(); - } - - /** if I am linking vertices **/ - if (this.args.linkEnabled) { - - if (!this.args.linking) { - this.args.linking = true; - if (this.isVertex(evt.target)) { - this.linkStartX = p.x; - this.linkStartY = p.y; - this.linkSVGNode = SVG.drawLine(p.x, p.y, p.x, p.y, this._svg, { - "stroke" : "#FF0000" - }); - this.linkNodeSource = this.getVertexIdFromSVGId(evt.target.id); - } - } else { - this.linkNodeTarget = this.getVertexIdFromSVGId(evt.target.id); - this.args.linking = false; - this.args.linkEnabled = false; - if (this.isVertex(evt.target)) { - this.getDataset().addEdge(this.linkNodeSource + "_" + this.linkNodeTarget, this.linkNodeSource, this.linkNodeTarget, {}); - } - this.linkSVGNode.parentNode.removeChild(this.linkSVGNode); - } - return; - } - - /** Id is a vertex or the canvas **/ - if (this.isVertex(evt.target) || this.isNodeCanvas(evt.target) || this.isNodeBackground(evt.target)) { - this._startDragging(evt); - } - /** if i is edge **/ - if (this.isEdge(evt.target)) { - this.selectEdge(this.getEdgeIdFromSVGId(evt.target.getAttribute("id"))); - } - - if (this.args.multipleSelectionEnabled) { - if (!this.dragging) { - this.setSelecting(true); - this.selectorX = p.x; - this.selectorY = p.y; - this.displaySelection(p.x, p.y, 1, 1); - } - } - - } - if (event.button == 1) { - this.setLinking(false); - this.setMultipleSelection(false); - this.selecting = false; - - /** Id is a vertex or the canvas **/ - if (this.isVertex(evt.target) || this.isNodeCanvas(evt.target) || this.isNodeBackground(evt.target)) { - this._startDragging(evt); - } - } -}; - -GraphCanvas.prototype.mouseUp = function(event) { - if (!this.args.interactive) { - return; - } - - if (this.dragging) { - this._stopDragging(event); - if (this.isVertex(event.target)) { - var vertexId = this.getVertexIdFromSVGId(event.target.id); - if (this.getDataset().getVertexById(vertexId).getEdges().length >= this.args.maxNumberEdgesMoving) { - this.moveEdge(vertexId); - } - } - } - - if (this.selecting) { - this.setSelecting(false); - - var x1 = (parseFloat(this.selectorSVGNode.getAttribute("x")) - DOM.select(this.id).getAttribute("dragx")) / this.getFormatter().getWidth(); - var y1 = (parseFloat(this.selectorSVGNode.getAttribute("y")) - DOM.select(this.id).getAttribute("dragy")) / this.getFormatter().getHeight(); - var x2 = (x1 + parseFloat(this.selectorSVGNode.getAttribute("width") / this.formatter.getWidth())); - var y2 = (y1 + parseFloat(this.selectorSVGNode.getAttribute("height") / this.formatter.getHeight())); - - var verticesSelected = this.getLayout().getVerticesByArea(x1 / this.getFormatter().getZoomScale, y1 / this.getFormatter().getZoomScale, - x2 / this.getFormatter().getZoomScale, y2 / this.getFormatter().getZoomScale); - - for ( var i = 0; i < verticesSelected.length; i++) { - this.selectNode(verticesSelected[i].getId()); - } - - if (this.selectorSVGNode != null) { - this._svg.removeChild(this.selectorSVGNode); - } - - if (this.args.labeled) { - this.clearLabels(); - this.renderLabels(); - } - - this.selectorSVGNode = null; - // this.renderLabels(); - } -}; - -/** SELECTION **/ -GraphCanvas.prototype.displaySelection = function(x, y, width, height) { - if (this.selectorSVGNode != null) { - this.selectorSVGNode.setAttribute("x", x); - this.selectorSVGNode.setAttribute("y", y); - this.selectorSVGNode.setAttribute("width", width); - this.selectorSVGNode.setAttribute("height", height); - } else { - this.selectorSVGNode = SVG.drawRectangle(x, y, width, height, this._svg, { - "fill" : "red", - "stroke" : "black", - "opacity" : "0.2", - "stroke-opacity" : "1" - }); - } -}; - -/** DRAGGING **/ -GraphCanvas.prototype._startDragging = function(evt) { - if (!this.isDraggingCanvasEnabled()) { - if (this.isNodeCanvas(evt.target)) { - this.draggingElement = null; - } - } - - if (this.isVertex(evt.target) || (this.isNodeBackground(evt.target) && (this.isDraggingCanvasEnabled()))|| (this.isNodeCanvas(evt.target) && (this.isDraggingCanvasEnabled()))) { - this.clearLabels(); - this.draggingElement = evt.target; - this.dragging = true; - var p = this.getSVGCoordenates(evt); - - this.nMouseOffsetX = p.x - parseInt(evt.target.getAttribute("dragx")); - this.nMouseOffsetY = p.y - parseInt(evt.target.getAttribute("dragy")); - - if (this.isVertex(evt.target)) { - this.dragStartX = parseInt(this.draggingElement.getAttribute("dragx")) * this.getFormatter().getZoomScale() - + parseFloat(DOM.select(this.id).getAttribute("dragx")); - this.dragStartY = parseInt(this.draggingElement.getAttribute("dragy")) * this.getFormatter().getZoomScale() - + parseFloat(DOM.select(this.id).getAttribute("dragy")); - } else { - this.dragStartX = p.x - parseInt(this.draggingElement.getAttribute("dragx"));// + parseFloat(DOM.select(this.id).getAttribute("dragx")); - this.dragStartY = p.y - parseInt(this.draggingElement.getAttribute("dragy"));// + parseFloat(DOM.select(this.id).getAttribute("dragy")); - } - } -}; - -GraphCanvas.prototype._stopDragging = function(event) { - this.nMouseOffsetX = 0; - this.nMouseOffsetX = 0; - /** despues del evento up viene el evento click entonces acabo el dragging en el mouseclick **/ - this.dragging = false; - this.draggingElement = null; - this.renderLabels(); - - this.setLinking(false); - this.setMultipleSelection(true); - this.selecting = false; - -}; - -/** Move the edges of the vertex with the vertexId indicado **/ -GraphCanvas.prototype.moveEdge = function(vertexId) { - var x = this.getLayout().getNodeById(vertexId).x * this.getFormatter().getWidth(); - var y = this.getLayout().getNodeById(vertexId).y * this.getFormatter().getHeight(); - - /** Moving edges out **/ - for ( var i = 0; i < this.getDataset().getVertexById(vertexId).getEdgesOut().length; i++) { - var edgeId = this.getDataset().getVertexById(vertexId).getEdgesOut()[i].getId(); - var svgEdgeId = this.getSVGEdgeId(edgeId); - var edgeFormatter = this.getFormatter().getEdgeById(edgeId); - if (edgeFormatter instanceof LineEdgeGraphFormatter) { - DOM.select(svgEdgeId + "_shadow").setAttribute("x2", x); - DOM.select(svgEdgeId + "_shadow").setAttribute("y2", y); - DOM.select(svgEdgeId).setAttribute("x2", x); - DOM.select(svgEdgeId).setAttribute("y2", y); - } - - if ((edgeFormatter instanceof DirectedLineEdgeGraphFormatter) || (edgeFormatter instanceof OdirectedLineEdgeGraphFormatter) - || (edgeFormatter instanceof OdotDirectedLineEdgeGraphFormatter) || (edgeFormatter instanceof DotDirectedLineEdgeGraphFormatter) - || (edgeFormatter instanceof CutDirectedLineEdgeGraphFormatter)) { - this.removeEdge(edgeId); - this.renderEdge(edgeId); - } - } - - /** Moving edges in **/ - for ( var i = 0; i < this.getDataset().getVertexById(vertexId).getEdgesIn().length; i++) { - var edgeId = this.getDataset().getVertexById(vertexId).getEdgesIn()[i].getId(); - var svgEdgeId = this.getSVGEdgeId(edgeId); - var edgeFormatter = this.getFormatter().getEdgeById(edgeId); - if (edgeFormatter instanceof LineEdgeGraphFormatter) { - DOM.select(svgEdgeId).setAttribute("x1", x); - DOM.select(svgEdgeId).setAttribute("y1", y); - DOM.select(svgEdgeId + "_shadow").setAttribute("x1", x); - DOM.select(svgEdgeId + "_shadow").setAttribute("y1", y); - } - - if ((edgeFormatter instanceof DirectedLineEdgeGraphFormatter) || (edgeFormatter instanceof OdirectedLineEdgeGraphFormatter) - || (edgeFormatter instanceof OdotDirectedLineEdgeGraphFormatter) || (edgeFormatter instanceof DotDirectedLineEdgeGraphFormatter) - || (edgeFormatter instanceof CutDirectedLineEdgeGraphFormatter)) { - this.removeEdge(edgeId); - this.renderEdge(edgeId); - } - - if (edgeFormatter instanceof BezierEdgeGraphFormatter) { - var radius = this.getFormatter().getVertexById(vertexId).getDefault().getSize() * this.getFormatter().getNodesMaxSize(); - var d = this.calculateCoordenatesBezier(radius, x, y); - DOM.select(svgEdgeId).setAttribute("d", d); - } - } -}; - -GraphCanvas.prototype.moveNode = function(vertexId) { - var x = this.getLayout().getNodeById(vertexId).x * this.getFormatter().getWidth(); - var y = this.getLayout().getNodeById(vertexId).y * this.getFormatter().getHeight(); - var svgNodeElement = DOM.select(this.getSVGNodeId(vertexId)); - - svgNodeElement.setAttribute("dragx", x); - svgNodeElement.setAttribute("dragy", y); - svgNodeElement.setAttribute("transform", "translate(" + x + "," + y + ")"); - - if (this.getDataset().getVertexById(vertexId).getEdges().length < this.args.maxNumberEdgesMoving) { - this.moveEdge(vertexId); - } -}; - -GraphCanvas.prototype._movingNode = function(svgNodeElement, x, y) { - var vertexId = this.getVertexIdFromSVGId(svgNodeElement.getAttribute("id")); - this.getLayout().getNodeById(vertexId).setCoordinates(x / this.getFormatter().getWidth(), y / this.getFormatter().getHeight()); - this.desplazamientoX = 0; - this.desplazamientoY = 0; - this.removeLabel(vertexId); - this.renderLabel(vertexId); -}; - -/** INIT **/ -GraphCanvas.prototype.init = function() { - - this._svg = this.createSVGDom(this.targetID, this.id, this.getFormatter().getWidth(), this.getFormatter().getHeight(), this.getFormatter() - .getBackgroundColor()); - this.GraphGroup = SVG.drawGroup(this._svg, [ [ "id", this.args.idGraph ], [ "transform", "translate(0,0), scale(1)" ] ]); - this.GraphBackground = SVG.drawGroup(this.GraphGroup, [ [ "id", this.args.idBackground ] ]); - this.GraphEdgeGroup = SVG.drawGroup(this.GraphGroup, [ [ "id", this.args.idEdgesGraph ] ]); - this.GraphNodeGroup = SVG.drawGroup(this.GraphGroup, [ [ "id", this.args.idNodesGraph ] ]); - this.GraphLabelGroup = SVG.drawGroup(this.GraphGroup, [ [ "id", this.args.idLabelGraph ] ]); - - if ((this.getFormatter().getBackgroundImage() != null) && (this.getFormatter().getBackgroundImage() != "")) { - this.setBackgroundImage(this.getFormatter().getBackgroundImage()); - } - /** SVG Events listener */ - var _this = this; - this._svg.addEventListener("click", function(event) { - _this.mouseClick(event); - }, false); - this._svg.addEventListener("mousemove", function(event) { - _this.mouseMove(event, _this); - }, false); - this._svg.addEventListener("mousedown", function(event) { - _this.mouseDown(event, _this); - }, false); - this._svg.addEventListener("mouseup", function(event) { - _this.mouseUp(event, _this); - }, false); -}; - -/* - GraphCanvas.prototype.backgroungToSVG = function(){ - var _this = this; - var canvas = document.createElement('canvas'); - canvas.setAttribute("id", "canvas"); - canvas.width = this.formatter.getWidth(); - canvas.height = this.formatter.getHeight(); - - this._svg.parentNode.parentNode.appendChild(canvas); - var ctx = document.getElementById('canvas').getContext('2d'); - var img = new Image(); - - img.src = this.formatter.getBackgroundImage(); - ctx.drawImage(img,0,0 ,_this.formatter.getWidth(), _this.formatter.getHeight()); - - - img.onload = function() { - canvas.parentNode.removeChild(canvas); - } - - this.NodeSVGbackgroundImage.setAttribute("xlink:href", document.getElementById("canvas").toDataURL()); - this.NodeSVGbackgroundImage.removeAttribute("href"); - - // - - };*/ - -GraphCanvas.prototype.setBackgroundImage = function() { - if (this.NodeSVGbackgroundImage != null) { - this.NodeSVGbackgroundImage.parentNode.removeChild(this.NodeSVGbackgroundImage); - } - $('#' + this.targetID).svg(); - $('#' + this.targetID).svg("get"); - - $('#' + this.targetID).svg("get")._svg = document.getElementById(this.id); - - var svg = $('#' + this.targetID).svg("get"); - this.NodeSVGbackgroundImage = svg.image(0, 0, this.getFormatter().getWidth(), this.getFormatter().getHeight(), this.getFormatter() - .getBackgroundImage()); - this.NodeSVGbackgroundImage.setAttribute("id", this.args.idBackgroundNode); - - this.NodeSVGbackgroundImage.setAttribute("x", 0); - this.NodeSVGbackgroundImage.setAttribute("y", 0); - - this.NodeSVGbackgroundImage.setAttribute("dragx", 0); - this.NodeSVGbackgroundImage.setAttribute("dragy", 0); - - if (this.getFormatter().args.backgroundImageHeight != null) { - this.NodeSVGbackgroundImage.setAttribute("height", this.getFormatter().args.backgroundImageHeight); - } - if (this.getFormatter().args.backgroundImageWidth != null) { - this.NodeSVGbackgroundImage.setAttribute("width", this.getFormatter().args.backgroundImageWidth); - } - - if (this.getFormatter().args.backgroundImageX != null) { - this.NodeSVGbackgroundImage.setAttribute("x", this.getFormatter().args.backgroundImageX); - } - if (this.getFormatter().args.backgroundImageY != null) { - this.NodeSVGbackgroundImage.setAttribute("y", this.getFormatter().args.backgroundImageY); - } - - this.GraphBackground.appendChild(this.NodeSVGbackgroundImage); - this.NodeSVGbackgroundImage.removeAttribute("href"); - this.NodeSVGbackgroundImage.setAttribute("xlink:href", this.getFormatter().getBackgroundImage()); -}; - -GraphCanvas.prototype.removeBackgroundImage = function() { - if (this.NodeSVGbackgroundImage != null) { - this.NodeSVGbackgroundImage.parentNode.removeChild(this.NodeSVGbackgroundImage); - } -}; - -GraphCanvas.prototype._setBackgroundColor = function(color) { - var attributes = [ [ "fill", color ] ]; - SVG.drawRectangle(0, 0, this.getFormatter().getWidth(), this.getFormatter().getHeight(), this.GraphBackground, attributes); -}; - -/** Serialize **/ -GraphCanvas.prototype.toJSON = function() { - var json = {}; - json.dataset = {}; - json.formatter = {}; - json.layout = {}; - json.dataset = this.getDataset().toJSON(); - json.formatter = this.getFormatter().toJSON(); - json.layout = this.getLayout().toJSON(); - return json; -}; - -GraphCanvas.prototype.toHTML = function() { - //this.backgroungToSVG(); - var html = this._svg.parentElement.innerHTML; - - var start = html.indexOf("") + 6; - - return html.substr(start, end); -}; - -/** DRAW **/ -GraphCanvas.prototype.draw = function(graphdataset, graphformatter, graphlayout) { - this.setDataset(graphdataset); - this.setFormatter(graphformatter); - this.setLayout(graphlayout); - - var _this = this; - this.getFormatter().changed.attach(function(sender, item) { - _this.removeNode(item.getId()); - _this.renderNode(item.getId()); - if (_this.args.labeled) { - _this.removeLabel(item.getId()); - _this.renderLabel(item.getId()); - } - - }); - //TODO - this.getFormatter().edgeChanged.attach(function(sender, item) { - _this.removeEdge(item.getId()); - _this.renderEdge(item.getId()); - }); - - this.getFormatter().resized.attach(function(sender, item) { - _this.resize(_this.getFormatter().getWidth(), _this.getFormatter().getHeight()); - }); - - this.getFormatter().backgroundImageChanged.attach(function(sender, item) { - _this.setBackgroundImage(_this.getFormatter().getBackgroundImage()); - }); - - this.getFormatter().backgroundColorChanged.attach(function(sender, item) { - _this._setBackgroundColor(_this.getFormatter().getBackgroundColor()); - }); - - this.getLayout().changed.attach(function(sender, item) { - _this.moveNode(item.getId()); - _this.moveEdge(item.getId()); - if (_this.args.labeled) { - _this.removeLabel(item.getId()); - _this.renderLabel(item.getId()); - } - }); - - this.getDataset().newVertex.attach(function(sender, item) { - - _this.renderNode(item.getId()); - if (_this.args.labeled) { - _this.renderLabel(item.getId()); - } - }); - - this.getDataset().newEdge.attach(function(sender, item) { - _this.renderEdge(item.getId()); - }); - - this.getDataset().vertexDeleted.attach(function(sender, item) { - _this.removeNode(item.getId()); - if (_this.args.labeled) { - _this.removeLabel(item.getId()); - } - }); - - this.getDataset().edgeDeleted.attach(function(sender, item) { - _this.removeEdge(item.getId()); - }); - - this.getDataset().vertexNameChanged.attach(function(sender, args) { - if (_this.args.labeled) { - _this.removeLabel(args.item.getId()); - _this.removeLabel(args.item.getId()); - _this.renderLabel(args.item.getId()); - } - }); - this.init(); - this.render(); -}; - -GraphCanvas.prototype.render = function() { - for ( var id in this.getDataset().getVertices()) { - this.renderNode(id); - } - this.renderLabels(); - this.renderEdges(); -}; - -GraphCanvas.prototype.renderLabels = function() { - if (this.args.labeled) { - for ( var id in this.getDataset().getVertices()) { - this.renderLabel(id); - } - } -}; - -GraphCanvas.prototype.removeLabels = function() { - for ( var id in this.getDataset().getVertices()) { - this.removeLabel(id); - } -}; - -/** Utilities method for nodes **/ -GraphCanvas.prototype.isNodeCanvas = function(node) { - return ((node.id == this.args.idGraph) || (node.id == this.id)); -}; - -GraphCanvas.prototype.isNodeBackground = function(node) { - return ((node.id == this.args.idBackgroundNode)); -}; - -GraphCanvas.prototype.isVertex = function(node) { - if (node.getAttribute("id") != null) { - if (node.getAttribute("id").indexOf("_v_") != -1) { - return true; - } - } - return false; -}; - -GraphCanvas.prototype.isLabel = function(node) { - if (node.getAttribute("id") != null) { - if (node.getAttribute("id").indexOf("_l_") != -1) { - return true; - } - } - return false; -}; - -GraphCanvas.prototype.isEdge = function(node) { - if (node.getAttribute("id") != null) { - if (node.getAttribute("id").indexOf("_e_") != -1) { - return true; - } - } - return false; -}; - -/** Resize **/ -GraphCanvas.prototype.resize = function(width, height) { - // this._svg.setAttribute("width", width); - // this._svg.setAttribute("height", height); - if (this.NodeSVGbackgroundImage != null) { - this.NodeSVGbackgroundImage.setAttribute("width", width); - this.NodeSVGbackgroundImage.setAttribute("height", height); - } - - this._svg.setAttribute("width", width); - this._svg.setAttribute("height", height); - - this.clearCanvas(); - this.render(); -}; - -GraphCanvas.prototype.clearCanvas = function() { - DOM.removeChilds(this.GraphEdgeGroup.getAttribute("id")); - DOM.removeChilds(this.GraphNodeGroup.getAttribute("id")); - this.clearLabels(); -}; - -GraphCanvas.prototype.clearLabels = function() { - DOM.removeChilds(this.GraphLabelGroup.getAttribute("id")); -}; - -/** ID'S converter **/ -GraphCanvas.prototype.getSVGNodeId = function(nodeId) { - return this.id + "_v_" + nodeId; -}; - -GraphCanvas.prototype.getSVGEdgeId = function(edgeId) { - return this.id + "_e_" + edgeId; -}; - -GraphCanvas.prototype.getSVGArrowEdgeId = function(edgeId) { - return this.id + "_arrow_" + edgeId; -}; - -GraphCanvas.prototype.getSVGLabelId = function(edgeId) { - return this.id + "_l_" + edgeId; -}; - -GraphCanvas.prototype.blinkVertexById = function(vertexId) { - $("#" + this.getSVGNodeId(vertexId)).fadeIn().fadeOut().fadeIn().fadeOut().fadeIn().fadeOut(); -}; - -GraphCanvas.prototype.getVertexIdFromSVGId = function(svgVertexId) { - return svgVertexId.replace(this.id, "").replace("_v_", ""); -}; - -GraphCanvas.prototype.getEdgeIdFromSVGId = function(svgEdgeId) { - return svgEdgeId.replace(this.id, "").replace("_e_", ""); -}; - -/** VERTEX **/ -GraphCanvas.prototype.getVertexById = function(id) { - return document.getElementById(this.getSVGNodeId(id)); -}; - -GraphCanvas.prototype.renderNodes = function() { - for ( var id in this.getDataset().getVertices()) { - this.renderNode(id); - } -}; - -GraphCanvas.prototype.overNode = function(nodeId) { - if (!this.args.interactive) { - return; - } - /** If selected we don't change the format **/ - if (this.args.isVertexSelected[nodeId] == null) { - var args = this.getFormatter().getVertexById(nodeId).getOver(); - args.args["cursor"] = 'pointer'; - this.changeVertexFormat(nodeId, args); - } -}; - -GraphCanvas.prototype.outNode = function(nodeId) { - if (!this.args.interactive) { - return; - } - - /** If selected we don't change the format **/ - if (this.args.isVertexSelected[nodeId] == null) { - this.changeVertexFormat(nodeId, this.getFormatter().getVertexById(nodeId).getDefault()); - } -}; - -GraphCanvas.prototype.overLabel = function(nodeId) { - this.overNode(nodeId); - // this.svgLabels[nodeId].setAttribute("cursor", "pointer"); -}; - -GraphCanvas.prototype.outLabel = function(nodeId) { - this.outNode(nodeId); - // this.svgLabels[nodeId].setAttribute("cursor", ""); -}; - -GraphCanvas.prototype.clickNode = function(nodeId) { - if (!this.args.interactive) { - return; - } - - /** si el evento se dispara oprque estaba dragging entonces no activo nada **/ - if (this.args.isVertexSelected[nodeId] == null) { - this.selectNode(nodeId); - } else { - this.deselectNode(nodeId); - } -}; - -GraphCanvas.prototype.selectNode = function(nodeId) { - for ( var i = 0; i < this.args.selectedVertices.length; i++) { - var format = this.getFormatter().getVertexById(nodeId).getSelected(); - format.opacity = 0.2; - this.changeVertexFormat(nodeId, this.getFormatter().getVertexById(nodeId).getSelected()); - } - - if (this.args.isVertexSelected[nodeId] == null) { - var format = this.getFormatter().getVertexById(nodeId).getSelected(); - format.opacity = 1; - this.changeVertexFormat(nodeId, this.getFormatter().getVertexById(nodeId).getSelected()); - this.args.selectedVertices.push(nodeId); - this.args.isVertexSelected[nodeId] = this.args.selectedVertices.length - 1; - this.onVertexSelect.notify(nodeId); - } -}; - -GraphCanvas.prototype.selectAllEdges = function() { - this.deselectNodes(); - this.deselectEdges(); - - for ( var edgesId in this.getDataset().edges) { - this.selectEdge(edgesId); - } -}; - -GraphCanvas.prototype.selectAllNodes = function() { - this.deselectNodes(); - this.deselectEdges(); - - for ( var vertexId in this.getDataset().vertices) { - this.selectNode(vertexId); - } -}; - -GraphCanvas.prototype.selectAll = function() { - this.deselectNodes(); - this.deselectEdges(); - - for ( var vertexId in this.getDataset().vertices) { - this.selectNode(vertexId); - } - - for ( var edgesId in this.getDataset().edges) { - this.selectEdge(edgesId); - } -}; - -GraphCanvas.prototype.selectEdge = function(edgeId) { - if (this.args.isEdgeSelected[edgeId] == null) { - this.changeEdgeFormat(edgeId, this.getFormatter().getEdgeById(edgeId).getSelected()); - //this.args.selectedEdges.push(edgeId); - this.args.isEdgeSelected[edgeId] = true; //this.args.selectedEdges.length - 1; - this.onEdgeSelect.notify(edgeId); - } -}; - -GraphCanvas.prototype.selectEdges = function(edges) { - - for ( var i = 0; i < edges.length; i++) { - this.selectEdge(edges[i]); - } -}; - -GraphCanvas.prototype.deselectNode = function(nodeId) { - if (this.args.isVertexSelected[nodeId] != null) { - this.changeVertexFormat(nodeId, this.getFormatter().getVertexById(nodeId).getDefault()); - this.args.selectedVertices.splice(this.args.isVertexSelected[nodeId], 1); - var index = this.args.isVertexSelected[nodeId]; - delete this.args.isVertexSelected[nodeId]; - - for ( var vertex in this.args.isVertexSelected) { - if (this.args.isVertexSelected[vertex] > index) { - this.args.isVertexSelected[vertex] = this.args.isVertexSelected[vertex] - 1; - } - } - } -}; - -GraphCanvas.prototype.deselectNodes = function() { - var selected = JSON.parse(JSON.stringify(this.getSelectedVertices())); - for ( var i = 0; i < selected.length; i++) { - this.deselectNode(selected[i]); - } -}; -GraphCanvas.prototype.selectNodes = function(idNodes) { - - for ( var i = 0; i < idNodes.length; i++) { - this.selectNode(idNodes[i]); - } - - // for ( var vertex in this.args.isVertexSelected) { - // if (this.args.isVertexSelected[vertex] > index){ - // this.args.isVertexSelected[vertex] = this.args.isVertexSelected[vertex] - 1; - // } - // } - -}; - -GraphCanvas.prototype.changeVertexFormat = function(nodeId, format) { - var svgNode = DOM.select(this.getSVGNodeId(nodeId)); - if (svgNode != null) { - var properties = format.toJSON(); - for ( var item in properties) { - svgNode.setAttribute(item, properties[item]); - } - - if (this.getFormatter().getVertexById(nodeId) instanceof CircleVertexGraphFormatter) { - var transform = "translate(" + svgNode.getAttribute("dragx") + "," + svgNode.getAttribute("dragy") + "), scale(" + format.getSize() + ")"; - svgNode.setAttribute("transform", transform); - } - } -}; - -GraphCanvas.prototype.renderLabel = function(nodeId) { - var x = Math.ceil(this.getLayout().getNodeById(nodeId).x * this.getFormatter().getWidth()); - var y = Math.ceil(this.getLayout().getNodeById(nodeId).y * this.getFormatter().getHeight()); - - var svgAttributesNode = JSON.parse(JSON.stringify(this.getFormatter().getVertexById(nodeId).getDefault().toJSON().title)); - svgAttributesNode.id = this.getSVGLabelId(this.getDataset().getVertexById(nodeId).getId()); - svgAttributesNode.dx = (-1) * (this.getDataset().getVertexById(nodeId).getName().length * svgAttributesNode["font-size"]) / 4 - 4; - - svgAttributesNode.dy = parseFloat((this.getFormatter().getVertexById(nodeId).getDefault().getSize())) - + parseFloat(svgAttributesNode["font-size"]) + parseFloat(this.getFormatter().getVertexById(nodeId).getDefault().getStrokeWidth()) - 4; - svgAttributesNode.dragx = Math.ceil(this.getLayout().getNodeById(nodeId).x * this.getFormatter().getWidth()); - - var gragy = parseFloat(this.getFormatter().getVertexById(nodeId).getDefault().getSize()) - + Math.ceil(this.getLayout().getNodeById(nodeId).y * this.getFormatter().getHeight()); - svgAttributesNode.dragy = gragy; - svgAttributesNode.transform = "translate(" + svgAttributesNode.dragx + "," + svgAttributesNode.dragy + ")";//, scale("+this.formatter.getVertexById(nodeId).getDefault().getSize()+")"; - - var nodeSVG = SVG.drawText(0, 0, this.getDataset().getVertexById(nodeId).getName(), this.GraphLabelGroup, svgAttributesNode); - - this.svgLabels[nodeId] = nodeSVG; - - /** Events for the SVG node **/ - var _this = this; - if (nodeSVG != null) { - nodeSVG.addEventListener("mouseover", function() { - _this.overLabel(nodeId); - }, false); - nodeSVG.addEventListener("mouseout", function() { - _this.outLabel(nodeId); - }, false); - } - -}; - -GraphCanvas.prototype.removeLabel = function(labelId) { - if (DOM.select(this.getSVGLabelId(labelId)) != null) { - DOM.select(this.getSVGLabelId(labelId)).parentNode.removeChild(DOM.select(this.getSVGLabelId(labelId))); - } -}; - -GraphCanvas.prototype.renderNode = function(nodeId) { - var svgAttributesNode = JSON.parse(JSON.stringify(this.getFormatter().getVertexById(nodeId).getDefault().toJSON())); - svgAttributesNode.dragx = Math.ceil(this.getLayout().getNodeById(nodeId).x * this.getFormatter().getWidth()); - svgAttributesNode.dragy = Math.ceil(this.getLayout().getNodeById(nodeId).y * this.getFormatter().getHeight()); - svgAttributesNode.transform = "translate(" + svgAttributesNode.dragx + "," + svgAttributesNode.dragy + ")"; - svgAttributesNode.id = this.getSVGNodeId(nodeId); - /*svgAttributesNode["stroke-width"] = 3 ; - svgAttributesNode["stroke-opacity"] = 1 ; - svgAttributesNode["fill-opacity"] = svgAttributesNode["opacity"] ; - svgAttributesNode["opacity"] = 1 ;*/ - this.circleDefaultRadius = this.getFormatter().getVertexById(nodeId).getDefault().getSize(); - var nodeSVG; - - if (this.getFormatter().getVertexById(nodeId) instanceof CircleVertexGraphFormatter) { - nodeSVG = SVG.drawCircle(0, 0, this.circleDefaultRadius, this.GraphNodeGroup, svgAttributesNode); - } - - if (this.getFormatter().getVertexById(nodeId) instanceof SquareVertexGraphFormatter) { - //nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius) ,0 - (this.formatter.getVertexById(nodeId).getDefault().getSize()) , (this.getFormatter().getVertexById(nodeId).getDefault().getSize()*2), (this.getFormatter().getVertexById(nodeId).getDefault().getSize()*2), this.GraphNodeGroup, svgAttributesNode); - nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius), 0 - (this.circleDefaultRadius), (this.circleDefaultRadius * 2), - (this.circleDefaultRadius * 2), this.GraphNodeGroup, svgAttributesNode); - } - - if (this.getFormatter().getVertexById(nodeId) instanceof EllipseVertexGraphFormatter) { - nodeSVG = SVG.drawEllipse(0, 0, this.circleDefaultRadius * 1.5, this.circleDefaultRadius, this.GraphNodeGroup, svgAttributesNode); - } - - if (this.getFormatter().getVertexById(nodeId) instanceof RectangleVertexGraphFormatter) { - //nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius) ,0 - ((this.circleDefaultRadius*2)/2) , (this.circleDefaultRadius*2), (this.circleDefaultRadius), this.GraphNodeGroup, svgAttributesNode); - nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius * 1.5), 0 - (this.circleDefaultRadius), (this.circleDefaultRadius * 2 * 1.5), - (this.circleDefaultRadius * 2), this.GraphNodeGroup, svgAttributesNode); - - } - - if (this.getFormatter().getVertexById(nodeId) instanceof RoundedVertexGraphFormatter) { - svgAttributesNode.ry = 2;// this.formatter.getVertexById(nodeId).getDefault().getSize()/4; - svgAttributesNode.rx = 2;// this.formatter.getVertexById(nodeId).getDefault().getSize()/4; - nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius * 1.5), 0 - (this.circleDefaultRadius), (this.circleDefaultRadius * 2 * 1.5), - (this.circleDefaultRadius * 2), this.GraphNodeGroup, svgAttributesNode); - } - - // - - if (this.getFormatter().getVertexById(nodeId) instanceof OctagonVertexGraphFormatter) { - svgAttributesNode.ry = 2; - svgAttributesNode.rx = 2; - nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius * 1.5), 0 - (this.circleDefaultRadius), (this.circleDefaultRadius * 2 * 1.5), - (this.circleDefaultRadius * 2), this.GraphNodeGroup, svgAttributesNode); - } - - nodeSVG.internalId = nodeId; - // - var _this = this; - - /** Events for the SVG node **/ - if (nodeSVG != null) { - nodeSVG.addEventListener("mouseover", function() { - _this.onVertexOver.notify(nodeId); - _this.overNode(nodeId); - }, false); - nodeSVG.addEventListener("mouseout", function() { - _this.onVertexOut.notify(nodeId); - _this.outNode(nodeId); - }, false); - //nodeSVG.addEventListener("click", function(){_this.clickNode(nodeId);}, false); - // - nodeSVG.addEventListener("mouseup", function() { - _this.onVertexUp.notify(nodeId); - }, false); - } -}; - -GraphCanvas.prototype.removeNode = function(nodeId) { - DOM.select(this.getSVGNodeId(nodeId)).parentNode.removeChild(DOM.select(this.getSVGNodeId(nodeId))); - if (this.args.labeled) { - this.removeLabel(nodeId); - } -}; - -/** REMOVING **/ -GraphCanvas.prototype.removeSelected = function() { - /** El orden importa **/ - this.removeSelectedEdges(); - this.removeSelectedNode(); - -}; - -GraphCanvas.prototype.removeSelectedNode = function() { - var selected = JSON.parse(JSON.stringify(this.getSelectedVertices())); - this.deselectNodes(); - var sorted = selected.sort(function(a, b) { - return a - b - }); - for ( var i = 0; i < sorted.length; i++) { - if (this.getDataset().getVertexById(sorted[i]) != null) { - this.getDataset().getVertexById(sorted[i]).remove(); - } - } -}; - -/** EDGES **/ -GraphCanvas.prototype.removeEdge = function(edgeId) { - if (DOM.select(this.getSVGEdgeId(edgeId)) != null) { - DOM.select(this.getSVGEdgeId(edgeId)).parentNode.removeChild(DOM.select(this.getSVGEdgeId(edgeId))); - } - - if (DOM.select(this.getSVGEdgeId(edgeId) + "_shadow") != null) { - DOM.select(this.getSVGEdgeId(edgeId) + "_shadow").parentNode.removeChild(DOM.select(this.getSVGEdgeId(edgeId) + "_shadow")); - } - - if (DOM.select(this.getSVGArrowEdgeId(edgeId)) != null) { - DOM.select(this.getSVGArrowEdgeId(edgeId)).parentNode.removeChild(DOM.select(this.getSVGArrowEdgeId(edgeId))); - } -}; - -GraphCanvas.prototype.overEdge = function(edgeId) { - if ((!this.args.interactive) || this.dragging || this.selecting) { - return; - } - - /** If selected we don't change the format **/ - if (this.args.isEdgeSelected[edgeId] == null) { - var format = this.getFormatter().getEdgeById(edgeId).getOver(); - format.args["cursor"] = "pointer"; - this.changeEdgeFormat(edgeId, format); - } -}; - -GraphCanvas.prototype.outEdge = function(edgeId) { - if (!this.args.interactive) { - return; - } - - /** If selected we don't change the format **/ - if (this.args.isEdgeSelected[edgeId] == null) { - this.changeEdgeFormat(edgeId, this.getFormatter().getEdgeById(edgeId).getDefault()); - } -}; - -GraphCanvas.prototype.changeEdgeFormat = function(edgeId, format) { - var svgEdge = DOM.select(this.getSVGEdgeId(edgeId) + "_shadow"); - if (svgEdge != null) { - var properties = format.toJSON(); - for ( var item in properties) { - svgEdge.setAttribute(item, properties[item]); - } - } -}; - -GraphCanvas.prototype.deselectEdge = function(edgeID) { - if (this.args.isEdgeSelected[edgeID] != null) { - this.changeEdgeFormat(edgeID, this.getFormatter().getEdgeById(edgeID).getDefault()); - var index = this.args.isEdgeSelected[edgeID]; - delete this.args.isEdgeSelected[edgeID]; - } -}; - -GraphCanvas.prototype.deselectEdges = function() { - var selected = JSON.parse(JSON.stringify(this.getSelectedEdges())); - for ( var i = 0; i < selected.length; i++) { - this.deselectEdge(selected[i]); - } -}; - -GraphCanvas.prototype.removeSelectedEdges = function() { - var selected = JSON.parse(JSON.stringify(this.getSelectedEdges())); - this.deselectEdges(); - for ( var i = 0; i < selected.length; i++) { - if (this.getDataset().getEdgeById(selected[i]) != null) { - this.getDataset().getEdgeById(selected[i]).remove(); - } - } -}; - -GraphCanvas.prototype.renderEdge = function(edgeId) { - var svgAttributesEdge = this.getFormatter().getEdgeById(edgeId).getDefault().toJSON(); - var edge = this.getDataset().getEdgeById(edgeId); - - var svgNodeTarget = this.getVertexById(edge.getNodeTarget().getId()); - var svgNodeSource = this.getVertexById(edge.getNodeSource().getId()); - svgAttributesEdge.id = this.getSVGEdgeId(edge.getId()) + "_shadow"; - - var svgEdge = null; - - if (this.getFormatter().getEdgeById(edgeId) instanceof LineEdgeGraphFormatter) { - var coordenateSourceX = svgNodeSource.getAttribute("dragx"); - var coordenateSourceY = svgNodeSource.getAttribute("dragy"); - var coordenateTargetX = svgNodeTarget.getAttribute("dragx"); - var coordenateTargetY = svgNodeTarget.getAttribute("dragy"); - - SVG.drawLine(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, this.GraphEdgeGroup, svgAttributesEdge); - var attributesShadow = {}; - attributesShadow.id = this.getSVGEdgeId(edge.getId()); - attributesShadow["stroke-opacity"] = 0; - attributesShadow["stroke-width"] = 4; - attributesShadow["stroke"] = "black"; - svgEdge = SVG.drawLine(svgNodeSource.getAttribute("dragx"), svgNodeSource.getAttribute("dragy"), svgNodeTarget.getAttribute("dragx"), - svgNodeTarget.getAttribute("dragy"), this.GraphEdgeGroup, attributesShadow); - } - - if (this.getFormatter().getEdgeById(edgeId) instanceof BezierEdgeGraphFormatter) { - var nodeId = edge.getNodeTarget().getId(); - var nodeSize = this.formatter.getVertexById(nodeId).getDefault().getSize() * this.getFormatter().getNodesMaxSize(); - svgAttributesEdge.fill = "none"; - svgAttributesEdge.id = this.getSVGEdgeId(edgeId); - var d = this.calculateCoordenatesBezier(nodeSize, svgNodeSource.getAttribute("dragx"), svgNodeSource.getAttribute("dragy")); - svgEdge = SVG.drawPath(d, this.GraphEdgeGroup, svgAttributesEdge); - } - ; - - if ((this.getFormatter().getEdgeById(edgeId) instanceof DirectedLineEdgeGraphFormatter) - || (this.getFormatter().getEdgeById(edgeId) instanceof CutDirectedLineEdgeGraphFormatter) - || (this.getFormatter().getEdgeById(edgeId) instanceof DotDirectedLineEdgeGraphFormatter) - || (this.getFormatter().getEdgeById(edgeId) instanceof OdotDirectedLineEdgeGraphFormatter) - || (this.getFormatter().getEdgeById(edgeId) instanceof OdirectedLineEdgeGraphFormatter)) { - var coordenateSourceX = svgNodeSource.getAttribute("dragx"); - var coordenateSourceY = svgNodeSource.getAttribute("dragy"); - var coordenateTargetX = svgNodeTarget.getAttribute("dragx"); - var coordenateTargetY = svgNodeTarget.getAttribute("dragy"); - - var offset = parseFloat(this.getFormatter().getVertexById(this.getDataset().getEdgeById(edgeId).getNodeTarget().getId()).getDefault() - .getSize() - * this.circleDefaultRadius); - var point = this._calculateEdgePointerPosition(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, offset); - coordenateTargetX = point.x; - coordenateTargetY = point.y; - SVG.drawLine(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, this.GraphEdgeGroup, svgAttributesEdge); - - var attributesShadow = {}; - attributesShadow.id = this.getSVGEdgeId(edge.getId()); - attributesShadow["stroke-opacity"] = 0; - attributesShadow["stroke-width"] = 4; - attributesShadow["stroke"] = "black"; - svgEdge = SVG.drawLine(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, this.GraphEdgeGroup, attributesShadow); - } - - if (this.getFormatter().getEdgeById(edgeId) instanceof DirectedLineEdgeGraphFormatter - || (this.getFormatter().getEdgeById(edgeId) instanceof OdirectedLineEdgeGraphFormatter)) { - var coordenateSourceX = svgNodeSource.getAttribute("dragx"); - var coordenateSourceY = svgNodeSource.getAttribute("dragy"); - var coordenateTargetX = svgNodeTarget.getAttribute("dragx"); - var coordenateTargetY = svgNodeTarget.getAttribute("dragy"); - - var point = this._calculateEdgePointerPosition(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, offset); - coordenateTargetX = point.x; - coordenateTargetY = point.y; - - var angle = Geometry.toDegree(point.angle) + 90; - this.arrowDefaultSize = this.getFormatter().getEdgeById(edgeId).getArrowSize(); //getDefault().getArrowSize(); - var d = "-" + this.arrowDefaultSize + ",0 0,-" + parseFloat(this.arrowDefaultSize) * 2 + " " + this.arrowDefaultSize + ",0"; - - var attributes; - - if (this.getFormatter().getEdgeById(edgeId) instanceof DirectedLineEdgeGraphFormatter) { - attributes = [ - [ "fill", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], - [ "stroke", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], [ "id", this.getSVGArrowEdgeId(edgeId) ] ]; - } else { - attributes = [ - [ "fill", "#FFFFFF" ], [ "stroke", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], - [ "id", this.getSVGArrowEdgeId(edgeId) ] ]; - } - - var flechaSVGNode = SVG.drawPoligon(d, this.GraphEdgeGroup, attributes);//, ["transform", "rotate("+angle+"), translate(0,0)"]]); - flechaSVGNode.setAttribute("transform", " translate(" + coordenateTargetX + ", " + coordenateTargetY + "), rotate(" + angle + ")"); - } - ; - - if (this.getFormatter().getEdgeById(edgeId) instanceof CutDirectedLineEdgeGraphFormatter) { - var coordenateSourceX = svgNodeSource.getAttribute("dragx"); - var coordenateSourceY = svgNodeSource.getAttribute("dragy"); - var coordenateTargetX = svgNodeTarget.getAttribute("dragx"); - var coordenateTargetY = svgNodeTarget.getAttribute("dragy"); - - var point = this._calculateEdgePointerPosition(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, offset); - coordenateTargetX = point.x; - coordenateTargetY = point.y; - - var angle = Geometry.toDegree(point.angle) + 90; - - //this.arrowDefaultSize = 2; //getDefault().getArrowSize(); - var d = "-4,0 4,0 4,-2 -4,-2"; - - var flechaSVGNode = SVG.drawPoligon(d, this.GraphEdgeGroup, [ - [ "fill", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], - [ "stroke", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], [ "id", this.getSVGArrowEdgeId(edgeId) ] ]);//, ["transform", "rotate("+angle+"), translate(0,0)"]]); - flechaSVGNode.setAttribute("transform", " translate(" + coordenateTargetX + ", " + coordenateTargetY + "), rotate(" + angle + ")"); - } - ; - - if ((this.getFormatter().getEdgeById(edgeId) instanceof DotDirectedLineEdgeGraphFormatter) - || (this.getFormatter().getEdgeById(edgeId) instanceof OdotDirectedLineEdgeGraphFormatter)) { - var coordenateSourceX = svgNodeSource.getAttribute("dragx"); - var coordenateSourceY = svgNodeSource.getAttribute("dragy"); - var coordenateTargetX = svgNodeTarget.getAttribute("dragx"); - var coordenateTargetY = svgNodeTarget.getAttribute("dragy"); - var point = this._calculateEdgePointerPosition(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, offset); - coordenateTargetX = point.x; - coordenateTargetY = point.y; - var angle = Geometry.toDegree(point.angle) + 90; - // this.arrowDefaultSize = this.formatter.getEdgeById(edgeId).getArrowSize(); //getDefault().getArrowSize(); - var attributes = []; - if (this.getFormatter().getEdgeById(edgeId) instanceof OdotDirectedLineEdgeGraphFormatter) { - attributes = [ - [ "fill", "#FFFFFF" ], [ "stroke", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], - [ "id", this.getSVGArrowEdgeId(edgeId) ] ]; - } else { - attributes = [ - [ "fill", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], - [ "stroke", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], [ "id", this.getSVGArrowEdgeId(edgeId) ] ]; - } - var flechaSVGNode = SVG.drawCircle(0, 0, 4, this.GraphEdgeGroup, attributes); - flechaSVGNode.setAttribute("transform", " translate(" + coordenateTargetX + ", " + coordenateTargetY + "), rotate(" + angle + ")"); - } - ; - - var _this = this; - /** Events for the SVG edge **/ - if (svgEdge != null) { - if (this.getDataset().getEdgesCount() < this.args.maxNumberEdgesFiringEvents) { - svgEdge.addEventListener("mouseover", function() { - _this.overEdge(edgeId); - }, false); - svgEdge.addEventListener("mouseout", function() { - _this.outEdge(edgeId); - }, false); - } - } -}; - -GraphCanvas.prototype._calculateEdgePointerPosition = function(sourceX, sourceY, targetX, targetY, radius) { - var angle = Geometry.getAngleBetweenTwoPoints(sourceX, sourceY, targetX, targetY); - - /** Suponiendo el node source que este a la derecha **/ - if ((targetX - sourceX) < 0) { - var b = Geometry.getAdjacentSideOfRectangleRight(angle, radius); - targetX = parseFloat(targetX) + parseFloat(b); - arrowX = parseFloat(targetX) + parseFloat(b) + this.arrowDefaultSize / 2; - } else { - var b = Geometry.getAdjacentSideOfRectangleRight(angle, radius); - targetX = parseFloat(targetX) - parseFloat(b); - arrowX = parseFloat(targetX) - parseFloat(b) - this.arrowDefaultSize / 2; - } - - /** Suponiendo el node source que este a la arriba **/ - if ((targetY - sourceY) > 0) { - var a = Geometry.getOppositeSideOfRectangleRight(angle, radius); - targetY = parseFloat(targetY) - parseFloat(a); - arrowY = parseFloat(targetY) - parseFloat(a) - this.arrowDefaultSize / 2; - } else { - var a = Geometry.getOppositeSideOfRectangleRight(angle, radius); - targetY = parseFloat(targetY) + parseFloat(a); - arrowY = parseFloat(targetY) + parseFloat(a) - this.arrowDefaultSize / 2; - - } - - return { - "x" : arrowX, - "y" : arrowY, - "angle" : angle - }; -}; - -GraphCanvas.prototype.calculateCoordenatesBezier = function(nodeSize, x1, y1) { - var x11 = x1 - (nodeSize / 2); - var y11 = y1 - (nodeSize / 2); - - var x12 = parseFloat(x1) + parseFloat(nodeSize / 2); - var y12 = y1 - (nodeSize / 2); - - var curvePointX = (x12 - x11) / 2 + x11; - var curvePointY = y1 - (nodeSize * 2); - var d = "M" + x11 + "," + y11 + " T" + curvePointX + "," + curvePointY + " " + x12 + "," + y12; - return d; - -}; - -GraphCanvas.prototype.renderEdges = function() { - for ( var edge in this.getDataset().getEdges()) { - this.renderEdge(this.getDataset().getEdgeById(edge).getId()); - - } -}; - -GraphCanvas.prototype.getLastSelectedNode = function() { - var node = null; - if (this.getSelectedVertices().length > 0) { - var nodeId = this.getSelectedVertices()[this.getSelectedVertices().length - 1]; - node = this.getDataset().getVertexById(nodeId); - } - return node; -}; -/* - GraphCanvas.prototype.getNodeByNameAndIndex = function(node, index){ - var nodeId = this.getDataset().verticesIndex[node][index]; - var nodeItem = this.getDataset().getVertexById(nodeId); - return nodeItem; - }; - */ - -GraphCanvas.prototype.setDataset = function(dataset) { - this.dataset = dataset; -}; - -GraphCanvas.prototype.setFormatter = function(formatter) { - this.formatter = formatter; -}; - -GraphCanvas.prototype.setLayout = function(layout) { - this.layout = layout; -}; - -/** API **/ -GraphCanvas.prototype.getDataset = function() { - return this.dataset; -}; - -GraphCanvas.prototype.getFormatter = function() { - return this.formatter; -}; - -GraphCanvas.prototype.getLayout = function() { - return this.layout; -}; - -/** API DATASET **/ -GraphCanvas.prototype.addVertex = function(name, args) { - this.getDataset().addNode(name, args); -}; - -GraphCanvas.prototype.removeVertex = function(vertexId) { - this.getDataset().getVertexById(vertexId).remove(); -}; - -GraphCanvas.prototype.addEdge = function(edgeName, nodeSourceId, nodeTargetId, args) { - this.getDataset().addEdge(edgeName, nodeSourceId, nodeTargetId, args); -}; -/* - GraphCanvas.prototype.removeEdge = function(edgeId){ - this.getDataset().getEdgeById(edgeId).remove(); - }; - */ - -/** API FORMATTER **/ -GraphCanvas.prototype.getWidth = function() { - return this.getFormatter().getWidth(); -}; - -GraphCanvas.prototype.getHeight = function() { - return this.getFormatter().getHeight(); -}; - -GraphCanvas.prototype.getBackgroundImage = function() { - return this.getFormatter().getBackgroundImage(); -}; - -//GraphCanvas.prototype.setBackgroundImage = function(value){ -// this.getFormatter().setBackgroundImage(value); -//}; - -GraphCanvas.prototype.getBackgroundColor = function() { - return this.getFormatter().getBackgroundColor(); -}; - -GraphCanvas.prototype.setBackgroundColor = function() { - this.getFormatter().setBackgroundColor(value); -}; - -//GraphCanvas.prototype.setEdgeFill = function(edgeId, value){ -// this.getFormatter().getEdgeById(edgeId).getDefault().setFill(value); -//}; -// -//GraphCanvas.prototype.getEdgeFill = function(edgeId){ -// return this.getFormatter().getEdgeById(edgeId).getDefault().getFill(); -//}; - -/** VERTICES FORMATTER **/ -GraphCanvas.prototype.setVertexSize = function(vertexId, value) { - this.getFormatter().getVertexById(vertexId).getDefault().setSize(value); -}; - -GraphCanvas.prototype.getVertexSize = function(vertexId) { - return this.getFormatter().getVertexById(vertexId).getDefault().getSize(); -}; - -GraphCanvas.prototype.setVertexStroke = function(vertexId, value) { - this.getFormatter().getVertexById(vertexId).getDefault().setStroke(value); -}; - -GraphCanvas.prototype.getVertexStroke = function(vertexId) { - return this.getFormatter().getVertexById(vertexId).getDefault().getStroke(); -}; - -GraphCanvas.prototype.setVertexStrokeOpacity = function(vertexId, value) { - this.getFormatter().getVertexById(vertexId).getDefault().setStrokeOpacity(value); -}; - -GraphCanvas.prototype.getVertexStrokeOpacity = function(vertexId) { - return this.getFormatter().getVertexById(vertexId).getDefault().getStrokeOpacity(); -}; - -GraphCanvas.prototype.setVertexOpacity = function(vertexId, value) { - this.getFormatter().getVertexById(vertexId).getDefault().setOpacity(value); -}; - -GraphCanvas.prototype.getVertexOpacity = function(vertexId) { - return this.getFormatter().getVertexById(vertexId).getDefault().getOpacity(); -}; - -GraphCanvas.prototype.setVertexFill = function(vertexId, color) { - this.getFormatter().getVertexById(vertexId).getDefault().setFill(color); -}; - -GraphCanvas.prototype.getVertexFill = function(vertexId) { - return this.getFormatter().getVertexById(vertexId).getDefault().getFill(); -}; - -/** EDGES FORMATTER **/ -GraphCanvas.prototype.setEdgeSize = function(edgeId, value) { - this.getFormatter().getEdgeById(edgeId).getDefault().setSize(value); -}; - -GraphCanvas.prototype.getEdgeSize = function(edgeId) { - return this.getFormatter().getEdgeById(edgeId).getDefault().getSize(); -}; - -GraphCanvas.prototype.setEdgeStroke = function(edgeId, value) { - this.getFormatter().getEdgeById(edgeId).getDefault().setStroke(value); -}; - -GraphCanvas.prototype.getEdgeStroke = function(edgeId) { - return this.getFormatter().getEdgeById(edgeId).getDefault().getStroke(); -}; - -GraphCanvas.prototype.setEdgeStrokeOpacity = function(edgeId, value) { - this.getFormatter().getEdgeById(edgeId).getDefault().setStrokeOpacity(value); -}; - -GraphCanvas.prototype.getEdgeStrokeOpacity = function(edgeId) { - return this.getFormatter().getEdgeById(edgeId).getDefault().getStrokeOpacity(); -}; - -GraphCanvas.prototype.setEdgeFill = function(edgeId, color) { - this.getFormatter().getEdgeById(edgeId).getDefault().setFill(color); -}; - -GraphCanvas.prototype.getEdgeFill = function(edgeId) { - return this.getFormatter().getEdgeById(edgeId).getDefault().getFill(); -}; - -/** API LAYOUT **/ -GraphCanvas.prototype.setCoordinates = function(vertexId, x, y) { - return this.getLayout().getEdgeById(vertexId).setCoordinates(x, y); -}; - - - -function HPLCGraph(args) { - this.width = 600; - this.height = 600; - this.title = ''; - this.bbar = false; - this.plotInnerPanelPadding = 10; - this.plotPanelPadding = 5; - this.id = BUI.id(); - - this.hidePlots = null; - this.xlabel = ""; - this.scaled = false; - this.xParam = null; - this.showRangeSelector = true; - this.interactionModel = null; - - /** for each stat the max and minimum value when it is scaled in order to show correctly in the legend **/ - this.ranges = {}; - if (args != null) { - if (args.interactionModel != null) { - this.interactionModel = args.interactionModel; - } - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; - } - if (args.bbar != null) { - this.bbar = args.bbar; - } - if (args.title != null) { - this.title = args.title; - } - if (args.plots != null) { - this.plots = args.plots; - } - - if (args.scaled != null) { - this.scaled = args.scaled; - } - if (args.xlabel != null) { - this.xlabel = args.xlabel; - } - if (args.xParam != null) { - this.xParam = args.xParam; - } - if (args.showRangeSelector != null) { - this.showRangeSelector = args.showRangeSelector; - } - } - - this.onZoomX = new Event(this); - this.onResetZoom = new Event(this); - this.dblclick = new Event(this); -} - -HPLCGraph.prototype.getMenu = function () { - var _this = this; - /** Actions buttons **/ - var actions = []; - - function toggle(item, pressed) { - if (pressed) { - _this.plots[item.param] = true; - } else { - delete _this.plots[item.param]; - } - _this.reloadData(this.hplcData); - } - - for (var i = 0; i < this.hplcData.length; i++) { - if (this.hplcData[i].showOnMenu != false) { - var param = this.hplcData[i].param; - var style = "style='padding:0 0px 0 5px;'"; - actions.push({ - text : "
" + BUI.getRectangleColorDIV(this.hplcData[i].color, 10, 10) + " " + this.hplcData[i].label + "
", - id : _this.id + param, - param : param, - enableToggle : true, - scope : this, - toggleHandler : toggle, - pressed : (_this.plots[param] != null) - }); - } - } - actions.push("-"); - - actions.push({ - text : "Scale", - enableToggle : true, - scope : this, - pressed : this.scaled, - icon : '../images/icon_graph.png', - toggleHandler : function (item, pressed) { - _this.scaled = pressed; - _this.reloadData(this.hplcData); - } - }); - - actions.push("->"); - actions.push({ - text : "Save", - scope : this, - icon : '../images/save.gif', - handler : function (item, pressed) { - var largeImage = document.createElement("img"); - largeImage.style.display = 'block'; - largeImage.style.width = 200 + "px"; - largeImage.style.height = 200 + "px"; - largeImage.setAttribute('src', Dygraph.Export.asCanvas(this.dygraphObject.dygraph).toDataURL()); - window.open(Dygraph.Export.asCanvas(this.dygraphObject.dygraph).toDataURL(), 'Image', ''); - } - }); - - return actions; -}; - -/** Looks for the maximum value and then divide everything but that value **/ -HPLCGraph.prototype.scaledData = function (data) { - for (var i = 0; i < data.length; i++) { - var values = this.getMaxAndMinValue(data[i]); - data[i] = this.divideValuesByMax(data[i], values.max); - this.ranges[data[i].label] = values; - } - return data; -}; - - -/** Given a stat float[] and a max number it will divide each value by max **/ -HPLCGraph.prototype.divideValuesByMax = function (stat, max) { - for (var j = 0; j < stat.data.length; j++) { - if (max != 0) { - stat.data[j] = Number(stat.data[j]) / max; - stat.std[j] = Number(stat.std[j]) / max; - } - } - return stat; -}; - -/** returns max value of a stat **/ -HPLCGraph.prototype.getMaxAndMinValue = function (stat) { - var max = 0; - var min = stat.data[0]; - for (var j = 0; j < stat.data.length; j++) { - if (Number(stat.data[j]) > max) { - max = Number(stat.data[j]); - } - if (Number(stat.std[j]) > max) { - max = Number(stat.std[j]); - } - if (Number(stat.data[j]) < min) { - min = Number(stat.data[j]); - } - } - return { - max : Number(max), - min : Number(min) - }; -}; - -HPLCGraph.prototype.getPoint = function (data, i) { - var point = [ 10, 10, 10 ]; - var y = parseFloat(data.data[i]); - var error = parseFloat(data.std[i]); - if (data.fdata == null) { - return [ y - error, y, y + error ]; - } else { - if (data.fstd != null) { - return [ data.fstd(y - error), data.fdata(y), data.fstd(y + error) ]; - } - return [ data.fdata(y) - error, data.fdata(y), data.fdata(y) + error ]; - } - return point; -}; - -HPLCGraph.prototype.reloadData = function(hplcData) { - this.panel.setLoading(false); - this.hplcData = hplcData; - - var data = hplcData; - - - /** In case of having peaks **/ - if (this.peaks != null) { - for (var peak in this.peaks) { - var values = []; - var std = []; - for (var i = 0; i < this.peaks[peak].length; i++) { - values.push(this.peaks[peak][i][1]); - std.push(this.peaks[peak][i][2]); - } - data.push({ - param : peak, - data : values, - showOnMenu : false, - fdata : function (a) { - var value = (Math.log(parseFloat(a))); - if (isNumber(value)) { - return value; - } - }, - fstd : function (a) { - var value = Math.log(Math.abs(parseFloat(a))); - if (isNumber(value)) - return value; - }, - std : std, - color : this.colorPeak[peak], - label : peak - }); - - } - } - - - if (this.scaled) { - data = this.scaledData(JSON.parse(JSON.stringify(hplcData))); - } - - var paramIndex = {}; - var parsed = []; - var j = 0; - for (var i = 0; i < data[0].data.length - 1; i++) { - var aux = []; - for (j = 0; j < data.length; j++) { - if (this.plots != null) { - if (this.plots[data[j].param] != null) { - aux.push(this.getPoint(data[j], i)); - paramIndex[data[j].param] = aux.length - 1; - } - } else { - aux.push([ data[j].data[i] - data[j].std[i], data[j].data[i], data[j].data[i] + data[j].std[i] ]); - } - } - parsed.push([]); - - var index = i; - if (this.xParam != null) { - index = parseFloat(data[this.xParam].data[i]); - } - - parsed[parsed.length - 1].push(index); - - for (j = 0; j < data.length; j++) { - if (this.plots != null) { - if (this.plots[data[j].param] != null) { - parsed[parsed.length - 1].push(aux[paramIndex[data[j].param]]); - } - } else { - parsed[parsed.length - 1].push(aux[j]); - } - } - } - - var colors = []; - var labels = [ "" ]; - for (j = 0; j < data.length; j++) { - if (this.plots != null) { - if (this.plots[data[j].param] != null) { - colors.push(data[j].color); - labels.push(data[j].label); - } - } else { - parsed[parsed.length - 1].push(aux[j]); - } - } - - this._renderDygraph(parsed, colors, labels); -}; - -HPLCGraph.prototype._renderDygraph = function (parsed, colors, labels) { - this.dygraphObject = new StdDevDyGraph(this.id, { - width : this.width, - height : this.height - 10, - xlabel : this.xlabel, - showRangeSelector : this.showRangeSelector, - interactionModel : this.interactionModel, - scaled : this.scaled, - ranges : this.ranges - }); - this.dygraphObject.draw(parsed, colors, labels); - - var _this = this; - this.dygraphObject.onZoomX.attach(function (sender, args) { - try { - _this.onZoomX.notify(args); - } catch (e) { - } - }); - - this.dygraphObject.onResetZoom.attach(function (sender, args) { - try { - _this.onResetZoom.notify(args); - } catch (e) { - } - }); - - this.dygraphObject.dblclick.attach(function (sender, args) { - try { - _this.dblclick.notify(args); - } catch (e) { - } - }); - -}; - -HPLCGraph.prototype.loadData = function (data) { - var _this = this; - this.reloadData(data); - this.panel.addDocked({ - xtype : 'toolbar', - items : this.getMenu() - }); - - - if (this.bbar == true){ - this.panel.addDocked({ - xtype : 'toolbar', - dock: 'bottom', - items : [ - { - xtype: 'numberfield', - id: 'main_field_start', - fieldLabel: 'Range from', - width: 170, - labelWidth : 70, - value: 0, - minValue: 0 - }, - { - xtype: 'numberfield', - id: 'main_field_end', - fieldLabel: 'to', - width: 130, - labelWidth : 30, - value: 0, - minValue: 0 - }, - { - xtype: 'button', - text: 'Go', - handler: function () { - var start = parseFloat(Ext.getCmp("main_field_start").getValue()); - var end = parseFloat(Ext.getCmp("main_field_end").getValue()); - - if (start < 0) { - start = 0; - } - if (end < 0) { - end = 0; - } - if (start > end) { - var aux = end; - end = start; - start = aux; - } - - _this.dygraphObject.dygraph.updateOptions({ isZoomedIgnoreProgrammaticZoom: true, dateWindow: [start, end] }); - } - } - ] - }); - } -}; - -HPLCGraph.prototype.getPanel = function () { - this.panel = Ext.create('Ext.panel.Panel', { - padding : this.plotPanelPadding, - width : this.width + 4 * this.plotInnerPanelPadding, - height : this.height + 4 * this.plotInnerPanelPadding, - items : [ { - html : "", - id : this.id, - width : this.width, - height : this.height - } ] - }); - - return this.panel; -}; - -HPLCGraph.prototype.input = function () { - return DATADOC.getHPLCData(); -}; - -HPLCGraph.prototype.getDataByFrameNumber = function (frameNumber) { - var data = {}; - data.frameNumber = frameNumber; - for (var key in this.hplcData){ - data[this.hplcData[key].label] = this.hplcData[key].data[frameNumber]; - } - console.log(data); - return data; -}; - - -HPLCGraph.prototype.test = function (targetId) { - var mainPlotPanel = new HPLCGraph({ - title : 'I0', - width : 800, - height : 400, - plots : { - "I0" : true, - "Rg" : true, - "Mass" : true - }, - xlabel : "HPLC Frames", - scaled : this.scaled, - interactionModel : { - 'dblclick' : function (event, g, context) { - } - } - }); - mainPlotPanel.getPanel().render(targetId); - mainPlotPanel.loadData(mainPlotPanel.input()); - -}; - - -function MergesHPLCGraph(args) { - HPLCGraph.prototype.constructor.call(this, args); - -// this.peakColors = ["#00FB42", "#00BA31", "#007C21", "#003E10"]; - this.peakColors = ["#DEBD00", "#6D9100", "#872900", "#0092CC"]; -} - - -MergesHPLCGraph.prototype.scaledData = HPLCGraph.prototype.scaledData; -MergesHPLCGraph.prototype.divideValuesByMax = HPLCGraph.prototype.divideValuesByMax; -MergesHPLCGraph.prototype.getMaxAndMinValue = HPLCGraph.prototype.getMaxAndMinValue; -MergesHPLCGraph.prototype.getPoint = HPLCGraph.prototype.getPoint; -MergesHPLCGraph.prototype.reloadData = HPLCGraph.prototype.reloadData; -MergesHPLCGraph.prototype._renderDygraph = HPLCGraph.prototype._renderDygraph; -MergesHPLCGraph.prototype.loadData = HPLCGraph.prototype.loadData; -MergesHPLCGraph.prototype.getPanel = HPLCGraph.prototype.getPanel; -MergesHPLCGraph.prototype.getDataByFrameNumber = HPLCGraph.prototype.getDataByFrameNumber; - - -MergesHPLCGraph.prototype.setPeaks = function (data) { - this.peaks = data; - /** get size of peaks **/ - this.peakKeys = []; - this.colorPeak = {}; - var colorCount = 1; - for (var key in this.peaks) { - if (this.peaks.hasOwnProperty(key)) { - var color = this.peakColors[colorCount % this.peakColors.length]; - colorCount = colorCount + 1; - this.peakKeys.push(key); - this.colorPeak[key] = color; - } - } - this.peakKeys.sort(); -}; - - -MergesHPLCGraph.prototype.getMenu = function () { - var _this = this; - /** Actions buttons **/ - var actions = []; - - function toggle(item, pressed) { - if (pressed) { - _this.plots[item.param] = true; - } else { - delete _this.plots[item.param]; - } - _this.reloadData(_this.hplcData); - } - - - /** Toolbar for peaks Average **/ - if (this.peaks != null) { - var items = []; - for (var i = 0; i < this.peakKeys.length; i++) { - var color = this.colorPeak[this.peakKeys[i]]; - items.push({ - text: "Peak #" + i + " " + this.peakKeys[i].replace("- ", " to #").replace(".0", "").replace(".0", "") + "", - peakid : this.peakKeys[i], - checked: false, - checkHandler: function (sender, pressed) { - var item = new Object(); - item.param = sender.peakid; - toggle(item, pressed); - } - }); - } - - var menu = Ext.create('Ext.menu.Menu', { - id: 'mainMenu', - style: { - overflow: 'visible' - }, - items: items - }); - var tb = Ext.create('Ext.toolbar.Toolbar'); - tb.add({ - text: 'Peaks Avg.', - menu: menu - }); - actions.push(tb); - } - - - - for (var i = 0; i < this.hplcData.length; i++) { - if (this.hplcData[i].showOnMenu != false) { - var param = this.hplcData[i].param; - var style = "style='padding:0 0px 0 5px;'"; - actions.push({ - text : "
" + BUI.getRectangleColorDIV(this.hplcData[i].color, 10, 10) + " " + this.hplcData[i].label + "
", - id : _this.id + param, - param : param, - enableToggle : true, - scope : this, - margin : 5, - toggleHandler : toggle, - pressed : (_this.plots[param] != null) - }); - } - } - - actions.push("->"); - actions.push({ - text : "Save", - scope : this, - icon : '../images/save.gif', - handler : function (item, pressed) { - var largeImage = document.createElement("img"); - largeImage.style.display = 'block'; - largeImage.style.width = 200 + "px"; - largeImage.style.height = 200 + "px"; - largeImage.setAttribute('src', Dygraph.Export.asCanvas(this.dygraphObject.dygraph).toDataURL()); - window.open(Dygraph.Export.asCanvas(this.dygraphObject.dygraph).toDataURL(), 'Image', ''); - } - }); - - return actions; -}; - - -MergesHPLCGraph.prototype.input = function () { - return DATADOC.getScatteringHPLCFrameData(); -}; - -MergesHPLCGraph.prototype.test = function (targetId) { - var mainPlotPanel = new MergesHPLCGraph({ - title : 'Scattering', - width : this.plotWidth, - height : 500, - showRangeSelector : false, - xParam : 0, - xlabel : "scattering_I", - plots : { - "scattering_I" : true, - "subtracted_I" : true, - "buffer_I" : true - } - }); - mainPlotPanel.getPanel().render(targetId); - mainPlotPanel.loadData(mainPlotPanel.input()); -}; - - -function NetworkWidget(args) { - this.id = "NetworkViewer_" + Math.random().toString().replace(".", "_"); - - this.label = true; - if (args != null) { - if (args.targetId != null) { - this.targetId = args.targetId; - } - if (args.label != null) { - this.label = args.label; - } - } - - this.onVertexOver = new Event(this); - this.onVertexOut = new Event(this); -} - -NetworkWidget.prototype.draw = function(dataset, formatter, layout) { - - this.graphCanvas = new GraphCanvas(this.id, document.getElementById(this.targetId), { - "labeled" : this.label, - "multipleSelectionEnabled" : false, - "draggingCanvasEnabled" : false - }); - this.graphCanvas.draw(dataset, formatter, layout); - - var _this = this; - this.graphCanvas.onVertexOver.attach(function(sender, nodeId) { - _this.onVertexOver.notify(nodeId); - }); - - this.graphCanvas.onVertexOut.attach(function(sender, nodeId) { - _this.onVertexOut.notify(nodeId); - }); -}; - -/** SELECT VERTICES BY NAME * */ -NetworkWidget.prototype.selectVertexByName = function(vertexName) { - var vertices = this.getDataset().getVertexByName(vertexName); - if (vertices != null) { - for ( var nodeId in vertices) { - if (vertices.hasOwnProperty(nodeId)) { - var vertexId = vertices[nodeId].getId(); - this.selectVertexById(vertexId); - } - } - } -}; - -NetworkWidget.prototype.selectVerticesByName = function(verticesName) { - for ( var i = 0; i < verticesName.length; i++) { - this.selectVertexByName(verticesName[i]); - } -}; - -/** SELECT VERTICES BY ID * */ -NetworkWidget.prototype.selectVertexById = function(vertexId) { - this.graphCanvas.selectNode(vertexId); - this.blinkVertexById(vertexId); -}; - -NetworkWidget.prototype.selectVerticesById = function(verticesId) { - for ( var i = 0; i < verticesId.length; i++) { - this.selectVertexById(verticesId[i]); - } -}; - -/** VECINDARIO * */ -NetworkWidget.prototype.selectNeighbourhood = function() { - this.selectEdgesFromVertices(); - this.selectAdjacent(); -}; - -/** DESELECT * */ -NetworkWidget.prototype.deselectNodes = function() { - this.graphCanvas.deselectNodes(); -}; - -/** SELECT ALL NODES * */ -NetworkWidget.prototype.selectAllNodes = function() { - this.getGraphCanvas().selectAllNodes(); -}; - -/** SELECT EVERYTHING * */ -NetworkWidget.prototype.selectAll = function() { - this.getGraphCanvas().selectAll(); -}; - -/** SELECT ALL EDGES * */ -NetworkWidget.prototype.selectAllEdges = function() { - this.getGraphCanvas().selectAllEdges(); -}; - -/** ZOOM * */ -NetworkWidget.prototype.setScale = function(value) { - this.graphCanvas.setScale(value); -}; - -NetworkWidget.prototype.getScale = function() { - return this.graphCanvas.getScale(value); -}; - -/** SELECT ADJACENT VERTICES FROM SELECTED VERTICES * */ -NetworkWidget.prototype.selectAdjacent = function() { - var selectedVertices = this.getGraphCanvas().getSelectedVertices(); - var edges = []; - for ( var i = 0; i < selectedVertices.length; i++) { - edges = edges.concat(this.getGraphCanvas().getDataset().getVertexById(selectedVertices[i]).getEdges()); - } - var vertices = []; - for ( i = 0; i < edges.length; i++) { - vertices.push(edges[i].getNodeSource().getId()); - vertices.push(edges[i].getNodeTarget().getId()); - } - - this.selectVerticesById(vertices); -}; - -/** SELECT EDGES FROM SELECTED VERTICES * */ -NetworkWidget.prototype.selectEdgesFromVertices = function() { - var selectedVertices = this.getGraphCanvas().getSelectedVertices(); - var edges = []; - for ( var i = 0; i < selectedVertices.length; i++) { - edges = edges.concat(this.getGraphCanvas().getDataset().getVertexById(selectedVertices[i]).getEdges()); - } - var edgesId = []; - for ( i = 0; i < edges.length; i++) { - edgesId.push(edges[i].getId()); - } - this.getGraphCanvas().selectEdges(edgesId); -}; - -/** BLINKING * */ -NetworkWidget.prototype.blinkVertexById = function(vertexId) { - this.graphCanvas.blinkVertexById(vertexId); -}; - -/** COMPONENTE CONEXA DE LOS NODOS SELECCIONADOS * */ -NetworkWidget.prototype.selectConnectedComponent = function() { - var elements = this.getConnectedComponent(); - this.selectVerticesById(elements.nodes); - this.graphCanvas.selectEdges(elements.edges); -}; - -NetworkWidget.prototype.getConnectedComponent = function() { - var nodosVisitados = {}; - var aristasVisitadas = {}; - var arrNodos = []; - var arrAristas = []; - var selectedGraphNodesId = this.getGraphCanvas().getSelectedVertices(); - for ( var i = 0; i < selectedGraphNodesId.length; i++) { - this.visitNode(selectedGraphNodesId[i], nodosVisitados, aristasVisitadas, arrNodos, arrAristas); - } - return { - nodes : arrNodos, - edges : arrAristas - }; -}; - -NetworkWidget.prototype.visitNode = function(nodeId, nodosVisitados, aristasVisitadas, arrNodos, arrAristas) { - nodosVisitados[nodeId] = true; - arrNodos.push(nodeId); - var nodeEdges = this.getDataset().getVertexById(nodeId).getEdges(); - for ( var j = 0; j < nodeEdges.length; j++) { - var edge = nodeEdges[j]; - var edgeId = edge.getId(); - if (aristasVisitadas[edgeId] == null) { - aristasVisitadas[edgeId] = true; - arrAristas.push(edgeId); - var nodeTargetId = edge.getNodeTarget().getId(); - if (nodosVisitados[nodeTargetId] == null) { - this.visitNode(nodeTargetId, nodosVisitados, aristasVisitadas, arrNodos, arrAristas); - } - var nodeSourceId = edge.getNodeSource().getId(); - if (nodosVisitados[nodeSourceId] == null) { - this.visitNode(nodeSourceId, nodosVisitados, aristasVisitadas, arrNodos, arrAristas); - } - } - } -}; - -/** COLLAPSE SELECTED VERTICES * */ -NetworkWidget.prototype.collapse = function() { - var selectedVertices = this.getGraphCanvas().getSelectedVertices(); - var xMin = -Infinity; - var xMax = Infinity; - var yMin = -Infinity; - var yMax = Infinity; - - for ( var i = 0; i < selectedVertices.length; i++) { - var vertex = this.getGraphCanvas().getLayout().getNodeById(selectedVertices[i]); - if (xMin < vertex.x) { - xMin = vertex.x; - } - if (xMax > vertex.x) { - xMax = vertex.x; - } - if (yMin < vertex.y) { - yMin = vertex.y; - } - if (yMax > vertex.y) { - yMax = vertex.y; - } - } - - var centerX = xMin - xMax; - var centerY = yMin - yMax; - var radius = (xMax - xMin) / 4; - - var count = selectedVertices.length; - var verticesCoordinates = []; - - for ( i = 0; i < selectedVertices.length; i++) { - x = centerX + radius * Math.sin(i * 2 * Math.PI / count); - y = centerY + radius * Math.cos(i * 2 * Math.PI / count); - verticesCoordinates.push({ - 'x' : x, - 'y' : y - }); - } - - for ( i = 0; i < selectedVertices.length; i++) { - this.getGraphCanvas().getLayout().getNodeById(selectedVertices[i]).setCoordinates(verticesCoordinates[i].x, verticesCoordinates[i].y); - } -}; - -/** SETTER FONT SIZE * */ -NetworkWidget.prototype.setVerticesFontSize = function(value) { - for ( var nodeId in this.getDataset().getVertices()) { - if (this.getDataset().getVertices().hasOwnProperty(nodeId)) { - this.getFormatter().getVertexById(nodeId).getDefault().setFontSize(value); - } - } -}; - -/** GETTERS * */ -NetworkWidget.prototype.getFormatter = function() { - return this.getGraphCanvas().getFormatter(); -}; -NetworkWidget.prototype.getLayout = function() { - return this.getGraphCanvas().getLayout(); -}; - -NetworkWidget.prototype.getDataset = function() { - return this.getGraphCanvas().getDataset(); -}; - -NetworkWidget.prototype.getGraphCanvas = function() { - return this.graphCanvas; -}; - -RangeWhiskerGraph.prototype.cleanArray = GenericGraph.prototype.cleanArray; -RangeWhiskerGraph.prototype.plotAxes = GenericGraph.prototype.plotAxes; -RangeWhiskerGraph.prototype.plotRuler = GenericGraph.prototype.plotRuler; -RangeWhiskerGraph.prototype.drawSVGVerticalText = GenericGraph.prototype.drawSVGVerticalText; -RangeWhiskerGraph.prototype.getClassColor = GenericGraph.prototype.getClassColor; -RangeWhiskerGraph.prototype.getDimensions = GenericGraph.prototype.getDimensions; -RangeWhiskerGraph.prototype.calculate = GenericGraph.prototype.calculate; -RangeWhiskerGraph.prototype.getMedian = GenericGraph.prototype.getMedian; -RangeWhiskerGraph.prototype.pointToPixel = GenericGraph.prototype.pointToPixel; -RangeWhiskerGraph.prototype.maxValueWhisker = GenericGraph.prototype.maxValueWhisker; -RangeWhiskerGraph.prototype.refresh = GenericGraph.prototype.refresh; - -/** - * Subclass of GenericGraph - * - * @plotHorizontalByCluster - */ -function RangeWhiskerGraph(args) { - this.maxBoxWidth = 25; - - if (args == null) { - args = {}; - } - args.plotHorizontalByCluster = false; - - GenericGraph.call(this, args); - - if (args.maxBoxWidth != null) { - this.maxBoxWidth = args.maxBoxWidth; - } -} - -RangeWhiskerGraph.prototype.refresh = function(data) { - document.getElementById(this.targetId).innerHTML = ""; - this.draw(this.targetId, data); -}; - -RangeWhiskerGraph.prototype.isNumber = function(value) { - if (value == "") - return false; - - var d = parseInt(value); - if (!isNaN(d)) - return true; - else - return false; - -}; - -/** - There are several different methods for calculating quartiles.[1] This calculator uses a method described by Moore and McCabe to find quartile values. - The same method also used by The TI-83 to calculate quartile values. - With this method, the first quartile is the median of the numbers below the median, the third quartile is the median of the numbers above the median. - - http://www.miniwebtool.com/quartile-calculator/ - http://www.alcula.com/calculators/statistics/box-plot/ - - **/ -RangeWhiskerGraph.prototype.getQ1 = function(array) { - array = array.slice(0, array.length / 2); - return this.getMedian(array); -}; - -RangeWhiskerGraph.prototype.getQ3 = function(array) { - array = array.slice((array.length + 1) / 2); - return this.getMedian(array); - -}; - -RangeWhiskerGraph.prototype.getQ2 = function(array) { - return this.getMedian(array); -}; - -RangeWhiskerGraph.prototype.getBelowOutliers = function(belowLimit, array) { - var points = []; - for ( var i = 0; i < array.length; i++) { - if (array[i] <= belowLimit) { - points.push(array[i]); - } - } - return points; -}; - -RangeWhiskerGraph.prototype.getAboveOutliers = function(aboveLimit, array) { - var points = []; - for ( var i = 0; i < array.length; i++) { - if (array[i] >= aboveLimit) { - points.push(array[i]); - } - } - return points; -}; - -RangeWhiskerGraph.prototype.minValueWhisker = function(belowLimit, q1, array) { - var points = []; - - for ( var i = 0; i < array.length; i++) { - if ((array[i] < q1) && (array[i]) > belowLimit) { - points.push(array[i]); - } - } - - if (points.length > 0) { - points.sort(function(a, b) { - return a - b; - }); - return points[0]; - } - return null; -}; - -//RangeWhiskerGraph.prototype.maxValueWhisker = function(aboveLimit, q3, array){ -// var points = []; -// for (var i = 0; i < array.length; i++){ -// if ((array[i] > q3) && (array[i]) <= aboveLimit){ -// points.push(array[i]); -// } -// } -// if (points.length > 0){ -// points.sort(function(a, b){return a - b;}); -// return points[points.length - 1]; -// } -// return null; -//}; - -RangeWhiskerGraph.prototype.drawPoints = function(boxProperties) { - if (this.plotPoints) { - for ( var i = 0; i < boxProperties.values.length; i++) { - var value = boxProperties.values[i]; - var toPixel = this.pointToPixel(value, boxProperties); - SVG.drawCircle(boxProperties.x, toPixel, this.pointRadius, this.svg, - [ - [ "fill", "green" ], [ "fill-opacity", this.fillOpacityPoint ], [ 'stroke-opacity', this.strokeOpacityPoint ], - [ "stroke", "black" ] ]); - } - } -}; - -RangeWhiskerGraph.prototype.plotRangeQ1Q3 = function(data, properties) { - var posX = this.left + this.rulerWidth; - - var boxBordersPointsQ1 = []; - var boxBordersPointsQ3 = []; - var Q2 = []; - - for ( var i = 0; i < data.clusters.length; i++) { - var cluster = data.clusters[i]; - /** inter cluster space **/ - posX = posX + this.interClustersSpace; - - for ( var j = 0; j < cluster.classes.length; j++) { - var ratio = properties.width / (properties.xValues.range); - var coorX = (cluster.x - properties.xValues.min) * ratio + this.rulerWidth; - var boxProperties = { - name : cluster.classes[j].name, - values : cluster.classes[j].values, - minPoint : properties.minPoint, - maxPoint : properties.maxPoint, - x : coorX + this.left, - y : this.top, - width : properties.classWidth, - height : this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight - }; - - var result = this.calculate(boxProperties.values); - var boxColor = this.getClassColor(boxProperties.name); - - if (this.isNumber(result.Q1) && this.isNumber(result.Q3)) { - var x = boxProperties.x; - var y = this.pointToPixel(result.Q1, boxProperties); - if (boxBordersPointsQ1[cluster.classes[j].name] == null) { - boxBordersPointsQ1[cluster.classes[j].name] = []; - } - boxBordersPointsQ1[cluster.classes[j].name].push({ - x : x, - y : y - }); - - x = boxProperties.x; - y = this.pointToPixel(result.Q3, boxProperties); - if (boxBordersPointsQ3[cluster.classes[j].name] == null) { - boxBordersPointsQ3[cluster.classes[j].name] = []; - } - boxBordersPointsQ3[cluster.classes[j].name].push({ - x : x, - y : y - }); - } else { - - if (this.isNumber(result.Q2)) { - - if (boxBordersPointsQ1[cluster.classes[j].name] == null) { - boxBordersPointsQ1[cluster.classes[j].name] = []; - } - - if (boxBordersPointsQ3[cluster.classes[j].name] == null) { - boxBordersPointsQ3[cluster.classes[j].name] = []; - } - - boxBordersPointsQ1[cluster.classes[j].name].push({ - x : boxProperties.x, - y : this.pointToPixel(result.Q2, boxProperties) - }); - boxBordersPointsQ3[cluster.classes[j].name].push({ - x : boxProperties.x, - y : this.pointToPixel(result.Q2, boxProperties) - }); - } - } - } - } - for ( var classe in boxBordersPointsQ1) { - var points = boxBordersPointsQ1[classe]; - var pointsSVG = ""; - for (var k = 0; k < points.length; k++) { - pointsSVG = Number(points[k].x).toFixed(1) + "," + Number(points[k].y).toFixed(1) + " " + pointsSVG; - } - - points = boxBordersPointsQ3[classe]; - for (var z = points.length - 1; z >= 0; z--) { - pointsSVG = Number(points[z].x).toFixed(1) + "," + Number(points[z].y).toFixed(1) + " " + pointsSVG; - } - - SVG.drawPoligon(pointsSVG, this.svg, [ - [ "fill", this.getClassColor(classe) ], [ "opacity", "0.3" ], [ "stroke", "black" ], [ "stroke-width", 1 ] ]); - } -}; - -RangeWhiskerGraph.prototype.plotWhisters = function(data, properties) { - var colors = [ "yellow", "orange", "green" ]; - - this.plotRangeQ1Q3(data, properties); - var Q2 = {}; - - for ( var i = 0; i < data.clusters.length; i++) { - var cluster = data.clusters[i]; - for ( var j = 0; j < cluster.classes.length; j++) { - var ratio = properties.width / (properties.xValues.range); - var coorX = (cluster.x - properties.xValues.min) * ratio + this.left + this.rulerWidth - this.rulerStroke; - var boxProperties = { - name : cluster.classes[j].name, - values : cluster.classes[j].values, - minPoint : properties.minPoint, - maxPoint : properties.maxPoint, - x : coorX, - y : this.top, - width : properties.classWidth, - height : this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight - }; - - this.drawPoints(boxProperties); - - /** PLOTTING Q2 **/ - var result = this.calculate(boxProperties.values); - var boxColor = this.getClassColor(boxProperties.name); - if (this.isNumber(result.Q2)) { - if (Q2[boxProperties.name] != null) { - SVG.drawLine(boxProperties.x, this.pointToPixel(result.Q2, boxProperties), Q2[boxProperties.name].x, Q2[boxProperties.name].y, - this.svg, [ [ "stroke", boxColor ], [ "stroke-width", "2" ] ]); - } - Q2[boxProperties.name] = { - x : boxProperties.x, - y : this.pointToPixel(result.Q2, boxProperties) - } - } - } - } - -}; - -RangeWhiskerGraph.prototype.draw = function(targetId, data) { - //this.calculate(data); - this.targetId = targetId; - var properties = (this.getDimensions(data)); - this.svg = SVG.createSVGCanvas(document.getElementById(this.targetId), [ [ "width", this.width ], [ "height", this.height ] ]); - this.plotAxes(properties); - this.plotWhisters(data, properties); -}; - -RangeWhiskerGraph.prototype.input = function() { - return DATADOC.getBoxWhikerData(); -}; - -RangeWhiskerGraph.prototype.test = function(targetId) { - var plot = new RangeWhiskerGraph({ - targetId : targetId, - height : 350, - width : 450, - maxBoxWidth : 25 - }); - plot.refresh(this.input()); -}; - -StdDevDyGraph.prototype.dblclick = DygraphWidget.prototype.dblclick; -StdDevDyGraph.prototype._createHTLMWrapper = DygraphWidget.prototype._createHTLMWrapper; -StdDevDyGraph.prototype.draw = DygraphWidget.prototype.draw; - -function StdDevDyGraph(targetId, args) { - this.scaled = false; - if (args == null) { - args = {}; - } - args.customBars = true; - DygraphWidget.prototype.constructor.call(this, targetId, args); -} - -StdDevDyGraph.prototype.input = function () { - return { - data : [ [ 1, [ 2, 3, 3.5 ], [ 4, 4.2, 5 ] ], [ 2, [ 5, 5.5, 5.7 ], [ 4, 4.2, 5 ] ] ], - colors : [ "blue", "red" ], - labels : [ "", 'data1', 'data2' ] - }; -}; - -StdDevDyGraph.prototype.test = function (targetId) { - var dygraphObject = new StdDevDyGraph(targetId, { - width : 500, - height : 400, - xlabel : "xLabel", - showRangeSelector : false - }); - - dygraphObject.draw(dygraphObject.input().data, dygraphObject.input().colors, dygraphObject.input().labels); -}; - - - -function AbinitioGrid(args) { - this.height = null; - this.width = null; - this.id = BUI.id(); - - if (args != null) { - if (args.height != null) { - this.height = args.height; - - if (args.width != null) { - this.width = args.width; - } - } - } - - this.onSelected = new Event(this); -}; - - -AbinitioGrid.prototype.refresh = function(subtractions){ - this.store.loadData(this._prepareData(subtractions)); -}; - -AbinitioGrid.prototype._prepareData = function(subtractions){ - /** Parsing data * */ - var models = []; - for (var l = 0; l < subtractions.length; l++) { - var subtraction = subtractions[l]; - for (var k = 0; k < subtraction.substractionToAbInitioModel3VOs.length; k++) { - var data = subtraction.substractionToAbInitioModel3VOs[k].abinitiomodel3VO; - if (data.averagedModel != null) { - models.push(data.averagedModel); - models[models.length - 1].type = "Reference"; - } - - if (data.shapeDeterminationModel != null) { - models.push(data.shapeDeterminationModel); - models[models.length - 1].type = "Refined"; - } - - if (data.modelList3VO != null) { - if (data.modelList3VO.modeltolist3VOs != null) { - for (var i = 0; i < data.modelList3VO.modeltolist3VOs.length; i++) { - models.push(data.modelList3VO.modeltolist3VOs[i].model3VO); - models[models.length - 1].type = "Model"; - } - } - } - } - } - return models; -}; - -AbinitioGrid.prototype.getPanel = function(){ - var _this = this; - - - var modelFields = [ "modelId", "type", "chiSqrt", "dmax", "firFile", "logFile", "fitFile", "pdbFile", "rfactor", "rg", "volume" ]; - Ext.define('AbinitioModel', { - extend : 'Ext.data.Model', - fields : modelFields - - }); - - /** - * Store in Memory - */ - this.store = Ext.create('Ext.data.Store', { - model : 'AbinitioModel', - autoload : true, - groupField : 'type' - }); - - - var groupingFeature = Ext.create('Ext.grid.feature.Grouping',{ - groupHeaderTpl: '{name} ({rows.length} model{[values.rows.length > 1 ? "s" : ""]})', - startCollapsed: true, - collapsible : true - }); - - this.grid = Ext.create('Ext.grid.Panel', { - collapsible : false, - resizable : true, - features: [groupingFeature], - autoscroll : true, - multiSelect : true, - store : this.store, - height : this.height, - width : this.width, - margin : 10, - columns : [ { - text : "Type", - dataindex : "type", - hidden : true, - renderer : function(a, b, record) { - return record.data.type; - }, - flex : 1 - }, - { - text : "ModelId", - dataindex : "modelId", - hidden : true, - renderer : function(a, b, record) { - return record.data.modelId; - - }, - flex : 1 - }, - - { - text : "chiSqrt", - dataindex : "chiSqrt", - renderer : function(a, b, record) { - if (record.data.dmax != null) { - return BUI.formatValuesUnits(record.data.chiSqrt, "", 12, this.decimals); - } - - }, - flex : 1 - }, - { - text : "Dmax", - dataindex : "dmax", - renderer : function(a, b, record) { - if (record.data.dmax != null) { - return BUI.formatValuesUnits(record.data.dmax, "nm", 12, this.decimals); - } - - }, - flex : 1 - }, { - text : "rFactor", - dataindex : "rfactor", - hidden : true, - renderer : function(a, b, record) { - if (record.data.rfactor != null) { - return record.data.rfactor; - } - }, - flex : 1 - }, { - text : "Rg", - dataindex : "rg", - renderer : function(a, b, record) { - if (record.data.rg != null) { - return BUI.formatValuesUnits(record.data.rg, "nm", 12, this.decimals); - } - - }, - flex : 1 - }, - { - text : "Volume", - dataindex : "volume", - renderer : function(a, b, record) { - if (record.raw.volume != null){ - return BUI.formatValuesUnits(record.raw.volume, '') + " nm3"; - } - }, - flex : 1 - }, - { - text : "PDB", - dataindex : "pdbFile", - renderer : function(a, b, record) { - if (record.data.pdbFile != null){ - return record.data.pdbFile.split("/")[record.data.pdbFile.split("/").length - 1]; - } - }, - flex : 1 - }, { - text : "Fir", - dataindex : "firFile", - renderer : function(a, b, record) { - if (record.data.firFile != null){ - return record.data.firFile.split("/")[record.data.firFile.split("/").length - 1]; - } - }, - flex : 1 - }, { - text : "LOG", - dataindex : "logFile", - hidden : true, - renderer : function(a, b, record) { - if (record.data.logFile != null){ - return record.data.logFile.split("/")[record.data.logFile.split("/").length - 1]; - } - }, - flex : 1 - } - ], - viewConfig : { - enableTextSelection : true, - preserveScrollOnRefresh : true, - stripeRows : true, - listeners : { - 'celldblclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - }, - 'cellclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - var models = []; - for (var i = 0; i < grid.getSelectionModel().selected.items.length; i++) { - models.push(grid.getSelectionModel().selected.items[i].raw); - } - _this.onSelected.notify(models); - } - } - } - }); - return this.grid; - -}; - - -function AdditiveGrid(args) { - this.onRemoveButtonClicked = new Event(this); -} - -AdditiveGrid.prototype.getBuffer = function() { - return this.buffer; -}; - -AdditiveGrid.prototype._getActions = function() { - var _this = this; - /** Actions buttons **/ - var actions = []; - - actions.push(Ext.create('Ext.Action', { - icon : '../images/add.png', - text : 'Add', - disabled : true, - alwaysEnabled : true, - handler : function(widget, event) { - _this.buffer.bufferhasadditive3VOs.push(BIOSAXS_BEANS.getBufferhasAdditive3VO()); - _this.refresh(_this.buffer, _this.experiment); - } - })); - - return actions; -}; - -AdditiveGrid.prototype.refresh = function(buffer, experiment) { - this.buffer = buffer; - this.experiment = experiment; - if (buffer) { - if (buffer.bufferhasadditive3VOs) { - this.features = buffer.bufferhasadditive3VOs; - } - } - this.experiment = experiment; - this.store.loadData(this._prepareData(), false); -}; - -AdditiveGrid.prototype.getAdditives = function() { - var additives = []; - for ( var i = 0; i < this.store.getCount(); i++) { - var bufferHasAdditive = BIOSAXS_BEANS.getBufferhasAdditive3VO(); - var data = this.store.getAt(i).getData(); - - bufferHasAdditive.additive3VO.name = data.name; - bufferHasAdditive.additive3VO.comments = data.comments; - bufferHasAdditive.additive3VO.additiveType = data.additiveType; - - bufferHasAdditive.bufferId = this.buffer.bufferId; - bufferHasAdditive.bufferHasAdditiveId = data.bufferHasAdditiveId; - bufferHasAdditive.quantity = data.quantity; - additives.push(bufferHasAdditive); - } - - return additives; -}; - -AdditiveGrid.prototype._getFields = function(buffers) { - var columns = [ - - { - header : 'Name', - dataIndex : 'name', - type : 'string', - editor : { - allowBlank : true - }, - flex : 1 - }, - { - header : 'Type', - name : 'additiveType', - dataIndex : 'additiveType', - editor : { - xtype : 'combobox', - typeAhead : true, - triggerAction : 'all', - selectOnTab : true, - store : BIOSAXS.proposal.getAdditiveTypes(), - lazyRender : true, - listClass : 'x-combo-list-small' - }, - flex : 0.6 - }, - { - header : 'Quantity', - dataIndex : 'quantity', - name : 'quantity', - editor : { - allowBlank : true - }, - type : 'string', - flex : 1 - }, - { - xtype : 'actioncolumn', - items : [ { - icon : '../images/cancel.png', - tooltip : 'Delete additive', - scope : this, - handler : function(grid, rowIndex, colIndex) { - if ((grid.getStore().getAt(rowIndex).data.bufferHasAdditiveId == null)|| (grid.getStore().getAt(rowIndex).data.bufferHasAdditiveId == "")) { - grid.getStore().removeAt(rowIndex); - } else { - this.onRemoveButtonClicked.notify({ - 'bufferId' : this.buffer.bufferId, - 'bufferHasAdditiveId' : this.store.getAt(rowIndex).data.bufferHasAdditiveId - }); - } - } - } ] - } ]; - - return columns; -}; - -AdditiveGrid.prototype._prepareData = function() { - var data = []; - if (this.features == null) { - this.features = []; - } - for (var i = 0; i < this.features.length; i++) { - var object = this.features[i]; - object.name = this.features[i].additive3VO.name; - object.additiveType = this.features[i].additive3VO.additiveType; - object.comments = this.features[i].additive3VO.comments; - object.additiveId = this.features[i].additive3VO.additiveId; - data.push(object); - } - return data; -}; - -AdditiveGrid.prototype.getPanel = function(buffer, experiment) { - this.buffer = buffer; - this.features = buffer.bufferhasadditive3VOs; - this.experiment = experiment; - return this._renderGrid(); -}; - -AdditiveGrid.prototype.getStore = function() { - var _this = this; - var store = Ext.create('Ext.data.Store', { - fields : [ "name", "additiveType", "comments", "additiveId", "bufferHasAdditiveId", "quantity" ], - autoload : false, - data : this._prepareData(), - listeners : { - update : function(store, record) { - record.index = _this.grid.getSelectionModel().getCurrentPosition().row; - _this.buffer.bufferhasadditive3VOs[record.index].additive3VO.name = record.data.name; - _this.buffer.bufferhasadditive3VOs[record.index].additive3VO.additiveType = record.data.additiveType; - _this.buffer.bufferhasadditive3VOs[record.index].additive3VO.comments = record.data.comments; - _this.buffer.bufferhasadditive3VOs[record.index].quantity = record.data.quantity; - } - } - }); - - // store.sort('bufferHasAdditiveId', 'ASC'); - store.loadData(this._prepareData(), false); - return store; -}; - -AdditiveGrid.prototype._renderGrid = function() { - var _this = this; - this.store = this.getStore(); - - var cellEditing = Ext.create('Ext.grid.plugin.CellEditing', { - clicksToEdit : 1 - }); - - this.grid = Ext.create('Ext.grid.Panel', { - dockedItems : [ { - xtype : 'toolbar', - items : this._getActions() - } ], - store : this.store, - height : 230, - title : "Additives", - width : "100%", - columns : _this._getFields(), - plugins : [ cellEditing ], - viewConfig : { - stripeRows : true, - listeners : { - itemcontextmenu : function(view, rec, node, index, e) { - e.stopEvent(); - contextMenu.showAt(e.getXY()); - return false; - } - } - }, - selModel : { - mode : 'SINGLE' - } - }); - - return this.grid; -}; - -AdditiveGrid.prototype.input = function() { -}; - -AdditiveGrid.prototype.test = function(targetId) { - var grid = new AdditiveGrid(); - var panel = grid.getPanel([]); - panel.render(targetId); - -}; - -/** AnalysisGrid **/ -function AnalysisGrid(args) { - var _this = this; - - this.id = BUI.id(); - if (Ext.get("mainPanel")){ - this.width = Ext.get("mainPanel").getWidth(); - } - else{ - this.width = this.maxWidth; - } - this.maxWidth = 1500; - - /** Visibles **/ - this.isGuinierTabVisible = true; - this.isGnomTabVisible = true; - this.isPorodTabVisible = true; - this.isScatteringPlotVisible = true; - this.isAbinitioTabVisible = true; - this.showButtonsVisible = true; - this.isI0Visible = true; - - this.margin = null; - this.grouped = true; - - this.hideNulls = false; - this.decimals = 4; - this.height = null; - this.sorters = [ { - property : 'conc', - direction : 'ASC' - } ]; - - if (args != null) { - if (args.grouped != null) { - this.grouped = args.grouped; - } - - if (args.showButtonsVisible != null) { - this.showButtonsVisible = args.showButtonsVisible; - } - if (args.isI0Visible != null) { - this.isI0Visible = args.isI0Visible; - } - if (args.sorters != null) { - this.sorters = args.sorters; - } - if (args.isScatteringPlotVisible != null) { - this.isScatteringPlotVisible = args.isScatteringPlotVisible; - } - if (args.isGuinierTabVisible != null) { - this.isGuinierTabVisible = args.isGuinierTabVisible; - } - if (args.isGnomTabVisible != null) { - this.isGnomTabVisible = args.isGnomTabVisible; - } - if (args.isPorodTabVisible != null) { - this.isPorodTabVisible = args.isPorodTabVisible; - } - if (args.hideNulls != null) { - this.hideNulls = args.hideNulls; - } - if (args.height != null) { - this.height = args.height; - } - if (args.width != null) { - this.width = args.width; - } - if (args.maxWidth != null) { - this.maxWidth = args.maxWidth; - } - } -} - -AnalysisGrid.prototype.refresh = function(data, args) { - this.store.loadData(this._prepareData(data), false); - if (args != null){ - if (args.experiment != null){ - this.experiment = args.experiment; - } - } -}; - -AnalysisGrid.prototype._getPorod = function() { - return { - text : 'Porod', - name : 'Porod', - columns : [ - { - text : 'Volume', - dataIndex : 'volumeEdna', - width : 75, - sortable : true, - hidden : !this.isPorodTabVisible, - renderer : function(val, y, sample) { - if (sample.raw.volume != null) - return BUI.formatValuesUnits(sample.raw.volume, '') + " nm3"; - } - }, - { - text : 'MM Vol. est.', - dataIndex : 'volumeEdna', - tooltip : '[Volume/2 - Volume/1.5] (Guinier)', - sortable : true, - width : 95, - hidden : !this.isPorodTabVisible, - renderer : function(val, y, sample) { - if (sample.raw.volume != null) - return Number(sample.raw.volume / 2).toFixed(1) + " - " + Number(sample.raw.volume / 1.5).toFixed(1)+ "kD"; - } - } ] - }; -}; - - -AnalysisGrid.prototype._getFramesColumn = function() { - var _this = this; - return { - text : 'Frames (Averaged/Total)', - dataIndex : 'datacollection', - name : 'datacollection', - sortable : true, - width : 150, - renderer : function(dataCollections, y, data) { - /** Bug of Webservices: frames count were swapped with frames averages **/ - if (data.raw.bufferAfterFramesCount){ - if (data.raw.bufferAfterFramesMerged){ - if (parseInt(data.raw.bufferAfterFramesMerged) > parseInt(data.raw.bufferAfterFramesCount)){ - var aux = parseInt(data.raw.bufferAfterFramesCount); - data.raw.bufferAfterFramesCount= data.raw.bufferAfterFramesMerged; - data.raw.bufferAfterFramesMerged = aux; - } - } - } - - if (data.raw.bufferBeforeFramesCount){ - if (data.raw.bufferBeforeFramesMerged){ - if (parseInt(data.raw.bufferBeforeFramesMerged) > parseInt(data.raw.bufferBeforeFramesCount)){ - var aux = parseInt(data.raw.bufferBeforeFramesCount); - data.raw.bufferBeforeFramesCount= data.raw.bufferBeforeFramesMerged; - data.raw.bufferBeforeFramesMerged = aux; - } - } - - } - - var bufferAcronym = data.raw.bufferAcronym; - var macromoleculeAcronym = data.raw.macromoleculeAcronym; - var bbmerges = data.raw.bufferBeforeFramesMerged; - var molmerges = data.raw.framesMerge; - var bamerges = data.raw.bufferAfterFramesMerged; - var totalframes = data.raw.framesCount; - var bufferId = data.raw.bufferId; - var macromoleculeId = data.raw.macromoleculeId; - var macromoleculeColor = null; - if (_this.experiment != null){ - macromoleculeColor = _this.experiment.macromoleculeColors[data.raw.macromoleculeId]; - } - - /** BUG in the database to be fixed **/ - try{ - if (totalframes != null){ - if(molmerges != null){ - if (parseFloat(totalframes) < parseFloat(molmerges)){ - var aux = totalframes; - totalframes = molmerges; - molmerges = aux; - } - } - } - } - catch(e){ - - } - - return BUI.getHTMLTableForFrameAveraged(bufferAcronym, - macromoleculeAcronym, - bbmerges, - molmerges, - bamerges, - totalframes, - bufferId, - macromoleculeId, - macromoleculeColor); - } - }; -}; - -AnalysisGrid.prototype._getColumns = function() { - var _this = this; - return [ - { - name : 'groupeField', - dataIndex : 'groupeField', - hidden : true - - }, - { - "header" : "subtractionId", - hidden : true, - "dataIndex" : "subtractionId", - "name" : "subtractionId" - }, - { - header : "Macromolecule", - dataIndex : "macromoleculeAcronym", - name : "macromoleculeAcronym", - renderer : function(val, y, sample) { - return '
' + val + '
' + - BUI.formatValuesUnits(sample.raw.conc, "mg/ml", 10, this.decimals) + '
' + - BUI.formatValuesUnits(sample.raw.exposureTemperature, "C", 10, this.decimals) + '
' - } - }, - { - header : "Order", - dataIndex : "priorityLevelId", - name : "priorityLevelId", - hidden : true - }, - { - header : "Code", - dataIndex : "code", - name : "code", - hidden : true - }, - { - header : "Conc.", - dataIndex : "conc", - width : 80, - name : "conc", - type : "number", - hidden : true, - renderer : function(val, y, sample) { - return BUI.formatValuesUnits(val, "mg/ml", 10, this.decimals); - } - }, - { - text : 'Scattering', - width : 100, - dataIndex : 'subtractionId', - name : 'subtractionId', - hidden : !this.isScatteringPlotVisible, - renderer : function(val, y, sample) { - var url = BUI.getURL() + '&type=scattering&subtractionId=' + sample.raw.subtractionId; - var event = "OnClick= window.open('" + url + "')"; - return ''; - } - }, - { - text : 'Kratky', - width : 100, - dataIndex : 'subtractionId', - hidden : true, - name : 'subtractionId', - renderer : function(val, y, sample) { - var url = BUI.getURL() + '&type=kratky&subtractionId=' + sample.raw.subtractionId; - var event = "OnClick= window.open('" + url + "')"; - return ''; - } - }, - this._getFramesColumn(), - { - text : 'File Name', - dataIndex : 'averageFilePath', - name : 'averageFilePath', - sortable : true, - width : 150, - hidden : true, - renderer : function(dataCollections, y, data) { - return BUI.getHTMLTableForPrefixes(data.raw.bufferBeforeAverageFilePath, data.raw.averageFilePath, - data.raw.bufferAfterAverageFilePath); - } - }, - - { - text : 'Guinier', - name : 'Guinier', - columns : [ - { - text : 'Rg', - dataIndex : 'rgGuinier', - name : 'rgGuinier', - hidden : !this.isGuinierTabVisible, - width : 75, - tooltip : 'In polymer physics, the radius of gyration is used to describe the dimensions of a polymer chain.', - sortable : true, - renderer : function(val, y, sample) { - if (sample.raw.rgGuinier != null) { - /** Show warning if rgGuinier and rgGnom differ more than 10% **/ - if (Math.abs(sample.raw.rgGuinier - sample.raw.rgGnom) > (sample.raw.rgGuinier * 0.1)) { - return "" + BUI.formatValuesUnits(sample.raw.rgGuinier, "") + ""; - - } - return BUI.formatValuesUnits(sample.raw.rgGuinier, "nm", 12, this.decimals); - } - } - }, - { - text : 'Points', - dataIndex : 'points', - sortable : true, - width : 100, - type : 'string', - hidden : !this.isGuinierTabVisible, - renderer : function(val, y, sample) { - if ((sample.raw.firstPointUsed == "") || (sample.raw.firstPointUsed == null)) - return; - return "" + sample.raw.firstPointUsed + " - " + sample.raw.lastPointUsed + " (" + - (sample.raw.lastPointUsed - sample.raw.firstPointUsed) + " )"; - } - }, - { - text : 'Quality', - dataIndex : 'quality', - hidden : !this.isGuinierTabVisible, - tooltip : 'Estimated data quality. 1.0 - means ideal quality, 0.0 - unusable data. In table format it is given in percent (100% - ideal quality, 0% - unusable data). Please note that this estimation is based only on the Guinier interval (very low angles).', - width : 60, - sortable : true, - renderer : function(val, y, sample) { - if (sample.raw.quality != null) { - val = sample.raw.quality; - if ((val != null) && (val != "")) { - return "" + (Number(val) * 100).toFixed(2) + " %"; - } - } - } - }, { - text : 'I(0)', - dataIndex : 'I0', - sortable : true, - hidden : !this.isI0Visible, - tooltip : 'Extrapolated scattering intensity at zero angle I(0) (forward scattering)', - width : 75, - type : 'string', - renderer : function(val, y, sample) { - if (sample.raw.I0 != null) { - return BUI.formatValuesErrorUnitsScientificFormat(sample.raw.I0, sample.raw.i0stdev, ""); - } - } - }, { - text : 'Aggregated', - tooltip : "If aggregation was detected from the slope of the data curve at low angles the value is '1', otherwise '0'.", - dataIndex : 'isagregated', - hidden : true, - width : 75, - renderer : function(val, y, sample) { - if ((sample.raw.isagregated != null)) { - if (val == true) { - return "Yes"; - } else { - return "No"; - } - } - } - }, { - text : 'Guinier', - sortable : true, - dataIndex : 'subtractionId', - type : 'string', - width : 100, - hidden : true, - renderer : function(val, y, sample) { - - if (sample.raw.subtractionId != null) { - var url = BUI.getURL() + '&type=guinier&subtractionId=' + sample.raw.subtractionId; - var event = "OnClick= window.open('" + url + "')"; - return ''; - } - } - } ] - }, - { - text : 'Gnom', - name : 'Gnom', - - columns : [ { - text : 'Rg', - dataIndex : 'rgGnom', - type : 'string', - width : 65, - hidden : !this.isGnomTabVisible, - sortable : true, - renderer : function(val, y, sample) { - /** Show warning if rgGuinier and rgGnom differ more than 10% **/ - if (sample.raw.rgGnom != null) { - if (Math.abs(sample.raw.rgGuinier - sample.raw.rgGnom) > (sample.raw.rgGuinier * 0.1)) { - return "" + BUI.formatValuesUnits(sample.raw.rgGnom, "") + ""; - - } - return BUI.formatValuesUnits(sample.raw.rgGnom, "nm"); - } - } - }, { - text : 'Total', - dataIndex : 'total', - width : 65, - hidden : !this.isGnomTabVisible, - sortable : true, - renderer : function(val, y, sample) { - if (sample.raw.total != null) - return BUI.formatValuesUnits(sample.raw.total, ''); - } - }, { - text : 'Dmax', - dataIndex : 'dmax', - sortable : true, - width : 75, - hidden : !this.isGnomTabVisible, - renderer : function(val, y, sample) { - if (sample.raw.dmax != null) - return BUI.formatValuesUnits(sample.raw.dmax, "") + " nm"; - } - }, { - text : 'P(r)', - sortable : true, - hidden : true, - width : 100, - dataIndex : 'subtractionId', - type : 'string', - renderer : function(val, y, sample) { - var url = BUI.getURL() + '&type=gnom&subtractionId=' + sample.raw.subtractionId; - var event = "OnClick= window.open('" + url + "')"; - return ''; - } - } ] - }, - this._getPorod(), - { - text : 'AbInitio Modeling', - name : 'AbInitio_modeling', - - columns : [ - { - text : 'NSD', - dataIndex : 'volumeEdna', - width : 100, - sortable : true, - hidden : true, - renderer : function(val, y, sample) { - var url = BUI.getNSDImageURL(sample.raw.modelListId); - var event = "OnClick= window.open('" + url + "')"; - return ''; - } - }, - { - text : 'Chi2', - dataIndex : 'volumeEdna', - sortable : true, - hidden : true, - width : 100, - renderer : function(val, y, sample) { - var url = BUI.getCHI2ImageURL(sample.raw.modelListId); - var event = "OnClick= window.open('" + url + "')"; - return ''; - } - }, - { - text : 'Pdb', - dataIndex : 'volumeEdna', - tooltip : 'Damaver: The program suite DAMAVER is a set of programs to align ab initio models, select the most typical one and build an averaged model. Dammif : Rapid ab initio shape determination by simulated annealing using a single phase dummy atom model. Dammin :Ab initio shape determination by simulated annealing using a single phase dummy atom model', - sortable : true, - width : 125, - hidden : !this.isAbinitioTabVisible, - renderer : function(val, y, sample) { - var html = new String(); - var split = null; - var url = null; - var file = sample.raw.averagedModel; - if (file != null) { - split = file.split("/"); - if (split.length > 0) { - url = BUI.getPdbURL() + '&type=AVERAGED&abInitioModelId=' + sample.raw.abInitioModelId; - html = html + ''+ split[split.length - 1] + '

'; - - } - } - - file = sample.raw.rapidShapeDeterminationModel; - if (file != null) { - split = file.split("/"); - if (split.length > 0) { - url = BUI.getPdbURL() + '&type=RAPIDSHAPEDETERMINATIONMODEL&abInitioModelId=' + sample.raw.abInitioModelId; - html = html + '' + split[split.length - 1] + '

'; - } - } - - file = sample.raw.shapeDeterminationModel; - if (file != null) { - split = file.split("/"); - if (split.length > 0) { - url = BUI.getPdbURL() + '&type=SHAPEDETERMINATIONMODEL&abInitioModelId=' + sample.raw.abInitioModelId; - html = html + ''+ split[split.length - 1] + ''; - } - } - return html; - } - }, - { - text : 'Damaver', - dataIndex : 'volumeEdna', - hidden : true, - tooltip : 'Damaver: The program suite DAMAVER is a set of programs to align ab initio models, select the most typical one and build an averaged model. ', - sortable : true, - width : 125, - renderer : function(val, y, sample) { - var file = sample.raw.averagedModel; - if (file != null) { - var split = file.split("/"); - if (split.length > 0) { - var url = BUI.getPdbURL() + '&type=AVERAGED&abInitioModelId=' + sample.raw.abInitioModelId; - return '' + split[split.length - 1]+ ''; - } - } - return sample.raw.averagedModel; - } - }, - { - text : 'Dammif', - dataIndex : 'volumeEdna', - hidden : true, - tooltip : 'Dammif : Rapid ab initio shape determination by simulated annealing using a single phase dummy atom model', - sortable : true, - width : 125, - renderer : function(val, y, sample) { - var file = sample.raw.rapidShapeDeterminationModel; - if (file != null) { - var split = file.split("/"); - if (split.length > 0) { - var url = BUI.getPdbURL() + '&type=RAPIDSHAPEDETERMINATIONMODEL&abInitioModelId=' + sample.raw.abInitioModelId; - return '' + split[split.length - 1] + ''; - } - } - return sample.raw.averagedModel; - } - }, - { - text : 'Dammin', - dataIndex : 'volumeEdna', - hidden : true, - tooltip : 'Dammin :Ab initio shape determination by simulated annealing using a single phase dummy atom model', - sortable : true, - width : 125, - renderer : function(val, y, sample) { - var file = sample.raw.shapeDeterminationModel; - if (file != null) { - var split = file.split("/"); - if (split.length > 0) { - var url = BUI.getPdbURL() + '&type=SHAPEDETERMINATIONMODEL&abInitioModelId=' + sample.raw.abInitioModelId; - return '' + split[split.length - 1]+ ''; - } - } - return sample.raw.averagedModel; - } - } ] - }, { - text : 'Time', - dataIndex : 'substractionCreationTime', - name : 'substractionCreationTime', - hidden : true, - width : 80, - sortable : true, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - try { - if (record.raw.substractionCreationTime != null) { - return moment(record.raw.substractionCreationTime).format('h:mm:ss a'); - } - } catch (e) { - return "NA"; - } - } - }, { - text : 'Date', - dataIndex : 'substractionCreationTime', - name : 'substractionCreationTime', - hidden : true, - width : 80, - sortable : true, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - try { - if (record.raw.substractionCreationTime != null) { - return moment(record.raw.substractionCreationTime).format("LL"); - } - } catch (e) { - return "NA"; - } - } - }, - this._getButtons()]; -}; - -AnalysisGrid.prototype._getButtons = function() { - return { - id : this.id + 'buttonPlot', - name : 'buttonPlot', - hidden : !this.showButtonsVisible, - width : 110, - sortable : false, - renderer : function(value, metaData, sample, rowIndex, colIndex, store) { - var html = ""; - - if (sample.raw.subtractionId) { - html = html + ""; - if (sample.raw.rapidShapeDeterminationModelId != null) { - html = html + ""; - } - } - return html + "
" + BUI.getGreenButton('Calibration', { - height : 20, - width : 100 - }) + "
" + BUI.getGreenButton('Primary Data Proc.', { - height : 20, - width : 100 - }) + "
" + BUI.getGreenButton('AbInitio Modeling', { - height : 20, - width : 100 - }) + "
"; - } - }; -}; -AnalysisGrid.prototype._prepareData = function(data) { - if (this.hideNulls) { - var result = []; - for ( var i = 0; i < data.length; i++) { - if (data[i].subtractionId != null) { - data[i].groupeField = data[i].macromoleculeAcronym + " " + data[i].bufferAcronym; - result.push(data[i]); - } - } - return result; - } else { - return data; - } -}; - -AnalysisGrid.prototype.getPanel = function(data) { - var _this = this; - var columns = this._getColumns(); - - var fields = JSON.parse(JSON.stringify(columns)); - fields.push({ - name : 'experimentId', - dataIndex : 'experimentId' - - }); - this.store = Ext.create('Ext.data.Store', { - fields : fields, - autoload : true, - data : this._prepareData(data), - groupField : 'groupeField' - }); - - this.store.sort(this.sorters); - - var features = []; - - if (this.grouped) { - features.push({ - ftype : 'grouping', - groupHeaderTpl : '{name}', - hideGroupedHeader : false, - startCollapsed : false - }); - } - - this.grid = Ext.create('Ext.grid.Panel', { - style : { - padding : 5 - }, - maxWidth : this.maxWidth, - width : this.width, - height : this.height, - store : this.store, - columns : columns, - resizable : true, - features : features, - viewConfig : { - preserveScrollOnRefresh : true, - stripeRows : true, - listeners : { - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonPlot') { - if (e.target.defaultValue == 'AbInitio Modeling') { - var url = BUI.getPDBVisualizerURL(record.raw.averagedModelId, record.raw.subtractionId, record.raw.experimentId); - window.open(url, "_blank"); - } - - if (e.target.defaultValue == 'Primary Data Proc.') { - _this._edit(record.raw); - } - - if (e.target.defaultValue == 'Calibration') { - _this._showCalibration(record.raw); - } - } - } - } - }, - selModel : { - mode : 'SINGLE' - } - }); - - return this.grid; - -}; - -AnalysisGrid.prototype._openVisualizarBySubstractionId = function(record) { - //experimentId, subtractionId) { - var experimentId = record.experimentId; - var subtractionId = record.subtractionId; - - var _this = this; - var adapter = new BiosaxsDataAdapter(); - this.subtractionId = subtractionId; - - adapter.onSuccess.attach(function(sender, data) { - var experiment = new Experiment(data); - var experimentList = new ExperimentList([ experiment ]); - var subtraction = experiment.getSubtractionById(_this.subtractionId); - _this.grid.setLoading(false); - _this._openVisualizer(experimentList, subtraction, record); - }); - this.grid.setLoading("ISPyB: Fetching experiment"); - adapter.getExperimentById(experimentId, "MEDIUM"); -}; - -AnalysisGrid.prototype._edit = function(record) { - var experimentId = record.experimentId; - var _this = this; - - if (BIOSAXS.proposal.macromolecules == null) { - this.grid.setLoading("ISPyB: Fetching proposal"); - BIOSAXS.proposal.onInitialized.attach(function(sender, data) { - _this._openVisualizarBySubstractionId(record); - }); - BIOSAXS.proposal.init(); - } else { - this._openVisualizarBySubstractionId(record); - } -}; - - -AnalysisGrid.prototype._showCalibration = function(row) { - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - Ext.create('Ext.window.Window', { - title : 'Calibration', - width : 900, - resizable : true, - height : 400, - modal : true, - frame : false, - draggable : true, - closable : true, - autoscroll : true, - paddin : 5, - layout : { - type : 'vbox', - align : 'stretch' - }, - items : [ new AnalysisGrid({ - isGuinierTabVisible : false, - isGnomTabVisible : false, - isPorodTabVisible : false, - isAbinitioTabVisible : false, - isI0Visible : true, - showButtonsVisible : false, - height : 350, - sorters : [ { - property : 'experimentId', - direction : 'DESC' - } ] - }).getPanel(data) ] - }).show(); - }); - adapter.getAnalysisCalibrationByProposalId(); -}; - -AnalysisGrid.prototype._openVisualizer = function(experimentList, subtraction, record) { - var merges = experimentList.getMergesByDataCollectionId(subtraction.dataCollectionId); - var mergeIdList = []; - for ( var i = 0; i < merges.length; i++) { - mergeIdList.push(merges[i].mergeId); - } - - var dataAdapter = new BiosaxsDataAdapter(); - dataAdapter.onSuccess.attach(function(sender, merges) { - var dataCollectionCurveVisualizer = new DataCollectionCurveVisualizer(); - dataCollectionCurveVisualizer.draw(); - dataCollectionCurveVisualizer.refresh(merges, experimentList, subtraction.dataCollectionId, record); - }); - - dataAdapter.onError.attach(function(sender, error) { - }); - - dataAdapter.getMergesByIdsList(mergeIdList); -}; - -AnalysisGrid.prototype.input = function() { - return { - data : DATADOC.getData_3367().slice(20, 30),//[{"total":"0.447505552082","bufferBeforeMeasurementId":22150,"sampleMergeId":12373,"averagedModelId":43636,"I0":"32.50776","proposalCode":"OPD","averagedModel":"/data/pyarch/bm29/opd29/1137/1d/damaver.pdb","bufferAfterMergeId":12374,"framesCount":"10","bufferBeforeMergeId":12372,"averageFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_016_ave.dat","bufferAfterMeasurementId":22152,"rgGuinier":"2.96883","subtractedFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_016_sub.dat","firstPointUsed":"30","chi2RgFilePath":"/data/pyarch/bm29/opd29/1137/1d/chi2_R.png","abInitioModelId":272,"macromoleculeId":112,"code":"_20.0_1.25","transmission":"100.0","timeStart":"2013-07-17 17:10:25.743734","bufferAcronym":"MES","quality":"0.87091","shapeDeterminationModelId":43638,"expermientComments":"[BsxCube] Generated from BsxCube","bufferId":707,"isagregated":"False","dmax":"10.390905","bufferBeforeAverageFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_015_ave.dat","exposureTemperature":"20.0","subtractionId":5165,"conc":"1.25","rapidShapeDeterminationModel":"/data/pyarch/bm29/opd29/1137/1d/damfilt.pdb","experimentCreationDate":"Jul 17, 2013 5:08:37 PM","lastPointUsed":"92","modelListId":272,"framesMerge":"10","rapidShapeDeterminationModelId":43637,"bufferAfterAverageFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_017_ave.dat","nsdFilePath":"/data/pyarch/bm29/opd29/1137/1d/nsd.png","bufferAfterFramesMerged":"10","experimentId":1137,"macromoleculeAcronym":"MG386","i0stdev":"0.05726128","sampleMeasurementId":22151,"measurementComments":"[1] MES","priorityLevelId":2,"bufferBeforeFramesMerged":"10","substractionCreationTime":"Jul 17, 2013 5:12:32 PM","proposalNumber":"29","rgGnom":"3.05242714339","volume":"44.1406","shapeDeterminationModel":"/data/pyarch/bm29/opd29/1137/1d/dammin.pdb","comments":null},{"total":"0.582641941147","bufferBeforeMeasurementId":22152,"sampleMergeId":12375,"averagedModelId":43809,"I0":"31.4366153846","proposalCode":"OPD","averagedModel":"/data/pyarch/bm29/opd29/1137/1d/damaver.pdb","bufferAfterMergeId":12376,"framesCount":"10","bufferBeforeMergeId":12374,"averageFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_018_ave.dat","bufferAfterMeasurementId":22155,"rgGuinier":"2.95541","subtractedFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_018_sub.dat","firstPointUsed":"21","chi2RgFilePath":"/data/pyarch/bm29/opd29/1137/1d/chi2_R.png","abInitioModelId":273,"macromoleculeId":112,"code":"_20.0_0.65000000000000002","transmission":"100.0","timeStart":"2013-07-17 17:12:55.837462","bufferAcronym":"MES","quality":"0.870164","shapeDeterminationModelId":43811,"expermientComments":"[BsxCube] Generated from BsxCube","bufferId":707,"isagregated":"False","dmax":"10.343935","bufferBeforeAverageFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_017_ave.dat","exposureTemperature":"20.0","subtractionId":5166,"conc":"0.65000000000000002","rapidShapeDeterminationModel":"/data/pyarch/bm29/opd29/1137/1d/damfilt.pdb","experimentCreationDate":"Jul 17, 2013 5:08:37 PM","lastPointUsed":"80","modelListId":273,"framesMerge":"10","rapidShapeDeterminationModelId":43810,"bufferAfterAverageFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_019_ave.dat","nsdFilePath":"/data/pyarch/bm29/opd29/1137/1d/nsd.png","bufferAfterFramesMerged":"10","experimentId":1137,"macromoleculeAcronym":"MG386","i0stdev":"0.100250461538","sampleMeasurementId":22154,"measurementComments":"[2] MES","priorityLevelId":4,"bufferBeforeFramesMerged":"10","substractionCreationTime":"Jul 17, 2013 5:15:02 PM","proposalNumber":"29","rgGnom":"2.9963404542","volume":"42.2255","shapeDeterminationModel":"/data/pyarch/bm29/opd29/1137/1d/dammin.pdb","comments":null}], - proposal : new ResultsAssemblyGrid().input().proposal - }; -}; - -AnalysisGrid.prototype.test = function(targetId) { - var analysisGrid = new AnalysisGrid(); - BIOSAXS.proposal = new Proposal(analysisGrid.input().proposal); - var panel = analysisGrid.getPanel(analysisGrid.input().data); - panel.render(targetId); -}; - - -function HPLCAnalysisGrid(args) { - AnalysisGrid.prototype.constructor.call(this, args); -} - -HPLCAnalysisGrid.prototype._edit = AnalysisGrid.prototype._edit; -HPLCAnalysisGrid.prototype._getColumns = AnalysisGrid.prototype._getColumns; -HPLCAnalysisGrid.prototype._openVisualizarBySubstractionId = AnalysisGrid.prototype._openVisualizarBySubstractionId; -HPLCAnalysisGrid.prototype._openVisualizer = AnalysisGrid.prototype._openVisualizer; -HPLCAnalysisGrid.prototype._prepareData = AnalysisGrid.prototype._prepareData; -HPLCAnalysisGrid.prototype._showCalibration = AnalysisGrid.prototype._showCalibration; -HPLCAnalysisGrid.prototype.getPanel = AnalysisGrid.prototype.getPanel; -HPLCAnalysisGrid.prototype.input = AnalysisGrid.prototype.input; -HPLCAnalysisGrid.prototype.test = AnalysisGrid.prototype.test; -HPLCAnalysisGrid.prototype.refresh = AnalysisGrid.prototype.refresh; -HPLCAnalysisGrid.prototype._getPorod = AnalysisGrid.prototype._getPorod; - -HPLCAnalysisGrid.prototype._getButtons = function() { - return { - id : this.id + 'buttonPlot', - name : 'buttonPlot', - hidden : !this.showButtonsVisible, - width : 110, - sortable : false, - renderer : function(value, metaData, sample, rowIndex, colIndex, store) { - var html = ""; - - if (sample.raw.subtractionId) { - if (sample.raw.rapidShapeDeterminationModelId != null) { - html = html + ""; - } - } - return html + "
" + BUI.getGreenButton('AbInitio Modeling', { - height : 20, - width : 100 - }) + "
"; - } - }; -}; - -HPLCAnalysisGrid.prototype._getFramesColumn = function() { - return { - text : 'Frames', - dataIndex : 'datacollection', - name : 'datacollection', - sortable : true, - width : 150, - renderer : function(dataCollections, y, data) { - molmerges = data.raw.framesMerge; - totalframes = data.raw.framesCount; - return molmerges +" - "+ totalframes; - } - }; -}; - - - - -/** - * Rigid body grid to show PDB, symmetry and multiplicity - * - * - * #onUploadFile click on upload file - */ -function AprioriRigidBodyGrid(args) { - - this.height = 250; - this.btnEditVisible = true; - this.btnRemoveVisible = true; - - if (args != null) { - if (args.height != null) { - this.height = args.height; - } - if (args.btnEditVisible != null) { - this.btnEditVisible = args.btnEditVisible; - } - if (args.btnRemoveVisible != null) { - this.btnRemoveVisible = args.btnRemoveVisible; - } - } - - /** Events **/ - this.onUploadFile = new Event(this); - this.onRemove = new Event(this); -} - -AprioriRigidBodyGrid.prototype._getColumns = function() { -}; - -AprioriRigidBodyGrid.prototype._getTopButtons = function() { - var _this = this; - /** Actions buttons **/ - var actions = []; - - /** ADD BUTTON **/ - actions.push(Ext.create('Ext.Action', { - icon : '../images/add.png', - text : 'Add', - disabled : false, - handler : function(widget, event) { - _this.onAddButtonClicked.notify(); - } - })); - - return actions; -}; - -AprioriRigidBodyGrid.prototype.refresh = function(macromolecule) { - this.macromolecule = macromolecule; - if (macromolecule != null){ - this.pdbStore.loadData(macromolecule.structure3VOs); - } -}; - -AprioriRigidBodyGrid.prototype._prepareData = function() { - var data = []; - for ( var i = 0; i < this.features.length; i++) { - data.push(this.features[i]); - } - return data; -}; - -AprioriRigidBodyGrid.prototype._getPlugins = function() { - var _this = this; - var plugins = []; - plugins.push(Ext.create('Ext.grid.plugin.RowEditing', { - clicksToEdit : 1, - listeners : { - validateedit : function(grid, e) { - /** Comments are always updatable* */ - e.record.raw.symmetry = e.newValues.symmetry; - e.record.raw.multiplicity = e.newValues.multiplicity; - - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, proposal) { - BIOSAXS.proposal.setItems(proposal); - _this.refresh(BIOSAXS.proposal.getMacromoleculeById(_this.macromolecule.macromoleculeId)); - _this.panel.setLoading(false); - }); - adapter.onError.attach(function() { - alert("Error"); - }); - - _this.panel.setLoading(); - adapter.saveStructure(e.record.raw); - } - } - })); - return plugins; -}; - -AprioriRigidBodyGrid.prototype.getPanel = function() { - var _this = this; - - this.pdbStore = Ext.create('Ext.data.Store', { - fields : [ 'filePath', 'structureId', 'structureType', 'symmetry', 'structureId', 'name', 'multiplicity' ], - groupField : 'structureType', - sorters : { - property : 'structureId', - direction : 'DESC' - } - }); - - var groupingFeature = Ext.create('Ext.grid.feature.Grouping', { - groupHeaderTpl : Ext.create('Ext.XTemplate', - "
{name:this.formatName}
", { - formatName : function(name) { - return name; - } - }), - hideGroupedHeader : true, - startCollapsed : false - }); - - this.panel = Ext.create('Ext.grid.Panel', { - margin : "15 10 0 10", - height : this.height, - store : this.pdbStore, - plugins : _this._getPlugins(), - tbar : [ { - text : 'Add Modeling Option (PDB)', - icon : '../images/add.png', - handler : function() { - _this.onUploadFile.notify('PDB', 'Upload PDB File'); - } - } - - ], - columns : [ - { - text : "structureId", - flex : 0.2, - hidden : true, - dataIndex : 'structureId', - sortable : true - }, - { - text : "File", - flex : 0.5, - dataIndex : 'filePath', - sortable : true, - hidden : true - }, - { - text : "PDB", - flex : 0.4, - dataIndex : 'name', - sortable : true - }, - { - text : "Symmetry", - flex : 0.2, - dataIndex : 'symmetry', - sortable : true, - editor : { - xtype : 'combobox', - typeAhead : true, - triggerAction : 'all', - selectOnTab : true, - store : [ [ "P1", "P1" ], [ "P2", "P2" ], [ "P3", "P3" ], [ "P4", "P4" ], [ "P5", "P5" ], [ "P6", "P6" ], [ "P32", "P32" ], [ "P42", "P42" ], - [ "P52", "P52" ], [ "P62", "P62" ], [ "P222", "P222" ] ], - } - }, { - text : "Multiplicity", - flex : 0.2, - dataIndex : 'multiplicity', - sortable : true, - editor : { - xtype : 'textfield' - } - - }, { - text : "Subunit", - flex : 0.2, - dataIndex : 'isSubunit', - sortable : true, - hidden : true - }, { - text : "Type", - flex : 0.2, - dataIndex : 'structureType', - sortable : true, - hidden : true - }, - - { - id : this.id + 'REMOVE', - flex : 0.2, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - return BUI.getRedButton('REMOVE'); - } - }, ], - - listeners : { - itemdblclick : function(dataview, record, item, e) { - _this._editExperiment(record.raw.experimentId); - }, - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'REMOVE') { - var dataAdapter = new BiosaxsDataAdapter(); - dataAdapter.onSuccess.attach(function() { - _this.panel.setLoading(false); - _this.onRemove.notify(); - }); - _this.panel.setLoading("Removing PDB file"); - dataAdapter.removeStructure(record.data.structureId); - } - - } - }, - viewConfig : { - getRowClass : function(record, rowIdx, params, store) { - if (record.raw.isSubunit != null) { - return "blue-row"; - } - } - } - }); - - return this.panel; -}; - - - - -AprioriRigidBodyGrid.prototype.input = function() { - return { - proposal : DATADOC.getProposal_10(), - dewars : DATADOC.getDewars_10() - - }; -}; - -AprioriRigidBodyGrid.prototype.test = function(targetId) { - var AprioriRigidBodyGrid = new AprioriRigidBodyGrid({ - height : 150 - }); - BIOSAXS.proposal = new Proposal(AprioriRigidBodyGrid.input().proposal); - var panel = AprioriRigidBodyGrid.getPanel(AprioriRigidBodyGrid.input().dewars); - panel.render(targetId); - -}; - -/** - * It shows buffer grid with a top bar with "Add" button - * - * @height - * @searchBar - * @collapsed - * @width - */ -function BufferGrid(args) { - this.height = 500; - this.searchBar = false; - this.tbar = false; - this.collapsed = false; - this.id = BUI.id(); - - if (args != null) { - if (args.height != null) { - this.height = args.height; - } - if (args.searchBar != null) { - this.searchBar = args.searchBar; - } - - if (args.tbar != null) { - this.tbar = args.tbar; - } - - if (args.collapsed != null) { - this.collapsed = args.collapsed; - } - - if (args.width != null) { - this.width = args.width; - } - } -} - -BufferGrid.prototype._edit = function(bufferId) { - var _this = this; - var window = new BufferWindow(); - window.onSuccess.attach(function(sender, proposal) { - _this.store.loadData(BIOSAXS.proposal.getBuffers()); - }); - window.draw(BIOSAXS.proposal.getBufferById(bufferId)); -}; - -BufferGrid.prototype.refresh = function(buffers) { - this.store.loadData(this._prepareData(buffers), false); -}; - -BufferGrid.prototype._prepareData = function(buffers) { - return buffers; -}; - -BufferGrid.prototype._getTbar = function() { - var _this = this; - var actions = []; - - actions.push(Ext.create('Ext.Action', { - icon : '../images/add.png', - text : 'Add buffer', - disabled : false, - handler : function(widget, event) { - var window = new BufferWindow(); - window.onSuccess.attach(function(sender) { - _this.store.loadData(BIOSAXS.proposal.getBuffers()); - }); - window.draw({}); - } - })); - return actions; -}; - -BufferGrid.prototype.getPanel = function(buffers) { - var _this = this; - - this.store = Ext.create('Ext.data.Store', { - fields : [ 'bufferId', 'acronym', 'name', 'composition' ], - data : buffers - }); - - this.store.sort('acronym'); - - var type = 'Ext.grid.Panel'; - if (this.searchBar == true) { - type = 'Ext.ux.LiveSearchGridPanel'; - } - - this.grid = Ext.create(type, { - title : 'Buffers', - collapsible : true, - collapsed : this.collapsed, - store : this.store, - height : this.height, - width : this.width, - columns : [ - /*{ - text : '', - dataIndex : 'bufferId', - width : 20, - renderer : function(val, y, sample) { - return BUI.getRectangleColorDIV(BIOSAXS.proposal.bufferColors[val], 10, 10); - } - },*/ - { - text : 'Acronym', - dataIndex : 'acronym', - flex : 1 - }, { - text : 'Name', - dataIndex : 'name', - flex : 1, - hidden : true - }, { - text : 'Composition', - dataIndex : 'composition', - flex : 1, - hidden : true - }, { - id : _this.id + 'buttonEditBuffer', - width : 80, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - return BUI.getGreenButton('EDIT'); - } - }, { - id : _this.id + 'buttonRemoveBuffer', - width : 85, - hidden : true, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - return BUI.getRedButton('REMOVE'); - } - } ], - flex : 1, - viewConfig : { - stripeRows : true, - listeners : { - 'celldblclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - _this._edit(record.data.bufferId); - }, - 'cellclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEditBuffer') { - _this._edit(record.data.bufferId); - } - - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemoveBuffer') { - BUI.showBetaWarning(); - } - } - - } - } - }); - - /** Adding the tbar **/ - if (this.tbar) { - this.grid.addDocked({ - xtype : 'toolbar', - items : this._getTbar() - }); - } - return this.grid; -}; - -BufferGrid.prototype.input = function() { - return new MacromoleculeGrid().input(); -}; - -BufferGrid.prototype.test = function(targetId) { - var bufferGrid = new BufferGrid({ - width : 800, - height : 350, - collapsed : false, - tbar : true - }); - - BIOSAXS.proposal = new Proposal(bufferGrid.input().proposal); - var panel = bufferGrid.getPanel(BIOSAXS.proposal.macromolecules); - panel.render(targetId); -}; - -/** - * A shipment may contains one or more cases where stock solutions and sample plates are stored - * - * @height - * @btnEditVisible - * @btnRemoveVisible - * - * #onEditButtonClicked - * #onAddButtonClicked - * #onRemoveButtonClicked - * #onDuplicateButtonClicked - */ -function CaseGrid(args) { - - this.height = 100; - this.btnEditVisible = true; - this.btnRemoveVisible = true; - - if (args != null) { - if (args.height != null) { - this.height = args.height; - } - if (args.btnEditVisible != null) { - this.btnEditVisible = args.btnEditVisible; - } - if (args.btnRemoveVisible != null) { - this.btnRemoveVisible = args.btnRemoveVisible; - } - } - - /** Events **/ - this.onEditButtonClicked = new Event(this); - this.onAddButtonClicked = new Event(this); - this.onRemoveButtonClicked = new Event(this); - this.onDuplicateButtonClicked = new Event(this); -} - -CaseGrid.prototype._getColumns = function() { - var _this = this; - - function actionItemRenderer(value, meta, record, rowIx, ColIx, store) { - /*if (record.raw.specimen3VOs.length > 0){ - return 'x-hide-display'; - }*/ - } - - var columns = [ - { - header : 'Code', - dataIndex : 'code', - name : 'code', - type : 'string', - flex : 1 - }, - { - header : 'Bar Code', - dataIndex : 'barCode', - name : 'barCode', - type : 'string', - flex : 1, - hidden : true - }, - { - header : 'BeamLine', - dataIndex : 'barCode', - type : 'string', - flex : 1, - renderer : function(comp, val, record) { - if (record.raw.sessionVO != null) { - return "" + record.raw.sessionVO.beamlineName + ""; - } - } - }, - { - header : 'Session', - dataIndex : 'barCode', - type : 'string', - flex : 1, - renderer : function(comp, val, record) { - if (record.raw.sessionVO != null) { - return "" + moment(record.raw.sessionVO.startDate).format("MMM Do YY") + ""; - } - } - }, - { - header : 'Status', - dataIndex : 'dewarStatus', - name : 'dewarStatus', - type : 'string', - flex : 1, - renderer : function(comp, val, record) { - if (new String(record.raw.dewarStatus).toUpperCase() == 'OPENED') { - return "" + new String(record.raw.dewarStatus).toUpperCase() + ""; - } - return "" + new String(record.raw.dewarStatus).toUpperCase() + ""; - } - }, - { - header : 'Type', - dataIndex : 'type', - name : 'type', - type : 'string', - flex : 1, - hidden : true - }, - { - header : 'Sample Plates', - dataIndex : 'plates', - name : 'plates', - type : 'string', - flex : 1, - hidden : true - }, - { - header : 'Stock Solutions', - dataIndex : 'plates', - name : 'plates', - type : 'string', - width : 100, - renderer : function(comp, val, record) { - var html = "
"; - var stockSolutions = BIOSAXS.proposal.getStockSolutionsByDewarId(record.raw.dewarId); - html = html + "" + stockSolutions.length + " x"; - return html + "
"; - } - }, { - header : 'isStorageDewar', - dataIndex : 'isStorageDewar', - name : 'isStorageDewar', - type : 'string', - flex : 1, - hidden : true - }, { - header : 'Tracking Number From Synchrotron', - dataIndex : 'trackingNumberFromSynchrotron', - name : 'trackingNumberFromSynchrotron', - type : 'string', - flex : 1, - hidden : true - }, { - header : 'Tracking Number To Synchrotron', - dataIndex : 'trackingNumberToSynchrotron', - name : 'trackingNumberToSynchrotron', - type : 'string', - flex : 1, - hidden : true - }, { - header : 'Storage Location', - dataIndex : 'storageLocation', - name : 'storageLocation', - type : 'string', - flex : 1, - hidden : false - }, { - header : 'Comments', - dataIndex : 'comments', - name : 'comments', - type : 'string', - flex : 1, - hidden : false - } - ]; - - if (this.btnEditVisible) { - columns.push({ - id : _this.id + 'buttonEdit', - text : '', - hidden : !_this.btnEditVisible, - width : 85, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - return BUI.getGreenButton('EDIT'); - } - }); - } - - if (this.btnRemoveVisible) { - columns.push({ - id : _this.id + 'buttonRemove', - width : 85, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - if (_this.btnRemoveVisible) { - return BUI.getRedButton('REMOVE'); - } - } - }); - } - - columns.push({ - dataIndex : 'comments', - type : 'string', - width : 85, - hidden : false, - renderer : function(comp, val, record) { - return BUI.getBlueButton("LABELS", { - href : BUI.getPrintcomponentURL(record.raw.dewarId) - }); - } - }); - - return columns; -}; - -CaseGrid.prototype._getTopButtons = function() { - var _this = this; - /** Actions buttons **/ - var actions = []; - - /** ADD BUTTON **/ - actions.push(Ext.create('Ext.Action', { - icon : '../images/add.png', - text : 'Add', - disabled : false, - handler : function(widget, event) { - _this.onAddButtonClicked.notify(); - } - })); - - return actions; -}; - -CaseGrid.prototype.refresh = function(dewars) { - this.features = dewars; - this.store.loadData(this._prepareData(dewars), false); -}; - -CaseGrid.prototype._sort = function(store) { - store.sort('dewarId', 'DESC'); -}; - -CaseGrid.prototype._prepareData = function() { - var data = []; - for ( var i = 0; i < this.features.length; i++) { - data.push(this.features[i]); - } - return data; -}; - -CaseGrid.prototype.getPanel = function(dewars, plates) { - this.features = dewars; - this.plates = plates; - return this._renderGrid(); -}; - -CaseGrid.prototype._edit = function(dewar) { - var _this = this; - var caseWindow = new CaseWindow(); - /**SAVED **/ - caseWindow.onSaved.attach(function(sender, dewar) { - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, shipment) { - _this.refresh(shipment.dewarVOs); - }); - adapter.saveCase(BIOSAXS.proposal.getShipmentByDewarId(dewar.dewarId).shippingId, dewar); - }); - caseWindow.draw(dewar); -}; - -CaseGrid.prototype._getStoreFields = function(data) { - return [ { - name : 'dewarId', - type : 'string' - }, { - name : 'barCode', - type : 'string' - }, { - name : 'code', - type : 'string' - }, { - name : 'comments', - type : 'string' - }, { - name : 'dewarStatus', - type : 'string' - }, { - name : 'isStorageDewar', - type : 'string' - }, { - name : 'plates', - type : 'string' - }, { - name : 'transportValue', - type : 'string' - }, { - name : 'trackingNumberFromSynchrotron', - type : 'string' - }, { - name : 'trackingNumberToSynchrotron', - type : 'string' - }, { - name : 'timeStamp', - type : 'string' - }, { - name : 'storageLocation', - type : 'string' - }, { - name : 'type', - type : 'string' - } - - ]; -}; - -CaseGrid.prototype._renderGrid = function() { - var _this = this; - - /** Store **/ - var data = this._prepareData(); - this.store = Ext.create('Ext.data.Store', { - fields : this._getStoreFields(data), - autoload : true, - data : data - }); - this._sort(this.store); - - this.store.loadData(data, false); - - this.grid = Ext.create('Ext.grid.Panel', { - style : { - padding : 5 - }, - height : this.height, - store : this.store, - columns : this._getColumns(), - viewConfig : { - stripeRows : true, - listeners : { - itemdblclick : function(dataview, record, item, e) { - _this._edit(record.raw); - }, - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEdit') { - _this._edit(record.raw); - } - - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemove') { - _this.onRemoveButtonClicked.notify(_this.store.getAt(rowIndex).raw.dewarId); - } - } - } - }, - selModel : { - mode : 'SINGLE' - } - }); - - var actions = _this._getTopButtons(); - this.grid.addDocked({ - xtype : 'toolbar', - items : actions - }); - - this.grid.getSelectionModel().on({ - selectionchange : function(sm, selections) { - if (selections.length) { - for ( var i = 0; i < actions.length; i++) { - if (actions[i].enable) { - actions[i].enable(); - } - } - } else { - for ( var i = 0; i < actions.length; i++) { - if (actions[i].alwaysEnabled == false) { - if (actions[i].disable) { - actions[i].disable(); - } - } - } - } - } - }); - return this.grid; -}; - -CaseGrid.prototype.input = function() { - return { - proposal : DATADOC.getProposal_10(), - dewars : DATADOC.getDewars_10() - - }; -}; - -CaseGrid.prototype.test = function(targetId) { - var CaseGrid = new CaseGrid({ - height : 150 - }); - BIOSAXS.proposal = new Proposal(CaseGrid.input().proposal); - var panel = CaseGrid.getPanel(CaseGrid.input().dewars); - panel.render(targetId); - -}; - -/** - * A shipment may contains one or more cases where stock solutions and sample plates are stored - * - * @height - * @btnEditVisible - * @btnRemoveVisible - * - * #onEditButtonClicked - * #onAddButtonClicked - * #onRemoveButtonClicked - * #onDuplicateButtonClicked - */ -function ExampleGrid(args) { - - this.height = 100; - this.btnEditVisible = true; - this.btnRemoveVisible = true; - - if (args != null) { - if (args.height != null) { - this.height = args.height; - } - if (args.btnEditVisible != null) { - this.btnEditVisible = args.btnEditVisible; - } - if (args.btnRemoveVisible != null) { - this.btnRemoveVisible = args.btnRemoveVisible; - } - } - - /** Events **/ - this.onEditButtonClicked = new Event(this); - this.onAddButtonClicked = new Event(this); - this.onRemoveButtonClicked = new Event(this); - this.onDuplicateButtonClicked = new Event(this); -} - -ExampleGrid.prototype._getColumns = function() { - var _this = this; - - function actionItemRenderer(value, meta, record, rowIx, ColIx, store) { - /*if (record.raw.specimen3VOs.length > 0){ - return 'x-hide-display'; - }*/ - } - - var columns = [ - { - header : 'Code', - dataIndex : 'code', - name : 'code', - type : 'string', - flex : 1 - }, - { - header : 'Bar Code', - dataIndex : 'barCode', - name : 'barCode', - type : 'string', - flex : 1, - hidden : true - }, - { - header : 'BeamLine', - dataIndex : 'barCode', - type : 'string', - flex : 1, - renderer : function(comp, val, record) { - if (record.raw.sessionVO != null) { - return "" + record.raw.sessionVO.beamlineName + ""; - } - } - }, - { - header : 'Session', - dataIndex : 'barCode', - type : 'string', - flex : 1, - renderer : function(comp, val, record) { - if (record.raw.sessionVO != null) { - return "" + moment(record.raw.sessionVO.startDate).format("MMM Do YY") + ""; - } - } - }, - { - header : 'Status', - dataIndex : 'dewarStatus', - name : 'dewarStatus', - type : 'string', - flex : 1, - renderer : function(comp, val, record) { - if (new String(record.raw.dewarStatus).toUpperCase() == 'OPENED') { - return "" + new String(record.raw.dewarStatus).toUpperCase() + ""; - } - return "" + new String(record.raw.dewarStatus).toUpperCase() + ""; - } - }, - { - header : 'Type', - dataIndex : 'type', - name : 'type', - type : 'string', - flex : 1, - hidden : true - }, - { - header : 'Sample Plates', - dataIndex : 'plates', - name : 'plates', - type : 'string', - flex : 1, - hidden : true - }, - { - header : 'Stock Solutions', - dataIndex : 'plates', - name : 'plates', - type : 'string', - width : 100, - renderer : function(comp, val, record) { - var html = "
"; - var stockSolutions = BIOSAXS.proposal.getStockSolutionsByDewarId(record.raw.dewarId); - html = html + "" + stockSolutions.length + " x"; - return html + "
"; - } - }, { - header : 'isStorageDewar', - dataIndex : 'isStorageDewar', - name : 'isStorageDewar', - type : 'string', - flex : 1, - hidden : true - }, { - header : 'Tracking Number From Synchrotron', - dataIndex : 'trackingNumberFromSynchrotron', - name : 'trackingNumberFromSynchrotron', - type : 'string', - flex : 1, - hidden : true - }, { - header : 'Tracking Number To Synchrotron', - dataIndex : 'trackingNumberToSynchrotron', - name : 'trackingNumberToSynchrotron', - type : 'string', - flex : 1, - hidden : true - }, { - header : 'Storage Location', - dataIndex : 'storageLocation', - name : 'storageLocation', - type : 'string', - flex : 1, - hidden : false - }, { - header : 'Comments', - dataIndex : 'comments', - name : 'comments', - type : 'string', - flex : 1, - hidden : false - } - ]; - - if (this.btnEditVisible) { - columns.push({ - id : _this.id + 'buttonEdit', - text : '', - hidden : !_this.btnEditVisible, - width : 85, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - return BUI.getGreenButton('EDIT'); - } - }); - } - - if (this.btnRemoveVisible) { - columns.push({ - id : _this.id + 'buttonRemove', - width : 85, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - if (_this.btnRemoveVisible) { - return BUI.getRedButton('REMOVE'); - } - } - }); - } - - columns.push({ - dataIndex : 'comments', - type : 'string', - width : 85, - hidden : false, - renderer : function(comp, val, record) { - return BUI.getBlueButton("LABELS", { - href : BUI.getPrintcomponentURL(record.raw.dewarId) - }); - } - }); - - return columns; -}; - -ExampleGrid.prototype._getTopButtons = function() { - var _this = this; - /** Actions buttons **/ - var actions = []; - - /** ADD BUTTON **/ - actions.push(Ext.create('Ext.Action', { - icon : '../images/add.png', - text : 'Add', - disabled : false, - handler : function(widget, event) { - _this.onAddButtonClicked.notify(); - } - })); - - return actions; -}; - -ExampleGrid.prototype.refresh = function(dewars) { - this.features = dewars; - this.store.loadData(this._prepareData(dewars), false); -}; - -ExampleGrid.prototype._sort = function(store) { - store.sort('dewarId', 'DESC'); -}; - -ExampleGrid.prototype._prepareData = function() { - var data = []; - for ( var i = 0; i < this.features.length; i++) { - data.push(this.features[i]); - } - return data; -}; - -ExampleGrid.prototype.getPanel = function() { - this.grid = Ext.create('Ext.grid.Panel', { - style : { - padding : 5 - }, - height : this.height, - store : this.store, - columns : this._getColumns(), - viewConfig : { - stripeRows : true, - listeners : { - itemdblclick : function(dataview, record, item, e) { - _this._edit(record.raw); - }, - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEdit') { - _this._edit(record.raw); - } - - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemove') { - _this.onRemoveButtonClicked.notify(_this.store.getAt(rowIndex).raw.dewarId); - } - } - } - }, - selModel : { - mode : 'SINGLE' - } - }); - - var actions = _this._getTopButtons(); - this.grid.addDocked({ - xtype : 'toolbar', - items : actions - }); - - this.grid.getSelectionModel().on({ - selectionchange : function(sm, selections) { - if (selections.length) { - for ( var i = 0; i < actions.length; i++) { - if (actions[i].enable) { - actions[i].enable(); - } - } - } else { - for ( var i = 0; i < actions.length; i++) { - if (actions[i].alwaysEnabled == false) { - if (actions[i].disable) { - actions[i].disable(); - } - } - } - } - } - }); - return this.grid; -}; - - -ExampleGrid.prototype._getStoreFields = function(data) { - return [ { - name : 'dewarId', - type : 'string' - }, { - name : 'barCode', - type : 'string' - }, { - name : 'code', - type : 'string' - }, { - name : 'comments', - type : 'string' - }, { - name : 'dewarStatus', - type : 'string' - }, { - name : 'isStorageDewar', - type : 'string' - }, { - name : 'plates', - type : 'string' - }, { - name : 'transportValue', - type : 'string' - }, { - name : 'trackingNumberFromSynchrotron', - type : 'string' - }, { - name : 'trackingNumberToSynchrotron', - type : 'string' - }, { - name : 'timeStamp', - type : 'string' - }, { - name : 'storageLocation', - type : 'string' - }, { - name : 'type', - type : 'string' - } - - ]; -}; - -ExampleGrid.prototype._renderGrid = function() { - var _this = this; - - /** Store **/ - var data = this._prepareData(); - this.store = Ext.create('Ext.data.Store', { - fields : this._getStoreFields(data), - autoload : true, - data : data - }); - this._sort(this.store); - - this.store.loadData(data, false); - - this.grid = Ext.create('Ext.grid.Panel', { - style : { - padding : 5 - }, - height : this.height, - store : this.store, - columns : this._getColumns(), - viewConfig : { - stripeRows : true, - listeners : { - itemdblclick : function(dataview, record, item, e) { - _this._edit(record.raw); - }, - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEdit') { - _this._edit(record.raw); - } - - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemove') { - _this.onRemoveButtonClicked.notify(_this.store.getAt(rowIndex).raw.dewarId); - } - } - } - }, - selModel : { - mode : 'SINGLE' - } - }); - - var actions = _this._getTopButtons(); - this.grid.addDocked({ - xtype : 'toolbar', - items : actions - }); - - this.grid.getSelectionModel().on({ - selectionchange : function(sm, selections) { - if (selections.length) { - for ( var i = 0; i < actions.length; i++) { - if (actions[i].enable) { - actions[i].enable(); - } - } - } else { - for ( var i = 0; i < actions.length; i++) { - if (actions[i].alwaysEnabled == false) { - if (actions[i].disable) { - actions[i].disable(); - } - } - } - } - } - }); - return this.grid; -}; - -ExampleGrid.prototype.input = function() { - return { - proposal : DATADOC.getProposal_10(), - dewars : DATADOC.getDewars_10() - - }; -}; - -ExampleGrid.prototype.test = function(targetId) { - var ExampleGrid = new ExampleGrid({ - height : 150 - }); - BIOSAXS.proposal = new Proposal(ExampleGrid.input().proposal); - var panel = ExampleGrid.getPanel(ExampleGrid.input().dewars); - panel.render(targetId); - -}; - - -/** - * Shows a list of experiment AKA data acquisitions - * @height - * @sorters - * @minHeight - * @gridType: Ext.ux.LiveSearchGridPanel or Ext.grid.Panel - * @tbar true or false - * @grouping true or false - * @width - * @title - * #onEditButtonClicked - */ -function ExperimentGrid(args) { - this.width = "100%"; - this.height = 700; - this.minHeight = 500; - - this.id = BUI.id(); - this.gridType = 'Ext.grid.Panel'; //'Ext.ux.LiveSearchGridPanel'; - this.tbar = false; - this.hideHeaders = false; - this.grouping = true; - this.title = null; - - this.filtered = null; - - /** maximum row count **/ - this.limit = 100; - - this.sessionIdFilter = null; - - /** if not null filtered by date **/ - this.date = null; - - this.sorters = [ { - property : 'date', - direction : 'DESC' - }, { - property : 'time', - direction : 'DESC' - } ]; - - this.dates = {}; - if (args != null) { - if (args.height != null) { - this.height = args.height; - } - if (args.limit != null) { - this.limit = args.limit; - } - if (args.sorters != null) { - this.sorters = args.sorters; - } - if (args.sessionId != null){ - this.sessionIdFilter = args.sessionId; - } - if (args.filtered != null) { - this.filtered = args.filtered; - } - if (args.minHeight != null) { - this.minHeight = args.minHeight; - } - if (args.gridType != null) { - this.gridType = args.gridType; - } - if (args.tbar != null) { - this.tbar = args.tbar; - } - if (args.grouping != null) { - this.grouping = args.grouping; - } - if (args.width != null) { - this.width = args.width; - } - if (args.title != null) { - this.title = args.title; - } - - } - /** Events **/ - this.onEditButtonClicked = new Event(this); -} - -ExperimentGrid.prototype._getFilterTypes = function() { - return []; -}; - -ExperimentGrid.prototype._prepareData = function(rows) { - var data = []; - var count = 0; - - rows.sort(function(a,b){return b.experimentId - a.experimentId;}); - for ( var i = 0; i < rows.length; i++) { - var row = rows[i]; - this.dates[moment(row.creationDate).format("YYYYMMDD")] = moment(row.creationDate).format("MMM Do YY"); - if ( - ( this.filtered == null || row.experimentType == this.filtered ) && (count < this.limit || this.limit == null ) && (this.sessionIdFilter == null || this.date != null || (this.date == null && this.sessionIdFilter == row.sessionId)) - ){ - - data.push({ - experimentId : row.experimentId, - status : row.status, - dataAcquisitionFilePath : row.dataAcquisitionFilePath, - type : row.experimentType, - name : row.name, - macromolecules_names : row.macromolecules, - percentageAnalysed : { - value : (row.dataCollectionDoneCount / row.dataCollectionCount) * 100, - text : row.dataCollectionDoneCount + " of " + row.dataCollectionCount - }, - percentageCollected : { - value : (row.measurementDoneCount / row.measurementCount) * 100, - text : row.measurementDoneCount + " of " + row.measurementCount - }, - percentageMerged : { - value : (row.measurementAveragedCount / row.measurementCount) * 100, - text : row.measurementAveragedCount + " of " + row.measurementCount - }, - date : moment(row.creationDate).format("YYYYMMDD"), - time : moment(row.creationDate).format("YYYYMMDDHHmmss"), - creationDate : row.creationDate - }); - count ++; - } - } - return data; -}; - -ExperimentGrid.prototype.getPanel = function(experiments) { - this.features = experiments; - return this._renderGrid(experiments); -}; - -ExperimentGrid.prototype.refresh = function(experiments) { - this.experiments = experiments; - var filtered = []; - for ( var i = 0; i < experiments.length; i++) { - if (experiments[i].experimentType != "TEMPLATE") { - filtered.push(experiments[i]); - } - } - - this.parsedData = this._prepareData(filtered); - - var day = {}; - var dates = []; - for ( var i = 0; i < this.experiments.length; i++) { - var date = moment(this.experiments[i].creationDate).format("MMM Do YYYY"); - if (day[date] == null){ - dates.push({ - date : date, - value : moment(this.experiments[i].creationDate) - }); - day[date] = true; - } - } - - this.storeDate.loadData(dates, false); - this.store.loadData(this.parsedData, false); - - /** If it has already been filtered by date we keep the filter **/ - if (this.date != null){ - this._filterByDate(this.date); - } -}; - -ExperimentGrid.prototype._getTopButtons = function() { - var _this = this; - /** Actions buttons **/ - var actions = []; - - actions.push(Ext.create('Ext.Action', { - icon : '../images/calendar_icon.png', - text : 'Show Calendar', - disabled : false, - handler : function(widget, event) { - var window = Ext.create('Ext.window.Window', { - title : 'Calendar', - width : 600, - height : 600, - modal : true, - closable : true, - layout : { - type : 'vbox', - align : 'stretch' - }, - items : [ { - xtype : 'label', - html : 'Click on a data acquisition to select:', - margin : '5 5 5 5' - }, { - html : '
', - margin : '5 5 5 5' - } - - ] - }).show(); - - var calendarWidget = new CalendarWidget({ - height : 450 - }); - var aux = _this.limit; - /** we remove the limit temporarily **/ - _this.limit = null; - _this.sessionIdFilter = null; - calendarWidget.loadData(_this._prepareData(_this.experiments)); - _this.limit = aux; - calendarWidget.draw('calendar'); - calendarWidget.onClick.attach(function(sender, date) { - date = moment(date, "YYYY-MM-DD"); - _this._filterByDate(date); - window.close(); - - }); - - } - })); - this.storeDate = Ext.create('Ext.data.ArrayStore', { - fields: ['date', 'value'], - data : [] - }); - - this.dateMenu = Ext.create('Ext.form.field.ComboBox', { - hideLabel: true, - store: this.storeDate, - displayField: 'date', - typeAhead: true, - queryMode: 'local', - margin : '0 0 0 30', - triggerAction: 'all', - emptyText:'Select a date...', - selectOnFocus:true, - width:135, - listeners:{ - scope: this, - 'select': function (a,b,c){ - _this.limit = null; - _this._filterByDate(moment(b[0].raw.value, "YYYY-MM-DD")); - } - } - }); - - actions.push(this.dateMenu); - - actions.push("->"); - if (_this.filtered != null){ - actions.push({ - html : "Experiment Type: " + _this.filtered +"" - }); - } - else{ - actions.push({ - html : "Experiment Type: ALL" - }); - } - return actions; -}; - -/** - * Date format: "YYYY-MM-DD" - */ -ExperimentGrid.prototype._filterByDate = function(date) { - var experimentsFiltered = []; - /** Getting all the experiments of date**/ - for ( var i = 0; i < this.experiments.length; i++) { - var experiment = this.experiments[i]; - if (experiment.creationDate != null) { - var experimentDate = moment(experiment.creationDate); - if (experimentDate.year() == date.year()) { - if (experimentDate.month() == date.month()) { - if (experimentDate.date() == date.date()) { - experimentsFiltered.push(experiment); - } - } - } - } - } - var parsedData = this._prepareData(experimentsFiltered); - this.store.loadData(parsedData); - this.date = date; -}; - -/** Only for templates **/ -ExperimentGrid.prototype._removeExperimentById = function(experimentId) { - var _this = this; - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(evt, args) { - _this.grid.setLoading(false); - document.getElementById(BIOSAXS.targetId).innerHTML = ""; - BIOSAXS.start(BIOSAXS.targetId); - }); - this.grid.setLoading("Removing experiment "); - adapter.removeExperimentById(experimentId); -}; - -ExperimentGrid.prototype._renderGrid = function() { - var _this = this; - - /** Store **/ - this.store = Ext.create('Ext.data.Store', { - fields : this._getColumns(), - groupField : 'date', - autoload : true, - data : [], - remoteSort: false, - sorters : this.sorters - }); - - - - - var groupingFeature = Ext.create('Ext.grid.feature.Grouping', { - groupHeaderTpl : Ext.create('Ext.XTemplate', - "
{name:this.formatName}
", { - formatName : function(name) { - return _this.dates[name]; - } - }), - hideGroupedHeader : true, - startCollapsed : false - }); - - this.features = []; - if (this.grouping) { - this.features.push(groupingFeature); - } - - /** Grid **/ - this.grid = Ext.create(this.gridType, { - hideHeaders : this.hideHeaders, - resizable : true, - title : this.title, - width : this.width, - minHeight : this.minHeight, - height : this.height, - features : this.features, - store : this.store, - columns : this._getColumns(), - selModel : { - mode : 'SINGLE' - }, - viewConfig : { - stripeRows : true, - getRowClass : function(record, rowIdx, params, store) { - if (record.raw.type == "TEMPLATE") { - return "template-color-row"; - } - if ((record.raw.type == "CALIBRATION") && (record.raw.status == "FINISHED")) { - return "blue-row"; - } - }, - listeners : { - itemdblclick : function(dataview, record, item, e) { - _this._editExperiment(record.raw.experimentId); - }, - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'GO') { - _this._editExperiment(record.raw.experimentId); - } - - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'REMOVE') { - _this._removeExperimentById(record.raw.experimentId); - } - - } - } - } - }); - - var actions = _this._getTopButtons(); - - if (this.tbar) { - this.grid.addDocked({ - xtype : 'toolbar', - items : actions - }); - this.grid.getSelectionModel().on({ - selectionchange : function(sm, selections) { - if (selections.length) { - for ( var i = 0; i < actions.length; i++) { - if (actions[i].enable) { - actions[i].enable(); - } - } - } else { - for ( var i = 0; i < actions.length; i++) { - if (actions[i].alwaysEnabled == false) { - if (actions[i].disable) { - actions[i].disable(); - } - } - } - } - } - }); - } - - return this.grid; -}; - -ExperimentGrid.prototype._getColumns = function() { - var _this = this; - function actionItemRenderer(value, meta, record, rowIx, ColIx, store) { - if (record.raw.buffer3VOs != null) { - if (record.raw.buffer3VOs.length > 0) { - return 'x-hide-display'; - } - } - - if (record.data.platesCount > 0) { - return 'x-hide-display'; - } - } - - return [ - { - text : 'experimentId', - dataIndex : 'experimentId', - name : 'experimentId', - type : 'string', - hidden : true - }, - { - xtype : 'rownumberer', - width : 40 - }, - { - text : 'Name', - dataIndex : 'name', - name : 'name', - type : 'string', - flex : 1 - }, - - { - text : 'Type', - dataIndex : 'type', - name : 'type', - type : 'string', - flex : 1, - renderer : function(val) { - if (val == "CALIBRATION") { - return "" + val + ""; - } - - return val; - } - }, - { - text : 'Macromolecules', - name : 'macromolecules_names', - dataIndex : 'macromolecules_names', - flex : 1, - renderer : function(val) { - if (val != null) { - return " " + val + ""; - } - return " Information not available"; - } - }, - { - text : 'Buffers', - dataIndex : 'buffer_names', - name : 'buffer_names', - flex : 1, - hidden : true, - renderer : function(val) { - return "Buffer/s: " + val + ""; - } - }, - { - text : 'Status', - dataIndex : 'status', - name : 'status', - type : 'string', - flex : 1, - renderer : function(val, x, sample) { - if (sample.raw.type == "TEMPLATE") { - return "READY"; - } - if (sample.raw.status == "ABORTED") { - return "" + val + ""; - } - return "" + val + ""; - } - }, - { - text : 'Download', - dataIndex : 'creationDate', - name : 'creationDate', - renderer : function(val, x, sample) { - if (sample != null) { - if (sample.raw.type == "HPLC") { - return; - } - return BUI.getZipHTMLByExperimentId(sample.raw.experimentId, sample.raw.name); - } - }, - width : 100 - - }, - { - header : 'Measurements', - dataIndex : 'percentageCollected', - name : 'percentageCollected', - type : 'string', - renderer : function(val, y, sample) { - if ((sample.raw.type == "TEMPLATE") || (sample.raw.type == "HPLC")) { - return; - } - return "
" + BUI.getProgessBar(sample.raw.percentageCollected.value, sample.raw.percentageCollected.text) + "
"; - }, - width : 100 - }, - { - header : 'Averaged', - dataIndex : 'percentageMerged', - name : 'percentageMerged', - type : 'string', - renderer : function(val, y, sample) { - if ((sample.raw.type == "TEMPLATE") || (sample.raw.type == "HPLC")) { - return; - } - return "
" + BUI.getProgessBar(sample.raw.percentageMerged.value, sample.raw.percentageMerged.text) + "
"; - }, - width : 100 - }, - { - header : 'Subtractions', - dataIndex : 'percentageAnalysed', - name : 'percentageAnalysed', - type : 'string', - renderer : function(val, y, sample) { - if ((sample.raw.type == "TEMPLATE") || (sample.raw.type == "HPLC")) { - return; - } - return "
" + BUI.getProgessBar(sample.raw.percentageAnalysed.value, sample.raw.percentageAnalysed.text) + "
"; - }, - width : 100 - }, - - { - text : 'time', - dataIndex : 'time', - name : 'time', - hidden : true, - renderer : function(val) { - return val; - }, - width : 100 - - }, { - text : 'Date', - dataIndex : 'date', - name : 'date', - renderer : function(val) { - return val; - }, - width : 100 - - }, - - { - text : 'Time', - dataIndex : 'creationDate', - name : 'creationDate', - renderer : function(val) { - return moment(val).format(" HH:mm:ss"); - }, - width : 100 - - }, { - id : _this.id + 'GO', - width : 80, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - return BUI.getGreenButton('GO'); - } - } ]; -}; - -/** Changes location.href in order to edit the experiment **/ -ExperimentGrid.prototype._editExperiment = function(experimentId) { - if (Ext.urlDecode(window.location.href).sessionId != null) { - location.href = 'viewProjectList.do?reqCode=display&experimentId=' + experimentId + '&sessionId='+ Ext.urlDecode(window.location.href).sessionId; - } else { - location.href = 'viewProjectList.do?reqCode=display&experimentId=' + experimentId; - } -}; - -ExperimentGrid.prototype.input = function() { - var experiments = DATADOC.getExperimentList_10(); - return { - experiments : experiments, - proposal : new MeasurementGrid().input().proposal - - }; -}; - -ExperimentGrid.prototype.test = function(targetId) { - var experimentGrid = new ExperimentGrid({ - height : 350, - minHeight : 350, - width : 1000 - - }); - BIOSAXS.proposal = new Proposal(experimentGrid.input().proposal); - var panel = experimentGrid.getPanel(experimentGrid.input().experiments); - experimentGrid.refresh(experimentGrid.input().experiments); - panel.render(targetId); -}; - -function FitStructureToExperimentDataGrid(args) { - this.height = null; - this.width = null; - this.id = BUI.id(); - - if (args != null) { - if (args.height != null) { - this.height = args.height; - - if (args.width != null) { - this.width = args.width; - } - } - } - - this.onSelected = new Event(this); -} - -FitStructureToExperimentDataGrid.prototype.getStructuresByMacromolecule = function(macromolecule) { - var structures = []; - if (macromolecule.structure3VOs != null) { - if (macromolecule.structure3VOs.length > 0) { - for (var i = 0; i < macromolecule.structure3VOs.length; i++) { - structures.push(macromolecule.structure3VOs[i]); - } - } - } - return structures; -}; - -FitStructureToExperimentDataGrid.prototype._prepareData = function(subtractions) { - var data = []; - for (var i = 0; i < subtractions.length; i++) { - - for (var j = 0; j < subtractions[i].fitStructureToExperimentalData3VOs.length; j++) { - var fit = subtractions[i].fitStructureToExperimentalData3VOs[j]; - data.push({ - fit : fit.fitFilePath, - fitStructureToExperimentalDataId : fit.fitStructureToExperimentalDataId, - mixtureToStructure3VOs : fit.mixtureToStructure3VOs, - subtractedFile : subtractions[i].substractedFilePath - }); - } - } - return data; - -}; - -FitStructureToExperimentDataGrid.prototype.refresh = function(subtractions) { - this.store.loadData(this._prepareData(subtractions), false); -}; - -FitStructureToExperimentDataGrid.prototype.getPanel = function() { - var _this = this; - this.store = Ext.create('Ext.data.Store', { - fields : [ 'fit', 'subtractedFile', 'structureId', 'fitFilePath', 'mixtureToStructure3VOs' ], - data : [] - }); - - this.store.sort([ { - property : 'name', - direction : 'ASC' - } ]); - - this.selModel = Ext.create('Ext.selection.RowModel', { - allowDeselect : true, - mode : 'MULTI', - listeners : { - selectionchange : function(sm, selections) { - var selected = []; - for (var i = 0; i < selections.length; i++) { - selected.push(selections[i].raw); - } - _this.onSelected.notify(selected); - } - } - }); - - this.panel = Ext.create('Ext.grid.Panel', { - store : this.store, - deferredRender : false, - width : this.width, - height : this.height, - margin : 10, - selModel : this.selModel, - columns : [ { - text : 'Name', - dataIndex : 'fit', - flex : 1, - renderer : function(val, b, record) { - return BUI.getFileName(val); - } - }, { - text : 'PDB', - dataIndex : 'mixtureToStructure3VOs', - flex : 1, - renderer : function(values, b, record) { - var html = ""; - for (var i = 0; i < values.length; i++) { - var structure = BIOSAXS.proposal.getStructuresById(values[i].structureId); - html = html + ""; - if (structure != null){ - html = html + ""; - } - html = html + ""; - } - return html + "
" + structure.name + "
"; - } - }, { - text : 'Volume Fraction', - dataIndex : 'mixtureToStructure3VOs', - flex : 1, - renderer : function(values, b, record) { - var html = ""; - for (var i = 0; i < values.length; i++) { - html = html + ""; - html = html + ""; - html = html + ""; - } - - return html + "
" + values[i].volumeFraction + "
"; - } - },{ - text : 'Subtraction', - dataIndex : 'subtractedFile', - flex : 1, - renderer : function(values, b, record) { - return values.split("/")[values.split("/").length - 1]; - } - },], - - viewConfig : { - enableTextSelection : true, - preserveScrollOnRefresh : true - }, - listeners : { - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - }, - afterrender : function() { - } - } - }); - return this.panel; -}; - -/** Static method **/ -FitStructureToExperimentDataGrid.prototype.RUNFitScattering = function(subtractionId, structureId) { - var _this = this; - /** Add to Workflow **/ - var adapter = new BiosaxsDataAdapter(); - var workflow = { - 'workflowTitle' : 'FitExperimentalDatatoStructure', - 'comments' : 'FitExperimentalDatatoStructure run from ISPyB for subtractionId: ' + subtractionId + ' and structureId ' + structureId - } - - var inputs = [ { - name : 'subtractionId', - value : subtractionId - }, { - name : 'structureId', - value : structureId - } ]; - - adapter.onSuccess.attach(function(sender, data) { - /** Add to Fit **/ - var adapter2 = new BiosaxsDataAdapter(); - var fit = { - 'workflowId' : data.workflowId, - 'subtractionId' : subtractionId, - 'structureId' : structureId, - 'comments' : 'Sent to workflow engine' - } - adapter2.onSuccess.attach(function(sender, fit) { - _this.refresh(_this.subtractionId, _this.macromolecule); - }); - adapter2.addFitStructureData(fit); - - }); - adapter.addWorkflow(workflow, inputs); - -}; +/** + * Example form + * + * @witdh + * @height + */ +function MolarityForm(args) { + this.id = BUI.id(); + this.width = 700; + this.height = 500; + + if (args != null) { + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + } + + this.onSave = new Event(this); + this.onClose = new Event(this); +} + -/** - * It shows buffer grid with a top bar with "Add" button - * - * @height - * @searchBar - * @collapsed - * @width - */ -function FrameGrid(args) { - this.height = 500; - this.width = 500; - this.searchBar = false; - this.tbar = false; - this.collapsed = false; - - - if (args != null) { - if (args.height != null) { - this.height = args.height; - } - - if (args.searchBar != null) { - this.searchBar = args.searchBar; - } - - if (args.tbar != null) { - this.tbar = args.tbar; - } - - if (args.collapsed != null) { - this.collapsed = args.collapsed; - } - - if (args.width != null) { - this.width = args.width; - } - } -} - -FrameGrid.prototype._edit = function(bufferId) { - var _this = this; - var window = new BufferWindow(); - window.onSuccess.attach(function(sender, proposal) { - _this.store.loadData(BIOSAXS.proposal.getBuffers()); - }); - window.draw(BIOSAXS.proposal.getBufferById(bufferId)); -}; - -FrameGrid.prototype.refresh = function(buffers, experimentId) { - this.experimentId = experimentId; - this.store.loadData(this._prepareData(buffers), false); -}; - -FrameGrid.prototype._prepareData = function(buffers) { - return buffers; -}; - -FrameGrid.prototype._getTbar = function() { - var _this = this; - var actions = []; - - actions.push(Ext.create('Ext.Action', { - icon : '../images/add.png', - text : 'Add Buffer', - disabled : false, - handler : function(widget, event) { - var window = new BufferWindow(); - window.onSuccess.attach(function(sender) { - _this.store.loadData(BIOSAXS.proposal.getBuffers()); - }); - window.draw({}); - } - })); - return actions; -}; - -FrameGrid.prototype.getPanel = function(buffers) { - var _this = this; - - this.store = Ext.create('Ext.data.Store', { - fields : [ 'frameNumber', 'I0', 'Rg', 'Mass', 'Vc', 'Qr', 'quality'], - data : buffers - }); - - this.store.sort('frameNumber'); - - var type = 'Ext.grid.Panel'; - if (this.searchBar == true) { - type = 'Ext.ux.LiveSearchGridPanel'; - } - - this.grid = Ext.create(type, { - store : this.store, - height : this.height, - width : this.width, - margin : 5, - columns : [{ - text : 'Frame', - dataIndex : 'frameNumber', - flex : 1 - },{ - text : 'I0', - dataIndex : 'I0', - flex : 1, - renderer : function(val, y, sample) { - return BUI.formatValuesUnits(sample.data.I0, "", 12, 3); - } - },{ - text : 'Rg', - dataIndex : 'Rg', - flex : 1, - renderer : function(val, y, sample) { - return BUI.formatValuesUnits(sample.data.Rg, "nm", 12, 3); - } - },{ - text : 'Mass', - dataIndex : 'Mass', - flex : 1, - renderer : function(val, y, sample) { - return BUI.formatValuesUnits(sample.data.Mass, "", 12, 3); - } - },{ - text : 'Vc', - dataIndex : 'Vc', - flex : 1, - renderer : function(val, y, sample) { - return BUI.formatValuesUnits(sample.data.Vc, "", 12, 3); - } - },{ - text : 'Qr', - dataIndex : 'Qr', - flex : 1, - renderer : function(val, y, sample) { - return BUI.formatValuesUnits(sample.data.Qr, "", 12, 3); - } - },{ - text : 'Quality', - dataIndex : 'quality', - flex : 1, - renderer : function(val, y, sample) { - return (Number(sample.data.quality) * 100).toFixed(2) + "%"; - } - }, - { - text : '', - renderer : function(val, x, sample) { - if (sample != null) { - return BUI.getZipHTMLByFrameRangeId(_this.experimentId, sample.raw.frameNumber, sample.raw.frameNumber); - } - }, - width : 100 - }], - flex : 1, - viewConfig : { - stripeRows : true - } - }); - - /** Adding the tbar **/ - if (this.tbar) { - this.grid.addDocked({ - xtype : 'toolbar', - items : this._getTbar() - }); - } - return this.grid; -}; - -FrameGrid.prototype.input = function() { - return []; -}; - -FrameGrid.prototype.test = function(targetId) { - var frameGrid = new FrameGrid({ - width : 800, - height : 350, - collapsed : false, - tbar : true - }); - - var panel = frameGrid.getPanel([]); - panel.render(targetId); -}; - - -function PeakGrid(args) { - this.height = 500; - this.searchBar = false; - this.tbar = false; - this.collapsed = false; - this.width = 500; - this.showExtendedColumns = false; - - if (args != null) { - if (args.showExtendedColumns != null) { - this.showExtendedColumns = args.showExtendedColumns; - } - if (args.height != null) { - this.height = args.height; - } - if (args.searchBar != null) { - this.searchBar = args.searchBar; - } - - if (args.tbar != null) { - this.tbar = args.tbar; - } - - if (args.collapsed != null) { - this.collapsed = args.collapsed; - } - - if (args.width != null) { - this.width = args.width; - } - } -} - - -PeakGrid.prototype.refresh = function(buffers) { - this.store.loadData(this._prepareData(buffers), false); -}; - -PeakGrid.prototype._prepareData = function(buffers) { - -// for ( var i = 0; i < buffers.length; i++) { -// buffers[i].name = "Peak #" + (i+1); +MolarityForm.prototype._getNumericWithHelp = function(type, fieldLabel, fieldName, help) { + return Ext.create('Ext.container.Container', { + margin : "10 0 0 10", + items : [ { + xtype : type, + fieldLabel : fieldLabel, + name : fieldName, + id : this.id + fieldName, + decimalPrecision : 6 + }, { + xtype : 'label', + forId : 'myFieldId', + text : help, + margin : "5 0 0 105", + cls : "inline-help" + } ] + }); +}; + + +MolarityForm.prototype._getItems = function() { + this.macromoleculeCombo = BIOSAXS_COMBOMANAGER.getComboMacromoleculeByMacromolecules(this.getMacromuleculesCandidates(this.macromolecule), { + width : 250, + labelWidth : 100, + margin : 10 + }); + + return [ { + xtype : 'container', + flex : 1, + margin : '10 0 0 10', + border : 0, + layout : 'anchor', + defaultType : 'requiredtext', + items : [ this.macromoleculeCombo, + this._getNumericWithHelp("textfield", "Ratio", "ratio", "Number in assymmetric units") + ] + } ]; +}; + +MolarityForm.prototype._persist = function() { + var _this = this; + var macromoleculeId = this.macromoleculeCombo.getValue(); + var ratio = Ext.getCmp(this.id + "ratio").getValue(); + var comments = "Not used yet"; + var dataAdapter = new BiosaxsDataAdapter(); + this.panel.setLoading("Saving"); + dataAdapter.onSuccess.attach(function(sender, args) { + _this.onSave.notify(); + }); + dataAdapter.saveStoichiometry(this.macromolecule.macromoleculeId, macromoleculeId, ratio, comments); +}; + +MolarityForm.prototype._getButtons = function() { + var _this = this; + + function onClose() { + _this.onClose.notify(); + } + + return [ { + text : 'Save', + handler : function() { + _this._persist(); + } + }, { + text : 'Cancel', + handler : function() { + onClose(); + } + } ]; +}; + +MolarityForm.prototype.getPanel = function() { + this.panel = Ext.create('Ext.form.Panel', { +// width : null, + height : this.height, + margin : 2, + border : 1, + defaultType : 'requiredtext', + items : this._getItems(), + buttons : this._getButtons() + }); + return this.panel; +}; + +/** macromolecules contains all macromolecules except this one **/ +MolarityForm.prototype.getMacromuleculesCandidates = function(macromolecule) { + var macromolecules = []; + if ( BIOSAXS.proposal.macromolecules){ + for (var i = 0; i < BIOSAXS.proposal.macromolecules.length; i++) { + var m = BIOSAXS.proposal.macromolecules[i]; + if (this.macromolecule != null){ + if (m.macromoleculeId != this.macromolecule.macromoleculeId) { + macromolecules.push(m); + } + } + } + } + return macromolecules; +}; + + +/** It populates the form **/ +MolarityForm.prototype.refresh = function(macromolecule) { + this.macromolecule = macromolecule; + +}; + + +MolarityForm.prototype.input = function() { + return {}; +}; + + +/** It populates the form **/ +MolarityForm.prototype.test = function(targetId) { + var macromoleculeForm = new MolarityForm(); + var panel = macromoleculeForm.getPanel(); + panel.render(targetId); +}; + +///** +// * +// * @witdh +// * @height +// */ +//function MacromoleculeForm(args) { +// this.id = BUI.id(); +// this.width = 700; +// this.height = 500; +// +// if (args != null) { +// if (args.width != null) { +// this.width = args.width; +// } +// if (args.height != null) { +// this.height = args.height; +// } +// } +// +// this.onClose = new Event(this); +//} +// +//MacromoleculeForm.prototype.getMacromolecule = function() { +// this.macromolecule.name = Ext.getCmp(this.panel.getItemId()).getValues().name; +// this.macromolecule.acronym = Ext.getCmp(this.panel.getItemId()).getValues().acronym; +// this.macromolecule.comments = Ext.getCmp(this.panel.getItemId()).getValues().comments; +// this.macromolecule.extintionCoefficient = Ext.getCmp(this.panel.getItemId()).getValues().extintionCoefficient; +// this.macromolecule.molecularMass = Ext.getCmp(this.panel.getItemId()).getValues().molecularMass; +// return this.macromolecule; +//}; +// +//MacromoleculeForm.prototype.setMacromolecule = function(macromolecule) { +// this.pdbStore.loadData(macromolecule.structure3VOs); +// +//}; +// +//MacromoleculeForm.prototype.getForm = function(macromolecule) { +// this.panel = Ext.createWidget('form', { +// frame : false, +// border : 0, +// padding : 15, +// width : 550, +// height : 350, +// items : [ { +// xtype : 'container', +// layout : 'hbox', +// items : [ { +// xtype : 'container', +// flex : 1, +// border : false, +// layout : 'anchor', +// defaultType : 'requiredtext', +// items : [ { +// fieldLabel : 'Name', +// name : 'name', +// anchor : '95%', +// tooltip : "Name of the macromolecule", +// value : macromolecule.name +// }, { +// fieldLabel : 'Acronym', +// name : 'acronym', +// anchor : '95%', +// value : macromolecule.acronym +// } ] +// }, { +// xtype : 'container', +// flex : 1, +// layout : 'anchor', +// defaultType : 'textfield', +// items : [ { +// xtype : 'numberfield', +// fieldLabel : 'Mol. Mass (Da)', +// name : 'molecularMass', +// value : macromolecule.molecularMass, +// decimalPrecision : 6 +// }, { +// xtype : 'numberfield', +// fieldLabel : 'Extinction coef.', +// name : 'extintionCoefficient', +// value : macromolecule.extintionCoefficient, +// decimalPrecision : 6 +// } ] +// } ] +// }, { +// xtype : 'textareafield', +// name : 'comments', +// fieldLabel : 'Comments', +// value : macromolecule.comments, +// width : this.width - 10 +// }, +// +// { +// html : BUI.getWarningHTML("The macromolecule is unsaved. Save the macromolecule to get access to other tabs"), +// margin : "150 10 10 10", +// id : this.id + "unsavedWarning", +// hidden : !(!macromolecule.macromoleculeId) +// } +// +// ] +// }); +// return this.panel; +//}; +// +//MacromoleculeForm.prototype.save = function() { +// var _this = this; +// +// var adapter = new BiosaxsDataAdapter(); +// adapter.onSuccess.attach(function(sender, proposal) { +// BIOSAXS.proposal.setItems(proposal); +// _this.panel.setLoading(false); +// +// Ext.getCmp(_this.id + "assembly").enable() +// Ext.getCmp(_this.id + "advanced").enable(); +// Ext.getCmp(_this.id + "unsavedWarning").hide(); +// }); +// +// if (this.getMacromolecule().name == "") { +// BUI.showError("Name field is mandatory"); +// return; +// } +// if (this.getMacromolecule().acronym == "") { +// BUI.showError("Acroynm field is mandatory"); +// return; +// } +// +// /** Check if acronym is unique * */ +// if (this.getMacromolecule().macromoleculeId == null) { +// if (BIOSAXS.proposal.getMacromoleculeByAcronym(this.getMacromolecule().acronym) == null) { +// this.panel.setLoading("ISPyB: Saving Macromolecule") +// adapter.saveMacromolecule(this.getMacromolecule()); +// } else { +// alert("There is already an existing macromolecule with the same acronym"); +// +// } +// } else { +// this.panel.setLoading("ISPyB: Saving Macromolecule") +// adapter.saveMacromolecule(this.getMacromolecule()); +// } +// +//}; +// +//MacromoleculeForm.prototype.getPanel = function(macromolecule) { +// var _this = this; +// this.macromolecule = macromolecule; +// return Ext.createWidget('tabpanel', { +// height : this.height, +// margin : 5, +// plain : true, +// style : { +// padding : 5 +// }, +// items : [ { +// tabConfig : { +// title : "General", +// disabled : false +// }, +// items : [ this.getForm(macromolecule) ], +// bbar : [ "->", { +// text : 'Save', +// cls : 'btn-with-border', +// style : { +// +// border : 1 +// }, +// handler : function() { +// _this.save(); +// } +// }, { +// text : 'Close', +// cls : 'btn-with-border', +// handler : function() { +// _this.onClose.notify(); +// } +// } ] +// }, { +// tabConfig : { +// id : this.id + "assembly", +// title : "Assembly", +// tooltip : 'Description of subunits present in the macromolecule', +// // hidden : (!macromolecule.macromoleculeId), +// disabled : (!macromolecule.macromoleculeId) +// }, +// items : [ this.getMolarityGrid(macromolecule) ] +// }, { +// tabConfig : { +// id : this.id + "advanced", +// title : "Advanced Modeling", +// // hidden : (!macromolecule.macromoleculeId), +// tooltip : 'Definition of the description contacts and symetries', +// disabled : (!macromolecule.macromoleculeId) +// }, +// items : [ this.getRigidBodyForm(macromolecule) ] +// } ] +// }); +//}; +// +//MacromoleculeForm.prototype.getRigidBodyForm = function(macromolecule) { +// var _this = this; +// +// // [P1, P2, P3, P4 ,P5 ,P6 ,32, P42, P52, P62] + P222 +// var symmetry = Ext.create('Ext.data.Store', { +// fields : [ 's' ], +// data : [ { +// "s" : "P1" +// }, { +// "s" : "P2" +// }, { +// "s" : "P3" +// }, { +// "s" : "P4" +// }, { +// "s" : "P5" +// }, { +// "s" : "P6" +// }, { +// "s" : "P32" +// }, { +// "s" : "P42" +// }, { +// "s" : "P52" +// }, { +// "s" : "P62" +// }, { +// "s" : "P222" +// } ] +// }); +// +// if (macromolecule.symmetry == null) { +// macromolecule.symmetry = "P1"; +// } +// var comboBox = Ext.create('Ext.form.ComboBox', { +// fieldLabel : 'Symmetry', +// store : symmetry, +// id : 'comboSym', +// queryMode : 'local', +// displayField : 's', +// valueField : 's', +// value : macromolecule.symmetry, +// margin : "10 0 0 0", +// listeners : { +// change : function(combo, newValue, oldValue, eOpts) { +// macromolecule.symmetry = newValue; +// } +// } +// }); +// +// this.rigidBodyPanel = Ext.createWidget('form', { +// frame : false, +// border : 0, +// padding : 10, +// width : 550, +// height : 400, +// items : [ { +// xtype : 'container', +// layout : 'hbox', +// items : [ { +// xtype : 'container', +// border : false, +// layout : 'hbox', +// items : [ { +// xtype : 'label', +// forId : 'myFieldId', +// text : 'Contact Desc:', +// width : 105, +// margin : '0 0 0 0' +// }, { +// xtype : 'textfield', +// hideLabel : true, +// id : "contactsDescriptionFilePath", +// margin : '0 0 0 0', +// width : 300, +// value : macromolecule.contactsDescriptionFilePath +// }, { +// text : 'Upload', +// xtype : 'button', +// margin : "0 0 0 20", +// width : 100, +// handler : function() { +// _this._openUploadDialog(macromolecule.macromoleculeId, "CONTACTS", "Upload Contact Description File"); +// } +// } ] +// } ] +// }, +// +// comboBox, { +// xtype : 'checkbox', +// margin : '10 0 0 5', +// boxLabel : "I want rigid body modeling run on this stuff", +// checked : true, +// width : 300 +// }, _this.getPDBGrid(macromolecule) ] +// }); +// return this.rigidBodyPanel; +//}; +// +//MacromoleculeForm.prototype.update = function() { +// var _this = this; +// BIOSAXS.proposal.onInitialized.attach(function() { +// if (BIOSAXS.proposal != null) { +// var macromolecules = BIOSAXS.proposal.macromolecules; +// for (var i = 0; i < macromolecules.length; i++) { +// if (macromolecules[i].macromoleculeId == _this.macromolecule.macromoleculeId) { +// _this.macromolecule = macromolecules[i]; +// _this.setMacromolecule(_this.macromolecule); +// _this.molarityStore.loadData(_this.parseMolarityData(_this.macromolecule)); +// _this.pdbGrid.setLoading(false); +// Ext.getCmp("contactsDescriptionFilePath").setValue(_this.macromolecule.contactsDescriptionFilePath) +// _this.molarityGrid.setLoading(false); +// +// } +// } +// } +// }); +// this.molarityGrid.setLoading("Updating"); +// this.pdbGrid.setLoading("Updating"); +// BIOSAXS.proposal.init(); +//}; +// +///******************************************************************************* +// * MOLARITY GRID +// ******************************************************************************/ +// +//MacromoleculeForm.prototype.parseMolarityData = function(macromolecule) { +// var data = []; +// if (macromolecule.stoichiometry != null) { +// for (var i = 0; i < macromolecule.stoichiometry.length; i++) { +// data.push({ +// ratio : macromolecule.stoichiometry[i].ratio, +// acronym : macromolecule.stoichiometry[i].macromolecule3VO.acronym, +// comments : macromolecule.stoichiometry[i].macromolecule3VO.comments, +// stoichiometryId : macromolecule.stoichiometry[i].stoichiometryId, +// name : macromolecule.stoichiometry[i].macromolecule3VO.name +// }); +// } +// } +// return data; +//}; +// +//MacromoleculeForm.prototype.getMolarityGrid = function(macromolecule) { +// var _this = this; +// +// this.molarityStore = Ext.create('Ext.data.Store', { +// fields : [ 'acronym', 'ratio', 'comments', 'stoichiometryId', 'name' ], +// data : this.parseMolarityData(macromolecule), +// sorters : { +// property : 'ratio', +// direction : 'DESC' +// } +// }); +// +// this.molarityGrid = Ext.create('Ext.grid.Panel', { +// store : this.molarityStore, +// height : 350, +// padding : 5, +// columns : [ +// +// { +// text : 'Subunit', +// columns : [ { +// text : "Acronym", +// width : 100, +// hidden : false, +// dataIndex : 'acronym', +// sortable : true +// }, { +// text : "Name", +// width : 100, +// hidden : false, +// dataIndex : 'name', +// sortable : true +// }, { +// text : "Comments", +// width : 100, +// dataIndex : 'comments', +// sortable : true +// } ] +// }, { +// text : "Number
in assymmetric units", +// width : 150, +// dataIndex : 'ratio', +// tooltip : 'Number of times this subunit is present in the macromolecule', +// sortable : true +// }, { +// id : this.id + 'MOLARITY_REMOVE', +// flex : 0.1, +// sortable : false, +// renderer : function(value, metaData, record, rowIndex, colIndex, store) { +// return BUI.getRedButton('REMOVE'); +// } +// } ], +// listeners : { +// cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { +// if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'MOLARITY_REMOVE') { +// var dataAdapter = new BiosaxsDataAdapter(); +// dataAdapter.onSuccess.attach(function() { +// _this.molarityGrid.setLoading(false); +// _this.update(); +// }); +// dataAdapter.removeStoichiometry(record.data.stoichiometryId); +// _this.molarityGrid.setLoading("Removing Structure"); +// } +// } +// }, +// buttons : [ { +// text : 'Add molarity', +// handler : function() { +// +// function onClose() { +// w.destroy(); +// _this.update(); +// } +// var w = Ext.create('Ext.window.Window', { +// title : 'Molarity', +// height : 300, +// width : 500, +// modal : true, +// buttons : [ { +// text : 'Save', +// handler : function() { +// var macromoleculeId = (_this.macromoleculeCombo.getValue()); +// var ratio = Ext.getCmp(_this.id + "ratio").getValue(); +// var comments = ""; +// var dataAdapter = new BiosaxsDataAdapter(); +// dataAdapter.onSuccess.attach(function(sender, args) { +// _this.update(); +// w.destroy(); +// }); +// dataAdapter.saveStoichiometry(_this.macromolecule.macromoleculeId, macromoleculeId, ratio, comments); +// } +// }, { +// text : 'Cancel', +// handler : function() { +// onClose(); +// } +// } ], +// items : [ _this.getMolarityForm(macromolecule) ], +// listeners : { +// onEsc : function() { +// onClose(); +// }, +// close : function() { +// onClose(); +// } +// } +// }).show(); +// } +// } ] +// }); +// return this.molarityGrid; +//}; +// +///******************************************************************************* +// * PDB GRID +// ******************************************************************************/ +// +//MacromoleculeForm.prototype._openUploadDialog = function(macromoleculeId, type, title) { +// var _this = this; +// function onClose() { +// w.destroy(); +// _this.update(); +// } +// +// var w = Ext.create('Ext.window.Window', { +// title : title, +// height : 200, +// width : 400, +// modal : true, +// buttons : [ { +// text : 'Close', +// handler : function() { +// onClose(); +// } +// } ], +// layout : 'fit', +// items : { +// html : "" +// }, +// listeners : { +// onEsc : function() { +// onClose(); +// }, +// close : function() { +// onClose(); +// } +// } +// }).show(); +//}; +// +//MacromoleculeForm.prototype._getPlugins = function() { +// var _this = this; +// var plugins = []; +// // if (this.updateRowEnabled) { +// plugins.push(Ext.create('Ext.grid.plugin.RowEditing', { +// clicksToEdit : 1, +// listeners : { +// validateedit : function(grid, e) { +// /** Comments are always updatable* */ +// e.record.raw.symmetry = e.newValues.symmetry; +// e.record.raw.multiplicity = e.newValues.multiplicity; +// +// var adapter = new BiosaxsDataAdapter(); +// adapter.onSuccess.attach(function(sender, measurement) { +// // _this.grid.setLoading(false); +// }); +// adapter.onError.attach(function() { +// alert("Error"); +// // _this.grid.setLoading(false); +// }); +// +// // _this.grid.setLoading(); +// adapter.saveStructure(e.record.raw); +// } +// } +// })); +// // } +// return plugins; +//}; +// +//MacromoleculeForm.prototype.getPDBGrid = function(macromolecule) { +// var _this = this; +// +// var data = macromolecule.structure3VOs; +// +// // /** Getting PDB from subunits **/ +// // if (macromolecule != null){ +// // if (macromolecule.stoichiometry != null){ +// // for (var i =0; i < macromolecule.stoichiometry.length; i++){ +// // var stoichiometry = macromolecule.stoichiometry[i]; +// // if (stoichiometry.macromolecule3VO != null){ +// // if (stoichiometry.macromolecule3VO.structure3VOs != null){ +// // for (var j = 0; j < stoichiometry.macromolecule3VO.structure3VOs.length; +// // j++) { +// // var structure = stoichiometry.macromolecule3VO.structure3VOs[j]; +// // structure["isSubunit"] = stoichiometry.macromolecule3VO.acronym; +// // data.push(structure) +// // } +// // } +// // } +// // } +// // } +// // } +// +// this.pdbStore = Ext.create('Ext.data.Store', { +// fields : [ 'filePath', 'structureId', 'structureType', 'symmetry', 'structureId', 'name', 'multiplicity' ], +// data : macromolecule.structure3VOs, +// groupField : 'structureType', +// sorters : { +// property : 'structureId', +// direction : 'DESC' +// } +// }); +// +// var groupingFeature = Ext.create('Ext.grid.feature.Grouping', { +// groupHeaderTpl : Ext.create('Ext.XTemplate', +// "
{name:this.formatName}
", { +// formatName : function(name) { +// return name; +// } +// }), +// hideGroupedHeader : true, +// startCollapsed : false +// }); +// +// this.pdbGrid = Ext.create('Ext.grid.Panel', { +// margin : "15 0 0 5", +// height : 250, +// store : this.pdbStore, +// plugins : _this._getPlugins(), +// buttons : [ { +// // text : 'Add PDB file', +// text : 'Add Modeling Option', +// handler : function() { +// _this._openUploadDialog(macromolecule.macromoleculeId, "PDB", 'Upload PDB File'); +// } +// } +// +// ], +// columns : [ +// { +// text : "structureId", +// flex : 0.2, +// hidden : true, +// dataIndex : 'structureId', +// sortable : true +// }, +// { +// text : "File", +// flex : 0.5, +// dataIndex : 'filePath', +// sortable : true, +// hidden : true +// }, +// { +// text : "PDB", +// flex : 0.4, +// dataIndex : 'name', +// sortable : true +// }, +// { +// text : "Symmetry", +// flex : 0.4, +// dataIndex : 'symmetry', +// sortable : true, +// editor : { +// xtype : 'combobox', +// typeAhead : true, +// triggerAction : 'all', +// selectOnTab : true, +// store : [ [ "P1", "P1" ], [ "P2", "P2" ], [ "P3", "P3" ], [ "P4", "P4" ], [ "P5", "P5" ], [ "P6", "P6" ], [ "P32", "P32" ], [ "P42", "P42" ], +// [ "P52", "P52" ], [ "P62", "P62" ], [ "P222", "P222" ] ], +// } +// }, { +// text : "Multiplicity", +// flex : 0.4, +// dataIndex : 'multiplicity', +// sortable : true, +// editor : { +// xtype : 'textfield' +// } +// +// }, { +// text : "Subunit", +// flex : 0.2, +// dataIndex : 'isSubunit', +// sortable : true, +// hidden : true +// }, { +// text : "Type", +// flex : 0.2, +// dataIndex : 'structureType', +// sortable : true, +// hidden : true +// }, +// +// { +// id : this.id + 'REMOVE', +// flex : 0.2, +// hidden : true, +// sortable : false, +// renderer : function(value, metaData, record, rowIndex, colIndex, store) { +// return BUI.getRedButton('REMOVE'); +// } +// }, ], +// +// listeners : { +// itemdblclick : function(dataview, record, item, e) { +// _this._editExperiment(record.raw.experimentId); +// }, +// cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { +// +// if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'REMOVE') { +// var dataAdapter = new BiosaxsDataAdapter(); +// dataAdapter.onSuccess.attach(function() { +// _this.pdbGrid.setLoading(false); +// _this.update(); +// }); +// dataAdapter.removeStructure(record.data.structureId); +// _this.pdbGrid.setLoading("Removing PDB file"); +// } +// +// } +// }, +// viewConfig : { +// getRowClass : function(record, rowIdx, params, store) { +// if (record.raw.isSubunit != null) { +// return "blue-row"; +// } +// } +// } +// }); +// +// return this.pdbGrid; +//}; +// +//MacromoleculeForm.prototype.getMolarityForm = function(macromolecule) { +// var _this = this; +// var data = []; +// for (var i = 0; i < BIOSAXS.proposal.macromolecules.length; i++) { +// var m = BIOSAXS.proposal.macromolecules[i]; +// if (m.macromoleculeId != macromolecule.macromoleculeId) { +// data.push(m); +// } +// // } - /** Adding information of buffer **/ - if (buffers.length > 0){ - buffers.unshift({ - name : "BUFFER", - start : 0, - experimentId : buffers[0].experimentId, - end : buffers[0].start - 1 - }); - } - - - return buffers; -}; - -PeakGrid.prototype._getTbar = function() { - var _this = this; - var actions = []; +// this.macromoleculeCombo = BIOSAXS_COMBOMANAGER.getComboMacromoleculeByMacromolecules(data, { +// width : 250, +// labelWidth : 100, +// margin : 10 +// }); +// +// return Ext.createWidget('form', { +// +// frame : false, +// border : 0, +// // padding : 15, +// width : 550, +// height : 350, +// items : [ { +// xtype : 'container', +// flex : 1, +// border : false, +// layout : 'anchor', +// defaultType : 'requiredtext', +// items : [ this.macromoleculeCombo, { +// xtype : 'numberfield', +// name : 'Ratio', +// id : _this.id + "ratio", +// fieldLabel : 'Number in assymmetric units', +// value : 1, +// decimalPrecision : 6, +// margin : 10 +// }, { +// xtype : 'textareafield', +// name : 'comments', +// fieldLabel : 'Comments', +// margin : 10, +// width : 400, +// value : "" +// +// } ] +// } ] +// }); +// +//}; +// +///******************************************************************************* +// * JAVASCRIPT DOC +// ******************************************************************************/ +//MacromoleculeForm.prototype.input = function() { +// return { +// macromolecule : DATADOC.getMacromolecule_10() +// }; +//}; +// +//MacromoleculeForm.prototype.test = function(targetId) { +// var macromoleculeForm = new MacromoleculeForm(); +// var panel = macromoleculeForm.getPanel(macromoleculeForm.input().macromolecule); +// panel.render(targetId); +//}; + +function ResultSummaryForm() { + this.radiationDamageThreshold = BUI.getRadiationDamageThreshold(); + this.qualityThreshold = BUI.getQualityThreshold(); - actions.push(Ext.create('Ext.Action', { - icon : '../images/add.png', - text : 'Add Buffer', - disabled : false, - handler : function(widget, event) { - var window = new BufferWindow(); - window.onSuccess.attach(function(sender) { - _this.store.loadData(BIOSAXS.proposal.getBuffers()); - }); - window.draw({}); - } - })); - return actions; -}; + /** Data clusters with bufers **/ + this.clusterByBuffers = false; + + /** Visualization are groupeb by concenttrations. Ex: 4.5mg/ml and 4.7mg/ml will be clusterized together **/ + this.collapseConcentrations = true; + + this.summaryHeight = 350; + this.id = BUI.id(); -PeakGrid.prototype.getPanel = function(buffers) { var _this = this; - this.peakCount = 0; - this.store = Ext.create('Ext.data.Store', { - fields : ['name', {name:'start', type : 'int'}, {name:'end', type : 'int'}], - data : buffers - - }); - - this.store.sort('start'); - var type = 'Ext.grid.Panel'; - if (this.searchBar == true) { - type = 'Ext.ux.LiveSearchGridPanel'; - } - this.grid = Ext.create(type, { - store : this.store, - height : this.height, - width : this.width, - margin : 5, - columns : [ - { - text : '', - dataIndex : 'name', - width : 100, - hidden : _this.showExtendedColumns, - renderer : function(val, y, sample) { - if (sample.data.name == "BUFFER") - return "BUFFER"; - _this.peakCount++; - return "Peak #" + _this.peakCount; - } - - - }, - { - text : 'Peaks', - dataIndex : 'start', - sortable : true, - width : 100, - hidden: !_this.showExtendedColumns, - renderer : function(val, y, sample) { - return "From " + Number(sample.raw.start) + " to " + Number(sample.raw.end); - } - }, - { - text : 'Frames', - hidden : _this.showExtendedColumns, - columns : [ - { - text : 'Start', - dataIndex : 'start', - sortable : true, - hidden : _this.showExtendedColumns, - width : 100, - renderer : function(val, y, sample) { - return Number(val); - } - },{ - text : 'End', - dataIndex : 'end', - width : 100, - hidden : _this.showExtendedColumns, - renderer : function(val, y, sample) { - return Number(val); - } - },{ - text : 'Total', - dataIndex : 'end', - width : 100, - hidden : _this.showExtendedColumns, - renderer : function(val, y, sample) { - return "" + (sample.raw.end - sample.raw.start) + " frames"; - } - } - ] - } -// , -// { -// text : '', -// hidden : _this.showExtendedColumns, -// renderer : function(val, x, sample) { -// if (sample != null) { -// return BUI.getZipHTMLByFrameRangeId(sample.raw.experimentId, sample.raw.start, sample.raw.end); -// } -// }, -// width : 100 -// } - ], - flex : 1, - viewConfig : { - stripeRows : true, - getRowClass : function(record, rowIdx, params, store) { - if (record.raw.name == "BUFFER") { - return "blue-row"; - } - } - } + this.qualityControlResultsWidget = new QualityControlResultsWidget({ + qualityThreshold : this.radiationDamageThreshold, + radiationDamageThreshold : this.qualityThreshold + + }); + this.qualityControlResultsWidget.onQualityChanged.attach(function(sender, value) { + _this.qualityThreshold = value; + _this.thresholdsChanged(); }); - /** Adding the tbar **/ - if (this.tbar) { - this.grid.addDocked({ - xtype : 'toolbar', - items : this._getTbar() - }); - } - return this.grid; -}; + this.qualityControlResultsWidget.onRadiationDatamageChanged.attach(function(sender, value) { + _this.radiationDamageThreshold = value; + _this.thresholdsChanged(); -PeakGrid.prototype.input = function() { - return []; -}; + }); + this.concentrationHTMLTableWidget = new ConcentrationHTMLTableWidget({ + height : 250, + showBufferColumns : this.clusterByBuffers + }); -PeakGrid.prototype.test = function(targetId) { - var PeakGrid = new PeakGrid({ - width : 800, + this.plot = new BoxWhiskerGraph({ + targetId : _this.id + '_boxPlot', height : 350, - collapsed : false, - tbar : true + width : 450, + maxBoxWidth : 25 }); - var panel = PeakGrid.getPanel([]); - panel.render(targetId); -}; - -/** - * Macromolecule Grid showing macromolecules and adding anb updating buttons - * - * @height - * @maxHeight - * @width - * @cssFontStyle - * @searchBar makes this grid as Ext.ux.LiveSearchGridPanel - * @tbar top bar containing "Add" and "Update From SMIS" button - * @collapsed - * @collapsible - * @btnEditVisible - * @btnRemoveVisible - * @multiselect makes it multiselect using Ext.selection.CheckboxModel - * - * #onSelected - * #onMacromoleculesChanged - */ -function MacromoleculeGrid(args) { - this.height = 500; - this.width = 500; - this.id = BUI.id(); - this.maxHeight = this.height; + this.rangePlot = new RangeWhiskerGraph({ + targetId : _this.id + '_rangePlot', + height : 350, + width : 450, + maxBoxWidth : 25 + }); +} - this.searchBar = false; - this.tbar = false; +ResultSummaryForm.prototype.thresholdsChanged = function() { + var parsedData = this.prepareData(this.rawData); - this.collapsible = true; - this.collapsed = true; + var filtered = JSON.parse(JSON.stringify(parsedData)); + filtered.concentration.concentrations = []; + for ( var conc in parsedData.concentration.concentrations) { + if (parsedData.concentration.concentrations[conc].calculation.rgGnom.validNumber > 0) { + filtered.concentration.concentrations.push(parsedData.concentration.concentrations[conc]); + } + } - this.btnEditVisible = true; - this.btnRemoveVisible = false; - this.multiselect = false; + this.plotWhisker(filtered); + this.plotRange(filtered); - /** Font style applied to the acronym column **/ - this.cssFontStyle = null; + this.concentrationHTMLTableWidget.refresh(parsedData); +}; - if (args != null) { - if (args.height != null) { - this.height = args.height; - this.maxHeight = this.height; - } - if (args.maxHeight != null) { - this.maxHeight = args.maxHeight; - } - if (args.width != null) { - this.width = args.width; - } - if (args.cssFontStyle != null) { - this.cssFontStyle = args.cssFontStyle; - } +/** Given a frame object (object returned by analyzeFrames()) and depending of the threshold indicates if a datacollection has radiation damage **/ +ResultSummaryForm.prototype.hasRadiationDamage = function(frameObject) { + var bb = frameObject.bufferBeforeFramesMerged / frameObject.framesCount; + var ba = frameObject.bufferAfterFramesMerged / frameObject.framesCount; + var mol = frameObject.framesMerge / frameObject.framesCount; + return !((bb >= this.radiationDamageThreshold) && (ba >= this.radiationDamageThreshold) && (mol >= this.radiationDamageThreshold)); +}; - if (args.searchBar != null) { - this.searchBar = args.searchBar; - } - if (args.tbar != null) { - this.tbar = args.tbar; - } - if (args.collapsible != null) { - this.collapsible = args.collapsible; - } - if (args.collapsed != null) { - this.collapsed = args.collapsed; - } - if (args.btnEditVisible != null) { - this.btnEditVisible = args.btnEditVisible; - } - if (args.btnRemoveVisible != null) { - this.btnRemoveVisible = args.btnRemoveVisible; - } - if (args.multiselect != null) { - this.multiselect = args.multiselect; - } +/** Return (frameObject) an object with the information about the frames for a data collection**/ +ResultSummaryForm.prototype.analyzeFrames = function(dataCollectionRow) { + return { + bufferAfterFramesMerged : dataCollectionRow.bufferAfterFramesMerged, + bufferBeforeFramesMerged : dataCollectionRow.bufferBeforeFramesMerged, + framesCount : dataCollectionRow.framesCount, + framesMerge : dataCollectionRow.framesMerge + }; +}; + +ResultSummaryForm.prototype.detectDataCollectionWarnings = function(dataCollectionRow) { + var frameObject = this.analyzeFrames(dataCollectionRow); + var warnings = { + count : 0, + type : [] + }; + + if (this.hasRadiationDamage(frameObject)) { + warnings.count = warnings.count + 1; + warnings.type.push("RADIATION DAMAGE"); } - this.onSelected = new Event(); - - this.onMacromoleculesChanged = new Event(); -} + if (Number(dataCollectionRow.quality) < this.qualityThreshold) { + warnings.count = 1;//warnings.count + 1; + warnings.type.push("Quality <" + this.qualityThreshold); + } + return warnings; +}; +/** Return array composed by {concentration} objects **/ +ResultSummaryForm.prototype.getConcentrations = function(data) { + var concentrationsId = {}; + for ( var i = 0; i < data.length; i++) { + var warning = this.detectDataCollectionWarnings(data[i]); + var id = data[i].conc;// + "_" + data[i].bufferId; + if (this.clusterByBuffers) { + id = data[i].conc + "_" + data[i].bufferId; + } + if (concentrationsId[id] == null) { + concentrationsId[id] = { + id : id, + concentration : Number(data[i].conc).toFixed(2), + bufferId : data[i].bufferId, + bufferAcronym : data[i].bufferAcronym, + rgGuinier : [], + i0Guinier : [], + rgGnom : [], + dMax : [], + quality : [], + frames : [], + frames_warning : warning.count + }; + } else { + concentrationsId[id].frames_warning = concentrationsId[id].frames_warning + warning.count; + } + concentrationsId[id].frames.push(data[i]); -MacromoleculeGrid.prototype.edit = function(macromolecule) { - var _this = this; - var window = new MacromoleculeWindow(); - window.onSave.attach(function(sender) { - _this.store.loadData(BIOSAXS.proposal.getMacromolecules()); - _this.onMacromoleculesChanged.notify(); - }); - window.draw(macromolecule); -}; + if (warning.count == 0) { + concentrationsId[id].rgGuinier.push(data[i].rgGuinier); + concentrationsId[id].i0Guinier.push(data[i].I0); + concentrationsId[id].quality.push(data[i].quality); + concentrationsId[id].rgGnom.push(data[i].rgGnom); + concentrationsId[id].dMax.push(data[i].dmax); + } -MacromoleculeGrid.prototype.getTbar = function() { - var _this = this; - var actions = []; + } + var concentrations = []; + for ( var item in concentrationsId) { + if (concentrationsId.hasOwnProperty(item)) { + concentrations.push({ + concentration : concentrationsId[item].concentration, + id : item, + bufferId : Number(concentrationsId[item].bufferId).toFixed(2), + bufferAcronym : concentrationsId[item].bufferAcronym, + rgGuinier : concentrationsId[item].rgGuinier, + /** Frames **/ + frames : concentrationsId[item].frames, + frames_warning : concentrationsId[item].frames_warning, + /** Calculation **/ + calculation : { + rgGuinier : BUI.getStandardDeviation(concentrationsId[item].rgGuinier), + i0Guinier : BUI.getStandardDeviation(concentrationsId[item].i0Guinier), + quality : BUI.getStandardDeviation(concentrationsId[item].quality), + rgGnom : BUI.getStandardDeviation(concentrationsId[item].rgGnom), + dMax : BUI.getStandardDeviation(concentrationsId[item].dMax) - actions.push(Ext.create('Ext.Action', { - icon : '../images/add.png', - text : 'Add macromolecule', - disabled : false, - handler : function(widget, event) { - _this.edit(); - } - })); - actions.push("->"); - actions.push(Ext.create('Ext.Action', { - icon : '../images/folder_go.png', - text : 'Update From SMIS', - tooltip : "Retrieve all the macromolecules of your proposal from SMIS database", - disabled : false, - handler : function(widget, event) { - _this.grid.setLoading("Connecting to SMIS"); - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - BIOSAXS.proposal.setMacromolecules(data.macromolecules); - _this.refresh(BIOSAXS.proposal.macromolecules); - _this.grid.setLoading(false); - }); - adapter.onError.attach(function(sender, data) { - _this.grid.setLoading(false); + } }); - adapter.updateDataBaseFromSMIS(); } - })); - return actions; -}; + } -MacromoleculeGrid.prototype.deselectAll = function() { - this.grid.getSelectionModel().deselectAll(); + return { + concentrations : concentrations + }; }; -MacromoleculeGrid.prototype.selectById = function(macromoleculeId) { - this.grid.getSelectionModel().deselectAll(); - for ( var i = 0; i < this.grid.getStore().data.items.length; i++) { - var item = this.grid.getStore().data.items[i].raw; - if (item.macromoleculeId == macromoleculeId) { - this.grid.getSelectionModel().select(i); +ResultSummaryForm.prototype.prepareData = function(data) { + /** Return array composed by {acronym, bufferId} objects **/ + function getBuffers(data) { + var buffersId = {}; + for ( var i = 0; i < data.length; i++) { + buffersId[data[i].bufferId] = data[i].acronym; + } + var buffers = []; + for ( var id in buffersId) { + if (buffersId.hasOwnProperty(id)) { + buffers.push({ + acronym : buffersId[id], + bufferId : id + }); + } } + return buffers; } -}; -MacromoleculeGrid.prototype.refresh = function(macromolecules) { - this.store.loadData(macromolecules, false); + /** Get a string with all the concentrations **/ + function getConcentrationString(parseConcentrations) { + var concentrations = []; + for ( var i = 0; i < parseConcentrations.concentrations.length; i++) { + concentrations.push(parseConcentrations.concentrations[i].concentration + " mg/ml "); + } + return concentrations.toString(); + } + + var parseConcentrations = this.getConcentrations(data); + + return { + dataCollectionCount : data.length, + buffers : getBuffers(data), + concentration : parseConcentrations, + concentrationLabel : getConcentrationString(parseConcentrations) + }; }; -MacromoleculeGrid.prototype.getColumns = function() { - var _this = this; - var columns = [ - { - text : 'Acronym', - dataIndex : 'acronym', - id : this.id + "acronym", - flex : 1, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - if (_this.cssFontStyle != null) { - return "" + value + ""; +ResultSummaryForm.prototype.getDataForWhisker = function(data) { + var clusters = []; + + var concentrations = {}; + var i = 0; + var conc = 0; + if (this.collapseConcentrations) { + for (i = 0; i < data.concentration.concentrations.length; i++) { + conc = data.concentration.concentrations[i]; + var concentration = Number(conc.concentration).toFixed(0); + if (concentrations[concentration] == null) { + concentrations[concentration] = {}; + concentrations[concentration].concentration = concentration; + concentrations[concentration].calculation = {}; + concentrations[concentration].calculation.rgGuinier = {}; + concentrations[concentration].calculation.rgGuinier.values = []; + concentrations[concentration].calculation.rgGuinier.values = conc.calculation.rgGuinier.values; + concentrations[concentration].calculation.rgGnom = {}; + concentrations[concentration].calculation.rgGnom.values = []; + concentrations[concentration].calculation.rgGnom.values = conc.calculation.rgGnom.values; + } else { + concentrations[concentration].calculation.rgGuinier.values = concentrations[concentration].calculation.rgGuinier.values + .concat(conc.calculation.rgGuinier.values); + concentrations[concentration].calculation.rgGnom.values = concentrations[concentration].calculation.rgGnom.values + .concat(conc.calculation.rgGnom.values); } - return value; } - }, { - text : 'Name', - dataIndex : 'name', - id : this.id + "name", - flex : 1, - hidden : true - } ]; - if (this.btnEditVisible) { - columns.push({ - id : _this.id + 'buttonEditMacromolecule', - width : 85, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - if (_this.btnEditVisible) { - return BUI.getGreenButton('EDIT'); - } - return null; + /** From object to array **/ + var array = []; + for ( var key in concentrations) { + if (concentrations.hasOwnProperty(key)) { + array.push(concentrations[key]); } + } + data.concentration.concentrations = array; + } + + for (i = 0; i < data.concentration.concentrations.length; i++) { + conc = data.concentration.concentrations[i]; + clusters.push({ + name : conc.concentration + "mg/ml", + concentration : Number(conc.concentration), + x : Number(conc.concentration), + classes : [] + }); + clusters[clusters.length - 1].classes.push({ + name : "Guinier", + color : '#9A2EFE', + values : conc.calculation.rgGuinier.values + + }); + clusters[clusters.length - 1].classes.push({ + name : "P(r)", + color : '#2E64FE', + values : conc.calculation.rgGnom.values + }); } - if (this.btnRemoveVisible) { - columns.push({ - id : _this.id + 'buttonRemoveMacromolecule', - width : 85, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - if (_this.btnRemoveVisible) { - return BUI.getRedButton('REMOVE'); - } - return null; - } + return { + clusters : clusters.sort(function(a, b) { + return a.concentration - b.concentration; + }) + }; +}; + +ResultSummaryForm.prototype.getDataForWhiskerQuality = function(data) { + var clusters = []; + + for ( var i = 0; i < data.concentration.concentrations.length; i++) { + var conc = data.concentration.concentrations[i]; + clusters.push({ + name : conc.concentration + "mg/ml", + classes : [] + }); + clusters[clusters.length - 1].classes.push({ + name : "Quality", + values : conc.calculation.quality.values + }); } - return columns; + return { + clusters : clusters + }; +}; + +ResultSummaryForm.prototype.plotQualityWhisker = function(parsedData) { + this.qualityPlot.refresh(this.getDataForWhiskerQuality(parsedData)); }; +ResultSummaryForm.prototype.plotWhisker = function(parsedData) { + this.plot.refresh(this.getDataForWhisker(parsedData)); +}; -/** Returns the grid **/ -MacromoleculeGrid.prototype.getPanel = function() { +ResultSummaryForm.prototype.plotRange = function(parsedData) { + this.rangePlot.refresh(this.getDataForWhisker(parsedData)); +}; + +ResultSummaryForm.prototype.getPanel = function(data) { var _this = this; + _this.rawData = data; + var parsedData = this.prepareData(data); - this.store = Ext.create('Ext.data.Store', { - fields : [ 'macromoleculeId', 'name', 'acronym' ] - }); + this.panel = Ext + .createWidget( + 'form', + { + bodyPadding : 20, + frame : false, + border : 0, + width : this.width, + height : this.summaryHeight + 1000, + items : [ { + xtype : 'container', + layout : 'hbox', + items : [ { + xtype : 'container', + flex : 1, + border : false, + layout : 'anchor', + defaultType : 'textfield', + items : [ + _this.qualityControlResultsWidget.getPanel(), + { + xtype : 'fieldset', + width : 950, + margin : "20, 0 0 0", + height : this.summaryHeight + 500, + items : [ + { + html : "
Concentration Analysis
", + border : 0, + width : 900 - var type = 'Ext.grid.Panel'; - if (this.searchBar == true) { - type = 'Ext.ux.LiveSearchGridPanel'; - } + }, + { + html : this.concentrationHTMLTableWidget.getPanel(parsedData), + border : 0, + width : 900, + margin : "10, 0 0 10" - this.selModel = Ext.create('Ext.selection.RowModel', { -// allowDeselect : true, -// mode : 'MULTI', - listeners : { - selectionchange : function(sm, selections) { - var selected = []; - for (var i = 0; i < selections.length; i++) { - selected.push(selections[i].raw); - } - _this.onSelected.notify(selected); - } - } - }); + }, + { + xtype : 'container', + layout : 'vbox', + border : 5, + items : [ + { + html : "
Rg based on Guinier and Gnom
", + border : 8, + width : 900, + margin : "20 0 0 10" - this.grid = Ext.create(type, { - id : this.id, - title : 'Macromolecules', - collapsible : this.collapsible, - collapsed : this.collapsed, - store : this.store, - height : this.height, - maxHeight : this.maxHeight, - selModel : this.selModel, - columns : this.getColumns(), - width : this.width, - viewConfig : { - stripeRows : true, - listeners : { - 'celldblclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - _this.edit(BIOSAXS.proposal.getMacromoleculeById(record.data.macromoleculeId)); - }, - 'cellclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEditMacromolecule') { - _this.edit(BIOSAXS.proposal.getMacromoleculeById(record.data.macromoleculeId)); - } - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemoveMacromolecule') { - BUI.showBetaWarning(); - } - } + }, { + xtype : 'container', + layout : 'hbox', + items : [ { + xtype : 'container', + layout : 'vbox', + items : [ { + html : "
", + border : 0, + width : this.plot.width, + padding : "10 0 0 20", + listeners : { + afterrender : function() { + _this.plotWhisker(parsedData); - } - } - }); + } + } + }, { + html : "
Concentration (mg/ml)
", + width : 450, + border : 0, + margin : "-50 0 0 0" + + } ] + }, { + xtype : 'container', + layout : 'vbox', + items : [ { + html : "
", + border : 0, + width : this.rangePlot.width, + padding : "10 0 0 10", + listeners : { + afterrender : function() { + _this.plotRange(parsedData); + } + } + }, { + html : "
Concentration (mg/ml)
", + width : 450, + border : 0, + margin : "-50 0 0 0" + + } ] + } ] + } ] + } ] + } ] + } + + ] + } ] + }); + return this.panel; - /** Adding the tbar **/ - if (this.tbar) { - this.grid.addDocked({ - xtype : 'toolbar', - items : this.getTbar() - }); - } - return this.grid; }; -MacromoleculeGrid.prototype.input = function() { +ResultSummaryForm.prototype.input = function() { return { - proposal : DATADOC.getProposal_10() + data : DATADOC.getData_3367() }; }; -MacromoleculeGrid.prototype.test = function(targetId) { - var macromoleculeGrid = new MacromoleculeGrid({ - width : 800, - height : 350, - collapsed : false, - tbar : true - }); - - BIOSAXS.proposal = new Proposal(macromoleculeGrid.input().proposal); - var panel = macromoleculeGrid.getPanel(BIOSAXS.proposal.macromolecules); +ResultSummaryForm.prototype.test = function(targetId) { + var resultSummaryForm = new ResultSummaryForm(); + var panel = resultSummaryForm.getPanel(resultSummaryForm.input().data); panel.render(targetId); + }; -/** - * Shows measurements with their attributes as specimen, exposure temperature, - * volume to load, transmission etc... - * - * @addBtnMultipleEdit: if true add a button for changing measurements' - * parameters by choosing multiple measurements. It opens - * MultipleEditMeasurementGridWindow - * @collapsed: if true it doesn't show buffer's measurements - * @editor: hashmap containing columns to be edited. It is an array of a json - * like editor of Ext - * @selModel - * @collapseBtnEnable - * @removeBtnEnabled Ext.selection.RowModel - * @addBtnEnable - * @updateRowEnabled true/false if update plugin is set to the grid - * @showTitle - * @title - * @isStatusColumnHidden - * @isPriorityColumnHidden - * @isTimeColumnHidden - * @estimateTime - * @margin - * @tbar - * @height - * @maxHeight - * @minHeight - * @width - * @maxWidth - * @resizable - * @experimentColorBased when colors for buffers and macromolecules are not - * selected by the proposal but by experiment, so the - * number of colors is smaller +/** + * Example form + * + * @witdh + * @height + */ +function RigibBodyModelingForm(args) { + this.id = BUI.id(); + this.width = 700; + this.height = 500; + + if (args != null) { + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + } + + var _this = this; + this.rigidBodyGrid = new AprioriRigidBodyGrid(); + + this.rigidBodyGrid.onUploadFile.attach(function(sender, type, title){ + _this._openUploadDialog(_this.macromolecule.macromoleculeId, type, title); + }); + + this.rigidBodyGrid.onRemove.attach(function(sender, type, title){ + _this._update(); + }); + + this.onSave = new Event(this); + +} + +RigibBodyModelingForm.prototype._getItems = function() { + var _this = this; + + + return [ { + xtype : 'label', + forId : 'myFieldId', + text : 'Information for model fit, mixture analysis and rigid body modeling', + margin : '15 0 20 10', + cls : "inline-help" + }, + this.rigidBodyGrid.getPanel(), + { + xtype : 'label', + forId : 'myFieldId', + text : 'Distance restraints may be imposed on the model using contacts conditions file (OPTIONAL)', + margin : '25 0 5 10', + cls : "inline-help" + }, + { + xtype : 'container', + layout : 'hbox', + items : [ { + xtype : 'container', + border : false, + layout : 'hbox', + items : [ { + xtype : 'label', + forId : 'myFieldId', + text : 'Contact Description File: (Optional)', + width : 150, + margin : '10 0 0 10' + }, { + id : this.id + "contactsDescriptionFilePath", + xtype : 'textfield', + hideLabel : true, + margin : '10 0 0 0', + width : 200, + disabled: true + }, { + text : 'Upload', + xtype : 'button', + margin : "10 0 0 10", + width : 80, + handler : function() { + + _this._openUploadDialog(_this.macromolecule.macromoleculeId, "CONTACTS", "Upload Contact Description File"); + } + }, { + text : 'Remove', + id : _this.id + "_remove", + xtype : 'button', + margin : "10 0 0 10", + width : 80, + handler : function() { + _this.macromolecule.contactsDescriptionFilePath = null; + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, proposal) { + /** Updating the proposal global object **/ + BIOSAXS.proposal.setItems(proposal); + _this.panel.setLoading(false); + + var saved = BIOSAXS.proposal.getMacromoleculeByAcronym(_this.macromolecule.acronym); + /** Refreshing to check that everything is ok **/ + _this.refresh(saved); + _this.onSave.notify(saved); + }); + + _this.panel.setLoading("Saving Macromolecule") + adapter.saveMacromolecule(_this.macromolecule); + } + } ] + } ] + }, { + xtype : 'panel', + html : "Go to SASREF manual for further information", + margin : "10 0 0 160", + border : 0 + + }, + { + xtype : 'checkbox', + margin : '10 0 0 5', + boxLabel : "I want rigid body modeling run on this stuff", + checked : true, + width : 300 + } ] + +}; + +/** Because update is a jsp page we don't know if the user has uploaded a file or not then we need to refresh **/ +RigibBodyModelingForm.prototype._update = function(macromoleculeId, type, title) { + var _this = this; + BIOSAXS.proposal.onInitialized.attach(function() { + if (BIOSAXS.proposal != null) { + _this.refresh(BIOSAXS.proposal.getMacromoleculeById(_this.macromolecule.macromoleculeId)); + _this.panel.setLoading(false); + } + }); + this.panel.setLoading(); + BIOSAXS.proposal.init(); +}; + +RigibBodyModelingForm.prototype._openUploadDialog = function(macromoleculeId, type, title) { + var _this = this; + function onClose() { + w.destroy(); + _this._update(); + + } + + var w = Ext.create('Ext.window.Window', { + title : title, + height : 200, + width : 400, + modal : true, + buttons : [ { + text : 'Close', + handler : function() { + onClose(); + } + } ], + layout : 'fit', + items : { + html : "" + }, + listeners : { + onEsc : function() { + onClose(); + }, + close : function() { + onClose(); + } + } + }).show(); +}; + +RigibBodyModelingForm.prototype._getButtons = function() { + return []; +}; + +RigibBodyModelingForm.prototype.getPanel = function() { + var _this = this; + this.panel = Ext.create('Ext.form.Panel', { + width : this.width, + height : this.height, + margin : 10, + border : 1, + defaultType : 'textfield', + items : this._getItems(), + buttons : this._getButtons(), + listeners : { + afterrender : function(){ + _this._populate(); + + } + } + }); + return this.panel; +}; + +/** Populates could be call when the DOM is not filled yet **/ +RigibBodyModelingForm.prototype._populate = function() { + if (this.macromolecule != null){ + if (Ext.getCmp(this.id + "contactsDescriptionFilePath") != null){ + if (this.macromolecule.contactsDescriptionFilePath != null){ + Ext.getCmp(this.id + "contactsDescriptionFilePath").setValue(this.macromolecule.contactsDescriptionFilePath); + Ext.getCmp(this.id + "_remove").enable(); + } + else{ + Ext.getCmp(this.id + "_remove").disable(); + Ext.getCmp(this.id + "contactsDescriptionFilePath").setValue(""); + + } + } + } +}; + +/** It populates the form * */ +RigibBodyModelingForm.prototype.refresh = function(macromolecule) { + this.macromolecule = macromolecule; + this.rigidBodyGrid.refresh(macromolecule); + this._populate(); +}; + +RigibBodyModelingForm.prototype.input = function() { + return {}; +}; + + +/** It populates the form **/ +RigibBodyModelingForm.prototype.test = function(targetId) { + var macromoleculeForm = new RigibBodyModelingForm(); + var panel = macromoleculeForm.getPanel(); + panel.render(targetId); +}; + + +/** + * Same form as MX part * - * #onClick #onSelected #onRemoved #onUpdateTime #onMeasurementChanged - * #onExperimentChanged + * @creationMode if true a create button appears instead of save + * @showTitle true or false */ -function MeasurementGrid(args) { +function ShipmentForm(args) { this.id = BUI.id(); - this.height = 500; - this.width = 900; - - this.maxWidth = 1200; - this.maxHeight = 600; - this.minHeight = 500; - - this.unitsFontSize = 9; - this.title = "Measurements"; - this.estimateTime = false; - this.collapsed = true; - this.tbar = true; - + this.creationMode = false; this.showTitle = true; - this.resizable = true; - this.updateRowEnabled = true; - - /** - * Hash map containing the keys of the editable columns. Ex: - * 'exposureTemperature' * - */ - this.editor = { - comments : { - xtype : 'textfield', - allowBlank : true + if (args != null) { + if (args.creationMode != null) { + this.creationMode = args.creationMode; } - }; + if (args.showTitle != null) { + this.showTitle = args.showTitle; + } + } - this.isTimeColumnHidden = false; - this.isStatusColumnHidden = false; - this.isPriorityColumnHidden = true; - this.margin = "0 0 0 0"; + this.onSaved = new Event(this); +} - this.addBtnEnable = true; - this.sorter = [ { - property : 'priority', - direction : 'ASC' - } ]; +ShipmentForm.prototype.fillStores = function() { + this.panel.setLoading("Loading Labcontacts from database"); + this.labContactForSendingStore.loadData(BIOSAXS.proposal.getLabcontacts(), false); + this.labContactForReturnStore.loadData(BIOSAXS.proposal.getLabcontacts(), false); + this.panel.setLoading(false); + if (this.shipment != null) { + this.setShipment(this.shipment); + } +}; - this.removeBtnEnabled = false; - this.collapseBtnEnable = true; - this.addBtnMultipleEdit = false; - this.sortingBtnEnable = false; +ShipmentForm.prototype.draw = function(targetId) { + this.getPanel().render(targetId); +}; +ShipmentForm.prototype.setShipment = function(shipment) { + this.shipment = shipment; var _this = this; - this.selModel = Ext.create('Ext.selection.RowModel', { - allowDeselect : true, - mode : 'MULTI', - listeners : { - selectionchange : function(sm, selections) { - var selected = []; - for (var i = 0; i < selections.length; i++) { - selected.push(selections[i].raw); - } - _this.onSelected.notify(selected); - } - } - }); - - if (args != null) { - - if (args.selModel != null) { - this.selModel = args.selModel; - } + Ext.getCmp(_this.id + "shippingName").setValue(shipment.json.shippingName); + Ext.getCmp(_this.id + "shippingStatus").setValue(shipment.json.shippingStatus); + Ext.getCmp(_this.id + "comments").setValue(shipment.json.comments); + if (shipment.json.sendingLabContactVO != null) { + this.labContactsSendingCombo.setValue(shipment.json.sendingLabContactVO.labContactId); + } + if (shipment.json.returnLabContactVO != null) { + this.labContactsReturnCombo.setValue(shipment.json.returnLabContactVO.labContactId); + } - if (args.removeBtnEnabled != null) { - this.removeBtnEnabled = args.removeBtnEnabled; - } +}; - if (args.addBtnMultipleEdit != null) { - this.addBtnMultipleEdit = args.addBtnMultipleEdit; - } +ShipmentForm.prototype._saveShipment = function() { + var _this = this; + var shippingId = null; + if (this.shipment != null) { + shippingId = this.shipment.json.shippingId; + } + var json = { + shippingId : shippingId, + name : Ext.getCmp(_this.id + "shippingName").getValue(), + status : Ext.getCmp(_this.id + "shippingStatus").getValue(), + sendingLabContactId : Ext.getCmp(_this.id + "shipmentform_sendingLabContactId").getValue(), + returnLabContactId : Ext.getCmp(_this.id + "returnLabContactId").getValue(), + returnCourier : Ext.getCmp(_this.id + "returnCourier").getValue(), + courierAccount : Ext.getCmp(_this.id + "courierAccount").getValue(), + BillingReference : Ext.getCmp(_this.id + "BillingReference").getValue(), + dewarAvgCustomsValue : Ext.getCmp(_this.id + "dewarAvgCustomsValue").getValue(), + dewarAvgTransportValue : Ext.getCmp(_this.id + "dewarAvgTransportValue").getValue(), + comments : Ext.getCmp(_this.id + "comments").getValue() + }; - // if (args.experimentColorBased != null) { - // this.experimentColorBased = args.experimentColorBased; - // } + var dataAdapter = new BiosaxsDataAdapter(); + dataAdapter.onSuccess.attach(function(sender, shipment) { + window.location = BUI.getShippingURL(shipment.shippingId); + }); - if (args.collapsed != null) { - this.collapsed = args.collapsed; - } - if (args.resizable != null) { - this.resizable = args.resizable; - } + dataAdapter.onError.attach(function(sender, error) { + _this.onError.notify(error); + }); - if (args.editor != null) { - this.editor = args.editor; - } + /** Cheking params **/ + if (json.name == "") { + BUI.showError("Name field is mandatory"); + return; + } - if (args.collapseBtnEnable != null) { - this.collapseBtnEnable = args.collapseBtnEnable; - } + if (json.sendingLabContactId == null) { + BUI.showError("Lab contact for sending field is mandatory"); + return; + } - if (args.addBtnEnable != null) { - this.addBtnEnable = args.addBtnEnable; - } - if (args.sortingBtnEnable != null) { - this.sortingBtnEnable = args.sortingBtnEnable; - } + if (json.returnLabContactId == null) { + BUI.showError("Lab contact for return field is mandatory"); + return; + } - if (args.isPriorityColumnHidden != null) { - this.isPriorityColumnHidden = args.isPriorityColumnHidden; - } + dataAdapter.createShipment(json.shippingId, json.name, json.status, json.comments, json.sendingLabContactId, json.returnLabContactId, + json.returnCourier, json.courierAccount, json.BillingReference, json.dewarAvgCustomsValue, json.dewarAvgTransportValue); - if (args.width != null) { - this.width = args.width; - } +}; - if (args.updateRowEnabled != null) { - this.updateRowEnabled = args.updateRowEnabled; - } +ShipmentForm.prototype.getPanel = function(shipment) { + var _this = this; + this.shipment = shipment; + var required = '*'; + var buttons = []; - if (args.showTitle != null) { - this.showTitle = args.showTitle; - if (this.showTitle == false) { - this.title = null; + if (_this.creationMode) { + buttons.push({ + text : 'Create', + scope : this, + handler : function() { + _this._saveShipment(); } - } - - if (args.height != null) { - this.height = args.height; - } - - if (args.maxHeight != null) { - this.maxHeight = args.maxHeight; - } - - if (args.minHeight != null) { - this.minHeight = args.minHeight; - } + }); + } else { + buttons.push({ + text : 'Save', + scope : this, + handler : function() { + _this._saveShipment(); + } + }); - if (args.maxWidth != null) { - this.maxWidth = args.maxWidth; - } + } - if (args.isStatusColumnHidden != null) { - this.isStatusColumnHidden = args.isStatusColumnHidden; - } - if (args.isTimeColumnHidden != null) { - this.isTimeColumnHidden = args.isTimeColumnHidden; - } + this.labContactForSendingStore = Ext.create('Ext.data.Store', { + fields : [ 'cardName', 'labContactId' ] + }); - if (args.title != null) { - this.title = args.title; - } - if (args.estimateTime != null) { - this.estimateTime = args.estimateTime; - } + this.labContactForReturnStore = Ext.create('Ext.data.Store', { + fields : [ 'cardName', 'labContactId' ] + }); - if (args.margin != null) { - this.margin = args.margin; - } + // Create the combo box, attached to the states data store + this.labContactsSendingCombo = Ext.create('Ext.form.ComboBox', { + id : _this.id + "shipmentform_sendingLabContactId", + fieldLabel : 'Lab contact for sending', + afterLabelTextTpl : required, + store : this.labContactForSendingStore, + queryMode : 'local', + labelWidth : 200, + displayField : 'cardName', + valueField : 'labContactId' + }); - if (args.tbar != null) { - this.tbar = args.tbar; + this.labContactsReturnCombo = Ext.create('Ext.form.ComboBox', { + id : _this.id + "returnLabContactId", + fieldLabel : 'If No, Lab-Contact for Return', + afterLabelTextTpl : required, + store : this.labContactForReturnStore, + queryMode : 'local', + labelWidth : 200, + displayField : 'cardName', + valueField : 'labContactId', + listeners : { + change : function(x, newValue) { + for ( var i = 0; i < x.getStore().data.items.length; i++) { + if (x.getStore().data.items[i].raw.labContactId == newValue) { + Ext.getCmp(_this.id + "returnCourier").setValue(x.getStore().data.items[i].raw.defaultCourrierCompany); + Ext.getCmp(_this.id + "courierAccount").setValue(x.getStore().data.items[i].raw.courierAccount); + Ext.getCmp(_this.id + "BillingReference").setValue(x.getStore().data.items[i].raw.billingReference); + Ext.getCmp(_this.id + "dewarAvgCustomsValue").setValue(x.getStore().data.items[i].raw.dewarAvgCustomsValue); + Ext.getCmp(_this.id + "dewarAvgTransportValue").setValue(x.getStore().data.items[i].raw.dewarAvgTransportValue); + } + } + } } + }); - if (args.sorter != null) { - this.sorter = args.sorter; - } + if (this.panel == null) { + this.panel = Ext.create('Ext.form.Panel', { + bodyPadding : 5, + width : 600, + border : 1, + items : [ { + xtype : 'fieldset', + title : 'Details', + collapsible : false, + defaultType : 'textfield', + layout : 'anchor', + defaults : { + anchor : '100%' + }, + items : [ { + xtype : 'requiredtext', + fieldLabel : 'Shipment Label', + allowBlank : false, + name : 'shippingName', + id : _this.id + 'shippingName', + value : '', + anchor : '50%' + }, { + xtype : 'textareafield', + name : 'comments', + id : _this.id + 'comments', + fieldLabel : 'Comments', + value : '' + }, { + fieldLabel : 'Status', + readOnly : true, + id : _this.id + 'shippingStatus', + value : 'Opened', + anchor : '50%' + } ] + }, { + xtype : 'fieldset', + title : 'Lab-Contacts', + collapsible : false, + defaultType : 'textfield', + layout : 'anchor', + defaults : { + anchor : '100%' + }, + items : [ this.labContactsSendingCombo, this.labContactsReturnCombo ] + }, { + border : 0, + html : BUI.getWarningHTML("These informations are relevant for all shipments") + }, { + xtype : 'fieldset', + title : 'Courier accounts details for return', + collapsible : false, + layout : 'anchor', + defaults : { + anchor : '100%' + }, + items : [ { + xtype : 'textfield', + labelWidth : 400, + fieldLabel : 'Courier company for return (if ESRF sends a dewar back)', + id : _this.id + 'returnCourier', + value : '' + }, { + xtype : 'textfield', + labelWidth : 400, + fieldLabel : 'Courier account', + id : _this.id + 'courierAccount', + value : '' + }, { + xtype : 'textfield', + labelWidth : 400, + fieldLabel : 'Billing reference', + id : _this.id + 'BillingReference', + value : '' + }, { + xtype : 'numberfield', + labelWidth : 400, + fieldLabel : 'Average Customs value of a dewar (Euro)', + id : _this.id + 'dewarAvgCustomsValue', + value : '' + }, { + xtype : 'numberfield', + labelWidth : 400, + fieldLabel : 'Average Transport value of a dewar (Euro)', + id : _this.id + 'dewarAvgTransportValue', + value : '' + } ] + } ], + buttons : buttons + }); } - this.onClick = new Event(this); - this.onSelected = new Event(this); - this.onRemoved = new Event(this); - this.onUpdateTime = new Event(this); - this.onMeasurementChanged = new Event(this); - this.onExperimentChanged = new Event(this); -} - -MeasurementGrid.prototype._sortBy = function(sort) { - var _this = this; - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - _this.onExperimentChanged.notify(data); - _this.grid.setLoading(false); - // wizardWidget.window.close(); - }); - adapter.onError.attach(function(sender, data) { - _this.grid.setLoading(false); - alert("Oops, there was a problem"); - }); - _this.grid.setLoading("Sorting"); - adapter.sortMeasurements(this.experiments.experiments[0].experimentId, sort); + this.fillStores(); + if (this.showTitle) { + this.panel.setTitle('Create a new Shipment'); + } + return this.panel; }; -MeasurementGrid.prototype._getMenu = function() { - var _this = this; - if (this.tbar) { +ShipmentForm.prototype.input = function() { + return { + proposal : DATADOC.getProposal_10() - var items = []; - if (_this.addBtnEnable) { - items.push({ - icon : '../images/add.png', - text : 'Add measurements', - handler : function() { - _this._openAddMeasurementWindow(); - } - }); - } + }; +}; - if (_this.addBtnMultipleEdit) { - items.push({ - icon : '../images/Edit_16x16_01.png', - text : 'Multiple Edit', - handler : function() { - var multipleEditMeasurementGridWindow = new MultipleEditMeasurementGridWindow(); - multipleEditMeasurementGridWindow.onExperimentChanged.attach(function(sender, data) { - _this.onExperimentChanged.notify(data); - }); +ShipmentForm.prototype.test = function(targetId) { + var shipmentForm = new ShipmentForm({ + creationMode : true - multipleEditMeasurementGridWindow.draw(_this.measurements, _this.experiments); + }); + BIOSAXS.proposal = new Proposal(shipmentForm.input().proposal); + shipmentForm.getPanel().render(targetId); +}; + +/** + * #onSaved + */ +function StockSolutionForm(args) { + this.id = BUI.id(); + this.actions = []; - } - }); + if (args != null) { + if (args.actions != null) { + this.actions = args.actions; } + } + this.onSaved = new Event(this); +} - items.push("->"); +StockSolutionForm.prototype.getStockSolution = function() { + if (this.stockSolution != null) { + this.stockSolution.concentration = Ext.getCmp(this.id + "stockSolution_concentration").getValue(); + this.stockSolution.storageTemperature = Ext.getCmp(this.id + "stockSolution_storageTemperature").getValue(); + this.stockSolution.volume = Ext.getCmp(this.id + "stockSolution_volume").getValue(); + this.stockSolution.comments = Ext.getCmp(this.id + "stockSolution_comments").getValue(); + this.stockSolution.name = Ext.getCmp(this.id + "stockSolution_name").getValue(); + this.stockSolution.bufferId = this.bufferCombo.getValue(); - if (_this.sortingBtnEnable) { - var split = Ext.create('Ext.button.Split', { - text : 'Sort by', - // handle a click on the button itself - handler : function() { - // alert("The button was clicked"); - }, - menu : new Ext.menu.Menu({ - items : [ - { - text : 'First Created First Measured', - handler : function() { - _this._sortBy("FIFO"); - } - }, "-", { - text : 'Default', - handler : function() { - _this._sortBy("DEFAULT"); - } - } ] - }) - }); - items.push(split); + if (this.macromoleculeCombo.getValue() != null) { + this.stockSolution.macromoleculeId = this.macromoleculeCombo.getValue(); + } else { + this.stockSolution.macromolecule3VO = null; } - if (_this.collapseBtnEnable) { - items.push({ - text : 'Collapse buffers', - enableToggle : true, - scope : this, - toggleHandler : function(item, pressed) { - this.collapsed = pressed; - this.grid.getStore().loadData(this._prepareData(this.measurements, this.experiments), false); - }, - pressed : this.collapsed - }); + } else { + return { + concentration : Ext.getCmp(this.id + "stockSolution_concentration").getValue(), + storageTemperature : Ext.getCmp(this.id + "stockSolution_storageTemperature").getValue(), + volume : Ext.getCmp(this.id + "stockSolution_volume").getValue(), + comments : Ext.getCmp(this.id + "stockSolution_comments").getValue(), + name : Ext.getCmp(this.id + "stockSolution_name").getValue(), + bufferId : this.bufferCombo.getValue(), + macromoleculeId : this.macromoleculeCombo.getValue() + }; + } + return this.stockSolution; +}; + +StockSolutionForm.prototype.setStockSolution = function(stockSolution) { + if (stockSolution != null) { + if (stockSolution.macromoleculeId != null) { + this.macromoleculeCombo.setValue(stockSolution.macromoleculeId); } - var tb = Ext.create('Ext.toolbar.Toolbar', { - items : items - }); - return tb; + this.bufferCombo.setValue(stockSolution.bufferId); + Ext.getCmp(this.id + "stockSolution_concentration").setValue(this.stockSolution.concentration); + Ext.getCmp(this.id + "stockSolution_storageTemperature").setValue(this.stockSolution.storageTemperature); + Ext.getCmp(this.id + "stockSolution_volume").setValue(this.stockSolution.volume); + Ext.getCmp(this.id + "stockSolution_name").setValue(this.stockSolution.name); + Ext.getCmp(this.id + "stockSolution_comments").setValue(this.stockSolution.comments); } - return null; }; -/** Opens WizardWidget for adding new measurements * */ -MeasurementGrid.prototype._openAddMeasurementWindow = function(measurements, experiments) { - var _this = this; - var wizardWidget = new WizardWidget(); - wizardWidget.onFinished.attach(function(sender, result) { - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - _this.onExperimentChanged.notify(data); - _this.grid.setLoading(false); - wizardWidget.window.close(); - }); - wizardWidget.current.setLoading("ISPyB: Adding measurements"); - adapter.addMeasurements(result.name, "comments", result.data, _this.experiments.experiments[0].experimentId); +StockSolutionForm.prototype.getBufferCombo = function() { + this.bufferCombo = BIOSAXS_COMBOMANAGER.getComboBuffers(BIOSAXS.proposal.getBuffers(), { + labelWidth : 120, + margin : '0 0 10 0', + width : 220 + }); + return this.bufferCombo; +}; - wizardWidget.draw(null, new MeasurementCreatorStepWizardForm(BIOSAXS.proposal.getMacromolecules(), { - noNext : true - })); +StockSolutionForm.prototype.getMacromoleculeCombo = function() { + this.macromoleculeCombo = BIOSAXS_COMBOMANAGER.getComboMacromoleculeByMacromolecules(BIOSAXS.proposal.getMacromolecules(), { + labelWidth : 120, + margin : '0 0 10 0', + width : 220 + + }); + return this.macromoleculeCombo; }; -/******************************************************************************* - * Opens WizardWidget for adding new measurements - * - * @Measurements - * @Experiments experimentList Object - ******************************************************************************/ -MeasurementGrid.prototype._prepareData = function(measurements, experiments) { - var data = []; - for (var i = 0; i < measurements.length; i++) { - var measurement = measurements[i]; - var specimen = experiments.getSampleById(measurement.specimenId); - var buffer = experiments.getBufferById(specimen.bufferId); - measurement.buffer_acronym = buffer.acronym; - measurement.bufferId = buffer.bufferId; - measurement.volume = specimen.volume; - if (specimen.macromolecule3VO != null) { - measurement.acronym = specimen.macromolecule3VO.acronym; - measurement.macromoleculeId = specimen.macromolecule3VO.macromoleculeId; - } - measurement.concentration = specimen.concentration; - if (measurement.run3VO != null) { - measurement.energy = measurement.run3VO.energy; - measurement.expExposureTemperature = measurement.run3VO.exposureTemperature; - measurement.storageTemperature = measurement.run3VO.storageTemperature; - measurement.timePerFrame = measurement.run3VO.timePerFrame; - measurement.radiationAbsolute = measurement.run3VO.radiationAbsolute; - measurement.radiationRelative = measurement.run3VO.radiationRelative; - measurement.status = "DONE"; +StockSolutionForm.prototype.refresh = function() { +}; - try { - if (measurement.run3VO.timeStart != null) { - if (measurement.run3VO.timeStart != "") { - measurement.miliseconds = moment(measurement.run3VO.timeStart).format("X"); - } - } - } catch (E) { - console.log(E); - } - } +StockSolutionForm.prototype._getTopPanel = function() { + return { + xtype : 'container', + layout : 'hbox', + border : 0, + items : [ { + xtype : 'container', + layout : 'hbox', + items : [ { + xtype : 'container', + flex : 1, + border : false, + layout : 'anchor', + defaultType : 'textfield', + items : [ - if (experiments.getDataCollectionByMeasurementId(measurement.measurementId).length > 0) { - var measurementtodatacollection3VOs = experiments.getDataCollectionByMeasurementId(measurement.measurementId)[0].measurementtodatacollection3VOs; - for (var k = 0; k < measurementtodatacollection3VOs.length; k++) { - if (measurementtodatacollection3VOs[k].dataCollectionOrder == 1) { - var specimenBuffer = experiments.getSampleById(experiments.getMeasurementById(measurementtodatacollection3VOs[k].measurementId).specimenId); - if (specimenBuffer.sampleplateposition3VO != null) { - measurement.bufferSampleplateposition3VO = specimenBuffer.sampleplateposition3VO; - measurement.bufferSampleplate = (experiments.getSamplePlateById(specimenBuffer.sampleplateposition3VO.samplePlateId)); - } - } - } - } + this.getMacromoleculeCombo(), { + xtype : 'requiredtext', + id : this.id + 'stockSolution_name', + fieldLabel : 'Acronym', + labelWidth : 120, + width : 250 + }, { + xtype : 'requiredtext', + id : this.id + 'stockSolution_concentration', + fieldLabel : 'Conc. (mg/ml)', + labelWidth : 120, + width : 250 + }, - if (this.collapsed) { - /** If collapsed only the samples * */ - if (specimen.macromolecule3VO != null) { - data.push(measurement); - } - } else { - data.push(measurement); - } + { + id : this.id + 'stockSolution_storageTemperature', + fieldLabel : 'Storage Temp.(C)', + labelWidth : 120, + width : 250 + }, { + xtype : 'requiredtext', + id : this.id + 'stockSolution_volume', + fieldLabel : 'Volume in Well (µl)', + labelWidth : 120, + width : 250 + } ] + } ] + }, { + xtype : 'container', + flex : 1, + layout : 'anchor', + defaultType : 'textfield', + margin : '0 0 0 10', + items : [ this.getBufferCombo() ] + } ] + }; - } - return data; }; -/** - * Refresh data grid with the measurements and the experiments - * - * @measurements array with measurement3VO objects - * @experiments array with experiments objects - */ -MeasurementGrid.prototype.refresh = function(measurements, experiments) { - this.experiments = experiments; - this.measurements = measurements; - this.store.loadData(this._prepareData(measurements, experiments), false); +StockSolutionForm.prototype.getPanel = function(stockSolution) { + this.stockSolution = stockSolution; + this.panel = Ext.createWidget({ + xtype : 'container', + layout : 'vbox', + border : 0, + style : { + padding : '10px' + }, + fieldDefaults : { + labelAlign : 'left', + labelWidth : 50 + }, + items : [ this._getTopPanel(stockSolution), { + id : this.id + 'stockSolution_comments', + xtype : 'textareafield', + name : 'comments', + fieldLabel : 'Comments', + labelWidth : 120, + width : '100%' + } ] + }); + + this.setStockSolution(stockSolution); + return this.panel; +}; + +StockSolutionForm.prototype.input = function() { + return { + stock : { + "stockSolutionId" : 6, + "proposalId" : 3124, + "macromoleculeId" : 5933, + "bufferId" : 811, + "instructionSet3VO" : null, + "boxId" : 305861, + "storageTemperature" : "20", + "volume" : "300", + "concentration" : "1.2", + "comments" : "Buffer EDTA with A", + "name" : "A_EDTA_1.2", + "samples" : [], + "buffer" : "EDTA", + "macromolecule" : "A" + }, + proposal : new MeasurementGrid().input().proposal + }; +}; + +StockSolutionForm.prototype.test = function(targetId) { + var stockSolutionForm = new StockSolutionForm(); + BIOSAXS.proposal = new Proposal(stockSolutionForm.input().proposal); + var panel = stockSolutionForm.getPanel(new Shipment(stockSolutionForm.input().stock)); + panel.render(targetId); }; + + +BoxWhiskerGraph.prototype.cleanArray = GenericGraph.prototype.cleanArray; +BoxWhiskerGraph.prototype.plotAxes = GenericGraph.prototype.plotAxes; +BoxWhiskerGraph.prototype.plotRuler = GenericGraph.prototype.plotRuler; +BoxWhiskerGraph.prototype.drawSVGVerticalText = GenericGraph.prototype.drawSVGVerticalText; +BoxWhiskerGraph.prototype.getClassColor = GenericGraph.prototype.getClassColor; +BoxWhiskerGraph.prototype.getDimensions = GenericGraph.prototype.getDimensions; +BoxWhiskerGraph.prototype.calculate = GenericGraph.prototype.calculate; +BoxWhiskerGraph.prototype.getMedian = GenericGraph.prototype.getMedian; +BoxWhiskerGraph.prototype.pointToPixel = GenericGraph.prototype.pointToPixel; +BoxWhiskerGraph.prototype.maxValueWhisker = GenericGraph.prototype.maxValueWhisker; +BoxWhiskerGraph.prototype.refresh = GenericGraph.prototype.refresh; /** - * Set status bar to busy (refreshing icon) + * Subclass of GenericGraph * - * @msg message to be displayed on the bar + * @maxBoxWidth */ -MeasurementGrid.prototype._showStatusBarBusy = function(msg) { - var statusBar = Ext.getCmp(this.id + 'basic-statusbar'); - statusBar.setStatus({ - text : msg, - iconCls : 'x-status-busy', - clear : false - }); +function BoxWhiskerGraph(args){ + this.maxBoxWidth = 25; + + if (args == null){ + args = new Object(); + } + args["plotHorizontalByCluster"] = true; + + GenericGraph.call(this, args); + + if (args.maxBoxWidth != null){ + this.maxBoxWidth = args.maxBoxWidth; + } }; + + /** - * Set status bar to ready (ok icon) - * - * @msg message to be displayed on the bar - */ -MeasurementGrid.prototype._showStatusBarReady = function(msg) { - var statusBar = Ext.getCmp(this.id + 'basic-statusbar'); - statusBar.setStatus({ - text : msg, - iconCls : 'x-status-valid', - clear : false - }); +There are several different methods for calculating quartiles.[1] This calculator uses a method described by Moore and McCabe to find quartile values. +The same method also used by The TI-83 to calculate quartile values. +With this method, the first quartile is the median of the numbers below the median, the third quartile is the median of the numbers above the median. + +http://www.miniwebtool.com/quartile-calculator/ +http://www.alcula.com/calculators/statistics/box-plot/ +**/ +BoxWhiskerGraph.prototype.getQ1 = function(array){ + array = array.slice(0, array.length/2); + return this.getMedian(array); }; -/** - * If updateRowEnabled returns an array with Ext.grid.plugin.RowEditing - */ -MeasurementGrid.prototype._getPlugins = function() { - var _this = this; - var plugins = []; - if (this.updateRowEnabled) { - plugins.push(Ext.create('Ext.grid.plugin.RowEditing', { - clicksToEdit : 1, - listeners : { - validateedit : function(grid, e) { - /** Setting values * */ - for ( var key in _this.editor) { - e.record.raw[key] = e.newValues[key]; - } - /** Comments are always updatable* */ - e.record.raw.comments = e.newValues.comments; +BoxWhiskerGraph.prototype.getQ3 = function(array){ + array = array.slice((array.length + 1)/2); + return this.getMedian(array); + +}; - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, measurement) { - _this.onMeasurementChanged.notify(measurement); - _this.grid.setLoading(false); - }); - adapter.onError.attach(function() { - alert("Error"); - _this.grid.setLoading(false); - }); +BoxWhiskerGraph.prototype.getQ2 = function(array){ + return this.getMedian(array); +}; - _this.grid.setLoading(); - adapter.saveMeasurement(e.record.raw, _this.experiments.experiments[0]); - } - } - })); +BoxWhiskerGraph.prototype.getBelowOutliers = function(belowLimit, array){ + var points = new Array(); + for (var i = 0; i < array.length; i++){ + if (array[i] <= belowLimit){ + points.push(array[i]); + } } - return plugins; + return points; }; -/** - * @key name of the columns mathing the this.editor[key] - */ -MeasurementGrid.prototype._getEditor = function(key) { - if (this.editor[key] != null) { - return this.editor[key]; +BoxWhiskerGraph.prototype.getAboveOutliers = function(aboveLimit, array){ + var points = new Array(); + for (var i = 0; i < array.length; i++){ + if (array[i] >= aboveLimit){ + points.push(array[i]); + } } - return null; + return points; }; -MeasurementGrid.prototype.getPanel = function(measurements, experiments) { - this.experiments = experiments; - this.measurements = measurements; - var _this = this; - this.store = Ext.create('Ext.data.Store', { - fields : [ { - name : 'miliseconds', - type : 'int' - }, 'priority', 'bufferId', { - name : 'exposureTemperature', - type : 'numeric' - }, 'volumeToLoad','code', 'transmission', 'viscosity', 'waitTime', 'flow', 'buffer_acronym', 'macromoleculeId', 'acronym', 'concentration', 'extraFlowTime', 'volume', 'energy', - 'expExposureTemperature', 'storageTemperature', 'timePerFrame', 'radiationAbsolute', 'radiationRelative', 'status', 'comments' ], - data : this._prepareData(measurements, experiments) - }); - this.store.sort(this.sorter); - var bbar = {}; - try { - bbar = Ext.create('Ext.ux.StatusBar', { - id : _this.id + 'basic-statusbar', - defaultText : 'Ready', - text : 'Ready', - iconCls : 'x-status-valid', - items : [] - }); - } catch (exp) { - console.log("bbar error"); + +BoxWhiskerGraph.prototype.minValueWhisker = function(belowLimit, q1, array){ + var points = new Array(); + + for (var i = 0; i < array.length; i++){ + if ((array[i] < q1) && (array[i]) > belowLimit){ + points.push(array[i]); + } + } + + if (points.length > 0){ + points.sort(function(a, b){return a - b;}); + return points[0]; } + return null; +}; - this.grid = Ext - .create( - 'Ext.grid.Panel', - { - id : this.id, - title : this.title, - store : this.store, - selModel : this.selModel, - plugins : this._getPlugins(), - resizable : this.resizable, - margin : this.margin, - maxHeight : this.maxHeight, - minHeight : this.minHeight, - maxWidth : this.maxWidth, - width : this.width, - tbar : this._getMenu(), - columns : [ - { - text : 'Order', - dataIndex : 'priority', - width : 50, - hidden : _this.isPriorityColumnHidden, - sortable : true +BoxWhiskerGraph.prototype.isNumber = function(value){ + if (value=="") return false; - }, - { - text : 'Run Number', - dataIndex : 'code', - width : 50, - hidden : true, - sortable : true + var d = parseInt(value); + if (!isNaN(d)) return true; else return false; - }, +}; - { - text : 'Specimen', - columns : [ +BoxWhiskerGraph.prototype.plotBoxWhisker = function(boxProperties){ + if (this.maxBoxWidth != null){ + if (boxProperties.width > this.maxBoxWidth){ + boxProperties.x = boxProperties.x + (boxProperties.width/2) - (this.maxBoxWidth/2); + boxProperties.width = this.maxBoxWidth; + } + + } - { - text : '', - dataIndex : 'macromoleculeId', - width : 30, - renderer : function(val, y, sample) { - if (val != null) { - if (_this.experiments == null) { - return BUI.getRectangleColorDIV(BIOSAXS.proposal.macromoleculeColors[val], 10, 10); - } else { - return BUI.getRectangleColorDIV(_this.experiments.macromoleculeColors[val], 10, 10); - } - } - }, - sortable : true - }, - { - text : 'Macromo.', - dataIndex : 'acronym', - width : 80, - renderer : function(val, y, sample) { - return val; - }, - sortable : true - }, - { - text : 'Conc. ', - dataIndex : 'concentration', - width : 80, - renderer : function(val, y, sample) { - if (sample.raw.macromoleculeId == null) { - return ""; - } - if (isNaN(val)) - return val; + if (this.plotPoints){ + for(var i = 0; i < boxProperties.values.length; i++){ + var value = boxProperties.values[i]; + var toPixel = this.pointToPixel(value, boxProperties); + SVG.drawCircle(boxProperties.x + (boxProperties.width/2) + 2, toPixel, this.pointRadius, this.svg, [["fill", "green"], ["fill-opacity", this.fillOpacityPoint],['stroke-opacity', this.strokeOpacityPoint], ["stroke", "black"]]); + } + } + - if (val != 0) { - return BUI.formatValuesUnits(val, '', { - fontSize : 16, - decimals : 3, - unitsFontSize : this.unitsFontSize - }); - } else { - return; - } + var boxColor = this.getClassColor(boxProperties.name); + var result = this.calculate(boxProperties.values); + /** Q1 **/ + + if (this.isNumber(result.Q1)){ + SVG.drawLine(boxProperties.x, this.pointToPixel(result.Q1, boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result.Q1, boxProperties), this.svg, [["stroke", boxColor]]); + } + /** Q2 **/ + if (this.isNumber(result.Q2)){ + SVG.drawLine(boxProperties.x, this.pointToPixel(result.Q2, boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result.Q2, boxProperties), this.svg, [["stroke", "blue"], ["stroke-width", "2"]]); + } + + /** Q3 **/ + if (this.isNumber(result.Q3)){ + SVG.drawLine(boxProperties.x, this.pointToPixel(result.Q3, boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result.Q3, boxProperties), this.svg, [["stroke", boxColor]]); + } + + /** Concenting Q1 and Q3 **/ + if (this.isNumber(result.Q1)&&this.isNumber(result.Q3)){ + SVG.drawLine(boxProperties.x, this.pointToPixel(result.Q1, boxProperties), boxProperties.x, this.pointToPixel(result.Q3, boxProperties), this.svg, [["stroke", boxColor]]); + SVG.drawLine(boxProperties.x + boxProperties.width, this.pointToPixel(result.Q1, boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result.Q3, boxProperties), this.svg, [["stroke", boxColor]]); + } + + /** min-whisker **/ + if (result["min-whisker"] != null){ + if (this.isNumber(result.Q1)){ + SVG.drawLine(boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result.Q1, boxProperties), boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result["min-whisker"], boxProperties), this.svg, [["stroke", boxColor]]); + } + SVG.drawLine(boxProperties.x,this.pointToPixel(result["min-whisker"], boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result["min-whisker"], boxProperties) , this.svg, [["stroke", boxColor]]); + + } + + /** max-whisker **/ + if (result["max-whisker"] != null){ + if (this.isNumber(result.Q3)){ + SVG.drawLine(boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result.Q3, boxProperties), boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result["max-whisker"], boxProperties), this.svg, [["stroke", boxColor]]); + } + SVG.drawLine(boxProperties.x , this.pointToPixel(result["max-whisker"], boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result["max-whisker"], boxProperties), this.svg, [["stroke", boxColor]]); + + } + + /** outliners **/ + if (result["above-outliers"] != null){ + for (var point in result["above-outliers"]){ + SVG.drawCircle(boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result["above-outliers"][point], boxProperties), this.pointRadius, this.svg, [["fill", "red"], ["fill-opacity", "1"]]); + //SVG.drawText(boxProperties.x + (boxProperties.width/2) - 2, this.pointToPixel(result["above-outliers"][point], boxProperties) + 2, "x",this.svg, [["fill", "black"], ["font-size", "x-small"]]); + } + } + if (result["below-outliers"] != null){ + for (var point in result["below-outliers"]){ + SVG.drawCircle(boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result["below-outliers"][point], boxProperties), this.pointRadius, this.svg, [["fill", "red"], ["fill-opacity", "1"]]); + //SVG.drawText(boxProperties.x + (boxProperties.width/2) - 2, this.pointToPixel(result["below-outliers"][point], boxProperties) + 2, "x",this.svg, [["fill", "black"], ["font-size", "x-small"]]); + } + } +}; - }, - sortable : true - }, - { - text : '', - dataIndex : 'bufferId', - width : 30, - hidden : false, - renderer : function(val, y, sample) { - if (val != null) { - var color = '#FFCCFF'; - if (_this.experiments != null) { - var dc = _this.experiments.getDataCollectionByMeasurementId(sample.raw.measurementId); - if (dc != null) { - if (dc.length > 0) { - color = _this.experiments.getSpecimenColorByBufferId(_this.experiments - .getMeasurementById(dc[0].measurementtodatacollection3VOs[0].measurementId).specimenId); - } - } - } else { - color = BIOSAXS.proposal.bufferColors[val]; - } - return BUI.getRectangleColorDIV(color, 10, 10); - } - }, - sortable : true - }, - { - text : 'Buffer', - dataIndex : 'buffer_acronym', - width : 120, - renderer : function(val, y, sample) { - if (sample.raw.bufferSampleplateposition3VO != null) { - return BIOSAXS.proposal.getBufferById(sample.raw.bufferId).acronym + " Plate: [" - + sample.raw.bufferSampleplate.slotPositionColumn + ", " - + BUI.getSamplePlateLetters()[sample.raw.bufferSampleplateposition3VO.rowNumber - 1] + "-" - + sample.raw.bufferSampleplateposition3VO.columnNumber + "]"; - } - return val; - }, - sortable : true - }, { - text : 'Position', - width : 100, - hidden : true, - renderer : function(val, y, sample) { - if (_this.experiments != null) { - return BUI.getSamplePositionHTML(_this.experiments.getSampleById(sample.raw.specimenId), _this.experiments.experiments[0]); - } - } - } ] - }, - { - text : 'Parameters', - columns : [ - { - text : 'Ex. Flow. time (s)', - dataIndex : 'extraFlowTime', - width : 100, - hidden : true, - renderer : function(val, y, sample) { - return BUI.formatValuesUnits(val, 's', { - fontSize : 12, - decimals : 0, - unitsFontSize : this.unitsFontSize - }); - } - }, - { - text : 'Exp. Temp.', - dataIndex : 'exposureTemperature', - width : 70, - renderer : function(val, y, sample) { - if (Number(val)) { - return BUI.formatValuesUnits(val, 'C', { - fontSize : 12, - decimals : 2, - unitsFontSize : this.unitsFontSize - }); - } - return null; - }, - sortable : true, - editor : this._getEditor("exposureTemperature") - }, - { - text : 'Vol. Load', - dataIndex : 'volumeToLoad', - width : 60, - hidden : false, - editor : this._getEditor("volumeToLoad"), - renderer : function(val, y, sample) { - // return val+ " µl"; - return BUI.formatValuesUnits(val, 'µl', { - fontSize : 12, - decimals : 2, - unitsFontSize : this.unitsFontSize - }); - } - }, - { - text : 'Volume in Well', - dataIndex : 'volume', - hidden : true, - editor : this._getEditor("volume"), - width : 80, - renderer : function(val, y, sample) { - // return val + "(µl)"; - return BUI.formatValuesUnits(val, 'µl', { - fontSize : 12, - decimals : 2, - unitsFontSize : this.unitsFontSize - }); - } - }, - { - text : 'Trans.', - dataIndex : 'transmission', - width : 60, - editor : this._getEditor("transmission"), - renderer : function(val, y, sample) { - return BUI.formatValuesUnits(val, '%', { - fontSize : 12, - decimals : 0, - unitsFontSize : this.unitsFontSize - }); - } - }, - { - text : 'Wait T.', - dataIndex : 'waitTime', - editor : this._getEditor("waitTime"), - width : 50, - renderer : function(val, y, sample) { - // if (val != 0) { - return BUI.formatValuesUnits(val, 's', { - fontSize : 12, - decimals : 0, - unitsFontSize : this.unitsFontSize - }); - // } - } - }, - { - text : 'Flow', - dataIndex : 'flow', - editor : this._getEditor("flow"), - width : 50, - renderer : function(val, y, sample) { - if (val == true) { - return "yes"; - } - return null; - } - }, - { - text : 'Viscosity', - dataIndex : 'viscosity', - tooltip : 'The viscosity of a fluid is a measure of its resistance to gradual deformation by shear stress or tensile stress. For liquids, it corresponds to the informal notion of "thickness"', - editor : this._getEditor("viscosity"), - width : 50, - renderer : function(val, y, sample) { - return val; - } - } ] - }, { - text : 'Status', - dataIndex : 'status', - width : 50, - hidden : _this.isStatusColumnHidden, - renderer : function(val, y, sample) { - if (val != null) { - if (val == 'DONE') { - return "" + val + " "; - } - } - } - }, { - text : 'Time', - dataIndex : 'time', - width : 80, - hidden : _this.isTimeColumnHidden, - renderer : function(val, y, sample) { - if (sample.raw.run3VO != null) { - if (sample.raw.run3VO.timeStart != null) { - if (sample.raw.run3VO.timeStart != "") { - var m = moment(sample.raw.run3VO.timeStart); - return m.format("hh:mm:ss a"); - } - } - } - } - }, { - text : 'Energy', - dataIndex : 'energy', - width : 100, - hidden : true - }, { - text : 'Real Exp. Temp.(C)', - width : 100, - dataIndex : 'expExposureTemperature', - hidden : true - }, { - text : 'Storage Temp.(C)', - width : 100, - dataIndex : 'storageTemperature', - hidden : true - }, { - text : 'Time/Frame (s)', - width : 100, - dataIndex : 'timePerFrame', - hidden : true - }, { - text : 'Radiation Relative', - dataIndex : 'radiationRelative', - width : 100, - hidden : true - }, { - text : 'Radiation Absolute', - dataIndex : 'radiationAbsolute', - width : 100, - hidden : true - }, { - text : 'Comments', - dataIndex : 'comments', - flex : 1, - hidden : false, - editor : this._getEditor("comments") - }, { - id : _this.id + 'buttonRemoveSample', - text : '', - hidden : !_this.removeBtnEnabled, - width : 100, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - if (record.raw.macromoleculeId != null) { - if (_this.removeBtnEnabled) { - return BUI.getRedButton('REMOVE'); - } - } - } - } ], - bbar : bbar, - viewConfig : { - stripeRows : true, - getRowClass : function(record, index, rowParams, store) { - if (record.data.status == "DONE") { - return 'green-row'; - } - }, - listeners : { - 'itemclick' : function(grid, record, item, index, e, eOpts) { - _this.onClick.notify({ - specimen : record.raw - }); - }, - 'cellclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemoveSample') { - grid.getStore().removeAt(rowIndex); +BoxWhiskerGraph.prototype.plotClusterTitles = function(properties){ + /** Cluster Titles **/ + var posX = this.left + this.rulerWidth; + var data = this.data; + for(var i = 0; i < data.clusters.length; i++ ){ + /** title for the clusters **/ + posX = posX + this.interClustersSpace; + + /** Drawing title of classes **/ + var cluster = data.clusters[i]; + var posXClasses = posX; + for(var j = 0; j < cluster.classes.length; j++){ + //SVG.drawRectangle(posXClasses, this.height - (this.bottom + this.clusterTitleHeight + this.rulerHeight), properties.classWidth, this.rulerHeight, this.svg, [["fill", "green"]]); +// SVG.drawText(posXClasses + 1/6*properties.classWidth, this.height - (this.bottom + this.clusterTitleHeight + (this.rulerHeight*1/4)), cluster.classes[j].name, this.svg, [["style", "font-size:xx-small"]]); + var color = cluster.classes[j].color; + this.drawSVGVerticalText(posXClasses + 1/2*(properties.classWidth), this.height - (this.bottom - this.clusterTitleHeight + (this.rulerHeight)), cluster.classes[j].name , [["style", "font-size:x-small;"], ["fill", color]]); + + // SVG.drawRectangle(posXClasses, this.height - (this.bottom + this.clusterTitleHeight), properties.classWidth, 2, this.svg, [["fill", "black"]]); + posXClasses = posXClasses + properties.classWidth + this.interClassesSpace; + } + + var clusterTitleSpace = (data.clusters[i].classes.length * properties.classWidth) + ((data.clusters[i].classes.length - 1) * this.interClassesSpace); + //SVG.drawRectangle(posX, this.height - (this.bottom + this.clusterTitleHeight), clusterTitleSpace, this.clusterTitleHeight, this.svg, [["fill", "pink"]]); + SVG.drawRectangle(posX, this.height - (this.clusterTitleHeight+this.bottom), clusterTitleSpace, 1, this.svg, []); + +// var transform = ["translate", "(" + posX + 1/3*clusterTitleSpace +", " + this.height - (this.bottom + (this.clusterTitleHeight*1/4)) +")"], ["transform", "rotate(180)"]; +// var transform = ["transform", "translate(" + (posX + 1/3*clusterTitleSpace) +", " + (this.height - (this.bottom + (this.clusterTitleHeight*1/4))) + "), rotate(-90) "]; +// this.drawSVGVerticalText(posX + 1/3*clusterTitleSpace, this.height - (this.bottom + (this.clusterTitleHeight*1/4)),data.clusters[i].name, [["style", "font-size:x-small"]]); + SVG.drawText(posX , this.height - (this.bottom + (this.clusterTitleHeight*1/4)),data.clusters[i].name ,this.svg, [["style", "font-size:x-small"]]); + posX = posX + clusterTitleSpace; + } +}; + +BoxWhiskerGraph.prototype.plotWhisters = function(data, properties){ + var colors = ["yellow", "orange", "green"]; + var posX = this.left + this.rulerWidth; + for(var i = 0; i < data.clusters.length; i++ ){ + var cluster = data.clusters[i]; + /** inter cluster space **/ + //SVG.drawRectangle(posX, this.top, this.interClustersSpace, this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight, this.svg, [["fill", "black"]]); + posX = posX + this.interClustersSpace; + + for (var j = 0; j < cluster.classes.length; j ++){ + + //SVG.drawRectangle(posX, this.top, properties.classWidth, this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight, this.svg, [["fill", colors[j]]]); + this.plotBoxWhisker( + { + name : cluster.classes[j].name, + values : cluster.classes[j].values, + minPoint : properties.minPoint, + maxPoint : properties.maxPoint, + x : posX, + y : this.top, + width : properties.classWidth, + height : this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight + + + } + ); + posX = posX + properties.classWidth; + //SVG.drawRectangle(posX, this.top, this.interClassesSpace, this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight, this.svg, [["fill", "black"]]); + if (j < cluster.classes.length - 1){ + posX = posX + this.interClassesSpace; + } + } + } +}; + +BoxWhiskerGraph.prototype.draw = function(targetId, data){ + this.targetId = targetId; + var properties = (this.getDimensions(data)); + this.svg = SVG.createSVGCanvas(document.getElementById(this.targetId), [["width", this.width], ["height", this.height]]); + this.plotAxes(properties); + this.plotClusterTitles(properties); + this.plotWhisters(data,properties); +}; + +BoxWhiskerGraph.prototype.input = function(){ + return DATADOC.getBoxWhikerData(); +}; + +BoxWhiskerGraph.prototype.test = function(targetId){ + var plot = new BoxWhiskerGraph( + { + targetId : targetId, + height : 350, + width : 450, + maxBoxWidth : 25 + } + ); + plot.refresh(this.input()); +}; + + + + + + + +function DataSet(){ + this.json = null; + +}; + + +DataSet.prototype.loadFromJSON = function(json){ + if(json != null) { + if(this.validate(json)) { + this.json = json; + } + } +}; + + +DataSet.prototype.toJSON = function(json){ + return this.json; +}; + + +/** Abstract method to be override on childs classes **/ +DataSet.prototype.validate = function(json){ + if (true){ + return true; + } + /*else{ + throw "Data validation failed"; + }*/ +}; + + + + +Edge.prototype.getName = GraphItem.prototype.getName; +Edge.prototype.setName = GraphItem.prototype.setName; +Edge.prototype.getId = GraphItem.prototype.getId; + +function Edge(id, name, nodeSource, nodeTarget, args){ + GraphItem.prototype.constructor.call(this, id, name, args); + + this.sourceNode = nodeSource; + this.targetNode = nodeTarget; + +}; + +Edge.prototype.toJSON = function(){ + return {"index": this.id,"sourceIndex":this.sourceNode.getId(),"targetIndex":this.targetNode.getId(),"args":this.args}; +}; + +Edge.prototype.getNodeSource = function(){ + return this.sourceNode; +}; + +Edge.prototype.getNodeTarget = function(){ + return this.targetNode; +}; + +Edge.prototype.remove = function(){ + //Remove edge object in the nodes + this.getNodeSource().removeEdge(this); + this.getNodeTarget().removeEdge(this); + + this.deleted.notify(this); +}; + + +EdgeGraphFormatter.prototype.setProperties = ItemGraphFormatter.prototype.setProperties; +EdgeGraphFormatter.prototype.getDefault = ItemGraphFormatter.prototype.getDefault; +EdgeGraphFormatter.prototype.getSelected = ItemGraphFormatter.prototype.getSelected; +EdgeGraphFormatter.prototype.getOver = ItemGraphFormatter.prototype.getOver; +EdgeGraphFormatter.prototype.getDragging = ItemGraphFormatter.prototype.getDragging; +EdgeGraphFormatter.prototype.getId = ItemGraphFormatter.prototype.getId; +EdgeGraphFormatter.prototype.toJSON = ItemGraphFormatter.prototype.toJSON; +EdgeGraphFormatter.prototype.loadFromJSON = ItemGraphFormatter.prototype.loadFromJSON; +EdgeGraphFormatter.prototype._setEvents = ItemGraphFormatter.prototype._setEvents; + +function EdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ + ItemGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); + + this.getDefault().args.type = "EdgeGraphFormatter"; +}; + + + + +LineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; +LineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; +LineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; +LineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; +LineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; +LineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; +LineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; +LineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; +LineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; + +function LineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ + EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); + this.args.type = "LineEdgeGraphFormatter"; +}; + +/** DIRECTED **/ +DirectedLineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; +DirectedLineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; +DirectedLineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; +DirectedLineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; +DirectedLineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; +DirectedLineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; +DirectedLineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; +DirectedLineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; +DirectedLineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; + +function DirectedLineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ + EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); + this.args.type = "DirectedLineEdgeGraphFormatter"; + this.args.arrowSize = "3"; +}; +DirectedLineEdgeGraphFormatter.prototype.getArrowSize = function(){ + return this.args.arrowSize; +}; + +OdirectedLineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; +OdirectedLineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; +OdirectedLineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; +OdirectedLineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; +OdirectedLineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; +OdirectedLineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; +OdirectedLineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; +OdirectedLineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; +OdirectedLineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; + +function OdirectedLineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ + EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); + this.args.type = "DirectedLineEdgeGraphFormatter"; + this.args.arrowSize = "3"; +}; + +OdirectedLineEdgeGraphFormatter.prototype.getArrowSize = function(){ + return this.args.arrowSize; +}; + + +/** CUT (inhibition) **/ +CutDirectedLineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; +CutDirectedLineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; +CutDirectedLineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; +CutDirectedLineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; +CutDirectedLineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; +CutDirectedLineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; +CutDirectedLineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; +CutDirectedLineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; +CutDirectedLineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; + +function CutDirectedLineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ + EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); + this.args.type = "CutDirectedLineEdgeGraphFormatter"; +}; + + + + +BezierEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; +BezierEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; +BezierEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; +BezierEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; +BezierEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; +BezierEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; +BezierEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; +BezierEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; +BezierEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; +BezierEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; + +function BezierEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ + EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); + this.args.type = "BezierEdgeGraphFormatter"; +}; + + + +DotDirectedLineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; +DotDirectedLineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; +DotDirectedLineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; +DotDirectedLineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; +DotDirectedLineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; +DotDirectedLineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; +DotDirectedLineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; +DotDirectedLineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; +DotDirectedLineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; + +function DotDirectedLineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ + EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); + this.args.type = "DotDirectedLineEdgeGraphFormatter"; +}; + + +OdotDirectedLineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; +OdotDirectedLineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; +OdotDirectedLineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; +OdotDirectedLineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; +OdotDirectedLineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; +OdotDirectedLineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; +OdotDirectedLineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; +OdotDirectedLineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; +OdotDirectedLineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; + +function OdotDirectedLineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ + EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); + this.args.type = "OdotDirectedLineEdgeGraphFormatter"; +}; + + + +function GraphDataset(){ + DataSet.prototype.constructor.call(this); + this.edges = new Object(); + this.vertices = new Object(); + this.verticesIndex = new Object(); + + //Events + this.newVertex = new Event(this); + this.vertexNameChanged = new Event(this); + this.vertexDeleted = new Event(this); + + this.newEdge = new Event(this); + this.edgeNameChanged = new Event(this); + this.edgeDeleted = new Event(this); + + this.json = new Object(); + this.json.vertices = new Array(); + this.json.edges = new Array(); + this.json.relations = new Array(); +}; + +GraphDataset.prototype.loadFromJSON = DataSet.prototype.loadFromJSON; +GraphDataset.prototype.toJSON = DataSet.prototype.toJSON; +GraphDataset.prototype.validate = DataSet.prototype.validate; + +/** Devuelve el numero de edges incidentes sobre el nodo con mas edges **/ +GraphDataset.prototype.getMaxClass = function(){ + var maxClassNode = 0; + for ( var node in this.vertices) { + if (this.vertices[node].getEdgesCount() > maxClassNode){ + maxClassNode = this.vertices[node].getEdgesCount(); + } + } + return maxClassNode; +}; + +/** Devuelve el numero de edges incidentes sobre el nodo con mas edges **/ +GraphDataset.prototype.getMinClass = function(){ + var minClassNode = Math.min(); + for ( var node in this.vertices) { + if (this.vertices[node].getEdgesCount() < minClassNode){ + minClassNode = this.vertices[node].getEdgesCount(); + } + } + return minClassNode; +}; + +GraphDataset.prototype.getVertexByName = function(nodeName){ + var results = new Array(); + + for (var vertexId in this.verticesIndex[nodeName]){ + var vertexByid = this.getVertexById(this.verticesIndex[nodeName][vertexId]); + results.push(vertexByid); + //* añadido nuevo porque fallaba el anterior codigo + return vertexByid + } + + if (results <= 1){ + return this.getVertexById(this.verticesIndex[nodeName]); + } + else{ + return results; + } +}; + +GraphDataset.prototype.getVertexById = function(id){ + return this.vertices[id]; +}; + +GraphDataset.prototype.toSIF = function(){ + var sifDataAdapter = new SifFileDataAdapter(); + return sifDataAdapter.toSIF(this); +}; + +GraphDataset.prototype.toSIFID = function(){ + var sifDataAdapter = new SifFileDataAdapter(); + return sifDataAdapter.toSIFID(this); +}; + +GraphDataset.prototype.toDOT = function(){ + var dotFileDataAdapter = new DotFileDataAdapter(); + return dotFileDataAdapter.toDOT(this); +}; + +GraphDataset.prototype.toDOTID = function(){ + var dotFileDataAdapter = new DotFileDataAdapter(); + return dotFileDataAdapter.toDOTID(this); +}; + +GraphDataset.prototype._addNode = function(nodeName, args){ + return new Vertex(this._getVerticesCount()-1, nodeName, args); +}; + +GraphDataset.prototype.addNode = function(nodeName, args){ + this.json.vertices.push(nodeName); + this._addVerticesIndex(nodeName, this._getVerticesCount() - 1); + var vertex = this._addNode(nodeName, args); + this.vertices[this._getVerticesCount()-1] = vertex; + this._setNodeEvents(vertex); + this.newVertex.notify(vertex); +}; + +GraphDataset.prototype._addVerticesIndex = function(nodeName, id){ + if (this.verticesIndex[nodeName] == null){ + this.verticesIndex[nodeName] = new Array(); + } + this.verticesIndex[nodeName].push(id); +}; + +GraphDataset.prototype.addEdge = function(edgeName, nodeSourceId, nodeTargetId, args){ + this.json.edges.push(edgeName); + var nodeSource = this.getVertexById(nodeSourceId); + var nodeTarget = this.getVertexById(nodeTargetId); + var index = this.getEdgesCount() - 1; + this.edges[index] = new Edge(index, edgeName, nodeSource, nodeTarget, args); + this.json.relations.push({"index": index, "sourceIndex": nodeSourceId, "targetIndex": nodeTargetId, "args": args }); + + nodeSource.addEdge(this.edges[index]); + nodeTarget.addEdge(this.edges[index]); + this._setEdgeEvents(this.edges[index]); + this.newEdge.notify(this.edges[index]); +}; + +GraphDataset.prototype.getVertices = function(){ + return this.vertices; +}; + +GraphDataset.prototype.getEdges = function(){ + return this.edges; +}; + +GraphDataset.prototype.getEdgeById = function(edgeId){ + return this.edges[edgeId]; +}; + +GraphDataset.prototype._getVerticesCount = function(){ + return this.json.vertices.length; +}; + + +GraphDataset.prototype.getVerticesCount = function(){ + var count = 0; + for ( var vertex in this.getVertices()) { + count ++; + } + return count; +}; + + +GraphDataset.prototype.getEdgesCount = function(){ + return this.json.edges.length; +}; + +GraphDataset.prototype.init = function(){ + this.edges = new Object(); + this.vertices = new Object(); +}; + +GraphDataset.prototype._setNodeEvents = function(node){ + var _this = this; + //NODE EVENTS + node.deleted.attach(function (sender, node){ + _this._removeNode(node); + }); + + node.nameChanged.attach(function (sender, args){ + var item = args.item; + var newName = item.name; + var indexes = _this.verticesIndex[args.previousName]; + for(var i = 0; i < indexes.length; i++){ + if(indexes[i] == item.id) + indexes.splice(i,1); + } + if(indexes.length == 0){ + delete _this.verticesIndex[args.previousName]; + } + _this._addVerticesIndex(newName, item.id); + _this.json.vertices[item.id] = newName; + _this.vertexNameChanged.notify(args); + }); +}; + +GraphDataset.prototype._setEdgeEvents = function(edge){ + var _this = this; + //EDGE EVENTS + edge.nameChanged.attach(function (sender, edge){ + _this.edgeNameChanged.notify(edge); + + }); + + edge.deleted.attach(function (sender, edge){ + _this._removeEdge(edge); + }); +}; + +GraphDataset.prototype._connectVerticesByName = function(nodeNameSource, nodeNameTarget){ + var source = this.getVertexByName(nodeNameSource); + var target = this.getVertexByName(nodeNameTarget); + + if ((source != null)&&(target!=null)){ + this.addEdge(source.getName() +"_" + target.getName(), source.getId(), target.getId(), {}); + } + else{ + if (source == null){ + console.log("No encontrado: " + nodeNameSource) + } + if (target == null){ + console.log("No encontrado: " + nodeNameTarget) + } + } +}; + +GraphDataset.prototype.loadFromJSON = function(json){ + var json = json; + this.init(); + this.json = new Object(); + this.json.vertices = new Array(); + this.json.edges = new Array(); + this.json.relations = new Array(); + + for ( var i = 0; i < json.nodes.length; i++) { + if (json.nodes[i] != null){ + var name = json.nodes[i]; + this.addNode(name); + } + else{ + this.json.vertices.push(null); + } + } + + for ( var i = 0; i < json.edges.length; i++) { + if (json.edges[i] != null){ + if (json.relations[i] != null){ + var name = json.edges[i]; + this.addEdge(name, json.relations[i].sourceIndex, json.relations[i].targetIndex, json.relations[i].args); + } + } + else{ + this.json.edges.push(null); + this.json.relations.push(null); + } + } +}; + +GraphDataset.prototype.prettyPrint = function(){ + for ( var node in this.vertices) { + console.log(this.vertices[node].getName() ); + for ( var j = 0; j < this.vertices[node].getEdgesIn().length; j++) { + console.log(" --> " + this.vertices[node].getEdgesIn()[j].getNodeTarget().getName() ); + } + } +}; + +GraphDataset.prototype._removeEdge = function(edge){ + this.json.edges[edge.getId()] = null; + this.json.relations[edge.getId()] = null; + + delete this.edges[edge.getId()]; + this.edgeDeleted.notify(edge); + + +}; + +GraphDataset.prototype._removeNode = function(node){ + this.json.vertices[node.getId()] = null; + delete this.vertices[node.getId()]; + this.vertexDeleted.notify(node); +}; + +GraphDataset.prototype.toJSON = function(){ + var json = new Object(); + var nodes = new Array(); + json.nodes = this.json.vertices; //nodes; + json.edges = this.json.edges; //edges; + json.relations = this.json.relations; + return json; +}; + +GraphDataset.prototype.clone = function(){ + var dsDataset = new GraphDataset(); + dsDataset.loadFromJSON(this.toJSON()); + return dsDataset; +}; +//GraphDataset.prototype.test = function(){ +// this.loadFromJSON(this.toJSON()); +//}; + +function labels(){ + var names = new Array(); + + var dataset = interactomeViewer.graphEditorWidget.dataset; + var layout = interactomeViewer.graphEditorWidget.layout; + + for ( var vertexId in interactomeViewer.graphEditorWidget.dataset.getVertices()) { + names.push(interactomeViewer.graphEditorWidget.dataset.getVertexById(vertexId).getName()); + } + + var sorted = (names.sort()); + console.log(sorted) + var distance = 0.01; + var altura = 0.6; + for ( var i = 0; i < names.length; i++) { + var id =dataset.getVertexByName(names[i]).getId(); + + layout.getNodeById(id).setCoordenates(distance, altura); + + + distance = parseFloat(distance) + parseFloat(0.03); + + altura = parseFloat(altura) + parseFloat(0.02); + + if (parseFloat(altura) == 0.9800000000000003){ + + altura = 0.6; + distance = distance - 0.51; + } + + } + + +}; + +function GraphItem(id, name, args){ + this.id = id; + this.name = name; + this.type = "NONE"; + + this.args = new Object(); + + + if (args!=null){ + this.args = args; + if (args.type !=null){ + this.type = args.type; + } + } + + //Events + this.nameChanged = new Event(this); + this.deleted = new Event(this); +} + +GraphItem.prototype.getName = function(){ + return this.name; +}; + +GraphItem.prototype.getId = function(){ + return this.id; +}; + +GraphItem.prototype.setName = function(name){ + var oldName = this.getName(); + this.name = name; + this.nameChanged.notify({"item": this, "previousName" : oldName}); +}; + + + + + +function LayoutDataset(){ + this.dataset = null; + this.vertices = new Object(); + this.changed = new Event(this); + + + this.args = new Object(); + + //RANDOM, CIRCLE + this.args.type = "CIRCLE"; +}; + +LayoutDataset.prototype.loadFromJSON = function(dataset, json){ + var _this = this; + this.vertices = new Object(); + this.dataset = dataset; //new GraphDataset(); + for ( var vertex in json) { + this.vertices[vertex] = new NodeLayout(vertex, json[vertex].x, json[vertex].y); + this.vertices[vertex].changed.attach(function (sender, item){ + _this.changed.notify(item); + }); + } + this._attachDatasetEvents(); +}; + + +LayoutDataset.prototype.toJSON = function(){ + var serialize = new Object(); + for ( var vertex in this.vertices) { + serialize[vertex] = new Object(); + serialize[vertex].x = this.vertices[vertex].x; + serialize[vertex].y = this.vertices[vertex].y; + } + serialize.dataset = new Object(); + serialize.dataset =this.dataset.toJSON(); + return serialize; +}; + +LayoutDataset.prototype.dataBind = function(graphDataset){ + this.dataset = graphDataset; + this._attachDatasetEvents(); + this._calculateLayout(); +}; + +LayoutDataset.prototype._removeVertex = function(vertexId){ + delete this.vertices[vertexId]; +}; + +LayoutDataset.prototype._attachDatasetEvents = function(){ + var _this = this; + + this.dataset.vertexDeleted.attach(function (sender, item){ + _this._removeVertex(item.getId()); + }); + + this.dataset.newVertex.attach(function (sender, item){ + _this.vertices[item.getId()] = new NodeLayout(item.getId(), 0.5, 0.5); + _this.vertices[item.getId()].changed.attach(function (sender, item){ + _this.changed.notify(item); + }); + }); +}; + +LayoutDataset.prototype.getType = function(){ + return this.args.type; +}; + +LayoutDataset.prototype._calculateLayoutVertices = function(type, count){ + + if (type == "CIRCLE"){ + var radius = 0.4; + var centerX = 0.5; + var centerY = 0.5; + var verticesCoordinates = new Array(); + for(var i = 0; i < count; i++){ + x = centerX + radius * Math.sin(i * 2 * Math.PI/count); + y = centerY + radius * Math.cos(i * 2 * Math.PI/count); + verticesCoordinates.push({'x':x,'y':y}); + } + return verticesCoordinates; + } +}; + + +LayoutDataset.prototype._calculateLayout = function(){ + var _this = this; + if (this.getType() == "RANDOM"){ + for ( var vertex in this.dataset.getVertices()) { + if (this.vertices[vertex] == null){ + this.vertices[vertex] = new NodeLayout(vertex, 0, 0); + } + this.vertices[vertex].setCoordinates(Math.random(), Math.random()); + this.vertices[vertex].changed.attach(function (sender, item){ + _this.changed.notify(item); + }); + } + } + + if ( this.getType() == "CIRCLE"){ + + var count = this.dataset._getVerticesCount(); + var verticesCoordinates = this._calculateLayoutVertices(this.getType(), count); + + var aux = 0; + for ( var vertex in this.dataset.getVertices()) { + if (this.vertices[vertex] == null){ + this.vertices[vertex] = new NodeLayout(vertex, 0, 0); + } + this.vertices[vertex].setCoordinates(verticesCoordinates[aux].x, verticesCoordinates[aux].y);//{"x":, "y":}; + aux++; + this.vertices[vertex].changed.attach(function (sender, item){ + _this.changed.notify(item); + }); + } + } + + + if (this.getType() == "SQUARE"){ + + var count = this.dataset._getVerticesCount(); + var xMin = 0.1; + var xMax = 0.9; + var yMin = 0.1; + var yMax = 0.9; + + var rows = Math.sqrt(count); + var step = (xMax - xMin) / rows; + + var verticesCoordinates = new Array(); + for(var i = 0; i < rows; i ++){ + for ( var j = 0; j < rows; j++) { + x = i * step + xMin; + y = j * step + yMin; + verticesCoordinates.push({'x':x,'y':y}); + } + } + + var aux = 0; + for ( var vertex in this.dataset.getVertices()) { + if (this.vertices[vertex] == null){ + this.vertices[vertex] = new NodeLayout(vertex, 0, 0); + } + this.vertices[vertex].setCoordinates(verticesCoordinates[aux].x, verticesCoordinates[aux].y);//{"x":, "y":}; + aux++; + this.vertices[vertex].changed.attach(function (sender, item){ + _this.changed.notify(item); + }); + } + } + +}; + +LayoutDataset.prototype.getNodeById = function(id){ + return this.vertices[id]; +}; + +LayoutDataset.prototype.getVerticesByArea = function(x1, y1, x2, y2){ + var vertices = new Array(); + for ( var vertex in this.dataset.getVertices()) { + if ((this.vertices[vertex].x >= x1)&&(this.vertices[vertex].x <= x2)){ + if ((this.vertices[vertex].y >= y1)&&(this.vertices[vertex].y <= y2)){ + vertices.push(this.vertices[vertex]); + } + } + } + return vertices; +}; + + + + +LayoutDataset.prototype.getLayout = function(type){ + + if (type == "CIRCLE"){ + this.args.type = "CIRCLE"; + this._calculateLayout(); + return; + } + + if (type == "SQUARE"){ + this.args.type = "SQUARE"; + this._calculateLayout(); + return; + } + + if (type == "RANDOM"){ + this.args.type = "RANDOM"; + this._calculateLayout(); + return; + } + + + var dotText = this.dataset.toDOTID(); + var url = "http://bioinfo.cipf.es/utils/ws/rest/network/layout/"+type+".coords"; + var _this = this; + + $.ajax({ + async: true, + type: "POST", + url: url, + dataType: "text", + data: { + dot :dotText + }, + cache: false, + success: function(data){ + var response = JSON.parse(data); + for ( var vertexId in response) { + _this.vertices[vertexId].setCoordinates(response[vertexId].x, response[vertexId].y); + } + } + }); + +// $.ajax({ +// async: true, +// type: "POST", +// url: url, +// dataType: "script", +// data: { +// dot :dotText +// }, +// cache: false, +// success: function(data){ +// var response = JSON.parse(data); +// for ( var vertexId in response) { +// _this.vertices[vertexId].setCoordinates(response[vertexId].x, response[vertexId].y); +// } +// } +// }); + +}; + +function NodeLayout(id, x, y, args){ + this.id = id; + this.x = x; + this.y = y; + this.changed = new Event(this); +}; + +NodeLayout.prototype.getId = function(id){ + return this.id; +}; + +NodeLayout.prototype.setCoordinates = function(x, y){ + this.x = x; + this.y = y; + this.changed.notify(this); +}; + + + +function NetworkDataSetFormatter(vertexFormatProperties, defaultEdgeProperties, args){ + DataSet.prototype.constructor.call(this); + + this.args = new Object(); + + this.vertices = new Object(); + this.edges = new Object(); + this.dataset = null; + this.maxClass = 0; + this.minClass = 0; + + /** Coordenates with default Setting */ + this.args.width = 1100; + this.args.height = 500; + + /** Optional parameters */ + this.args.backgroundColor = "#FFFFFF"; + this.args.backgroundImage = null; + this.args.backgroundImageHeight = null; + this.args.backgroundImageWidth = null; + this.args.backgroundImageX = null; + this.args.backgroundImageY = null; + + + this.args.balanceNodes = false; + this.args.nodesMaxSize = 3; + this.args.nodesMinSize = 0.5; + + + /** Zoom **/ + this.args.zoomScale = 1; + this.args.zoomScaleStepFactor = 0.4; + + if (args != null){ + if (args.backgroundImage != null){ + this.args.backgroundImage = args.backgroundImage; + } + + if (args.width != null){ + this.args.width = args.width; + } + + if (args.height != null){ + this.args.height = args.height; + this.args.svgHeight = args.height; + } + + if (args.svgHeight != null){ + this.args.svgHeight = args.svgHeight; + } + + if (args.backgroundColor != null){ + this.args.backgroundColor = args.backgroundColor; + } + + if(args.balanceNodes != null){ + this.args.balanceNodes = args.balanceNodes; + } + + if(args.nodesMaxSize != null){ + this.args.nodesMaxSize = args.nodesMaxSize; + } + if(args.nodesMinSize != null){ + this.args.nodesMinSize = args.nodesMinSize; + } + } + + this.args.defaultEdgeProperties = {"fill":"#000000", "radius":"1", "stroke":"#000000", "size":1, "title":{"fontSize":10, "fontColor":"#000000"}}; + this.args.vertexFormatProperties = { "fill":"#000000", "stroke":"#000000", "stroke-opacity":"#000000"}; + + if (vertexFormatProperties!= null){ + this.args.vertexFormatProperties = vertexFormatProperties; + } + if (defaultEdgeProperties!= null){ + this.args.defaultEdgeProperties = defaultEdgeProperties; + } + + /** Events **/ + this.changed = new Event(this); + this.edgeChanged = new Event(this); + this.resized = new Event(this); + this.backgroundImageChanged= new Event(this); + this.backgroundColorChanged= new Event(this); +}; + +NetworkDataSetFormatter.prototype.loadFromJSON = function(dataset, json){ + this.args = new Object(); + this.vertices = new Object(); + this.args = json; + this._setDataset(dataset); + var _this = this; + + for ( var vertex in json.vertices) { + this.addVertex(vertex, json.vertices[vertex]); + } + + for ( var edgeId in json.edges) { + this.addEdge(edgeId, json.edges[edgeId]); + } +}; + + +NetworkDataSetFormatter.prototype.toJSON = function(){ + + +// this.args.vertices = new Object(); +// this.args.edges = new Object(); +// +// for ( var vertex in this.vertices) { +// this.args.vertices[vertex] = this.getVertexById(vertex).toJSON(); +// } +// for ( var edge in this.edges) { +// this.args.edges[edge] = this.getEdgeById(edge).toJSON(); +// } +// +// return (this.args); + + + var serialize = new Object(); + serialize = JSON.parse(JSON.stringify(this.args)); + serialize.vertices = new Object(); + serialize.edges = new Object(); + + for ( var vertex in this.vertices) { + serialize.vertices[vertex] = this.getVertexById(vertex).toJSON(); + } + for ( var edge in this.edges) { + serialize.edges[edge] = this.getEdgeById(edge).toJSON(); + } + + return (serialize); +}; + + + +NetworkDataSetFormatter.prototype._getNodeSize = function(nodeId){ + if (this.isVerticesBalanced()){ + var total = this.maxClass - this.minClass; + if (total == 0){ total = 1;} + var nodeConnection = this.dataset.getVertexById(nodeId).getEdges().length; + return ((nodeConnection*this.args.nodesMaxSize)/total) + this.args.nodesMinSize; + } + return this.getVertexById(nodeId).getDefault().getSize(); +}; + +NetworkDataSetFormatter.prototype._recalculateSize = function(){ + if (this.isVerticesBalanced()){ + this.maxClass = this.dataset.getMaxClass(); + this.minClass = this.dataset.getMinClass(); + for ( var vertexIdAll in this.vertices) { + var size = this._getNodeSize(vertexIdAll); + this.vertices[vertexIdAll].getDefault().setSize(size); + this.vertices[vertexIdAll].getSelected().setSize(size); + this.vertices[vertexIdAll].getOver().setSize(size); + } + } +}; + + +NetworkDataSetFormatter.prototype.addVertex = function(vertexId, json){ + + + if (json == null){ + this.vertices[vertexId] = new CircleVertexGraphFormatter(vertexId, this.args.vertexFormatProperties.defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); + } + else{ + + /** Cargo los attributos desde el json **/ + if (json.type == null){ + this.vertices[vertexId] = new CircleVertexGraphFormatter(vertexId, this.args.vertexFormatProperties.defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); + } + + if ((json.type == "SquareVertexGraphFormatter")||(json.type == "SquareVertexNetworkFormatter")){ + this.vertices[vertexId] = new SquareVertexGraphFormatter(vertexId); + this.vertices[vertexId].loadFromJSON(json); + } + + if ((json.type == "CircleVertexGraphFormatter")||(json.type == "CircleVertexNetworkFormatter")){ + this.vertices[vertexId] = new CircleVertexGraphFormatter(vertexId); + this.vertices[vertexId].loadFromJSON(json); + } + + if ((json.type == "EllipseVertexGraphFormatter")||(json.type == "EllipseVertexNetworkFormatter")){ + this.vertices[vertexId] = new EllipseVertexGraphFormatter(vertexId); + this.vertices[vertexId].loadFromJSON(json); + } + + if ((json.type == "RectangleVertexGraphFormatter")||(json.type == "RectangleVertexNetworkFormatter")){ + this.vertices[vertexId] = new RectangleVertexGraphFormatter(vertexId); + this.vertices[vertexId].loadFromJSON(json); + } + + if ((json.type == "RoundedVertexGraphFormatter")||(json.type == "RoundedVertexNetworkFormatter")){ + this.vertices[vertexId] = new RoundedVertexGraphFormatter(vertexId); + this.vertices[vertexId].loadFromJSON(json); + } + + } + + + var _this = this; + this.vertices[vertexId].stateChanged.attach(function (sender, item){ + _this.changed.notify(item); + }); + + var size = this._getNodeSize(vertexId); + this.vertices[vertexId].defaultFormat.args.size = size; + this.vertices[vertexId].selected.args.size = size; + this.vertices[vertexId].over.args.size = size; + +}; + +NetworkDataSetFormatter.prototype.addEdge = function(edgeId, json){ + + /** Es un edge nuevo que le doy los atributos por defecto **/ + if (json == null){ + if (this.dataset.getEdgeById(edgeId).getNodeSource().getId() == this.dataset.getEdgeById(edgeId).getNodeTarget().getId()){ + this.edges[edgeId] = new BezierEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); + }else{ + this.edges[edgeId] = new DirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); + } + } + else{ + /** Cargo los attributos desde el json **/ + if (json.type == null){ + this.edges[edgeId] = new LineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); + } + + if ((json.type == "LineEdgeGraphFormatter")||(json.type == "LineEdgeNetworkFormatter")){ + this.edges[edgeId] = new LineEdgeGraphFormatter(edgeId); + this.edges[edgeId].loadFromJSON(json); + } + if ((json.type == "DirectedLineEdgeGraphFormatter")||(json.type == "DirectedLineEdgeNetworkFormatter")){ + this.edges[edgeId] = new DirectedLineEdgeGraphFormatter(edgeId); + this.edges[edgeId].loadFromJSON(json); + } + + if ((json.type == "BezierEdgeGraphFormatter")||(json.type == "BezierEdgeNetworkFormatter")){ + this.edges[edgeId] = new BezierEdgeGraphFormatter(edgeId); + this.edges[edgeId].loadFromJSON(json); + } + + + if ((json.type == "CutDirectedLineEdgeGraphFormatter")||(json.type == "CutDirectedLineEdgeNetworkFormatter")){ + this.edges[edgeId] = new CutDirectedLineEdgeGraphFormatter(edgeId); + this.edges[edgeId].loadFromJSON(json); + } + + if ((json.type == "DotDirectedLineEdgeGraphFormatter")||(json.type == "DotDirectedLineEdgeNetworkFormatter")){ + this.edges[edgeId] = new DotDirectedLineEdgeGraphFormatter(edgeId); + this.edges[edgeId].loadFromJSON(json); + } + if ((json.type == "OdotDirectedLineEdgeGraphFormatter")||(json.type == "OdotDirectedLineEdgeNetworkFormatter")){ + this.edges[edgeId] = new OdotDirectedLineEdgeGraphFormatter(edgeId); + this.edges[edgeId].loadFromJSON(json); + } + + if ((json.type == "OdirectedLineEdgeGraphFormatter")||(json.type == "OdirectedLineEdgeNetworkFormatter")){ + this.edges[edgeId] = new OdirectedLineEdgeGraphFormatter(edgeId); + this.edges[edgeId].loadFromJSON(json); + } + } + + var _this = this; + this.edges[edgeId].stateChanged.attach(function (sender, item){ + _this.edgeChanged.notify(item); + }); + + this._recalculateSize(); +}; + +NetworkDataSetFormatter.prototype._setDataset = function(dataset){ + this.dataset = dataset; + this.maxClass = dataset.getMaxClass(); + this.minClass = dataset.getMinClass(); + this._attachDatasetEvents(); +}; + +NetworkDataSetFormatter.prototype.changeEdgeType = function(edgeId, type){ + if ((type == "LineEdgeGraphFormatter")||(type == "LineEdgeNetworkFormatter")){ + this.edges[edgeId] = new LineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); + + } + if ((type == "DirectedLineEdgeGraphFormatter")||(type == "DirectedLineEdgeNetworkFormatter")){ + this.edges[edgeId] = new DirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); + } + + if ((type == "CutDirectedLineEdgeGraphFormatter")||(type == "CutDirectedLineEdgeNetworkFormatter")){ + this.edges[edgeId] = new CutDirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); + } + + if ((type == "DotDirectedLineEdgeGraphFormatter")||(type == "DotDirectedLineEdgeNetworkFormatter")){ + this.edges[edgeId] = new DotDirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); + } + + if ((type == "OdotDirectedLineEdgeGraphFormatter")||(type == "OdotDirectedLineEdgeNetworkFormatter")){ + this.edges[edgeId] = new OdotDirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); + } + + if ((type == "OdirectedLineEdgeGraphFormatter")||(type == "OdirectedLineEdgeNetworkFormatter")){ + this.edges[edgeId] = new OdirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); + } + + + + var _this = this; + this.edges[edgeId].stateChanged.attach(function (sender, item){ + _this.edgeChanged.notify(item); + }); + _this.edgeChanged.notify(this.edges[edgeId]); +}; +/* +classe = "SquareNetworkNodeFormatter"; +} +if (value == "circle"){ + classe = "CircleNetworkNodeFormatter"; + **/ +NetworkDataSetFormatter.prototype.changeNodeType = function(vertexId, type){ + var defaultFormat = JSON.parse(JSON.stringify(this.vertices[vertexId].getDefault())); + var selectedFormat = JSON.parse(JSON.stringify(this.vertices[vertexId].getSelected())); + var defaultFormat = JSON.parse(JSON.stringify(this.vertices[vertexId].getDefault())); + var defaultFormat = JSON.parse(JSON.stringify(this.vertices[vertexId].getDefault())); + + if ((type == "SquareVertexGraphFormatter")||(type == "SquareVertexNetworkFormatter")){ + this.vertices[vertexId] = new SquareVertexGraphFormatter(vertexId,defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); + } + + if ((type == "CircleVertexGraphFormatter")||(type == "CircleVertexNetworkFormatter")){ + this.vertices[vertexId] = new CircleVertexGraphFormatter(vertexId, defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); + } + + if ((type == "EllipseVertexGraphFormatter")||(type == "EllipseVertexNetworkFormatter")){ + this.vertices[vertexId] = new EllipseVertexGraphFormatter(vertexId, defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); + } + + if ((type == "RectangleVertexGraphFormatter")||(type == "RectangleVertexNetworkFormatter")){ + this.vertices[vertexId] = new RectangleVertexGraphFormatter(vertexId, defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); + } + + if ((type == "RoundedVertexGraphFormatter")||(type == "RoundedVertexNetworkFormatter")){ + this.vertices[vertexId] = new RoundedVertexGraphFormatter(vertexId, defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); + } + + if ((type == "OctagonVertexGraphFormatter")||(type == "OctagonVertexNetworkhFormatter")){ + this.vertices[vertexId] = new OctagonVertexGraphFormatter(vertexId, defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); + } + + + var _this = this; + this.vertices[vertexId].stateChanged.attach(function (sender, item){ + _this.changed.notify(item); + }); + _this.changed.notify(this.vertices[vertexId]); +}; + + + +NetworkDataSetFormatter.prototype.dataBind = function(networkDataSet){ + var _this = this; + this._setDataset(networkDataSet); + + for ( var vertex in this.dataset.getVertices()) { + this.addVertex(vertex); + } + + for ( var edge in this.dataset.getEdges()) { + this.addEdge(edge); + } +}; + +NetworkDataSetFormatter.prototype._removeEdge = function(edgeId){ + delete this.edges[edgeId]; +}; + +NetworkDataSetFormatter.prototype._removeVertex = function(vertexId){ + delete this.vertices[vertexId]; +}; + +NetworkDataSetFormatter.prototype._attachDatasetEvents = function(id){ + var _this = this; + this.dataset.vertexDeleted.attach(function (sender, item){ + _this._removeVertex(item.getId()); + }); + + this.dataset.edgeDeleted.attach(function (sender, item){ + _this._removeEdge(item.getId()); + }); + + this.dataset.newVertex.attach(function (sender, item){ + _this.addVertex(item.getId()); + }); + + this.dataset.newEdge.attach(function (sender, item){ + _this.addEdge(item.getId()); + }); +}; + + +NetworkDataSetFormatter.prototype.getVertexById = function(id){ + return this.vertices[id]; +}; + +NetworkDataSetFormatter.prototype.getEdgeById = function(id){ + return this.edges[id]; +}; + +NetworkDataSetFormatter.prototype.makeLabelsBigger = function(){ +for ( var vertexId in this.vertices) { + var fontSize = this.vertices[vertexId].getDefault().getFontSize() + 2; + this.vertices[vertexId].getDefault().setFontSize(fontSize); + } +}; + +NetworkDataSetFormatter.prototype.makeLabelsSmaller = function(){ + for ( var vertexId in this.vertices) { + var fontSize = this.vertices[vertexId].getDefault().getFontSize() - 2; + this.vertices[vertexId].getDefault().setFontSize(fontSize); + } +}; + + +NetworkDataSetFormatter.prototype.resize = function(width, height){ + this.args.width = width; + this.args.height = height; + this.resized.notify(); +}; + +/** ZOOM GETTERS **/ +NetworkDataSetFormatter.prototype.getZoomScaleStepFactor = function(){return this.args.zoomScaleStepFactor;}; +NetworkDataSetFormatter.prototype.setZoomScaleStepFactor = function(scaleFactor){this.args.zoomScaleStepFactor = scaleFactor;}; +NetworkDataSetFormatter.prototype.getZoomScale = function(){return this.args.zoomScale;}; +NetworkDataSetFormatter.prototype.setZoomScale = function(scale){this.args.zoomScale = scale;}; + +NetworkDataSetFormatter.prototype.getNodesMaxSize = function(){return this.args.nodesMaxSize;}; +NetworkDataSetFormatter.prototype.getNodesMinSize = function(){return this.args.nodesMinSize;}; + +/** SIZE SETTERS AND GETTERS **/ +NetworkDataSetFormatter.prototype.isVerticesBalanced = function(){return this.args.balanceNodes;}; +NetworkDataSetFormatter.prototype.getWidth = function(){return this.args.width;}; +NetworkDataSetFormatter.prototype.getHeight = function(){return this.args.height;}; + +/** OPTIONAL PARAMETERS GETTERS AND SETTERS **/ +NetworkDataSetFormatter.prototype.getBackgroundImage = function(){return this.args.backgroundImage;}; +NetworkDataSetFormatter.prototype.setBackgroundImage = function(value){this.args.backgroundImage = value; this.backgroundImageChanged.notify(this);}; + + +NetworkDataSetFormatter.prototype.getBackgroundImageWidth = function(){return this.args.backgroundImageWidth;}; +NetworkDataSetFormatter.prototype.setBackgroundImageWidth = function(value){this.args.backgroundImageWidth = value; this.backgroundImageChanged.notify(this);}; + +NetworkDataSetFormatter.prototype.getBackgroundImageHeight = function(){return this.args.backgroundImageHeight;}; +NetworkDataSetFormatter.prototype.setBackgroundImageHeight = function(value){this.args.backgroundImageHeight = value; this.backgroundImageChanged.notify(this);}; + +NetworkDataSetFormatter.prototype.getBackgroundImageX = function(){return this.args.backgroundImageX;}; +NetworkDataSetFormatter.prototype.setBackgroundImageX = function(value){this.args.backgroundImageX = value; this.backgroundImageChanged.notify(this);}; + +NetworkDataSetFormatter.prototype.getBackgroundImageY = function(){return this.args.backgroundImageX;}; +NetworkDataSetFormatter.prototype.setBackgroundImageY = function(value){this.args.backgroundImageY = value; this.backgroundImageChanged.notify(this);}; + + + +NetworkDataSetFormatter.prototype.getBackgroundColor = function(){return this.args.backgroundColor;}; +NetworkDataSetFormatter.prototype.setBackgroundColor = function(value){this.args.backgroundColor = value; this.backgroundColorChanged.notify(this);}; + +NetworkDataSetFormatter.prototype.getWidth = function(){return this.args.width;}; +NetworkDataSetFormatter.prototype.setWidth = function(value){this.args.width = value;}; + +NetworkDataSetFormatter.prototype.getHeight = function(){return this.args.height;}; +NetworkDataSetFormatter.prototype.setHeight = function(value){this.args.height = value;}; + + + + +Vertex.prototype.getName = GraphItem.prototype.getName; +Vertex.prototype.setName = GraphItem.prototype.setName; +Vertex.prototype.getId = GraphItem.prototype.getId; + +function Vertex(id, name, args){ + GraphItem.prototype.constructor.call(this, id, name, args); + this.edgesIn= new Array(); + this.edgesOut= new Array(); +}; + +Vertex.prototype.getEdges = function(){ + return this.edgesIn.concat(this.edgesOut); +}; + +Vertex.prototype.getEdgesCount = function(){ + return this.getEdges().length; +}; + +Vertex.prototype.getEdgesIn = function(){ + return this.edgesIn; +}; + +Vertex.prototype.getEdgesOut = function(){ + return this.edgesOut; +}; + +Vertex.prototype.addEdge = function(edge){ + if (edge.getNodeSource().getId() == this.id){ + this.edgesIn.push(edge); + } + else{ + this.edgesOut.push(edge); + } +}; + +Vertex.prototype.removeEdge = function(edge){ + for ( var i = 0; i < this.getEdgesIn().length; i++) { + var edgeIn = this.edgesIn[i]; + if (edgeIn.getId() == edge.getId()){ + this.edgesIn.splice(i, 1); + } + } + for ( var i = 0; i < this.getEdgesOut().length; i++) { + var edgeIn = this.edgesOut[i]; + if (edgeIn.getId() == edge.getId()){ + this.edgesOut.splice(i, 1); + } + } +}; + +Vertex.prototype.remove = function(){ + var edges = this.getEdges(); + for ( var i = 0; i < edges.length; i++) { + var edge = edges[i]; + edge.remove(); + } + this.deleted.notify(this); +}; + + + + + +VertexGraphFormatter.prototype.getDefault = ItemGraphFormatter.prototype.getDefault; +VertexGraphFormatter.prototype.getSelected = ItemGraphFormatter.prototype.getSelected; +VertexGraphFormatter.prototype.getOver = ItemGraphFormatter.prototype.getOver; +VertexGraphFormatter.prototype.getDragging = ItemGraphFormatter.prototype.getDragging; +VertexGraphFormatter.prototype.getId = ItemGraphFormatter.prototype.getId; +VertexGraphFormatter.prototype.toJSON = ItemGraphFormatter.prototype.toJSON; +VertexGraphFormatter.prototype.loadFromJSON = ItemGraphFormatter.prototype.loadFromJSON; +VertexGraphFormatter.prototype._setEvents = ItemGraphFormatter.prototype._setEvents; + + +function VertexGraphFormatter(defaultFormat, selectedFormat, overFormat, draggingFormat){ + ItemGraphFormatter.prototype.constructor.call(this, defaultFormat, selectedFormat, overFormat, draggingFormat); +}; + + +CircleVertexGraphFormatter.prototype.getDefault = VertexGraphFormatter.prototype.getDefault; +CircleVertexGraphFormatter.prototype.getSelected = VertexGraphFormatter.prototype.getSelected; +CircleVertexGraphFormatter.prototype.getOver = VertexGraphFormatter.prototype.getOver; +CircleVertexGraphFormatter.prototype.getDragging = VertexGraphFormatter.prototype.getDragging; +CircleVertexGraphFormatter.prototype.getId = VertexGraphFormatter.prototype.getId; +CircleVertexGraphFormatter.prototype.toJSON = VertexGraphFormatter.prototype.toJSON; +CircleVertexGraphFormatter.prototype.loadFromJSON = VertexGraphFormatter.prototype.loadFromJSON; +CircleVertexGraphFormatter.prototype._setEvents = VertexGraphFormatter.prototype._setEvents; + +function CircleVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ + VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); + this.args.type = "CircleVertexGraphFormatter"; + if (defaultFormat != null){ + if (defaultFormat.radius != null){ + this.defaultFormat.args.radius = defaultFormat.radius; + } + } + + if (selectedFormat != null){ + if (selectedFormat.radius != null){ + this.selected.args.radius = selectedFormat.radius; + } + } + + if (overFormat != null){ + if (overFormat.radius != null){ + this.over.args.radius = overFormat.radius; + } + } + + if (draggingFormat != null){ + if (draggingFormat.radius != null){ + this.dragging.args.draggingFormat = draggingFormat.radius; + } + } +}; + + + +SquareVertexGraphFormatter.prototype.getDefault = VertexGraphFormatter.prototype.getDefault; +SquareVertexGraphFormatter.prototype.getSelected = VertexGraphFormatter.prototype.getSelected; +SquareVertexGraphFormatter.prototype.getOver = VertexGraphFormatter.prototype.getOver; +SquareVertexGraphFormatter.prototype.getDragging = VertexGraphFormatter.prototype.getDragging; +SquareVertexGraphFormatter.prototype.getId = VertexGraphFormatter.prototype.getId; +SquareVertexGraphFormatter.prototype.toJSON = VertexGraphFormatter.prototype.toJSON; +SquareVertexGraphFormatter.prototype.loadFromJSON = VertexGraphFormatter.prototype.loadFromJSON; +SquareVertexGraphFormatter.prototype._setEvents = VertexGraphFormatter.prototype._setEvents; + +function SquareVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ + VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); + this.args.type = "SquareVertexGraphFormatter"; + if (defaultFormat != null){ + if (defaultFormat.radius != null){ + this.defaultFormat.args.radius = defaultFormat.radius; + } + } + + if (selectedFormat != null){ + if (selectedFormat.radius != null){ + this.selected.args.radius = selectedFormat.radius; + } + } + + if (overFormat != null){ + if (overFormat.radius != null){ + this.over.args.radius = overFormat.radius; + } + } + + if (draggingFormat != null){ + if (draggingFormat.radius != null){ + this.dragging.args.draggingFormat = draggingFormat.radius; + } + } +}; + + +EllipseVertexGraphFormatter.prototype.getDefault = VertexGraphFormatter.prototype.getDefault; +EllipseVertexGraphFormatter.prototype.getSelected = VertexGraphFormatter.prototype.getSelected; +EllipseVertexGraphFormatter.prototype.getOver = VertexGraphFormatter.prototype.getOver; +EllipseVertexGraphFormatter.prototype.getDragging = VertexGraphFormatter.prototype.getDragging; +EllipseVertexGraphFormatter.prototype.getId = VertexGraphFormatter.prototype.getId; +EllipseVertexGraphFormatter.prototype.toJSON = VertexGraphFormatter.prototype.toJSON; +EllipseVertexGraphFormatter.prototype.loadFromJSON = VertexGraphFormatter.prototype.loadFromJSON; +EllipseVertexGraphFormatter.prototype._setEvents = VertexGraphFormatter.prototype._setEvents; + +function EllipseVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ + VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); + this.args.type = "EllipseVertexGraphFormatter"; + if (defaultFormat != null){ + if (defaultFormat.radius != null){ + this.defaultFormat.args.radius = defaultFormat.radius; + } + } + + if (selectedFormat != null){ + if (selectedFormat.radius != null){ + this.selected.args.radius = selectedFormat.radius; + } + } + + if (overFormat != null){ + if (overFormat.radius != null){ + this.over.args.radius = overFormat.radius; + } + } + + if (draggingFormat != null){ + if (draggingFormat.radius != null){ + this.dragging.args.draggingFormat = draggingFormat.radius; + } + } +}; + + + +RectangleVertexGraphFormatter.prototype.getDefault = ItemGraphFormatter.prototype.getDefault; +RectangleVertexGraphFormatter.prototype.getSelected = ItemGraphFormatter.prototype.getSelected; +RectangleVertexGraphFormatter.prototype.getOver = ItemGraphFormatter.prototype.getOver; +RectangleVertexGraphFormatter.prototype.getDragging = ItemGraphFormatter.prototype.getDragging; +RectangleVertexGraphFormatter.prototype.getId = ItemGraphFormatter.prototype.getId; +RectangleVertexGraphFormatter.prototype.toJSON = ItemGraphFormatter.prototype.toJSON; +RectangleVertexGraphFormatter.prototype.loadFromJSON = ItemGraphFormatter.prototype.loadFromJSON; +RectangleVertexGraphFormatter.prototype._setEvents = ItemGraphFormatter.prototype._setEvents; + +function RectangleVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ + VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); + this.args.type = "RectangleVertexGraphFormatter"; + if (defaultFormat != null){ + if (defaultFormat.radius != null){ + this.defaultFormat.args.radius = defaultFormat.radius; + } + } + + if (selectedFormat != null){ + if (selectedFormat.radius != null){ + this.selected.args.radius = selectedFormat.radius; + } + } + + if (overFormat != null){ + if (overFormat.radius != null){ + this.over.args.radius = overFormat.radius; + } + } + + if (draggingFormat != null){ + if (draggingFormat.radius != null){ + this.dragging.args.draggingFormat = draggingFormat.radius; + } + } +}; + + + +RoundedVertexGraphFormatter.prototype.getDefault = ItemGraphFormatter.prototype.getDefault; +RoundedVertexGraphFormatter.prototype.getSelected = ItemGraphFormatter.prototype.getSelected; +RoundedVertexGraphFormatter.prototype.getOver = ItemGraphFormatter.prototype.getOver; +RoundedVertexGraphFormatter.prototype.getDragging = ItemGraphFormatter.prototype.getDragging; +RoundedVertexGraphFormatter.prototype.getId = ItemGraphFormatter.prototype.getId; +RoundedVertexGraphFormatter.prototype.toJSON = ItemGraphFormatter.prototype.toJSON; +RoundedVertexGraphFormatter.prototype.loadFromJSON = ItemGraphFormatter.prototype.loadFromJSON; +RoundedVertexGraphFormatter.prototype._setEvents = ItemGraphFormatter.prototype._setEvents; + +function RoundedVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ + VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); + this.args.type = "RoundedVertexGraphFormatter"; + if (defaultFormat != null){ + if (defaultFormat.radius != null){ + this.defaultFormat.args.radius = defaultFormat.radius; + } + } + + if (selectedFormat != null){ + if (selectedFormat.radius != null){ + this.selected.args.radius = selectedFormat.radius; + } + } + + if (overFormat != null){ + if (overFormat.radius != null){ + this.over.args.radius = overFormat.radius; + } + } + + if (draggingFormat != null){ + if (draggingFormat.radius != null){ + this.dragging.args.draggingFormat = draggingFormat.radius; + } + } +}; + + + +OctagonVertexGraphFormatter.prototype.getDefault = ItemGraphFormatter.prototype.getDefault; +OctagonVertexGraphFormatter.prototype.getSelected = ItemGraphFormatter.prototype.getSelected; +OctagonVertexGraphFormatter.prototype.getOver = ItemGraphFormatter.prototype.getOver; +OctagonVertexGraphFormatter.prototype.getDragging = ItemGraphFormatter.prototype.getDragging; +OctagonVertexGraphFormatter.prototype.getId = ItemGraphFormatter.prototype.getId; +OctagonVertexGraphFormatter.prototype.toJSON = ItemGraphFormatter.prototype.toJSON; +OctagonVertexGraphFormatter.prototype.loadFromJSON = ItemGraphFormatter.prototype.loadFromJSON; +OctagonVertexGraphFormatter.prototype._setEvents = ItemGraphFormatter.prototype._setEvents; + +function OctagonVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ + VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); + this.args.type = "OctagonVertexGraphFormatter"; + if (defaultFormat != null){ + if (defaultFormat.radius != null){ + this.defaultFormat.args.radius = defaultFormat.radius; + } + } + + if (selectedFormat != null){ + if (selectedFormat.radius != null){ + this.selected.args.radius = selectedFormat.radius; + } + } + + if (overFormat != null){ + if (overFormat.radius != null){ + this.over.args.radius = overFormat.radius; + } + } + + if (draggingFormat != null){ + if (draggingFormat.radius != null){ + this.dragging.args.draggingFormat = draggingFormat.radius; + } + } +}; + + + +var Colors = new function() +{ + this.hashColor = []; + this.getColorByScoreArrayValue = function (arrayScore) + { + var array = new Array(); + + for (var i = 0; i< arrayScore.length; i++) + { + + var color = this.getColorByScoreValue(arrayScore[i]) + array.push( color); + + } + return array; + }; + + this.getHexStringByScoreArrayValue = function (arrayScore) + { + var arrayColor = this.getColorByScoreArrayValue(arrayScore); + var arrayHex = new Array(); + for (var i = 0; i< arrayColor.length; i++) + { + arrayHex.push( arrayColor[i].HexString()); + } + return arrayHex; + }; + + this.getColorByScoreValue = function (score) + { + + var truncate = score.toString().substr(0,4); + if (this.hashColor[truncate]!=null) + { + return this.hashColor[truncate]; + } + + + if(isNaN(score)) { + return Colors.ColorFromRGB(0,0,0); + } + var value; + + var from, to; + if(score < 0.5) { + from = Colors.ColorFromRGB(0,0,255); + to = Colors.ColorFromRGB(255,255,255); + value = (score * 2); + } else { + from = Colors.ColorFromRGB(255,255,255); + to = Colors.ColorFromRGB(255,0,0); + value = (score * 2) - 1; + } + + var x = value; + var y = 1.0 - value; + var color = Colors.ColorFromRGB(y * from.Red() + x * to.Red(), y * from.Green() + x * to.Green(), y * from.Blue() + x * to.Blue()); + + this.hashColor[truncate] = color; + + return color; + }; + + this.ColorFromHSV = function(hue, sat, val) + { + var color = new Color(); + color.SetHSV(hue,sat,val); + return color; + }; + + this.ColorFromRGB = function(r, g, b) + { + var color = new Color(); + color.SetRGB(r,g,b); + return color; + }; + + this.ColorFromHex = function(hexStr) + { + var color = new Color(); + color.SetHexString(hexStr); + return color; + }; + + function Color() { + //Stored as values between 0 and 1 + var red = 0; + var green = 0; + var blue = 0; + + //Stored as values between 0 and 360 + var hue = 0; + + //Strored as values between 0 and 1 + var saturation = 0; + var value = 0; + + this.SetRGB = function(r, g, b) + { + red = r/255.0; + green = g/255.0; + blue = b/255.0; + calculateHSV(); + }; + + this.Red = function() { return Math.round(red*255); }; + + this.Green = function() { return Math.round(green*255); }; + + this.Blue = function() { return Math.round(blue*255); }; + + this.SetHSV = function(h, s, v) + { + hue = h; + saturation = s; + value = v; + calculateRGB(); + }; + + this.Hue = function() + { return hue; }; + + this.Saturation = function() + { return saturation; }; + + this.Value = function() + { return value; }; + + this.SetHexString = function(hexString) + { + if(hexString == null || typeof(hexString) != "string") + { + this.SetRGB(0,0,0); + return; + } + + if (hexString.substr(0, 1) == '#') + hexString = hexString.substr(1); + + if(hexString.length != 6) + { + this.SetRGB(0,0,0); + return; + } + + var r = parseInt(hexString.substr(0, 2), 16); + var g = parseInt(hexString.substr(2, 2), 16); + var b = parseInt(hexString.substr(4, 2), 16); + if (isNaN(r) || isNaN(g) || isNaN(b)) + { + this.SetRGB(0,0,0); + return; + } + + this.SetRGB(r,g,b); + }; + + this.HexString = function() + { + + var rStr = this.Red().toString(16); + if (rStr.length == 1) + rStr = '0' + rStr; + var gStr = this.Green().toString(16); + if (gStr.length == 1) + gStr = '0' + gStr; + var bStr = this.Blue().toString(16); + if (bStr.length == 1) + bStr = '0' + bStr; + return ('#' + rStr + gStr + bStr).toUpperCase(); + }; + + this.Complement = function() + { + var newHue = (hue >= 180) ? hue - 180 : hue + 180; + var newVal = (value * (saturation - 1) + 1); + var newSat = (value*saturation) / newVal; + var newColor = new Color(); + newColor.SetHSV(newHue, newSat, newVal); + return newColor; + } ; + + function calculateHSV() + { + var max = Math.max(Math.max(red, green), blue); + var min = Math.min(Math.min(red, green), blue); + + value = max; + + saturation = 0; + if(max != 0) + saturation = 1 - min/max; + + hue = 0; + if(min == max) + return; + + var delta = (max - min); + if (red == max) + hue = (green - blue) / delta; + else if (green == max) + hue = 2 + ((blue - red) / delta); + else + hue = 4 + ((red - green) / delta); + hue = hue * 60; + if(hue < 0) + hue += 360; + } + + function calculateRGB() + { + red = value; + green = value; + blue = value; + + if(value == 0 || saturation == 0) + return; + + var tHue = (hue / 60); + var i = Math.floor(tHue); + var f = tHue - i; + var p = value * (1 - saturation); + var q = value * (1 - saturation * f); + var t = value * (1 - saturation * (1 - f)); + switch(i) + { + case 0: + red = value; green = t; blue = p; + break; + case 1: + red = q; green = value; blue = p; + break; + case 2: + red = p; green = value; blue = t; + break; + case 3: + red = p; green = q; blue = value; + break; + case 4: + red = t; green = p; blue = value; + break; + default: + red = value; green = p; blue = q; + break; + } + } + } +} +(); +/* + * Clase gestiona la insercción, eliminación de los elementos en el DOM + * + * Vital hacerla SIEMPRE compatible hacia atrás + * + * Last update: 28-10-2010 + * + */ + + +var DOM = {}; + +DOM.createNewElement = function(type, nodeParent, attributes) +{ + + var node = document.createElement(type); + for (var i=0; i0) + { + parent.removeChild(parent.childNodes[0]); + + } +}; + +DOM.select = function(targetID) +{ + return document.getElementById(targetID); +// return $("#"+targetID); +}; +var Geometry = +{ + + /** From tow points obtains the angles formed with the cartesian side **/ + getAngleBetweenTwoPoints : function(x1, y1, x2, y2){ + //var m = (y1 - y2)/ (x1 - x2); + return Math.atan2(y2-y1, x2-x1); + }, + + getAdjacentSideOfRectangleRight : function(angle, hypotenuse){ + return Math.abs(Math.cos(angle)*hypotenuse); + }, + + getOppositeSideOfRectangleRight : function(angle, hypotenuse){ + return Math.abs(Math.sin(angle)*hypotenuse); + }, + + toDegree: function(radian){ + return radian*180/Math.PI; + + } + + +}; + +var SVG = +{ + svgns : 'http://www.w3.org/2000/svg', + xlinkns : "http://www.w3.org/1999/xlink", + + createSVGCanvas: function(parentNode, attributes) + { + + attributes.push( ['xmlns', SVG.svgns], ['xmlns:xlink', 'http://www.w3.org/1999/xlink']); + var svg = document.createElementNS("http://www.w3.org/2000/svg", "svg"); + this._setProperties(svg, attributes); + parentNode.appendChild( svg); + return svg; + + }, + + createRectangle : function (x, y, width, height, attributes){ + var rect = document.createElementNS(this.svgns, "rect"); + rect.setAttribute("x",x); + rect.setAttribute("y",y); + rect.setAttribute("width",width); + rect.setAttribute("height",height); + SVG._setProperties(rect, attributes); + return rect; + }, + + drawImage64 : function (x, y, width, height, base64, svgNode, attributes) { + var node = SVG.createImage64(x, y, width, height, base64, attributes); + svgNode.appendChild(node); + return node; + }, + + createImage64 : function (x, y, width, height, base64, attributes) { + var img = document.createElementNS(this.svgns, "image"); + img.setAttribute("x",x); + img.setAttribute("y",y); + img.setAttribute("width",width); + img.setAttribute("height",height); + img.setAttribute("xlink:href",base64); + SVG._setProperties(img, attributes); + return img; + }, + + createLine: function (x1, y1, x2, y2, attributes){ + var line = document.createElementNS(this.svgns,"line"); + line.setAttribute("x1",x1); + line.setAttribute("y1",y1); + line.setAttribute("x2", x2); + line.setAttribute("y2", y2); + SVG._setProperties(line, attributes); + return line; + }, + + createClip: function (id, nodeToClip, attributes){ + var clip = document.createElementNS(this.svgns,"clipPath"); + clip.setAttribute("id",id); + clip.appendChild(nodeToClip); + return clip; + }, + + drawClip : function (id, nodeToClip, svgNode) { + var node = SVG.createClip(id, nodeToClip); + svgNode.appendChild(node); + return node; + }, + + drawRectangle : function (cx, cy, width, height, svgNode, attributes) { + try{ + var node = SVG.createRectangle(cx, cy, width, height, attributes); + svgNode.appendChild(node); + } + catch(e){ + + console.log("-------------------- "); + console.log("Error on drawRectangle " + e); + console.log(attributes); + console.log("-------------------- "); + } + return node; + }, + + createEllipse : function (x, y, rx, ry, attributes){ + var rect = document.createElementNS(this.svgns, "ellipse"); + rect.setAttribute("cx",x); + rect.setAttribute("cy",y); + rect.setAttribute("rx",rx); + rect.setAttribute("ry",ry); + SVG._setProperties(rect, attributes); + return rect; + }, + + drawEllipse : function (cx, cy, rx, ry, svgNode, attributes) { + var node = SVG.createEllipse(cx, cy, rx, ry, attributes); + svgNode.appendChild(node); + return node; + }, + + drawImage : function (x, y, canvasSVG, attributes) { + var image = document.createElementNS(this.svgns, "image"); + image.setAttribute("x",x); + image.setAttribute("y",y); + canvasSVG.appendChild(image); + SVG._setProperties(image, attributes); + }, + + drawLine : function (x1, y1, x2, y2, nodeSVG, attributes) { + try{ + var line = SVG.createLine(x1, y1, x2, y2, attributes); + nodeSVG.appendChild(line); + }catch(e){ + } + return line; + }, + + + drawPath: function (d, nodeSVG, attributes) { + var path = SVG.createPath(d, attributes); + nodeSVG.appendChild(path); + return path; + }, + + createPoligon : function (points, attributes){ + var poligon = document.createElementNS(this.svgns, "polygon"); + poligon.setAttribute("points",points); + SVG._setProperties(poligon, attributes); + return poligon; + }, + + drawPoligon : function (points, canvasSVG, attributes){ + var poligon = SVG.createPoligon(points, attributes); + canvasSVG.appendChild(poligon); + return poligon; + }, + // + + createPath : function (d, attributes){ + var path = document.createElementNS(this.svgns, "path"); + path.setAttribute("d",d); + SVG._setProperties(path, attributes); + return path; + }, + + drawCircle : function (x, y, radio, canvasSVG, attributes) { + + var newText = document.createElementNS(this.svgns,"circle"); + newText.setAttribute("cx",x); + newText.setAttribute("cy",y); + newText.setAttribute("r",radio); + + canvasSVG.appendChild(newText); + attributes["cursor"] = "pointer"; + this._setProperties(newText, attributes); + return newText; + }, + + + _setProperties: function(node, attributes) + { + if (attributes instanceof Array){ + for (var i=0; i< attributes.length; i++) + { + node.setAttribute(attributes[i][0], attributes[i][1]); + } + } + else{ + for ( var key in attributes){ + node.setAttribute(key, attributes[key]); + } + } + }, + +/* drawPath: function(pointsArray, canvasSVG, attributes){ + var path = document.createElementNS(this.svgns,"polyline"); + path.setAttribute ('id', id); + + var d= pointsArray[0].x+ " "+ pointsArray[0].y; + for (var i=1; i< pointsArray.length; i++) + { + d=d+" "+pointsArray[i].x+" "+pointsArray[i].y; + } + path.setAttribute ('points', d); + canvasSVG.appendChild(path); + },*/ + + createText : function (x, y, text, attributes) { + var node = document.createElementNS(this.svgns,"text"); + node.setAttributeNS(null , "x",x); + node.setAttributeNS(null, "y",y); + + var textNode = document.createTextNode(text); + node.appendChild(textNode); + + this._setProperties(node, attributes); + return node; + }, + + drawText : function (x, y, text, canvasSVG, attributes) { + var text = SVG.createText(x, y, text, attributes); + canvasSVG.appendChild(text); + return text; + }, + + + + drawGroup: function(svgNode, attributes) + { + var group = SVG.createGroup(attributes); + svgNode.appendChild(group); + return group; + }, + + createGroup: function(attributes){ + var group = document.createElementNS(this.svgns,"g"); + this._setProperties(group, attributes); + return group; + } + +}; + + + +var CanvasToSVG = { + + convert: function(sourceCanvas, targetSVG, x, y, id, attributes) { + + var img = this._convert(sourceCanvas, targetSVG, x, y, id); + + for (var i=0; i< attributes.length; i++) + { + img.setAttribute(attributes[i][0], attributes[i][1]); + } + }, + + _convert: function(sourceCanvas, targetSVG, x, y, id) { + var svgNS = "http://www.w3.org/2000/svg"; + var xlinkNS = "http://www.w3.org/1999/xlink"; + // get base64 encoded png from Canvas + var image = sourceCanvas.toDataURL(); + + // must be careful with the namespaces + var svgimg = document.createElementNS(svgNS, "image"); + + svgimg.setAttribute('id', id); + + //svgimg.setAttribute('class', class); + //svgimg.setAttribute('xlink:href', image); + svgimg.setAttributeNS(xlinkNS, 'xlink:href', image); + + + + + svgimg.setAttribute('x', x ? x : 0); + svgimg.setAttribute('y', y ? y : 0); + svgimg.setAttribute('width', sourceCanvas.width); + svgimg.setAttribute('height', sourceCanvas.height); + //svgimg.setAttribute('cursor', 'pointer'); + svgimg.imageData = image; + + targetSVG.appendChild(svgimg); + return svgimg; + }, + + importSVG: function(sourceSVG, targetCanvas) { + svg_xml = sourceSVG;//(new XMLSerializer()).serializeToString(sourceSVG); + var ctx = targetCanvas.getContext('2d'); + + var img = new Image(); + img.src = "data:image/svg+xml;base64," + btoa(svg_xml); +// img.onload = function() { + ctx.drawImage(img, 0, 0); +// }; + } + +}; +/* +Graph.prototype.importSVG = function(sourceSVG, targetCanvas) { + sourceSVG = this._svg; + targetCanvas = document.createElementNS('canvas'); + // https://developer.mozilla.org/en/XMLSerializer + svg_xml = (new XMLSerializer()).serializeToString(sourceSVG); + var ctx = targetCanvas.getContext('2d'); + // this is just a JavaScript (HTML) image + var img = new Image(); + // http://en.wikipedia.org/wiki/SVG#Native_support + // https://developer.mozilla.org/en/DOM/window.btoa + img.src = "data:image/svg+xml;base64," + btoa(svg_xml); + img.onload = function() { + // after this, Canvas’ origin-clean is DIRTY + ctx.drawImage(img, 0, 0); + } +}; +*/ + +/* + +Normalizacion de datos para dibujar colores +Issues: + No sé como debería llamarse esta libreria + No sé si ya existe una funciçon en javascript que lo haga + + +*/ + + +var Normalizer = new function() +{ + this.normalizeArray = function (arrayData) + { + + return this.standardizeArray(this.normal(arrayData)); + +// var result = this._getMaxAndMin(arrayData); +// var min =result[0]; +// var max = result[1]; +// +// +// //los hacemos todos positivos +// for (var i = 0; i< arrayData.length; i++) +// { +// arrayData[i]= Math.abs(min) + parseFloat(arrayData[i]); +// } +// +// var result = this._getMaxAndMin(arrayData); +// var min =result[0]; +// var max = result[1]; +// +// +// var resultArray = new Array(); +// for (var i = 0; i< arrayData.length; i++) +// { +// resultArray.push(arrayData[i]*1/max); +// } +// return resultArray; + }; + + this.normal = function(arrayData){ + var mean = this._getMean(arrayData); + var deviation = this._getStdDeviation(arrayData); + var result = this._getMaxAndMin(arrayData); + var min = result[0]; + var max = result[1]; + + var resultArray = new Array(); + for (var i = 0; i< arrayData.length; i++) { + if (deviation!=0){ + resultArray.push((arrayData[i]-mean)/deviation); + }else{ + resultArray.push(arrayData[i]); + } + } + return resultArray; + }; + + this.standardizeArray = function(arrayData) + { + var result = this._getMaxAndMin(arrayData); + var min = result[0]; + var max = result[1]; + + var offset = ( min <= 0 ) ? Math.abs(min) : (-1 * min); + var resultArray = new Array(); + for (var i = 0; i< arrayData.length; i++) { + if(max + offset!=0){ + resultArray.push((arrayData[i] + offset) / (max + offset)); + }else{ + resultArray.push(arrayData[i]+offset); + } + } + return resultArray; + }; + + + this._getMean = function(arrayData) { + var sum = 0; + for (var i = 0; i< arrayData.length; i++) { + sum = sum + parseFloat(arrayData[i]); + } + return sum/arrayData.length; + }; + + this._getStdDeviation = function(arrayData) { + var mean = this._getMean(arrayData); + var acum = 0.0; + for(var i=0; i max) max = parseFloat(arrayData[i]); + } + + return [min, max]; + }; +}; +function GraphCanvas(componentID, targetNode, args) { + this.args = {}; + /** target */ + this.targetID = targetNode.id; + + /** id manage */ + this.id = componentID; + this.args.idGraph = this.id + "main"; + this.args.idBackgroundNode = this.id + "background"; + + this.args.idEdgesGraph = this.id + "edges"; + this.args.idNodesGraph = this.id + "vertices"; + this.args.idLabelGraph = this.id + "label"; + this.args.idBackground = this.id + "background"; + + /** Objects Graph **/ + this.dataset = null; + this.formatter = null; + this.layout = null; + + /** Drawing **/ + this.circleDefaultRadius = 2; + this.squareDefaultSide = this.circleDefaultRadius * 1.5; + + /** Directed Arrow **/ + this.arrowDefaultSize = this.circleDefaultRadius; + + /** Groups **/ + this.GraphGroup = null; + this.GraphNodeGroup = null; + this.GraphLabelGroup = null; + this.GraphBackground = null; + + /** SETTINGS FLAGS **/ + this.args.draggingCanvasEnabled = false; //Flag to set if the canvas can be dragged + this.args.multipleSelectionEnabled = false; + this.args.interactive = false; + this.args.labeled = false; + this.args.linkEnabled = false; + + /** If numberEdge > maxNumberEdgesMoving then only it will move edges when mouse up **/ + this.args.maxNumberEdgesMoving = 3; + this.args.maxNumberEdgesFiringEvents = 50; + + /** Linking edges **/ + this.args.linking = false; + this.linkStartX = 0; + this.linkStartY = 0; + this.linkSVGNode = null; + this.linkNodeSource = null; + this.linkNodeTarget = null; + + /** Dragging Control **/ + this.draggingElement = null; + this.dragging = false; + this.nMouseOffsetX = 0; + this.nMouseOffsetY = 0; + this.dragStartX = 0; + this.dragStartY = 0; + this.desplazamientoX = 0; + this.desplazamientoY = 0; + + /** Selection Control **/ + this.selecting = false; + this.selectorX = null; + this.selectorY = null; + this.selectorSVGNode = null; + + /** Node status **/ + this.args.isVertexSelected = {}; + this.args.selectedVertices = []; + + /** Edges status **/ + this.args.isEdgeSelected = {}; + //this.args.selectedEdges = []; + + if (args != null) { + if (args.multipleSelectionEnabled != null) { + this.args.multipleSelectionEnabled = args.multipleSelectionEnabled; + this.args.draggingCanvasEnabled = !(this.args.multipleSelectionEnabled); + } + if (args.draggingCanvasEnabled != null) { + this.args.draggingCanvasEnabled = args.draggingCanvasEnabled; + this.args.multipleSelectionEnabled = !(this.args.draggingCanvasEnabled); + } + if (args.interactive != null) { + this.args.interactive = args.interactive; + } + if (args.labeled != null) { + this.args.labeled = args.labeled; + } + + } + + /** Hashmap with the svg node labels **/ + this.svgLabels = {}; + + /** EVENTS **/ + this.onVertexOut = new Event(this); + this.onVertexOver = new Event(this); + this.onVertexSelect = new Event(this); + this.onEdgeSelect = new Event(this); + this.onCanvasClicked = new Event(this); + this.onVertexUp = new Event(this); +} + +GraphCanvas.prototype.showLabels = function(value) { + this.args.labeled = value; + this.removeLabels(); + if (value) { + this.renderLabels(); + } +}; + +GraphCanvas.prototype.getSelectedVertices = function() { + return this.args.selectedVertices; +}; + +GraphCanvas.prototype.getSelectedEdges = function() { + var selected = []; + for ( var selectedEdge in this.args.isEdgeSelected) { + selected.push(selectedEdge); + } + return selected; +}; + +GraphCanvas.prototype.createSVGDom = function(targetID, id, width, height, backgroundColor) { + var container = document.getElementById(targetID); + this._svg = SVG.createSVGCanvas(container, [ + [ "style", "background-color:" + backgroundColor + ";" ], [ "id", id ], [ "dragx", 0 ], [ "dragy", 0 ], + [ "height", this.getFormatter().getHeight() ], [ "width", this.getFormatter().getWidth() ] ]); + return this._svg; +}; + +/** MULTIPLE SELECTION **/ +GraphCanvas.prototype.isMultipleSelectionEnabled = function() { + return this.args.multipleSelectionEnabled; +}; + +GraphCanvas.prototype.setMultipleSelection = function(value) { + this.args.multipleSelectionEnabled = value; + this.args.draggingCanvasEnabled = (!value); +}; + +GraphCanvas.prototype.setSelecting = function(value) { + this.selecting = value; +}; + +/** linking **/ +GraphCanvas.prototype.setLinking = function(value) { + this.args.linkEnabled = value; + this.selecting = !value; + this.dragging = !value; +}; + +/** CANVAS MOVING **/ +GraphCanvas.prototype.setDraggingCanvas = function(value) { + this.args.draggingCanvasEnabled = value; + this.args.multipleSelectionEnabled = !value; +}; + +GraphCanvas.prototype.isDraggingCanvasEnabled = function() { + return this.args.draggingCanvasEnabled; +}; +/** ZOOM **/ +GraphCanvas.prototype.getScale = function() { + return this.getFormatter().getZoomScale(); +}; + +GraphCanvas.prototype.setScale = function(scale) { + var graphNode = document.getElementById(this.args.idGraph); + graphNode.setAttribute("transform", graphNode.getAttribute("transform").replace("scale(" + this.getScale() + ")", "scale(" + scale + ")")); + this.getFormatter().setZoomScale(scale); +}; + +GraphCanvas.prototype.zoomIn = function() { + this.setScale(this.getScale() + this.getFormatter().getZoomScaleStepFactor()); +}; + +GraphCanvas.prototype.zoomOut = function() { + this.setScale(this.getScale() - this.getFormatter().getZoomScaleStepFactor()); + +}; + +/** SVG COORDENATES **/ +GraphCanvas.prototype.getSVGCoordenates = function(evt) { + var p = this._svg.createSVGPoint(); + p.x = evt.clientX; + p.y = evt.clientY; + + var m = this._svg.getScreenCTM(document.documentElement); + p = p.matrixTransform(m.inverse()); + return p; +}; + +/** SVG EVENTS **/ +GraphCanvas.prototype.mouseClick = function(event) { + if (event.button == 0) { + if (!this.args.interactive) { + return; + } + + if (this.isVertex(event.target)) { + this.clickNode(this.getVertexIdFromSVGId(event.target.id)); + } + /** Como el evento mouseClick viene despues del mouse up es aqui donde manejo el tema de deseccionar los elementos que estoy dragging **/ + if (this.dragging) { + this.dragging = false; + } + } +}; + +GraphCanvas.prototype.mouseMove = function(evt) { + if (this.selecting) { + this.clearLabels(); + + var width = (this.getSVGCoordenates(evt).x - this.selectorX); + var height = (this.getSVGCoordenates(evt).y - this.selectorY); + if ((width > 0) && (height > 0)) { + this.displaySelection(this.selectorX, this.selectorY, width, height); + } + if ((width > 0) && (height < 0)) { + this.displaySelection(this.selectorX, this.getSVGCoordenates(evt).y, width, Math.abs(height)); + } + if ((width < 0) && (height < 0)) { + this.displaySelection(this.getSVGCoordenates(evt).x, this.getSVGCoordenates(evt).y, Math.abs(width), Math.abs(height)); + } + if ((width < 0) && (height > 0)) { + this.displaySelection(this.selectorX + width, this.selectorY, Math.abs(width), Math.abs(height)); + } + + var x1 = (parseFloat(this.selectorSVGNode.getAttribute("x")) - DOM.select(this.id).getAttribute("dragx")) / this.getFormatter().getWidth(); + var y1 = (parseFloat(this.selectorSVGNode.getAttribute("y")) - DOM.select(this.id).getAttribute("dragy")) / this.getFormatter().getHeight(); + var x2 = (x1 + parseFloat(this.selectorSVGNode.getAttribute("width") / this.getFormatter().getWidth())); + var y2 = (y1 + parseFloat(this.selectorSVGNode.getAttribute("height") / this.getFormatter().getHeight())); + + this.deselectNodes(this.getLayout()); + var verticesSelected = this.getLayout().getVerticesByArea(x1 / this.getFormatter().getZoomScale(), y1 / this.getFormatter().getZoomScale(), + x2 / this.getFormatter().getZoomScale(), y2 / this.getFormatter().getZoomScale()); + for ( var i = 0; i < verticesSelected.length; i++) { + this.selectNode(verticesSelected[i].getId()); + this.renderLabel(verticesSelected[i].getId()); + } + + } + var p = null; + if (this.args.linking) { + p = this.getSVGCoordenates(evt); + if (this.linkSVGNode != null) { + this.linkSVGNode.setAttribute("x2", p.x - 2); + this.linkSVGNode.setAttribute("y2", p.y - 2); + } + } + + if (this.dragging) { + p = this.getSVGCoordenates(evt); + p.x -= this.nMouseOffsetX; + p.y -= this.nMouseOffsetY; + this.desplazamientoX = (this.getSVGCoordenates(evt).x - this.dragStartX);// + parseFloat(DOM.select(this.id).getAttribute("dragx")); + this.desplazamientoY = (this.getSVGCoordenates(evt).y - this.dragStartY);// + parseFloat(DOM.select(this.id).getAttribute("dragy")); + + if (this.draggingElement != null) { + /** Click sobre el recct del banground que provoca que mueva todo el canvas **/ + if (this.isNodeCanvas(this.draggingElement)) { + + p = this.getSVGCoordenates(evt); + p.x = this.desplazamientoX; + p.y = this.desplazamientoY; + + this.draggingElement.setAttribute("dragx", p.x); + this.draggingElement.setAttribute("dragy", p.y); + this.draggingElement = document.getElementById(this.args.idGraph); + this.draggingElement.setAttribute("transform", "translate(" + p.x + "," + p.y + "), scale(" + this.getScale() + ")"); + + DOM.select(this.id).setAttribute("dragx", p.x); + DOM.select(this.id).setAttribute("dragy", p.y); + + if (this.NodeSVGbackgroundImage != null) { + this.NodeSVGbackgroundImage.setAttribute("dragx", p.x); + this.NodeSVGbackgroundImage.setAttribute("dragy", p.y); + } + } else { + if (this.isVertex(this.draggingElement)) { + this.selectNode(this.getVertexIdFromSVGId(this.draggingElement.id)); + this.desplazamientoX = this.desplazamientoX / this.getFormatter().getZoomScale(); + this.desplazamientoY = this.desplazamientoY / this.getFormatter().getZoomScale(); + this.moveSelectedNodes(this.desplazamientoX, this.desplazamientoY); + + this.dragStartX = this.getSVGCoordenates(evt).x; + this.dragStartY = this.getSVGCoordenates(evt).y; + } else { + if (this.isNodeBackground(this.draggingElement)) { + + this.draggingElement.setAttribute("dragx", p.x); + this.draggingElement.setAttribute("dragy", p.y); + this.draggingElement = document.getElementById(this.args.idGraph); + this.draggingElement.setAttribute("transform", "translate(" + p.x + "," + p.y + "), scale(" + this.getScale() + ")"); + } else { + this.draggingElement.setAttribute("transform", "translate(" + p.x + "," + p.y + ")"); + } + } + } + } + } +}; + +GraphCanvas.prototype.moveSelectedNodes = function(offsetX, offsetY) { + for ( var i = 0; i < this.getSelectedVertices().length; i++) { + + var nodeId = this.getSelectedVertices()[i]; + var svgNodeId = this.getSVGNodeId(nodeId); + + var x = parseFloat(DOM.select(svgNodeId).getAttribute("dragx")) + parseFloat(offsetX);// - parseFloat(DOM.select(this.id).getAttribute("dragx")); + var y = parseFloat(DOM.select(svgNodeId).getAttribute("dragy")) + parseFloat(offsetY);// + parseFloat(DOM.select(this.id).getAttribute("dragy")); + + this._movingNode(DOM.select(svgNodeId), x, y); + } +}; + +GraphCanvas.prototype.mouseDown = function(evt) { + if (event.button == 0) { + + /** if !no interactive mouse events do anything **/ + if (!this.args.interactive) { + return; + } + + var p = this.getSVGCoordenates(evt); + + /** When click on canvas or background deselect all **/ + if (this.isNodeCanvas(evt.target) || this.isNodeBackground(evt.target)) { + this.deselectNodes(); + this.deselectEdges(); + this.onCanvasClicked.notify(); + } + + /** if I am linking vertices **/ + if (this.args.linkEnabled) { + + if (!this.args.linking) { + this.args.linking = true; + if (this.isVertex(evt.target)) { + this.linkStartX = p.x; + this.linkStartY = p.y; + this.linkSVGNode = SVG.drawLine(p.x, p.y, p.x, p.y, this._svg, { + "stroke" : "#FF0000" + }); + this.linkNodeSource = this.getVertexIdFromSVGId(evt.target.id); + } + } else { + this.linkNodeTarget = this.getVertexIdFromSVGId(evt.target.id); + this.args.linking = false; + this.args.linkEnabled = false; + if (this.isVertex(evt.target)) { + this.getDataset().addEdge(this.linkNodeSource + "_" + this.linkNodeTarget, this.linkNodeSource, this.linkNodeTarget, {}); + } + this.linkSVGNode.parentNode.removeChild(this.linkSVGNode); + } + return; + } + + /** Id is a vertex or the canvas **/ + if (this.isVertex(evt.target) || this.isNodeCanvas(evt.target) || this.isNodeBackground(evt.target)) { + this._startDragging(evt); + } + /** if i is edge **/ + if (this.isEdge(evt.target)) { + this.selectEdge(this.getEdgeIdFromSVGId(evt.target.getAttribute("id"))); + } + + if (this.args.multipleSelectionEnabled) { + if (!this.dragging) { + this.setSelecting(true); + this.selectorX = p.x; + this.selectorY = p.y; + this.displaySelection(p.x, p.y, 1, 1); + } + } + + } + if (event.button == 1) { + this.setLinking(false); + this.setMultipleSelection(false); + this.selecting = false; + + /** Id is a vertex or the canvas **/ + if (this.isVertex(evt.target) || this.isNodeCanvas(evt.target) || this.isNodeBackground(evt.target)) { + this._startDragging(evt); + } + } +}; + +GraphCanvas.prototype.mouseUp = function(event) { + if (!this.args.interactive) { + return; + } + + if (this.dragging) { + this._stopDragging(event); + if (this.isVertex(event.target)) { + var vertexId = this.getVertexIdFromSVGId(event.target.id); + if (this.getDataset().getVertexById(vertexId).getEdges().length >= this.args.maxNumberEdgesMoving) { + this.moveEdge(vertexId); + } + } + } + + if (this.selecting) { + this.setSelecting(false); + + var x1 = (parseFloat(this.selectorSVGNode.getAttribute("x")) - DOM.select(this.id).getAttribute("dragx")) / this.getFormatter().getWidth(); + var y1 = (parseFloat(this.selectorSVGNode.getAttribute("y")) - DOM.select(this.id).getAttribute("dragy")) / this.getFormatter().getHeight(); + var x2 = (x1 + parseFloat(this.selectorSVGNode.getAttribute("width") / this.formatter.getWidth())); + var y2 = (y1 + parseFloat(this.selectorSVGNode.getAttribute("height") / this.formatter.getHeight())); + + var verticesSelected = this.getLayout().getVerticesByArea(x1 / this.getFormatter().getZoomScale, y1 / this.getFormatter().getZoomScale, + x2 / this.getFormatter().getZoomScale, y2 / this.getFormatter().getZoomScale); + + for ( var i = 0; i < verticesSelected.length; i++) { + this.selectNode(verticesSelected[i].getId()); + } + + if (this.selectorSVGNode != null) { + this._svg.removeChild(this.selectorSVGNode); + } + + if (this.args.labeled) { + this.clearLabels(); + this.renderLabels(); + } + + this.selectorSVGNode = null; + // this.renderLabels(); + } +}; + +/** SELECTION **/ +GraphCanvas.prototype.displaySelection = function(x, y, width, height) { + if (this.selectorSVGNode != null) { + this.selectorSVGNode.setAttribute("x", x); + this.selectorSVGNode.setAttribute("y", y); + this.selectorSVGNode.setAttribute("width", width); + this.selectorSVGNode.setAttribute("height", height); + } else { + this.selectorSVGNode = SVG.drawRectangle(x, y, width, height, this._svg, { + "fill" : "red", + "stroke" : "black", + "opacity" : "0.2", + "stroke-opacity" : "1" + }); + } +}; + +/** DRAGGING **/ +GraphCanvas.prototype._startDragging = function(evt) { + if (!this.isDraggingCanvasEnabled()) { + if (this.isNodeCanvas(evt.target)) { + this.draggingElement = null; + } + } + + if (this.isVertex(evt.target) || (this.isNodeBackground(evt.target) && (this.isDraggingCanvasEnabled()))|| (this.isNodeCanvas(evt.target) && (this.isDraggingCanvasEnabled()))) { + this.clearLabels(); + this.draggingElement = evt.target; + this.dragging = true; + var p = this.getSVGCoordenates(evt); + + this.nMouseOffsetX = p.x - parseInt(evt.target.getAttribute("dragx")); + this.nMouseOffsetY = p.y - parseInt(evt.target.getAttribute("dragy")); + + if (this.isVertex(evt.target)) { + this.dragStartX = parseInt(this.draggingElement.getAttribute("dragx")) * this.getFormatter().getZoomScale() + + parseFloat(DOM.select(this.id).getAttribute("dragx")); + this.dragStartY = parseInt(this.draggingElement.getAttribute("dragy")) * this.getFormatter().getZoomScale() + + parseFloat(DOM.select(this.id).getAttribute("dragy")); + } else { + this.dragStartX = p.x - parseInt(this.draggingElement.getAttribute("dragx"));// + parseFloat(DOM.select(this.id).getAttribute("dragx")); + this.dragStartY = p.y - parseInt(this.draggingElement.getAttribute("dragy"));// + parseFloat(DOM.select(this.id).getAttribute("dragy")); + } + } +}; + +GraphCanvas.prototype._stopDragging = function(event) { + this.nMouseOffsetX = 0; + this.nMouseOffsetX = 0; + /** despues del evento up viene el evento click entonces acabo el dragging en el mouseclick **/ + this.dragging = false; + this.draggingElement = null; + this.renderLabels(); + + this.setLinking(false); + this.setMultipleSelection(true); + this.selecting = false; + +}; + +/** Move the edges of the vertex with the vertexId indicado **/ +GraphCanvas.prototype.moveEdge = function(vertexId) { + var x = this.getLayout().getNodeById(vertexId).x * this.getFormatter().getWidth(); + var y = this.getLayout().getNodeById(vertexId).y * this.getFormatter().getHeight(); + + /** Moving edges out **/ + for ( var i = 0; i < this.getDataset().getVertexById(vertexId).getEdgesOut().length; i++) { + var edgeId = this.getDataset().getVertexById(vertexId).getEdgesOut()[i].getId(); + var svgEdgeId = this.getSVGEdgeId(edgeId); + var edgeFormatter = this.getFormatter().getEdgeById(edgeId); + if (edgeFormatter instanceof LineEdgeGraphFormatter) { + DOM.select(svgEdgeId + "_shadow").setAttribute("x2", x); + DOM.select(svgEdgeId + "_shadow").setAttribute("y2", y); + DOM.select(svgEdgeId).setAttribute("x2", x); + DOM.select(svgEdgeId).setAttribute("y2", y); + } + + if ((edgeFormatter instanceof DirectedLineEdgeGraphFormatter) || (edgeFormatter instanceof OdirectedLineEdgeGraphFormatter) + || (edgeFormatter instanceof OdotDirectedLineEdgeGraphFormatter) || (edgeFormatter instanceof DotDirectedLineEdgeGraphFormatter) + || (edgeFormatter instanceof CutDirectedLineEdgeGraphFormatter)) { + this.removeEdge(edgeId); + this.renderEdge(edgeId); + } + } + + /** Moving edges in **/ + for ( var i = 0; i < this.getDataset().getVertexById(vertexId).getEdgesIn().length; i++) { + var edgeId = this.getDataset().getVertexById(vertexId).getEdgesIn()[i].getId(); + var svgEdgeId = this.getSVGEdgeId(edgeId); + var edgeFormatter = this.getFormatter().getEdgeById(edgeId); + if (edgeFormatter instanceof LineEdgeGraphFormatter) { + DOM.select(svgEdgeId).setAttribute("x1", x); + DOM.select(svgEdgeId).setAttribute("y1", y); + DOM.select(svgEdgeId + "_shadow").setAttribute("x1", x); + DOM.select(svgEdgeId + "_shadow").setAttribute("y1", y); + } + + if ((edgeFormatter instanceof DirectedLineEdgeGraphFormatter) || (edgeFormatter instanceof OdirectedLineEdgeGraphFormatter) + || (edgeFormatter instanceof OdotDirectedLineEdgeGraphFormatter) || (edgeFormatter instanceof DotDirectedLineEdgeGraphFormatter) + || (edgeFormatter instanceof CutDirectedLineEdgeGraphFormatter)) { + this.removeEdge(edgeId); + this.renderEdge(edgeId); + } + + if (edgeFormatter instanceof BezierEdgeGraphFormatter) { + var radius = this.getFormatter().getVertexById(vertexId).getDefault().getSize() * this.getFormatter().getNodesMaxSize(); + var d = this.calculateCoordenatesBezier(radius, x, y); + DOM.select(svgEdgeId).setAttribute("d", d); + } + } +}; + +GraphCanvas.prototype.moveNode = function(vertexId) { + var x = this.getLayout().getNodeById(vertexId).x * this.getFormatter().getWidth(); + var y = this.getLayout().getNodeById(vertexId).y * this.getFormatter().getHeight(); + var svgNodeElement = DOM.select(this.getSVGNodeId(vertexId)); + + svgNodeElement.setAttribute("dragx", x); + svgNodeElement.setAttribute("dragy", y); + svgNodeElement.setAttribute("transform", "translate(" + x + "," + y + ")"); + + if (this.getDataset().getVertexById(vertexId).getEdges().length < this.args.maxNumberEdgesMoving) { + this.moveEdge(vertexId); + } +}; + +GraphCanvas.prototype._movingNode = function(svgNodeElement, x, y) { + var vertexId = this.getVertexIdFromSVGId(svgNodeElement.getAttribute("id")); + this.getLayout().getNodeById(vertexId).setCoordinates(x / this.getFormatter().getWidth(), y / this.getFormatter().getHeight()); + this.desplazamientoX = 0; + this.desplazamientoY = 0; + this.removeLabel(vertexId); + this.renderLabel(vertexId); +}; + +/** INIT **/ +GraphCanvas.prototype.init = function() { + + this._svg = this.createSVGDom(this.targetID, this.id, this.getFormatter().getWidth(), this.getFormatter().getHeight(), this.getFormatter() + .getBackgroundColor()); + this.GraphGroup = SVG.drawGroup(this._svg, [ [ "id", this.args.idGraph ], [ "transform", "translate(0,0), scale(1)" ] ]); + this.GraphBackground = SVG.drawGroup(this.GraphGroup, [ [ "id", this.args.idBackground ] ]); + this.GraphEdgeGroup = SVG.drawGroup(this.GraphGroup, [ [ "id", this.args.idEdgesGraph ] ]); + this.GraphNodeGroup = SVG.drawGroup(this.GraphGroup, [ [ "id", this.args.idNodesGraph ] ]); + this.GraphLabelGroup = SVG.drawGroup(this.GraphGroup, [ [ "id", this.args.idLabelGraph ] ]); + + if ((this.getFormatter().getBackgroundImage() != null) && (this.getFormatter().getBackgroundImage() != "")) { + this.setBackgroundImage(this.getFormatter().getBackgroundImage()); + } + /** SVG Events listener */ + var _this = this; + this._svg.addEventListener("click", function(event) { + _this.mouseClick(event); + }, false); + this._svg.addEventListener("mousemove", function(event) { + _this.mouseMove(event, _this); + }, false); + this._svg.addEventListener("mousedown", function(event) { + _this.mouseDown(event, _this); + }, false); + this._svg.addEventListener("mouseup", function(event) { + _this.mouseUp(event, _this); + }, false); +}; + +/* + GraphCanvas.prototype.backgroungToSVG = function(){ + var _this = this; + var canvas = document.createElement('canvas'); + canvas.setAttribute("id", "canvas"); + canvas.width = this.formatter.getWidth(); + canvas.height = this.formatter.getHeight(); + + this._svg.parentNode.parentNode.appendChild(canvas); + var ctx = document.getElementById('canvas').getContext('2d'); + var img = new Image(); + + img.src = this.formatter.getBackgroundImage(); + ctx.drawImage(img,0,0 ,_this.formatter.getWidth(), _this.formatter.getHeight()); + + + img.onload = function() { + canvas.parentNode.removeChild(canvas); + } + + this.NodeSVGbackgroundImage.setAttribute("xlink:href", document.getElementById("canvas").toDataURL()); + this.NodeSVGbackgroundImage.removeAttribute("href"); + + // + + };*/ + +GraphCanvas.prototype.setBackgroundImage = function() { + if (this.NodeSVGbackgroundImage != null) { + this.NodeSVGbackgroundImage.parentNode.removeChild(this.NodeSVGbackgroundImage); + } + $('#' + this.targetID).svg(); + $('#' + this.targetID).svg("get"); + + $('#' + this.targetID).svg("get")._svg = document.getElementById(this.id); + + var svg = $('#' + this.targetID).svg("get"); + this.NodeSVGbackgroundImage = svg.image(0, 0, this.getFormatter().getWidth(), this.getFormatter().getHeight(), this.getFormatter() + .getBackgroundImage()); + this.NodeSVGbackgroundImage.setAttribute("id", this.args.idBackgroundNode); + + this.NodeSVGbackgroundImage.setAttribute("x", 0); + this.NodeSVGbackgroundImage.setAttribute("y", 0); + + this.NodeSVGbackgroundImage.setAttribute("dragx", 0); + this.NodeSVGbackgroundImage.setAttribute("dragy", 0); + + if (this.getFormatter().args.backgroundImageHeight != null) { + this.NodeSVGbackgroundImage.setAttribute("height", this.getFormatter().args.backgroundImageHeight); + } + if (this.getFormatter().args.backgroundImageWidth != null) { + this.NodeSVGbackgroundImage.setAttribute("width", this.getFormatter().args.backgroundImageWidth); + } + + if (this.getFormatter().args.backgroundImageX != null) { + this.NodeSVGbackgroundImage.setAttribute("x", this.getFormatter().args.backgroundImageX); + } + if (this.getFormatter().args.backgroundImageY != null) { + this.NodeSVGbackgroundImage.setAttribute("y", this.getFormatter().args.backgroundImageY); + } + + this.GraphBackground.appendChild(this.NodeSVGbackgroundImage); + this.NodeSVGbackgroundImage.removeAttribute("href"); + this.NodeSVGbackgroundImage.setAttribute("xlink:href", this.getFormatter().getBackgroundImage()); +}; + +GraphCanvas.prototype.removeBackgroundImage = function() { + if (this.NodeSVGbackgroundImage != null) { + this.NodeSVGbackgroundImage.parentNode.removeChild(this.NodeSVGbackgroundImage); + } +}; + +GraphCanvas.prototype._setBackgroundColor = function(color) { + var attributes = [ [ "fill", color ] ]; + SVG.drawRectangle(0, 0, this.getFormatter().getWidth(), this.getFormatter().getHeight(), this.GraphBackground, attributes); +}; + +/** Serialize **/ +GraphCanvas.prototype.toJSON = function() { + var json = {}; + json.dataset = {}; + json.formatter = {}; + json.layout = {}; + json.dataset = this.getDataset().toJSON(); + json.formatter = this.getFormatter().toJSON(); + json.layout = this.getLayout().toJSON(); + return json; +}; + +GraphCanvas.prototype.toHTML = function() { + //this.backgroungToSVG(); + var html = this._svg.parentElement.innerHTML; + + var start = html.indexOf("") + 6; + + return html.substr(start, end); +}; + +/** DRAW **/ +GraphCanvas.prototype.draw = function(graphdataset, graphformatter, graphlayout) { + this.setDataset(graphdataset); + this.setFormatter(graphformatter); + this.setLayout(graphlayout); + + var _this = this; + this.getFormatter().changed.attach(function(sender, item) { + _this.removeNode(item.getId()); + _this.renderNode(item.getId()); + if (_this.args.labeled) { + _this.removeLabel(item.getId()); + _this.renderLabel(item.getId()); + } + + }); + //TODO + this.getFormatter().edgeChanged.attach(function(sender, item) { + _this.removeEdge(item.getId()); + _this.renderEdge(item.getId()); + }); + + this.getFormatter().resized.attach(function(sender, item) { + _this.resize(_this.getFormatter().getWidth(), _this.getFormatter().getHeight()); + }); + + this.getFormatter().backgroundImageChanged.attach(function(sender, item) { + _this.setBackgroundImage(_this.getFormatter().getBackgroundImage()); + }); + + this.getFormatter().backgroundColorChanged.attach(function(sender, item) { + _this._setBackgroundColor(_this.getFormatter().getBackgroundColor()); + }); + + this.getLayout().changed.attach(function(sender, item) { + _this.moveNode(item.getId()); + _this.moveEdge(item.getId()); + if (_this.args.labeled) { + _this.removeLabel(item.getId()); + _this.renderLabel(item.getId()); + } + }); + + this.getDataset().newVertex.attach(function(sender, item) { + + _this.renderNode(item.getId()); + if (_this.args.labeled) { + _this.renderLabel(item.getId()); + } + }); + + this.getDataset().newEdge.attach(function(sender, item) { + _this.renderEdge(item.getId()); + }); + + this.getDataset().vertexDeleted.attach(function(sender, item) { + _this.removeNode(item.getId()); + if (_this.args.labeled) { + _this.removeLabel(item.getId()); + } + }); + + this.getDataset().edgeDeleted.attach(function(sender, item) { + _this.removeEdge(item.getId()); + }); + + this.getDataset().vertexNameChanged.attach(function(sender, args) { + if (_this.args.labeled) { + _this.removeLabel(args.item.getId()); + _this.removeLabel(args.item.getId()); + _this.renderLabel(args.item.getId()); + } + }); + this.init(); + this.render(); +}; + +GraphCanvas.prototype.render = function() { + for ( var id in this.getDataset().getVertices()) { + this.renderNode(id); + } + this.renderLabels(); + this.renderEdges(); +}; + +GraphCanvas.prototype.renderLabels = function() { + if (this.args.labeled) { + for ( var id in this.getDataset().getVertices()) { + this.renderLabel(id); + } + } +}; + +GraphCanvas.prototype.removeLabels = function() { + for ( var id in this.getDataset().getVertices()) { + this.removeLabel(id); + } +}; + +/** Utilities method for nodes **/ +GraphCanvas.prototype.isNodeCanvas = function(node) { + return ((node.id == this.args.idGraph) || (node.id == this.id)); +}; + +GraphCanvas.prototype.isNodeBackground = function(node) { + return ((node.id == this.args.idBackgroundNode)); +}; + +GraphCanvas.prototype.isVertex = function(node) { + if (node.getAttribute("id") != null) { + if (node.getAttribute("id").indexOf("_v_") != -1) { + return true; + } + } + return false; +}; + +GraphCanvas.prototype.isLabel = function(node) { + if (node.getAttribute("id") != null) { + if (node.getAttribute("id").indexOf("_l_") != -1) { + return true; + } + } + return false; +}; + +GraphCanvas.prototype.isEdge = function(node) { + if (node.getAttribute("id") != null) { + if (node.getAttribute("id").indexOf("_e_") != -1) { + return true; + } + } + return false; +}; + +/** Resize **/ +GraphCanvas.prototype.resize = function(width, height) { + // this._svg.setAttribute("width", width); + // this._svg.setAttribute("height", height); + if (this.NodeSVGbackgroundImage != null) { + this.NodeSVGbackgroundImage.setAttribute("width", width); + this.NodeSVGbackgroundImage.setAttribute("height", height); + } + + this._svg.setAttribute("width", width); + this._svg.setAttribute("height", height); + + this.clearCanvas(); + this.render(); +}; + +GraphCanvas.prototype.clearCanvas = function() { + DOM.removeChilds(this.GraphEdgeGroup.getAttribute("id")); + DOM.removeChilds(this.GraphNodeGroup.getAttribute("id")); + this.clearLabels(); +}; + +GraphCanvas.prototype.clearLabels = function() { + DOM.removeChilds(this.GraphLabelGroup.getAttribute("id")); +}; + +/** ID'S converter **/ +GraphCanvas.prototype.getSVGNodeId = function(nodeId) { + return this.id + "_v_" + nodeId; +}; + +GraphCanvas.prototype.getSVGEdgeId = function(edgeId) { + return this.id + "_e_" + edgeId; +}; + +GraphCanvas.prototype.getSVGArrowEdgeId = function(edgeId) { + return this.id + "_arrow_" + edgeId; +}; + +GraphCanvas.prototype.getSVGLabelId = function(edgeId) { + return this.id + "_l_" + edgeId; +}; + +GraphCanvas.prototype.blinkVertexById = function(vertexId) { + $("#" + this.getSVGNodeId(vertexId)).fadeIn().fadeOut().fadeIn().fadeOut().fadeIn().fadeOut(); +}; + +GraphCanvas.prototype.getVertexIdFromSVGId = function(svgVertexId) { + return svgVertexId.replace(this.id, "").replace("_v_", ""); +}; + +GraphCanvas.prototype.getEdgeIdFromSVGId = function(svgEdgeId) { + return svgEdgeId.replace(this.id, "").replace("_e_", ""); +}; + +/** VERTEX **/ +GraphCanvas.prototype.getVertexById = function(id) { + return document.getElementById(this.getSVGNodeId(id)); +}; + +GraphCanvas.prototype.renderNodes = function() { + for ( var id in this.getDataset().getVertices()) { + this.renderNode(id); + } +}; + +GraphCanvas.prototype.overNode = function(nodeId) { + if (!this.args.interactive) { + return; + } + /** If selected we don't change the format **/ + if (this.args.isVertexSelected[nodeId] == null) { + var args = this.getFormatter().getVertexById(nodeId).getOver(); + args.args["cursor"] = 'pointer'; + this.changeVertexFormat(nodeId, args); + } +}; + +GraphCanvas.prototype.outNode = function(nodeId) { + if (!this.args.interactive) { + return; + } + + /** If selected we don't change the format **/ + if (this.args.isVertexSelected[nodeId] == null) { + this.changeVertexFormat(nodeId, this.getFormatter().getVertexById(nodeId).getDefault()); + } +}; + +GraphCanvas.prototype.overLabel = function(nodeId) { + this.overNode(nodeId); + // this.svgLabels[nodeId].setAttribute("cursor", "pointer"); +}; + +GraphCanvas.prototype.outLabel = function(nodeId) { + this.outNode(nodeId); + // this.svgLabels[nodeId].setAttribute("cursor", ""); +}; + +GraphCanvas.prototype.clickNode = function(nodeId) { + if (!this.args.interactive) { + return; + } + + /** si el evento se dispara oprque estaba dragging entonces no activo nada **/ + if (this.args.isVertexSelected[nodeId] == null) { + this.selectNode(nodeId); + } else { + this.deselectNode(nodeId); + } +}; + +GraphCanvas.prototype.selectNode = function(nodeId) { + for ( var i = 0; i < this.args.selectedVertices.length; i++) { + var format = this.getFormatter().getVertexById(nodeId).getSelected(); + format.opacity = 0.2; + this.changeVertexFormat(nodeId, this.getFormatter().getVertexById(nodeId).getSelected()); + } + + if (this.args.isVertexSelected[nodeId] == null) { + var format = this.getFormatter().getVertexById(nodeId).getSelected(); + format.opacity = 1; + this.changeVertexFormat(nodeId, this.getFormatter().getVertexById(nodeId).getSelected()); + this.args.selectedVertices.push(nodeId); + this.args.isVertexSelected[nodeId] = this.args.selectedVertices.length - 1; + this.onVertexSelect.notify(nodeId); + } +}; + +GraphCanvas.prototype.selectAllEdges = function() { + this.deselectNodes(); + this.deselectEdges(); + + for ( var edgesId in this.getDataset().edges) { + this.selectEdge(edgesId); + } +}; + +GraphCanvas.prototype.selectAllNodes = function() { + this.deselectNodes(); + this.deselectEdges(); + + for ( var vertexId in this.getDataset().vertices) { + this.selectNode(vertexId); + } +}; + +GraphCanvas.prototype.selectAll = function() { + this.deselectNodes(); + this.deselectEdges(); + + for ( var vertexId in this.getDataset().vertices) { + this.selectNode(vertexId); + } + + for ( var edgesId in this.getDataset().edges) { + this.selectEdge(edgesId); + } +}; + +GraphCanvas.prototype.selectEdge = function(edgeId) { + if (this.args.isEdgeSelected[edgeId] == null) { + this.changeEdgeFormat(edgeId, this.getFormatter().getEdgeById(edgeId).getSelected()); + //this.args.selectedEdges.push(edgeId); + this.args.isEdgeSelected[edgeId] = true; //this.args.selectedEdges.length - 1; + this.onEdgeSelect.notify(edgeId); + } +}; + +GraphCanvas.prototype.selectEdges = function(edges) { + + for ( var i = 0; i < edges.length; i++) { + this.selectEdge(edges[i]); + } +}; + +GraphCanvas.prototype.deselectNode = function(nodeId) { + if (this.args.isVertexSelected[nodeId] != null) { + this.changeVertexFormat(nodeId, this.getFormatter().getVertexById(nodeId).getDefault()); + this.args.selectedVertices.splice(this.args.isVertexSelected[nodeId], 1); + var index = this.args.isVertexSelected[nodeId]; + delete this.args.isVertexSelected[nodeId]; + + for ( var vertex in this.args.isVertexSelected) { + if (this.args.isVertexSelected[vertex] > index) { + this.args.isVertexSelected[vertex] = this.args.isVertexSelected[vertex] - 1; + } + } + } +}; + +GraphCanvas.prototype.deselectNodes = function() { + var selected = JSON.parse(JSON.stringify(this.getSelectedVertices())); + for ( var i = 0; i < selected.length; i++) { + this.deselectNode(selected[i]); + } +}; +GraphCanvas.prototype.selectNodes = function(idNodes) { + + for ( var i = 0; i < idNodes.length; i++) { + this.selectNode(idNodes[i]); + } + + // for ( var vertex in this.args.isVertexSelected) { + // if (this.args.isVertexSelected[vertex] > index){ + // this.args.isVertexSelected[vertex] = this.args.isVertexSelected[vertex] - 1; + // } + // } + +}; + +GraphCanvas.prototype.changeVertexFormat = function(nodeId, format) { + var svgNode = DOM.select(this.getSVGNodeId(nodeId)); + if (svgNode != null) { + var properties = format.toJSON(); + for ( var item in properties) { + svgNode.setAttribute(item, properties[item]); + } + + if (this.getFormatter().getVertexById(nodeId) instanceof CircleVertexGraphFormatter) { + var transform = "translate(" + svgNode.getAttribute("dragx") + "," + svgNode.getAttribute("dragy") + "), scale(" + format.getSize() + ")"; + svgNode.setAttribute("transform", transform); + } + } +}; + +GraphCanvas.prototype.renderLabel = function(nodeId) { + var x = Math.ceil(this.getLayout().getNodeById(nodeId).x * this.getFormatter().getWidth()); + var y = Math.ceil(this.getLayout().getNodeById(nodeId).y * this.getFormatter().getHeight()); + + var svgAttributesNode = JSON.parse(JSON.stringify(this.getFormatter().getVertexById(nodeId).getDefault().toJSON().title)); + svgAttributesNode.id = this.getSVGLabelId(this.getDataset().getVertexById(nodeId).getId()); + svgAttributesNode.dx = (-1) * (this.getDataset().getVertexById(nodeId).getName().length * svgAttributesNode["font-size"]) / 4 - 4; + + svgAttributesNode.dy = parseFloat((this.getFormatter().getVertexById(nodeId).getDefault().getSize())) + + parseFloat(svgAttributesNode["font-size"]) + parseFloat(this.getFormatter().getVertexById(nodeId).getDefault().getStrokeWidth()) - 4; + svgAttributesNode.dragx = Math.ceil(this.getLayout().getNodeById(nodeId).x * this.getFormatter().getWidth()); + + var gragy = parseFloat(this.getFormatter().getVertexById(nodeId).getDefault().getSize()) + + Math.ceil(this.getLayout().getNodeById(nodeId).y * this.getFormatter().getHeight()); + svgAttributesNode.dragy = gragy; + svgAttributesNode.transform = "translate(" + svgAttributesNode.dragx + "," + svgAttributesNode.dragy + ")";//, scale("+this.formatter.getVertexById(nodeId).getDefault().getSize()+")"; + + var nodeSVG = SVG.drawText(0, 0, this.getDataset().getVertexById(nodeId).getName(), this.GraphLabelGroup, svgAttributesNode); + + this.svgLabels[nodeId] = nodeSVG; + + /** Events for the SVG node **/ + var _this = this; + if (nodeSVG != null) { + nodeSVG.addEventListener("mouseover", function() { + _this.overLabel(nodeId); + }, false); + nodeSVG.addEventListener("mouseout", function() { + _this.outLabel(nodeId); + }, false); + } + +}; + +GraphCanvas.prototype.removeLabel = function(labelId) { + if (DOM.select(this.getSVGLabelId(labelId)) != null) { + DOM.select(this.getSVGLabelId(labelId)).parentNode.removeChild(DOM.select(this.getSVGLabelId(labelId))); + } +}; + +GraphCanvas.prototype.renderNode = function(nodeId) { + var svgAttributesNode = JSON.parse(JSON.stringify(this.getFormatter().getVertexById(nodeId).getDefault().toJSON())); + svgAttributesNode.dragx = Math.ceil(this.getLayout().getNodeById(nodeId).x * this.getFormatter().getWidth()); + svgAttributesNode.dragy = Math.ceil(this.getLayout().getNodeById(nodeId).y * this.getFormatter().getHeight()); + svgAttributesNode.transform = "translate(" + svgAttributesNode.dragx + "," + svgAttributesNode.dragy + ")"; + svgAttributesNode.id = this.getSVGNodeId(nodeId); + /*svgAttributesNode["stroke-width"] = 3 ; + svgAttributesNode["stroke-opacity"] = 1 ; + svgAttributesNode["fill-opacity"] = svgAttributesNode["opacity"] ; + svgAttributesNode["opacity"] = 1 ;*/ + this.circleDefaultRadius = this.getFormatter().getVertexById(nodeId).getDefault().getSize(); + var nodeSVG; + + if (this.getFormatter().getVertexById(nodeId) instanceof CircleVertexGraphFormatter) { + nodeSVG = SVG.drawCircle(0, 0, this.circleDefaultRadius, this.GraphNodeGroup, svgAttributesNode); + } + + if (this.getFormatter().getVertexById(nodeId) instanceof SquareVertexGraphFormatter) { + //nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius) ,0 - (this.formatter.getVertexById(nodeId).getDefault().getSize()) , (this.getFormatter().getVertexById(nodeId).getDefault().getSize()*2), (this.getFormatter().getVertexById(nodeId).getDefault().getSize()*2), this.GraphNodeGroup, svgAttributesNode); + nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius), 0 - (this.circleDefaultRadius), (this.circleDefaultRadius * 2), + (this.circleDefaultRadius * 2), this.GraphNodeGroup, svgAttributesNode); + } + + if (this.getFormatter().getVertexById(nodeId) instanceof EllipseVertexGraphFormatter) { + nodeSVG = SVG.drawEllipse(0, 0, this.circleDefaultRadius * 1.5, this.circleDefaultRadius, this.GraphNodeGroup, svgAttributesNode); + } + + if (this.getFormatter().getVertexById(nodeId) instanceof RectangleVertexGraphFormatter) { + //nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius) ,0 - ((this.circleDefaultRadius*2)/2) , (this.circleDefaultRadius*2), (this.circleDefaultRadius), this.GraphNodeGroup, svgAttributesNode); + nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius * 1.5), 0 - (this.circleDefaultRadius), (this.circleDefaultRadius * 2 * 1.5), + (this.circleDefaultRadius * 2), this.GraphNodeGroup, svgAttributesNode); + + } + + if (this.getFormatter().getVertexById(nodeId) instanceof RoundedVertexGraphFormatter) { + svgAttributesNode.ry = 2;// this.formatter.getVertexById(nodeId).getDefault().getSize()/4; + svgAttributesNode.rx = 2;// this.formatter.getVertexById(nodeId).getDefault().getSize()/4; + nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius * 1.5), 0 - (this.circleDefaultRadius), (this.circleDefaultRadius * 2 * 1.5), + (this.circleDefaultRadius * 2), this.GraphNodeGroup, svgAttributesNode); + } + + // + + if (this.getFormatter().getVertexById(nodeId) instanceof OctagonVertexGraphFormatter) { + svgAttributesNode.ry = 2; + svgAttributesNode.rx = 2; + nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius * 1.5), 0 - (this.circleDefaultRadius), (this.circleDefaultRadius * 2 * 1.5), + (this.circleDefaultRadius * 2), this.GraphNodeGroup, svgAttributesNode); + } + + nodeSVG.internalId = nodeId; + // + var _this = this; + + /** Events for the SVG node **/ + if (nodeSVG != null) { + nodeSVG.addEventListener("mouseover", function() { + _this.onVertexOver.notify(nodeId); + _this.overNode(nodeId); + }, false); + nodeSVG.addEventListener("mouseout", function() { + _this.onVertexOut.notify(nodeId); + _this.outNode(nodeId); + }, false); + //nodeSVG.addEventListener("click", function(){_this.clickNode(nodeId);}, false); + // + nodeSVG.addEventListener("mouseup", function() { + _this.onVertexUp.notify(nodeId); + }, false); + } +}; + +GraphCanvas.prototype.removeNode = function(nodeId) { + DOM.select(this.getSVGNodeId(nodeId)).parentNode.removeChild(DOM.select(this.getSVGNodeId(nodeId))); + if (this.args.labeled) { + this.removeLabel(nodeId); + } +}; + +/** REMOVING **/ +GraphCanvas.prototype.removeSelected = function() { + /** El orden importa **/ + this.removeSelectedEdges(); + this.removeSelectedNode(); + +}; + +GraphCanvas.prototype.removeSelectedNode = function() { + var selected = JSON.parse(JSON.stringify(this.getSelectedVertices())); + this.deselectNodes(); + var sorted = selected.sort(function(a, b) { + return a - b + }); + for ( var i = 0; i < sorted.length; i++) { + if (this.getDataset().getVertexById(sorted[i]) != null) { + this.getDataset().getVertexById(sorted[i]).remove(); + } + } +}; + +/** EDGES **/ +GraphCanvas.prototype.removeEdge = function(edgeId) { + if (DOM.select(this.getSVGEdgeId(edgeId)) != null) { + DOM.select(this.getSVGEdgeId(edgeId)).parentNode.removeChild(DOM.select(this.getSVGEdgeId(edgeId))); + } + + if (DOM.select(this.getSVGEdgeId(edgeId) + "_shadow") != null) { + DOM.select(this.getSVGEdgeId(edgeId) + "_shadow").parentNode.removeChild(DOM.select(this.getSVGEdgeId(edgeId) + "_shadow")); + } + + if (DOM.select(this.getSVGArrowEdgeId(edgeId)) != null) { + DOM.select(this.getSVGArrowEdgeId(edgeId)).parentNode.removeChild(DOM.select(this.getSVGArrowEdgeId(edgeId))); + } +}; + +GraphCanvas.prototype.overEdge = function(edgeId) { + if ((!this.args.interactive) || this.dragging || this.selecting) { + return; + } + + /** If selected we don't change the format **/ + if (this.args.isEdgeSelected[edgeId] == null) { + var format = this.getFormatter().getEdgeById(edgeId).getOver(); + format.args["cursor"] = "pointer"; + this.changeEdgeFormat(edgeId, format); + } +}; + +GraphCanvas.prototype.outEdge = function(edgeId) { + if (!this.args.interactive) { + return; + } + + /** If selected we don't change the format **/ + if (this.args.isEdgeSelected[edgeId] == null) { + this.changeEdgeFormat(edgeId, this.getFormatter().getEdgeById(edgeId).getDefault()); + } +}; + +GraphCanvas.prototype.changeEdgeFormat = function(edgeId, format) { + var svgEdge = DOM.select(this.getSVGEdgeId(edgeId) + "_shadow"); + if (svgEdge != null) { + var properties = format.toJSON(); + for ( var item in properties) { + svgEdge.setAttribute(item, properties[item]); + } + } +}; + +GraphCanvas.prototype.deselectEdge = function(edgeID) { + if (this.args.isEdgeSelected[edgeID] != null) { + this.changeEdgeFormat(edgeID, this.getFormatter().getEdgeById(edgeID).getDefault()); + var index = this.args.isEdgeSelected[edgeID]; + delete this.args.isEdgeSelected[edgeID]; + } +}; + +GraphCanvas.prototype.deselectEdges = function() { + var selected = JSON.parse(JSON.stringify(this.getSelectedEdges())); + for ( var i = 0; i < selected.length; i++) { + this.deselectEdge(selected[i]); + } +}; + +GraphCanvas.prototype.removeSelectedEdges = function() { + var selected = JSON.parse(JSON.stringify(this.getSelectedEdges())); + this.deselectEdges(); + for ( var i = 0; i < selected.length; i++) { + if (this.getDataset().getEdgeById(selected[i]) != null) { + this.getDataset().getEdgeById(selected[i]).remove(); + } + } +}; + +GraphCanvas.prototype.renderEdge = function(edgeId) { + var svgAttributesEdge = this.getFormatter().getEdgeById(edgeId).getDefault().toJSON(); + var edge = this.getDataset().getEdgeById(edgeId); + + var svgNodeTarget = this.getVertexById(edge.getNodeTarget().getId()); + var svgNodeSource = this.getVertexById(edge.getNodeSource().getId()); + svgAttributesEdge.id = this.getSVGEdgeId(edge.getId()) + "_shadow"; + + var svgEdge = null; + + if (this.getFormatter().getEdgeById(edgeId) instanceof LineEdgeGraphFormatter) { + var coordenateSourceX = svgNodeSource.getAttribute("dragx"); + var coordenateSourceY = svgNodeSource.getAttribute("dragy"); + var coordenateTargetX = svgNodeTarget.getAttribute("dragx"); + var coordenateTargetY = svgNodeTarget.getAttribute("dragy"); + + SVG.drawLine(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, this.GraphEdgeGroup, svgAttributesEdge); + var attributesShadow = {}; + attributesShadow.id = this.getSVGEdgeId(edge.getId()); + attributesShadow["stroke-opacity"] = 0; + attributesShadow["stroke-width"] = 4; + attributesShadow["stroke"] = "black"; + svgEdge = SVG.drawLine(svgNodeSource.getAttribute("dragx"), svgNodeSource.getAttribute("dragy"), svgNodeTarget.getAttribute("dragx"), + svgNodeTarget.getAttribute("dragy"), this.GraphEdgeGroup, attributesShadow); + } + + if (this.getFormatter().getEdgeById(edgeId) instanceof BezierEdgeGraphFormatter) { + var nodeId = edge.getNodeTarget().getId(); + var nodeSize = this.formatter.getVertexById(nodeId).getDefault().getSize() * this.getFormatter().getNodesMaxSize(); + svgAttributesEdge.fill = "none"; + svgAttributesEdge.id = this.getSVGEdgeId(edgeId); + var d = this.calculateCoordenatesBezier(nodeSize, svgNodeSource.getAttribute("dragx"), svgNodeSource.getAttribute("dragy")); + svgEdge = SVG.drawPath(d, this.GraphEdgeGroup, svgAttributesEdge); + } + ; + + if ((this.getFormatter().getEdgeById(edgeId) instanceof DirectedLineEdgeGraphFormatter) + || (this.getFormatter().getEdgeById(edgeId) instanceof CutDirectedLineEdgeGraphFormatter) + || (this.getFormatter().getEdgeById(edgeId) instanceof DotDirectedLineEdgeGraphFormatter) + || (this.getFormatter().getEdgeById(edgeId) instanceof OdotDirectedLineEdgeGraphFormatter) + || (this.getFormatter().getEdgeById(edgeId) instanceof OdirectedLineEdgeGraphFormatter)) { + var coordenateSourceX = svgNodeSource.getAttribute("dragx"); + var coordenateSourceY = svgNodeSource.getAttribute("dragy"); + var coordenateTargetX = svgNodeTarget.getAttribute("dragx"); + var coordenateTargetY = svgNodeTarget.getAttribute("dragy"); + + var offset = parseFloat(this.getFormatter().getVertexById(this.getDataset().getEdgeById(edgeId).getNodeTarget().getId()).getDefault() + .getSize() + * this.circleDefaultRadius); + var point = this._calculateEdgePointerPosition(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, offset); + coordenateTargetX = point.x; + coordenateTargetY = point.y; + SVG.drawLine(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, this.GraphEdgeGroup, svgAttributesEdge); + + var attributesShadow = {}; + attributesShadow.id = this.getSVGEdgeId(edge.getId()); + attributesShadow["stroke-opacity"] = 0; + attributesShadow["stroke-width"] = 4; + attributesShadow["stroke"] = "black"; + svgEdge = SVG.drawLine(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, this.GraphEdgeGroup, attributesShadow); + } + + if (this.getFormatter().getEdgeById(edgeId) instanceof DirectedLineEdgeGraphFormatter + || (this.getFormatter().getEdgeById(edgeId) instanceof OdirectedLineEdgeGraphFormatter)) { + var coordenateSourceX = svgNodeSource.getAttribute("dragx"); + var coordenateSourceY = svgNodeSource.getAttribute("dragy"); + var coordenateTargetX = svgNodeTarget.getAttribute("dragx"); + var coordenateTargetY = svgNodeTarget.getAttribute("dragy"); + + var point = this._calculateEdgePointerPosition(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, offset); + coordenateTargetX = point.x; + coordenateTargetY = point.y; + + var angle = Geometry.toDegree(point.angle) + 90; + this.arrowDefaultSize = this.getFormatter().getEdgeById(edgeId).getArrowSize(); //getDefault().getArrowSize(); + var d = "-" + this.arrowDefaultSize + ",0 0,-" + parseFloat(this.arrowDefaultSize) * 2 + " " + this.arrowDefaultSize + ",0"; + + var attributes; + + if (this.getFormatter().getEdgeById(edgeId) instanceof DirectedLineEdgeGraphFormatter) { + attributes = [ + [ "fill", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], + [ "stroke", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], [ "id", this.getSVGArrowEdgeId(edgeId) ] ]; + } else { + attributes = [ + [ "fill", "#FFFFFF" ], [ "stroke", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], + [ "id", this.getSVGArrowEdgeId(edgeId) ] ]; + } + + var flechaSVGNode = SVG.drawPoligon(d, this.GraphEdgeGroup, attributes);//, ["transform", "rotate("+angle+"), translate(0,0)"]]); + flechaSVGNode.setAttribute("transform", " translate(" + coordenateTargetX + ", " + coordenateTargetY + "), rotate(" + angle + ")"); + } + ; + + if (this.getFormatter().getEdgeById(edgeId) instanceof CutDirectedLineEdgeGraphFormatter) { + var coordenateSourceX = svgNodeSource.getAttribute("dragx"); + var coordenateSourceY = svgNodeSource.getAttribute("dragy"); + var coordenateTargetX = svgNodeTarget.getAttribute("dragx"); + var coordenateTargetY = svgNodeTarget.getAttribute("dragy"); + + var point = this._calculateEdgePointerPosition(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, offset); + coordenateTargetX = point.x; + coordenateTargetY = point.y; + + var angle = Geometry.toDegree(point.angle) + 90; + + //this.arrowDefaultSize = 2; //getDefault().getArrowSize(); + var d = "-4,0 4,0 4,-2 -4,-2"; + + var flechaSVGNode = SVG.drawPoligon(d, this.GraphEdgeGroup, [ + [ "fill", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], + [ "stroke", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], [ "id", this.getSVGArrowEdgeId(edgeId) ] ]);//, ["transform", "rotate("+angle+"), translate(0,0)"]]); + flechaSVGNode.setAttribute("transform", " translate(" + coordenateTargetX + ", " + coordenateTargetY + "), rotate(" + angle + ")"); + } + ; + + if ((this.getFormatter().getEdgeById(edgeId) instanceof DotDirectedLineEdgeGraphFormatter) + || (this.getFormatter().getEdgeById(edgeId) instanceof OdotDirectedLineEdgeGraphFormatter)) { + var coordenateSourceX = svgNodeSource.getAttribute("dragx"); + var coordenateSourceY = svgNodeSource.getAttribute("dragy"); + var coordenateTargetX = svgNodeTarget.getAttribute("dragx"); + var coordenateTargetY = svgNodeTarget.getAttribute("dragy"); + var point = this._calculateEdgePointerPosition(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, offset); + coordenateTargetX = point.x; + coordenateTargetY = point.y; + var angle = Geometry.toDegree(point.angle) + 90; + // this.arrowDefaultSize = this.formatter.getEdgeById(edgeId).getArrowSize(); //getDefault().getArrowSize(); + var attributes = []; + if (this.getFormatter().getEdgeById(edgeId) instanceof OdotDirectedLineEdgeGraphFormatter) { + attributes = [ + [ "fill", "#FFFFFF" ], [ "stroke", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], + [ "id", this.getSVGArrowEdgeId(edgeId) ] ]; + } else { + attributes = [ + [ "fill", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], + [ "stroke", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], [ "id", this.getSVGArrowEdgeId(edgeId) ] ]; + } + var flechaSVGNode = SVG.drawCircle(0, 0, 4, this.GraphEdgeGroup, attributes); + flechaSVGNode.setAttribute("transform", " translate(" + coordenateTargetX + ", " + coordenateTargetY + "), rotate(" + angle + ")"); + } + ; + + var _this = this; + /** Events for the SVG edge **/ + if (svgEdge != null) { + if (this.getDataset().getEdgesCount() < this.args.maxNumberEdgesFiringEvents) { + svgEdge.addEventListener("mouseover", function() { + _this.overEdge(edgeId); + }, false); + svgEdge.addEventListener("mouseout", function() { + _this.outEdge(edgeId); + }, false); + } + } +}; + +GraphCanvas.prototype._calculateEdgePointerPosition = function(sourceX, sourceY, targetX, targetY, radius) { + var angle = Geometry.getAngleBetweenTwoPoints(sourceX, sourceY, targetX, targetY); + + /** Suponiendo el node source que este a la derecha **/ + if ((targetX - sourceX) < 0) { + var b = Geometry.getAdjacentSideOfRectangleRight(angle, radius); + targetX = parseFloat(targetX) + parseFloat(b); + arrowX = parseFloat(targetX) + parseFloat(b) + this.arrowDefaultSize / 2; + } else { + var b = Geometry.getAdjacentSideOfRectangleRight(angle, radius); + targetX = parseFloat(targetX) - parseFloat(b); + arrowX = parseFloat(targetX) - parseFloat(b) - this.arrowDefaultSize / 2; + } + + /** Suponiendo el node source que este a la arriba **/ + if ((targetY - sourceY) > 0) { + var a = Geometry.getOppositeSideOfRectangleRight(angle, radius); + targetY = parseFloat(targetY) - parseFloat(a); + arrowY = parseFloat(targetY) - parseFloat(a) - this.arrowDefaultSize / 2; + } else { + var a = Geometry.getOppositeSideOfRectangleRight(angle, radius); + targetY = parseFloat(targetY) + parseFloat(a); + arrowY = parseFloat(targetY) + parseFloat(a) - this.arrowDefaultSize / 2; + + } + + return { + "x" : arrowX, + "y" : arrowY, + "angle" : angle + }; +}; + +GraphCanvas.prototype.calculateCoordenatesBezier = function(nodeSize, x1, y1) { + var x11 = x1 - (nodeSize / 2); + var y11 = y1 - (nodeSize / 2); + + var x12 = parseFloat(x1) + parseFloat(nodeSize / 2); + var y12 = y1 - (nodeSize / 2); + + var curvePointX = (x12 - x11) / 2 + x11; + var curvePointY = y1 - (nodeSize * 2); + var d = "M" + x11 + "," + y11 + " T" + curvePointX + "," + curvePointY + " " + x12 + "," + y12; + return d; + +}; + +GraphCanvas.prototype.renderEdges = function() { + for ( var edge in this.getDataset().getEdges()) { + this.renderEdge(this.getDataset().getEdgeById(edge).getId()); + + } +}; + +GraphCanvas.prototype.getLastSelectedNode = function() { + var node = null; + if (this.getSelectedVertices().length > 0) { + var nodeId = this.getSelectedVertices()[this.getSelectedVertices().length - 1]; + node = this.getDataset().getVertexById(nodeId); + } + return node; +}; +/* + GraphCanvas.prototype.getNodeByNameAndIndex = function(node, index){ + var nodeId = this.getDataset().verticesIndex[node][index]; + var nodeItem = this.getDataset().getVertexById(nodeId); + return nodeItem; + }; + */ + +GraphCanvas.prototype.setDataset = function(dataset) { + this.dataset = dataset; +}; + +GraphCanvas.prototype.setFormatter = function(formatter) { + this.formatter = formatter; +}; + +GraphCanvas.prototype.setLayout = function(layout) { + this.layout = layout; +}; + +/** API **/ +GraphCanvas.prototype.getDataset = function() { + return this.dataset; +}; + +GraphCanvas.prototype.getFormatter = function() { + return this.formatter; +}; + +GraphCanvas.prototype.getLayout = function() { + return this.layout; +}; + +/** API DATASET **/ +GraphCanvas.prototype.addVertex = function(name, args) { + this.getDataset().addNode(name, args); +}; + +GraphCanvas.prototype.removeVertex = function(vertexId) { + this.getDataset().getVertexById(vertexId).remove(); +}; + +GraphCanvas.prototype.addEdge = function(edgeName, nodeSourceId, nodeTargetId, args) { + this.getDataset().addEdge(edgeName, nodeSourceId, nodeTargetId, args); +}; +/* + GraphCanvas.prototype.removeEdge = function(edgeId){ + this.getDataset().getEdgeById(edgeId).remove(); + }; + */ + +/** API FORMATTER **/ +GraphCanvas.prototype.getWidth = function() { + return this.getFormatter().getWidth(); +}; + +GraphCanvas.prototype.getHeight = function() { + return this.getFormatter().getHeight(); +}; + +GraphCanvas.prototype.getBackgroundImage = function() { + return this.getFormatter().getBackgroundImage(); +}; + +//GraphCanvas.prototype.setBackgroundImage = function(value){ +// this.getFormatter().setBackgroundImage(value); +//}; + +GraphCanvas.prototype.getBackgroundColor = function() { + return this.getFormatter().getBackgroundColor(); +}; + +GraphCanvas.prototype.setBackgroundColor = function() { + this.getFormatter().setBackgroundColor(value); +}; + +//GraphCanvas.prototype.setEdgeFill = function(edgeId, value){ +// this.getFormatter().getEdgeById(edgeId).getDefault().setFill(value); +//}; +// +//GraphCanvas.prototype.getEdgeFill = function(edgeId){ +// return this.getFormatter().getEdgeById(edgeId).getDefault().getFill(); +//}; + +/** VERTICES FORMATTER **/ +GraphCanvas.prototype.setVertexSize = function(vertexId, value) { + this.getFormatter().getVertexById(vertexId).getDefault().setSize(value); +}; + +GraphCanvas.prototype.getVertexSize = function(vertexId) { + return this.getFormatter().getVertexById(vertexId).getDefault().getSize(); +}; + +GraphCanvas.prototype.setVertexStroke = function(vertexId, value) { + this.getFormatter().getVertexById(vertexId).getDefault().setStroke(value); +}; + +GraphCanvas.prototype.getVertexStroke = function(vertexId) { + return this.getFormatter().getVertexById(vertexId).getDefault().getStroke(); +}; + +GraphCanvas.prototype.setVertexStrokeOpacity = function(vertexId, value) { + this.getFormatter().getVertexById(vertexId).getDefault().setStrokeOpacity(value); +}; + +GraphCanvas.prototype.getVertexStrokeOpacity = function(vertexId) { + return this.getFormatter().getVertexById(vertexId).getDefault().getStrokeOpacity(); +}; + +GraphCanvas.prototype.setVertexOpacity = function(vertexId, value) { + this.getFormatter().getVertexById(vertexId).getDefault().setOpacity(value); +}; + +GraphCanvas.prototype.getVertexOpacity = function(vertexId) { + return this.getFormatter().getVertexById(vertexId).getDefault().getOpacity(); +}; + +GraphCanvas.prototype.setVertexFill = function(vertexId, color) { + this.getFormatter().getVertexById(vertexId).getDefault().setFill(color); +}; + +GraphCanvas.prototype.getVertexFill = function(vertexId) { + return this.getFormatter().getVertexById(vertexId).getDefault().getFill(); +}; + +/** EDGES FORMATTER **/ +GraphCanvas.prototype.setEdgeSize = function(edgeId, value) { + this.getFormatter().getEdgeById(edgeId).getDefault().setSize(value); +}; + +GraphCanvas.prototype.getEdgeSize = function(edgeId) { + return this.getFormatter().getEdgeById(edgeId).getDefault().getSize(); +}; + +GraphCanvas.prototype.setEdgeStroke = function(edgeId, value) { + this.getFormatter().getEdgeById(edgeId).getDefault().setStroke(value); +}; + +GraphCanvas.prototype.getEdgeStroke = function(edgeId) { + return this.getFormatter().getEdgeById(edgeId).getDefault().getStroke(); +}; + +GraphCanvas.prototype.setEdgeStrokeOpacity = function(edgeId, value) { + this.getFormatter().getEdgeById(edgeId).getDefault().setStrokeOpacity(value); +}; + +GraphCanvas.prototype.getEdgeStrokeOpacity = function(edgeId) { + return this.getFormatter().getEdgeById(edgeId).getDefault().getStrokeOpacity(); +}; + +GraphCanvas.prototype.setEdgeFill = function(edgeId, color) { + this.getFormatter().getEdgeById(edgeId).getDefault().setFill(color); +}; + +GraphCanvas.prototype.getEdgeFill = function(edgeId) { + return this.getFormatter().getEdgeById(edgeId).getDefault().getFill(); +}; + +/** API LAYOUT **/ +GraphCanvas.prototype.setCoordinates = function(vertexId, x, y) { + return this.getLayout().getEdgeById(vertexId).setCoordinates(x, y); +}; + + + +function HPLCGraph(args) { + this.width = 600; + this.height = 600; + this.title = ''; + this.bbar = false; + this.plotInnerPanelPadding = 10; + this.plotPanelPadding = 5; + this.id = BUI.id(); - if (record.raw.measurementId != null) { - /** For testing * */ - grid.setLoading("ISPyB: Removing measurement"); - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - grid.setLoading(false); - /** - * We get and refresh experiment - * because specimens has changed * - */ - var adapter2 = new BiosaxsDataAdapter(); - adapter2.onSuccess.attach(function(sender, experiment) { - _this.onRemoved.notify(experiment); - _this._showStatusBarReady('Ready'); - }); - if (_this.experiments.experiments[0].experimentId != null) { - adapter2.getExperimentById(_this.experiments.experiments[0].experimentId, "MEDIUM"); - _this._showStatusBarBusy("ISPyB: Removing Unused Specimens"); - } - }); + this.hidePlots = null; + this.xlabel = ""; + this.scaled = false; + this.xParam = null; + this.showRangeSelector = true; + this.interactionModel = null; + + /** for each stat the max and minimum value when it is scaled in order to show correctly in the legend **/ + this.ranges = {}; + if (args != null) { + if (args.interactionModel != null) { + this.interactionModel = args.interactionModel; + } + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + if (args.bbar != null) { + this.bbar = args.bbar; + } + if (args.title != null) { + this.title = args.title; + } + if (args.plots != null) { + this.plots = args.plots; + } + + if (args.scaled != null) { + this.scaled = args.scaled; + } + if (args.xlabel != null) { + this.xlabel = args.xlabel; + } + if (args.xParam != null) { + this.xParam = args.xParam; + } + if (args.showRangeSelector != null) { + this.showRangeSelector = args.showRangeSelector; + } + } + + this.onZoomX = new Event(this); + this.onResetZoom = new Event(this); + this.dblclick = new Event(this); +} + +HPLCGraph.prototype.getMenu = function () { + var _this = this; + /** Actions buttons **/ + var actions = []; + + function toggle(item, pressed) { + if (pressed) { + _this.plots[item.param] = true; + } else { + delete _this.plots[item.param]; + } + _this.reloadData(this.hplcData); + } + + for (var i = 0; i < this.hplcData.length; i++) { + if (this.hplcData[i].showOnMenu != false) { + var param = this.hplcData[i].param; + var style = "style='padding:0 0px 0 5px;'"; + actions.push({ + text : "
" + BUI.getRectangleColorDIV(this.hplcData[i].color, 10, 10) + " " + this.hplcData[i].label + "
", + id : _this.id + param, + param : param, + enableToggle : true, + scope : this, + toggleHandler : toggle, + pressed : (_this.plots[param] != null) + }); + } + } + actions.push("-"); + + actions.push({ + text : "Scale", + enableToggle : true, + scope : this, + pressed : this.scaled, + icon : '../images/icon_graph.png', + toggleHandler : function (item, pressed) { + _this.scaled = pressed; + _this.reloadData(this.hplcData); + } + }); + + actions.push("->"); + actions.push({ + text : "Save", + scope : this, + icon : '../images/save.gif', + handler : function (item, pressed) { + var largeImage = document.createElement("img"); + largeImage.style.display = 'block'; + largeImage.style.width = 200 + "px"; + largeImage.style.height = 200 + "px"; + largeImage.setAttribute('src', Dygraph.Export.asCanvas(this.dygraphObject.dygraph).toDataURL()); + window.open(Dygraph.Export.asCanvas(this.dygraphObject.dygraph).toDataURL(), 'Image', ''); + } + }); + + return actions; +}; - adapter.onError.attach(function(sender, data) { - alert("Error: " + data); - grid.setLoading(false); - }); +/** Looks for the maximum value and then divide everything but that value **/ +HPLCGraph.prototype.scaledData = function (data) { + for (var i = 0; i < data.length; i++) { + var values = this.getMaxAndMinValue(data[i]); + data[i] = this.divideValuesByMax(data[i], values.max); + this.ranges[data[i].label] = values; + } + return data; +}; - adapter.removeMeasurement(record.raw); - } - } - } +/** Given a stat float[] and a max number it will divide each value by max **/ +HPLCGraph.prototype.divideValuesByMax = function (stat, max) { + for (var j = 0; j < stat.data.length; j++) { + if (max != 0) { + stat.data[j] = Number(stat.data[j]) / max; + stat.std[j] = Number(stat.std[j]) / max; + } + } + return stat; +}; - } - } - }); +/** returns max value of a stat **/ +HPLCGraph.prototype.getMaxAndMinValue = function (stat) { + var max = 0; + var min = stat.data[0]; + for (var j = 0; j < stat.data.length; j++) { + if (Number(stat.data[j]) > max) { + max = Number(stat.data[j]); + } + if (Number(stat.std[j]) > max) { + max = Number(stat.std[j]); + } + if (Number(stat.data[j]) < min) { + min = Number(stat.data[j]); + } + } + return { + max : Number(max), + min : Number(min) + }; +}; - this.grid.on("afterrender", function() { +HPLCGraph.prototype.getPoint = function (data, i) { + var point = [ 10, 10, 10 ]; + var y = parseFloat(data.data[i]); + var error = parseFloat(data.std[i]); + if (data.fdata == null) { + return [ y - error, y, y + error ]; + } else { + if (data.fstd != null) { + return [ data.fstd(y - error), data.fdata(y), data.fstd(y + error) ]; + } + return [ data.fdata(y) - error, data.fdata(y), data.fdata(y) + error ]; + } + return point; +}; - function updateTime() { - try { - _this.estimatedTime = _this.estimatedTime - 1; +HPLCGraph.prototype.reloadData = function(hplcData) { + this.panel.setLoading(false); + this.hplcData = hplcData; - _this.onUpdateTime.notify({ - hours : (Number(_this.estimatedTime / 3600).toFixed()), - minutes : (Number((_this.estimatedTime / 60) % 60).toFixed()), - seconds : (Number(_this.estimatedTime % 60).toFixed()) + var data = hplcData; + - }); + /** In case of having peaks **/ + if (this.peaks != null) { + for (var peak in this.peaks) { + var values = []; + var std = []; + for (var i = 0; i < this.peaks[peak].length; i++) { + values.push(this.peaks[peak][i][1]); + std.push(this.peaks[peak][i][2]); + } + data.push({ + param : peak, + data : values, + showOnMenu : false, + fdata : function (a) { + var value = (Math.log(parseFloat(a))); + if (isNumber(value)) { + return value; + } + }, + fstd : function (a) { + var value = Math.log(Math.abs(parseFloat(a))); + if (isNumber(value)) + return value; + }, + std : std, + color : this.colorPeak[peak], + label : peak + }); + + } + } + + + if (this.scaled) { + data = this.scaledData(JSON.parse(JSON.stringify(hplcData))); + } - if (Number(_this.estimatedTime) < 0) { - _this.timer = null; - grid.setTitle(_this.title); + var paramIndex = {}; + var parsed = []; + var j = 0; + for (var i = 0; i < data[0].data.length - 1; i++) { + var aux = []; + for (j = 0; j < data.length; j++) { + if (this.plots != null) { + if (this.plots[data[j].param] != null) { + aux.push(this.getPoint(data[j], i)); + paramIndex[data[j].param] = aux.length - 1; } + } else { + aux.push([ data[j].data[i] - data[j].std[i], data[j].data[i], data[j].data[i] + data[j].std[i] ]); + } + } + parsed.push([]); - } catch (e) { - console.log(e); - _this.timer = null; + var index = i; + if (this.xParam != null) { + index = parseFloat(data[this.xParam].data[i]); + } + + parsed[parsed.length - 1].push(index); + + for (j = 0; j < data.length; j++) { + if (this.plots != null) { + if (this.plots[data[j].param] != null) { + parsed[parsed.length - 1].push(aux[paramIndex[data[j].param]]); + } + } else { + parsed[parsed.length - 1].push(aux[j]); } } + } - if (_this.estimateTime) { - var experimentList = _this.experiments; - var collected = experimentList.getMeasurementsCollected(); - if (collected.length > 0) { - if (collected[0].run3VO != null) { - try { - var end = collected[0].run3VO.timeEnd; - var start = collected[0].run3VO.timeStart; - var dstart = moment(start); - var dend = moment(end); - var seconds = Number(dend.diff(dstart) / 1000).toFixed(); + var colors = []; + var labels = [ "" ]; + for (j = 0; j < data.length; j++) { + if (this.plots != null) { + if (this.plots[data[j].param] != null) { + colors.push(data[j].color); + labels.push(data[j].label); + } + } else { + parsed[parsed.length - 1].push(aux[j]); + } + } - _this.estimatedTime = (seconds * experimentList.getMeasurementsNotCollected().length); + this._renderDygraph(parsed, colors, labels); +}; - if (_this.estimatedTime > 0) { - updateTime(); - _this.timer = setInterval(function() { - updateTime(); - }, 1000); +HPLCGraph.prototype._renderDygraph = function (parsed, colors, labels) { + this.dygraphObject = new StdDevDyGraph(this.id, { + width : this.width, + height : this.height - 10, + xlabel : this.xlabel, + showRangeSelector : this.showRangeSelector, + interactionModel : this.interactionModel, + scaled : this.scaled, + ranges : this.ranges + }); + this.dygraphObject.draw(parsed, colors, labels); + + var _this = this; + this.dygraphObject.onZoomX.attach(function (sender, args) { + try { + _this.onZoomX.notify(args); + } catch (e) { + } + }); + + this.dygraphObject.onResetZoom.attach(function (sender, args) { + try { + _this.onResetZoom.notify(args); + } catch (e) { + } + }); + + this.dygraphObject.dblclick.attach(function (sender, args) { + try { + _this.dblclick.notify(args); + } catch (e) { + } + }); + +}; + +HPLCGraph.prototype.loadData = function (data) { + var _this = this; + this.reloadData(data); + this.panel.addDocked({ + xtype : 'toolbar', + items : this.getMenu() + }); + + + if (this.bbar == true){ + this.panel.addDocked({ + xtype : 'toolbar', + dock: 'bottom', + items : [ + { + xtype: 'numberfield', + id: 'main_field_start', + fieldLabel: 'Range from', + width: 170, + labelWidth : 70, + value: 0, + minValue: 0 + }, + { + xtype: 'numberfield', + id: 'main_field_end', + fieldLabel: 'to', + width: 130, + labelWidth : 30, + value: 0, + minValue: 0 + }, + { + xtype: 'button', + text: 'Go', + handler: function () { + var start = parseFloat(Ext.getCmp("main_field_start").getValue()); + var end = parseFloat(Ext.getCmp("main_field_end").getValue()); + + if (start < 0) { + start = 0; + } + if (end < 0) { + end = 0; + } + if (start > end) { + var aux = end; + end = start; + start = aux; + } + + _this.dygraphObject.dygraph.updateOptions({ isZoomedIgnoreProgrammaticZoom: true, dateWindow: [start, end] }); + } } + ] + }); + } +}; - } catch (e) { - } - } - } - } +HPLCGraph.prototype.getPanel = function () { + this.panel = Ext.create('Ext.panel.Panel', { + padding : this.plotPanelPadding, + width : this.width + 4 * this.plotInnerPanelPadding, + height : this.height + 4 * this.plotInnerPanelPadding, + items : [ { + html : "", + id : this.id, + width : this.width, + height : this.height + } ] }); - return this.grid; + return this.panel; }; -/** Method for testing * */ -MeasurementGrid.prototype.input = function() { - var experiment = DATADOC.getExperiment_10(); - var measurements = DATADOC.getMeasurements_10(); - var proposal = DATADOC.getProposal_10(); - return { - experiment : experiment, - measurements : measurements, - proposal : proposal - }; +HPLCGraph.prototype.input = function () { + return DATADOC.getHPLCData(); }; -MeasurementGrid.prototype.test = function(targetId) { - var measurementGrid = new MeasurementGrid({ - tbar : true - - }); - BIOSAXS.proposal = new Proposal(measurementGrid.input().proposal); - var panel = measurementGrid.getPanel(measurementGrid.input().measurements, new ExperimentList([ new Experiment(measurementGrid.input().experiment) ])); - panel.render(targetId); +HPLCGraph.prototype.getDataByFrameNumber = function (frameNumber) { + var data = {}; + data.frameNumber = frameNumber; + for (var key in this.hplcData){ + data[this.hplcData[key].label] = this.hplcData[key].data[frameNumber]; + } + console.log(data); + return data; }; - -/** - * A shipment may contains one or more cases where stock solutions and sample - * plates are stored - * - * @height - * @btnEditVisible - * @btnRemoveVisible - * - * #onEditButtonClicked - */ -function MolarityGrid(args) { - this.height = 100; - this.width = 100; - if (args != null) { - if (args.height != null) { - this.height = args.height; - } - if (args.width != null) { - this.width = args.width; + +HPLCGraph.prototype.test = function (targetId) { + var mainPlotPanel = new HPLCGraph({ + title : 'I0', + width : 800, + height : 400, + plots : { + "I0" : true, + "Rg" : true, + "Mass" : true + }, + xlabel : "HPLC Frames", + scaled : this.scaled, + interactionModel : { + 'dblclick' : function (event, g, context) { + } } - } + }); + mainPlotPanel.getPanel().render(targetId); + mainPlotPanel.loadData(mainPlotPanel.input()); - var _this = this; - - this.molarityForm = new MolarityForm({height : 180, width : 455}); +}; - this.molarityForm.onSave.attach(function(sender){ - _this.molarityWindow.destroy(); - _this.updateProposal(); - - }); - - this.molarityForm.onClose.attach(function(sender){ - _this.molarityWindow.destroy(); - - }); + +function MergesHPLCGraph(args) { + HPLCGraph.prototype.constructor.call(this, args); - /** Events * */ - this.onEditButtonClicked = new Event(this); +// this.peakColors = ["#00FB42", "#00BA31", "#007C21", "#003E10"]; + this.peakColors = ["#DEBD00", "#6D9100", "#872900", "#0092CC"]; } -MolarityGrid.prototype._getColumns = function() { - return [ { - text : 'Subunit', - columns : [ { - text : "Acronym", - width : 100, - hidden : false, - dataIndex : 'acronym', - sortable : true - }, { - text : "Name", - width : 125, - hidden : false, - dataIndex : 'name', - sortable : true - }, { - text : "MM Est.", - width : 100, - dataIndex : 'molecularMass', - sortable : true, - renderer : function(grid, cls, record){ - return BUI.formatValuesUnits(record.data.molecularMass , "Da", 10, 2); - - } - } ] - }, { -// text : "Number
in assymmetric units", - text : "Ratio", - width : 100, - dataIndex : 'ratio', - tooltip : 'Number of times the subunit is present in the macromolecule', - sortable : true - }, { - id : this.id + 'MOLARITY_REMOVE', - flex : 0.1, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - return BUI.getRedButton('REMOVE'); - } - } ]; -}; -MolarityGrid.prototype._openMolarityWindow = function() { - this.molarityWindow = Ext.create('Ext.window.Window', { - title : 'Molarity', - height : 220, - width : 500, - modal : true, - items : [this.molarityForm.getPanel() ] - }).show(); -}; +MergesHPLCGraph.prototype.scaledData = HPLCGraph.prototype.scaledData; +MergesHPLCGraph.prototype.divideValuesByMax = HPLCGraph.prototype.divideValuesByMax; +MergesHPLCGraph.prototype.getMaxAndMinValue = HPLCGraph.prototype.getMaxAndMinValue; +MergesHPLCGraph.prototype.getPoint = HPLCGraph.prototype.getPoint; +MergesHPLCGraph.prototype.reloadData = HPLCGraph.prototype.reloadData; +MergesHPLCGraph.prototype._renderDygraph = HPLCGraph.prototype._renderDygraph; +MergesHPLCGraph.prototype.loadData = HPLCGraph.prototype.loadData; +MergesHPLCGraph.prototype.getPanel = HPLCGraph.prototype.getPanel; +MergesHPLCGraph.prototype.getDataByFrameNumber = HPLCGraph.prototype.getDataByFrameNumber; -MolarityGrid.prototype._getButtons = function() { - var _this = this; - return [ { - text : 'Add subunit', - icon : '../images/add.png', - handler : function() { - _this._openMolarityWindow(); + +MergesHPLCGraph.prototype.setPeaks = function (data) { + this.peaks = data; + /** get size of peaks **/ + this.peakKeys = []; + this.colorPeak = {}; + var colorCount = 1; + for (var key in this.peaks) { + if (this.peaks.hasOwnProperty(key)) { + var color = this.peakColors[colorCount % this.peakColors.length]; + colorCount = colorCount + 1; + this.peakKeys.push(key); + this.colorPeak[key] = color; } - }]; + } + this.peakKeys.sort(); }; -MolarityGrid.prototype.updateProposal = function() { +MergesHPLCGraph.prototype.getMenu = function () { var _this = this; - this.panel.setLoading(); - BIOSAXS.proposal.onInitialized.attach(function() { - if (BIOSAXS.proposal != null) { - var macromolecules = BIOSAXS.proposal.macromolecules; - for (var i = 0; i < macromolecules.length; i++) { - - if (macromolecules[i].macromoleculeId == _this.macromolecule.macromoleculeId) { - _this.refresh(macromolecules[i]); - _this.panel.setLoading(false); + /** Actions buttons **/ + var actions = []; + + function toggle(item, pressed) { + if (pressed) { + _this.plots[item.param] = true; + } else { + delete _this.plots[item.param]; + } + _this.reloadData(_this.hplcData); + } + + + /** Toolbar for peaks Average **/ + if (this.peaks != null) { + var items = []; + for (var i = 0; i < this.peakKeys.length; i++) { + var color = this.colorPeak[this.peakKeys[i]]; + items.push({ + text: "Peak #" + i + " " + this.peakKeys[i].replace("- ", " to #").replace(".0", "").replace(".0", "") + "", + peakid : this.peakKeys[i], + checked: false, + checkHandler: function (sender, pressed) { + var item = new Object(); + item.param = sender.peakid; + toggle(item, pressed); } - } + }); } - }); - BIOSAXS.proposal.init(); -}; - + + var menu = Ext.create('Ext.menu.Menu', { + id: 'mainMenu', + style: { + overflow: 'visible' + }, + items: items + }); + var tb = Ext.create('Ext.toolbar.Toolbar'); + tb.add({ + text: 'Peaks Avg.', + menu: menu + }); + actions.push(tb); + } -MolarityGrid.prototype.getPanel = function() { - var _this = this; + - this.molarityStore = Ext.create('Ext.data.Store', { - fields : [ 'acronym', 'ratio', 'comments', 'stoichiometryId', 'name', 'molecularMass' ], - sorters : { - property : 'ratio', - direction : 'DESC' + for (var i = 0; i < this.hplcData.length; i++) { + if (this.hplcData[i].showOnMenu != false) { + var param = this.hplcData[i].param; + var style = "style='padding:0 0px 0 5px;'"; + actions.push({ + text : "
" + BUI.getRectangleColorDIV(this.hplcData[i].color, 10, 10) + " " + this.hplcData[i].label + "
", + id : _this.id + param, + param : param, + enableToggle : true, + scope : this, + margin : 5, + toggleHandler : toggle, + pressed : (_this.plots[param] != null) + }); } - }); - - this.panel = Ext.create('Ext.grid.Panel', { - store : this.molarityStore, - height : this.height, - padding : 5, - columns : this._getColumns(), - listeners : { - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - - /** Remove entry * */ - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'MOLARITY_REMOVE') { - var dataAdapter = new BiosaxsDataAdapter(); - dataAdapter.onSuccess.attach(function(sender) { - _this.updateProposal(); - - }); - dataAdapter.removeStoichiometry(record.data.stoichiometryId); - _this.panel.setLoading("Removing Structure"); - } - } - }, - tbar : this._getButtons() - }); - return this.panel; -}; + } -MolarityGrid.prototype._prepareData = function(macromolecule) { - /** Return an array of [{ratio,acronym, stoichiometryId, name}] **/ - var data = []; - if (macromolecule.stoichiometry != null) { - for (var i = 0; i < macromolecule.stoichiometry.length; i++) { - var hostMacromolecule = BIOSAXS.proposal.getMacromoleculeById(macromolecule.stoichiometry[i].macromoleculeId); - data.push({ - ratio : macromolecule.stoichiometry[i].ratio, - acronym : hostMacromolecule.acronym, - comments : hostMacromolecule.comments, - molecularMass : hostMacromolecule.molecularMass, - stoichiometryId : macromolecule.stoichiometry[i].stoichiometryId, - name : hostMacromolecule.name - }); - } + actions.push("->"); + actions.push({ + text : "Save", + scope : this, + icon : '../images/save.gif', + handler : function (item, pressed) { + var largeImage = document.createElement("img"); + largeImage.style.display = 'block'; + largeImage.style.width = 200 + "px"; + largeImage.style.height = 200 + "px"; + largeImage.setAttribute('src', Dygraph.Export.asCanvas(this.dygraphObject.dygraph).toDataURL()); + window.open(Dygraph.Export.asCanvas(this.dygraphObject.dygraph).toDataURL(), 'Image', ''); } - return data; -}; + }); -MolarityGrid.prototype.refresh = function(macromolecule) { - if (macromolecule != null){ - this.molarityStore.loadData(this._prepareData(macromolecule)); - this.molarityForm.refresh(macromolecule); - this.macromolecule = macromolecule; - } + return actions; }; -MolarityGrid.prototype.input = function() { - return { - proposal : DATADOC.getProposal_10(), - dewars : DATADOC.getDewars_10() - }; +MergesHPLCGraph.prototype.input = function () { + return DATADOC.getScatteringHPLCFrameData(); }; -MolarityGrid.prototype.test = function(targetId) { - var MolarityGrid = new MolarityGrid({ - height : 150 +MergesHPLCGraph.prototype.test = function (targetId) { + var mainPlotPanel = new MergesHPLCGraph({ + title : 'Scattering', + width : this.plotWidth, + height : 500, + showRangeSelector : false, + xParam : 0, + xlabel : "scattering_I", + plots : { + "scattering_I" : true, + "subtracted_I" : true, + "buffer_I" : true + } }); - BIOSAXS.proposal = new Proposal(MolarityGrid.input().proposal); - var panel = MolarityGrid.getPanel(MolarityGrid.input().dewars); - panel.render(targetId); - + mainPlotPanel.getPanel().render(targetId); + mainPlotPanel.loadData(mainPlotPanel.input()); }; + + +function NetworkWidget(args) { + this.id = "NetworkViewer_" + Math.random().toString().replace(".", "_"); + + this.label = true; + if (args != null) { + if (args.targetId != null) { + this.targetId = args.targetId; + } + if (args.label != null) { + this.label = args.label; + } + } + + this.onVertexOver = new Event(this); + this.onVertexOut = new Event(this); +} + +NetworkWidget.prototype.draw = function(dataset, formatter, layout) { + + this.graphCanvas = new GraphCanvas(this.id, document.getElementById(this.targetId), { + "labeled" : this.label, + "multipleSelectionEnabled" : false, + "draggingCanvasEnabled" : false + }); + this.graphCanvas.draw(dataset, formatter, layout); + + var _this = this; + this.graphCanvas.onVertexOver.attach(function(sender, nodeId) { + _this.onVertexOver.notify(nodeId); + }); + + this.graphCanvas.onVertexOut.attach(function(sender, nodeId) { + _this.onVertexOut.notify(nodeId); + }); +}; + +/** SELECT VERTICES BY NAME * */ +NetworkWidget.prototype.selectVertexByName = function(vertexName) { + var vertices = this.getDataset().getVertexByName(vertexName); + if (vertices != null) { + for ( var nodeId in vertices) { + if (vertices.hasOwnProperty(nodeId)) { + var vertexId = vertices[nodeId].getId(); + this.selectVertexById(vertexId); + } + } + } +}; + +NetworkWidget.prototype.selectVerticesByName = function(verticesName) { + for ( var i = 0; i < verticesName.length; i++) { + this.selectVertexByName(verticesName[i]); + } +}; + +/** SELECT VERTICES BY ID * */ +NetworkWidget.prototype.selectVertexById = function(vertexId) { + this.graphCanvas.selectNode(vertexId); + this.blinkVertexById(vertexId); +}; + +NetworkWidget.prototype.selectVerticesById = function(verticesId) { + for ( var i = 0; i < verticesId.length; i++) { + this.selectVertexById(verticesId[i]); + } +}; + +/** VECINDARIO * */ +NetworkWidget.prototype.selectNeighbourhood = function() { + this.selectEdgesFromVertices(); + this.selectAdjacent(); +}; +/** DESELECT * */ +NetworkWidget.prototype.deselectNodes = function() { + this.graphCanvas.deselectNodes(); +}; + +/** SELECT ALL NODES * */ +NetworkWidget.prototype.selectAllNodes = function() { + this.getGraphCanvas().selectAllNodes(); +}; + +/** SELECT EVERYTHING * */ +NetworkWidget.prototype.selectAll = function() { + this.getGraphCanvas().selectAll(); +}; + +/** SELECT ALL EDGES * */ +NetworkWidget.prototype.selectAllEdges = function() { + this.getGraphCanvas().selectAllEdges(); +}; + +/** ZOOM * */ +NetworkWidget.prototype.setScale = function(value) { + this.graphCanvas.setScale(value); +}; + +NetworkWidget.prototype.getScale = function() { + return this.graphCanvas.getScale(value); +}; + +/** SELECT ADJACENT VERTICES FROM SELECTED VERTICES * */ +NetworkWidget.prototype.selectAdjacent = function() { + var selectedVertices = this.getGraphCanvas().getSelectedVertices(); + var edges = []; + for ( var i = 0; i < selectedVertices.length; i++) { + edges = edges.concat(this.getGraphCanvas().getDataset().getVertexById(selectedVertices[i]).getEdges()); + } + var vertices = []; + for ( i = 0; i < edges.length; i++) { + vertices.push(edges[i].getNodeSource().getId()); + vertices.push(edges[i].getNodeTarget().getId()); + } + + this.selectVerticesById(vertices); +}; + +/** SELECT EDGES FROM SELECTED VERTICES * */ +NetworkWidget.prototype.selectEdgesFromVertices = function() { + var selectedVertices = this.getGraphCanvas().getSelectedVertices(); + var edges = []; + for ( var i = 0; i < selectedVertices.length; i++) { + edges = edges.concat(this.getGraphCanvas().getDataset().getVertexById(selectedVertices[i]).getEdges()); + } + var edgesId = []; + for ( i = 0; i < edges.length; i++) { + edgesId.push(edges[i].getId()); + } + this.getGraphCanvas().selectEdges(edgesId); +}; + +/** BLINKING * */ +NetworkWidget.prototype.blinkVertexById = function(vertexId) { + this.graphCanvas.blinkVertexById(vertexId); +}; + +/** COMPONENTE CONEXA DE LOS NODOS SELECCIONADOS * */ +NetworkWidget.prototype.selectConnectedComponent = function() { + var elements = this.getConnectedComponent(); + this.selectVerticesById(elements.nodes); + this.graphCanvas.selectEdges(elements.edges); +}; + +NetworkWidget.prototype.getConnectedComponent = function() { + var nodosVisitados = {}; + var aristasVisitadas = {}; + var arrNodos = []; + var arrAristas = []; + var selectedGraphNodesId = this.getGraphCanvas().getSelectedVertices(); + for ( var i = 0; i < selectedGraphNodesId.length; i++) { + this.visitNode(selectedGraphNodesId[i], nodosVisitados, aristasVisitadas, arrNodos, arrAristas); + } + return { + nodes : arrNodos, + edges : arrAristas + }; +}; + +NetworkWidget.prototype.visitNode = function(nodeId, nodosVisitados, aristasVisitadas, arrNodos, arrAristas) { + nodosVisitados[nodeId] = true; + arrNodos.push(nodeId); + var nodeEdges = this.getDataset().getVertexById(nodeId).getEdges(); + for ( var j = 0; j < nodeEdges.length; j++) { + var edge = nodeEdges[j]; + var edgeId = edge.getId(); + if (aristasVisitadas[edgeId] == null) { + aristasVisitadas[edgeId] = true; + arrAristas.push(edgeId); + var nodeTargetId = edge.getNodeTarget().getId(); + if (nodosVisitados[nodeTargetId] == null) { + this.visitNode(nodeTargetId, nodosVisitados, aristasVisitadas, arrNodos, arrAristas); + } + var nodeSourceId = edge.getNodeSource().getId(); + if (nodosVisitados[nodeSourceId] == null) { + this.visitNode(nodeSourceId, nodosVisitados, aristasVisitadas, arrNodos, arrAristas); + } + } + } +}; + +/** COLLAPSE SELECTED VERTICES * */ +NetworkWidget.prototype.collapse = function() { + var selectedVertices = this.getGraphCanvas().getSelectedVertices(); + var xMin = -Infinity; + var xMax = Infinity; + var yMin = -Infinity; + var yMax = Infinity; + + for ( var i = 0; i < selectedVertices.length; i++) { + var vertex = this.getGraphCanvas().getLayout().getNodeById(selectedVertices[i]); + if (xMin < vertex.x) { + xMin = vertex.x; + } + if (xMax > vertex.x) { + xMax = vertex.x; + } + if (yMin < vertex.y) { + yMin = vertex.y; + } + if (yMax > vertex.y) { + yMax = vertex.y; + } + } + + var centerX = xMin - xMax; + var centerY = yMin - yMax; + var radius = (xMax - xMin) / 4; + + var count = selectedVertices.length; + var verticesCoordinates = []; + + for ( i = 0; i < selectedVertices.length; i++) { + x = centerX + radius * Math.sin(i * 2 * Math.PI / count); + y = centerY + radius * Math.cos(i * 2 * Math.PI / count); + verticesCoordinates.push({ + 'x' : x, + 'y' : y + }); + } + + for ( i = 0; i < selectedVertices.length; i++) { + this.getGraphCanvas().getLayout().getNodeById(selectedVertices[i]).setCoordinates(verticesCoordinates[i].x, verticesCoordinates[i].y); + } +}; +/** SETTER FONT SIZE * */ +NetworkWidget.prototype.setVerticesFontSize = function(value) { + for ( var nodeId in this.getDataset().getVertices()) { + if (this.getDataset().getVertices().hasOwnProperty(nodeId)) { + this.getFormatter().getVertexById(nodeId).getDefault().setFontSize(value); + } + } +}; + +/** GETTERS * */ +NetworkWidget.prototype.getFormatter = function() { + return this.getGraphCanvas().getFormatter(); +}; +NetworkWidget.prototype.getLayout = function() { + return this.getGraphCanvas().getLayout(); +}; + +NetworkWidget.prototype.getDataset = function() { + return this.getGraphCanvas().getDataset(); +}; + +NetworkWidget.prototype.getGraphCanvas = function() { + return this.graphCanvas; +}; + +RangeWhiskerGraph.prototype.cleanArray = GenericGraph.prototype.cleanArray; +RangeWhiskerGraph.prototype.plotAxes = GenericGraph.prototype.plotAxes; +RangeWhiskerGraph.prototype.plotRuler = GenericGraph.prototype.plotRuler; +RangeWhiskerGraph.prototype.drawSVGVerticalText = GenericGraph.prototype.drawSVGVerticalText; +RangeWhiskerGraph.prototype.getClassColor = GenericGraph.prototype.getClassColor; +RangeWhiskerGraph.prototype.getDimensions = GenericGraph.prototype.getDimensions; +RangeWhiskerGraph.prototype.calculate = GenericGraph.prototype.calculate; +RangeWhiskerGraph.prototype.getMedian = GenericGraph.prototype.getMedian; +RangeWhiskerGraph.prototype.pointToPixel = GenericGraph.prototype.pointToPixel; +RangeWhiskerGraph.prototype.maxValueWhisker = GenericGraph.prototype.maxValueWhisker; +RangeWhiskerGraph.prototype.refresh = GenericGraph.prototype.refresh; + /** - * Given data analysis parsed with ResultsAssemblyWidget makes a selector grid with buffer/protein - **/ -function SpecimenSelectorResultGrid() { - this.id = BUI.id(); -} + * Subclass of GenericGraph + * + * @plotHorizontalByCluster + */ +function RangeWhiskerGraph(args) { + this.maxBoxWidth = 25; -SpecimenSelectorResultGrid.prototype._prepareData = function(data) { - var parsed = []; - for ( var i = 0; i < data.length; i++) { - var row = data[i]; - for ( var j = 0; j < row.conditions.length; j++) { - parsed.push({ - bufferId : row.conditions[j].bufferId, - macromoleculeId : row.macromoleculeId, - macromoleculeAcronym : BIOSAXS.proposal.getMacromoleculeById(row.macromoleculeId).acronym, - bufferAcronym : BIOSAXS.proposal.getBufferById(row.conditions[j].bufferId).acronym - }); - } + if (args == null) { + args = {}; } - return parsed; -}; - -SpecimenSelectorResultGrid.prototype.refresh = function(data) { - this.store.loadData(this._prepareData(data)); -}; - -SpecimenSelectorResultGrid.prototype.getPanel = function(data) { - var _this = this; - this.store = Ext.create('Ext.data.Store', { - fields : [ 'macromoleculeId', 'bufferId', 'macromoleculeAcronym', 'bufferAcronym', 'concentration' ], - data : this._prepareData(data), - groupField : 'macromoleculeAcronym' - }); + args.plotHorizontalByCluster = false; - this.store.sort('concentration'); - this.grid = Ext.create('Ext.grid.Panel', { - id : this.id, - store : this.store, - width : this.width, - height : this.height, - maxHeight : this.maxHeight, - border : 1, - features : [ { - ftype : 'grouping', - groupHeaderTpl : '{name}', - hideGroupedHeader : true, - startCollapsed : false - } ], - selModel : Ext.create('Ext.selection.CheckboxModel', { - allowDeselect : true, - mode : 'MULTI', - listeners : { - selectionchange : function(sm, selections) { - _this.selected = []; - for ( var i = 0; i < selections.length; i++) { - _this.selected.push(selections[i].raw); - } - } - } - }), - margin : 10, - sortableColumns : true, - columns : [ { - text : 'Macromolecule', - dataIndex : 'macromoleculeAcronym', - flex : 1 - }, { - text : '', - dataIndex : 'bufferId', - width : 20, - hidden : false, - renderer : function(val, y, sample) { - return BUI.getRectangleColorDIV(BIOSAXS.proposal.bufferColors[val], 10, 10); - } - }, { - text : 'Buffer', - dataIndex : 'bufferAcronym', - flex : 1 - }, { - text : 'Concentration', - dataIndex : 'concentration', - flex : 1, - renderer : function(val, y, sample) { - return val + " mg/ml"; - } - } ] - }); + GenericGraph.call(this, args); - /** Adding the tbar **/ - if (this.tbar) { - this.grid.addDocked({ - xtype : 'toolbar', - items : this.getTbar() - }); + if (args.maxBoxWidth != null) { + this.maxBoxWidth = args.maxBoxWidth; } - return this.grid; -}; +} -SpecimenSelectorResultGrid.prototype.input = function() { - return { - data : new ResultsAssemblyGrid()._prepareData(new ResultsAssemblyGrid().input().data), - proposal : new ResultsAssemblyGrid().input().proposal - }; +RangeWhiskerGraph.prototype.refresh = function(data) { + document.getElementById(this.targetId).innerHTML = ""; + this.draw(this.targetId, data); }; -SpecimenSelectorResultGrid.prototype.test = function(targetId) { - var specimenSelectorResultGrid = new SpecimenSelectorResultGrid(); - BIOSAXS.proposal = new Proposal(specimenSelectorResultGrid.input().proposal); - var panel = specimenSelectorResultGrid.getPanel(specimenSelectorResultGrid.input().data); - panel.render(targetId); -}; +RangeWhiskerGraph.prototype.isNumber = function(value) { + if (value == "") + return false; -/** - * Show all buffer conditions for each macromolecules pointing out the measurements quality - * - * @height - * @maxHeight - * @width - * @searchBar - * @tbar - * @btnResultVisible - * - * #onClick - */ -function ResultsAssemblyGrid(args) { - this.height = 500; - this.id = BUI.id(); - this.maxHeight = this.height; + var d = parseInt(value); + if (!isNaN(d)) + return true; + else + return false; - this.width = 900; - this.searchBar = false; - this.tbar = false; - this.btnResultVisible = false; +}; - /** For processing **/ - this.processed = {}; - this.renderedPlotIndex = 0; +/** + There are several different methods for calculating quartiles.[1] This calculator uses a method described by Moore and McCabe to find quartile values. + The same method also used by The TI-83 to calculate quartile values. + With this method, the first quartile is the median of the numbers below the median, the third quartile is the median of the numbers above the median. - this.plotWidth = 210; - this.plotHeight = 80; + http://www.miniwebtool.com/quartile-calculator/ + http://www.alcula.com/calculators/statistics/box-plot/ - /** Colors **/ - this.validColor = BUI.getValidColor(); - this.warningColor = BUI.getWarningColor(); - this.notValidColor = BUI.getErrorColor(); + **/ +RangeWhiskerGraph.prototype.getQ1 = function(array) { + array = array.slice(0, array.length / 2); + return this.getMedian(array); +}; - /** Show warning if guinier quality less than **/ - this.guinierQuality = BUI.getQualityThreshold(); - this.framePercentageThreshold = BUI.getRadiationDamageThreshold(); +RangeWhiskerGraph.prototype.getQ3 = function(array) { + array = array.slice((array.length + 1) / 2); + return this.getMedian(array); - if (args != null) { - if (args.height != null) { - this.height = args.height; - this.maxHeight = this.height; - } - if (args.maxHeight != null) { - this.maxHeight = args.maxHeight; - } - if (args.width != null) { - this.width = args.width; - } - if (args.searchBar != null) { - this.searchBar = args.searchBar; +}; + +RangeWhiskerGraph.prototype.getQ2 = function(array) { + return this.getMedian(array); +}; + +RangeWhiskerGraph.prototype.getBelowOutliers = function(belowLimit, array) { + var points = []; + for ( var i = 0; i < array.length; i++) { + if (array[i] <= belowLimit) { + points.push(array[i]); } + } + return points; +}; - if (args.tbar != null) { - this.tbar = args.tbar; +RangeWhiskerGraph.prototype.getAboveOutliers = function(aboveLimit, array) { + var points = []; + for ( var i = 0; i < array.length; i++) { + if (array[i] >= aboveLimit) { + points.push(array[i]); } - if (args.btnResultVisible != null) { - this.btnResultVisible = args.btnResultVisible; + } + return points; +}; + +RangeWhiskerGraph.prototype.minValueWhisker = function(belowLimit, q1, array) { + var points = []; + + for ( var i = 0; i < array.length; i++) { + if ((array[i] < q1) && (array[i]) > belowLimit) { + points.push(array[i]); } + } + if (points.length > 0) { + points.sort(function(a, b) { + return a - b; + }); + return points[0]; } + return null; +}; - this.onClick = new Event(); -} +//RangeWhiskerGraph.prototype.maxValueWhisker = function(aboveLimit, q3, array){ +// var points = []; +// for (var i = 0; i < array.length; i++){ +// if ((array[i] > q3) && (array[i]) <= aboveLimit){ +// points.push(array[i]); +// } +// } +// if (points.length > 0){ +// points.sort(function(a, b){return a - b;}); +// return points[points.length - 1]; +// } +// return null; +//}; -ResultsAssemblyGrid.prototype.edit = function(macromoleculeId) { - var _this = this; - var window = new MacromoleculeWindow(); - window.onSuccess.attach(function(sender, proposal) { - _this.store.loadData(_this._prepareData(BIOSAXS.proposal.getMacromolecules())); - }); - window.draw(BIOSAXS.proposal.getMacromoleculeById(macromoleculeId)); +RangeWhiskerGraph.prototype.drawPoints = function(boxProperties) { + if (this.plotPoints) { + for ( var i = 0; i < boxProperties.values.length; i++) { + var value = boxProperties.values[i]; + var toPixel = this.pointToPixel(value, boxProperties); + SVG.drawCircle(boxProperties.x, toPixel, this.pointRadius, this.svg, + [ + [ "fill", "green" ], [ "fill-opacity", this.fillOpacityPoint ], [ 'stroke-opacity', this.strokeOpacityPoint ], + [ "stroke", "black" ] ]); + } + } }; -ResultsAssemblyGrid.prototype.getTbar = function() { - var _this = this; - var actions = []; +RangeWhiskerGraph.prototype.plotRangeQ1Q3 = function(data, properties) { + var posX = this.left + this.rulerWidth; - actions.push(Ext.create('Ext.Action', { - icon : '../images/add.png', - text : 'Add Macromolecule', - disabled : false, - handler : function(widget, event) { - var window = new MacromoleculeWindow(); - window.onSuccess.attach(function(sender) { - _this.refresh(); - }); - window.draw({}); - } - })); + var boxBordersPointsQ1 = []; + var boxBordersPointsQ3 = []; + var Q2 = []; - actions.push(Ext.create('Ext.Action', { - icon : '../images/add.png', - text : 'Define an Assembly', - disabled : false, - handler : function(widget, event) { - var createAssemblywindow = new CreateAssemblyWindow(); - createAssemblywindow.onSaved.attach(function(evt, args) { - if (args.macromoleculeIds.length > 0) { - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, proposal) { - _this.refresh(); - }); - adapter.saveAssembly(args.assemblyId, args.macromoleculeIds); + for ( var i = 0; i < data.clusters.length; i++) { + var cluster = data.clusters[i]; + /** inter cluster space **/ + posX = posX + this.interClustersSpace; - } + for ( var j = 0; j < cluster.classes.length; j++) { + var ratio = properties.width / (properties.xValues.range); + var coorX = (cluster.x - properties.xValues.min) * ratio + this.rulerWidth; + var boxProperties = { + name : cluster.classes[j].name, + values : cluster.classes[j].values, + minPoint : properties.minPoint, + maxPoint : properties.maxPoint, + x : coorX + this.left, + y : this.top, + width : properties.classWidth, + height : this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight + }; - }); - createAssemblywindow.draw(_this.experiment); - } - })); + var result = this.calculate(boxProperties.values); + var boxColor = this.getClassColor(boxProperties.name); - return actions; -}; + if (this.isNumber(result.Q1) && this.isNumber(result.Q3)) { + var x = boxProperties.x; + var y = this.pointToPixel(result.Q1, boxProperties); + if (boxBordersPointsQ1[cluster.classes[j].name] == null) { + boxBordersPointsQ1[cluster.classes[j].name] = []; + } + boxBordersPointsQ1[cluster.classes[j].name].push({ + x : x, + y : y + }); -ResultsAssemblyGrid.prototype.refresh = function() { - this.store.loadData(this._prepareData()); -}; + x = boxProperties.x; + y = this.pointToPixel(result.Q3, boxProperties); + if (boxBordersPointsQ3[cluster.classes[j].name] == null) { + boxBordersPointsQ3[cluster.classes[j].name] = []; + } + boxBordersPointsQ3[cluster.classes[j].name].push({ + x : x, + y : y + }); + } else { -ResultsAssemblyGrid.prototype.addCondition = function(record, data_parsed, i) { - function getCondition(record) { - return { - concentration : record.conc, - quality : record.quality, - bufferBeforeFramesMerged : record.bufferBeforeFramesMerged, - bufferAfterFramesMerged : record.bufferAfterFramesMerged, - framesCount : record.framesCount, - framesMerge : record.framesMerge - }; - } + if (this.isNumber(result.Q2)) { - if (data_parsed[i].conditions != null) { - var bufferFound = false; - for ( var index in data_parsed[i].conditions) { - condition = data_parsed[i].conditions[index]; + if (boxBordersPointsQ1[cluster.classes[j].name] == null) { + boxBordersPointsQ1[cluster.classes[j].name] = []; + } - if ((condition.macromoleculeId == record.macromoleculeId) && (condition.bufferId == record.bufferId)) { - data_parsed[i].conditions[index].concentrations.push(getCondition(record)); - bufferFound = true; + if (boxBordersPointsQ3[cluster.classes[j].name] == null) { + boxBordersPointsQ3[cluster.classes[j].name] = []; + } + + boxBordersPointsQ1[cluster.classes[j].name].push({ + x : boxProperties.x, + y : this.pointToPixel(result.Q2, boxProperties) + }); + boxBordersPointsQ3[cluster.classes[j].name].push({ + x : boxProperties.x, + y : this.pointToPixel(result.Q2, boxProperties) + }); + } } } - if (!bufferFound) { - data_parsed[i].conditions.push({ - macromoleculeId : record.macromoleculeId, - bufferId : record.bufferId, - concentrations : [ getCondition(record) ] - }); + } + for ( var classe in boxBordersPointsQ1) { + var points = boxBordersPointsQ1[classe]; + var pointsSVG = ""; + for (var k = 0; k < points.length; k++) { + pointsSVG = Number(points[k].x).toFixed(1) + "," + Number(points[k].y).toFixed(1) + " " + pointsSVG; + } + + points = boxBordersPointsQ3[classe]; + for (var z = points.length - 1; z >= 0; z--) { + pointsSVG = Number(points[z].x).toFixed(1) + "," + Number(points[z].y).toFixed(1) + " " + pointsSVG; } + + SVG.drawPoligon(pointsSVG, this.svg, [ + [ "fill", this.getClassColor(classe) ], [ "opacity", "0.3" ], [ "stroke", "black" ], [ "stroke-width", 1 ] ]); } }; -ResultsAssemblyGrid.prototype.process = function(record, data_parsed) { - if (this.processed[record.macromoleculeId] == null) { - this.processed[record.macromoleculeId] = true; - record.measurementCount = 1; - record.subtractionCount = 1; - record.averageCount = 1; - record.conditions = []; - data_parsed.push(record); - } +RangeWhiskerGraph.prototype.plotWhisters = function(data, properties) { + var colors = [ "yellow", "orange", "green" ]; - for ( var i = 0; i < data_parsed.length; i++) { - if (data_parsed[i].macromoleculeId == record.macromoleculeId) { - data_parsed[i].measurementCount = data_parsed[i].measurementCount + 1; + this.plotRangeQ1Q3(data, properties); + var Q2 = {}; - if (record.subtractionId != null) { - data_parsed[i].subtractionCount = data_parsed[i].subtractionCount + 1; - this.addCondition(record, data_parsed, i); - } + for ( var i = 0; i < data.clusters.length; i++) { + var cluster = data.clusters[i]; + for ( var j = 0; j < cluster.classes.length; j++) { + var ratio = properties.width / (properties.xValues.range); + var coorX = (cluster.x - properties.xValues.min) * ratio + this.left + this.rulerWidth - this.rulerStroke; + var boxProperties = { + name : cluster.classes[j].name, + values : cluster.classes[j].values, + minPoint : properties.minPoint, + maxPoint : properties.maxPoint, + x : coorX, + y : this.top, + width : properties.classWidth, + height : this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight + }; - if (record.framesMerge != null) { - data_parsed[i].averageCount = data_parsed[i].averageCount + 1; - } + this.drawPoints(boxProperties); - if (record.timeStart != null) { - if (data_parsed[i].timeStart != null) { - if (moment(data_parsed[i].timeStart).format("X") > moment(record.timeStart).format("X")) { - data_parsed[i].timeStart = record.timeStart; - } + /** PLOTTING Q2 **/ + var result = this.calculate(boxProperties.values); + var boxColor = this.getClassColor(boxProperties.name); + if (this.isNumber(result.Q2)) { + if (Q2[boxProperties.name] != null) { + SVG.drawLine(boxProperties.x, this.pointToPixel(result.Q2, boxProperties), Q2[boxProperties.name].x, Q2[boxProperties.name].y, + this.svg, [ [ "stroke", boxColor ], [ "stroke-width", "2" ] ]); + } + Q2[boxProperties.name] = { + x : boxProperties.x, + y : this.pointToPixel(result.Q2, boxProperties) } } } } - return data_parsed; - }; -ResultsAssemblyGrid.prototype._prepareData = function(data) { - var data_parsed = []; - for ( var i = 0; i < data.length; i++) { - data_parsed = this.process(data[i], data_parsed); - } - this.data = data_parsed; - return data_parsed; +RangeWhiskerGraph.prototype.draw = function(targetId, data) { + //this.calculate(data); + this.targetId = targetId; + var properties = (this.getDimensions(data)); + this.svg = SVG.createSVGCanvas(document.getElementById(this.targetId), [ [ "width", this.width ], [ "height", this.height ] ]); + this.plotAxes(properties); + this.plotWhisters(data, properties); }; -/** Given an array of conditions it returns distinct(concentrations) order by concentration and hash map with number of ocurrences**/ -ResultsAssemblyGrid.prototype.parseConcentrations = function(val, conditions, differentConcentration, quality) { - var conditions = []; - var differentConcentration = {}; - var quality = []; - for ( var i = 0; i < val.length; i++) { - var conc = Number(val[i].concentration).toFixed(1); - var quality = Number(val[i].quality).toFixed(2); - if (differentConcentration[conc] == null) { - differentConcentration[conc] = 0; - conditions.push({ - concentration : conc, - quality : [ quality ], - frames : [ { - bufferAfterFramesMerged : val[i].bufferAfterFramesMerged, - bufferBeforeFramesMerged : val[i].bufferBeforeFramesMerged, - framesMerge : val[i].framesMerge, - framesCount : val[i].framesCount - } ] - }); - } else { - /** Add quality **/ - for ( var j = 0; j < conditions.length; j++) { - if (conditions[j].concentration == conc) { - conditions[j].quality.push(quality); - conditions[j].frames.push({ - bufferAfterFramesMerged : val[i].bufferAfterFramesMerged, - bufferBeforeFramesMerged : val[i].bufferBeforeFramesMerged, - framesMerge : val[i].framesMerge, - framesCount : val[i].framesCount - }); - } - } - } +RangeWhiskerGraph.prototype.input = function() { + return DATADOC.getBoxWhikerData(); +}; - differentConcentration[conc] = differentConcentration[conc] + 1; - } - /** sorting concentrations **/ - conditions.sort(function(a, b) { - return a.concentration - b.concentration; +RangeWhiskerGraph.prototype.test = function(targetId) { + var plot = new RangeWhiskerGraph({ + targetId : targetId, + height : 350, + width : 450, + maxBoxWidth : 25 }); - return { - concentrations : conditions, - differentConcentration : differentConcentration - }; + plot.refresh(this.input()); }; + +StdDevDyGraph.prototype.dblclick = DygraphWidget.prototype.dblclick; +StdDevDyGraph.prototype._createHTLMWrapper = DygraphWidget.prototype._createHTLMWrapper; +StdDevDyGraph.prototype.draw = DygraphWidget.prototype.draw; -ResultsAssemblyGrid.prototype.getConditionWarnings = function(condition) { - - var withWarnings = 0; - - for ( var i = 0; i < condition.frames.length; i++) { - if (condition.quality[i] == null) { - withWarnings = withWarnings + 1; - continue; - } else { - if (Number(condition.quality[i]) < this.guinierQuality) { - withWarnings = withWarnings + 1; - continue; - } - } - - if (condition.frames[i].bufferBeforeFramesMerged / condition.frames[i].framesCount < this.framePercentageThreshold|| condition.frames[i].framesMerged / condition.frames[i].framesCount < this.framePercentageThreshold|| condition.frames[i].bufferAfterFramesMerged / condition.frames[i].framesCount < this.framePercentageThreshold) { - withWarnings = withWarnings + 1; - continue; - } +function StdDevDyGraph(targetId, args) { + this.scaled = false; + if (args == null) { + args = {}; } + args.customBars = true; + DygraphWidget.prototype.constructor.call(this, targetId, args); +} +StdDevDyGraph.prototype.input = function () { return { - withWarnings : withWarnings, - withoutWarnings : condition.frames.length - withWarnings + data : [ [ 1, [ 2, 3, 3.5 ], [ 4, 4.2, 5 ] ], [ 2, [ 5, 5.5, 5.7 ], [ 4, 4.2, 5 ] ] ], + colors : [ "blue", "red" ], + labels : [ "", 'data1', 'data2' ] }; }; -ResultsAssemblyGrid.prototype.getFrameHTMLTable = function(warnings) { - var html = ""; - if (warnings.withWarnings > 0) { - html = html + "
" + warnings.withWarnings + - "x
"; - } - - if (warnings.withoutWarnings > 0) { - html = html + "
" + warnings.withoutWarnings + - "x
"; - } - return html; -}; +StdDevDyGraph.prototype.test = function (targetId) { + var dygraphObject = new StdDevDyGraph(targetId, { + width : 500, + height : 400, + xlabel : "xLabel", + showRangeSelector : false + }); -ResultsAssemblyGrid.prototype.createConcentrationRow = function(numberOcu, condition, warnings){ - var html = ""; - if (numberOcu > 1){ - html = html + "" +numberOcu + "x " + BUI.formatConcentration(condition.concentration); - } - else{ - html = html + BUI.formatConcentration(condition.concentration); - } - html = html + ""; - html = html + this.getFrameHTMLTable(warnings); + ""; - html = html + ""; - return html; + dygraphObject.draw(dygraphObject.input().data, dygraphObject.input().colors, dygraphObject.input().labels); }; + + + +function AbinitioGrid(args) { + this.height = null; + this.width = null; + this.id = BUI.id(); + + if (args != null) { + if (args.height != null) { + this.height = args.height; + + if (args.width != null) { + this.width = args.width; + } + } + } + + this.onSelected = new Event(this); +}; + + +AbinitioGrid.prototype.refresh = function(subtractions){ + this.store.loadData(this._prepareData(subtractions)); +}; + +AbinitioGrid.prototype._prepareData = function(subtractions){ + /** Parsing data * */ + var models = []; + for (var l = 0; l < subtractions.length; l++) { + var subtraction = subtractions[l]; + for (var k = 0; k < subtraction.substractionToAbInitioModel3VOs.length; k++) { + var data = subtraction.substractionToAbInitioModel3VOs[k].abinitiomodel3VO; + if (data.averagedModel != null) { + models.push(data.averagedModel); + models[models.length - 1].type = "Reference"; + } + + if (data.shapeDeterminationModel != null) { + models.push(data.shapeDeterminationModel); + models[models.length - 1].type = "Refined"; + } + + if (data.modelList3VO != null) { + if (data.modelList3VO.modeltolist3VOs != null) { + for (var i = 0; i < data.modelList3VO.modeltolist3VOs.length; i++) { + models.push(data.modelList3VO.modeltolist3VOs[i].model3VO); + models[models.length - 1].type = "Model"; + } + } + } + } + } + return models; +}; + +AbinitioGrid.prototype.getPanel = function(){ + var _this = this; + + + var modelFields = [ "modelId", "type", "chiSqrt", "dmax", "firFile", "logFile", "fitFile", "pdbFile", "rfactor", "rg", "volume" ]; + Ext.define('AbinitioModel', { + extend : 'Ext.data.Model', + fields : modelFields + + }); + + /** + * Store in Memory + */ + this.store = Ext.create('Ext.data.Store', { + model : 'AbinitioModel', + autoload : true, + groupField : 'type' + }); + + + var groupingFeature = Ext.create('Ext.grid.feature.Grouping',{ + groupHeaderTpl: '{name} ({rows.length} model{[values.rows.length > 1 ? "s" : ""]})', + startCollapsed: true, + collapsible : true + }); + + this.grid = Ext.create('Ext.grid.Panel', { + collapsible : false, + resizable : true, + features: [groupingFeature], + autoscroll : true, + multiSelect : true, + store : this.store, + height : this.height, + width : this.width, + margin : 10, + columns : [ { + text : "Type", + dataindex : "type", + hidden : true, + renderer : function(a, b, record) { + return record.data.type; + }, + flex : 1 + }, + { + text : "ModelId", + dataindex : "modelId", + hidden : true, + renderer : function(a, b, record) { + return record.data.modelId; + + }, + flex : 1 + }, + + { + text : "chiSqrt", + dataindex : "chiSqrt", + renderer : function(a, b, record) { + if (record.data.dmax != null) { + return BUI.formatValuesUnits(record.data.chiSqrt, "", 12, this.decimals); + } + + }, + flex : 1 + }, + { + text : "Dmax", + dataindex : "dmax", + renderer : function(a, b, record) { + if (record.data.dmax != null) { + return BUI.formatValuesUnits(record.data.dmax, "nm", 12, this.decimals); + } + + }, + flex : 1 + }, { + text : "rFactor", + dataindex : "rfactor", + hidden : true, + renderer : function(a, b, record) { + if (record.data.rfactor != null) { + return record.data.rfactor; + } + }, + flex : 1 + }, { + text : "Rg", + dataindex : "rg", + renderer : function(a, b, record) { + if (record.data.rg != null) { + return BUI.formatValuesUnits(record.data.rg, "nm", 12, this.decimals); + } + + }, + flex : 1 + }, + { + text : "Volume", + dataindex : "volume", + renderer : function(a, b, record) { + if (record.raw.volume != null){ + return BUI.formatValuesUnits(record.raw.volume, '') + " nm3"; + } + }, + flex : 1 + }, + { + text : "PDB", + dataindex : "pdbFile", + renderer : function(a, b, record) { + if (record.data.pdbFile != null){ + return record.data.pdbFile.split("/")[record.data.pdbFile.split("/").length - 1]; + } + }, + flex : 1 + }, { + text : "Fir", + dataindex : "firFile", + renderer : function(a, b, record) { + if (record.data.firFile != null){ + return record.data.firFile.split("/")[record.data.firFile.split("/").length - 1]; + } + }, + flex : 1 + }, { + text : "LOG", + dataindex : "logFile", + hidden : true, + renderer : function(a, b, record) { + if (record.data.logFile != null){ + return record.data.logFile.split("/")[record.data.logFile.split("/").length - 1]; + } + }, + flex : 1 + } + ], + viewConfig : { + enableTextSelection : true, + preserveScrollOnRefresh : true, + stripeRows : true, + listeners : { + 'celldblclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + }, + 'cellclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + var models = []; + for (var i = 0; i < grid.getSelectionModel().selected.items.length; i++) { + models.push(grid.getSelectionModel().selected.items[i].raw); + } + _this.onSelected.notify(models); + } + } + } + }); + return this.grid; + +}; + +function AdditiveGrid(args) { + this.onRemoveButtonClicked = new Event(this); +} -ResultsAssemblyGrid.prototype.getConditionHTMLTable = function(val, style, record) { - var maxNumberColumns = 2; - var html = "
"; - var nColumns = 0; - for ( var r = 0; r < val.length; r++) { - if (nColumns == maxNumberColumns) { - nColumns = 0; - html = html + ""; - } - html = html + ""; - nColumns = nColumns + 1; - } - html = html + "
"; - var value = val[r]; - - var bufferAcronym = (BIOSAXS.proposal.getBufferById(value.bufferId).acronym); - - var parsed = (this.parseConcentrations(value.concentrations)); - var conditions = parsed.concentrations; - var differentConcentration = parsed.differentConcentration; - - /** Checking warnings **/ - var warnings = []; - var concentrationValidPerconcentration = 0; - var measurements = 0; - for ( var i = 0; i < conditions.length; i++) { - measurements = measurements + conditions[i].frames.length; - var warning = this.getConditionWarnings(conditions[i]); - warnings.push(warning); - if (warning.withoutWarnings > 0) { - concentrationValidPerconcentration = concentrationValidPerconcentration + 1; - } - } - - this.validColor = '#E0F8E0'; - this.warningColor = '#F5DA81'; - this.notValidColor = '#F6CED8'; - - var color = this.warningColor; - if (concentrationValidPerconcentration > 2) { - color = this.validColor; - } - /** More measurement need to be done **/ - if (measurements < 3) { - color = this.notValidColor; - } - - html = html + ""; - html = html + ""; - for ( var i = 0; i < conditions.length; i++) { - html = html + this.createConcentrationRow(differentConcentration[conditions[i].concentration], conditions[i], warnings[i]); - } - - html = html + ""; - html = html + "
" + bufferAcronym.toUpperCase() + - "
"; - - html = html + "
"; - return html; +AdditiveGrid.prototype.getBuffer = function() { + return this.buffer; }; -ResultsAssemblyGrid.prototype._getTbar = function() { - function goTo(url) { - window.location = url; - } - +AdditiveGrid.prototype._getActions = function() { var _this = this; - return [ { - icon : '../images/application_view_list.png', - text : 'Multiple Select', - handler : function() { - var specimenSelectorResultGrid = new SpecimenSelectorResultGrid(); - var window = Ext.create('Ext.window.Window', { - title : 'Multiple select', - height : 600, - width : 600, - layout : 'fit', - items : [ specimenSelectorResultGrid.getPanel(_this.data) ], - buttons : [ { - text : 'Go', - handler : function() { - var array = []; - for ( var i = 0; i < specimenSelectorResultGrid.selected.length; i++) { - var row = specimenSelectorResultGrid.selected[i]; - array.push({ - macromoleculeId : row.macromoleculeId, - bufferId : row.bufferId - }); - } - goTo(BUI.getMacromoleculeResultsURLByMultipleSearch(array)); + /** Actions buttons **/ + var actions = []; - } - }, { - text : 'Cancel', - handler : function() { - window.close(); - } - } ] + actions.push(Ext.create('Ext.Action', { + icon : '../images/add.png', + text : 'Add', + disabled : true, + alwaysEnabled : true, + handler : function(widget, event) { + _this.buffer.bufferhasadditive3VOs.push(BIOSAXS_BEANS.getBufferhasAdditive3VO()); + _this.refresh(_this.buffer, _this.experiment); + } + })); - }).show(); + return actions; +}; +AdditiveGrid.prototype.refresh = function(buffer, experiment) { + this.buffer = buffer; + this.experiment = experiment; + if (buffer) { + if (buffer.bufferhasadditive3VOs) { + this.features = buffer.bufferhasadditive3VOs; } - } ]; + } + this.experiment = experiment; + this.store.loadData(this._prepareData(), false); }; -ResultsAssemblyGrid.prototype.getLegendPanel = function() { - return { - html : '
' + BUI.getRectangleColorDIV(this.validColor, 10, 10) + - 'Good quality measurements' + - BUI.getRectangleColorDIV(this.warningColor, 10, 10) + - 'Probably valid with manual processing' + - BUI.getRectangleColorDIV(this.notValidColor, 10, 10) + - 'More measurements need to be done
' - }; -}; -/** Returns the grid **/ -ResultsAssemblyGrid.prototype.getPanel = function(macromolecules) { - var _this = this; +AdditiveGrid.prototype.getAdditives = function() { + var additives = []; + for ( var i = 0; i < this.store.getCount(); i++) { + var bufferHasAdditive = BIOSAXS_BEANS.getBufferhasAdditive3VO(); + var data = this.store.getAt(i).getData(); - this.store = Ext.create('Ext.data.Store', { - fields : [ - 'macromoleculeId', 'macromoleculeAcronym', 'measurementCount', 'subtractionCount', 'averageCount', 'timeStart', 'concentrationArray', - 'bufferConditions', 'conditions' ], - data : this._prepareData(macromolecules) - }); + bufferHasAdditive.additive3VO.name = data.name; + bufferHasAdditive.additive3VO.comments = data.comments; + bufferHasAdditive.additive3VO.additiveType = data.additiveType; - this.store.sort('macromoleculeAcronym'); + bufferHasAdditive.bufferId = this.buffer.bufferId; + bufferHasAdditive.bufferHasAdditiveId = data.bufferHasAdditiveId; + bufferHasAdditive.quantity = data.quantity; + additives.push(bufferHasAdditive); + } - this.grid = Ext.create('Ext.grid.Panel', { - id : this.id, - title : 'Macromolecules', - store : this.store, - tbar : this._getTbar(), - bbar : [ this.getLegendPanel() ], - width : this.width, - height : this.height, - maxHeight : this.maxHeight, - sortableColumns : true, - columns : [ - { - text : '', - dataIndex : 'macromoleculeId', - width : 20, - hidden : false, - renderer : function(val, y, sample) { - return BUI.getRectangleColorDIV(BIOSAXS.proposal.macromoleculeColors[val], 10, 10); - } - }, - { - text : 'Macromolecule', - dataIndex : 'macromoleculeAcronym', - width : 200 + return additives; +}; + +AdditiveGrid.prototype._getFields = function(buffers) { + var columns = [ + + { + header : 'Name', + dataIndex : 'name', + type : 'string', + editor : { + allowBlank : true }, - { - text : 'Buffer Conditions', - dataIndex : 'conditions', - flex : 1, - renderer : function(val, style, record) { - return _this.getConditionHTMLTable(val, style, record); - } + flex : 1 + }, + { + header : 'Type', + name : 'additiveType', + dataIndex : 'additiveType', + editor : { + xtype : 'combobox', + typeAhead : true, + triggerAction : 'all', + selectOnTab : true, + store : BIOSAXS.proposal.getAdditiveTypes(), + lazyRender : true, + listClass : 'x-combo-list-small' }, - { - header : 'Average', - dataIndex : 'percentageCollected', - name : 'percentageCollected', - type : 'string', - hidden : true, - renderer : function(val, y, sample) { - return "
" + - BUI.getProgessBar((sample.raw.averageCount / sample.raw.measurementCount) * 100, sample.raw.averageCount + "/" + - sample.raw.measurementCount) + "
"; - }, - width : 100, - sorter : false + flex : 0.6 + }, + { + header : 'Quantity', + dataIndex : 'quantity', + name : 'quantity', + editor : { + allowBlank : true }, - { - header : 'Subtractions', - dataIndex : 'percentageCollected', - name : 'percentageCollected', - type : 'string', - hidden : true, - renderer : function(val, y, sample) { - return "
"+ BUI.getProgessBar((sample.raw.subtractionCount / sample.raw.measurementCount) * 100, sample.raw.subtractionCount + "/" + - sample.raw.measurementCount) + "
"; - }, - width : 100 - }, { - header : 'Date', - dataIndex : 'timeStart', - name : 'timeStart', - type : 'string', - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - if (record.raw.timeStart != null) { - return moment(record.raw.timeStart).format("MMM Do YY"); + type : 'string', + flex : 1 + }, + { + xtype : 'actioncolumn', + items : [ { + icon : '../images/cancel.png', + tooltip : 'Delete additive', + scope : this, + handler : function(grid, rowIndex, colIndex) { + if ((grid.getStore().getAt(rowIndex).data.bufferHasAdditiveId == null)|| (grid.getStore().getAt(rowIndex).data.bufferHasAdditiveId == "")) { + grid.getStore().removeAt(rowIndex); + } else { + this.onRemoveButtonClicked.notify({ + 'bufferId' : this.buffer.bufferId, + 'bufferHasAdditiveId' : this.store.getAt(rowIndex).data.bufferHasAdditiveId + }); } } - }, { - header : 'Download', - dataIndex : 'percentageCollected', - name : 'percentageCollected', - type : 'string', - renderer : function(val, y, sample) { - return BUI.getZipHTMLByMacromoleculeId(sample.raw.macromoleculeId); - }, - width : 100 - }, + } ] + } ]; + + return columns; +}; + +AdditiveGrid.prototype._prepareData = function() { + var data = []; + if (this.features == null) { + this.features = []; + } + for (var i = 0; i < this.features.length; i++) { + var object = this.features[i]; + object.name = this.features[i].additive3VO.name; + object.additiveType = this.features[i].additive3VO.additiveType; + object.comments = this.features[i].additive3VO.comments; + object.additiveId = this.features[i].additive3VO.additiveId; + data.push(object); + } + return data; +}; - { - id : 'btnResultVisible', - width : 85, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - return BUI.getGreenButton('GO'); - } - } ], +AdditiveGrid.prototype.getPanel = function(buffer, experiment) { + this.buffer = buffer; + this.features = buffer.bufferhasadditive3VOs; + this.experiment = experiment; + return this._renderGrid(); +}; + +AdditiveGrid.prototype.getStore = function() { + var _this = this; + var store = Ext.create('Ext.data.Store', { + fields : [ "name", "additiveType", "comments", "additiveId", "bufferHasAdditiveId", "quantity" ], + autoload : false, + data : this._prepareData(), + listeners : { + update : function(store, record) { + record.index = _this.grid.getSelectionModel().getCurrentPosition().row; + _this.buffer.bufferhasadditive3VOs[record.index].additive3VO.name = record.data.name; + _this.buffer.bufferhasadditive3VOs[record.index].additive3VO.additiveType = record.data.additiveType; + _this.buffer.bufferhasadditive3VOs[record.index].additive3VO.comments = record.data.comments; + _this.buffer.bufferhasadditive3VOs[record.index].quantity = record.data.quantity; + } + } + }); + + // store.sort('bufferHasAdditiveId', 'ASC'); + store.loadData(this._prepareData(), false); + return store; +}; + +AdditiveGrid.prototype._renderGrid = function() { + var _this = this; + this.store = this.getStore(); + + var cellEditing = Ext.create('Ext.grid.plugin.CellEditing', { + clicksToEdit : 1 + }); + + this.grid = Ext.create('Ext.grid.Panel', { + dockedItems : [ { + xtype : 'toolbar', + items : this._getActions() + } ], + store : this.store, + height : 230, + title : "Additives", + width : "100%", + columns : _this._getFields(), + plugins : [ cellEditing ], viewConfig : { stripeRows : true, listeners : { - afterrender : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - }, - celldblclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - _this.edit(record.data.macromoleculeId); - }, - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - if (grid.getGridColumns()[cellIndex].getId() == 'buttonEditMacromolecule') { - _this.edit(record.data.macromoleculeId); - } - if (grid.getGridColumns()[cellIndex].getId() == 'buttonRemoveMacromolecule') { - BUI.showBetaWarning(); - } - if (grid.getGridColumns()[cellIndex].getId() == 'btnResultVisible') { - window.location = BUI.getMacromoleculeResultsURL(record.data.macromoleculeId); - } + itemcontextmenu : function(view, rec, node, index, e) { + e.stopEvent(); + contextMenu.showAt(e.getXY()); + return false; } } + }, + selModel : { + mode : 'SINGLE' } }); - /** Adding the tbar **/ - if (this.tbar) { - this.grid.addDocked({ - xtype : 'toolbar', - items : this.getTbar() - }); - } return this.grid; }; -ResultsAssemblyGrid.prototype.input = function(targetId) { - return { - data : DATADOC.getData_3367(), - proposal : DATADOC.getProposal_3367() - }; +AdditiveGrid.prototype.input = function() { }; -ResultsAssemblyGrid.prototype.test = function(targetId) { - var grid = new ResultsAssemblyGrid({ - height : 600, - searchBar : false, - tbar : false, - btnResultVisible : true, - width : 1000 - }); - BIOSAXS.proposal = new Proposal(grid.input().proposal); - var panel = grid.getPanel(grid.input().data); +AdditiveGrid.prototype.test = function(targetId) { + var grid = new AdditiveGrid(); + var panel = grid.getPanel([]); panel.render(targetId); }; +/** AnalysisGrid **/ +function AnalysisGrid(args) { + var _this = this; -function RigidModelGrid(args) { - this.height = null; - this.width = null; this.id = BUI.id(); + if (Ext.get("mainPanel")){ + this.width = Ext.get("mainPanel").getWidth(); + } + else{ + this.width = this.maxWidth; + } + this.maxWidth = 1500; + + /** Visibles **/ + this.isGuinierTabVisible = true; + this.isGnomTabVisible = true; + this.isPorodTabVisible = true; + this.isScatteringPlotVisible = true; + this.isAbinitioTabVisible = true; + this.showButtonsVisible = true; + this.isI0Visible = true; + + this.margin = null; + this.grouped = true; + + this.hideNulls = false; + this.decimals = 4; + this.height = null; + this.sorters = [ { + property : 'conc', + direction : 'ASC' + } ]; if (args != null) { + if (args.grouped != null) { + this.grouped = args.grouped; + } + + if (args.showButtonsVisible != null) { + this.showButtonsVisible = args.showButtonsVisible; + } + if (args.isI0Visible != null) { + this.isI0Visible = args.isI0Visible; + } + if (args.sorters != null) { + this.sorters = args.sorters; + } + if (args.isScatteringPlotVisible != null) { + this.isScatteringPlotVisible = args.isScatteringPlotVisible; + } + if (args.isGuinierTabVisible != null) { + this.isGuinierTabVisible = args.isGuinierTabVisible; + } + if (args.isGnomTabVisible != null) { + this.isGnomTabVisible = args.isGnomTabVisible; + } + if (args.isPorodTabVisible != null) { + this.isPorodTabVisible = args.isPorodTabVisible; + } + if (args.hideNulls != null) { + this.hideNulls = args.hideNulls; + } if (args.height != null) { this.height = args.height; + } + if (args.width != null) { + this.width = args.width; + } + if (args.maxWidth != null) { + this.maxWidth = args.maxWidth; + } + } +} - if (args.width != null) { - this.width = args.width; +AnalysisGrid.prototype.refresh = function(data, args) { + this.store.loadData(this._prepareData(data), false); + if (args != null){ + if (args.experiment != null){ + this.experiment = args.experiment; + } + } +}; + +AnalysisGrid.prototype._getPorod = function() { + return { + text : 'Porod', + name : 'Porod', + columns : [ + { + text : 'Volume', + dataIndex : 'volumeEdna', + width : 75, + sortable : true, + hidden : !this.isPorodTabVisible, + renderer : function(val, y, sample) { + if (sample.raw.volume != null) + return BUI.formatValuesUnits(sample.raw.volume, '') + " nm3"; + } + }, + { + text : 'MM Vol. est.', + dataIndex : 'volumeEdna', + tooltip : '[Volume/2 - Volume/1.5] (Guinier)', + sortable : true, + width : 95, + hidden : !this.isPorodTabVisible, + renderer : function(val, y, sample) { + if (sample.raw.volume != null) + return Number(sample.raw.volume / 2).toFixed(1) + " - " + Number(sample.raw.volume / 1.5).toFixed(1)+ "kD"; + } + } ] + }; +}; + + +AnalysisGrid.prototype._getFramesColumn = function() { + var _this = this; + return { + text : 'Frames (Averaged/Total)', + dataIndex : 'datacollection', + name : 'datacollection', + sortable : true, + width : 150, + renderer : function(dataCollections, y, data) { + /** Bug of Webservices: frames count were swapped with frames averages **/ + if (data.raw.bufferAfterFramesCount){ + if (data.raw.bufferAfterFramesMerged){ + if (parseInt(data.raw.bufferAfterFramesMerged) > parseInt(data.raw.bufferAfterFramesCount)){ + var aux = parseInt(data.raw.bufferAfterFramesCount); + data.raw.bufferAfterFramesCount= data.raw.bufferAfterFramesMerged; + data.raw.bufferAfterFramesMerged = aux; + } + } + } + + if (data.raw.bufferBeforeFramesCount){ + if (data.raw.bufferBeforeFramesMerged){ + if (parseInt(data.raw.bufferBeforeFramesMerged) > parseInt(data.raw.bufferBeforeFramesCount)){ + var aux = parseInt(data.raw.bufferBeforeFramesCount); + data.raw.bufferBeforeFramesCount= data.raw.bufferBeforeFramesMerged; + data.raw.bufferBeforeFramesMerged = aux; + } + } + + } + + var bufferAcronym = data.raw.bufferAcronym; + var macromoleculeAcronym = data.raw.macromoleculeAcronym; + var bbmerges = data.raw.bufferBeforeFramesMerged; + var molmerges = data.raw.framesMerge; + var bamerges = data.raw.bufferAfterFramesMerged; + var totalframes = data.raw.framesCount; + var bufferId = data.raw.bufferId; + var macromoleculeId = data.raw.macromoleculeId; + var macromoleculeColor = null; + if (_this.experiment != null){ + macromoleculeColor = _this.experiment.macromoleculeColors[data.raw.macromoleculeId]; } - } - } - - this.onSelected = new Event(this); -} - - -RigidModelGrid.prototype.refresh = function(subtractions) { - var data = []; - if (subtractions != null){ - if (subtractions.length > 0){ - for (j in subtractions){ - var subtraction = subtractions[j]; - if (subtraction.rigidBodyModeling3VOs != null){ - for (i in subtraction.rigidBodyModeling3VOs){ - data.push(subtraction.rigidBodyModeling3VOs[i]); + + /** BUG in the database to be fixed **/ + try{ + if (totalframes != null){ + if(molmerges != null){ + if (parseFloat(totalframes) < parseFloat(molmerges)){ + var aux = totalframes; + totalframes = molmerges; + molmerges = aux; + } } } } + catch(e){ + + } + + return BUI.getHTMLTableForFrameAveraged(bufferAcronym, + macromoleculeAcronym, + bbmerges, + molmerges, + bamerges, + totalframes, + bufferId, + macromoleculeId, + macromoleculeColor); } - } - this.store.loadData(data); + }; }; -RigidModelGrid.prototype.getPanel = function() { +AnalysisGrid.prototype._getColumns = function() { var _this = this; - this.store = Ext.create('Ext.data.Store', { - fields : [ 'symmetry', 'subtractionId', 'subUnitConfigFilePath', 'rigidBodyModelingId', 'rigidBodyModelFilePath', 'logFilePath', 'fitFilePath', 'curveConfigFilePath', - 'crossCorrConfigFilePath', 'contactDescriptionFilePath' ], - data : [] - }); - - this.store.sort([ { - property : 'name', - direction : 'ASC' - } ]); + return [ + { + name : 'groupeField', + dataIndex : 'groupeField', + hidden : true - this.panel = Ext.create('Ext.grid.Panel', { - store : this.store, - width : this.width, - height : this.height, - margin : 10, - deferredRender : false, - columns : [ { - text : 'RBM', - dataIndex : 'rigidBodyModelFilePath', - hidden : false, - flex : 1, - renderer : function(val){ - return BUI.getFileName(val); - } - }, { - text : 'Sub Unit Conf.', - dataIndex : 'subUnitConfigFilePath', + }, + { + "header" : "subtractionId", hidden : true, - flex : 1, - renderer : function(val){ - return BUI.getFileName(val); + "dataIndex" : "subtractionId", + "name" : "subtractionId" + }, + { + header : "Macromolecule", + dataIndex : "macromoleculeAcronym", + name : "macromoleculeAcronym", + renderer : function(val, y, sample) { + return '
' + val + '
' + + BUI.formatValuesUnits(sample.raw.conc, "mg/ml", 10, this.decimals) + '
' + + BUI.formatValuesUnits(sample.raw.exposureTemperature, "C", 10, this.decimals) + '
' } - }, { - text : 'Log', - dataIndex : 'logFilePath', + }, + { + header : "Order", + dataIndex : "priorityLevelId", + name : "priorityLevelId", + hidden : true + }, + { + header : "Code", + dataIndex : "code", + name : "code", + hidden : true + }, + { + header : "Conc.", + dataIndex : "conc", + width : 80, + name : "conc", + type : "number", hidden : true, - flex : 1, - renderer : function(val){ - return BUI.getFileName(val); - } - }, { - text : 'Fit', - dataIndex : 'fitFilePath', - hidden : false, - flex : 1, - renderer : function(val){ - return BUI.getFileName(val); - } - }, { - text : 'Curve Conf.', - dataIndex : 'curveConfigFilePath', - hidden : false, - flex : 1, - renderer : function(val){ - return BUI.getFileName(val); + renderer : function(val, y, sample) { + return BUI.formatValuesUnits(val, "mg/ml", 10, this.decimals); } - }, { - text : 'Cross Corr.', - dataIndex : 'crossCorrConfigFilePath', - hidden : false, - flex : 1, - renderer : function(val){ - return BUI.getFileName(val); + }, + { + text : 'Scattering', + width : 100, + dataIndex : 'subtractionId', + name : 'subtractionId', + hidden : !this.isScatteringPlotVisible, + renderer : function(val, y, sample) { + var url = BUI.getURL() + '&type=scattering&subtractionId=' + sample.raw.subtractionId; + var event = "OnClick= window.open('" + url + "')"; + return ''; } - }, { - text : 'Contact Desc.', - dataIndex : 'contactDescriptionFilePath', + }, + { + text : 'Kratky', + width : 100, + dataIndex : 'subtractionId', hidden : true, - flex : 1, - renderer : function(val){ - return BUI.getFileName(val); + name : 'subtractionId', + renderer : function(val, y, sample) { + var url = BUI.getURL() + '&type=kratky&subtractionId=' + sample.raw.subtractionId; + var event = "OnClick= window.open('" + url + "')"; + return ''; } - } ], - - viewConfig : { - enableTextSelection : true, - preserveScrollOnRefresh : true }, - listeners : { - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - - }, - afterrender : function() { + this._getFramesColumn(), + { + text : 'File Name', + dataIndex : 'averageFilePath', + name : 'averageFilePath', + sortable : true, + width : 150, + hidden : true, + renderer : function(dataCollections, y, data) { + return BUI.getHTMLTableForPrefixes(data.raw.bufferBeforeAverageFilePath, data.raw.averageFilePath, + data.raw.bufferAfterAverageFilePath); } - } - }); - return this.panel; -}; + }, - -/** - * shows shipments - * - * @height - * @width - * @minHeight - * @btnEditVisible - */ -function ShipmentGrid(args) { - this.id = BUI.id(); - this.height = 100; - this.width = null; - this.minHeight = null; - this.btnEditVisible = true; + { + text : 'Guinier', + name : 'Guinier', + columns : [ + { + text : 'Rg', + dataIndex : 'rgGuinier', + name : 'rgGuinier', + hidden : !this.isGuinierTabVisible, + width : 75, + tooltip : 'In polymer physics, the radius of gyration is used to describe the dimensions of a polymer chain.', + sortable : true, + renderer : function(val, y, sample) { + if (sample.raw.rgGuinier != null) { + /** Show warning if rgGuinier and rgGnom differ more than 10% **/ + if (Math.abs(sample.raw.rgGuinier - sample.raw.rgGnom) > (sample.raw.rgGuinier * 0.1)) { + return "" + BUI.formatValuesUnits(sample.raw.rgGuinier, "") + ""; - if (args != null) { - if (args.height != null) { - this.height = args.height; - } - if (args.width != null) { - this.width = args.width; - } - if (args.minHeight != null) { - this.minHeight = args.minHeight; - } - if (args.btnEditVisible != null) { - this.btnEditVisible = args.btnEditVisible; - } - } -} + } + return BUI.formatValuesUnits(sample.raw.rgGuinier, "nm", 12, this.decimals); + } + } + }, + { + text : 'Points', + dataIndex : 'points', + sortable : true, + width : 100, + type : 'string', + hidden : !this.isGuinierTabVisible, + renderer : function(val, y, sample) { + if ((sample.raw.firstPointUsed == "") || (sample.raw.firstPointUsed == null)) + return; + return "" + sample.raw.firstPointUsed + " - " + sample.raw.lastPointUsed + " (" + + (sample.raw.lastPointUsed - sample.raw.firstPointUsed) + " )"; + } + }, + { + text : 'Quality', + dataIndex : 'quality', + hidden : !this.isGuinierTabVisible, + tooltip : 'Estimated data quality. 1.0 - means ideal quality, 0.0 - unusable data. In table format it is given in percent (100% - ideal quality, 0% - unusable data). Please note that this estimation is based only on the Guinier interval (very low angles).', + width : 60, + sortable : true, + renderer : function(val, y, sample) { + if (sample.raw.quality != null) { + val = sample.raw.quality; + if ((val != null) && (val != "")) { + return "" + (Number(val) * 100).toFixed(2) + " %"; + } + } + } + }, { + text : 'I(0)', + dataIndex : 'I0', + sortable : true, + hidden : !this.isI0Visible, + tooltip : 'Extrapolated scattering intensity at zero angle I(0) (forward scattering)', + width : 75, + type : 'string', + renderer : function(val, y, sample) { + if (sample.raw.I0 != null) { + return BUI.formatValuesErrorUnitsScientificFormat(sample.raw.I0, sample.raw.i0stdev, ""); + } + } + }, { + text : 'Aggregated', + tooltip : "If aggregation was detected from the slope of the data curve at low angles the value is '1', otherwise '0'.", + dataIndex : 'isagregated', + hidden : true, + width : 75, + renderer : function(val, y, sample) { + if ((sample.raw.isagregated != null)) { + if (val == true) { + return "Yes"; + } else { + return "No"; + } + } + } + }, { + text : 'Guinier', + sortable : true, + dataIndex : 'subtractionId', + type : 'string', + width : 100, + hidden : true, + renderer : function(val, y, sample) { -ShipmentGrid.prototype._getColumns = function() { - var _this = this; - var columns = [ - { - text : 'Name', - dataIndex : 'shippingName', - flex : 1 + if (sample.raw.subtractionId != null) { + var url = BUI.getURL() + '&type=guinier&subtractionId=' + sample.raw.subtractionId; + var event = "OnClick= window.open('" + url + "')"; + return ''; + } + } + } ] }, { - header : 'Type', - dataIndex : 'shippingType', - flex : 1, - hidden : true, - renderer : function(val, comp, record) { - if (val != null) { - return val.toUpperCase(); - } + text : 'Gnom', + name : 'Gnom', - } - }, - { - header : 'Status', - type : 'string', - flex : 1, - hidden : false, - renderer : function(comp, val, record) { - if (record.raw.shippingStatus != null) { - if (new String(record.raw.shippingStatus).toUpperCase() == 'OPENED') { - return "" + new String(record.raw.shippingStatus).toUpperCase() + ""; + columns : [ { + text : 'Rg', + dataIndex : 'rgGnom', + type : 'string', + width : 65, + hidden : !this.isGnomTabVisible, + sortable : true, + renderer : function(val, y, sample) { + /** Show warning if rgGuinier and rgGnom differ more than 10% **/ + if (sample.raw.rgGnom != null) { + if (Math.abs(sample.raw.rgGuinier - sample.raw.rgGnom) > (sample.raw.rgGuinier * 0.1)) { + return "" + BUI.formatValuesUnits(sample.raw.rgGnom, "") + ""; + + } + return BUI.formatValuesUnits(sample.raw.rgGnom, "nm"); } - return "" + new String(record.raw.shippingStatus).toUpperCase() + ""; } - } + }, { + text : 'Total', + dataIndex : 'total', + width : 65, + hidden : !this.isGnomTabVisible, + sortable : true, + renderer : function(val, y, sample) { + if (sample.raw.total != null) + return BUI.formatValuesUnits(sample.raw.total, ''); + } + }, { + text : 'Dmax', + dataIndex : 'dmax', + sortable : true, + width : 75, + hidden : !this.isGnomTabVisible, + renderer : function(val, y, sample) { + if (sample.raw.dmax != null) + return BUI.formatValuesUnits(sample.raw.dmax, "") + " nm"; + } + }, { + text : 'P(r)', + sortable : true, + hidden : true, + width : 100, + dataIndex : 'subtractionId', + type : 'string', + renderer : function(val, y, sample) { + var url = BUI.getURL() + '&type=gnom&subtractionId=' + sample.raw.subtractionId; + var event = "OnClick= window.open('" + url + "')"; + return ''; + } + } ] }, + this._getPorod(), { - text : 'Cases', - flex : 1, - hidden : false, - renderer : function(comp, val, record) { - var shipment = BIOSAXS.proposal.getShipmentById(record.data.shippingId); - var container = ""; - if (shipment.dewarVOs.length > 0) { - container = container + ""; - } else { - return "Empty"; - } - return container + "
" + shipment.dewarVOs.length + "x
"; - } - }, { - header : 'Comments', - dataIndex : 'comments', - flex : 1, - hidden : false - }, { - header : 'Creation Date', - dataIndex : 'creationDate', - hidden : true - } ]; - - if (this.btnEditVisible) { - columns.push({ - id : _this.id + 'buttonEdit', - text : '', - hidden : !_this.btnEditVisible, - width : 100, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - return BUI.getGreenButton('EDIT'); - } - }); - } - - columns.push({ - id : _this.id + 'buttonRemove', - text : '', - width : 100, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - var shipment = BIOSAXS.proposal.getShipmentById(record.data.shippingId); - if (shipment.dewarVOs.length == 0) { - return BUI.getRedButton('REMOVE'); - } - - } - }); - - return columns; -}; - -ShipmentGrid.prototype._getTopButtons = function() { - var _this = this; - /** Actions buttons **/ - var actions = []; - actions.push(Ext.create('Ext.Action', { - icon : '../images/add.png', - text : 'Add Shipment', - handler : function(widget, event) { - //window.location = BUI.getCreateShipmentURL(); - var _this = this; - - var shipmentForm = new ShipmentForm({ - creationMode : true, - showTitle : false - }); - shipmentForm.onSaved.attach(function(sender, shipment) { - _this.showShipmentTabs(shipment, targetId); - }); - - var window = Ext.create('Ext.window.Window', { - title : 'New Shipment', - height : 600, - width : 800, - layout : 'fit', - items : [ shipmentForm.getPanel() ] - }).show(); - - } - })); - return actions; -}; - -ShipmentGrid.prototype.refresh = function(shippings) { - this.features = shippings; - this.store.loadData(this._prepareData(), false); -}; - -ShipmentGrid.prototype._prepareData = function() { - var data = []; - for ( var i = 0; i < this.features.length; i++) { - data.push(this.features[i]); - } - return data; -}; - -ShipmentGrid.prototype.getPanel = function(shipments) { - this.features = shipments; - return this._renderGrid(); -}; - -ShipmentGrid.prototype.edit = function(shippingId) { - window.location = BUI.getShippingURL(shippingId); -}; - -ShipmentGrid.prototype._getStoreFields = function(data) { - var _this = this; - return [ { - name : 'shippingId' - }, { - name : 'shippingName' - }, { - name : 'shippingStatus' - }, { - name : 'shippingType' - }, { - name : 'creationDate' - }, { - name : 'comments' - } ]; -}; - -ShipmentGrid.prototype._renderGrid = function() { - var _this = this; - - /** Store **/ - var data = this._prepareData(); - this.store = Ext.create('Ext.data.Store', { - fields : this._getStoreFields(data), - autoload : true, - data : data - }); - - this.store.loadData(data, false); + text : 'AbInitio Modeling', + name : 'AbInitio_modeling', - this.grid = Ext.create('Ext.grid.Panel', { - title : "Shipping", - icon : '/ispyb/images/plane.gif', - width : this.width, - minWidth : this.minWidth, - height : this.height, - store : this.store, - columns : this._getColumns(), - viewConfig : { - stripeRows : true, - listeners : { - itemdblclick : function(dataview, record, item, e) { - _this.edit(record.raw.shippingId); + columns : [ + { + text : 'NSD', + dataIndex : 'volumeEdna', + width : 100, + sortable : true, + hidden : true, + renderer : function(val, y, sample) { + var url = BUI.getNSDImageURL(sample.raw.modelListId); + var event = "OnClick= window.open('" + url + "')"; + return ''; + } }, - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEdit') { - _this.edit(record.data.shippingId); + { + text : 'Chi2', + dataIndex : 'volumeEdna', + sortable : true, + hidden : true, + width : 100, + renderer : function(val, y, sample) { + var url = BUI.getCHI2ImageURL(sample.raw.modelListId); + var event = "OnClick= window.open('" + url + "')"; + return ''; } + }, + { + text : 'Pdb', + dataIndex : 'volumeEdna', + tooltip : 'Damaver: The program suite DAMAVER is a set of programs to align ab initio models, select the most typical one and build an averaged model. Dammif : Rapid ab initio shape determination by simulated annealing using a single phase dummy atom model. Dammin :Ab initio shape determination by simulated annealing using a single phase dummy atom model', + sortable : true, + width : 125, + hidden : !this.isAbinitioTabVisible, + renderer : function(val, y, sample) { + var html = new String(); + var split = null; + var url = null; + var file = sample.raw.averagedModel; + if (file != null) { + split = file.split("/"); + if (split.length > 0) { + url = BUI.getPdbURL() + '&type=AVERAGED&abInitioModelId=' + sample.raw.abInitioModelId; + html = html + ''+ split[split.length - 1] + '

'; - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemove') { - var shipment = BIOSAXS.proposal.getShipmentById(record.data.shippingId); - if (shipment.dewarVOs.length == 0) { + } + } - var adapter = new BiosaxsDataAdapter(); - _this.grid.setLoading("ISPyB: Removing shipment"); - adapter.onSuccess.attach(function(sender) { - BIOSAXS.proposal.onInitialized.attach(function(sender) { - _this.refresh(BIOSAXS.proposal.getShipments()); - _this.grid.setLoading(false); - }); - BIOSAXS.proposal.init(); - }); + file = sample.raw.rapidShapeDeterminationModel; + if (file != null) { + split = file.split("/"); + if (split.length > 0) { + url = BUI.getPdbURL() + '&type=RAPIDSHAPEDETERMINATIONMODEL&abInitioModelId=' + sample.raw.abInitioModelId; + html = html + '' + split[split.length - 1] + '

'; + } + } - adapter.onError.attach(function(sender) { - alert("Error"); - _this.grid.setLoading(false); - }); - adapter.removeShipment(record.data.shippingId); + file = sample.raw.shapeDeterminationModel; + if (file != null) { + split = file.split("/"); + if (split.length > 0) { + url = BUI.getPdbURL() + '&type=SHAPEDETERMINATIONMODEL&abInitioModelId=' + sample.raw.abInitioModelId; + html = html + ''+ split[split.length - 1] + ''; + } } + return html; } - } - } - }, - selModel : { - mode : 'SINGLE' - } - }); - - var actions = _this._getTopButtons(); - this.grid.addDocked({ - xtype : 'toolbar', - items : actions - }); - - this.grid.getSelectionModel().on({ - selectionchange : function(sm, selections) { - if (selections.length) { - for ( var i = 0; i < actions.length; i++) { - if (actions[i].enable) { - actions[i].enable(); + }, + { + text : 'Damaver', + dataIndex : 'volumeEdna', + hidden : true, + tooltip : 'Damaver: The program suite DAMAVER is a set of programs to align ab initio models, select the most typical one and build an averaged model. ', + sortable : true, + width : 125, + renderer : function(val, y, sample) { + var file = sample.raw.averagedModel; + if (file != null) { + var split = file.split("/"); + if (split.length > 0) { + var url = BUI.getPdbURL() + '&type=AVERAGED&abInitioModelId=' + sample.raw.abInitioModelId; + return '' + split[split.length - 1]+ ''; + } + } + return sample.raw.averagedModel; } - } - } else { - for ( var i = 0; i < actions.length; i++) { - if (actions[i].alwaysEnabled == false) { - if (actions[i].disable) { - actions[i].disable(); + }, + { + text : 'Dammif', + dataIndex : 'volumeEdna', + hidden : true, + tooltip : 'Dammif : Rapid ab initio shape determination by simulated annealing using a single phase dummy atom model', + sortable : true, + width : 125, + renderer : function(val, y, sample) { + var file = sample.raw.rapidShapeDeterminationModel; + if (file != null) { + var split = file.split("/"); + if (split.length > 0) { + var url = BUI.getPdbURL() + '&type=RAPIDSHAPEDETERMINATIONMODEL&abInitioModelId=' + sample.raw.abInitioModelId; + return '' + split[split.length - 1] + ''; + } } + return sample.raw.averagedModel; } - } - } - } - }); - return this.grid; -}; - -ShipmentGrid.prototype.input = function() { - return { - proposal : new MeasurementGrid().input().proposal, - shippings : DATADOC.getShippings_10() - }; -}; - -ShipmentGrid.prototype.test = function(targetId) { - var shipmentGrid = new ShipmentGrid({ - minHeight : 300, - height : 440 - }); - BIOSAXS.proposal = new Proposal(shipmentGrid.input().proposal); - var panel = shipmentGrid.getPanel(targetId); - panel.render(targetId); - shipmentGrid.refresh(shipmentGrid.input().shippings); -}; - -function SpecimenGrid(args) { - this.id = BUI.id(); - this.height = 500; - this.unitsFontSize = 9; - this.editEnabled = false; - this.isPositionColumnHidden = false; - this.removeBtnEnabled = false; - - this.selectionMode = "MULTI"; - this.updateRowEnabled = false; - this.grouped = true; - this.width = 900; - this.title = 'Specimens'; - - this.margin = "0 0 0 0"; -// this.experimentColorBased = false; - - if (args != null) { - if (args.height != null) { - this.height = args.height; - } - - if (args.showTitle == false) { - this.title = null; - } - - if (args.margin == false) { - this.margin = args.margin; - } - - if (args.grouped == false) { - this.grouped = null; - } - - if (args.width != null) { - this.width = args.width; - } - - - if (args.editEnabled != null) { - this.editEnabled = args.editEnabled; - } - if (args.removeBtnEnabled != null) { - this.removeBtnEnabled = args.removeBtnEnabled; - } - if (args.isPositionColumnHidden != null) { - this.isPositionColumnHidden = args.isPositionColumnHidden; - } - if (args.selectionMode != null) { - this.selectionMode = args.selectionMode; - } - if (args.updateRowEnabled != null) { - this.updateRowEnabled = args.updateRowEnabled; - } - - } - this.onClick = new Event(this); - this.onSelected = new Event(this); - this.onRemoved = new Event(this); - this.onSpecimenChanged = new Event(); -} - -SpecimenGrid.prototype._prepareData = function(experiment) { - var data = []; - - var samples = experiment.getSamples(); - for ( var i = 0; i < samples.length; i++) { - var sample = samples[i]; - if (sample.macromolecule3VO != null) { - sample.macromolecule = sample.macromolecule3VO.acronym; - sample.exposureTemperature = []; - sample.macromoleculeId = sample.macromolecule3VO.macromoleculeId; - } + }, + { + text : 'Dammin', + dataIndex : 'volumeEdna', + hidden : true, + tooltip : 'Dammin :Ab initio shape determination by simulated annealing using a single phase dummy atom model', + sortable : true, + width : 125, + renderer : function(val, y, sample) { + var file = sample.raw.shapeDeterminationModel; + if (file != null) { + var split = file.split("/"); + if (split.length > 0) { + var url = BUI.getPdbURL() + '&type=SHAPEDETERMINATIONMODEL&abInitioModelId=' + sample.raw.abInitioModelId; + return '' + split[split.length - 1]+ ''; + } + } + return sample.raw.averagedModel; + } + } ] + }, { + text : 'Time', + dataIndex : 'substractionCreationTime', + name : 'substractionCreationTime', + hidden : true, + width : 80, + sortable : true, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + try { + if (record.raw.substractionCreationTime != null) { + return moment(record.raw.substractionCreationTime).format('h:mm:ss a'); + } + } catch (e) { + return "NA"; + } + } + }, { + text : 'Date', + dataIndex : 'substractionCreationTime', + name : 'substractionCreationTime', + hidden : true, + width : 80, + sortable : true, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + try { + if (record.raw.substractionCreationTime != null) { + return moment(record.raw.substractionCreationTime).format("LL"); + } + } catch (e) { + return "NA"; + } + } + }, + this._getButtons()]; +}; - if (sample.sampleplateposition3VO != null) { - if (sample.sampleplateposition3VO.samplePlateId != null) { - sample.samplePlateId = sample.sampleplateposition3VO.samplePlateId; - sample.rowNumber = sample.sampleplateposition3VO.rowNumber; - sample.columnNumber = sample.sampleplateposition3VO.columnNumber; - if (experiment.getSamplePlateById(sample.sampleplateposition3VO.samplePlateId).plategroup3VO != null) { - sample.plateGroupName = experiment.getSamplePlateById(sample.sampleplateposition3VO.samplePlateId).plategroup3VO.name; - sample.samplePlateName = experiment.getSamplePlateById(sample.sampleplateposition3VO.samplePlateId).name + " [" + sample.plateGroupName + "]"; - sample.slotPositionColumn = experiment.getSamplePlateById(sample.sampleplateposition3VO.samplePlateId).slotPositionColumn; +AnalysisGrid.prototype._getButtons = function() { + return { + id : this.id + 'buttonPlot', + name : 'buttonPlot', + hidden : !this.showButtonsVisible, + width : 110, + sortable : false, + renderer : function(value, metaData, sample, rowIndex, colIndex, store) { + var html = ""; + + if (sample.raw.subtractionId) { + html = html + ""; + if (sample.raw.rapidShapeDeterminationModelId != null) { + html = html + ""; } } - } else { - sample.samplePlateName = "Unallocated Specimens"; + return html + "
" + BUI.getGreenButton('Calibration', { + height : 20, + width : 100 + }) + "
" + BUI.getGreenButton('Primary Data Proc.', { + height : 20, + width : 100 + }) + "
" + BUI.getGreenButton('AbInitio Modeling', { + height : 20, + width : 100 + }) + "
"; } - - /** For grouping, because sencha has not option for multiple grouping I add a field to your store with a convert function that concatenates these two fields and then group by that field.**/ - sample.groupIndex = sample.bufferId + sample.macromoleculeId; - var macromolecule = BIOSAXS.proposal.getMacromoleculeById(sample.macromoleculeId); - - sample.acronym = "Buffers"; - if (macromolecule != null) { - sample.acronym = BIOSAXS.proposal.getMacromoleculeById(sample.macromoleculeId).acronym; + }; +}; +AnalysisGrid.prototype._prepareData = function(data) { + if (this.hideNulls) { + var result = []; + for ( var i = 0; i < data.length; i++) { + if (data[i].subtractionId != null) { + data[i].groupeField = data[i].macromoleculeAcronym + " " + data[i].bufferAcronym; + result.push(data[i]); + } } - - sample.buffer = experiment.getBufferById(sample.bufferId); - - sample.volumeToLoad = experiment.getVolumeToLoadBySampleId(sample.sampleId); - data.push(sample); + return result; + } else { + return data; } - return data; }; -SpecimenGrid.prototype.deselectAll = function() { - this.grid.getSelectionModel().deselectAll(); -}; +AnalysisGrid.prototype.getPanel = function(data) { + var _this = this; + var columns = this._getColumns(); -SpecimenGrid.prototype.selectById = function(specimenId) { - this.grid.getSelectionModel().deselectAll(); - for ( var i = 0; i < this.grid.getStore().data.items.length; i++) { - var item = this.grid.getStore().data.items[i].raw; - if (item.specimenId == specimenId) { - this.grid.getSelectionModel().select(i); - } - } -}; + var fields = JSON.parse(JSON.stringify(columns)); + fields.push({ + name : 'experimentId', + dataIndex : 'experimentId' -SpecimenGrid.prototype.getStore = function() { - return this.store; -}; + }); + this.store = Ext.create('Ext.data.Store', { + fields : fields, + autoload : true, + data : this._prepareData(data), + groupField : 'groupeField' + }); -SpecimenGrid.prototype.getPlugins = function() { - var _this = this; + this.store.sort(this.sorters); - var plugins = []; + var features = []; - if (this.updateRowEnabled) { - plugins.push(Ext.create('Ext.grid.plugin.RowEditing', { - clicksToEdit : 1, + if (this.grouped) { + features.push({ + ftype : 'grouping', + groupHeaderTpl : '{name}', + hideGroupedHeader : false, + startCollapsed : false + }); + } + + this.grid = Ext.create('Ext.grid.Panel', { + style : { + padding : 5 + }, + maxWidth : this.maxWidth, + width : this.width, + height : this.height, + store : this.store, + columns : columns, + resizable : true, + features : features, + viewConfig : { + preserveScrollOnRefresh : true, + stripeRows : true, listeners : { - validateedit : function(grid, e) { - var measurements = []; + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - if (e.newValues.bufferId != e.record.raw.bufferId) { - /** If buffer has changed we have to change all the specimens sharing same datacollection **/ - var dataCollections = []; - if (e.record.raw.macromoleculeId == null) { - dataCollections = dataCollections.concat(_this.experiment.getDataCollectionsBySpecimenId(e.record.raw.specimenId)); - } else { - var sampleDataCollections = _this.experiment.getDataCollectionsBySpecimenId(e.record.raw.specimenId); - for ( var i = 0; i < sampleDataCollections.length; i++) { - var sampleDataCollection = sampleDataCollections[i]; - if (sampleDataCollection != null) { - for ( var j = 0; j < sampleDataCollection.measurementtodatacollection3VOs.length; j++) { - var measurementTODc = sampleDataCollection.measurementtodatacollection3VOs[j]; - if (measurementTODc.dataCollectionOrder == 1) { - dataCollections = dataCollections.concat(_this.experiment.getDataCollectionsBySpecimenId(_this.experiment - .getMeasurementById(measurementTODc.measurementId).specimenId)); - } - } - } - } - } - var i = null; - for ( i = 0; i < dataCollections.length; i++) { - var dataCollection = dataCollections[i]; - var specimens = _this.experiment.getSpecimenByDataCollectionId(dataCollection.dataCollectionId); - measurements = measurements.concat(specimens); + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonPlot') { + if (e.target.defaultValue == 'AbInitio Modeling') { + var url = BUI.getPDBVisualizerURL(record.raw.averagedModelId, record.raw.subtractionId, record.raw.experimentId); + window.open(url, "_blank"); } - for ( i = 0; i < measurements.length; i++) { - var measurement = measurements[i]; - var specimen = _this.experiment.getSpecimenById(measurement.specimenId); - specimen.bufferId = e.newValues.bufferId; - new BiosaxsDataAdapter().saveSpecimen(specimen, _this.experiment); + if (e.target.defaultValue == 'Primary Data Proc.') { + _this._edit(record.raw); } - } - - /** Setting values **/ - e.record.raw.concentration = e.newValues.concentration; - e.record.raw.volume = e.newValues.volume; - /** Position **/ - if (e.record.raw.sampleplateposition3VO != null) { - var samplePlate = _this.experiment.getSamplePlateBySlotPositionColumn(e.newValues.slotPositionColumn); - if (samplePlate != null) { - e.record.raw.sampleplateposition3VO = { - columnNumber : e.newValues.columnNumber, - rowNumber : e.newValues.rowNumber, - samplePlateId : samplePlate.samplePlateId - }; - } - } else { - if (e.newValues.slotPositionColumn != null) { - var samplePlate = _this.experiment.getSamplePlateBySlotPositionColumn(e.newValues.slotPositionColumn); - if (samplePlate != null) { - e.record.raw.sampleplateposition3VO = { - columnNumber : e.newValues.columnNumber, - rowNumber : e.newValues.rowNumber, - samplePlateId : samplePlate.samplePlateId - }; - } + if (e.target.defaultValue == 'Calibration') { + _this._showCalibration(record.raw); } } - - var macromoleculeId = e.record.data.macromoleculeId; - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, specimen) { - /** Because macromolecule3VO is fecthed LAZY **/ - if (macromoleculeId != null) { - specimen.macromolecule3VO = BIOSAXS.proposal.getMacromoleculeById(macromoleculeId); - } - _this.onSpecimenChanged.notify(specimen); - _this.grid.setLoading(false); - }); - adapter.onError.attach(function() { - alert("Error"); - _this.grid.setLoading(false); - }); - _this.grid.setLoading(); - adapter.saveSpecimen(e.record.raw, _this.experiment); } } - })); - } - return plugins; + }, + selModel : { + mode : 'SINGLE' + } + }); + + return this.grid; + +}; + +AnalysisGrid.prototype._openVisualizarBySubstractionId = function(record) { + //experimentId, subtractionId) { + var experimentId = record.experimentId; + var subtractionId = record.subtractionId; + + var _this = this; + var adapter = new BiosaxsDataAdapter(); + this.subtractionId = subtractionId; + + adapter.onSuccess.attach(function(sender, data) { + var experiment = new Experiment(data); + var experimentList = new ExperimentList([ experiment ]); + var subtraction = experiment.getSubtractionById(_this.subtractionId); + _this.grid.setLoading(false); + _this._openVisualizer(experimentList, subtraction, record); + }); + this.grid.setLoading("ISPyB: Fetching experiment"); + adapter.getExperimentById(experimentId, "MEDIUM"); }; -SpecimenGrid.prototype._getRowCombo = function() { - var data = []; - for ( var i = 1; i <= 8; i++) { - data.push({ - rowNumber : i, - name : BUI.getSamplePlateLetters()[i - 1] +AnalysisGrid.prototype._edit = function(record) { + var experimentId = record.experimentId; + var _this = this; + + if (BIOSAXS.proposal.macromolecules == null) { + this.grid.setLoading("ISPyB: Fetching proposal"); + BIOSAXS.proposal.onInitialized.attach(function(sender, data) { + _this._openVisualizarBySubstractionId(record); }); + BIOSAXS.proposal.init(); + } else { + this._openVisualizarBySubstractionId(record); } +}; - var positionsStore = Ext.create('Ext.data.Store', { - fields : [ 'rowNumber', 'name' ], - data : data - }); - return Ext.create('Ext.form.ComboBox', { - store : positionsStore, - queryMode : 'local', - displayField : 'name', - valueField : 'rowNumber' +AnalysisGrid.prototype._showCalibration = function(row) { + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + Ext.create('Ext.window.Window', { + title : 'Calibration', + width : 900, + resizable : true, + height : 400, + modal : true, + frame : false, + draggable : true, + closable : true, + autoscroll : true, + paddin : 5, + layout : { + type : 'vbox', + align : 'stretch' + }, + items : [ new AnalysisGrid({ + isGuinierTabVisible : false, + isGnomTabVisible : false, + isPorodTabVisible : false, + isAbinitioTabVisible : false, + isI0Visible : true, + showButtonsVisible : false, + height : 350, + sorters : [ { + property : 'experimentId', + direction : 'DESC' + } ] + }).getPanel(data) ] + }).show(); }); + adapter.getAnalysisCalibrationByProposalId(); }; -SpecimenGrid.prototype._getColumnCombo = function() { - var data = []; - for ( var i = 1; i <= 12; i++) { - data.push({ - columnNumber : i - }); +AnalysisGrid.prototype._openVisualizer = function(experimentList, subtraction, record) { + var merges = experimentList.getMergesByDataCollectionId(subtraction.dataCollectionId); + var mergeIdList = []; + for ( var i = 0; i < merges.length; i++) { + mergeIdList.push(merges[i].mergeId); } - var positionsStore = Ext.create('Ext.data.Store', { - fields : [ 'columnNumber' ], - data : data + var dataAdapter = new BiosaxsDataAdapter(); + dataAdapter.onSuccess.attach(function(sender, merges) { + var dataCollectionCurveVisualizer = new DataCollectionCurveVisualizer(); + dataCollectionCurveVisualizer.draw(); + dataCollectionCurveVisualizer.refresh(merges, experimentList, subtraction.dataCollectionId, record); }); - return Ext.create('Ext.form.ComboBox', { - store : positionsStore, - queryMode : 'local', - displayField : 'columnNumber', - valueField : 'columnNumber' + dataAdapter.onError.attach(function(sender, error) { }); + + dataAdapter.getMergesByIdsList(mergeIdList); }; -SpecimenGrid.prototype._getSlotColumBombo = function() { - if (this.experiment){ - var length = this.experiment.getSamplePlates().length; - - var data = []; - for ( var i = 1; i <= length; i++) { - data.push({ - slotPositionColumn : i - }); - } +AnalysisGrid.prototype.input = function() { + return { + data : DATADOC.getData_3367().slice(20, 30),//[{"total":"0.447505552082","bufferBeforeMeasurementId":22150,"sampleMergeId":12373,"averagedModelId":43636,"I0":"32.50776","proposalCode":"OPD","averagedModel":"/data/pyarch/bm29/opd29/1137/1d/damaver.pdb","bufferAfterMergeId":12374,"framesCount":"10","bufferBeforeMergeId":12372,"averageFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_016_ave.dat","bufferAfterMeasurementId":22152,"rgGuinier":"2.96883","subtractedFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_016_sub.dat","firstPointUsed":"30","chi2RgFilePath":"/data/pyarch/bm29/opd29/1137/1d/chi2_R.png","abInitioModelId":272,"macromoleculeId":112,"code":"_20.0_1.25","transmission":"100.0","timeStart":"2013-07-17 17:10:25.743734","bufferAcronym":"MES","quality":"0.87091","shapeDeterminationModelId":43638,"expermientComments":"[BsxCube] Generated from BsxCube","bufferId":707,"isagregated":"False","dmax":"10.390905","bufferBeforeAverageFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_015_ave.dat","exposureTemperature":"20.0","subtractionId":5165,"conc":"1.25","rapidShapeDeterminationModel":"/data/pyarch/bm29/opd29/1137/1d/damfilt.pdb","experimentCreationDate":"Jul 17, 2013 5:08:37 PM","lastPointUsed":"92","modelListId":272,"framesMerge":"10","rapidShapeDeterminationModelId":43637,"bufferAfterAverageFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_017_ave.dat","nsdFilePath":"/data/pyarch/bm29/opd29/1137/1d/nsd.png","bufferAfterFramesMerged":"10","experimentId":1137,"macromoleculeAcronym":"MG386","i0stdev":"0.05726128","sampleMeasurementId":22151,"measurementComments":"[1] MES","priorityLevelId":2,"bufferBeforeFramesMerged":"10","substractionCreationTime":"Jul 17, 2013 5:12:32 PM","proposalNumber":"29","rgGnom":"3.05242714339","volume":"44.1406","shapeDeterminationModel":"/data/pyarch/bm29/opd29/1137/1d/dammin.pdb","comments":null},{"total":"0.582641941147","bufferBeforeMeasurementId":22152,"sampleMergeId":12375,"averagedModelId":43809,"I0":"31.4366153846","proposalCode":"OPD","averagedModel":"/data/pyarch/bm29/opd29/1137/1d/damaver.pdb","bufferAfterMergeId":12376,"framesCount":"10","bufferBeforeMergeId":12374,"averageFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_018_ave.dat","bufferAfterMeasurementId":22155,"rgGuinier":"2.95541","subtractedFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_018_sub.dat","firstPointUsed":"21","chi2RgFilePath":"/data/pyarch/bm29/opd29/1137/1d/chi2_R.png","abInitioModelId":273,"macromoleculeId":112,"code":"_20.0_0.65000000000000002","transmission":"100.0","timeStart":"2013-07-17 17:12:55.837462","bufferAcronym":"MES","quality":"0.870164","shapeDeterminationModelId":43811,"expermientComments":"[BsxCube] Generated from BsxCube","bufferId":707,"isagregated":"False","dmax":"10.343935","bufferBeforeAverageFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_017_ave.dat","exposureTemperature":"20.0","subtractionId":5166,"conc":"0.65000000000000002","rapidShapeDeterminationModel":"/data/pyarch/bm29/opd29/1137/1d/damfilt.pdb","experimentCreationDate":"Jul 17, 2013 5:08:37 PM","lastPointUsed":"80","modelListId":273,"framesMerge":"10","rapidShapeDeterminationModelId":43810,"bufferAfterAverageFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_019_ave.dat","nsdFilePath":"/data/pyarch/bm29/opd29/1137/1d/nsd.png","bufferAfterFramesMerged":"10","experimentId":1137,"macromoleculeAcronym":"MG386","i0stdev":"0.100250461538","sampleMeasurementId":22154,"measurementComments":"[2] MES","priorityLevelId":4,"bufferBeforeFramesMerged":"10","substractionCreationTime":"Jul 17, 2013 5:15:02 PM","proposalNumber":"29","rgGnom":"2.9963404542","volume":"42.2255","shapeDeterminationModel":"/data/pyarch/bm29/opd29/1137/1d/dammin.pdb","comments":null}], + proposal : new ResultsAssemblyGrid().input().proposal + }; +}; + +AnalysisGrid.prototype.test = function(targetId) { + var analysisGrid = new AnalysisGrid(); + BIOSAXS.proposal = new Proposal(analysisGrid.input().proposal); + var panel = analysisGrid.getPanel(analysisGrid.input().data); + panel.render(targetId); +}; + + +function HPLCAnalysisGrid(args) { + AnalysisGrid.prototype.constructor.call(this, args); +} - var positionsStore = Ext.create('Ext.data.Store', { - fields : [ 'slotPositionColumn' ], - data : data - }); +HPLCAnalysisGrid.prototype._edit = AnalysisGrid.prototype._edit; +HPLCAnalysisGrid.prototype._getColumns = AnalysisGrid.prototype._getColumns; +HPLCAnalysisGrid.prototype._openVisualizarBySubstractionId = AnalysisGrid.prototype._openVisualizarBySubstractionId; +HPLCAnalysisGrid.prototype._openVisualizer = AnalysisGrid.prototype._openVisualizer; +HPLCAnalysisGrid.prototype._prepareData = AnalysisGrid.prototype._prepareData; +HPLCAnalysisGrid.prototype._showCalibration = AnalysisGrid.prototype._showCalibration; +HPLCAnalysisGrid.prototype.getPanel = AnalysisGrid.prototype.getPanel; +HPLCAnalysisGrid.prototype.input = AnalysisGrid.prototype.input; +HPLCAnalysisGrid.prototype.test = AnalysisGrid.prototype.test; +HPLCAnalysisGrid.prototype.refresh = AnalysisGrid.prototype.refresh; +HPLCAnalysisGrid.prototype._getPorod = AnalysisGrid.prototype._getPorod; + +HPLCAnalysisGrid.prototype._getButtons = function() { + return { + id : this.id + 'buttonPlot', + name : 'buttonPlot', + hidden : !this.showButtonsVisible, + width : 110, + sortable : false, + renderer : function(value, metaData, sample, rowIndex, colIndex, store) { + var html = ""; - return Ext.create('Ext.form.ComboBox', { - store : positionsStore, - queryMode : 'local', - displayField : 'slotPositionColumn', - valueField : 'slotPositionColumn' - }); + if (sample.raw.subtractionId) { + if (sample.raw.rapidShapeDeterminationModelId != null) { + html = html + ""; + } + } + return html + "
" + BUI.getGreenButton('AbInitio Modeling', { + height : 20, + width : 100 + }) + "
"; + } + }; +}; + +HPLCAnalysisGrid.prototype._getFramesColumn = function() { + return { + text : 'Frames', + dataIndex : 'datacollection', + name : 'datacollection', + sortable : true, + width : 150, + renderer : function(dataCollections, y, data) { + molmerges = data.raw.framesMerge; + totalframes = data.raw.framesCount; + return molmerges +" - "+ totalframes; + } + }; +}; + + + + +/** + * Rigid body grid to show PDB, symmetry and multiplicity + * + * + * #onUploadFile click on upload file + */ +function AprioriRigidBodyGrid(args) { + + this.height = 250; + this.btnEditVisible = true; + this.btnRemoveVisible = true; + + if (args != null) { + if (args.height != null) { + this.height = args.height; + } + if (args.btnEditVisible != null) { + this.btnEditVisible = args.btnEditVisible; + } + if (args.btnRemoveVisible != null) { + this.btnRemoveVisible = args.btnRemoveVisible; + } + } + + /** Events **/ + this.onUploadFile = new Event(this); + this.onRemove = new Event(this); +} + +AprioriRigidBodyGrid.prototype._getColumns = function() { +}; + +AprioriRigidBodyGrid.prototype._getTopButtons = function() { + var _this = this; + /** Actions buttons **/ + var actions = []; + + /** ADD BUTTON **/ + actions.push(Ext.create('Ext.Action', { + icon : '../images/add.png', + text : 'Add', + disabled : false, + handler : function(widget, event) { + _this.onAddButtonClicked.notify(); + } + })); + + return actions; +}; + +AprioriRigidBodyGrid.prototype.refresh = function(macromolecule) { + this.macromolecule = macromolecule; + if (macromolecule != null){ + this.pdbStore.loadData(macromolecule.structure3VOs); + } +}; + +AprioriRigidBodyGrid.prototype._prepareData = function() { + var data = []; + for ( var i = 0; i < this.features.length; i++) { + data.push(this.features[i]); + } + return data; +}; + +AprioriRigidBodyGrid.prototype._getPlugins = function() { + var _this = this; + var plugins = []; + plugins.push(Ext.create('Ext.grid.plugin.RowEditing', { + clicksToEdit : 1, + listeners : { + validateedit : function(grid, e) { + /** Comments are always updatable* */ + e.record.raw.symmetry = e.newValues.symmetry; + e.record.raw.multiplicity = e.newValues.multiplicity; + + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, proposal) { + BIOSAXS.proposal.setItems(proposal); + _this.refresh(BIOSAXS.proposal.getMacromoleculeById(_this.macromolecule.macromoleculeId)); + _this.panel.setLoading(false); + }); + adapter.onError.attach(function() { + alert("Error"); + }); + + _this.panel.setLoading(); + adapter.saveStructure(e.record.raw); + } + } + })); + return plugins; +}; + +AprioriRigidBodyGrid.prototype.getPanel = function() { + var _this = this; + + this.pdbStore = Ext.create('Ext.data.Store', { + fields : [ 'filePath', 'structureId', 'structureType', 'symmetry', 'structureId', 'name', 'multiplicity' ], + groupField : 'structureType', + sorters : { + property : 'structureId', + direction : 'DESC' + } + }); + + var groupingFeature = Ext.create('Ext.grid.feature.Grouping', { + groupHeaderTpl : Ext.create('Ext.XTemplate', + "
{name:this.formatName}
", { + formatName : function(name) { + return name; + } + }), + hideGroupedHeader : true, + startCollapsed : false + }); + + this.panel = Ext.create('Ext.grid.Panel', { + margin : "15 10 0 10", + height : this.height, + store : this.pdbStore, + plugins : _this._getPlugins(), + tbar : [ { + text : 'Add Modeling Option (PDB)', + icon : '../images/add.png', + handler : function() { + _this.onUploadFile.notify('PDB', 'Upload PDB File'); + } + } + + ], + columns : [ + { + text : "structureId", + flex : 0.2, + hidden : true, + dataIndex : 'structureId', + sortable : true + }, + { + text : "File", + flex : 0.5, + dataIndex : 'filePath', + sortable : true, + hidden : true + }, + { + text : "PDB", + flex : 0.4, + dataIndex : 'name', + sortable : true + }, + { + text : "Symmetry", + flex : 0.2, + dataIndex : 'symmetry', + sortable : true, + editor : { + xtype : 'combobox', + typeAhead : true, + triggerAction : 'all', + selectOnTab : true, + store : [ [ "P1", "P1" ], [ "P2", "P2" ], [ "P3", "P3" ], [ "P4", "P4" ], [ "P5", "P5" ], [ "P6", "P6" ], [ "P32", "P32" ], [ "P42", "P42" ], + [ "P52", "P52" ], [ "P62", "P62" ], [ "P222", "P222" ] ], + } + }, { + text : "Multiplicity", + flex : 0.2, + dataIndex : 'multiplicity', + sortable : true, + editor : { + xtype : 'textfield' + } + + }, { + text : "Subunit", + flex : 0.2, + dataIndex : 'isSubunit', + sortable : true, + hidden : true + }, { + text : "Type", + flex : 0.2, + dataIndex : 'structureType', + sortable : true, + hidden : true + }, + + { + id : this.id + 'REMOVE', + flex : 0.2, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + return BUI.getRedButton('REMOVE'); + } + }, ], + + listeners : { + itemdblclick : function(dataview, record, item, e) { + _this._editExperiment(record.raw.experimentId); + }, + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'REMOVE') { + var dataAdapter = new BiosaxsDataAdapter(); + dataAdapter.onSuccess.attach(function() { + _this.panel.setLoading(false); + _this.onRemove.notify(); + }); + _this.panel.setLoading("Removing PDB file"); + dataAdapter.removeStructure(record.data.structureId); + } + + } + }, + viewConfig : { + getRowClass : function(record, rowIdx, params, store) { + if (record.raw.isSubunit != null) { + return "blue-row"; + } + } + } + }); + + return this.panel; +}; + + + + +AprioriRigidBodyGrid.prototype.input = function() { + return { + proposal : DATADOC.getProposal_10(), + dewars : DATADOC.getDewars_10() + + }; +}; + +AprioriRigidBodyGrid.prototype.test = function(targetId) { + var AprioriRigidBodyGrid = new AprioriRigidBodyGrid({ + height : 150 + }); + BIOSAXS.proposal = new Proposal(AprioriRigidBodyGrid.input().proposal); + var panel = AprioriRigidBodyGrid.getPanel(AprioriRigidBodyGrid.input().dewars); + panel.render(targetId); + +}; + +/** + * It shows buffer grid with a top bar with "Add" button + * + * @height + * @searchBar + * @collapsed + * @width + */ +function BufferGrid(args) { + this.height = 500; + this.searchBar = false; + this.tbar = false; + this.collapsed = false; + this.id = BUI.id(); + + if (args != null) { + if (args.height != null) { + this.height = args.height; + } + if (args.searchBar != null) { + this.searchBar = args.searchBar; + } + + if (args.tbar != null) { + this.tbar = args.tbar; + } + + if (args.collapsed != null) { + this.collapsed = args.collapsed; + } + + if (args.width != null) { + this.width = args.width; + } } +} + +BufferGrid.prototype._edit = function(bufferId) { + var _this = this; + var window = new BufferWindow(); + window.onSuccess.attach(function(sender, proposal) { + _this.store.loadData(BIOSAXS.proposal.getBuffers()); + }); + window.draw(BIOSAXS.proposal.getBufferById(bufferId)); }; -SpecimenGrid.prototype.getPanelByExperiment = function(experiment) { - this.experiment = experiment; - var data = this._prepareData(experiment); - return this.getPanel(data); +BufferGrid.prototype.refresh = function(buffers) { + this.store.loadData(this._prepareData(buffers), false); }; -SpecimenGrid.prototype.refresh = function(experiment) { - this.experiment = experiment; - var data = this._prepareData(experiment); - this.store.loadData(data); +BufferGrid.prototype._prepareData = function(buffers) { + return buffers; }; -SpecimenGrid.prototype.getPanel = function() { +BufferGrid.prototype._getTbar = function() { var _this = this; - this.store = Ext.create('Ext.data.Store', { - fields : [ - 'buffer', 'bufferId', 'code', 'macromolecule', 'acronym', 'macromoleculeId', 'concentration', 'volume', 'samplePlateId', - 'slotPositionColumn', 'rowNumber', 'columnNumber', 'groupIndex' ], - data : [], - groupField : 'acronym' - }); - this.store.sort([ { - property : 'concentration', - direction : 'ASC' - }, { - property : 'buffer', - direction : 'ASC' - } ]); + var actions = []; - var selModel = Ext.create('Ext.selection.RowModel', { - allowDeselect : true, - mode : this.selectionMode, - listeners : { - selectionchange : function(sm, selections) { - var selected = []; - for ( var i = 0; i < selections.length; i++) { - selected.push(selections[i].raw); - } - _this.onSelected.notify(selected); - } + actions.push(Ext.create('Ext.Action', { + icon : '../images/add.png', + text : 'Add buffer', + disabled : false, + handler : function(widget, event) { + var window = new BufferWindow(); + window.onSuccess.attach(function(sender) { + _this.store.loadData(BIOSAXS.proposal.getBuffers()); + }); + window.draw({}); } - }); - - var features = []; - - if (this.grouped) { - features.push({ - ftype : 'grouping', - groupHeaderTpl : '{name}', - hideGroupedHeader : false, - startCollapsed : false, - id : 'myGroupedStore' - }); - } + })); + return actions; +}; - this.grid = Ext.create( - 'Ext.grid.Panel', - { - title : this.title, - height : this.height, - width : this.width, - selModel : selModel, - store : this.store, - features : features, - margin : this.margin, - plugins : this.getPlugins(), - columns : [ - { - text : '', - dataIndex : 'macromolecule', - width : 20, - renderer : function(val, y, sample) { - var macromoleculeId = null; - if (sample.raw.macromolecule3VO != null) { - macromoleculeId = sample.raw.macromolecule3VO.macromoleculeId; - } - else{ - macromoleculeId = sample.raw.macromoleculeId; - } - - if (macromoleculeId == null) return; - return BUI.getRectangleColorDIV(_this.experiment.macromoleculeColors[macromoleculeId], 10, 10); - } - }, - { - text : 'Macromolecule', - dataIndex : 'macromolecule', - width : 100 - }, - { - text : '', - dataIndex : 'buffer', - width : 20, - renderer : function(val, y, sample) { - var color = "black"; - if (sample.raw.bufferId != null) { - if (_this.experiment.getDataCollectionsBySpecimenId(sample.raw.specimenId)[0] != null){ - color = _this.experiment.getSpecimenColorByBufferId(_this.experiment.getMeasurementById(_this.experiment.getDataCollectionsBySpecimenId(sample.raw.specimenId)[0].measurementtodatacollection3VOs[0].measurementId).specimenId); - } - return BUI.getRectangleColorDIV(color, 10, 10); - } - } - }, { - text : 'Buffer', - dataIndex : 'bufferId', - width : 140, - renderer : function(val, y, sample) { - if (sample.raw.bufferId != null) { - return BIOSAXS.proposal.getBufferById(val).acronym; - } - }, - editor : BIOSAXS_COMBOMANAGER.getComboBuffers(BIOSAXS.proposal.getBuffers(), { - noLabel : true, - width : 300 - }) - }, { - text : 'Conc.', - dataIndex : 'concentration', - width : 100, - editor : { - allowBlank : false - }, - renderer : function(val, meta, sample) { - if (isNaN(val)) { - meta.tdCls = 'yellow-cell'; - return val; - } else { - if (val != 0) { - return BUI.formatValuesUnits(val, 'mg/ml', { - fontSize : 16, - decimals : 3, - unitsFontSize : this.unitsFontSize - }); - } else { - return; - } - } - } - }, { - text : 'Vol. Well', - dataIndex : 'volume', - width : 70, - editor : { - allowBlank : true - }, - renderer : function(val, y, sample) { - return BUI.formatValuesUnits(sample.data.volume, 'µl', { - fontSize : 12, - decimals : 2, - unitsFontSize : this.unitsFontSize - }); - } - }, { - text : 'Position', - hidden : true, - flex : 1, - renderer : function(val, y, sample) { - return BUI.getSamplePositionHTML(sample.raw, _this.experiment); - } - }, { - text : 'samplePlateId', - dataIndex : 'samplePlateId', - hidden : true - }, { - text : 'Plate', - hidden : this.isPositionColumnHidden, - dataIndex : 'slotPositionColumn', - editor : _this._getSlotColumBombo(), - flex : 1, - renderer : function(val, meta, sample) { - if ((val != null) & (val != "")) { - return val; - } else { - meta.tdCls = 'yellow-cell'; - } - } - }, { - text : 'Row', - hidden : this.isPositionColumnHidden, - dataIndex : 'rowNumber', - editor : this._getRowCombo(), - flex : 1, - renderer : function(val, meta, sample) { - if ((val != null) && (val != "")) { - return BUI.getSamplePlateLetters()[val - 1]; - } else { - meta.tdCls = 'yellow-cell'; - } - } - }, { - text : 'Well', - hidden : this.isPositionColumnHidden, - dataIndex : 'columnNumber', - editor : this._getColumnCombo(), - flex : 1, - renderer : function(val, meta, sample) { - if ((val != null) && (val != "")) { - return val; - } else { - meta.tdCls = 'yellow-cell'; - } - } - }, { - id : _this.id + 'buttonEditSample', - text : 'Edit', - width : 80, - sortable : false, - hidden : !_this.editEnabled, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - if (_this.editEnabled) { - return BUI.getGreenButton('EDIT'); - } - } - }, { - id : _this.id + 'buttonRemoveSample', - text : '', - hidden : !_this.removeBtnEnabled, - width : 100, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - if (_this.removeBtnEnabled) { - return BUI.getRedButton('REMOVE'); - } - } - } +BufferGrid.prototype.getPanel = function(buffers) { + var _this = this; - ], - viewConfig : { - preserveScrollOnRefresh : true, - stripeRows : true, - getRowClass : function(record) { - var specimens = _this.experiment.getSampleByPosition(record.data.samplePlateId, record.data.rowNumber, - record.data.columnNumber); - if (specimens.length > 1) { - return 'red-row'; + this.store = Ext.create('Ext.data.Store', { + fields : [ 'bufferId', 'acronym', 'name', 'composition' ], + data : buffers + }); - } - }, - listeners : { - selectionchange : function(grid, selected) { - _this.onClick.notify(record.raw); - }, - cellclick : function(grid, td, cellIndex, record, tr) { - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEditSample') { - } - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemoveSample') { - grid.getStore().removeAt(rowIndex); - _this.onRemoved.notify(); - } + this.store.sort('acronym'); - } + var type = 'Ext.grid.Panel'; + if (this.searchBar == true) { + type = 'Ext.ux.LiveSearchGridPanel'; + } - } - } - }); + this.grid = Ext.create(type, { + title : 'Buffers', + collapsible : true, + collapsed : this.collapsed, + store : this.store, + height : this.height, + width : this.width, + columns : [ + /*{ + text : '', + dataIndex : 'bufferId', + width : 20, + renderer : function(val, y, sample) { + return BUI.getRectangleColorDIV(BIOSAXS.proposal.bufferColors[val], 10, 10); + } + },*/ + { + text : 'Acronym', + dataIndex : 'acronym', + flex : 1 + }, { + text : 'Name', + dataIndex : 'name', + flex : 1, + hidden : true + }, { + text : 'Composition', + dataIndex : 'composition', + flex : 1, + hidden : true + }, { + id : _this.id + 'buttonEditBuffer', + width : 80, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + return BUI.getGreenButton('EDIT'); + } + }, { + id : _this.id + 'buttonRemoveBuffer', + width : 85, + hidden : true, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + return BUI.getRedButton('REMOVE'); + } + } ], + flex : 1, + viewConfig : { + stripeRows : true, + listeners : { + 'celldblclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + _this._edit(record.data.bufferId); + }, + 'cellclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEditBuffer') { + _this._edit(record.data.bufferId); + } + + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemoveBuffer') { + BUI.showBetaWarning(); + } + } + + } + } + }); + + /** Adding the tbar **/ + if (this.tbar) { + this.grid.addDocked({ + xtype : 'toolbar', + items : this._getTbar() + }); + } return this.grid; }; -SpecimenGrid.prototype.input = function() { - return { - experiment : DATADOC.getExperiment_10(), - proposal : DATADOC.getProposal_10() - }; +BufferGrid.prototype.input = function() { + return new MacromoleculeGrid().input(); }; -SpecimenGrid.prototype.test = function(targetId) { - var specimenGrid = new SpecimenGrid({ - height : 400, - maxHeight : 400, - width : 1000 +BufferGrid.prototype.test = function(targetId) { + var bufferGrid = new BufferGrid({ + width : 800, + height : 350, + collapsed : false, + tbar : true }); - BIOSAXS.proposal = new Proposal(specimenGrid.input().proposal); - var experiment = new Experiment(specimenGrid.input().experiment); - var panel = specimenGrid.getPanelByExperiment(experiment); + BIOSAXS.proposal = new Proposal(bufferGrid.input().proposal); + var panel = bufferGrid.getPanel(BIOSAXS.proposal.macromolecules); panel.render(targetId); - }; /** - * Shows a list of stock solutions with macromolecule, buffer, storage temperature, concentration, shipment and comments + * A shipment may contains one or more cases where stock solutions and sample plates are stored * - * @multiselect allows multiple selection - * @height - * @minHeight - * @width - * @tbar - * @showTitle - * @isPackedVisible shows is stock solution is in a box - * @btnEditVisible shows edit button - * @btnAddVisible - * @btnAddExisting - * @btnUnpackVisible allows to unpack a stock solution - * @btnRemoveVisible allow to remove a stock solution + * @height + * @btnEditVisible + * @btnRemoveVisible + * + * #onEditButtonClicked + * #onAddButtonClicked + * #onRemoveButtonClicked + * #onDuplicateButtonClicked */ +function CaseGrid(args) { -function StockSolutionGrid(args) { - this.id = BUI.id(); this.height = 100; - this.width = null; - this.minHeight = null; - this.tbar = true; - - this.title = "Stock Solutions"; - - /** Visible buttons and actions **/ this.btnEditVisible = true; this.btnRemoveVisible = true; - this.btnAddVisible = true; - this.btnAddExisting = false; - this.isPackedVisible = true; - this.btnUnpackVisible = false; - - /** Selectors **/ - this.multiselect = false; - this.selectedStockSolutions = []; if (args != null) { - if (args.btnUnpackVisible != null) { - this.btnUnpackVisible = args.btnUnpackVisible; - } - if (args.multiselect != null) { - this.multiselect = args.multiselect; - } if (args.height != null) { this.height = args.height; } if (args.btnEditVisible != null) { this.btnEditVisible = args.btnEditVisible; } - if (args.btnAddVisible != null) { - this.btnAddVisible = args.btnAddVisible; - } - if (args.btnAddExisting != null) { - this.btnAddExisting = args.btnAddExisting; - } - if (args.width != null) { - this.width = args.width; - } - if (args.minHeight != null) { - this.minHeight = args.minHeight; - } - if (args.tbar != null) { - this.tbar = args.tbar; - } if (args.btnRemoveVisible != null) { this.btnRemoveVisible = args.btnRemoveVisible; } - if (args.isPackedVisible != null) { - this.isPackedVisible = args.isPackedVisible; - } - if (args.showTitle != null) { - this.showTitle = args.showTitle; - if (this.showTitle == false) { - this.title = null; + } + + /** Events **/ + this.onEditButtonClicked = new Event(this); + this.onAddButtonClicked = new Event(this); + this.onRemoveButtonClicked = new Event(this); + this.onDuplicateButtonClicked = new Event(this); +} + +CaseGrid.prototype._getColumns = function() { + var _this = this; + + function actionItemRenderer(value, meta, record, rowIx, ColIx, store) { + /*if (record.raw.specimen3VOs.length > 0){ + return 'x-hide-display'; + }*/ + } + + var columns = [ + { + header : 'Code', + dataIndex : 'code', + name : 'code', + type : 'string', + flex : 1 + }, + { + header : 'Bar Code', + dataIndex : 'barCode', + name : 'barCode', + type : 'string', + flex : 1, + hidden : true + }, + { + header : 'BeamLine', + dataIndex : 'barCode', + type : 'string', + flex : 1, + renderer : function(comp, val, record) { + if (record.raw.sessionVO != null) { + return "" + record.raw.sessionVO.beamlineName + ""; + } + } + }, + { + header : 'Session', + dataIndex : 'barCode', + type : 'string', + flex : 1, + renderer : function(comp, val, record) { + if (record.raw.sessionVO != null) { + return "" + moment(record.raw.sessionVO.startDate).format("MMM Do YY") + ""; + } } - } - - } - - /** Events **/ - this.onProposalChanged = new Event(this); - this.onStockSolutionSelected = new Event(this); -} - -StockSolutionGrid.prototype._getColumns = function() { - var _this = this; - var columns = [ - - { - header : 'Macromolecule', - dataIndex : 'macromolecule', - id : _this.id + 'macromolecule', - type : 'string', - renderer : function(val, y, specimen) { - return '' + val + ''; }, - hidden : false, - flex : 1 - }, { - header : 'Buffer', - dataIndex : 'buffer', - name : 'buffer', - hidden : false, - renderer : function(val, y, specimen) { - return '' + val + ''; + { + header : 'Status', + dataIndex : 'dewarStatus', + name : 'dewarStatus', + type : 'string', + flex : 1, + renderer : function(comp, val, record) { + if (new String(record.raw.dewarStatus).toUpperCase() == 'OPENED') { + return "" + new String(record.raw.dewarStatus).toUpperCase() + ""; + } + return "" + new String(record.raw.dewarStatus).toUpperCase() + ""; + } }, - type : 'string', - flex : 1 - }, { - header : 'Acronym', - dataIndex : 'name', - name : 'name', - type : 'string', - flex : 1, - hidden : true - }, { - header : 'Storage Temp.', - dataIndex : 'storageTemperature', - name : 'storageTemperature', - type : 'string', - flex : 1, - hidden : false, - renderer : function(val) { - return BUI.formatValuesUnits(val, 'C', { - fontSize : 12, - decimals : 2, - unitsFontSize : 10 - }); - } - }, { - header : 'Volume', - dataIndex : 'volume', - type : 'string', - flex : 1, - hidden : false, - renderer : function(val) { - return BUI.formatValuesUnits(val, 'µl', { - fontSize : 12, - decimals : 2, - unitsFontSize : 10 - }); - } - }, { - header : 'Concentration', - dataIndex : 'concentration', - name : 'concentration', - type : 'string', - flex : 1, - renderer : function(val) { - return BUI.formatValuesUnits(val, 'mg/ml', { - fontSize : 12, - decimals : 2, - unitsFontSize : 10 - }); - } - }, { - header : 'Packed', - dataIndex : 'comments', - id : _this.id + "box", - type : 'string', - width : 50, - hidden : !this.isPackedVisible, - renderer : function(val, cmp, a) { - if (a.raw.boxId != null) { - return "
"; + { + header : 'Type', + dataIndex : 'type', + name : 'type', + type : 'string', + flex : 1, + hidden : true + }, + { + header : 'Sample Plates', + dataIndex : 'plates', + name : 'plates', + type : 'string', + flex : 1, + hidden : true + }, + { + header : 'Stock Solutions', + dataIndex : 'plates', + name : 'plates', + type : 'string', + width : 100, + renderer : function(comp, val, record) { + var html = "
"; + var stockSolutions = BIOSAXS.proposal.getStockSolutionsByDewarId(record.raw.dewarId); + html = html + "" + stockSolutions.length + " x"; + return html + "
"; } - + }, { + header : 'isStorageDewar', + dataIndex : 'isStorageDewar', + name : 'isStorageDewar', + type : 'string', + flex : 1, + hidden : true + }, { + header : 'Tracking Number From Synchrotron', + dataIndex : 'trackingNumberFromSynchrotron', + name : 'trackingNumberFromSynchrotron', + type : 'string', + flex : 1, + hidden : true + }, { + header : 'Tracking Number To Synchrotron', + dataIndex : 'trackingNumberToSynchrotron', + name : 'trackingNumberToSynchrotron', + type : 'string', + flex : 1, + hidden : true + }, { + header : 'Storage Location', + dataIndex : 'storageLocation', + name : 'storageLocation', + type : 'string', + flex : 1, + hidden : false + }, { + header : 'Comments', + dataIndex : 'comments', + name : 'comments', + type : 'string', + flex : 1, + hidden : false } - }, { - header : 'Comments', - dataIndex : 'comments', - type : 'string', - flex : 1 - } ]; + ]; if (this.btnEditVisible) { columns.push({ id : _this.id + 'buttonEdit', + text : '', + hidden : !_this.btnEditVisible, width : 85, sortable : false, renderer : function(value, metaData, record, rowIndex, colIndex, store) { - if (_this.btnEditVisible) { - return BUI.getGreenButton('EDIT'); - } + return BUI.getGreenButton('EDIT'); } }); } @@ -22014,4646 +16857,9803 @@ StockSolutionGrid.prototype._getColumns = function() { }); } - if (this.btnUnpackVisible) { - columns.push({ - id : _this.id + 'buttonUnpack', - width : 85, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - if (_this.btnUnpackVisible) { - return BUI.getBlueButton('UNPACK'); - } - } - }); - } + columns.push({ + dataIndex : 'comments', + type : 'string', + width : 85, + hidden : false, + renderer : function(comp, val, record) { + return BUI.getBlueButton("LABELS", { + href : BUI.getPrintcomponentURL(record.raw.dewarId) + }); + } + }); + return columns; }; -StockSolutionGrid.prototype._getTopButtons = function() { - var _this = this; - /** Actions buttons **/ - var actions = []; - - /** ADD BUTTON **/ - if (this.btnAddVisible) { - actions.push(Ext.create('Ext.Action', { - icon : '../images/add.png', - text : 'Add Stock Solution', - tooltip : 'Will create a new stock solution', - disabled : false, - alwaysEnabled : true, - handler : function(widget, event) { - _this.edit(); - } - })); - } - - if (this.btnAddExisting) { - actions.push(Ext.create('Ext.Action', { - icon : '../images/add.png', - text : 'Add Existing', - tooltip : 'Allows to select upacked stock solutions', - disabled : false, - alwaysEnabled : true, - handler : function(widget, event) { - var stockSolutionGrid = new StockSolutionGrid({ - btnAddVisible : false, - btnEditVisible : false, - btnRemoveVisible : false, - btnAddExisting : false, - isPackedVisible : true, - multiselect : true - }); - - var window = Ext.create('Ext.window.Window', { - title : 'Select', - height : 400, - width : 800, - layout : 'fit', - items : [ stockSolutionGrid.getPanel() ], - buttons : [ { - text : 'Pack', - handler : function() { - _this.onStockSolutionSelected.notify(stockSolutionGrid.selectedStockSolutions); - window.close(); - } - }, { - text : 'Cancel', - handler : function() { - window.close(); - } - } ] - - }).show(); +CaseGrid.prototype._getTopButtons = function() { + var _this = this; + /** Actions buttons **/ + var actions = []; - stockSolutionGrid.refresh(BIOSAXS.proposal.getUnpackedStockSolutions()); - } - })); - } + /** ADD BUTTON **/ + actions.push(Ext.create('Ext.Action', { + icon : '../images/add.png', + text : 'Add', + disabled : false, + handler : function(widget, event) { + _this.onAddButtonClicked.notify(); + } + })); return actions; }; -StockSolutionGrid.prototype.refresh = function(stockSolutions) { - this.features = stockSolutions; - this.store.loadData(this._prepareData(), false); +CaseGrid.prototype.refresh = function(dewars) { + this.features = dewars; + this.store.loadData(this._prepareData(dewars), false); }; -StockSolutionGrid.prototype._prepareData = function() { +CaseGrid.prototype._sort = function(store) { + store.sort('dewarId', 'DESC'); +}; + +CaseGrid.prototype._prepareData = function() { var data = []; for ( var i = 0; i < this.features.length; i++) { - var stockSolution = this.features[i]; - stockSolution.buffer = BIOSAXS.proposal.getBufferById(stockSolution.bufferId).acronym; - if (stockSolution.macromoleculeId != null) { - stockSolution.macromolecule = BIOSAXS.proposal.getMacromoleculeById(stockSolution.macromoleculeId).acronym; - } - data.push(stockSolution); + data.push(this.features[i]); } return data; }; -StockSolutionGrid.prototype.getPanel = function() { +CaseGrid.prototype.getPanel = function(dewars, plates) { + this.features = dewars; + this.plates = plates; return this._renderGrid(); }; -StockSolutionGrid.prototype.edit = function(stockSolutionId) { +CaseGrid.prototype._edit = function(dewar) { var _this = this; - var stockSolutionWindow = new StockSolutionWindow(); - /** On stock solution SAVED **/ - stockSolutionWindow.onSaved.attach(function(sender, stockSolution) { - _this.onProposalChanged.notify(stockSolution); + var caseWindow = new CaseWindow(); + /**SAVED **/ + caseWindow.onSaved.attach(function(sender, dewar) { + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, shipment) { + _this.refresh(shipment.dewarVOs); + }); + adapter.saveCase(BIOSAXS.proposal.getShipmentByDewarId(dewar.dewarId).shippingId, dewar); }); - stockSolutionWindow.draw(BIOSAXS.proposal.getStockSolutionById(stockSolutionId)); + caseWindow.draw(dewar); }; -StockSolutionGrid.prototype._getStoreFields = function() { +CaseGrid.prototype._getStoreFields = function(data) { return [ { - name : 'name', + name : 'dewarId', type : 'string' }, { - name : 'stockSolutionId', + name : 'barCode', type : 'string' }, { - name : 'macromolecule', + name : 'code', type : 'string' }, { - name : 'buffer', + name : 'comments', type : 'string' }, { - name : 'storageTemperature', - type : 'numeric' + name : 'dewarStatus', + type : 'string' }, { - name : 'volume', + name : 'isStorageDewar', type : 'string' }, { - name : 'concentration', + name : 'plates', type : 'string' }, { - name : 'buffer', + name : 'transportValue', type : 'string' }, { - name : 'comments', + name : 'trackingNumberFromSynchrotron', type : 'string' - } ]; -}; + }, { + name : 'trackingNumberToSynchrotron', + type : 'string' + }, { + name : 'timeStamp', + type : 'string' + }, { + name : 'storageLocation', + type : 'string' + }, { + name : 'type', + type : 'string' + } -//StockSolutionGrid.prototype.refresh = function() { -// this.proposal.onInitialized.attach(function(sender){ -// -// }); -// this.proposal.init(Ext.urlDecode(window.location.href).sessionId); -//}; + ]; +}; -StockSolutionGrid.prototype._renderGrid = function() { +CaseGrid.prototype._renderGrid = function() { var _this = this; /** Store **/ + var data = this._prepareData(); this.store = Ext.create('Ext.data.Store', { - fields : this._getStoreFields(), //columns, - autoload : true + fields : this._getStoreFields(data), + autoload : true, + data : data }); + this._sort(this.store); - var filters = { - ftype : 'filters', - local : true, - filters : this.filters - }; - - var selModel = null; - - if (this.multiselect) { - selModel = Ext.create('Ext.selection.CheckboxModel', { - //multiSelect : false,//this.multiselect, - mode : 'SINGLE', - listeners : { - selectionchange : function(sm, selections) { - _this.selectedStockSolutions = []; - for ( var i = 0; i < selections.length; i++) { - _this.selectedStockSolutions.push(selections[i].raw); - } - } - } - }); - } else { - selModel = { - mode : 'SINGLE' - }; - } - - this.store.sort("stockSolutionId", "desc"); + this.store.loadData(data, false); this.grid = Ext.create('Ext.grid.Panel', { style : { padding : 5 }, - icon : '/ispyb/images/SampleHolder_24x24_01.png', - title : this.title, height : this.height, - width : this.width, - minWidth : this.minWidth, - selModel : selModel, store : this.store, columns : this._getColumns(), viewConfig : { stripeRows : true, listeners : { itemdblclick : function(dataview, record, item, e) { - _this.edit(record.raw.stockSolutionId); - }, - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - var adapter = null; - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonUnpack') { - _this.grid.setLoading("ISPyB: Unpacking stock solution"); - adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender) { - _this.onProposalChanged.notify(); - _this.grid.setLoading(false); - }); - adapter.onError.attach(function(sender) { - _this.onProposalChanged.notify(); - _this.grid.setLoading(false); - }); - record.raw.boxId = null; - adapter.saveStockSolution(record.raw); - } - - if (grid.getGridColumns()[cellIndex].getId() == _this.id + "box") { - window.location = BUI.getShippingURL(BIOSAXS.proposal.getShipmentByDewarId(record.raw.boxId).shippingId); - } - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEdit') { - _this.edit(record.data.stockSolutionId); - } - - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemove') { - _this.grid.setLoading("ISPyB: Removing stock solution"); - adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender) { - _this.onProposalChanged.notify(); - _this.grid.setLoading(false); - }); - adapter.onError.attach(function(sender) { - _this.onProposalChanged.notify(); - _this.grid.setLoading(false); - }); - adapter.removeStockSolution(record.data.stockSolutionId); - } - } - } - } - - }); - - var actions = _this._getTopButtons(); - this.grid.addDocked({ - xtype : 'toolbar', - items : actions - }); - - var i = null; - this.grid.getSelectionModel().on({ - selectionchange : function(sm, selections) { - if (selections.length) { - for ( i = 0; i < actions.length; i++) { - if (actions[i].enable) { - actions[i].enable(); - } - } - } else { - for ( i = 0; i < actions.length; i++) { - if (actions[i].alwaysEnabled == false) { - if (actions[i].disable) { - actions[i].disable(); - } - } - } - } - } - }); - return this.grid; -}; - -StockSolutionGrid.prototype.input = function() { - return { - proposal : DATADOC.getProposal_10() - }; -}; - -StockSolutionGrid.prototype.test = function(targetId) { - var stockSolutionGrid = new StockSolutionGrid({ - height : 300, - width : 900 - }); - BIOSAXS.proposal = new Proposal(stockSolutionGrid.input().proposal); - var panel = stockSolutionGrid.getPanel(); - stockSolutionGrid.refresh(BIOSAXS.proposal.getStockSolutions()); - panel.render(targetId); -}; - - -function SuperpositionGrid(args) { - this.height = null; - this.width = null; - this.id = BUI.id(); - - if (args != null) { - if (args.height != null) { - this.height = args.height; - - if (args.width != null) { - this.width = args.width; - } - } - } - - this.onSelected = new Event(this); -} - -SuperpositionGrid.prototype._prepareData = function(data) { - return data; -}; + _this._edit(record.raw); + }, + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEdit') { + _this._edit(record.raw); + } -SuperpositionGrid.prototype.refresh = function(subtractions) { - var data = []; - if (subtractions != null){ - if (subtractions.length > 0){ - for (j in subtractions){ - var subtraction = subtractions[j]; - if (subtraction.superposition3VOs != null){ - for (i in subtraction.superposition3VOs){ - data.push(subtraction.superposition3VOs[i]); + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemove') { + _this.onRemoveButtonClicked.notify(_this.store.getAt(rowIndex).raw.dewarId); } } } + }, + selModel : { + mode : 'SINGLE' } - } - this.store.loadData(data); -}; + }); -SuperpositionGrid.prototype.getPanel = function() { - var _this = this; - this.store = Ext.create('Ext.data.Store', { - fields : [ 'abinitioModelPdbFilePath', 'aprioriPdbFilePath', 'alignedPdbFilePath' ], - data : [] + var actions = _this._getTopButtons(); + this.grid.addDocked({ + xtype : 'toolbar', + items : actions }); - this.selModel = Ext.create('Ext.selection.RowModel', { - allowDeselect : true, - mode : 'MULTI', - listeners : { - selectionchange : function(sm, selections) { - var selected = []; - for (var i = 0; i < selections.length; i++) { - selected.push(selections[i].raw); + this.grid.getSelectionModel().on({ + selectionchange : function(sm, selections) { + if (selections.length) { + for ( var i = 0; i < actions.length; i++) { + if (actions[i].enable) { + actions[i].enable(); + } + } + } else { + for ( var i = 0; i < actions.length; i++) { + if (actions[i].alwaysEnabled == false) { + if (actions[i].disable) { + actions[i].disable(); + } + } } - _this.onSelected.notify(selected); } } }); - - this.store.sort([ { - property : 'name', - direction : 'ASC' - } ]); + return this.grid; +}; - this.panel = Ext.create('Ext.grid.Panel', { - store : this.store, - selModel : this.selModel, - width : this.width, - height : this.height, - margin : 10, - deferredRender : false, - columns : [ { - text : 'Abinitio', - dataIndex : 'abinitioModelPdbFilePath', - hidden : false, - flex : 1, - renderer : function(val){ - return BUI.getFileName(val); - } - }, { - text : 'Apriori', - dataIndex : 'aprioriPdbFilePath', - hidden : false, - flex : 1, - renderer : function(val){ - return BUI.getFileName(val); - } - }, { - text : 'Aligned', - dataIndex : 'alignedPdbFilePath', - hidden : false, - flex : 1, - renderer : function(val){ - return BUI.getFileName(val); - } - } ], +CaseGrid.prototype.input = function() { + return { + proposal : DATADOC.getProposal_10(), + dewars : DATADOC.getDewars_10() - viewConfig : { - enableTextSelection : true, - preserveScrollOnRefresh : true - }, - listeners : { - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + }; +}; - }, - afterrender : function() { - } - } +CaseGrid.prototype.test = function(targetId) { + var CaseGrid = new CaseGrid({ + height : 150 }); - return this.panel; + BIOSAXS.proposal = new Proposal(CaseGrid.input().proposal); + var panel = CaseGrid.getPanel(CaseGrid.input().dewars); + panel.render(targetId); + }; +/** + * A shipment may contains one or more cases where stock solutions and sample plates are stored + * + * @height + * @btnEditVisible + * @btnRemoveVisible + * + * #onEditButtonClicked + * #onAddButtonClicked + * #onRemoveButtonClicked + * #onDuplicateButtonClicked + */ +function ExampleGrid(args) { + + this.height = 100; + this.btnEditVisible = true; + this.btnRemoveVisible = true; + + if (args != null) { + if (args.height != null) { + this.height = args.height; + } + if (args.btnEditVisible != null) { + this.btnEditVisible = args.btnEditVisible; + } + if (args.btnRemoveVisible != null) { + this.btnRemoveVisible = args.btnRemoveVisible; + } + } + + /** Events **/ + this.onEditButtonClicked = new Event(this); + this.onAddButtonClicked = new Event(this); + this.onRemoveButtonClicked = new Event(this); + this.onDuplicateButtonClicked = new Event(this); +} + +ExampleGrid.prototype._getColumns = function() { + var _this = this; + + function actionItemRenderer(value, meta, record, rowIx, ColIx, store) { + /*if (record.raw.specimen3VOs.length > 0){ + return 'x-hide-display'; + }*/ + } + + var columns = [ + { + header : 'Code', + dataIndex : 'code', + name : 'code', + type : 'string', + flex : 1 + }, + { + header : 'Bar Code', + dataIndex : 'barCode', + name : 'barCode', + type : 'string', + flex : 1, + hidden : true + }, + { + header : 'BeamLine', + dataIndex : 'barCode', + type : 'string', + flex : 1, + renderer : function(comp, val, record) { + if (record.raw.sessionVO != null) { + return "" + record.raw.sessionVO.beamlineName + ""; + } + } + }, + { + header : 'Session', + dataIndex : 'barCode', + type : 'string', + flex : 1, + renderer : function(comp, val, record) { + if (record.raw.sessionVO != null) { + return "" + moment(record.raw.sessionVO.startDate).format("MMM Do YY") + ""; + } + } + }, + { + header : 'Status', + dataIndex : 'dewarStatus', + name : 'dewarStatus', + type : 'string', + flex : 1, + renderer : function(comp, val, record) { + if (new String(record.raw.dewarStatus).toUpperCase() == 'OPENED') { + return "" + new String(record.raw.dewarStatus).toUpperCase() + ""; + } + return "" + new String(record.raw.dewarStatus).toUpperCase() + ""; + } + }, + { + header : 'Type', + dataIndex : 'type', + name : 'type', + type : 'string', + flex : 1, + hidden : true + }, + { + header : 'Sample Plates', + dataIndex : 'plates', + name : 'plates', + type : 'string', + flex : 1, + hidden : true + }, + { + header : 'Stock Solutions', + dataIndex : 'plates', + name : 'plates', + type : 'string', + width : 100, + renderer : function(comp, val, record) { + var html = "
"; + var stockSolutions = BIOSAXS.proposal.getStockSolutionsByDewarId(record.raw.dewarId); + html = html + "" + stockSolutions.length + " x"; + return html + "
"; + } + }, { + header : 'isStorageDewar', + dataIndex : 'isStorageDewar', + name : 'isStorageDewar', + type : 'string', + flex : 1, + hidden : true + }, { + header : 'Tracking Number From Synchrotron', + dataIndex : 'trackingNumberFromSynchrotron', + name : 'trackingNumberFromSynchrotron', + type : 'string', + flex : 1, + hidden : true + }, { + header : 'Tracking Number To Synchrotron', + dataIndex : 'trackingNumberToSynchrotron', + name : 'trackingNumberToSynchrotron', + type : 'string', + flex : 1, + hidden : true + }, { + header : 'Storage Location', + dataIndex : 'storageLocation', + name : 'storageLocation', + type : 'string', + flex : 1, + hidden : false + }, { + header : 'Comments', + dataIndex : 'comments', + name : 'comments', + type : 'string', + flex : 1, + hidden : false + } + ]; + + if (this.btnEditVisible) { + columns.push({ + id : _this.id + 'buttonEdit', + text : '', + hidden : !_this.btnEditVisible, + width : 85, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + return BUI.getGreenButton('EDIT'); + } + }); + } + + if (this.btnRemoveVisible) { + columns.push({ + id : _this.id + 'buttonRemove', + width : 85, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + if (_this.btnRemoveVisible) { + return BUI.getRedButton('REMOVE'); + } + } + }); + } + + columns.push({ + dataIndex : 'comments', + type : 'string', + width : 85, + hidden : false, + renderer : function(comp, val, record) { + return BUI.getBlueButton("LABELS", { + href : BUI.getPrintcomponentURL(record.raw.dewarId) + }); + } + }); + + return columns; +}; + +ExampleGrid.prototype._getTopButtons = function() { + var _this = this; + /** Actions buttons **/ + var actions = []; + + /** ADD BUTTON **/ + actions.push(Ext.create('Ext.Action', { + icon : '../images/add.png', + text : 'Add', + disabled : false, + handler : function(widget, event) { + _this.onAddButtonClicked.notify(); + } + })); + + return actions; +}; + +ExampleGrid.prototype.refresh = function(dewars) { + this.features = dewars; + this.store.loadData(this._prepareData(dewars), false); +}; + +ExampleGrid.prototype._sort = function(store) { + store.sort('dewarId', 'DESC'); +}; + +ExampleGrid.prototype._prepareData = function() { + var data = []; + for ( var i = 0; i < this.features.length; i++) { + data.push(this.features[i]); + } + return data; +}; + +ExampleGrid.prototype.getPanel = function() { + this.grid = Ext.create('Ext.grid.Panel', { + style : { + padding : 5 + }, + height : this.height, + store : this.store, + columns : this._getColumns(), + viewConfig : { + stripeRows : true, + listeners : { + itemdblclick : function(dataview, record, item, e) { + _this._edit(record.raw); + }, + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEdit') { + _this._edit(record.raw); + } + + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemove') { + _this.onRemoveButtonClicked.notify(_this.store.getAt(rowIndex).raw.dewarId); + } + } + } + }, + selModel : { + mode : 'SINGLE' + } + }); + + var actions = _this._getTopButtons(); + this.grid.addDocked({ + xtype : 'toolbar', + items : actions + }); + + this.grid.getSelectionModel().on({ + selectionchange : function(sm, selections) { + if (selections.length) { + for ( var i = 0; i < actions.length; i++) { + if (actions[i].enable) { + actions[i].enable(); + } + } + } else { + for ( var i = 0; i < actions.length; i++) { + if (actions[i].alwaysEnabled == false) { + if (actions[i].disable) { + actions[i].disable(); + } + } + } + } + } + }); + return this.grid; +}; + + +ExampleGrid.prototype._getStoreFields = function(data) { + return [ { + name : 'dewarId', + type : 'string' + }, { + name : 'barCode', + type : 'string' + }, { + name : 'code', + type : 'string' + }, { + name : 'comments', + type : 'string' + }, { + name : 'dewarStatus', + type : 'string' + }, { + name : 'isStorageDewar', + type : 'string' + }, { + name : 'plates', + type : 'string' + }, { + name : 'transportValue', + type : 'string' + }, { + name : 'trackingNumberFromSynchrotron', + type : 'string' + }, { + name : 'trackingNumberToSynchrotron', + type : 'string' + }, { + name : 'timeStamp', + type : 'string' + }, { + name : 'storageLocation', + type : 'string' + }, { + name : 'type', + type : 'string' + } + + ]; +}; + +ExampleGrid.prototype._renderGrid = function() { + var _this = this; + + /** Store **/ + var data = this._prepareData(); + this.store = Ext.create('Ext.data.Store', { + fields : this._getStoreFields(data), + autoload : true, + data : data + }); + this._sort(this.store); + + this.store.loadData(data, false); + + this.grid = Ext.create('Ext.grid.Panel', { + style : { + padding : 5 + }, + height : this.height, + store : this.store, + columns : this._getColumns(), + viewConfig : { + stripeRows : true, + listeners : { + itemdblclick : function(dataview, record, item, e) { + _this._edit(record.raw); + }, + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEdit') { + _this._edit(record.raw); + } + + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemove') { + _this.onRemoveButtonClicked.notify(_this.store.getAt(rowIndex).raw.dewarId); + } + } + } + }, + selModel : { + mode : 'SINGLE' + } + }); + + var actions = _this._getTopButtons(); + this.grid.addDocked({ + xtype : 'toolbar', + items : actions + }); + + this.grid.getSelectionModel().on({ + selectionchange : function(sm, selections) { + if (selections.length) { + for ( var i = 0; i < actions.length; i++) { + if (actions[i].enable) { + actions[i].enable(); + } + } + } else { + for ( var i = 0; i < actions.length; i++) { + if (actions[i].alwaysEnabled == false) { + if (actions[i].disable) { + actions[i].disable(); + } + } + } + } + } + }); + return this.grid; +}; + +ExampleGrid.prototype.input = function() { + return { + proposal : DATADOC.getProposal_10(), + dewars : DATADOC.getDewars_10() + + }; +}; + +ExampleGrid.prototype.test = function(targetId) { + var ExampleGrid = new ExampleGrid({ + height : 150 + }); + BIOSAXS.proposal = new Proposal(ExampleGrid.input().proposal); + var panel = ExampleGrid.getPanel(ExampleGrid.input().dewars); + panel.render(targetId); + +}; + + /** - * See ExperimentGrid - * + * Shows a list of experiment AKA data acquisitions + * @height + * @sorters + * @minHeight + * @gridType: Ext.ux.LiveSearchGridPanel or Ext.grid.Panel + * @tbar true or false + * @grouping true or false + * @width + * @title + * #onEditButtonClicked */ -function TemplateGrid(args) { - - if (args == null) { - args = {}; - } - args.sorters = [ { - property : 'experimentId', - direction : 'DESC' - } ]; - - ExperimentGrid.prototype.constructor.call(this, args); -} - -TemplateGrid.prototype._getFilterTypes = ExperimentGrid.prototype._getFilterTypes; -TemplateGrid.prototype._prettyPrintMacromolecules = ExperimentGrid.prototype._prettyPrintMacromolecules; -TemplateGrid.prototype._getPercentage = ExperimentGrid.prototype._getPercentage; -TemplateGrid.prototype._getPercentageCollected = ExperimentGrid.prototype._getPercentageCollected; -TemplateGrid.prototype.getPercentageMerged = ExperimentGrid.prototype.getPercentageMerged; -TemplateGrid.prototype._prepareData = ExperimentGrid.prototype._prepareData; -TemplateGrid.prototype.getPanel = ExperimentGrid.prototype.getPanel; -TemplateGrid.prototype._renderGrid = ExperimentGrid.prototype._renderGrid; -TemplateGrid.prototype._editExperiment = ExperimentGrid.prototype._editExperiment; -TemplateGrid.prototype._removeExperimentById = ExperimentGrid.prototype._removeExperimentById; - -TemplateGrid.prototype._getTopButtons = function() { - /** Actions buttons * */ - var actions = []; - - actions.push(Ext.create('Ext.Action', { - icon : '../images/add.png', - text : 'Add experiment', - handler : function(widget, event) { - var wizardWidget = new WizardWidget({ - windowMode : true - }); - - wizardWidget.onFinished.attach(function(sender, result) { - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - var experiment = new Experiment(data); - BIOSAXS.openExperimentByExperiment(experiment); - wizardWidget.window.close(); - }); - wizardWidget.current.setLoading("ISPyB: Creating experiment"); - adapter.createTemplate(result.name, "comments", result.data); - }); - -// wizardWidget.draw(this.targetId, new ExperimentTypeWizardForm()); - wizardWidget.draw(this.targetId, new MeasurementCreatorStepWizardForm(BIOSAXS.proposal.getMacromolecules())); - } - })); - return actions; -}; - -TemplateGrid.prototype.refresh = function(data) { - var filtered = []; - for ( var i = 0; i < data.length; i++) { - if (data[i].experimentType == "TEMPLATE") { - filtered.push(data[i]); - } - } - this.store.loadData(this._prepareData(filtered), false); -}; - -TemplateGrid.prototype._getColumns = function() { - var _this = this; - function actionItemRenderer(value, meta, record, rowIx, ColIx, store) { - if (record.raw.buffer3VOs != null) { - if (record.raw.buffer3VOs.length > 0) { - return 'x-hide-display'; - } - } +function ExperimentGrid(args) { + this.width = "100%"; + this.height = 700; + this.minHeight = 500; - if (record.data.platesCount > 0) { - return 'x-hide-display'; - } - } + this.id = BUI.id(); + this.gridType = 'Ext.grid.Panel'; //'Ext.ux.LiveSearchGridPanel'; + this.tbar = false; + this.hideHeaders = false; + this.grouping = true; + this.title = null; - return [ { - xtype : 'rownumberer', - width : 40 - }, { - text : 'experimentId', - dataIndex : 'experimentId', - name : 'experimentId', - type : 'string', - hidden : true + this.filtered = null; + + /** maximum row count **/ + this.limit = 100; + + this.sessionIdFilter = null; + + /** if not null filtered by date **/ + this.date = null; + + this.sorters = [ { + property : 'date', + direction : 'DESC' }, { - text : 'Name', - dataIndex : 'name', - name : 'name', - type : 'string', - flex : 1 - }, + property : 'time', + direction : 'DESC' + } ]; - { - text : 'Type', - dataIndex : 'type', - name : 'type', - type : 'string', - hidden : true, - flex : 1, - renderer : function(val) { - return val; + this.dates = {}; + if (args != null) { + if (args.height != null) { + this.height = args.height; } - }, { - text : 'Macromolecules', - name : 'macromolecules_names', - dataIndex : 'macromolecules_names', - flex : 1, - renderer : function(val) { - return " " + val + ""; + if (args.limit != null) { + this.limit = args.limit; } - }, { - id : _this.id + 'GO', - width : 80, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - return BUI.getGreenButton('EDIT'); + if (args.sorters != null) { + this.sorters = args.sorters; } - }, { - id : _this.id + 'REMOVE', - width : 100, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - return BUI.getRedButton('REMOVE'); + if (args.sessionId != null){ + this.sessionIdFilter = args.sessionId; + } + if (args.filtered != null) { + this.filtered = args.filtered; + } + if (args.minHeight != null) { + this.minHeight = args.minHeight; + } + if (args.gridType != null) { + this.gridType = args.gridType; + } + if (args.tbar != null) { + this.tbar = args.tbar; + } + if (args.grouping != null) { + this.grouping = args.grouping; + } + if (args.width != null) { + this.width = args.width; + } + if (args.title != null) { + this.title = args.title; } - } ]; -}; - -TemplateGrid.prototype.input = function() { - var experiments = DATADOC.getExperimentList_10(); - return { - experiments : experiments, - proposal : new MeasurementGrid().input().proposal - - }; -}; - -TemplateGrid.prototype.test = function(targetId) { - var experimentGrid = new TemplateGrid({ - height : 350, - minHeight : 350, - width : 1000, - gridType : 'Ext.grid.Panel', - title : 'Experiments', - grouping : false, - tbar : true - }); - BIOSAXS.proposal = new Proposal(experimentGrid.input().proposal); - var panel = experimentGrid.getPanel(experimentGrid.input().experiments); - experimentGrid.refresh(experimentGrid.input().experiments); - panel.render(targetId); -}; - -function VolumeGrid() { - this.id = BUI.id(); + } + /** Events **/ + this.onEditButtonClicked = new Event(this); } -VolumeGrid.prototype.getPanel = function(experiment) { - this.experiment = experiment; - return this.render(); +ExperimentGrid.prototype._getFilterTypes = function() { + return []; }; -VolumeGrid.prototype.getVolumesPanel = function(data, title) { - var _this = this; - var store = Ext.create('Ext.data.Store', { - fields : [ 'name', 'volume', 'macromoleculeId', 'bufferId' ], - data : data - }); - store.sort([ { - property : 'name', - direction : 'ASC' - } ]); - - var grid = Ext.create('Ext.grid.Panel', { - title : title, - height : 400, - maxHeight : 400, - width : 900, - store : store, - margin : '10 0 50 10', - tbar : [ { - text : 'Go to Shipment', - icon : '../images/plane-small.gif', - handler : function() { - window.location = BUI.getCreateShipmentList(); - } - } ], - viewConfig : { - stripeRows : true, - listeners : { - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonCreate') { - var stockSolutionWindow = new StockSolutionWindow(); - /** On stock solution SAVED **/ - stockSolutionWindow.onSaved.attach(function(sender, stockSolution) { - BIOSAXS.proposal.onInitialized.attach(function(sender, data) { - _this.refresh(_this.experiment); - }); - BIOSAXS.proposal.init(); - }); - var acronym = "ST"; - if (record.raw.macromoleculeId != null) { - acronym = acronym + "_" + BIOSAXS.proposal.getMacromoleculeById(record.raw.macromoleculeId).acronym; - } - if (record.raw.bufferId != null) { - acronym = acronym + "_" + BIOSAXS.proposal.getBufferById(record.raw.bufferId).acronym; - } - stockSolutionWindow.draw({ - concentration : record.raw.concentration, - macromoleculeId : record.raw.macromoleculeId, - bufferId : record.raw.bufferId, - name : acronym, - volume : record.raw.volume - }); - } - - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonStockSolutions') { - var stockSolutionGrid = new StockSolutionGrid({ - btnAddVisible : false, - btnEditVisible : false, - btnRemoveVisible : false, - btnAddExisting : false, - isPackedVisible : true, - multiselect : false - }); - - var window = Ext.create('Ext.window.Window', { - title : 'Stock solutions by specimen', - height : 400, - width : 800, - layout : 'fit', - items : [ stockSolutionGrid.getPanel() ], - buttons : [ { - text : 'Close', - handler : function() { - window.close(); - } - } ] - - }).show(); - stockSolutionGrid.refresh(BIOSAXS.proposal.getStockSolutionsBySpecimen(record.raw.macromoleculeId, record.raw.bufferId)); - } - } - } - }, - columns : [ -// { -// text : '', -// dataIndex : 'macromoleculeId', -// width : 20, -// renderer : function(val, y, sample) { -// if (val != null) { -//// return BUI.getRectangleColorDIV(BIOSAXS.proposal.macromoleculeColors[val], 10, 10); -// return BUI.getRectangleColorDIV(_this.experiment.macromoleculeColors[val], 10, 10); -// } -// } -// }, -// { -// text : '', -// dataIndex : 'bufferId', -// width : 20, -// renderer : function(val, y, sample) { -// if (val != null) { -// return BUI.getRectangleColorDIV(_this.experiment.getSpecimenColorByBufferId(val), 10, 10); -// } -// } -// }, - { - text : 'Specimen', - dataIndex : 'name', - flex : 0.5 - }, - { - text : 'Estimated Volume', - dataIndex : 'volume', - tooltip : 'Estimation of the maximum volume needed for making this experiment', - flex : 0.5, - editor : { - allowBlank : true - }, - renderer : function(val, y, sample) { - return BUI.formatValuesUnits(sample.data.volume, 'µl', { - fontSize : 16, - decimals : 2, - unitsFontSize : this.unitsFontSize - }); - } - }, - { - text : 'Stock Solution', - id : _this.id + 'buttonStockSolutions', - dataIndex : 'name', - flex : 0.5, - tooltip : 'Stock Solutions containing this specimen in this proposal', - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - var macromoleculeId = record.raw.macromoleculeId; - var bufferId = record.raw.bufferId; - var stockSolutions = BIOSAXS.proposal.getStockSolutionsBySpecimen(macromoleculeId, bufferId); - if (stockSolutions.length > 0) { - return "
" + stockSolutions.length + " x
"; - } +ExperimentGrid.prototype._prepareData = function(rows) { + var data = []; + var count = 0; + + rows.sort(function(a,b){return b.experimentId - a.experimentId;}); + for ( var i = 0; i < rows.length; i++) { + var row = rows[i]; + this.dates[moment(row.creationDate).format("YYYYMMDD")] = moment(row.creationDate).format("MMM Do YY"); + if ( + ( this.filtered == null || row.experimentType == this.filtered ) && (count < this.limit || this.limit == null ) && (this.sessionIdFilter == null || this.date != null || (this.date == null && this.sessionIdFilter == row.sessionId)) + ){ - } - }, { - id : _this.id + 'buttonCreate', - text : '', - tooltip : 'Create a new stock solution for shipping', - width : 170, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - return BUI.getGreenButton('NEW STOCK SOLUTION', { - width : 160 + data.push({ + experimentId : row.experimentId, + status : row.status, + dataAcquisitionFilePath : row.dataAcquisitionFilePath, + type : row.experimentType, + name : row.name, + macromolecules_names : row.macromolecules, + percentageAnalysed : { + value : (row.dataCollectionDoneCount / row.dataCollectionCount) * 100, + text : row.dataCollectionDoneCount + " of " + row.dataCollectionCount + }, + percentageCollected : { + value : (row.measurementDoneCount / row.measurementCount) * 100, + text : row.measurementDoneCount + " of " + row.measurementCount + }, + percentageMerged : { + value : (row.measurementAveragedCount / row.measurementCount) * 100, + text : row.measurementAveragedCount + " of " + row.measurementCount + }, + date : moment(row.creationDate).format("YYYYMMDD"), + time : moment(row.creationDate).format("YYYYMMDDHHmmss"), + creationDate : row.creationDate }); - } - } ] - }); - return grid; + count ++; + } + } + return data; +}; +ExperimentGrid.prototype.getPanel = function(experiments) { + this.features = experiments; + return this._renderGrid(experiments); }; -VolumeGrid.prototype._prepareData = function(experiment) { - var keys = {}; - for ( var i = 0; i < experiment.getSamples().length; i++) { - var sample = experiment.getSamples()[i]; - var key = ""; - if (sample.macromoleculeId == null) { - key = experiment.getBufferById(sample.bufferId).acronym; - if (keys[key] == null) { - keys[key] = { - macromoleculeId : sample.macromoleculeId, - name : key, - bufferId : sample.bufferId, - volume : 0 - }; - } - keys[key].volume = Number(sample.volume) + Number(keys[key].volume); +ExperimentGrid.prototype.refresh = function(experiments) { + this.experiments = experiments; + var filtered = []; + for ( var i = 0; i < experiments.length; i++) { + if (experiments[i].experimentType != "TEMPLATE") { + filtered.push(experiments[i]); } + } - if ((sample.macromolecule3VO != null) || (sample.macromoleculeId != null)) { - macromoleculeId = sample.macromoleculeId; - if (sample.macromoleculeId == null) { - sample.macromoleculeId = sample.macromolecule3VO.macromoleculeId; - } - key = BIOSAXS.proposal.getMacromoleculeById(sample.macromoleculeId).acronym + " + " + experiment.getBufferById(sample.bufferId).acronym; - if (keys[key] == null) { - keys[key] = { - macromoleculeId : sample.macromoleculeId, - name : key, - bufferId : sample.bufferId, - volume : 0 - }; - } - keys[key].volume = Number(sample.volume) + Number(keys[key].volume); + this.parsedData = this._prepareData(filtered); + + var day = {}; + var dates = []; + for ( var i = 0; i < this.experiments.length; i++) { + var date = moment(this.experiments[i].creationDate).format("MMM Do YYYY"); + if (day[date] == null){ + dates.push({ + date : date, + value : moment(this.experiments[i].creationDate) + }); + day[date] = true; } } - var data = []; - for (var keyId in keys) { - data.push(keys[keyId]); + + this.storeDate.loadData(dates, false); + this.store.loadData(this.parsedData, false); + + /** If it has already been filtered by date we keep the filter **/ + if (this.date != null){ + this._filterByDate(this.date); } - - return data; }; -VolumeGrid.prototype.refresh = function(experiment) { - this.experiment = experiment; - this.macromoleculeGrid.getStore().loadData(this._prepareData(this.experiment), false); -}; +ExperimentGrid.prototype._getTopButtons = function() { + var _this = this; + /** Actions buttons **/ + var actions = []; -VolumeGrid.prototype.render = function() { - this.macromoleculeGrid = this.getVolumesPanel(this._prepareData(this.experiment), "Estimation of required Volume"); + actions.push(Ext.create('Ext.Action', { + icon : '../images/calendar_icon.png', + text : 'Show Calendar', + disabled : false, + handler : function(widget, event) { + var window = Ext.create('Ext.window.Window', { + title : 'Calendar', + width : 600, + height : 600, + modal : true, + closable : true, + layout : { + type : 'vbox', + align : 'stretch' + }, + items : [ { + xtype : 'label', + html : 'Click on a data acquisition to select:', + margin : '5 5 5 5' + }, { + html : '
', + margin : '5 5 5 5' + } - return { - xtype : 'container', - layout : 'vbox', - margin : "0, 0, 0, 5", - items : [ { - xtype : 'container', - layout : 'hbox', - margin : "0, 0, 0, 0", - items : [ this.macromoleculeGrid ] - } ] - }; + ] + }).show(); + + var calendarWidget = new CalendarWidget({ + height : 450 + }); + var aux = _this.limit; + /** we remove the limit temporarily **/ + _this.limit = null; + _this.sessionIdFilter = null; + calendarWidget.loadData(_this._prepareData(_this.experiments)); + _this.limit = aux; + calendarWidget.draw('calendar'); + calendarWidget.onClick.attach(function(sender, date) { + date = moment(date, "YYYY-MM-DD"); + _this._filterByDate(date); + window.close(); + + }); + + } + })); + this.storeDate = Ext.create('Ext.data.ArrayStore', { + fields: ['date', 'value'], + data : [] + }); + + this.dateMenu = Ext.create('Ext.form.field.ComboBox', { + hideLabel: true, + store: this.storeDate, + displayField: 'date', + typeAhead: true, + queryMode: 'local', + margin : '0 0 0 30', + triggerAction: 'all', + emptyText:'Select a date...', + selectOnFocus:true, + width:135, + listeners:{ + scope: this, + 'select': function (a,b,c){ + _this.limit = null; + _this._filterByDate(moment(b[0].raw.value, "YYYY-MM-DD")); + } + } + }); + + actions.push(this.dateMenu); + + actions.push("->"); + if (_this.filtered != null){ + actions.push({ + html : "Experiment Type: " + _this.filtered +"" + }); + } + else{ + actions.push({ + html : "Experiment Type: ALL" + }); + } + return actions; }; -VolumeGrid.prototype.input = function(experiment) { - return { - experiment : DATADOC.getExperiment_10() - }; +/** + * Date format: "YYYY-MM-DD" + */ +ExperimentGrid.prototype._filterByDate = function(date) { + var experimentsFiltered = []; + /** Getting all the experiments of date**/ + for ( var i = 0; i < this.experiments.length; i++) { + var experiment = this.experiments[i]; + if (experiment.creationDate != null) { + var experimentDate = moment(experiment.creationDate); + if (experimentDate.year() == date.year()) { + if (experimentDate.month() == date.month()) { + if (experimentDate.date() == date.date()) { + experimentsFiltered.push(experiment); + } + } + } + } + } + var parsedData = this._prepareData(experimentsFiltered); + this.store.loadData(parsedData); + this.date = date; }; -VolumeGrid.prototype.test = function(targetId) { - var volumeGrid = new VolumeGrid(); - BIOSAXS.proposal = new Proposal(new MeasurementGrid().input().proposal); - var panel = volumeGrid.getPanel(new Experiment(new VolumeGrid().input().experiment)); - Ext.create('Ext.panel.Panel', { - height : 500, - width : 1000, - renderTo : targetId, - items : [ panel ] +/** Only for templates **/ +ExperimentGrid.prototype._removeExperimentById = function(experimentId) { + var _this = this; + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(evt, args) { + _this.grid.setLoading(false); + document.getElementById(BIOSAXS.targetId).innerHTML = ""; + BIOSAXS.start(BIOSAXS.targetId); }); + this.grid.setLoading("Removing experiment "); + adapter.removeExperimentById(experimentId); }; - -/** - * Example of a tab panel to be populated with widgets - * - * @width width in pixels - * @height height in pixels - * - * #myEvent event that this class is supposed to throw - * - **/ -function ExampleTabs(args) { - this.width = 500; - this.height = 500; + +ExperimentGrid.prototype._renderGrid = function() { + var _this = this; + + /** Store **/ + this.store = Ext.create('Ext.data.Store', { + fields : this._getColumns(), + groupField : 'date', + autoload : true, + data : [], + remoteSort: false, + sorters : this.sorters + }); + - if (args != null){ - if (args.width != null){ - this.width= args.width; - } - if (args.height != null){ - this.height= args.height; - } - } - /** Events **/ - this.myEvent = new Event(); -} - -/** Populate the widget **/ -ExampleTabs.prototype.refresh = function(macromolecule) { -}; + var groupingFeature = Ext.create('Ext.grid.feature.Grouping', { + groupHeaderTpl : Ext.create('Ext.XTemplate', + "
{name:this.formatName}
", { + formatName : function(name) { + return _this.dates[name]; + } + }), + hideGroupedHeader : true, + startCollapsed : false + }); -/** It creates a tab panel with the specified with and height **/ -ExampleTabs.prototype.getPanel = function() { - this.panel = Ext.createWidget('tabpanel', { - height : this.height, - width : this.width, - style : { - padding : 2 + this.features = []; + if (this.grouping) { + this.features.push(groupingFeature); + } + + /** Grid **/ + this.grid = Ext.create(this.gridType, { + hideHeaders : this.hideHeaders, + resizable : true, + title : this.title, + width : this.width, + minHeight : this.minHeight, + height : this.height, + features : this.features, + store : this.store, + columns : this._getColumns(), + selModel : { + mode : 'SINGLE' }, - items : [ { - tabConfig : { - title : 'Test', - icon : '/ispyb/images/plane-small.gif' + viewConfig : { + stripeRows : true, + getRowClass : function(record, rowIdx, params, store) { + if (record.raw.type == "TEMPLATE") { + return "template-color-row"; + } + if ((record.raw.type == "CALIBRATION") && (record.raw.status == "FINISHED")) { + return "blue-row"; + } }, - items : [ { - xtype : 'container', - margin : '5 5 5 5', - items : [ ] - } ] - } ] + listeners : { + itemdblclick : function(dataview, record, item, e) { + _this._editExperiment(record.raw.experimentId); + }, + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'GO') { + _this._editExperiment(record.raw.experimentId); + } + + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'REMOVE') { + _this._removeExperimentById(record.raw.experimentId); + } + + } + } + } }); - return this.panel; -}; - -/** - * Shows an experiments with the specimens, measurements, analysis tabs where - * results are shown and the frames widget - * - * @targetId - */ -function ExperimentTabs(targetId) { - this.height = 900; - this.targetId = targetId; + var actions = _this._getTopButtons(); - this.id = BUI.id(); - var _this = this; + if (this.tbar) { + this.grid.addDocked({ + xtype : 'toolbar', + items : actions + }); + this.grid.getSelectionModel().on({ + selectionchange : function(sm, selections) { + if (selections.length) { + for ( var i = 0; i < actions.length; i++) { + if (actions[i].enable) { + actions[i].enable(); + } + } + } else { + for ( var i = 0; i < actions.length; i++) { + if (actions[i].alwaysEnabled == false) { + if (actions[i].disable) { + actions[i].disable(); + } + } + } + } + } + }); + } - this.INTERVAL_UPDATE = BUI.getUpdateInterval(); + return this.grid; +}; - this.gridHeight = 1000; - /** data * */ - this.experiment = null; +ExperimentGrid.prototype._getColumns = function() { + var _this = this; + function actionItemRenderer(value, meta, record, rowIx, ColIx, store) { + if (record.raw.buffer3VOs != null) { + if (record.raw.buffer3VOs.length > 0) { + return 'x-hide-display'; + } + } - - /** Specimen Widget contains a specimenGrid and a sampleChangerWidget than can be displayed with are vertical or horizontal layout **/ - this.specimenWidget = new SpecimenWidget({ - height : 600 - }); - - - /** For Overview * */ - /*this.samplePlateGroupWidget = new SamplePlateGroupWidget({ - showTitle : false, - height : 250, - margin : 5, - border : 0 + if (record.data.platesCount > 0) { + return 'x-hide-display'; + } + } - });*/ + return [ + { + text : 'experimentId', + dataIndex : 'experimentId', + name : 'experimentId', + type : 'string', + hidden : true + }, + { + xtype : 'rownumberer', + width : 40 + }, + { + text : 'Name', + dataIndex : 'name', + name : 'name', + type : 'string', + flex : 1 + }, - /** For Measurements * */ - /*this.measurementSamplePlateGroupWidget = new SamplePlateGroupWidget({ - showTitle : false, - height : 250, - margin : '5 0 0 0', - border : 0 - });*/ + { + text : 'Type', + dataIndex : 'type', + name : 'type', + type : 'string', + flex : 1, + renderer : function(val) { + if (val == "CALIBRATION") { + return "" + val + ""; + } + + return val; + } + }, + { + text : 'Macromolecules', + name : 'macromolecules_names', + dataIndex : 'macromolecules_names', + flex : 1, + renderer : function(val) { + if (val != null) { + return " " + val + ""; + } + return " Information not available"; + } + }, + { + text : 'Buffers', + dataIndex : 'buffer_names', + name : 'buffer_names', + flex : 1, + hidden : true, + renderer : function(val) { + return "Buffer/s: " + val + ""; + } + }, + { + text : 'Status', + dataIndex : 'status', + name : 'status', + type : 'string', + flex : 1, + renderer : function(val, x, sample) { + if (sample.raw.type == "TEMPLATE") { + return "READY"; + } + if (sample.raw.status == "ABORTED") { + return "" + val + ""; + } + return "" + val + ""; + } + }, + { + text : 'Download', + dataIndex : 'creationDate', + name : 'creationDate', + renderer : function(val, x, sample) { + if (sample != null) { + if (sample.raw.type == "HPLC") { + return; + } + return BUI.getZipHTMLByExperimentId(sample.raw.experimentId, sample.raw.name); + } + }, + width : 100 - this.measurementGridDone = new MeasurementGrid({ - height : 600, - minHeight : 400, - maxHeight : 800, - positionColumnsHidden : true, - showTitle : false, - estimateTime : true, - width : 900, - maxWidth : 1500, - addBtnEnable : false, - markDone : true, - removeBtnEnabled : false - }); - this.measurementGridDone.onSelected.attach(function(sender, measurements) { - var specimens = []; - for ( var i = 0; i < measurements.length; i++) { - specimens.push(_this.experiment.getSampleById(measurements[i].specimenId)); - } - //_this.measurementSamplePlateGroupWidget.selectSpecimens(specimens); - }); + }, + { + header : 'Measurements', + dataIndex : 'percentageCollected', + name : 'percentageCollected', + type : 'string', + renderer : function(val, y, sample) { + if ((sample.raw.type == "TEMPLATE") || (sample.raw.type == "HPLC")) { + return; + } + return "
" + BUI.getProgessBar(sample.raw.percentageCollected.value, sample.raw.percentageCollected.text) + "
"; + }, + width : 100 + }, + { + header : 'Averaged', + dataIndex : 'percentageMerged', + name : 'percentageMerged', + type : 'string', + renderer : function(val, y, sample) { + if ((sample.raw.type == "TEMPLATE") || (sample.raw.type == "HPLC")) { + return; + } + return "
" + BUI.getProgessBar(sample.raw.percentageMerged.value, sample.raw.percentageMerged.text) + "
"; + }, + width : 100 + }, + { + header : 'Subtractions', + dataIndex : 'percentageAnalysed', + name : 'percentageAnalysed', + type : 'string', + renderer : function(val, y, sample) { + if ((sample.raw.type == "TEMPLATE") || (sample.raw.type == "HPLC")) { + return; + } + return "
" + BUI.getProgessBar(sample.raw.percentageAnalysed.value, sample.raw.percentageAnalysed.text) + "
"; + }, + width : 100 + }, - /** AnalysisGrid * */ - this.analysisGrid = new AnalysisGrid({ - height : Ext.getBody().getViewSize().height * 0.9 - 300, - positionColumnsHidden : true, - sorters : [ { - property : 'priorityLevelId', - direction : 'ASC' - } ] - }); - - - /** Queue * */ - this.queueGrid = new QueueGrid({ - url : BUI.getQueueUrlByExperiment(), - height : Ext.getBody().getViewSize().height * 0.9 - 300, - width : Ext.getBody().getViewSize().width * 0.9 - 300, - isGrouped : true, - tbar : false, - bbar : false, - sorter : [{ - property: 'measurementId', - direction: 'DESC' - }] - }); + { + text : 'time', + dataIndex : 'time', + name : 'time', + hidden : true, + renderer : function(val) { + return val; + }, + width : 100 -} + }, { + text : 'Date', + dataIndex : 'date', + name : 'date', + renderer : function(val) { + return val; + }, + width : 100 -ExperimentTabs.prototype.error = function(error) { - var e = JSON.parse(error); - showError(e); - this.panel.setLoading(false); -}; + }, -ExperimentTabs.prototype.draw = function(experiment) { - this.renderDataAcquisition(experiment); -}; + { + text : 'Time', + dataIndex : 'creationDate', + name : 'creationDate', + renderer : function(val) { + return moment(val).format(" HH:mm:ss"); + }, + width : 100 -ExperimentTabs.prototype.refreshAnalysisData = function() { - var _this = this; - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - _this.analysisGrid.refresh(data, {experiment : _this.experiment}); - }); - adapter.getAnalysisInformationByExperimentId(this.experiment.experimentId); - - /** Auto load **/ - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - _this.queueGrid.refresh(data); - }); - adapter.getCompactAnalysisByExperimentId(this.experiment.experimentId); - this.queueGrid.store.proxy.url = BUI.getQueueUrlByExperiment(this.experiment.experimentId); - this.queueGrid.refresh(); + }, { + id : _this.id + 'GO', + width : 80, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + return BUI.getGreenButton('GO'); + } + } ]; }; -ExperimentTabs.prototype.getSpecimenContainerHeight = function(experiment) { - var maxItems = 0; - if (maxItems < experiment.getSamples().length + 1) { - maxItems = experiment.getSamples().length + 1; - } - - var height = (maxItems + 1) * 40 + 40; - if (height > 400) { - height = 400; +/** Changes location.href in order to edit the experiment **/ +ExperimentGrid.prototype._editExperiment = function(experimentId) { + if (Ext.urlDecode(window.location.href).sessionId != null) { + location.href = 'viewProjectList.do?reqCode=display&experimentId=' + experimentId + '&sessionId='+ Ext.urlDecode(window.location.href).sessionId; + } else { + location.href = 'viewProjectList.do?reqCode=display&experimentId=' + experimentId; } - return height; -}; - -ExperimentTabs.prototype.getExperimentTitle = function() { - var experimentHeaderForm = new ExperimentHeaderForm(); - return experimentHeaderForm.getPanel(this.experiment); }; -ExperimentTabs.prototype.renderDataAcquisition = function(experiment) { - var _this = this; - this.experiment = experiment; +ExperimentGrid.prototype.input = function() { + var experiments = DATADOC.getExperimentList_10(); + return { + experiments : experiments, + proposal : new MeasurementGrid().input().proposal - var specimenGrid = new SpecimenGrid({ - height : 400, - maxHeight : 500, - width : 890 - }); + }; +}; - specimenGrid.onClick.attach(function(sender, args) { - }); +ExperimentGrid.prototype.test = function(targetId) { + var experimentGrid = new ExperimentGrid({ + height : 350, + minHeight : 350, + width : 1000 - specimenGrid.onSelected.attach(function(sender, specimens) { - //_this.samplePlateGroupWidget.selectSpecimens(specimens); - }); - var specimenContainer = this.specimenWidget.getPanel(); - this.specimenWidget.refresh(experiment); - /* - var specimenContainer = Ext.create('Ext.container.Container', { - layout : 'hbox', - width : 900, - padding : '10 0 0 2', - items : [ specimenGrid.getPanel() ] }); + BIOSAXS.proposal = new Proposal(experimentGrid.input().proposal); + var panel = experimentGrid.getPanel(experimentGrid.input().experiments); + experimentGrid.refresh(experimentGrid.input().experiments); + panel.render(targetId); +}; + + +function FitStructureToExperimentDataGrid(args) { + this.height = null; + this.width = null; + this.id = BUI.id(); + + if (args != null) { + if (args.height != null) { + this.height = args.height; + + if (args.width != null) { + this.width = args.width; + } + } + } + + this.onSelected = new Event(this); +} + +FitStructureToExperimentDataGrid.prototype.getStructuresByMacromolecule = function(macromolecule) { + var structures = []; + if (macromolecule.structure3VOs != null) { + if (macromolecule.structure3VOs.length > 0) { + for (var i = 0; i < macromolecule.structure3VOs.length; i++) { + structures.push(macromolecule.structure3VOs[i]); + } + } + } + return structures; +}; + +FitStructureToExperimentDataGrid.prototype._prepareData = function(subtractions) { + var data = []; + for (var i = 0; i < subtractions.length; i++) { + + for (var j = 0; j < subtractions[i].fitStructureToExperimentalData3VOs.length; j++) { + var fit = subtractions[i].fitStructureToExperimentalData3VOs[j]; + data.push({ + fit : fit.fitFilePath, + fitStructureToExperimentalDataId : fit.fitStructureToExperimentalDataId, + mixtureToStructure3VOs : fit.mixtureToStructure3VOs, + subtractedFile : subtractions[i].substractedFilePath + }); + } + } + return data; + +}; + +FitStructureToExperimentDataGrid.prototype.refresh = function(subtractions) { + this.store.loadData(this._prepareData(subtractions), false); +}; + +FitStructureToExperimentDataGrid.prototype.getPanel = function() { + var _this = this; + this.store = Ext.create('Ext.data.Store', { + fields : [ 'fit', 'subtractedFile', 'structureId', 'fitFilePath', 'mixtureToStructure3VOs' ], + data : [] + }); + + this.store.sort([ { + property : 'name', + direction : 'ASC' + } ]); + + this.selModel = Ext.create('Ext.selection.RowModel', { + allowDeselect : true, + mode : 'MULTI', + listeners : { + selectionchange : function(sm, selections) { + var selected = []; + for (var i = 0; i < selections.length; i++) { + selected.push(selections[i].raw); + } + _this.onSelected.notify(selected); + } + } + }); + + this.panel = Ext.create('Ext.grid.Panel', { + store : this.store, + deferredRender : false, + width : this.width, + height : this.height, + margin : 10, + selModel : this.selModel, + columns : [ { + text : 'Name', + dataIndex : 'fit', + flex : 1, + renderer : function(val, b, record) { + return BUI.getFileName(val); + } + }, { + text : 'PDB', + dataIndex : 'mixtureToStructure3VOs', + flex : 1, + renderer : function(values, b, record) { + var html = ""; + for (var i = 0; i < values.length; i++) { + var structure = BIOSAXS.proposal.getStructuresById(values[i].structureId); + html = html + ""; + if (structure != null){ + html = html + ""; + } + html = html + ""; + } + return html + "
" + structure.name + "
"; + } + }, { + text : 'Volume Fraction', + dataIndex : 'mixtureToStructure3VOs', + flex : 1, + renderer : function(values, b, record) { + var html = ""; + for (var i = 0; i < values.length; i++) { + html = html + ""; + html = html + ""; + html = html + ""; + } + + return html + "
" + values[i].volumeFraction + "
"; + } + },{ + text : 'Subtraction', + dataIndex : 'subtractedFile', + flex : 1, + renderer : function(values, b, record) { + return values.split("/")[values.split("/").length - 1]; + } + },], + + viewConfig : { + enableTextSelection : true, + preserveScrollOnRefresh : true + }, + listeners : { + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + }, + afterrender : function() { + } + } + }); + return this.panel; +}; + +/** Static method **/ +FitStructureToExperimentDataGrid.prototype.RUNFitScattering = function(subtractionId, structureId) { + var _this = this; + /** Add to Workflow **/ + var adapter = new BiosaxsDataAdapter(); + var workflow = { + 'workflowTitle' : 'FitExperimentalDatatoStructure', + 'comments' : 'FitExperimentalDatatoStructure run from ISPyB for subtractionId: ' + subtractionId + ' and structureId ' + structureId + } + + var inputs = [ { + name : 'subtractionId', + value : subtractionId + }, { + name : 'structureId', + value : structureId + } ]; + + adapter.onSuccess.attach(function(sender, data) { + /** Add to Fit **/ + var adapter2 = new BiosaxsDataAdapter(); + var fit = { + 'workflowId' : data.workflowId, + 'subtractionId' : subtractionId, + 'structureId' : structureId, + 'comments' : 'Sent to workflow engine' + } + adapter2.onSuccess.attach(function(sender, fit) { + _this.refresh(_this.subtractionId, _this.macromolecule); + }); + adapter2.addFitStructureData(fit); + + }); + adapter.addWorkflow(workflow, inputs); + +}; + +/** + * It shows buffer grid with a top bar with "Add" button + * + * @height + * @searchBar + * @collapsed + * @width + */ +function FrameGrid(args) { + this.height = 500; + this.width = 500; + this.searchBar = false; + this.tbar = false; + this.collapsed = false; - specimenGrid.refresh(experiment);*/ - var experimentList = new ExperimentList([ _this.experiment ]); - var measurementContainer = Ext.create('Ext.container.Container', { - layout : 'vbox', - padding : '5px 0px 0px 10px', - items : [] - }); - measurementContainer.insert(0, _this.measurementGridDone.getPanel(this.experiment.getMeasurements(), experimentList)); -// measurementContainer.insert(1, _this.measurementSamplePlateGroupWidget.getPanel(experiment)); + if (args != null) { + if (args.height != null) { + this.height = args.height; + } + + if (args.searchBar != null) { + this.searchBar = args.searchBar; + } - // this.dataCollectionCurveVisualizer = new DataCollectionCurveVisualizer(); - // this.dataCollectionCurveVisualizer.experiments = [experiment]; - // this.dataCollectionCurveVisualizer.dataCollectionFrameTree.experiments = - // [experiment]; - // this.dataCollectionCurveVisualizer.dataCollections = - // experiment.getDataCollections(); + if (args.tbar != null) { + this.tbar = args.tbar; + } - this.panel = Ext.createWidget('tabpanel', { - plain : true, - style : { - padding : 2 - }, - items : [ { - tabConfig : { - id : 'genralTabl', - title : "Overview" - }, - items : [ specimenContainer ] - }, { - tabConfig : { - title : 'Measurements' - }, - items : [ measurementContainer] - }, { - tabConfig : { - id : 'SpecimenTab', - title : 'Analysis', - hidden : this.isTemplate() - }, - items : [ { - xtype : 'container', - layout : 'vbox', - padding : '5px 0px 10px 10px', - items : [ _this.analysisGrid.getPanel([]) ] - } ] - }, - { - tabConfig : { - id : 'newAnalysisTab', - title : 'Analysis BETA', - hidden : this.isTemplate() - }, - items : [ { - xtype : 'container', - layout : 'vbox', - padding : '5px 0px 10px 10px', - items : [ _this.queueGrid.getPanel([]) ] - } ] + if (args.collapsed != null) { + this.collapsed = args.collapsed; } - ] + + if (args.width != null) { + this.width = args.width; + } + } +} + +FrameGrid.prototype._edit = function(bufferId) { + var _this = this; + var window = new BufferWindow(); + window.onSuccess.attach(function(sender, proposal) { + _this.store.loadData(BIOSAXS.proposal.getBuffers()); }); + window.draw(BIOSAXS.proposal.getBufferById(bufferId)); +}; - return this.getPanel(this.panel); +FrameGrid.prototype.refresh = function(buffers, experimentId) { + this.experimentId = experimentId; + this.store.loadData(this._prepareData(buffers), false); }; -ExperimentTabs.prototype.isTemplate = function() { - if (this.experiment.json.type == "TEMPLATE") { - return true; - } - return false; +FrameGrid.prototype._prepareData = function(buffers) { + return buffers; }; -ExperimentTabs.prototype.update = function() { +FrameGrid.prototype._getTbar = function() { var _this = this; - var inter; - if (!_this.isTemplate()) { - function updateExperiments() { - _this.refreshAnalysisData(); - window.clearInterval(inter); - inter = setInterval(function() { - updateExperiments(); - }, _this.INTERVAL_UPDATE); - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - var experiment = new Experiment(data); - _this.measurementGridDone.refresh(experiment.getMeasurements(), new ExperimentList([ experiment ])); + var actions = []; + + actions.push(Ext.create('Ext.Action', { + icon : '../images/add.png', + text : 'Add Buffer', + disabled : false, + handler : function(widget, event) { + var window = new BufferWindow(); + window.onSuccess.attach(function(sender) { + _this.store.loadData(BIOSAXS.proposal.getBuffers()); }); - adapter.getExperimentById(_this.experiment.json.experimentId, "MEDIUM"); + window.draw({}); } - inter = setInterval(function() { - updateExperiments(); - }, _this.INTERVAL_UPDATE); - } + })); + return actions; }; -ExperimentTabs.prototype.getPanel = function(panel) { +FrameGrid.prototype.getPanel = function(buffers) { var _this = this; - if (this.experimentPanel == null) { - this.experimentPanel = Ext.create('Ext.container.Container', { - bodyPadding : 2, - width : Ext.getBody().getViewSize().width * 0.9, - renderTo : this.targetId, - style : { - padding : 2 - }, - items : [ this.getExperimentTitle(), this.panel ], - listeners : { - afterrender : function() { - _this.refreshAnalysisData(); - _this.update(); - } - } - }); - } - - return this.experimentPanel; -}; - -ExperimentTabs.prototype.input = function() { - return { - experiment : DATADOC.getExperiment_10(), - proposal : DATADOC.getProposal_10() - }; -}; - -ExperimentTabs.prototype.test = function(targetId) { - var experimentTabs = new ExperimentTabs(targetId); - BIOSAXS.proposal = new Proposal(experimentTabs.input().proposal); - experimentTabs.draw(new Experiment(experimentTabs.input().experiment)); -}; + this.store = Ext.create('Ext.data.Store', { + fields : [ 'frameNumber', 'I0', 'Rg', 'Mass', 'Vc', 'Qr', 'quality'], + data : buffers + }); - -/** - * Shows an experiments with the specimens, measurements, analysis tabs where results are shown and the frames widget - * - * @targetId - */ -function HPLCTabs(targetId) { - this.height = 1400; - this.targetId = targetId; + this.store.sort('frameNumber'); - this.id = BUI.id(); + var type = 'Ext.grid.Panel'; + if (this.searchBar == true) { + type = 'Ext.ux.LiveSearchGridPanel'; + } - this.gridHeight = 600; - this.pointsCount = 1036; - this.plotHeight = 350; - this.plotWidth = 800; - this.plotPanelPadding = 5; + this.grid = Ext.create(type, { + store : this.store, + height : this.height, + width : this.width, + margin : 5, + columns : [{ + text : 'Frame', + dataIndex : 'frameNumber', + flex : 1 + },{ + text : 'I0', + dataIndex : 'I0', + flex : 1, + renderer : function(val, y, sample) { + return BUI.formatValuesUnits(sample.data.I0, "", 12, 3); + } + },{ + text : 'Rg', + dataIndex : 'Rg', + flex : 1, + renderer : function(val, y, sample) { + return BUI.formatValuesUnits(sample.data.Rg, "nm", 12, 3); + } + },{ + text : 'Mass', + dataIndex : 'Mass', + flex : 1, + renderer : function(val, y, sample) { + return BUI.formatValuesUnits(sample.data.Mass, "", 12, 3); + } + },{ + text : 'Vc', + dataIndex : 'Vc', + flex : 1, + renderer : function(val, y, sample) { + return BUI.formatValuesUnits(sample.data.Vc, "", 12, 3); + } + },{ + text : 'Qr', + dataIndex : 'Qr', + flex : 1, + renderer : function(val, y, sample) { + return BUI.formatValuesUnits(sample.data.Qr, "", 12, 3); + } + },{ + text : 'Quality', + dataIndex : 'quality', + flex : 1, + renderer : function(val, y, sample) { + return (Number(sample.data.quality) * 100).toFixed(2) + "%"; + } + }, + { + text : '', + renderer : function(val, x, sample) { + if (sample != null) { + return BUI.getZipHTMLByFrameRangeId(_this.experimentId, sample.raw.frameNumber, sample.raw.frameNumber); + } + }, + width : 100 + }], + flex : 1, + viewConfig : { + stripeRows : true + } + }); - var _this = this; + /** Adding the tbar **/ + if (this.tbar) { + this.grid.addDocked({ + xtype : 'toolbar', + items : this._getTbar() + }); + } + return this.grid; +}; - this.analysisGrid = new HPLCAnalysisGrid({ - height : Ext.getBody().getViewSize().height * 0.9 - 300, - positionColumnsHidden : true, - sorters : [ { - property : 'priorityLevelId', - direction : 'ASC' - } ] - }); +FrameGrid.prototype.input = function() { + return []; +}; - this.frameGrid = new FrameGrid({ - width : 600, - height : 60, - collapsed : false, - tbar : false - }); - - this.peakGrid = new PeakGrid({ - width : 550, - height : 500, - collapsed : false, - tbar : false - }); - - this.peakGrid2 = new PeakGrid({ - width : 102, - height : this.plotHeight, +FrameGrid.prototype.test = function(targetId) { + var frameGrid = new FrameGrid({ + width : 800, + height : 350, collapsed : false, - tbar : false, - showExtendedColumns : true + tbar : true }); - - this.mainPlotPanel = new HPLCGraph({ - title : 'I0', - width : this.plotWidth - 110, - height : this.plotHeight, - bbar : true, - plots : { - "I0" : true, - "Rg" : true - }, - xlabel : "HPLC Frames", - scaled : true, - interactionModel : { - 'dblclick' : function(event, g, context) { - _this._selectFrame(g.lastx_); - var annotations = []; - annotations.push({ - series : g.selPoints_[0].name, - x : g.lastx_, - width : 100, - height : 23, - tickHeight : 4, - shortText : g.lastx_, - text : g.lastx_, - attachAtBottom : true - }); - g.setAnnotations(annotations); - } + var panel = frameGrid.getPanel([]); + panel.render(targetId); +}; + + +function PeakGrid(args) { + this.height = 500; + this.searchBar = false; + this.tbar = false; + this.collapsed = false; + this.width = 500; + this.showExtendedColumns = false; + + if (args != null) { + if (args.showExtendedColumns != null) { + this.showExtendedColumns = args.showExtendedColumns; + } + if (args.height != null) { + this.height = args.height; + } + if (args.searchBar != null) { + this.searchBar = args.searchBar; } - }); - this.intensityPlotPanel = new MergesHPLCGraph({ - title : 'Scattering', - width : this.plotWidth, - height : 500, - showRangeSelector : false, - xParam : 0, - xlabel : "scattering_I", - plots : { - "scattering_I" : true, - "subtracted_I" : true, - "buffer_I" : true + if (args.tbar != null) { + this.tbar = args.tbar; } - }); -} + if (args.collapsed != null) { + this.collapsed = args.collapsed; + } -HPLCTabs.prototype._selectFrame = function(frameNumber) { - try{ - this._renderScatteringCurve(frameNumber); - this.frameGrid.refresh([this.mainPlotPanel.getDataByFrameNumber(frameNumber)], this.experiment.experimentId); - } - catch(e){ - console.log(e); + if (args.width != null) { + this.width = args.width; + } } -}; +} -HPLCTabs.prototype.error = function(error) { - var e = JSON.parse(error); - showError(e); - this.panel.setLoading(false); -}; -HPLCTabs.prototype.loadDataMainPlot = function(data) { - var zeroArray = []; - for ( var i = 0; i < data.I0.length; i++) { - zeroArray.push(0); - } - data = [ { - param : "I0", - data : data.I0, - std : data.I0_Stdev, - color : '#0066CC', - label : "I0" - }, - { - param : "sum_I", - label : "sum_I", - color : "#00FF00", - data : data.sum_I, - std : zeroArray - }, - { - param : "Rg", - label : "Rg", - color : "#21610B", - data : data.Rg, - std : data.Rg_Stdev - }, { - param : "Mass", - data : data.mass, - std : data.mass_Stdev, - color : '#FF9900', - label : "Mass" - }, { - param : "Vc", - data : data.Vc, - std : data.Vc_Stdev, - color : '#990099', - label : "Vc" - }, { - param : "Qr", - data : data.Qr, - std : data.Qr_Stdev, - color : '#FF0066', - label : "Qr" - }, { - param : "quality", - label : "quality", - color : "#FF00FF", - data : data.quality, - std : zeroArray - } ]; - this.data = data; - this.mainPlotPanel.loadData(data); +PeakGrid.prototype.refresh = function(buffers) { + this.store.loadData(this._prepareData(buffers), false); }; -HPLCTabs.prototype._loadIntensityPlotByFrameNumber = function(frameNumber) { - var _this = this; +PeakGrid.prototype._prepareData = function(buffers) { - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - var array = []; - data = [ { - param : "q", - data : data[frameNumber].q, - std : data[frameNumber].q, - fstd : function(a) { - return parseFloat(a); - }, - color : '#green', - label : "q", - showOnMenu : false - }, - { - param : "scattering_I", - data : data[frameNumber].scattering_I, - fdata : function(a) { - return Math.log(parseFloat(a)); - }, - std : data[frameNumber].scattering_Stdev, - fstd : function(a) { - return Math.log(Math.abs(parseFloat(a))); - }, - color : 'green', - label : "Log(I) Sample" - }, - { - param : "buffer_I", - data : data[frameNumber].buffer_I, - fdata : function(a) { - return Math.log(parseFloat(a)); - }, - fstd : function(a) { - return Math.log(Math.abs(parseFloat(a))); - }, - std : data[frameNumber].subtracted_Stdev, - color : '#0000FF', - label : "Log(I) Avg Buf." - }, - { - param : "subtracted_I", - data : data[frameNumber].subtracted_I, - fdata : function(a) { - var value = (Math.log(parseFloat(a))); - if (isNumber(value)) - return value; - }, - fstd : function(a) { - var value = Math.log(Math.abs(parseFloat(a))); - if (isNumber(value)) - return value; - }, - std : data[frameNumber].subtracted_Stdev, - color : 'red', - label : "Log(I) Sub." - } - ]; +// for ( var i = 0; i < buffers.length; i++) { +// buffers[i].name = "Peak #" + (i+1); +// } + /** Adding information of buffer **/ + if (buffers.length > 0){ + buffers.unshift({ + name : "BUFFER", + start : 0, + experimentId : buffers[0].experimentId, + end : buffers[0].start - 1 + }); + } + + + return buffers; +}; - _this.intensityPlotPanel.xlabel = "Frame " + frameNumber + " (q, nm-1)"; +PeakGrid.prototype._getTbar = function() { + var _this = this; + var actions = []; - if (_this.intensityPlotPanel.hplcData == null) { - /** It creates also top bar **/ - _this.intensityPlotPanel.loadData(data); - } else { - _this.intensityPlotPanel.reloadData(data); - + actions.push(Ext.create('Ext.Action', { + icon : '../images/add.png', + text : 'Add Buffer', + disabled : false, + handler : function(widget, event) { + var window = new BufferWindow(); + window.onSuccess.attach(function(sender) { + _this.store.loadData(BIOSAXS.proposal.getBuffers()); + }); + window.draw({}); } - _this.intensityPlotPanel.panel.setLoading(false); - }); - adapter.onError.attach(function(sender, data) { - _this.intensityPlotPanel.panel.setLoading(false); - }); - this.intensityPlotPanel.panel.setLoading("Retrieving Frame " + frameNumber); - adapter.getH5FrameScattering(this.experiment.json.experimentId, frameNumber); + })); + return actions; }; -HPLCTabs.prototype._renderScatteringCurve = function(frameNumber) { +PeakGrid.prototype.getPanel = function(buffers) { var _this = this; + this.peakCount = 0; + this.store = Ext.create('Ext.data.Store', { + fields : ['name', {name:'start', type : 'int'}, {name:'end', type : 'int'}], + data : buffers + + }); - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - _this.intensityPlotPanel.setPeaks(data); - _this._loadIntensityPlotByFrameNumber(frameNumber); - try{ - var peaks = []; - for(key in data){ - peaks.push({ - start : key.split("-")[0], - end : key.split("-")[1], - experimentId : _this.experiment.json.experimentId - }); + this.store.sort('start'); + + var type = 'Ext.grid.Panel'; + if (this.searchBar == true) { + type = 'Ext.ux.LiveSearchGridPanel'; + } + this.grid = Ext.create(type, { + store : this.store, + height : this.height, + width : this.width, + margin : 5, + columns : [ + { + text : '', + dataIndex : 'name', + width : 100, + hidden : _this.showExtendedColumns, + renderer : function(val, y, sample) { + if (sample.data.name == "BUFFER") + return "BUFFER"; + _this.peakCount++; + return "Peak #" + _this.peakCount; + } + + + }, + { + text : 'Peaks', + dataIndex : 'start', + sortable : true, + width : 100, + hidden: !_this.showExtendedColumns, + renderer : function(val, y, sample) { + return "From " + Number(sample.raw.start) + " to " + Number(sample.raw.end); + } + }, + { + text : 'Frames', + hidden : _this.showExtendedColumns, + columns : [ + { + text : 'Start', + dataIndex : 'start', + sortable : true, + hidden : _this.showExtendedColumns, + width : 100, + renderer : function(val, y, sample) { + return Number(val); + } + },{ + text : 'End', + dataIndex : 'end', + width : 100, + hidden : _this.showExtendedColumns, + renderer : function(val, y, sample) { + return Number(val); + } + },{ + text : 'Total', + dataIndex : 'end', + width : 100, + hidden : _this.showExtendedColumns, + renderer : function(val, y, sample) { + return "" + (sample.raw.end - sample.raw.start) + " frames"; + } + } + ] + } +// , +// { +// text : '', +// hidden : _this.showExtendedColumns, +// renderer : function(val, x, sample) { +// if (sample != null) { +// return BUI.getZipHTMLByFrameRangeId(sample.raw.experimentId, sample.raw.start, sample.raw.end); +// } +// }, +// width : 100 +// } + ], + flex : 1, + viewConfig : { + stripeRows : true, + getRowClass : function(record, rowIdx, params, store) { + if (record.raw.name == "BUFFER") { + return "blue-row"; + } } - _this.peakGrid2.refresh(JSON.parse(JSON.stringify(peaks))); - _this.peakGrid.refresh(peaks); -// console.log(peaks); - } - catch(e){ - showError(e); } }); - adapter.onError.attach(function(sender, data) { - _this.intensityPlotPanel.setLoading(false); + + /** Adding the tbar **/ + if (this.tbar) { + this.grid.addDocked({ + xtype : 'toolbar', + items : this._getTbar() + }); + } + return this.grid; +}; + +PeakGrid.prototype.input = function() { + return []; +}; + +PeakGrid.prototype.test = function(targetId) { + var PeakGrid = new PeakGrid({ + width : 800, + height : 350, + collapsed : false, + tbar : true }); - this.intensityPlotPanel.panel.setLoading("Reading HDF5 File "); - adapter.getH5FramesMerge(this.experiment.json.experimentId); + + var panel = PeakGrid.getPanel([]); + panel.render(targetId); }; + +/** + * Macromolecule Grid showing macromolecules and adding anb updating buttons + * + * @height + * @maxHeight + * @width + * @cssFontStyle + * @searchBar makes this grid as Ext.ux.LiveSearchGridPanel + * @tbar top bar containing "Add" and "Update From SMIS" button + * @collapsed + * @collapsible + * @btnEditVisible + * @btnRemoveVisible + * @multiselect makes it multiselect using Ext.selection.CheckboxModel + * + * #onSelected + * #onMacromoleculesChanged + */ +function MacromoleculeGrid(args) { + this.height = 500; + this.width = 500; + this.id = BUI.id(); + this.maxHeight = this.height; -HPLCTabs.prototype._postRenderOverviewPanel = function() { - var _this = this; - var adapter = new BiosaxsDataAdapter(); - adapter.onError.attach(function(sender, data) { - data = data.replace(/NaN/g, '0'); - _this.loadDataMainPlot(JSON.parse(data)); - + this.searchBar = false; + this.tbar = false; + + this.collapsible = true; + this.collapsed = true; + + this.btnEditVisible = true; + this.btnRemoveVisible = false; + this.multiselect = false; + + /** Font style applied to the acronym column **/ + this.cssFontStyle = null; + + if (args != null) { + if (args.height != null) { + this.height = args.height; + this.maxHeight = this.height; + } + if (args.maxHeight != null) { + this.maxHeight = args.maxHeight; + } + if (args.width != null) { + this.width = args.width; + } + if (args.cssFontStyle != null) { + this.cssFontStyle = args.cssFontStyle; + } + + if (args.searchBar != null) { + this.searchBar = args.searchBar; + } + if (args.tbar != null) { + this.tbar = args.tbar; + } + if (args.collapsible != null) { + this.collapsible = args.collapsible; + } + if (args.collapsed != null) { + this.collapsed = args.collapsed; + } + if (args.btnEditVisible != null) { + this.btnEditVisible = args.btnEditVisible; + } + if (args.btnRemoveVisible != null) { + this.btnRemoveVisible = args.btnRemoveVisible; + } + if (args.multiselect != null) { + this.multiselect = args.multiselect; + } + } - }); - adapter.onSuccess.attach(function(sender, data) { - _this.loadDataMainPlot(data); - _this._renderScatteringCurve(0); - }); - adapter.getH5fileParameters(this.experiment.json.experimentId, [ - "I0", "I0_Stdev", "sum_I","Rg", "Rg_Stdev", "Vc", "Vc_Stdev", "Qr", "Qr_Stdev", "mass", "mass_Stdev", "quality" ]); + this.onSelected = new Event(); -}; + this.onMacromoleculesChanged = new Event(); +} -HPLCTabs.prototype._postRenderDetailsPanel = function() { - if (this.data != null) { - this.I0PlotPanel.loadData(this.data); - this.RgPlotPanel.loadData(this.data); - this.MassPlotPanel.loadData(this.data); - this.VcPlotPanel.loadData(this.data); - } -}; -HPLCTabs.prototype.draw = function(experiment) { - var _this = this; - this.renderDataAcquisition(experiment); -}; -HPLCTabs.prototype.getExperimentTitle = function() { - var experimentHeaderForm = new ExperimentHeaderForm(); - return experimentHeaderForm.getPanel(this.experiment); -}; -HPLCTabs.prototype.renderDataAcquisition = function(experiment) { +MacromoleculeGrid.prototype.edit = function(macromolecule) { var _this = this; - this.experiment = experiment; - if (this.experimentPanel == null) { - this.experimentPanel = Ext.create('Ext.container.Container', { - bodyPadding : 2, - height : this.height, - width : Ext.getBody().getViewSize().width * 0.9, - renderTo : this.targetId, - style : { - padding : 2 - }, - items : [ this.getExperimentTitle(), this.getPanel() ], - listeners : { - afterrender : function() { - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - _this.analysisGrid.refresh(data); - }); - adapter.getAnalysisInformationByExperimentId(_this.experiment.experimentId); - } - } - }); - } - return this.experimentPanel; + var window = new MacromoleculeWindow(); + window.onSave.attach(function(sender) { + _this.store.loadData(BIOSAXS.proposal.getMacromolecules()); + _this.onMacromoleculesChanged.notify(); + }); + window.draw(macromolecule); }; -HPLCTabs.prototype.getPanel = function() { +MacromoleculeGrid.prototype.getTbar = function() { var _this = this; - this.panel = Ext.createWidget('tabpanel', - { - plain : true, - height : this.height, -// width : 900, - style : { - padding : 2 - }, - items : [ - { - tabConfig : { - title : "Overview" + var actions = []; - }, - items : [ { - xtype : 'container', - layout : 'hbox', - border : 1, - flex : 1, - items : [ { - xtype : 'container', - layout : 'vbox', - border : 1, - items : [ { - xtype : 'container', - margin : '10px', - border : 1, - items : [ - { - xtype : 'container', - margin : '0px', - layout : 'hbox', - border : 1, - items : [ - this.peakGrid2.getPanel([]), - this.mainPlotPanel.getPanel() - ] - }, - { - xtype : 'container', - layout : 'vbox', - border : 1, - items : [ - { - html: '
Select a frame by double-clicking on the HPLC Frames plot
', - margin: 5, - border : 0 - }, - this.frameGrid.getPanel([]), - this.intensityPlotPanel.getPanel() - ] - } - - ] - }], - listeners : { - afterrender : function() { - _this._postRenderOverviewPanel(); - } - } - } ] - } ] - }, -// { -// tabConfig : { -// title : "Details" -// }, -// items : [ { -// xtype : 'container', -// layout : 'hbox', -// border : 1, -// flex : 1, -// items : [ { -// xtype : 'container', -// layout : 'vbox', -// border : 1, -// items : [ { -// xtype : 'container', -// padding : '1px', -// items : [ -// this.I0PlotPanel.getPanel(), this.RgPlotPanel.getPanel(), this.MassPlotPanel.getPanel(), -// this.VcPlotPanel.getPanel() ] -// } ], -// listeners : { -// afterrender : function() { -// _this._postRenderDetailsPanel(); -// } -// } -// } ] -// } ] -// }, - { - tabConfig : { - title : "Analysis" - }, - items : [ { - xtype : 'container', - layout : 'vbox', - padding : '5px 0px 10px 10px', - items : [ _this.analysisGrid.getPanel([]) ] - } ] - }, - { - tabConfig : { - title : "File Manager" - }, - items : [ { - xtype : 'container', - layout : 'vbox', - padding : '5px 0px 10px 10px', - items : [ - { - html: '
Custom Download
', - margin : '10 0 10 5', - border : 0 - }, - { - html: '
Download has been temporary disabled. Contact your labcontact if you want to extract the frames from the HDF5 file
', - margin : '10 0 10 5', - hidden : _this.experiment.experimentId == 2602, - border : 0 - }, - { - xtype : 'container', - layout : 'hbox', - margin : '0 0 0 20', - flex : 1, - items :[ - { - xtype: 'numberfield', - id: 'field_start', - fieldLabel: 'Frames from', - value: 0, - minValue: 0 - }, - { - xtype: 'numberfield', - id: 'field_end', - fieldLabel: 'to', - labelWidth : 20, - margin : '0 0 0 10', - minValue: 0 - }, - { - xtype: 'button', - /** allowing test account to download frames **/ - disabled : _this.experiment.experimentId != 2602, - text : 'Download', - margin : '0 0 0 10', - handler : function() { - var experimentId = _this.experiment.experimentId; - var start = Ext.getCmp("field_start").getValue(); - var end = Ext.getCmp("field_end").getValue(); - /** Checking if start is bigger than end **/ - if (start > end){ - var aux = end; - end = start; - start = aux; - } - var url = BUI.getZipFrameHPLCUrl(experimentId, start, end); - window.open(url) - } - } - ] - }, - _this.peakGrid.getPanel([]) - - ] - } - ] - } - ] + actions.push(Ext.create('Ext.Action', { + icon : '../images/add.png', + text : 'Add macromolecule', + disabled : false, + handler : function(widget, event) { + _this.edit(); + } + })); + actions.push("->"); + actions.push(Ext.create('Ext.Action', { + icon : '../images/folder_go.png', + text : 'Update From SMIS', + tooltip : "Retrieve all the macromolecules of your proposal from SMIS database", + disabled : false, + handler : function(widget, event) { + _this.grid.setLoading("Connecting to SMIS"); + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + BIOSAXS.proposal.setMacromolecules(data.macromolecules); + _this.refresh(BIOSAXS.proposal.macromolecules); + _this.grid.setLoading(false); + }); + adapter.onError.attach(function(sender, data) { + _this.grid.setLoading(false); }); + adapter.updateDataBaseFromSMIS(); + } + })); + return actions; +}; - return this.panel; +MacromoleculeGrid.prototype.deselectAll = function() { + this.grid.getSelectionModel().deselectAll(); +}; + +MacromoleculeGrid.prototype.selectById = function(macromoleculeId) { + this.grid.getSelectionModel().deselectAll(); + for ( var i = 0; i < this.grid.getStore().data.items.length; i++) { + var item = this.grid.getStore().data.items[i].raw; + if (item.macromoleculeId == macromoleculeId) { + this.grid.getSelectionModel().select(i); + } + } +}; + +MacromoleculeGrid.prototype.refresh = function(macromolecules) { + this.store.loadData(macromolecules, false); +}; + +MacromoleculeGrid.prototype.getColumns = function() { + var _this = this; + var columns = [ + { + text : 'Acronym', + dataIndex : 'acronym', + id : this.id + "acronym", + flex : 1, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + if (_this.cssFontStyle != null) { + return "" + value + ""; + } + return value; + } + }, { + text : 'Name', + dataIndex : 'name', + id : this.id + "name", + flex : 1, + hidden : true + } ]; + + if (this.btnEditVisible) { + columns.push({ + id : _this.id + 'buttonEditMacromolecule', + width : 85, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + if (_this.btnEditVisible) { + return BUI.getGreenButton('EDIT'); + } + return null; + } + }); + } + if (this.btnRemoveVisible) { + columns.push({ + id : _this.id + 'buttonRemoveMacromolecule', + width : 85, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + if (_this.btnRemoveVisible) { + return BUI.getRedButton('REMOVE'); + } + return null; + } + }); + } + + return columns; +}; + + +/** Returns the grid **/ +MacromoleculeGrid.prototype.getPanel = function() { + var _this = this; + + this.store = Ext.create('Ext.data.Store', { + fields : [ 'macromoleculeId', 'name', 'acronym' ] + }); + + var type = 'Ext.grid.Panel'; + if (this.searchBar == true) { + type = 'Ext.ux.LiveSearchGridPanel'; + } + + this.selModel = Ext.create('Ext.selection.RowModel', { +// allowDeselect : true, +// mode : 'MULTI', + listeners : { + selectionchange : function(sm, selections) { + var selected = []; + for (var i = 0; i < selections.length; i++) { + selected.push(selections[i].raw); + } + _this.onSelected.notify(selected); + } + } + }); + + this.grid = Ext.create(type, { + id : this.id, + title : 'Macromolecules', + collapsible : this.collapsible, + collapsed : this.collapsed, + store : this.store, + height : this.height, + maxHeight : this.maxHeight, + selModel : this.selModel, + columns : this.getColumns(), + width : this.width, + viewConfig : { + stripeRows : true, + listeners : { + 'celldblclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + _this.edit(BIOSAXS.proposal.getMacromoleculeById(record.data.macromoleculeId)); + }, + 'cellclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEditMacromolecule') { + _this.edit(BIOSAXS.proposal.getMacromoleculeById(record.data.macromoleculeId)); + } + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemoveMacromolecule') { + BUI.showBetaWarning(); + } + } + + } + } + }); + + /** Adding the tbar **/ + if (this.tbar) { + this.grid.addDocked({ + xtype : 'toolbar', + items : this.getTbar() + }); + } + return this.grid; +}; + +MacromoleculeGrid.prototype.input = function() { + return { + proposal : DATADOC.getProposal_10() + }; +}; + +MacromoleculeGrid.prototype.test = function(targetId) { + var macromoleculeGrid = new MacromoleculeGrid({ + width : 800, + height : 350, + collapsed : false, + tbar : true + }); + + BIOSAXS.proposal = new Proposal(macromoleculeGrid.input().proposal); + var panel = macromoleculeGrid.getPanel(BIOSAXS.proposal.macromolecules); + panel.render(targetId); }; /** - * Main form tab for macromolecule + * Shows measurements with their attributes as specimen, exposure temperature, + * volume to load, transmission etc... * - * @width + * @addBtnMultipleEdit: if true add a button for changing measurements' + * parameters by choosing multiple measurements. It opens + * MultipleEditMeasurementGridWindow + * @collapsed: if true it doesn't show buffer's measurements + * @editor: hashmap containing columns to be edited. It is an array of a json + * like editor of Ext + * @selModel + * @collapseBtnEnable + * @removeBtnEnabled Ext.selection.RowModel + * @addBtnEnable + * @updateRowEnabled true/false if update plugin is set to the grid + * @showTitle + * @title + * @isStatusColumnHidden + * @isPriorityColumnHidden + * @isTimeColumnHidden + * @estimateTime + * @margin + * @tbar * @height + * @maxHeight + * @minHeight + * @width + * @maxWidth + * @resizable + * @experimentColorBased when colors for buffers and macromolecules are not + * selected by the proposal but by experiment, so the + * number of colors is smaller * - * #onClose when user clicks on close button in the MacromoleculeForm - * #onSave when macromole is saved by macromoleculeForm + * #onClick #onSelected #onRemoved #onUpdateTime #onMeasurementChanged + * #onExperimentChanged */ -function MacromoleculeTabs(args) { - this.width = 500; +function MeasurementGrid(args) { + this.id = BUI.id(); + this.height = 500; + this.width = 900; - if (args != null) { - if (args.width != null) { - this.width = args.width; + this.maxWidth = 1200; + this.maxHeight = 600; + this.minHeight = 500; + + this.unitsFontSize = 9; + this.title = "Measurements"; + this.estimateTime = false; + this.collapsed = true; + this.tbar = true; + + this.showTitle = true; + this.resizable = true; + this.updateRowEnabled = true; + + /** + * Hash map containing the keys of the editable columns. Ex: + * 'exposureTemperature' * + */ + this.editor = { + comments : { + xtype : 'textfield', + allowBlank : true } - if (args.height != null) { - this.height = args.height; + }; + + this.isTimeColumnHidden = false; + this.isStatusColumnHidden = false; + this.isPriorityColumnHidden = true; + this.margin = "0 0 0 0"; + + this.addBtnEnable = true; + this.sorter = [ { + property : 'priority', + direction : 'ASC' + } ]; + + this.removeBtnEnabled = false; + this.collapseBtnEnable = true; + this.addBtnMultipleEdit = false; + this.sortingBtnEnable = false; + + var _this = this; + this.selModel = Ext.create('Ext.selection.RowModel', { + allowDeselect : true, + mode : 'MULTI', + listeners : { + selectionchange : function(sm, selections) { + var selected = []; + for (var i = 0; i < selections.length; i++) { + selected.push(selections[i].raw); + } + _this.onSelected.notify(selected); + } } - } + }); - var _this = this; + if (args != null) { - /** Widgets **/ + if (args.selModel != null) { + this.selModel = args.selModel; + } - /** Macromolecule Form **/ - this.macromoleculeForm = new MacromoleculeForm({ - width : this.width - 30, - height : this.height - 50, - }); + if (args.removeBtnEnabled != null) { + this.removeBtnEnabled = args.removeBtnEnabled; + } - this.macromoleculeForm.onClose.attach(function(sender) { - _this.onClose.notify(); - }); + if (args.addBtnMultipleEdit != null) { + this.addBtnMultipleEdit = args.addBtnMultipleEdit; + } - this.macromoleculeForm.onSave.attach(function(sender, macromolecule) { - _this.onSave.notify(macromolecule); - }); + // if (args.experimentColorBased != null) { + // this.experimentColorBased = args.experimentColorBased; + // } - this.assemblyForm = new AssemblyForm({ - width : this.width - 30, - height : this.height - 50, - }); - - this.rigibBodyModelingForm = new RigibBodyModelingForm({ - width : this.width - 30, - height : this.height - 50, - }); - - this.rigibBodyModelingForm.onSave.attach(function(sender, macromolecule) { - _this.onSave.notify(macromolecule); - }); - + if (args.collapsed != null) { + this.collapsed = args.collapsed; + } + if (args.resizable != null) { + this.resizable = args.resizable; + } - /** Events **/ - this.onClose = new Event(this); - this.onSave = new Event(this); -} + if (args.editor != null) { + this.editor = args.editor; + } -/** Populate the widget **/ -MacromoleculeTabs.prototype.refresh = function(macromolecule) { - this.macromoleculeForm.refresh(macromolecule); - this.assemblyForm.refresh(macromolecule); - this.rigibBodyModelingForm.refresh(macromolecule); + if (args.collapseBtnEnable != null) { + this.collapseBtnEnable = args.collapseBtnEnable; + } - if (macromolecule != null){ - if (macromolecule.macromoleculeId == null){ - Ext.getCmp(this.id + "_advancedTab").disable(); - Ext.getCmp(this.id + "_assemblyTab").disable(); + if (args.addBtnEnable != null) { + this.addBtnEnable = args.addBtnEnable; } - else{ - Ext.getCmp(this.id + "_advancedTab").enable(); - Ext.getCmp(this.id + "_assemblyTab").enable(); + if (args.sortingBtnEnable != null) { + this.sortingBtnEnable = args.sortingBtnEnable; } - } - else{ - Ext.getCmp(this.id + "_advancedTab").disable(); - Ext.getCmp(this.id + "_assemblyTab").disable(); - } -}; -MacromoleculeTabs.prototype.getItems = function() { - return [ { - tabConfig : { - title : 'General' - }, - items : [ { - xtype : 'container', - items : [ this.macromoleculeForm.getPanel() ] - } ] - }, { - id : this.id + "_assemblyTab", - tabConfig : { - title : 'Assembly' - }, - items : [ { - xtype : 'container', - items : [ this.assemblyForm.getPanel() ] - } ] - },{ - id : this.id + "_advancedTab", - tabConfig : { - title : 'Advanced' - }, - items : [ this.rigibBodyModelingForm.getPanel() ] - } ]; -}; + if (args.isPriorityColumnHidden != null) { + this.isPriorityColumnHidden = args.isPriorityColumnHidden; + } -MacromoleculeTabs.prototype.getPanel = function() { - this.panel = Ext.createWidget('tabpanel', { - height : this.height, - width : this.width, - plain : true, - margin : 5, - border : 0, - items : this.getItems() - }); - return this.panel; -}; - -function ResultTabs() { -} + if (args.width != null) { + this.width = args.width; + } -ResultTabs.prototype.draw = function(targetId, data, macromoleculeId) { - var panel = this.getPanel(targetId, data, macromoleculeId); - return Ext.create('Ext.container.Container', { - renderTo : targetId, - items : [ BUI.getMacromoleculeHeader(macromoleculeId), panel ] - }); + if (args.updateRowEnabled != null) { + this.updateRowEnabled = args.updateRowEnabled; + } -}; + if (args.showTitle != null) { + this.showTitle = args.showTitle; + if (this.showTitle == false) { + this.title = null; + } + } -ResultTabs.prototype._splitBySpecimen = function(data) { - var splitted = {}; + if (args.height != null) { + this.height = args.height; + } - for ( var i = 0; i < data.length; i++) { - var row = data[i]; - if (splitted[row.macromoleculeId + "_" + row.bufferId] == null) { - splitted[row.macromoleculeId + "_" + row.bufferId] = []; + if (args.maxHeight != null) { + this.maxHeight = args.maxHeight; } - splitted[row.macromoleculeId + "_" + row.bufferId].push(row); - } - return splitted; -}; + if (args.minHeight != null) { + this.minHeight = args.minHeight; + } -ResultTabs.prototype._getTabTitle = function(key, data) { - var macromoleculeId = key.split("_")[0]; - var bufferId = key.split("_")[1]; + if (args.maxWidth != null) { + this.maxWidth = args.maxWidth; + } - return BIOSAXS.proposal.getMacromoleculeById(macromoleculeId).acronym + " + " + BIOSAXS.proposal.getBufferById(bufferId).acronym + "(" + data.length + ")"; -}; + if (args.isStatusColumnHidden != null) { + this.isStatusColumnHidden = args.isStatusColumnHidden; + } + if (args.isTimeColumnHidden != null) { + this.isTimeColumnHidden = args.isTimeColumnHidden; + } -ResultTabs.prototype.getPanel = function(targetId, data, macromoleculeId) { + if (args.title != null) { + this.title = args.title; + } + if (args.estimateTime != null) { + this.estimateTime = args.estimateTime; + } - var dataFiltered = new AnalysisGrid({ - hideNulls : true, - grouped : true, - sorters : [ { - property : 'quality', - direction : 'DESC' - } ] - })._prepareData(data); + if (args.margin != null) { + this.margin = args.margin; + } - var items = [ { - tabConfig : { - title : 'Analysis (' + dataFiltered.length + ')' - }, - items : [ { - xtype : 'container', - layout : 'vbox', - padding : 10, - items : [ new AnalysisGrid({ - isScatteringPlotVisible : false - }).getPanel(dataFiltered) ] - } ] - }, { - tabConfig : { - title : 'Concentration Effects' - }, - items : [ new ResultSummaryForm().getPanel(data) ] - } ]; + if (args.tbar != null) { + this.tbar = args.tbar; + } + + if (args.sorter != null) { + this.sorter = args.sorter; + } - var splitted = this._splitBySpecimen(dataFiltered); - for ( var key in splitted) { - items.push({ - tabConfig : { - title : this._getTabTitle(key, splitted[key]) - }, - items : [ new ResultSummaryForm().getPanel(splitted[key]) ] - }); } + this.onClick = new Event(this); + this.onSelected = new Event(this); + this.onRemoved = new Event(this); + this.onUpdateTime = new Event(this); + this.onMeasurementChanged = new Event(this); + this.onExperimentChanged = new Event(this); +} - this.panel = Ext.createWidget('tabpanel', { - style : { - padding : 2 - }, - items : items +MeasurementGrid.prototype._sortBy = function(sort) { + var _this = this; + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + _this.onExperimentChanged.notify(data); + _this.grid.setLoading(false); + // wizardWidget.window.close(); }); - return this.panel; - + adapter.onError.attach(function(sender, data) { + _this.grid.setLoading(false); + alert("Oops, there was a problem"); + }); + _this.grid.setLoading("Sorting"); + adapter.sortMeasurements(this.experiments.experiments[0].experimentId, sort); }; - - -function ShipmentTabs(targetId) { - this.targetId = targetId; +MeasurementGrid.prototype._getMenu = function() { var _this = this; - this.gridHeight = 500; - /** data **/ - this.shipment = null; - - /** Shipment Form **/ - this.shipmentForm = new ShipmentForm({ - creationMode : false, - showTitle : false - }); - this.shipmentForm.onSaved.attach(function(sender, data) { - _this.refresh(data); + if (this.tbar) { - }); + var items = []; + if (_this.addBtnEnable) { + items.push({ + icon : '../images/add.png', + text : 'Add measurements', + handler : function() { + _this._openAddMeasurementWindow(); + } + }); + } + if (_this.addBtnMultipleEdit) { + items.push({ + icon : '../images/Edit_16x16_01.png', + text : 'Multiple Edit', + handler : function() { + var multipleEditMeasurementGridWindow = new MultipleEditMeasurementGridWindow(); + multipleEditMeasurementGridWindow.onExperimentChanged.attach(function(sender, data) { + _this.onExperimentChanged.notify(data); + }); - /** Cases grid **/ - this.caseGrid = new CaseGrid({ - height : this.gridHeight - }); + multipleEditMeasurementGridWindow.draw(_this.measurements, _this.experiments); - this.caseGrid.onAddButtonClicked.attach(function(sender, dewar) { - _this.caseGrid.grid.setLoading("ISPyB: Creating a new case"); - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, shipment) { - /** updateing shipment on proposal **/ - for ( var i = 0; i < BIOSAXS.proposal.shippings.length; i++) { - if (BIOSAXS.proposal.shippings[i].shippingId == shipment.shippingId) { - BIOSAXS.proposal.shippings[i] = shipment; } - } - _this.refresh(shipment); - }); - adapter.onError.attach(function(sender, shipment) { - _this.caseGrid.grid.setLoading(false); - }); - adapter.addCase(_this.shipment.json.shippingId); - }); + }); + } - this.caseGrid.onRemoveButtonClicked.attach(function(sender, dewarId) { - _this.panel.setLoading("ISPyB: removing case"); - _this.shipment.onSaved.attach(function(sender, shipment) { - _this.refresh(shipment); + items.push("->"); - }); - _this.shipment.removeCase(dewarId); - }); -} + if (_this.sortingBtnEnable) { + var split = Ext.create('Ext.button.Split', { + text : 'Sort by', + // handle a click on the button itself + handler : function() { + // alert("The button was clicked"); + }, + menu : new Ext.menu.Menu({ + items : [ + { + text : 'First Created First Measured', + handler : function() { + _this._sortBy("FIFO"); + } + }, "-", { + text : 'Default', + handler : function() { + _this._sortBy("DEFAULT"); + } + } ] + }) + }); + items.push(split); + } -ShipmentTabs.prototype.refresh = function(shipment) { + if (_this.collapseBtnEnable) { + items.push({ + text : 'Collapse buffers', + enableToggle : true, + scope : this, + toggleHandler : function(item, pressed) { + this.collapsed = pressed; + this.grid.getStore().loadData(this._prepareData(this.measurements, this.experiments), false); + }, + pressed : this.collapsed + }); + } + var tb = Ext.create('Ext.toolbar.Toolbar', { + items : items + }); + return tb; + } + return null; +}; +/** Opens WizardWidget for adding new measurements * */ +MeasurementGrid.prototype._openAddMeasurementWindow = function(measurements, experiments) { var _this = this; - this.shipment = shipment; - var proposal = new Proposal(); - proposal.onDataRetrieved.attach(function(sender, plates) { - - _this.refreshWithPlates(shipment, plates); - _this.caseGrid.grid.setLoading(false); + var wizardWidget = new WizardWidget(); + wizardWidget.onFinished.attach(function(sender, result) { + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + _this.onExperimentChanged.notify(data); + _this.grid.setLoading(false); + wizardWidget.window.close(); + }); + wizardWidget.current.setLoading("ISPyB: Adding measurements"); + adapter.addMeasurements(result.name, "comments", result.data, _this.experiments.experiments[0].experimentId); }); - proposal.getPlatesByProposal(); + + wizardWidget.draw(null, new MeasurementCreatorStepWizardForm(BIOSAXS.proposal.getMacromolecules(), { + noNext : true + })); }; -ShipmentTabs.prototype.refreshWithPlates = function(shipment, plates) { - this.shipment = new Shipment(shipment); +/******************************************************************************* + * Opens WizardWidget for adding new measurements + * + * @Measurements + * @Experiments experimentList Object + ******************************************************************************/ +MeasurementGrid.prototype._prepareData = function(measurements, experiments) { + var data = []; + for (var i = 0; i < measurements.length; i++) { + var measurement = measurements[i]; + var specimen = experiments.getSampleById(measurement.specimenId); + var buffer = experiments.getBufferById(specimen.bufferId); + measurement.buffer_acronym = buffer.acronym; + measurement.bufferId = buffer.bufferId; + measurement.volume = specimen.volume; + if (specimen.macromolecule3VO != null) { + measurement.acronym = specimen.macromolecule3VO.acronym; + measurement.macromoleculeId = specimen.macromolecule3VO.macromoleculeId; + } + measurement.concentration = specimen.concentration; + if (measurement.run3VO != null) { + measurement.energy = measurement.run3VO.energy; + measurement.expExposureTemperature = measurement.run3VO.exposureTemperature; + measurement.storageTemperature = measurement.run3VO.storageTemperature; + measurement.timePerFrame = measurement.run3VO.timePerFrame; + measurement.radiationAbsolute = measurement.run3VO.radiationAbsolute; + measurement.radiationRelative = measurement.run3VO.radiationRelative; + measurement.status = "DONE"; - this.caseGrid.refresh(this.shipment.getDewars(), plates); - this.panel.setLoading(false); + try { + if (measurement.run3VO.timeStart != null) { + if (measurement.run3VO.timeStart != "") { + measurement.miliseconds = moment(measurement.run3VO.timeStart).format("X"); + } + } + } catch (E) { + console.log(E); + } + } + + if (experiments.getDataCollectionByMeasurementId(measurement.measurementId).length > 0) { + var measurementtodatacollection3VOs = experiments.getDataCollectionByMeasurementId(measurement.measurementId)[0].measurementtodatacollection3VOs; + for (var k = 0; k < measurementtodatacollection3VOs.length; k++) { + if (measurementtodatacollection3VOs[k].dataCollectionOrder == 1) { + var specimenBuffer = experiments.getSampleById(experiments.getMeasurementById(measurementtodatacollection3VOs[k].measurementId).specimenId); + if (specimenBuffer.sampleplateposition3VO != null) { + measurement.bufferSampleplateposition3VO = specimenBuffer.sampleplateposition3VO; + measurement.bufferSampleplate = (experiments.getSamplePlateById(specimenBuffer.sampleplateposition3VO.samplePlateId)); + } + } + } + } + + if (this.collapsed) { + /** If collapsed only the samples * */ + if (specimen.macromolecule3VO != null) { + data.push(measurement); + } + } else { + data.push(measurement); + } + + } + return data; }; -ShipmentTabs.prototype.error = function(error) { - var e = JSON.parse(error); - showError(e); - this.panel.setLoading(false); +/** + * Refresh data grid with the measurements and the experiments + * + * @measurements array with measurement3VO objects + * @experiments array with experiments objects + */ +MeasurementGrid.prototype.refresh = function(measurements, experiments) { + this.experiments = experiments; + this.measurements = measurements; + this.store.loadData(this._prepareData(measurements, experiments), false); }; -//ShipmentTabs.prototype.refreshTabTitles = function() { -/*Ext.getCmp("MacromoleculeTab").setText(this.getMacromoleculeTitle()); -Ext.getCmp("BufferTab").setText(this.getBuffersTitle()); -Ext.getCmp("SpecimenTab").setText(this.getSpecimenTitle()); -Ext.getCmp("PlatesTab").setText(this.getPlatesTitle()); -Ext.getCmp("AssembliesTab").setText(this.getShipmentTitle()); -Ext.getCmp("PlateGroupsTab").setText(this.getPlateGroupsTitle());*/ -//}; -ShipmentTabs.prototype.draw = function(shipment) { - var _this = this; - _this.plates = []; - _this.shipment = shipment; - _this.render(shipment); +/** + * Set status bar to busy (refreshing icon) + * + * @msg message to be displayed on the bar + */ +MeasurementGrid.prototype._showStatusBarBusy = function(msg) { + var statusBar = Ext.getCmp(this.id + 'basic-statusbar'); + statusBar.setStatus({ + text : msg, + iconCls : 'x-status-busy', + clear : false + }); +}; - // var proposal = new Proposal(); - // proposal.onDataRetrieved.attach(function(sender, plates){ - // _this.plates = plates; - // _this.shipment = shipment; - // _this.render(shipment); - // - // }); - // proposal.getPlatesByProposal(); +/** + * Set status bar to ready (ok icon) + * + * @msg message to be displayed on the bar + */ +MeasurementGrid.prototype._showStatusBarReady = function(msg) { + var statusBar = Ext.getCmp(this.id + 'basic-statusbar'); + statusBar.setStatus({ + text : msg, + iconCls : 'x-status-valid', + clear : false + }); }; -//ShipmentTabs.prototype.getShipmentTitle = function() { -// return 'Shipment'; -//}; +/** + * If updateRowEnabled returns an array with Ext.grid.plugin.RowEditing + */ +MeasurementGrid.prototype._getPlugins = function() { + var _this = this; + var plugins = []; + if (this.updateRowEnabled) { + plugins.push(Ext.create('Ext.grid.plugin.RowEditing', { + clicksToEdit : 1, + listeners : { + validateedit : function(grid, e) { + /** Setting values * */ + for ( var key in _this.editor) { + e.record.raw[key] = e.newValues[key]; + } + /** Comments are always updatable* */ + e.record.raw.comments = e.newValues.comments; -//ShipmentTabs.prototype.getMacromoleculeTitle = function() { -// return 'Macromolecules (' + this.experiment.getMacromolecules().length + ')'; -//}; + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, measurement) { + _this.onMeasurementChanged.notify(measurement); + _this.grid.setLoading(false); + }); + adapter.onError.attach(function() { + alert("Error"); + _this.grid.setLoading(false); + }); -//ShipmentTabs.prototype.getBuffersTitle = function() { -// return 'Buffers (' + this.experiment.getBuffers().length + ')'; -//}; + _this.grid.setLoading(); + adapter.saveMeasurement(e.record.raw, _this.experiments.experiments[0]); + } + } + })); + } + return plugins; +}; -//ShipmentTabs.prototype.getPlateGroupsTitle = function() { -// return 'Plate Groups (' + this.experiment.getPlateGroups().length + ')'; -//}; +/** + * @key name of the columns mathing the this.editor[key] + */ +MeasurementGrid.prototype._getEditor = function(key) { + if (this.editor[key] != null) { + return this.editor[key]; + } + return null; +}; -//ShipmentTabs.prototype.getSampleChangerTitle = function() { -// return 'Sample Changer'; -//}; +MeasurementGrid.prototype.getPanel = function(measurements, experiments) { + this.experiments = experiments; + this.measurements = measurements; + var _this = this; + this.store = Ext.create('Ext.data.Store', { + fields : [ { + name : 'miliseconds', + type : 'int' + }, 'priority', 'bufferId', { + name : 'exposureTemperature', + type : 'numeric' + }, 'volumeToLoad','code', 'transmission', 'viscosity', 'waitTime', 'flow', 'buffer_acronym', 'macromoleculeId', 'acronym', 'concentration', 'extraFlowTime', 'volume', 'energy', + 'expExposureTemperature', 'storageTemperature', 'timePerFrame', 'radiationAbsolute', 'radiationRelative', 'status', 'comments' ], + data : this._prepareData(measurements, experiments) + }); + this.store.sort(this.sorter); + var bbar = {}; + try { + bbar = Ext.create('Ext.ux.StatusBar', { + id : _this.id + 'basic-statusbar', + defaultText : 'Ready', + text : 'Ready', + iconCls : 'x-status-valid', + items : [] + }); + } catch (exp) { + console.log("bbar error"); + } -//ShipmentTabs.prototype.getSpecimenTitle = function() { -// return 'Specimens(' + this.experiment.getSpecimenCount() + ')'; -//}; + this.grid = Ext + .create( + 'Ext.grid.Panel', + { + id : this.id, + title : this.title, + store : this.store, + selModel : this.selModel, + plugins : this._getPlugins(), + resizable : this.resizable, + margin : this.margin, + maxHeight : this.maxHeight, + minHeight : this.minHeight, + maxWidth : this.maxWidth, + width : this.width, + tbar : this._getMenu(), + columns : [ + { + text : 'Order', + dataIndex : 'priority', + width : 50, + hidden : _this.isPriorityColumnHidden, + sortable : true -//ShipmentTabs.prototype.getPlatesTitle = function() { -// return 'Plates(' + this.experiment.getSamplePlates().length + ')'; -//}; + }, + { + text : 'Run Number', + dataIndex : 'code', + width : 50, + hidden : true, + sortable : true -//ShipmentTabs.prototype.getBuffersTip = function() { -/*if (this.experiment.getBuffers().length == 0){ - return BUI.getWarningHTML("There are no buffers. Click on add to create new ones. Click on edit button or double click to edit them"); - -} -else{ - return BUI.getTipHTML("Click on edit button or double click to edit them. Click on duplicate to create an identical buffer including its additives") -}*/ -//}; + }, -//ShipmentTabs.prototype.refreshTips = function() { -/*Ext.getCmp("BufferTabTip").update(this.getBuffersTip()); -Ext.getCmp("SpecimenTabTip").update(this.getSpecimensTip());*/ -//}; + { + text : 'Specimen', + columns : [ -ShipmentTabs.prototype.render = function(shipment) { - return this.getPanel(shipment); -}; + { + text : '', + dataIndex : 'macromoleculeId', + width : 30, + renderer : function(val, y, sample) { + if (val != null) { + if (_this.experiments == null) { + return BUI.getRectangleColorDIV(BIOSAXS.proposal.macromoleculeColors[val], 10, 10); + } else { + return BUI.getRectangleColorDIV(_this.experiments.macromoleculeColors[val], 10, 10); + } + } + }, + sortable : true + }, + { + text : 'Macromo.', + dataIndex : 'acronym', + width : 80, + renderer : function(val, y, sample) { + return val; + }, + sortable : true + }, + { + text : 'Conc. ', + dataIndex : 'concentration', + width : 80, + renderer : function(val, y, sample) { + if (sample.raw.macromoleculeId == null) { + return ""; + } + if (isNaN(val)) + return val; -ShipmentTabs.prototype.getShipmentHeader = function(shipment) { - var _this = this; - function getHTMLSource() { - var name = shipment.json.shippingName; - var status = shipment.json.shippingStatus; - var creationDate = shipment.json.creationDate; - var html = BUI.createFormLabel("Name :", name, 75, 400); - html = html + BUI.createFormLabel("Status :", status, 75, 400); - html = html + BUI.createFormLabel("Date :", creationDate, 75, 400); - return html; - } + if (val != 0) { + return BUI.formatValuesUnits(val, '', { + fontSize : 16, + decimals : 3, + unitsFontSize : this.unitsFontSize + }); + } else { + return; + } - return Ext.create('Ext.container.Container', { - frame : false, - layout : 'hbox', - title : 'General', - padding : 5, - bodyPadding : '5 5 0 0', - width : 890, - margin : '0 0 10 0', - height : 100, - style : { - borderColor : '#BDBDBD', - borderStyle : 'solid', - borderWidth : '1px' - }, - fieldDefaults : { - msgTarget : 'side', - labelWidth : 100 - }, - items : [ { - margin : "0 0 0 0", - width : 475, - border : 0, - html : getHTMLSource() - } - ] - }); -}; + }, + sortable : true + }, + { + text : '', + dataIndex : 'bufferId', + width : 30, + hidden : false, + renderer : function(val, y, sample) { + if (val != null) { + var color = '#FFCCFF'; + if (_this.experiments != null) { + var dc = _this.experiments.getDataCollectionByMeasurementId(sample.raw.measurementId); + if (dc != null) { + if (dc.length > 0) { + color = _this.experiments.getSpecimenColorByBufferId(_this.experiments + .getMeasurementById(dc[0].measurementtodatacollection3VOs[0].measurementId).specimenId); + } + } + } else { + color = BIOSAXS.proposal.bufferColors[val]; + } + return BUI.getRectangleColorDIV(color, 10, 10); + } + }, + sortable : true + }, + { + text : 'Buffer', + dataIndex : 'buffer_acronym', + width : 120, + renderer : function(val, y, sample) { + if (sample.raw.bufferSampleplateposition3VO != null) { + return BIOSAXS.proposal.getBufferById(sample.raw.bufferId).acronym + " Plate: [" + + sample.raw.bufferSampleplate.slotPositionColumn + ", " + + BUI.getSamplePlateLetters()[sample.raw.bufferSampleplateposition3VO.rowNumber - 1] + "-" + + sample.raw.bufferSampleplateposition3VO.columnNumber + "]"; + } + return val; + }, + sortable : true + }, { + text : 'Position', + width : 100, + hidden : true, + renderer : function(val, y, sample) { + if (_this.experiments != null) { + return BUI.getSamplePositionHTML(_this.experiments.getSampleById(sample.raw.specimenId), _this.experiments.experiments[0]); + } + } + } ] + }, + { + text : 'Parameters', + columns : [ + { + text : 'Ex. Flow. time (s)', + dataIndex : 'extraFlowTime', + width : 100, + hidden : true, + renderer : function(val, y, sample) { + return BUI.formatValuesUnits(val, 's', { + fontSize : 12, + decimals : 0, + unitsFontSize : this.unitsFontSize + }); + } + }, + { + text : 'Exp. Temp.', + dataIndex : 'exposureTemperature', + width : 70, + renderer : function(val, y, sample) { + if (Number(val)) { + return BUI.formatValuesUnits(val, 'C', { + fontSize : 12, + decimals : 2, + unitsFontSize : this.unitsFontSize + }); + } + return null; + }, + sortable : true, + editor : this._getEditor("exposureTemperature") + }, + { + text : 'Vol. Load', + dataIndex : 'volumeToLoad', + width : 60, + hidden : false, + editor : this._getEditor("volumeToLoad"), + renderer : function(val, y, sample) { + // return val+ " µl"; + return BUI.formatValuesUnits(val, 'µl', { + fontSize : 12, + decimals : 2, + unitsFontSize : this.unitsFontSize + }); + } + }, + { + text : 'Volume in Well', + dataIndex : 'volume', + hidden : true, + editor : this._getEditor("volume"), + width : 80, + renderer : function(val, y, sample) { + // return val + "(µl)"; + return BUI.formatValuesUnits(val, 'µl', { + fontSize : 12, + decimals : 2, + unitsFontSize : this.unitsFontSize + }); + } + }, + { + text : 'Trans.', + dataIndex : 'transmission', + width : 60, + editor : this._getEditor("transmission"), + renderer : function(val, y, sample) { + return BUI.formatValuesUnits(val, '%', { + fontSize : 12, + decimals : 0, + unitsFontSize : this.unitsFontSize + }); + } + }, + { + text : 'Wait T.', + dataIndex : 'waitTime', + editor : this._getEditor("waitTime"), + width : 50, + renderer : function(val, y, sample) { + // if (val != 0) { + return BUI.formatValuesUnits(val, 's', { + fontSize : 12, + decimals : 0, + unitsFontSize : this.unitsFontSize + }); + // } + } + }, + { + text : 'Flow', + dataIndex : 'flow', + editor : this._getEditor("flow"), + width : 50, + renderer : function(val, y, sample) { + if (val == true) { + return "yes"; + } + return null; + } + }, + { + text : 'Viscosity', + dataIndex : 'viscosity', + tooltip : 'The viscosity of a fluid is a measure of its resistance to gradual deformation by shear stress or tensile stress. For liquids, it corresponds to the informal notion of "thickness"', + editor : this._getEditor("viscosity"), + width : 50, + renderer : function(val, y, sample) { + return val; + } + } ] + }, { + text : 'Status', + dataIndex : 'status', + width : 50, + hidden : _this.isStatusColumnHidden, + renderer : function(val, y, sample) { + if (val != null) { + if (val == 'DONE') { + return "" + val + " "; + } + } + } + }, { + text : 'Time', + dataIndex : 'time', + width : 80, + hidden : _this.isTimeColumnHidden, + renderer : function(val, y, sample) { + if (sample.raw.run3VO != null) { + if (sample.raw.run3VO.timeStart != null) { + if (sample.raw.run3VO.timeStart != "") { + var m = moment(sample.raw.run3VO.timeStart); + return m.format("hh:mm:ss a"); + } + } + } + } + }, { + text : 'Energy', + dataIndex : 'energy', + width : 100, + hidden : true + }, { + text : 'Real Exp. Temp.(C)', + width : 100, + dataIndex : 'expExposureTemperature', + hidden : true + }, { + text : 'Storage Temp.(C)', + width : 100, + dataIndex : 'storageTemperature', + hidden : true + }, { + text : 'Time/Frame (s)', + width : 100, + dataIndex : 'timePerFrame', + hidden : true + }, { + text : 'Radiation Relative', + dataIndex : 'radiationRelative', + width : 100, + hidden : true + }, { + text : 'Radiation Absolute', + dataIndex : 'radiationAbsolute', + width : 100, + hidden : true + }, { + text : 'Comments', + dataIndex : 'comments', + flex : 1, + hidden : false, + editor : this._getEditor("comments") -ShipmentTabs.prototype.getTabPanel = function(shipment) { - this.panel = Ext.createWidget('tabpanel', { - height : 600, - style : { - padding : 2 - }, - items : [ { - tabConfig : { - id : 'Shipment', - title : 'Shipment', - icon : '/ispyb/images/plane-small.gif' - }, - items : [ { - xtype : 'container', - margin : '5 5 5 5', - items : [ this.shipmentForm.getPanel(shipment) ] - } ] - }, { - tabConfig : { - id : 'Cases', - title : 'Cases', - icon : '../images/box-icon-very-small.png' - }, - items : [ { - xtype : 'container', - margin : '5 5 5 5', - items : [ this.caseGrid.getPanel(shipment.getDewars(), this.plates) ] - } ] - } ] - }); - return this.panel; -}; + }, { + id : _this.id + 'buttonRemoveSample', + text : '', + hidden : !_this.removeBtnEnabled, + width : 100, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + if (record.raw.macromoleculeId != null) { + if (_this.removeBtnEnabled) { + return BUI.getRedButton('REMOVE'); + } + } + } + } ], + bbar : bbar, + viewConfig : { + stripeRows : true, + getRowClass : function(record, index, rowParams, store) { + if (record.data.status == "DONE") { + return 'green-row'; + } -ShipmentTabs.prototype.getPanel = function(shipment) { - var _this = this; - this.shipment = shipment; - if (this.plates == null) { - this.plates = []; - } + }, + listeners : { + 'itemclick' : function(grid, record, item, index, e, eOpts) { + _this.onClick.notify({ + specimen : record.raw + }); + }, + 'cellclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemoveSample') { + grid.getStore().removeAt(rowIndex); - if (this.shipPanel == null) { - this.shipPanel = Ext.create('Ext.container.Container', { - bodyPadding : 2, - width : Ext.getBody().getViewSize().width * 0.9, - renderTo : this.targetId, - style : { - padding : 2 - }, - items : [ this.getShipmentHeader(shipment), this.getTabPanel(shipment) ] - }); - } + if (record.raw.measurementId != null) { + /** For testing * */ + grid.setLoading("ISPyB: Removing measurement"); + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + grid.setLoading(false); + /** + * We get and refresh experiment + * because specimens has changed * + */ + var adapter2 = new BiosaxsDataAdapter(); + adapter2.onSuccess.attach(function(sender, experiment) { + _this.onRemoved.notify(experiment); + _this._showStatusBarReady('Ready'); + }); + if (_this.experiments.experiments[0].experimentId != null) { + adapter2.getExperimentById(_this.experiments.experiments[0].experimentId, "MEDIUM"); + _this._showStatusBarBusy("ISPyB: Removing Unused Specimens"); + } + }); - return this.shipPanel; -}; - -/** - * Shows an template with the specimens, measurements and the experiment's - * requirement - * - * @targetId - */ -function TemplateTabs(targetId) { - this.height = 600; - this.targetId = targetId; + adapter.onError.attach(function(sender, data) { + alert("Error: " + data); + grid.setLoading(false); + }); - this.id = BUI.id(); - var _this = this; + adapter.removeMeasurement(record.raw); + } + } - this.gridHeight = 1000; - /** data * */ - this.experiment = null; + } - this.specimenSelected = null; + } + } + }); - /** Specimen Widget contains a specimenGrid and a sampleChangerWidget than can be displayed with are vertical or horizontal layout **/ - this.specimenWidget = new SpecimenWidget({ - height : this.height - }); - - this.samplePlateGroupWidget = new SamplePlateGroupWidget({ - showTitle : false, - height : 250, - margin : 5, - bbar : true - }); - - this.samplePlateGroupWidget.onExperimentChanged.attach(function(sender, experiment) { - _this.refresh(experiment); - }); + this.grid.on("afterrender", function() { - this.samplePlateGroupWidget.onClick.attach(function(sender, args) { - }); + function updateTime() { + try { + _this.estimatedTime = _this.estimatedTime - 1; - this.volumePlanificator = new VolumeGrid(); + _this.onUpdateTime.notify({ + hours : (Number(_this.estimatedTime / 3600).toFixed()), + minutes : (Number((_this.estimatedTime / 60) % 60).toFixed()), + seconds : (Number(_this.estimatedTime % 60).toFixed()) - /** For Measurements * */ - var storeViscosity = Ext.create('Ext.data.Store', { - fields : [ 'name' ], - data : [ { - "name" : "low" - }, { - "name" : "medium" - }, { - "name" : "high" - } ] - }); + }); - // Create the combo box, attached to the states data store - var viscosityEditor = Ext.create('Ext.form.ComboBox', { - fieldLabel : '', - store : storeViscosity, - queryMode : 'local', - displayField : 'name', - valueField : 'name' - }); + if (Number(_this.estimatedTime) < 0) { + _this.timer = null; + grid.setTitle(_this.title); + } - this.measurementGrid = new MeasurementGrid({ - maxWidth : 1500, - estimateTime : false, - positionColumnsHidden : true, - isPriorityColumnHidden : true, - isStatusColumnHidden : true, - isTimeColumnHidden : true, - updateRowEnabled : true, - collapsed : true, - removeBtnEnabled : true, - showTitle : false, - collapseBtnEnable : false, - addBtnMultipleEdit : true, - sortingBtnEnable : true, - editor : { - exposureTemperature : { - xtype : 'textfield', - allowBlank : true - }, - comments : { - xtype : 'textfield', - allowBlank : true - }, - volumeToLoad : { - xtype : 'numberfield', - allowBlank : true - }, - transmission : { - xtype : 'numberfield', - allowBlank : true - }, - viscosity : viscosityEditor, - waitTime : { - xtype : 'numberfield', - allowBlank : true - }, - flow : { - xtype : 'checkbox', - allowBlank : true + } catch (e) { + console.log(e); + _this.timer = null; } } - }); - - this.measurementGrid.onSelected.attach(function(sender, measurements) { - var specimens = []; - for ( var i = 0; i < measurements.length; i++) { - specimens.push(_this.experiment.getSampleById(measurements[i].specimenId)); - } - }); - this.measurementGrid.onMeasurementChanged.attach(function(sender, measurement) { - _this.experiment.setMeasurement(measurement); - _this.refresh(_this.experiment); - }); + if (_this.estimateTime) { + var experimentList = _this.experiments; + var collected = experimentList.getMeasurementsCollected(); + if (collected.length > 0) { + if (collected[0].run3VO != null) { + try { + var end = collected[0].run3VO.timeEnd; + var start = collected[0].run3VO.timeStart; + var dstart = moment(start); + var dend = moment(end); + var seconds = Number(dend.diff(dstart) / 1000).toFixed(); - this.measurementGrid.onExperimentChanged.attach(function(sender, json) { - _this.refresh(new Experiment(json)); - }); + _this.estimatedTime = (seconds * experimentList.getMeasurementsNotCollected().length); - this.measurementGrid.onRemoved.attach(function(sender, experiment) { - _this.refreshSpecimen(new Experiment(experiment)); - }); + if (_this.estimatedTime > 0) { + updateTime(); + _this.timer = setInterval(function() { + updateTime(); + }, 1000); + } - this.measurementGrid.onUpdateTime.attach(function(sender, args) { - document.getElementById(_this.id + "_counter").innerHTML = args.hours + 'h, ' + args.minutes + 'min and ' + args.seconds + ' seconds'; + } catch (e) { + } + } + } + } }); - -} - -TemplateTabs.prototype.refreshMeasurement = function(experiment) { - this.experiment = experiment; - this.experiment.onSaved = new Event(this); - this.experiment.onSpecimenSaved = new Event(this); - var experimentList = new ExperimentList([ this.experiment ]); - this.measurementGrid.refresh(experimentList.getMeasurementsNotCollected(), experimentList); -}; -TemplateTabs.prototype.refreshSpecimen = function(experiment) { - this.experiment = experiment; - this.experiment.onSaved = new Event(this); - this.experiment.onSpecimenSaved = new Event(this); - this.samplePlateGroupWidget.refresh(this.experiment); - this.specimenWidget.refresh(this.experiment); - this.volumePlanificator.refresh(this.experiment); + return this.grid; }; -TemplateTabs.prototype.refresh = function(experiment) { - // var start = new Date().getTime(); - this.experiment = experiment; - this.experiment.onSaved = new Event(this); - this.experiment.onSpecimenSaved = new Event(this); - - // var experimentList = new ExperimentList([this.experiment]); - this.refreshMeasurement(experiment); - this.refreshSpecimen(experiment); - /** Refreshing grids * */ - this.panel.setLoading(false); - +/** Method for testing * */ +MeasurementGrid.prototype.input = function() { + var experiment = DATADOC.getExperiment_10(); + var measurements = DATADOC.getMeasurements_10(); + var proposal = DATADOC.getProposal_10(); + return { + experiment : experiment, + measurements : measurements, + proposal : proposal + }; }; -TemplateTabs.prototype.error = function(error) { - var e = JSON.parse(error); - showError(e); - this.panel.setLoading(false); +MeasurementGrid.prototype.test = function(targetId) { + var measurementGrid = new MeasurementGrid({ + tbar : true + }); + BIOSAXS.proposal = new Proposal(measurementGrid.input().proposal); + var panel = measurementGrid.getPanel(measurementGrid.input().measurements, new ExperimentList([ new Experiment(measurementGrid.input().experiment) ])); + panel.render(targetId); }; + +/** + * A shipment may contains one or more cases where stock solutions and sample + * plates are stored + * + * @height + * @btnEditVisible + * @btnRemoveVisible + * + * #onEditButtonClicked + */ +function MolarityGrid(args) { + this.height = 100; + this.width = 100; + + if (args != null) { + if (args.height != null) { + this.height = args.height; + } + if (args.width != null) { + this.width = args.width; + } + } + + var _this = this; + + this.molarityForm = new MolarityForm({height : 180, width : 455}); + + this.molarityForm.onSave.attach(function(sender){ + _this.molarityWindow.destroy(); + _this.updateProposal(); + + }); + + this.molarityForm.onClose.attach(function(sender){ + _this.molarityWindow.destroy(); + + }); + + /** Events * */ + this.onEditButtonClicked = new Event(this); +} + +MolarityGrid.prototype._getColumns = function() { + return [ { + text : 'Subunit', + columns : [ { + text : "Acronym", + width : 100, + hidden : false, + dataIndex : 'acronym', + sortable : true + }, { + text : "Name", + width : 125, + hidden : false, + dataIndex : 'name', + sortable : true + }, { + text : "MM Est.", + width : 100, + dataIndex : 'molecularMass', + sortable : true, + renderer : function(grid, cls, record){ + return BUI.formatValuesUnits(record.data.molecularMass , "Da", 10, 2); + + } + } ] + }, { +// text : "Number
in assymmetric units", + text : "Ratio", + width : 100, + dataIndex : 'ratio', + tooltip : 'Number of times the subunit is present in the macromolecule', + sortable : true + }, { + id : this.id + 'MOLARITY_REMOVE', + flex : 0.1, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + return BUI.getRedButton('REMOVE'); + } + } ]; +}; + +MolarityGrid.prototype._openMolarityWindow = function() { + this.molarityWindow = Ext.create('Ext.window.Window', { + title : 'Molarity', + height : 220, + width : 500, + modal : true, + items : [this.molarityForm.getPanel() ] + }).show(); +}; + +MolarityGrid.prototype._getButtons = function() { + var _this = this; + return [ { + text : 'Add subunit', + icon : '../images/add.png', + handler : function() { + _this._openMolarityWindow(); + } + }]; +}; + + +MolarityGrid.prototype.updateProposal = function() { + var _this = this; + this.panel.setLoading(); + BIOSAXS.proposal.onInitialized.attach(function() { + if (BIOSAXS.proposal != null) { + var macromolecules = BIOSAXS.proposal.macromolecules; + for (var i = 0; i < macromolecules.length; i++) { + + if (macromolecules[i].macromoleculeId == _this.macromolecule.macromoleculeId) { + _this.refresh(macromolecules[i]); + _this.panel.setLoading(false); + } + } + } + }); + BIOSAXS.proposal.init(); +}; + + +MolarityGrid.prototype.getPanel = function() { + var _this = this; + + this.molarityStore = Ext.create('Ext.data.Store', { + fields : [ 'acronym', 'ratio', 'comments', 'stoichiometryId', 'name', 'molecularMass' ], + sorters : { + property : 'ratio', + direction : 'DESC' + } + }); + + this.panel = Ext.create('Ext.grid.Panel', { + store : this.molarityStore, + height : this.height, + padding : 5, + columns : this._getColumns(), + listeners : { + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + + /** Remove entry * */ + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'MOLARITY_REMOVE') { + var dataAdapter = new BiosaxsDataAdapter(); + dataAdapter.onSuccess.attach(function(sender) { + _this.updateProposal(); + + }); + dataAdapter.removeStoichiometry(record.data.stoichiometryId); + _this.panel.setLoading("Removing Structure"); + } + } + }, + tbar : this._getButtons() + }); + return this.panel; +}; + +MolarityGrid.prototype._prepareData = function(macromolecule) { + /** Return an array of [{ratio,acronym, stoichiometryId, name}] **/ + var data = []; + if (macromolecule.stoichiometry != null) { + for (var i = 0; i < macromolecule.stoichiometry.length; i++) { + var hostMacromolecule = BIOSAXS.proposal.getMacromoleculeById(macromolecule.stoichiometry[i].macromoleculeId); + data.push({ + ratio : macromolecule.stoichiometry[i].ratio, + acronym : hostMacromolecule.acronym, + comments : hostMacromolecule.comments, + molecularMass : hostMacromolecule.molecularMass, + stoichiometryId : macromolecule.stoichiometry[i].stoichiometryId, + name : hostMacromolecule.name + }); + } + } + return data; +}; + +MolarityGrid.prototype.refresh = function(macromolecule) { + if (macromolecule != null){ + this.molarityStore.loadData(this._prepareData(macromolecule)); + this.molarityForm.refresh(macromolecule); + this.macromolecule = macromolecule; + } +}; + +MolarityGrid.prototype.input = function() { + return { + proposal : DATADOC.getProposal_10(), + dewars : DATADOC.getDewars_10() + + }; +}; + +MolarityGrid.prototype.test = function(targetId) { + var MolarityGrid = new MolarityGrid({ + height : 150 + }); + BIOSAXS.proposal = new Proposal(MolarityGrid.input().proposal); + var panel = MolarityGrid.getPanel(MolarityGrid.input().dewars); + panel.render(targetId); + +}; + + +/** + * Given data analysis parsed with ResultsAssemblyWidget makes a selector grid with buffer/protein + **/ +function SpecimenSelectorResultGrid() { + this.id = BUI.id(); +} -TemplateTabs.prototype.draw = function(experiment) { - this.render(experiment); +SpecimenSelectorResultGrid.prototype._prepareData = function(data) { + var parsed = []; + for ( var i = 0; i < data.length; i++) { + var row = data[i]; + for ( var j = 0; j < row.conditions.length; j++) { + parsed.push({ + bufferId : row.conditions[j].bufferId, + macromoleculeId : row.macromoleculeId, + macromoleculeAcronym : BIOSAXS.proposal.getMacromoleculeById(row.macromoleculeId).acronym, + bufferAcronym : BIOSAXS.proposal.getBufferById(row.conditions[j].bufferId).acronym + }); + } + } + return parsed; }; - -TemplateTabs.prototype.getExperimentTitle = function() { - var _this = this; - var experimentHeaderForm = new ExperimentHeaderForm(); - return experimentHeaderForm.getPanel(this.experiment); +SpecimenSelectorResultGrid.prototype.refresh = function(data) { + this.store.loadData(this._prepareData(data)); }; -TemplateTabs.prototype.render = function(experiment) { +SpecimenSelectorResultGrid.prototype.getPanel = function(data) { var _this = this; - this.experiment = experiment; + this.store = Ext.create('Ext.data.Store', { + fields : [ 'macromoleculeId', 'bufferId', 'macromoleculeAcronym', 'bufferAcronym', 'concentration' ], + data : this._prepareData(data), + groupField : 'macromoleculeAcronym' + }); - /** - * - * Depending on the sample Changer configuration we want to display the plates vertically or horizontally - * Default is vertical - * - * */ - - var specimenContainer = this.specimenWidget.getPanel(); - this.specimenWidget.refresh(experiment); - - var experimentList = new ExperimentList([ _this.experiment ]); - var measurementContainer = Ext.create('Ext.container.Container', { - layout : { - type : 'vbox' - }, - defaults : { - style : { - padding : '5px 0px 0px 10px' + this.store.sort('concentration'); + this.grid = Ext.create('Ext.grid.Panel', { + id : this.id, + store : this.store, + width : this.width, + height : this.height, + maxHeight : this.maxHeight, + border : 1, + features : [ { + ftype : 'grouping', + groupHeaderTpl : '{name}', + hideGroupedHeader : true, + startCollapsed : false + } ], + selModel : Ext.create('Ext.selection.CheckboxModel', { + allowDeselect : true, + mode : 'MULTI', + listeners : { + selectionchange : function(sm, selections) { + _this.selected = []; + for ( var i = 0; i < selections.length; i++) { + _this.selected.push(selections[i].raw); + } + } } - }, - items : [ _this.measurementGrid.getPanel(experimentList.getMeasurementsNotCollected(), experimentList) ] + }), + margin : 10, + sortableColumns : true, + columns : [ { + text : 'Macromolecule', + dataIndex : 'macromoleculeAcronym', + flex : 1 + }, { + text : '', + dataIndex : 'bufferId', + width : 20, + hidden : false, + renderer : function(val, y, sample) { + return BUI.getRectangleColorDIV(BIOSAXS.proposal.bufferColors[val], 10, 10); + } + }, { + text : 'Buffer', + dataIndex : 'bufferAcronym', + flex : 1 + }, { + text : 'Concentration', + dataIndex : 'concentration', + flex : 1, + renderer : function(val, y, sample) { + return val + " mg/ml"; + } + } ] }); - this.panel = Ext - .createWidget( - 'tabpanel', - { - plain : true, - items : [ - { - tabConfig : { - title : 'Measurements' - }, - items : [ { - xtype : 'container', - layout : 'vbox', - border : 1, -// height : _this.gridHeight, - margin : "0 0 10 0", - items : [ measurementContainer ] - } - - ] - }, - { - tabConfig : { - id : 'genralTabl', - title : "Specimens" - // width : 900, - // border : 3 - - }, - items : [ specimenContainer ] - }, - { - tabConfig : { - title : "Requirements" + /** Adding the tbar **/ + if (this.tbar) { + this.grid.addDocked({ + xtype : 'toolbar', + items : this.getTbar() + }); + } + return this.grid; +}; - }, - items : [ - { - html : BUI.getTipHTML("Estimated volume is the maximum volume required. Depending on the order of your measurements you may use less. Click on create stock solutions if you plan to ship these stock solutions"), - margin : "10 10 10 10", - border : 0 - }, this.volumePlanificator.getPanel(experiment) ] - } ] - }); - // ); - return this.getPanel(this.panel); +SpecimenSelectorResultGrid.prototype.input = function() { + return { + data : new ResultsAssemblyGrid()._prepareData(new ResultsAssemblyGrid().input().data), + proposal : new ResultsAssemblyGrid().input().proposal + }; }; -TemplateTabs.prototype.isTemplate = function() { - if (this.experiment.json.type == "TEMPLATE") { - return true; - } - return false; +SpecimenSelectorResultGrid.prototype.test = function(targetId) { + var specimenSelectorResultGrid = new SpecimenSelectorResultGrid(); + BIOSAXS.proposal = new Proposal(specimenSelectorResultGrid.input().proposal); + var panel = specimenSelectorResultGrid.getPanel(specimenSelectorResultGrid.input().data); + panel.render(targetId); }; +/** + * Show all buffer conditions for each macromolecules pointing out the measurements quality + * + * @height + * @maxHeight + * @width + * @searchBar + * @tbar + * @btnResultVisible + * + * #onClick + */ +function ResultsAssemblyGrid(args) { + this.height = 500; + this.id = BUI.id(); + this.maxHeight = this.height; -TemplateTabs.prototype.getPanel = function(panel) { - var _this = this; - if (this.experimentPanel == null) { - this.experimentPanel = Ext.create('Ext.container.Container', { - bodyPadding : 2, - width : 1000,//Ext.getBody().getViewSize().width * 0.9, - renderTo : this.targetId, - height : 500, -// style : { -// padding : 2 -// }, - items : [ - this.getExperimentTitle(), - this.panel - ], - listeners : { - afterrender : function(thisCmp) { - $("#SchemeReport" + _this.experiment.experimentId).click(function() { - $(this).target = "_blank"; - window.open('viewProjectList.do?reqCode=display&menu=platescheme&experimentId=' + _this.experiment.experimentId); - return false; - }); + this.width = 900; + this.searchBar = false; + this.tbar = false; + this.btnResultVisible = false; - } - } - }); - } - return this.experimentPanel; -}; + /** For processing **/ + this.processed = {}; + this.renderedPlotIndex = 0; -TemplateTabs.prototype.input = function(targetId) { - return new ExperimentTabs().input(); -}; + this.plotWidth = 210; + this.plotHeight = 80; -TemplateTabs.prototype.test = function(targetId) { - var experimentTabs = new TemplateTabs(targetId); - BIOSAXS.proposal = new Proposal(experimentTabs.input().proposal); - experimentTabs.draw(new Experiment(experimentTabs.input().experiment)); -}; - -var BUI = { - //interval : 60000, - interval : 40000, - rainbow : function(numOfSteps, step) { - // This function generates vibrant, "evenly spaced" colours (i.e. no clustering). This is ideal for creating easily distinguishable vibrant markers in Google Maps and other apps. - // Adam Cole, 2011-Sept-14 - // HSV to RBG adapted from: http://mjijackson.com/2008/02/rgb-to-hsl-and-rgb-to-hsv-color-model-conversion-algorithms-in-javascript - var r, g, b; - var h = step / numOfSteps; - var i = ~~(h * 6); - var f = h * 6 - i; - var q = 1 - f; - switch (i % 6) { - case 0: - r = 1, g = f, b = 0; - break; - case 1: - r = q, g = 1, b = 0; - break; - case 2: - r = 0, g = 1, b = f; - break; - case 3: - r = 0, g = q, b = 1; - break; - case 4: - r = f, g = 0, b = 1; - break; - case 5: - r = 1, g = 0, b = q; - break; + /** Colors **/ + this.validColor = BUI.getValidColor(); + this.warningColor = BUI.getWarningColor(); + this.notValidColor = BUI.getErrorColor(); + + /** Show warning if guinier quality less than **/ + this.guinierQuality = BUI.getQualityThreshold(); + this.framePercentageThreshold = BUI.getRadiationDamageThreshold(); + + if (args != null) { + if (args.height != null) { + this.height = args.height; + this.maxHeight = this.height; } - var c = "#" + ("00" + (~~(r * 255)).toString(16)).slice(-2) + ("00" + (~~(g * 255)).toString(16)).slice(-2) - + ("00" + (~~(b * 255)).toString(16)).slice(-2); - return (c); - }, - getFileNameByPath : function(filePath) { - if (filePath != null){ - var split = filePath.split("/"); - if (split.length > 0){ - return split[split.length - 1]; - } + if (args.maxHeight != null) { + this.maxHeight = args.maxHeight; + } + if (args.width != null) { + this.width = args.width; + } + if (args.searchBar != null) { + this.searchBar = args.searchBar; } - return "Not file"; - }, - getUpdateInterval : function() { - this.interval = this.interval + 2000; - return this.interval; - }, - getRadiationDamageThreshold : function() { - return 0.7; - }, - getQualityThreshold : function() { - return 0.7; - }, - getCreateShipmentURL : function() { - return '/ispyb/user/viewProjectList.do?reqCode=display&menu=create_shipment'; - }, - getCreateShipmentList : function() { - return '/ispyb/user/viewProjectList.do?reqCode=display&menu=list_shipment'; - }, - getShippingURL : function(shippingId) { - return '/ispyb/user/viewProjectList.do?reqCode=display&menu=shipment&shippingId=' + shippingId; - }, - getMacromoleculeResultsURLByMultipleSearch : function(array) { - return '/ispyb/user/viewProjectList.do?reqCode=display&menu=macromolecule&search=' - + JSON.stringify(array).replace(new RegExp("\"", 'g'), "'"); - }, - getMacromoleculeResultsURL : function(macromoleculeId) { - return '/ispyb/user/viewProjectList.do?reqCode=display&menu=macromolecule¯omoleculeId=' + macromoleculeId; - }, - getMacromoleculeBufferResultsURL : function(macromoleculeId, bufferId) { - return '/ispyb/user/viewProjectList.do?reqCode=display&menu=macromolecule&bufferId=' + bufferId + '¯omoleculeId=' + macromoleculeId; - }, + if (args.tbar != null) { + this.tbar = args.tbar; + } + if (args.btnResultVisible != null) { + this.btnResultVisible = args.btnResultVisible; + } - getMacromoleculeHeader : function(macromoleculeId) { + } - function getHTMLSource(macromoleculeId) { - if (macromoleculeId != null) { - var html = BUI.createFormLabel("Name :", BIOSAXS.proposal.getMacromoleculeById(macromoleculeId).name, 75, 400); - html = html + BUI.createFormLabel("Acronym :", BIOSAXS.proposal.getMacromoleculeById(macromoleculeId).acronym, 75, 400); - if (BIOSAXS.proposal.getMacromoleculeById(macromoleculeId).comments != null) { - html = html + BUI.createFormLabel("Comments :", BIOSAXS.proposal.getMacromoleculeById(macromoleculeId).comments, 75, 400); - } - return html; - } - } + this.onClick = new Event(); +} - return Ext.create('Ext.container.Container', { - frame : false, - layout : 'hbox', - title : 'Macromolecule', - bodyPadding : '5', - width : 890, - margin : '0 0 10 0', - height : 100, - style : { - borderColor : '#BDBDBD', - borderStyle : 'solid', - borderWidth : '1px' - }, - fieldDefaults : { - msgTarget : 'side', - labelWidth : 100 - }, - items : [ { - margin : "10 0 0 10", - width : 475, - border : 0, - html : getHTMLSource(macromoleculeId) - }, { - margin : "10 0 0 10", - width : 475, - border : 0, - html : BUI.getZipHTMLByMacromoleculeId(macromoleculeId) - } - ] - }); - }, +ResultsAssemblyGrid.prototype.edit = function(macromoleculeId) { + var _this = this; + var window = new MacromoleculeWindow(); + window.onSuccess.attach(function(sender, proposal) { + _this.store.loadData(_this._prepareData(BIOSAXS.proposal.getMacromolecules())); + }); + window.draw(BIOSAXS.proposal.getMacromoleculeById(macromoleculeId)); +}; - getZipHTMLByMacromoleculeId : function(macromoleculeId) { - if (macromoleculeId != null) { - var fileName = BIOSAXS.proposal.getMacromoleculeById(macromoleculeId).acronym; - return ""; - } - }, - getZipHTMLByExperimentId : function(experimentId, filename) { - if (filename == null){ - filename = "experiment"; - } - return ""; - }, - - getZipURLByAverageId : function(averageId, filename) { - if (filename == null){ - filename = "experiment"; - } - return "/ispyb/user/dataadapter.do?reqCode=getZipFileByAverageListId&f&mergeIdsList=" + averageId + "&fileName=" + filename; - }, - getZipURLBySubtractionId : function(subtractionId, filename) { - if (filename == null){ - filename = "experiment"; +ResultsAssemblyGrid.prototype.getTbar = function() { + var _this = this; + var actions = []; + + actions.push(Ext.create('Ext.Action', { + icon : '../images/add.png', + text : 'Add Macromolecule', + disabled : false, + handler : function(widget, event) { + var window = new MacromoleculeWindow(); + window.onSuccess.attach(function(sender) { + _this.refresh(); + }); + window.draw({}); } - return "/ispyb/user/dataadapter.do?reqCode=getZipFileByAverageListId&f&subtractionIdList=" + subtractionId + "&fileName=" + filename; - }, - - - getZipHTMLByFrameRangeId : function(experimentId, start, end) { - var fileName = "experiment"; - return ""; - }, - getZipFrameHPLCUrl : function(experimentId, start, end) { - return "/ispyb/user/dataadapter.do?reqCode=getZipFileH5ByFramesRange&f&experimentId=" + experimentId + "&start=" + Number(start) +"&end="+ Number(end); - }, - - getQueueUrl : function() { - return "/ispyb/user/dataadapter.do?reqCode=getPagingCompactAnalysisByProposalId"; - }, - - getQueueUrlByExperiment: function(experimentId) { - return "/ispyb/user/dataadapter.do?reqCode=getPagingCompactAnalysisByExperimentId&f&experimentId=" + experimentId; - }, - getStandardDeviation : function(values) { - var sum = 0; - var count = 0; - var avg = null; + })); + + actions.push(Ext.create('Ext.Action', { + icon : '../images/add.png', + text : 'Define an Assembly', + disabled : false, + handler : function(widget, event) { + var createAssemblywindow = new CreateAssemblyWindow(); + createAssemblywindow.onSaved.attach(function(evt, args) { + if (args.macromoleculeIds.length > 0) { + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, proposal) { + _this.refresh(); + }); + adapter.saveAssembly(args.assemblyId, args.macromoleculeIds); - var curatedValues = new Array(); - for ( var i = 0; i < values.length; i++) { - var value = values[i]; - if (value != null) { - if (!isNaN(value)) { - count = count + 1; - sum = sum + Number(value); - curatedValues.push(Number(value)); } - } - } - if (count > 0) { - avg = sum / count; - } else { - avg = sum; - } - var aux = 0; - for ( var i = 0; i < curatedValues.length; i++) { - var value = curatedValues[i]; - aux = aux + Math.pow(value - avg, 2); + }); + createAssemblywindow.draw(_this.experiment); } - /** std **/ - var std = Math.sqrt(aux / count); + })); + + return actions; +}; + +ResultsAssemblyGrid.prototype.refresh = function() { + this.store.loadData(this._prepareData()); +}; + +ResultsAssemblyGrid.prototype.addCondition = function(record, data_parsed, i) { + function getCondition(record) { return { - std : (std), - sum : (sum), - avg : (avg), - validNumber : count, - totalNumber : values.length, - values : values + concentration : record.conc, + quality : record.quality, + bufferBeforeFramesMerged : record.bufferBeforeFramesMerged, + bufferAfterFramesMerged : record.bufferAfterFramesMerged, + framesCount : record.framesCount, + framesMerge : record.framesMerge }; - }, - - getHTMLTableForFrameAveraged : function(bufferAcronym, macromoleculeAcronym, bbmerges, molmerges, bamerges, totalframes, bufferId,macromoleculeId, macromoleculeColor) { - - function getFrameSpan(framesMerged, total) { - return "(" + framesMerged + " of " + total + ")"; - } + } - function getColorFrame(framesMerged, total) { - if (framesMerged / total < 0.5) { - return "#FA5858"; - } - if ((framesMerged / total >= 0.5) && (framesMerged / total < 0.8)) { - return "#FF9900"; + if (data_parsed[i].conditions != null) { + var bufferFound = false; + for ( var index in data_parsed[i].conditions) { + condition = data_parsed[i].conditions[index]; + + if ((condition.macromoleculeId == record.macromoleculeId) && (condition.bufferId == record.bufferId)) { + data_parsed[i].conditions[index].concentrations.push(getCondition(record)); + bufferFound = true; } - return "white"; } - - function getRow(color, acroynm, framesMerged, totalframes) { - return " " - + BUI.getRectangleColorDIV(color, 10, 10) - + " " + acroynm + "" - + getFrameSpan(framesMerged, totalframes) + ""; + if (!bufferFound) { + data_parsed[i].conditions.push({ + macromoleculeId : record.macromoleculeId, + bufferId : record.bufferId, + concentrations : [ getCondition(record) ] + }); } + } +}; - var html = ""; +ResultsAssemblyGrid.prototype.process = function(record, data_parsed) { + if (this.processed[record.macromoleculeId] == null) { + this.processed[record.macromoleculeId] = true; + record.measurementCount = 1; + record.subtractionCount = 1; + record.averageCount = 1; + record.conditions = []; + data_parsed.push(record); + } - /** Buffer Before **/ - if (bufferAcronym != null) { - if (bbmerges != null) { - color = BIOSAXS.proposal.bufferColors[bufferId]; - html = html + getRow(color, bufferAcronym, bbmerges, totalframes); + for ( var i = 0; i < data_parsed.length; i++) { + if (data_parsed[i].macromoleculeId == record.macromoleculeId) { + data_parsed[i].measurementCount = data_parsed[i].measurementCount + 1; + + if (record.subtractionId != null) { + data_parsed[i].subtractionCount = data_parsed[i].subtractionCount + 1; + this.addCondition(record, data_parsed, i); } - } - /** Molecule **/ - if (macromoleculeAcronym != null) { - if (molmerges != null) { - if (macromoleculeColor == null){ - color = BIOSAXS.proposal.macromoleculeColors[macromoleculeId]; - } - else{ - color = macromoleculeColor; //BIOSAXS.proposal.macromoleculeColors[macromoleculeId]; + if (record.framesMerge != null) { + data_parsed[i].averageCount = data_parsed[i].averageCount + 1; + } + + if (record.timeStart != null) { + if (data_parsed[i].timeStart != null) { + if (moment(data_parsed[i].timeStart).format("X") > moment(record.timeStart).format("X")) { + data_parsed[i].timeStart = record.timeStart; + } } - html = html + getRow(color, macromoleculeAcronym, molmerges, totalframes); } } + } - /** Buffer After **/ - if (bufferAcronym != null) { - if (bamerges != null) { - color = BIOSAXS.proposal.bufferColors[bufferId]; - html = html + getRow(color, bufferAcronym, bamerges, totalframes); + return data_parsed; + +}; + +ResultsAssemblyGrid.prototype._prepareData = function(data) { + var data_parsed = []; + for ( var i = 0; i < data.length; i++) { + data_parsed = this.process(data[i], data_parsed); + } + this.data = data_parsed; + return data_parsed; +}; + +/** Given an array of conditions it returns distinct(concentrations) order by concentration and hash map with number of ocurrences**/ +ResultsAssemblyGrid.prototype.parseConcentrations = function(val, conditions, differentConcentration, quality) { + var conditions = []; + var differentConcentration = {}; + var quality = []; + for ( var i = 0; i < val.length; i++) { + var conc = Number(val[i].concentration).toFixed(1); + var quality = Number(val[i].quality).toFixed(2); + if (differentConcentration[conc] == null) { + differentConcentration[conc] = 0; + conditions.push({ + concentration : conc, + quality : [ quality ], + frames : [ { + bufferAfterFramesMerged : val[i].bufferAfterFramesMerged, + bufferBeforeFramesMerged : val[i].bufferBeforeFramesMerged, + framesMerge : val[i].framesMerge, + framesCount : val[i].framesCount + } ] + }); + } else { + /** Add quality **/ + for ( var j = 0; j < conditions.length; j++) { + if (conditions[j].concentration == conc) { + conditions[j].quality.push(quality); + conditions[j].frames.push({ + bufferAfterFramesMerged : val[i].bufferAfterFramesMerged, + bufferBeforeFramesMerged : val[i].bufferBeforeFramesMerged, + framesMerge : val[i].framesMerge, + framesCount : val[i].framesCount + }); + } } } - return html + "
"; - }, - isWebGLEnabled : function(return_context) { - if (!!window.WebGLRenderingContext) { - var canvas = document.createElement("canvas"); - names = [ "webgl", "experimental-webgl", "moz-webgl", "webkit-3d" ]; - context = false; - for ( var i = 0; i < 4; i++) { - try { - context = canvas.getContext(names[i]); - if (context && typeof context.getParameter == "function") { - // WebGL is enabled - if (return_context) { - // return WebGL object if the function's argument is present - return { - name : names[i], - gl : context - }; - } - // else, return just true - return true; - } - } catch (e) { - } + + differentConcentration[conc] = differentConcentration[conc] + 1; + } + /** sorting concentrations **/ + conditions.sort(function(a, b) { + return a.concentration - b.concentration; + }); + return { + concentrations : conditions, + differentConcentration : differentConcentration + }; +}; + +ResultsAssemblyGrid.prototype.getConditionWarnings = function(condition) { + + var withWarnings = 0; + + for ( var i = 0; i < condition.frames.length; i++) { + if (condition.quality[i] == null) { + withWarnings = withWarnings + 1; + continue; + } else { + if (Number(condition.quality[i]) < this.guinierQuality) { + withWarnings = withWarnings + 1; + continue; } - // WebGL is supported, but disabled - return false; } - // WebGL not supported28. - return false; - }, - getHTMLTableForPrefixes : function(bufferBeforeaverageFilePath, averageFilePath, bufferAfterAverageFilePath) { - function getRow(bufferBeforeaverageFilePath) { - file = bufferBeforeaverageFilePath; - try { - file = bufferBeforeaverageFilePath.split("/")[bufferBeforeaverageFilePath.split("/").length - 1]; - } catch (e) { - file = "NA"; + if (condition.frames[i].bufferBeforeFramesMerged / condition.frames[i].framesCount < this.framePercentageThreshold|| condition.frames[i].framesMerged / condition.frames[i].framesCount < this.framePercentageThreshold|| condition.frames[i].bufferAfterFramesMerged / condition.frames[i].framesCount < this.framePercentageThreshold) { + withWarnings = withWarnings + 1; + continue; + } + } + + return { + withWarnings : withWarnings, + withoutWarnings : condition.frames.length - withWarnings + }; +}; + +ResultsAssemblyGrid.prototype.getFrameHTMLTable = function(warnings) { + var html = ""; + if (warnings.withWarnings > 0) { + html = html + "
" + warnings.withWarnings + + "x
"; + } + + if (warnings.withoutWarnings > 0) { + html = html + "
" + warnings.withoutWarnings + + "x
"; + } + return html; +}; + +ResultsAssemblyGrid.prototype.createConcentrationRow = function(numberOcu, condition, warnings){ + var html = ""; + if (numberOcu > 1){ + html = html + "" +numberOcu + "x " + BUI.formatConcentration(condition.concentration); + } + else{ + html = html + BUI.formatConcentration(condition.concentration); + } + html = html + ""; + html = html + this.getFrameHTMLTable(warnings); + ""; + html = html + ""; + return html; +}; + + +ResultsAssemblyGrid.prototype.getConditionHTMLTable = function(val, style, record) { + var maxNumberColumns = 2; + var html = "
"; + var nColumns = 0; + for ( var r = 0; r < val.length; r++) { + if (nColumns == maxNumberColumns) { + nColumns = 0; + html = html + ""; + } + html = html + ""; } - var html = "
"; + var value = val[r]; + + var bufferAcronym = (BIOSAXS.proposal.getBufferById(value.bufferId).acronym); + + var parsed = (this.parseConcentrations(value.concentrations)); + var conditions = parsed.concentrations; + var differentConcentration = parsed.differentConcentration; + + /** Checking warnings **/ + var warnings = []; + var concentrationValidPerconcentration = 0; + var measurements = 0; + for ( var i = 0; i < conditions.length; i++) { + measurements = measurements + conditions[i].frames.length; + var warning = this.getConditionWarnings(conditions[i]); + warnings.push(warning); + if (warning.withoutWarnings > 0) { + concentrationValidPerconcentration = concentrationValidPerconcentration + 1; } - return "
" + file + "
"; - /** Buffer Before **/ - if (bufferBeforeaverageFilePath != null) { - html = html + getRow(bufferBeforeaverageFilePath); - } + this.validColor = '#E0F8E0'; + this.warningColor = '#F5DA81'; + this.notValidColor = '#F6CED8'; - /** Molecule **/ - if (averageFilePath != null) { - html = html + getRow(averageFilePath); + var color = this.warningColor; + if (concentrationValidPerconcentration > 2) { + color = this.validColor; + } + /** More measurement need to be done **/ + if (measurements < 3) { + color = this.notValidColor; } - /** Buffer After **/ - if (bufferAfterAverageFilePath != null) { - html = html + getRow(bufferAfterAverageFilePath); + html = html + "
"; + html = html + ""; + for ( var i = 0; i < conditions.length; i++) { + html = html + this.createConcentrationRow(differentConcentration[conditions[i].concentration], conditions[i], warnings[i]); } - return html + "
" + bufferAcronym.toUpperCase() + + "
"; - }, - getBaseURL : function() { - return '/ispyb/user/dataadapter.do'; - }, + html = html + ""; + html = html + ""; - getPrintcomponentURL : function(dewarId) { - return '/ispyb/user/viewDewarAction.do?reqCode=generateLabels&dewarId=' + dewarId; + html = html + ""; + nColumns = nColumns + 1; + } + html = html + "
"; + return html; +}; - }, - getPDBVisualizerURL : function(modelId, subtractionId, experimentId) { - return '/ispyb/user/viewProjectList.do?reqCode=display&menu=PDBVisualizer&modelId=' + modelId + '&experimentId=' + experimentId - + '&subtractionId=' + subtractionId; - }, +ResultsAssemblyGrid.prototype._getTbar = function() { + function goTo(url) { + window.location = url; + } - getURL : function() { - return this.getBaseURL() + '?reqCode=getImage'; + var _this = this; + return [ { + icon : '../images/application_view_list.png', + text : 'Multiple Select', + handler : function() { + var specimenSelectorResultGrid = new SpecimenSelectorResultGrid(); + var window = Ext.create('Ext.window.Window', { + title : 'Multiple select', + height : 600, + width : 600, + layout : 'fit', + items : [ specimenSelectorResultGrid.getPanel(_this.data) ], + buttons : [ { + text : 'Go', + handler : function() { + var array = []; + for ( var i = 0; i < specimenSelectorResultGrid.selected.length; i++) { + var row = specimenSelectorResultGrid.selected[i]; + array.push({ + macromoleculeId : row.macromoleculeId, + bufferId : row.bufferId + }); + } + goTo(BUI.getMacromoleculeResultsURLByMultipleSearch(array)); + + } + }, { + text : 'Cancel', + handler : function() { + window.close(); + } + } ] + + }).show(); - }, - getAbinitioImageURL : function() { - return this.getBaseURL() + '?reqCode=getAbinitioImage'; - }, - getNSDImageURL : function(modelListId) { - return BUI.getAbinitioImageURL() + '&type=NSD&modelListId=' + modelListId; - }, - getCHI2ImageURL : function(modelListId) { - return BUI.getAbinitioImageURL() + '&type=CHI2&modelListId=' + modelListId; - }, - getModelFile : function(type, modelId, format) { - return this.getBaseURL() + '?reqCode=getModelFile' + "&type=" + type + "&modelId=" + modelId + "&format=" + format; - }, - getPdbURL : function() { - return this.getBaseURL() + '?reqCode=getPdbFiles'; - }, - getStvArray : function(value, error) { - value = Number(value); - error = Number(error); - return [ value - error, value, value + error ]; - }, - getPointArrayForDygraph : function(x, y, error) { - return [ x, BUI.getStvArray(y, error) ]; - }, - createDIV : function(text, width, className, backgroundColor) { - var nameContainer = document.createElement("div"); - var nameSpan = document.createElement("span"); - if (className != null) { - nameSpan.setAttribute("class", className); - } - if (backgroundColor != null) { - nameSpan.setAttribute("style", "float:left;width:" + width + "px;height:18px;background-color:" + backgroundColor); - } else { - nameSpan.setAttribute("style", "float:left;width:" + width + "px;height:18px;"); } - nameSpan.appendChild(document.createTextNode(text)); - nameContainer.appendChild(nameSpan); - return nameContainer; - }, + } ]; +}; - createFormLabel : function(labelText, text, labelWidth, textWidth, backgroundColor) { - var div = document.createElement("div"); +ResultsAssemblyGrid.prototype.getLegendPanel = function() { + return { + html : '
' + BUI.getRectangleColorDIV(this.validColor, 10, 10) + + 'Good quality measurements' + + BUI.getRectangleColorDIV(this.warningColor, 10, 10) + + 'Probably valid with manual processing' + + BUI.getRectangleColorDIV(this.notValidColor, 10, 10) + + 'More measurements need to be done
' + }; +}; +/** Returns the grid **/ +ResultsAssemblyGrid.prototype.getPanel = function(macromolecules) { + var _this = this; - div.appendChild(BUI.createDIV(labelText, labelWidth, "bLabel", backgroundColor)); - div.appendChild(BUI.createDIV(text, textWidth, "btext", backgroundColor)); - return div.innerHTML; - }, + this.store = Ext.create('Ext.data.Store', { + fields : [ + 'macromoleculeId', 'macromoleculeAcronym', 'measurementCount', 'subtractionCount', 'averageCount', 'timeStart', 'concentrationArray', + 'bufferConditions', 'conditions' ], + data : this._prepareData(macromolecules) + }); - createTextArea : function(labelText, text, labelWidth, rows, cols) { - var div = document.createElement("div"); - div.appendChild(BUI.createDIV(labelText, labelWidth, "bLabel")); - var textArea = document.createElement("textarea"); - textArea.setAttribute("rows", rows); - textArea.setAttribute("cols", cols); - textArea.appendChild(document.createTextNode(text)); - div.appendChild(textArea); - return div.innerHTML; - }, + this.store.sort('macromoleculeAcronym'); - showBetaWarning : function() { - alert("ISPyB for Biosaxs version Beta has not this functionality enabled"); - }, + this.grid = Ext.create('Ext.grid.Panel', { + id : this.id, + title : 'Macromolecules', + store : this.store, + tbar : this._getTbar(), + bbar : [ this.getLegendPanel() ], + width : this.width, + height : this.height, + maxHeight : this.maxHeight, + sortableColumns : true, + columns : [ + { + text : '', + dataIndex : 'macromoleculeId', + width : 20, + hidden : false, + renderer : function(val, y, sample) { + return BUI.getRectangleColorDIV(BIOSAXS.proposal.macromoleculeColors[val], 10, 10); + } + }, + { + text : 'Macromolecule', + dataIndex : 'macromoleculeAcronym', + width : 200 + }, + { + text : 'Buffer Conditions', + dataIndex : 'conditions', + flex : 1, + renderer : function(val, style, record) { + return _this.getConditionHTMLTable(val, style, record); + } + }, + { + header : 'Average', + dataIndex : 'percentageCollected', + name : 'percentageCollected', + type : 'string', + hidden : true, + renderer : function(val, y, sample) { + return "
" + + BUI.getProgessBar((sample.raw.averageCount / sample.raw.measurementCount) * 100, sample.raw.averageCount + "/" + + sample.raw.measurementCount) + "
"; + }, + width : 100, + sorter : false + }, + { + header : 'Subtractions', + dataIndex : 'percentageCollected', + name : 'percentageCollected', + type : 'string', + hidden : true, + renderer : function(val, y, sample) { + return "
"+ BUI.getProgessBar((sample.raw.subtractionCount / sample.raw.measurementCount) * 100, sample.raw.subtractionCount + "/" + + sample.raw.measurementCount) + "
"; + }, + width : 100 + }, { + header : 'Date', + dataIndex : 'timeStart', + name : 'timeStart', + type : 'string', + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + if (record.raw.timeStart != null) { + return moment(record.raw.timeStart).format("MMM Do YY"); + } + } + }, { + header : 'Download', + dataIndex : 'percentageCollected', + name : 'percentageCollected', + type : 'string', + renderer : function(val, y, sample) { + return BUI.getZipHTMLByMacromoleculeId(sample.raw.macromoleculeId); + }, + width : 100 + }, - formatValuesErrorUnitsScientificFormat : function(val, error, unit, args) { - var fontSize = 14; - var decimals = 2; - var errorFontSize = 10; - /** line break **/ - var lineBreak = true; - if (args != null) { - if (args.fontSize != null) { - fontSize = args.fontSize; - } - if (args.decimals != null) { - decimals = args.decimals; - } - if (args.errorFontSize != null) { - errorFontSize = args.errorFontSize; - } - if (args.lineBreak != null) { - lineBreak = args.lineBreak; + { + id : 'btnResultVisible', + width : 85, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + return BUI.getGreenButton('GO'); + } + } ], + viewConfig : { + stripeRows : true, + listeners : { + afterrender : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + }, + celldblclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + _this.edit(record.data.macromoleculeId); + }, + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + if (grid.getGridColumns()[cellIndex].getId() == 'buttonEditMacromolecule') { + _this.edit(record.data.macromoleculeId); + } + if (grid.getGridColumns()[cellIndex].getId() == 'buttonRemoveMacromolecule') { + BUI.showBetaWarning(); + } + if (grid.getGridColumns()[cellIndex].getId() == 'btnResultVisible') { + window.location = BUI.getMacromoleculeResultsURL(record.data.macromoleculeId); + } + } } - } + }); - if (val == "") { - return ""; - } - if (error == null) { - return "" + Number(val).toFixed(decimals) + ""; - } - var html = "" + Number(val).toFixed(decimals) + " " + unit + ""; - if (lineBreak) { - html = html + "
"; - } - return html + " ± " + Number(Number(error).toFixed(3)).toExponential() - + ""; - }, + /** Adding the tbar **/ + if (this.tbar) { + this.grid.addDocked({ + xtype : 'toolbar', + items : this.getTbar() + }); + } + return this.grid; +}; - formatValuesErrorUnits : function(val, error, unit, args) { - var fontSize = 16; - var decimals = 2; - var errorFontSize = 10; - /** line break **/ - var lineBreak = true; - if (args != null) { - if (args.fontSize != null) { - fontSize = args.fontSize; - } - if (args.decimals != null) { - decimals = args.decimals; - } - if (args.errorFontSize != null) { - errorFontSize = args.errorFontSize; - } - if (args.lineBreak != null) { - lineBreak = args.lineBreak; - } +ResultsAssemblyGrid.prototype.input = function(targetId) { + return { + data : DATADOC.getData_3367(), + proposal : DATADOC.getProposal_3367() + }; +}; - } +ResultsAssemblyGrid.prototype.test = function(targetId) { + var grid = new ResultsAssemblyGrid({ + height : 600, + searchBar : false, + tbar : false, + btnResultVisible : true, + width : 1000 + }); + BIOSAXS.proposal = new Proposal(grid.input().proposal); + var panel = grid.getPanel(grid.input().data); + panel.render(targetId); - if (val == "") { - return ""; +}; + + +function RigidModelGrid(args) { + this.height = null; + this.width = null; + this.id = BUI.id(); + + if (args != null) { + if (args.height != null) { + this.height = args.height; + + if (args.width != null) { + this.width = args.width; + } + } + } + + this.onSelected = new Event(this); +} + + +RigidModelGrid.prototype.refresh = function(subtractions) { + var data = []; + if (subtractions != null){ + if (subtractions.length > 0){ + for (j in subtractions){ + var subtraction = subtractions[j]; + if (subtraction.rigidBodyModeling3VOs != null){ + for (i in subtraction.rigidBodyModeling3VOs){ + data.push(subtraction.rigidBodyModeling3VOs[i]); + } + } + } + } + } + this.store.loadData(data); +}; + +RigidModelGrid.prototype.getPanel = function() { + var _this = this; + this.store = Ext.create('Ext.data.Store', { + fields : [ 'symmetry', 'subtractionId', 'subUnitConfigFilePath', 'rigidBodyModelingId', 'rigidBodyModelFilePath', 'logFilePath', 'fitFilePath', 'curveConfigFilePath', + 'crossCorrConfigFilePath', 'contactDescriptionFilePath' ], + data : [] + }); + + this.store.sort([ { + property : 'name', + direction : 'ASC' + } ]); + + this.panel = Ext.create('Ext.grid.Panel', { + store : this.store, + width : this.width, + height : this.height, + margin : 10, + deferredRender : false, + columns : [ { + text : 'RBM', + dataIndex : 'rigidBodyModelFilePath', + hidden : false, + flex : 1, + renderer : function(val){ + return BUI.getFileName(val); + } + }, { + text : 'Sub Unit Conf.', + dataIndex : 'subUnitConfigFilePath', + hidden : true, + flex : 1, + renderer : function(val){ + return BUI.getFileName(val); + } + }, { + text : 'Log', + dataIndex : 'logFilePath', + hidden : true, + flex : 1, + renderer : function(val){ + return BUI.getFileName(val); + } + }, { + text : 'Fit', + dataIndex : 'fitFilePath', + hidden : false, + flex : 1, + renderer : function(val){ + return BUI.getFileName(val); + } + }, { + text : 'Curve Conf.', + dataIndex : 'curveConfigFilePath', + hidden : false, + flex : 1, + renderer : function(val){ + return BUI.getFileName(val); + } + }, { + text : 'Cross Corr.', + dataIndex : 'crossCorrConfigFilePath', + hidden : false, + flex : 1, + renderer : function(val){ + return BUI.getFileName(val); + } + }, { + text : 'Contact Desc.', + dataIndex : 'contactDescriptionFilePath', + hidden : true, + flex : 1, + renderer : function(val){ + return BUI.getFileName(val); + } + } ], + + viewConfig : { + enableTextSelection : true, + preserveScrollOnRefresh : true + }, + listeners : { + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + + }, + afterrender : function() { + } + } + }); + return this.panel; +}; + + +/** + * shows shipments + * + * @height + * @width + * @minHeight + * @btnEditVisible + */ +function ShipmentGrid(args) { + this.id = BUI.id(); + this.height = 100; + this.width = null; + this.minHeight = null; + this.btnEditVisible = true; + + if (args != null) { + if (args.height != null) { + this.height = args.height; } - if (error == null) { - return "" + Number(val).toFixed(decimals) + ""; + if (args.width != null) { + this.width = args.width; } - var html = "" + Number(val).toFixed(decimals) + " " + unit + ""; - if (lineBreak) { - html = html + "
"; + if (args.minHeight != null) { + this.minHeight = args.minHeight; } - return html + " ± " + Number(Number(error).toFixed(8)).toExponential() - + ""; - }, - - formatValuesUnits : function(val, unit, args) { - var fontSize = 12; - var decimals = 2; - var unitsFontSize = 10; - if (args != null) { - if (args.fontSize != null) { - fontSize = args.fontSize; - } - if (args.decimals != null) { - decimals = args.decimals; - } - if (args.unitsFontSize != null) { - unitsFontSize = args.unitsFontSize; - } - + if (args.btnEditVisible != null) { + this.btnEditVisible = args.btnEditVisible; } + } +} - if (val === "") { - return ""; - } - if (unit == null) { - return "" + Number(val).toFixed(decimals) + ""; - } - return "" + Number(val).toFixed(decimals) + " " + unit + ""; - }, +ShipmentGrid.prototype._getColumns = function() { + var _this = this; + var columns = [ + { + text : 'Name', + dataIndex : 'shippingName', + flex : 1 + }, + { + header : 'Type', + dataIndex : 'shippingType', + flex : 1, + hidden : true, + renderer : function(val, comp, record) { + if (val != null) { + return val.toUpperCase(); + } - getGreenButton : function(text, args) { - var width = 70; - var height = 20; - if (args != null) { - if (args.width != null) { - width = args.width; } - if (args.height != null) { - height = args.height; + }, + { + header : 'Status', + type : 'string', + flex : 1, + hidden : false, + renderer : function(comp, val, record) { + if (record.raw.shippingStatus != null) { + if (new String(record.raw.shippingStatus).toUpperCase() == 'OPENED') { + return "" + new String(record.raw.shippingStatus).toUpperCase() + ""; + } + return "" + new String(record.raw.shippingStatus).toUpperCase() + ""; + } + } + }, + { + text : 'Cases', + flex : 1, + hidden : false, + renderer : function(comp, val, record) { + var shipment = BIOSAXS.proposal.getShipmentById(record.data.shippingId); + var container = ""; + if (shipment.dewarVOs.length > 0) { + container = container + ""; + } else { + return "Empty"; + } + return container + "
" + shipment.dewarVOs.length + "x
"; } - } - - return ''; - }, -// getBlueButton : function(text, args) { -// var width = 70; -// var height = 20; -// if (args != null) { -// if (args.width != null) { -// width = args.width; -// } -// if (args.height != null) { -// height = args.height; -// } -// } -// -// return ''; -// }, + }, { + header : 'Comments', + dataIndex : 'comments', + flex : 1, + hidden : false + }, { + header : 'Creation Date', + dataIndex : 'creationDate', + hidden : true + } ]; - getBlueButton : function(text, args) { - var width = 70; - var height = 20; - var href = null; - if (args != null) { - if (args.width != null) { - width = args.width; - } - if (args.height != null) { - height = args.height; + if (this.btnEditVisible) { + columns.push({ + id : _this.id + 'buttonEdit', + text : '', + hidden : !_this.btnEditVisible, + width : 100, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + return BUI.getGreenButton('EDIT'); } - if (args.href != null) { - href = args.href; + }); + } + + columns.push({ + id : _this.id + 'buttonRemove', + text : '', + width : 100, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + var shipment = BIOSAXS.proposal.getShipmentById(record.data.shippingId); + if (shipment.dewarVOs.length == 0) { + return BUI.getRedButton('REMOVE'); } + } - if (href != null) { - return ''; - } else { - return ''; -// return ''; - } - }, - - getSubmitGreenButton : function(text) { - return ''; - }, + }); - getRedButton : function(text) { - return ''; + return columns; +}; - }, - getRectangleColorDIV : function(color, height, width) { - return '
'; - }, +ShipmentGrid.prototype._getTopButtons = function() { + var _this = this; + /** Actions buttons **/ + var actions = []; + actions.push(Ext.create('Ext.Action', { + icon : '../images/add.png', + text : 'Add Shipment', + handler : function(widget, event) { + //window.location = BUI.getCreateShipmentURL(); + var _this = this; - openBufferWindow : function(bufferId) { - var window = new BufferWindow(); - window.draw(tabs.experiment.getBufferById(bufferId), tabs.experiment); - }, + var shipmentForm = new ShipmentForm({ + creationMode : true, + showTitle : false + }); + shipmentForm.onSaved.attach(function(sender, shipment) { + _this.showShipmentTabs(shipment, targetId); + }); + + var window = Ext.create('Ext.window.Window', { + title : 'New Shipment', + height : 600, + width : 800, + layout : 'fit', + items : [ shipmentForm.getPanel() ] + }).show(); - /** Render for safety levels on grids **/ - safetyRenderer : function(val, y, specimen) { - var color = val; - if (val == "YELLOW") { - color = "#E9AB17"; } - return '' + val + ''; - }, + })); + return actions; +}; - getSampleColor : function() { - return '#CB181D'; - }, +ShipmentGrid.prototype.refresh = function(shippings) { + this.features = shippings; + this.store.loadData(this._prepareData(), false); +}; - getLightSampleColor : function() { - return '#FCBBA1'; - }, +ShipmentGrid.prototype._prepareData = function() { + var data = []; + for ( var i = 0; i < this.features.length; i++) { + data.push(this.features[i]); + } + return data; +}; - getBufferColor : function() { - return '#6A51A3'; - }, - getLightBufferColor : function() { - return '#BCBDDC'; - }, +ShipmentGrid.prototype.getPanel = function(shipments) { + this.features = shipments; + return this._renderGrid(); +}; - formatConcentration : function(val) { - if (val != null) { - return "" + Number(val).toFixed(2) + " mg/ml "; - } - return val; - }, +ShipmentGrid.prototype.edit = function(shippingId) { + window.location = BUI.getShippingURL(shippingId); +}; - formatVolume : function(sample, volume) { - if (Number(sample.data.volumeToLoad) > Number(sample.data.volume)) { - return "" + volume + " �l"; - } - if (Number(sample.data.volumeToLoad) == Number(sample.data.volume)) { - return "" + volume + " �l"; - } - return "" + volume + " �l"; - }, +ShipmentGrid.prototype._getStoreFields = function(data) { + var _this = this; + return [ { + name : 'shippingId' + }, { + name : 'shippingName' + }, { + name : 'shippingStatus' + }, { + name : 'shippingType' + }, { + name : 'creationDate' + }, { + name : 'comments' + } ]; +}; - getProposal : function() { - return new Proposal(); - }, +ShipmentGrid.prototype._renderGrid = function() { + var _this = this; - getSampleNameRenderer : function(val, y, record) { - var sample = record.data; - if (record.raw.macromolecule3VO == null) { - return '' + sample.code + ''; - } else { - return '' + sample.code + ''; - } - }, + /** Store **/ + var data = this._prepareData(); + this.store = Ext.create('Ext.data.Store', { + fields : this._getStoreFields(data), + autoload : true, + data : data + }); - getSafetyLevels : function() { - var safetyLevels = new Array(); - safetyLevels.push({ - safetyLevelId : "", - name : "UNKNOWN" - }); - safetyLevels.push({ - safetyLevelId : 1, - name : "GREEN" - }); - safetyLevels.push({ - safetyLevelId : 2, - name : "YELLOW" - }); - safetyLevels.push({ - safetyLevelId : 3, - name : "RED" - }); - return safetyLevels; - }, + this.store.loadData(data, false); + + this.grid = Ext.create('Ext.grid.Panel', { + title : "Shipping", + icon : '/ispyb/images/plane.gif', + width : this.width, + minWidth : this.minWidth, + height : this.height, + store : this.store, + columns : this._getColumns(), + viewConfig : { + stripeRows : true, + listeners : { + itemdblclick : function(dataview, record, item, e) { + _this.edit(record.raw.shippingId); + }, + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEdit') { + _this.edit(record.data.shippingId); + } - getErrorColor : function() { - return '#F6CED8'; - }, - getWarningColor : function() { - return '#F5DA81'; - }, - getValidColor : function() { - return '#E0F8E0'; - }, - getSamplePlateLetters : function() { - return [ "A", "B", "C", "D", "E", "F", "G", "H" ]; - }, - getSamplePositionHTML : function(sample, experiment) { - var plate = ""; - var row = ""; - var column = ""; - var rows = this.getSamplePlateLetters(); - if (sample.sampleplateposition3VO != null) { - var samplePlate = experiment.getSamplePlateById(sample.sampleplateposition3VO.samplePlateId); - if (samplePlate != null) { - plate = (samplePlate.slotPositionColumn); - row = (sample.sampleplateposition3VO.rowNumber); - column = (sample.sampleplateposition3VO.columnNumber); - // var html = "Plate: " + "" + plate + ""; - // html = html + ", Row: " + "" + rows[row - 1] + ""; - // html = html + ", Column: " + "" + column + ""; - var html = "Plate: " + plate - + "-" + rows[row - 1] + "" + column + ""; - return html; + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemove') { + var shipment = BIOSAXS.proposal.getShipmentById(record.data.shippingId); + if (shipment.dewarVOs.length == 0) { + + var adapter = new BiosaxsDataAdapter(); + _this.grid.setLoading("ISPyB: Removing shipment"); + adapter.onSuccess.attach(function(sender) { + BIOSAXS.proposal.onInitialized.attach(function(sender) { + _this.refresh(BIOSAXS.proposal.getShipments()); + _this.grid.setLoading(false); + }); + BIOSAXS.proposal.init(); + }); + + adapter.onError.attach(function(sender) { + alert("Error"); + _this.grid.setLoading(false); + }); + adapter.removeShipment(record.data.shippingId); + } + } + } } + }, + selModel : { + mode : 'SINGLE' } - return ""; - }, + }); - getSafetyLabelName : function(safetyLevelId) { - var safetyLevels = BUI.getSafetyLevels(); - for ( var i = 0; i < safetyLevels.length; i++) { - if (safetyLevels[i].safetyLevelId == safetyLevelId) { - return safetyLevels[i].name; + var actions = _this._getTopButtons(); + this.grid.addDocked({ + xtype : 'toolbar', + items : actions + }); + + this.grid.getSelectionModel().on({ + selectionchange : function(sm, selections) { + if (selections.length) { + for ( var i = 0; i < actions.length; i++) { + if (actions[i].enable) { + actions[i].enable(); + } + } + } else { + for ( var i = 0; i < actions.length; i++) { + if (actions[i].alwaysEnabled == false) { + if (actions[i].disable) { + actions[i].disable(); + } + } + } } } - return "UNKNOWN"; - }, - /** generate random id **/ - id : function() { - var text = ""; - var possible = "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789"; - - for ( var i = 0; i < 5; i++) - text += possible.charAt(Math.floor(Math.random() * possible.length)); + }); + return this.grid; +}; - return text; - }, - showWarning : function(message) { - Ext.Msg.show({ - title : 'Warning', - msg : message, - icon : Ext.Msg.WARNING, - animEl : 'elId' - }); - }, - showError : function(message) { - Ext.Msg.show({ - title : 'Warning', - msg : message, - icon : Ext.Msg.ERROR, - animEl : 'elId' - }); - }, - getTipHTML : function(message) { - //return "
Tip
" - // + message + "
"; - return "
Tip
" - + message + "
"; - }, +ShipmentGrid.prototype.input = function() { + return { + proposal : new MeasurementGrid().input().proposal, + shippings : DATADOC.getShippings_10() + }; +}; - getWarningHTML : function(message) { - return "
Warning
" - + message + "
"; - }, +ShipmentGrid.prototype.test = function(targetId) { + var shipmentGrid = new ShipmentGrid({ + minHeight : 300, + height : 440 + }); + BIOSAXS.proposal = new Proposal(shipmentGrid.input().proposal); + var panel = shipmentGrid.getPanel(targetId); + panel.render(targetId); + shipmentGrid.refresh(shipmentGrid.input().shippings); +}; + +function SpecimenGrid(args) { + this.id = BUI.id(); + this.height = 500; + this.unitsFontSize = 9; + this.editEnabled = false; + this.isPositionColumnHidden = false; + this.removeBtnEnabled = false; - getErrorHTML : function(message) { - return "
Error
" - + message + "
"; - }, + this.selectionMode = "MULTI"; + this.updateRowEnabled = false; + this.grouped = true; + this.width = 900; + this.title = 'Specimens'; + + this.margin = "0 0 0 0"; +// this.experimentColorBased = false; - getProgessBar : function(percentage, text) { - /** percentage 100% green **/ - var color = "#0a0"; + if (args != null) { + if (args.height != null) { + this.height = args.height; + } - color = "#99CC00"; - if (percentage > 100) { - color = "yellow"; - percentage = 100; + if (args.showTitle == false) { + this.title = null; } - if (isNaN(percentage)) { - color = "white"; - percentage = 0; + + if (args.margin == false) { + this.margin = args.margin; } - var defaultText = percentage + "%"; - if (text != null) { - defaultText = text; + if (args.grouped == false) { + this.grouped = null; } - return "
" + defaultText + "
"; - }, - getFileName : function(filePath){ - if (filePath != null){ - return filePath.split("/")[filePath.split("/").length - 1] + if (args.width != null) { + this.width = args.width; } - return ""; - } -}; -Ext.ux.form.RequiredCombo = Ext.extend(Ext.form.ComboBox, { - config : { - cls : 'custom-field-text-required' - }, - initComponent : function() { - Ext.ux.form.RequiredCombo.superclass.initComponent.apply(this, arguments); - }, - checkChange : function() { - if ((this.getValue() == null) || String(this.getValue()).length == 0) { - this.addCls('custom-field-text-required'); - } else { - this.removeCls('custom-field-text-required'); + if (args.editEnabled != null) { + this.editEnabled = args.editEnabled; + } + if (args.removeBtnEnabled != null) { + this.removeBtnEnabled = args.removeBtnEnabled; + } + if (args.isPositionColumnHidden != null) { + this.isPositionColumnHidden = args.isPositionColumnHidden; + } + if (args.selectionMode != null) { + this.selectionMode = args.selectionMode; + } + if (args.updateRowEnabled != null) { + this.updateRowEnabled = args.updateRowEnabled; } + } -}); + this.onClick = new Event(this); + this.onSelected = new Event(this); + this.onRemoved = new Event(this); + this.onSpecimenChanged = new Event(); +} -Ext.define('Ext.form.field.RequiredNumber', { - extend : 'Ext.form.field.Number', - alias : 'widget.requirednumberfield', - alternateClassName : [ 'Ext.form.RequiredNumberField', 'Ext.form.RequiredNumber' ], - config : { - cls : 'custom-field-text-required' - }, +SpecimenGrid.prototype._prepareData = function(experiment) { + var data = []; - initComponent : function() { - var me = this; - me.callParent(); - me.setMinValue(me.minValue); - me.setMaxValue(me.maxValue); - }, + var samples = experiment.getSamples(); + for ( var i = 0; i < samples.length; i++) { + var sample = samples[i]; + if (sample.macromolecule3VO != null) { + sample.macromolecule = sample.macromolecule3VO.acronym; + sample.exposureTemperature = []; + sample.macromoleculeId = sample.macromolecule3VO.macromoleculeId; + } - onChange : function() { - if ((this.getValue() == null) || String(this.getValue()).length == 0) { - this.addCls('custom-field-text-required'); + if (sample.sampleplateposition3VO != null) { + if (sample.sampleplateposition3VO.samplePlateId != null) { + sample.samplePlateId = sample.sampleplateposition3VO.samplePlateId; + sample.rowNumber = sample.sampleplateposition3VO.rowNumber; + sample.columnNumber = sample.sampleplateposition3VO.columnNumber; + if (experiment.getSamplePlateById(sample.sampleplateposition3VO.samplePlateId).plategroup3VO != null) { + sample.plateGroupName = experiment.getSamplePlateById(sample.sampleplateposition3VO.samplePlateId).plategroup3VO.name; + sample.samplePlateName = experiment.getSamplePlateById(sample.sampleplateposition3VO.samplePlateId).name + " [" + sample.plateGroupName + "]"; + sample.slotPositionColumn = experiment.getSamplePlateById(sample.sampleplateposition3VO.samplePlateId).slotPositionColumn; + } + } } else { - this.removeCls('custom-field-text-required'); + sample.samplePlateName = "Unallocated Specimens"; } - this.toggleSpinners(); - this.callParent(arguments); - } -}); -Ext.define('Ext.form.field.RequiredText', { - extend : 'Ext.form.field.Text', - alias : 'widget.requiredtext', - requires : [ 'Ext.form.field.VTypes', 'Ext.layout.component.field.Text' ], - alternateClassName : [ 'Ext.form.RequiredTextField', 'Ext.form.RequiredText' ], - config : { - cls : 'custom-field-text-required' - }, - initComponent : function() { - var me = this; - if (me.allowOnlyWhitespace === false) { - me.allowBlank = false; + /** For grouping, because sencha has not option for multiple grouping I add a field to your store with a convert function that concatenates these two fields and then group by that field.**/ + sample.groupIndex = sample.bufferId + sample.macromoleculeId; + var macromolecule = BIOSAXS.proposal.getMacromoleculeById(sample.macromoleculeId); + + sample.acronym = "Buffers"; + if (macromolecule != null) { + sample.acronym = BIOSAXS.proposal.getMacromoleculeById(sample.macromoleculeId).acronym; } - me.callParent(); - me.addEvents( - /** - * @event autosize - * Fires when the **{@link #autoSize}** function is triggered and the field is resized according to the - * {@link #grow}/{@link #growMin}/{@link #growMax} configs as a result. This event provides a hook for the - * developer to apply additional logic at runtime to resize the field if needed. - * @param {Ext.form.field.Text} this This text field - * @param {Number} width The new field width - */ - 'autosize', - /** - * @event keydown - * Keydown input field event. This event only fires if **{@link #enableKeyEvents}** is set to true. - * @param {Ext.form.field.Text} this This text field - * @param {Ext.EventObject} e - */ - 'keydown', - /** - * @event keyup - * Keyup input field event. This event only fires if **{@link #enableKeyEvents}** is set to true. - * @param {Ext.form.field.Text} this This text field - * @param {Ext.EventObject} e - */ - 'keyup', - /** - * @event keypress - * Keypress input field event. This event only fires if **{@link #enableKeyEvents}** is set to true. - * @param {Ext.form.field.Text} this This text field - * @param {Ext.EventObject} e - */ - 'keypress'); - me.addStateEvents('change'); - me.setGrowSizePolicy(); - }, - checkChange : function() { - if ((this.getValue() == null) || String(this.getValue()).length == 0) { - this.addCls('custom-field-text-required'); - } else { - this.removeCls('custom-field-text-required'); + sample.buffer = experiment.getBufferById(sample.bufferId); + + sample.volumeToLoad = experiment.getVolumeToLoadBySampleId(sample.sampleId); + data.push(sample); + } + return data; +}; + +SpecimenGrid.prototype.deselectAll = function() { + this.grid.getSelectionModel().deselectAll(); +}; + +SpecimenGrid.prototype.selectById = function(specimenId) { + this.grid.getSelectionModel().deselectAll(); + for ( var i = 0; i < this.grid.getStore().data.items.length; i++) { + var item = this.grid.getStore().data.items[i].raw; + if (item.specimenId == specimenId) { + this.grid.getSelectionModel().select(i); } } -}); +}; -var BIOSAXS_COMBOMANAGER = { +SpecimenGrid.prototype.getStore = function() { + return this.store; +}; - getComboMacromoleculeByMacromolecules : function(macromolecules, args) { - var labelWidth = 150; - var margin = "0 0 5 0"; - var width = 300; +SpecimenGrid.prototype.getPlugins = function() { + var _this = this; - if (args != null) { - if (args.labelWidth != null) { - labelWidth = args.labelWidth; - } - if (args.margin != null) { - margin = args.margin; - } - if (args.width != null) { - width = args.width; - } - } + var plugins = []; - var store = Ext.create('Ext.data.Store', { - fields : [ 'macromoleculeId', 'acronym' ], - data : macromolecules, - sorters : [ 'acronym' ] - }); + if (this.updateRowEnabled) { + plugins.push(Ext.create('Ext.grid.plugin.RowEditing', { + clicksToEdit : 1, + listeners : { + validateedit : function(grid, e) { + var measurements = []; - return Ext.create('Ext.form.ComboBox', { - fieldLabel : 'Macromolecules', - labelWidth : labelWidth, - width : width, - margin : margin, - store : store, - editable: false, - queryMode : 'local', - displayField : 'acronym', - valueField : 'macromoleculeId' - }); - }, - getComboBuffers : function(buffers, args) { - var labelWidth = 150; - var margin = "0 0 5 0"; - var width = 300; - var fieldLabel = 'Buffer'; + if (e.newValues.bufferId != e.record.raw.bufferId) { + /** If buffer has changed we have to change all the specimens sharing same datacollection **/ + var dataCollections = []; + if (e.record.raw.macromoleculeId == null) { + dataCollections = dataCollections.concat(_this.experiment.getDataCollectionsBySpecimenId(e.record.raw.specimenId)); + } else { + var sampleDataCollections = _this.experiment.getDataCollectionsBySpecimenId(e.record.raw.specimenId); + for ( var i = 0; i < sampleDataCollections.length; i++) { + var sampleDataCollection = sampleDataCollections[i]; + if (sampleDataCollection != null) { + for ( var j = 0; j < sampleDataCollection.measurementtodatacollection3VOs.length; j++) { + var measurementTODc = sampleDataCollection.measurementtodatacollection3VOs[j]; + if (measurementTODc.dataCollectionOrder == 1) { + dataCollections = dataCollections.concat(_this.experiment.getDataCollectionsBySpecimenId(_this.experiment + .getMeasurementById(measurementTODc.measurementId).specimenId)); + } + } + } + } + } + var i = null; + for ( i = 0; i < dataCollections.length; i++) { + var dataCollection = dataCollections[i]; + var specimens = _this.experiment.getSpecimenByDataCollectionId(dataCollection.dataCollectionId); + measurements = measurements.concat(specimens); + } - if (args != null) { - if (args.labelWidth != null) { - labelWidth = args.labelWidth; - } - if (args.margin != null) { - margin = args.margin; - } - if (args.width != null) { - width = args.width; - } - if (args.noLabel != null) { - fieldLabel = null; - } - } + for ( i = 0; i < measurements.length; i++) { + var measurement = measurements[i]; + var specimen = _this.experiment.getSpecimenById(measurement.specimenId); + specimen.bufferId = e.newValues.bufferId; + new BiosaxsDataAdapter().saveSpecimen(specimen, _this.experiment); + } + } - var store = Ext.create('Ext.data.Store', { - fields : [ 'bufferId', 'acronym' ], - data : buffers, - sorters : [ 'acronym' ] - }); + /** Setting values **/ + e.record.raw.concentration = e.newValues.concentration; + e.record.raw.volume = e.newValues.volume; - return Ext.create('Ext.form.ComboBox', { - fieldLabel : fieldLabel, - labelWidth : labelWidth, - width : width, - margin : margin, - editable: false, - store : store, - queryMode : 'local', - displayField : 'acronym', - valueField : 'bufferId' - }); - }, - getComboSessions : function(sessions, args) { - var labelWidth = 150; - var margin = "0 0 5 0"; - var width = 300; + /** Position **/ + if (e.record.raw.sampleplateposition3VO != null) { + var samplePlate = _this.experiment.getSamplePlateBySlotPositionColumn(e.newValues.slotPositionColumn); + if (samplePlate != null) { + e.record.raw.sampleplateposition3VO = { + columnNumber : e.newValues.columnNumber, + rowNumber : e.newValues.rowNumber, + samplePlateId : samplePlate.samplePlateId + }; + } + } else { + if (e.newValues.slotPositionColumn != null) { + var samplePlate = _this.experiment.getSamplePlateBySlotPositionColumn(e.newValues.slotPositionColumn); + if (samplePlate != null) { + e.record.raw.sampleplateposition3VO = { + columnNumber : e.newValues.columnNumber, + rowNumber : e.newValues.rowNumber, + samplePlateId : samplePlate.samplePlateId + }; + } + } + } - if (args != null) { - if (args.labelWidth != null) { - labelWidth = args.labelWidth; - } - if (args.margin != null) { - margin = args.margin; - } - if (args.width != null) { - width = args.width; + var macromoleculeId = e.record.data.macromoleculeId; + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, specimen) { + /** Because macromolecule3VO is fecthed LAZY **/ + if (macromoleculeId != null) { + specimen.macromolecule3VO = BIOSAXS.proposal.getMacromoleculeById(macromoleculeId); + } + _this.onSpecimenChanged.notify(specimen); + _this.grid.setLoading(false); + }); + adapter.onError.attach(function() { + alert("Error"); + _this.grid.setLoading(false); + }); + _this.grid.setLoading(); + adapter.saveSpecimen(e.record.raw, _this.experiment); + } } - } - - for ( var i = 0; i < sessions.length; i++) { - sessions[i]["startDateFormatted"] = moment(sessions[i].startDate).format("MMM Do YY"); - sessions[i]["sorter"] = moment(sessions[i].startDate).format("YYYYMMDD"); - } + })); + } + return plugins; +}; - var store = Ext.create('Ext.data.Store', { - fields : [ 'sessionId', 'startDateFormatted', 'beamlineName', 'startDate', 'endDate', 'beamlineOperator' ], - data : sessions, - sorters : [ 'sorter' ] +SpecimenGrid.prototype._getRowCombo = function() { + var data = []; + for ( var i = 1; i <= 8; i++) { + data.push({ + rowNumber : i, + name : BUI.getSamplePlateLetters()[i - 1] }); + } - return Ext.create('Ext.form.ComboBox', { - fieldLabel : 'Sessions', - labelWidth : labelWidth, - width : width, - margin : margin, - store : store, - queryMode : 'local', - // displayField : 'startDate', - valueField : 'sessionId', - // Template for the dropdown menu. - // Note the use of "x-boundlist-item" class, - // this is required to make the items selectable. - tpl : Ext.create('Ext.XTemplate', '', - '
{startDateFormatted} {beamlineName}
', ''), - // template for the content inside text field - displayTpl : Ext.create('Ext.XTemplate', '', '{startDateFormatted}', '') + var positionsStore = Ext.create('Ext.data.Store', { + fields : [ 'rowNumber', 'name' ], + data : data + }); - }); - } + return Ext.create('Ext.form.ComboBox', { + store : positionsStore, + queryMode : 'local', + displayField : 'name', + valueField : 'rowNumber' + }); }; - - function GenericWindow(args){ - this.title = "title"; - this.width = 700; - this.height = 500; - this.id = BUI.id(); - - this.close = false; - this.draggable = true; - this.modal = true; - - if (args != null){ - if (args.actions != null){ - this.actions = args.actions; - } - if (args.form != null){ - this.form = args.form; - } - if (args.width != null){ - this.width = args.width; - } - if (args.modal != null){ - this.modal = args.modal; - } - - if (args.height != null){ - this.height = args.height; - } - if (args.title != null){ - this.title = args.title; - } - if (args.form != null){ - this.form = args.form; - } - if (args.close != null){ - this.close = args.close; - } - if (args.draggable != null){ - this.draggable = args.draggable; - } - - } - /** Events **/ - this.onSaved = new Event(this); - }; - - -GenericWindow.prototype.getButtons = function() { - var _this = this; - - if (this.close){ - return [ { - text : 'Close', - handler : function() { - _this.panel.close(); - } - } ]; - } - else{ - return [ { - text : 'Save', - handler : function() { - _this.save(); - - } - }, { - text : 'Cancel', - handler : function() { - _this.panel.close(); - } - } ]; +SpecimenGrid.prototype._getColumnCombo = function() { + var data = []; + for ( var i = 1; i <= 12; i++) { + data.push({ + columnNumber : i + }); } -}; -GenericWindow.prototype.save = function (){ - alert("Method save of GenerciWindow class is abstract"); + var positionsStore = Ext.create('Ext.data.Store', { + fields : [ 'columnNumber' ], + data : data + }); + + return Ext.create('Ext.form.ComboBox', { + store : positionsStore, + queryMode : 'local', + displayField : 'columnNumber', + valueField : 'columnNumber' + }); }; -GenericWindow.prototype._postRender = function(data, experiment){ +SpecimenGrid.prototype._getSlotColumBombo = function() { + if (this.experiment){ + var length = this.experiment.getSamplePlates().length; + + var data = []; + for ( var i = 1; i <= length; i++) { + data.push({ + slotPositionColumn : i + }); + } + + var positionsStore = Ext.create('Ext.data.Store', { + fields : [ 'slotPositionColumn' ], + data : data + }); + return Ext.create('Ext.form.ComboBox', { + store : positionsStore, + queryMode : 'local', + displayField : 'slotPositionColumn', + valueField : 'slotPositionColumn' + }); + } }; - -GenericWindow.prototype.draw = function (data, experiment){ - this._render(data, experiment); +SpecimenGrid.prototype.getPanelByExperiment = function(experiment) { + this.experiment = experiment; + var data = this._prepareData(experiment); + return this.getPanel(data); }; -GenericWindow.prototype.refresh = function(data, experiment){ - this.data = data; - this.experiment = experiment; - this.form.refresh(data, experiment); +SpecimenGrid.prototype.refresh = function(experiment) { + this.experiment = experiment; + var data = this._prepareData(experiment); + this.store.loadData(data); }; -GenericWindow.prototype._render = function(data, experiment){ - this.data = data; - var _this = this; - if (this.panel == null){ - this.panel = Ext.create('Ext.Window', { - id : this.id, - title : this.title, - resizable : true, - constrain : true, - border : 1, - modal : this.modal, - frame : false, - draggable : this.draggable, - closable : true, - autoscroll : true, - layout : { type: 'vbox',align: 'stretch'}, - width : this.width, - height : this.form.height, - buttonAlign :'right', - buttons : this.getButtons(), - items : this.form.getPanel(data, experiment), - listeners: { - scope : this, - minimize : function(){ - this.panel.hide(); - }, - destroy : function(){ - delete this.panel; - } - } - }); - this.panel.setLoading(); - } - - this.panel.show(); - this._postRender(); -}; -function CalendarWidget(args) { - this.height = 740; +SpecimenGrid.prototype.getPanel = function() { + var _this = this; + this.store = Ext.create('Ext.data.Store', { + fields : [ + 'buffer', 'bufferId', 'code', 'macromolecule', 'acronym', 'macromoleculeId', 'concentration', 'volume', 'samplePlateId', + 'slotPositionColumn', 'rowNumber', 'columnNumber', 'groupIndex' ], + data : [], + groupField : 'acronym' + }); + this.store.sort([ { + property : 'concentration', + direction : 'ASC' + }, { + property : 'buffer', + direction : 'ASC' + } ]); - if (args != null) { - if (args.height != null) { - this.height = args.height; + var selModel = Ext.create('Ext.selection.RowModel', { + allowDeselect : true, + mode : this.selectionMode, + listeners : { + selectionchange : function(sm, selections) { + var selected = []; + for ( var i = 0; i < selections.length; i++) { + selected.push(selections[i].raw); + } + _this.onSelected.notify(selected); + } } + }); + + var features = []; + + if (this.grouped) { + features.push({ + ftype : 'grouping', + groupHeaderTpl : '{name}', + hideGroupedHeader : false, + startCollapsed : false, + id : 'myGroupedStore' + }); } - this.onClick = new Event(); -} + this.grid = Ext.create( + 'Ext.grid.Panel', + { + title : this.title, + height : this.height, + width : this.width, + selModel : selModel, + store : this.store, + features : features, + margin : this.margin, + plugins : this.getPlugins(), + columns : [ + { + text : '', + dataIndex : 'macromolecule', + width : 20, + renderer : function(val, y, sample) { + var macromoleculeId = null; + if (sample.raw.macromolecule3VO != null) { + macromoleculeId = sample.raw.macromolecule3VO.macromoleculeId; + } + else{ + macromoleculeId = sample.raw.macromoleculeId; + } + + if (macromoleculeId == null) return; + return BUI.getRectangleColorDIV(_this.experiment.macromoleculeColors[macromoleculeId], 10, 10); + } + }, + { + text : 'Macromolecule', + dataIndex : 'macromolecule', + width : 100 + }, + { + text : '', + dataIndex : 'buffer', + width : 20, + renderer : function(val, y, sample) { + var color = "black"; + if (sample.raw.bufferId != null) { + if (_this.experiment.getDataCollectionsBySpecimenId(sample.raw.specimenId)[0] != null){ + color = _this.experiment.getSpecimenColorByBufferId(_this.experiment.getMeasurementById(_this.experiment.getDataCollectionsBySpecimenId(sample.raw.specimenId)[0].measurementtodatacollection3VOs[0].measurementId).specimenId); + } + return BUI.getRectangleColorDIV(color, 10, 10); + } + } + }, { + text : 'Buffer', + dataIndex : 'bufferId', + width : 140, + renderer : function(val, y, sample) { + if (sample.raw.bufferId != null) { + return BIOSAXS.proposal.getBufferById(val).acronym; + } + }, + editor : BIOSAXS_COMBOMANAGER.getComboBuffers(BIOSAXS.proposal.getBuffers(), { + noLabel : true, + width : 300 + }) + }, { + text : 'Conc.', + dataIndex : 'concentration', + width : 100, + editor : { + allowBlank : false + }, + renderer : function(val, meta, sample) { + if (isNaN(val)) { + meta.tdCls = 'yellow-cell'; + return val; + } else { + if (val != 0) { + return BUI.formatValuesUnits(val, 'mg/ml', { + fontSize : 16, + decimals : 3, + unitsFontSize : this.unitsFontSize + }); + } else { + return; + } + } + } + }, { + text : 'Vol. Well', + dataIndex : 'volume', + width : 70, + editor : { + allowBlank : true + }, + renderer : function(val, y, sample) { + return BUI.formatValuesUnits(sample.data.volume, 'µl', { + fontSize : 12, + decimals : 2, + unitsFontSize : this.unitsFontSize + }); + } + }, { + text : 'Position', + hidden : true, + flex : 1, + renderer : function(val, y, sample) { + return BUI.getSamplePositionHTML(sample.raw, _this.experiment); + } + }, { + text : 'samplePlateId', + dataIndex : 'samplePlateId', + hidden : true + }, { + text : 'Plate', + hidden : this.isPositionColumnHidden, + dataIndex : 'slotPositionColumn', + editor : _this._getSlotColumBombo(), + flex : 1, + renderer : function(val, meta, sample) { + if ((val != null) & (val != "")) { + return val; + } else { + meta.tdCls = 'yellow-cell'; + } + } + }, { + text : 'Row', + hidden : this.isPositionColumnHidden, + dataIndex : 'rowNumber', + editor : this._getRowCombo(), + flex : 1, + renderer : function(val, meta, sample) { + if ((val != null) && (val != "")) { + return BUI.getSamplePlateLetters()[val - 1]; + } else { + meta.tdCls = 'yellow-cell'; + } + } + }, { + text : 'Well', + hidden : this.isPositionColumnHidden, + dataIndex : 'columnNumber', + editor : this._getColumnCombo(), + flex : 1, + renderer : function(val, meta, sample) { + if ((val != null) && (val != "")) { + return val; + } else { + meta.tdCls = 'yellow-cell'; + } + } + }, { + id : _this.id + 'buttonEditSample', + text : 'Edit', + width : 80, + sortable : false, + hidden : !_this.editEnabled, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + if (_this.editEnabled) { + return BUI.getGreenButton('EDIT'); + } + } + }, { + id : _this.id + 'buttonRemoveSample', + text : '', + hidden : !_this.removeBtnEnabled, + width : 100, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + if (_this.removeBtnEnabled) { + return BUI.getRedButton('REMOVE'); + } + } + } -CalendarWidget.prototype.loadData = function(data) { - this.events = []; + ], + viewConfig : { + preserveScrollOnRefresh : true, + stripeRows : true, + getRowClass : function(record) { + var specimens = _this.experiment.getSampleByPosition(record.data.samplePlateId, record.data.rowNumber, + record.data.columnNumber); + if (specimens.length > 1) { + return 'red-row'; - for ( var i = 0; i < data.length; i++) { - var date = moment(data[i].creationDate); - var textColor = 'black'; + } + }, + listeners : { + selectionchange : function(grid, selected) { + _this.onClick.notify(record.raw); + }, + cellclick : function(grid, td, cellIndex, record, tr) { + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEditSample') { + } + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemoveSample') { + grid.getStore().removeAt(rowIndex); + _this.onRemoved.notify(); + } - if (data[i].status == "FINISHED") { - textColor = 'green'; - } - if (data[i].status == "ABORTED") { - textColor = 'red'; - } - this.events.push({ - title : data[i].name, - start : date.format("YYYY-MM-DD HH:mm:ss"), - end : date.format("YYYY-MM-DD HH:mm:ss"), - date : date, - allDay : false, - color : textColor, - className : date.format("YYYY-MM-DD") - }); - } + } + } + } + }); + return this.grid; }; -CalendarWidget.prototype.draw = function(targetId) { - var _this = this; - $('#' + targetId).fullCalendar({ - eventClick : function(calEvent, jsEvent, view) { - _this.onClick.notify(calEvent.className[0]); - - }, - contentHeight : _this.height, - header : { - left : 'prev,next today', - center : 'title', - right : 'month,basicWeek,basicDay' - }, - editable : false, - events : this.events +SpecimenGrid.prototype.input = function() { + return { + experiment : DATADOC.getExperiment_10(), + proposal : DATADOC.getProposal_10() + }; +}; + +SpecimenGrid.prototype.test = function(targetId) { + var specimenGrid = new SpecimenGrid({ + height : 400, + maxHeight : 400, + width : 1000 }); + BIOSAXS.proposal = new Proposal(specimenGrid.input().proposal); + + var experiment = new Experiment(specimenGrid.input().experiment); + var panel = specimenGrid.getPanelByExperiment(experiment); + panel.render(targetId); }; /** - * It shows a table with the guinier and gnom data as well as passed and - * discarded measurements + * Shows a list of stock solutions with macromolecule, buffer, storage temperature, concentration, shipment and comments * - * @height - * @showBufferColumns + * @multiselect allows multiple selection + * @height + * @minHeight + * @width + * @tbar + * @showTitle + * @isPackedVisible shows is stock solution is in a box + * @btnEditVisible shows edit button + * @btnAddVisible + * @btnAddExisting + * @btnUnpackVisible allows to unpack a stock solution + * @btnRemoveVisible allow to remove a stock solution */ -function ConcentrationHTMLTableWidget(args) { + +function StockSolutionGrid(args) { this.id = BUI.id(); + this.height = 100; + this.width = null; + this.minHeight = null; + this.tbar = true; - this.showBufferColumns = true; + this.title = "Stock Solutions"; + + /** Visible buttons and actions **/ + this.btnEditVisible = true; + this.btnRemoveVisible = true; + this.btnAddVisible = true; + this.btnAddExisting = false; + this.isPackedVisible = true; + this.btnUnpackVisible = false; + + /** Selectors **/ + this.multiselect = false; + this.selectedStockSolutions = []; if (args != null) { + if (args.btnUnpackVisible != null) { + this.btnUnpackVisible = args.btnUnpackVisible; + } + if (args.multiselect != null) { + this.multiselect = args.multiselect; + } if (args.height != null) { this.height = args.height; } - if (args.showBufferColumns != null) { - this.showBufferColumns = args.showBufferColumns; + if (args.btnEditVisible != null) { + this.btnEditVisible = args.btnEditVisible; + } + if (args.btnAddVisible != null) { + this.btnAddVisible = args.btnAddVisible; + } + if (args.btnAddExisting != null) { + this.btnAddExisting = args.btnAddExisting; + } + if (args.width != null) { + this.width = args.width; + } + if (args.minHeight != null) { + this.minHeight = args.minHeight; + } + if (args.tbar != null) { + this.tbar = args.tbar; + } + if (args.btnRemoveVisible != null) { + this.btnRemoveVisible = args.btnRemoveVisible; + } + if (args.isPackedVisible != null) { + this.isPackedVisible = args.isPackedVisible; + } + if (args.showTitle != null) { + this.showTitle = args.showTitle; + if (this.showTitle == false) { + this.title = null; + } } - } -} - -ConcentrationHTMLTableWidget.prototype.refresh = function(parsedData) { - document.getElementById(this.id).innerHTML = this.getPanel(parsedData); -}; - -ConcentrationHTMLTableWidget.prototype.getPanel = function(parsedData) { - var html = "
"; - html = html + ""; - /** Title * */ - html = html + ""; - html = html + ""; - if (this.showBufferColumns) { - html = html + ""; } - html = html + ""; - html = html + ""; - html = html + ""; - html = html + ""; - html = html + ""; - html = html + ""; - html = html + ""; - html = html + ""; - html = html + ""; - html = html + ""; - html = html + ""; - html = html + ""; - html = html + ""; + /** Events **/ + this.onProposalChanged = new Event(this); + this.onStockSolutionSelected = new Event(this); +} - parsedData.concentration.concentrations.sort(function(a, b) { - return a.concentration - b.concentration; - }); - /** Row * */ - for ( var i = 0; i < parsedData.concentration.concentrations.length; i++) { - var row = parsedData[i]; +StockSolutionGrid.prototype._getColumns = function() { + var _this = this; + var columns = [ - var tr = ""; - if (i % 2 == 1) { - tr = ""; + { + header : 'Macromolecule', + dataIndex : 'macromolecule', + id : _this.id + 'macromolecule', + type : 'string', + renderer : function(val, y, specimen) { + return '' + val + ''; + }, + hidden : false, + flex : 1 + }, { + header : 'Buffer', + dataIndex : 'buffer', + name : 'buffer', + hidden : false, + renderer : function(val, y, specimen) { + return '' + val + ''; + }, + type : 'string', + flex : 1 + }, { + header : 'Acronym', + dataIndex : 'name', + name : 'name', + type : 'string', + flex : 1, + hidden : true + }, { + header : 'Storage Temp.', + dataIndex : 'storageTemperature', + name : 'storageTemperature', + type : 'string', + flex : 1, + hidden : false, + renderer : function(val) { + return BUI.formatValuesUnits(val, 'C', { + fontSize : 12, + decimals : 2, + unitsFontSize : 10 + }); } - var goodMeasurements = (parsedData.concentration.concentrations[i].frames.length - parsedData.concentration.concentrations[i].frames_warning); - if (goodMeasurements == 0) { - tr = ""; + }, { + header : 'Volume', + dataIndex : 'volume', + type : 'string', + flex : 1, + hidden : false, + renderer : function(val) { + return BUI.formatValuesUnits(val, 'µl', { + fontSize : 12, + decimals : 2, + unitsFontSize : 10 + }); } - html = html + tr; - html = html + ""; - if (this.showBufferColumns) { - html = html + ""; + }, { + header : 'Concentration', + dataIndex : 'concentration', + name : 'concentration', + type : 'string', + flex : 1, + renderer : function(val) { + return BUI.formatValuesUnits(val, 'mg/ml', { + fontSize : 12, + decimals : 2, + unitsFontSize : 10 + }); } - html = html + ""; - html = html + ""; - html = html + ""; - html = html + ""; - html = html + ""; - html = html + ""; - html = html + ""; - html = html + ""; + }, { + header : 'Packed', + dataIndex : 'comments', + id : _this.id + "box", + type : 'string', + width : 50, + hidden : !this.isPackedVisible, + renderer : function(val, cmp, a) { + if (a.raw.boxId != null) { + return "
"; + } + + } + }, { + header : 'Comments', + dataIndex : 'comments', + type : 'string', + flex : 1 + } ]; + + if (this.btnEditVisible) { + columns.push({ + id : _this.id + 'buttonEdit', + width : 85, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + if (_this.btnEditVisible) { + return BUI.getGreenButton('EDIT'); + } + } + }); + } + + if (this.btnRemoveVisible) { + columns.push({ + id : _this.id + 'buttonRemove', + width : 85, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + if (_this.btnRemoveVisible) { + return BUI.getRedButton('REMOVE'); + } + } + }); } - return html + "
ConcentrationBufferMeasurementsGuinierGnom
PassedDiscardedRgI0QualityRgdMax
" + parsedData.concentration.concentrations[i].concentration + "" + parsedData.concentration.concentrations[i].bufferAcronym + "" + goodMeasurements + " of " + parsedData.concentration.concentrations[i].frames.length + "" + parsedData.concentration.concentrations[i].frames_warning + "" + BUI.formatValuesErrorUnits(parsedData.concentration.concentrations[i].calculation.rgGuinier.avg, parsedData.concentration.concentrations[i].calculation.rgGuinier.std, "nm", { - lineBreak : false - }) + "" + BUI.formatValuesErrorUnits(parsedData.concentration.concentrations[i].calculation.i0Guinier.avg, parsedData.concentration.concentrations[i].calculation.i0Guinier.std, " ", { - lineBreak : false - }) + "" + BUI.formatValuesErrorUnits(parsedData.concentration.concentrations[i].calculation.quality.avg, parsedData.concentration.concentrations[i].calculation.quality.std, " ", { - lineBreak : false - }) + "" + BUI.formatValuesErrorUnits(parsedData.concentration.concentrations[i].calculation.rgGnom.avg, parsedData.concentration.concentrations[i].calculation.rgGnom.std, " ", { - lineBreak : false - }) + "" + BUI.formatValuesErrorUnits(parsedData.concentration.concentrations[i].calculation.dMax.avg, parsedData.concentration.concentrations[i].calculation.dMax.std, " ", { - lineBreak : false - }) + "
"; + + if (this.btnUnpackVisible) { + columns.push({ + id : _this.id + 'buttonUnpack', + width : 85, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + if (_this.btnUnpackVisible) { + return BUI.getBlueButton('UNPACK'); + } + } + }); + } + return columns; }; -ConcentrationHTMLTableWidget.prototype.input = function() { - return { - data : { - "dataCollectionCount" : 4, - "buffers" : [ { - "bufferId" : "422" - } ], - "concentration" : { - "concentrations" : [ { - "concentration" : "7.17", - "id" : "7.1699999999999999", - "bufferId" : "422.00", - "bufferAcronym" : "B1", - "rgGuinier" : [ "5.12723" ], - "frames" : [ { - "total" : "0.515705406286", - "bufferBeforeMeasurementId" : 15045, - "sampleMergeId" : 8176, - "averagedModelId" : null, - "I0" : "183.457461646", - "proposalCode" : "OPD", - "averagedModel" : null, - "bufferAfterMergeId" : 8177, - "framesCount" : "10", - "bufferBeforeMergeId" : 8175, - "averageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_065_ave.dat", - "bufferAfterMeasurementId" : 15048, - "rgGuinier" : "5.12723", - "subtractedFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_065_sub.dat", - "firstPointUsed" : "17", - "chi2RgFilePath" : null, - "abInitioModelId" : null, - "macromoleculeId" : 649, - "code" : "_4.0_7.17", - "transmission" : "100.0", - "timeStart" : "2013-06-05 15:43:54.348723", - "bufferAcronym" : "B1", - "quality" : "0.853011", - "shapeDeterminationModelId" : null, - "expermientComments" : "[BsxCube] Generated from BsxCube", - "bufferId" : 422, - "isagregated" : "False", - "dmax" : "25.63615", - "bufferBeforeAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_064_ave.dat", - "exposureTemperature" : "4.0", - "subtractionId" : 3377, - "conc" : "7.1699999999999999", - "rapidShapeDeterminationModel" : null, - "experimentCreationDate" : "Jun 5, 2013 3:30:30 PM", - "lastPointUsed" : "36", - "modelListId" : null, - "framesMerge" : "9", - "rapidShapeDeterminationModelId" : null, - "bufferAfterAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_066_ave.dat", - "nsdFilePath" : null, - "bufferAfterFramesMerged" : "10", - "experimentId" : 700, - "macromoleculeAcronym" : "L9", - "i0stdev" : "0.139364435146", - "sampleMeasurementId" : 15047, - "measurementComments" : "[5]", - "priorityLevelId" : 10, - "bufferBeforeFramesMerged" : "10", - "substractionCreationTime" : "Jun 5, 2013 3:46:31 PM", - "proposalNumber" : "29", - "rgGnom" : "5.40297914939", - "volume" : "475.302", - "shapeDeterminationModel" : null, - "comments" : null, - "groupeField" : "L9 B1" - } ], - "frames_warning" : 0, - "calculation" : { - "rgGuinier" : { - "std" : 0, - "sum" : 5.12723, - "avg" : 5.12723, - "validNumber" : 1, - "totalNumber" : 1, - "values" : [ "5.12723" ] - }, - "i0Guinier" : { - "std" : 0, - "sum" : 183.457461646, - "avg" : 183.457461646, - "validNumber" : 1, - "totalNumber" : 1, - "values" : [ "183.457461646" ] - }, - "quality" : { - "std" : 0, - "sum" : 0.853011, - "avg" : 0.853011, - "validNumber" : 1, - "totalNumber" : 1, - "values" : [ "0.853011" ] - }, - "rgGnom" : { - "std" : 0, - "sum" : 5.40297914939, - "avg" : 5.40297914939, - "validNumber" : 1, - "totalNumber" : 1, - "values" : [ "5.40297914939" ] - }, - "dMax" : { - "std" : 0, - "sum" : 25.63615, - "avg" : 25.63615, - "validNumber" : 1, - "totalNumber" : 1, - "values" : [ "25.63615" ] - } - } - }, { - "concentration" : "3.53", - "id" : "3.5299999999999998", - "bufferId" : "422.00", - "bufferAcronym" : "B1", - "rgGuinier" : [ "4.38278" ], - "frames" : [ { - "total" : "0.497164741078", - "bufferBeforeMeasurementId" : 15048, - "sampleMergeId" : 8178, - "averagedModelId" : null, - "I0" : "160.023229462", - "proposalCode" : "OPD", - "averagedModel" : null, - "bufferAfterMergeId" : 8179, - "framesCount" : "10", - "bufferBeforeMergeId" : 8177, - "averageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_067_ave.dat", - "bufferAfterMeasurementId" : 15051, - "rgGuinier" : "4.38278", - "subtractedFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_067_sub.dat", - "firstPointUsed" : "36", - "chi2RgFilePath" : null, - "abInitioModelId" : null, - "macromoleculeId" : 649, - "code" : "_4.0_3.53", - "transmission" : "100.0", - "timeStart" : "2013-06-05 15:47:04.630129", - "bufferAcronym" : "B1", - "quality" : "0.742825", - "shapeDeterminationModelId" : null, - "expermientComments" : "[BsxCube] Generated from BsxCube", - "bufferId" : 422, - "isagregated" : "False", - "dmax" : "15.33973", - "bufferBeforeAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_066_ave.dat", - "exposureTemperature" : "4.0", - "subtractionId" : 3378, - "conc" : "3.5299999999999998", - "rapidShapeDeterminationModel" : null, - "experimentCreationDate" : "Jun 5, 2013 3:30:30 PM", - "lastPointUsed" : "61", - "modelListId" : null, - "framesMerge" : "10", - "rapidShapeDeterminationModelId" : null, - "bufferAfterAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_068_ave.dat", - "nsdFilePath" : null, - "bufferAfterFramesMerged" : "10", - "experimentId" : 700, - "macromoleculeAcronym" : "L9", - "i0stdev" : "0.1499898017", - "sampleMeasurementId" : 15050, - "measurementComments" : "[6]", - "priorityLevelId" : 12, - "bufferBeforeFramesMerged" : "10", - "substractionCreationTime" : "Jun 5, 2013 3:49:42 PM", - "proposalNumber" : "29", - "rgGnom" : "4.40615474861", - "volume" : "372.656", - "shapeDeterminationModel" : null, - "comments" : null, - "groupeField" : "L9 B1" - } ], - "frames_warning" : 0, - "calculation" : { - "rgGuinier" : { - "std" : 0, - "sum" : 4.38278, - "avg" : 4.38278, - "validNumber" : 1, - "totalNumber" : 1, - "values" : [ "4.38278" ] - }, - "i0Guinier" : { - "std" : 0, - "sum" : 160.023229462, - "avg" : 160.023229462, - "validNumber" : 1, - "totalNumber" : 1, - "values" : [ "160.023229462" ] - }, - "quality" : { - "std" : 0, - "sum" : 0.742825, - "avg" : 0.742825, - "validNumber" : 1, - "totalNumber" : 1, - "values" : [ "0.742825" ] - }, - "rgGnom" : { - "std" : 0, - "sum" : 4.40615474861, - "avg" : 4.40615474861, - "validNumber" : 1, - "totalNumber" : 1, - "values" : [ "4.40615474861" ] - }, - "dMax" : { - "std" : 0, - "sum" : 15.33973, - "avg" : 15.33973, - "validNumber" : 1, - "totalNumber" : 1, - "values" : [ "15.33973" ] +StockSolutionGrid.prototype._getTopButtons = function() { + var _this = this; + /** Actions buttons **/ + var actions = []; + + /** ADD BUTTON **/ + if (this.btnAddVisible) { + actions.push(Ext.create('Ext.Action', { + icon : '../images/add.png', + text : 'Add Stock Solution', + tooltip : 'Will create a new stock solution', + disabled : false, + alwaysEnabled : true, + handler : function(widget, event) { + _this.edit(); + } + })); + } + + if (this.btnAddExisting) { + actions.push(Ext.create('Ext.Action', { + icon : '../images/add.png', + text : 'Add Existing', + tooltip : 'Allows to select upacked stock solutions', + disabled : false, + alwaysEnabled : true, + handler : function(widget, event) { + var stockSolutionGrid = new StockSolutionGrid({ + btnAddVisible : false, + btnEditVisible : false, + btnRemoveVisible : false, + btnAddExisting : false, + isPackedVisible : true, + multiselect : true + }); + + var window = Ext.create('Ext.window.Window', { + title : 'Select', + height : 400, + width : 800, + layout : 'fit', + items : [ stockSolutionGrid.getPanel() ], + buttons : [ { + text : 'Pack', + handler : function() { + _this.onStockSolutionSelected.notify(stockSolutionGrid.selectedStockSolutions); + window.close(); + } + }, { + text : 'Cancel', + handler : function() { + window.close(); } + } ] + + }).show(); + + stockSolutionGrid.refresh(BIOSAXS.proposal.getUnpackedStockSolutions()); + } + })); + } + + return actions; +}; + +StockSolutionGrid.prototype.refresh = function(stockSolutions) { + this.features = stockSolutions; + this.store.loadData(this._prepareData(), false); +}; + +StockSolutionGrid.prototype._prepareData = function() { + var data = []; + for ( var i = 0; i < this.features.length; i++) { + var stockSolution = this.features[i]; + stockSolution.buffer = BIOSAXS.proposal.getBufferById(stockSolution.bufferId).acronym; + if (stockSolution.macromoleculeId != null) { + stockSolution.macromolecule = BIOSAXS.proposal.getMacromoleculeById(stockSolution.macromoleculeId).acronym; + } + data.push(stockSolution); + } + return data; +}; + +StockSolutionGrid.prototype.getPanel = function() { + return this._renderGrid(); +}; + +StockSolutionGrid.prototype.edit = function(stockSolutionId) { + var _this = this; + var stockSolutionWindow = new StockSolutionWindow(); + /** On stock solution SAVED **/ + stockSolutionWindow.onSaved.attach(function(sender, stockSolution) { + _this.onProposalChanged.notify(stockSolution); + }); + stockSolutionWindow.draw(BIOSAXS.proposal.getStockSolutionById(stockSolutionId)); +}; + +StockSolutionGrid.prototype._getStoreFields = function() { + return [ { + name : 'name', + type : 'string' + }, { + name : 'stockSolutionId', + type : 'string' + }, { + name : 'macromolecule', + type : 'string' + }, { + name : 'buffer', + type : 'string' + }, { + name : 'storageTemperature', + type : 'numeric' + }, { + name : 'volume', + type : 'string' + }, { + name : 'concentration', + type : 'string' + }, { + name : 'buffer', + type : 'string' + }, { + name : 'comments', + type : 'string' + } ]; +}; + +//StockSolutionGrid.prototype.refresh = function() { +// this.proposal.onInitialized.attach(function(sender){ +// +// }); +// this.proposal.init(Ext.urlDecode(window.location.href).sessionId); +//}; + +StockSolutionGrid.prototype._renderGrid = function() { + var _this = this; + + /** Store **/ + this.store = Ext.create('Ext.data.Store', { + fields : this._getStoreFields(), //columns, + autoload : true + }); + + var filters = { + ftype : 'filters', + local : true, + filters : this.filters + }; + + var selModel = null; + + if (this.multiselect) { + selModel = Ext.create('Ext.selection.CheckboxModel', { + //multiSelect : false,//this.multiselect, + mode : 'SINGLE', + listeners : { + selectionchange : function(sm, selections) { + _this.selectedStockSolutions = []; + for ( var i = 0; i < selections.length; i++) { + _this.selectedStockSolutions.push(selections[i].raw); } - }, { - "concentration" : "1.75", - "id" : "1.75", - "bufferId" : "422.00", - "bufferAcronym" : "B1", - "rgGuinier" : [], - "frames" : [ { - "total" : "0.5538035065", - "bufferBeforeMeasurementId" : 15051, - "sampleMergeId" : 8180, - "averagedModelId" : null, - "I0" : "146.927428571", - "proposalCode" : "OPD", - "averagedModel" : null, - "bufferAfterMergeId" : 8181, - "framesCount" : "10", - "bufferBeforeMergeId" : 8179, - "averageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_069_ave.dat", - "bufferAfterMeasurementId" : 15054, - "rgGuinier" : "4.27139", - "subtractedFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_069_sub.dat", - "firstPointUsed" : "33", - "chi2RgFilePath" : null, - "abInitioModelId" : null, - "macromoleculeId" : 649, - "code" : "_4.0_1.75", - "transmission" : "100.0", - "timeStart" : "2013-06-05 15:50:09.395824", - "bufferAcronym" : "B1", - "quality" : "0.765999", - "shapeDeterminationModelId" : null, - "expermientComments" : "[BsxCube] Generated from BsxCube", - "bufferId" : 422, - "isagregated" : "False", - "dmax" : "14.949865", - "bufferBeforeAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_068_ave.dat", - "exposureTemperature" : "4.0", - "subtractionId" : 3379, - "conc" : "1.75", - "rapidShapeDeterminationModel" : null, - "experimentCreationDate" : "Jun 5, 2013 3:30:30 PM", - "lastPointUsed" : "62", - "modelListId" : null, - "framesMerge" : "6", - "rapidShapeDeterminationModelId" : null, - "bufferAfterAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_070_ave.dat", - "nsdFilePath" : null, - "bufferAfterFramesMerged" : "10", - "experimentId" : 700, - "macromoleculeAcronym" : "L9", - "i0stdev" : "0.191914285714", - "sampleMeasurementId" : 15053, - "measurementComments" : "[7]", - "priorityLevelId" : 14, - "bufferBeforeFramesMerged" : "10", - "substractionCreationTime" : "Jun 5, 2013 3:52:31 PM", - "proposalNumber" : "29", - "rgGnom" : "4.28379338749", - "volume" : "356.326", - "shapeDeterminationModel" : null, - "comments" : null, - "groupeField" : "L9 B1" - } ], - "frames_warning" : 1, - "calculation" : { - "rgGuinier" : { - "std" : null, - "sum" : 0, - "avg" : 0, - "validNumber" : 0, - "totalNumber" : 0, - "values" : [] - }, - "i0Guinier" : { - "std" : null, - "sum" : 0, - "avg" : 0, - "validNumber" : 0, - "totalNumber" : 0, - "values" : [] - }, - "quality" : { - "std" : null, - "sum" : 0, - "avg" : 0, - "validNumber" : 0, - "totalNumber" : 0, - "values" : [] - }, - "rgGnom" : { - "std" : null, - "sum" : 0, - "avg" : 0, - "validNumber" : 0, - "totalNumber" : 0, - "values" : [] - }, - "dMax" : { - "std" : null, - "sum" : 0, - "avg" : 0, - "validNumber" : 0, - "totalNumber" : 0, - "values" : [] + } + } + }); + } else { + selModel = { + mode : 'SINGLE' + }; + } + + this.store.sort("stockSolutionId", "desc"); + + this.grid = Ext.create('Ext.grid.Panel', { + style : { + padding : 5 + }, + icon : '/ispyb/images/SampleHolder_24x24_01.png', + title : this.title, + height : this.height, + width : this.width, + minWidth : this.minWidth, + selModel : selModel, + store : this.store, + columns : this._getColumns(), + viewConfig : { + stripeRows : true, + listeners : { + itemdblclick : function(dataview, record, item, e) { + _this.edit(record.raw.stockSolutionId); + }, + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + var adapter = null; + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonUnpack') { + _this.grid.setLoading("ISPyB: Unpacking stock solution"); + adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender) { + _this.onProposalChanged.notify(); + _this.grid.setLoading(false); + }); + adapter.onError.attach(function(sender) { + _this.onProposalChanged.notify(); + _this.grid.setLoading(false); + }); + record.raw.boxId = null; + adapter.saveStockSolution(record.raw); + } + + if (grid.getGridColumns()[cellIndex].getId() == _this.id + "box") { + window.location = BUI.getShippingURL(BIOSAXS.proposal.getShipmentByDewarId(record.raw.boxId).shippingId); + } + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEdit') { + _this.edit(record.data.stockSolutionId); + } + + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemove') { + _this.grid.setLoading("ISPyB: Removing stock solution"); + adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender) { + _this.onProposalChanged.notify(); + _this.grid.setLoading(false); + }); + adapter.onError.attach(function(sender) { + _this.onProposalChanged.notify(); + _this.grid.setLoading(false); + }); + adapter.removeStockSolution(record.data.stockSolutionId); + } + } + } + } + + }); + + var actions = _this._getTopButtons(); + this.grid.addDocked({ + xtype : 'toolbar', + items : actions + }); + + var i = null; + this.grid.getSelectionModel().on({ + selectionchange : function(sm, selections) { + if (selections.length) { + for ( i = 0; i < actions.length; i++) { + if (actions[i].enable) { + actions[i].enable(); + } + } + } else { + for ( i = 0; i < actions.length; i++) { + if (actions[i].alwaysEnabled == false) { + if (actions[i].disable) { + actions[i].disable(); + } + } + } + } + } + }); + return this.grid; +}; + +StockSolutionGrid.prototype.input = function() { + return { + proposal : DATADOC.getProposal_10() + }; +}; + +StockSolutionGrid.prototype.test = function(targetId) { + var stockSolutionGrid = new StockSolutionGrid({ + height : 300, + width : 900 + }); + BIOSAXS.proposal = new Proposal(stockSolutionGrid.input().proposal); + var panel = stockSolutionGrid.getPanel(); + stockSolutionGrid.refresh(BIOSAXS.proposal.getStockSolutions()); + panel.render(targetId); +}; + + +function SuperpositionGrid(args) { + this.height = null; + this.width = null; + this.id = BUI.id(); + + if (args != null) { + if (args.height != null) { + this.height = args.height; + + if (args.width != null) { + this.width = args.width; + } + } + } + + this.onSelected = new Event(this); +} + +SuperpositionGrid.prototype._prepareData = function(data) { + return data; +}; + +SuperpositionGrid.prototype.refresh = function(subtractions) { + var data = []; + if (subtractions != null){ + if (subtractions.length > 0){ + for (j in subtractions){ + var subtraction = subtractions[j]; + if (subtraction.superposition3VOs != null){ + for (i in subtraction.superposition3VOs){ + data.push(subtraction.superposition3VOs[i]); + } + } + } + } + } + this.store.loadData(data); +}; + +SuperpositionGrid.prototype.getPanel = function() { + var _this = this; + this.store = Ext.create('Ext.data.Store', { + fields : [ 'abinitioModelPdbFilePath', 'aprioriPdbFilePath', 'alignedPdbFilePath' ], + data : [] + }); + + this.selModel = Ext.create('Ext.selection.RowModel', { + allowDeselect : true, + mode : 'MULTI', + listeners : { + selectionchange : function(sm, selections) { + var selected = []; + for (var i = 0; i < selections.length; i++) { + selected.push(selections[i].raw); + } + _this.onSelected.notify(selected); + } + } + }); + + this.store.sort([ { + property : 'name', + direction : 'ASC' + } ]); + + this.panel = Ext.create('Ext.grid.Panel', { + store : this.store, + selModel : this.selModel, + width : this.width, + height : this.height, + margin : 10, + deferredRender : false, + columns : [ { + text : 'Abinitio', + dataIndex : 'abinitioModelPdbFilePath', + hidden : false, + flex : 1, + renderer : function(val){ + return BUI.getFileName(val); + } + }, { + text : 'Apriori', + dataIndex : 'aprioriPdbFilePath', + hidden : false, + flex : 1, + renderer : function(val){ + return BUI.getFileName(val); + } + }, { + text : 'Aligned', + dataIndex : 'alignedPdbFilePath', + hidden : false, + flex : 1, + renderer : function(val){ + return BUI.getFileName(val); + } + } ], + + viewConfig : { + enableTextSelection : true, + preserveScrollOnRefresh : true + }, + listeners : { + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + + }, + afterrender : function() { + } + } + }); + return this.panel; +}; + +/** + * See ExperimentGrid + * + */ +function TemplateGrid(args) { + + if (args == null) { + args = {}; + } + args.sorters = [ { + property : 'experimentId', + direction : 'DESC' + } ]; + + ExperimentGrid.prototype.constructor.call(this, args); +} + +TemplateGrid.prototype._getFilterTypes = ExperimentGrid.prototype._getFilterTypes; +TemplateGrid.prototype._prettyPrintMacromolecules = ExperimentGrid.prototype._prettyPrintMacromolecules; +TemplateGrid.prototype._getPercentage = ExperimentGrid.prototype._getPercentage; +TemplateGrid.prototype._getPercentageCollected = ExperimentGrid.prototype._getPercentageCollected; +TemplateGrid.prototype.getPercentageMerged = ExperimentGrid.prototype.getPercentageMerged; +TemplateGrid.prototype._prepareData = ExperimentGrid.prototype._prepareData; +TemplateGrid.prototype.getPanel = ExperimentGrid.prototype.getPanel; +TemplateGrid.prototype._renderGrid = ExperimentGrid.prototype._renderGrid; +TemplateGrid.prototype._editExperiment = ExperimentGrid.prototype._editExperiment; +TemplateGrid.prototype._removeExperimentById = ExperimentGrid.prototype._removeExperimentById; + +TemplateGrid.prototype._getTopButtons = function() { + /** Actions buttons * */ + var actions = []; + + actions.push(Ext.create('Ext.Action', { + icon : '../images/add.png', + text : 'Add experiment', + handler : function(widget, event) { + var wizardWidget = new WizardWidget({ + windowMode : true + }); + + wizardWidget.onFinished.attach(function(sender, result) { + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + var experiment = new Experiment(data); + BIOSAXS.openExperimentByExperiment(experiment); + wizardWidget.window.close(); + }); + wizardWidget.current.setLoading("ISPyB: Creating experiment"); + adapter.createTemplate(result.name, "comments", result.data); + }); + +// wizardWidget.draw(this.targetId, new ExperimentTypeWizardForm()); + wizardWidget.draw(this.targetId, new MeasurementCreatorStepWizardForm(BIOSAXS.proposal.getMacromolecules())); + } + })); + return actions; +}; + +TemplateGrid.prototype.refresh = function(data) { + var filtered = []; + for ( var i = 0; i < data.length; i++) { + if (data[i].experimentType == "TEMPLATE") { + filtered.push(data[i]); + } + } + this.store.loadData(this._prepareData(filtered), false); +}; + +TemplateGrid.prototype._getColumns = function() { + var _this = this; + function actionItemRenderer(value, meta, record, rowIx, ColIx, store) { + if (record.raw.buffer3VOs != null) { + if (record.raw.buffer3VOs.length > 0) { + return 'x-hide-display'; + } + } + + if (record.data.platesCount > 0) { + return 'x-hide-display'; + } + } + + return [ { + xtype : 'rownumberer', + width : 40 + }, { + text : 'experimentId', + dataIndex : 'experimentId', + name : 'experimentId', + type : 'string', + hidden : true + }, { + text : 'Name', + dataIndex : 'name', + name : 'name', + type : 'string', + flex : 1 + }, + + { + text : 'Type', + dataIndex : 'type', + name : 'type', + type : 'string', + hidden : true, + flex : 1, + renderer : function(val) { + return val; + } + }, { + text : 'Macromolecules', + name : 'macromolecules_names', + dataIndex : 'macromolecules_names', + flex : 1, + renderer : function(val) { + return " " + val + ""; + } + }, { + id : _this.id + 'GO', + width : 80, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + return BUI.getGreenButton('EDIT'); + } + }, { + id : _this.id + 'REMOVE', + width : 100, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + return BUI.getRedButton('REMOVE'); + } + } ]; +}; + +TemplateGrid.prototype.input = function() { + var experiments = DATADOC.getExperimentList_10(); + return { + experiments : experiments, + proposal : new MeasurementGrid().input().proposal + + }; +}; + +TemplateGrid.prototype.test = function(targetId) { + var experimentGrid = new TemplateGrid({ + height : 350, + minHeight : 350, + width : 1000, + gridType : 'Ext.grid.Panel', + title : 'Experiments', + grouping : false, + tbar : true + + }); + BIOSAXS.proposal = new Proposal(experimentGrid.input().proposal); + var panel = experimentGrid.getPanel(experimentGrid.input().experiments); + experimentGrid.refresh(experimentGrid.input().experiments); + panel.render(targetId); +}; + +function VolumeGrid() { + this.id = BUI.id(); +} + +VolumeGrid.prototype.getPanel = function(experiment) { + this.experiment = experiment; + return this.render(); +}; + +VolumeGrid.prototype.getVolumesPanel = function(data, title) { + var _this = this; + var store = Ext.create('Ext.data.Store', { + fields : [ 'name', 'volume', 'macromoleculeId', 'bufferId' ], + data : data + }); + store.sort([ { + property : 'name', + direction : 'ASC' + } ]); + + var grid = Ext.create('Ext.grid.Panel', { + title : title, + height : 400, + maxHeight : 400, + width : 900, + store : store, + margin : '10 0 50 10', + tbar : [ { + text : 'Go to Shipment', + icon : '../images/plane-small.gif', + handler : function() { + window.location = BUI.getCreateShipmentList(); + } + } ], + viewConfig : { + stripeRows : true, + listeners : { + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonCreate') { + var stockSolutionWindow = new StockSolutionWindow(); + /** On stock solution SAVED **/ + stockSolutionWindow.onSaved.attach(function(sender, stockSolution) { + BIOSAXS.proposal.onInitialized.attach(function(sender, data) { + _this.refresh(_this.experiment); + }); + BIOSAXS.proposal.init(); + }); + var acronym = "ST"; + if (record.raw.macromoleculeId != null) { + acronym = acronym + "_" + BIOSAXS.proposal.getMacromoleculeById(record.raw.macromoleculeId).acronym; + } + if (record.raw.bufferId != null) { + acronym = acronym + "_" + BIOSAXS.proposal.getBufferById(record.raw.bufferId).acronym; } + stockSolutionWindow.draw({ + concentration : record.raw.concentration, + macromoleculeId : record.raw.macromoleculeId, + bufferId : record.raw.bufferId, + name : acronym, + volume : record.raw.volume + }); } - }, { - "concentration" : "0.91", - "id" : "0.91000000000000003", - "bufferId" : "422.00", - "bufferAcronym" : "B1", - "rgGuinier" : [], - "frames" : [ { - "total" : null, - "bufferBeforeMeasurementId" : 15054, - "sampleMergeId" : 8182, - "averagedModelId" : null, - "I0" : "0.0", - "proposalCode" : "OPD", - "averagedModel" : null, - "bufferAfterMergeId" : 8183, - "framesCount" : "10", - "bufferBeforeMergeId" : 8181, - "averageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_071_ave.dat", - "bufferAfterMeasurementId" : 15057, - "rgGuinier" : null, - "subtractedFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_071_sub.dat", - "firstPointUsed" : "0", - "chi2RgFilePath" : null, - "abInitioModelId" : null, - "macromoleculeId" : 649, - "code" : "_4.0_.91", - "transmission" : "100.0", - "timeStart" : "2013-06-05 15:52:58.133705", - "bufferAcronym" : "B1", - "quality" : "0.0", - "shapeDeterminationModelId" : null, - "expermientComments" : "[BsxCube] Generated from BsxCube", - "bufferId" : 422, - "isagregated" : "False", - "dmax" : null, - "bufferBeforeAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_070_ave.dat", - "exposureTemperature" : "4.0", - "subtractionId" : 3380, - "conc" : "0.91000000000000003", - "rapidShapeDeterminationModel" : null, - "experimentCreationDate" : "Jun 5, 2013 3:30:30 PM", - "lastPointUsed" : "0", - "modelListId" : null, - "framesMerge" : "10", - "rapidShapeDeterminationModelId" : null, - "bufferAfterAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_072_ave.dat", - "nsdFilePath" : null, - "bufferAfterFramesMerged" : "10", - "experimentId" : 700, - "macromoleculeAcronym" : "L9", - "i0stdev" : "0.0", - "sampleMeasurementId" : 15056, - "measurementComments" : "[8]", - "priorityLevelId" : 16, - "bufferBeforeFramesMerged" : "10", - "substractionCreationTime" : "Jun 5, 2013 3:55:35 PM", - "proposalNumber" : "29", - "rgGnom" : null, - "volume" : null, - "shapeDeterminationModel" : null, - "comments" : null, - "groupeField" : "L9 B1" - } ], - "frames_warning" : 1, - "calculation" : { - "rgGuinier" : { - "std" : null, - "sum" : 0, - "avg" : 0, - "validNumber" : 0, - "totalNumber" : 0, - "values" : [] - }, - "i0Guinier" : { - "std" : null, - "sum" : 0, - "avg" : 0, - "validNumber" : 0, - "totalNumber" : 0, - "values" : [] + + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonStockSolutions') { + var stockSolutionGrid = new StockSolutionGrid({ + btnAddVisible : false, + btnEditVisible : false, + btnRemoveVisible : false, + btnAddExisting : false, + isPackedVisible : true, + multiselect : false + }); + + var window = Ext.create('Ext.window.Window', { + title : 'Stock solutions by specimen', + height : 400, + width : 800, + layout : 'fit', + items : [ stockSolutionGrid.getPanel() ], + buttons : [ { + text : 'Close', + handler : function() { + window.close(); + } + } ] + + }).show(); + stockSolutionGrid.refresh(BIOSAXS.proposal.getStockSolutionsBySpecimen(record.raw.macromoleculeId, record.raw.bufferId)); + } + } + } + }, + columns : [ +// { +// text : '', +// dataIndex : 'macromoleculeId', +// width : 20, +// renderer : function(val, y, sample) { +// if (val != null) { +//// return BUI.getRectangleColorDIV(BIOSAXS.proposal.macromoleculeColors[val], 10, 10); +// return BUI.getRectangleColorDIV(_this.experiment.macromoleculeColors[val], 10, 10); +// } +// } +// }, +// { +// text : '', +// dataIndex : 'bufferId', +// width : 20, +// renderer : function(val, y, sample) { +// if (val != null) { +// return BUI.getRectangleColorDIV(_this.experiment.getSpecimenColorByBufferId(val), 10, 10); +// } +// } +// }, + { + text : 'Specimen', + dataIndex : 'name', + flex : 0.5 + }, + { + text : 'Estimated Volume', + dataIndex : 'volume', + tooltip : 'Estimation of the maximum volume needed for making this experiment', + flex : 0.5, + editor : { + allowBlank : true + }, + renderer : function(val, y, sample) { + return BUI.formatValuesUnits(sample.data.volume, 'µl', { + fontSize : 16, + decimals : 2, + unitsFontSize : this.unitsFontSize + }); + } + }, + { + text : 'Stock Solution', + id : _this.id + 'buttonStockSolutions', + dataIndex : 'name', + flex : 0.5, + tooltip : 'Stock Solutions containing this specimen in this proposal', + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + var macromoleculeId = record.raw.macromoleculeId; + var bufferId = record.raw.bufferId; + var stockSolutions = BIOSAXS.proposal.getStockSolutionsBySpecimen(macromoleculeId, bufferId); + if (stockSolutions.length > 0) { + return "
" + stockSolutions.length + " x
"; + } + + } + }, { + id : _this.id + 'buttonCreate', + text : '', + tooltip : 'Create a new stock solution for shipping', + width : 170, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + return BUI.getGreenButton('NEW STOCK SOLUTION', { + width : 160 + }); + } + } ] + }); + return grid; + +}; + +VolumeGrid.prototype._prepareData = function(experiment) { + var keys = {}; + for ( var i = 0; i < experiment.getSamples().length; i++) { + var sample = experiment.getSamples()[i]; + var key = ""; + if (sample.macromoleculeId == null) { + key = experiment.getBufferById(sample.bufferId).acronym; + if (keys[key] == null) { + keys[key] = { + macromoleculeId : sample.macromoleculeId, + name : key, + bufferId : sample.bufferId, + volume : 0 + }; + } + keys[key].volume = Number(sample.volume) + Number(keys[key].volume); + } + + if ((sample.macromolecule3VO != null) || (sample.macromoleculeId != null)) { + macromoleculeId = sample.macromoleculeId; + if (sample.macromoleculeId == null) { + sample.macromoleculeId = sample.macromolecule3VO.macromoleculeId; + } + key = BIOSAXS.proposal.getMacromoleculeById(sample.macromoleculeId).acronym + " + " + experiment.getBufferById(sample.bufferId).acronym; + if (keys[key] == null) { + keys[key] = { + macromoleculeId : sample.macromoleculeId, + name : key, + bufferId : sample.bufferId, + volume : 0 + }; + } + keys[key].volume = Number(sample.volume) + Number(keys[key].volume); + } + } + var data = []; + for (var keyId in keys) { + data.push(keys[keyId]); + } + + return data; +}; + +VolumeGrid.prototype.refresh = function(experiment) { + this.experiment = experiment; + this.macromoleculeGrid.getStore().loadData(this._prepareData(this.experiment), false); +}; + +VolumeGrid.prototype.render = function() { + this.macromoleculeGrid = this.getVolumesPanel(this._prepareData(this.experiment), "Estimation of required Volume"); + + return { + xtype : 'container', + layout : 'vbox', + margin : "0, 0, 0, 5", + items : [ { + xtype : 'container', + layout : 'hbox', + margin : "0, 0, 0, 0", + items : [ this.macromoleculeGrid ] + } ] + }; +}; + +VolumeGrid.prototype.input = function(experiment) { + return { + experiment : DATADOC.getExperiment_10() + }; +}; + +VolumeGrid.prototype.test = function(targetId) { + var volumeGrid = new VolumeGrid(); + BIOSAXS.proposal = new Proposal(new MeasurementGrid().input().proposal); + var panel = volumeGrid.getPanel(new Experiment(new VolumeGrid().input().experiment)); + Ext.create('Ext.panel.Panel', { + height : 500, + width : 1000, + renderTo : targetId, + items : [ panel ] + }); +}; + +/** + * Example of a tab panel to be populated with widgets + * + * @width width in pixels + * @height height in pixels + * + * #myEvent event that this class is supposed to throw + * + **/ +function ExampleTabs(args) { + this.width = 500; + this.height = 500; + + if (args != null){ + if (args.width != null){ + this.width= args.width; + } + if (args.height != null){ + this.height= args.height; + } + } + + /** Events **/ + this.myEvent = new Event(); +} + +/** Populate the widget **/ +ExampleTabs.prototype.refresh = function(macromolecule) { + +}; + +/** It creates a tab panel with the specified with and height **/ +ExampleTabs.prototype.getPanel = function() { + this.panel = Ext.createWidget('tabpanel', { + height : this.height, + width : this.width, + style : { + padding : 2 + }, + items : [ { + tabConfig : { + title : 'Test', + icon : '/ispyb/images/plane-small.gif' + }, + items : [ { + xtype : 'container', + margin : '5 5 5 5', + items : [ ] + } ] + } ] + }); + return this.panel; +}; + + +/** + * Shows an experiments with the specimens, measurements, analysis tabs where + * results are shown and the frames widget + * + * @targetId + */ +function ExperimentTabs(targetId) { + this.height = 900; + this.targetId = targetId; + + this.id = BUI.id(); + var _this = this; + + this.INTERVAL_UPDATE = BUI.getUpdateInterval(); + + this.gridHeight = 1000; + /** data * */ + this.experiment = null; + + + /** Specimen Widget contains a specimenGrid and a sampleChangerWidget than can be displayed with are vertical or horizontal layout **/ + this.specimenWidget = new SpecimenWidget({ + height : 600 + }); + + + /** For Overview * */ + /*this.samplePlateGroupWidget = new SamplePlateGroupWidget({ + showTitle : false, + height : 250, + margin : 5, + border : 0 + + });*/ + + /** For Measurements * */ + /*this.measurementSamplePlateGroupWidget = new SamplePlateGroupWidget({ + showTitle : false, + height : 250, + margin : '5 0 0 0', + border : 0 + });*/ + + this.measurementGridDone = new MeasurementGrid({ + height : 600, + minHeight : 400, + maxHeight : 800, + positionColumnsHidden : true, + showTitle : false, + estimateTime : true, + width : 900, + maxWidth : 1500, + addBtnEnable : false, + markDone : true, + removeBtnEnabled : false + }); + this.measurementGridDone.onSelected.attach(function(sender, measurements) { + var specimens = []; + for ( var i = 0; i < measurements.length; i++) { + specimens.push(_this.experiment.getSampleById(measurements[i].specimenId)); + } + //_this.measurementSamplePlateGroupWidget.selectSpecimens(specimens); + }); + + /** AnalysisGrid * */ + this.analysisGrid = new AnalysisGrid({ + height : Ext.getBody().getViewSize().height * 0.9 - 300, + positionColumnsHidden : true, + sorters : [ { + property : 'priorityLevelId', + direction : 'ASC' + } ] + }); + + + /** Queue * */ + this.queueGrid = new QueueGrid({ + url : BUI.getQueueUrlByExperiment(), + height : Ext.getBody().getViewSize().height * 0.9 - 300, + width : Ext.getBody().getViewSize().width * 0.9 - 300, + isGrouped : true, + tbar : false, + bbar : false, + sorter : [{ + property: 'measurementId', + direction: 'DESC' + }] + }); + +} + +ExperimentTabs.prototype.error = function(error) { + var e = JSON.parse(error); + showError(e); + this.panel.setLoading(false); +}; + +ExperimentTabs.prototype.draw = function(experiment) { + this.renderDataAcquisition(experiment); +}; + +ExperimentTabs.prototype.refreshAnalysisData = function() { + var _this = this; + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + _this.analysisGrid.refresh(data, {experiment : _this.experiment}); + }); + adapter.getAnalysisInformationByExperimentId(this.experiment.experimentId); + + /** Auto load **/ + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + _this.queueGrid.refresh(data); + }); + adapter.getCompactAnalysisByExperimentId(this.experiment.experimentId); + this.queueGrid.store.proxy.url = BUI.getQueueUrlByExperiment(this.experiment.experimentId); + this.queueGrid.refresh(); +}; + +ExperimentTabs.prototype.getSpecimenContainerHeight = function(experiment) { + var maxItems = 0; + if (maxItems < experiment.getSamples().length + 1) { + maxItems = experiment.getSamples().length + 1; + } + + var height = (maxItems + 1) * 40 + 40; + if (height > 400) { + height = 400; + } + return height; +}; + +ExperimentTabs.prototype.getExperimentTitle = function() { + var experimentHeaderForm = new ExperimentHeaderForm(); + return experimentHeaderForm.getPanel(this.experiment); +}; + +ExperimentTabs.prototype.renderDataAcquisition = function(experiment) { + var _this = this; + this.experiment = experiment; + + var specimenGrid = new SpecimenGrid({ + height : 400, + maxHeight : 500, + width : 890 + }); + + specimenGrid.onClick.attach(function(sender, args) { + }); + + specimenGrid.onSelected.attach(function(sender, specimens) { + //_this.samplePlateGroupWidget.selectSpecimens(specimens); + }); + var specimenContainer = this.specimenWidget.getPanel(); + this.specimenWidget.refresh(experiment); + /* + var specimenContainer = Ext.create('Ext.container.Container', { + layout : 'hbox', + width : 900, + padding : '10 0 0 2', + items : [ specimenGrid.getPanel() ] + }); + + specimenGrid.refresh(experiment);*/ + + var experimentList = new ExperimentList([ _this.experiment ]); + var measurementContainer = Ext.create('Ext.container.Container', { + layout : 'vbox', + padding : '5px 0px 0px 10px', + items : [] + }); + measurementContainer.insert(0, _this.measurementGridDone.getPanel(this.experiment.getMeasurements(), experimentList)); +// measurementContainer.insert(1, _this.measurementSamplePlateGroupWidget.getPanel(experiment)); + + // this.dataCollectionCurveVisualizer = new DataCollectionCurveVisualizer(); + // this.dataCollectionCurveVisualizer.experiments = [experiment]; + // this.dataCollectionCurveVisualizer.dataCollectionFrameTree.experiments = + // [experiment]; + // this.dataCollectionCurveVisualizer.dataCollections = + // experiment.getDataCollections(); + + this.panel = Ext.createWidget('tabpanel', { + plain : true, + style : { + padding : 2 + }, + items : [ { + tabConfig : { + id : 'genralTabl', + title : "Overview" + }, + items : [ specimenContainer ] + }, { + tabConfig : { + title : 'Measurements' + }, + items : [ measurementContainer] + }, { + tabConfig : { + id : 'SpecimenTab', + title : 'Analysis', + hidden : this.isTemplate() + }, + items : [ { + xtype : 'container', + layout : 'vbox', + padding : '5px 0px 10px 10px', + items : [ _this.analysisGrid.getPanel([]) ] + } ] + }, + { + tabConfig : { + id : 'newAnalysisTab', + title : 'Analysis BETA', + hidden : this.isTemplate() + }, + items : [ { + xtype : 'container', + layout : 'vbox', + padding : '5px 0px 10px 10px', + items : [ _this.queueGrid.getPanel([]) ] + } ] + } + ] + }); + + return this.getPanel(this.panel); +}; + +ExperimentTabs.prototype.isTemplate = function() { + if (this.experiment.json.type == "TEMPLATE") { + return true; + } + return false; +}; + +ExperimentTabs.prototype.update = function() { + var _this = this; + var inter; + if (!_this.isTemplate()) { + function updateExperiments() { + _this.refreshAnalysisData(); + window.clearInterval(inter); + inter = setInterval(function() { + updateExperiments(); + }, _this.INTERVAL_UPDATE); + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + var experiment = new Experiment(data); + _this.measurementGridDone.refresh(experiment.getMeasurements(), new ExperimentList([ experiment ])); + }); + adapter.getExperimentById(_this.experiment.json.experimentId, "MEDIUM"); + } + inter = setInterval(function() { + updateExperiments(); + }, _this.INTERVAL_UPDATE); + } +}; + +ExperimentTabs.prototype.getPanel = function(panel) { + var _this = this; + if (this.experimentPanel == null) { + this.experimentPanel = Ext.create('Ext.container.Container', { + bodyPadding : 2, + width : Ext.getBody().getViewSize().width * 0.9, + renderTo : this.targetId, + style : { + padding : 2 + }, + items : [ this.getExperimentTitle(), this.panel ], + listeners : { + afterrender : function() { + _this.refreshAnalysisData(); + _this.update(); + } + } + }); + } + + return this.experimentPanel; +}; + +ExperimentTabs.prototype.input = function() { + return { + experiment : DATADOC.getExperiment_10(), + proposal : DATADOC.getProposal_10() + }; +}; + +ExperimentTabs.prototype.test = function(targetId) { + var experimentTabs = new ExperimentTabs(targetId); + BIOSAXS.proposal = new Proposal(experimentTabs.input().proposal); + experimentTabs.draw(new Experiment(experimentTabs.input().experiment)); +}; + + + +/** + * Shows an experiments with the specimens, measurements, analysis tabs where results are shown and the frames widget + * + * @targetId + */ +function HPLCTabs(targetId) { + this.height = 1400; + this.targetId = targetId; + + this.id = BUI.id(); + + this.gridHeight = 600; + this.pointsCount = 1036; + this.plotHeight = 350; + this.plotWidth = 800; + this.plotPanelPadding = 5; + + var _this = this; + + this.analysisGrid = new HPLCAnalysisGrid({ + height : Ext.getBody().getViewSize().height * 0.9 - 300, + positionColumnsHidden : true, + sorters : [ { + property : 'priorityLevelId', + direction : 'ASC' + } ] + }); + + this.frameGrid = new FrameGrid({ + width : 600, + height : 60, + collapsed : false, + tbar : false + }); + + this.peakGrid = new PeakGrid({ + width : 550, + height : 500, + collapsed : false, + tbar : false + }); + + this.peakGrid2 = new PeakGrid({ + width : 102, + height : this.plotHeight, + collapsed : false, + tbar : false, + showExtendedColumns : true + }); + + this.mainPlotPanel = new HPLCGraph({ + title : 'I0', + width : this.plotWidth - 110, + height : this.plotHeight, + bbar : true, + plots : { + "I0" : true, + "Rg" : true + }, + xlabel : "HPLC Frames", + scaled : true, + interactionModel : { + 'dblclick' : function(event, g, context) { + _this._selectFrame(g.lastx_); + var annotations = []; + annotations.push({ + series : g.selPoints_[0].name, + x : g.lastx_, + width : 100, + height : 23, + tickHeight : 4, + shortText : g.lastx_, + text : g.lastx_, + attachAtBottom : true + }); + g.setAnnotations(annotations); + + } + } + }); + + this.intensityPlotPanel = new MergesHPLCGraph({ + title : 'Scattering', + width : this.plotWidth, + height : 500, + showRangeSelector : false, + xParam : 0, + xlabel : "scattering_I", + plots : { + "scattering_I" : true, + "subtracted_I" : true, + "buffer_I" : true + } + }); + +} + +HPLCTabs.prototype._selectFrame = function(frameNumber) { + try{ + this._renderScatteringCurve(frameNumber); + this.frameGrid.refresh([this.mainPlotPanel.getDataByFrameNumber(frameNumber)], this.experiment.experimentId); + } + catch(e){ + console.log(e); + } +}; + +HPLCTabs.prototype.error = function(error) { + var e = JSON.parse(error); + showError(e); + this.panel.setLoading(false); +}; + +HPLCTabs.prototype.loadDataMainPlot = function(data) { + var zeroArray = []; + for ( var i = 0; i < data.I0.length; i++) { + zeroArray.push(0); + } + data = [ { + param : "I0", + data : data.I0, + std : data.I0_Stdev, + color : '#0066CC', + label : "I0" + }, + { + param : "sum_I", + label : "sum_I", + color : "#00FF00", + data : data.sum_I, + std : zeroArray + }, + { + param : "Rg", + label : "Rg", + color : "#21610B", + data : data.Rg, + std : data.Rg_Stdev + }, { + param : "Mass", + data : data.mass, + std : data.mass_Stdev, + color : '#FF9900', + label : "Mass" + }, { + param : "Vc", + data : data.Vc, + std : data.Vc_Stdev, + color : '#990099', + label : "Vc" + }, { + param : "Qr", + data : data.Qr, + std : data.Qr_Stdev, + color : '#FF0066', + label : "Qr" + }, { + param : "quality", + label : "quality", + color : "#FF00FF", + data : data.quality, + std : zeroArray + } ]; + this.data = data; + this.mainPlotPanel.loadData(data); +}; + +HPLCTabs.prototype._loadIntensityPlotByFrameNumber = function(frameNumber) { + var _this = this; + + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + var array = []; + data = [ { + param : "q", + data : data[frameNumber].q, + std : data[frameNumber].q, + fstd : function(a) { + return parseFloat(a); + }, + color : '#green', + label : "q", + showOnMenu : false + }, + { + param : "scattering_I", + data : data[frameNumber].scattering_I, + fdata : function(a) { + return Math.log(parseFloat(a)); + }, + std : data[frameNumber].scattering_Stdev, + fstd : function(a) { + return Math.log(Math.abs(parseFloat(a))); + }, + color : 'green', + label : "Log(I) Sample" + }, + { + param : "buffer_I", + data : data[frameNumber].buffer_I, + fdata : function(a) { + return Math.log(parseFloat(a)); + }, + fstd : function(a) { + return Math.log(Math.abs(parseFloat(a))); + }, + std : data[frameNumber].subtracted_Stdev, + color : '#0000FF', + label : "Log(I) Avg Buf." + }, + { + param : "subtracted_I", + data : data[frameNumber].subtracted_I, + fdata : function(a) { + var value = (Math.log(parseFloat(a))); + if (isNumber(value)) + return value; + }, + fstd : function(a) { + var value = Math.log(Math.abs(parseFloat(a))); + if (isNumber(value)) + return value; + }, + std : data[frameNumber].subtracted_Stdev, + color : 'red', + label : "Log(I) Sub." + } + ]; + + _this.intensityPlotPanel.xlabel = "Frame " + frameNumber + " (q, nm-1)"; + + if (_this.intensityPlotPanel.hplcData == null) { + /** It creates also top bar **/ + _this.intensityPlotPanel.loadData(data); + } else { + _this.intensityPlotPanel.reloadData(data); + + } + _this.intensityPlotPanel.panel.setLoading(false); + }); + adapter.onError.attach(function(sender, data) { + _this.intensityPlotPanel.panel.setLoading(false); + }); + this.intensityPlotPanel.panel.setLoading("Retrieving Frame " + frameNumber); + adapter.getH5FrameScattering(this.experiment.json.experimentId, frameNumber); +}; + +HPLCTabs.prototype._renderScatteringCurve = function(frameNumber) { + var _this = this; + + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + _this.intensityPlotPanel.setPeaks(data); + _this._loadIntensityPlotByFrameNumber(frameNumber); + try{ + var peaks = []; + for(key in data){ + peaks.push({ + start : key.split("-")[0], + end : key.split("-")[1], + experimentId : _this.experiment.json.experimentId + }); + } + _this.peakGrid2.refresh(JSON.parse(JSON.stringify(peaks))); + _this.peakGrid.refresh(peaks); +// console.log(peaks); + } + catch(e){ + showError(e); + } + }); + adapter.onError.attach(function(sender, data) { + _this.intensityPlotPanel.setLoading(false); + }); + this.intensityPlotPanel.panel.setLoading("Reading HDF5 File "); + adapter.getH5FramesMerge(this.experiment.json.experimentId); +}; + +HPLCTabs.prototype._postRenderOverviewPanel = function() { + var _this = this; + var adapter = new BiosaxsDataAdapter(); + adapter.onError.attach(function(sender, data) { + data = data.replace(/NaN/g, '0'); + _this.loadDataMainPlot(JSON.parse(data)); + + + }); + adapter.onSuccess.attach(function(sender, data) { + _this.loadDataMainPlot(data); + _this._renderScatteringCurve(0); + }); + adapter.getH5fileParameters(this.experiment.json.experimentId, [ + "I0", "I0_Stdev", "sum_I","Rg", "Rg_Stdev", "Vc", "Vc_Stdev", "Qr", "Qr_Stdev", "mass", "mass_Stdev", "quality" ]); + +}; + +HPLCTabs.prototype._postRenderDetailsPanel = function() { + if (this.data != null) { + this.I0PlotPanel.loadData(this.data); + this.RgPlotPanel.loadData(this.data); + this.MassPlotPanel.loadData(this.data); + this.VcPlotPanel.loadData(this.data); + } + +}; + +HPLCTabs.prototype.draw = function(experiment) { + var _this = this; + this.renderDataAcquisition(experiment); +}; + +HPLCTabs.prototype.getExperimentTitle = function() { + var experimentHeaderForm = new ExperimentHeaderForm(); + return experimentHeaderForm.getPanel(this.experiment); +}; + +HPLCTabs.prototype.renderDataAcquisition = function(experiment) { + var _this = this; + this.experiment = experiment; + if (this.experimentPanel == null) { + this.experimentPanel = Ext.create('Ext.container.Container', { + bodyPadding : 2, + height : this.height, + width : Ext.getBody().getViewSize().width * 0.9, + renderTo : this.targetId, + style : { + padding : 2 + }, + items : [ this.getExperimentTitle(), this.getPanel() ], + listeners : { + afterrender : function() { + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + _this.analysisGrid.refresh(data); + }); + adapter.getAnalysisInformationByExperimentId(_this.experiment.experimentId); + } + } + }); + } + return this.experimentPanel; +}; + +HPLCTabs.prototype.getPanel = function() { + var _this = this; + this.panel = Ext.createWidget('tabpanel', + { + plain : true, + height : this.height, +// width : 900, + style : { + padding : 2 + }, + items : [ + { + tabConfig : { + title : "Overview" + }, - "quality" : { - "std" : null, - "sum" : 0, - "avg" : 0, - "validNumber" : 0, - "totalNumber" : 0, - "values" : [] + items : [ { + xtype : 'container', + layout : 'hbox', + border : 1, + flex : 1, + items : [ { + xtype : 'container', + layout : 'vbox', + border : 1, + items : [ { + xtype : 'container', + margin : '10px', + border : 1, + items : [ + { + xtype : 'container', + margin : '0px', + layout : 'hbox', + border : 1, + items : [ + this.peakGrid2.getPanel([]), + this.mainPlotPanel.getPanel() + ] + }, + { + xtype : 'container', + layout : 'vbox', + border : 1, + items : [ + { + html: '
Select a frame by double-clicking on the HPLC Frames plot
', + margin: 5, + border : 0 + }, + this.frameGrid.getPanel([]), + this.intensityPlotPanel.getPanel() + ] + } + + ] + }], + listeners : { + afterrender : function() { + _this._postRenderOverviewPanel(); + } + } + } ] + } ] + }, +// { +// tabConfig : { +// title : "Details" +// }, +// items : [ { +// xtype : 'container', +// layout : 'hbox', +// border : 1, +// flex : 1, +// items : [ { +// xtype : 'container', +// layout : 'vbox', +// border : 1, +// items : [ { +// xtype : 'container', +// padding : '1px', +// items : [ +// this.I0PlotPanel.getPanel(), this.RgPlotPanel.getPanel(), this.MassPlotPanel.getPanel(), +// this.VcPlotPanel.getPanel() ] +// } ], +// listeners : { +// afterrender : function() { +// _this._postRenderDetailsPanel(); +// } +// } +// } ] +// } ] +// }, + { + tabConfig : { + title : "Analysis" }, - "rgGnom" : { - "std" : null, - "sum" : 0, - "avg" : 0, - "validNumber" : 0, - "totalNumber" : 0, - "values" : [] + items : [ { + xtype : 'container', + layout : 'vbox', + padding : '5px 0px 10px 10px', + items : [ _this.analysisGrid.getPanel([]) ] + } ] + }, + { + tabConfig : { + title : "File Manager" }, - "dMax" : { - "std" : null, - "sum" : 0, - "avg" : 0, - "validNumber" : 0, - "totalNumber" : 0, - "values" : [] + items : [ { + xtype : 'container', + layout : 'vbox', + padding : '5px 0px 10px 10px', + items : [ + { + html: '
Custom Download
', + margin : '10 0 10 5', + border : 0 + }, + { + html: '
Download has been temporary disabled. Contact your labcontact if you want to extract the frames from the HDF5 file
', + margin : '10 0 10 5', + hidden : _this.experiment.experimentId == 2602, + border : 0 + }, + { + xtype : 'container', + layout : 'hbox', + margin : '0 0 0 20', + flex : 1, + items :[ + { + xtype: 'numberfield', + id: 'field_start', + fieldLabel: 'Frames from', + value: 0, + minValue: 0 + }, + { + xtype: 'numberfield', + id: 'field_end', + fieldLabel: 'to', + labelWidth : 20, + margin : '0 0 0 10', + minValue: 0 + }, + { + xtype: 'button', + /** allowing test account to download frames **/ + disabled : _this.experiment.experimentId != 2602, + text : 'Download', + margin : '0 0 0 10', + handler : function() { + var experimentId = _this.experiment.experimentId; + var start = Ext.getCmp("field_start").getValue(); + var end = Ext.getCmp("field_end").getValue(); + /** Checking if start is bigger than end **/ + if (start > end){ + var aux = end; + end = start; + start = aux; + } + var url = BUI.getZipFrameHPLCUrl(experimentId, start, end); + window.open(url) + } + } + ] + }, + _this.peakGrid.getPanel([]) + + ] + } + ] + } + ] + }); + + return this.panel; +}; + +/** + * Main form tab for macromolecule + * + * @width + * @height + * + * #onClose when user clicks on close button in the MacromoleculeForm + * #onSave when macromole is saved by macromoleculeForm + */ +function MacromoleculeTabs(args) { + this.width = 500; + this.height = 500; + + if (args != null) { + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + } + + var _this = this; + + /** Widgets **/ + + /** Macromolecule Form **/ + this.macromoleculeForm = new MacromoleculeForm({ + width : this.width - 30, + height : this.height - 50, + }); + + this.macromoleculeForm.onClose.attach(function(sender) { + _this.onClose.notify(); + }); + + this.macromoleculeForm.onSave.attach(function(sender, macromolecule) { + _this.onSave.notify(macromolecule); + }); + + this.assemblyForm = new AssemblyForm({ + width : this.width - 30, + height : this.height - 50, + }); + + this.rigibBodyModelingForm = new RigibBodyModelingForm({ + width : this.width - 30, + height : this.height - 50, + }); + + this.rigibBodyModelingForm.onSave.attach(function(sender, macromolecule) { + _this.onSave.notify(macromolecule); + }); + + + /** Events **/ + this.onClose = new Event(this); + this.onSave = new Event(this); +} + +/** Populate the widget **/ +MacromoleculeTabs.prototype.refresh = function(macromolecule) { + this.macromoleculeForm.refresh(macromolecule); + this.assemblyForm.refresh(macromolecule); + this.rigibBodyModelingForm.refresh(macromolecule); + + if (macromolecule != null){ + if (macromolecule.macromoleculeId == null){ + Ext.getCmp(this.id + "_advancedTab").disable(); + Ext.getCmp(this.id + "_assemblyTab").disable(); + } + else{ + Ext.getCmp(this.id + "_advancedTab").enable(); + Ext.getCmp(this.id + "_assemblyTab").enable(); + } + } + else{ + Ext.getCmp(this.id + "_advancedTab").disable(); + Ext.getCmp(this.id + "_assemblyTab").disable(); + } +}; + +MacromoleculeTabs.prototype.getItems = function() { + return [ { + tabConfig : { + title : 'General' + }, + items : [ { + xtype : 'container', + items : [ this.macromoleculeForm.getPanel() ] + } ] + }, { + id : this.id + "_assemblyTab", + tabConfig : { + title : 'Assembly' + }, + items : [ { + xtype : 'container', + items : [ this.assemblyForm.getPanel() ] + } ] + },{ + id : this.id + "_advancedTab", + tabConfig : { + title : 'Advanced' + }, + items : [ this.rigibBodyModelingForm.getPanel() ] + } ]; +}; + +MacromoleculeTabs.prototype.getPanel = function() { + this.panel = Ext.createWidget('tabpanel', { + height : this.height, + width : this.width, + plain : true, + margin : 5, + border : 0, + items : this.getItems() + }); + return this.panel; +}; + +function ResultTabs() { +} + +ResultTabs.prototype.draw = function(targetId, data, macromoleculeId) { + var panel = this.getPanel(targetId, data, macromoleculeId); + return Ext.create('Ext.container.Container', { + renderTo : targetId, + items : [ BUI.getMacromoleculeHeader(macromoleculeId), panel ] + }); + +}; + +ResultTabs.prototype._splitBySpecimen = function(data) { + var splitted = {}; + + for ( var i = 0; i < data.length; i++) { + var row = data[i]; + if (splitted[row.macromoleculeId + "_" + row.bufferId] == null) { + splitted[row.macromoleculeId + "_" + row.bufferId] = []; + } + splitted[row.macromoleculeId + "_" + row.bufferId].push(row); + } + return splitted; + +}; + +ResultTabs.prototype._getTabTitle = function(key, data) { + var macromoleculeId = key.split("_")[0]; + var bufferId = key.split("_")[1]; + + return BIOSAXS.proposal.getMacromoleculeById(macromoleculeId).acronym + " + " + BIOSAXS.proposal.getBufferById(bufferId).acronym + "(" + data.length + ")"; +}; + +ResultTabs.prototype.getPanel = function(targetId, data, macromoleculeId) { + + var dataFiltered = new AnalysisGrid({ + hideNulls : true, + grouped : true, + sorters : [ { + property : 'quality', + direction : 'DESC' + } ] + })._prepareData(data); + + var items = [ { + tabConfig : { + title : 'Analysis (' + dataFiltered.length + ')' + }, + items : [ { + xtype : 'container', + layout : 'vbox', + padding : 10, + items : [ new AnalysisGrid({ + isScatteringPlotVisible : false + }).getPanel(dataFiltered) ] + } ] + }, { + tabConfig : { + title : 'Concentration Effects' + }, + items : [ new ResultSummaryForm().getPanel(data) ] + } ]; + + var splitted = this._splitBySpecimen(dataFiltered); + for ( var key in splitted) { + items.push({ + tabConfig : { + title : this._getTabTitle(key, splitted[key]) + }, + items : [ new ResultSummaryForm().getPanel(splitted[key]) ] + }); + } + + this.panel = Ext.createWidget('tabpanel', { + style : { + padding : 2 + }, + items : items + }); + return this.panel; + +}; + + +function ShipmentTabs(targetId) { + this.targetId = targetId; + + var _this = this; + this.gridHeight = 500; + /** data **/ + this.shipment = null; + + /** Shipment Form **/ + this.shipmentForm = new ShipmentForm({ + creationMode : false, + showTitle : false + }); + this.shipmentForm.onSaved.attach(function(sender, data) { + _this.refresh(data); + + }); + + + /** Cases grid **/ + this.caseGrid = new CaseGrid({ + height : this.gridHeight + }); + + this.caseGrid.onAddButtonClicked.attach(function(sender, dewar) { + _this.caseGrid.grid.setLoading("ISPyB: Creating a new case"); + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, shipment) { + /** updateing shipment on proposal **/ + for ( var i = 0; i < BIOSAXS.proposal.shippings.length; i++) { + if (BIOSAXS.proposal.shippings[i].shippingId == shipment.shippingId) { + BIOSAXS.proposal.shippings[i] = shipment; + } + } + _this.refresh(shipment); + }); + adapter.onError.attach(function(sender, shipment) { + _this.caseGrid.grid.setLoading(false); + }); + adapter.addCase(_this.shipment.json.shippingId); + }); + + this.caseGrid.onRemoveButtonClicked.attach(function(sender, dewarId) { + _this.panel.setLoading("ISPyB: removing case"); + _this.shipment.onSaved.attach(function(sender, shipment) { + _this.refresh(shipment); + + }); + _this.shipment.removeCase(dewarId); + }); +} + +ShipmentTabs.prototype.refresh = function(shipment) { + + var _this = this; + this.shipment = shipment; + var proposal = new Proposal(); + proposal.onDataRetrieved.attach(function(sender, plates) { + + _this.refreshWithPlates(shipment, plates); + _this.caseGrid.grid.setLoading(false); + }); + proposal.getPlatesByProposal(); +}; + +ShipmentTabs.prototype.refreshWithPlates = function(shipment, plates) { + this.shipment = new Shipment(shipment); + + this.caseGrid.refresh(this.shipment.getDewars(), plates); + this.panel.setLoading(false); +}; + +ShipmentTabs.prototype.error = function(error) { + var e = JSON.parse(error); + showError(e); + this.panel.setLoading(false); +}; + +//ShipmentTabs.prototype.refreshTabTitles = function() { +/*Ext.getCmp("MacromoleculeTab").setText(this.getMacromoleculeTitle()); +Ext.getCmp("BufferTab").setText(this.getBuffersTitle()); +Ext.getCmp("SpecimenTab").setText(this.getSpecimenTitle()); +Ext.getCmp("PlatesTab").setText(this.getPlatesTitle()); +Ext.getCmp("AssembliesTab").setText(this.getShipmentTitle()); +Ext.getCmp("PlateGroupsTab").setText(this.getPlateGroupsTitle());*/ +//}; +ShipmentTabs.prototype.draw = function(shipment) { + var _this = this; + _this.plates = []; + _this.shipment = shipment; + _this.render(shipment); + + // var proposal = new Proposal(); + // proposal.onDataRetrieved.attach(function(sender, plates){ + // _this.plates = plates; + // _this.shipment = shipment; + // _this.render(shipment); + // + // }); + // proposal.getPlatesByProposal(); +}; + +//ShipmentTabs.prototype.getShipmentTitle = function() { +// return 'Shipment'; +//}; + +//ShipmentTabs.prototype.getMacromoleculeTitle = function() { +// return 'Macromolecules (' + this.experiment.getMacromolecules().length + ')'; +//}; + +//ShipmentTabs.prototype.getBuffersTitle = function() { +// return 'Buffers (' + this.experiment.getBuffers().length + ')'; +//}; + +//ShipmentTabs.prototype.getPlateGroupsTitle = function() { +// return 'Plate Groups (' + this.experiment.getPlateGroups().length + ')'; +//}; + +//ShipmentTabs.prototype.getSampleChangerTitle = function() { +// return 'Sample Changer'; +//}; + +//ShipmentTabs.prototype.getSpecimenTitle = function() { +// return 'Specimens(' + this.experiment.getSpecimenCount() + ')'; +//}; + +//ShipmentTabs.prototype.getPlatesTitle = function() { +// return 'Plates(' + this.experiment.getSamplePlates().length + ')'; +//}; + +//ShipmentTabs.prototype.getBuffersTip = function() { +/*if (this.experiment.getBuffers().length == 0){ + return BUI.getWarningHTML("There are no buffers. Click on add to create new ones. Click on edit button or double click to edit them"); + +} +else{ + return BUI.getTipHTML("Click on edit button or double click to edit them. Click on duplicate to create an identical buffer including its additives") +}*/ +//}; + +//ShipmentTabs.prototype.refreshTips = function() { +/*Ext.getCmp("BufferTabTip").update(this.getBuffersTip()); +Ext.getCmp("SpecimenTabTip").update(this.getSpecimensTip());*/ +//}; + +ShipmentTabs.prototype.render = function(shipment) { + return this.getPanel(shipment); +}; + +ShipmentTabs.prototype.getShipmentHeader = function(shipment) { + var _this = this; + function getHTMLSource() { + var name = shipment.json.shippingName; + var status = shipment.json.shippingStatus; + var creationDate = shipment.json.creationDate; + var html = BUI.createFormLabel("Name :", name, 75, 400); + html = html + BUI.createFormLabel("Status :", status, 75, 400); + html = html + BUI.createFormLabel("Date :", creationDate, 75, 400); + return html; + } + + return Ext.create('Ext.container.Container', { + frame : false, + layout : 'hbox', + title : 'General', + padding : 5, + bodyPadding : '5 5 0 0', + width : 890, + margin : '0 0 10 0', + height : 100, + style : { + borderColor : '#BDBDBD', + borderStyle : 'solid', + borderWidth : '1px' + }, + fieldDefaults : { + msgTarget : 'side', + labelWidth : 100 + }, + items : [ { + margin : "0 0 0 0", + width : 475, + border : 0, + html : getHTMLSource() + } + ] + }); +}; + +ShipmentTabs.prototype.getTabPanel = function(shipment) { + this.panel = Ext.createWidget('tabpanel', { + height : 600, + style : { + padding : 2 + }, + items : [ { + tabConfig : { + id : 'Shipment', + title : 'Shipment', + icon : '/ispyb/images/plane-small.gif' + }, + items : [ { + xtype : 'container', + margin : '5 5 5 5', + items : [ this.shipmentForm.getPanel(shipment) ] + } ] + }, { + tabConfig : { + id : 'Cases', + title : 'Cases', + icon : '../images/box-icon-very-small.png' + }, + items : [ { + xtype : 'container', + margin : '5 5 5 5', + items : [ this.caseGrid.getPanel(shipment.getDewars(), this.plates) ] + } ] + } ] + }); + return this.panel; +}; + +ShipmentTabs.prototype.getPanel = function(shipment) { + var _this = this; + this.shipment = shipment; + if (this.plates == null) { + this.plates = []; + } + + if (this.shipPanel == null) { + this.shipPanel = Ext.create('Ext.container.Container', { + bodyPadding : 2, + width : Ext.getBody().getViewSize().width * 0.9, + renderTo : this.targetId, + style : { + padding : 2 + }, + items : [ this.getShipmentHeader(shipment), this.getTabPanel(shipment) ] + }); + } + + return this.shipPanel; +}; + +/** + * Shows an template with the specimens, measurements and the experiment's + * requirement + * + * @targetId + */ +function TemplateTabs(targetId) { + this.height = 600; + this.targetId = targetId; + + this.id = BUI.id(); + var _this = this; + + this.gridHeight = 1000; + /** data * */ + this.experiment = null; + + this.specimenSelected = null; + + /** Specimen Widget contains a specimenGrid and a sampleChangerWidget than can be displayed with are vertical or horizontal layout **/ + this.specimenWidget = new SpecimenWidget({ + height : this.height + }); + + this.samplePlateGroupWidget = new SamplePlateGroupWidget({ + showTitle : false, + height : 250, + margin : 5, + bbar : true + }); + + this.samplePlateGroupWidget.onExperimentChanged.attach(function(sender, experiment) { + _this.refresh(experiment); + }); + + this.samplePlateGroupWidget.onClick.attach(function(sender, args) { + }); + + this.volumePlanificator = new VolumeGrid(); + + /** For Measurements * */ + var storeViscosity = Ext.create('Ext.data.Store', { + fields : [ 'name' ], + data : [ { + "name" : "low" + }, { + "name" : "medium" + }, { + "name" : "high" + } ] + }); + + // Create the combo box, attached to the states data store + var viscosityEditor = Ext.create('Ext.form.ComboBox', { + fieldLabel : '', + store : storeViscosity, + queryMode : 'local', + displayField : 'name', + valueField : 'name' + }); + + this.measurementGrid = new MeasurementGrid({ + maxWidth : 1500, + estimateTime : false, + positionColumnsHidden : true, + isPriorityColumnHidden : true, + isStatusColumnHidden : true, + isTimeColumnHidden : true, + updateRowEnabled : true, + collapsed : true, + removeBtnEnabled : true, + showTitle : false, + collapseBtnEnable : false, + addBtnMultipleEdit : true, + sortingBtnEnable : true, + editor : { + exposureTemperature : { + xtype : 'textfield', + allowBlank : true + }, + comments : { + xtype : 'textfield', + allowBlank : true + }, + volumeToLoad : { + xtype : 'numberfield', + allowBlank : true + }, + transmission : { + xtype : 'numberfield', + allowBlank : true + }, + viscosity : viscosityEditor, + waitTime : { + xtype : 'numberfield', + allowBlank : true + }, + flow : { + xtype : 'checkbox', + allowBlank : true + } + } + }); + + this.measurementGrid.onSelected.attach(function(sender, measurements) { + var specimens = []; + for ( var i = 0; i < measurements.length; i++) { + specimens.push(_this.experiment.getSampleById(measurements[i].specimenId)); + } + }); + + this.measurementGrid.onMeasurementChanged.attach(function(sender, measurement) { + _this.experiment.setMeasurement(measurement); + _this.refresh(_this.experiment); + }); + + this.measurementGrid.onExperimentChanged.attach(function(sender, json) { + _this.refresh(new Experiment(json)); + }); + + this.measurementGrid.onRemoved.attach(function(sender, experiment) { + _this.refreshSpecimen(new Experiment(experiment)); + }); + + this.measurementGrid.onUpdateTime.attach(function(sender, args) { + document.getElementById(_this.id + "_counter").innerHTML = args.hours + 'h, ' + args.minutes + 'min and ' + args.seconds + ' seconds'; + }); + +} + +TemplateTabs.prototype.refreshMeasurement = function(experiment) { + this.experiment = experiment; + this.experiment.onSaved = new Event(this); + this.experiment.onSpecimenSaved = new Event(this); + var experimentList = new ExperimentList([ this.experiment ]); + this.measurementGrid.refresh(experimentList.getMeasurementsNotCollected(), experimentList); +}; + +TemplateTabs.prototype.refreshSpecimen = function(experiment) { + this.experiment = experiment; + this.experiment.onSaved = new Event(this); + this.experiment.onSpecimenSaved = new Event(this); + this.samplePlateGroupWidget.refresh(this.experiment); + this.specimenWidget.refresh(this.experiment); + this.volumePlanificator.refresh(this.experiment); +}; + +TemplateTabs.prototype.refresh = function(experiment) { + // var start = new Date().getTime(); + this.experiment = experiment; + this.experiment.onSaved = new Event(this); + this.experiment.onSpecimenSaved = new Event(this); + + // var experimentList = new ExperimentList([this.experiment]); + this.refreshMeasurement(experiment); + this.refreshSpecimen(experiment); + /** Refreshing grids * */ + this.panel.setLoading(false); + +}; + +TemplateTabs.prototype.error = function(error) { + var e = JSON.parse(error); + showError(e); + this.panel.setLoading(false); + +}; + +TemplateTabs.prototype.draw = function(experiment) { + this.render(experiment); +}; + + +TemplateTabs.prototype.getExperimentTitle = function() { + var _this = this; + var experimentHeaderForm = new ExperimentHeaderForm(); + return experimentHeaderForm.getPanel(this.experiment); +}; + +TemplateTabs.prototype.render = function(experiment) { + var _this = this; + this.experiment = experiment; + + /** + * + * Depending on the sample Changer configuration we want to display the plates vertically or horizontally + * Default is vertical + * + * */ + + var specimenContainer = this.specimenWidget.getPanel(); + this.specimenWidget.refresh(experiment); + + var experimentList = new ExperimentList([ _this.experiment ]); + var measurementContainer = Ext.create('Ext.container.Container', { + layout : { + type : 'vbox' + }, + defaults : { + style : { + padding : '5px 0px 0px 10px' + } + }, + items : [ _this.measurementGrid.getPanel(experimentList.getMeasurementsNotCollected(), experimentList) ] + }); + + this.panel = Ext + .createWidget( + 'tabpanel', + { + plain : true, + items : [ + { + tabConfig : { + title : 'Measurements' + }, + items : [ { + xtype : 'container', + layout : 'vbox', + border : 1, +// height : _this.gridHeight, + margin : "0 0 10 0", + items : [ measurementContainer ] + } + + ] + }, + { + tabConfig : { + id : 'genralTabl', + title : "Specimens" + // width : 900, + // border : 3 + + }, + items : [ specimenContainer ] + }, + { + tabConfig : { + title : "Requirements" + + }, + items : [ + { + html : BUI.getTipHTML("Estimated volume is the maximum volume required. Depending on the order of your measurements you may use less. Click on create stock solutions if you plan to ship these stock solutions"), + margin : "10 10 10 10", + border : 0 + }, this.volumePlanificator.getPanel(experiment) ] + } ] + }); + // ); + return this.getPanel(this.panel); +}; + +TemplateTabs.prototype.isTemplate = function() { + if (this.experiment.json.type == "TEMPLATE") { + return true; + } + return false; +}; + + +TemplateTabs.prototype.getPanel = function(panel) { + var _this = this; + if (this.experimentPanel == null) { + this.experimentPanel = Ext.create('Ext.container.Container', { + bodyPadding : 2, + width : 1000,//Ext.getBody().getViewSize().width * 0.9, + renderTo : this.targetId, + height : 500, +// style : { +// padding : 2 +// }, + items : [ + this.getExperimentTitle(), + this.panel + ], + listeners : { + afterrender : function(thisCmp) { + $("#SchemeReport" + _this.experiment.experimentId).click(function() { + $(this).target = "_blank"; + window.open('viewProjectList.do?reqCode=display&menu=platescheme&experimentId=' + _this.experiment.experimentId); + return false; + }); + + } + } + }); + } + return this.experimentPanel; +}; + +TemplateTabs.prototype.input = function(targetId) { + return new ExperimentTabs().input(); +}; + +TemplateTabs.prototype.test = function(targetId) { + var experimentTabs = new TemplateTabs(targetId); + BIOSAXS.proposal = new Proposal(experimentTabs.input().proposal); + experimentTabs.draw(new Experiment(experimentTabs.input().experiment)); +}; + +var BUI = { + //interval : 60000, + interval : 40000, + rainbow : function(numOfSteps, step) { + // This function generates vibrant, "evenly spaced" colours (i.e. no clustering). This is ideal for creating easily distinguishable vibrant markers in Google Maps and other apps. + // Adam Cole, 2011-Sept-14 + // HSV to RBG adapted from: http://mjijackson.com/2008/02/rgb-to-hsl-and-rgb-to-hsv-color-model-conversion-algorithms-in-javascript + var r, g, b; + var h = step / numOfSteps; + var i = ~~(h * 6); + var f = h * 6 - i; + var q = 1 - f; + switch (i % 6) { + case 0: + r = 1, g = f, b = 0; + break; + case 1: + r = q, g = 1, b = 0; + break; + case 2: + r = 0, g = 1, b = f; + break; + case 3: + r = 0, g = q, b = 1; + break; + case 4: + r = f, g = 0, b = 1; + break; + case 5: + r = 1, g = 0, b = q; + break; + } + var c = "#" + ("00" + (~~(r * 255)).toString(16)).slice(-2) + ("00" + (~~(g * 255)).toString(16)).slice(-2) + + ("00" + (~~(b * 255)).toString(16)).slice(-2); + return (c); + }, + getFileNameByPath : function(filePath) { + if (filePath != null){ + var split = filePath.split("/"); + if (split.length > 0){ + return split[split.length - 1]; + } + } + return "Not file"; + }, + getUpdateInterval : function() { + this.interval = this.interval + 2000; + return this.interval; + }, + getRadiationDamageThreshold : function() { + return 0.7; + }, + getQualityThreshold : function() { + return 0.7; + }, + getCreateShipmentURL : function() { + return '/ispyb/user/viewProjectList.do?reqCode=display&menu=create_shipment'; + }, + getCreateShipmentList : function() { + return '/ispyb/user/viewProjectList.do?reqCode=display&menu=list_shipment'; + }, + getShippingURL : function(shippingId) { + return '/ispyb/user/viewProjectList.do?reqCode=display&menu=shipment&shippingId=' + shippingId; + }, + + getMacromoleculeResultsURLByMultipleSearch : function(array) { + return '/ispyb/user/viewProjectList.do?reqCode=display&menu=macromolecule&search=' + + JSON.stringify(array).replace(new RegExp("\"", 'g'), "'"); + }, + getMacromoleculeResultsURL : function(macromoleculeId) { + return '/ispyb/user/viewProjectList.do?reqCode=display&menu=macromolecule¯omoleculeId=' + macromoleculeId; + }, + getMacromoleculeBufferResultsURL : function(macromoleculeId, bufferId) { + return '/ispyb/user/viewProjectList.do?reqCode=display&menu=macromolecule&bufferId=' + bufferId + '¯omoleculeId=' + macromoleculeId; + }, + + getMacromoleculeHeader : function(macromoleculeId) { + + function getHTMLSource(macromoleculeId) { + if (macromoleculeId != null) { + var html = BUI.createFormLabel("Name :", BIOSAXS.proposal.getMacromoleculeById(macromoleculeId).name, 75, 400); + html = html + BUI.createFormLabel("Acronym :", BIOSAXS.proposal.getMacromoleculeById(macromoleculeId).acronym, 75, 400); + if (BIOSAXS.proposal.getMacromoleculeById(macromoleculeId).comments != null) { + html = html + BUI.createFormLabel("Comments :", BIOSAXS.proposal.getMacromoleculeById(macromoleculeId).comments, 75, 400); + } + return html; + } + } + + return Ext.create('Ext.container.Container', { + frame : false, + layout : 'hbox', + title : 'Macromolecule', + bodyPadding : '5', + width : 890, + margin : '0 0 10 0', + height : 100, + style : { + borderColor : '#BDBDBD', + borderStyle : 'solid', + borderWidth : '1px' + }, + fieldDefaults : { + msgTarget : 'side', + labelWidth : 100 + }, + items : [ { + margin : "10 0 0 10", + width : 475, + border : 0, + html : getHTMLSource(macromoleculeId) + }, { + margin : "10 0 0 10", + width : 475, + border : 0, + html : BUI.getZipHTMLByMacromoleculeId(macromoleculeId) + } + ] + }); + }, + + getZipHTMLByMacromoleculeId : function(macromoleculeId) { + if (macromoleculeId != null) { + var fileName = BIOSAXS.proposal.getMacromoleculeById(macromoleculeId).acronym; + return ""; + } + }, + getZipHTMLByExperimentId : function(experimentId, filename) { + if (filename == null){ + filename = "experiment"; + } + return ""; + }, + + getZipURLByAverageId : function(averageId, filename) { + if (filename == null){ + filename = "experiment"; + } + return "/ispyb/user/dataadapter.do?reqCode=getZipFileByAverageListId&f&mergeIdsList=" + averageId + "&fileName=" + filename; + }, + getZipURLBySubtractionId : function(subtractionId, filename) { + if (filename == null){ + filename = "experiment"; + } + return "/ispyb/user/dataadapter.do?reqCode=getZipFileByAverageListId&f&subtractionIdList=" + subtractionId + "&fileName=" + filename; + }, + + + getZipHTMLByFrameRangeId : function(experimentId, start, end) { + var fileName = "experiment"; + return ""; + }, + getZipFrameHPLCUrl : function(experimentId, start, end) { + return "/ispyb/user/dataadapter.do?reqCode=getZipFileH5ByFramesRange&f&experimentId=" + experimentId + "&start=" + Number(start) +"&end="+ Number(end); + }, + + getQueueUrl : function() { + return "/ispyb/user/dataadapter.do?reqCode=getPagingCompactAnalysisByProposalId"; + }, + + getQueueUrlByExperiment: function(experimentId) { + return "/ispyb/user/dataadapter.do?reqCode=getPagingCompactAnalysisByExperimentId&f&experimentId=" + experimentId; + }, + getStandardDeviation : function(values) { + var sum = 0; + var count = 0; + var avg = null; + + var curatedValues = new Array(); + for ( var i = 0; i < values.length; i++) { + var value = values[i]; + if (value != null) { + if (!isNaN(value)) { + count = count + 1; + sum = sum + Number(value); + curatedValues.push(Number(value)); + } + } + } + + if (count > 0) { + avg = sum / count; + } else { + avg = sum; + } + var aux = 0; + for ( var i = 0; i < curatedValues.length; i++) { + var value = curatedValues[i]; + aux = aux + Math.pow(value - avg, 2); + } + /** std **/ + var std = Math.sqrt(aux / count); + return { + std : (std), + sum : (sum), + avg : (avg), + validNumber : count, + totalNumber : values.length, + values : values + }; + }, + + getHTMLTableForFrameAveraged : function(bufferAcronym, macromoleculeAcronym, bbmerges, molmerges, bamerges, totalframes, bufferId,macromoleculeId, macromoleculeColor) { + + function getFrameSpan(framesMerged, total) { + return "(" + framesMerged + " of " + total + ")"; + } + + function getColorFrame(framesMerged, total) { + if (framesMerged / total < 0.5) { + return "#FA5858"; + } + if ((framesMerged / total >= 0.5) && (framesMerged / total < 0.8)) { + return "#FF9900"; + } + return "white"; + } + + function getRow(color, acroynm, framesMerged, totalframes) { + return " " + + BUI.getRectangleColorDIV(color, 10, 10) + + " " + acroynm + "" + + getFrameSpan(framesMerged, totalframes) + ""; + } + + var html = ""; + + /** Buffer Before **/ + if (bufferAcronym != null) { + if (bbmerges != null) { + color = BIOSAXS.proposal.bufferColors[bufferId]; + html = html + getRow(color, bufferAcronym, bbmerges, totalframes); + } + } + + /** Molecule **/ + if (macromoleculeAcronym != null) { + if (molmerges != null) { + if (macromoleculeColor == null){ + color = BIOSAXS.proposal.macromoleculeColors[macromoleculeId]; + } + else{ + color = macromoleculeColor; //BIOSAXS.proposal.macromoleculeColors[macromoleculeId]; + } + html = html + getRow(color, macromoleculeAcronym, molmerges, totalframes); + } + } + + /** Buffer After **/ + if (bufferAcronym != null) { + if (bamerges != null) { + color = BIOSAXS.proposal.bufferColors[bufferId]; + html = html + getRow(color, bufferAcronym, bamerges, totalframes); + } + } + return html + "
"; + }, + isWebGLEnabled : function(return_context) { + if (!!window.WebGLRenderingContext) { + var canvas = document.createElement("canvas"); + names = [ "webgl", "experimental-webgl", "moz-webgl", "webkit-3d" ]; + context = false; + for ( var i = 0; i < 4; i++) { + try { + context = canvas.getContext(names[i]); + if (context && typeof context.getParameter == "function") { + // WebGL is enabled + if (return_context) { + // return WebGL object if the function's argument is present + return { + name : names[i], + gl : context + }; } + // else, return just true + return true; } - } ] - }, - "concentrationLabel" : "7.17 mg/ml ,3.53 mg/ml ,1.75 mg/ml ,0.91 mg/ml " + } catch (e) { + } + } + // WebGL is supported, but disabled + return false; + } + // WebGL not supported28. + return false; + }, + getHTMLTableForPrefixes : function(bufferBeforeaverageFilePath, averageFilePath, bufferAfterAverageFilePath) { + + function getRow(bufferBeforeaverageFilePath) { + file = bufferBeforeaverageFilePath; + try { + file = bufferBeforeaverageFilePath.split("/")[bufferBeforeaverageFilePath.split("/").length - 1]; + } catch (e) { + file = "NA"; + } + return "" + file + ""; + } + var html = ""; + + /** Buffer Before **/ + if (bufferBeforeaverageFilePath != null) { + html = html + getRow(bufferBeforeaverageFilePath); + } + + /** Molecule **/ + if (averageFilePath != null) { + html = html + getRow(averageFilePath); + } + + /** Buffer After **/ + if (bufferAfterAverageFilePath != null) { + html = html + getRow(bufferAfterAverageFilePath); + } + return html + "
"; + }, + + getBaseURL : function() { + return '/ispyb/user/dataadapter.do'; + }, + + getPrintcomponentURL : function(dewarId) { + return '/ispyb/user/viewDewarAction.do?reqCode=generateLabels&dewarId=' + dewarId; + + }, + getPDBVisualizerURL : function(modelId, subtractionId, experimentId) { + return '/ispyb/user/viewProjectList.do?reqCode=display&menu=PDBVisualizer&modelId=' + modelId + '&experimentId=' + experimentId + + '&subtractionId=' + subtractionId; + }, + + getURL : function() { + return this.getBaseURL() + '?reqCode=getImage'; + + }, + getAbinitioImageURL : function() { + return this.getBaseURL() + '?reqCode=getAbinitioImage'; + }, + getNSDImageURL : function(modelListId) { + return BUI.getAbinitioImageURL() + '&type=NSD&modelListId=' + modelListId; + }, + getCHI2ImageURL : function(modelListId) { + return BUI.getAbinitioImageURL() + '&type=CHI2&modelListId=' + modelListId; + }, + getModelFile : function(type, modelId, format) { + return this.getBaseURL() + '?reqCode=getModelFile' + "&type=" + type + "&modelId=" + modelId + "&format=" + format; + }, + getPdbURL : function() { + return this.getBaseURL() + '?reqCode=getPdbFiles'; + }, + getStvArray : function(value, error) { + value = Number(value); + error = Number(error); + return [ value - error, value, value + error ]; + }, + getPointArrayForDygraph : function(x, y, error) { + return [ x, BUI.getStvArray(y, error) ]; + }, + createDIV : function(text, width, className, backgroundColor) { + var nameContainer = document.createElement("div"); + var nameSpan = document.createElement("span"); + if (className != null) { + nameSpan.setAttribute("class", className); + } + if (backgroundColor != null) { + nameSpan.setAttribute("style", "float:left;width:" + width + "px;height:18px;background-color:" + backgroundColor); + } else { + nameSpan.setAttribute("style", "float:left;width:" + width + "px;height:18px;"); + } + nameSpan.appendChild(document.createTextNode(text)); + nameContainer.appendChild(nameSpan); + return nameContainer; + }, + + createFormLabel : function(labelText, text, labelWidth, textWidth, backgroundColor) { + var div = document.createElement("div"); + + div.appendChild(BUI.createDIV(labelText, labelWidth, "bLabel", backgroundColor)); + div.appendChild(BUI.createDIV(text, textWidth, "btext", backgroundColor)); + return div.innerHTML; + }, + + createTextArea : function(labelText, text, labelWidth, rows, cols) { + var div = document.createElement("div"); + div.appendChild(BUI.createDIV(labelText, labelWidth, "bLabel")); + var textArea = document.createElement("textarea"); + textArea.setAttribute("rows", rows); + textArea.setAttribute("cols", cols); + textArea.appendChild(document.createTextNode(text)); + div.appendChild(textArea); + return div.innerHTML; + }, + + showBetaWarning : function() { + alert("ISPyB for Biosaxs version Beta has not this functionality enabled"); + }, + + formatValuesErrorUnitsScientificFormat : function(val, error, unit, args) { + var fontSize = 14; + var decimals = 2; + var errorFontSize = 10; + /** line break **/ + var lineBreak = true; + if (args != null) { + if (args.fontSize != null) { + fontSize = args.fontSize; + } + if (args.decimals != null) { + decimals = args.decimals; + } + if (args.errorFontSize != null) { + errorFontSize = args.errorFontSize; + } + if (args.lineBreak != null) { + lineBreak = args.lineBreak; + } + + } + + if (val == "") { + return ""; + } + if (error == null) { + return "" + Number(val).toFixed(decimals) + ""; + } + var html = "" + Number(val).toFixed(decimals) + " " + unit + ""; + if (lineBreak) { + html = html + "
"; + } + return html + " ± " + Number(Number(error).toFixed(3)).toExponential() + + ""; + }, + + formatValuesErrorUnits : function(val, error, unit, args) { + var fontSize = 16; + var decimals = 2; + var errorFontSize = 10; + /** line break **/ + var lineBreak = true; + if (args != null) { + if (args.fontSize != null) { + fontSize = args.fontSize; + } + if (args.decimals != null) { + decimals = args.decimals; + } + if (args.errorFontSize != null) { + errorFontSize = args.errorFontSize; + } + if (args.lineBreak != null) { + lineBreak = args.lineBreak; + } + + } + + if (val == "") { + return ""; + } + if (error == null) { + return "" + Number(val).toFixed(decimals) + ""; + } + var html = "" + Number(val).toFixed(decimals) + " " + unit + ""; + if (lineBreak) { + html = html + "
"; + } + return html + " ± " + Number(Number(error).toFixed(8)).toExponential() + + ""; + }, + + formatValuesUnits : function(val, unit, args) { + var fontSize = 12; + var decimals = 2; + var unitsFontSize = 10; + if (args != null) { + if (args.fontSize != null) { + fontSize = args.fontSize; + } + if (args.decimals != null) { + decimals = args.decimals; + } + if (args.unitsFontSize != null) { + unitsFontSize = args.unitsFontSize; + } + + } + + if (val === "") { + return ""; + } + if (unit == null) { + return "" + Number(val).toFixed(decimals) + ""; + } + return "" + Number(val).toFixed(decimals) + " " + unit + ""; + }, + + getGreenButton : function(text, args) { + var width = 70; + var height = 20; + if (args != null) { + if (args.width != null) { + width = args.width; + } + if (args.height != null) { + height = args.height; + } + } + + return ''; + }, +// getBlueButton : function(text, args) { +// var width = 70; +// var height = 20; +// if (args != null) { +// if (args.width != null) { +// width = args.width; +// } +// if (args.height != null) { +// height = args.height; +// } +// } +// +// return ''; +// }, + + getBlueButton : function(text, args) { + var width = 70; + var height = 20; + var href = null; + if (args != null) { + if (args.width != null) { + width = args.width; + } + if (args.height != null) { + height = args.height; + } + if (args.href != null) { + href = args.href; + } + } + if (href != null) { + return ''; + } else { + return ''; +// return ''; + } + }, + + getSubmitGreenButton : function(text) { + return ''; + }, + + getRedButton : function(text) { + return ''; + + }, + getRectangleColorDIV : function(color, height, width) { + return '
'; + }, + + openBufferWindow : function(bufferId) { + var window = new BufferWindow(); + window.draw(tabs.experiment.getBufferById(bufferId), tabs.experiment); + }, + + /** Render for safety levels on grids **/ + safetyRenderer : function(val, y, specimen) { + var color = val; + if (val == "YELLOW") { + color = "#E9AB17"; + } + return '' + val + ''; + }, + + getSampleColor : function() { + return '#CB181D'; + }, + + getLightSampleColor : function() { + return '#FCBBA1'; + }, + + getBufferColor : function() { + return '#6A51A3'; + }, + getLightBufferColor : function() { + return '#BCBDDC'; + }, + + formatConcentration : function(val) { + if (val != null) { + return "" + Number(val).toFixed(2) + " mg/ml "; + } + return val; + }, + + formatVolume : function(sample, volume) { + if (Number(sample.data.volumeToLoad) > Number(sample.data.volume)) { + return "" + volume + " �l"; + } + if (Number(sample.data.volumeToLoad) == Number(sample.data.volume)) { + return "" + volume + " �l"; + } + return "" + volume + " �l"; + }, + + getProposal : function() { + return new Proposal(); + }, + + getSampleNameRenderer : function(val, y, record) { + var sample = record.data; + if (record.raw.macromolecule3VO == null) { + return '' + sample.code + ''; + } else { + return '' + sample.code + ''; + } + }, + + getSafetyLevels : function() { + var safetyLevels = new Array(); + safetyLevels.push({ + safetyLevelId : "", + name : "UNKNOWN" + }); + safetyLevels.push({ + safetyLevelId : 1, + name : "GREEN" + }); + safetyLevels.push({ + safetyLevelId : 2, + name : "YELLOW" + }); + safetyLevels.push({ + safetyLevelId : 3, + name : "RED" + }); + return safetyLevels; + }, + + getErrorColor : function() { + return '#F6CED8'; + }, + getWarningColor : function() { + return '#F5DA81'; + }, + getValidColor : function() { + return '#E0F8E0'; + }, + getSamplePlateLetters : function() { + return [ "A", "B", "C", "D", "E", "F", "G", "H" ]; + }, + getSamplePositionHTML : function(sample, experiment) { + var plate = ""; + var row = ""; + var column = ""; + var rows = this.getSamplePlateLetters(); + if (sample.sampleplateposition3VO != null) { + var samplePlate = experiment.getSamplePlateById(sample.sampleplateposition3VO.samplePlateId); + if (samplePlate != null) { + plate = (samplePlate.slotPositionColumn); + row = (sample.sampleplateposition3VO.rowNumber); + column = (sample.sampleplateposition3VO.columnNumber); + // var html = "Plate: " + "" + plate + ""; + // html = html + ", Row: " + "" + rows[row - 1] + ""; + // html = html + ", Column: " + "" + column + ""; + var html = "Plate: " + plate + + "-" + rows[row - 1] + "" + column + ""; + return html; + } + } + return ""; + }, + + getSafetyLabelName : function(safetyLevelId) { + var safetyLevels = BUI.getSafetyLevels(); + for ( var i = 0; i < safetyLevels.length; i++) { + if (safetyLevels[i].safetyLevelId == safetyLevelId) { + return safetyLevels[i].name; + } + } + return "UNKNOWN"; + }, + /** generate random id **/ + id : function() { + var text = ""; + var possible = "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789"; + + for ( var i = 0; i < 5; i++) + text += possible.charAt(Math.floor(Math.random() * possible.length)); + + return text; + }, + showWarning : function(message) { + Ext.Msg.show({ + title : 'Warning', + msg : message, + icon : Ext.Msg.WARNING, + animEl : 'elId' + }); + }, + showError : function(message) { + Ext.Msg.show({ + title : 'Warning', + msg : message, + icon : Ext.Msg.ERROR, + animEl : 'elId' + }); + }, + getTipHTML : function(message) { + //return "
Tip
" + // + message + "
"; + return "
Tip
" + + message + "
"; + }, + + getWarningHTML : function(message) { + return "
Warning
" + + message + "
"; + }, + + getErrorHTML : function(message) { + return "
Error
" + + message + "
"; + }, + + getProgessBar : function(percentage, text) { + /** percentage 100% green **/ + var color = "#0a0"; + + color = "#99CC00"; + if (percentage > 100) { + color = "yellow"; + percentage = 100; + } + if (isNaN(percentage)) { + color = "white"; + percentage = 0; + } + + var defaultText = percentage + "%"; + if (text != null) { + defaultText = text; + } + + return "
" + defaultText + "
"; + }, + getFileName : function(filePath){ + if (filePath != null){ + return filePath.split("/")[filePath.split("/").length - 1] + } + return ""; + } + +}; + +Ext.ux.form.RequiredCombo = Ext.extend(Ext.form.ComboBox, { + config : { + cls : 'custom-field-text-required' + }, + initComponent : function() { + Ext.ux.form.RequiredCombo.superclass.initComponent.apply(this, arguments); + }, + checkChange : function() { + if ((this.getValue() == null) || String(this.getValue()).length == 0) { + this.addCls('custom-field-text-required'); + } else { + this.removeCls('custom-field-text-required'); + } + } +}); + +Ext.define('Ext.form.field.RequiredNumber', { + extend : 'Ext.form.field.Number', + alias : 'widget.requirednumberfield', + alternateClassName : [ 'Ext.form.RequiredNumberField', 'Ext.form.RequiredNumber' ], + config : { + cls : 'custom-field-text-required' + }, + + initComponent : function() { + var me = this; + me.callParent(); + me.setMinValue(me.minValue); + me.setMaxValue(me.maxValue); + }, + + onChange : function() { + if ((this.getValue() == null) || String(this.getValue()).length == 0) { + this.addCls('custom-field-text-required'); + } else { + this.removeCls('custom-field-text-required'); + } + this.toggleSpinners(); + this.callParent(arguments); + } +}); + +Ext.define('Ext.form.field.RequiredText', { + extend : 'Ext.form.field.Text', + alias : 'widget.requiredtext', + requires : [ 'Ext.form.field.VTypes', 'Ext.layout.component.field.Text' ], + alternateClassName : [ 'Ext.form.RequiredTextField', 'Ext.form.RequiredText' ], + config : { + cls : 'custom-field-text-required' + }, + initComponent : function() { + var me = this; + if (me.allowOnlyWhitespace === false) { + me.allowBlank = false; } - }; -}; + me.callParent(); + me.addEvents( + /** + * @event autosize + * Fires when the **{@link #autoSize}** function is triggered and the field is resized according to the + * {@link #grow}/{@link #growMin}/{@link #growMax} configs as a result. This event provides a hook for the + * developer to apply additional logic at runtime to resize the field if needed. + * @param {Ext.form.field.Text} this This text field + * @param {Number} width The new field width + */ + 'autosize', -ConcentrationHTMLTableWidget.prototype.test = function(targetId) { - var concentrationHTMLTableWidget = new ConcentrationHTMLTableWidget(); - document.getElementById(targetId).innerHTML = concentrationHTMLTableWidget.getPanel(concentrationHTMLTableWidget.input().data); -}; - -function DataCollectionWidget() { + /** + * @event keydown + * Keydown input field event. This event only fires if **{@link #enableKeyEvents}** is set to true. + * @param {Ext.form.field.Text} this This text field + * @param {Ext.EventObject} e + */ + 'keydown', + /** + * @event keyup + * Keyup input field event. This event only fires if **{@link #enableKeyEvents}** is set to true. + * @param {Ext.form.field.Text} this This text field + * @param {Ext.EventObject} e + */ + 'keyup', + /** + * @event keypress + * Keypress input field event. This event only fires if **{@link #enableKeyEvents}** is set to true. + * @param {Ext.form.field.Text} this This text field + * @param {Ext.EventObject} e + */ + 'keypress'); + me.addStateEvents('change'); + me.setGrowSizePolicy(); + }, + checkChange : function() { + if ((this.getValue() == null) || String(this.getValue()).length == 0) { + this.addCls('custom-field-text-required'); + } else { + this.removeCls('custom-field-text-required'); + } + } +}); -}; +var BIOSAXS_COMBOMANAGER = { -DataCollectionWidget.prototype.refresh = function(subtractionId) { + getComboMacromoleculeByMacromolecules : function(macromolecules, args) { + var labelWidth = 150; + var margin = "0 0 5 0"; + var width = 300; -}; + if (args != null) { + if (args.labelWidth != null) { + labelWidth = args.labelWidth; + } + if (args.margin != null) { + margin = args.margin; + } + if (args.width != null) { + width = args.width; + } + } -DataCollectionWidget.prototype.getMacromolecule = function(data) { - for (var i = 0; i < data.length; i++) { - if (data[i].macromoleculeId != null) { - return BIOSAXS.proposal.getMacromoleculeById(data[i].macromoleculeId); + var store = Ext.create('Ext.data.Store', { + fields : [ 'macromoleculeId', 'acronym' ], + data : macromolecules, + sorters : [ 'acronym' ] + }); + + return Ext.create('Ext.form.ComboBox', { + fieldLabel : 'Macromolecules', + labelWidth : labelWidth, + width : width, + margin : margin, + store : store, + editable: false, + queryMode : 'local', + displayField : 'acronym', + valueField : 'macromoleculeId' + }); + }, + getComboBuffers : function(buffers, args) { + var labelWidth = 150; + var margin = "0 0 5 0"; + var width = 300; + var fieldLabel = 'Buffer'; + + if (args != null) { + if (args.labelWidth != null) { + labelWidth = args.labelWidth; + } + if (args.margin != null) { + margin = args.margin; + } + if (args.width != null) { + width = args.width; + } + if (args.noLabel != null) { + fieldLabel = null; + } } - } - return null; -}; -DataCollectionWidget.prototype.getMacromoleculeContainer = function(data) { - var macromolecule = this.getMacromolecule(data); + var store = Ext.create('Ext.data.Store', { + fields : [ 'bufferId', 'acronym' ], + data : buffers, + sorters : [ 'acronym' ] + }); - var disabled = false; - if (macromolecule == null) { - disabled = true; - } + return Ext.create('Ext.form.ComboBox', { + fieldLabel : fieldLabel, + labelWidth : labelWidth, + width : width, + margin : margin, + editable: false, + store : store, + queryMode : 'local', + displayField : 'acronym', + valueField : 'bufferId' + }); + }, + getComboSessions : function(sessions, args) { + var labelWidth = 150; + var margin = "0 0 5 0"; + var width = 300; - var acronym = (macromolecule == null ? "" : macromolecule.acronym); - var mm = (macromolecule == null ? "" : macromolecule.molecularMass); - var comments = (macromolecule == null ? "" : macromolecule.comments); + if (args != null) { + if (args.labelWidth != null) { + labelWidth = args.labelWidth; + } + if (args.margin != null) { + margin = args.margin; + } + if (args.width != null) { + width = args.width; + } + } - return Ext.create('Ext.Panel', { - width : 500, - height : 200, - disabled : disabled, - title : "Macromolecule", - layout : 'form', - bodyPadding : 5, - defaultType : 'textfield', - tbar : { - defaultButtonUI : 'default', - items : [ { - xtype : 'button', - text : 'Edit', - cls : 'btn-with-border', - handler : function() { - var macromoleculeWindow = new MacromoleculeWindow(); - macromoleculeWindow.draw(macromolecule); - /** TODO: update when save **/ - } - } ] - }, - items : [ { - fieldLabel : 'Acronym', - name : 'first', - readOnly : true, - value : acronym - }, { - fieldLabel : 'Molecular Mass', - name : 'last', - readOnly : true, - value : mm - }, { - xtype : 'textareafield', - fieldLabel : 'Comments', - value : '', - name : 'last', - readOnly : true, - value : comments - } ] - }); -}; + for ( var i = 0; i < sessions.length; i++) { + sessions[i]["startDateFormatted"] = moment(sessions[i].startDate).format("MMM Do YY"); + sessions[i]["sorter"] = moment(sessions[i].startDate).format("YYYYMMDD"); + } -DataCollectionWidget.prototype.getBufferContainer = function(data) { - var _this = this; - var buffer = BIOSAXS.proposal.getBufferById(data[0].bufferId); + var store = Ext.create('Ext.data.Store', { + fields : [ 'sessionId', 'startDateFormatted', 'beamlineName', 'startDate', 'endDate', 'beamlineOperator' ], + data : sessions, + sorters : [ 'sorter' ] + }); - return Ext.create('Ext.Panel', { - width : 500, - height : 200, - title : "Buffer", - layout : 'form', - // collapsed : true, - // collapsible : true, - bodyPadding : 5, - defaultType : 'textfield', - style : { - padding : '0px 0px 0px 2px' - }, - tbar : { - defaultButtonUI : 'default', - items : [ { - xtype : 'button', - text : 'Edit', - cls : 'btn-with-border', - handler : function() { - var bufferWindow = new BufferWindow(); - bufferWindow.draw(BIOSAXS.proposal.getBufferById(data[0].bufferId)); - /** TODO: update when save **/ - } + return Ext.create('Ext.form.ComboBox', { + fieldLabel : 'Sessions', + labelWidth : labelWidth, + width : width, + margin : margin, + store : store, + queryMode : 'local', + // displayField : 'startDate', + valueField : 'sessionId', + // Template for the dropdown menu. + // Note the use of "x-boundlist-item" class, + // this is required to make the items selectable. + tpl : Ext.create('Ext.XTemplate', '', + '
{startDateFormatted} {beamlineName}
', ''), + // template for the content inside text field + displayTpl : Ext.create('Ext.XTemplate', '', '{startDateFormatted}', '') - } ] - }, - items : [ { - fieldLabel : 'Buffer', - name : 'acronym', - readOnly : true, - value : buffer.acronym - }, { - fieldLabel : 'Composition', - name : 'last', - readOnly : true, - value : buffer.composition + }); + } +}; + + function GenericWindow(args){ + this.title = "title"; + this.width = 700; + this.height = 500; + this.id = BUI.id(); + + this.close = false; + this.draggable = true; + this.modal = true; + + if (args != null){ + if (args.actions != null){ + this.actions = args.actions; + } + if (args.form != null){ + this.form = args.form; + } + if (args.width != null){ + this.width = args.width; + } + if (args.modal != null){ + this.modal = args.modal; + } + + if (args.height != null){ + this.height = args.height; + } + if (args.title != null){ + this.title = args.title; + } + if (args.form != null){ + this.form = args.form; + } + if (args.close != null){ + this.close = args.close; + } + if (args.draggable != null){ + this.draggable = args.draggable; + } + + } + /** Events **/ + this.onSaved = new Event(this); + }; + + + +GenericWindow.prototype.getButtons = function() { + var _this = this; + + if (this.close){ + return [ { + text : 'Close', + handler : function() { + _this.panel.close(); + } + } ]; + } + else{ + return [ { + text : 'Save', + handler : function() { + _this.save(); + + } }, { - xtype : 'textareafield', - fieldLabel : 'Comments', - value : buffer.comments, - name : 'last', - readOnly : true - - } ] - }); + text : 'Cancel', + handler : function() { + _this.panel.close(); + } + } ]; + } }; -DataCollectionWidget.prototype.getSpecimenContainer = function(data) { - return Ext.create('Ext.container.Container', { - layout : { - type : 'hbox' - }, - style : { - margin : '10px 10px 10px 10px' - }, - border : 0, - style : { - borderColor : '#000000', - borderStyle : 'solid', - borderWidth : '1px' - }, - defaults : { - labelWidth : 80, - // implicitly create Container by specifying xtype - xtype : 'datefield', - flex : 1, - - }, - items : [ this.getMacromoleculeContainer(data), this.getBufferContainer(data) ] - }); +GenericWindow.prototype.save = function (){ + alert("Method save of GenerciWindow class is abstract"); }; -DataCollectionWidget.prototype.getSeparator = function() { - return { - html : "
", - border : 0 - } +GenericWindow.prototype._postRender = function(data, experiment){ + }; -DataCollectionWidget.prototype.getFitStructurePanel = function(data) { - var _this = this; - - return Ext.create('Ext.container.Container', { - layout : { - type : 'hbox' - }, - style : { - margin : '10px 10px 10px 10px' - }, - border : 0, - style : { - borderColor : '#000000', - borderStyle : 'solid', - borderWidth : '1px' - }, - defaults : { - labelWidth : 80, - xtype : 'datefield', - flex : 1 - }, - items : [ - ] - }); +GenericWindow.prototype.draw = function (data, experiment){ + this._render(data, experiment); }; -DataCollectionWidget.prototype.getFitStructurePanelWorkflow = function(data) { - var _this = this; - var macromolecule = this.getMacromolecule(data); - - var items = []; +GenericWindow.prototype.refresh = function(data, experiment){ + this.data = data; + this.experiment = experiment; + this.form.refresh(data, experiment); +}; - /** Adding all the pdb files linked to the macromolecule **/ - // if (macromolecule.structure3VOs != null) { - // if (macromolecule.structure3VOs.length > 0) { - // - // items.push(); - // } - // } else { - // items.push({ - // html : "No apriori information added to this macromolecule. Apriori information needed for further analysis", - // margin : "5 5 5 5" - // }); - // } - var fitStructureToExperimentDataGrid = new FitStructureToExperimentDataGrid(); - - fitStructureToExperimentDataGrid.refresh(_this.data[0].subtractionId, _this.getMacromolecule(data)); - return Ext.create('Ext.container.Container', { - style : { - margin : '10px 10px 10px 10px' - }, - border : 0, +GenericWindow.prototype._render = function(data, experiment){ + this.data = data; + var _this = this; + if (this.panel == null){ + this.panel = Ext.create('Ext.Window', { + id : this.id, + title : this.title, + resizable : true, + constrain : true, + border : 1, + modal : this.modal, + frame : false, + draggable : this.draggable, + closable : true, + autoscroll : true, + layout : { type: 'vbox',align: 'stretch'}, + width : this.width, + height : this.form.height, + buttonAlign :'right', + buttons : this.getButtons(), + items : this.form.getPanel(data, experiment), + listeners: { + scope : this, + minimize : function(){ + this.panel.hide(); + }, + destroy : function(){ + delete this.panel; + } + } + }); + this.panel.setLoading(); + } + + this.panel.show(); + this._postRender(); +}; +function CalendarWidget(args) { + this.height = 740; - style : { - borderColor : '#000000', - borderStyle : 'solid', - borderWidth : '1px' - }, - defaults : { - labelWidth : 80, - xtype : 'datefield', - flex : 1 - }, - items : [ fitStructureToExperimentDataGrid.getPanel() ], - listeners : { - afterrender : function() { - } + if (args != null) { + if (args.height != null) { + this.height = args.height; } - }); -}; -/** Static method **/ -DataCollectionWidget.prototype.RUNFitScattering = function(subtractionId, structureId) { - var _this = this; - /** Add to Workflow **/ - var adapter = new BiosaxsDataAdapter(); - var workflow = { - 'workflowTitle' : 'FitExperimentalDatatoStructure', - 'comments' : 'FitExperimentalDatatoStructure run from ISPyB for subtractionId: ' + subtractionId + ' and structureId ' + structureId } - var inputs = [ { - name : 'subtractionId', - value : subtractionId - }, { - name : 'structureId', - value : structureId - } ]; + this.onClick = new Event(); +} - adapter.onSuccess.attach(function(sender, data) { - /** Add to Fit **/ - var adapter2 = new BiosaxsDataAdapter(); - var fit = { - 'workflowId' : data.workflowId, - 'subtractionId' : subtractionId, - 'structureId' : structureId, - 'comments' : 'Sent to workflow engine' - } - adapter2.onSuccess.attach(function(sender, fit) { +CalendarWidget.prototype.loadData = function(data) { + this.events = []; - }); - adapter2.addFitStructureData(fit); + for ( var i = 0; i < data.length; i++) { + var date = moment(data[i].creationDate); + var textColor = 'black'; - }); - adapter.addWorkflow(workflow, inputs); + if (data[i].status == "FINISHED") { + textColor = 'green'; + } + if (data[i].status == "ABORTED") { + textColor = 'red'; + } + this.events.push({ + title : data[i].name, + start : date.format("YYYY-MM-DD HH:mm:ss"), + end : date.format("YYYY-MM-DD HH:mm:ss"), + date : date, + allDay : false, + color : textColor, + className : date.format("YYYY-MM-DD") + }); + } }; -DataCollectionWidget.prototype.getSuperpositionTab = function(data) { +CalendarWidget.prototype.draw = function(targetId) { var _this = this; + $('#' + targetId).fullCalendar({ + eventClick : function(calEvent, jsEvent, view) { + _this.onClick.notify(calEvent.className[0]); - this.superpositionGrid = new SuperpositionGrid(); - - return Ext.create('Ext.container.Container', { - style : { - margin : '10px 10px 10px 10px' - }, - border : 0, - style : { - borderColor : '#000000', - borderStyle : 'solid', - borderWidth : '1px' - }, - items : [ _this.superpositionGrid.getPanel() ], - listeners : { - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - - }, - afterrender : function() { - /** Getting Rigid bodies **/ - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, result) { - _this.superpositionGrid.refresh(result); - }); - adapter.getSuperpositionBySubtractionId(data[1].subtractionId); - } - } - }); -}; - -DataCollectionWidget.prototype.getAdvancedTab = function(data) { - var _this = this; - return Ext.create('Ext.container.Container', { - style : { - margin : '10px 10px 10px 10px' }, - border : 0, - style : { - borderColor : '#000000', - borderStyle : 'solid', - borderWidth : '1px' + contentHeight : _this.height, + header : { + left : 'prev,next today', + center : 'title', + right : 'month,basicWeek,basicDay' }, - items : [ _this.getFitStructurePanel(data), _this.getFitStructurePanelWorkflow(data) ] + editable : false, + events : this.events }); -}; - -DataCollectionWidget.prototype.getRigiBodyForm = function(data) { - var _this = this; - _this.rigiBodyGrid = new RigidModelGrid(); - return _this.rigiBodyGrid.getPanel(); }; + +/** + * It shows a table with the guinier and gnom data as well as passed and + * discarded measurements + * + * @height + * @showBufferColumns + */ +function ConcentrationHTMLTableWidget(args) { + this.id = BUI.id(); -DataCollectionWidget.prototype.getRigidBodyModelingTab = function(data) { - var _this = this; - return Ext.create('Ext.container.Container', { - style : { - margin : '10px 10px 10px 10px' - }, - border : 0, - style : { - borderColor : '#000000', - borderStyle : 'solid', - borderWidth : '1px' - }, - items : [ _this.getRigiBodyForm(data) ], - listeners : { - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + this.showBufferColumns = true; - }, - afterrender : function() { - /** Getting Rigid bodies **/ - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, result) { - _this.rigiBodyGrid.refresh(result); - }); - adapter.getRigidBodyModelingBySubtractionId(data[1].subtractionId); - } + if (args != null) { + if (args.height != null) { + this.height = args.height; } - }); -}; - -DataCollectionWidget.prototype.getTabs = function(data) { - var _this = this; - - this.subtractionCurveVisualizer = new SubtractionCurveVisualizer(); - - this.tabs = Ext.createWidget('tabpanel', { - activeTab : 1, - plain : true, - defaults : { - autoScroll : true, - bodyPadding : 10 - }, - items : [ { - title : 'Solution', - items : [ _this.getSpecimenContainer(data) ] - }, { - title : 'Primary Data Reduction', - active : true, - tabConfig : { - xtype : 'tab', - margins : '0 0 0 20', - }, - items : [ _this.subtractionCurveVisualizer.getPanel() ] - }, { - title : 'Abinitio', - items : [ _this.getAbinitioModellingContainer(data), _this.getSeparator(), _this.getModelViz(data) ] - }, { - title : 'Mixtures', - items : [ _this.getAdvancedTab(data) ] - }, { - title : 'Superpositions', - items : [ _this.getSuperpositionTab(data) ] - }, { - title : 'Rigid Body Modeling', - items : [ _this.getRigidBodyModelingTab(data) ] - } ] - }); - return this.tabs; -}; + if (args.showBufferColumns != null) { + this.showBufferColumns = args.showBufferColumns; + } + } +} -DataCollectionWidget.prototype.getPanel = function(data) { - var _this = this; - _this.data = data; - this.panel = Ext.create('Ext.container.Container', { - width : 1000, - layout : { - type : 'vbox', - align : 'stretch', - padding : 5 - }, - items : [ _this.getTabs(data) +ConcentrationHTMLTableWidget.prototype.refresh = function(parsedData) { + document.getElementById(this.id).innerHTML = this.getPanel(parsedData); +}; - ] - }); +ConcentrationHTMLTableWidget.prototype.getPanel = function(parsedData) { + var html = "
"; + html = html + ""; - this.panel.on("afterrender", function() { - _this.subtractionCurveVisualizer.refresh([ _this.data[1].mergeId ], [ _this.data[1].subtractionId ]); - }); - return this.panel; -}; + /** Title * */ + html = html + ""; + html = html + ""; + if (this.showBufferColumns) { + html = html + ""; + } + html = html + ""; + html = html + ""; + html = html + ""; + html = html + ""; -DataCollectionWidget.prototype.getModelViz = function(data) { - this.modelViz = new ModelVisualizerForm({ - height : 800, - width : 1000 - }); - return this.modelViz.getPanel(); -}; + html = html + ""; + html = html + ""; + html = html + ""; + html = html + ""; + html = html + ""; + html = html + ""; + html = html + ""; + html = html + ""; + html = html + ""; -/** - * PRIMARY DATA PROCESSING - */ -DataCollectionWidget.prototype.getPrimaryDataProcessingContainer = function(data) { - var _this = this; - this.primaryDataProcessingGrid = new PrimaryDataProcessingGrid({ - height : 250, - width : 1000, - title : 'Primary Data Processing' + parsedData.concentration.concentrations.sort(function(a, b) { + return a.concentration - b.concentration; }); + /** Row * */ + for ( var i = 0; i < parsedData.concentration.concentrations.length; i++) { + var row = parsedData[i]; - this.primaryDataProcessingGrid.onSelected.attach(function(sender, selected) { - /** Refresh tabs **/ - var averagesId = []; - var subtractionIds = []; - - var subtractionKeys = {}; - for (var i = 0; i < selected.length; i++) { - if (selected[i].mergeId != null) { - averagesId.push(selected[i].mergeId); - } + var tr = ""; + if (i % 2 == 1) { + tr = ""; + } + var goodMeasurements = (parsedData.concentration.concentrations[i].frames.length - parsedData.concentration.concentrations[i].frames_warning); + if (goodMeasurements == 0) { + tr = ""; + } + html = html + tr; + html = html + ""; + if (this.showBufferColumns) { + html = html + ""; + } + html = html + ""; + html = html + ""; + html = html + ""; + html = html + ""; + html = html + ""; + html = html + ""; + html = html + ""; + html = html + ""; + } + return html + "
ConcentrationBufferMeasurementsGuinierGnom
PassedDiscardedRgI0QualityRgdMax
" + parsedData.concentration.concentrations[i].concentration + "" + parsedData.concentration.concentrations[i].bufferAcronym + "" + goodMeasurements + " of " + parsedData.concentration.concentrations[i].frames.length + "" + parsedData.concentration.concentrations[i].frames_warning + "" + BUI.formatValuesErrorUnits(parsedData.concentration.concentrations[i].calculation.rgGuinier.avg, parsedData.concentration.concentrations[i].calculation.rgGuinier.std, "nm", { + lineBreak : false + }) + "" + BUI.formatValuesErrorUnits(parsedData.concentration.concentrations[i].calculation.i0Guinier.avg, parsedData.concentration.concentrations[i].calculation.i0Guinier.std, " ", { + lineBreak : false + }) + "" + BUI.formatValuesErrorUnits(parsedData.concentration.concentrations[i].calculation.quality.avg, parsedData.concentration.concentrations[i].calculation.quality.std, " ", { + lineBreak : false + }) + "" + BUI.formatValuesErrorUnits(parsedData.concentration.concentrations[i].calculation.rgGnom.avg, parsedData.concentration.concentrations[i].calculation.rgGnom.std, " ", { + lineBreak : false + }) + "" + BUI.formatValuesErrorUnits(parsedData.concentration.concentrations[i].calculation.dMax.avg, parsedData.concentration.concentrations[i].calculation.dMax.std, " ", { + lineBreak : false + }) + "
"; +}; - if (selected[i].subtractionId != null) { - if (selected[i].macromoleculeId != null) { - if (subtractionKeys[selected[i].subtractionId] == null) { - subtractionIds.push(selected[i].subtractionId); +ConcentrationHTMLTableWidget.prototype.input = function() { + return { + data : { + "dataCollectionCount" : 4, + "buffers" : [ { + "bufferId" : "422" + } ], + "concentration" : { + "concentrations" : [ { + "concentration" : "7.17", + "id" : "7.1699999999999999", + "bufferId" : "422.00", + "bufferAcronym" : "B1", + "rgGuinier" : [ "5.12723" ], + "frames" : [ { + "total" : "0.515705406286", + "bufferBeforeMeasurementId" : 15045, + "sampleMergeId" : 8176, + "averagedModelId" : null, + "I0" : "183.457461646", + "proposalCode" : "OPD", + "averagedModel" : null, + "bufferAfterMergeId" : 8177, + "framesCount" : "10", + "bufferBeforeMergeId" : 8175, + "averageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_065_ave.dat", + "bufferAfterMeasurementId" : 15048, + "rgGuinier" : "5.12723", + "subtractedFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_065_sub.dat", + "firstPointUsed" : "17", + "chi2RgFilePath" : null, + "abInitioModelId" : null, + "macromoleculeId" : 649, + "code" : "_4.0_7.17", + "transmission" : "100.0", + "timeStart" : "2013-06-05 15:43:54.348723", + "bufferAcronym" : "B1", + "quality" : "0.853011", + "shapeDeterminationModelId" : null, + "expermientComments" : "[BsxCube] Generated from BsxCube", + "bufferId" : 422, + "isagregated" : "False", + "dmax" : "25.63615", + "bufferBeforeAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_064_ave.dat", + "exposureTemperature" : "4.0", + "subtractionId" : 3377, + "conc" : "7.1699999999999999", + "rapidShapeDeterminationModel" : null, + "experimentCreationDate" : "Jun 5, 2013 3:30:30 PM", + "lastPointUsed" : "36", + "modelListId" : null, + "framesMerge" : "9", + "rapidShapeDeterminationModelId" : null, + "bufferAfterAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_066_ave.dat", + "nsdFilePath" : null, + "bufferAfterFramesMerged" : "10", + "experimentId" : 700, + "macromoleculeAcronym" : "L9", + "i0stdev" : "0.139364435146", + "sampleMeasurementId" : 15047, + "measurementComments" : "[5]", + "priorityLevelId" : 10, + "bufferBeforeFramesMerged" : "10", + "substractionCreationTime" : "Jun 5, 2013 3:46:31 PM", + "proposalNumber" : "29", + "rgGnom" : "5.40297914939", + "volume" : "475.302", + "shapeDeterminationModel" : null, + "comments" : null, + "groupeField" : "L9 B1" + } ], + "frames_warning" : 0, + "calculation" : { + "rgGuinier" : { + "std" : 0, + "sum" : 5.12723, + "avg" : 5.12723, + "validNumber" : 1, + "totalNumber" : 1, + "values" : [ "5.12723" ] + }, + "i0Guinier" : { + "std" : 0, + "sum" : 183.457461646, + "avg" : 183.457461646, + "validNumber" : 1, + "totalNumber" : 1, + "values" : [ "183.457461646" ] + }, + "quality" : { + "std" : 0, + "sum" : 0.853011, + "avg" : 0.853011, + "validNumber" : 1, + "totalNumber" : 1, + "values" : [ "0.853011" ] + }, + "rgGnom" : { + "std" : 0, + "sum" : 5.40297914939, + "avg" : 5.40297914939, + "validNumber" : 1, + "totalNumber" : 1, + "values" : [ "5.40297914939" ] + }, + "dMax" : { + "std" : 0, + "sum" : 25.63615, + "avg" : 25.63615, + "validNumber" : 1, + "totalNumber" : 1, + "values" : [ "25.63615" ] + } + } + }, { + "concentration" : "3.53", + "id" : "3.5299999999999998", + "bufferId" : "422.00", + "bufferAcronym" : "B1", + "rgGuinier" : [ "4.38278" ], + "frames" : [ { + "total" : "0.497164741078", + "bufferBeforeMeasurementId" : 15048, + "sampleMergeId" : 8178, + "averagedModelId" : null, + "I0" : "160.023229462", + "proposalCode" : "OPD", + "averagedModel" : null, + "bufferAfterMergeId" : 8179, + "framesCount" : "10", + "bufferBeforeMergeId" : 8177, + "averageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_067_ave.dat", + "bufferAfterMeasurementId" : 15051, + "rgGuinier" : "4.38278", + "subtractedFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_067_sub.dat", + "firstPointUsed" : "36", + "chi2RgFilePath" : null, + "abInitioModelId" : null, + "macromoleculeId" : 649, + "code" : "_4.0_3.53", + "transmission" : "100.0", + "timeStart" : "2013-06-05 15:47:04.630129", + "bufferAcronym" : "B1", + "quality" : "0.742825", + "shapeDeterminationModelId" : null, + "expermientComments" : "[BsxCube] Generated from BsxCube", + "bufferId" : 422, + "isagregated" : "False", + "dmax" : "15.33973", + "bufferBeforeAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_066_ave.dat", + "exposureTemperature" : "4.0", + "subtractionId" : 3378, + "conc" : "3.5299999999999998", + "rapidShapeDeterminationModel" : null, + "experimentCreationDate" : "Jun 5, 2013 3:30:30 PM", + "lastPointUsed" : "61", + "modelListId" : null, + "framesMerge" : "10", + "rapidShapeDeterminationModelId" : null, + "bufferAfterAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_068_ave.dat", + "nsdFilePath" : null, + "bufferAfterFramesMerged" : "10", + "experimentId" : 700, + "macromoleculeAcronym" : "L9", + "i0stdev" : "0.1499898017", + "sampleMeasurementId" : 15050, + "measurementComments" : "[6]", + "priorityLevelId" : 12, + "bufferBeforeFramesMerged" : "10", + "substractionCreationTime" : "Jun 5, 2013 3:49:42 PM", + "proposalNumber" : "29", + "rgGnom" : "4.40615474861", + "volume" : "372.656", + "shapeDeterminationModel" : null, + "comments" : null, + "groupeField" : "L9 B1" + } ], + "frames_warning" : 0, + "calculation" : { + "rgGuinier" : { + "std" : 0, + "sum" : 4.38278, + "avg" : 4.38278, + "validNumber" : 1, + "totalNumber" : 1, + "values" : [ "4.38278" ] + }, + "i0Guinier" : { + "std" : 0, + "sum" : 160.023229462, + "avg" : 160.023229462, + "validNumber" : 1, + "totalNumber" : 1, + "values" : [ "160.023229462" ] + }, + "quality" : { + "std" : 0, + "sum" : 0.742825, + "avg" : 0.742825, + "validNumber" : 1, + "totalNumber" : 1, + "values" : [ "0.742825" ] + }, + "rgGnom" : { + "std" : 0, + "sum" : 4.40615474861, + "avg" : 4.40615474861, + "validNumber" : 1, + "totalNumber" : 1, + "values" : [ "4.40615474861" ] + }, + "dMax" : { + "std" : 0, + "sum" : 15.33973, + "avg" : 15.33973, + "validNumber" : 1, + "totalNumber" : 1, + "values" : [ "15.33973" ] + } + } + }, { + "concentration" : "1.75", + "id" : "1.75", + "bufferId" : "422.00", + "bufferAcronym" : "B1", + "rgGuinier" : [], + "frames" : [ { + "total" : "0.5538035065", + "bufferBeforeMeasurementId" : 15051, + "sampleMergeId" : 8180, + "averagedModelId" : null, + "I0" : "146.927428571", + "proposalCode" : "OPD", + "averagedModel" : null, + "bufferAfterMergeId" : 8181, + "framesCount" : "10", + "bufferBeforeMergeId" : 8179, + "averageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_069_ave.dat", + "bufferAfterMeasurementId" : 15054, + "rgGuinier" : "4.27139", + "subtractedFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_069_sub.dat", + "firstPointUsed" : "33", + "chi2RgFilePath" : null, + "abInitioModelId" : null, + "macromoleculeId" : 649, + "code" : "_4.0_1.75", + "transmission" : "100.0", + "timeStart" : "2013-06-05 15:50:09.395824", + "bufferAcronym" : "B1", + "quality" : "0.765999", + "shapeDeterminationModelId" : null, + "expermientComments" : "[BsxCube] Generated from BsxCube", + "bufferId" : 422, + "isagregated" : "False", + "dmax" : "14.949865", + "bufferBeforeAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_068_ave.dat", + "exposureTemperature" : "4.0", + "subtractionId" : 3379, + "conc" : "1.75", + "rapidShapeDeterminationModel" : null, + "experimentCreationDate" : "Jun 5, 2013 3:30:30 PM", + "lastPointUsed" : "62", + "modelListId" : null, + "framesMerge" : "6", + "rapidShapeDeterminationModelId" : null, + "bufferAfterAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_070_ave.dat", + "nsdFilePath" : null, + "bufferAfterFramesMerged" : "10", + "experimentId" : 700, + "macromoleculeAcronym" : "L9", + "i0stdev" : "0.191914285714", + "sampleMeasurementId" : 15053, + "measurementComments" : "[7]", + "priorityLevelId" : 14, + "bufferBeforeFramesMerged" : "10", + "substractionCreationTime" : "Jun 5, 2013 3:52:31 PM", + "proposalNumber" : "29", + "rgGnom" : "4.28379338749", + "volume" : "356.326", + "shapeDeterminationModel" : null, + "comments" : null, + "groupeField" : "L9 B1" + } ], + "frames_warning" : 1, + "calculation" : { + "rgGuinier" : { + "std" : null, + "sum" : 0, + "avg" : 0, + "validNumber" : 0, + "totalNumber" : 0, + "values" : [] + }, + "i0Guinier" : { + "std" : null, + "sum" : 0, + "avg" : 0, + "validNumber" : 0, + "totalNumber" : 0, + "values" : [] + }, + "quality" : { + "std" : null, + "sum" : 0, + "avg" : 0, + "validNumber" : 0, + "totalNumber" : 0, + "values" : [] + }, + "rgGnom" : { + "std" : null, + "sum" : 0, + "avg" : 0, + "validNumber" : 0, + "totalNumber" : 0, + "values" : [] + }, + "dMax" : { + "std" : null, + "sum" : 0, + "avg" : 0, + "validNumber" : 0, + "totalNumber" : 0, + "values" : [] + } + } + }, { + "concentration" : "0.91", + "id" : "0.91000000000000003", + "bufferId" : "422.00", + "bufferAcronym" : "B1", + "rgGuinier" : [], + "frames" : [ { + "total" : null, + "bufferBeforeMeasurementId" : 15054, + "sampleMergeId" : 8182, + "averagedModelId" : null, + "I0" : "0.0", + "proposalCode" : "OPD", + "averagedModel" : null, + "bufferAfterMergeId" : 8183, + "framesCount" : "10", + "bufferBeforeMergeId" : 8181, + "averageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_071_ave.dat", + "bufferAfterMeasurementId" : 15057, + "rgGuinier" : null, + "subtractedFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_071_sub.dat", + "firstPointUsed" : "0", + "chi2RgFilePath" : null, + "abInitioModelId" : null, + "macromoleculeId" : 649, + "code" : "_4.0_.91", + "transmission" : "100.0", + "timeStart" : "2013-06-05 15:52:58.133705", + "bufferAcronym" : "B1", + "quality" : "0.0", + "shapeDeterminationModelId" : null, + "expermientComments" : "[BsxCube] Generated from BsxCube", + "bufferId" : 422, + "isagregated" : "False", + "dmax" : null, + "bufferBeforeAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_070_ave.dat", + "exposureTemperature" : "4.0", + "subtractionId" : 3380, + "conc" : "0.91000000000000003", + "rapidShapeDeterminationModel" : null, + "experimentCreationDate" : "Jun 5, 2013 3:30:30 PM", + "lastPointUsed" : "0", + "modelListId" : null, + "framesMerge" : "10", + "rapidShapeDeterminationModelId" : null, + "bufferAfterAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_072_ave.dat", + "nsdFilePath" : null, + "bufferAfterFramesMerged" : "10", + "experimentId" : 700, + "macromoleculeAcronym" : "L9", + "i0stdev" : "0.0", + "sampleMeasurementId" : 15056, + "measurementComments" : "[8]", + "priorityLevelId" : 16, + "bufferBeforeFramesMerged" : "10", + "substractionCreationTime" : "Jun 5, 2013 3:55:35 PM", + "proposalNumber" : "29", + "rgGnom" : null, + "volume" : null, + "shapeDeterminationModel" : null, + "comments" : null, + "groupeField" : "L9 B1" + } ], + "frames_warning" : 1, + "calculation" : { + "rgGuinier" : { + "std" : null, + "sum" : 0, + "avg" : 0, + "validNumber" : 0, + "totalNumber" : 0, + "values" : [] + }, + "i0Guinier" : { + "std" : null, + "sum" : 0, + "avg" : 0, + "validNumber" : 0, + "totalNumber" : 0, + "values" : [] + }, + "quality" : { + "std" : null, + "sum" : 0, + "avg" : 0, + "validNumber" : 0, + "totalNumber" : 0, + "values" : [] + }, + "rgGnom" : { + "std" : null, + "sum" : 0, + "avg" : 0, + "validNumber" : 0, + "totalNumber" : 0, + "values" : [] + }, + "dMax" : { + "std" : null, + "sum" : 0, + "avg" : 0, + "validNumber" : 0, + "totalNumber" : 0, + "values" : [] + } } - subtractionKeys[selected[i].subtractionId] = true; - } - } + } ] + }, + "concentrationLabel" : "7.17 mg/ml ,3.53 mg/ml ,1.75 mg/ml ,0.91 mg/ml " } - - /** Refreshing Primary Data Reduction **/ - _this.subtractionCurveVisualizer.refresh(averagesId, subtractionIds); - - }); - return this.primaryDataProcessingGrid.getPanel(data); + }; }; -/** - * getAbinitioModellingContainer - */ -DataCollectionWidget.prototype.getAbinitioModellingContainer = function(data) { - var _this = this; - - this.abinitioGrid = new AbinitioGrid(); - this.abinitioGrid.onSelected.attach(function(sender, models) { - _this.modelViz.refresh(models); - - }); - /** It may be abinitio models linked to the buffers **/ - var abinitioIdList = []; - for (var i = 0; i < data.length; i++) { - abinitioIdList.push(data[i].abInitioId); - } - - var uniqueIds = []; - $.each(abinitioIdList, function(i, el) { - if ($.inArray(el, uniqueIds) === -1) - uniqueIds.push(el); - }); - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - _this.abinitioGrid.refresh(data); - }); - adapter.getAbinitioByIdsList(uniqueIds); - return this.abinitioGrid.getPanel([]); +ConcentrationHTMLTableWidget.prototype.test = function(targetId) { + var concentrationHTMLTableWidget = new ConcentrationHTMLTableWidget(); + document.getElementById(targetId).innerHTML = concentrationHTMLTableWidget.getPanel(concentrationHTMLTableWidget.input().data); }; +function DataCollectionWidget() { + +}; + +DataCollectionWidget.prototype.refresh = function(subtractionId) { + +}; + +DataCollectionWidget.prototype.getMacromolecule = function(data) { + for (var i = 0; i < data.length; i++) { + if (data[i].macromoleculeId != null) { + return BIOSAXS.proposal.getMacromoleculeById(data[i].macromoleculeId); + } + } + return null; +}; + +DataCollectionWidget.prototype.getMacromoleculeContainer = function(data) { + var macromolecule = this.getMacromolecule(data); + + var disabled = false; + if (macromolecule == null) { + disabled = true; + } + + var acronym = (macromolecule == null ? "" : macromolecule.acronym); + var mm = (macromolecule == null ? "" : macromolecule.molecularMass); + var comments = (macromolecule == null ? "" : macromolecule.comments); + + return Ext.create('Ext.Panel', { + width : 500, + height : 200, + disabled : disabled, + title : "Macromolecule", + layout : 'form', + bodyPadding : 5, + defaultType : 'textfield', + tbar : { + defaultButtonUI : 'default', + items : [ { + xtype : 'button', + text : 'Edit', + cls : 'btn-with-border', + handler : function() { + var macromoleculeWindow = new MacromoleculeWindow(); + macromoleculeWindow.draw(macromolecule); + /** TODO: update when save **/ + } + } ] + }, + items : [ { + fieldLabel : 'Acronym', + name : 'first', + readOnly : true, + value : acronym + }, { + fieldLabel : 'Molecular Mass', + name : 'last', + readOnly : true, + value : mm + }, { + xtype : 'textareafield', + fieldLabel : 'Comments', + value : '', + name : 'last', + readOnly : true, + value : comments + } ] + }); +}; + +DataCollectionWidget.prototype.getBufferContainer = function(data) { + var _this = this; + var buffer = BIOSAXS.proposal.getBufferById(data[0].bufferId); + + return Ext.create('Ext.Panel', { + width : 500, + height : 200, + title : "Buffer", + layout : 'form', + // collapsed : true, + // collapsible : true, + bodyPadding : 5, + defaultType : 'textfield', + style : { + padding : '0px 0px 0px 2px' + }, + tbar : { + defaultButtonUI : 'default', + items : [ { + xtype : 'button', + text : 'Edit', + cls : 'btn-with-border', + handler : function() { + var bufferWindow = new BufferWindow(); + bufferWindow.draw(BIOSAXS.proposal.getBufferById(data[0].bufferId)); + /** TODO: update when save **/ + } + + } ] + }, + items : [ { + fieldLabel : 'Buffer', + name : 'acronym', + readOnly : true, + value : buffer.acronym + }, { + fieldLabel : 'Composition', + name : 'last', + readOnly : true, + value : buffer.composition + }, { + xtype : 'textareafield', + fieldLabel : 'Comments', + value : buffer.comments, + name : 'last', + readOnly : true + + } ] + }); +}; + +DataCollectionWidget.prototype.getSpecimenContainer = function(data) { + return Ext.create('Ext.container.Container', { + layout : { + type : 'hbox' + }, + style : { + margin : '10px 10px 10px 10px' + }, + border : 0, + style : { + borderColor : '#000000', + borderStyle : 'solid', + borderWidth : '1px' + }, + defaults : { + labelWidth : 80, + // implicitly create Container by specifying xtype + xtype : 'datefield', + flex : 1, + + }, + items : [ this.getMacromoleculeContainer(data), this.getBufferContainer(data) ] + }); +}; + +DataCollectionWidget.prototype.getSeparator = function() { + return { + html : "
", + border : 0 + } +}; + +DataCollectionWidget.prototype.getFitStructurePanel = function(data) { + var _this = this; + + return Ext.create('Ext.container.Container', { + layout : { + type : 'hbox' + }, + style : { + margin : '10px 10px 10px 10px' + }, + border : 0, + style : { + borderColor : '#000000', + borderStyle : 'solid', + borderWidth : '1px' + }, + defaults : { + labelWidth : 80, + xtype : 'datefield', + flex : 1 + }, + items : [ + + ] + }); +}; + +DataCollectionWidget.prototype.getFitStructurePanelWorkflow = function(data) { + var _this = this; + var macromolecule = this.getMacromolecule(data); + + var items = []; + + /** Adding all the pdb files linked to the macromolecule **/ + // if (macromolecule.structure3VOs != null) { + // if (macromolecule.structure3VOs.length > 0) { + // + // items.push(); + // } + // } else { + // items.push({ + // html : "No apriori information added to this macromolecule. Apriori information needed for further analysis", + // margin : "5 5 5 5" + // }); + // } + var fitStructureToExperimentDataGrid = new FitStructureToExperimentDataGrid(); + + fitStructureToExperimentDataGrid.refresh(_this.data[0].subtractionId, _this.getMacromolecule(data)); + return Ext.create('Ext.container.Container', { + style : { + margin : '10px 10px 10px 10px' + }, + border : 0, + + style : { + borderColor : '#000000', + borderStyle : 'solid', + borderWidth : '1px' + }, + defaults : { + labelWidth : 80, + xtype : 'datefield', + flex : 1 + }, + items : [ fitStructureToExperimentDataGrid.getPanel() ], + listeners : { + afterrender : function() { + } + } + }); +}; +/** Static method **/ +DataCollectionWidget.prototype.RUNFitScattering = function(subtractionId, structureId) { + var _this = this; + /** Add to Workflow **/ + var adapter = new BiosaxsDataAdapter(); + var workflow = { + 'workflowTitle' : 'FitExperimentalDatatoStructure', + 'comments' : 'FitExperimentalDatatoStructure run from ISPyB for subtractionId: ' + subtractionId + ' and structureId ' + structureId + } + + var inputs = [ { + name : 'subtractionId', + value : subtractionId + }, { + name : 'structureId', + value : structureId + } ]; + + adapter.onSuccess.attach(function(sender, data) { + /** Add to Fit **/ + var adapter2 = new BiosaxsDataAdapter(); + var fit = { + 'workflowId' : data.workflowId, + 'subtractionId' : subtractionId, + 'structureId' : structureId, + 'comments' : 'Sent to workflow engine' + } + adapter2.onSuccess.attach(function(sender, fit) { + + }); + adapter2.addFitStructureData(fit); + + }); + adapter.addWorkflow(workflow, inputs); + +}; + +DataCollectionWidget.prototype.getSuperpositionTab = function(data) { + var _this = this; + + this.superpositionGrid = new SuperpositionGrid(); + + return Ext.create('Ext.container.Container', { + style : { + margin : '10px 10px 10px 10px' + }, + border : 0, + style : { + borderColor : '#000000', + borderStyle : 'solid', + borderWidth : '1px' + }, + items : [ _this.superpositionGrid.getPanel() ], + listeners : { + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + + }, + afterrender : function() { + /** Getting Rigid bodies **/ + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, result) { + _this.superpositionGrid.refresh(result); + }); + adapter.getSuperpositionBySubtractionId(data[1].subtractionId); + } + } + }); +}; + +DataCollectionWidget.prototype.getAdvancedTab = function(data) { + var _this = this; + return Ext.create('Ext.container.Container', { + style : { + margin : '10px 10px 10px 10px' + }, + border : 0, + style : { + borderColor : '#000000', + borderStyle : 'solid', + borderWidth : '1px' + }, + items : [ _this.getFitStructurePanel(data), _this.getFitStructurePanelWorkflow(data) ] + }); +}; + +DataCollectionWidget.prototype.getRigiBodyForm = function(data) { + var _this = this; + _this.rigiBodyGrid = new RigidModelGrid(); + return _this.rigiBodyGrid.getPanel(); + +}; + +DataCollectionWidget.prototype.getRigidBodyModelingTab = function(data) { + var _this = this; + return Ext.create('Ext.container.Container', { + style : { + margin : '10px 10px 10px 10px' + }, + border : 0, + style : { + borderColor : '#000000', + borderStyle : 'solid', + borderWidth : '1px' + }, + items : [ _this.getRigiBodyForm(data) ], + listeners : { + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + + }, + afterrender : function() { + /** Getting Rigid bodies **/ + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, result) { + _this.rigiBodyGrid.refresh(result); + }); + adapter.getRigidBodyModelingBySubtractionId(data[1].subtractionId); + } + } + }); +}; + +DataCollectionWidget.prototype.getTabs = function(data) { + var _this = this; + + this.subtractionCurveVisualizer = new SubtractionCurveVisualizer(); + + this.tabs = Ext.createWidget('tabpanel', { + activeTab : 1, + plain : true, + defaults : { + autoScroll : true, + bodyPadding : 10 + }, + items : [ { + title : 'Solution', + items : [ _this.getSpecimenContainer(data) ] + }, { + title : 'Primary Data Reduction', + active : true, + tabConfig : { + xtype : 'tab', + margins : '0 0 0 20', + }, + items : [ _this.subtractionCurveVisualizer.getPanel() ] + }, { + title : 'Abinitio', + items : [ _this.getAbinitioModellingContainer(data), _this.getSeparator(), _this.getModelViz(data) ] + }, { + title : 'Mixtures', + items : [ _this.getAdvancedTab(data) ] + }, { + title : 'Superpositions', + items : [ _this.getSuperpositionTab(data) ] + }, { + title : 'Rigid Body Modeling', + items : [ _this.getRigidBodyModelingTab(data) ] + } ] + }); + return this.tabs; +}; + +DataCollectionWidget.prototype.getPanel = function(data) { + var _this = this; + _this.data = data; + this.panel = Ext.create('Ext.container.Container', { + width : 1000, + layout : { + type : 'vbox', + align : 'stretch', + padding : 5 + }, + items : [ _this.getTabs(data) + + ] + }); + + this.panel.on("afterrender", function() { + _this.subtractionCurveVisualizer.refresh([ _this.data[1].mergeId ], [ _this.data[1].subtractionId ]); + }); + return this.panel; +}; + +DataCollectionWidget.prototype.getModelViz = function(data) { + this.modelViz = new ModelVisualizerForm({ + height : 800, + width : 1000 + }); + return this.modelViz.getPanel(); +}; + +/** + * PRIMARY DATA PROCESSING + */ +DataCollectionWidget.prototype.getPrimaryDataProcessingContainer = function(data) { + var _this = this; + this.primaryDataProcessingGrid = new PrimaryDataProcessingGrid({ + height : 250, + width : 1000, + title : 'Primary Data Processing' + }); + + this.primaryDataProcessingGrid.onSelected.attach(function(sender, selected) { + /** Refresh tabs **/ + var averagesId = []; + var subtractionIds = []; + + var subtractionKeys = {}; + for (var i = 0; i < selected.length; i++) { + if (selected[i].mergeId != null) { + averagesId.push(selected[i].mergeId); + } + + if (selected[i].subtractionId != null) { + if (selected[i].macromoleculeId != null) { + if (subtractionKeys[selected[i].subtractionId] == null) { + subtractionIds.push(selected[i].subtractionId); + } + subtractionKeys[selected[i].subtractionId] = true; + } + } + } + + /** Refreshing Primary Data Reduction **/ + _this.subtractionCurveVisualizer.refresh(averagesId, subtractionIds); + + }); + return this.primaryDataProcessingGrid.getPanel(data); +}; +/** + * getAbinitioModellingContainer + */ +DataCollectionWidget.prototype.getAbinitioModellingContainer = function(data) { + var _this = this; + + this.abinitioGrid = new AbinitioGrid(); + this.abinitioGrid.onSelected.attach(function(sender, models) { + _this.modelViz.refresh(models); + + }); + /** It may be abinitio models linked to the buffers **/ + var abinitioIdList = []; + for (var i = 0; i < data.length; i++) { + abinitioIdList.push(data[i].abInitioId); + } + + var uniqueIds = []; + $.each(abinitioIdList, function(i, el) { + if ($.inArray(el, uniqueIds) === -1) + uniqueIds.push(el); + }); + + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + _this.abinitioGrid.refresh(data); + }); + adapter.getAbinitioByIdsList(uniqueIds); + return this.abinitioGrid.getPanel([]); +}; + /** * Edit the information of a buffer * @@ -29163,258 +29163,258 @@ ShippingWidget.prototype.refresh = function() { }; -/** - * Widget container of Specimen grid and samplePlate widget - * Depending of the sample changer layout it may be displayed vertically or horizontally - * - * @param args - * - * #onExperimentChanged It happens when specimen are modified - */ -function SpecimenWidget(args){ - - this.width = 1000; - this.height = 600; - - if (args != null){ - if (args.width != null){ - this.width = args.width; - } - if (args.height != null){ - this.height = args.height; - } - } - - var _this = this; - - /** Specimen Grid **/ - this.specimenGrid = new SpecimenGrid({ - minHeight : 425, - selectionMode : "SINGLE", - editEnabled : false, - updateRowEnabled : true, - width : 900, - showTitle : false - }); - - - this.specimenGrid.onSpecimenChanged.attach(function(sender, specimen) { - _this.experiment.setSpecimenById(specimen); - _this.refresh(_this.experiment); - }); - - this.specimenGrid.onSelected.attach(function(sender, specimens) { - if (specimens.length > 0) { - _this.specimenSelected = specimens[0]; - } else { - _this.specimenSelected = null; - } - _this.samplePlateGroupWidget.selectSpecimens(specimens); - }); - - - /** Sample plate Widget **/ - this.samplePlateGroupWidget = new SamplePlateGroupWidget({ - showTitle : false, - height : 250, - margin : 5, - bbar : true - }); - - - this.samplePlateGroupWidget.onExperimentChanged.attach(function(sender, json) { - _this.refresh(new Experiment(json)); - }); - - this.samplePlateGroupWidget.onClick.attach(function(sender, args) { - /** Clicking on a plate * */ - var row = args.row; - var column = args.column; - var samplePlateId = args.samplePlate.samplePlateId; - - /** is specimen selected on the grid? * */ - if (_this.specimenSelected != null) { - /** Is position target empty * */ - if (_this.experiment.getSampleByPosition(args.samplePlate.samplePlateId, args.row, args.column).length == 0) { - var specimen = _this.experiment.getSampleById(_this.specimenSelected.specimenId); - if (specimen.sampleplateposition3VO == null) { - specimen.sampleplateposition3VO = {}; - } - - specimen.sampleplateposition3VO = { - columnNumber : column, - rowNumber : row, - samplePlateId : samplePlateId - }; - - _this.samplePlateGroupWidget.panel.setLoading("ISPyB: Saving specimen"); - var adapter = new BiosaxsDataAdapter(); - /** If success * */ - adapter.onSuccess.attach(function(sender, experiment) { - _this.samplePlateGroupWidget.panel.setLoading(false); - }); - - adapter.onError.attach(function(sender, error) { - _this.samplePlateGroupWidget.panel.setLoading(false); - showError(error); - }); - - adapter.saveSpecimen(specimen, _this.experiment); - - _this.samplePlateGroupWidget.refresh(_this.experiment); - _this.specimenGrid.refresh(_this.experiment); - //_this.refresh(_this.experiment); - _this.specimenGrid.deselectAll(); - - } else { - /** - * Can we merge? We can merge when specimen are the - * same. So, same buffer, macromolecule, concentration * - */ - var target = _this.experiment.getSampleByPosition(args.samplePlate.samplePlateId, args.row, args.column)[0]; - var specimen = _this.experiment.getSampleById(_this.specimenSelected.specimenId); - - if ((specimen.bufferId == target.bufferId) && (specimen.concentration == target.concentration)) { - if (((specimen.macromolecule3VO != null) && (target.macromolecule3VO != null) && (specimen.macromolecule3VO.macromoleculeId == target.macromolecule3VO.macromoleculeId)) || - ((specimen.macromolecule3VO == null) && (target.macromolecule3VO == null))) { - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - _this.refresh(new Experiment(data)); - _this.samplePlateGroupWidget.panel.setLoading(false); - - _this.onExperimentChanged.notify(experiment); - }); - adapter.onError.attach(function(sender, error) { - _this.samplePlateGroupWidget.panel.setLoading(false); - showError(error); - }); - _this.samplePlateGroupWidget.panel.setLoading("ISPyB: Merging specimens"); - adapter.mergeSpecimens(specimen.specimenId, target.specimenId); - } - } else { - alert("Well is not empty. Select another well!"); - } - } - } else { - var specimen = _this.experiment.getSampleByPosition(args.samplePlate.samplePlateId, args.row, args.column)[0]; - if (specimen != null) { - _this.specimenGrid.selectById(specimen.specimenId); - } - } - }); - - /** Events **/ - this.onExperimentChanged = new Event(this); -}; - -/** - * Return vbox or hbox depending on the slot positions of the plates - */ -SpecimenWidget.prototype.getContainerLayoutConfiguration = function(experiment){ - var dimensions = this.samplePlateGroupWidget.getDimensions(experiment.getSamplePlates()); - if (dimensions.maxSlotPositionRow < dimensions.maxSlotPositionColumn){ - return { - layout : "vbox", - specimenGridWidth : this.width - 10, - specimenGridHeight : this.height - 260, - samplePlateGroupWidth : this.width - 10, - samplePlateGroupHeight : 250 - }; - } - return { - layout : "hbox", - samplePlateGroupWidth : this.width*1/3 -10, - samplePlateGroupHeight : this.height - 10, - specimenGridWidth : this.width*2/3, - specimenGridHeight : this.height - 10 - }; - -}; - - -SpecimenWidget.prototype.refresh = function(experiment){ - this.experiment = experiment; - - /** Removing all components **/ - this.panel.removeAll(); - - var layoutConfiguration = this.getContainerLayoutConfiguration(experiment); - - /** Setting new width and height for layout vbox and hbox **/ - this.specimenGrid.width = layoutConfiguration.specimenGridWidth; - this.specimenGrid.height = layoutConfiguration.specimenGridHeight; - - this.samplePlateGroupWidget.width = layoutConfiguration.samplePlateGroupWidth; - this.samplePlateGroupWidget.height = layoutConfiguration.samplePlateGroupHeight; - - if (layoutConfiguration.layout == "hbox"){ - this.specimenGrid.margin = "0 0 0 5"; - this.specimenGrid.width =this.specimenGrid.width - 5; - } - /** Insert container depending on layout [vertical|horizontal] */ - var container = Ext.create('Ext.container.Container', { - layout : layoutConfiguration.layout, - height : this.height, - width : this.width, - padding : '2px', - items : [ ] - }); - if (layoutConfiguration.layout == "vbox"){ - container.insert(this.specimenGrid.getPanel()); - container.insert(this.samplePlateGroupWidget.getPanel()); - } - else{ - container.insert(this.samplePlateGroupWidget.getPanel()); - container.insert(this.specimenGrid.getPanel()); - } - - /** Insert Widget **/ - this.panel.insert(container); - - /** Load data **/ - this.specimenGrid.refresh(experiment); - this.samplePlateGroupWidget.refresh(experiment); - - -}; - -/** It creates a dummy container to be inserted the plates once the method refresh has been called - * This is necessay because we can not know the sample changer layout before hand - * **/ -SpecimenWidget.prototype.getPanel = function(){ - this.panel = Ext.create('Ext.container.Container', { - layout : 'vbox', - height : this.height, - border : 0, - margin : 5, - width : this.width, - items : [] - }); - return this.panel; -}; - - -SpecimenWidget.prototype.input = function() { - return { - experiment : DATADOC.getExperiment_10(), - proposal : DATADOC.getProposal_10() - }; -}; - -SpecimenWidget.prototype.test = function(targetId) { - var specimenWidget = new SpecimenWidget({ - height : 500, - width : 1000 - }); - BIOSAXS.proposal = new Proposal(specimenWidget.input().proposal); - var experiment = new Experiment(specimenWidget.input().experiment); - var panel = specimenWidget.getPanel(); - panel.render(targetId); - specimenWidget.refresh(experiment); - -}; - - +/** + * Widget container of Specimen grid and samplePlate widget + * Depending of the sample changer layout it may be displayed vertically or horizontally + * + * @param args + * + * #onExperimentChanged It happens when specimen are modified + */ +function SpecimenWidget(args){ + + this.width = 1000; + this.height = 600; + + if (args != null){ + if (args.width != null){ + this.width = args.width; + } + if (args.height != null){ + this.height = args.height; + } + } + + var _this = this; + + /** Specimen Grid **/ + this.specimenGrid = new SpecimenGrid({ + minHeight : 425, + selectionMode : "SINGLE", + editEnabled : false, + updateRowEnabled : true, + width : 900, + showTitle : false + }); + + + this.specimenGrid.onSpecimenChanged.attach(function(sender, specimen) { + _this.experiment.setSpecimenById(specimen); + _this.refresh(_this.experiment); + }); + + this.specimenGrid.onSelected.attach(function(sender, specimens) { + if (specimens.length > 0) { + _this.specimenSelected = specimens[0]; + } else { + _this.specimenSelected = null; + } + _this.samplePlateGroupWidget.selectSpecimens(specimens); + }); + + + /** Sample plate Widget **/ + this.samplePlateGroupWidget = new SamplePlateGroupWidget({ + showTitle : false, + height : 250, + margin : 5, + bbar : true + }); + + + this.samplePlateGroupWidget.onExperimentChanged.attach(function(sender, json) { + _this.refresh(new Experiment(json)); + }); + + this.samplePlateGroupWidget.onClick.attach(function(sender, args) { + /** Clicking on a plate * */ + var row = args.row; + var column = args.column; + var samplePlateId = args.samplePlate.samplePlateId; + + /** is specimen selected on the grid? * */ + if (_this.specimenSelected != null) { + /** Is position target empty * */ + if (_this.experiment.getSampleByPosition(args.samplePlate.samplePlateId, args.row, args.column).length == 0) { + var specimen = _this.experiment.getSampleById(_this.specimenSelected.specimenId); + if (specimen.sampleplateposition3VO == null) { + specimen.sampleplateposition3VO = {}; + } + + specimen.sampleplateposition3VO = { + columnNumber : column, + rowNumber : row, + samplePlateId : samplePlateId + }; + + _this.samplePlateGroupWidget.panel.setLoading("ISPyB: Saving specimen"); + var adapter = new BiosaxsDataAdapter(); + /** If success * */ + adapter.onSuccess.attach(function(sender, experiment) { + _this.samplePlateGroupWidget.panel.setLoading(false); + }); + + adapter.onError.attach(function(sender, error) { + _this.samplePlateGroupWidget.panel.setLoading(false); + showError(error); + }); + + adapter.saveSpecimen(specimen, _this.experiment); + + _this.samplePlateGroupWidget.refresh(_this.experiment); + _this.specimenGrid.refresh(_this.experiment); + //_this.refresh(_this.experiment); + _this.specimenGrid.deselectAll(); + + } else { + /** + * Can we merge? We can merge when specimen are the + * same. So, same buffer, macromolecule, concentration * + */ + var target = _this.experiment.getSampleByPosition(args.samplePlate.samplePlateId, args.row, args.column)[0]; + var specimen = _this.experiment.getSampleById(_this.specimenSelected.specimenId); + + if ((specimen.bufferId == target.bufferId) && (specimen.concentration == target.concentration)) { + if (((specimen.macromolecule3VO != null) && (target.macromolecule3VO != null) && (specimen.macromolecule3VO.macromoleculeId == target.macromolecule3VO.macromoleculeId)) || + ((specimen.macromolecule3VO == null) && (target.macromolecule3VO == null))) { + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + _this.refresh(new Experiment(data)); + _this.samplePlateGroupWidget.panel.setLoading(false); + + _this.onExperimentChanged.notify(experiment); + }); + adapter.onError.attach(function(sender, error) { + _this.samplePlateGroupWidget.panel.setLoading(false); + showError(error); + }); + _this.samplePlateGroupWidget.panel.setLoading("ISPyB: Merging specimens"); + adapter.mergeSpecimens(specimen.specimenId, target.specimenId); + } + } else { + alert("Well is not empty. Select another well!"); + } + } + } else { + var specimen = _this.experiment.getSampleByPosition(args.samplePlate.samplePlateId, args.row, args.column)[0]; + if (specimen != null) { + _this.specimenGrid.selectById(specimen.specimenId); + } + } + }); + + /** Events **/ + this.onExperimentChanged = new Event(this); +}; + +/** + * Return vbox or hbox depending on the slot positions of the plates + */ +SpecimenWidget.prototype.getContainerLayoutConfiguration = function(experiment){ + var dimensions = this.samplePlateGroupWidget.getDimensions(experiment.getSamplePlates()); + if (dimensions.maxSlotPositionRow < dimensions.maxSlotPositionColumn){ + return { + layout : "vbox", + specimenGridWidth : this.width - 10, + specimenGridHeight : this.height - 260, + samplePlateGroupWidth : this.width - 10, + samplePlateGroupHeight : 250 + }; + } + return { + layout : "hbox", + samplePlateGroupWidth : this.width*1/3 -10, + samplePlateGroupHeight : this.height - 10, + specimenGridWidth : this.width*2/3, + specimenGridHeight : this.height - 10 + }; + +}; + + +SpecimenWidget.prototype.refresh = function(experiment){ + this.experiment = experiment; + + /** Removing all components **/ + this.panel.removeAll(); + + var layoutConfiguration = this.getContainerLayoutConfiguration(experiment); + + /** Setting new width and height for layout vbox and hbox **/ + this.specimenGrid.width = layoutConfiguration.specimenGridWidth; + this.specimenGrid.height = layoutConfiguration.specimenGridHeight; + + this.samplePlateGroupWidget.width = layoutConfiguration.samplePlateGroupWidth; + this.samplePlateGroupWidget.height = layoutConfiguration.samplePlateGroupHeight; + + if (layoutConfiguration.layout == "hbox"){ + this.specimenGrid.margin = "0 0 0 5"; + this.specimenGrid.width =this.specimenGrid.width - 5; + } + /** Insert container depending on layout [vertical|horizontal] */ + var container = Ext.create('Ext.container.Container', { + layout : layoutConfiguration.layout, + height : this.height, + width : this.width, + padding : '2px', + items : [ ] + }); + if (layoutConfiguration.layout == "vbox"){ + container.insert(this.specimenGrid.getPanel()); + container.insert(this.samplePlateGroupWidget.getPanel()); + } + else{ + container.insert(this.samplePlateGroupWidget.getPanel()); + container.insert(this.specimenGrid.getPanel()); + } + + /** Insert Widget **/ + this.panel.insert(container); + + /** Load data **/ + this.specimenGrid.refresh(experiment); + this.samplePlateGroupWidget.refresh(experiment); + + +}; + +/** It creates a dummy container to be inserted the plates once the method refresh has been called + * This is necessay because we can not know the sample changer layout before hand + * **/ +SpecimenWidget.prototype.getPanel = function(){ + this.panel = Ext.create('Ext.container.Container', { + layout : 'vbox', + height : this.height, + border : 0, + margin : 5, + width : this.width, + items : [] + }); + return this.panel; +}; + + +SpecimenWidget.prototype.input = function() { + return { + experiment : DATADOC.getExperiment_10(), + proposal : DATADOC.getProposal_10() + }; +}; + +SpecimenWidget.prototype.test = function(targetId) { + var specimenWidget = new SpecimenWidget({ + height : 500, + width : 1000 + }); + BIOSAXS.proposal = new Proposal(specimenWidget.input().proposal); + var experiment = new Experiment(specimenWidget.input().experiment); + var panel = specimenWidget.getPanel(); + panel.render(targetId); + specimenWidget.refresh(experiment); + +}; + + function WarningWidget(args) { this.actions = []; diff --git a/ispyb-ws/src/main/java/ispyb/ws/rest/mx/DataCollectionRestWebService.java b/ispyb-ws/src/main/java/ispyb/ws/rest/mx/DataCollectionRestWebService.java index 82f7cae2b..5a80a23f0 100644 --- a/ispyb-ws/src/main/java/ispyb/ws/rest/mx/DataCollectionRestWebService.java +++ b/ispyb-ws/src/main/java/ispyb/ws/rest/mx/DataCollectionRestWebService.java @@ -217,16 +217,16 @@ public Response getViewDataCollectionBySessionId(@PathParam("token") String toke @RolesAllowed({"User", "Manager", "Industrial", "Localcontact"}) @GET - @Path("{token}/proposal/{proposal}/mx/datacollection/session/{sessionId}/report/{reportType}/pdf") + @Path("{token}/proposal/{proposal}/mx/datacollection/session/{sessionId}/report/{nbRows}/pdf") @Produces({ "application/pdf" }) public Response getDataCollectionsReportBySessionIdPDF(@PathParam("token") String token, @PathParam("proposal") String proposal, - @PathParam("sessionId") String sessionId, @PathParam("reportType") String reportType) throws NamingException { + @PathParam("sessionId") String sessionId, @PathParam("nbRows") String nbRows) throws NamingException { String methodName = "getDataCollectionReportyBySessionIdPdf"; long start = this.logInit(methodName, logger, token, proposal, sessionId); try { - byte[] byteToExport = this.getPdfRtf(sessionId, proposal, reportType, false); + byte[] byteToExport = this.getPdfRtf(sessionId, proposal, nbRows, false); this.logFinish(methodName, start, logger); return this.downloadFile(byteToExport, "DataCollectionsReport.pdf"); @@ -237,16 +237,16 @@ public Response getDataCollectionsReportBySessionIdPDF(@PathParam("token") Strin @RolesAllowed({"User", "Manager", "Industrial", "Localcontact"}) @GET - @Path("{token}/proposal/{proposal}/mx/datacollection/session/{sessionId}/report/{reportType}/rtf") + @Path("{token}/proposal/{proposal}/mx/datacollection/session/{sessionId}/report/{nbRows}/rtf") @Produces({ "application/rtf" }) public Response getDataCollectionsReportBySessionIdRTF(@PathParam("token") String token, @PathParam("proposal") String proposal, - @PathParam("sessionId") String sessionId, @PathParam("reportType") String reportType) throws NamingException { + @PathParam("sessionId") String sessionId, @PathParam("nbRows") String nbRows) throws NamingException { String methodName = "getDataCollectionReportyBySessionIdRtf"; long start = this.logInit(methodName, logger, token, proposal, sessionId); try { - byte[] byteToExport = this.getPdfRtf(sessionId, proposal, reportType, true); + byte[] byteToExport = this.getPdfRtf(sessionId, proposal, nbRows, true); this.logFinish(methodName, start, logger); return this.downloadFile(byteToExport, "DataCollectionsReport.rtf"); @@ -355,22 +355,18 @@ public Response getViewDataCollectionByProteinAcronym(@PathParam("token") String } } - private byte [] getPdfRtf(String sessionId, String proposal, String reportType, boolean isRtf) throws NamingException, Exception { + private byte [] getPdfRtf(String sessionId, String proposal, String nbRows, boolean isRtf) throws NamingException, Exception { Integer id = new Integer(sessionId); List> dataCollections = this.getWebServiceDataCollectionGroup3Service().getViewDataCollectionBySessionId(this.getProposalId(proposal), id); - // for testing purposes, to be removed later - Integer nbRowsMax = new Integer(reportType); + Integer nbRowsMax = new Integer(nbRows); ExiPdfRtfExporter pdf = new ExiPdfRtfExporter(proposal, id , dataCollections, nbRowsMax); byte [] byteToExport = pdf.exportDataCollectionReport(isRtf).toByteArray(); - if (reportType.equals("1")) { - byteToExport = pdf.exportDataCollectionReport(isRtf).toByteArray(); - } return byteToExport; } From 7087e7b15847557329797a450ef69adb40e1a745 Mon Sep 17 00:00:00 2001 From: delageniere Date: Tue, 17 Oct 2017 17:36:14 +0200 Subject: [PATCH 13/38] reports improvements --- .../common/util/export/ExiPdfRtfExporter.java | 62 ++++++++++--------- 1 file changed, 34 insertions(+), 28 deletions(-) diff --git a/ispyb-ejb/src/main/java/ispyb/common/util/export/ExiPdfRtfExporter.java b/ispyb-ejb/src/main/java/ispyb/common/util/export/ExiPdfRtfExporter.java index ce9035ac5..be8cd28be 100644 --- a/ispyb-ejb/src/main/java/ispyb/common/util/export/ExiPdfRtfExporter.java +++ b/ispyb-ejb/src/main/java/ispyb/common/util/export/ExiPdfRtfExporter.java @@ -154,7 +154,8 @@ public class ExiPdfRtfExporter { public final static float CRYSTAL_IMAGE_HEIGHT = 174; - public final static float IMAGE_HEIGHT = 120; + //public final static float IMAGE_HEIGHT = 120; + public final static float IMAGE_HEIGHT = 100; // public final static float CRYSTAL_IMAGE_WIDTH = 160; // public final static float CRYSTAL_IMAGE_HEIGHT = 99; @@ -425,10 +426,10 @@ private void setDataCollectionTable(Document document) throws Exception { LOG.info("dcMap=" + dataCollectionMapData.toString()); setDataCollectionMapData(document, dataCollectionMapData); - if (getCellParam(dataCollectionMapData, "DataCollectionGroup_crystalClass") != null) { - String dcgId = getCellParam(dataCollectionMapData, "DataCollectionGroup_dataCollectionGroupId"); + if (getCellParam(dataCollectionMapData, "DataCollectionGroup_crystalClass", null) != null) { + String dcgId = getCellParam(dataCollectionMapData, "DataCollectionGroup_dataCollectionGroupId", null); if (!mapDataCollectionGroupIdCClass.containsKey(dcgId)){ - mapDataCollectionGroupIdCClass.put(dcgId, getCellParam(dataCollectionMapData, "DataCollectionGroup_crystalClass")); + mapDataCollectionGroupIdCClass.put(dcgId, getCellParam(dataCollectionMapData, "DataCollectionGroup_crystalClass", null)); } } i++; @@ -454,19 +455,20 @@ private void setDataCollectionTable(Document document) throws Exception { private void setDataCollectionMapData(Document document, Map dataCollectionMapItem) throws Exception { // 1st row - String parag = getCellParam(dataCollectionMapItem, "DataCollectionGroup_experimentType") - + " " + getCellParam(dataCollectionMapItem, "DataCollection_startTime"); + String parag = getCellParam(dataCollectionMapItem, "DataCollectionGroup_experimentType", null) + + " " + getCellParam(dataCollectionMapItem, "DataCollection_startTime", null); Paragraph p = new Paragraph(parag, FONT_DOC_BLUE); document.add(p); //row2 - parag = getCellParam(dataCollectionMapItem,"DataCollection_imageDirectory"); + parag = getCellParam(dataCollectionMapItem,"DataCollection_imageDirectory", null); document.add(new Paragraph(parag, FONT_DOC_ITALIC)); //row3 Table table = new Table(NB_COL_DATACOLLECTION); table.getDefaultCell().setHorizontalAlignment(Element.ALIGN_LEFT); table.getDefaultCell().setBorderWidth(0); + table.setBorder(0); // 1st Cell parag = "Workflow: \n" @@ -481,13 +483,13 @@ private void setDataCollectionMapData(Document document, Map dat table.addCell(p); // Cell2 - parag = getCellParam(dataCollectionMapItem, "Workflow_workflowType") + "\n" - + getCellParam(dataCollectionMapItem, "Protein_acronym") + "\n" - + getCellParam(dataCollectionMapItem, "BLSample_name") + "\n" - + getCellParam(dataCollectionMapItem, "DataCollection_imagePrefix") + "\n" - + getCellParam(dataCollectionMapItem, "DataCollection_dataCollectionNumber") + "\n" - + getCellParam(dataCollectionMapItem, "Protein_acronym") + "\n" - + getCellParam(dataCollectionMapItem, "DataCollection_transmission") + "\n"; + parag = getCellParam(dataCollectionMapItem, "Workflow_workflowType", null) + "\n" + + getCellParam(dataCollectionMapItem, "Protein_acronym", null) + "\n" + + getCellParam(dataCollectionMapItem, "BLSample_name", null) + "\n" + + getCellParam(dataCollectionMapItem, "DataCollection_imagePrefix", null) + "\n" + + getCellParam(dataCollectionMapItem, "DataCollection_dataCollectionNumber", null) + "\n" + + getCellParam(dataCollectionMapItem, "DataCollection_numberOfImages", null) + "\n" + + getCellParam(dataCollectionMapItem, "DataCollection_transmission", df2) + "\n"; LOG.info("parag=" + parag); p = new Paragraph(parag, FONT_DOC_BOLD); table.addCell(p); @@ -506,13 +508,13 @@ private void setDataCollectionMapData(Document document, Map dat // Cell 4 - parag = getCellParam(dataCollectionMapItem, "DataCollection_resolutionAtCorner")+ "\n" - + getCellParam(dataCollectionMapItem, "DataCollection_wavelength") + "\n" - + getCellParam(dataCollectionMapItem, "DataCollection_axisRange") + "\n" - + getCellParam(dataCollectionMapItem, "DataCollection_omegaStart") + "\n" - + getCellParam(dataCollectionMapItem, "exposureTime") + "\n" - + getCellParam(dataCollectionMapItem, "DataCollection_flux") + "\n" - + getCellParam(dataCollectionMapItem, "DataCollection_flux_end") + "\n" ; + parag = getCellParam(dataCollectionMapItem, "DataCollection_resolutionAtCorner", df2)+ "\n" + + getCellParam(dataCollectionMapItem, "DataCollection_wavelength", df3) + "\n" + + getCellParam(dataCollectionMapItem, "DataCollection_axisRange", df2) + "\n" + + getCellParam(dataCollectionMapItem, "DataCollection_omegaStart", df2) + "\n" + + getCellParam(dataCollectionMapItem, "exposureTime", df2) + "\n" + + getCellParam(dataCollectionMapItem, "DataCollection_flux", null) + "\n" + + getCellParam(dataCollectionMapItem, "DataCollection_flux_end", null) + "\n" ; table.addCell(new Paragraph(parag, FONT_DOC_BOLD)); @@ -523,8 +525,8 @@ private void setDataCollectionMapData(Document document, Map dat // 6 Cell : thumbnail - if (!getCellParam(dataCollectionMapItem, "lastImageId").isEmpty()) { - String thumbnailPath = (imageService.findByPk(new Integer(getCellParam(dataCollectionMapItem, "lastImageId")))).getJpegThumbnailFileFullPath(); + if (!getCellParam(dataCollectionMapItem, "lastImageId", null).isEmpty()) { + String thumbnailPath = (imageService.findByPk(new Integer(getCellParam(dataCollectionMapItem, "lastImageId", null)))).getJpegThumbnailFileFullPath(); Cell cellThumbnail = getCellImage(thumbnailPath); cellThumbnail.setBorderWidth(0); table.addCell(cellThumbnail); @@ -542,8 +544,8 @@ private void setDataCollectionMapData(Document document, Map dat table.addCell(cellSnapshot); // 8 Cell : graph or other plot - if (!getCellParam(dataCollectionMapItem, "DataCollection_dataCollectionId").isEmpty()) { - String plotPath = (dcService.findByPk(new Integer(getCellParam(dataCollectionMapItem, "DataCollection_dataCollectionId")), false, false)).getImageQualityIndicatorsPlotPath(); + if (!getCellParam(dataCollectionMapItem, "DataCollection_dataCollectionId", null).isEmpty()) { + String plotPath = (dcService.findByPk(new Integer(getCellParam(dataCollectionMapItem, "DataCollection_dataCollectionId", null)), false, false)).getImageQualityIndicatorsPlotPath(); Cell cellGraph = getCellImage(plotPath); cellGraph.setBorderWidth(0); table.addCell(cellGraph); @@ -569,11 +571,15 @@ private void setDataCollectionMapData(Document document, Map dat * @param dataCollectionMap * @throws Exception */ - private String getCellParam(Map dataCollectionMap, String param) throws Exception { + private String getCellParam(Map dataCollectionMap, String param, DecimalFormat df) throws Exception { String paramValue = ""; - if (dataCollectionMap.get(param) != null) { - paramValue = dataCollectionMap.get(param).toString(); + if (dataCollectionMap.get(param) != null) { + if (df == null){ + paramValue = dataCollectionMap.get(param).toString(); + } else { + paramValue = df.format(dataCollectionMap.get(param)).toString(); + } } return paramValue; From 1831bb4f53c348fd40bc27b57e2d3cf573f66504 Mon Sep 17 00:00:00 2001 From: delageniere Date: Wed, 18 Oct 2017 12:23:24 +0200 Subject: [PATCH 14/38] new type of report with analalysis data --- .../common/util/export/ExiPdfRtfExporter.java | 152 +++++++++++++++++- 1 file changed, 145 insertions(+), 7 deletions(-) diff --git a/ispyb-ejb/src/main/java/ispyb/common/util/export/ExiPdfRtfExporter.java b/ispyb-ejb/src/main/java/ispyb/common/util/export/ExiPdfRtfExporter.java index be8cd28be..7318750d4 100644 --- a/ispyb-ejb/src/main/java/ispyb/common/util/export/ExiPdfRtfExporter.java +++ b/ispyb-ejb/src/main/java/ispyb/common/util/export/ExiPdfRtfExporter.java @@ -130,6 +130,8 @@ public class ExiPdfRtfExporter { public final static Font FONT_INDEXING_SUCCESS = new Font(Font.HELVETICA, 8, Font.NORMAL, GREEN_COLOR); public final static int NB_COL_DATACOLLECTION = 8; + + public final static int NB_COL_DATA_ANALYSIS = 11; public final static int SIZE_FONT = 8; @@ -156,6 +158,7 @@ public class ExiPdfRtfExporter { //public final static float IMAGE_HEIGHT = 120; public final static float IMAGE_HEIGHT = 100; + public final static float IMAGE_HEIGHT_SMALL = 50; // public final static float CRYSTAL_IMAGE_WIDTH = 160; // public final static float CRYSTAL_IMAGE_HEIGHT = 99; @@ -440,6 +443,36 @@ private void setDataCollectionTable(Document document) throws Exception { document.add(new Paragraph(" ")); } + + /** + * set the dataCollection table + * + * @param document + * @throws Exception + */ + private void setDataAnalysisTable(Document document) throws Exception { + document.add(new Paragraph("Data Collections + Analysis:", FONT_TITLE)); + document.add(new Paragraph(" ")); + if (dataCollections.isEmpty()) { + document.add(new Paragraph("There is no data collection in this report", FONT_DOC)); + } else { + document.add(new Paragraph(" ")); + + // DataCollection Rows + Iterator> it = dataCollections.iterator(); + int i = 0; + while (it.hasNext() && i < nbRowsMax) { + Map dataCollectionMapData = it.next(); + LOG.info("dcMap=" + dataCollectionMapData.toString()); + setDataAnalysisMapData(document, dataCollectionMapData); + + i++; + } + document.add(new Paragraph(" ")); + } + document.add(new Paragraph(" ")); + + } /** * set a line for a specified dataCollection in the dataCollection table @@ -527,7 +560,7 @@ private void setDataCollectionMapData(Document document, Map dat if (!getCellParam(dataCollectionMapItem, "lastImageId", null).isEmpty()) { String thumbnailPath = (imageService.findByPk(new Integer(getCellParam(dataCollectionMapItem, "lastImageId", null)))).getJpegThumbnailFileFullPath(); - Cell cellThumbnail = getCellImage(thumbnailPath); + Cell cellThumbnail = getCellImage(thumbnailPath, IMAGE_HEIGHT); cellThumbnail.setBorderWidth(0); table.addCell(cellThumbnail); } else { @@ -538,7 +571,7 @@ private void setDataCollectionMapData(Document document, Map dat // 7 Cell : snapshot - Cell cellSnapshot = getCellImage(dataCollectionMapItem,"DataCollection_xtalSnapshotFullPath1"); + Cell cellSnapshot = getCellImage(dataCollectionMapItem,"DataCollection_xtalSnapshotFullPath1", IMAGE_HEIGHT); //cellSnapshot.setRowspan(nbRows); cellSnapshot.setBorderWidth(0); table.addCell(cellSnapshot); @@ -546,7 +579,7 @@ private void setDataCollectionMapData(Document document, Map dat // 8 Cell : graph or other plot if (!getCellParam(dataCollectionMapItem, "DataCollection_dataCollectionId", null).isEmpty()) { String plotPath = (dcService.findByPk(new Integer(getCellParam(dataCollectionMapItem, "DataCollection_dataCollectionId", null)), false, false)).getImageQualityIndicatorsPlotPath(); - Cell cellGraph = getCellImage(plotPath); + Cell cellGraph = getCellImage(plotPath, IMAGE_HEIGHT); cellGraph.setBorderWidth(0); table.addCell(cellGraph); } else { @@ -564,6 +597,111 @@ private void setDataCollectionMapData(Document document, Map dat return; } + /** + * set a line for a specified dataCollection in the dataCollection table + * + * @param document + * @param table + * @param col + * @param session + * @param df2 + * @param df3 + * @throws Exception + */ + private void setDataAnalysisMapData(Document document, Map dataCollectionMapItem) throws Exception { + + // 1st row + String parag = getCellParam(dataCollectionMapItem, "DataCollectionGroup_experimentType", null) + + " " + getCellParam(dataCollectionMapItem, "DataCollection_startTime", null); + Paragraph p = new Paragraph(parag, FONT_DOC_BLUE); + document.add(p); + + //row2 + parag = getCellParam(dataCollectionMapItem,"DataCollection_imageDirectory", null); + document.add(new Paragraph(parag, FONT_DOC_ITALIC)); + + //row 1 + Table table = new Table(NB_COL_DATA_ANALYSIS); + table.getDefaultCell().setHorizontalAlignment(Element.ALIGN_LEFT); + table.getDefaultCell().setBorderWidth(0); + table.setBorder(0); + + // 1st Cell + parag = "Protein: \n" + + " \n" + + "Prefix: \n" + + " \n" + + "Images: \n" + + " \n"; + LOG.info("parag=" + parag); + p = new Paragraph(parag, FONT_DOC); + table.addCell(p); + + // Cell 2 + parag = getCellParam(dataCollectionMapItem, "Protein_acronym", null) + "\n\n" + + getCellParam(dataCollectionMapItem, "DataCollection_imagePrefix", null) + "\n\n" + + getCellParam(dataCollectionMapItem, "DataCollection_numberOfImages", null) + "\n\n" ; + LOG.info("parag=" + parag); + p = new Paragraph(parag, FONT_DOC_BOLD); + table.addCell(p); + + // Cell 3 + parag = "Type: \n" + + "Res. (corner): \n" + + "Wavelength: \n" ; + LOG.info("parag=" + parag); + p = new Paragraph(parag, FONT_DOC); + table.addCell(p); + + // Cell 4 + parag = getCellParam(dataCollectionMapItem, "Workflow_workflowType", null) + "\n" + + getCellParam(dataCollectionMapItem, "DataCollection_resolutionAtCorner", df2)+ "\n" + + getCellParam(dataCollectionMapItem, "DataCollection_wavelength", df3) + "\n" ; + LOG.info("parag=" + parag); + p = new Paragraph(parag, FONT_DOC_BOLD); + table.addCell(p); + + // Cell 5 : image quality indicator plot + if (!getCellParam(dataCollectionMapItem, "DataCollection_dataCollectionId", null).isEmpty()) { + String plotPath = (dcService.findByPk(new Integer(getCellParam(dataCollectionMapItem, "DataCollection_dataCollectionId", null)), false, false)).getImageQualityIndicatorsPlotPath(); + Cell cellGraph = getCellImage(plotPath, IMAGE_HEIGHT); + cellGraph.setBorderWidth(0); + table.addCell(cellGraph); + } else { + table.addCell(" "); + } + + // Cell 6 indexed/strategy or completeness + //dataCollectionGroup.ScreeningOutput_indexingSuccess + //ScreeningOutput_strategySuccess + table.addCell(" "); + + // Cell 7 + //dataCollectionGroup.ScreeningOutput_mosaicity + //dataCollectionGroup.ScreeningOutputLattice_spaceGroup + table.addCell(" "); + + // Cell 8 + + //if (dataCollectionGroup.ScreeningOutputLattice_spaceGroup){ +//dataCollectionGroup.ScreeningOutputLattice_unitCell_a + ", " + dataCollectionGroup.ScreeningOutputLattice_unitCell_b + ", " + dataCollectionGroup.ScreeningOutputLattice_unitCell_c, + + table.addCell(" "); + + // Cell 9 + table.addCell(" "); + + // Cell 10 + table.addCell(" "); + + // Cell 11 + table.addCell(" "); + + document.add(table); + + return; + } + /** * get the value or replace by blank if null to fill a cell paragraph * @@ -606,14 +744,14 @@ private Cell getCellValue(String value) { * @return * @throws Exception */ - private Cell getCellImage(Map dataCollectionMapItem, String imageParam) throws Exception { + private Cell getCellImage(Map dataCollectionMapItem, String imageParam, float image_size) throws Exception { if (dataCollectionMapItem.get(imageParam) != null && !(dataCollectionMapItem.get(imageParam).toString()).equals("") ) { String image = dataCollectionMapItem.get(imageParam).toString(); image = PathUtils.getPath(image); try { Image jpg1 = Image.getInstance(image); - jpg1.scaleAbsolute(jpg1.getWidth() * IMAGE_HEIGHT / jpg1.getHeight(), IMAGE_HEIGHT); + jpg1.scaleAbsolute(jpg1.getWidth() * image_size / jpg1.getHeight(), image_size); Cell cell = new Cell(jpg1); cell.setLeading(0); cell.setBorderWidth(0); @@ -634,13 +772,13 @@ private Cell getCellImage(Map dataCollectionMapItem, String imag * @return * @throws Exception */ - private Cell getCellImage(String imagePath) throws Exception { + private Cell getCellImage(String imagePath, float image_size) throws Exception { if (imagePath != null ) { String image = PathUtils.getPath(imagePath); try { Image jpg1 = Image.getInstance(image); - jpg1.scaleAbsolute(jpg1.getWidth() * IMAGE_HEIGHT / jpg1.getHeight(), IMAGE_HEIGHT); + jpg1.scaleAbsolute(jpg1.getWidth() * image_size / jpg1.getHeight(), image_size); Cell cell = new Cell(jpg1); cell.setLeading(0); cell.setBorderWidth(0); From 3fda215b046f2585b0a6fcd755dbdb561266c775 Mon Sep 17 00:00:00 2001 From: delageniere Date: Thu, 19 Oct 2017 10:43:59 +0200 Subject: [PATCH 15/38] new ws for new report type --- .../common/util/export/ExiPdfRtfExporter.java | 67 +++++++++++++++---- .../rest/mx/DataCollectionRestWebService.java | 56 ++++++++++++++++ 2 files changed, 111 insertions(+), 12 deletions(-) diff --git a/ispyb-ejb/src/main/java/ispyb/common/util/export/ExiPdfRtfExporter.java b/ispyb-ejb/src/main/java/ispyb/common/util/export/ExiPdfRtfExporter.java index 7318750d4..2096c7c06 100644 --- a/ispyb-ejb/src/main/java/ispyb/common/util/export/ExiPdfRtfExporter.java +++ b/ispyb-ejb/src/main/java/ispyb/common/util/export/ExiPdfRtfExporter.java @@ -271,6 +271,50 @@ public ByteArrayOutputStream exportDataCollectionReport(boolean rtfFormat) throw } + public ByteArrayOutputStream exportDataCollectionAnalysisReport(boolean rtfFormat) throws Exception { + + this.init(); + // create simple doc and write to a ByteArrayOutputStream + Document document = new Document(PageSize.A4.rotate(), 20, 20, 20, 20); + ByteArrayOutputStream baos = new ByteArrayOutputStream(); + if (!rtfFormat) { + PdfWriter.getInstance(document, baos); + } else { + RtfWriter2.getInstance(document, baos); + } + + // ============================= + // Header + footer + // ============================= + + setHeader(document); + setFooter(document); + document.open(); + + // =============================== + // Body + // =============================== + // Crystallographer added only for IFX proposal in case of MXPress + // experiment + setCrystallographer(document); + // Session comments + setSessionComments(document); + // session title& info + setSessionTable(document); + + // ====================== + // Data Collection analysis table + // ====================== + document.add(new Paragraph(" ")); + setDataAnalysisTable(document); + + // ====================== + // End of file + // ====================== + document.close(); + return baos; + + } /** * sets the header in the specified document * @@ -609,16 +653,6 @@ private void setDataCollectionMapData(Document document, Map dat * @throws Exception */ private void setDataAnalysisMapData(Document document, Map dataCollectionMapItem) throws Exception { - - // 1st row - String parag = getCellParam(dataCollectionMapItem, "DataCollectionGroup_experimentType", null) - + " " + getCellParam(dataCollectionMapItem, "DataCollection_startTime", null); - Paragraph p = new Paragraph(parag, FONT_DOC_BLUE); - document.add(p); - - //row2 - parag = getCellParam(dataCollectionMapItem,"DataCollection_imageDirectory", null); - document.add(new Paragraph(parag, FONT_DOC_ITALIC)); //row 1 Table table = new Table(NB_COL_DATA_ANALYSIS); @@ -627,14 +661,14 @@ private void setDataAnalysisMapData(Document document, Map dataC table.setBorder(0); // 1st Cell - parag = "Protein: \n" + String parag = "Protein: \n" + " \n" + "Prefix: \n" + " \n" + "Images: \n" + " \n"; LOG.info("parag=" + parag); - p = new Paragraph(parag, FONT_DOC); + Paragraph p = new Paragraph(parag, FONT_DOC); table.addCell(p); // Cell 2 @@ -672,6 +706,15 @@ private void setDataAnalysisMapData(Document document, Map dataC } // Cell 6 indexed/strategy or completeness + String indexed = "success"; + if (!getCellParam(dataCollectionMapItem, "ScreeningOutput_indexingSuccess", null){ + indexed = "failed"; + } + parag = "Indexed: \n" + + "Strategy: \n" + ; + p = new Paragraph(parag, FONT_DOC); + table.addCell(p); //dataCollectionGroup.ScreeningOutput_indexingSuccess //ScreeningOutput_strategySuccess table.addCell(" "); diff --git a/ispyb-ws/src/main/java/ispyb/ws/rest/mx/DataCollectionRestWebService.java b/ispyb-ws/src/main/java/ispyb/ws/rest/mx/DataCollectionRestWebService.java index 5a80a23f0..dc246eb55 100644 --- a/ispyb-ws/src/main/java/ispyb/ws/rest/mx/DataCollectionRestWebService.java +++ b/ispyb-ws/src/main/java/ispyb/ws/rest/mx/DataCollectionRestWebService.java @@ -255,6 +255,46 @@ public Response getDataCollectionsReportBySessionIdRTF(@PathParam("token") Strin } } + @RolesAllowed({"User", "Manager", "Industrial", "Localcontact"}) + @GET + @Path("{token}/proposal/{proposal}/mx/datacollection/session/{sessionId}/analysisreport/{nbRows}/pdf") + @Produces({ "application/pdf" }) + public Response getDataCollectionsAnalysisReportBySessionIdPDF(@PathParam("token") String token, + @PathParam("proposal") String proposal, + @PathParam("sessionId") String sessionId, @PathParam("nbRows") String nbRows) throws NamingException { + + String methodName = "getDataCollectionAnalysisReportyBySessionIdPdf"; + long start = this.logInit(methodName, logger, token, proposal, sessionId); + try { + byte[] byteToExport = this.getAnalysisPdfRtf(sessionId, proposal, nbRows, false); + this.logFinish(methodName, start, logger); + return this.downloadFile(byteToExport, "DataCollectionsAnalysisReport.pdf"); + + } catch (Exception e) { + return this.logError(methodName, e, start, logger); + } + } + + @RolesAllowed({"User", "Manager", "Industrial", "Localcontact"}) + @GET + @Path("{token}/proposal/{proposal}/mx/datacollection/session/{sessionId}/analysisreport/{nbRows}/rtf") + @Produces({ "application/rtf" }) + public Response getDataCollectionsAnalysisReportBySessionIdRTF(@PathParam("token") String token, + @PathParam("proposal") String proposal, + @PathParam("sessionId") String sessionId, @PathParam("nbRows") String nbRows) throws NamingException { + + String methodName = "getDataCollectionReportyBySessionIdRtf"; + long start = this.logInit(methodName, logger, token, proposal, sessionId); + try { + byte[] byteToExport = this.getAnalysisPdfRtf(sessionId, proposal, nbRows, true); + this.logFinish(methodName, start, logger); + return this.downloadFile(byteToExport, "DataCollectionsAnalysisReport.rtf"); + + } catch (Exception e) { + return this.logError(methodName, e, start, logger); + } + } + @RolesAllowed({ "User", "Manager", "Industrial", "Localcontact" }) @GET @@ -370,4 +410,20 @@ public Response getViewDataCollectionByProteinAcronym(@PathParam("token") String return byteToExport; } + + private byte [] getAnalysisPdfRtf(String sessionId, String proposal, String nbRows, boolean isRtf) throws NamingException, Exception { + + Integer id = new Integer(sessionId); + + List> dataCollections = + this.getWebServiceDataCollectionGroup3Service().getViewDataCollectionBySessionId(this.getProposalId(proposal), id); + + Integer nbRowsMax = new Integer(nbRows); + + ExiPdfRtfExporter pdf = new ExiPdfRtfExporter(proposal, id , dataCollections, nbRowsMax); + + byte [] byteToExport = pdf.exportDataCollectionAnalysisReport(isRtf).toByteArray(); + + return byteToExport; + } } From 3bb2af8fbe928a59b87d842ce326a3c93983d055 Mon Sep 17 00:00:00 2001 From: delageniere Date: Thu, 19 Oct 2017 11:32:23 +0200 Subject: [PATCH 16/38] new ws for new report type --- .../common/util/export/ExiPdfRtfExporter.java | 55 ++++++++++++++++--- 1 file changed, 47 insertions(+), 8 deletions(-) diff --git a/ispyb-ejb/src/main/java/ispyb/common/util/export/ExiPdfRtfExporter.java b/ispyb-ejb/src/main/java/ispyb/common/util/export/ExiPdfRtfExporter.java index 2096c7c06..b1ce118d3 100644 --- a/ispyb-ejb/src/main/java/ispyb/common/util/export/ExiPdfRtfExporter.java +++ b/ispyb-ejb/src/main/java/ispyb/common/util/export/ExiPdfRtfExporter.java @@ -706,15 +706,32 @@ private void setDataAnalysisMapData(Document document, Map dataC } // Cell 6 indexed/strategy or completeness - String indexed = "success"; - if (!getCellParam(dataCollectionMapItem, "ScreeningOutput_indexingSuccess", null){ - indexed = "failed"; + String indexed = "failed"; + String strateg = "failed"; + Boolean indexing = getBoolean(dataCollectionMapItem, "ScreeningOutput_indexingSuccess"); + Boolean strategy = getBoolean(dataCollectionMapItem, "ScreeningOutput_strategySuccess"); + + if (indexing != null && strategy != null){ + + if (indexing ){ + indexed = "success"; + } + + if (strategy ){ + strateg = "success"; + } + + parag = "Indexed: "+ indexed + "\n" + + "Strategy:"+ strateg + "\n" + ; + p = new Paragraph(parag, FONT_DOC); + table.addCell(p); + + } else { + table.addCell(" "); } - parag = "Indexed: \n" - + "Strategy: \n" - ; - p = new Paragraph(parag, FONT_DOC); - table.addCell(p); + + //dataCollectionGroup.ScreeningOutput_indexingSuccess //ScreeningOutput_strategySuccess table.addCell(" "); @@ -765,6 +782,28 @@ private String getCellParam(Map dataCollectionMap, String param, return paramValue; } + + /** + * get the value as boolean to fill a cell and return a null value if no value or not an integer + * + * @param param + * @param dataCollectionMap + * @throws Exception + */ + private Boolean getBoolean(Map dataCollectionMap, String param) throws Exception { + + Boolean cellBool = null; + + if (dataCollectionMap.get(param) != null) { + + if (dataCollectionMap.get(param).equals("1") ){ + cellBool = true; + } else { + cellBool = false; + } + } + return cellBool; + } /** * returns a simple cell witha given value inside From d4e8fbe62c7ad5041f2aeb6f2071a7531437d34c Mon Sep 17 00:00:00 2001 From: delageniere Date: Thu, 19 Oct 2017 16:04:54 +0200 Subject: [PATCH 17/38] new ws for new report type --- .../common/util/export/ExiPdfRtfExporter.java | 129 ++++++++++-------- 1 file changed, 75 insertions(+), 54 deletions(-) diff --git a/ispyb-ejb/src/main/java/ispyb/common/util/export/ExiPdfRtfExporter.java b/ispyb-ejb/src/main/java/ispyb/common/util/export/ExiPdfRtfExporter.java index b1ce118d3..54ca6757a 100644 --- a/ispyb-ejb/src/main/java/ispyb/common/util/export/ExiPdfRtfExporter.java +++ b/ispyb-ejb/src/main/java/ispyb/common/util/export/ExiPdfRtfExporter.java @@ -61,6 +61,7 @@ import ispyb.server.mx.vos.collections.DataCollectionGroup3VO; import ispyb.server.mx.vos.collections.IspybCrystalClass3VO; import ispyb.server.mx.vos.collections.Session3VO; +import sun.tools.jstat.Alignment; /** * allows creation of PDF or RTF report - general report for EXI, available in the @@ -108,6 +109,8 @@ public class ExiPdfRtfExporter { public final static Font FONT_DOC = new Font(Font.HELVETICA, 8, Font.NORMAL, Color.BLACK); + public final static Font FONT_DOC_SMALL = new Font(Font.HELVETICA, 6, Font.NORMAL, Color.BLACK); + public final static Font FONT_DOC_BLUE = new Font(Font.HELVETICA, 8, Font.NORMAL, Color.BLUE); public final static Font FONT_DOC_ITALIC = new Font(Font.HELVETICA, 8, Font.ITALIC, Color.BLACK); @@ -121,6 +124,11 @@ public class ExiPdfRtfExporter { public final static Font FONT_DOC_EXPONENT_BLUE = new Font(Font.HELVETICA, 11, Font.NORMAL, Color.BLUE); public final static Font FONT_DOC_BOLD = new Font(Font.HELVETICA, 8, Font.BOLD); + + public final static Font FONT_DOC_SMALL_BOLD = new Font(Font.HELVETICA, 6, Font.BOLD); + + public final static Font FONT_DOC_SMALL_CENTERED = new Font(Font.HELVETICA, 6, Font.BOLD); + public final static Font FONT_DOC_PARAM_TITLE = new Font(Font.HELVETICA, 8, Font.NORMAL, LIGHT_GREY_COLOR); public final static Font FONT_INDEXING_NOTDONE = new Font(Font.HELVETICA, 8, Font.NORMAL, LIGHT_GREY_COLOR); @@ -495,12 +503,12 @@ private void setDataCollectionTable(Document document) throws Exception { * @throws Exception */ private void setDataAnalysisTable(Document document) throws Exception { - document.add(new Paragraph("Data Collections + Analysis:", FONT_TITLE)); + document.add(new Paragraph("Data Collections & Analysis results:", FONT_TITLE)); document.add(new Paragraph(" ")); if (dataCollections.isEmpty()) { document.add(new Paragraph("There is no data collection in this report", FONT_DOC)); } else { - document.add(new Paragraph(" ")); + //document.add(new Paragraph(" ")); // DataCollection Rows Iterator> it = dataCollections.iterator(); @@ -658,41 +666,40 @@ private void setDataAnalysisMapData(Document document, Map dataC Table table = new Table(NB_COL_DATA_ANALYSIS); table.getDefaultCell().setHorizontalAlignment(Element.ALIGN_LEFT); table.getDefaultCell().setBorderWidth(0); - table.setBorder(0); + table.setBorder(1); // 1st Cell - String parag = "Protein: \n" - + " \n" - + "Prefix: \n" - + " \n" - + "Images: \n" - + " \n"; + String parag = "Protein: \n\n" + + "Prefix: \n\n" + + "Images: \n\n" ; + LOG.info("parag=" + parag); - Paragraph p = new Paragraph(parag, FONT_DOC); + Paragraph p = new Paragraph(parag, FONT_DOC_SMALL); table.addCell(p); - // Cell 2 - parag = getCellParam(dataCollectionMapItem, "Protein_acronym", null) + "\n\n" - + getCellParam(dataCollectionMapItem, "DataCollection_imagePrefix", null) + "\n\n" - + getCellParam(dataCollectionMapItem, "DataCollection_numberOfImages", null) + "\n\n" ; + // 2st Cell + parag = getCellParam(dataCollectionMapItem, "Protein_acronym", null)+ "\n\n" + + getCellParam(dataCollectionMapItem, "DataCollection_imagePrefix", null) + "\n\n" + + getCellParam(dataCollectionMapItem, "DataCollection_numberOfImages", null) + "\n\n" ; + LOG.info("parag=" + parag); - p = new Paragraph(parag, FONT_DOC_BOLD); + p = new Paragraph(parag, FONT_DOC_SMALL_BOLD); table.addCell(p); - + // Cell 3 parag = "Type: \n" - + "Res. (corner): \n" - + "Wavelength: \n" ; + + "Res. (corner): \n" + + "Wavelength: \n" ; LOG.info("parag=" + parag); - p = new Paragraph(parag, FONT_DOC); + p = new Paragraph(parag, FONT_DOC_SMALL); table.addCell(p); // Cell 4 parag = getCellParam(dataCollectionMapItem, "Workflow_workflowType", null) + "\n" + getCellParam(dataCollectionMapItem, "DataCollection_resolutionAtCorner", df2)+ "\n" + getCellParam(dataCollectionMapItem, "DataCollection_wavelength", df3) + "\n" ; - LOG.info("parag=" + parag); - p = new Paragraph(parag, FONT_DOC_BOLD); + + p = new Paragraph(parag, FONT_DOC_SMALL_BOLD); table.addCell(p); // Cell 5 : image quality indicator plot @@ -706,56 +713,76 @@ private void setDataAnalysisMapData(Document document, Map dataC } // Cell 6 indexed/strategy or completeness - String indexed = "failed"; - String strateg = "failed"; Boolean indexing = getBoolean(dataCollectionMapItem, "ScreeningOutput_indexingSuccess"); Boolean strategy = getBoolean(dataCollectionMapItem, "ScreeningOutput_strategySuccess"); + p = new Paragraph(); + + Chunk chu1 = new Chunk("Indexed: ", FONT_DOC_SMALL); if (indexing != null && strategy != null){ + + Chunk chu2 = new Chunk( "Failed", FONT_INDEXING_FAILED); + if (indexing.booleanValue() ){ + chu2 = new Chunk( "Success", FONT_INDEXING_SUCCESS); + } + p.add(chu1); + p.add(chu2); - if (indexing ){ - indexed = "success"; - } - - if (strategy ){ - strateg = "success"; + chu1 = new Chunk("Strategy: ", FONT_DOC_SMALL); + chu2 = new Chunk( "Failed", FONT_INDEXING_FAILED); + if (strategy.booleanValue() ){ + chu2 = new Chunk( "Success", FONT_INDEXING_SUCCESS); } + p.add(chu1); + p.add(chu2); - parag = "Indexed: "+ indexed + "\n" - + "Strategy:"+ strateg + "\n" - ; - p = new Paragraph(parag, FONT_DOC); table.addCell(p); } else { table.addCell(" "); } - + LOG.info("parag=" + p.toString()); - //dataCollectionGroup.ScreeningOutput_indexingSuccess - //ScreeningOutput_strategySuccess - table.addCell(" "); - // Cell 7 - //dataCollectionGroup.ScreeningOutput_mosaicity - //dataCollectionGroup.ScreeningOutputLattice_spaceGroup - table.addCell(" "); + parag = "Space group: \n" + + "Mosaicity: \n" ; + LOG.info("parag=" + parag); + p = new Paragraph(parag, FONT_DOC_SMALL); + table.addCell(p); + // Cell 8 + parag = getCellParam(dataCollectionMapItem, "ScreeningOutputLattice_spaceGroup", null) + "\n" + + getCellParam(dataCollectionMapItem, "ScreeningOutput_mosaicity", null)+ "\n" ; + p = new Paragraph(parag, FONT_DOC_SMALL_BOLD); + table.addCell(p); + //if (dataCollectionGroup.ScreeningOutputLattice_spaceGroup){ //dataCollectionGroup.ScreeningOutputLattice_unitCell_a + ", " + dataCollectionGroup.ScreeningOutputLattice_unitCell_b + ", " + dataCollectionGroup.ScreeningOutputLattice_unitCell_c, - table.addCell(" "); // Cell 9 - table.addCell(" "); + parag = "a \n" + getCellParam(dataCollectionMapItem, "ScreeningOutputLattice_unitCell_a", null) + + "\n alpha \n" + getCellParam(dataCollectionMapItem, "ScreeningOutputLattice_unitCell_alpha", null) ; + p = new Paragraph(parag, FONT_DOC_SMALL_CENTERED); + p.setAlignment(Element.ALIGN_CENTER); + table.addCell(p); // Cell 10 - table.addCell(" "); + parag = "b \n" + getCellParam(dataCollectionMapItem, "ScreeningOutputLattice_unitCell_b", null) + + "\n beta \n" + getCellParam(dataCollectionMapItem, "ScreeningOutputLattice_unitCell_beta", null) ; + p = new Paragraph(parag, FONT_DOC_SMALL_CENTERED); + p.setAlignment(Element.ALIGN_CENTER); + table.addCell(p); // Cell 11 - table.addCell(" "); + parag = "c \n" + getCellParam(dataCollectionMapItem, "ScreeningOutputLattice_unitCell_c", null) + + "\n gamma \n" + getCellParam(dataCollectionMapItem, "ScreeningOutputLattice_unitCell_gama", null) ; + + p = new Paragraph(parag, FONT_DOC_SMALL_CENTERED); + p.setAlignment(Element.ALIGN_CENTER); + table.addCell(p); document.add(table); @@ -792,15 +819,9 @@ private String getCellParam(Map dataCollectionMap, String param, */ private Boolean getBoolean(Map dataCollectionMap, String param) throws Exception { - Boolean cellBool = null; - - if (dataCollectionMap.get(param) != null) { - - if (dataCollectionMap.get(param).equals("1") ){ - cellBool = true; - } else { - cellBool = false; - } + Boolean cellBool = null; + if (dataCollectionMap.get(param) != null) { + cellBool = new Boolean (dataCollectionMap.get(param).toString()); } return cellBool; } From fc90306d8dbaee56c9a635320b4eaae4ac1e2ffd Mon Sep 17 00:00:00 2001 From: delageniere Date: Thu, 19 Oct 2017 16:26:58 +0200 Subject: [PATCH 18/38] new version 5.2.1 --- ispyb-bcr-ear/pom.xml | 4 ++-- ispyb-bcr/pom.xml | 2 +- ispyb-ear/pom.xml | 6 +++--- ispyb-ejb/pom.xml | 2 +- ispyb-ui/pom.xml | 2 +- ispyb-ui/src/main/webapp/help/release_notes.txt | 9 +++++++++ ispyb-ws/pom.xml | 4 ++-- pom.xml | 2 +- 8 files changed, 20 insertions(+), 11 deletions(-) diff --git a/ispyb-bcr-ear/pom.xml b/ispyb-bcr-ear/pom.xml index cdac8b23b..14062c216 100644 --- a/ispyb-bcr-ear/pom.xml +++ b/ispyb-bcr-ear/pom.xml @@ -4,7 +4,7 @@ ispyb ispyb-parent - 5.2.0 + 5.2.1 ispyb-bcr-ear ear @@ -15,7 +15,7 @@ ispyb ispyb-ejb3 ejb - 5.2.0 + 5.2.1 provided diff --git a/ispyb-bcr/pom.xml b/ispyb-bcr/pom.xml index a3a64ce4b..c3ffd9a25 100644 --- a/ispyb-bcr/pom.xml +++ b/ispyb-bcr/pom.xml @@ -31,7 +31,7 @@ ispyb ispyb-ejb3 - 5.2.0 + 5.2.1 provided diff --git a/ispyb-ear/pom.xml b/ispyb-ear/pom.xml index ce16ed6b7..9f7d773e1 100644 --- a/ispyb-ear/pom.xml +++ b/ispyb-ear/pom.xml @@ -4,7 +4,7 @@ ispyb ispyb-parent - 5.2.0 + 5.2.1 ispyb-ear ear @@ -13,7 +13,7 @@ ispyb ispyb-ejb3 ejb - 5.2.0 + 5.2.1 @@ -26,7 +26,7 @@ ispyb ispyb-ws war - 5.2.0 + 5.2.1 diff --git a/ispyb-ejb/pom.xml b/ispyb-ejb/pom.xml index c6632b948..26e05d19d 100644 --- a/ispyb-ejb/pom.xml +++ b/ispyb-ejb/pom.xml @@ -4,7 +4,7 @@ ispyb ispyb-parent - 5.2.0 + 5.2.1 ispyb-ejb3 jar diff --git a/ispyb-ui/pom.xml b/ispyb-ui/pom.xml index 8710e2a4b..dd69688fc 100644 --- a/ispyb-ui/pom.xml +++ b/ispyb-ui/pom.xml @@ -22,7 +22,7 @@ ispyb ispyb-ejb3 - 5.2.0 + 5.2.1 provided diff --git a/ispyb-ui/src/main/webapp/help/release_notes.txt b/ispyb-ui/src/main/webapp/help/release_notes.txt index fd87424b4..b107e4d6f 100644 --- a/ispyb-ui/src/main/webapp/help/release_notes.txt +++ b/ispyb-ui/src/main/webapp/help/release_notes.txt @@ -1,3 +1,12 @@ +New TAG : 5.2.1 + + +************** +* 19.10.2017 * +************** + +- work in progress: #135 + ************** * 22.09.2017 * ************** diff --git a/ispyb-ws/pom.xml b/ispyb-ws/pom.xml index e3f4f6072..a4ba244f9 100644 --- a/ispyb-ws/pom.xml +++ b/ispyb-ws/pom.xml @@ -4,7 +4,7 @@ ispyb ispyb-parent - 5.2.0 + 5.2.1 ispyb-ws war @@ -12,7 +12,7 @@ ispyb ispyb-ejb3 - 5.2.0 + 5.2.1 provided diff --git a/pom.xml b/pom.xml index 3ab16191a..cbcba335f 100644 --- a/pom.xml +++ b/pom.xml @@ -4,7 +4,7 @@ 4.0.0 ispyb ispyb-parent - 5.2.0 + 5.2.1 pom ispyb-ejb From 8a24edbbacde3da0031f890531c0f949755845ed Mon Sep 17 00:00:00 2001 From: delageniere Date: Thu, 19 Oct 2017 16:32:12 +0200 Subject: [PATCH 19/38] new version 5.3.2 --- ispyb-bcr-ear/pom.xml | 4 ++-- ispyb-bcr/pom.xml | 2 +- ispyb-ear/pom.xml | 6 +++--- ispyb-ejb/pom.xml | 2 +- ispyb-ui/pom.xml | 2 +- ispyb-ws/pom.xml | 4 ++-- pom.xml | 2 +- 7 files changed, 11 insertions(+), 11 deletions(-) diff --git a/ispyb-bcr-ear/pom.xml b/ispyb-bcr-ear/pom.xml index 14062c216..f68ff45ae 100644 --- a/ispyb-bcr-ear/pom.xml +++ b/ispyb-bcr-ear/pom.xml @@ -4,7 +4,7 @@ ispyb ispyb-parent - 5.2.1 + 5.3.2 ispyb-bcr-ear ear @@ -15,7 +15,7 @@ ispyb ispyb-ejb3 ejb - 5.2.1 + 5.3.2 provided diff --git a/ispyb-bcr/pom.xml b/ispyb-bcr/pom.xml index c3ffd9a25..7ec9b4460 100644 --- a/ispyb-bcr/pom.xml +++ b/ispyb-bcr/pom.xml @@ -31,7 +31,7 @@ ispyb ispyb-ejb3 - 5.2.1 + 5.3.2 provided diff --git a/ispyb-ear/pom.xml b/ispyb-ear/pom.xml index 9f7d773e1..cbbe85d12 100644 --- a/ispyb-ear/pom.xml +++ b/ispyb-ear/pom.xml @@ -4,7 +4,7 @@ ispyb ispyb-parent - 5.2.1 + 5.3.2 ispyb-ear ear @@ -13,7 +13,7 @@ ispyb ispyb-ejb3 ejb - 5.2.1 + 5.3.2 @@ -26,7 +26,7 @@ ispyb ispyb-ws war - 5.2.1 + 5.3.2 diff --git a/ispyb-ejb/pom.xml b/ispyb-ejb/pom.xml index 26e05d19d..a2132d7f1 100644 --- a/ispyb-ejb/pom.xml +++ b/ispyb-ejb/pom.xml @@ -4,7 +4,7 @@ ispyb ispyb-parent - 5.2.1 + 5.3.2 ispyb-ejb3 jar diff --git a/ispyb-ui/pom.xml b/ispyb-ui/pom.xml index dd69688fc..0b3af3d9c 100644 --- a/ispyb-ui/pom.xml +++ b/ispyb-ui/pom.xml @@ -22,7 +22,7 @@ ispyb ispyb-ejb3 - 5.2.1 + 5.3.2 provided diff --git a/ispyb-ws/pom.xml b/ispyb-ws/pom.xml index a4ba244f9..c05712229 100644 --- a/ispyb-ws/pom.xml +++ b/ispyb-ws/pom.xml @@ -4,7 +4,7 @@ ispyb ispyb-parent - 5.2.1 + 5.3.2 ispyb-ws war @@ -12,7 +12,7 @@ ispyb ispyb-ejb3 - 5.2.1 + 5.3.2 provided diff --git a/pom.xml b/pom.xml index cbcba335f..1d979d091 100644 --- a/pom.xml +++ b/pom.xml @@ -4,7 +4,7 @@ 4.0.0 ispyb ispyb-parent - 5.2.1 + 5.3.2 pom ispyb-ejb From b511554f1930342cdb69eaeb83d2d83d3706c4f5 Mon Sep 17 00:00:00 2001 From: delageniere Date: Fri, 20 Oct 2017 16:48:20 +0200 Subject: [PATCH 20/38] modifications in reports --- .../util/beamlines/ESRFBeamlineEnum.java | 48 ++++++++++++------ .../common/util/export/ExiPdfRtfExporter.java | 50 ++++++++++--------- .../rest/mx/DataCollectionRestWebService.java | 37 ++++++++------ 3 files changed, 81 insertions(+), 54 deletions(-) diff --git a/ispyb-ejb/src/main/java/ispyb/common/util/beamlines/ESRFBeamlineEnum.java b/ispyb-ejb/src/main/java/ispyb/common/util/beamlines/ESRFBeamlineEnum.java index b99a02f86..13a97882c 100644 --- a/ispyb-ejb/src/main/java/ispyb/common/util/beamlines/ESRFBeamlineEnum.java +++ b/ispyb-ejb/src/main/java/ispyb/common/util/beamlines/ESRFBeamlineEnum.java @@ -30,37 +30,53 @@ public enum ESRFBeamlineEnum { ID14_1("ID14-1", "id14eh1", new String[] { "ID14 1" }, "+33476882323", - null, false, false), ID14_2("ID14-2", "id14eh2", new String[] { "ID14 2" }, + null, false, false), + ID14_2("ID14-2", "id14eh2", new String[] { "ID14 2" }, "+33476882565", - null, false, false), ID14_3("ID14-3", "id14eh3", new String[] { "ID14 3" }, + null, false, false), + ID14_3("ID14-3", "id14eh3", new String[] { "ID14 3" }, "+33476882786", - null, false, false), ID14_4("ID14-4", "id14eh4", new String[] { "ID14 4" }, + null, false, false), + ID14_4("ID14-4", "id14eh4", new String[] { "ID14 4" }, "+33476882322", - null, false, false), ID23_1("ID23-1", "id23eh1", new String[] { "ID23 1" }, + null, false, false), + ID23_1("ID23-1", "id23eh1", new String[] { "ID23 1" }, "+33476882261", - new String[] { "x_geo_corr.cbf", "y_geo_corr.cbf" }, false, true), ID23_2("ID23-2", "id23eh2", new String[] { "ID23 2" }, + new String[] { "x_geo_corr.cbf", "y_geo_corr.cbf" }, false, true), + ID23_2("ID23-2", "id23eh2", new String[] { "ID23 2" }, "+33476882590", - new String[] { "x_geo_corr.cbf", "y_geo_corr.cbf" }, false, true), ID29("ID29", "id29", new String[] { "ID29" }, + new String[] { "x_geo_corr.cbf", "y_geo_corr.cbf" }, false, true), + ID29("ID29", "id29", new String[] { "ID29" }, "+33476882805", - new String[] { "x_geo_corr.cbf", "y_geo_corr.cbf" }, false, true), ID30A1("ID30A-1", "id30a1", new String[] { "ID30A1" }, + new String[] { "x_geo_corr.cbf", "y_geo_corr.cbf" }, false, true), + ID30A1("ID30A-1", "id30a1", new String[] { "ID30A1" }, "+3347688****", - null, true, true), ID30A2("ID30A-2", "id30a2", new String[] { "ID30A2" }, + null, true, true), + ID30A2("ID30A-2", "id30a2", new String[] { "ID30A2" }, "+3347688****", - null, true, true), ID30A3("ID30A-3", "id30a3", new String[] { "ID30A3" }, + null, true, true), + ID30A3("ID30A-3", "id30a3", new String[] { "ID30A3" }, "+3347688****", - null, true, true), ID30B("ID30B", "id30b", null, + null, true, true), + ID30B("ID30B", "id30b", null, "+3347688****", - null, true, true), BM14("BM14", "bm14", new String[] { "BM14U" }, + null, true, true), + BM14("BM14", "bm14", new String[] { "BM14U" }, "+33476882703", - null, false, true), BM16("BM16", "bm16", null, + null, false, true), + BM16("BM16", "bm16", null, "+33476882614", - null, false, false), BM29("BM29", "bm29", null, + null, false, false), + BM29("BM29", "bm29", null, "+33476882628", - null, false, true), BM30A("BM30A", "bm30a", null, + null, false, true), + BM30A("BM30A", "bm30a", null, "+33476882787", - null, false, true), ID19("ID19", "id19", null, + null, false, true), + ID19("ID19", "id19", null, "+33476882700", - null, false, true); + null, false, true), + CM01("CM01", "cm01", null,"+3347688****", null, false, true); private ESRFBeamlineEnum(String beamlineName, String directoryName, String[] associatedName, String phoneNumber, String[] correctionFiles, boolean emailNotification, boolean inActivity) { diff --git a/ispyb-ejb/src/main/java/ispyb/common/util/export/ExiPdfRtfExporter.java b/ispyb-ejb/src/main/java/ispyb/common/util/export/ExiPdfRtfExporter.java index 54ca6757a..d77581366 100644 --- a/ispyb-ejb/src/main/java/ispyb/common/util/export/ExiPdfRtfExporter.java +++ b/ispyb-ejb/src/main/java/ispyb/common/util/export/ExiPdfRtfExporter.java @@ -137,7 +137,7 @@ public class ExiPdfRtfExporter { public final static Font FONT_INDEXING_SUCCESS = new Font(Font.HELVETICA, 8, Font.NORMAL, GREEN_COLOR); - public final static int NB_COL_DATACOLLECTION = 8; + public final static int NB_COL_DATACOLLECTION = 7; public final static int NB_COL_DATA_ANALYSIS = 11; @@ -593,22 +593,18 @@ private void setDataCollectionMapData(Document document, Map dat // Cell 4 - parag = getCellParam(dataCollectionMapItem, "DataCollection_resolutionAtCorner", df2)+ "\n" + parag = getCellParam(dataCollectionMapItem, "DataCollection_resolution", df2) + + "("+ getCellParam(dataCollectionMapItem, "DataCollection_resolutionAtCorner", df2) + ") \n" + getCellParam(dataCollectionMapItem, "DataCollection_wavelength", df3) + "\n" + getCellParam(dataCollectionMapItem, "DataCollection_axisRange", df2) + "\n" + getCellParam(dataCollectionMapItem, "DataCollection_omegaStart", df2) + "\n" - + getCellParam(dataCollectionMapItem, "exposureTime", df2) + "\n" + + getCellParam(dataCollectionMapItem, "DataCollection_exposureTime", df2) + "\n" + getCellParam(dataCollectionMapItem, "DataCollection_flux", null) + "\n" + getCellParam(dataCollectionMapItem, "DataCollection_flux_end", null) + "\n" ; table.addCell(new Paragraph(parag, FONT_DOC_BOLD)); - - - - // 5 Cell add cell containing autoproc results - table.addCell(" "); - // 6 Cell : thumbnail + // 5 Cell : thumbnail if (!getCellParam(dataCollectionMapItem, "lastImageId", null).isEmpty()) { String thumbnailPath = (imageService.findByPk(new Integer(getCellParam(dataCollectionMapItem, "lastImageId", null)))).getJpegThumbnailFileFullPath(); @@ -622,13 +618,13 @@ private void setDataCollectionMapData(Document document, Map dat //cellThumbnail.setRowspan(nbRows); - // 7 Cell : snapshot + // 6 Cell : snapshot Cell cellSnapshot = getCellImage(dataCollectionMapItem,"DataCollection_xtalSnapshotFullPath1", IMAGE_HEIGHT); //cellSnapshot.setRowspan(nbRows); cellSnapshot.setBorderWidth(0); table.addCell(cellSnapshot); - // 8 Cell : graph or other plot + // 7 Cell : graph or other plot if (!getCellParam(dataCollectionMapItem, "DataCollection_dataCollectionId", null).isEmpty()) { String plotPath = (dcService.findByPk(new Integer(getCellParam(dataCollectionMapItem, "DataCollection_dataCollectionId", null)), false, false)).getImageQualityIndicatorsPlotPath(); Cell cellGraph = getCellImage(plotPath, IMAGE_HEIGHT); @@ -696,7 +692,8 @@ private void setDataAnalysisMapData(Document document, Map dataC // Cell 4 parag = getCellParam(dataCollectionMapItem, "Workflow_workflowType", null) + "\n" - + getCellParam(dataCollectionMapItem, "DataCollection_resolutionAtCorner", df2)+ "\n" + + getCellParam(dataCollectionMapItem, "DataCollection_resolution", df2) + + "("+ getCellParam(dataCollectionMapItem, "DataCollection_resolutionAtCorner", df2) + ") \n" + getCellParam(dataCollectionMapItem, "DataCollection_wavelength", df3) + "\n" ; p = new Paragraph(parag, FONT_DOC_SMALL_BOLD); @@ -715,6 +712,7 @@ private void setDataAnalysisMapData(Document document, Map dataC // Cell 6 indexed/strategy or completeness Boolean indexing = getBoolean(dataCollectionMapItem, "ScreeningOutput_indexingSuccess"); Boolean strategy = getBoolean(dataCollectionMapItem, "ScreeningOutput_strategySuccess"); + String autoprocSpaceGroup = getCellParam(dataCollectionMapItem, "AutoProc_spaceGroup", null); p = new Paragraph(); @@ -734,34 +732,38 @@ private void setDataAnalysisMapData(Document document, Map dataC chu2 = new Chunk( "Success", FONT_INDEXING_SUCCESS); } p.add(chu1); - p.add(chu2); - + p.add(chu2); table.addCell(p); + } else if (autoprocSpaceGroup != null && !autoprocSpaceGroup.isEmpty()){ + parag = autoprocSpaceGroup + " Completeness \n" + + "Overall" + "\n" + + "Inner" + "\n" + + "Outer" + "\n"; + p = new Paragraph(parag, FONT_DOC_SMALL); + } else { + table.addCell(" "); + } - LOG.info("parag=" + p.toString()); // Cell 7 - parag = "Space group: \n" + if (indexing != null && strategy != null){ + parag = "Space group: \n" + "Mosaicity: \n" ; - LOG.info("parag=" + parag); - p = new Paragraph(parag, FONT_DOC_SMALL); + p = new Paragraph(parag, FONT_DOC_SMALL); + } else { + p = new Paragraph(" "); + } table.addCell(p); - // Cell 8 parag = getCellParam(dataCollectionMapItem, "ScreeningOutputLattice_spaceGroup", null) + "\n" + getCellParam(dataCollectionMapItem, "ScreeningOutput_mosaicity", null)+ "\n" ; p = new Paragraph(parag, FONT_DOC_SMALL_BOLD); table.addCell(p); - - //if (dataCollectionGroup.ScreeningOutputLattice_spaceGroup){ -//dataCollectionGroup.ScreeningOutputLattice_unitCell_a + ", " + dataCollectionGroup.ScreeningOutputLattice_unitCell_b + ", " + dataCollectionGroup.ScreeningOutputLattice_unitCell_c, - - // Cell 9 parag = "a \n" + getCellParam(dataCollectionMapItem, "ScreeningOutputLattice_unitCell_a", null) + "\n alpha \n" + getCellParam(dataCollectionMapItem, "ScreeningOutputLattice_unitCell_alpha", null) ; diff --git a/ispyb-ws/src/main/java/ispyb/ws/rest/mx/DataCollectionRestWebService.java b/ispyb-ws/src/main/java/ispyb/ws/rest/mx/DataCollectionRestWebService.java index dc246eb55..ad02d3c92 100644 --- a/ispyb-ws/src/main/java/ispyb/ws/rest/mx/DataCollectionRestWebService.java +++ b/ispyb-ws/src/main/java/ispyb/ws/rest/mx/DataCollectionRestWebService.java @@ -1,8 +1,5 @@ package ispyb.ws.rest.mx; -import ispyb.common.util.export.ExiPdfRtfExporter; -import ispyb.server.mx.vos.collections.DataCollection3VO; - import java.io.File; import java.nio.file.Files; import java.nio.file.Paths; @@ -18,11 +15,15 @@ import javax.ws.rs.Path; import javax.ws.rs.PathParam; import javax.ws.rs.Produces; +import javax.ws.rs.QueryParam; import javax.ws.rs.core.Response; import org.apache.log4j.Logger; import org.jboss.resteasy.annotations.GZIP; +import ispyb.common.util.export.ExiPdfRtfExporter; +import ispyb.server.mx.vos.collections.DataCollection3VO; + @Path("/") public class DataCollectionRestWebService extends MXRestWebService { @@ -217,11 +218,11 @@ public Response getViewDataCollectionBySessionId(@PathParam("token") String toke @RolesAllowed({"User", "Manager", "Industrial", "Localcontact"}) @GET - @Path("{token}/proposal/{proposal}/mx/datacollection/session/{sessionId}/report/{nbRows}/pdf") + @Path("{token}/proposal/{proposal}/mx/datacollection/session/{sessionId}/report/pdf") @Produces({ "application/pdf" }) public Response getDataCollectionsReportBySessionIdPDF(@PathParam("token") String token, @PathParam("proposal") String proposal, - @PathParam("sessionId") String sessionId, @PathParam("nbRows") String nbRows) throws NamingException { + @PathParam("sessionId") String sessionId, @QueryParam("nbRows") String nbRows) throws NamingException { String methodName = "getDataCollectionReportyBySessionIdPdf"; long start = this.logInit(methodName, logger, token, proposal, sessionId); @@ -237,11 +238,11 @@ public Response getDataCollectionsReportBySessionIdPDF(@PathParam("token") Strin @RolesAllowed({"User", "Manager", "Industrial", "Localcontact"}) @GET - @Path("{token}/proposal/{proposal}/mx/datacollection/session/{sessionId}/report/{nbRows}/rtf") + @Path("{token}/proposal/{proposal}/mx/datacollection/session/{sessionId}/report/rtf") @Produces({ "application/rtf" }) public Response getDataCollectionsReportBySessionIdRTF(@PathParam("token") String token, @PathParam("proposal") String proposal, - @PathParam("sessionId") String sessionId, @PathParam("nbRows") String nbRows) throws NamingException { + @PathParam("sessionId") String sessionId, @QueryParam("nbRows") String nbRows) throws NamingException { String methodName = "getDataCollectionReportyBySessionIdRtf"; long start = this.logInit(methodName, logger, token, proposal, sessionId); @@ -257,11 +258,11 @@ public Response getDataCollectionsReportBySessionIdRTF(@PathParam("token") Strin @RolesAllowed({"User", "Manager", "Industrial", "Localcontact"}) @GET - @Path("{token}/proposal/{proposal}/mx/datacollection/session/{sessionId}/analysisreport/{nbRows}/pdf") + @Path("{token}/proposal/{proposal}/mx/datacollection/session/{sessionId}/analysisreport/pdf") @Produces({ "application/pdf" }) public Response getDataCollectionsAnalysisReportBySessionIdPDF(@PathParam("token") String token, @PathParam("proposal") String proposal, - @PathParam("sessionId") String sessionId, @PathParam("nbRows") String nbRows) throws NamingException { + @PathParam("sessionId") String sessionId, @QueryParam("nbRows") String nbRows) throws NamingException { String methodName = "getDataCollectionAnalysisReportyBySessionIdPdf"; long start = this.logInit(methodName, logger, token, proposal, sessionId); @@ -277,11 +278,11 @@ public Response getDataCollectionsAnalysisReportBySessionIdPDF(@PathParam("token @RolesAllowed({"User", "Manager", "Industrial", "Localcontact"}) @GET - @Path("{token}/proposal/{proposal}/mx/datacollection/session/{sessionId}/analysisreport/{nbRows}/rtf") + @Path("{token}/proposal/{proposal}/mx/datacollection/session/{sessionId}/analysisreport/rtf") @Produces({ "application/rtf" }) public Response getDataCollectionsAnalysisReportBySessionIdRTF(@PathParam("token") String token, @PathParam("proposal") String proposal, - @PathParam("sessionId") String sessionId, @PathParam("nbRows") String nbRows) throws NamingException { + @PathParam("sessionId") String sessionId, @QueryParam("nbRows") String nbRows) throws NamingException { String methodName = "getDataCollectionReportyBySessionIdRtf"; long start = this.logInit(methodName, logger, token, proposal, sessionId); @@ -401,8 +402,12 @@ public Response getViewDataCollectionByProteinAcronym(@PathParam("token") String List> dataCollections = this.getWebServiceDataCollectionGroup3Service().getViewDataCollectionBySessionId(this.getProposalId(proposal), id); - - Integer nbRowsMax = new Integer(nbRows); + + Integer nbRowsMax = dataCollections.size(); + + if (nbRows != null && !nbRows.isEmpty()) { + nbRowsMax = new Integer(nbRows); + } ExiPdfRtfExporter pdf = new ExiPdfRtfExporter(proposal, id , dataCollections, nbRowsMax); @@ -418,7 +423,11 @@ public Response getViewDataCollectionByProteinAcronym(@PathParam("token") String List> dataCollections = this.getWebServiceDataCollectionGroup3Service().getViewDataCollectionBySessionId(this.getProposalId(proposal), id); - Integer nbRowsMax = new Integer(nbRows); + Integer nbRowsMax = dataCollections.size(); + + if (nbRows != null && !nbRows.isEmpty()) { + nbRowsMax = new Integer(nbRows); + } ExiPdfRtfExporter pdf = new ExiPdfRtfExporter(proposal, id , dataCollections, nbRowsMax); From 131ef93d599abd093799a47048d5af7b30ba4e88 Mon Sep 17 00:00:00 2001 From: delageniere Date: Mon, 23 Oct 2017 16:31:21 +0200 Subject: [PATCH 21/38] improvements for reports --- .../common/util/export/ExiPdfRtfExporter.java | 257 +++++++++++++----- .../rest/mx/DataCollectionRestWebService.java | 6 +- 2 files changed, 197 insertions(+), 66 deletions(-) diff --git a/ispyb-ejb/src/main/java/ispyb/common/util/export/ExiPdfRtfExporter.java b/ispyb-ejb/src/main/java/ispyb/common/util/export/ExiPdfRtfExporter.java index d77581366..1613ddb08 100644 --- a/ispyb-ejb/src/main/java/ispyb/common/util/export/ExiPdfRtfExporter.java +++ b/ispyb-ejb/src/main/java/ispyb/common/util/export/ExiPdfRtfExporter.java @@ -26,6 +26,7 @@ import java.text.DecimalFormat; import java.text.NumberFormat; import java.util.ArrayList; +import java.util.Arrays; import java.util.HashMap; import java.util.Iterator; import java.util.List; @@ -57,11 +58,9 @@ import ispyb.server.mx.services.collections.DataCollection3Service; import ispyb.server.mx.services.collections.Image3Service; import ispyb.server.mx.services.collections.IspybCrystalClass3Service; -import ispyb.server.mx.vos.collections.DataCollection3VO; -import ispyb.server.mx.vos.collections.DataCollectionGroup3VO; +import ispyb.server.mx.services.ws.rest.datacollectiongroup.DataCollectionGroupRestWsService; import ispyb.server.mx.vos.collections.IspybCrystalClass3VO; import ispyb.server.mx.vos.collections.Session3VO; -import sun.tools.jstat.Alignment; /** * allows creation of PDF or RTF report - general report for EXI, available in the @@ -133,13 +132,13 @@ public class ExiPdfRtfExporter { public final static Font FONT_INDEXING_NOTDONE = new Font(Font.HELVETICA, 8, Font.NORMAL, LIGHT_GREY_COLOR); - public final static Font FONT_INDEXING_FAILED = new Font(Font.HELVETICA, 8, Font.NORMAL, RED_COLOR); + public final static Font FONT_INDEXING_FAILED = new Font(Font.HELVETICA, 6, Font.BOLD, RED_COLOR); - public final static Font FONT_INDEXING_SUCCESS = new Font(Font.HELVETICA, 8, Font.NORMAL, GREEN_COLOR); + public final static Font FONT_INDEXING_SUCCESS = new Font(Font.HELVETICA, 6, Font.BOLD, GREEN_COLOR); public final static int NB_COL_DATACOLLECTION = 7; - public final static int NB_COL_DATA_ANALYSIS = 11; + public final static int NB_COL_DATA_ANALYSIS = 12; public final static int SIZE_FONT = 8; @@ -174,6 +173,8 @@ public class ExiPdfRtfExporter { public final static float DIFF_IMAGE_HEIGHT = 174; + //proposalId + int proposalId; // proposal String proposalDesc; @@ -199,9 +200,11 @@ public class ExiPdfRtfExporter { private DataCollection3Service dcService; + private DataCollectionGroupRestWsService dcGroupService; + private Image3Service imageService; - public ExiPdfRtfExporter(String proposalDesc, Integer sessionId, + public ExiPdfRtfExporter(int proposalId, String proposalDesc, Integer sessionId, List> dataCollections, Integer nbRowsMax) throws Exception { this.proposalDesc = proposalDesc; this.sessionId = sessionId; @@ -220,6 +223,8 @@ private void init() throws Exception { .getLocalService(Session3Service.class); dcService = (DataCollection3Service) ejb3ServiceLocator .getLocalService(DataCollection3Service.class); + dcGroupService = (DataCollectionGroupRestWsService) ejb3ServiceLocator + .getLocalService(DataCollectionGroupRestWsService.class); imageService = (Image3Service) ejb3ServiceLocator .getLocalService(Image3Service.class); @@ -516,8 +521,7 @@ private void setDataAnalysisTable(Document document) throws Exception { while (it.hasNext() && i < nbRowsMax) { Map dataCollectionMapData = it.next(); LOG.info("dcMap=" + dataCollectionMapData.toString()); - setDataAnalysisMapData(document, dataCollectionMapData); - + setDataAnalysisMapData(document, dataCollectionMapData); i++; } document.add(new Paragraph(" ")); @@ -709,82 +713,138 @@ private void setDataAnalysisMapData(Document document, Map dataC table.addCell(" "); } - // Cell 6 indexed/strategy or completeness + // Cell 6 7 8 9 10 11 indexed/strategy or completeness Boolean indexing = getBoolean(dataCollectionMapItem, "ScreeningOutput_indexingSuccess"); Boolean strategy = getBoolean(dataCollectionMapItem, "ScreeningOutput_strategySuccess"); String autoprocSpaceGroup = getCellParam(dataCollectionMapItem, "AutoProc_spaceGroup", null); p = new Paragraph(); - - Chunk chu1 = new Chunk("Indexed: ", FONT_DOC_SMALL); + String [] bestRmerge = null; + if (indexing != null && strategy != null){ - - Chunk chu2 = new Chunk( "Failed", FONT_INDEXING_FAILED); + // Cell 6 + parag = "\nIndexed: \n " + + "\nStrategy: \n"; + p = new Paragraph(parag, FONT_DOC_SMALL); + table.addCell(p); + + // Cell 6 + p = new Paragraph(); + Chunk chu2 = new Chunk( "KO", FONT_INDEXING_FAILED); if (indexing.booleanValue() ){ - chu2 = new Chunk( "Success", FONT_INDEXING_SUCCESS); + chu2 = new Chunk( "OK", FONT_INDEXING_SUCCESS); } - p.add(chu1); p.add(chu2); - chu1 = new Chunk("Strategy: ", FONT_DOC_SMALL); - chu2 = new Chunk( "Failed", FONT_INDEXING_FAILED); + chu2 = new Chunk( "KO", FONT_INDEXING_FAILED); if (strategy.booleanValue() ){ - chu2 = new Chunk( "Success", FONT_INDEXING_SUCCESS); + chu2 = new Chunk( "OK", FONT_INDEXING_SUCCESS); } - p.add(chu1); + p.add("\n"); p.add(chu2); table.addCell(p); - - } else if (autoprocSpaceGroup != null && !autoprocSpaceGroup.isEmpty()){ - parag = autoprocSpaceGroup + " Completeness \n" - + "Overall" + "\n" - + "Inner" + "\n" - + "Outer" + "\n"; + + // Cell 7 + parag = "Space group: \n" + + "Mosaicity: \n" ; p = new Paragraph(parag, FONT_DOC_SMALL); - - } else { - - table.addCell(" "); + table.addCell(p); - } - - // Cell 7 - if (indexing != null && strategy != null){ - parag = "Space group: \n" - + "Mosaicity: \n" ; + // Cell 8 + parag = getCellParam(dataCollectionMapItem, "ScreeningOutputLattice_spaceGroup", null) + "\n" + + getCellParam(dataCollectionMapItem, "ScreeningOutput_mosaicity", null)+ "\n" ; + p = new Paragraph(parag, FONT_DOC_SMALL_BOLD); + table.addCell(p); + + // Cell 9 + parag = "a \n" + getCellParam(dataCollectionMapItem, "ScreeningOutputLattice_unitCell_a", null) + + "\n alpha \n" + getCellParam(dataCollectionMapItem, "ScreeningOutputLattice_unitCell_alpha", null) ; + p = new Paragraph(parag, FONT_DOC_SMALL_CENTERED); + p.setAlignment(Element.ALIGN_CENTER); + table.addCell(p); + + // Cell 10 + parag = "b \n" + getCellParam(dataCollectionMapItem, "ScreeningOutputLattice_unitCell_b", null) + + "\n beta \n" + getCellParam(dataCollectionMapItem, "ScreeningOutputLattice_unitCell_beta", null) ; + p = new Paragraph(parag, FONT_DOC_SMALL_CENTERED); + p.setAlignment(Element.ALIGN_CENTER); + table.addCell(p); + + // Cell 11 + parag = "c \n" + getCellParam(dataCollectionMapItem, "ScreeningOutputLattice_unitCell_c", null) + + "\n gamma \n" + getCellParam(dataCollectionMapItem, "ScreeningOutputLattice_unitCell_gama", null) ; + + p = new Paragraph(parag, FONT_DOC_SMALL_CENTERED); + p.setAlignment(Element.ALIGN_CENTER); + table.addCell(p); + + + } else if (autoprocSpaceGroup != null && !autoprocSpaceGroup.isEmpty() && extractBestRmerge(dataCollectionMapItem) != null){ + // Cell 6 + bestRmerge = extractBestRmerge(dataCollectionMapItem); + parag = autoprocSpaceGroup + "\n" + + "Overall\n" + + "Inner\n" + + "Outer\n"; p = new Paragraph(parag, FONT_DOC_SMALL); - } else { - p = new Paragraph(" "); - } - table.addCell(p); + table.addCell(p); - // Cell 8 - parag = getCellParam(dataCollectionMapItem, "ScreeningOutputLattice_spaceGroup", null) + "\n" - + getCellParam(dataCollectionMapItem, "ScreeningOutput_mosaicity", null)+ "\n" ; - p = new Paragraph(parag, FONT_DOC_SMALL_BOLD); - table.addCell(p); + // Cell 7 + parag ="Completeness\n" + + bestRmerge[16] + "\n" + + bestRmerge[2] + "\n" + + bestRmerge[12] + "\n"; + p = new Paragraph(parag, FONT_DOC_SMALL); + table.addCell(p); - // Cell 9 - parag = "a \n" + getCellParam(dataCollectionMapItem, "ScreeningOutputLattice_unitCell_a", null) - + "\n alpha \n" + getCellParam(dataCollectionMapItem, "ScreeningOutputLattice_unitCell_alpha", null) ; - p = new Paragraph(parag, FONT_DOC_SMALL_CENTERED); - p.setAlignment(Element.ALIGN_CENTER); - table.addCell(p); + // Cell 8 + parag = "Res. \n" + + bestRmerge[17]+ "\n " + + bestRmerge[3] + "\n" + + bestRmerge[13] + "\n" ; + p = new Paragraph(parag, FONT_DOC_SMALL); + table.addCell(p); - // Cell 10 - parag = "b \n" + getCellParam(dataCollectionMapItem, "ScreeningOutputLattice_unitCell_b", null) - + "\n beta \n" + getCellParam(dataCollectionMapItem, "ScreeningOutputLattice_unitCell_beta", null) ; - p = new Paragraph(parag, FONT_DOC_SMALL_CENTERED); - p.setAlignment(Element.ALIGN_CENTER); - table.addCell(p); + // Cell 9 + parag = "Rmerge \n" + + bestRmerge[15] + "\n" + + bestRmerge[1] + "\n" + + bestRmerge[11] + "\n"; + p = new Paragraph(parag, FONT_DOC_SMALL); + table.addCell(p); - // Cell 11 - parag = "c \n" + getCellParam(dataCollectionMapItem, "ScreeningOutputLattice_unitCell_c", null) - + "\n gamma \n" + getCellParam(dataCollectionMapItem, "ScreeningOutputLattice_unitCell_gama", null) ; + // cell parameters of innerShell + // Cell 10 a alpha + parag = "a \n" + bestRmerge[4] + + "\n alpha \n" + bestRmerge[7] ; + p = new Paragraph(parag, FONT_DOC_SMALL_CENTERED); + p.setAlignment(Element.ALIGN_CENTER); + table.addCell(p); + + // Cell 11 b beta + parag = "b \n" + bestRmerge[5] + + "\n beta \n" + bestRmerge[8] ; + p = new Paragraph(parag, FONT_DOC_SMALL_CENTERED); + p.setAlignment(Element.ALIGN_CENTER); + table.addCell(p); - p = new Paragraph(parag, FONT_DOC_SMALL_CENTERED); - p.setAlignment(Element.ALIGN_CENTER); - table.addCell(p); + // Cell 12 + parag = "c \n" + bestRmerge[6] + + "\n gamma \n" + bestRmerge[9] ; + + p = new Paragraph(parag, FONT_DOC_SMALL_CENTERED); + p.setAlignment(Element.ALIGN_CENTER); + table.addCell(p); + + } else { + table.addCell(" "); + table.addCell(" "); + table.addCell(" "); + table.addCell(" "); + table.addCell(" "); + table.addCell(" "); + table.addCell(" "); + } document.add(table); @@ -1010,5 +1070,76 @@ private List getListOfNbCrystalPerClass(List list return listOfNbCrystalPerClass; } + private String[] extractBestRmerge(Map dataCollectionMapItem) throws Exception { + + String listString = (String)dataCollectionMapItem.get("completenessList"); + listString.trim(); + List completenessList = new ArrayList(Arrays.asList((listString.split(",")))); + LOG.info("completenessList = " + completenessList.toString()); + + String [] bestRmerge = null; + + if (completenessList != null && !completenessList.isEmpty()) { + + bestRmerge = new String[18]; + List rmergesList = new ArrayList(Arrays.asList(((String)dataCollectionMapItem.get("rMerges")).trim().split(","))); + LOG.info("rmergesList = " + rmergesList.size() + rmergesList.toString() ); + List scalingStatisticsTypesList = new ArrayList(Arrays.asList(((String)dataCollectionMapItem.get("scalingStatisticsTypes")).trim().split(","))); + LOG.info("scalingStatisticsTypesList = " + scalingStatisticsTypesList.size() + scalingStatisticsTypesList.toString()); + int i = 0; + Double rmergeMin = 1000.0; + int indexRmergeMin = 0; + + for (Iterator iterator = scalingStatisticsTypesList.iterator(); iterator.hasNext();) { + String type = (String) iterator.next(); + if (type.equals("innerShell")){ + if (new Double(rmergesList.get(i)) < rmergeMin) { + rmergeMin = new Double(rmergesList.get(i)); + indexRmergeMin = i; + } + } + i=i+1; + } + List spaceGroupsList = new ArrayList(Arrays.asList(((String)dataCollectionMapItem.get("AutoProc_spaceGroups")).trim().split(","))); + LOG.info("spaceGroupsList = " + spaceGroupsList.size() + spaceGroupsList.toString()); + List resolutionsLimitLowList = new ArrayList(Arrays.asList(((String)dataCollectionMapItem.get("resolutionsLimitLow")).trim().split(","))); + LOG.info("resolutionsLimitLowList = " + resolutionsLimitLowList.size() + resolutionsLimitLowList.toString()); + List resolutionsLimitHighList = new ArrayList(Arrays.asList(((String)dataCollectionMapItem.get("resolutionsLimitHigh")).trim().split(","))); + LOG.info("resolutionsLimitHighList = " + resolutionsLimitHighList.toString()); + + + bestRmerge[0] = spaceGroupsList.get(indexRmergeMin); + bestRmerge[1] = rmergeMin.toString(); + bestRmerge[2]= completenessList.get(indexRmergeMin); + bestRmerge[3] = resolutionsLimitLowList.get(indexRmergeMin) + "/" + resolutionsLimitHighList.get(indexRmergeMin); + + List tmpList = new ArrayList(Arrays.asList(((String)dataCollectionMapItem.get("Autoprocessing_cell_a")).trim().split(","))); + bestRmerge[4] = tmpList.get(indexRmergeMin); + tmpList = new ArrayList(Arrays.asList(((String)dataCollectionMapItem.get("Autoprocessing_cell_b")).trim().split(","))); + bestRmerge[5] = tmpList.get(indexRmergeMin); + tmpList = new ArrayList(Arrays.asList(((String)dataCollectionMapItem.get("Autoprocessing_cell_c")).trim().split(","))); + bestRmerge[6] = tmpList.get(indexRmergeMin); + tmpList = new ArrayList(Arrays.asList(((String)dataCollectionMapItem.get("Autoprocessing_cell_alpha")).trim().split(","))); + bestRmerge[7] = tmpList.get(indexRmergeMin); + tmpList = new ArrayList(Arrays.asList(((String)dataCollectionMapItem.get("Autoprocessing_cell_beta")).trim().split(","))); + bestRmerge[8] = tmpList.get(indexRmergeMin); + tmpList = new ArrayList(Arrays.asList(((String)dataCollectionMapItem.get("Autoprocessing_cell_gamma")).trim().split(","))); + bestRmerge[9] = tmpList.get(indexRmergeMin); + + //outer + bestRmerge[10] = spaceGroupsList.get(indexRmergeMin+1); + bestRmerge[11] = rmergesList.get(indexRmergeMin+1); + bestRmerge[12]= completenessList.get(indexRmergeMin+1); + bestRmerge[13] = resolutionsLimitLowList.get(indexRmergeMin+1) + "/" + resolutionsLimitHighList.get(indexRmergeMin+1); + + //overall + bestRmerge[14] = spaceGroupsList.get(indexRmergeMin+2); + bestRmerge[15] = rmergesList.get(indexRmergeMin+2); + bestRmerge[16]= completenessList.get(indexRmergeMin+2); + bestRmerge[17] = resolutionsLimitLowList.get(indexRmergeMin+2) + "/" + resolutionsLimitHighList.get(indexRmergeMin+2); + } + LOG.info("bestRmerge = " + "- " + bestRmerge[0] + "- " + bestRmerge[1]+ "- " + bestRmerge[2]+ "- " + bestRmerge[3]); + return bestRmerge; + } } diff --git a/ispyb-ws/src/main/java/ispyb/ws/rest/mx/DataCollectionRestWebService.java b/ispyb-ws/src/main/java/ispyb/ws/rest/mx/DataCollectionRestWebService.java index ad02d3c92..0b2a26526 100644 --- a/ispyb-ws/src/main/java/ispyb/ws/rest/mx/DataCollectionRestWebService.java +++ b/ispyb-ws/src/main/java/ispyb/ws/rest/mx/DataCollectionRestWebService.java @@ -404,12 +404,12 @@ public Response getViewDataCollectionByProteinAcronym(@PathParam("token") String this.getWebServiceDataCollectionGroup3Service().getViewDataCollectionBySessionId(this.getProposalId(proposal), id); Integer nbRowsMax = dataCollections.size(); - + if (nbRows != null && !nbRows.isEmpty()) { nbRowsMax = new Integer(nbRows); } - ExiPdfRtfExporter pdf = new ExiPdfRtfExporter(proposal, id , dataCollections, nbRowsMax); + ExiPdfRtfExporter pdf = new ExiPdfRtfExporter(this.getProposalId(proposal), proposal, id , dataCollections, nbRowsMax); byte [] byteToExport = pdf.exportDataCollectionReport(isRtf).toByteArray(); @@ -429,7 +429,7 @@ public Response getViewDataCollectionByProteinAcronym(@PathParam("token") String nbRowsMax = new Integer(nbRows); } - ExiPdfRtfExporter pdf = new ExiPdfRtfExporter(proposal, id , dataCollections, nbRowsMax); + ExiPdfRtfExporter pdf = new ExiPdfRtfExporter(this.getProposalId(proposal), proposal, id , dataCollections, nbRowsMax); byte [] byteToExport = pdf.exportDataCollectionAnalysisReport(isRtf).toByteArray(); From 81e1baae4ebc06f2e82043786a79cb57874de43f Mon Sep 17 00:00:00 2001 From: delageniere Date: Mon, 23 Oct 2017 17:10:47 +0200 Subject: [PATCH 22/38] improvements for reports --- .../ispyb/common/util/export/ExiPdfRtfExporter.java | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/ispyb-ejb/src/main/java/ispyb/common/util/export/ExiPdfRtfExporter.java b/ispyb-ejb/src/main/java/ispyb/common/util/export/ExiPdfRtfExporter.java index 1613ddb08..095a08356 100644 --- a/ispyb-ejb/src/main/java/ispyb/common/util/export/ExiPdfRtfExporter.java +++ b/ispyb-ejb/src/main/java/ispyb/common/util/export/ExiPdfRtfExporter.java @@ -47,6 +47,8 @@ import com.lowagie.text.Paragraph; import com.lowagie.text.Phrase; import com.lowagie.text.Table; +import com.lowagie.text.pdf.PdfPCell; +import com.lowagie.text.pdf.PdfPTable; import com.lowagie.text.pdf.PdfWriter; import com.lowagie.text.rtf.RtfWriter2; @@ -666,7 +668,6 @@ private void setDataAnalysisMapData(Document document, Map dataC Table table = new Table(NB_COL_DATA_ANALYSIS); table.getDefaultCell().setHorizontalAlignment(Element.ALIGN_LEFT); table.getDefaultCell().setBorderWidth(0); - table.setBorder(1); // 1st Cell String parag = "Protein: \n\n" @@ -845,8 +846,12 @@ private void setDataAnalysisMapData(Document document, Map dataC table.addCell(" "); table.addCell(" "); } - - document.add(table); + // to avoid splitting table + Table containingTable = new Table(1); + Cell cell = new Cell(table); + containingTable.addCell(cell); + + document.add(containingTable); return; } From 31896ee93ff9b7fd4848805b6a8e27605fcac69e Mon Sep 17 00:00:00 2001 From: delageniere Date: Tue, 24 Oct 2017 11:50:07 +0200 Subject: [PATCH 23/38] modif for reports + IM proposal update --- .../common/util/export/ExiPdfRtfExporter.java | 68 ++++++++++++++----- .../bodies/common/proposal/updateISPYBdb.jsp | 3 +- 2 files changed, 53 insertions(+), 18 deletions(-) diff --git a/ispyb-ejb/src/main/java/ispyb/common/util/export/ExiPdfRtfExporter.java b/ispyb-ejb/src/main/java/ispyb/common/util/export/ExiPdfRtfExporter.java index 095a08356..6a3bbc43a 100644 --- a/ispyb-ejb/src/main/java/ispyb/common/util/export/ExiPdfRtfExporter.java +++ b/ispyb-ejb/src/main/java/ispyb/common/util/export/ExiPdfRtfExporter.java @@ -113,6 +113,8 @@ public class ExiPdfRtfExporter { public final static Font FONT_DOC_SMALL = new Font(Font.HELVETICA, 6, Font.NORMAL, Color.BLACK); public final static Font FONT_DOC_BLUE = new Font(Font.HELVETICA, 8, Font.NORMAL, Color.BLUE); + public final static Font FONT_DOC_ORANGE = new Font(Font.HELVETICA, 8, Font.NORMAL, Color.ORANGE); + public final static Font FONT_DOC_RED = new Font(Font.HELVETICA, 8, Font.NORMAL, Color.RED); public final static Font FONT_DOC_ITALIC = new Font(Font.HELVETICA, 8, Font.ITALIC, Color.BLACK); @@ -718,6 +720,9 @@ private void setDataAnalysisMapData(Document document, Map dataC Boolean indexing = getBoolean(dataCollectionMapItem, "ScreeningOutput_indexingSuccess"); Boolean strategy = getBoolean(dataCollectionMapItem, "ScreeningOutput_strategySuccess"); String autoprocSpaceGroup = getCellParam(dataCollectionMapItem, "AutoProc_spaceGroup", null); + boolean existAutoProcSpaceGroup = (autoprocSpaceGroup != null && !autoprocSpaceGroup.isEmpty() ) + || ( dataCollectionMapItem.get("AutoProc_spaceGroups") != null && !((String)dataCollectionMapItem.get("AutoProc_spaceGroups")).isEmpty()); + p = new Paragraph(); String [] bestRmerge = null; @@ -780,22 +785,27 @@ private void setDataAnalysisMapData(Document document, Map dataC table.addCell(p); - } else if (autoprocSpaceGroup != null && !autoprocSpaceGroup.isEmpty() && extractBestRmerge(dataCollectionMapItem) != null){ + } else if (existAutoProcSpaceGroup && extractBestRmerge(dataCollectionMapItem) != null){ // Cell 6 bestRmerge = extractBestRmerge(dataCollectionMapItem); - parag = autoprocSpaceGroup + "\n" + parag = bestRmerge[0] + "\n" + "Overall\n" + "Inner\n" + "Outer\n"; p = new Paragraph(parag, FONT_DOC_SMALL); table.addCell(p); - // Cell 7 - parag ="Completeness\n" - + bestRmerge[16] + "\n" - + bestRmerge[2] + "\n" - + bestRmerge[12] + "\n"; - p = new Paragraph(parag, FONT_DOC_SMALL); + // Cell 7 + p = new Paragraph("Completeness\n", FONT_DOC_SMALL); + Chunk chu = getCompletenessChunk(bestRmerge[16]); + p.add(chu); + p.add("\n"); + chu = getCompletenessChunk(bestRmerge[2]); + p.add(chu); + p.add("\n"); + chu = getCompletenessChunk(bestRmerge[12]); + p.add(chu); + table.addCell(p); // Cell 8 @@ -1092,15 +1102,20 @@ private String[] extractBestRmerge(Map dataCollectionMapItem) th List scalingStatisticsTypesList = new ArrayList(Arrays.asList(((String)dataCollectionMapItem.get("scalingStatisticsTypes")).trim().split(","))); LOG.info("scalingStatisticsTypesList = " + scalingStatisticsTypesList.size() + scalingStatisticsTypesList.toString()); int i = 0; - Double rmergeMin = 1000.0; + Double rmergeMin = 1000.000; int indexRmergeMin = 0; for (Iterator iterator = scalingStatisticsTypesList.iterator(); iterator.hasNext();) { String type = (String) iterator.next(); - if (type.equals("innerShell")){ - if (new Double(rmergesList.get(i)) < rmergeMin) { - rmergeMin = new Double(rmergesList.get(i)); + if (type.contains("innerShell")){ + double rm = new Double(rmergesList.get(i)).doubleValue(); + LOG.info("rm = " + rm); + if (rm > 0 && rm < rmergeMin) { + rmergeMin = rm; indexRmergeMin = i; + // TODO replace this by a look for the higher spacegroup + if (rmergeMin < 10) + break; } } i=i+1; @@ -1138,13 +1153,32 @@ private String[] extractBestRmerge(Map dataCollectionMapItem) th bestRmerge[13] = resolutionsLimitLowList.get(indexRmergeMin+1) + "/" + resolutionsLimitHighList.get(indexRmergeMin+1); //overall - bestRmerge[14] = spaceGroupsList.get(indexRmergeMin+2); - bestRmerge[15] = rmergesList.get(indexRmergeMin+2); - bestRmerge[16]= completenessList.get(indexRmergeMin+2); - bestRmerge[17] = resolutionsLimitLowList.get(indexRmergeMin+2) + "/" + resolutionsLimitHighList.get(indexRmergeMin+2); + int overallIndex = indexRmergeMin-1; + if (overallIndex < 0 || scalingStatisticsTypesList.get(0).contains("innerShell")) { + overallIndex = indexRmergeMin+2; + } + + bestRmerge[14] = spaceGroupsList.get(overallIndex); + bestRmerge[15] = rmergesList.get(overallIndex); + bestRmerge[16]= completenessList.get(overallIndex); + //TODO format to 2 figures after . + bestRmerge[17] = resolutionsLimitLowList.get(overallIndex) + "/" + resolutionsLimitHighList.get(overallIndex); } - LOG.info("bestRmerge = " + "- " + bestRmerge[0] + "- " + bestRmerge[1]+ "- " + bestRmerge[2]+ "- " + bestRmerge[3]); + LOG.info("bestRmerge = " + bestRmerge[0] + "- " + bestRmerge[1]+ "- " + bestRmerge[2]+ "- " + bestRmerge[3]); return bestRmerge; } + + private Chunk getCompletenessChunk(String completeness) { + Chunk chu = new Chunk( completeness, FONT_DOC_SMALL_BOLD); + chu.setBackground(BLUE_COLOR); + if (completeness != null && new Double(completeness) < 80 ) { + if (new Double(completeness) < 10) { + chu.setBackground(RED_COLOR); + } else { + chu.setBackground(LIGHT_YELLOW_COLOR); + } + } + return chu; + } } diff --git a/ispyb-ui/src/main/webapp/tiles/bodies/common/proposal/updateISPYBdb.jsp b/ispyb-ui/src/main/webapp/tiles/bodies/common/proposal/updateISPYBdb.jsp index badc48481..692b6a7af 100644 --- a/ispyb-ui/src/main/webapp/tiles/bodies/common/proposal/updateISPYBdb.jsp +++ b/ispyb-ui/src/main/webapp/tiles/bodies/common/proposal/updateISPYBdb.jsp @@ -66,7 +66,8 @@ Contributors : S. Delageniere, R. Leal, L. Launer, K. Levik, S. Veyrier, P. Bren - + + From de9c172f312a487253971d58b0c3eb3e19353c48 Mon Sep 17 00:00:00 2001 From: delageniere Date: Thu, 26 Oct 2017 15:39:49 +0200 Subject: [PATCH 24/38] analysis report improvement --- .../common/util/export/ExiPdfRtfExporter.java | 84 +++++++++++++------ .../getViewTableQuery.sql | 2 +- .../getViewTableQuery.sql | 2 +- 3 files changed, 60 insertions(+), 28 deletions(-) diff --git a/ispyb-ejb/src/main/java/ispyb/common/util/export/ExiPdfRtfExporter.java b/ispyb-ejb/src/main/java/ispyb/common/util/export/ExiPdfRtfExporter.java index 6a3bbc43a..a99b77023 100644 --- a/ispyb-ejb/src/main/java/ispyb/common/util/export/ExiPdfRtfExporter.java +++ b/ispyb-ejb/src/main/java/ispyb/common/util/export/ExiPdfRtfExporter.java @@ -28,10 +28,12 @@ import java.util.ArrayList; import java.util.Arrays; import java.util.HashMap; +import java.util.HashSet; import java.util.Iterator; import java.util.List; import java.util.Locale; import java.util.Map; +import java.util.Set; import org.apache.log4j.Logger; @@ -47,8 +49,6 @@ import com.lowagie.text.Paragraph; import com.lowagie.text.Phrase; import com.lowagie.text.Table; -import com.lowagie.text.pdf.PdfPCell; -import com.lowagie.text.pdf.PdfPTable; import com.lowagie.text.pdf.PdfWriter; import com.lowagie.text.rtf.RtfWriter2; @@ -57,10 +57,12 @@ import ispyb.common.util.PathUtils; import ispyb.server.common.services.sessions.Session3Service; import ispyb.server.common.util.ejb.Ejb3ServiceLocator; +import ispyb.server.mx.services.autoproc.SpaceGroup3Service; import ispyb.server.mx.services.collections.DataCollection3Service; import ispyb.server.mx.services.collections.Image3Service; import ispyb.server.mx.services.collections.IspybCrystalClass3Service; import ispyb.server.mx.services.ws.rest.datacollectiongroup.DataCollectionGroupRestWsService; +import ispyb.server.mx.vos.autoproc.SpaceGroup3VO; import ispyb.server.mx.vos.collections.IspybCrystalClass3VO; import ispyb.server.mx.vos.collections.Session3VO; @@ -176,6 +178,8 @@ public class ExiPdfRtfExporter { public final static float DIFF_IMAGE_WIDTH = 174; public final static float DIFF_IMAGE_HEIGHT = 174; + + public final static double MIN_RMERGE = 10; //proposalId int proposalId; @@ -207,6 +211,10 @@ public class ExiPdfRtfExporter { private DataCollectionGroupRestWsService dcGroupService; private Image3Service imageService; + + private SpaceGroup3Service spacegroupService; + + private Map spgMap = new HashMap (); public ExiPdfRtfExporter(int proposalId, String proposalDesc, Integer sessionId, List> dataCollections, Integer nbRowsMax) throws Exception { @@ -231,8 +239,18 @@ private void init() throws Exception { .getLocalService(DataCollectionGroupRestWsService.class); imageService = (Image3Service) ejb3ServiceLocator .getLocalService(Image3Service.class); + spacegroupService = (SpaceGroup3Service) ejb3ServiceLocator + .getLocalService(SpaceGroup3Service.class); slv = sessionService.findByPk(sessionId, false/*withDataCollectionGroup*/, false/*withEnergyScan*/, false/*withXFESpectrum*/); + + List spaceGroups = spacegroupService.findAll(); + + for (Iterator iterator = spaceGroups.iterator(); iterator.hasNext();) { + SpaceGroup3VO spg = (SpaceGroup3VO) iterator.next(); + spgMap.put(spg.getSpaceGroupName(), spg.getSpaceGroupNumber()); + } + LOG.info("spgMap=" + spgMap.toString()); } @@ -785,9 +803,9 @@ private void setDataAnalysisMapData(Document document, Map dataC table.addCell(p); - } else if (existAutoProcSpaceGroup && extractBestRmerge(dataCollectionMapItem) != null){ + } else if (existAutoProcSpaceGroup && extractBestAutoproc(dataCollectionMapItem) != null){ // Cell 6 - bestRmerge = extractBestRmerge(dataCollectionMapItem); + bestRmerge = extractBestAutoproc(dataCollectionMapItem); parag = bestRmerge[0] + "\n" + "Overall\n" + "Inner\n" @@ -1085,51 +1103,64 @@ private List getListOfNbCrystalPerClass(List list return listOfNbCrystalPerClass; } - private String[] extractBestRmerge(Map dataCollectionMapItem) throws Exception { + private String[] extractBestAutoproc(Map dataCollectionMapItem) throws Exception { - String listString = (String)dataCollectionMapItem.get("completenessList"); - listString.trim(); - List completenessList = new ArrayList(Arrays.asList((listString.split(",")))); - LOG.info("completenessList = " + completenessList.toString()); - String [] bestRmerge = null; + String listString = (String)dataCollectionMapItem.get("completenessList"); - if (completenessList != null && !completenessList.isEmpty()) { - - bestRmerge = new String[18]; + if (dataCollectionMapItem.get("completenessList") != null && !listString.isEmpty() && dataCollectionMapItem.get("AutoProc_spaceGroups") != null) { + + listString.trim(); + List completenessList = new ArrayList(Arrays.asList((listString.split(",")))); + LOG.info("completenessList = " + completenessList.toString()); + List spaceGroupsList = new ArrayList(Arrays.asList(((String)dataCollectionMapItem.get("AutoProc_spaceGroups")).trim().split(","))); + LOG.info("spaceGroupsList = " + spaceGroupsList.size() + spaceGroupsList.toString()); + List resolutionsLimitLowList = new ArrayList(Arrays.asList(((String)dataCollectionMapItem.get("resolutionsLimitLow")).trim().split(","))); + LOG.info("resolutionsLimitLowList = " + resolutionsLimitLowList.size() + resolutionsLimitLowList.toString()); + List resolutionsLimitHighList = new ArrayList(Arrays.asList(((String)dataCollectionMapItem.get("resolutionsLimitHigh")).trim().split(","))); + LOG.info("resolutionsLimitHighList = " + resolutionsLimitHighList.toString()); List rmergesList = new ArrayList(Arrays.asList(((String)dataCollectionMapItem.get("rMerges")).trim().split(","))); LOG.info("rmergesList = " + rmergesList.size() + rmergesList.toString() ); List scalingStatisticsTypesList = new ArrayList(Arrays.asList(((String)dataCollectionMapItem.get("scalingStatisticsTypes")).trim().split(","))); LOG.info("scalingStatisticsTypesList = " + scalingStatisticsTypesList.size() + scalingStatisticsTypesList.toString()); + + bestRmerge = new String[18]; int i = 0; Double rmergeMin = 1000.000; int indexRmergeMin = 0; + Set indexSet = new HashSet(); - for (Iterator iterator = scalingStatisticsTypesList.iterator(); iterator.hasNext();) { + for (Iterator iterator = scalingStatisticsTypesList.iterator(); iterator.hasNext();) { String type = (String) iterator.next(); if (type.contains("innerShell")){ double rm = new Double(rmergesList.get(i)).doubleValue(); LOG.info("rm = " + rm); if (rm > 0 && rm < rmergeMin) { rmergeMin = rm; - indexRmergeMin = i; - // TODO replace this by a look for the higher spacegroup - if (rmergeMin < 10) - break; + indexRmergeMin = i; + if (rmergeMin < MIN_RMERGE) + indexSet.add(i); } } i=i+1; } - List spaceGroupsList = new ArrayList(Arrays.asList(((String)dataCollectionMapItem.get("AutoProc_spaceGroups")).trim().split(","))); - LOG.info("spaceGroupsList = " + spaceGroupsList.size() + spaceGroupsList.toString()); - List resolutionsLimitLowList = new ArrayList(Arrays.asList(((String)dataCollectionMapItem.get("resolutionsLimitLow")).trim().split(","))); - LOG.info("resolutionsLimitLowList = " + resolutionsLimitLowList.size() + resolutionsLimitLowList.toString()); - List resolutionsLimitHighList = new ArrayList(Arrays.asList(((String)dataCollectionMapItem.get("resolutionsLimitHigh")).trim().split(","))); - LOG.info("resolutionsLimitHighList = " + resolutionsLimitHighList.toString()); + if (!indexSet.isEmpty()) { + String spgTemp; + Integer spgNb = 0; + for (Iterator iterator = indexSet.iterator(); iterator.hasNext();) { + Integer index = (Integer) iterator.next(); + spgTemp = spaceGroupsList.get(index); + + if (spgMap.get(spgTemp)!= null && spgNb < spgMap.get(spgTemp)) { + spgNb = spgMap.get(spgTemp); + indexRmergeMin = index; + } + } + } bestRmerge[0] = spaceGroupsList.get(indexRmergeMin); - bestRmerge[1] = rmergeMin.toString(); + bestRmerge[1] = rmergesList.get(indexRmergeMin); bestRmerge[2]= completenessList.get(indexRmergeMin); bestRmerge[3] = resolutionsLimitLowList.get(indexRmergeMin) + "/" + resolutionsLimitHighList.get(indexRmergeMin); @@ -1163,8 +1194,9 @@ private String[] extractBestRmerge(Map dataCollectionMapItem) th bestRmerge[16]= completenessList.get(overallIndex); //TODO format to 2 figures after . bestRmerge[17] = resolutionsLimitLowList.get(overallIndex) + "/" + resolutionsLimitHighList.get(overallIndex); + LOG.info("bestRmerge = " + bestRmerge[0] + "- " + bestRmerge[1]+ "- " + bestRmerge[2]+ "- " + bestRmerge[3]); } - LOG.info("bestRmerge = " + bestRmerge[0] + "- " + bestRmerge[1]+ "- " + bestRmerge[2]+ "- " + bestRmerge[3]); + return bestRmerge; } diff --git a/ispyb-ejb/src/main/resources/queries/DataCollectionGroupRestWsServiceBean/getViewTableQuery.sql b/ispyb-ejb/src/main/resources/queries/DataCollectionGroupRestWsServiceBean/getViewTableQuery.sql index ce9f0a09a..85fd97aa0 100644 --- a/ispyb-ejb/src/main/resources/queries/DataCollectionGroupRestWsServiceBean/getViewTableQuery.sql +++ b/ispyb-ejb/src/main/resources/queries/DataCollectionGroupRestWsServiceBean/getViewTableQuery.sql @@ -20,7 +20,7 @@ GROUP_CONCAT(`scalingStatisticsType` SEPARATOR ', ') AS `scalingStatisticsTypes` GROUP_CONCAT(`resolutionLimitHigh` SEPARATOR ', ') AS `resolutionsLimitHigh`, GROUP_CONCAT(`resolutionLimitLow` SEPARATOR ', ') AS `resolutionsLimitLow`, GROUP_CONCAT(`rMerge` SEPARATOR ', ') AS `rMerges`, -GROUP_CONCAT(`completeness` SEPARATOR ', ') AS `completenessList`, +GROUP_CONCAT(`completeness` SEPARATOR ', ') AS `completenessList`, GROUP_CONCAT(`AutoProc_spaceGroup` SEPARATOR ', ') AS `AutoProc_spaceGroups`, (SELECT count(*) diff --git a/ispyb-ejb/src/main/resources/queries/DataCollectionRestWsServiceBean/getViewTableQuery.sql b/ispyb-ejb/src/main/resources/queries/DataCollectionRestWsServiceBean/getViewTableQuery.sql index 89b48324c..c90e57e0c 100644 --- a/ispyb-ejb/src/main/resources/queries/DataCollectionRestWsServiceBean/getViewTableQuery.sql +++ b/ispyb-ejb/src/main/resources/queries/DataCollectionRestWsServiceBean/getViewTableQuery.sql @@ -16,7 +16,7 @@ GROUP_CONCAT(`scalingStatisticsType` SEPARATOR ', ') AS `scalingStatisticsTypes` GROUP_CONCAT(`resolutionLimitHigh` SEPARATOR ', ') AS `resolutionsLimitHigh`, GROUP_CONCAT(`resolutionLimitLow` SEPARATOR ', ') AS `resolutionsLimitLow`, GROUP_CONCAT(`rMerge` SEPARATOR ', ') AS `rMerges`, -GROUP_CONCAT(`completeness` SEPARATOR ', ') AS `completenessList`, +GROUP_CONCAT(`completeness` SEPARATOR ', ') AS `completenessList`, GROUP_CONCAT(`AutoProc_spaceGroup` SEPARATOR ', ') AS `AutoProc_spaceGroups`, (SELECT count(*) From 3db304f02120622a17379b2764371a72871c3528 Mon Sep 17 00:00:00 2001 From: delageniere Date: Thu, 26 Oct 2017 16:38:49 +0200 Subject: [PATCH 25/38] change the name of reports + reverse order --- .../common/util/export/ExiPdfRtfExporter.java | 19 ++++++++++++------- .../rest/mx/DataCollectionRestWebService.java | 14 ++++++++++---- 2 files changed, 22 insertions(+), 11 deletions(-) diff --git a/ispyb-ejb/src/main/java/ispyb/common/util/export/ExiPdfRtfExporter.java b/ispyb-ejb/src/main/java/ispyb/common/util/export/ExiPdfRtfExporter.java index a99b77023..d6a93da60 100644 --- a/ispyb-ejb/src/main/java/ispyb/common/util/export/ExiPdfRtfExporter.java +++ b/ispyb-ejb/src/main/java/ispyb/common/util/export/ExiPdfRtfExporter.java @@ -36,6 +36,7 @@ import java.util.Set; import org.apache.log4j.Logger; +import org.jboss.util.collection.ReverseListIterator; import com.lowagie.text.BadElementException; import com.lowagie.text.Cell; @@ -501,10 +502,12 @@ private void setDataCollectionTable(Document document) throws Exception { Map mapDataCollectionGroupIdCClass = new HashMap(); // DataCollection Rows - Iterator> it = dataCollections.iterator(); + //Iterator> it = dataCollections.iterator(); + Iterator> it2 = new ReverseListIterator >(dataCollections); + int i = 0; - while (it.hasNext() && i < nbRowsMax) { - Map dataCollectionMapData = it.next(); + while (it2.hasNext() && i < nbRowsMax) { + Map dataCollectionMapData = it2.next(); LOG.info("dcMap=" + dataCollectionMapData.toString()); setDataCollectionMapData(document, dataCollectionMapData); @@ -516,7 +519,7 @@ private void setDataCollectionTable(Document document) throws Exception { } i++; } - setCrystalClassSummary(document, mapDataCollectionGroupIdCClass); + //setCrystalClassSummary(document, mapDataCollectionGroupIdCClass); document.add(new Paragraph(" ")); } document.add(new Paragraph(" ")); @@ -538,10 +541,12 @@ private void setDataAnalysisTable(Document document) throws Exception { //document.add(new Paragraph(" ")); // DataCollection Rows - Iterator> it = dataCollections.iterator(); + //Iterator> it = dataCollections.iterator(); + Iterator> it2 = new ReverseListIterator >(dataCollections); + int i = 0; - while (it.hasNext() && i < nbRowsMax) { - Map dataCollectionMapData = it.next(); + while (it2.hasNext() && i < nbRowsMax) { + Map dataCollectionMapData = it2.next(); LOG.info("dcMap=" + dataCollectionMapData.toString()); setDataAnalysisMapData(document, dataCollectionMapData); i++; diff --git a/ispyb-ws/src/main/java/ispyb/ws/rest/mx/DataCollectionRestWebService.java b/ispyb-ws/src/main/java/ispyb/ws/rest/mx/DataCollectionRestWebService.java index 0b2a26526..b5197f889 100644 --- a/ispyb-ws/src/main/java/ispyb/ws/rest/mx/DataCollectionRestWebService.java +++ b/ispyb-ws/src/main/java/ispyb/ws/rest/mx/DataCollectionRestWebService.java @@ -23,6 +23,7 @@ import ispyb.common.util.export.ExiPdfRtfExporter; import ispyb.server.mx.vos.collections.DataCollection3VO; +import ispyb.server.mx.vos.collections.Session3VO; @Path("/") public class DataCollectionRestWebService extends MXRestWebService { @@ -229,7 +230,8 @@ public Response getDataCollectionsReportBySessionIdPDF(@PathParam("token") Strin try { byte[] byteToExport = this.getPdfRtf(sessionId, proposal, nbRows, false); this.logFinish(methodName, start, logger); - return this.downloadFile(byteToExport, "DataCollectionsReport.pdf"); + Session3VO ses = this.getSession3Service().findByPk(new Integer(sessionId), false, false, false); + return this.downloadFile(byteToExport, "Report_" + proposal + "_"+ ses.getBeamlineName()+ "_" + ses.getStartDate() + ".pdf"); } catch (Exception e) { return this.logError(methodName, e, start, logger); @@ -249,7 +251,8 @@ public Response getDataCollectionsReportBySessionIdRTF(@PathParam("token") Strin try { byte[] byteToExport = this.getPdfRtf(sessionId, proposal, nbRows, true); this.logFinish(methodName, start, logger); - return this.downloadFile(byteToExport, "DataCollectionsReport.rtf"); + Session3VO ses = this.getSession3Service().findByPk(new Integer(sessionId), false, false, false); + return this.downloadFile(byteToExport, "Report_" + proposal + "_"+ ses.getBeamlineName()+ "_" + ses.getStartDate() + ".rtf"); } catch (Exception e) { return this.logError(methodName, e, start, logger); @@ -269,7 +272,9 @@ public Response getDataCollectionsAnalysisReportBySessionIdPDF(@PathParam("token try { byte[] byteToExport = this.getAnalysisPdfRtf(sessionId, proposal, nbRows, false); this.logFinish(methodName, start, logger); - return this.downloadFile(byteToExport, "DataCollectionsAnalysisReport.pdf"); + Session3VO ses = this.getSession3Service().findByPk(new Integer(sessionId), false, false, false); + return this.downloadFile(byteToExport, "AnalysisReport_" + proposal + "_"+ ses.getBeamlineName()+ "_" + ses.getStartDate() + ".pdf"); + } catch (Exception e) { return this.logError(methodName, e, start, logger); @@ -289,7 +294,8 @@ public Response getDataCollectionsAnalysisReportBySessionIdRTF(@PathParam("token try { byte[] byteToExport = this.getAnalysisPdfRtf(sessionId, proposal, nbRows, true); this.logFinish(methodName, start, logger); - return this.downloadFile(byteToExport, "DataCollectionsAnalysisReport.rtf"); + Session3VO ses = this.getSession3Service().findByPk(new Integer(sessionId), false, false, false); + return this.downloadFile(byteToExport, "AnalysisReport_" + proposal + "_"+ ses.getBeamlineName()+ "_" + ses.getStartDate() + ".rtf"); } catch (Exception e) { return this.logError(methodName, e, start, logger); From 9d2539d6a1ff5959019a698f1747b1f441825fc2 Mon Sep 17 00:00:00 2001 From: delageniere Date: Fri, 27 Oct 2017 09:49:46 +0200 Subject: [PATCH 26/38] change the version of java in doc --- documentation/ISPyB_DevelopersGuide.doc | Bin 206336 -> 207360 bytes 1 file changed, 0 insertions(+), 0 deletions(-) diff --git a/documentation/ISPyB_DevelopersGuide.doc b/documentation/ISPyB_DevelopersGuide.doc index f5ca5375e93d6644fb114ae5863d11ec624f0f0c..65267a340e0591758ce0c0de5773e13591b99997 100644 GIT binary patch delta 13192 zcmd_xiC<0W~ED~uU1NMZ@NMe z`d3vURXf8?wA`3QC$7ke;><+nGkv33sG5w zjtd=EoL8Ku|M1hLxv{lq#_86lg#=5%Df&+vB&{^INs3exHFH!UjynnALU@(y>Ob9g zL5Quqf8SXMS99KX6N0Y@ch>Ut`P!nH5Uq(#ptlgg9Jjd@-{E|AoQGZEz*@fkhjrus z_JIrU49pTDjUy{v5n>Aa9XNp-QLa(3q)yoZ;*u}B)=n~H`7*38`Rex#>kb!^N{wo3 z3=!6UsK0<*b|N{iHS3QN`cFPz%hT8rq9Ihnc|PBl7y9YTaGvt_l8yv6YG#PiKYdpo z)7^+%JtRb`nzT2tyXMd_{Rs@gQcTLq$q1Lnx8C%+LJI3&hW8(SDMU^MAr7Sr5n}j| zbp@hVll6So?yP10%9q^{A+`|YT#{M7PH@m#j+grjg)kC_juDT}-DNy-_}uWlvM;kR zB*W_CLQJYC$Q1o2hP5FX4Etr7*1+lS-T(Z$%w_o^(^eWcFc}(7DXhSzlkYzrVYrZg z`utLogXy;|4AK6_Z+#YRqPaJ)eYOAg_0%?Is)N!hsl9Wbq&C8Ue zWZ>- z7II5e<^sjnScW((#{nFKA^b;de;$WY-jngLAlz!Ofh}abzJwue;cSn>WF)zm3bC4v zHNQ+#;*Btbh&E`8p$OIuP?epE zpFE%8T=G1DIFGIkgxCXzhC;+cxC*fZMKFX_7LLx(Sou{6k>Q;!56_73WSF(!f=Nh+ zc@rT9U^AY=mw3o{$vBNg1ja$Q3E_+$=!r{i+B+tSxAvKd((peQmfCivG7m?ya5q)5 zG{GD`28PpV*p9^#tUv-1u?jL63s}J#j;M_~a6)tVqBZ>Bk3e*XjM`L0V+G=ontwVybqA{*`8&SNFHSDj z7AM8WE#xmYZcgl+X>r6|TWY3^*T$GD)wH9{6&oYZ9;dXi=89&Vn;`~HoOKS~;{!gz zsW~YNAGE@8oWM=wU>IFP2!>-Ge!~SkK|2p2+9Mn{P@>)JuME+~k5DXiSrrv`MN@Vi zpM_YRv(`X87(zFMTvQ%n1ZR&zHtv>()RhqWmxuI{^*c;&L1tne7Gnu+!r4=ZMxLUp zXv{_vG(}fz^%7zmw&Mqo$j=|%&A*$IpPhd>Ka;<6nddT&XB^@0+`;1q)4omCF49h< z;kMBgR8p!b8bOQm{L3sM*Td&t5)I{*-$Z12_+OXDp)$dJ8hn@XDE!3w8J=S-QHa2D zd=Ep^>{|*k9{X?!CFHOErJGP$NmPc(xbH(M4kI1caRa~OE?(dz-l7D86Dg>M>ac|! z>Yy%~p*i~NhE-L*Q#AeA9*SZ33XzzH`S==3u>wEfN9@5~WZ*O|A`1`k2(M6x5|p9> z149$kL0!0_5t_l>o3UjpHhj?weeflMF&Ytw(rvD;3|BNVg-qFRjUgC|i>T{E3yOs} zhyqk*6zYiDsDp0kjunVU0#4!--olb$z;I;1skIO@a2Rh58A8LVsj19UG*N^&6)~8L zL?j^v8?X)A@e_9A7o;Hrr*Q$9$i{X2iTkK1V~wh)jXLl`OSC~-6x=wj(^$(`$UQ#{ z#V~{+9J3IO`B;DyY``{b$G@-}`*8r5aRs@^!(IG=CwK~#v@u2{nMSCBYORF5a9~3w zZdb^J?Sa1Nr(0*Mj8O*nV|yS5Ap~PE6SJT}EaD(DVjGU*1Z1XU;2N@#gIwIjJv`M7 zwpX?*nx||R;0=mViubS}11q5hYN9Ucp*|WQ2))n`{V@z7h`>0^z)Z|R4AvtVo3I%t zaLQNI5m{`=QDQ!B;~xIN2YmF^ZLFn)Dw>b%7*mWYpbqMxDcsN+ZO{Q7F$$yc6(TVe z(=i_lkbsp~jWyVbUD%6#IDkVqjWf8`TGSTVY~&yp1$c%+6ycq2Lv1BY(Y#~(J>pfCDkI7VPRCSVGpuoz3Q9N!=r8?XaELWli0jPy1{@**2qxQ1-x zAP*1lP`9D3jHIlLAMge5ZNx3Ow-urbf-w=3uo8(l4AXX03XH;N9KvCo!$myD3%o>& z_6?S^jZ$GX4PO{oPB-Gbz~p%s;fWJM?~;f;=% zfQgudb@&;XFeOAYn8OgOTwPyRWw+Au)7V54@;baiAr|@zu?Xz~7?NNrreV9TWn<;M z(oM#6DrR6N4991)or7HD;RWP54d)5v9ASt;**SIHnkqepRLK6GMq0aLvC`0M{77rV zJ<0xv2<};G2<}T3H&%qL^;iaBW$%pdDvT#!n*I}Q;bNspwexi!k^Y8*+0(i&Q7$SC z(!N&ARI3{VaT7Vng`CxSudQaK*lD!^jBbNEC=GS#kJTtedn-d49eQ%?)%TykYF}5Kev?kuF zyJdYrV_D8s8{n;e>nm@89 zwLn#3wRinhuL|{uoU6_uKy7cXvFB8-<<_&_isyKbw#4=$_ejp%ADuu`?rFM0_V3F{ zi1uyt8j%P_6tn8^quAQ?qFVGOHTuyKW9=8Tinud?VHQ!8{z9XXLL*v@q|LzOP#74O&R#my+bm=}*3)-QoHdVh7R_ zXfa8PDx}4Ub+ovsvYs9~xe8rhGBZTTfTeD9klI_(4(_Se)Ra1KDWvWglA#`#?~NPi zOcE551Y1dh&^G$cU@%Egnai(_Ad;XVNiecE<%P>Hz#IHP670hRl3^K_FFk_~SKk=} zF^3dbg$H3IO^t9anPfOmGQ^S$ZD;dE^n(jYFj6K3$q-5sOvi5|LobqHKgke6G9-`; 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z_iaAwg?Np((BI^ew~T(rNN4&T$Xh`3oN3VVAN5p)y!Yb_tLEjmc;vsjS%_8Gj9(#d z?VNSt3`Bib&M?e@ymgb91%z76IyN6ipUY23mc$gAwfsMDUa z2l5K)1@sp_R$b_!aU2(5(Urp3v-k}e=-!jIgYEbk2YYd9Bcl&TjFm&E4wOQP{xoOQ z&k^-g!`d-aBlJ^3^RLRMgqz2*Z_FA`-Q&=B>i<^~JtlBAU_KT>PT?Y9mcSen&8AaD zct&*<$|_6ZY(gw1!+2KtaIPP||21s$xg4F>VLd*L!t6{A!}{U(18LQ41|PJ9e)K%c z;FeV}z%^sgie?-dh6DHo3geIoE;Ah5f#DK{Yt(}r1}syE2xL#I?^$I>nmj~HC?NY4 z*{8_;kuEZE{c6g%O^n6 z^FfSPgQ)X78c!+Y1H0Cc&#WZ*(9T>_{)9$8rK!Z=R2>$u#4nJ~wAK&_sejsk)bR-e zVF=ya1l2x8*KV5X#Q(!s{Ig~J--Cg!UXtpFqI)<~HLkm1+fy&ibiJ>u+89}AR5W72 znT3atuVuO)ZmR-Sx@S4614g=SzpLgeTCWGHYajm`fE;_|OTmY>N|K`7rzJ`9rSPXu z>(?q;)W?_XAh))r_huI~`RbzW$2C0}Yu&Jisv=e63C8p5isu=s2ZkeM4kBt}k9ij( zzT9G3Wlyrv$C6g9%iS35%*QGVrHfAcSk*_d^zf8l{q&NLJgcV3e~oR%;fZJi`H@-6 zEnV|es{Q$@wu<7V4JuGIF{o>vq8(kJs_(E={jNU$GG2bs8gec3k!$&+(LlGmK-HzH z=37I$yhGL^rzvHTwxXZViJ*2=(G`M6nyV(Xe)8+@xYm!HP5IT`Vof~iPA zBIM`OStt(C+hQ@BODaB=UrCi|ox794VP&PA!Dy3RelcwU2#pc7nz6 mo?fkdT|C{x!d!wq+ Date: Fri, 27 Oct 2017 14:14:55 +0200 Subject: [PATCH 27/38] reports enhancement --- .../common/util/export/ExiPdfRtfExporter.java | 21 +++++++++++------- .../rest/mx/DataCollectionRestWebService.java | 22 ++++++++++++++----- 2 files changed, 29 insertions(+), 14 deletions(-) diff --git a/ispyb-ejb/src/main/java/ispyb/common/util/export/ExiPdfRtfExporter.java b/ispyb-ejb/src/main/java/ispyb/common/util/export/ExiPdfRtfExporter.java index d6a93da60..9b3ac7606 100644 --- a/ispyb-ejb/src/main/java/ispyb/common/util/export/ExiPdfRtfExporter.java +++ b/ispyb-ejb/src/main/java/ispyb/common/util/export/ExiPdfRtfExporter.java @@ -553,8 +553,6 @@ private void setDataAnalysisTable(Document document) throws Exception { } document.add(new Paragraph(" ")); } - document.add(new Paragraph(" ")); - } /** @@ -691,6 +689,9 @@ private void setDataAnalysisMapData(Document document, Map dataC //row 1 Table table = new Table(NB_COL_DATA_ANALYSIS); + table.setCellsFitPage(true); + table.setBorder(0); + table.getDefaultCell().setHorizontalAlignment(Element.ALIGN_LEFT); table.getDefaultCell().setBorderWidth(0); @@ -757,7 +758,7 @@ private void setDataAnalysisMapData(Document document, Map dataC p = new Paragraph(parag, FONT_DOC_SMALL); table.addCell(p); - // Cell 6 + // Cell 7 p = new Paragraph(); Chunk chu2 = new Chunk( "KO", FONT_INDEXING_FAILED); if (indexing.booleanValue() ){ @@ -773,33 +774,33 @@ private void setDataAnalysisMapData(Document document, Map dataC p.add(chu2); table.addCell(p); - // Cell 7 + // Cell 8 parag = "Space group: \n" + "Mosaicity: \n" ; p = new Paragraph(parag, FONT_DOC_SMALL); table.addCell(p); - // Cell 8 + // Cell 9 parag = getCellParam(dataCollectionMapItem, "ScreeningOutputLattice_spaceGroup", null) + "\n" + getCellParam(dataCollectionMapItem, "ScreeningOutput_mosaicity", null)+ "\n" ; p = new Paragraph(parag, FONT_DOC_SMALL_BOLD); table.addCell(p); - // Cell 9 + // Cell 10 parag = "a \n" + getCellParam(dataCollectionMapItem, "ScreeningOutputLattice_unitCell_a", null) + "\n alpha \n" + getCellParam(dataCollectionMapItem, "ScreeningOutputLattice_unitCell_alpha", null) ; p = new Paragraph(parag, FONT_DOC_SMALL_CENTERED); p.setAlignment(Element.ALIGN_CENTER); table.addCell(p); - // Cell 10 + // Cell 11 parag = "b \n" + getCellParam(dataCollectionMapItem, "ScreeningOutputLattice_unitCell_b", null) + "\n beta \n" + getCellParam(dataCollectionMapItem, "ScreeningOutputLattice_unitCell_beta", null) ; p = new Paragraph(parag, FONT_DOC_SMALL_CENTERED); p.setAlignment(Element.ALIGN_CENTER); table.addCell(p); - // Cell 11 + // Cell 12 parag = "c \n" + getCellParam(dataCollectionMapItem, "ScreeningOutputLattice_unitCell_c", null) + "\n gamma \n" + getCellParam(dataCollectionMapItem, "ScreeningOutputLattice_unitCell_gama", null) ; @@ -881,6 +882,10 @@ private void setDataAnalysisMapData(Document document, Map dataC } // to avoid splitting table Table containingTable = new Table(1); + containingTable.setCellsFitPage(true); + containingTable.setBorder(0); + containingTable.getDefaultCell().setBorderWidth(0); + Cell cell = new Cell(table); containingTable.addCell(cell); diff --git a/ispyb-ws/src/main/java/ispyb/ws/rest/mx/DataCollectionRestWebService.java b/ispyb-ws/src/main/java/ispyb/ws/rest/mx/DataCollectionRestWebService.java index b5197f889..45f112b79 100644 --- a/ispyb-ws/src/main/java/ispyb/ws/rest/mx/DataCollectionRestWebService.java +++ b/ispyb-ws/src/main/java/ispyb/ws/rest/mx/DataCollectionRestWebService.java @@ -231,7 +231,10 @@ public Response getDataCollectionsReportBySessionIdPDF(@PathParam("token") Strin byte[] byteToExport = this.getPdfRtf(sessionId, proposal, nbRows, false); this.logFinish(methodName, start, logger); Session3VO ses = this.getSession3Service().findByPk(new Integer(sessionId), false, false, false); - return this.downloadFile(byteToExport, "Report_" + proposal + "_"+ ses.getBeamlineName()+ "_" + ses.getStartDate() + ".pdf"); + if (ses != null) + return this.downloadFile(byteToExport, "Report_" + proposal + "_"+ ses.getBeamlineName()+ "_" + ses.getStartDate() + ".pdf"); + else + return this.downloadFile(byteToExport, "No_session.pdf"); } catch (Exception e) { return this.logError(methodName, e, start, logger); @@ -252,7 +255,10 @@ public Response getDataCollectionsReportBySessionIdRTF(@PathParam("token") Strin byte[] byteToExport = this.getPdfRtf(sessionId, proposal, nbRows, true); this.logFinish(methodName, start, logger); Session3VO ses = this.getSession3Service().findByPk(new Integer(sessionId), false, false, false); - return this.downloadFile(byteToExport, "Report_" + proposal + "_"+ ses.getBeamlineName()+ "_" + ses.getStartDate() + ".rtf"); + if (ses != null) + return this.downloadFile(byteToExport, "Report_" + proposal + "_"+ ses.getBeamlineName()+ "_" + ses.getStartDate() + ".rtf"); + else + return this.downloadFile(byteToExport, "No_session.pdf"); } catch (Exception e) { return this.logError(methodName, e, start, logger); @@ -273,8 +279,10 @@ public Response getDataCollectionsAnalysisReportBySessionIdPDF(@PathParam("token byte[] byteToExport = this.getAnalysisPdfRtf(sessionId, proposal, nbRows, false); this.logFinish(methodName, start, logger); Session3VO ses = this.getSession3Service().findByPk(new Integer(sessionId), false, false, false); - return this.downloadFile(byteToExport, "AnalysisReport_" + proposal + "_"+ ses.getBeamlineName()+ "_" + ses.getStartDate() + ".pdf"); - + if (ses !=null) + return this.downloadFile(byteToExport, "AnalysisReport_" + proposal + "_"+ ses.getBeamlineName()+ "_" + ses.getStartDate() + ".pdf"); + else + return this.downloadFile(byteToExport, "No_session.pdf"); } catch (Exception e) { return this.logError(methodName, e, start, logger); @@ -295,8 +303,10 @@ public Response getDataCollectionsAnalysisReportBySessionIdRTF(@PathParam("token byte[] byteToExport = this.getAnalysisPdfRtf(sessionId, proposal, nbRows, true); this.logFinish(methodName, start, logger); Session3VO ses = this.getSession3Service().findByPk(new Integer(sessionId), false, false, false); - return this.downloadFile(byteToExport, "AnalysisReport_" + proposal + "_"+ ses.getBeamlineName()+ "_" + ses.getStartDate() + ".rtf"); - + if (ses !=null) + return this.downloadFile(byteToExport, "AnalysisReport_" + proposal + "_"+ ses.getBeamlineName()+ "_" + ses.getStartDate() + ".rtf"); + else + return this.downloadFile(byteToExport, "No_session.pdf"); } catch (Exception e) { return this.logError(methodName, e, start, logger); } From 5c8b688387d39b9d6012265d013f7a487bcb04e9 Mon Sep 17 00:00:00 2001 From: delageniere Date: Mon, 30 Oct 2017 15:53:54 +0100 Subject: [PATCH 28/38] fixes #176 --- .../main/webapp/tiles/bodies/biosaxs/welcome.jsp | 4 +++- .../tiles/bodies/common/help/mxcubeHelp.jsp | 13 +++++++------ .../tiles/bodies/common/help/prepareHelp.jsp | 16 +++++++++------- .../bodies/mx/prepare/fillSampleChanger.jsp | 12 +++++++----- 4 files changed, 26 insertions(+), 19 deletions(-) diff --git a/ispyb-ui/src/main/webapp/tiles/bodies/biosaxs/welcome.jsp b/ispyb-ui/src/main/webapp/tiles/bodies/biosaxs/welcome.jsp index 37f289009..bd9e8d15c 100644 --- a/ispyb-ui/src/main/webapp/tiles/bodies/biosaxs/welcome.jsp +++ b/ispyb-ui/src/main/webapp/tiles/bodies/biosaxs/welcome.jsp @@ -91,8 +91,10 @@ <% String targetDataAcquisitions = request.getContextPath() + "/user/viewProjectList.do?reqCode=display"; %> <% String targetListShipment = request.getContextPath() + "/user/viewProjectList.do?reqCode=display&menu=list_shipment"; %> <% String targetPrepareExperiment = request.getContextPath() + "/user/viewProjectList.do?reqCode=display&menu=prepareexperiment"; %> +<% String toUpdateDB = request.getContextPath() + "/updateDB.do?reqCode=updateProposal"; %> -

In case of problems when creating shipments/samples, update ISPyB database (this may take a few minutes). + +

In case of problems when creating shipments/samples, update ISPyB database (this may take a few minutes).


diff --git a/ispyb-ui/src/main/webapp/tiles/bodies/common/help/mxcubeHelp.jsp b/ispyb-ui/src/main/webapp/tiles/bodies/common/help/mxcubeHelp.jsp index 7c010e569..2f9bc3f28 100644 --- a/ispyb-ui/src/main/webapp/tiles/bodies/common/help/mxcubeHelp.jsp +++ b/ispyb-ui/src/main/webapp/tiles/bodies/common/help/mxcubeHelp.jsp @@ -18,6 +18,7 @@ Contributors : S. Delageniere, R. Leal, L. Launer, K. Levik, S. Veyrier, P. Bren --------------------------------------------------------------------------------------------------%> <%@ taglib uri="http://java.sun.com/jsp/jstl/core" prefix="c" %> <%@page import="ispyb.common.util.Constants"%> +<%@ page isELIgnored="false" %> Help page for MxCube @@ -33,25 +34,25 @@ Contributors : S. Delageniere, R. Leal, L. Launer, K. Levik, S. Veyrier, P. Bren <%-- 1) Select shipment --%> - 1- Select the dewars you want for processing.
+ 1- Select the dewars you want for processing.
 <%-- 2) Fill Sample changer --%> - 2- Fill the sample changer: assign a location for your containers (only required if not using Damatrix codes)
+ 2- Fill the sample changer: assign a location for your containers (only required if not using Damatrix codes)
 - 2- Fill the sample changer: assign a location for your containers
+ 2- Fill the sample changer: assign a location for your containers
 - 2- Fill the sample changer: assign a location for your containers
+ 2- Fill the sample changer: assign a location for your containers
 - 2- Fill the sample changer: assign a location for your containers
+ 2- Fill the sample changer: assign a location for your containers
 - 2- Fill the sample changer: assign a location for your containers
+ 2- Fill the sample changer: assign a location for your containers
 diff --git a/ispyb-ui/src/main/webapp/tiles/bodies/common/help/prepareHelp.jsp b/ispyb-ui/src/main/webapp/tiles/bodies/common/help/prepareHelp.jsp index e265a0fac..633193999 100644 --- a/ispyb-ui/src/main/webapp/tiles/bodies/common/help/prepareHelp.jsp +++ b/ispyb-ui/src/main/webapp/tiles/bodies/common/help/prepareHelp.jsp @@ -19,6 +19,8 @@ Contributors : S. Delageniere, R. Leal, L. Launer, K. Levik, S. Veyrier, P. Bren <%@ taglib uri="http://java.sun.com/jsp/jstl/core" prefix="c" %> <%@page import="ispyb.common.util.Constants"%> +<%@ page isELIgnored="false" %> + Help page for Prepare Experiment @@ -29,25 +31,25 @@ Contributors : S. Delageniere, R. Leal, L. Launer, K. Levik, S. Veyrier, P. Bren <%-- 1) Select shipment --%> - 1- Select the dewars you want for processing.
+ 1- Select the dewars you want for processing.
 <%-- 2) Fill Sample changer --%> - 2- Fill the sample changer: assign a location for your containers (only required if not using Damatrix codes)
+ 2- Fill the sample changer: assign a location for your containers (only required if not using Damatrix codes)
 - 2- Fill the sample changer: assign a location for your containers
+ 2- Fill the sample changer: assign a location for your containers
 - 2- Fill the sample changer: assign a location for your containers
+ 2- Fill the sample changer: assign a location for your containers
 - 2- Fill the sample changer: assign a location for your containers
+ 2- Fill the sample changer: assign a location for your containers
 - 2- Fill the sample changer: assign a location for your containers
+ 2- Fill the sample changer: assign a location for your containers
 @@ -66,7 +68,7 @@ Contributors : S. Delageniere, R. Leal, L. Launer, K. Levik, S. Veyrier, P. Bren - +

diff --git a/ispyb-ui/src/main/webapp/tiles/bodies/mx/prepare/fillSampleChanger.jsp b/ispyb-ui/src/main/webapp/tiles/bodies/mx/prepare/fillSampleChanger.jsp index a799d3335..6f31ef7a4 100644 --- a/ispyb-ui/src/main/webapp/tiles/bodies/mx/prepare/fillSampleChanger.jsp +++ b/ispyb-ui/src/main/webapp/tiles/bodies/mx/prepare/fillSampleChanger.jsp @@ -25,6 +25,8 @@ Contributors : S. Delageniere, R. Leal, L. Launer, K. Levik, S. Veyrier, P. Bren <%@page import="ispyb.common.util.Constants"%> +<%@ page isELIgnored="false" %> + <% String buttonLabel = "Next step: Link Samples in " + Constants.BCM_NAME; %> @@ -42,25 +44,25 @@ Contributors : S. Delageniere, R. Leal, L. Launer, K. Levik, S. Veyrier, P. Bren <%-- 1) Select shipment --%> - 1- Select the dewars you want for processing.
+ 1- Select the dewars you want for processing.
 <%-- 2) Fill Sample changer --%> - 2- Fill the sample changer: assign a location for your containers (only required if not using Damatrix codes)
+ 2- Fill the sample changer: assign a location for your containers (only required if not using Damatrix codes)
 - 2- Fill the sample changer: assign a location for your containers
+ 2- Fill the sample changer: assign a location for your containers
 - 2- Fill the sample changer: assign a location for your containers
+ 2- Fill the sample changer: assign a location for your containers
 - 2- Fill the sample changer: assign a location for your containers
+ 2- Fill the sample changer: assign a location for your containers
 From c4f83777fc321493bfbe75f5ac643c435a112d75 Mon Sep 17 00:00:00 2001 From: Alejandro De Maria Antolinos Date: Tue, 31 Oct 2017 10:24:22 +0100 Subject: [PATCH 29/38] Added security cheks for downloads --- .../services/sessions/Session3Service.java | 4 + .../sessions/Session3ServiceBean.java | 41 + .../src/main/webapp/js/ispyb/min/ispyb-bx.js | 24046 ++++++++-------- .../mx/AutoprocintegrationRestWebService.java | 62 +- 4 files changed, 12115 insertions(+), 12038 deletions(-) diff --git a/ispyb-ejb/src/main/java/ispyb/server/common/services/sessions/Session3Service.java b/ispyb-ejb/src/main/java/ispyb/server/common/services/sessions/Session3Service.java index a3fe103c2..472d285e6 100644 --- a/ispyb-ejb/src/main/java/ispyb/server/common/services/sessions/Session3Service.java +++ b/ispyb-ejb/src/main/java/ispyb/server/common/services/sessions/Session3Service.java @@ -175,6 +175,8 @@ public List findByStartDateAndBeamLineNameAndNbShifts(final Integer */ public Session3VO findByAutoProcScalingId(final Integer autoProcScalingId) throws Exception; + public Session3VO findByAutoProcProgramAttachmentId(final Integer autoProcProgramAttachmentId) throws Exception; + public void protectSession(Integer sessionId) throws Exception; /** @@ -195,6 +197,8 @@ public List findByStartDateAndBeamLineNameAndNbShifts(final Integer */ public Integer getNbOfTests(final Integer sesId) throws Exception; + public Session3VO findByAutoProcProgramId(int autoProcProgramId); + } \ No newline at end of file diff --git a/ispyb-ejb/src/main/java/ispyb/server/common/services/sessions/Session3ServiceBean.java b/ispyb-ejb/src/main/java/ispyb/server/common/services/sessions/Session3ServiceBean.java index 401f24495..27b4debdc 100644 --- a/ispyb-ejb/src/main/java/ispyb/server/common/services/sessions/Session3ServiceBean.java +++ b/ispyb-ejb/src/main/java/ispyb/server/common/services/sessions/Session3ServiceBean.java @@ -111,6 +111,19 @@ private static final String FIND_ALL(boolean fetchDataCollectionGroup, boolean f + " where s.sessionId = g.sessionId and " + " g.dataCollectionGroupId = c.dataCollectionGroupId and " + " c.dataCollectionId = api.dataCollectionId and " + " api.autoProcIntegrationId = apshi.autoProcIntegrationId and " + " apshi.autoProcScalingId = aps.autoProcScalingId and " + " aps.autoProcScalingId = :autoProcScalingId "; + + private static final String FIND_BY_AUTOPROCPROGRAMATTACHMENT_ID = "select s.* from BLSession s, " + + " DataCollectionGroup g, DataCollection c, AutoProcIntegration api, AutoProcProgram autoprocProgram, AutoProcProgramAttachment autoProcProgramAttachment" + + " where s.sessionId = g.sessionId and g.dataCollectionGroupId = c.dataCollectionGroupId and autoprocProgram.autoProcProgramId = api.autoProcProgramId" + + " and c.dataCollectionId = api.dataCollectionId and autoprocProgram.autoProcProgramId = autoProcProgramAttachment.autoProcProgramId " + + " and autoProcProgramAttachment.autoProcProgramAttachmentId = :autoProcProgramAttachmentId "; + + + private static final String FIND_BY_AUTOPROCPROGRAM_ID = "select s.* from BLSession s, " + + " DataCollectionGroup g, DataCollection c, AutoProcIntegration api, AutoProcProgram autoprocProgram " + + " where s.sessionId = g.sessionId and g.dataCollectionGroupId = c.dataCollectionGroupId and autoprocProgram.autoProcProgramId = api.autoProcProgramId" + + " and c.dataCollectionId = api.dataCollectionId and autoprocProgram.autoProcProgramId = :autoProcProgramId "; + private static String getProposalCodeNumberQuery() { String query = "select * " + " FROM BLSession ses, Proposal pro " @@ -525,6 +538,32 @@ public Session3VO findByAutoProcScalingId(final Integer autoProcScalingId) throw } return null; } + + + @SuppressWarnings("unchecked") + public Session3VO findByAutoProcProgramAttachmentId(final Integer autoProcProgramAttachmentId) throws Exception { + String query = FIND_BY_AUTOPROCPROGRAMATTACHMENT_ID; + List col = this.entityManager.createNativeQuery(query, "sessionNativeQuery") + .setParameter("autoProcProgramAttachmentId", autoProcProgramAttachmentId).getResultList(); + if (col != null && col.size() > 0) { + return col.get(0); + } + return null; + } + + + @Override + public Session3VO findByAutoProcProgramId(int autoProcProgramId) { + String query = FIND_BY_AUTOPROCPROGRAM_ID; + @SuppressWarnings("unchecked") + List col = this.entityManager.createNativeQuery(query, "sessionNativeQuery") + .setParameter("autoProcProgramId", autoProcProgramId).getResultList(); + if (col != null && col.size() > 0) { + return col.get(0); + } + return null; + } + /** @@ -818,4 +857,6 @@ private void checkChangeRemoveAccess(Session3VO vo) throws AccessDeniedException + + } \ No newline at end of file diff --git a/ispyb-ui/src/main/webapp/js/ispyb/min/ispyb-bx.js b/ispyb-ui/src/main/webapp/js/ispyb/min/ispyb-bx.js index 23e07209a..a98a06520 100644 --- a/ispyb-ui/src/main/webapp/js/ispyb/min/ispyb-bx.js +++ b/ispyb-ui/src/main/webapp/js/ispyb/min/ispyb-bx.js @@ -38,321 +38,321 @@ Event.prototype = { } }; -function GenericGraph(args) { - this.width = 600; - this.height = 400; - - this.targetId = null; - /** Free spaces in the borders * */ - this.top = 10; - this.left = 10; - this.bottom = 50; - this.right = 40; - - /** Ruler * */ - this.rulerHeight = 50; - this.rulerWidth = 50; - this.rulerStroke = 2; - this.rulerVerticalMarksNumber = 5; - - this.rulerMaxValue = null; - this.rulerMinValue = null; - - /** plot options * */ - this.plotPoints = true; - this.pointRadius = 2; - this.fillOpacityPoint = 0.2; - this.strokeOpacityPoint = 0.2; - - /** Cluster titles * */ - this.clusterTitleHeight = 20; - this.interClassesSpace = 2; - this.interClustersSpace = 4; - this.fontSize = 7; - - /** - * If true classes and title will be rendender in the rule otherwise will be - * integer values - */ - this.plotHorizontalByCluster = true; - - if (args != null) { - if (args.targetId != null) { - this.targetId = args.targetId; - } - if (args.plotHorizontalByCluster != null) { - this.plotHorizontalByCluster = args.plotHorizontalByCluster; - } - if (args.height != null) { - this.height = args.height; - } - if (args.width != null) { - this.width = args.width; - } - if (args.rulerMinValue != null) { - this.rulerMinValue = args.rulerMinValue; - } - if (args.rulerMaxValue != null) { - this.rulerMaxValue = args.rulerMaxValue; - } - if (args.rulerHeight != null) { - this.rulerHeight = args.rulerHeight; - } - - } -} - -GenericGraph.prototype.calculate = function(data) { - var result = {}; - - var checked = this.cleanArray(data); - - /** sorting array * */ - checked.sort(function(a, b) { - return a - b; - }); - - var median = this.getMedian(checked); - - result.median = median; - result.Q1 = Number(this.getQ1(checked)); - result.Q2 = Number(this.getQ2(checked)); - result.Q3 = Number(this.getQ3(checked)); - result.population = checked; - - result.IQR = Number(result.Q3 - result.Q1); - result.outlier_below_limit = result.Q1 - (1.5 * result.IQR); - result.outlier_above_limit = result.Q3 + (1.5 * result.IQR); - result.below_outliers = this.getBelowOutliers(result.outlier_below_limit, checked); - result.above_outliers = this.getAboveOutliers(result.outlier_above_limit, checked); - - result.min_whisker = this.minValueWhisker(result.outlier_below_limit, result.Q1, checked); - result.max_whisker = this.maxValueWhisker(result.outlier_above_limit, result.Q3, checked); - - return result; -}; - -GenericGraph.prototype.drawSVGVerticalText = function(x, y, text, properties) { - var transform = [ "transform", "translate(" + x + ", " + y + "), rotate(-90) " ]; - properties.push(transform); - SVG.drawText(0, 0, text, this.svg, properties); -}; - -/** Plot the numbers on the axis * */ -GenericGraph.prototype.plotRuler = function(rulerProperties) { - - SVG.drawRectangle(rulerProperties.vertical.x, rulerProperties.vertical.y, rulerProperties.vertical.width, rulerProperties.vertical.height, - this.svg, [ [ "fill", "black" ] ]); - var distance = rulerProperties.vertical.height / (this.rulerVerticalMarksNumber + 1); - for ( var i = 0; i <= this.rulerVerticalMarksNumber + 1; i++) { - var deltaHeight = distance * i; - var aux = rulerProperties.vertical.height - deltaHeight; - - var text = Number((aux / rulerProperties.vertical.height) * (rulerProperties.maxPoint - rulerProperties.minPoint) + rulerProperties.minPoint) - .toFixed(3); - - SVG.drawLine(rulerProperties.horizontal.x, this.top + deltaHeight, rulerProperties.horizontal.x - rulerProperties.markWidth, - this.top + deltaHeight, this.svg, [ [ "stroke", "black" ] ]); - SVG.drawText(this.left, this.top + distance * i + 5, text, this.svg, [ [ "style", "font-size:xx-small" ] ]); - /** Drawing the mark up to the end * */ - SVG.drawLine(rulerProperties.horizontal.x, this.top + deltaHeight, this.width - this.right, this.top + deltaHeight, this.svg, [ - [ "stroke", rulerProperties.markColor ], [ "stroke-width", "0.3" ] ]); - - if (i == this.rulerVerticalMarksNumber + 1) { - SVG.drawLine(rulerProperties.horizontal.x, this.top + deltaHeight, this.width - this.right, this.top + deltaHeight, this.svg, [ [ - "stroke", rulerProperties.markColor ] ]); - } - } - - /** Drawing horizontal rulers * */ - if (!this.plotHorizontalByCluster) { - var width = rulerProperties.horizontal.width; - var ratio = width / (rulerProperties.horizontal.xValues.range); - for ( i = 0; i < rulerProperties.horizontal.xValues.values.length; i++) { - var coorX = rulerProperties.horizontal.xValues.values[i] - rulerProperties.horizontal.xValues.min; - SVG.drawText(rulerProperties.horizontal.x + coorX * ratio, this.height - (this.bottom + (this.clusterTitleHeight)), - rulerProperties.horizontal.xValues.values[i], this.svg, [ [ "style", "font-size:small" ] ]); - } - } -}; - -GenericGraph.prototype.plotAxes = function(properties) { - /** - * Drawing canvas plot-free spaces SVG.drawRectangle(0, this.top, this.left, - * this.height, this.svg, [["fill", "pink"]]); SVG.drawRectangle(this.width - - * this.right, this.top, plot.width, plot.height, this.svg, [["fill", - * "pink"]]); SVG.drawRectangle(0, 0, this.width, this.top, this.svg, - * [["fill", "red"]]); SVG.drawRectangle(0, this.height - this.bottom, - * this.width, this.bottom, this.svg, [["fill", "red"]]); - */ - - /** Drawing ruler Space * */ - this.plotRuler({ - minPoint : Number(properties.minPoint), - maxPoint : Number(properties.maxPoint), - markColor : "black", - markWidth : 20, - vertical : { - x : this.left + this.rulerWidth - this.rulerStroke, - y : this.top, - width : this.rulerStroke, - height : this.height - (this.top + this.bottom + this.clusterTitleHeight) - this.rulerHeight - }, - horizontal : { - x : this.left + this.rulerWidth - this.rulerStroke, - y : this.height - (this.bottom + this.clusterTitleHeight + this.rulerHeight), - width : properties.width, - height : this.rulerStroke, - xValues : properties.xValues - } - }); - -}; - -/** Remove nulls and NaN elements in the array * */ -GenericGraph.prototype.cleanArray = function(data) { - var checked = []; - - /** checking data are numbers * */ - for ( var i = 0; i < data.length; i++) { - if (data[i] != null) { - if (!isNaN(data[i])) { - checked.push(data[i]); - } - } - } - return checked; -}; - -GenericGraph.prototype.refresh = function(data) { - document.getElementById(this.targetId).innerHTML = ""; - this.draw(this.targetId, data); -}; - -GenericGraph.prototype.getClassColor = function(className) { - for ( var i = 0; i < this.data.clusters.length; i++) { - var cluster = this.data.clusters[i]; - for ( var j = 0; j < cluster.classes.length; j++) { - var classes = cluster.classes[j]; - if (classes.name == className) { - if (classes.color != null) { - return classes.color; - } - } - } - } - return "black"; -}; - -GenericGraph.prototype.getDimensions = function(data) { - var results = {}; - var points = []; - - this.data = data; - var classesNumber = 0; - var xValues = []; - - for ( var i = 0; i < data.clusters.length; i++) { - var cluster = data.clusters[i]; - if (!this.plotHorizontalByCluster) { - xValues.push(data.clusters[i].x); - } - for ( var j = 0; j < cluster.classes.length; j++) { - var classes = cluster.classes[j]; - points = points.concat(classes.values); - classesNumber = classesNumber + 1; - } - } - - var checked = this.cleanArray(points); - - checked.sort(function(a, b) { - return a - b; - }); - - results.minPoint = checked[0]; - if (this.rulerMinValue != null) { - results.minPoint = this.rulerMinValue; - } - results.maxPoint = checked[checked.length - 1]; - if (this.rulerMaxValue != null) { - results.maxPoint = this.rulerMaxValue; - } - - results.classesNumber = classesNumber; - results.clusterNumber = data.clusters.length; - - var totalInterClassesFreeSpace = (classesNumber - data.clusters.length) * this.interClassesSpace; - var totalInterClusterFreeSpace = (data.clusters.length) * this.interClustersSpace; - results.classWidth = (this.width - (this.rulerWidth + this.left + this.right + totalInterClassesFreeSpace + totalInterClusterFreeSpace))/ classesNumber; - results.width = this.width - (this.right + this.left) - this.rulerWidth + this.rulerStroke; - - results.xValues = {}; - - xValues.sort(function(a, b) { - return a - b; - }); - results.xValues.values = xValues; - if (xValues.length > 0) { - results.xValues.min = xValues[0]; - results.xValues.max = xValues[xValues.length - 1]; - results.xValues.range = results.xValues.max - results.xValues.min; - } - return results; - -}; - -GenericGraph.prototype.draw = function(targetId, data) { - this.targetId = targetId; - var properties = (this.getDimensions(data)); - this.svg = SVG.createSVGCanvas(document.getElementById(this.targetId), [ [ "width", this.width ], [ "height", this.height ] ]); - this.plotAxes(properties); -}; - -GenericGraph.prototype.getMedian = function(checked) { - /** Calculating median * */ - if (checked.length % 2 == 1) { - return checked[Math.floor(checked.length / 2)]; - } else { - return (Number(checked[(checked.length / 2) - 1]) + Number(checked[checked.length / 2])) / 2; - } -}; - -GenericGraph.prototype.pointToPixel = function(value, boxProperties) { - var ratio = (value - boxProperties.minPoint) / (boxProperties.maxPoint - boxProperties.minPoint); - var pixelLength = boxProperties.height - boxProperties.y + this.top; - return (-1 * ratio) * (pixelLength) + (boxProperties.y + boxProperties.height); -}; - -GenericGraph.prototype.maxValueWhisker = function(aboveLimit, q3, array) { - var points = []; - for ( var i = 0; i < array.length; i++) { - if ((array[i] > q3) && (array[i]) <= aboveLimit) { - points.push(array[i]); - } - } - if (points.length > 0) { - points.sort(function(a, b) { - return a - b; - }); - return points[points.length - 1]; - } - return null; -}; - -GenericGraph.prototype.input = function() { - return DATADOC.getBoxWhikerData(); -}; - -GenericGraph.prototype.test = function(targetId) { - var plot = new GenericGraph({ - targetId : targetId, - height : 350, - width : 450, - maxBoxWidth : 25 - }); - plot.refresh(this.input()); -}; +function GenericGraph(args) { + this.width = 600; + this.height = 400; + + this.targetId = null; + /** Free spaces in the borders * */ + this.top = 10; + this.left = 10; + this.bottom = 50; + this.right = 40; + + /** Ruler * */ + this.rulerHeight = 50; + this.rulerWidth = 50; + this.rulerStroke = 2; + this.rulerVerticalMarksNumber = 5; + + this.rulerMaxValue = null; + this.rulerMinValue = null; + + /** plot options * */ + this.plotPoints = true; + this.pointRadius = 2; + this.fillOpacityPoint = 0.2; + this.strokeOpacityPoint = 0.2; + + /** Cluster titles * */ + this.clusterTitleHeight = 20; + this.interClassesSpace = 2; + this.interClustersSpace = 4; + this.fontSize = 7; + + /** + * If true classes and title will be rendender in the rule otherwise will be + * integer values + */ + this.plotHorizontalByCluster = true; + + if (args != null) { + if (args.targetId != null) { + this.targetId = args.targetId; + } + if (args.plotHorizontalByCluster != null) { + this.plotHorizontalByCluster = args.plotHorizontalByCluster; + } + if (args.height != null) { + this.height = args.height; + } + if (args.width != null) { + this.width = args.width; + } + if (args.rulerMinValue != null) { + this.rulerMinValue = args.rulerMinValue; + } + if (args.rulerMaxValue != null) { + this.rulerMaxValue = args.rulerMaxValue; + } + if (args.rulerHeight != null) { + this.rulerHeight = args.rulerHeight; + } + + } +} + +GenericGraph.prototype.calculate = function(data) { + var result = {}; + + var checked = this.cleanArray(data); + + /** sorting array * */ + checked.sort(function(a, b) { + return a - b; + }); + + var median = this.getMedian(checked); + + result.median = median; + result.Q1 = Number(this.getQ1(checked)); + result.Q2 = Number(this.getQ2(checked)); + result.Q3 = Number(this.getQ3(checked)); + result.population = checked; + + result.IQR = Number(result.Q3 - result.Q1); + result.outlier_below_limit = result.Q1 - (1.5 * result.IQR); + result.outlier_above_limit = result.Q3 + (1.5 * result.IQR); + result.below_outliers = this.getBelowOutliers(result.outlier_below_limit, checked); + result.above_outliers = this.getAboveOutliers(result.outlier_above_limit, checked); + + result.min_whisker = this.minValueWhisker(result.outlier_below_limit, result.Q1, checked); + result.max_whisker = this.maxValueWhisker(result.outlier_above_limit, result.Q3, checked); + + return result; +}; + +GenericGraph.prototype.drawSVGVerticalText = function(x, y, text, properties) { + var transform = [ "transform", "translate(" + x + ", " + y + "), rotate(-90) " ]; + properties.push(transform); + SVG.drawText(0, 0, text, this.svg, properties); +}; + +/** Plot the numbers on the axis * */ +GenericGraph.prototype.plotRuler = function(rulerProperties) { + + SVG.drawRectangle(rulerProperties.vertical.x, rulerProperties.vertical.y, rulerProperties.vertical.width, rulerProperties.vertical.height, + this.svg, [ [ "fill", "black" ] ]); + var distance = rulerProperties.vertical.height / (this.rulerVerticalMarksNumber + 1); + for ( var i = 0; i <= this.rulerVerticalMarksNumber + 1; i++) { + var deltaHeight = distance * i; + var aux = rulerProperties.vertical.height - deltaHeight; + + var text = Number((aux / rulerProperties.vertical.height) * (rulerProperties.maxPoint - rulerProperties.minPoint) + rulerProperties.minPoint) + .toFixed(3); + + SVG.drawLine(rulerProperties.horizontal.x, this.top + deltaHeight, rulerProperties.horizontal.x - rulerProperties.markWidth, + this.top + deltaHeight, this.svg, [ [ "stroke", "black" ] ]); + SVG.drawText(this.left, this.top + distance * i + 5, text, this.svg, [ [ "style", "font-size:xx-small" ] ]); + /** Drawing the mark up to the end * */ + SVG.drawLine(rulerProperties.horizontal.x, this.top + deltaHeight, this.width - this.right, this.top + deltaHeight, this.svg, [ + [ "stroke", rulerProperties.markColor ], [ "stroke-width", "0.3" ] ]); + + if (i == this.rulerVerticalMarksNumber + 1) { + SVG.drawLine(rulerProperties.horizontal.x, this.top + deltaHeight, this.width - this.right, this.top + deltaHeight, this.svg, [ [ + "stroke", rulerProperties.markColor ] ]); + } + } + + /** Drawing horizontal rulers * */ + if (!this.plotHorizontalByCluster) { + var width = rulerProperties.horizontal.width; + var ratio = width / (rulerProperties.horizontal.xValues.range); + for ( i = 0; i < rulerProperties.horizontal.xValues.values.length; i++) { + var coorX = rulerProperties.horizontal.xValues.values[i] - rulerProperties.horizontal.xValues.min; + SVG.drawText(rulerProperties.horizontal.x + coorX * ratio, this.height - (this.bottom + (this.clusterTitleHeight)), + rulerProperties.horizontal.xValues.values[i], this.svg, [ [ "style", "font-size:small" ] ]); + } + } +}; + +GenericGraph.prototype.plotAxes = function(properties) { + /** + * Drawing canvas plot-free spaces SVG.drawRectangle(0, this.top, this.left, + * this.height, this.svg, [["fill", "pink"]]); SVG.drawRectangle(this.width - + * this.right, this.top, plot.width, plot.height, this.svg, [["fill", + * "pink"]]); SVG.drawRectangle(0, 0, this.width, this.top, this.svg, + * [["fill", "red"]]); SVG.drawRectangle(0, this.height - this.bottom, + * this.width, this.bottom, this.svg, [["fill", "red"]]); + */ + + /** Drawing ruler Space * */ + this.plotRuler({ + minPoint : Number(properties.minPoint), + maxPoint : Number(properties.maxPoint), + markColor : "black", + markWidth : 20, + vertical : { + x : this.left + this.rulerWidth - this.rulerStroke, + y : this.top, + width : this.rulerStroke, + height : this.height - (this.top + this.bottom + this.clusterTitleHeight) - this.rulerHeight + }, + horizontal : { + x : this.left + this.rulerWidth - this.rulerStroke, + y : this.height - (this.bottom + this.clusterTitleHeight + this.rulerHeight), + width : properties.width, + height : this.rulerStroke, + xValues : properties.xValues + } + }); + +}; + +/** Remove nulls and NaN elements in the array * */ +GenericGraph.prototype.cleanArray = function(data) { + var checked = []; + + /** checking data are numbers * */ + for ( var i = 0; i < data.length; i++) { + if (data[i] != null) { + if (!isNaN(data[i])) { + checked.push(data[i]); + } + } + } + return checked; +}; + +GenericGraph.prototype.refresh = function(data) { + document.getElementById(this.targetId).innerHTML = ""; + this.draw(this.targetId, data); +}; + +GenericGraph.prototype.getClassColor = function(className) { + for ( var i = 0; i < this.data.clusters.length; i++) { + var cluster = this.data.clusters[i]; + for ( var j = 0; j < cluster.classes.length; j++) { + var classes = cluster.classes[j]; + if (classes.name == className) { + if (classes.color != null) { + return classes.color; + } + } + } + } + return "black"; +}; + +GenericGraph.prototype.getDimensions = function(data) { + var results = {}; + var points = []; + + this.data = data; + var classesNumber = 0; + var xValues = []; + + for ( var i = 0; i < data.clusters.length; i++) { + var cluster = data.clusters[i]; + if (!this.plotHorizontalByCluster) { + xValues.push(data.clusters[i].x); + } + for ( var j = 0; j < cluster.classes.length; j++) { + var classes = cluster.classes[j]; + points = points.concat(classes.values); + classesNumber = classesNumber + 1; + } + } + + var checked = this.cleanArray(points); + + checked.sort(function(a, b) { + return a - b; + }); + + results.minPoint = checked[0]; + if (this.rulerMinValue != null) { + results.minPoint = this.rulerMinValue; + } + results.maxPoint = checked[checked.length - 1]; + if (this.rulerMaxValue != null) { + results.maxPoint = this.rulerMaxValue; + } + + results.classesNumber = classesNumber; + results.clusterNumber = data.clusters.length; + + var totalInterClassesFreeSpace = (classesNumber - data.clusters.length) * this.interClassesSpace; + var totalInterClusterFreeSpace = (data.clusters.length) * this.interClustersSpace; + results.classWidth = (this.width - (this.rulerWidth + this.left + this.right + totalInterClassesFreeSpace + totalInterClusterFreeSpace))/ classesNumber; + results.width = this.width - (this.right + this.left) - this.rulerWidth + this.rulerStroke; + + results.xValues = {}; + + xValues.sort(function(a, b) { + return a - b; + }); + results.xValues.values = xValues; + if (xValues.length > 0) { + results.xValues.min = xValues[0]; + results.xValues.max = xValues[xValues.length - 1]; + results.xValues.range = results.xValues.max - results.xValues.min; + } + return results; + +}; + +GenericGraph.prototype.draw = function(targetId, data) { + this.targetId = targetId; + var properties = (this.getDimensions(data)); + this.svg = SVG.createSVGCanvas(document.getElementById(this.targetId), [ [ "width", this.width ], [ "height", this.height ] ]); + this.plotAxes(properties); +}; + +GenericGraph.prototype.getMedian = function(checked) { + /** Calculating median * */ + if (checked.length % 2 == 1) { + return checked[Math.floor(checked.length / 2)]; + } else { + return (Number(checked[(checked.length / 2) - 1]) + Number(checked[checked.length / 2])) / 2; + } +}; + +GenericGraph.prototype.pointToPixel = function(value, boxProperties) { + var ratio = (value - boxProperties.minPoint) / (boxProperties.maxPoint - boxProperties.minPoint); + var pixelLength = boxProperties.height - boxProperties.y + this.top; + return (-1 * ratio) * (pixelLength) + (boxProperties.y + boxProperties.height); +}; + +GenericGraph.prototype.maxValueWhisker = function(aboveLimit, q3, array) { + var points = []; + for ( var i = 0; i < array.length; i++) { + if ((array[i] > q3) && (array[i]) <= aboveLimit) { + points.push(array[i]); + } + } + if (points.length > 0) { + points.sort(function(a, b) { + return a - b; + }); + return points[points.length - 1]; + } + return null; +}; + +GenericGraph.prototype.input = function() { + return DATADOC.getBoxWhikerData(); +}; + +GenericGraph.prototype.test = function(targetId) { + var plot = new GenericGraph({ + targetId : targetId, + height : 350, + width : 450, + maxBoxWidth : 25 + }); + plot.refresh(this.input()); +}; /** * Using dygraph it plots a chart. Params: targetId, labelsContainerId, args @@ -2087,338 +2087,338 @@ MacromoleculeConditionGrid.prototype.test = function(targetId) { panel.render(targetId); }; - -function ItemGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ - this.id = id; - this.args = new Object(); - - this.defaultFormat = new ItemFormat(defaultFormat); - - if(selectedFormat != null){ - this.selected = new ItemFormat(selectedFormat); - } - else{ - this.selected = new ItemFormat(defaultFormat); - } - - if(overFormat != null){ - this.over = new ItemFormat(overFormat); - } - else{ - this.over = new ItemFormat(defaultFormat); - } - - if(draggingFormat != null){ - this.dragging = new ItemFormat(draggingFormat); - } - else{ - this.dragging = new ItemFormat(defaultFormat); - } - - //Events - this.stateChanged = new Event(this); - - - //Attaching events - var _this = this; - this._setEvents(); -}; - -ItemGraphFormatter.prototype.getType = function(){ - return this.args.type; -}; - - -ItemGraphFormatter.prototype.toJSON = function(){ - var json = this.args; - json.defaultFormat = this.getDefault().toJSON(); - json.over = this.getOver().toJSON(); - json.selected = this.getSelected().toJSON(); - json.dragging = this.getDragging().toJSON(); - json.id = this.id; - return json; -}; - -ItemGraphFormatter.prototype.loadFromJSON = function(json){ - this.args = json; - this.defaultFormat = new ItemFormat(json.defaultFormat); - this.over = new ItemFormat(json.over); - this.selected = new ItemFormat(json.selected); - this.dragging = new ItemFormat(json.dragging); - this._setEvents(); -}; - -ItemGraphFormatter.prototype._setEvents = function(){ - //Attaching events - var _this = this; - - this.defaultFormat.changed.attach(function (sender, item){ - _this.over.setSize(_this.defaultFormat.getSize()); - _this.selected.setSize(_this.defaultFormat.getSize()); - _this.dragging.setSize(_this.defaultFormat.getSize()); - _this.stateChanged.notify(_this); - }); - - this.selected.changed.attach(function (sender, item){ - _this.stateChanged.notify(_this); - }); - - this.over.changed.attach(function (sender, item){ - _this.stateChanged.notify(_this); - }); - - this.dragging.changed.attach(function (sender, item){ - _this.stateChanged.notify(_this); - }); -}; - -/** Getters **/ -ItemGraphFormatter.prototype.getId = function(){return this.id;}; -ItemGraphFormatter.prototype.getDefault = function(){return this.defaultFormat;}; -ItemGraphFormatter.prototype.getSelected = function(){return this.selected;}; -ItemGraphFormatter.prototype.getOver = function(){return this.over;}; -ItemGraphFormatter.prototype.getDragging = function(){return this.dragging;}; - -function ItemFormat(args){ - this.defaultFormat = new Object(); - this.args = new Object(); - this.args.title = new Object(); - //Defult properties - this.args.visible = true; - this.args.hidden = false; - this.args.stroke = "#000000"; - this.args.strokeOpacity = 0.8; - this.args["stroke-width"] = 1; - this.args.fill = "#000000"; - this.args["fill-opacity"] = 1; - this.args.size = 1; - this.args.opacity = 1; - this.args.fontSize = "8"; - this.args.fontColor = "#000000"; - - /** For directed edge with arrow **/ - //this.args.arrowSize = 1; - - - if (args != null){ - if (args.visible != null){ - this.args.visible = args.visible; - } - if (args.opacity != null){ - this.args.opacity = args.opacity; - } - if (args.size != null){ - this.args.size = args.size; - } - if (args.hidden != null){ - this.args.hidden = args.hidden; - } - if (args.stroke != null){ - this.args.stroke = this._fixColor(args.stroke); - } - if (args.strokeOpacity != null){ - this.args.strokeOpacity = args.strokeOpacity; - } - if (args["stroke-width"]!=null){ - this.args["stroke-width"] = args["stroke-width"]; - } - if (args["fill-opacity"]!=null){ - this.args["fill-opacity"] = args["fill-opacity"]; - } - if (args.shape!=null){ - this.args.shape = args.shape; - } - if (args.fill!=null){ - this.args.fill = this._fixColor(args.fill); - } - - - if (args.title!=null){ - if (args.title.fontSize!=null){ - this.args.title.fontSize = args.title.fontSize; - } - if (args.title.fill!=null){ - this.args.title.fill = this._fixColor(args.title.fill); - } - } - - /** For directed edge with arrow **/ - /*if (args.arrowSize!=null){ - this.args.arrowSize = args.arrowSize; - }*/ - - } - - this.changed = new Event(); -}; - -ItemFormat.prototype._fixColor = function(color){ - var fixed = color; - if (color.indexOf("green") != -1){ - fixed = '#04B431'; - } - - if (color.indexOf("blue") != -1){ - fixed = '#045FB4'; - } - - if (color.indexOf("red") != -1){ - fixed = '#DF0101'; - } - - if (color.indexOf("black") != -1){ - fixed = '#000000'; - } - - if (color.indexOf("white") != -1){ - fixed = '#FFFFFF'; - } - - if (color.indexOf("#") == -1){ - fixed = "#" + color; - } - return fixed; -}; - -ItemFormat.prototype.toJSON = function(){ - if(this.args.strokeOpacity != null){ - this.args["stroke-opacity"] = this.args.strokeOpacity; - delete this.args.strokeOpacity; - } - -// if(this.args.strokeWidth != null){ -// this.args["stroke-width"] = this.args.strokeWidth; -// delete this.args["stroke-width"]; -// } - - if(this.args.title.fontColor != null){ - this.args.title["font-color"] = this.args.title.fontColor; - } - else{ - this.args.title["font-color"] = this.args.fontColor;//;this.args.title.fontColor; - } - - if(this.args.title.fontSize != null){ - this.args.title["font-size"] = this.args.title.fontSize;//;this.args.title.fontColor; - } - else{ - this.args.title["font-size"] = this.args.fontSize;//;this.args.title.fontColor; - } - //return this.args; - return this.args; -}; - -ItemFormat.prototype.getAttribute = function(name){return this.args[name];}; - -//Getters and Setters -ItemFormat.prototype.setVisible = function(visible){ - if (this.args.visible != visible){ - this.args.visible = visible; - this.changed.notify(this); - } -}; - -ItemFormat.prototype.getVisible = function(){return this.args.visible;}; - -ItemFormat.prototype.setHidden = function(hidden){ - if (this.args.hidden != hidden){ - this.args.hidden = hidden; - this.changed.notify(this); - } -}; - -ItemFormat.prototype.getHidden = function(){return this.args.hidden;}; - - -ItemFormat.prototype.setStroke = function(stroke){ - if (this.args.stroke != stroke){ - this.args.stroke = stroke; - this.changed.notify(this); - } -}; - -ItemFormat.prototype.getStroke = function(){return this.args.stroke;}; - -ItemFormat.prototype.setStrokeOpacity = function(strokeOpacity){ - if (this.args.strokeOpacity != strokeOpacity){ - this.args.strokeOpacity = strokeOpacity; - this.changed.notify(this); - } -}; - -ItemFormat.prototype.getStrokeOpacity = function(){return this.args["stroke-opacity"];}; - -ItemFormat.prototype.setStrokeWidth = function(strokeWidth){ - if (this.args["stroke-width"] != strokeWidth){ - this.args["stroke-width"] = strokeWidth; - this.changed.notify(this); - } -}; - - -ItemFormat.prototype.getFillOpacity = function(){return this.args["fill-opacity"];}; - -ItemFormat.prototype.setfillOpacity = function(strokeWidth){ - if (this.args["fill-opacity"] != strokeWidth){ - this.args["fill-opacity"] = strokeWidth; - this.changed.notify(this); - } -}; - - -ItemFormat.prototype.getStrokeWidth = function(){ - return this.args["stroke-width"]; -}; - -ItemFormat.prototype.setFill = function(fill){ - if (this.args.fill != fill){ - this.args.fill = fill; - this.changed.notify(this); - } -}; - -ItemFormat.prototype.getFill = function(){return this.args.fill;}; - -ItemFormat.prototype.setSize = function(size){ - if (this.args.size != size){ - this.args.size = size; - this.changed.notify(this); - } -}; - -ItemFormat.prototype.getSize = function(){return this.args.size;}; - -ItemFormat.prototype.setOpacity = function(opacity){ - if (this.args.opacity != opacity){ - this.args.opacity = opacity; - this.changed.notify(this); - } -}; - -ItemFormat.prototype.getOpacity = function(){return this.args.opacity;}; - -ItemFormat.prototype.getArrowSize = function(){return this.args.arrowSize;}; - -ItemFormat.prototype.setArrowSize = function(arrowSize){ - if (this.args.arrowSize != arrowSize){ - this.args.arrowSize = arrowSize; - this.changed.notify(this); - } -}; - -ItemFormat.prototype.getFontSize = function(){return this.args.title.fontSize;}; - -ItemFormat.prototype.setFontSize = function(fontSize){ - - if (this.args.title.fontSize != fontSize){ - this.args.title.fontSize = fontSize; - this.changed.notify(this); - } -}; - - - - + +function ItemGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ + this.id = id; + this.args = new Object(); + + this.defaultFormat = new ItemFormat(defaultFormat); + + if(selectedFormat != null){ + this.selected = new ItemFormat(selectedFormat); + } + else{ + this.selected = new ItemFormat(defaultFormat); + } + + if(overFormat != null){ + this.over = new ItemFormat(overFormat); + } + else{ + this.over = new ItemFormat(defaultFormat); + } + + if(draggingFormat != null){ + this.dragging = new ItemFormat(draggingFormat); + } + else{ + this.dragging = new ItemFormat(defaultFormat); + } + + //Events + this.stateChanged = new Event(this); + + + //Attaching events + var _this = this; + this._setEvents(); +}; + +ItemGraphFormatter.prototype.getType = function(){ + return this.args.type; +}; + + +ItemGraphFormatter.prototype.toJSON = function(){ + var json = this.args; + json.defaultFormat = this.getDefault().toJSON(); + json.over = this.getOver().toJSON(); + json.selected = this.getSelected().toJSON(); + json.dragging = this.getDragging().toJSON(); + json.id = this.id; + return json; +}; + +ItemGraphFormatter.prototype.loadFromJSON = function(json){ + this.args = json; + this.defaultFormat = new ItemFormat(json.defaultFormat); + this.over = new ItemFormat(json.over); + this.selected = new ItemFormat(json.selected); + this.dragging = new ItemFormat(json.dragging); + this._setEvents(); +}; + +ItemGraphFormatter.prototype._setEvents = function(){ + //Attaching events + var _this = this; + + this.defaultFormat.changed.attach(function (sender, item){ + _this.over.setSize(_this.defaultFormat.getSize()); + _this.selected.setSize(_this.defaultFormat.getSize()); + _this.dragging.setSize(_this.defaultFormat.getSize()); + _this.stateChanged.notify(_this); + }); + + this.selected.changed.attach(function (sender, item){ + _this.stateChanged.notify(_this); + }); + + this.over.changed.attach(function (sender, item){ + _this.stateChanged.notify(_this); + }); + + this.dragging.changed.attach(function (sender, item){ + _this.stateChanged.notify(_this); + }); +}; + +/** Getters **/ +ItemGraphFormatter.prototype.getId = function(){return this.id;}; +ItemGraphFormatter.prototype.getDefault = function(){return this.defaultFormat;}; +ItemGraphFormatter.prototype.getSelected = function(){return this.selected;}; +ItemGraphFormatter.prototype.getOver = function(){return this.over;}; +ItemGraphFormatter.prototype.getDragging = function(){return this.dragging;}; + +function ItemFormat(args){ + this.defaultFormat = new Object(); + this.args = new Object(); + this.args.title = new Object(); + //Defult properties + this.args.visible = true; + this.args.hidden = false; + this.args.stroke = "#000000"; + this.args.strokeOpacity = 0.8; + this.args["stroke-width"] = 1; + this.args.fill = "#000000"; + this.args["fill-opacity"] = 1; + this.args.size = 1; + this.args.opacity = 1; + this.args.fontSize = "8"; + this.args.fontColor = "#000000"; + + /** For directed edge with arrow **/ + //this.args.arrowSize = 1; + + + if (args != null){ + if (args.visible != null){ + this.args.visible = args.visible; + } + if (args.opacity != null){ + this.args.opacity = args.opacity; + } + if (args.size != null){ + this.args.size = args.size; + } + if (args.hidden != null){ + this.args.hidden = args.hidden; + } + if (args.stroke != null){ + this.args.stroke = this._fixColor(args.stroke); + } + if (args.strokeOpacity != null){ + this.args.strokeOpacity = args.strokeOpacity; + } + if (args["stroke-width"]!=null){ + this.args["stroke-width"] = args["stroke-width"]; + } + if (args["fill-opacity"]!=null){ + this.args["fill-opacity"] = args["fill-opacity"]; + } + if (args.shape!=null){ + this.args.shape = args.shape; + } + if (args.fill!=null){ + this.args.fill = this._fixColor(args.fill); + } + + + if (args.title!=null){ + if (args.title.fontSize!=null){ + this.args.title.fontSize = args.title.fontSize; + } + if (args.title.fill!=null){ + this.args.title.fill = this._fixColor(args.title.fill); + } + } + + /** For directed edge with arrow **/ + /*if (args.arrowSize!=null){ + this.args.arrowSize = args.arrowSize; + }*/ + + } + + this.changed = new Event(); +}; + +ItemFormat.prototype._fixColor = function(color){ + var fixed = color; + if (color.indexOf("green") != -1){ + fixed = '#04B431'; + } + + if (color.indexOf("blue") != -1){ + fixed = '#045FB4'; + } + + if (color.indexOf("red") != -1){ + fixed = '#DF0101'; + } + + if (color.indexOf("black") != -1){ + fixed = '#000000'; + } + + if (color.indexOf("white") != -1){ + fixed = '#FFFFFF'; + } + + if (color.indexOf("#") == -1){ + fixed = "#" + color; + } + return fixed; +}; + +ItemFormat.prototype.toJSON = function(){ + if(this.args.strokeOpacity != null){ + this.args["stroke-opacity"] = this.args.strokeOpacity; + delete this.args.strokeOpacity; + } + +// if(this.args.strokeWidth != null){ +// this.args["stroke-width"] = this.args.strokeWidth; +// delete this.args["stroke-width"]; +// } + + if(this.args.title.fontColor != null){ + this.args.title["font-color"] = this.args.title.fontColor; + } + else{ + this.args.title["font-color"] = this.args.fontColor;//;this.args.title.fontColor; + } + + if(this.args.title.fontSize != null){ + this.args.title["font-size"] = this.args.title.fontSize;//;this.args.title.fontColor; + } + else{ + this.args.title["font-size"] = this.args.fontSize;//;this.args.title.fontColor; + } + //return this.args; + return this.args; +}; + +ItemFormat.prototype.getAttribute = function(name){return this.args[name];}; + +//Getters and Setters +ItemFormat.prototype.setVisible = function(visible){ + if (this.args.visible != visible){ + this.args.visible = visible; + this.changed.notify(this); + } +}; + +ItemFormat.prototype.getVisible = function(){return this.args.visible;}; + +ItemFormat.prototype.setHidden = function(hidden){ + if (this.args.hidden != hidden){ + this.args.hidden = hidden; + this.changed.notify(this); + } +}; + +ItemFormat.prototype.getHidden = function(){return this.args.hidden;}; + + +ItemFormat.prototype.setStroke = function(stroke){ + if (this.args.stroke != stroke){ + this.args.stroke = stroke; + this.changed.notify(this); + } +}; + +ItemFormat.prototype.getStroke = function(){return this.args.stroke;}; + +ItemFormat.prototype.setStrokeOpacity = function(strokeOpacity){ + if (this.args.strokeOpacity != strokeOpacity){ + this.args.strokeOpacity = strokeOpacity; + this.changed.notify(this); + } +}; + +ItemFormat.prototype.getStrokeOpacity = function(){return this.args["stroke-opacity"];}; + +ItemFormat.prototype.setStrokeWidth = function(strokeWidth){ + if (this.args["stroke-width"] != strokeWidth){ + this.args["stroke-width"] = strokeWidth; + this.changed.notify(this); + } +}; + + +ItemFormat.prototype.getFillOpacity = function(){return this.args["fill-opacity"];}; + +ItemFormat.prototype.setfillOpacity = function(strokeWidth){ + if (this.args["fill-opacity"] != strokeWidth){ + this.args["fill-opacity"] = strokeWidth; + this.changed.notify(this); + } +}; + + +ItemFormat.prototype.getStrokeWidth = function(){ + return this.args["stroke-width"]; +}; + +ItemFormat.prototype.setFill = function(fill){ + if (this.args.fill != fill){ + this.args.fill = fill; + this.changed.notify(this); + } +}; + +ItemFormat.prototype.getFill = function(){return this.args.fill;}; + +ItemFormat.prototype.setSize = function(size){ + if (this.args.size != size){ + this.args.size = size; + this.changed.notify(this); + } +}; + +ItemFormat.prototype.getSize = function(){return this.args.size;}; + +ItemFormat.prototype.setOpacity = function(opacity){ + if (this.args.opacity != opacity){ + this.args.opacity = opacity; + this.changed.notify(this); + } +}; + +ItemFormat.prototype.getOpacity = function(){return this.args.opacity;}; + +ItemFormat.prototype.getArrowSize = function(){return this.args.arrowSize;}; + +ItemFormat.prototype.setArrowSize = function(arrowSize){ + if (this.args.arrowSize != arrowSize){ + this.args.arrowSize = arrowSize; + this.changed.notify(this); + } +}; + +ItemFormat.prototype.getFontSize = function(){return this.args.title.fontSize;}; + +ItemFormat.prototype.setFontSize = function(fontSize){ + + if (this.args.title.fontSize != fontSize){ + this.args.title.fontSize = fontSize; + this.changed.notify(this); + } +}; + + + + /** * This class executes the actions @@ -4952,2095 +4952,1101 @@ function openExperiment(experimentId) { BIOSAXS.openExperiment(experimentId); } -var SITE_CONF = { - SAMPLE_CHANGER_CONFIGURATION : { - "3":{ - "platetype3VO": {"plateTypeId":4,"name":"96 Well plate","rowCount":8,"columnCount":12,"shape":"REC"}, - "name":"96 Well plate", - "slotPositionRow":"1", - "slotPositionColumn":"3", - "storageTemperature":"0", - "sampleplateposition3VOs":[], - "experimentId":0 - }, - "2":{ - "platetype3VO":{"plateTypeId":2,"name":" 4 x ( 8 + 3 ) Block","rowCount":4,"columnCount":11,"shape":"REC"}, - "name":" 4 x ( 8 + 3 ) Block", - "slotPositionRow":"1", - "slotPositionColumn":"2", - "storageTemperature":"0", - "sampleplateposition3VOs":[],"experimentId":0 - }, - "1":{ - "platetype3VO":{"plateTypeId":1,"name":"Deep Well","rowCount":8,"columnCount":12,"shape":"REC"}, - "name":"Deep Well", - "slotPositionRow":"1", - "slotPositionColumn":"1", - "storageTemperature":"0", - "sampleplateposition3VOs":[], - "experimentId":0 - } - } +var SITE_CONF = { + SAMPLE_CHANGER_CONFIGURATION : { + "3":{ + "platetype3VO": {"plateTypeId":4,"name":"96 Well plate","rowCount":8,"columnCount":12,"shape":"REC"}, + "name":"96 Well plate", + "slotPositionRow":"1", + "slotPositionColumn":"3", + "storageTemperature":"0", + "sampleplateposition3VOs":[], + "experimentId":0 + }, + "2":{ + "platetype3VO":{"plateTypeId":2,"name":" 4 x ( 8 + 3 ) Block","rowCount":4,"columnCount":11,"shape":"REC"}, + "name":" 4 x ( 8 + 3 ) Block", + "slotPositionRow":"1", + "slotPositionColumn":"2", + "storageTemperature":"0", + "sampleplateposition3VOs":[],"experimentId":0 + }, + "1":{ + "platetype3VO":{"plateTypeId":1,"name":"Deep Well","rowCount":8,"columnCount":12,"shape":"REC"}, + "name":"Deep Well", + "slotPositionRow":"1", + "slotPositionColumn":"1", + "storageTemperature":"0", + "sampleplateposition3VOs":[], + "experimentId":0 + } + } }; - -var ISPYB_CONF = { - load : function(config) { - for (var key in config) { - ISPYB_CONF[key] = config[key]; - } - }, - SAMPLE_CHANGER_CONFIGURATION : { - "1": { - "platetype3VO": {"plateTypeId": 1, "name": "Deep Well", "rowCount": 8, "columnCount": 12, "shape": "REC"}, - "name": "Deep Well", - "slotPositionRow": "1", - "slotPositionColumn": "1", - "storageTemperature": "0", - "sampleplateposition3VOs": [], - "experimentId": 0 - } - } + +var ISPYB_CONF = { + load : function(config) { + for (var key in config) { + ISPYB_CONF[key] = config[key]; + } + }, + SAMPLE_CHANGER_CONFIGURATION : { + "1": { + "platetype3VO": {"plateTypeId": 1, "name": "Deep Well", "rowCount": 8, "columnCount": 12, "shape": "REC"}, + "name": "Deep Well", + "slotPositionRow": "1", + "slotPositionColumn": "1", + "storageTemperature": "0", + "sampleplateposition3VOs": [], + "experimentId": 0 + } + } }; -var SITE_CONF = { - -}; - -/** - * Example form - * - * @witdh - * @height - */ -function AbinitioForm(args) { - this.id = BUI.id(); - this.width = null; - this.height = null; - - if (args != null) { - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; - } - } - - var _this = this; - /** Widgets **/ - this.abinitioGrid = new AbinitioGrid({ - width : null, - height : 200 - }); - - this.abinitioGrid.onSelected.attach(function(sender, models) { - var modelsIdList = []; - for ( var i in models) { - modelsIdList.push(models[i].modelId); - } - _this._renderPlot(_this.subtractions[0].subtractionId, modelsIdList); - _this._renderPDB(modelsIdList); - }); - - /** Dygraph Widget that plots fir files**/ - this.plotWidget = new PlotWidget({ - width : 745 / 2, - height : 300, - margin : "10 0 5 10" - }); - - /** PDB viewer **/ - this.viewer = new PDBViewer({ - width : 745 / 2, - height : 300 - }); - -} - -AbinitioForm.prototype._renderPlot = function(subtractionId, modelsIdList) { - /** Trying to plot tje subtraction and the models **/ - try { - var colors = [ "#669900", "#0000FF" ]; - this.plotWidget.refresh([], [ ], modelsIdList, [], [], colors); - } catch (e) { - console.log(e); - } -}; - -AbinitioForm.prototype._renderPDB = function(modelsIdList) { - /** Trying to plot the PDB file **/ - try { - var viz = []; - for (var i = 0; i < modelsIdList.length; i++) { - viz.push({ - modelId : modelsIdList[i], - color : "0xFF6600", - opacity : 0.8 - }); - } - this.viewer.refresh(viz); - } catch (e) { - console.log(e); - } -}; - -AbinitioForm.prototype._getItems = function() { - var _this = this; - return [ { - xtype : 'label', - forId : 'myFieldId', - text : 'INLINE HELP: To be updated', - margin : '15 0 20 10', - cls : "inline-help" - }, this.abinitioGrid.getPanel(), { - xtype : 'container', - layout : 'hbox', - items : [ this.plotWidget.getPanel(), this.viewer.getPanel() ] - } ] -}; - -AbinitioForm.prototype._getButtons = function() { - return []; -}; - -AbinitioForm.prototype.getPanel = function() { - var _this = this; - this.panel = Ext.create('Ext.form.Panel', { - width : this.width, - height : this.height, - margin : 10, - border : 1, - defaultType : 'textfield', - items : this._getItems(), - buttons : this._getButtons(), - listeners : { - afterrender : function() { - _this._populate(); +var SITE_CONF = { + +}; - } - } - }); - return this.panel; -}; +/** + * Example form + * + * @witdh + * @height + */ +function AbinitioForm(args) { + this.id = BUI.id(); + this.width = null; + this.height = null; + + if (args != null) { + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + } + + var _this = this; + /** Widgets **/ + this.abinitioGrid = new AbinitioGrid({ + width : null, + height : 200 + }); + + this.abinitioGrid.onSelected.attach(function(sender, models) { + var modelsIdList = []; + for ( var i in models) { + modelsIdList.push(models[i].modelId); + } + _this._renderPlot(_this.subtractions[0].subtractionId, modelsIdList); + _this._renderPDB(modelsIdList); + }); + + /** Dygraph Widget that plots fir files**/ + this.plotWidget = new PlotWidget({ + width : 745 / 2, + height : 300, + margin : "10 0 5 10" + }); + + /** PDB viewer **/ + this.viewer = new PDBViewer({ + width : 745 / 2, + height : 300 + }); + +} + +AbinitioForm.prototype._renderPlot = function(subtractionId, modelsIdList) { + /** Trying to plot tje subtraction and the models **/ + try { + var colors = [ "#669900", "#0000FF" ]; + this.plotWidget.refresh([], [ ], modelsIdList, [], [], colors); + } catch (e) { + console.log(e); + } +}; + +AbinitioForm.prototype._renderPDB = function(modelsIdList) { + /** Trying to plot the PDB file **/ + try { + var viz = []; + for (var i = 0; i < modelsIdList.length; i++) { + viz.push({ + modelId : modelsIdList[i], + color : "0xFF6600", + opacity : 0.8 + }); + } + this.viewer.refresh(viz); + } catch (e) { + console.log(e); + } +}; + +AbinitioForm.prototype._getItems = function() { + var _this = this; + return [ { + xtype : 'label', + forId : 'myFieldId', + text : 'INLINE HELP: To be updated', + margin : '15 0 20 10', + cls : "inline-help" + }, this.abinitioGrid.getPanel(), { + xtype : 'container', + layout : 'hbox', + items : [ this.plotWidget.getPanel(), this.viewer.getPanel() ] + } ] +}; + +AbinitioForm.prototype._getButtons = function() { + return []; +}; + +AbinitioForm.prototype.getPanel = function() { + var _this = this; + this.panel = Ext.create('Ext.form.Panel', { + width : this.width, + height : this.height, + margin : 10, + border : 1, + defaultType : 'textfield', + items : this._getItems(), + buttons : this._getButtons(), + listeners : { + afterrender : function() { + _this._populate(); + + } + } + }); + return this.panel; +}; + +/** Populates could be call when the DOM is not filled yet **/ +AbinitioForm.prototype._populate = function() { +}; + +/** It populates the form * */ +AbinitioForm.prototype.refresh = function(subtractions) { + this.subtractions = subtractions; + this.abinitioGrid.refresh(subtractions); +}; + +AbinitioForm.prototype.input = function() { + return {}; +}; + +/** It populates the form **/ +AbinitioForm.prototype.test = function(targetId) { + var macromoleculeForm = new AbinitioForm(); + var panel = macromoleculeForm.getPanel(); + panel.render(targetId); +}; -/** Populates could be call when the DOM is not filled yet **/ -AbinitioForm.prototype._populate = function() { -}; - -/** It populates the form * */ -AbinitioForm.prototype.refresh = function(subtractions) { - this.subtractions = subtractions; - this.abinitioGrid.refresh(subtractions); -}; - -AbinitioForm.prototype.input = function() { - return {}; -}; - -/** It populates the form **/ -AbinitioForm.prototype.test = function(targetId) { - var macromoleculeForm = new AbinitioForm(); - var panel = macromoleculeForm.getPanel(); - panel.render(targetId); -}; - -/** - * Example form - * - * @witdh - * @height - */ -function DataReductionForm(args) { - this.id = BUI.id(); - this.width = null; - this.height = null; - - if (args != null) { - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; - } - } - - var _this = this; - - /** Widgets **/ - this.plotWidget = new PlotWidget({ - width : 650, - height : 490 - }); - - /** Selected frames to be displayed **/ - this.selectedItems = { - frames : [], - averages : [], - subtractions : [] - }; - -} - -DataReductionForm.prototype._parseSelectedItemsToIds = function(selectedArray) { - var ids = []; - if (selectedArray != null) { - for (var i = 0; i < selectedArray.length; i++) { - ids.push(selectedArray[i].id); - } - } - return ids; -}; - -DataReductionForm.prototype.onSelectionChanged = function(columnName, selected) { - if (selected != null) { - if (columnName == "Frames") { - this.selectedItems.frames = selected; - this.selectedItems.subtractions = []; - } - if (columnName == "Averages") { - this.selectedItems.averages = selected; - } - if (columnName == "Subtractions") { - this.selectedItems.frames = []; - this.selectedItems.subtractions = selected; - } - } - this.plotWidget.refresh(this._parseSelectedItemsToIds(this.selectedItems.frames), this._parseSelectedItemsToIds(this.selectedItems.subtractions)); -}; - -DataReductionForm.prototype._getFramesExtPanel = function(store, columnName, height) { - var _this = this; - - var selModel = Ext.create('Ext.selection.RowModel', { - allowDeselect : true, - mode : 'MULTI', - listeners : { - selectionchange : function(sm, selections) { - var selected = []; - for (var i = 0; i < selections.length; i++) { - selected.push(selections[i].raw); - } - _this.onSelectionChanged(columnName, selected); - } - } - }); - - return Ext.create('Ext.grid.Panel', { - store : store, - margin : 10, - height : height, - width : 200, - selModel : selModel, - columns : [ { - text : columnName, - dataIndex : 'fileName', - flex : 1 - } ], - viewConfig : { - } - }); -}; - -DataReductionForm.prototype._getFramesPanel = function() { - var fields = [ 'fileName', 'type', 'id' ]; - - this.framesStore = Ext.create('Ext.data.Store', { - fields : fields, - sorters : 'fileName' - }); - - this.averagesStore = Ext.create('Ext.data.Store', { - fields : fields - }); - - this.subtractionStore = Ext.create('Ext.data.Store', { - fields : fields - }); - - var gridFrames = this._getFramesExtPanel(this.framesStore, "Frames", 375); - var gridAvgs = this._getFramesExtPanel(this.averagesStore, "Averages", 125); - var subtractionAvgs = this._getFramesExtPanel(this.subtractionStore, "Subtractions", 75); - - return { - xtype : 'container', - layout : 'vbox', - items : [ gridFrames, subtractionAvgs ] - }; -}; - -DataReductionForm.prototype._getImageContainer = function(name, help) { - var html = "
" + name + "
" - return { - xtype : 'container', - layout : 'vbox', - items : [ { - html : html, - margin : "5 0 0 0", - height : 95, - width : 100 - }, { - xtype : 'label', - forId : 'myFieldId', - text : help, - margin : '5 0 0 0', - cls : "inline-help" - } ] - } -}; - -DataReductionForm.prototype._getItems = function() { - var _this = this; - return [ { - xtype : 'container', - layout : 'hbox', - items : [ - this._getFramesPanel(), - this.plotWidget.getPanel(), - { - xtype : 'panel', - width : 110, - frame : true, - margin : "10 5 5 5", - border : 0, - layout : 'vbox', - items : [ this._getImageContainer("scattering", "Scattering"), this._getImageContainer("guinier", "Guinier Region"), - this._getImageContainer("kratky", "Kratky Plot"), this._getImageContainer("gnom", "P(r) distribution") ] - } ] - } ] -}; - -DataReductionForm.prototype._getButtons = function() { - return []; -}; - -DataReductionForm.prototype.getPanel = function() { - var _this = this; - this.panel = Ext.create('Ext.form.Panel', { - width : this.width, - height : this.height, - border : 0, - items : this._getItems(), - buttons : this._getButtons(), - listeners : { - afterrender : function() { - _this._populate(); - } - } - }); - return this.panel; -}; - -/** Populates could be call when the DOM is not filled yet **/ -DataReductionForm.prototype._populate = function() { -}; - -/** It populates the form * */ -DataReductionForm.prototype.refresh = function(subtractions) { - if (subtractions != null) { - for (var i = 0; i < subtractions.length; i++) { - /** Loading frame grids **/ - var subtraction = subtractions[i]; - var averages = [ { - fileName : BUI.getFileName(subtraction.bufferAverageFilePath), - type : 'bufferAvg', - id : subtraction.subtractionId - }, { - fileName : BUI.getFileName(subtraction.sampleAverageFilePath), - type : 'sampleAvg', - id : subtraction.subtractionId - } - - ]; - this.averagesStore.loadData(averages, true); - this.subtractionStore.loadData([ { - fileName : BUI.getFileName(subtraction.substractedFilePath), - type : 'SUBTRACTION', - id : subtraction.subtractionId - } ], true); - - var frames = []; - /** Buffers **/ - if (subtraction.bufferOneDimensionalFiles != null) { - if (subtraction.bufferOneDimensionalFiles.frametolist3VOs != null) { - for (var j = 0; j < subtraction.bufferOneDimensionalFiles.frametolist3VOs.length; j++) { - var frametolist3VO = subtraction.bufferOneDimensionalFiles.frametolist3VOs[j]; - if (frametolist3VO.frame3VO != null) { - frames.push({ - fileName : BUI.getFileName(frametolist3VO.frame3VO.filePath), - type : 'BUFFER', - id : frametolist3VO.frame3VO.frameId - }); - } - } - } - } - /** Samples **/ - if (subtraction.sampleOneDimensionalFiles != null) { - if (subtraction.sampleOneDimensionalFiles.frametolist3VOs != null) { - for (var j = 0; j < subtraction.sampleOneDimensionalFiles.frametolist3VOs.length; j++) { - var frametolist3VO = subtraction.sampleOneDimensionalFiles.frametolist3VOs[j]; - if (frametolist3VO.frame3VO != null) { - frames.push({ - fileName : BUI.getFileName(frametolist3VO.frame3VO.filePath), - type : 'SAMPLE', - id : frametolist3VO.frame3VO.frameId - }); - } - } - } - } - - this.framesStore.loadData(frames, true); - - /** Loading images **/ - this._displayImage("scattering", subtraction.subtractionId); - this._displayImage("kratky", subtraction.subtractionId); - this._displayImage("guinier", subtraction.subtractionId); - this._displayImage("gnom", subtraction.subtractionId); - } - } -}; - -DataReductionForm.prototype._displayImage = function(name, subtractionId) { - var url = BUI.getURL() + '&type=' + name + '&subtractionId=' + subtractionId; - var event = "OnClick= window.open('" + url + "')"; - document.getElementById(this.id + "_" + name).innerHTML = ''; -}; - -DataReductionForm.prototype.input = function() { - return {}; -}; - -/** It populates the form **/ -DataReductionForm.prototype.test = function(targetId) { - var macromoleculeForm = new DataReductionForm(); - var panel = macromoleculeForm.getPanel(); - panel.render(targetId); -}; - -function PlotWidget(args) { - this.width = 600; - this.height = 600; - this.id = BUI.id(); - - this.linear = false; - - this.margin = "10 0 0 0"; - /** for each stat the max and minimum value when it is scaled in order to show correctly in the legend **/ - this.ranges = {}; - if (args != null) { - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; - } - if (args.margin != null) { - this.margin = args.margin; - } - } - -} - -PlotWidget.prototype.getMenu = function() { - var _this = this; - /** Actions buttons **/ - var actions = []; - actions.push("->"); - actions.push({ - text : "Export as Image", - scope : this, - icon : '../images/save.gif', - handler : function(item, pressed) { - var largeImage = document.createElement("img"); - largeImage.style.display = 'block'; - largeImage.style.width = 200 + "px"; - largeImage.style.height = 200 + "px"; - largeImage.setAttribute('src', Dygraph.Export.asCanvas(this.dygraphObject.dygraph).toDataURL()); - window.open(Dygraph.Export.asCanvas(this.dygraphObject.dygraph).toDataURL(), 'Image', ''); - } - }); - - return actions; -}; - -/** Looks for the maximum value and then divide everything but that value **/ -PlotWidget.prototype.scaledData = function(data) { - for (var i = 0; i < data.length; i++) { - var values = this.getMaxAndMinValue(data[i]); - data[i] = this.divideValuesByMax(data[i], values.max); - this.ranges[data[i].label] = values; - } - return data; -}; - -/** Given a stat float[] and a max number it will divide each value by max **/ -PlotWidget.prototype.divideValuesByMax = function(stat, max) { - for (var j = 0; j < stat.data.length; j++) { - if (max != 0) { - stat.data[j] = Number(stat.data[j]) / max; - stat.std[j] = Number(stat.std[j]) / max; - } - } - return stat; -}; - -/** returns max value of a stat **/ -PlotWidget.prototype.getMaxAndMinValue = function(stat) { - var max = 0; - var min = stat.data[0]; - for (var j = 0; j < stat.data.length; j++) { - if (Number(stat.data[j]) > max) { - max = Number(stat.data[j]); - } - if (Number(stat.std[j]) > max) { - max = Number(stat.std[j]); - } - if (Number(stat.data[j]) < min) { - min = Number(stat.data[j]); - } - } - return { - max : Number(max), - min : Number(min) - }; -}; - -PlotWidget.prototype._renderDygraph = function(parsed, colors, labels) { - this.dygraphObject = new StdDevDyGraph(this.id, { - width : this.width - 20, - height : this.height - 40, - xlabel : "", - }); - - this.dygraphObject.draw(parsed, colors, labels); - -}; - -PlotWidget.prototype.getPanel = function() { - this.panel = Ext.create('Ext.panel.Panel', { - width : this.width, - height : this.height, - margin : this.margin, - tbar : this.getMenu(), - items : [ { - html : "", - id : this.id, - width : this.width, - height : this.height, - padding : 10, - margin : "0 0 0 -30", - border : 0 - } ] - }); - - return this.panel; -}; - -PlotWidget.prototype.getPoint = function(y, error) { - var minus = y - error; - var max = y + error; - - if (this.linear) { - return [ Math.abs(minus), y, Math.abs(max) ]; - } - if ((minus != 0) && (max != 0)) { - return [ Math.log(Math.abs(minus)), Math.log(y), Math.log(Math.abs(max)) ]; - } else { - return [ Math.log(y), Math.log(y), Math.log(y) ]; - } - -}; - -PlotWidget.prototype.getDataPlot = function(frames, subtractions, models, fits, rbms) { - var files = []; - var labels = [ "Intensity" ]; - if (frames != null) { - for (var i = 0; i < frames.length; i++) { - files.push(frames[i].data); - labels.push(frames[i].fileName); - } - } - function splitData(data, column, errorColumn, name){ - var result = [] - for (var j = 0; j < data.length; j++) { - console.log(data[j][column]); - result.push([j,data[j][column],data[j][errorColumn]]);//[0, data[i][column],0]]); - } - files.push(result); - labels.push(name); - } - - if (subtractions != null) { - for (var i = 0; i < subtractions.length; i++) { - /** For subtraction **/ - files.push(subtractions[i].subtraction.data); - labels.push(subtractions[i].subtraction.fileName); - /** For sample average **/ -// files.push(subtractions[i].sampleAvg.data); -// labels.push(subtractions[i].sampleAvg.fileName); - /** For buffer average **/ -// files.push(subtractions[i].bufferAvg.data); -// labels.push(subtractions[i].bufferAvg.fileName); - } - } - - if (models != null) { - for (var i = 0; i < models.length; i++) { - for ( var key in models[i]) { - splitData(models[i][key].fir.data, 1, 2, "Intensity"); - splitData(models[i][key].fir.data, 3, 3, "Fit"); - } - } - } - - if (fits != null) { - for (var i = 0; i < fits.length; i++) { - for ( var key in fits[i]) { - - /** adding fit file to be plotted **/ - if (fits[i][key].fit.data[0].length == 3){ - splitData(fits[i][key].fit.data, 1, 1, "Intensity"); - splitData(fits[i][key].fit.data, 2, 2, "Fit"); - } - - /** s, Iexp(s), err, Ifit(s). **/ - if (fits[i][key].fit.data[0].length == 4){ - splitData(fits[i][key].fit.data, 1, 2, "Intensity"); - splitData(fits[i][key].fit.data, 3, 3, "Fit"); - } - - if (fits[i][key].fit.data[0].length == 5){ - /** X Intensity Fit Error Residues **/ - - splitData(fits[i][key].fit.data, 1, 3, "Intensity"); - splitData(fits[i][key].fit.data, 2, 2, "Fit"); - } - } - } - } - - var dataPoints = []; - if (files.length > 0) { - for (var i = 0; i < files[0].length; i++) { - dataPoints.push([ files[0][i][0], this.getPoint(files[0][i][1], files[0][i][2]) ]); - } - if (files.length > 1) { - for (var i = 1; i < files.length; i++) { - for (var j = 0; j < dataPoints.length; j++) { - if (files[i][j] != null){ - dataPoints[j].push(this.getPoint(files[i][j][1], files[i][j][2])); - } - else{ - dataPoints[j].push([0,0,0]); - } - } - } - } - } - - return { - dataPoints : dataPoints, - labels : labels - } -}; - -PlotWidget.prototype.refresh = function(frames, subtractions, models, fits, rbms, colors) { - - var _this = this; - this.panel.setLoading("Reading Files"); - - var dataAdapter = new BiosaxsDataAdapter(); - dataAdapter.onSuccess.attach(function(sender, data) { - _this.panel.setLoading("Rendering"); - var parsed = _this.getDataPlot(data.frames, data.subtractions, data.models, data.fits, rbms); - _this._renderDygraph(parsed.dataPoints, colors, parsed.labels); - _this.panel.setLoading(false); - }); - dataAdapter.onError.attach(function(sender, data) { - _this.panel.setLoading(false); - }); - dataAdapter.getDataPlot(frames, subtractions, models, fits, rbms); -}; - -PlotWidget.prototype.input = function() { - return DATADOC.getHPLCData(); -}; - - -/** - * Fit form - * - * @witdh - * @height - */ -function FitForm(args) { - this.id = BUI.id(); - this.width = null; - this.height = null; - - if (args != null) { - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; - } - } - - var _this = this; - - /** Widgets **/ - this.fitGrid = new FitStructureToExperimentDataGrid({ - width : null, - height : 200 - }); - - this.fitGrid.onSelected.attach(function(sender, fits) { - var modelsIdList = []; - for ( var i in fits) { - modelsIdList.push(fits[i].fitStructureToExperimentalDataId); - } - _this._renderPlot(_this.subtractions[0].subtractionId, modelsIdList); -// var adapter = new BiosaxsDataAdapter(); -// adapter.onSuccess.attach(function(sender, data) { -// -// }); -// adapter.getScatteringCurveByFrameIdsList([], [], [], ids); - }); - - - /** Dygraph Widget that plots fir files**/ - this.plotWidget = new PlotWidget({ - width : 745, - height : 300, - margin : "10 0 10 10" - }); -} - -FitForm.prototype._renderPlot = function(subtractionId, modelsIdList) { - /** Trying to plot tje subtraction and the models **/ - try { - var colors = [ "#669900", "#0000FF" ]; - - this.plotWidget.refresh([], [ ], [], modelsIdList, [], colors); - } catch (e) { - console.log(e); - } -}; - -FitForm.prototype._getItems = function() { - var _this = this; - return [ { - xtype : 'label', - forId : 'myFieldId', - text : 'INLINE HELP: To be updated', - margin : '15 0 20 10', - cls : "inline-help" - }, this.fitGrid.getPanel(), this.plotWidget.getPanel() ] - -}; - -FitForm.prototype._getButtons = function() { - return []; -}; - -FitForm.prototype.getPanel = function() { - var _this = this; - this.panel = Ext.create('Ext.form.Panel', { - width : this.width, - height : this.height, - margin : 10, - border : 1, - defaultType : 'textfield', - items : this._getItems(), - buttons : this._getButtons(), - listeners : { - afterrender : function() { - _this._populate(); - - } - } - }); - return this.panel; -}; - -/** Populates could be call when the DOM is not filled yet **/ -FitForm.prototype._populate = function() { -}; - -/** It populates the form * */ -FitForm.prototype.refresh = function(subtractions) { - this.subtractions = subtractions; - this.fitGrid.refresh(subtractions); -}; - -FitForm.prototype.input = function() { - return {}; -}; - -/** It populates the form **/ -FitForm.prototype.test = function(targetId) { - var macromoleculeForm = new FitForm(); - var panel = macromoleculeForm.getPanel(); - panel.render(targetId); -}; - -/** - * Example form - * - * @witdh - * @height - */ -function RigidBodyModelingResultForm(args) { - this.id = BUI.id(); - this.width = null; - this.height = null; - - if (args != null) { - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; - } - } - - var _this = this; - /** Widgets **/ - this.rigidModelGrid = new RigidModelGrid({ - width : null, - height : 200 - }); - - this.rigidModelGrid.onSelected.attach(function(sender, fits){ - var ids = []; - for ( var i in fits) { - ids.push(fits[i].fitStructureToExperimentalDataId); - } - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data){ -// debugger - - }); - - adapter.getScatteringCurveByFrameIdsList([], [], [], ids); - }); - -} - -RigidBodyModelingResultForm.prototype._getItems = function() { - var _this = this; - return [ { - xtype : 'label', - forId : 'myFieldId', - text : 'INLINE HELP: To be updated', - margin : '15 0 20 10', - cls : "inline-help" - }, this.rigidModelGrid.getPanel() ] - -}; - -RigidBodyModelingResultForm.prototype._getButtons = function() { - return []; -}; - -RigidBodyModelingResultForm.prototype.getPanel = function() { - var _this = this; - this.panel = Ext.create('Ext.form.Panel', { - width : this.width, - height : this.height, - margin : 10, - border : 1, - defaultType : 'textfield', - items : this._getItems(), - buttons : this._getButtons(), - listeners : { - afterrender : function() { - _this._populate(); - - } - } - }); - return this.panel; -}; - -/** Populates could be call when the DOM is not filled yet **/ -RigidBodyModelingResultForm.prototype._populate = function() { -}; - -/** It populates the form * */ -RigidBodyModelingResultForm.prototype.refresh = function(subtractions) { - this.rigidModelGrid.refresh(subtractions); -}; - -RigidBodyModelingResultForm.prototype.input = function() { - return {}; -}; - -/** It populates the form **/ -RigidBodyModelingResultForm.prototype.test = function(targetId) { - var macromoleculeForm = new RigidBodyModelingResultForm(); - var panel = macromoleculeForm.getPanel(); - panel.render(targetId); -}; - -/** - * Example form - * - * @witdh - * @height - */ -function SuperpositionForm(args) { - this.id = BUI.id(); - this.width = null; - this.height = null; - - if (args != null) { - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; - } - } - - var _this = this; - - /** Widgets **/ - this.superpositionGrid = new SuperpositionGrid({ - width : null, - height : 200 - }); - - this.superpositionGrid.onSelected.attach(function(sender, superpositions) { - var ids = []; - for ( var i in superpositions) { - ids.push(superpositions[i].superpositionId); - } -// _this._renderAbinitio(ids); -// _this.aprioriPDBViewer.refresh(); - _this._renderAligned(ids); - // getAlignedPDBContentBySuperpositionList - }); - - /** PDB viewer **/ -// this.abinitioPDBViewer = new PDBViewer({ -// width : 860 / 2, -// height : 300 / 2, -// margin : 0 -// }); -// -// /** PDB viewer **/ -// this.aprioriPDBViewer = new StructurePDBViewer({ -// width : 860 / 2, -// height : 300 / 2, -// margin : 0 -// }); - - this.alignedPDBViewer = new AlignedSuperpositionPDBViewer({ - width : 860 , - height : 300 - }); - -} - -SuperpositionForm.prototype._renderAligned = function(modelsIdList) { - /** Trying to plot the PDB file **/ - try { - this.alignedPDBViewer.refresh(modelsIdList); - } catch (e) { - console.log(e); - } -}; - -SuperpositionForm.prototype._renderAbinitio = function(modelsIdList) { - /** Trying to plot the PDB file **/ - try { - var viz = []; - for (var i = 0; i < modelsIdList.length; i++) { - viz.push({ - modelId : modelsIdList[i], - color : "0xFF6600", - opacity : 0.8 - }); - } - this.abinitioPDBViewer.refresh(viz); - } catch (e) { - console.log(e); - } -}; - -SuperpositionForm.prototype._getItems = function() { - var _this = this; - return [ { - xtype : 'label', - forId : 'myFieldId', - text : 'INLINE HELP: To be updated', - margin : '15 0 20 10', - cls : "inline-help" - }, this.superpositionGrid.getPanel(), { - xtype : 'container', - layout : 'hbox', - items : [ -// { -// xtype : 'container', -// layout : 'vbox', -// items : [ this.abinitioPDBViewer.getPanel(), this.aprioriPDBViewer.getPanel() -// -// ] -// }, - - this.alignedPDBViewer.getPanel() ] - } ] - -}; - -SuperpositionForm.prototype._getButtons = function() { - return []; -}; - -SuperpositionForm.prototype.getPanel = function() { - var _this = this; - this.panel = Ext.create('Ext.form.Panel', { - width : this.width, - height : this.height, - margin : 10, - border : 1, - defaultType : 'textfield', - items : this._getItems(), - buttons : this._getButtons(), - listeners : { - afterrender : function() { - _this._populate(); - - } - } - }); - return this.panel; -}; - -/** Populates could be call when the DOM is not filled yet **/ -SuperpositionForm.prototype._populate = function() { -}; - -/** It populates the form * */ -SuperpositionForm.prototype.refresh = function(subtractions) { - this.subtractions = subtractions; - this.superpositionGrid.refresh(subtractions); -}; - -SuperpositionForm.prototype.input = function() { - return {}; -}; - -/** It populates the form **/ -SuperpositionForm.prototype.test = function(targetId) { - var macromoleculeForm = new SuperpositionForm(); - var panel = macromoleculeForm.getPanel(); - panel.render(targetId); -}; - -/** - * Example form - * - * @witdh - * @height - */ -function AssemblyForm(args) { - this.id = BUI.id(); - this.width = 700; - this.height = 500; - - if (args != null) { - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; - } - } - - this.molarityGrid = new MolarityGrid({height : this.height - 50}); -} - -AssemblyForm.prototype._getItems = function() { - return [ { - xtype : 'label', - forId : 'myFieldId', - text : 'List of previously defined macromolecules present in the assembly. This information will be used for additional cross-checks where possible', - margin : '15 0 20 10', - cls : "inline-help" - }, this.molarityGrid.getPanel() ]; -}; - -AssemblyForm.prototype._getButtons = function() { - return []; -}; - -AssemblyForm.prototype.getPanel = function() { - this.panel = Ext.create('Ext.form.Panel', { - width : this.width, - height : this.height, - margin : 10, - border : 0, - defaultType : 'textfield', - items : this._getItems(), - buttons : this._getButtons() - }); - return this.panel; -}; - - -/** It populates the form **/ -AssemblyForm.prototype.refresh = function(macromolecule) { - this.macromolecule = macromolecule; - this.molarityGrid.refresh(macromolecule); -}; - -AssemblyForm.prototype.input = function() { - return {}; -}; - - -AssemblyForm.prototype.test = function(targetId) { - var assemblyForm = new AssemblyForm(); - - var panel = assemblyForm.getPanel(); - panel.render(targetId); -}; /** - * Edit the information of a buffer + * Example form * - * #onSaved - * #onRemoveAdditive + * @witdh + * @height */ -function BufferForm() { +function DataReductionForm(args) { + this.id = BUI.id(); + this.width = null; + this.height = null; + + if (args != null) { + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + } + var _this = this; - this.additiveGrid = new AdditiveGrid(); - this.additiveGrid.onRemoveButtonClicked.attach(function(sender, args) { - _this.onRemoveAdditive.notify(args); + /** Widgets **/ + this.plotWidget = new PlotWidget({ + width : 650, + height : 490 }); - this.onSaved = new Event(this); - this.onRemoveAdditive = new Event(this); + /** Selected frames to be displayed **/ + this.selectedItems = { + frames : [], + averages : [], + subtractions : [] + }; + } -BufferForm.prototype.getBuffer = function() { - this.buffer.name = Ext.getCmp("buffer_name").getValue(); - this.buffer.acronym = Ext.getCmp("buffer_acronym").getValue(); - this.buffer.comments = Ext.getCmp("buffer_comments").getValue(); - this.buffer.ph = Ext.getCmp("buffer_ph").getValue(); - this.buffer.composition = Ext.getCmp("buffer_composition").getValue(); - this.buffer.bufferhasadditive3VOs = this.additiveGrid.getAdditives(); - return this.buffer; +DataReductionForm.prototype._parseSelectedItemsToIds = function(selectedArray) { + var ids = []; + if (selectedArray != null) { + for (var i = 0; i < selectedArray.length; i++) { + ids.push(selectedArray[i].id); + } + } + return ids; }; -BufferForm.prototype._getTopPanel = function() { +DataReductionForm.prototype.onSelectionChanged = function(columnName, selected) { + if (selected != null) { + if (columnName == "Frames") { + this.selectedItems.frames = selected; + this.selectedItems.subtractions = []; + } + if (columnName == "Averages") { + this.selectedItems.averages = selected; + } + if (columnName == "Subtractions") { + this.selectedItems.frames = []; + this.selectedItems.subtractions = selected; + } + } + this.plotWidget.refresh(this._parseSelectedItemsToIds(this.selectedItems.frames), this._parseSelectedItemsToIds(this.selectedItems.subtractions)); +}; + +DataReductionForm.prototype._getFramesExtPanel = function(store, columnName, height) { + var _this = this; + + var selModel = Ext.create('Ext.selection.RowModel', { + allowDeselect : true, + mode : 'MULTI', + listeners : { + selectionchange : function(sm, selections) { + var selected = []; + for (var i = 0; i < selections.length; i++) { + selected.push(selections[i].raw); + } + _this.onSelectionChanged(columnName, selected); + } + } + }); + + return Ext.create('Ext.grid.Panel', { + store : store, + margin : 10, + height : height, + width : 200, + selModel : selModel, + columns : [ { + text : columnName, + dataIndex : 'fileName', + flex : 1 + } ], + viewConfig : { + } + }); +}; + +DataReductionForm.prototype._getFramesPanel = function() { + var fields = [ 'fileName', 'type', 'id' ]; + + this.framesStore = Ext.create('Ext.data.Store', { + fields : fields, + sorters : 'fileName' + }); + + this.averagesStore = Ext.create('Ext.data.Store', { + fields : fields + }); + + this.subtractionStore = Ext.create('Ext.data.Store', { + fields : fields + }); + + var gridFrames = this._getFramesExtPanel(this.framesStore, "Frames", 375); + var gridAvgs = this._getFramesExtPanel(this.averagesStore, "Averages", 125); + var subtractionAvgs = this._getFramesExtPanel(this.subtractionStore, "Subtractions", 75); + return { xtype : 'container', - layout : 'hbox', - border : 0, - frame : true, + layout : 'vbox', + items : [ gridFrames, subtractionAvgs ] + }; +}; + +DataReductionForm.prototype._getImageContainer = function(name, help) { + var html = "
" + name + "
" + return { + xtype : 'container', + layout : 'vbox', items : [ { - xtype : 'container', - layout : 'hbox', - items : [ { - xtype : 'container', - flex : 1, - border : false, - layout : 'anchor', - defaultType : 'textfield', - items : [ { - xtype : 'requiredtext', - id : 'buffer_name', - fieldLabel : 'Name', - name : 'name', - width : '200px', - value : this.buffer.name - }, { - xtype : 'requiredtext', - id : 'buffer_acronym', - fieldLabel : 'Acronym', - name : 'acronym', - width : '200px', - value : this.buffer.acronym - } ] - } ] + html : html, + margin : "5 0 0 0", + height : 95, + width : 100 }, { - xtype : 'container', - flex : 1, - layout : 'anchor', - defaultType : 'textfield', - margin : '0 0 0 10', - items : [ { - id : 'buffer_ph', - fieldLabel : 'pH', - name : 'ph', - value : this.buffer.ph, - xtype : 'numberfield', - width : 200, - minValue : 0, - maxValue : 15 - }, { - xtype : 'requiredtext', - id : 'buffer_composition', - fieldLabel : 'Composition', - name : 'composition', - width : 200, - value : this.buffer.composition - } ] + xtype : 'label', + forId : 'myFieldId', + text : help, + margin : '5 0 0 0', + cls : "inline-help" } ] - }; + } }; -BufferForm.prototype.getPanel = function(buffer) { - this.buffer = buffer; - this.panel = Ext.createWidget({ +DataReductionForm.prototype._getItems = function() { + var _this = this; + return [ { xtype : 'container', - layout : 'vbox', - style : { - padding : '10px' - }, - fieldDefaults : { - labelAlign : 'left', - labelWidth : 50 + layout : 'hbox', + items : [ + this._getFramesPanel(), + this.plotWidget.getPanel(), + { + xtype : 'panel', + width : 110, + frame : true, + margin : "10 5 5 5", + border : 0, + layout : 'vbox', + items : [ this._getImageContainer("scattering", "Scattering"), this._getImageContainer("guinier", "Guinier Region"), + this._getImageContainer("kratky", "Kratky Plot"), this._getImageContainer("gnom", "P(r) distribution") ] + } ] + } ] +}; - }, - items : [ this._getTopPanel(), { - id : 'buffer_comments', - xtype : 'textareafield', - name : 'comments', - fieldLabel : 'Comments', - width : '100%', - value : buffer.comments - }, this.additiveGrid.getPanel(buffer) ] +DataReductionForm.prototype._getButtons = function() { + return []; +}; + +DataReductionForm.prototype.getPanel = function() { + var _this = this; + this.panel = Ext.create('Ext.form.Panel', { + width : this.width, + height : this.height, + border : 0, + items : this._getItems(), + buttons : this._getButtons(), + listeners : { + afterrender : function() { + _this._populate(); + } + } }); return this.panel; }; -BufferForm.prototype.input = function() { - return { - buffer : { - "bufferId" : 422, - "proposalId" : 10, - "safetyLevelId" : null, - "name" : "B1", - "acronym" : "B1", - "ph" : null, - "composition" : null, - "bufferhasadditive3VOs" : [], - "comments" : null +/** Populates could be call when the DOM is not filled yet **/ +DataReductionForm.prototype._populate = function() { +}; + +/** It populates the form * */ +DataReductionForm.prototype.refresh = function(subtractions) { + if (subtractions != null) { + for (var i = 0; i < subtractions.length; i++) { + /** Loading frame grids **/ + var subtraction = subtractions[i]; + var averages = [ { + fileName : BUI.getFileName(subtraction.bufferAverageFilePath), + type : 'bufferAvg', + id : subtraction.subtractionId + }, { + fileName : BUI.getFileName(subtraction.sampleAverageFilePath), + type : 'sampleAvg', + id : subtraction.subtractionId + } + + ]; + this.averagesStore.loadData(averages, true); + this.subtractionStore.loadData([ { + fileName : BUI.getFileName(subtraction.substractedFilePath), + type : 'SUBTRACTION', + id : subtraction.subtractionId + } ], true); + + var frames = []; + /** Buffers **/ + if (subtraction.bufferOneDimensionalFiles != null) { + if (subtraction.bufferOneDimensionalFiles.frametolist3VOs != null) { + for (var j = 0; j < subtraction.bufferOneDimensionalFiles.frametolist3VOs.length; j++) { + var frametolist3VO = subtraction.bufferOneDimensionalFiles.frametolist3VOs[j]; + if (frametolist3VO.frame3VO != null) { + frames.push({ + fileName : BUI.getFileName(frametolist3VO.frame3VO.filePath), + type : 'BUFFER', + id : frametolist3VO.frame3VO.frameId + }); + } + } + } + } + /** Samples **/ + if (subtraction.sampleOneDimensionalFiles != null) { + if (subtraction.sampleOneDimensionalFiles.frametolist3VOs != null) { + for (var j = 0; j < subtraction.sampleOneDimensionalFiles.frametolist3VOs.length; j++) { + var frametolist3VO = subtraction.sampleOneDimensionalFiles.frametolist3VOs[j]; + if (frametolist3VO.frame3VO != null) { + frames.push({ + fileName : BUI.getFileName(frametolist3VO.frame3VO.filePath), + type : 'SAMPLE', + id : frametolist3VO.frame3VO.frameId + }); + } + } + } + } + + this.framesStore.loadData(frames, true); + + /** Loading images **/ + this._displayImage("scattering", subtraction.subtractionId); + this._displayImage("kratky", subtraction.subtractionId); + this._displayImage("guinier", subtraction.subtractionId); + this._displayImage("gnom", subtraction.subtractionId); } - }; + } }; -BufferForm.prototype.test = function(targetId) { - var bufferForm = new BufferForm(); - var panel = bufferForm.getPanel(bufferForm.input().buffer); +DataReductionForm.prototype._displayImage = function(name, subtractionId) { + var url = BUI.getURL() + '&type=' + name + '&subtractionId=' + subtractionId; + var event = "OnClick= window.open('" + url + "')"; + document.getElementById(this.id + "_" + name).innerHTML = ''; +}; + +DataReductionForm.prototype.input = function() { + return {}; +}; + +/** It populates the form **/ +DataReductionForm.prototype.test = function(targetId) { + var macromoleculeForm = new DataReductionForm(); + var panel = macromoleculeForm.getPanel(); panel.render(targetId); }; - -/** - * @showTitle - * - * #onSaved - * #onAddPlates - * #onRemovePlates - **/ -function CaseForm(args) { - this.width = 700; - this.showTitle = true; + +function PlotWidget(args) { + this.width = 600; + this.height = 600; + this.id = BUI.id(); + + this.linear = false; + + this.margin = "10 0 0 0"; + /** for each stat the max and minimum value when it is scaled in order to show correctly in the legend **/ + this.ranges = {}; if (args != null) { - if (args.showTitle != null) { - this.showTitle = args.showTitle; + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + if (args.margin != null) { + this.margin = args.margin; } } - var _this = this; - this.stockSolutionGrid = new StockSolutionGrid({ - width : this.width - 10, - minHeight : 300, - height : 300, - tbar : true, - showTitle : true, - isPackedVisible : false, - btnAddExisting : true, - btnRemoveVisible : false, - btnUnpackVisible : true - }); +} - /** When selecting existing stock solutions **/ - this.stockSolutionGrid.onStockSolutionSelected.attach(function(sender, stockSolutions) { - if (stockSolutions != null) { - for ( var i = 0; i < stockSolutions.length; i++) { - _this.saveStockSolution(stockSolutions[i]); - } +PlotWidget.prototype.getMenu = function() { + var _this = this; + /** Actions buttons **/ + var actions = []; + actions.push("->"); + actions.push({ + text : "Export as Image", + scope : this, + icon : '../images/save.gif', + handler : function(item, pressed) { + var largeImage = document.createElement("img"); + largeImage.style.display = 'block'; + largeImage.style.width = 200 + "px"; + largeImage.style.height = 200 + "px"; + largeImage.setAttribute('src', Dygraph.Export.asCanvas(this.dygraphObject.dygraph).toDataURL()); + window.open(Dygraph.Export.asCanvas(this.dygraphObject.dygraph).toDataURL(), 'Image', ''); } }); - /** it can be because it has been added a new one or removed **/ - this.stockSolutionGrid.onProposalChanged.attach(function(sender, stockSolution) { - if (stockSolution != null) { - _this.saveStockSolution(stockSolution); - } else { - BIOSAXS.proposal.onInitialized.attach(function() { - _this.stockSolutionGrid.refresh(BIOSAXS.proposal.getStockSolutionsByDewarId(_this.dewar.dewarId)); + return actions; +}; - _this.stockSolutionGrid.grid.setLoading(false); - }); - BIOSAXS.proposal.init(); +/** Looks for the maximum value and then divide everything but that value **/ +PlotWidget.prototype.scaledData = function(data) { + for (var i = 0; i < data.length; i++) { + var values = this.getMaxAndMinValue(data[i]); + data[i] = this.divideValuesByMax(data[i], values.max); + this.ranges[data[i].label] = values; + } + return data; +}; + +/** Given a stat float[] and a max number it will divide each value by max **/ +PlotWidget.prototype.divideValuesByMax = function(stat, max) { + for (var j = 0; j < stat.data.length; j++) { + if (max != 0) { + stat.data[j] = Number(stat.data[j]) / max; + stat.std[j] = Number(stat.std[j]) / max; + } + } + return stat; +}; +/** returns max value of a stat **/ +PlotWidget.prototype.getMaxAndMinValue = function(stat) { + var max = 0; + var min = stat.data[0]; + for (var j = 0; j < stat.data.length; j++) { + if (Number(stat.data[j]) > max) { + max = Number(stat.data[j]); + } + if (Number(stat.std[j]) > max) { + max = Number(stat.std[j]); + } + if (Number(stat.data[j]) < min) { + min = Number(stat.data[j]); } + } + return { + max : Number(max), + min : Number(min) + }; +}; +PlotWidget.prototype._renderDygraph = function(parsed, colors, labels) { + this.dygraphObject = new StdDevDyGraph(this.id, { + width : this.width - 20, + height : this.height - 40, + xlabel : "", }); - this.onSaved = new Event(this); - this.onAddPlates = new Event(this); - this.onRemovePlates = new Event(this); -} + this.dygraphObject.draw(parsed, colors, labels); -CaseForm.prototype.saveStockSolution = function(stockSolution) { - var _this = this; - var adapter = new BiosaxsDataAdapter(); - this.stockSolutionGrid.grid.setLoading("ISPyB: setting case to Stock solution"); - adapter.onSuccess.attach(function(sender, stockSolution) { - BIOSAXS.proposal.onInitialized.attach(function() { - _this.stockSolutionGrid.refresh(BIOSAXS.proposal.getStockSolutionsByDewarId(_this.dewar.dewarId)); - _this.stockSolutionGrid.grid.setLoading(false); - }); - BIOSAXS.proposal.init(); - }); - adapter.onError.attach(function(sender, data) { - _this.stockSolutionGrid.grid.setLoading(false); - BUI.showError(data); - }); - stockSolution.boxId = _this.dewar.dewarId; - adapter.saveStockSolution(stockSolution); }; -CaseForm.prototype.fillStores = function() { - var _this = this; - this.panel.setLoading("Loading Labcontacts from database"); - - var proposal = BUI.getProposal(); - proposal.onDataRetrieved.attach(function(sender, data) { - _this.labContactForSendingStore.loadData(data, false); - _this.labContactForReturnStore.loadData(data, false); - _this.panel.setLoading(false); +PlotWidget.prototype.getPanel = function() { + this.panel = Ext.create('Ext.panel.Panel', { + width : this.width, + height : this.height, + margin : this.margin, + tbar : this.getMenu(), + items : [ { + html : "", + id : this.id, + width : this.width, + height : this.height, + padding : 10, + margin : "0 0 0 -30", + border : 0 + } ] }); - proposal.getLabContactsByProposalId(); - -}; -CaseForm.prototype.refresh = function(dewar) { - this.setDewar(dewar); - this.stockSolutionGrid.refresh(BIOSAXS.proposal.getStockSolutionsByDewarId(dewar.dewarId)); + return this.panel; }; -CaseForm.prototype.getDewar = function() { - this.dewar.code = Ext.getCmp("dewar_code").getValue(); - this.dewar.comments = Ext.getCmp("dewar_comments").getValue(); - this.dewar.trackingNumberFromSynchrotron = Ext.getCmp("dewar_trackingNumberFromSynchrotron").getValue(); - this.dewar.trackingNumberToSynchrotron = Ext.getCmp("dewar_trackingNumberToSynchrotron").getValue(); - this.dewar.transportValue = Ext.getCmp("dewar_transportValue").getValue(); - this.dewar.storageLocation = Ext.getCmp("dewar_storageLocation").getValue(); - this.dewar.firstExperimentId = this.macromoleculeCombo.getValue(); - return this.dewar; -}; +PlotWidget.prototype.getPoint = function(y, error) { + var minus = y - error; + var max = y + error; -CaseForm.prototype.setDewar = function(dewar) { - this.dewar = dewar; - Ext.getCmp("dewar_code").setValue(this.dewar.code); - Ext.getCmp("dewar_dewarStatus").setText(new String(this.dewar.dewarStatus).toUpperCase()); - Ext.getCmp("dewar_comments").setValue(this.dewar.comments); - Ext.getCmp("dewar_trackingNumberFromSynchrotron").setValue(this.dewar.trackingNumberFromSynchrotron); - Ext.getCmp("dewar_trackingNumberToSynchrotron").setValue(this.dewar.trackingNumberToSynchrotron); - Ext.getCmp("dewar_transportValue").setValue(this.dewar.transportValue); - Ext.getCmp("dewar_storageLocation").setValue(this.dewar.storageLocation); - if (dewar.sessionVO != null) { - this.macromoleculeCombo.setValue(dewar.sessionVO.sessionId); + if (this.linear) { + return [ Math.abs(minus), y, Math.abs(max) ]; + } + if ((minus != 0) && (max != 0)) { + return [ Math.log(Math.abs(minus)), Math.log(y), Math.log(Math.abs(max)) ]; + } else { + return [ Math.log(y), Math.log(y), Math.log(y) ]; } -}; -CaseForm.prototype.getSessionCombo = function() { - this.macromoleculeCombo = BIOSAXS_COMBOMANAGER.getComboSessions(BIOSAXS.proposal.getSessions(), { - labelWidth : 100, - margin : '5 0 00 0', - width : 250 - }); - return this.macromoleculeCombo; }; -CaseForm.prototype.getInformationPanel = function() { - if (this.panel == null) { - this.informationPanel = Ext.create('Ext.form.Panel', { - width : this.width - 10, - border : 0, - items : [ { - xtype : 'container', - margin : "2 2 2 2", - collapsible : false, - defaultType : 'textfield', - layout : 'anchor', - items : [ { - xtype : 'container', - layout : 'hbox', - items : [ { - xtype : 'requiredtext', - fieldLabel : 'Code', - allowBlank : false, - name : 'code', - id : 'dewar_code', - anchor : '50%' - }, { - xtype : 'label', - margin : '0 0 0 20', - readOnly : true, - id : 'dewar_dewarStatus', - anchor : '50%' - } ] - }, this.getSessionCombo(), { - margin : '5 0 0 0', - xtype : 'textareafield', - name : 'comments', - id : 'dewar_comments', - width : this.width - 50, - fieldLabel : 'Comments' - } ] - }, { - xtype : 'fieldset', - title : 'Courier Accounts Details for Return', - collapsible : false, - layout : 'anchor', - defaults : { - anchor : '100%' - }, - items : [ { - xtype : 'container', - layout : 'hbox', - items : [ { - xtype : 'textfield', - labelWidth : 200, - width : 280, - fieldLabel : 'Track Number From Synchrotron', - id : 'dewar_trackingNumberFromSynchrotron' - }, { - xtype : 'numberfield', - width : 190, - labelWidth : 110, - margin : '0 0 0 30', - fieldLabel : 'Transport Value', - id : 'dewar_transportValue' +PlotWidget.prototype.getDataPlot = function(frames, subtractions, models, fits, rbms) { + var files = []; + var labels = [ "Intensity" ]; + if (frames != null) { + for (var i = 0; i < frames.length; i++) { + files.push(frames[i].data); + labels.push(frames[i].fileName); + } + } + function splitData(data, column, errorColumn, name){ + var result = [] + for (var j = 0; j < data.length; j++) { + console.log(data[j][column]); + result.push([j,data[j][column],data[j][errorColumn]]);//[0, data[i][column],0]]); + } + files.push(result); + labels.push(name); + } + + if (subtractions != null) { + for (var i = 0; i < subtractions.length; i++) { + /** For subtraction **/ + files.push(subtractions[i].subtraction.data); + labels.push(subtractions[i].subtraction.fileName); + /** For sample average **/ +// files.push(subtractions[i].sampleAvg.data); +// labels.push(subtractions[i].sampleAvg.fileName); + /** For buffer average **/ +// files.push(subtractions[i].bufferAvg.data); +// labels.push(subtractions[i].bufferAvg.fileName); + } + } + + if (models != null) { + for (var i = 0; i < models.length; i++) { + for ( var key in models[i]) { + splitData(models[i][key].fir.data, 1, 2, "Intensity"); + splitData(models[i][key].fir.data, 3, 3, "Fit"); + } + } + } + + if (fits != null) { + for (var i = 0; i < fits.length; i++) { + for ( var key in fits[i]) { + + /** adding fit file to be plotted **/ + if (fits[i][key].fit.data[0].length == 3){ + splitData(fits[i][key].fit.data, 1, 1, "Intensity"); + splitData(fits[i][key].fit.data, 2, 2, "Fit"); + } + + /** s, Iexp(s), err, Ifit(s). **/ + if (fits[i][key].fit.data[0].length == 4){ + splitData(fits[i][key].fit.data, 1, 2, "Intensity"); + splitData(fits[i][key].fit.data, 3, 3, "Fit"); + } + + if (fits[i][key].fit.data[0].length == 5){ + /** X Intensity Fit Error Residues **/ + + splitData(fits[i][key].fit.data, 1, 3, "Intensity"); + splitData(fits[i][key].fit.data, 2, 2, "Fit"); + } + } + } + } + + var dataPoints = []; + if (files.length > 0) { + for (var i = 0; i < files[0].length; i++) { + dataPoints.push([ files[0][i][0], this.getPoint(files[0][i][1], files[0][i][2]) ]); + } + if (files.length > 1) { + for (var i = 1; i < files.length; i++) { + for (var j = 0; j < dataPoints.length; j++) { + if (files[i][j] != null){ + dataPoints[j].push(this.getPoint(files[i][j][1], files[i][j][2])); } - - ] - }, { - xtype : 'container', - layout : 'hbox', - margin : '10 0 0 0', - items : [ - - { - xtype : 'textfield', - labelWidth : 200, - width : 280, - fieldLabel : 'Track Number To Synchrotron', - id : 'dewar_trackingNumberToSynchrotron' - }, { - xtype : 'textfield', - margin : '0 0 0 30', - width : 190, - labelWidth : 110, - fieldLabel : 'Storage Location', - id : 'dewar_storageLocation' + else{ + dataPoints[j].push([0,0,0]); } + } + } + } + } - ] - } ] - } ] - }); + return { + dataPoints : dataPoints, + labels : labels } +}; - return this.informationPanel; +PlotWidget.prototype.refresh = function(frames, subtractions, models, fits, rbms, colors) { + + var _this = this; + this.panel.setLoading("Reading Files"); + + var dataAdapter = new BiosaxsDataAdapter(); + dataAdapter.onSuccess.attach(function(sender, data) { + _this.panel.setLoading("Rendering"); + var parsed = _this.getDataPlot(data.frames, data.subtractions, data.models, data.fits, rbms); + _this._renderDygraph(parsed.dataPoints, colors, parsed.labels); + _this.panel.setLoading(false); + }); + dataAdapter.onError.attach(function(sender, data) { + _this.panel.setLoading(false); + }); + dataAdapter.getDataPlot(frames, subtractions, models, fits, rbms); }; -CaseForm.prototype.getPanel = function(dewar) { - this.dewar = dewar; - this.panel = Ext.createWidget({ - xtype : 'container', - layout : 'vbox', - width : this.width, - border : 0, - items : [ { - items : { - xtype : "container", - layout : "vbox", - margin : "5 5 5 5", - items : [ this.getInformationPanel(dewar), this.stockSolutionGrid.getPanel() ] +PlotWidget.prototype.input = function() { + return DATADOC.getHPLCData(); +}; - } - } ] + +/** + * Fit form + * + * @witdh + * @height + */ +function FitForm(args) { + this.id = BUI.id(); + this.width = null; + this.height = null; + + if (args != null) { + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + } + + var _this = this; + + /** Widgets **/ + this.fitGrid = new FitStructureToExperimentDataGrid({ + width : null, + height : 200 }); - this.refresh(dewar); - return this.panel; + this.fitGrid.onSelected.attach(function(sender, fits) { + var modelsIdList = []; + for ( var i in fits) { + modelsIdList.push(fits[i].fitStructureToExperimentalDataId); + } + _this._renderPlot(_this.subtractions[0].subtractionId, modelsIdList); +// var adapter = new BiosaxsDataAdapter(); +// adapter.onSuccess.attach(function(sender, data) { +// +// }); +// adapter.getScatteringCurveByFrameIdsList([], [], [], ids); + }); + + + /** Dygraph Widget that plots fir files**/ + this.plotWidget = new PlotWidget({ + width : 745, + height : 300, + margin : "10 0 10 10" + }); +} +FitForm.prototype._renderPlot = function(subtractionId, modelsIdList) { + /** Trying to plot tje subtraction and the models **/ + try { + var colors = [ "#669900", "#0000FF" ]; + + this.plotWidget.refresh([], [ ], [], modelsIdList, [], colors); + } catch (e) { + console.log(e); + } }; -CaseForm.prototype.input = function() { - return { - dewar : { - "dewarId" : 305861, - "code" : "ESRF-TEST", - "comments" : "comments", - "storageLocation" : "FRIDGE", - "dewarStatus" : "opened", - "timeStamp" : null, - "isStorageDewar" : null, - "barCode" : "ESRF305861", - "customsValue" : null, - "transportValue" : null, - "trackingNumberToSynchrotron" : "3333", - "trackingNumberFromSynchrotron" : "224466", - "type" : "Dewar", - "sessionVO" : { - "sessionId" : 31697, - "expSessionPk" : null, - "projectCode" : null, - "startDate" : "2012 07 21", - "endDate" : "2012 07 23", - "beamlineName" : "BM29", - "scheduled" : 1, - "nbShifts" : 2, - "comments" : null, - "beamlineOperator" : "PERNOT P", - "usedFlag" : null, - "sessionTitle" : null, - "structureDeterminations" : null, - "dewarTransport" : null, - "databackupFrance" : null, - "databackupEurope" : null, - "visit_number" : null, - "operatorSiteNumber" : "14061", - "timeStamp" : "2012 04 25" +FitForm.prototype._getItems = function() { + var _this = this; + return [ { + xtype : 'label', + forId : 'myFieldId', + text : 'INLINE HELP: To be updated', + margin : '15 0 20 10', + cls : "inline-help" + }, this.fitGrid.getPanel(), this.plotWidget.getPanel() ] + +}; + +FitForm.prototype._getButtons = function() { + return []; +}; + +FitForm.prototype.getPanel = function() { + var _this = this; + this.panel = Ext.create('Ext.form.Panel', { + width : this.width, + height : this.height, + margin : 10, + border : 1, + defaultType : 'textfield', + items : this._getItems(), + buttons : this._getButtons(), + listeners : { + afterrender : function() { + _this._populate(); + } - }, - proposal : { - "assemblies" : [], - "sessions" : [ { - "sessionId" : 31697, - "expSessionPk" : null, - "projectCode" : null, - "startDate" : "2012 07 21", - "endDate" : "2012 07 23", - "beamlineName" : "BM29", - "scheduled" : 1, - "nbShifts" : 2, - "comments" : null, - "beamlineOperator" : "PERNOT P", - "usedFlag" : null, - "sessionTitle" : null, - "structureDeterminations" : null, - "dewarTransport" : null, - "databackupFrance" : null, - "databackupEurope" : null, - "visit_number" : null, - "operatorSiteNumber" : "14061", - "timeStamp" : "2012 04 25" - } ], - "labcontacts" : [ { - "labContactId" : 787, - "personVO" : { - "personId" : 304252, - "personUUID" : null, - "familyName" : "KIM", - "givenName" : "Henry", - "title" : null, - "emailAddress" : "henry-sung.kim@ibs.fr", - "phoneNumber" : "", - "login" : "", - "passwd" : "", - "faxNumber" : "" - }, - "cardName" : "KIM-Institut de Bio", - "defaultCourrierCompany" : "22", - "courierAccount" : "", - "billingReference" : "", - "dewarAvgCustomsValue" : 0, - "dewarAvgTransportValue" : 0 - } ], - "buffers" : [ { - "bufferId" : 811, - "proposalId" : 3124, - "safetyLevelId" : null, - "name" : "EDTA", - "acronym" : "EDTA", - "ph" : null, - "composition" : "", - "bufferhasadditive3VOs" : [], - "comments" : "" - }, { - "bufferId" : 810, - "proposalId" : 3124, - "safetyLevelId" : null, - "name" : "HEPES", - "acronym" : "HEPES", - "ph" : null, - "composition" : "", - "bufferhasadditive3VOs" : [], - "comments" : "" - } ], - "shippings" : [ { - "shippingId" : 304107, - "shippingName" : "TEST", - "deliveryAgentAgentName" : null, - "deliveryAgentShippingDate" : null, - "deliveryAgentDeliveryDate" : null, - "deliveryAgentAgentCode" : null, - "deliveryAgentFlightCode" : null, - "shippingStatus" : "opened", - "timeStamp" : "2013 09 25", - "laboratoryId" : null, - "isStorageShipping" : null, - "creationDate" : "2013 09 25", - "comments" : "test", - "sendingLabContactVO" : { - "labContactId" : 787, - "personVO" : { - "personId" : 304252, - "personUUID" : null, - "familyName" : "KIM", - "givenName" : "Henry", - "title" : null, - "emailAddress" : "henry-sung.kim@ibs.fr", - "phoneNumber" : "", - "login" : "", - "passwd" : "", - "faxNumber" : "" - }, - "cardName" : "KIM-Institut de Bio", - "defaultCourrierCompany" : "22", - "courierAccount" : "", - "billingReference" : "", - "dewarAvgCustomsValue" : 0, - "dewarAvgTransportValue" : 0 - }, - "returnLabContactVO" : { - "labContactId" : 787, - "personVO" : { - "personId" : 304252, - "personUUID" : null, - "familyName" : "KIM", - "givenName" : "Henry", - "title" : null, - "emailAddress" : "henry-sung.kim@ibs.fr", - "phoneNumber" : "", - "login" : "", - "passwd" : "", - "faxNumber" : "" - }, - "cardName" : "KIM-Institut de Bio", - "defaultCourrierCompany" : "22", - "courierAccount" : "", - "billingReference" : "", - "dewarAvgCustomsValue" : 0, - "dewarAvgTransportValue" : 0 - }, - "returnCourier" : null, - "dateOfShippingToUser" : null, - "shippingType" : "DewarTracking", - "dewarVOs" : [ { - "dewarId" : 305861, - "code" : "ESRF-TEST", - "comments" : "comments", - "storageLocation" : "FRIDGE", - "dewarStatus" : "opened", - "timeStamp" : null, - "isStorageDewar" : null, - "barCode" : "ESRF305861", - "customsValue" : null, - "transportValue" : null, - "trackingNumberToSynchrotron" : "3333", - "trackingNumberFromSynchrotron" : "224466", - "type" : "Dewar", - "sessionVO" : { - "sessionId" : 31697, - "expSessionPk" : null, - "projectCode" : null, - "startDate" : "2012 07 21", - "endDate" : "2012 07 23", - "beamlineName" : "BM29", - "scheduled" : 1, - "nbShifts" : 2, - "comments" : null, - "beamlineOperator" : "PERNOT P", - "usedFlag" : null, - "sessionTitle" : null, - "structureDeterminations" : null, - "dewarTransport" : null, - "databackupFrance" : null, - "databackupEurope" : null, - "visit_number" : null, - "operatorSiteNumber" : "14061", - "timeStamp" : "2012 04 25" - } - } ] - } ], - "macromolecules" : [ { - "macromoleculeId" : 5933, - "safetylevelId" : null, - "proposalId" : 3124, - "name" : "A", - "acronym" : "A", - "molecularMass" : "", - "extintionCoefficient" : "", - "sequence" : null, - "creationDate" : null, - "comments" : "", - "macromoleculeregion3VOs" : [], - "stoichiometry3VOsForHostMacromoleculeId" : [], - "structure3VOs" : [] - } ], - "stockSolutions" : [ { - "stockSolutionId" : 6, - "proposalId" : 3124, - "macromoleculeId" : 5933, - "bufferId" : 811, - "instructionSet3VO" : null, - "boxId" : 305861, - "storageTemperature" : "20", - "volume" : "300", - "concentration" : "1.2", - "comments" : "Buffer EDTA with A", - "name" : "A_EDTA_1.2", - "samples" : [] - } ] } + }); + return this.panel; +}; - }; +/** Populates could be call when the DOM is not filled yet **/ +FitForm.prototype._populate = function() { }; -CaseForm.prototype.test = function(targetId) { - var caseForm = new CaseForm(); - BIOSAXS.proposal = new Proposal(caseForm.input().proposal); - var panel = caseForm.getPanel(caseForm.input().dewar); - panel.render(targetId); +/** It populates the form * */ +FitForm.prototype.refresh = function(subtractions) { + this.subtractions = subtractions; + this.fitGrid.refresh(subtractions); +}; + +FitForm.prototype.input = function() { + return {}; +}; + +/** It populates the form **/ +FitForm.prototype.test = function(targetId) { + var macromoleculeForm = new FitForm(); + var panel = macromoleculeForm.getPanel(); + panel.render(targetId); }; -/** - * Example form - * - * @witdh - * @height - */ -function ExampleForm(args) { - this.id = BUI.id(); - this.width = 700; - this.height = 500; - - if (args != null) { - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; - } - } -} - -ExampleForm.prototype._getItems = function() { - return [{ - fieldLabel : 'First Name', - name : 'first', - allowBlank : false - }, { - fieldLabel : 'Last Name', - name : 'last', - allowBlank : false - } ]; -}; - -ExampleForm.prototype._getItems = function() { - return [ ]; -}; - -ExampleForm.prototype._getButtons = function() { - return [ ]; -}; - -ExampleForm.prototype.getPanel = function() { - this.panel = Ext.create('Ext.form.Panel', { - width : this.width, - height : this.height, - margin : 10, - border : 1, - defaultType : 'textfield', - items : this._getItems(), - buttons : this._getButtons() - }); - return this.panel; -}; - -/** It populates the form **/ -ExampleForm.prototype.refresh = function(macromolecule) { -}; - -function ExperimentForm(args) { +/** + * Example form + * + * @witdh + * @height + */ +function RigidBodyModelingResultForm(args) { this.id = BUI.id(); + this.width = null; + this.height = null; if (args != null) { + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } } - this.onSaved = new Event(this); -} - -ExperimentForm.prototype._getItems = function(experiment) { - this.experiment = experiment; - var typeCombo = Ext.create('Ext.form.ComboBox', { - id : this.id + 'type', - fieldLabel : 'Type', - store : [ "STATIC", "CALIBRATION", "HPLC" ], - queryMode : 'local', - labelWidth : 120, - displayField : 'name', - valueField : 'name', - value : experiment.json.type, - disabled : (experiment.json.type == 'TEMPLATE') + var _this = this; + /** Widgets **/ + this.rigidModelGrid = new RigidModelGrid({ + width : null, + height : 200 }); - var items = []; - - - if (experiment.json.type == "HPLC" ){ - var typeMacromolecule = BIOSAXS_COMBOMANAGER.getComboMacromoleculeByMacromolecules(BIOSAXS.proposal.getMacromolecules(), {labelWidth : 120, width: "120px"}); - if (experiment.getHPLCMacromolecule() != null){ - typeMacromolecule.setValue(experiment.getHPLCMacromolecule().macromoleculeId); - items.push(typeMacromolecule); + this.rigidModelGrid.onSelected.attach(function(sender, fits){ + var ids = []; + for ( var i in fits) { + ids.push(fits[i].fitStructureToExperimentalDataId); } - } - - - items.push(typeCombo, { - id : this.id + 'name', - xtype : 'textfield', - fieldLabel : 'Name', - labelWidth : 120, - width : '100%', - value : experiment.json.name - }, { - id : this.id + 'comments', - xtype : 'textareafield', - name : 'comments', - fieldLabel : 'Comments', - labelWidth : 120, - height : 120, - width : '100%', - value : experiment.json.comments + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data){ +// debugger + + }); + + adapter.getScatteringCurveByFrameIdsList([], [], [], ids); }); - return items; + +} + +RigidBodyModelingResultForm.prototype._getItems = function() { + var _this = this; + return [ { + xtype : 'label', + forId : 'myFieldId', + text : 'INLINE HELP: To be updated', + margin : '15 0 20 10', + cls : "inline-help" + }, this.rigidModelGrid.getPanel() ] + }; -ExperimentForm.prototype.getPanel = function(experiment) { + +RigidBodyModelingResultForm.prototype._getButtons = function() { + return []; +}; + +RigidBodyModelingResultForm.prototype.getPanel = function() { var _this = this; - - this.panel = Ext.createWidget({ - xtype : 'container', - layout : 'vbox', - border : 0, - style : { - padding : '10px' - }, - fieldDefaults : { - labelAlign : 'left', - labelWidth : 50 - }, - items : this._getItems(experiment) + this.panel = Ext.create('Ext.form.Panel', { + width : this.width, + height : this.height, + margin : 10, + border : 1, + defaultType : 'textfield', + items : this._getItems(), + buttons : this._getButtons(), + listeners : { + afterrender : function() { + _this._populate(); + + } + } }); return this.panel; }; -ExperimentForm.prototype.input = function() { - return new ExperimentHeaderForm().input(); +/** Populates could be call when the DOM is not filled yet **/ +RigidBodyModelingResultForm.prototype._populate = function() { }; -ExperimentForm.prototype.test = function(targetId) { - var experimentForm = new ExperimentForm(); - var panel = experimentForm.getPanel(new Experiment(experimentForm.input().experiment)); +/** It populates the form * */ +RigidBodyModelingResultForm.prototype.refresh = function(subtractions) { + this.rigidModelGrid.refresh(subtractions); +}; + +RigidBodyModelingResultForm.prototype.input = function() { + return {}; +}; + +/** It populates the form **/ +RigidBodyModelingResultForm.prototype.test = function(targetId) { + var macromoleculeForm = new RigidBodyModelingResultForm(); + var panel = macromoleculeForm.getPanel(); panel.render(targetId); }; /** - * Shows the header for the experiments changing the color and parameters depending on experiment type + * Example form * + * @witdh + * @height */ -function ExperimentHeaderForm(args) { +function SuperpositionForm(args) { this.id = BUI.id(); - this.backgroundColor = '#FFFFFF'; -} + this.width = null; + this.height = null; -ExperimentHeaderForm.prototype.getHTMLSource = function(experiment) { - var html = BUI.createFormLabel("Name :", experiment.json.name, 75, 400, this.backgroundColor); - if (experiment.json.type == "HPLC") { - if (experiment.getHPLCMacromolecule() != null){ - html = html + BUI.createFormLabel("Molecule :", experiment.getHPLCMacromolecule().acronym, 75, 400, this.backgroundColor); + if (args != null) { + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; } } - else{ - html = html + BUI.createFormLabel("Type :", experiment.json.type, 75, 400, this.backgroundColor); - } - - html = html + BUI.createFormLabel("Date :", experiment.json.creationDate, 75, 400, this.backgroundColor); - return html; -}; -ExperimentHeaderForm.prototype.getHTMLDownload = function(experiment) { - var bgcolor = "background-color:" + this.backgroundColor + ";"; - var html = "
"; - if ((experiment.json.type == "CALIBATION") || (experiment.json.type == "STATIC")) { - html = html + " Download Source File
"; - html = html - + ""; - } - if (experiment.json.type == "TEMPLATE") { - html = html - + " Download Source File
"; - } + var _this = this; - if (experiment.json.type == "HPLC") { - html = html + " Download h5 File
"; - } + /** Widgets **/ + this.superpositionGrid = new SuperpositionGrid({ + width : null, + height : 200 + }); - return html; -}; + this.superpositionGrid.onSelected.attach(function(sender, superpositions) { + var ids = []; + for ( var i in superpositions) { + ids.push(superpositions[i].superpositionId); + } +// _this._renderAbinitio(ids); +// _this.aprioriPDBViewer.refresh(); + _this._renderAligned(ids); + // getAlignedPDBContentBySuperpositionList + }); -ExperimentHeaderForm.prototype.getTopPanel = function(experiment) { - return { - xtype : 'container', - layout : 'hbox', - items : [ { - margin : "0 0 0 0", - width : 475, - border : 0, - html : this.getHTMLSource(experiment) - }, { - margin : "0 0 0 0", - width : 475, - border : 0, - html : this.getHTMLDownload(experiment) - } ] - }; + /** PDB viewer **/ +// this.abinitioPDBViewer = new PDBViewer({ +// width : 860 / 2, +// height : 300 / 2, +// margin : 0 +// }); +// +// /** PDB viewer **/ +// this.aprioriPDBViewer = new StructurePDBViewer({ +// width : 860 / 2, +// height : 300 / 2, +// margin : 0 +// }); + + this.alignedPDBViewer = new AlignedSuperpositionPDBViewer({ + width : 860 , + height : 300 + }); + +} + +SuperpositionForm.prototype._renderAligned = function(modelsIdList) { + /** Trying to plot the PDB file **/ + try { + this.alignedPDBViewer.refresh(modelsIdList); + } catch (e) { + console.log(e); + } }; -ExperimentHeaderForm.prototype.getButton = function(experiment) { - var _this = this; - return Ext.create('Ext.Button', { - text : 'EDIT', - minWidth : '100', - margin : '10 0 0 30', - handler : function() { - var experimentWindow = new ExperimentWindow(); - experimentWindow.onSaved.attach(function(sender, data) { - _this.experiment.json.name = data.name; - _this.experiment.json.type = data.type; - _this.experiment.json.comments = data.comments; - _this.panel.remove(_this.panel.items.items[0]); - _this.panel.remove(_this.panel.items.items[0]); - _this.panel.insert(_this.getTopPanel(_this.experiment)); - _this.panel.insert(_this.getBottomPanel(_this.experiment)); +SuperpositionForm.prototype._renderAbinitio = function(modelsIdList) { + /** Trying to plot the PDB file **/ + try { + var viz = []; + for (var i = 0; i < modelsIdList.length; i++) { + viz.push({ + modelId : modelsIdList[i], + color : "0xFF6600", + opacity : 0.8 }); - experimentWindow.show(experiment); } - }); + this.abinitioPDBViewer.refresh(viz); + } catch (e) { + console.log(e); + } }; -ExperimentHeaderForm.prototype.getBottomPanel = function(experiment) { - return { +SuperpositionForm.prototype._getItems = function() { + var _this = this; + return [ { + xtype : 'label', + forId : 'myFieldId', + text : 'INLINE HELP: To be updated', + margin : '15 0 20 10', + cls : "inline-help" + }, this.superpositionGrid.getPanel(), { xtype : 'container', layout : 'hbox', - margin : '10 0 0 0', - items : [ this.getComments(experiment), this.getButton(experiment) ] - }; + items : [ +// { +// xtype : 'container', +// layout : 'vbox', +// items : [ this.abinitioPDBViewer.getPanel(), this.aprioriPDBViewer.getPanel() +// +// ] +// }, + + this.alignedPDBViewer.getPanel() ] + } ] + }; -ExperimentHeaderForm.prototype.getComments = function(experiment) { - return { - xtype : 'textareafield', - labelStyle : 'font-weight: bold;', - name : 'comments', - fieldLabel : 'Comments', - labelWidth : 70, - height : 40, - minWidth : '450', - readOnly : true, - value : experiment.json.comments - }; +SuperpositionForm.prototype._getButtons = function() { + return []; }; -ExperimentHeaderForm.prototype.getPanel = function(experiment) { - this.experiment = experiment; - - if (experiment.json.type == 'CALIBRATION') { - this.backgroundColor = '#EFFBFB'; - } - if (experiment.json.type == 'TEMPLATE') { - this.backgroundColor = '#E0F8E6'; - } +SuperpositionForm.prototype.getPanel = function() { + var _this = this; + this.panel = Ext.create('Ext.form.Panel', { + width : this.width, + height : this.height, + margin : 10, + border : 1, + defaultType : 'textfield', + items : this._getItems(), + buttons : this._getButtons(), + listeners : { + afterrender : function() { + _this._populate(); - this.panel = Ext.create('Ext.container.Container', { - frame : false, - layout : 'vbox', - padding : 5, - bodyPadding : '5 5 0 0', - width : 890, - margin : '0 0 10 0', - height : 120, - style : { - borderColor : '#99bce8', - borderStyle : 'solid', - borderWidth : '1px', - 'background-color' : this.backgroundColor - }, - fieldDefaults : { - msgTarget : 'side', - labelWidth : 100 - }, - items : [ this.getTopPanel(experiment), this.getBottomPanel(experiment) ] + } + } }); return this.panel; }; -ExperimentHeaderForm.prototype.input = function() { - return { - experiment : DATADOC.getExperiment_10() - }; +/** Populates could be call when the DOM is not filled yet **/ +SuperpositionForm.prototype._populate = function() { }; -ExperimentHeaderForm.prototype.test = function(targetId) { - var experimentHeaderForm = new ExperimentHeaderForm(); - var panel = experimentHeaderForm.getPanel(new Experiment(experimentHeaderForm.input().experiment)); - panel.render(targetId); +/** It populates the form * */ +SuperpositionForm.prototype.refresh = function(subtractions) { + this.subtractions = subtractions; + this.superpositionGrid.refresh(subtractions); +}; + +SuperpositionForm.prototype.input = function() { + return {}; +}; +/** It populates the form **/ +SuperpositionForm.prototype.test = function(targetId) { + var macromoleculeForm = new SuperpositionForm(); + var panel = macromoleculeForm.getPanel(); + panel.render(targetId); }; /** - * Macromolecule form with the general parameters of a macromolecule + * Example form * * @witdh * @height - * - * #onSave button save has been clicked - * #onClose button close has been clicked */ -function MacromoleculeForm(args) { +function AssemblyForm(args) { this.id = BUI.id(); this.width = 700; this.height = 500; @@ -7053,6751 +6059,7745 @@ function MacromoleculeForm(args) { this.height = args.height; } } - - /** Events **/ - this.onSave = new Event(this); - this.onClose = new Event(this); -} -/** Type : is the Ext type then requiredtext or textfield * */ -MacromoleculeForm.prototype._getFieldTextWithHelp = function(type, fieldLabel, fieldName, help) { - return Ext.create('Ext.container.Container', { - margin : "10 0 0 10", - items : [ { - xtype : type, - fieldLabel : fieldLabel, - name : fieldName, - id : this.id + fieldName - }, { - xtype : 'label', - forId : 'myFieldId', - text : help, - margin : "5 0 0 105", - cls : "inline-help" - } ] - }); -}; + this.molarityGrid = new MolarityGrid({height : this.height - 50}); +} -MacromoleculeForm.prototype._getNumericWithHelp = function(type, fieldLabel, fieldName, help) { - return Ext.create('Ext.container.Container', { - margin : "0 0 0 10", - items : [ { - xtype : type, - fieldLabel : fieldLabel, - name : fieldName, - id : this.id + fieldName, - decimalPrecision : 6, - width : 220 - }, { - xtype : 'label', - forId : 'myFieldId', - text : help, - margin : "5 0 0 10", - cls : "inline-help" - } ] - }); +AssemblyForm.prototype._getItems = function() { + return [ { + xtype : 'label', + forId : 'myFieldId', + text : 'List of previously defined macromolecules present in the assembly. This information will be used for additional cross-checks where possible', + margin : '15 0 20 10', + cls : "inline-help" + }, this.molarityGrid.getPanel() ]; }; -MacromoleculeForm.prototype._getButtons = function() { - var _this = this; - return [ { - text : 'Save', - handler : function() { - _this._save(); - } - },{ - text : 'Close', - handler : function() { - _this.onClose.notify(); - - } - } ]; +AssemblyForm.prototype._getButtons = function() { + return []; }; -/** It persits the macromolecule in the database **/ -MacromoleculeForm.prototype._persist = function(macromoleculeId, acronym, name, molecularMass, extintionCoefficient, comments, refractiveIndex, solventViscosity) { - - /** Checking not duplicated acronym **/ - if (((macromoleculeId == null) && (BIOSAXS.proposal.getMacromoleculeByAcronym(acronym) != null))== true){ - BUI.showError("Duplicated acronym"); - return; - } - - - if (macromoleculeId == null){ - /** new macromolecule **/ - this.macromolecule = {}; - this.macromolecule.macromoleculeId = null; - } - else{ - this.macromolecule.macromoleculeId = macromoleculeId; - } - - this.macromolecule["acronym"] = acronym; - this.macromolecule["name"] = name; - this.macromolecule["molecularMass"] = molecularMass; - this.macromolecule["extintionCoefficient"] = extintionCoefficient; - this.macromolecule["comments"] = comments; - this.macromolecule["symmetry"] = Ext.getCmp(this.id + 'comboSym').getValue(); - this.macromolecule["refractiveIndex"] = refractiveIndex; - this.macromolecule["solventViscosity"] = solventViscosity; - - var _this = this; - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, proposal) { - /** Updating the proposal global object **/ - BIOSAXS.proposal.setItems(proposal); - _this.panel.setLoading(false); - - var saved = BIOSAXS.proposal.getMacromoleculeByAcronym(acronym); - /** Refreshing to check that everything is ok **/ - _this.refresh(saved); - _this.onSave.notify(saved); +AssemblyForm.prototype.getPanel = function() { + this.panel = Ext.create('Ext.form.Panel', { + width : this.width, + height : this.height, + margin : 10, + border : 0, + defaultType : 'textfield', + items : this._getItems(), + buttons : this._getButtons() }); - - this.panel.setLoading("Saving Macromolecule") - adapter.saveMacromolecule(this.macromolecule); + return this.panel; }; -/** Save the macromolecule in the DB **/ -MacromoleculeForm.prototype._save = function() { - - var _this = this; - - var acronym = this._getField("acronym"); - var name = this._getField("name"); - var molecularMass = this._getField("molecularMass"); - var extintionCoefficient = this._getField("extintionCoefficient"); - var comments = this._getField("comments"); - - var refractiveIndex = this._getField("refractiveIndex"); - var solventViscosity = this._getField("solventViscosity"); - - /** Checking required fields **/ - if (name == "") { - BUI.showError("Name field is mandatory"); - return; - } - if (acronym == "") { - BUI.showError("Acroynm field is mandatory"); - return; - } - if (this.macromolecule != null){ - /** Checking if it is a new macromolecule **/ - if (this.macromolecule.macromoleculeId == null){ - /** Check if the acronym exists already **/ - this._persist(null, acronym, name, molecularMass, extintionCoefficient, comments, refractiveIndex, solventViscosity); - } - else{ - /** It is an update **/ - this._persist(this.macromolecule.macromoleculeId, acronym, name, molecularMass, extintionCoefficient, comments, refractiveIndex, solventViscosity); - } - } - else{ - /** It is a new macromolecule **/ - this._persist(null, acronym, name, molecularMass, extintionCoefficient, comments, refractiveIndex, solventViscosity); - } +/** It populates the form **/ +AssemblyForm.prototype.refresh = function(macromolecule) { + this.macromolecule = macromolecule; + this.molarityGrid.refresh(macromolecule); }; +AssemblyForm.prototype.input = function() { + return {}; +}; -MacromoleculeForm.prototype._getItems = function() { +AssemblyForm.prototype.test = function(targetId) { + var assemblyForm = new AssemblyForm(); + + var panel = assemblyForm.getPanel(); + panel.render(targetId); +}; +/** + * Edit the information of a buffer + * + * #onSaved + * #onRemoveAdditive + */ +function BufferForm() { var _this = this; - /** Symmetry combo box **/ - var symmetry = Ext.create('Ext.data.Store', { - fields : [ 's' ], - data : this._getSymmetries() - }); - this.symmetryComboBox = Ext.create('Ext.form.ComboBox', { - fieldLabel : 'Symmetry', - store : symmetry, - id : this.id + 'comboSym', - queryMode : 'local', - displayField : 's', - valueField : 's', - value : "P1", - margin : "0 0 0 30", - width : 220 + this.additiveGrid = new AdditiveGrid(); + this.additiveGrid.onRemoveButtonClicked.attach(function(sender, args) { + _this.onRemoveAdditive.notify(args); }); - - return [this._getFieldTextWithHelp("requiredtext", "Name", "name", "Long name. i.e: Bovine serum albumin"), - this._getFieldTextWithHelp("requiredtext", "Acronym", "acronym", "Acronym will be used in the files and analisys. i.e: BSA"), - this._getFieldTextWithHelp("textfield", "Mol. Mass (Da)", "molecularMass", "Atomic mass estimation measured in Da"), - { - xtype : 'container', - layout : 'hbox', - margin : "10 0 0 0", - items :[ - this._getNumericWithHelp("numberfield", "Extinction coef.", "extintionCoefficient", ""), - this.symmetryComboBox - ] - }, - { - xtype : 'container', - layout : 'hbox', - margin : "5 0 0 0", - items :[ - this._getNumericWithHelp("numberfield", "Refractive Index", "refractiveIndex", "How radiation propagates through the medium"), - this._getNumericWithHelp("numberfield", "Solvent Viscosity", "solventViscosity", "") - ] - }, - { - id : this.id + "comments", - xtype : 'textareafield', - name : 'comments', - margin : '35 0 0 10', - fieldLabel : 'Comments', - width : this.width - 100 - } ]; + + this.onSaved = new Event(this); + this.onRemoveAdditive = new Event(this); +} + +BufferForm.prototype.getBuffer = function() { + this.buffer.name = Ext.getCmp("buffer_name").getValue(); + this.buffer.acronym = Ext.getCmp("buffer_acronym").getValue(); + this.buffer.comments = Ext.getCmp("buffer_comments").getValue(); + this.buffer.ph = Ext.getCmp("buffer_ph").getValue(); + this.buffer.composition = Ext.getCmp("buffer_composition").getValue(); + this.buffer.bufferhasadditive3VOs = this.additiveGrid.getAdditives(); + return this.buffer; }; -MacromoleculeForm.prototype._getSymmetries = function() { - return [ { - "s" : "P1" - }, { - "s" : "P2" - }, { - "s" : "P3" - }, { - "s" : "P4" - }, { - "s" : "P5" - }, { - "s" : "P6" - }, { - "s" : "P32" - }, { - "s" : "P42" - }, { - "s" : "P52" - }, { - "s" : "P62" - }, { - "s" : "P222" - } ] +BufferForm.prototype._getTopPanel = function() { + return { + xtype : 'container', + layout : 'hbox', + border : 0, + frame : true, + items : [ { + xtype : 'container', + layout : 'hbox', + items : [ { + xtype : 'container', + flex : 1, + border : false, + layout : 'anchor', + defaultType : 'textfield', + items : [ { + xtype : 'requiredtext', + id : 'buffer_name', + fieldLabel : 'Name', + name : 'name', + width : '200px', + value : this.buffer.name + }, { + xtype : 'requiredtext', + id : 'buffer_acronym', + fieldLabel : 'Acronym', + name : 'acronym', + width : '200px', + value : this.buffer.acronym + } ] + } ] + }, { + xtype : 'container', + flex : 1, + layout : 'anchor', + defaultType : 'textfield', + margin : '0 0 0 10', + items : [ { + id : 'buffer_ph', + fieldLabel : 'pH', + name : 'ph', + value : this.buffer.ph, + xtype : 'numberfield', + width : 200, + minValue : 0, + maxValue : 15 + }, { + xtype : 'requiredtext', + id : 'buffer_composition', + fieldLabel : 'Composition', + name : 'composition', + width : 200, + value : this.buffer.composition + } ] + } ] + }; }; -MacromoleculeForm.prototype.getPanel = function() { - this.panel = Ext.create('Ext.form.Panel', { - width : this.width, - height : this.height, - margin : 10, - border : 1, - defaultType : 'textfield', - items : this._getItems(), - buttons : this._getButtons() +BufferForm.prototype.getPanel = function(buffer) { + this.buffer = buffer; + this.panel = Ext.createWidget({ + xtype : 'container', + layout : 'vbox', + style : { + padding : '10px' + }, + fieldDefaults : { + labelAlign : 'left', + labelWidth : 50 + + }, + items : [ this._getTopPanel(), { + id : 'buffer_comments', + xtype : 'textareafield', + name : 'comments', + fieldLabel : 'Comments', + width : '100%', + value : buffer.comments + }, this.additiveGrid.getPanel(buffer) ] }); return this.panel; }; - -/** Populates each text field by field name and value **/ -MacromoleculeForm.prototype._populateField = function(fieldName, value) { - if (value != null){ - Ext.getCmp(this.id + fieldName).setValue(value); - } +BufferForm.prototype.input = function() { + return { + buffer : { + "bufferId" : 422, + "proposalId" : 10, + "safetyLevelId" : null, + "name" : "B1", + "acronym" : "B1", + "ph" : null, + "composition" : null, + "bufferhasadditive3VOs" : [], + "comments" : null + } + }; }; -/** Gets the value of a textfield **/ -MacromoleculeForm.prototype._getField = function(fieldName) { - return Ext.getCmp(this.id + fieldName).getValue(); +BufferForm.prototype.test = function(targetId) { + var bufferForm = new BufferForm(); + var panel = bufferForm.getPanel(bufferForm.input().buffer); + panel.render(targetId); }; - - -/** It populates the form **/ -MacromoleculeForm.prototype.refresh = function(macromolecule) { - this.macromolecule = macromolecule; - if (macromolecule != null){ - this._populateField("name", macromolecule.name); - this._populateField("acronym", macromolecule.acronym); - this._populateField("extintionCoefficient", macromolecule.extintionCoefficient); - this._populateField("molecularMass", macromolecule.molecularMass); - this._populateField("comments", macromolecule.comments); - this._populateField("refractiveIndex", macromolecule.refractiveIndex); - this._populateField("solventViscosity", macromolecule.solventViscosity); - if (macromolecule.symmetry != null){ - Ext.getCmp(this.id + 'comboSym').setValue(macromolecule.symmetry); + +/** + * @showTitle + * + * #onSaved + * #onAddPlates + * #onRemovePlates + **/ +function CaseForm(args) { + this.width = 700; + this.showTitle = true; + if (args != null) { + if (args.showTitle != null) { + this.showTitle = args.showTitle; } } -}; - -MacromoleculeForm.prototype.input = function() { - return {}; -}; - - -/** It populates the form **/ -MacromoleculeForm.prototype.test = function(targetId) { - var macromoleculeForm = new MacromoleculeForm(); - macromoleculeForm.onClose.attach(function(sender){ - alert("Click on close"); + var _this = this; + this.stockSolutionGrid = new StockSolutionGrid({ + width : this.width - 10, + minHeight : 300, + height : 300, + tbar : true, + showTitle : true, + isPackedVisible : false, + btnAddExisting : true, + btnRemoveVisible : false, + btnUnpackVisible : true }); - var panel = macromoleculeForm.getPanel(); - panel.render(targetId); -}; + /** When selecting existing stock solutions **/ + this.stockSolutionGrid.onStockSolutionSelected.attach(function(sender, stockSolutions) { + if (stockSolutions != null) { + for ( var i = 0; i < stockSolutions.length; i++) { + _this.saveStockSolution(stockSolutions[i]); + } + } + }); - + /** it can be because it has been added a new one or removed **/ + this.stockSolutionGrid.onProposalChanged.attach(function(sender, stockSolution) { + if (stockSolution != null) { + _this.saveStockSolution(stockSolution); + } else { + BIOSAXS.proposal.onInitialized.attach(function() { + _this.stockSolutionGrid.refresh(BIOSAXS.proposal.getStockSolutionsByDewarId(_this.dewar.dewarId)); + _this.stockSolutionGrid.grid.setLoading(false); + }); + BIOSAXS.proposal.init(); -function ModelVisualizerForm(args){ - this.id =BUI.id(); - this.width = 600; - this.height = 400; - if (args!= null){ - if (args.width != null){ - this.width = args.width; - } - if (args.height != null){ - this.height = args.height; } - } -}; -ModelVisualizerForm.prototype._getFirHTML = function(modelId, width, height, type, desc) { - var html = ""; - html = html + ''; - html = html + ''; - html = html + ''; - html = html + '
dammin.' + type + '
' + desc + '
'; - return html; -}; - -ModelVisualizerForm.prototype.getItems = function(modelPanel){ - _this = this; - var height = _this.height/2 - 60; - var width = _this.width/2 - 10; - - return Ext.create('Ext.container.Container', { - layout: { - type: 'vbox', // Arrange child items vertically - }, - items: [ - modelPanel, - { - xtype : 'container', - layout: { - type: 'hbox', // Arrange child items vertically - }, - items : [{ - html : this._getFirHTML("id", width, height, "fir", "Fit of the simulated scattering curve versus a smoothed experimental data (spline interpolation)"), - height :height, - width : width, - padding: 2 - }, - { - html : this._getFirHTML("id", width, height, "fit", "Fit of the simulated scattering curve versus the experimental data."), - height : height, - width : width, - padding: 2 - }] - } - - ] }); -}; -ModelVisualizerForm.prototype.refresh = function(models){ - var input = []; -// var colors = ["008000", "F0A804", "0000FF", "800080", "C0C0C0"]; - for (var i = 0; i < models.length; i++) { - console.log(BUI.rainbow(models.length, i).replace("#", "0x")); - input.push({ - color: BUI.rainbow(models.length, i).replace("#", "0x"), - modelId: models[i].modelId, - opacity: 0.8, - radius: 3, - title: BUI.getFileNameByPath(models[i].pdbFile), - type: "SHAPEDETERMINATIONMODEL" - - }); - } - - this.panel.removeAll(); - this.panel.add( - _this.getItems( - new PDBViewer({ - width : this.width - 10, - height : (this.height/2) - 10, - title : "" - }).draw(input) - ) - ); - + this.onSaved = new Event(this); + this.onAddPlates = new Event(this); + this.onRemovePlates = new Event(this); +} + +CaseForm.prototype.saveStockSolution = function(stockSolution) { + var _this = this; var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - var splitted = data.toString().split("\n"); - var array = []; - for ( var i = 0; i < splitted.length; i++) { - var line = splitted[i].trim(); - var line_splited = line.split(/\s*[\s,]\s*/); - if (line_splited.length == 4) { - array.push([ Number(line_splited[0]), BUI.getStvArray(line_splited[1], line_splited[2]), BUI.getStvArray(line_splited[3], 0) ]); - } - } - - var id = (_this.id + "firid"); - var dygraphWidget = new StdDevDyGraph(id, { - width : (_this.width/2) - 10, - height :(_this.height/2) -110, - xlabel : 'q(nm-1)' + this.stockSolutionGrid.grid.setLoading("ISPyB: setting case to Stock solution"); + adapter.onSuccess.attach(function(sender, stockSolution) { + BIOSAXS.proposal.onInitialized.attach(function() { + _this.stockSolutionGrid.refresh(BIOSAXS.proposal.getStockSolutionsByDewarId(_this.dewar.dewarId)); + _this.stockSolutionGrid.grid.setLoading(false); }); - dygraphWidget.draw(array, [ "#FF0000", "#0000FF", "#FF00FF" ], [ 's', 'I(exp)', 'I(sim)' ]); + BIOSAXS.proposal.init(); }); - - adapter.getModelFile("FIR", models[0].modelId); - - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - var splitted = data.toString().split("\n"); - var array = []; - for ( var i = 0; i < splitted.length; i++) { - var line = splitted[i].trim(); - var line_splited = line.split(/\s*[\s,]\s*/); - if (line_splited.length == 3) { - array.push([ Number(line_splited[0]), BUI.getStvArray(line_splited[1], 0), BUI.getStvArray(line_splited[2], 0) ]); - } - } - - var id = (_this.id + "fitid"); - - var dygraphWidget = new StdDevDyGraph(id, { - width : (_this.width/2) - 10, - height : (_this.height/2) - 110, - xlabel : 'q(nm-1)' - }); - dygraphWidget.draw(array, [ "#FF0000", "#0000FF" ], [ "s", "I(exp)", "I(sim)" ]); + adapter.onError.attach(function(sender, data) { + _this.stockSolutionGrid.grid.setLoading(false); + BUI.showError(data); }); - adapter.getModelFile("FIT", models[0].modelId); + stockSolution.boxId = _this.dewar.dewarId; + adapter.saveStockSolution(stockSolution); }; -ModelVisualizerForm.prototype.getPanel = function(modelList){ - _this = this; - this.modelList = modelList; - this.panel = Ext.create('Ext.Panel', { - title: 'Results', - width: this.width, - height: this.height, - layout: { - type: 'vbox', // Arrange child items vertically -// align: 'stretch' // Each takes up full width - }, - items: [ - - ], - listeners : { - afterrender : function(grid, eOpts) { -// alert(_this.modelList) - } - } +CaseForm.prototype.fillStores = function() { + var _this = this; + this.panel.setLoading("Loading Labcontacts from database"); + + var proposal = BUI.getProposal(); + proposal.onDataRetrieved.attach(function(sender, data) { + _this.labContactForSendingStore.loadData(data, false); + _this.labContactForReturnStore.loadData(data, false); + _this.panel.setLoading(false); }); - - return this.panel; + proposal.getLabContactsByProposalId(); }; +CaseForm.prototype.refresh = function(dewar) { + this.setDewar(dewar); + this.stockSolutionGrid.refresh(BIOSAXS.proposal.getStockSolutionsByDewarId(dewar.dewarId)); +}; + +CaseForm.prototype.getDewar = function() { + this.dewar.code = Ext.getCmp("dewar_code").getValue(); + this.dewar.comments = Ext.getCmp("dewar_comments").getValue(); + this.dewar.trackingNumberFromSynchrotron = Ext.getCmp("dewar_trackingNumberFromSynchrotron").getValue(); + this.dewar.trackingNumberToSynchrotron = Ext.getCmp("dewar_trackingNumberToSynchrotron").getValue(); + this.dewar.transportValue = Ext.getCmp("dewar_transportValue").getValue(); + this.dewar.storageLocation = Ext.getCmp("dewar_storageLocation").getValue(); + this.dewar.firstExperimentId = this.macromoleculeCombo.getValue(); + return this.dewar; +}; + +CaseForm.prototype.setDewar = function(dewar) { + this.dewar = dewar; + Ext.getCmp("dewar_code").setValue(this.dewar.code); + Ext.getCmp("dewar_dewarStatus").setText(new String(this.dewar.dewarStatus).toUpperCase()); + Ext.getCmp("dewar_comments").setValue(this.dewar.comments); + Ext.getCmp("dewar_trackingNumberFromSynchrotron").setValue(this.dewar.trackingNumberFromSynchrotron); + Ext.getCmp("dewar_trackingNumberToSynchrotron").setValue(this.dewar.trackingNumberToSynchrotron); + Ext.getCmp("dewar_transportValue").setValue(this.dewar.transportValue); + Ext.getCmp("dewar_storageLocation").setValue(this.dewar.storageLocation); + if (dewar.sessionVO != null) { + this.macromoleculeCombo.setValue(dewar.sessionVO.sessionId); + } +}; + +CaseForm.prototype.getSessionCombo = function() { + this.macromoleculeCombo = BIOSAXS_COMBOMANAGER.getComboSessions(BIOSAXS.proposal.getSessions(), { + labelWidth : 100, + margin : '5 0 00 0', + width : 250 + }); + return this.macromoleculeCombo; +}; + +CaseForm.prototype.getInformationPanel = function() { + if (this.panel == null) { + this.informationPanel = Ext.create('Ext.form.Panel', { + width : this.width - 10, + border : 0, + items : [ { + xtype : 'container', + margin : "2 2 2 2", + collapsible : false, + defaultType : 'textfield', + layout : 'anchor', + items : [ { + xtype : 'container', + layout : 'hbox', + items : [ { + xtype : 'requiredtext', + fieldLabel : 'Code', + allowBlank : false, + name : 'code', + id : 'dewar_code', + anchor : '50%' + }, { + xtype : 'label', + margin : '0 0 0 20', + readOnly : true, + id : 'dewar_dewarStatus', + anchor : '50%' + } ] + }, this.getSessionCombo(), { + margin : '5 0 0 0', + xtype : 'textareafield', + name : 'comments', + id : 'dewar_comments', + width : this.width - 50, + fieldLabel : 'Comments' + } ] + }, { + xtype : 'fieldset', + title : 'Courier Accounts Details for Return', + collapsible : false, + layout : 'anchor', + defaults : { + anchor : '100%' + }, + items : [ { + xtype : 'container', + layout : 'hbox', + items : [ { + xtype : 'textfield', + labelWidth : 200, + width : 280, + fieldLabel : 'Track Number From Synchrotron', + id : 'dewar_trackingNumberFromSynchrotron' + }, { + xtype : 'numberfield', + width : 190, + labelWidth : 110, + margin : '0 0 0 30', + fieldLabel : 'Transport Value', + id : 'dewar_transportValue' + } + + ] + }, { + xtype : 'container', + layout : 'hbox', + margin : '10 0 0 0', + items : [ + + { + xtype : 'textfield', + labelWidth : 200, + width : 280, + fieldLabel : 'Track Number To Synchrotron', + id : 'dewar_trackingNumberToSynchrotron' + }, { + xtype : 'textfield', + margin : '0 0 0 30', + width : 190, + labelWidth : 110, + fieldLabel : 'Storage Location', + id : 'dewar_storageLocation' + } + + ] + } ] + } ] + }); + } + + return this.informationPanel; +}; + +CaseForm.prototype.getPanel = function(dewar) { + this.dewar = dewar; + this.panel = Ext.createWidget({ + xtype : 'container', + layout : 'vbox', + width : this.width, + border : 0, + items : [ { + items : { + xtype : "container", + layout : "vbox", + margin : "5 5 5 5", + items : [ this.getInformationPanel(dewar), this.stockSolutionGrid.getPanel() ] + + } + } ] + }); + + this.refresh(dewar); + return this.panel; + +}; + +CaseForm.prototype.input = function() { + return { + dewar : { + "dewarId" : 305861, + "code" : "ESRF-TEST", + "comments" : "comments", + "storageLocation" : "FRIDGE", + "dewarStatus" : "opened", + "timeStamp" : null, + "isStorageDewar" : null, + "barCode" : "ESRF305861", + "customsValue" : null, + "transportValue" : null, + "trackingNumberToSynchrotron" : "3333", + "trackingNumberFromSynchrotron" : "224466", + "type" : "Dewar", + "sessionVO" : { + "sessionId" : 31697, + "expSessionPk" : null, + "projectCode" : null, + "startDate" : "2012 07 21", + "endDate" : "2012 07 23", + "beamlineName" : "BM29", + "scheduled" : 1, + "nbShifts" : 2, + "comments" : null, + "beamlineOperator" : "PERNOT P", + "usedFlag" : null, + "sessionTitle" : null, + "structureDeterminations" : null, + "dewarTransport" : null, + "databackupFrance" : null, + "databackupEurope" : null, + "visit_number" : null, + "operatorSiteNumber" : "14061", + "timeStamp" : "2012 04 25" + } + }, + proposal : { + "assemblies" : [], + "sessions" : [ { + "sessionId" : 31697, + "expSessionPk" : null, + "projectCode" : null, + "startDate" : "2012 07 21", + "endDate" : "2012 07 23", + "beamlineName" : "BM29", + "scheduled" : 1, + "nbShifts" : 2, + "comments" : null, + "beamlineOperator" : "PERNOT P", + "usedFlag" : null, + "sessionTitle" : null, + "structureDeterminations" : null, + "dewarTransport" : null, + "databackupFrance" : null, + "databackupEurope" : null, + "visit_number" : null, + "operatorSiteNumber" : "14061", + "timeStamp" : "2012 04 25" + } ], + "labcontacts" : [ { + "labContactId" : 787, + "personVO" : { + "personId" : 304252, + "personUUID" : null, + "familyName" : "KIM", + "givenName" : "Henry", + "title" : null, + "emailAddress" : "henry-sung.kim@ibs.fr", + "phoneNumber" : "", + "login" : "", + "passwd" : "", + "faxNumber" : "" + }, + "cardName" : "KIM-Institut de Bio", + "defaultCourrierCompany" : "22", + "courierAccount" : "", + "billingReference" : "", + "dewarAvgCustomsValue" : 0, + "dewarAvgTransportValue" : 0 + } ], + "buffers" : [ { + "bufferId" : 811, + "proposalId" : 3124, + "safetyLevelId" : null, + "name" : "EDTA", + "acronym" : "EDTA", + "ph" : null, + "composition" : "", + "bufferhasadditive3VOs" : [], + "comments" : "" + }, { + "bufferId" : 810, + "proposalId" : 3124, + "safetyLevelId" : null, + "name" : "HEPES", + "acronym" : "HEPES", + "ph" : null, + "composition" : "", + "bufferhasadditive3VOs" : [], + "comments" : "" + } ], + "shippings" : [ { + "shippingId" : 304107, + "shippingName" : "TEST", + "deliveryAgentAgentName" : null, + "deliveryAgentShippingDate" : null, + "deliveryAgentDeliveryDate" : null, + "deliveryAgentAgentCode" : null, + "deliveryAgentFlightCode" : null, + "shippingStatus" : "opened", + "timeStamp" : "2013 09 25", + "laboratoryId" : null, + "isStorageShipping" : null, + "creationDate" : "2013 09 25", + "comments" : "test", + "sendingLabContactVO" : { + "labContactId" : 787, + "personVO" : { + "personId" : 304252, + "personUUID" : null, + "familyName" : "KIM", + "givenName" : "Henry", + "title" : null, + "emailAddress" : "henry-sung.kim@ibs.fr", + "phoneNumber" : "", + "login" : "", + "passwd" : "", + "faxNumber" : "" + }, + "cardName" : "KIM-Institut de Bio", + "defaultCourrierCompany" : "22", + "courierAccount" : "", + "billingReference" : "", + "dewarAvgCustomsValue" : 0, + "dewarAvgTransportValue" : 0 + }, + "returnLabContactVO" : { + "labContactId" : 787, + "personVO" : { + "personId" : 304252, + "personUUID" : null, + "familyName" : "KIM", + "givenName" : "Henry", + "title" : null, + "emailAddress" : "henry-sung.kim@ibs.fr", + "phoneNumber" : "", + "login" : "", + "passwd" : "", + "faxNumber" : "" + }, + "cardName" : "KIM-Institut de Bio", + "defaultCourrierCompany" : "22", + "courierAccount" : "", + "billingReference" : "", + "dewarAvgCustomsValue" : 0, + "dewarAvgTransportValue" : 0 + }, + "returnCourier" : null, + "dateOfShippingToUser" : null, + "shippingType" : "DewarTracking", + "dewarVOs" : [ { + "dewarId" : 305861, + "code" : "ESRF-TEST", + "comments" : "comments", + "storageLocation" : "FRIDGE", + "dewarStatus" : "opened", + "timeStamp" : null, + "isStorageDewar" : null, + "barCode" : "ESRF305861", + "customsValue" : null, + "transportValue" : null, + "trackingNumberToSynchrotron" : "3333", + "trackingNumberFromSynchrotron" : "224466", + "type" : "Dewar", + "sessionVO" : { + "sessionId" : 31697, + "expSessionPk" : null, + "projectCode" : null, + "startDate" : "2012 07 21", + "endDate" : "2012 07 23", + "beamlineName" : "BM29", + "scheduled" : 1, + "nbShifts" : 2, + "comments" : null, + "beamlineOperator" : "PERNOT P", + "usedFlag" : null, + "sessionTitle" : null, + "structureDeterminations" : null, + "dewarTransport" : null, + "databackupFrance" : null, + "databackupEurope" : null, + "visit_number" : null, + "operatorSiteNumber" : "14061", + "timeStamp" : "2012 04 25" + } + } ] + } ], + "macromolecules" : [ { + "macromoleculeId" : 5933, + "safetylevelId" : null, + "proposalId" : 3124, + "name" : "A", + "acronym" : "A", + "molecularMass" : "", + "extintionCoefficient" : "", + "sequence" : null, + "creationDate" : null, + "comments" : "", + "macromoleculeregion3VOs" : [], + "stoichiometry3VOsForHostMacromoleculeId" : [], + "structure3VOs" : [] + } ], + "stockSolutions" : [ { + "stockSolutionId" : 6, + "proposalId" : 3124, + "macromoleculeId" : 5933, + "bufferId" : 811, + "instructionSet3VO" : null, + "boxId" : 305861, + "storageTemperature" : "20", + "volume" : "300", + "concentration" : "1.2", + "comments" : "Buffer EDTA with A", + "name" : "A_EDTA_1.2", + "samples" : [] + } ] + } + + }; +}; + +CaseForm.prototype.test = function(targetId) { + var caseForm = new CaseForm(); + BIOSAXS.proposal = new Proposal(caseForm.input().proposal); + var panel = caseForm.getPanel(caseForm.input().dewar); + panel.render(targetId); +}; -/** - * Example form - * - * @witdh - * @height - */ -function MolarityForm(args) { - this.id = BUI.id(); - this.width = 700; - this.height = 500; - - if (args != null) { - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; - } - } - - this.onSave = new Event(this); - this.onClose = new Event(this); -} - - -MolarityForm.prototype._getNumericWithHelp = function(type, fieldLabel, fieldName, help) { - return Ext.create('Ext.container.Container', { - margin : "10 0 0 10", - items : [ { - xtype : type, - fieldLabel : fieldLabel, - name : fieldName, - id : this.id + fieldName, - decimalPrecision : 6 - }, { - xtype : 'label', - forId : 'myFieldId', - text : help, - margin : "5 0 0 105", - cls : "inline-help" - } ] - }); -}; - - -MolarityForm.prototype._getItems = function() { - this.macromoleculeCombo = BIOSAXS_COMBOMANAGER.getComboMacromoleculeByMacromolecules(this.getMacromuleculesCandidates(this.macromolecule), { - width : 250, - labelWidth : 100, - margin : 10 - }); - - return [ { - xtype : 'container', - flex : 1, - margin : '10 0 0 10', - border : 0, - layout : 'anchor', - defaultType : 'requiredtext', - items : [ this.macromoleculeCombo, - this._getNumericWithHelp("textfield", "Ratio", "ratio", "Number in assymmetric units") - ] - } ]; -}; - -MolarityForm.prototype._persist = function() { - var _this = this; - var macromoleculeId = this.macromoleculeCombo.getValue(); - var ratio = Ext.getCmp(this.id + "ratio").getValue(); - var comments = "Not used yet"; - var dataAdapter = new BiosaxsDataAdapter(); - this.panel.setLoading("Saving"); - dataAdapter.onSuccess.attach(function(sender, args) { - _this.onSave.notify(); - }); - dataAdapter.saveStoichiometry(this.macromolecule.macromoleculeId, macromoleculeId, ratio, comments); -}; - -MolarityForm.prototype._getButtons = function() { - var _this = this; - - function onClose() { - _this.onClose.notify(); - } - - return [ { - text : 'Save', - handler : function() { - _this._persist(); - } - }, { - text : 'Cancel', - handler : function() { - onClose(); - } - } ]; -}; - -MolarityForm.prototype.getPanel = function() { - this.panel = Ext.create('Ext.form.Panel', { -// width : null, - height : this.height, - margin : 2, - border : 1, - defaultType : 'requiredtext', - items : this._getItems(), - buttons : this._getButtons() - }); - return this.panel; -}; - -/** macromolecules contains all macromolecules except this one **/ -MolarityForm.prototype.getMacromuleculesCandidates = function(macromolecule) { - var macromolecules = []; - if ( BIOSAXS.proposal.macromolecules){ - for (var i = 0; i < BIOSAXS.proposal.macromolecules.length; i++) { - var m = BIOSAXS.proposal.macromolecules[i]; - if (this.macromolecule != null){ - if (m.macromoleculeId != this.macromolecule.macromoleculeId) { - macromolecules.push(m); - } - } - } - } - return macromolecules; -}; - - -/** It populates the form **/ -MolarityForm.prototype.refresh = function(macromolecule) { - this.macromolecule = macromolecule; - -}; - - -MolarityForm.prototype.input = function() { - return {}; -}; - - -/** It populates the form **/ -MolarityForm.prototype.test = function(targetId) { - var macromoleculeForm = new MolarityForm(); - var panel = macromoleculeForm.getPanel(); - panel.render(targetId); -}; - -///** -// * -// * @witdh -// * @height -// */ -//function MacromoleculeForm(args) { -// this.id = BUI.id(); -// this.width = 700; -// this.height = 500; -// -// if (args != null) { -// if (args.width != null) { -// this.width = args.width; -// } -// if (args.height != null) { -// this.height = args.height; -// } -// } -// -// this.onClose = new Event(this); -//} -// -//MacromoleculeForm.prototype.getMacromolecule = function() { -// this.macromolecule.name = Ext.getCmp(this.panel.getItemId()).getValues().name; -// this.macromolecule.acronym = Ext.getCmp(this.panel.getItemId()).getValues().acronym; -// this.macromolecule.comments = Ext.getCmp(this.panel.getItemId()).getValues().comments; -// this.macromolecule.extintionCoefficient = Ext.getCmp(this.panel.getItemId()).getValues().extintionCoefficient; -// this.macromolecule.molecularMass = Ext.getCmp(this.panel.getItemId()).getValues().molecularMass; -// return this.macromolecule; -//}; -// -//MacromoleculeForm.prototype.setMacromolecule = function(macromolecule) { -// this.pdbStore.loadData(macromolecule.structure3VOs); -// -//}; -// -//MacromoleculeForm.prototype.getForm = function(macromolecule) { -// this.panel = Ext.createWidget('form', { -// frame : false, -// border : 0, -// padding : 15, -// width : 550, -// height : 350, -// items : [ { -// xtype : 'container', -// layout : 'hbox', -// items : [ { -// xtype : 'container', -// flex : 1, -// border : false, -// layout : 'anchor', -// defaultType : 'requiredtext', -// items : [ { -// fieldLabel : 'Name', -// name : 'name', -// anchor : '95%', -// tooltip : "Name of the macromolecule", -// value : macromolecule.name -// }, { -// fieldLabel : 'Acronym', -// name : 'acronym', -// anchor : '95%', -// value : macromolecule.acronym -// } ] -// }, { -// xtype : 'container', -// flex : 1, -// layout : 'anchor', -// defaultType : 'textfield', -// items : [ { -// xtype : 'numberfield', -// fieldLabel : 'Mol. Mass (Da)', -// name : 'molecularMass', -// value : macromolecule.molecularMass, -// decimalPrecision : 6 -// }, { -// xtype : 'numberfield', -// fieldLabel : 'Extinction coef.', -// name : 'extintionCoefficient', -// value : macromolecule.extintionCoefficient, -// decimalPrecision : 6 -// } ] -// } ] -// }, { -// xtype : 'textareafield', -// name : 'comments', -// fieldLabel : 'Comments', -// value : macromolecule.comments, -// width : this.width - 10 -// }, -// -// { -// html : BUI.getWarningHTML("The macromolecule is unsaved. Save the macromolecule to get access to other tabs"), -// margin : "150 10 10 10", -// id : this.id + "unsavedWarning", -// hidden : !(!macromolecule.macromoleculeId) -// } -// -// ] -// }); -// return this.panel; -//}; -// -//MacromoleculeForm.prototype.save = function() { -// var _this = this; -// -// var adapter = new BiosaxsDataAdapter(); -// adapter.onSuccess.attach(function(sender, proposal) { -// BIOSAXS.proposal.setItems(proposal); -// _this.panel.setLoading(false); -// -// Ext.getCmp(_this.id + "assembly").enable() -// Ext.getCmp(_this.id + "advanced").enable(); -// Ext.getCmp(_this.id + "unsavedWarning").hide(); -// }); -// -// if (this.getMacromolecule().name == "") { -// BUI.showError("Name field is mandatory"); -// return; -// } -// if (this.getMacromolecule().acronym == "") { -// BUI.showError("Acroynm field is mandatory"); -// return; -// } -// -// /** Check if acronym is unique * */ -// if (this.getMacromolecule().macromoleculeId == null) { -// if (BIOSAXS.proposal.getMacromoleculeByAcronym(this.getMacromolecule().acronym) == null) { -// this.panel.setLoading("ISPyB: Saving Macromolecule") -// adapter.saveMacromolecule(this.getMacromolecule()); -// } else { -// alert("There is already an existing macromolecule with the same acronym"); -// -// } -// } else { -// this.panel.setLoading("ISPyB: Saving Macromolecule") -// adapter.saveMacromolecule(this.getMacromolecule()); -// } -// -//}; -// -//MacromoleculeForm.prototype.getPanel = function(macromolecule) { -// var _this = this; -// this.macromolecule = macromolecule; -// return Ext.createWidget('tabpanel', { -// height : this.height, -// margin : 5, -// plain : true, -// style : { -// padding : 5 -// }, -// items : [ { -// tabConfig : { -// title : "General", -// disabled : false -// }, -// items : [ this.getForm(macromolecule) ], -// bbar : [ "->", { -// text : 'Save', -// cls : 'btn-with-border', -// style : { -// -// border : 1 -// }, -// handler : function() { -// _this.save(); -// } -// }, { -// text : 'Close', -// cls : 'btn-with-border', -// handler : function() { -// _this.onClose.notify(); -// } -// } ] -// }, { -// tabConfig : { -// id : this.id + "assembly", -// title : "Assembly", -// tooltip : 'Description of subunits present in the macromolecule', -// // hidden : (!macromolecule.macromoleculeId), -// disabled : (!macromolecule.macromoleculeId) -// }, -// items : [ this.getMolarityGrid(macromolecule) ] -// }, { -// tabConfig : { -// id : this.id + "advanced", -// title : "Advanced Modeling", -// // hidden : (!macromolecule.macromoleculeId), -// tooltip : 'Definition of the description contacts and symetries', -// disabled : (!macromolecule.macromoleculeId) -// }, -// items : [ this.getRigidBodyForm(macromolecule) ] -// } ] -// }); -//}; -// -//MacromoleculeForm.prototype.getRigidBodyForm = function(macromolecule) { -// var _this = this; -// -// // [P1, P2, P3, P4 ,P5 ,P6 ,32, P42, P52, P62] + P222 -// var symmetry = Ext.create('Ext.data.Store', { -// fields : [ 's' ], -// data : [ { -// "s" : "P1" -// }, { -// "s" : "P2" -// }, { -// "s" : "P3" -// }, { -// "s" : "P4" -// }, { -// "s" : "P5" -// }, { -// "s" : "P6" -// }, { -// "s" : "P32" -// }, { -// "s" : "P42" -// }, { -// "s" : "P52" -// }, { -// "s" : "P62" -// }, { -// "s" : "P222" -// } ] -// }); -// -// if (macromolecule.symmetry == null) { -// macromolecule.symmetry = "P1"; -// } -// var comboBox = Ext.create('Ext.form.ComboBox', { -// fieldLabel : 'Symmetry', -// store : symmetry, -// id : 'comboSym', -// queryMode : 'local', -// displayField : 's', -// valueField : 's', -// value : macromolecule.symmetry, -// margin : "10 0 0 0", -// listeners : { -// change : function(combo, newValue, oldValue, eOpts) { -// macromolecule.symmetry = newValue; -// } -// } -// }); -// -// this.rigidBodyPanel = Ext.createWidget('form', { -// frame : false, -// border : 0, -// padding : 10, -// width : 550, -// height : 400, -// items : [ { -// xtype : 'container', -// layout : 'hbox', -// items : [ { -// xtype : 'container', -// border : false, -// layout : 'hbox', -// items : [ { -// xtype : 'label', -// forId : 'myFieldId', -// text : 'Contact Desc:', -// width : 105, -// margin : '0 0 0 0' -// }, { -// xtype : 'textfield', -// hideLabel : true, -// id : "contactsDescriptionFilePath", -// margin : '0 0 0 0', -// width : 300, -// value : macromolecule.contactsDescriptionFilePath -// }, { -// text : 'Upload', -// xtype : 'button', -// margin : "0 0 0 20", -// width : 100, -// handler : function() { -// _this._openUploadDialog(macromolecule.macromoleculeId, "CONTACTS", "Upload Contact Description File"); -// } -// } ] -// } ] -// }, -// -// comboBox, { -// xtype : 'checkbox', -// margin : '10 0 0 5', -// boxLabel : "I want rigid body modeling run on this stuff", -// checked : true, -// width : 300 -// }, _this.getPDBGrid(macromolecule) ] -// }); -// return this.rigidBodyPanel; -//}; -// -//MacromoleculeForm.prototype.update = function() { -// var _this = this; -// BIOSAXS.proposal.onInitialized.attach(function() { -// if (BIOSAXS.proposal != null) { -// var macromolecules = BIOSAXS.proposal.macromolecules; -// for (var i = 0; i < macromolecules.length; i++) { -// if (macromolecules[i].macromoleculeId == _this.macromolecule.macromoleculeId) { -// _this.macromolecule = macromolecules[i]; -// _this.setMacromolecule(_this.macromolecule); -// _this.molarityStore.loadData(_this.parseMolarityData(_this.macromolecule)); -// _this.pdbGrid.setLoading(false); -// Ext.getCmp("contactsDescriptionFilePath").setValue(_this.macromolecule.contactsDescriptionFilePath) -// _this.molarityGrid.setLoading(false); -// -// } -// } -// } -// }); -// this.molarityGrid.setLoading("Updating"); -// this.pdbGrid.setLoading("Updating"); -// BIOSAXS.proposal.init(); -//}; -// -///******************************************************************************* -// * MOLARITY GRID -// ******************************************************************************/ -// -//MacromoleculeForm.prototype.parseMolarityData = function(macromolecule) { -// var data = []; -// if (macromolecule.stoichiometry != null) { -// for (var i = 0; i < macromolecule.stoichiometry.length; i++) { -// data.push({ -// ratio : macromolecule.stoichiometry[i].ratio, -// acronym : macromolecule.stoichiometry[i].macromolecule3VO.acronym, -// comments : macromolecule.stoichiometry[i].macromolecule3VO.comments, -// stoichiometryId : macromolecule.stoichiometry[i].stoichiometryId, -// name : macromolecule.stoichiometry[i].macromolecule3VO.name -// }); -// } -// } -// return data; -//}; -// -//MacromoleculeForm.prototype.getMolarityGrid = function(macromolecule) { -// var _this = this; -// -// this.molarityStore = Ext.create('Ext.data.Store', { -// fields : [ 'acronym', 'ratio', 'comments', 'stoichiometryId', 'name' ], -// data : this.parseMolarityData(macromolecule), -// sorters : { -// property : 'ratio', -// direction : 'DESC' -// } -// }); -// -// this.molarityGrid = Ext.create('Ext.grid.Panel', { -// store : this.molarityStore, -// height : 350, -// padding : 5, -// columns : [ -// -// { -// text : 'Subunit', -// columns : [ { -// text : "Acronym", -// width : 100, -// hidden : false, -// dataIndex : 'acronym', -// sortable : true -// }, { -// text : "Name", -// width : 100, -// hidden : false, -// dataIndex : 'name', -// sortable : true -// }, { -// text : "Comments", -// width : 100, -// dataIndex : 'comments', -// sortable : true -// } ] -// }, { -// text : "Number
in assymmetric units", -// width : 150, -// dataIndex : 'ratio', -// tooltip : 'Number of times this subunit is present in the macromolecule', -// sortable : true -// }, { -// id : this.id + 'MOLARITY_REMOVE', -// flex : 0.1, -// sortable : false, -// renderer : function(value, metaData, record, rowIndex, colIndex, store) { -// return BUI.getRedButton('REMOVE'); -// } -// } ], -// listeners : { -// cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { -// if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'MOLARITY_REMOVE') { -// var dataAdapter = new BiosaxsDataAdapter(); -// dataAdapter.onSuccess.attach(function() { -// _this.molarityGrid.setLoading(false); -// _this.update(); -// }); -// dataAdapter.removeStoichiometry(record.data.stoichiometryId); -// _this.molarityGrid.setLoading("Removing Structure"); -// } -// } -// }, -// buttons : [ { -// text : 'Add molarity', -// handler : function() { -// -// function onClose() { -// w.destroy(); -// _this.update(); -// } -// var w = Ext.create('Ext.window.Window', { -// title : 'Molarity', -// height : 300, -// width : 500, -// modal : true, -// buttons : [ { -// text : 'Save', -// handler : function() { -// var macromoleculeId = (_this.macromoleculeCombo.getValue()); -// var ratio = Ext.getCmp(_this.id + "ratio").getValue(); -// var comments = ""; -// var dataAdapter = new BiosaxsDataAdapter(); -// dataAdapter.onSuccess.attach(function(sender, args) { -// _this.update(); -// w.destroy(); -// }); -// dataAdapter.saveStoichiometry(_this.macromolecule.macromoleculeId, macromoleculeId, ratio, comments); -// } -// }, { -// text : 'Cancel', -// handler : function() { -// onClose(); -// } -// } ], -// items : [ _this.getMolarityForm(macromolecule) ], -// listeners : { -// onEsc : function() { -// onClose(); -// }, -// close : function() { -// onClose(); -// } -// } -// }).show(); -// } -// } ] -// }); -// return this.molarityGrid; -//}; -// -///******************************************************************************* -// * PDB GRID -// ******************************************************************************/ -// -//MacromoleculeForm.prototype._openUploadDialog = function(macromoleculeId, type, title) { -// var _this = this; -// function onClose() { -// w.destroy(); -// _this.update(); -// } -// -// var w = Ext.create('Ext.window.Window', { -// title : title, -// height : 200, -// width : 400, -// modal : true, -// buttons : [ { -// text : 'Close', -// handler : function() { -// onClose(); -// } -// } ], -// layout : 'fit', -// items : { -// html : "" -// }, -// listeners : { -// onEsc : function() { -// onClose(); -// }, -// close : function() { -// onClose(); -// } -// } -// }).show(); -//}; -// -//MacromoleculeForm.prototype._getPlugins = function() { -// var _this = this; -// var plugins = []; -// // if (this.updateRowEnabled) { -// plugins.push(Ext.create('Ext.grid.plugin.RowEditing', { -// clicksToEdit : 1, -// listeners : { -// validateedit : function(grid, e) { -// /** Comments are always updatable* */ -// e.record.raw.symmetry = e.newValues.symmetry; -// e.record.raw.multiplicity = e.newValues.multiplicity; -// -// var adapter = new BiosaxsDataAdapter(); -// adapter.onSuccess.attach(function(sender, measurement) { -// // _this.grid.setLoading(false); -// }); -// adapter.onError.attach(function() { -// alert("Error"); -// // _this.grid.setLoading(false); -// }); -// -// // _this.grid.setLoading(); -// adapter.saveStructure(e.record.raw); -// } -// } -// })); -// // } -// return plugins; -//}; -// -//MacromoleculeForm.prototype.getPDBGrid = function(macromolecule) { -// var _this = this; -// -// var data = macromolecule.structure3VOs; -// -// // /** Getting PDB from subunits **/ -// // if (macromolecule != null){ -// // if (macromolecule.stoichiometry != null){ -// // for (var i =0; i < macromolecule.stoichiometry.length; i++){ -// // var stoichiometry = macromolecule.stoichiometry[i]; -// // if (stoichiometry.macromolecule3VO != null){ -// // if (stoichiometry.macromolecule3VO.structure3VOs != null){ -// // for (var j = 0; j < stoichiometry.macromolecule3VO.structure3VOs.length; -// // j++) { -// // var structure = stoichiometry.macromolecule3VO.structure3VOs[j]; -// // structure["isSubunit"] = stoichiometry.macromolecule3VO.acronym; -// // data.push(structure) -// // } -// // } -// // } -// // } -// // } -// // } -// -// this.pdbStore = Ext.create('Ext.data.Store', { -// fields : [ 'filePath', 'structureId', 'structureType', 'symmetry', 'structureId', 'name', 'multiplicity' ], -// data : macromolecule.structure3VOs, -// groupField : 'structureType', -// sorters : { -// property : 'structureId', -// direction : 'DESC' -// } -// }); -// -// var groupingFeature = Ext.create('Ext.grid.feature.Grouping', { -// groupHeaderTpl : Ext.create('Ext.XTemplate', -// "
{name:this.formatName}
", { -// formatName : function(name) { -// return name; -// } -// }), -// hideGroupedHeader : true, -// startCollapsed : false -// }); -// -// this.pdbGrid = Ext.create('Ext.grid.Panel', { -// margin : "15 0 0 5", -// height : 250, -// store : this.pdbStore, -// plugins : _this._getPlugins(), -// buttons : [ { -// // text : 'Add PDB file', -// text : 'Add Modeling Option', -// handler : function() { -// _this._openUploadDialog(macromolecule.macromoleculeId, "PDB", 'Upload PDB File'); -// } -// } -// -// ], -// columns : [ -// { -// text : "structureId", -// flex : 0.2, -// hidden : true, -// dataIndex : 'structureId', -// sortable : true -// }, -// { -// text : "File", -// flex : 0.5, -// dataIndex : 'filePath', -// sortable : true, -// hidden : true -// }, -// { -// text : "PDB", -// flex : 0.4, -// dataIndex : 'name', -// sortable : true -// }, -// { -// text : "Symmetry", -// flex : 0.4, -// dataIndex : 'symmetry', -// sortable : true, -// editor : { -// xtype : 'combobox', -// typeAhead : true, -// triggerAction : 'all', -// selectOnTab : true, -// store : [ [ "P1", "P1" ], [ "P2", "P2" ], [ "P3", "P3" ], [ "P4", "P4" ], [ "P5", "P5" ], [ "P6", "P6" ], [ "P32", "P32" ], [ "P42", "P42" ], -// [ "P52", "P52" ], [ "P62", "P62" ], [ "P222", "P222" ] ], -// } -// }, { -// text : "Multiplicity", -// flex : 0.4, -// dataIndex : 'multiplicity', -// sortable : true, -// editor : { -// xtype : 'textfield' -// } -// -// }, { -// text : "Subunit", -// flex : 0.2, -// dataIndex : 'isSubunit', -// sortable : true, -// hidden : true -// }, { -// text : "Type", -// flex : 0.2, -// dataIndex : 'structureType', -// sortable : true, -// hidden : true -// }, -// -// { -// id : this.id + 'REMOVE', -// flex : 0.2, -// hidden : true, -// sortable : false, -// renderer : function(value, metaData, record, rowIndex, colIndex, store) { -// return BUI.getRedButton('REMOVE'); -// } -// }, ], -// -// listeners : { -// itemdblclick : function(dataview, record, item, e) { -// _this._editExperiment(record.raw.experimentId); -// }, -// cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { -// -// if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'REMOVE') { -// var dataAdapter = new BiosaxsDataAdapter(); -// dataAdapter.onSuccess.attach(function() { -// _this.pdbGrid.setLoading(false); -// _this.update(); -// }); -// dataAdapter.removeStructure(record.data.structureId); -// _this.pdbGrid.setLoading("Removing PDB file"); -// } -// -// } -// }, -// viewConfig : { -// getRowClass : function(record, rowIdx, params, store) { -// if (record.raw.isSubunit != null) { -// return "blue-row"; -// } -// } -// } -// }); -// -// return this.pdbGrid; -//}; -// -//MacromoleculeForm.prototype.getMolarityForm = function(macromolecule) { -// var _this = this; -// var data = []; -// for (var i = 0; i < BIOSAXS.proposal.macromolecules.length; i++) { -// var m = BIOSAXS.proposal.macromolecules[i]; -// if (m.macromoleculeId != macromolecule.macromoleculeId) { -// data.push(m); -// } -// -// } -// this.macromoleculeCombo = BIOSAXS_COMBOMANAGER.getComboMacromoleculeByMacromolecules(data, { -// width : 250, -// labelWidth : 100, -// margin : 10 -// }); -// -// return Ext.createWidget('form', { -// -// frame : false, -// border : 0, -// // padding : 15, -// width : 550, -// height : 350, -// items : [ { -// xtype : 'container', -// flex : 1, -// border : false, -// layout : 'anchor', -// defaultType : 'requiredtext', -// items : [ this.macromoleculeCombo, { -// xtype : 'numberfield', -// name : 'Ratio', -// id : _this.id + "ratio", -// fieldLabel : 'Number in assymmetric units', -// value : 1, -// decimalPrecision : 6, -// margin : 10 -// }, { -// xtype : 'textareafield', -// name : 'comments', -// fieldLabel : 'Comments', -// margin : 10, -// width : 400, -// value : "" -// -// } ] -// } ] -// }); -// -//}; -// -///******************************************************************************* -// * JAVASCRIPT DOC -// ******************************************************************************/ -//MacromoleculeForm.prototype.input = function() { -// return { -// macromolecule : DATADOC.getMacromolecule_10() -// }; -//}; -// -//MacromoleculeForm.prototype.test = function(targetId) { -// var macromoleculeForm = new MacromoleculeForm(); -// var panel = macromoleculeForm.getPanel(macromoleculeForm.input().macromolecule); -// panel.render(targetId); -//}; - -function ResultSummaryForm() { - this.radiationDamageThreshold = BUI.getRadiationDamageThreshold(); - this.qualityThreshold = BUI.getQualityThreshold(); - - /** Data clusters with bufers **/ - this.clusterByBuffers = false; - - /** Visualization are groupeb by concenttrations. Ex: 4.5mg/ml and 4.7mg/ml will be clusterized together **/ - this.collapseConcentrations = true; - - this.summaryHeight = 350; - this.id = BUI.id(); - - var _this = this; - - this.qualityControlResultsWidget = new QualityControlResultsWidget({ - qualityThreshold : this.radiationDamageThreshold, - radiationDamageThreshold : this.qualityThreshold - - }); - this.qualityControlResultsWidget.onQualityChanged.attach(function(sender, value) { - _this.qualityThreshold = value; - _this.thresholdsChanged(); - }); - - this.qualityControlResultsWidget.onRadiationDatamageChanged.attach(function(sender, value) { - _this.radiationDamageThreshold = value; - _this.thresholdsChanged(); - - }); - this.concentrationHTMLTableWidget = new ConcentrationHTMLTableWidget({ - height : 250, - showBufferColumns : this.clusterByBuffers - }); - - this.plot = new BoxWhiskerGraph({ - targetId : _this.id + '_boxPlot', - height : 350, - width : 450, - maxBoxWidth : 25 - }); - - this.rangePlot = new RangeWhiskerGraph({ - targetId : _this.id + '_rangePlot', - height : 350, - width : 450, - maxBoxWidth : 25 - }); -} - -ResultSummaryForm.prototype.thresholdsChanged = function() { - var parsedData = this.prepareData(this.rawData); - - var filtered = JSON.parse(JSON.stringify(parsedData)); - filtered.concentration.concentrations = []; - for ( var conc in parsedData.concentration.concentrations) { - if (parsedData.concentration.concentrations[conc].calculation.rgGnom.validNumber > 0) { - filtered.concentration.concentrations.push(parsedData.concentration.concentrations[conc]); - } - } - - this.plotWhisker(filtered); - this.plotRange(filtered); - - this.concentrationHTMLTableWidget.refresh(parsedData); -}; - -/** Given a frame object (object returned by analyzeFrames()) and depending of the threshold indicates if a datacollection has radiation damage **/ -ResultSummaryForm.prototype.hasRadiationDamage = function(frameObject) { - var bb = frameObject.bufferBeforeFramesMerged / frameObject.framesCount; - var ba = frameObject.bufferAfterFramesMerged / frameObject.framesCount; - var mol = frameObject.framesMerge / frameObject.framesCount; - return !((bb >= this.radiationDamageThreshold) && (ba >= this.radiationDamageThreshold) && (mol >= this.radiationDamageThreshold)); -}; - -/** Return (frameObject) an object with the information about the frames for a data collection**/ -ResultSummaryForm.prototype.analyzeFrames = function(dataCollectionRow) { - return { - bufferAfterFramesMerged : dataCollectionRow.bufferAfterFramesMerged, - bufferBeforeFramesMerged : dataCollectionRow.bufferBeforeFramesMerged, - framesCount : dataCollectionRow.framesCount, - framesMerge : dataCollectionRow.framesMerge - }; -}; - -ResultSummaryForm.prototype.detectDataCollectionWarnings = function(dataCollectionRow) { - var frameObject = this.analyzeFrames(dataCollectionRow); - var warnings = { - count : 0, - type : [] - }; - - if (this.hasRadiationDamage(frameObject)) { - warnings.count = warnings.count + 1; - warnings.type.push("RADIATION DAMAGE"); - } - - if (Number(dataCollectionRow.quality) < this.qualityThreshold) { - warnings.count = 1;//warnings.count + 1; - warnings.type.push("Quality <" + this.qualityThreshold); - } - return warnings; -}; - -/** Return array composed by {concentration} objects **/ -ResultSummaryForm.prototype.getConcentrations = function(data) { - var concentrationsId = {}; - - for ( var i = 0; i < data.length; i++) { - var warning = this.detectDataCollectionWarnings(data[i]); - var id = data[i].conc;// + "_" + data[i].bufferId; - if (this.clusterByBuffers) { - id = data[i].conc + "_" + data[i].bufferId; - } - - if (concentrationsId[id] == null) { - concentrationsId[id] = { - id : id, - concentration : Number(data[i].conc).toFixed(2), - bufferId : data[i].bufferId, - bufferAcronym : data[i].bufferAcronym, - rgGuinier : [], - i0Guinier : [], - rgGnom : [], - dMax : [], - quality : [], - frames : [], - frames_warning : warning.count - }; - } else { - concentrationsId[id].frames_warning = concentrationsId[id].frames_warning + warning.count; - } - - concentrationsId[id].frames.push(data[i]); - - if (warning.count == 0) { - concentrationsId[id].rgGuinier.push(data[i].rgGuinier); - concentrationsId[id].i0Guinier.push(data[i].I0); - concentrationsId[id].quality.push(data[i].quality); - concentrationsId[id].rgGnom.push(data[i].rgGnom); - concentrationsId[id].dMax.push(data[i].dmax); - } - - } - var concentrations = []; - for ( var item in concentrationsId) { - if (concentrationsId.hasOwnProperty(item)) { - concentrations.push({ - concentration : concentrationsId[item].concentration, - id : item, - bufferId : Number(concentrationsId[item].bufferId).toFixed(2), - bufferAcronym : concentrationsId[item].bufferAcronym, - rgGuinier : concentrationsId[item].rgGuinier, - /** Frames **/ - frames : concentrationsId[item].frames, - frames_warning : concentrationsId[item].frames_warning, - /** Calculation **/ - calculation : { - rgGuinier : BUI.getStandardDeviation(concentrationsId[item].rgGuinier), - i0Guinier : BUI.getStandardDeviation(concentrationsId[item].i0Guinier), - quality : BUI.getStandardDeviation(concentrationsId[item].quality), - rgGnom : BUI.getStandardDeviation(concentrationsId[item].rgGnom), - dMax : BUI.getStandardDeviation(concentrationsId[item].dMax) - - } - }); - } - } - - return { - concentrations : concentrations - }; -}; - -ResultSummaryForm.prototype.prepareData = function(data) { - /** Return array composed by {acronym, bufferId} objects **/ - function getBuffers(data) { - var buffersId = {}; - for ( var i = 0; i < data.length; i++) { - buffersId[data[i].bufferId] = data[i].acronym; - } - var buffers = []; - for ( var id in buffersId) { - if (buffersId.hasOwnProperty(id)) { - buffers.push({ - acronym : buffersId[id], - bufferId : id - }); - } - } - return buffers; - } - - /** Get a string with all the concentrations **/ - function getConcentrationString(parseConcentrations) { - var concentrations = []; - for ( var i = 0; i < parseConcentrations.concentrations.length; i++) { - concentrations.push(parseConcentrations.concentrations[i].concentration + " mg/ml "); - } - return concentrations.toString(); - } - - var parseConcentrations = this.getConcentrations(data); - - return { - dataCollectionCount : data.length, - buffers : getBuffers(data), - concentration : parseConcentrations, - concentrationLabel : getConcentrationString(parseConcentrations) - }; -}; - -ResultSummaryForm.prototype.getDataForWhisker = function(data) { - var clusters = []; - - var concentrations = {}; - var i = 0; - var conc = 0; - if (this.collapseConcentrations) { - for (i = 0; i < data.concentration.concentrations.length; i++) { - conc = data.concentration.concentrations[i]; - var concentration = Number(conc.concentration).toFixed(0); - if (concentrations[concentration] == null) { - concentrations[concentration] = {}; - concentrations[concentration].concentration = concentration; - concentrations[concentration].calculation = {}; - concentrations[concentration].calculation.rgGuinier = {}; - concentrations[concentration].calculation.rgGuinier.values = []; - concentrations[concentration].calculation.rgGuinier.values = conc.calculation.rgGuinier.values; - concentrations[concentration].calculation.rgGnom = {}; - concentrations[concentration].calculation.rgGnom.values = []; - concentrations[concentration].calculation.rgGnom.values = conc.calculation.rgGnom.values; - } else { - concentrations[concentration].calculation.rgGuinier.values = concentrations[concentration].calculation.rgGuinier.values - .concat(conc.calculation.rgGuinier.values); - concentrations[concentration].calculation.rgGnom.values = concentrations[concentration].calculation.rgGnom.values - .concat(conc.calculation.rgGnom.values); - } - } - - /** From object to array **/ - var array = []; - for ( var key in concentrations) { - if (concentrations.hasOwnProperty(key)) { - array.push(concentrations[key]); - } - } - data.concentration.concentrations = array; - } - - for (i = 0; i < data.concentration.concentrations.length; i++) { - conc = data.concentration.concentrations[i]; - clusters.push({ - name : conc.concentration + "mg/ml", - concentration : Number(conc.concentration), - x : Number(conc.concentration), - classes : [] - }); - clusters[clusters.length - 1].classes.push({ - name : "Guinier", - color : '#9A2EFE', - values : conc.calculation.rgGuinier.values - - }); - clusters[clusters.length - 1].classes.push({ - name : "P(r)", - color : '#2E64FE', - values : conc.calculation.rgGnom.values - - }); - } - return { - clusters : clusters.sort(function(a, b) { - return a.concentration - b.concentration; - }) - }; -}; - -ResultSummaryForm.prototype.getDataForWhiskerQuality = function(data) { - var clusters = []; - - for ( var i = 0; i < data.concentration.concentrations.length; i++) { - var conc = data.concentration.concentrations[i]; - clusters.push({ - name : conc.concentration + "mg/ml", - classes : [] - }); - clusters[clusters.length - 1].classes.push({ - name : "Quality", - values : conc.calculation.quality.values - - }); - } - - return { - clusters : clusters - }; -}; - -ResultSummaryForm.prototype.plotQualityWhisker = function(parsedData) { - this.qualityPlot.refresh(this.getDataForWhiskerQuality(parsedData)); -}; - -ResultSummaryForm.prototype.plotWhisker = function(parsedData) { - this.plot.refresh(this.getDataForWhisker(parsedData)); -}; - -ResultSummaryForm.prototype.plotRange = function(parsedData) { - this.rangePlot.refresh(this.getDataForWhisker(parsedData)); -}; - -ResultSummaryForm.prototype.getPanel = function(data) { - var _this = this; - _this.rawData = data; - var parsedData = this.prepareData(data); - - this.panel = Ext - .createWidget( - 'form', - { - bodyPadding : 20, - frame : false, - border : 0, - width : this.width, - height : this.summaryHeight + 1000, - items : [ { - xtype : 'container', - layout : 'hbox', - items : [ { - xtype : 'container', - flex : 1, - border : false, - layout : 'anchor', - defaultType : 'textfield', - items : [ - _this.qualityControlResultsWidget.getPanel(), - { - xtype : 'fieldset', - width : 950, - margin : "20, 0 0 0", - height : this.summaryHeight + 500, - items : [ - { - html : "
Concentration Analysis
", - border : 0, - width : 900 - - }, - { - html : this.concentrationHTMLTableWidget.getPanel(parsedData), - border : 0, - width : 900, - margin : "10, 0 0 10" - - }, - { - xtype : 'container', - layout : 'vbox', - border : 5, - items : [ - { - html : "
Rg based on Guinier and Gnom
", - border : 8, - width : 900, - margin : "20 0 0 10" - - }, { - xtype : 'container', - layout : 'hbox', - items : [ { - xtype : 'container', - layout : 'vbox', - items : [ { - html : "
", - border : 0, - width : this.plot.width, - padding : "10 0 0 20", - listeners : { - afterrender : function() { - _this.plotWhisker(parsedData); - - } - } - }, { - html : "
Concentration (mg/ml)
", - width : 450, - border : 0, - margin : "-50 0 0 0" - - } ] - }, { - xtype : 'container', - layout : 'vbox', - items : [ { - html : "
", - border : 0, - width : this.rangePlot.width, - padding : "10 0 0 10", - listeners : { - afterrender : function() { - _this.plotRange(parsedData); - } - } - }, { - html : "
Concentration (mg/ml)
", - width : 450, - border : 0, - margin : "-50 0 0 0" - - } ] - } ] - } ] - } ] - } ] - } - - ] - } ] - }); - return this.panel; - -}; - -ResultSummaryForm.prototype.input = function() { - return { - data : DATADOC.getData_3367() - }; -}; - -ResultSummaryForm.prototype.test = function(targetId) { - var resultSummaryForm = new ResultSummaryForm(); - var panel = resultSummaryForm.getPanel(resultSummaryForm.input().data); - panel.render(targetId); - -}; - -/** - * Example form - * - * @witdh - * @height - */ -function RigibBodyModelingForm(args) { - this.id = BUI.id(); - this.width = 700; - this.height = 500; - - if (args != null) { - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; - } - } - - var _this = this; - this.rigidBodyGrid = new AprioriRigidBodyGrid(); - - this.rigidBodyGrid.onUploadFile.attach(function(sender, type, title){ - _this._openUploadDialog(_this.macromolecule.macromoleculeId, type, title); - }); - - this.rigidBodyGrid.onRemove.attach(function(sender, type, title){ - _this._update(); - }); - - this.onSave = new Event(this); - -} - -RigibBodyModelingForm.prototype._getItems = function() { - var _this = this; - - - return [ { - xtype : 'label', - forId : 'myFieldId', - text : 'Information for model fit, mixture analysis and rigid body modeling', - margin : '15 0 20 10', - cls : "inline-help" - }, - this.rigidBodyGrid.getPanel(), - { - xtype : 'label', - forId : 'myFieldId', - text : 'Distance restraints may be imposed on the model using contacts conditions file (OPTIONAL)', - margin : '25 0 5 10', - cls : "inline-help" - }, - { - xtype : 'container', - layout : 'hbox', - items : [ { - xtype : 'container', - border : false, - layout : 'hbox', - items : [ { - xtype : 'label', - forId : 'myFieldId', - text : 'Contact Description File: (Optional)', - width : 150, - margin : '10 0 0 10' - }, { - id : this.id + "contactsDescriptionFilePath", - xtype : 'textfield', - hideLabel : true, - margin : '10 0 0 0', - width : 200, - disabled: true - }, { - text : 'Upload', - xtype : 'button', - margin : "10 0 0 10", - width : 80, - handler : function() { - - _this._openUploadDialog(_this.macromolecule.macromoleculeId, "CONTACTS", "Upload Contact Description File"); - } - }, { - text : 'Remove', - id : _this.id + "_remove", - xtype : 'button', - margin : "10 0 0 10", - width : 80, - handler : function() { - _this.macromolecule.contactsDescriptionFilePath = null; - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, proposal) { - /** Updating the proposal global object **/ - BIOSAXS.proposal.setItems(proposal); - _this.panel.setLoading(false); - - var saved = BIOSAXS.proposal.getMacromoleculeByAcronym(_this.macromolecule.acronym); - /** Refreshing to check that everything is ok **/ - _this.refresh(saved); - _this.onSave.notify(saved); - }); - - _this.panel.setLoading("Saving Macromolecule") - adapter.saveMacromolecule(_this.macromolecule); - } - } ] - } ] - }, { - xtype : 'panel', - html : "Go to SASREF manual for further information", - margin : "10 0 0 160", - border : 0 - - }, - { - xtype : 'checkbox', - margin : '10 0 0 5', - boxLabel : "I want rigid body modeling run on this stuff", - checked : true, - width : 300 - } ] - -}; - -/** Because update is a jsp page we don't know if the user has uploaded a file or not then we need to refresh **/ -RigibBodyModelingForm.prototype._update = function(macromoleculeId, type, title) { - var _this = this; - BIOSAXS.proposal.onInitialized.attach(function() { - if (BIOSAXS.proposal != null) { - _this.refresh(BIOSAXS.proposal.getMacromoleculeById(_this.macromolecule.macromoleculeId)); - _this.panel.setLoading(false); - } - }); - this.panel.setLoading(); - BIOSAXS.proposal.init(); -}; - -RigibBodyModelingForm.prototype._openUploadDialog = function(macromoleculeId, type, title) { - var _this = this; - function onClose() { - w.destroy(); - _this._update(); - - } - - var w = Ext.create('Ext.window.Window', { - title : title, - height : 200, - width : 400, - modal : true, - buttons : [ { - text : 'Close', - handler : function() { - onClose(); - } - } ], - layout : 'fit', - items : { - html : "" - }, - listeners : { - onEsc : function() { - onClose(); - }, - close : function() { - onClose(); - } - } - }).show(); -}; - -RigibBodyModelingForm.prototype._getButtons = function() { - return []; -}; - -RigibBodyModelingForm.prototype.getPanel = function() { - var _this = this; - this.panel = Ext.create('Ext.form.Panel', { - width : this.width, - height : this.height, - margin : 10, - border : 1, - defaultType : 'textfield', - items : this._getItems(), - buttons : this._getButtons(), - listeners : { - afterrender : function(){ - _this._populate(); - - } - } - }); - return this.panel; -}; - -/** Populates could be call when the DOM is not filled yet **/ -RigibBodyModelingForm.prototype._populate = function() { - if (this.macromolecule != null){ - if (Ext.getCmp(this.id + "contactsDescriptionFilePath") != null){ - if (this.macromolecule.contactsDescriptionFilePath != null){ - Ext.getCmp(this.id + "contactsDescriptionFilePath").setValue(this.macromolecule.contactsDescriptionFilePath); - Ext.getCmp(this.id + "_remove").enable(); - } - else{ - Ext.getCmp(this.id + "_remove").disable(); - Ext.getCmp(this.id + "contactsDescriptionFilePath").setValue(""); - - } - } - } -}; - -/** It populates the form * */ -RigibBodyModelingForm.prototype.refresh = function(macromolecule) { - this.macromolecule = macromolecule; - this.rigidBodyGrid.refresh(macromolecule); - this._populate(); -}; - -RigibBodyModelingForm.prototype.input = function() { - return {}; -}; - - -/** It populates the form **/ -RigibBodyModelingForm.prototype.test = function(targetId) { - var macromoleculeForm = new RigibBodyModelingForm(); - var panel = macromoleculeForm.getPanel(); - panel.render(targetId); -}; - - -/** - * Same form as MX part - * - * @creationMode if true a create button appears instead of save - * @showTitle true or false - */ -function ShipmentForm(args) { - this.id = BUI.id(); - - this.creationMode = false; - this.showTitle = true; - if (args != null) { - if (args.creationMode != null) { - this.creationMode = args.creationMode; - } - if (args.showTitle != null) { - this.showTitle = args.showTitle; - } - } - - this.onSaved = new Event(this); -} - -ShipmentForm.prototype.fillStores = function() { - this.panel.setLoading("Loading Labcontacts from database"); - this.labContactForSendingStore.loadData(BIOSAXS.proposal.getLabcontacts(), false); - this.labContactForReturnStore.loadData(BIOSAXS.proposal.getLabcontacts(), false); - this.panel.setLoading(false); - if (this.shipment != null) { - this.setShipment(this.shipment); - } -}; - -ShipmentForm.prototype.draw = function(targetId) { - this.getPanel().render(targetId); -}; - -ShipmentForm.prototype.setShipment = function(shipment) { - this.shipment = shipment; - var _this = this; - Ext.getCmp(_this.id + "shippingName").setValue(shipment.json.shippingName); - Ext.getCmp(_this.id + "shippingStatus").setValue(shipment.json.shippingStatus); - Ext.getCmp(_this.id + "comments").setValue(shipment.json.comments); - if (shipment.json.sendingLabContactVO != null) { - this.labContactsSendingCombo.setValue(shipment.json.sendingLabContactVO.labContactId); - } - if (shipment.json.returnLabContactVO != null) { - this.labContactsReturnCombo.setValue(shipment.json.returnLabContactVO.labContactId); - } - -}; - -ShipmentForm.prototype._saveShipment = function() { - var _this = this; - var shippingId = null; - if (this.shipment != null) { - shippingId = this.shipment.json.shippingId; - } - var json = { - shippingId : shippingId, - name : Ext.getCmp(_this.id + "shippingName").getValue(), - status : Ext.getCmp(_this.id + "shippingStatus").getValue(), - sendingLabContactId : Ext.getCmp(_this.id + "shipmentform_sendingLabContactId").getValue(), - returnLabContactId : Ext.getCmp(_this.id + "returnLabContactId").getValue(), - returnCourier : Ext.getCmp(_this.id + "returnCourier").getValue(), - courierAccount : Ext.getCmp(_this.id + "courierAccount").getValue(), - BillingReference : Ext.getCmp(_this.id + "BillingReference").getValue(), - dewarAvgCustomsValue : Ext.getCmp(_this.id + "dewarAvgCustomsValue").getValue(), - dewarAvgTransportValue : Ext.getCmp(_this.id + "dewarAvgTransportValue").getValue(), - comments : Ext.getCmp(_this.id + "comments").getValue() - }; - - var dataAdapter = new BiosaxsDataAdapter(); - dataAdapter.onSuccess.attach(function(sender, shipment) { - window.location = BUI.getShippingURL(shipment.shippingId); - }); - - dataAdapter.onError.attach(function(sender, error) { - _this.onError.notify(error); - }); - - /** Cheking params **/ - if (json.name == "") { - BUI.showError("Name field is mandatory"); - return; - } - - if (json.sendingLabContactId == null) { - BUI.showError("Lab contact for sending field is mandatory"); - return; - } - - if (json.returnLabContactId == null) { - BUI.showError("Lab contact for return field is mandatory"); - return; - } - - dataAdapter.createShipment(json.shippingId, json.name, json.status, json.comments, json.sendingLabContactId, json.returnLabContactId, - json.returnCourier, json.courierAccount, json.BillingReference, json.dewarAvgCustomsValue, json.dewarAvgTransportValue); - -}; - -ShipmentForm.prototype.getPanel = function(shipment) { - var _this = this; - this.shipment = shipment; - var required = '*'; - var buttons = []; - - if (_this.creationMode) { - buttons.push({ - text : 'Create', - scope : this, - handler : function() { - _this._saveShipment(); - } - }); - } else { - buttons.push({ - text : 'Save', - scope : this, - handler : function() { - _this._saveShipment(); - } - }); - - } - - this.labContactForSendingStore = Ext.create('Ext.data.Store', { - fields : [ 'cardName', 'labContactId' ] - }); - - this.labContactForReturnStore = Ext.create('Ext.data.Store', { - fields : [ 'cardName', 'labContactId' ] - }); - - // Create the combo box, attached to the states data store - this.labContactsSendingCombo = Ext.create('Ext.form.ComboBox', { - id : _this.id + "shipmentform_sendingLabContactId", - fieldLabel : 'Lab contact for sending', - afterLabelTextTpl : required, - store : this.labContactForSendingStore, - queryMode : 'local', - labelWidth : 200, - displayField : 'cardName', - valueField : 'labContactId' - }); - - this.labContactsReturnCombo = Ext.create('Ext.form.ComboBox', { - id : _this.id + "returnLabContactId", - fieldLabel : 'If No, Lab-Contact for Return', - afterLabelTextTpl : required, - store : this.labContactForReturnStore, - queryMode : 'local', - labelWidth : 200, - displayField : 'cardName', - valueField : 'labContactId', - listeners : { - change : function(x, newValue) { - for ( var i = 0; i < x.getStore().data.items.length; i++) { - if (x.getStore().data.items[i].raw.labContactId == newValue) { - Ext.getCmp(_this.id + "returnCourier").setValue(x.getStore().data.items[i].raw.defaultCourrierCompany); - Ext.getCmp(_this.id + "courierAccount").setValue(x.getStore().data.items[i].raw.courierAccount); - Ext.getCmp(_this.id + "BillingReference").setValue(x.getStore().data.items[i].raw.billingReference); - Ext.getCmp(_this.id + "dewarAvgCustomsValue").setValue(x.getStore().data.items[i].raw.dewarAvgCustomsValue); - Ext.getCmp(_this.id + "dewarAvgTransportValue").setValue(x.getStore().data.items[i].raw.dewarAvgTransportValue); - } - } - } - } - }); - - if (this.panel == null) { - this.panel = Ext.create('Ext.form.Panel', { - bodyPadding : 5, - width : 600, - border : 1, - items : [ { - xtype : 'fieldset', - title : 'Details', - collapsible : false, - defaultType : 'textfield', - layout : 'anchor', - defaults : { - anchor : '100%' - }, - items : [ { - xtype : 'requiredtext', - fieldLabel : 'Shipment Label', - allowBlank : false, - name : 'shippingName', - id : _this.id + 'shippingName', - value : '', - anchor : '50%' - }, { - - xtype : 'textareafield', - name : 'comments', - id : _this.id + 'comments', - fieldLabel : 'Comments', - value : '' - }, { - fieldLabel : 'Status', - readOnly : true, - id : _this.id + 'shippingStatus', - value : 'Opened', - anchor : '50%' - } ] - }, { - xtype : 'fieldset', - title : 'Lab-Contacts', - collapsible : false, - defaultType : 'textfield', - layout : 'anchor', - defaults : { - anchor : '100%' - }, - items : [ this.labContactsSendingCombo, this.labContactsReturnCombo ] - }, { - border : 0, - html : BUI.getWarningHTML("These informations are relevant for all shipments") - }, { - xtype : 'fieldset', - title : 'Courier accounts details for return', - collapsible : false, - layout : 'anchor', - defaults : { - anchor : '100%' - }, - items : [ { - xtype : 'textfield', - labelWidth : 400, - fieldLabel : 'Courier company for return (if ESRF sends a dewar back)', - id : _this.id + 'returnCourier', - value : '' - }, { - xtype : 'textfield', - labelWidth : 400, - fieldLabel : 'Courier account', - id : _this.id + 'courierAccount', - value : '' - }, { - xtype : 'textfield', - labelWidth : 400, - fieldLabel : 'Billing reference', - id : _this.id + 'BillingReference', - value : '' - }, { - xtype : 'numberfield', - labelWidth : 400, - fieldLabel : 'Average Customs value of a dewar (Euro)', - id : _this.id + 'dewarAvgCustomsValue', - value : '' - }, { - xtype : 'numberfield', - labelWidth : 400, - fieldLabel : 'Average Transport value of a dewar (Euro)', - id : _this.id + 'dewarAvgTransportValue', - value : '' - } ] - } ], - buttons : buttons - }); - } - this.fillStores(); - if (this.showTitle) { - this.panel.setTitle('Create a new Shipment'); - } - return this.panel; -}; - -ShipmentForm.prototype.input = function() { - return { - proposal : DATADOC.getProposal_10() - - }; -}; - -ShipmentForm.prototype.test = function(targetId) { - var shipmentForm = new ShipmentForm({ - creationMode : true - - }); - BIOSAXS.proposal = new Proposal(shipmentForm.input().proposal); - shipmentForm.getPanel().render(targetId); -}; - -/** - * #onSaved - */ -function StockSolutionForm(args) { - this.id = BUI.id(); - this.actions = []; - - if (args != null) { - if (args.actions != null) { - this.actions = args.actions; - } - } - this.onSaved = new Event(this); -} - -StockSolutionForm.prototype.getStockSolution = function() { - if (this.stockSolution != null) { - this.stockSolution.concentration = Ext.getCmp(this.id + "stockSolution_concentration").getValue(); - this.stockSolution.storageTemperature = Ext.getCmp(this.id + "stockSolution_storageTemperature").getValue(); - this.stockSolution.volume = Ext.getCmp(this.id + "stockSolution_volume").getValue(); - this.stockSolution.comments = Ext.getCmp(this.id + "stockSolution_comments").getValue(); - this.stockSolution.name = Ext.getCmp(this.id + "stockSolution_name").getValue(); - this.stockSolution.bufferId = this.bufferCombo.getValue(); - - if (this.macromoleculeCombo.getValue() != null) { - this.stockSolution.macromoleculeId = this.macromoleculeCombo.getValue(); - } else { - this.stockSolution.macromolecule3VO = null; - } - - } else { - return { - concentration : Ext.getCmp(this.id + "stockSolution_concentration").getValue(), - storageTemperature : Ext.getCmp(this.id + "stockSolution_storageTemperature").getValue(), - volume : Ext.getCmp(this.id + "stockSolution_volume").getValue(), - comments : Ext.getCmp(this.id + "stockSolution_comments").getValue(), - name : Ext.getCmp(this.id + "stockSolution_name").getValue(), - bufferId : this.bufferCombo.getValue(), - macromoleculeId : this.macromoleculeCombo.getValue() - }; - } - return this.stockSolution; -}; - -StockSolutionForm.prototype.setStockSolution = function(stockSolution) { - if (stockSolution != null) { - if (stockSolution.macromoleculeId != null) { - this.macromoleculeCombo.setValue(stockSolution.macromoleculeId); - } - this.bufferCombo.setValue(stockSolution.bufferId); - Ext.getCmp(this.id + "stockSolution_concentration").setValue(this.stockSolution.concentration); - Ext.getCmp(this.id + "stockSolution_storageTemperature").setValue(this.stockSolution.storageTemperature); - Ext.getCmp(this.id + "stockSolution_volume").setValue(this.stockSolution.volume); - Ext.getCmp(this.id + "stockSolution_name").setValue(this.stockSolution.name); - Ext.getCmp(this.id + "stockSolution_comments").setValue(this.stockSolution.comments); - } -}; - -StockSolutionForm.prototype.getBufferCombo = function() { - this.bufferCombo = BIOSAXS_COMBOMANAGER.getComboBuffers(BIOSAXS.proposal.getBuffers(), { - labelWidth : 120, - margin : '0 0 10 0', - width : 220 - - }); - return this.bufferCombo; -}; - -StockSolutionForm.prototype.getMacromoleculeCombo = function() { - this.macromoleculeCombo = BIOSAXS_COMBOMANAGER.getComboMacromoleculeByMacromolecules(BIOSAXS.proposal.getMacromolecules(), { - labelWidth : 120, - margin : '0 0 10 0', - width : 220 - - }); - return this.macromoleculeCombo; -}; - -StockSolutionForm.prototype.refresh = function() { -}; - -StockSolutionForm.prototype._getTopPanel = function() { - return { - xtype : 'container', - layout : 'hbox', - border : 0, - items : [ { - xtype : 'container', - layout : 'hbox', - items : [ { - xtype : 'container', - flex : 1, - border : false, - layout : 'anchor', - defaultType : 'textfield', - items : [ - - this.getMacromoleculeCombo(), { - xtype : 'requiredtext', - id : this.id + 'stockSolution_name', - fieldLabel : 'Acronym', - labelWidth : 120, - width : 250 - }, { - xtype : 'requiredtext', - id : this.id + 'stockSolution_concentration', - fieldLabel : 'Conc. (mg/ml)', - labelWidth : 120, - width : 250 - }, - - { - id : this.id + 'stockSolution_storageTemperature', - fieldLabel : 'Storage Temp.(C)', - labelWidth : 120, - width : 250 - }, { - xtype : 'requiredtext', - id : this.id + 'stockSolution_volume', - fieldLabel : 'Volume in Well (µl)', - labelWidth : 120, - width : 250 - } ] - } ] - }, { - xtype : 'container', - flex : 1, - layout : 'anchor', - defaultType : 'textfield', - margin : '0 0 0 10', - items : [ this.getBufferCombo() ] - } ] - }; - -}; - -StockSolutionForm.prototype.getPanel = function(stockSolution) { - this.stockSolution = stockSolution; - this.panel = Ext.createWidget({ - xtype : 'container', - layout : 'vbox', - border : 0, - style : { - padding : '10px' - }, - fieldDefaults : { - labelAlign : 'left', - labelWidth : 50 - }, - items : [ this._getTopPanel(stockSolution), { - id : this.id + 'stockSolution_comments', - xtype : 'textareafield', - name : 'comments', - fieldLabel : 'Comments', - labelWidth : 120, - width : '100%' - } ] - }); - - this.setStockSolution(stockSolution); - return this.panel; -}; - -StockSolutionForm.prototype.input = function() { - return { - stock : { - "stockSolutionId" : 6, - "proposalId" : 3124, - "macromoleculeId" : 5933, - "bufferId" : 811, - "instructionSet3VO" : null, - "boxId" : 305861, - "storageTemperature" : "20", - "volume" : "300", - "concentration" : "1.2", - "comments" : "Buffer EDTA with A", - "name" : "A_EDTA_1.2", - "samples" : [], - "buffer" : "EDTA", - "macromolecule" : "A" - }, - proposal : new MeasurementGrid().input().proposal - }; -}; - -StockSolutionForm.prototype.test = function(targetId) { - var stockSolutionForm = new StockSolutionForm(); - BIOSAXS.proposal = new Proposal(stockSolutionForm.input().proposal); - var panel = stockSolutionForm.getPanel(new Shipment(stockSolutionForm.input().stock)); - panel.render(targetId); -}; - - -BoxWhiskerGraph.prototype.cleanArray = GenericGraph.prototype.cleanArray; -BoxWhiskerGraph.prototype.plotAxes = GenericGraph.prototype.plotAxes; -BoxWhiskerGraph.prototype.plotRuler = GenericGraph.prototype.plotRuler; -BoxWhiskerGraph.prototype.drawSVGVerticalText = GenericGraph.prototype.drawSVGVerticalText; -BoxWhiskerGraph.prototype.getClassColor = GenericGraph.prototype.getClassColor; -BoxWhiskerGraph.prototype.getDimensions = GenericGraph.prototype.getDimensions; -BoxWhiskerGraph.prototype.calculate = GenericGraph.prototype.calculate; -BoxWhiskerGraph.prototype.getMedian = GenericGraph.prototype.getMedian; -BoxWhiskerGraph.prototype.pointToPixel = GenericGraph.prototype.pointToPixel; -BoxWhiskerGraph.prototype.maxValueWhisker = GenericGraph.prototype.maxValueWhisker; -BoxWhiskerGraph.prototype.refresh = GenericGraph.prototype.refresh; - -/** - * Subclass of GenericGraph - * - * @maxBoxWidth - */ -function BoxWhiskerGraph(args){ - this.maxBoxWidth = 25; - - if (args == null){ - args = new Object(); - } - args["plotHorizontalByCluster"] = true; - - GenericGraph.call(this, args); - - if (args.maxBoxWidth != null){ - this.maxBoxWidth = args.maxBoxWidth; - } -}; - - - -/** -There are several different methods for calculating quartiles.[1] This calculator uses a method described by Moore and McCabe to find quartile values. -The same method also used by The TI-83 to calculate quartile values. -With this method, the first quartile is the median of the numbers below the median, the third quartile is the median of the numbers above the median. - -http://www.miniwebtool.com/quartile-calculator/ -http://www.alcula.com/calculators/statistics/box-plot/ -**/ -BoxWhiskerGraph.prototype.getQ1 = function(array){ - array = array.slice(0, array.length/2); - return this.getMedian(array); -}; - -BoxWhiskerGraph.prototype.getQ3 = function(array){ - array = array.slice((array.length + 1)/2); - return this.getMedian(array); - -}; - -BoxWhiskerGraph.prototype.getQ2 = function(array){ - return this.getMedian(array); -}; - -BoxWhiskerGraph.prototype.getBelowOutliers = function(belowLimit, array){ - var points = new Array(); - for (var i = 0; i < array.length; i++){ - if (array[i] <= belowLimit){ - points.push(array[i]); - } - } - return points; -}; - -BoxWhiskerGraph.prototype.getAboveOutliers = function(aboveLimit, array){ - var points = new Array(); - for (var i = 0; i < array.length; i++){ - if (array[i] >= aboveLimit){ - points.push(array[i]); - } - } - return points; -}; - - -BoxWhiskerGraph.prototype.minValueWhisker = function(belowLimit, q1, array){ - var points = new Array(); - - for (var i = 0; i < array.length; i++){ - if ((array[i] < q1) && (array[i]) > belowLimit){ - points.push(array[i]); - } - } - - if (points.length > 0){ - points.sort(function(a, b){return a - b;}); - return points[0]; - } - return null; -}; - -BoxWhiskerGraph.prototype.isNumber = function(value){ - if (value=="") return false; - - var d = parseInt(value); - if (!isNaN(d)) return true; else return false; - -}; - -BoxWhiskerGraph.prototype.plotBoxWhisker = function(boxProperties){ - if (this.maxBoxWidth != null){ - if (boxProperties.width > this.maxBoxWidth){ - boxProperties.x = boxProperties.x + (boxProperties.width/2) - (this.maxBoxWidth/2); - boxProperties.width = this.maxBoxWidth; - } - - } - - if (this.plotPoints){ - for(var i = 0; i < boxProperties.values.length; i++){ - var value = boxProperties.values[i]; - var toPixel = this.pointToPixel(value, boxProperties); - SVG.drawCircle(boxProperties.x + (boxProperties.width/2) + 2, toPixel, this.pointRadius, this.svg, [["fill", "green"], ["fill-opacity", this.fillOpacityPoint],['stroke-opacity', this.strokeOpacityPoint], ["stroke", "black"]]); - } - } - - - var boxColor = this.getClassColor(boxProperties.name); - var result = this.calculate(boxProperties.values); - /** Q1 **/ - - if (this.isNumber(result.Q1)){ - SVG.drawLine(boxProperties.x, this.pointToPixel(result.Q1, boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result.Q1, boxProperties), this.svg, [["stroke", boxColor]]); - } - /** Q2 **/ - if (this.isNumber(result.Q2)){ - SVG.drawLine(boxProperties.x, this.pointToPixel(result.Q2, boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result.Q2, boxProperties), this.svg, [["stroke", "blue"], ["stroke-width", "2"]]); - } - - /** Q3 **/ - if (this.isNumber(result.Q3)){ - SVG.drawLine(boxProperties.x, this.pointToPixel(result.Q3, boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result.Q3, boxProperties), this.svg, [["stroke", boxColor]]); - } - - /** Concenting Q1 and Q3 **/ - if (this.isNumber(result.Q1)&&this.isNumber(result.Q3)){ - SVG.drawLine(boxProperties.x, this.pointToPixel(result.Q1, boxProperties), boxProperties.x, this.pointToPixel(result.Q3, boxProperties), this.svg, [["stroke", boxColor]]); - SVG.drawLine(boxProperties.x + boxProperties.width, this.pointToPixel(result.Q1, boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result.Q3, boxProperties), this.svg, [["stroke", boxColor]]); - } - - /** min-whisker **/ - if (result["min-whisker"] != null){ - if (this.isNumber(result.Q1)){ - SVG.drawLine(boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result.Q1, boxProperties), boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result["min-whisker"], boxProperties), this.svg, [["stroke", boxColor]]); - } - SVG.drawLine(boxProperties.x,this.pointToPixel(result["min-whisker"], boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result["min-whisker"], boxProperties) , this.svg, [["stroke", boxColor]]); - - } - - /** max-whisker **/ - if (result["max-whisker"] != null){ - if (this.isNumber(result.Q3)){ - SVG.drawLine(boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result.Q3, boxProperties), boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result["max-whisker"], boxProperties), this.svg, [["stroke", boxColor]]); - } - SVG.drawLine(boxProperties.x , this.pointToPixel(result["max-whisker"], boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result["max-whisker"], boxProperties), this.svg, [["stroke", boxColor]]); - - } - - /** outliners **/ - if (result["above-outliers"] != null){ - for (var point in result["above-outliers"]){ - SVG.drawCircle(boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result["above-outliers"][point], boxProperties), this.pointRadius, this.svg, [["fill", "red"], ["fill-opacity", "1"]]); - //SVG.drawText(boxProperties.x + (boxProperties.width/2) - 2, this.pointToPixel(result["above-outliers"][point], boxProperties) + 2, "x",this.svg, [["fill", "black"], ["font-size", "x-small"]]); - } - } - if (result["below-outliers"] != null){ - for (var point in result["below-outliers"]){ - SVG.drawCircle(boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result["below-outliers"][point], boxProperties), this.pointRadius, this.svg, [["fill", "red"], ["fill-opacity", "1"]]); - //SVG.drawText(boxProperties.x + (boxProperties.width/2) - 2, this.pointToPixel(result["below-outliers"][point], boxProperties) + 2, "x",this.svg, [["fill", "black"], ["font-size", "x-small"]]); - } - } -}; - - - -BoxWhiskerGraph.prototype.plotClusterTitles = function(properties){ - /** Cluster Titles **/ - var posX = this.left + this.rulerWidth; - var data = this.data; - for(var i = 0; i < data.clusters.length; i++ ){ - /** title for the clusters **/ - posX = posX + this.interClustersSpace; - - /** Drawing title of classes **/ - var cluster = data.clusters[i]; - var posXClasses = posX; - for(var j = 0; j < cluster.classes.length; j++){ - //SVG.drawRectangle(posXClasses, this.height - (this.bottom + this.clusterTitleHeight + this.rulerHeight), properties.classWidth, this.rulerHeight, this.svg, [["fill", "green"]]); -// SVG.drawText(posXClasses + 1/6*properties.classWidth, this.height - (this.bottom + this.clusterTitleHeight + (this.rulerHeight*1/4)), cluster.classes[j].name, this.svg, [["style", "font-size:xx-small"]]); - var color = cluster.classes[j].color; - this.drawSVGVerticalText(posXClasses + 1/2*(properties.classWidth), this.height - (this.bottom - this.clusterTitleHeight + (this.rulerHeight)), cluster.classes[j].name , [["style", "font-size:x-small;"], ["fill", color]]); - - // SVG.drawRectangle(posXClasses, this.height - (this.bottom + this.clusterTitleHeight), properties.classWidth, 2, this.svg, [["fill", "black"]]); - posXClasses = posXClasses + properties.classWidth + this.interClassesSpace; - } - - var clusterTitleSpace = (data.clusters[i].classes.length * properties.classWidth) + ((data.clusters[i].classes.length - 1) * this.interClassesSpace); - //SVG.drawRectangle(posX, this.height - (this.bottom + this.clusterTitleHeight), clusterTitleSpace, this.clusterTitleHeight, this.svg, [["fill", "pink"]]); - SVG.drawRectangle(posX, this.height - (this.clusterTitleHeight+this.bottom), clusterTitleSpace, 1, this.svg, []); - -// var transform = ["translate", "(" + posX + 1/3*clusterTitleSpace +", " + this.height - (this.bottom + (this.clusterTitleHeight*1/4)) +")"], ["transform", "rotate(180)"]; -// var transform = ["transform", "translate(" + (posX + 1/3*clusterTitleSpace) +", " + (this.height - (this.bottom + (this.clusterTitleHeight*1/4))) + "), rotate(-90) "]; -// this.drawSVGVerticalText(posX + 1/3*clusterTitleSpace, this.height - (this.bottom + (this.clusterTitleHeight*1/4)),data.clusters[i].name, [["style", "font-size:x-small"]]); - SVG.drawText(posX , this.height - (this.bottom + (this.clusterTitleHeight*1/4)),data.clusters[i].name ,this.svg, [["style", "font-size:x-small"]]); - posX = posX + clusterTitleSpace; - } -}; - -BoxWhiskerGraph.prototype.plotWhisters = function(data, properties){ - var colors = ["yellow", "orange", "green"]; - var posX = this.left + this.rulerWidth; - for(var i = 0; i < data.clusters.length; i++ ){ - var cluster = data.clusters[i]; - /** inter cluster space **/ - //SVG.drawRectangle(posX, this.top, this.interClustersSpace, this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight, this.svg, [["fill", "black"]]); - posX = posX + this.interClustersSpace; - - for (var j = 0; j < cluster.classes.length; j ++){ - - //SVG.drawRectangle(posX, this.top, properties.classWidth, this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight, this.svg, [["fill", colors[j]]]); - this.plotBoxWhisker( - { - name : cluster.classes[j].name, - values : cluster.classes[j].values, - minPoint : properties.minPoint, - maxPoint : properties.maxPoint, - x : posX, - y : this.top, - width : properties.classWidth, - height : this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight - - - } - ); - posX = posX + properties.classWidth; - //SVG.drawRectangle(posX, this.top, this.interClassesSpace, this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight, this.svg, [["fill", "black"]]); - if (j < cluster.classes.length - 1){ - posX = posX + this.interClassesSpace; - } - } - } -}; - -BoxWhiskerGraph.prototype.draw = function(targetId, data){ - this.targetId = targetId; - var properties = (this.getDimensions(data)); - this.svg = SVG.createSVGCanvas(document.getElementById(this.targetId), [["width", this.width], ["height", this.height]]); - this.plotAxes(properties); - this.plotClusterTitles(properties); - this.plotWhisters(data,properties); -}; - -BoxWhiskerGraph.prototype.input = function(){ - return DATADOC.getBoxWhikerData(); -}; - -BoxWhiskerGraph.prototype.test = function(targetId){ - var plot = new BoxWhiskerGraph( - { - targetId : targetId, - height : 350, - width : 450, - maxBoxWidth : 25 - } - ); - plot.refresh(this.input()); -}; - - - - - - - -function DataSet(){ - this.json = null; - -}; - - -DataSet.prototype.loadFromJSON = function(json){ - if(json != null) { - if(this.validate(json)) { - this.json = json; - } - } -}; - - -DataSet.prototype.toJSON = function(json){ - return this.json; -}; - - -/** Abstract method to be override on childs classes **/ -DataSet.prototype.validate = function(json){ - if (true){ - return true; - } - /*else{ - throw "Data validation failed"; - }*/ -}; - - - - -Edge.prototype.getName = GraphItem.prototype.getName; -Edge.prototype.setName = GraphItem.prototype.setName; -Edge.prototype.getId = GraphItem.prototype.getId; - -function Edge(id, name, nodeSource, nodeTarget, args){ - GraphItem.prototype.constructor.call(this, id, name, args); - - this.sourceNode = nodeSource; - this.targetNode = nodeTarget; - -}; - -Edge.prototype.toJSON = function(){ - return {"index": this.id,"sourceIndex":this.sourceNode.getId(),"targetIndex":this.targetNode.getId(),"args":this.args}; -}; - -Edge.prototype.getNodeSource = function(){ - return this.sourceNode; -}; - -Edge.prototype.getNodeTarget = function(){ - return this.targetNode; -}; - -Edge.prototype.remove = function(){ - //Remove edge object in the nodes - this.getNodeSource().removeEdge(this); - this.getNodeTarget().removeEdge(this); - - this.deleted.notify(this); -}; - - -EdgeGraphFormatter.prototype.setProperties = ItemGraphFormatter.prototype.setProperties; -EdgeGraphFormatter.prototype.getDefault = ItemGraphFormatter.prototype.getDefault; -EdgeGraphFormatter.prototype.getSelected = ItemGraphFormatter.prototype.getSelected; -EdgeGraphFormatter.prototype.getOver = ItemGraphFormatter.prototype.getOver; -EdgeGraphFormatter.prototype.getDragging = ItemGraphFormatter.prototype.getDragging; -EdgeGraphFormatter.prototype.getId = ItemGraphFormatter.prototype.getId; -EdgeGraphFormatter.prototype.toJSON = ItemGraphFormatter.prototype.toJSON; -EdgeGraphFormatter.prototype.loadFromJSON = ItemGraphFormatter.prototype.loadFromJSON; -EdgeGraphFormatter.prototype._setEvents = ItemGraphFormatter.prototype._setEvents; - -function EdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ - ItemGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); - - this.getDefault().args.type = "EdgeGraphFormatter"; -}; - - - - -LineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; -LineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; -LineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; -LineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; -LineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; -LineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; -LineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; -LineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; -LineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; - -function LineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ - EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); - this.args.type = "LineEdgeGraphFormatter"; -}; - -/** DIRECTED **/ -DirectedLineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; -DirectedLineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; -DirectedLineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; -DirectedLineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; -DirectedLineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; -DirectedLineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; -DirectedLineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; -DirectedLineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; -DirectedLineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; - -function DirectedLineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ - EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); - this.args.type = "DirectedLineEdgeGraphFormatter"; - this.args.arrowSize = "3"; -}; -DirectedLineEdgeGraphFormatter.prototype.getArrowSize = function(){ - return this.args.arrowSize; -}; - -OdirectedLineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; -OdirectedLineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; -OdirectedLineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; -OdirectedLineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; -OdirectedLineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; -OdirectedLineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; -OdirectedLineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; -OdirectedLineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; -OdirectedLineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; - -function OdirectedLineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ - EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); - this.args.type = "DirectedLineEdgeGraphFormatter"; - this.args.arrowSize = "3"; -}; - -OdirectedLineEdgeGraphFormatter.prototype.getArrowSize = function(){ - return this.args.arrowSize; -}; - - -/** CUT (inhibition) **/ -CutDirectedLineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; -CutDirectedLineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; -CutDirectedLineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; -CutDirectedLineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; -CutDirectedLineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; -CutDirectedLineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; -CutDirectedLineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; -CutDirectedLineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; -CutDirectedLineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; - -function CutDirectedLineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ - EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); - this.args.type = "CutDirectedLineEdgeGraphFormatter"; -}; - - - - -BezierEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; -BezierEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; -BezierEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; -BezierEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; -BezierEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; -BezierEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; -BezierEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; -BezierEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; -BezierEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; -BezierEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; - -function BezierEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ - EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); - this.args.type = "BezierEdgeGraphFormatter"; -}; - - - -DotDirectedLineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; -DotDirectedLineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; -DotDirectedLineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; -DotDirectedLineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; -DotDirectedLineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; -DotDirectedLineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; -DotDirectedLineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; -DotDirectedLineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; -DotDirectedLineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; - -function DotDirectedLineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ - EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); - this.args.type = "DotDirectedLineEdgeGraphFormatter"; -}; - - -OdotDirectedLineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; -OdotDirectedLineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; -OdotDirectedLineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; -OdotDirectedLineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; -OdotDirectedLineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; -OdotDirectedLineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; -OdotDirectedLineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; -OdotDirectedLineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; -OdotDirectedLineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; - -function OdotDirectedLineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ - EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); - this.args.type = "OdotDirectedLineEdgeGraphFormatter"; -}; - - - -function GraphDataset(){ - DataSet.prototype.constructor.call(this); - this.edges = new Object(); - this.vertices = new Object(); - this.verticesIndex = new Object(); - - //Events - this.newVertex = new Event(this); - this.vertexNameChanged = new Event(this); - this.vertexDeleted = new Event(this); - - this.newEdge = new Event(this); - this.edgeNameChanged = new Event(this); - this.edgeDeleted = new Event(this); - - this.json = new Object(); - this.json.vertices = new Array(); - this.json.edges = new Array(); - this.json.relations = new Array(); -}; - -GraphDataset.prototype.loadFromJSON = DataSet.prototype.loadFromJSON; -GraphDataset.prototype.toJSON = DataSet.prototype.toJSON; -GraphDataset.prototype.validate = DataSet.prototype.validate; - -/** Devuelve el numero de edges incidentes sobre el nodo con mas edges **/ -GraphDataset.prototype.getMaxClass = function(){ - var maxClassNode = 0; - for ( var node in this.vertices) { - if (this.vertices[node].getEdgesCount() > maxClassNode){ - maxClassNode = this.vertices[node].getEdgesCount(); - } - } - return maxClassNode; -}; - -/** Devuelve el numero de edges incidentes sobre el nodo con mas edges **/ -GraphDataset.prototype.getMinClass = function(){ - var minClassNode = Math.min(); - for ( var node in this.vertices) { - if (this.vertices[node].getEdgesCount() < minClassNode){ - minClassNode = this.vertices[node].getEdgesCount(); - } - } - return minClassNode; -}; - -GraphDataset.prototype.getVertexByName = function(nodeName){ - var results = new Array(); - - for (var vertexId in this.verticesIndex[nodeName]){ - var vertexByid = this.getVertexById(this.verticesIndex[nodeName][vertexId]); - results.push(vertexByid); - //* añadido nuevo porque fallaba el anterior codigo - return vertexByid - } - - if (results <= 1){ - return this.getVertexById(this.verticesIndex[nodeName]); - } - else{ - return results; - } -}; - -GraphDataset.prototype.getVertexById = function(id){ - return this.vertices[id]; -}; - -GraphDataset.prototype.toSIF = function(){ - var sifDataAdapter = new SifFileDataAdapter(); - return sifDataAdapter.toSIF(this); -}; - -GraphDataset.prototype.toSIFID = function(){ - var sifDataAdapter = new SifFileDataAdapter(); - return sifDataAdapter.toSIFID(this); -}; - -GraphDataset.prototype.toDOT = function(){ - var dotFileDataAdapter = new DotFileDataAdapter(); - return dotFileDataAdapter.toDOT(this); -}; - -GraphDataset.prototype.toDOTID = function(){ - var dotFileDataAdapter = new DotFileDataAdapter(); - return dotFileDataAdapter.toDOTID(this); -}; - -GraphDataset.prototype._addNode = function(nodeName, args){ - return new Vertex(this._getVerticesCount()-1, nodeName, args); -}; - -GraphDataset.prototype.addNode = function(nodeName, args){ - this.json.vertices.push(nodeName); - this._addVerticesIndex(nodeName, this._getVerticesCount() - 1); - var vertex = this._addNode(nodeName, args); - this.vertices[this._getVerticesCount()-1] = vertex; - this._setNodeEvents(vertex); - this.newVertex.notify(vertex); -}; - -GraphDataset.prototype._addVerticesIndex = function(nodeName, id){ - if (this.verticesIndex[nodeName] == null){ - this.verticesIndex[nodeName] = new Array(); - } - this.verticesIndex[nodeName].push(id); -}; - -GraphDataset.prototype.addEdge = function(edgeName, nodeSourceId, nodeTargetId, args){ - this.json.edges.push(edgeName); - var nodeSource = this.getVertexById(nodeSourceId); - var nodeTarget = this.getVertexById(nodeTargetId); - var index = this.getEdgesCount() - 1; - this.edges[index] = new Edge(index, edgeName, nodeSource, nodeTarget, args); - this.json.relations.push({"index": index, "sourceIndex": nodeSourceId, "targetIndex": nodeTargetId, "args": args }); - - nodeSource.addEdge(this.edges[index]); - nodeTarget.addEdge(this.edges[index]); - this._setEdgeEvents(this.edges[index]); - this.newEdge.notify(this.edges[index]); -}; - -GraphDataset.prototype.getVertices = function(){ - return this.vertices; -}; - -GraphDataset.prototype.getEdges = function(){ - return this.edges; -}; - -GraphDataset.prototype.getEdgeById = function(edgeId){ - return this.edges[edgeId]; -}; - -GraphDataset.prototype._getVerticesCount = function(){ - return this.json.vertices.length; -}; - - -GraphDataset.prototype.getVerticesCount = function(){ - var count = 0; - for ( var vertex in this.getVertices()) { - count ++; - } - return count; -}; - - -GraphDataset.prototype.getEdgesCount = function(){ - return this.json.edges.length; -}; - -GraphDataset.prototype.init = function(){ - this.edges = new Object(); - this.vertices = new Object(); -}; - -GraphDataset.prototype._setNodeEvents = function(node){ - var _this = this; - //NODE EVENTS - node.deleted.attach(function (sender, node){ - _this._removeNode(node); - }); - - node.nameChanged.attach(function (sender, args){ - var item = args.item; - var newName = item.name; - var indexes = _this.verticesIndex[args.previousName]; - for(var i = 0; i < indexes.length; i++){ - if(indexes[i] == item.id) - indexes.splice(i,1); - } - if(indexes.length == 0){ - delete _this.verticesIndex[args.previousName]; - } - _this._addVerticesIndex(newName, item.id); - _this.json.vertices[item.id] = newName; - _this.vertexNameChanged.notify(args); - }); -}; - -GraphDataset.prototype._setEdgeEvents = function(edge){ - var _this = this; - //EDGE EVENTS - edge.nameChanged.attach(function (sender, edge){ - _this.edgeNameChanged.notify(edge); - - }); - - edge.deleted.attach(function (sender, edge){ - _this._removeEdge(edge); - }); -}; - -GraphDataset.prototype._connectVerticesByName = function(nodeNameSource, nodeNameTarget){ - var source = this.getVertexByName(nodeNameSource); - var target = this.getVertexByName(nodeNameTarget); - - if ((source != null)&&(target!=null)){ - this.addEdge(source.getName() +"_" + target.getName(), source.getId(), target.getId(), {}); - } - else{ - if (source == null){ - console.log("No encontrado: " + nodeNameSource) - } - if (target == null){ - console.log("No encontrado: " + nodeNameTarget) - } - } -}; - -GraphDataset.prototype.loadFromJSON = function(json){ - var json = json; - this.init(); - this.json = new Object(); - this.json.vertices = new Array(); - this.json.edges = new Array(); - this.json.relations = new Array(); - - for ( var i = 0; i < json.nodes.length; i++) { - if (json.nodes[i] != null){ - var name = json.nodes[i]; - this.addNode(name); - } - else{ - this.json.vertices.push(null); - } - } - - for ( var i = 0; i < json.edges.length; i++) { - if (json.edges[i] != null){ - if (json.relations[i] != null){ - var name = json.edges[i]; - this.addEdge(name, json.relations[i].sourceIndex, json.relations[i].targetIndex, json.relations[i].args); - } - } - else{ - this.json.edges.push(null); - this.json.relations.push(null); - } - } -}; - -GraphDataset.prototype.prettyPrint = function(){ - for ( var node in this.vertices) { - console.log(this.vertices[node].getName() ); - for ( var j = 0; j < this.vertices[node].getEdgesIn().length; j++) { - console.log(" --> " + this.vertices[node].getEdgesIn()[j].getNodeTarget().getName() ); - } - } -}; - -GraphDataset.prototype._removeEdge = function(edge){ - this.json.edges[edge.getId()] = null; - this.json.relations[edge.getId()] = null; - - delete this.edges[edge.getId()]; - this.edgeDeleted.notify(edge); - - -}; - -GraphDataset.prototype._removeNode = function(node){ - this.json.vertices[node.getId()] = null; - delete this.vertices[node.getId()]; - this.vertexDeleted.notify(node); -}; - -GraphDataset.prototype.toJSON = function(){ - var json = new Object(); - var nodes = new Array(); - json.nodes = this.json.vertices; //nodes; - json.edges = this.json.edges; //edges; - json.relations = this.json.relations; - return json; -}; - -GraphDataset.prototype.clone = function(){ - var dsDataset = new GraphDataset(); - dsDataset.loadFromJSON(this.toJSON()); - return dsDataset; -}; -//GraphDataset.prototype.test = function(){ -// this.loadFromJSON(this.toJSON()); -//}; - -function labels(){ - var names = new Array(); - - var dataset = interactomeViewer.graphEditorWidget.dataset; - var layout = interactomeViewer.graphEditorWidget.layout; - - for ( var vertexId in interactomeViewer.graphEditorWidget.dataset.getVertices()) { - names.push(interactomeViewer.graphEditorWidget.dataset.getVertexById(vertexId).getName()); - } - - var sorted = (names.sort()); - console.log(sorted) - var distance = 0.01; - var altura = 0.6; - for ( var i = 0; i < names.length; i++) { - var id =dataset.getVertexByName(names[i]).getId(); - - layout.getNodeById(id).setCoordenates(distance, altura); - - - distance = parseFloat(distance) + parseFloat(0.03); - - altura = parseFloat(altura) + parseFloat(0.02); - - if (parseFloat(altura) == 0.9800000000000003){ - - altura = 0.6; - distance = distance - 0.51; - } - - } - - -}; - -function GraphItem(id, name, args){ - this.id = id; - this.name = name; - this.type = "NONE"; - - this.args = new Object(); - - - if (args!=null){ - this.args = args; - if (args.type !=null){ - this.type = args.type; - } - } - - //Events - this.nameChanged = new Event(this); - this.deleted = new Event(this); -} - -GraphItem.prototype.getName = function(){ - return this.name; -}; - -GraphItem.prototype.getId = function(){ - return this.id; -}; - -GraphItem.prototype.setName = function(name){ - var oldName = this.getName(); - this.name = name; - this.nameChanged.notify({"item": this, "previousName" : oldName}); -}; - - - - - -function LayoutDataset(){ - this.dataset = null; - this.vertices = new Object(); - this.changed = new Event(this); - - - this.args = new Object(); - - //RANDOM, CIRCLE - this.args.type = "CIRCLE"; -}; - -LayoutDataset.prototype.loadFromJSON = function(dataset, json){ - var _this = this; - this.vertices = new Object(); - this.dataset = dataset; //new GraphDataset(); - for ( var vertex in json) { - this.vertices[vertex] = new NodeLayout(vertex, json[vertex].x, json[vertex].y); - this.vertices[vertex].changed.attach(function (sender, item){ - _this.changed.notify(item); - }); - } - this._attachDatasetEvents(); -}; - - -LayoutDataset.prototype.toJSON = function(){ - var serialize = new Object(); - for ( var vertex in this.vertices) { - serialize[vertex] = new Object(); - serialize[vertex].x = this.vertices[vertex].x; - serialize[vertex].y = this.vertices[vertex].y; - } - serialize.dataset = new Object(); - serialize.dataset =this.dataset.toJSON(); - return serialize; -}; - -LayoutDataset.prototype.dataBind = function(graphDataset){ - this.dataset = graphDataset; - this._attachDatasetEvents(); - this._calculateLayout(); -}; - -LayoutDataset.prototype._removeVertex = function(vertexId){ - delete this.vertices[vertexId]; -}; - -LayoutDataset.prototype._attachDatasetEvents = function(){ - var _this = this; - - this.dataset.vertexDeleted.attach(function (sender, item){ - _this._removeVertex(item.getId()); - }); - - this.dataset.newVertex.attach(function (sender, item){ - _this.vertices[item.getId()] = new NodeLayout(item.getId(), 0.5, 0.5); - _this.vertices[item.getId()].changed.attach(function (sender, item){ - _this.changed.notify(item); - }); - }); -}; - -LayoutDataset.prototype.getType = function(){ - return this.args.type; -}; - -LayoutDataset.prototype._calculateLayoutVertices = function(type, count){ - - if (type == "CIRCLE"){ - var radius = 0.4; - var centerX = 0.5; - var centerY = 0.5; - var verticesCoordinates = new Array(); - for(var i = 0; i < count; i++){ - x = centerX + radius * Math.sin(i * 2 * Math.PI/count); - y = centerY + radius * Math.cos(i * 2 * Math.PI/count); - verticesCoordinates.push({'x':x,'y':y}); - } - return verticesCoordinates; - } -}; - - -LayoutDataset.prototype._calculateLayout = function(){ - var _this = this; - if (this.getType() == "RANDOM"){ - for ( var vertex in this.dataset.getVertices()) { - if (this.vertices[vertex] == null){ - this.vertices[vertex] = new NodeLayout(vertex, 0, 0); - } - this.vertices[vertex].setCoordinates(Math.random(), Math.random()); - this.vertices[vertex].changed.attach(function (sender, item){ - _this.changed.notify(item); - }); - } - } - - if ( this.getType() == "CIRCLE"){ - - var count = this.dataset._getVerticesCount(); - var verticesCoordinates = this._calculateLayoutVertices(this.getType(), count); - - var aux = 0; - for ( var vertex in this.dataset.getVertices()) { - if (this.vertices[vertex] == null){ - this.vertices[vertex] = new NodeLayout(vertex, 0, 0); - } - this.vertices[vertex].setCoordinates(verticesCoordinates[aux].x, verticesCoordinates[aux].y);//{"x":, "y":}; - aux++; - this.vertices[vertex].changed.attach(function (sender, item){ - _this.changed.notify(item); - }); - } - } - - - if (this.getType() == "SQUARE"){ - - var count = this.dataset._getVerticesCount(); - var xMin = 0.1; - var xMax = 0.9; - var yMin = 0.1; - var yMax = 0.9; - - var rows = Math.sqrt(count); - var step = (xMax - xMin) / rows; - - var verticesCoordinates = new Array(); - for(var i = 0; i < rows; i ++){ - for ( var j = 0; j < rows; j++) { - x = i * step + xMin; - y = j * step + yMin; - verticesCoordinates.push({'x':x,'y':y}); - } - } - - var aux = 0; - for ( var vertex in this.dataset.getVertices()) { - if (this.vertices[vertex] == null){ - this.vertices[vertex] = new NodeLayout(vertex, 0, 0); - } - this.vertices[vertex].setCoordinates(verticesCoordinates[aux].x, verticesCoordinates[aux].y);//{"x":, "y":}; - aux++; - this.vertices[vertex].changed.attach(function (sender, item){ - _this.changed.notify(item); - }); - } - } - -}; - -LayoutDataset.prototype.getNodeById = function(id){ - return this.vertices[id]; -}; - -LayoutDataset.prototype.getVerticesByArea = function(x1, y1, x2, y2){ - var vertices = new Array(); - for ( var vertex in this.dataset.getVertices()) { - if ((this.vertices[vertex].x >= x1)&&(this.vertices[vertex].x <= x2)){ - if ((this.vertices[vertex].y >= y1)&&(this.vertices[vertex].y <= y2)){ - vertices.push(this.vertices[vertex]); - } - } - } - return vertices; -}; - - - - -LayoutDataset.prototype.getLayout = function(type){ - - if (type == "CIRCLE"){ - this.args.type = "CIRCLE"; - this._calculateLayout(); - return; - } - - if (type == "SQUARE"){ - this.args.type = "SQUARE"; - this._calculateLayout(); - return; - } - - if (type == "RANDOM"){ - this.args.type = "RANDOM"; - this._calculateLayout(); - return; - } - - - var dotText = this.dataset.toDOTID(); - var url = "http://bioinfo.cipf.es/utils/ws/rest/network/layout/"+type+".coords"; - var _this = this; - - $.ajax({ - async: true, - type: "POST", - url: url, - dataType: "text", - data: { - dot :dotText - }, - cache: false, - success: function(data){ - var response = JSON.parse(data); - for ( var vertexId in response) { - _this.vertices[vertexId].setCoordinates(response[vertexId].x, response[vertexId].y); - } - } - }); - -// $.ajax({ -// async: true, -// type: "POST", -// url: url, -// dataType: "script", -// data: { -// dot :dotText -// }, -// cache: false, -// success: function(data){ -// var response = JSON.parse(data); -// for ( var vertexId in response) { -// _this.vertices[vertexId].setCoordinates(response[vertexId].x, response[vertexId].y); -// } -// } -// }); - -}; - -function NodeLayout(id, x, y, args){ - this.id = id; - this.x = x; - this.y = y; - this.changed = new Event(this); -}; - -NodeLayout.prototype.getId = function(id){ - return this.id; -}; - -NodeLayout.prototype.setCoordinates = function(x, y){ - this.x = x; - this.y = y; - this.changed.notify(this); -}; - - - -function NetworkDataSetFormatter(vertexFormatProperties, defaultEdgeProperties, args){ - DataSet.prototype.constructor.call(this); - - this.args = new Object(); - - this.vertices = new Object(); - this.edges = new Object(); - this.dataset = null; - this.maxClass = 0; - this.minClass = 0; - - /** Coordenates with default Setting */ - this.args.width = 1100; - this.args.height = 500; - - /** Optional parameters */ - this.args.backgroundColor = "#FFFFFF"; - this.args.backgroundImage = null; - this.args.backgroundImageHeight = null; - this.args.backgroundImageWidth = null; - this.args.backgroundImageX = null; - this.args.backgroundImageY = null; - - - this.args.balanceNodes = false; - this.args.nodesMaxSize = 3; - this.args.nodesMinSize = 0.5; - - - /** Zoom **/ - this.args.zoomScale = 1; - this.args.zoomScaleStepFactor = 0.4; - - if (args != null){ - if (args.backgroundImage != null){ - this.args.backgroundImage = args.backgroundImage; - } - - if (args.width != null){ - this.args.width = args.width; - } - - if (args.height != null){ - this.args.height = args.height; - this.args.svgHeight = args.height; - } - - if (args.svgHeight != null){ - this.args.svgHeight = args.svgHeight; - } - - if (args.backgroundColor != null){ - this.args.backgroundColor = args.backgroundColor; - } - - if(args.balanceNodes != null){ - this.args.balanceNodes = args.balanceNodes; - } - - if(args.nodesMaxSize != null){ - this.args.nodesMaxSize = args.nodesMaxSize; - } - if(args.nodesMinSize != null){ - this.args.nodesMinSize = args.nodesMinSize; - } - } - - this.args.defaultEdgeProperties = {"fill":"#000000", "radius":"1", "stroke":"#000000", "size":1, "title":{"fontSize":10, "fontColor":"#000000"}}; - this.args.vertexFormatProperties = { "fill":"#000000", "stroke":"#000000", "stroke-opacity":"#000000"}; - - if (vertexFormatProperties!= null){ - this.args.vertexFormatProperties = vertexFormatProperties; - } - if (defaultEdgeProperties!= null){ - this.args.defaultEdgeProperties = defaultEdgeProperties; - } - - /** Events **/ - this.changed = new Event(this); - this.edgeChanged = new Event(this); - this.resized = new Event(this); - this.backgroundImageChanged= new Event(this); - this.backgroundColorChanged= new Event(this); -}; - -NetworkDataSetFormatter.prototype.loadFromJSON = function(dataset, json){ - this.args = new Object(); - this.vertices = new Object(); - this.args = json; - this._setDataset(dataset); - var _this = this; - - for ( var vertex in json.vertices) { - this.addVertex(vertex, json.vertices[vertex]); - } - - for ( var edgeId in json.edges) { - this.addEdge(edgeId, json.edges[edgeId]); - } -}; - - -NetworkDataSetFormatter.prototype.toJSON = function(){ - - -// this.args.vertices = new Object(); -// this.args.edges = new Object(); -// -// for ( var vertex in this.vertices) { -// this.args.vertices[vertex] = this.getVertexById(vertex).toJSON(); -// } -// for ( var edge in this.edges) { -// this.args.edges[edge] = this.getEdgeById(edge).toJSON(); -// } -// -// return (this.args); - - - var serialize = new Object(); - serialize = JSON.parse(JSON.stringify(this.args)); - serialize.vertices = new Object(); - serialize.edges = new Object(); - - for ( var vertex in this.vertices) { - serialize.vertices[vertex] = this.getVertexById(vertex).toJSON(); - } - for ( var edge in this.edges) { - serialize.edges[edge] = this.getEdgeById(edge).toJSON(); - } - - return (serialize); -}; - - - -NetworkDataSetFormatter.prototype._getNodeSize = function(nodeId){ - if (this.isVerticesBalanced()){ - var total = this.maxClass - this.minClass; - if (total == 0){ total = 1;} - var nodeConnection = this.dataset.getVertexById(nodeId).getEdges().length; - return ((nodeConnection*this.args.nodesMaxSize)/total) + this.args.nodesMinSize; - } - return this.getVertexById(nodeId).getDefault().getSize(); -}; - -NetworkDataSetFormatter.prototype._recalculateSize = function(){ - if (this.isVerticesBalanced()){ - this.maxClass = this.dataset.getMaxClass(); - this.minClass = this.dataset.getMinClass(); - for ( var vertexIdAll in this.vertices) { - var size = this._getNodeSize(vertexIdAll); - this.vertices[vertexIdAll].getDefault().setSize(size); - this.vertices[vertexIdAll].getSelected().setSize(size); - this.vertices[vertexIdAll].getOver().setSize(size); - } - } -}; - - -NetworkDataSetFormatter.prototype.addVertex = function(vertexId, json){ - - - if (json == null){ - this.vertices[vertexId] = new CircleVertexGraphFormatter(vertexId, this.args.vertexFormatProperties.defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); - } - else{ - - /** Cargo los attributos desde el json **/ - if (json.type == null){ - this.vertices[vertexId] = new CircleVertexGraphFormatter(vertexId, this.args.vertexFormatProperties.defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); - } - - if ((json.type == "SquareVertexGraphFormatter")||(json.type == "SquareVertexNetworkFormatter")){ - this.vertices[vertexId] = new SquareVertexGraphFormatter(vertexId); - this.vertices[vertexId].loadFromJSON(json); - } - - if ((json.type == "CircleVertexGraphFormatter")||(json.type == "CircleVertexNetworkFormatter")){ - this.vertices[vertexId] = new CircleVertexGraphFormatter(vertexId); - this.vertices[vertexId].loadFromJSON(json); - } - - if ((json.type == "EllipseVertexGraphFormatter")||(json.type == "EllipseVertexNetworkFormatter")){ - this.vertices[vertexId] = new EllipseVertexGraphFormatter(vertexId); - this.vertices[vertexId].loadFromJSON(json); - } - - if ((json.type == "RectangleVertexGraphFormatter")||(json.type == "RectangleVertexNetworkFormatter")){ - this.vertices[vertexId] = new RectangleVertexGraphFormatter(vertexId); - this.vertices[vertexId].loadFromJSON(json); - } - - if ((json.type == "RoundedVertexGraphFormatter")||(json.type == "RoundedVertexNetworkFormatter")){ - this.vertices[vertexId] = new RoundedVertexGraphFormatter(vertexId); - this.vertices[vertexId].loadFromJSON(json); - } - - } - - - var _this = this; - this.vertices[vertexId].stateChanged.attach(function (sender, item){ - _this.changed.notify(item); - }); - - var size = this._getNodeSize(vertexId); - this.vertices[vertexId].defaultFormat.args.size = size; - this.vertices[vertexId].selected.args.size = size; - this.vertices[vertexId].over.args.size = size; - -}; - -NetworkDataSetFormatter.prototype.addEdge = function(edgeId, json){ - - /** Es un edge nuevo que le doy los atributos por defecto **/ - if (json == null){ - if (this.dataset.getEdgeById(edgeId).getNodeSource().getId() == this.dataset.getEdgeById(edgeId).getNodeTarget().getId()){ - this.edges[edgeId] = new BezierEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); - }else{ - this.edges[edgeId] = new DirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); - } - } - else{ - /** Cargo los attributos desde el json **/ - if (json.type == null){ - this.edges[edgeId] = new LineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); - } - - if ((json.type == "LineEdgeGraphFormatter")||(json.type == "LineEdgeNetworkFormatter")){ - this.edges[edgeId] = new LineEdgeGraphFormatter(edgeId); - this.edges[edgeId].loadFromJSON(json); - } - if ((json.type == "DirectedLineEdgeGraphFormatter")||(json.type == "DirectedLineEdgeNetworkFormatter")){ - this.edges[edgeId] = new DirectedLineEdgeGraphFormatter(edgeId); - this.edges[edgeId].loadFromJSON(json); - } - - if ((json.type == "BezierEdgeGraphFormatter")||(json.type == "BezierEdgeNetworkFormatter")){ - this.edges[edgeId] = new BezierEdgeGraphFormatter(edgeId); - this.edges[edgeId].loadFromJSON(json); - } - - - if ((json.type == "CutDirectedLineEdgeGraphFormatter")||(json.type == "CutDirectedLineEdgeNetworkFormatter")){ - this.edges[edgeId] = new CutDirectedLineEdgeGraphFormatter(edgeId); - this.edges[edgeId].loadFromJSON(json); - } - - if ((json.type == "DotDirectedLineEdgeGraphFormatter")||(json.type == "DotDirectedLineEdgeNetworkFormatter")){ - this.edges[edgeId] = new DotDirectedLineEdgeGraphFormatter(edgeId); - this.edges[edgeId].loadFromJSON(json); - } - if ((json.type == "OdotDirectedLineEdgeGraphFormatter")||(json.type == "OdotDirectedLineEdgeNetworkFormatter")){ - this.edges[edgeId] = new OdotDirectedLineEdgeGraphFormatter(edgeId); - this.edges[edgeId].loadFromJSON(json); - } - - if ((json.type == "OdirectedLineEdgeGraphFormatter")||(json.type == "OdirectedLineEdgeNetworkFormatter")){ - this.edges[edgeId] = new OdirectedLineEdgeGraphFormatter(edgeId); - this.edges[edgeId].loadFromJSON(json); - } - } - - var _this = this; - this.edges[edgeId].stateChanged.attach(function (sender, item){ - _this.edgeChanged.notify(item); - }); - - this._recalculateSize(); -}; - -NetworkDataSetFormatter.prototype._setDataset = function(dataset){ - this.dataset = dataset; - this.maxClass = dataset.getMaxClass(); - this.minClass = dataset.getMinClass(); - this._attachDatasetEvents(); -}; - -NetworkDataSetFormatter.prototype.changeEdgeType = function(edgeId, type){ - if ((type == "LineEdgeGraphFormatter")||(type == "LineEdgeNetworkFormatter")){ - this.edges[edgeId] = new LineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); - - } - if ((type == "DirectedLineEdgeGraphFormatter")||(type == "DirectedLineEdgeNetworkFormatter")){ - this.edges[edgeId] = new DirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); - } - - if ((type == "CutDirectedLineEdgeGraphFormatter")||(type == "CutDirectedLineEdgeNetworkFormatter")){ - this.edges[edgeId] = new CutDirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); - } - - if ((type == "DotDirectedLineEdgeGraphFormatter")||(type == "DotDirectedLineEdgeNetworkFormatter")){ - this.edges[edgeId] = new DotDirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); - } - - if ((type == "OdotDirectedLineEdgeGraphFormatter")||(type == "OdotDirectedLineEdgeNetworkFormatter")){ - this.edges[edgeId] = new OdotDirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); - } - - if ((type == "OdirectedLineEdgeGraphFormatter")||(type == "OdirectedLineEdgeNetworkFormatter")){ - this.edges[edgeId] = new OdirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); - } - - - - var _this = this; - this.edges[edgeId].stateChanged.attach(function (sender, item){ - _this.edgeChanged.notify(item); - }); - _this.edgeChanged.notify(this.edges[edgeId]); -}; -/* -classe = "SquareNetworkNodeFormatter"; -} -if (value == "circle"){ - classe = "CircleNetworkNodeFormatter"; - **/ -NetworkDataSetFormatter.prototype.changeNodeType = function(vertexId, type){ - var defaultFormat = JSON.parse(JSON.stringify(this.vertices[vertexId].getDefault())); - var selectedFormat = JSON.parse(JSON.stringify(this.vertices[vertexId].getSelected())); - var defaultFormat = JSON.parse(JSON.stringify(this.vertices[vertexId].getDefault())); - var defaultFormat = JSON.parse(JSON.stringify(this.vertices[vertexId].getDefault())); - - if ((type == "SquareVertexGraphFormatter")||(type == "SquareVertexNetworkFormatter")){ - this.vertices[vertexId] = new SquareVertexGraphFormatter(vertexId,defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); - } - - if ((type == "CircleVertexGraphFormatter")||(type == "CircleVertexNetworkFormatter")){ - this.vertices[vertexId] = new CircleVertexGraphFormatter(vertexId, defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); - } - - if ((type == "EllipseVertexGraphFormatter")||(type == "EllipseVertexNetworkFormatter")){ - this.vertices[vertexId] = new EllipseVertexGraphFormatter(vertexId, defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); - } - - if ((type == "RectangleVertexGraphFormatter")||(type == "RectangleVertexNetworkFormatter")){ - this.vertices[vertexId] = new RectangleVertexGraphFormatter(vertexId, defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); - } - - if ((type == "RoundedVertexGraphFormatter")||(type == "RoundedVertexNetworkFormatter")){ - this.vertices[vertexId] = new RoundedVertexGraphFormatter(vertexId, defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); - } - - if ((type == "OctagonVertexGraphFormatter")||(type == "OctagonVertexNetworkhFormatter")){ - this.vertices[vertexId] = new OctagonVertexGraphFormatter(vertexId, defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); - } - - - var _this = this; - this.vertices[vertexId].stateChanged.attach(function (sender, item){ - _this.changed.notify(item); - }); - _this.changed.notify(this.vertices[vertexId]); -}; - - - -NetworkDataSetFormatter.prototype.dataBind = function(networkDataSet){ - var _this = this; - this._setDataset(networkDataSet); - - for ( var vertex in this.dataset.getVertices()) { - this.addVertex(vertex); - } - - for ( var edge in this.dataset.getEdges()) { - this.addEdge(edge); - } -}; - -NetworkDataSetFormatter.prototype._removeEdge = function(edgeId){ - delete this.edges[edgeId]; -}; - -NetworkDataSetFormatter.prototype._removeVertex = function(vertexId){ - delete this.vertices[vertexId]; -}; - -NetworkDataSetFormatter.prototype._attachDatasetEvents = function(id){ - var _this = this; - this.dataset.vertexDeleted.attach(function (sender, item){ - _this._removeVertex(item.getId()); - }); - - this.dataset.edgeDeleted.attach(function (sender, item){ - _this._removeEdge(item.getId()); - }); - - this.dataset.newVertex.attach(function (sender, item){ - _this.addVertex(item.getId()); - }); - - this.dataset.newEdge.attach(function (sender, item){ - _this.addEdge(item.getId()); - }); -}; - - -NetworkDataSetFormatter.prototype.getVertexById = function(id){ - return this.vertices[id]; -}; - -NetworkDataSetFormatter.prototype.getEdgeById = function(id){ - return this.edges[id]; -}; - -NetworkDataSetFormatter.prototype.makeLabelsBigger = function(){ -for ( var vertexId in this.vertices) { - var fontSize = this.vertices[vertexId].getDefault().getFontSize() + 2; - this.vertices[vertexId].getDefault().setFontSize(fontSize); - } -}; - -NetworkDataSetFormatter.prototype.makeLabelsSmaller = function(){ - for ( var vertexId in this.vertices) { - var fontSize = this.vertices[vertexId].getDefault().getFontSize() - 2; - this.vertices[vertexId].getDefault().setFontSize(fontSize); - } -}; - - -NetworkDataSetFormatter.prototype.resize = function(width, height){ - this.args.width = width; - this.args.height = height; - this.resized.notify(); -}; - -/** ZOOM GETTERS **/ -NetworkDataSetFormatter.prototype.getZoomScaleStepFactor = function(){return this.args.zoomScaleStepFactor;}; -NetworkDataSetFormatter.prototype.setZoomScaleStepFactor = function(scaleFactor){this.args.zoomScaleStepFactor = scaleFactor;}; -NetworkDataSetFormatter.prototype.getZoomScale = function(){return this.args.zoomScale;}; -NetworkDataSetFormatter.prototype.setZoomScale = function(scale){this.args.zoomScale = scale;}; - -NetworkDataSetFormatter.prototype.getNodesMaxSize = function(){return this.args.nodesMaxSize;}; -NetworkDataSetFormatter.prototype.getNodesMinSize = function(){return this.args.nodesMinSize;}; - -/** SIZE SETTERS AND GETTERS **/ -NetworkDataSetFormatter.prototype.isVerticesBalanced = function(){return this.args.balanceNodes;}; -NetworkDataSetFormatter.prototype.getWidth = function(){return this.args.width;}; -NetworkDataSetFormatter.prototype.getHeight = function(){return this.args.height;}; - -/** OPTIONAL PARAMETERS GETTERS AND SETTERS **/ -NetworkDataSetFormatter.prototype.getBackgroundImage = function(){return this.args.backgroundImage;}; -NetworkDataSetFormatter.prototype.setBackgroundImage = function(value){this.args.backgroundImage = value; this.backgroundImageChanged.notify(this);}; - - -NetworkDataSetFormatter.prototype.getBackgroundImageWidth = function(){return this.args.backgroundImageWidth;}; -NetworkDataSetFormatter.prototype.setBackgroundImageWidth = function(value){this.args.backgroundImageWidth = value; this.backgroundImageChanged.notify(this);}; - -NetworkDataSetFormatter.prototype.getBackgroundImageHeight = function(){return this.args.backgroundImageHeight;}; -NetworkDataSetFormatter.prototype.setBackgroundImageHeight = function(value){this.args.backgroundImageHeight = value; this.backgroundImageChanged.notify(this);}; - -NetworkDataSetFormatter.prototype.getBackgroundImageX = function(){return this.args.backgroundImageX;}; -NetworkDataSetFormatter.prototype.setBackgroundImageX = function(value){this.args.backgroundImageX = value; this.backgroundImageChanged.notify(this);}; - -NetworkDataSetFormatter.prototype.getBackgroundImageY = function(){return this.args.backgroundImageX;}; -NetworkDataSetFormatter.prototype.setBackgroundImageY = function(value){this.args.backgroundImageY = value; this.backgroundImageChanged.notify(this);}; - - - -NetworkDataSetFormatter.prototype.getBackgroundColor = function(){return this.args.backgroundColor;}; -NetworkDataSetFormatter.prototype.setBackgroundColor = function(value){this.args.backgroundColor = value; this.backgroundColorChanged.notify(this);}; - -NetworkDataSetFormatter.prototype.getWidth = function(){return this.args.width;}; -NetworkDataSetFormatter.prototype.setWidth = function(value){this.args.width = value;}; - -NetworkDataSetFormatter.prototype.getHeight = function(){return this.args.height;}; -NetworkDataSetFormatter.prototype.setHeight = function(value){this.args.height = value;}; - - - - -Vertex.prototype.getName = GraphItem.prototype.getName; -Vertex.prototype.setName = GraphItem.prototype.setName; -Vertex.prototype.getId = GraphItem.prototype.getId; - -function Vertex(id, name, args){ - GraphItem.prototype.constructor.call(this, id, name, args); - this.edgesIn= new Array(); - this.edgesOut= new Array(); -}; - -Vertex.prototype.getEdges = function(){ - return this.edgesIn.concat(this.edgesOut); -}; - -Vertex.prototype.getEdgesCount = function(){ - return this.getEdges().length; -}; - -Vertex.prototype.getEdgesIn = function(){ - return this.edgesIn; -}; - -Vertex.prototype.getEdgesOut = function(){ - return this.edgesOut; -}; - -Vertex.prototype.addEdge = function(edge){ - if (edge.getNodeSource().getId() == this.id){ - this.edgesIn.push(edge); - } - else{ - this.edgesOut.push(edge); - } -}; - -Vertex.prototype.removeEdge = function(edge){ - for ( var i = 0; i < this.getEdgesIn().length; i++) { - var edgeIn = this.edgesIn[i]; - if (edgeIn.getId() == edge.getId()){ - this.edgesIn.splice(i, 1); - } - } - for ( var i = 0; i < this.getEdgesOut().length; i++) { - var edgeIn = this.edgesOut[i]; - if (edgeIn.getId() == edge.getId()){ - this.edgesOut.splice(i, 1); - } - } -}; - -Vertex.prototype.remove = function(){ - var edges = this.getEdges(); - for ( var i = 0; i < edges.length; i++) { - var edge = edges[i]; - edge.remove(); - } - this.deleted.notify(this); -}; - - - - - -VertexGraphFormatter.prototype.getDefault = ItemGraphFormatter.prototype.getDefault; -VertexGraphFormatter.prototype.getSelected = ItemGraphFormatter.prototype.getSelected; -VertexGraphFormatter.prototype.getOver = ItemGraphFormatter.prototype.getOver; -VertexGraphFormatter.prototype.getDragging = ItemGraphFormatter.prototype.getDragging; -VertexGraphFormatter.prototype.getId = ItemGraphFormatter.prototype.getId; -VertexGraphFormatter.prototype.toJSON = ItemGraphFormatter.prototype.toJSON; -VertexGraphFormatter.prototype.loadFromJSON = ItemGraphFormatter.prototype.loadFromJSON; -VertexGraphFormatter.prototype._setEvents = ItemGraphFormatter.prototype._setEvents; - - -function VertexGraphFormatter(defaultFormat, selectedFormat, overFormat, draggingFormat){ - ItemGraphFormatter.prototype.constructor.call(this, defaultFormat, selectedFormat, overFormat, draggingFormat); -}; - - -CircleVertexGraphFormatter.prototype.getDefault = VertexGraphFormatter.prototype.getDefault; -CircleVertexGraphFormatter.prototype.getSelected = VertexGraphFormatter.prototype.getSelected; -CircleVertexGraphFormatter.prototype.getOver = VertexGraphFormatter.prototype.getOver; -CircleVertexGraphFormatter.prototype.getDragging = VertexGraphFormatter.prototype.getDragging; -CircleVertexGraphFormatter.prototype.getId = VertexGraphFormatter.prototype.getId; -CircleVertexGraphFormatter.prototype.toJSON = VertexGraphFormatter.prototype.toJSON; -CircleVertexGraphFormatter.prototype.loadFromJSON = VertexGraphFormatter.prototype.loadFromJSON; -CircleVertexGraphFormatter.prototype._setEvents = VertexGraphFormatter.prototype._setEvents; - -function CircleVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ - VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); - this.args.type = "CircleVertexGraphFormatter"; - if (defaultFormat != null){ - if (defaultFormat.radius != null){ - this.defaultFormat.args.radius = defaultFormat.radius; - } - } - - if (selectedFormat != null){ - if (selectedFormat.radius != null){ - this.selected.args.radius = selectedFormat.radius; - } - } - - if (overFormat != null){ - if (overFormat.radius != null){ - this.over.args.radius = overFormat.radius; - } - } - - if (draggingFormat != null){ - if (draggingFormat.radius != null){ - this.dragging.args.draggingFormat = draggingFormat.radius; - } - } -}; - - - -SquareVertexGraphFormatter.prototype.getDefault = VertexGraphFormatter.prototype.getDefault; -SquareVertexGraphFormatter.prototype.getSelected = VertexGraphFormatter.prototype.getSelected; -SquareVertexGraphFormatter.prototype.getOver = VertexGraphFormatter.prototype.getOver; -SquareVertexGraphFormatter.prototype.getDragging = VertexGraphFormatter.prototype.getDragging; -SquareVertexGraphFormatter.prototype.getId = VertexGraphFormatter.prototype.getId; -SquareVertexGraphFormatter.prototype.toJSON = VertexGraphFormatter.prototype.toJSON; -SquareVertexGraphFormatter.prototype.loadFromJSON = VertexGraphFormatter.prototype.loadFromJSON; -SquareVertexGraphFormatter.prototype._setEvents = VertexGraphFormatter.prototype._setEvents; - -function SquareVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ - VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); - this.args.type = "SquareVertexGraphFormatter"; - if (defaultFormat != null){ - if (defaultFormat.radius != null){ - this.defaultFormat.args.radius = defaultFormat.radius; - } - } - - if (selectedFormat != null){ - if (selectedFormat.radius != null){ - this.selected.args.radius = selectedFormat.radius; - } - } - - if (overFormat != null){ - if (overFormat.radius != null){ - this.over.args.radius = overFormat.radius; - } - } - - if (draggingFormat != null){ - if (draggingFormat.radius != null){ - this.dragging.args.draggingFormat = draggingFormat.radius; - } - } -}; - - -EllipseVertexGraphFormatter.prototype.getDefault = VertexGraphFormatter.prototype.getDefault; -EllipseVertexGraphFormatter.prototype.getSelected = VertexGraphFormatter.prototype.getSelected; -EllipseVertexGraphFormatter.prototype.getOver = VertexGraphFormatter.prototype.getOver; -EllipseVertexGraphFormatter.prototype.getDragging = VertexGraphFormatter.prototype.getDragging; -EllipseVertexGraphFormatter.prototype.getId = VertexGraphFormatter.prototype.getId; -EllipseVertexGraphFormatter.prototype.toJSON = VertexGraphFormatter.prototype.toJSON; -EllipseVertexGraphFormatter.prototype.loadFromJSON = VertexGraphFormatter.prototype.loadFromJSON; -EllipseVertexGraphFormatter.prototype._setEvents = VertexGraphFormatter.prototype._setEvents; - -function EllipseVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ - VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); - this.args.type = "EllipseVertexGraphFormatter"; - if (defaultFormat != null){ - if (defaultFormat.radius != null){ - this.defaultFormat.args.radius = defaultFormat.radius; - } - } - - if (selectedFormat != null){ - if (selectedFormat.radius != null){ - this.selected.args.radius = selectedFormat.radius; - } - } - - if (overFormat != null){ - if (overFormat.radius != null){ - this.over.args.radius = overFormat.radius; - } - } - - if (draggingFormat != null){ - if (draggingFormat.radius != null){ - this.dragging.args.draggingFormat = draggingFormat.radius; - } - } -}; - - - -RectangleVertexGraphFormatter.prototype.getDefault = ItemGraphFormatter.prototype.getDefault; -RectangleVertexGraphFormatter.prototype.getSelected = ItemGraphFormatter.prototype.getSelected; -RectangleVertexGraphFormatter.prototype.getOver = ItemGraphFormatter.prototype.getOver; -RectangleVertexGraphFormatter.prototype.getDragging = ItemGraphFormatter.prototype.getDragging; -RectangleVertexGraphFormatter.prototype.getId = ItemGraphFormatter.prototype.getId; -RectangleVertexGraphFormatter.prototype.toJSON = ItemGraphFormatter.prototype.toJSON; -RectangleVertexGraphFormatter.prototype.loadFromJSON = ItemGraphFormatter.prototype.loadFromJSON; -RectangleVertexGraphFormatter.prototype._setEvents = ItemGraphFormatter.prototype._setEvents; - -function RectangleVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ - VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); - this.args.type = "RectangleVertexGraphFormatter"; - if (defaultFormat != null){ - if (defaultFormat.radius != null){ - this.defaultFormat.args.radius = defaultFormat.radius; - } - } - - if (selectedFormat != null){ - if (selectedFormat.radius != null){ - this.selected.args.radius = selectedFormat.radius; - } - } - - if (overFormat != null){ - if (overFormat.radius != null){ - this.over.args.radius = overFormat.radius; - } - } - - if (draggingFormat != null){ - if (draggingFormat.radius != null){ - this.dragging.args.draggingFormat = draggingFormat.radius; - } - } -}; - - - -RoundedVertexGraphFormatter.prototype.getDefault = ItemGraphFormatter.prototype.getDefault; -RoundedVertexGraphFormatter.prototype.getSelected = ItemGraphFormatter.prototype.getSelected; -RoundedVertexGraphFormatter.prototype.getOver = ItemGraphFormatter.prototype.getOver; -RoundedVertexGraphFormatter.prototype.getDragging = ItemGraphFormatter.prototype.getDragging; -RoundedVertexGraphFormatter.prototype.getId = ItemGraphFormatter.prototype.getId; -RoundedVertexGraphFormatter.prototype.toJSON = ItemGraphFormatter.prototype.toJSON; -RoundedVertexGraphFormatter.prototype.loadFromJSON = ItemGraphFormatter.prototype.loadFromJSON; -RoundedVertexGraphFormatter.prototype._setEvents = ItemGraphFormatter.prototype._setEvents; - -function RoundedVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ - VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); - this.args.type = "RoundedVertexGraphFormatter"; - if (defaultFormat != null){ - if (defaultFormat.radius != null){ - this.defaultFormat.args.radius = defaultFormat.radius; - } - } - - if (selectedFormat != null){ - if (selectedFormat.radius != null){ - this.selected.args.radius = selectedFormat.radius; - } - } - - if (overFormat != null){ - if (overFormat.radius != null){ - this.over.args.radius = overFormat.radius; - } - } - - if (draggingFormat != null){ - if (draggingFormat.radius != null){ - this.dragging.args.draggingFormat = draggingFormat.radius; - } - } -}; - - - -OctagonVertexGraphFormatter.prototype.getDefault = ItemGraphFormatter.prototype.getDefault; -OctagonVertexGraphFormatter.prototype.getSelected = ItemGraphFormatter.prototype.getSelected; -OctagonVertexGraphFormatter.prototype.getOver = ItemGraphFormatter.prototype.getOver; -OctagonVertexGraphFormatter.prototype.getDragging = ItemGraphFormatter.prototype.getDragging; -OctagonVertexGraphFormatter.prototype.getId = ItemGraphFormatter.prototype.getId; -OctagonVertexGraphFormatter.prototype.toJSON = ItemGraphFormatter.prototype.toJSON; -OctagonVertexGraphFormatter.prototype.loadFromJSON = ItemGraphFormatter.prototype.loadFromJSON; -OctagonVertexGraphFormatter.prototype._setEvents = ItemGraphFormatter.prototype._setEvents; - -function OctagonVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ - VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); - this.args.type = "OctagonVertexGraphFormatter"; - if (defaultFormat != null){ - if (defaultFormat.radius != null){ - this.defaultFormat.args.radius = defaultFormat.radius; - } - } - - if (selectedFormat != null){ - if (selectedFormat.radius != null){ - this.selected.args.radius = selectedFormat.radius; - } - } - - if (overFormat != null){ - if (overFormat.radius != null){ - this.over.args.radius = overFormat.radius; - } - } - - if (draggingFormat != null){ - if (draggingFormat.radius != null){ - this.dragging.args.draggingFormat = draggingFormat.radius; - } - } -}; - - - -var Colors = new function() -{ - this.hashColor = []; - this.getColorByScoreArrayValue = function (arrayScore) - { - var array = new Array(); - - for (var i = 0; i< arrayScore.length; i++) - { - - var color = this.getColorByScoreValue(arrayScore[i]) - array.push( color); - - } - return array; - }; - - this.getHexStringByScoreArrayValue = function (arrayScore) - { - var arrayColor = this.getColorByScoreArrayValue(arrayScore); - var arrayHex = new Array(); - for (var i = 0; i< arrayColor.length; i++) - { - arrayHex.push( arrayColor[i].HexString()); - } - return arrayHex; - }; - - this.getColorByScoreValue = function (score) - { - - var truncate = score.toString().substr(0,4); - if (this.hashColor[truncate]!=null) - { - return this.hashColor[truncate]; - } - - - if(isNaN(score)) { - return Colors.ColorFromRGB(0,0,0); - } - var value; - - var from, to; - if(score < 0.5) { - from = Colors.ColorFromRGB(0,0,255); - to = Colors.ColorFromRGB(255,255,255); - value = (score * 2); - } else { - from = Colors.ColorFromRGB(255,255,255); - to = Colors.ColorFromRGB(255,0,0); - value = (score * 2) - 1; - } - - var x = value; - var y = 1.0 - value; - var color = Colors.ColorFromRGB(y * from.Red() + x * to.Red(), y * from.Green() + x * to.Green(), y * from.Blue() + x * to.Blue()); - - this.hashColor[truncate] = color; - - return color; - }; - - this.ColorFromHSV = function(hue, sat, val) - { - var color = new Color(); - color.SetHSV(hue,sat,val); - return color; - }; - - this.ColorFromRGB = function(r, g, b) - { - var color = new Color(); - color.SetRGB(r,g,b); - return color; - }; - - this.ColorFromHex = function(hexStr) - { - var color = new Color(); - color.SetHexString(hexStr); - return color; - }; - - function Color() { - //Stored as values between 0 and 1 - var red = 0; - var green = 0; - var blue = 0; - - //Stored as values between 0 and 360 - var hue = 0; - - //Strored as values between 0 and 1 - var saturation = 0; - var value = 0; - - this.SetRGB = function(r, g, b) - { - red = r/255.0; - green = g/255.0; - blue = b/255.0; - calculateHSV(); - }; - - this.Red = function() { return Math.round(red*255); }; - - this.Green = function() { return Math.round(green*255); }; - - this.Blue = function() { return Math.round(blue*255); }; - - this.SetHSV = function(h, s, v) - { - hue = h; - saturation = s; - value = v; - calculateRGB(); - }; - - this.Hue = function() - { return hue; }; - - this.Saturation = function() - { return saturation; }; - - this.Value = function() - { return value; }; - - this.SetHexString = function(hexString) - { - if(hexString == null || typeof(hexString) != "string") - { - this.SetRGB(0,0,0); - return; - } - - if (hexString.substr(0, 1) == '#') - hexString = hexString.substr(1); - - if(hexString.length != 6) - { - this.SetRGB(0,0,0); - return; - } - - var r = parseInt(hexString.substr(0, 2), 16); - var g = parseInt(hexString.substr(2, 2), 16); - var b = parseInt(hexString.substr(4, 2), 16); - if (isNaN(r) || isNaN(g) || isNaN(b)) - { - this.SetRGB(0,0,0); - return; - } - - this.SetRGB(r,g,b); - }; - - this.HexString = function() - { - - var rStr = this.Red().toString(16); - if (rStr.length == 1) - rStr = '0' + rStr; - var gStr = this.Green().toString(16); - if (gStr.length == 1) - gStr = '0' + gStr; - var bStr = this.Blue().toString(16); - if (bStr.length == 1) - bStr = '0' + bStr; - return ('#' + rStr + gStr + bStr).toUpperCase(); - }; - - this.Complement = function() - { - var newHue = (hue >= 180) ? hue - 180 : hue + 180; - var newVal = (value * (saturation - 1) + 1); - var newSat = (value*saturation) / newVal; - var newColor = new Color(); - newColor.SetHSV(newHue, newSat, newVal); - return newColor; - } ; - - function calculateHSV() - { - var max = Math.max(Math.max(red, green), blue); - var min = Math.min(Math.min(red, green), blue); - - value = max; - - saturation = 0; - if(max != 0) - saturation = 1 - min/max; - - hue = 0; - if(min == max) - return; - - var delta = (max - min); - if (red == max) - hue = (green - blue) / delta; - else if (green == max) - hue = 2 + ((blue - red) / delta); - else - hue = 4 + ((red - green) / delta); - hue = hue * 60; - if(hue < 0) - hue += 360; - } - - function calculateRGB() - { - red = value; - green = value; - blue = value; - - if(value == 0 || saturation == 0) - return; - - var tHue = (hue / 60); - var i = Math.floor(tHue); - var f = tHue - i; - var p = value * (1 - saturation); - var q = value * (1 - saturation * f); - var t = value * (1 - saturation * (1 - f)); - switch(i) - { - case 0: - red = value; green = t; blue = p; - break; - case 1: - red = q; green = value; blue = p; - break; - case 2: - red = p; green = value; blue = t; - break; - case 3: - red = p; green = q; blue = value; - break; - case 4: - red = t; green = p; blue = value; - break; - default: - red = value; green = p; blue = q; - break; - } - } - } -} -(); -/* - * Clase gestiona la insercción, eliminación de los elementos en el DOM - * - * Vital hacerla SIEMPRE compatible hacia atrás - * - * Last update: 28-10-2010 - * - */ - - -var DOM = {}; - -DOM.createNewElement = function(type, nodeParent, attributes) -{ - - var node = document.createElement(type); - for (var i=0; i0) - { - parent.removeChild(parent.childNodes[0]); - - } -}; - -DOM.select = function(targetID) -{ - return document.getElementById(targetID); -// return $("#"+targetID); -}; -var Geometry = -{ - - /** From tow points obtains the angles formed with the cartesian side **/ - getAngleBetweenTwoPoints : function(x1, y1, x2, y2){ - //var m = (y1 - y2)/ (x1 - x2); - return Math.atan2(y2-y1, x2-x1); - }, - - getAdjacentSideOfRectangleRight : function(angle, hypotenuse){ - return Math.abs(Math.cos(angle)*hypotenuse); - }, - - getOppositeSideOfRectangleRight : function(angle, hypotenuse){ - return Math.abs(Math.sin(angle)*hypotenuse); - }, - - toDegree: function(radian){ - return radian*180/Math.PI; - - } - - -}; - -var SVG = -{ - svgns : 'http://www.w3.org/2000/svg', - xlinkns : "http://www.w3.org/1999/xlink", - - createSVGCanvas: function(parentNode, attributes) - { - - attributes.push( ['xmlns', SVG.svgns], ['xmlns:xlink', 'http://www.w3.org/1999/xlink']); - var svg = document.createElementNS("http://www.w3.org/2000/svg", "svg"); - this._setProperties(svg, attributes); - parentNode.appendChild( svg); - return svg; - - }, - - createRectangle : function (x, y, width, height, attributes){ - var rect = document.createElementNS(this.svgns, "rect"); - rect.setAttribute("x",x); - rect.setAttribute("y",y); - rect.setAttribute("width",width); - rect.setAttribute("height",height); - SVG._setProperties(rect, attributes); - return rect; - }, - - drawImage64 : function (x, y, width, height, base64, svgNode, attributes) { - var node = SVG.createImage64(x, y, width, height, base64, attributes); - svgNode.appendChild(node); - return node; - }, - - createImage64 : function (x, y, width, height, base64, attributes) { - var img = document.createElementNS(this.svgns, "image"); - img.setAttribute("x",x); - img.setAttribute("y",y); - img.setAttribute("width",width); - img.setAttribute("height",height); - img.setAttribute("xlink:href",base64); - SVG._setProperties(img, attributes); - return img; - }, - - createLine: function (x1, y1, x2, y2, attributes){ - var line = document.createElementNS(this.svgns,"line"); - line.setAttribute("x1",x1); - line.setAttribute("y1",y1); - line.setAttribute("x2", x2); - line.setAttribute("y2", y2); - SVG._setProperties(line, attributes); - return line; - }, - - createClip: function (id, nodeToClip, attributes){ - var clip = document.createElementNS(this.svgns,"clipPath"); - clip.setAttribute("id",id); - clip.appendChild(nodeToClip); - return clip; - }, - - drawClip : function (id, nodeToClip, svgNode) { - var node = SVG.createClip(id, nodeToClip); - svgNode.appendChild(node); - return node; - }, - - drawRectangle : function (cx, cy, width, height, svgNode, attributes) { - try{ - var node = SVG.createRectangle(cx, cy, width, height, attributes); - svgNode.appendChild(node); - } - catch(e){ - - console.log("-------------------- "); - console.log("Error on drawRectangle " + e); - console.log(attributes); - console.log("-------------------- "); - } - return node; - }, - - createEllipse : function (x, y, rx, ry, attributes){ - var rect = document.createElementNS(this.svgns, "ellipse"); - rect.setAttribute("cx",x); - rect.setAttribute("cy",y); - rect.setAttribute("rx",rx); - rect.setAttribute("ry",ry); - SVG._setProperties(rect, attributes); - return rect; - }, - - drawEllipse : function (cx, cy, rx, ry, svgNode, attributes) { - var node = SVG.createEllipse(cx, cy, rx, ry, attributes); - svgNode.appendChild(node); - return node; - }, - - drawImage : function (x, y, canvasSVG, attributes) { - var image = document.createElementNS(this.svgns, "image"); - image.setAttribute("x",x); - image.setAttribute("y",y); - canvasSVG.appendChild(image); - SVG._setProperties(image, attributes); - }, - - drawLine : function (x1, y1, x2, y2, nodeSVG, attributes) { - try{ - var line = SVG.createLine(x1, y1, x2, y2, attributes); - nodeSVG.appendChild(line); - }catch(e){ - } - return line; - }, - - - drawPath: function (d, nodeSVG, attributes) { - var path = SVG.createPath(d, attributes); - nodeSVG.appendChild(path); - return path; - }, - - createPoligon : function (points, attributes){ - var poligon = document.createElementNS(this.svgns, "polygon"); - poligon.setAttribute("points",points); - SVG._setProperties(poligon, attributes); - return poligon; - }, - - drawPoligon : function (points, canvasSVG, attributes){ - var poligon = SVG.createPoligon(points, attributes); - canvasSVG.appendChild(poligon); - return poligon; - }, - // - - createPath : function (d, attributes){ - var path = document.createElementNS(this.svgns, "path"); - path.setAttribute("d",d); - SVG._setProperties(path, attributes); - return path; - }, - - drawCircle : function (x, y, radio, canvasSVG, attributes) { - - var newText = document.createElementNS(this.svgns,"circle"); - newText.setAttribute("cx",x); - newText.setAttribute("cy",y); - newText.setAttribute("r",radio); - - canvasSVG.appendChild(newText); - attributes["cursor"] = "pointer"; - this._setProperties(newText, attributes); - return newText; - }, - - - _setProperties: function(node, attributes) - { - if (attributes instanceof Array){ - for (var i=0; i< attributes.length; i++) - { - node.setAttribute(attributes[i][0], attributes[i][1]); - } - } - else{ - for ( var key in attributes){ - node.setAttribute(key, attributes[key]); - } - } - }, - -/* drawPath: function(pointsArray, canvasSVG, attributes){ - var path = document.createElementNS(this.svgns,"polyline"); - path.setAttribute ('id', id); - - var d= pointsArray[0].x+ " "+ pointsArray[0].y; - for (var i=1; i< pointsArray.length; i++) - { - d=d+" "+pointsArray[i].x+" "+pointsArray[i].y; - } - path.setAttribute ('points', d); - canvasSVG.appendChild(path); - },*/ - - createText : function (x, y, text, attributes) { - var node = document.createElementNS(this.svgns,"text"); - node.setAttributeNS(null , "x",x); - node.setAttributeNS(null, "y",y); - - var textNode = document.createTextNode(text); - node.appendChild(textNode); - - this._setProperties(node, attributes); - return node; - }, - - drawText : function (x, y, text, canvasSVG, attributes) { - var text = SVG.createText(x, y, text, attributes); - canvasSVG.appendChild(text); - return text; - }, - - - - drawGroup: function(svgNode, attributes) - { - var group = SVG.createGroup(attributes); - svgNode.appendChild(group); - return group; - }, - - createGroup: function(attributes){ - var group = document.createElementNS(this.svgns,"g"); - this._setProperties(group, attributes); - return group; - } - -}; - - - -var CanvasToSVG = { - - convert: function(sourceCanvas, targetSVG, x, y, id, attributes) { - - var img = this._convert(sourceCanvas, targetSVG, x, y, id); - - for (var i=0; i< attributes.length; i++) - { - img.setAttribute(attributes[i][0], attributes[i][1]); - } - }, - - _convert: function(sourceCanvas, targetSVG, x, y, id) { - var svgNS = "http://www.w3.org/2000/svg"; - var xlinkNS = "http://www.w3.org/1999/xlink"; - // get base64 encoded png from Canvas - var image = sourceCanvas.toDataURL(); - - // must be careful with the namespaces - var svgimg = document.createElementNS(svgNS, "image"); - - svgimg.setAttribute('id', id); - - //svgimg.setAttribute('class', class); - //svgimg.setAttribute('xlink:href', image); - svgimg.setAttributeNS(xlinkNS, 'xlink:href', image); - - - - - svgimg.setAttribute('x', x ? x : 0); - svgimg.setAttribute('y', y ? y : 0); - svgimg.setAttribute('width', sourceCanvas.width); - svgimg.setAttribute('height', sourceCanvas.height); - //svgimg.setAttribute('cursor', 'pointer'); - svgimg.imageData = image; - - targetSVG.appendChild(svgimg); - return svgimg; - }, - - importSVG: function(sourceSVG, targetCanvas) { - svg_xml = sourceSVG;//(new XMLSerializer()).serializeToString(sourceSVG); - var ctx = targetCanvas.getContext('2d'); - - var img = new Image(); - img.src = "data:image/svg+xml;base64," + btoa(svg_xml); -// img.onload = function() { - ctx.drawImage(img, 0, 0); -// }; - } - -}; -/* -Graph.prototype.importSVG = function(sourceSVG, targetCanvas) { - sourceSVG = this._svg; - targetCanvas = document.createElementNS('canvas'); - // https://developer.mozilla.org/en/XMLSerializer - svg_xml = (new XMLSerializer()).serializeToString(sourceSVG); - var ctx = targetCanvas.getContext('2d'); - // this is just a JavaScript (HTML) image - var img = new Image(); - // http://en.wikipedia.org/wiki/SVG#Native_support - // https://developer.mozilla.org/en/DOM/window.btoa - img.src = "data:image/svg+xml;base64," + btoa(svg_xml); - img.onload = function() { - // after this, Canvas’ origin-clean is DIRTY - ctx.drawImage(img, 0, 0); - } -}; -*/ - -/* - -Normalizacion de datos para dibujar colores -Issues: - No sé como debería llamarse esta libreria - No sé si ya existe una funciçon en javascript que lo haga - - -*/ - - -var Normalizer = new function() -{ - this.normalizeArray = function (arrayData) - { - - return this.standardizeArray(this.normal(arrayData)); - -// var result = this._getMaxAndMin(arrayData); -// var min =result[0]; -// var max = result[1]; -// -// -// //los hacemos todos positivos -// for (var i = 0; i< arrayData.length; i++) -// { -// arrayData[i]= Math.abs(min) + parseFloat(arrayData[i]); -// } -// -// var result = this._getMaxAndMin(arrayData); -// var min =result[0]; -// var max = result[1]; -// -// -// var resultArray = new Array(); -// for (var i = 0; i< arrayData.length; i++) -// { -// resultArray.push(arrayData[i]*1/max); -// } -// return resultArray; - }; - - this.normal = function(arrayData){ - var mean = this._getMean(arrayData); - var deviation = this._getStdDeviation(arrayData); - var result = this._getMaxAndMin(arrayData); - var min = result[0]; - var max = result[1]; - - var resultArray = new Array(); - for (var i = 0; i< arrayData.length; i++) { - if (deviation!=0){ - resultArray.push((arrayData[i]-mean)/deviation); - }else{ - resultArray.push(arrayData[i]); - } - } - return resultArray; - }; - - this.standardizeArray = function(arrayData) - { - var result = this._getMaxAndMin(arrayData); - var min = result[0]; - var max = result[1]; - - var offset = ( min <= 0 ) ? Math.abs(min) : (-1 * min); - var resultArray = new Array(); - for (var i = 0; i< arrayData.length; i++) { - if(max + offset!=0){ - resultArray.push((arrayData[i] + offset) / (max + offset)); - }else{ - resultArray.push(arrayData[i]+offset); - } - } - return resultArray; - }; - - - this._getMean = function(arrayData) { - var sum = 0; - for (var i = 0; i< arrayData.length; i++) { - sum = sum + parseFloat(arrayData[i]); - } - return sum/arrayData.length; - }; - - this._getStdDeviation = function(arrayData) { - var mean = this._getMean(arrayData); - var acum = 0.0; - for(var i=0; i max) max = parseFloat(arrayData[i]); - } - - return [min, max]; - }; -}; -function GraphCanvas(componentID, targetNode, args) { - this.args = {}; - /** target */ - this.targetID = targetNode.id; - - /** id manage */ - this.id = componentID; - this.args.idGraph = this.id + "main"; - this.args.idBackgroundNode = this.id + "background"; - - this.args.idEdgesGraph = this.id + "edges"; - this.args.idNodesGraph = this.id + "vertices"; - this.args.idLabelGraph = this.id + "label"; - this.args.idBackground = this.id + "background"; - - /** Objects Graph **/ - this.dataset = null; - this.formatter = null; - this.layout = null; - - /** Drawing **/ - this.circleDefaultRadius = 2; - this.squareDefaultSide = this.circleDefaultRadius * 1.5; - - /** Directed Arrow **/ - this.arrowDefaultSize = this.circleDefaultRadius; - - /** Groups **/ - this.GraphGroup = null; - this.GraphNodeGroup = null; - this.GraphLabelGroup = null; - this.GraphBackground = null; - - /** SETTINGS FLAGS **/ - this.args.draggingCanvasEnabled = false; //Flag to set if the canvas can be dragged - this.args.multipleSelectionEnabled = false; - this.args.interactive = false; - this.args.labeled = false; - this.args.linkEnabled = false; - - /** If numberEdge > maxNumberEdgesMoving then only it will move edges when mouse up **/ - this.args.maxNumberEdgesMoving = 3; - this.args.maxNumberEdgesFiringEvents = 50; - - /** Linking edges **/ - this.args.linking = false; - this.linkStartX = 0; - this.linkStartY = 0; - this.linkSVGNode = null; - this.linkNodeSource = null; - this.linkNodeTarget = null; - - /** Dragging Control **/ - this.draggingElement = null; - this.dragging = false; - this.nMouseOffsetX = 0; - this.nMouseOffsetY = 0; - this.dragStartX = 0; - this.dragStartY = 0; - this.desplazamientoX = 0; - this.desplazamientoY = 0; - - /** Selection Control **/ - this.selecting = false; - this.selectorX = null; - this.selectorY = null; - this.selectorSVGNode = null; - - /** Node status **/ - this.args.isVertexSelected = {}; - this.args.selectedVertices = []; - - /** Edges status **/ - this.args.isEdgeSelected = {}; - //this.args.selectedEdges = []; - - if (args != null) { - if (args.multipleSelectionEnabled != null) { - this.args.multipleSelectionEnabled = args.multipleSelectionEnabled; - this.args.draggingCanvasEnabled = !(this.args.multipleSelectionEnabled); - } - if (args.draggingCanvasEnabled != null) { - this.args.draggingCanvasEnabled = args.draggingCanvasEnabled; - this.args.multipleSelectionEnabled = !(this.args.draggingCanvasEnabled); - } - if (args.interactive != null) { - this.args.interactive = args.interactive; - } - if (args.labeled != null) { - this.args.labeled = args.labeled; - } - - } - - /** Hashmap with the svg node labels **/ - this.svgLabels = {}; - - /** EVENTS **/ - this.onVertexOut = new Event(this); - this.onVertexOver = new Event(this); - this.onVertexSelect = new Event(this); - this.onEdgeSelect = new Event(this); - this.onCanvasClicked = new Event(this); - this.onVertexUp = new Event(this); -} - -GraphCanvas.prototype.showLabels = function(value) { - this.args.labeled = value; - this.removeLabels(); - if (value) { - this.renderLabels(); - } -}; - -GraphCanvas.prototype.getSelectedVertices = function() { - return this.args.selectedVertices; -}; - -GraphCanvas.prototype.getSelectedEdges = function() { - var selected = []; - for ( var selectedEdge in this.args.isEdgeSelected) { - selected.push(selectedEdge); - } - return selected; -}; - -GraphCanvas.prototype.createSVGDom = function(targetID, id, width, height, backgroundColor) { - var container = document.getElementById(targetID); - this._svg = SVG.createSVGCanvas(container, [ - [ "style", "background-color:" + backgroundColor + ";" ], [ "id", id ], [ "dragx", 0 ], [ "dragy", 0 ], - [ "height", this.getFormatter().getHeight() ], [ "width", this.getFormatter().getWidth() ] ]); - return this._svg; -}; - -/** MULTIPLE SELECTION **/ -GraphCanvas.prototype.isMultipleSelectionEnabled = function() { - return this.args.multipleSelectionEnabled; -}; - -GraphCanvas.prototype.setMultipleSelection = function(value) { - this.args.multipleSelectionEnabled = value; - this.args.draggingCanvasEnabled = (!value); -}; - -GraphCanvas.prototype.setSelecting = function(value) { - this.selecting = value; -}; - -/** linking **/ -GraphCanvas.prototype.setLinking = function(value) { - this.args.linkEnabled = value; - this.selecting = !value; - this.dragging = !value; -}; - -/** CANVAS MOVING **/ -GraphCanvas.prototype.setDraggingCanvas = function(value) { - this.args.draggingCanvasEnabled = value; - this.args.multipleSelectionEnabled = !value; -}; - -GraphCanvas.prototype.isDraggingCanvasEnabled = function() { - return this.args.draggingCanvasEnabled; -}; -/** ZOOM **/ -GraphCanvas.prototype.getScale = function() { - return this.getFormatter().getZoomScale(); -}; - -GraphCanvas.prototype.setScale = function(scale) { - var graphNode = document.getElementById(this.args.idGraph); - graphNode.setAttribute("transform", graphNode.getAttribute("transform").replace("scale(" + this.getScale() + ")", "scale(" + scale + ")")); - this.getFormatter().setZoomScale(scale); -}; - -GraphCanvas.prototype.zoomIn = function() { - this.setScale(this.getScale() + this.getFormatter().getZoomScaleStepFactor()); -}; - -GraphCanvas.prototype.zoomOut = function() { - this.setScale(this.getScale() - this.getFormatter().getZoomScaleStepFactor()); - -}; - -/** SVG COORDENATES **/ -GraphCanvas.prototype.getSVGCoordenates = function(evt) { - var p = this._svg.createSVGPoint(); - p.x = evt.clientX; - p.y = evt.clientY; - - var m = this._svg.getScreenCTM(document.documentElement); - p = p.matrixTransform(m.inverse()); - return p; -}; - -/** SVG EVENTS **/ -GraphCanvas.prototype.mouseClick = function(event) { - if (event.button == 0) { - if (!this.args.interactive) { - return; - } - - if (this.isVertex(event.target)) { - this.clickNode(this.getVertexIdFromSVGId(event.target.id)); - } - /** Como el evento mouseClick viene despues del mouse up es aqui donde manejo el tema de deseccionar los elementos que estoy dragging **/ - if (this.dragging) { - this.dragging = false; - } - } -}; - -GraphCanvas.prototype.mouseMove = function(evt) { - if (this.selecting) { - this.clearLabels(); - - var width = (this.getSVGCoordenates(evt).x - this.selectorX); - var height = (this.getSVGCoordenates(evt).y - this.selectorY); - if ((width > 0) && (height > 0)) { - this.displaySelection(this.selectorX, this.selectorY, width, height); - } - if ((width > 0) && (height < 0)) { - this.displaySelection(this.selectorX, this.getSVGCoordenates(evt).y, width, Math.abs(height)); - } - if ((width < 0) && (height < 0)) { - this.displaySelection(this.getSVGCoordenates(evt).x, this.getSVGCoordenates(evt).y, Math.abs(width), Math.abs(height)); - } - if ((width < 0) && (height > 0)) { - this.displaySelection(this.selectorX + width, this.selectorY, Math.abs(width), Math.abs(height)); - } - - var x1 = (parseFloat(this.selectorSVGNode.getAttribute("x")) - DOM.select(this.id).getAttribute("dragx")) / this.getFormatter().getWidth(); - var y1 = (parseFloat(this.selectorSVGNode.getAttribute("y")) - DOM.select(this.id).getAttribute("dragy")) / this.getFormatter().getHeight(); - var x2 = (x1 + parseFloat(this.selectorSVGNode.getAttribute("width") / this.getFormatter().getWidth())); - var y2 = (y1 + parseFloat(this.selectorSVGNode.getAttribute("height") / this.getFormatter().getHeight())); - - this.deselectNodes(this.getLayout()); - var verticesSelected = this.getLayout().getVerticesByArea(x1 / this.getFormatter().getZoomScale(), y1 / this.getFormatter().getZoomScale(), - x2 / this.getFormatter().getZoomScale(), y2 / this.getFormatter().getZoomScale()); - for ( var i = 0; i < verticesSelected.length; i++) { - this.selectNode(verticesSelected[i].getId()); - this.renderLabel(verticesSelected[i].getId()); - } - - } - var p = null; - if (this.args.linking) { - p = this.getSVGCoordenates(evt); - if (this.linkSVGNode != null) { - this.linkSVGNode.setAttribute("x2", p.x - 2); - this.linkSVGNode.setAttribute("y2", p.y - 2); - } - } - - if (this.dragging) { - p = this.getSVGCoordenates(evt); - p.x -= this.nMouseOffsetX; - p.y -= this.nMouseOffsetY; - this.desplazamientoX = (this.getSVGCoordenates(evt).x - this.dragStartX);// + parseFloat(DOM.select(this.id).getAttribute("dragx")); - this.desplazamientoY = (this.getSVGCoordenates(evt).y - this.dragStartY);// + parseFloat(DOM.select(this.id).getAttribute("dragy")); - - if (this.draggingElement != null) { - /** Click sobre el recct del banground que provoca que mueva todo el canvas **/ - if (this.isNodeCanvas(this.draggingElement)) { - - p = this.getSVGCoordenates(evt); - p.x = this.desplazamientoX; - p.y = this.desplazamientoY; - - this.draggingElement.setAttribute("dragx", p.x); - this.draggingElement.setAttribute("dragy", p.y); - this.draggingElement = document.getElementById(this.args.idGraph); - this.draggingElement.setAttribute("transform", "translate(" + p.x + "," + p.y + "), scale(" + this.getScale() + ")"); - - DOM.select(this.id).setAttribute("dragx", p.x); - DOM.select(this.id).setAttribute("dragy", p.y); - - if (this.NodeSVGbackgroundImage != null) { - this.NodeSVGbackgroundImage.setAttribute("dragx", p.x); - this.NodeSVGbackgroundImage.setAttribute("dragy", p.y); - } - } else { - if (this.isVertex(this.draggingElement)) { - this.selectNode(this.getVertexIdFromSVGId(this.draggingElement.id)); - this.desplazamientoX = this.desplazamientoX / this.getFormatter().getZoomScale(); - this.desplazamientoY = this.desplazamientoY / this.getFormatter().getZoomScale(); - this.moveSelectedNodes(this.desplazamientoX, this.desplazamientoY); - - this.dragStartX = this.getSVGCoordenates(evt).x; - this.dragStartY = this.getSVGCoordenates(evt).y; - } else { - if (this.isNodeBackground(this.draggingElement)) { - - this.draggingElement.setAttribute("dragx", p.x); - this.draggingElement.setAttribute("dragy", p.y); - this.draggingElement = document.getElementById(this.args.idGraph); - this.draggingElement.setAttribute("transform", "translate(" + p.x + "," + p.y + "), scale(" + this.getScale() + ")"); - } else { - this.draggingElement.setAttribute("transform", "translate(" + p.x + "," + p.y + ")"); - } - } - } - } - } -}; - -GraphCanvas.prototype.moveSelectedNodes = function(offsetX, offsetY) { - for ( var i = 0; i < this.getSelectedVertices().length; i++) { - - var nodeId = this.getSelectedVertices()[i]; - var svgNodeId = this.getSVGNodeId(nodeId); - - var x = parseFloat(DOM.select(svgNodeId).getAttribute("dragx")) + parseFloat(offsetX);// - parseFloat(DOM.select(this.id).getAttribute("dragx")); - var y = parseFloat(DOM.select(svgNodeId).getAttribute("dragy")) + parseFloat(offsetY);// + parseFloat(DOM.select(this.id).getAttribute("dragy")); - - this._movingNode(DOM.select(svgNodeId), x, y); - } -}; - -GraphCanvas.prototype.mouseDown = function(evt) { - if (event.button == 0) { - - /** if !no interactive mouse events do anything **/ - if (!this.args.interactive) { - return; - } - - var p = this.getSVGCoordenates(evt); - - /** When click on canvas or background deselect all **/ - if (this.isNodeCanvas(evt.target) || this.isNodeBackground(evt.target)) { - this.deselectNodes(); - this.deselectEdges(); - this.onCanvasClicked.notify(); - } - - /** if I am linking vertices **/ - if (this.args.linkEnabled) { - - if (!this.args.linking) { - this.args.linking = true; - if (this.isVertex(evt.target)) { - this.linkStartX = p.x; - this.linkStartY = p.y; - this.linkSVGNode = SVG.drawLine(p.x, p.y, p.x, p.y, this._svg, { - "stroke" : "#FF0000" - }); - this.linkNodeSource = this.getVertexIdFromSVGId(evt.target.id); - } - } else { - this.linkNodeTarget = this.getVertexIdFromSVGId(evt.target.id); - this.args.linking = false; - this.args.linkEnabled = false; - if (this.isVertex(evt.target)) { - this.getDataset().addEdge(this.linkNodeSource + "_" + this.linkNodeTarget, this.linkNodeSource, this.linkNodeTarget, {}); - } - this.linkSVGNode.parentNode.removeChild(this.linkSVGNode); - } - return; - } - - /** Id is a vertex or the canvas **/ - if (this.isVertex(evt.target) || this.isNodeCanvas(evt.target) || this.isNodeBackground(evt.target)) { - this._startDragging(evt); - } - /** if i is edge **/ - if (this.isEdge(evt.target)) { - this.selectEdge(this.getEdgeIdFromSVGId(evt.target.getAttribute("id"))); - } - - if (this.args.multipleSelectionEnabled) { - if (!this.dragging) { - this.setSelecting(true); - this.selectorX = p.x; - this.selectorY = p.y; - this.displaySelection(p.x, p.y, 1, 1); - } - } - - } - if (event.button == 1) { - this.setLinking(false); - this.setMultipleSelection(false); - this.selecting = false; - - /** Id is a vertex or the canvas **/ - if (this.isVertex(evt.target) || this.isNodeCanvas(evt.target) || this.isNodeBackground(evt.target)) { - this._startDragging(evt); - } - } -}; - -GraphCanvas.prototype.mouseUp = function(event) { - if (!this.args.interactive) { - return; - } - - if (this.dragging) { - this._stopDragging(event); - if (this.isVertex(event.target)) { - var vertexId = this.getVertexIdFromSVGId(event.target.id); - if (this.getDataset().getVertexById(vertexId).getEdges().length >= this.args.maxNumberEdgesMoving) { - this.moveEdge(vertexId); - } - } - } - - if (this.selecting) { - this.setSelecting(false); - - var x1 = (parseFloat(this.selectorSVGNode.getAttribute("x")) - DOM.select(this.id).getAttribute("dragx")) / this.getFormatter().getWidth(); - var y1 = (parseFloat(this.selectorSVGNode.getAttribute("y")) - DOM.select(this.id).getAttribute("dragy")) / this.getFormatter().getHeight(); - var x2 = (x1 + parseFloat(this.selectorSVGNode.getAttribute("width") / this.formatter.getWidth())); - var y2 = (y1 + parseFloat(this.selectorSVGNode.getAttribute("height") / this.formatter.getHeight())); - - var verticesSelected = this.getLayout().getVerticesByArea(x1 / this.getFormatter().getZoomScale, y1 / this.getFormatter().getZoomScale, - x2 / this.getFormatter().getZoomScale, y2 / this.getFormatter().getZoomScale); - - for ( var i = 0; i < verticesSelected.length; i++) { - this.selectNode(verticesSelected[i].getId()); - } - - if (this.selectorSVGNode != null) { - this._svg.removeChild(this.selectorSVGNode); - } - - if (this.args.labeled) { - this.clearLabels(); - this.renderLabels(); - } - - this.selectorSVGNode = null; - // this.renderLabels(); - } -}; - -/** SELECTION **/ -GraphCanvas.prototype.displaySelection = function(x, y, width, height) { - if (this.selectorSVGNode != null) { - this.selectorSVGNode.setAttribute("x", x); - this.selectorSVGNode.setAttribute("y", y); - this.selectorSVGNode.setAttribute("width", width); - this.selectorSVGNode.setAttribute("height", height); - } else { - this.selectorSVGNode = SVG.drawRectangle(x, y, width, height, this._svg, { - "fill" : "red", - "stroke" : "black", - "opacity" : "0.2", - "stroke-opacity" : "1" - }); - } -}; - -/** DRAGGING **/ -GraphCanvas.prototype._startDragging = function(evt) { - if (!this.isDraggingCanvasEnabled()) { - if (this.isNodeCanvas(evt.target)) { - this.draggingElement = null; - } - } - - if (this.isVertex(evt.target) || (this.isNodeBackground(evt.target) && (this.isDraggingCanvasEnabled()))|| (this.isNodeCanvas(evt.target) && (this.isDraggingCanvasEnabled()))) { - this.clearLabels(); - this.draggingElement = evt.target; - this.dragging = true; - var p = this.getSVGCoordenates(evt); - - this.nMouseOffsetX = p.x - parseInt(evt.target.getAttribute("dragx")); - this.nMouseOffsetY = p.y - parseInt(evt.target.getAttribute("dragy")); - - if (this.isVertex(evt.target)) { - this.dragStartX = parseInt(this.draggingElement.getAttribute("dragx")) * this.getFormatter().getZoomScale() - + parseFloat(DOM.select(this.id).getAttribute("dragx")); - this.dragStartY = parseInt(this.draggingElement.getAttribute("dragy")) * this.getFormatter().getZoomScale() - + parseFloat(DOM.select(this.id).getAttribute("dragy")); - } else { - this.dragStartX = p.x - parseInt(this.draggingElement.getAttribute("dragx"));// + parseFloat(DOM.select(this.id).getAttribute("dragx")); - this.dragStartY = p.y - parseInt(this.draggingElement.getAttribute("dragy"));// + parseFloat(DOM.select(this.id).getAttribute("dragy")); - } - } -}; - -GraphCanvas.prototype._stopDragging = function(event) { - this.nMouseOffsetX = 0; - this.nMouseOffsetX = 0; - /** despues del evento up viene el evento click entonces acabo el dragging en el mouseclick **/ - this.dragging = false; - this.draggingElement = null; - this.renderLabels(); - - this.setLinking(false); - this.setMultipleSelection(true); - this.selecting = false; - -}; - -/** Move the edges of the vertex with the vertexId indicado **/ -GraphCanvas.prototype.moveEdge = function(vertexId) { - var x = this.getLayout().getNodeById(vertexId).x * this.getFormatter().getWidth(); - var y = this.getLayout().getNodeById(vertexId).y * this.getFormatter().getHeight(); - - /** Moving edges out **/ - for ( var i = 0; i < this.getDataset().getVertexById(vertexId).getEdgesOut().length; i++) { - var edgeId = this.getDataset().getVertexById(vertexId).getEdgesOut()[i].getId(); - var svgEdgeId = this.getSVGEdgeId(edgeId); - var edgeFormatter = this.getFormatter().getEdgeById(edgeId); - if (edgeFormatter instanceof LineEdgeGraphFormatter) { - DOM.select(svgEdgeId + "_shadow").setAttribute("x2", x); - DOM.select(svgEdgeId + "_shadow").setAttribute("y2", y); - DOM.select(svgEdgeId).setAttribute("x2", x); - DOM.select(svgEdgeId).setAttribute("y2", y); - } - - if ((edgeFormatter instanceof DirectedLineEdgeGraphFormatter) || (edgeFormatter instanceof OdirectedLineEdgeGraphFormatter) - || (edgeFormatter instanceof OdotDirectedLineEdgeGraphFormatter) || (edgeFormatter instanceof DotDirectedLineEdgeGraphFormatter) - || (edgeFormatter instanceof CutDirectedLineEdgeGraphFormatter)) { - this.removeEdge(edgeId); - this.renderEdge(edgeId); - } - } - - /** Moving edges in **/ - for ( var i = 0; i < this.getDataset().getVertexById(vertexId).getEdgesIn().length; i++) { - var edgeId = this.getDataset().getVertexById(vertexId).getEdgesIn()[i].getId(); - var svgEdgeId = this.getSVGEdgeId(edgeId); - var edgeFormatter = this.getFormatter().getEdgeById(edgeId); - if (edgeFormatter instanceof LineEdgeGraphFormatter) { - DOM.select(svgEdgeId).setAttribute("x1", x); - DOM.select(svgEdgeId).setAttribute("y1", y); - DOM.select(svgEdgeId + "_shadow").setAttribute("x1", x); - DOM.select(svgEdgeId + "_shadow").setAttribute("y1", y); - } - - if ((edgeFormatter instanceof DirectedLineEdgeGraphFormatter) || (edgeFormatter instanceof OdirectedLineEdgeGraphFormatter) - || (edgeFormatter instanceof OdotDirectedLineEdgeGraphFormatter) || (edgeFormatter instanceof DotDirectedLineEdgeGraphFormatter) - || (edgeFormatter instanceof CutDirectedLineEdgeGraphFormatter)) { - this.removeEdge(edgeId); - this.renderEdge(edgeId); - } - - if (edgeFormatter instanceof BezierEdgeGraphFormatter) { - var radius = this.getFormatter().getVertexById(vertexId).getDefault().getSize() * this.getFormatter().getNodesMaxSize(); - var d = this.calculateCoordenatesBezier(radius, x, y); - DOM.select(svgEdgeId).setAttribute("d", d); - } - } -}; - -GraphCanvas.prototype.moveNode = function(vertexId) { - var x = this.getLayout().getNodeById(vertexId).x * this.getFormatter().getWidth(); - var y = this.getLayout().getNodeById(vertexId).y * this.getFormatter().getHeight(); - var svgNodeElement = DOM.select(this.getSVGNodeId(vertexId)); - - svgNodeElement.setAttribute("dragx", x); - svgNodeElement.setAttribute("dragy", y); - svgNodeElement.setAttribute("transform", "translate(" + x + "," + y + ")"); - - if (this.getDataset().getVertexById(vertexId).getEdges().length < this.args.maxNumberEdgesMoving) { - this.moveEdge(vertexId); - } -}; - -GraphCanvas.prototype._movingNode = function(svgNodeElement, x, y) { - var vertexId = this.getVertexIdFromSVGId(svgNodeElement.getAttribute("id")); - this.getLayout().getNodeById(vertexId).setCoordinates(x / this.getFormatter().getWidth(), y / this.getFormatter().getHeight()); - this.desplazamientoX = 0; - this.desplazamientoY = 0; - this.removeLabel(vertexId); - this.renderLabel(vertexId); -}; - -/** INIT **/ -GraphCanvas.prototype.init = function() { - - this._svg = this.createSVGDom(this.targetID, this.id, this.getFormatter().getWidth(), this.getFormatter().getHeight(), this.getFormatter() - .getBackgroundColor()); - this.GraphGroup = SVG.drawGroup(this._svg, [ [ "id", this.args.idGraph ], [ "transform", "translate(0,0), scale(1)" ] ]); - this.GraphBackground = SVG.drawGroup(this.GraphGroup, [ [ "id", this.args.idBackground ] ]); - this.GraphEdgeGroup = SVG.drawGroup(this.GraphGroup, [ [ "id", this.args.idEdgesGraph ] ]); - this.GraphNodeGroup = SVG.drawGroup(this.GraphGroup, [ [ "id", this.args.idNodesGraph ] ]); - this.GraphLabelGroup = SVG.drawGroup(this.GraphGroup, [ [ "id", this.args.idLabelGraph ] ]); - - if ((this.getFormatter().getBackgroundImage() != null) && (this.getFormatter().getBackgroundImage() != "")) { - this.setBackgroundImage(this.getFormatter().getBackgroundImage()); - } - /** SVG Events listener */ - var _this = this; - this._svg.addEventListener("click", function(event) { - _this.mouseClick(event); - }, false); - this._svg.addEventListener("mousemove", function(event) { - _this.mouseMove(event, _this); - }, false); - this._svg.addEventListener("mousedown", function(event) { - _this.mouseDown(event, _this); - }, false); - this._svg.addEventListener("mouseup", function(event) { - _this.mouseUp(event, _this); - }, false); -}; - -/* - GraphCanvas.prototype.backgroungToSVG = function(){ - var _this = this; - var canvas = document.createElement('canvas'); - canvas.setAttribute("id", "canvas"); - canvas.width = this.formatter.getWidth(); - canvas.height = this.formatter.getHeight(); - - this._svg.parentNode.parentNode.appendChild(canvas); - var ctx = document.getElementById('canvas').getContext('2d'); - var img = new Image(); - - img.src = this.formatter.getBackgroundImage(); - ctx.drawImage(img,0,0 ,_this.formatter.getWidth(), _this.formatter.getHeight()); - - - img.onload = function() { - canvas.parentNode.removeChild(canvas); - } - - this.NodeSVGbackgroundImage.setAttribute("xlink:href", document.getElementById("canvas").toDataURL()); - this.NodeSVGbackgroundImage.removeAttribute("href"); - - // - - };*/ - -GraphCanvas.prototype.setBackgroundImage = function() { - if (this.NodeSVGbackgroundImage != null) { - this.NodeSVGbackgroundImage.parentNode.removeChild(this.NodeSVGbackgroundImage); - } - $('#' + this.targetID).svg(); - $('#' + this.targetID).svg("get"); - - $('#' + this.targetID).svg("get")._svg = document.getElementById(this.id); - - var svg = $('#' + this.targetID).svg("get"); - this.NodeSVGbackgroundImage = svg.image(0, 0, this.getFormatter().getWidth(), this.getFormatter().getHeight(), this.getFormatter() - .getBackgroundImage()); - this.NodeSVGbackgroundImage.setAttribute("id", this.args.idBackgroundNode); - - this.NodeSVGbackgroundImage.setAttribute("x", 0); - this.NodeSVGbackgroundImage.setAttribute("y", 0); - - this.NodeSVGbackgroundImage.setAttribute("dragx", 0); - this.NodeSVGbackgroundImage.setAttribute("dragy", 0); - - if (this.getFormatter().args.backgroundImageHeight != null) { - this.NodeSVGbackgroundImage.setAttribute("height", this.getFormatter().args.backgroundImageHeight); - } - if (this.getFormatter().args.backgroundImageWidth != null) { - this.NodeSVGbackgroundImage.setAttribute("width", this.getFormatter().args.backgroundImageWidth); - } - - if (this.getFormatter().args.backgroundImageX != null) { - this.NodeSVGbackgroundImage.setAttribute("x", this.getFormatter().args.backgroundImageX); - } - if (this.getFormatter().args.backgroundImageY != null) { - this.NodeSVGbackgroundImage.setAttribute("y", this.getFormatter().args.backgroundImageY); - } - - this.GraphBackground.appendChild(this.NodeSVGbackgroundImage); - this.NodeSVGbackgroundImage.removeAttribute("href"); - this.NodeSVGbackgroundImage.setAttribute("xlink:href", this.getFormatter().getBackgroundImage()); -}; - -GraphCanvas.prototype.removeBackgroundImage = function() { - if (this.NodeSVGbackgroundImage != null) { - this.NodeSVGbackgroundImage.parentNode.removeChild(this.NodeSVGbackgroundImage); - } -}; - -GraphCanvas.prototype._setBackgroundColor = function(color) { - var attributes = [ [ "fill", color ] ]; - SVG.drawRectangle(0, 0, this.getFormatter().getWidth(), this.getFormatter().getHeight(), this.GraphBackground, attributes); -}; - -/** Serialize **/ -GraphCanvas.prototype.toJSON = function() { - var json = {}; - json.dataset = {}; - json.formatter = {}; - json.layout = {}; - json.dataset = this.getDataset().toJSON(); - json.formatter = this.getFormatter().toJSON(); - json.layout = this.getLayout().toJSON(); - return json; -}; - -GraphCanvas.prototype.toHTML = function() { - //this.backgroungToSVG(); - var html = this._svg.parentElement.innerHTML; - - var start = html.indexOf("") + 6; - - return html.substr(start, end); -}; - -/** DRAW **/ -GraphCanvas.prototype.draw = function(graphdataset, graphformatter, graphlayout) { - this.setDataset(graphdataset); - this.setFormatter(graphformatter); - this.setLayout(graphlayout); - - var _this = this; - this.getFormatter().changed.attach(function(sender, item) { - _this.removeNode(item.getId()); - _this.renderNode(item.getId()); - if (_this.args.labeled) { - _this.removeLabel(item.getId()); - _this.renderLabel(item.getId()); - } - - }); - //TODO - this.getFormatter().edgeChanged.attach(function(sender, item) { - _this.removeEdge(item.getId()); - _this.renderEdge(item.getId()); - }); - - this.getFormatter().resized.attach(function(sender, item) { - _this.resize(_this.getFormatter().getWidth(), _this.getFormatter().getHeight()); - }); - - this.getFormatter().backgroundImageChanged.attach(function(sender, item) { - _this.setBackgroundImage(_this.getFormatter().getBackgroundImage()); - }); - - this.getFormatter().backgroundColorChanged.attach(function(sender, item) { - _this._setBackgroundColor(_this.getFormatter().getBackgroundColor()); - }); - - this.getLayout().changed.attach(function(sender, item) { - _this.moveNode(item.getId()); - _this.moveEdge(item.getId()); - if (_this.args.labeled) { - _this.removeLabel(item.getId()); - _this.renderLabel(item.getId()); - } - }); - - this.getDataset().newVertex.attach(function(sender, item) { - - _this.renderNode(item.getId()); - if (_this.args.labeled) { - _this.renderLabel(item.getId()); - } - }); - - this.getDataset().newEdge.attach(function(sender, item) { - _this.renderEdge(item.getId()); - }); - - this.getDataset().vertexDeleted.attach(function(sender, item) { - _this.removeNode(item.getId()); - if (_this.args.labeled) { - _this.removeLabel(item.getId()); - } - }); - - this.getDataset().edgeDeleted.attach(function(sender, item) { - _this.removeEdge(item.getId()); - }); - - this.getDataset().vertexNameChanged.attach(function(sender, args) { - if (_this.args.labeled) { - _this.removeLabel(args.item.getId()); - _this.removeLabel(args.item.getId()); - _this.renderLabel(args.item.getId()); - } - }); - this.init(); - this.render(); -}; - -GraphCanvas.prototype.render = function() { - for ( var id in this.getDataset().getVertices()) { - this.renderNode(id); - } - this.renderLabels(); - this.renderEdges(); -}; - -GraphCanvas.prototype.renderLabels = function() { - if (this.args.labeled) { - for ( var id in this.getDataset().getVertices()) { - this.renderLabel(id); - } - } -}; - -GraphCanvas.prototype.removeLabels = function() { - for ( var id in this.getDataset().getVertices()) { - this.removeLabel(id); - } -}; - -/** Utilities method for nodes **/ -GraphCanvas.prototype.isNodeCanvas = function(node) { - return ((node.id == this.args.idGraph) || (node.id == this.id)); -}; - -GraphCanvas.prototype.isNodeBackground = function(node) { - return ((node.id == this.args.idBackgroundNode)); -}; - -GraphCanvas.prototype.isVertex = function(node) { - if (node.getAttribute("id") != null) { - if (node.getAttribute("id").indexOf("_v_") != -1) { - return true; - } - } - return false; -}; - -GraphCanvas.prototype.isLabel = function(node) { - if (node.getAttribute("id") != null) { - if (node.getAttribute("id").indexOf("_l_") != -1) { - return true; - } - } - return false; -}; - -GraphCanvas.prototype.isEdge = function(node) { - if (node.getAttribute("id") != null) { - if (node.getAttribute("id").indexOf("_e_") != -1) { - return true; - } - } - return false; -}; - -/** Resize **/ -GraphCanvas.prototype.resize = function(width, height) { - // this._svg.setAttribute("width", width); - // this._svg.setAttribute("height", height); - if (this.NodeSVGbackgroundImage != null) { - this.NodeSVGbackgroundImage.setAttribute("width", width); - this.NodeSVGbackgroundImage.setAttribute("height", height); - } - - this._svg.setAttribute("width", width); - this._svg.setAttribute("height", height); - - this.clearCanvas(); - this.render(); -}; - -GraphCanvas.prototype.clearCanvas = function() { - DOM.removeChilds(this.GraphEdgeGroup.getAttribute("id")); - DOM.removeChilds(this.GraphNodeGroup.getAttribute("id")); - this.clearLabels(); -}; - -GraphCanvas.prototype.clearLabels = function() { - DOM.removeChilds(this.GraphLabelGroup.getAttribute("id")); -}; - -/** ID'S converter **/ -GraphCanvas.prototype.getSVGNodeId = function(nodeId) { - return this.id + "_v_" + nodeId; -}; - -GraphCanvas.prototype.getSVGEdgeId = function(edgeId) { - return this.id + "_e_" + edgeId; -}; - -GraphCanvas.prototype.getSVGArrowEdgeId = function(edgeId) { - return this.id + "_arrow_" + edgeId; -}; - -GraphCanvas.prototype.getSVGLabelId = function(edgeId) { - return this.id + "_l_" + edgeId; -}; - -GraphCanvas.prototype.blinkVertexById = function(vertexId) { - $("#" + this.getSVGNodeId(vertexId)).fadeIn().fadeOut().fadeIn().fadeOut().fadeIn().fadeOut(); -}; - -GraphCanvas.prototype.getVertexIdFromSVGId = function(svgVertexId) { - return svgVertexId.replace(this.id, "").replace("_v_", ""); -}; - -GraphCanvas.prototype.getEdgeIdFromSVGId = function(svgEdgeId) { - return svgEdgeId.replace(this.id, "").replace("_e_", ""); -}; - -/** VERTEX **/ -GraphCanvas.prototype.getVertexById = function(id) { - return document.getElementById(this.getSVGNodeId(id)); -}; - -GraphCanvas.prototype.renderNodes = function() { - for ( var id in this.getDataset().getVertices()) { - this.renderNode(id); - } -}; - -GraphCanvas.prototype.overNode = function(nodeId) { - if (!this.args.interactive) { - return; - } - /** If selected we don't change the format **/ - if (this.args.isVertexSelected[nodeId] == null) { - var args = this.getFormatter().getVertexById(nodeId).getOver(); - args.args["cursor"] = 'pointer'; - this.changeVertexFormat(nodeId, args); - } -}; - -GraphCanvas.prototype.outNode = function(nodeId) { - if (!this.args.interactive) { - return; - } - - /** If selected we don't change the format **/ - if (this.args.isVertexSelected[nodeId] == null) { - this.changeVertexFormat(nodeId, this.getFormatter().getVertexById(nodeId).getDefault()); - } -}; - -GraphCanvas.prototype.overLabel = function(nodeId) { - this.overNode(nodeId); - // this.svgLabels[nodeId].setAttribute("cursor", "pointer"); -}; - -GraphCanvas.prototype.outLabel = function(nodeId) { - this.outNode(nodeId); - // this.svgLabels[nodeId].setAttribute("cursor", ""); -}; - -GraphCanvas.prototype.clickNode = function(nodeId) { - if (!this.args.interactive) { - return; - } - - /** si el evento se dispara oprque estaba dragging entonces no activo nada **/ - if (this.args.isVertexSelected[nodeId] == null) { - this.selectNode(nodeId); - } else { - this.deselectNode(nodeId); - } -}; - -GraphCanvas.prototype.selectNode = function(nodeId) { - for ( var i = 0; i < this.args.selectedVertices.length; i++) { - var format = this.getFormatter().getVertexById(nodeId).getSelected(); - format.opacity = 0.2; - this.changeVertexFormat(nodeId, this.getFormatter().getVertexById(nodeId).getSelected()); - } - - if (this.args.isVertexSelected[nodeId] == null) { - var format = this.getFormatter().getVertexById(nodeId).getSelected(); - format.opacity = 1; - this.changeVertexFormat(nodeId, this.getFormatter().getVertexById(nodeId).getSelected()); - this.args.selectedVertices.push(nodeId); - this.args.isVertexSelected[nodeId] = this.args.selectedVertices.length - 1; - this.onVertexSelect.notify(nodeId); - } -}; - -GraphCanvas.prototype.selectAllEdges = function() { - this.deselectNodes(); - this.deselectEdges(); - - for ( var edgesId in this.getDataset().edges) { - this.selectEdge(edgesId); - } -}; - -GraphCanvas.prototype.selectAllNodes = function() { - this.deselectNodes(); - this.deselectEdges(); - - for ( var vertexId in this.getDataset().vertices) { - this.selectNode(vertexId); - } -}; - -GraphCanvas.prototype.selectAll = function() { - this.deselectNodes(); - this.deselectEdges(); - - for ( var vertexId in this.getDataset().vertices) { - this.selectNode(vertexId); - } - - for ( var edgesId in this.getDataset().edges) { - this.selectEdge(edgesId); - } -}; - -GraphCanvas.prototype.selectEdge = function(edgeId) { - if (this.args.isEdgeSelected[edgeId] == null) { - this.changeEdgeFormat(edgeId, this.getFormatter().getEdgeById(edgeId).getSelected()); - //this.args.selectedEdges.push(edgeId); - this.args.isEdgeSelected[edgeId] = true; //this.args.selectedEdges.length - 1; - this.onEdgeSelect.notify(edgeId); - } -}; - -GraphCanvas.prototype.selectEdges = function(edges) { - - for ( var i = 0; i < edges.length; i++) { - this.selectEdge(edges[i]); - } -}; - -GraphCanvas.prototype.deselectNode = function(nodeId) { - if (this.args.isVertexSelected[nodeId] != null) { - this.changeVertexFormat(nodeId, this.getFormatter().getVertexById(nodeId).getDefault()); - this.args.selectedVertices.splice(this.args.isVertexSelected[nodeId], 1); - var index = this.args.isVertexSelected[nodeId]; - delete this.args.isVertexSelected[nodeId]; - - for ( var vertex in this.args.isVertexSelected) { - if (this.args.isVertexSelected[vertex] > index) { - this.args.isVertexSelected[vertex] = this.args.isVertexSelected[vertex] - 1; - } - } - } -}; - -GraphCanvas.prototype.deselectNodes = function() { - var selected = JSON.parse(JSON.stringify(this.getSelectedVertices())); - for ( var i = 0; i < selected.length; i++) { - this.deselectNode(selected[i]); - } -}; -GraphCanvas.prototype.selectNodes = function(idNodes) { - - for ( var i = 0; i < idNodes.length; i++) { - this.selectNode(idNodes[i]); - } - - // for ( var vertex in this.args.isVertexSelected) { - // if (this.args.isVertexSelected[vertex] > index){ - // this.args.isVertexSelected[vertex] = this.args.isVertexSelected[vertex] - 1; - // } - // } - -}; - -GraphCanvas.prototype.changeVertexFormat = function(nodeId, format) { - var svgNode = DOM.select(this.getSVGNodeId(nodeId)); - if (svgNode != null) { - var properties = format.toJSON(); - for ( var item in properties) { - svgNode.setAttribute(item, properties[item]); - } - - if (this.getFormatter().getVertexById(nodeId) instanceof CircleVertexGraphFormatter) { - var transform = "translate(" + svgNode.getAttribute("dragx") + "," + svgNode.getAttribute("dragy") + "), scale(" + format.getSize() + ")"; - svgNode.setAttribute("transform", transform); - } - } -}; - -GraphCanvas.prototype.renderLabel = function(nodeId) { - var x = Math.ceil(this.getLayout().getNodeById(nodeId).x * this.getFormatter().getWidth()); - var y = Math.ceil(this.getLayout().getNodeById(nodeId).y * this.getFormatter().getHeight()); - - var svgAttributesNode = JSON.parse(JSON.stringify(this.getFormatter().getVertexById(nodeId).getDefault().toJSON().title)); - svgAttributesNode.id = this.getSVGLabelId(this.getDataset().getVertexById(nodeId).getId()); - svgAttributesNode.dx = (-1) * (this.getDataset().getVertexById(nodeId).getName().length * svgAttributesNode["font-size"]) / 4 - 4; - - svgAttributesNode.dy = parseFloat((this.getFormatter().getVertexById(nodeId).getDefault().getSize())) - + parseFloat(svgAttributesNode["font-size"]) + parseFloat(this.getFormatter().getVertexById(nodeId).getDefault().getStrokeWidth()) - 4; - svgAttributesNode.dragx = Math.ceil(this.getLayout().getNodeById(nodeId).x * this.getFormatter().getWidth()); - - var gragy = parseFloat(this.getFormatter().getVertexById(nodeId).getDefault().getSize()) - + Math.ceil(this.getLayout().getNodeById(nodeId).y * this.getFormatter().getHeight()); - svgAttributesNode.dragy = gragy; - svgAttributesNode.transform = "translate(" + svgAttributesNode.dragx + "," + svgAttributesNode.dragy + ")";//, scale("+this.formatter.getVertexById(nodeId).getDefault().getSize()+")"; - - var nodeSVG = SVG.drawText(0, 0, this.getDataset().getVertexById(nodeId).getName(), this.GraphLabelGroup, svgAttributesNode); - - this.svgLabels[nodeId] = nodeSVG; - - /** Events for the SVG node **/ - var _this = this; - if (nodeSVG != null) { - nodeSVG.addEventListener("mouseover", function() { - _this.overLabel(nodeId); - }, false); - nodeSVG.addEventListener("mouseout", function() { - _this.outLabel(nodeId); - }, false); - } - -}; - -GraphCanvas.prototype.removeLabel = function(labelId) { - if (DOM.select(this.getSVGLabelId(labelId)) != null) { - DOM.select(this.getSVGLabelId(labelId)).parentNode.removeChild(DOM.select(this.getSVGLabelId(labelId))); - } -}; - -GraphCanvas.prototype.renderNode = function(nodeId) { - var svgAttributesNode = JSON.parse(JSON.stringify(this.getFormatter().getVertexById(nodeId).getDefault().toJSON())); - svgAttributesNode.dragx = Math.ceil(this.getLayout().getNodeById(nodeId).x * this.getFormatter().getWidth()); - svgAttributesNode.dragy = Math.ceil(this.getLayout().getNodeById(nodeId).y * this.getFormatter().getHeight()); - svgAttributesNode.transform = "translate(" + svgAttributesNode.dragx + "," + svgAttributesNode.dragy + ")"; - svgAttributesNode.id = this.getSVGNodeId(nodeId); - /*svgAttributesNode["stroke-width"] = 3 ; - svgAttributesNode["stroke-opacity"] = 1 ; - svgAttributesNode["fill-opacity"] = svgAttributesNode["opacity"] ; - svgAttributesNode["opacity"] = 1 ;*/ - this.circleDefaultRadius = this.getFormatter().getVertexById(nodeId).getDefault().getSize(); - var nodeSVG; - - if (this.getFormatter().getVertexById(nodeId) instanceof CircleVertexGraphFormatter) { - nodeSVG = SVG.drawCircle(0, 0, this.circleDefaultRadius, this.GraphNodeGroup, svgAttributesNode); - } - - if (this.getFormatter().getVertexById(nodeId) instanceof SquareVertexGraphFormatter) { - //nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius) ,0 - (this.formatter.getVertexById(nodeId).getDefault().getSize()) , (this.getFormatter().getVertexById(nodeId).getDefault().getSize()*2), (this.getFormatter().getVertexById(nodeId).getDefault().getSize()*2), this.GraphNodeGroup, svgAttributesNode); - nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius), 0 - (this.circleDefaultRadius), (this.circleDefaultRadius * 2), - (this.circleDefaultRadius * 2), this.GraphNodeGroup, svgAttributesNode); - } - - if (this.getFormatter().getVertexById(nodeId) instanceof EllipseVertexGraphFormatter) { - nodeSVG = SVG.drawEllipse(0, 0, this.circleDefaultRadius * 1.5, this.circleDefaultRadius, this.GraphNodeGroup, svgAttributesNode); - } - - if (this.getFormatter().getVertexById(nodeId) instanceof RectangleVertexGraphFormatter) { - //nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius) ,0 - ((this.circleDefaultRadius*2)/2) , (this.circleDefaultRadius*2), (this.circleDefaultRadius), this.GraphNodeGroup, svgAttributesNode); - nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius * 1.5), 0 - (this.circleDefaultRadius), (this.circleDefaultRadius * 2 * 1.5), - (this.circleDefaultRadius * 2), this.GraphNodeGroup, svgAttributesNode); - - } - - if (this.getFormatter().getVertexById(nodeId) instanceof RoundedVertexGraphFormatter) { - svgAttributesNode.ry = 2;// this.formatter.getVertexById(nodeId).getDefault().getSize()/4; - svgAttributesNode.rx = 2;// this.formatter.getVertexById(nodeId).getDefault().getSize()/4; - nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius * 1.5), 0 - (this.circleDefaultRadius), (this.circleDefaultRadius * 2 * 1.5), - (this.circleDefaultRadius * 2), this.GraphNodeGroup, svgAttributesNode); - } - - // - - if (this.getFormatter().getVertexById(nodeId) instanceof OctagonVertexGraphFormatter) { - svgAttributesNode.ry = 2; - svgAttributesNode.rx = 2; - nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius * 1.5), 0 - (this.circleDefaultRadius), (this.circleDefaultRadius * 2 * 1.5), - (this.circleDefaultRadius * 2), this.GraphNodeGroup, svgAttributesNode); - } - - nodeSVG.internalId = nodeId; - // - var _this = this; - - /** Events for the SVG node **/ - if (nodeSVG != null) { - nodeSVG.addEventListener("mouseover", function() { - _this.onVertexOver.notify(nodeId); - _this.overNode(nodeId); - }, false); - nodeSVG.addEventListener("mouseout", function() { - _this.onVertexOut.notify(nodeId); - _this.outNode(nodeId); - }, false); - //nodeSVG.addEventListener("click", function(){_this.clickNode(nodeId);}, false); - // - nodeSVG.addEventListener("mouseup", function() { - _this.onVertexUp.notify(nodeId); - }, false); - } -}; - -GraphCanvas.prototype.removeNode = function(nodeId) { - DOM.select(this.getSVGNodeId(nodeId)).parentNode.removeChild(DOM.select(this.getSVGNodeId(nodeId))); - if (this.args.labeled) { - this.removeLabel(nodeId); - } -}; - -/** REMOVING **/ -GraphCanvas.prototype.removeSelected = function() { - /** El orden importa **/ - this.removeSelectedEdges(); - this.removeSelectedNode(); - -}; - -GraphCanvas.prototype.removeSelectedNode = function() { - var selected = JSON.parse(JSON.stringify(this.getSelectedVertices())); - this.deselectNodes(); - var sorted = selected.sort(function(a, b) { - return a - b - }); - for ( var i = 0; i < sorted.length; i++) { - if (this.getDataset().getVertexById(sorted[i]) != null) { - this.getDataset().getVertexById(sorted[i]).remove(); - } - } -}; - -/** EDGES **/ -GraphCanvas.prototype.removeEdge = function(edgeId) { - if (DOM.select(this.getSVGEdgeId(edgeId)) != null) { - DOM.select(this.getSVGEdgeId(edgeId)).parentNode.removeChild(DOM.select(this.getSVGEdgeId(edgeId))); - } - - if (DOM.select(this.getSVGEdgeId(edgeId) + "_shadow") != null) { - DOM.select(this.getSVGEdgeId(edgeId) + "_shadow").parentNode.removeChild(DOM.select(this.getSVGEdgeId(edgeId) + "_shadow")); - } - - if (DOM.select(this.getSVGArrowEdgeId(edgeId)) != null) { - DOM.select(this.getSVGArrowEdgeId(edgeId)).parentNode.removeChild(DOM.select(this.getSVGArrowEdgeId(edgeId))); - } -}; - -GraphCanvas.prototype.overEdge = function(edgeId) { - if ((!this.args.interactive) || this.dragging || this.selecting) { - return; - } - - /** If selected we don't change the format **/ - if (this.args.isEdgeSelected[edgeId] == null) { - var format = this.getFormatter().getEdgeById(edgeId).getOver(); - format.args["cursor"] = "pointer"; - this.changeEdgeFormat(edgeId, format); - } -}; - -GraphCanvas.prototype.outEdge = function(edgeId) { - if (!this.args.interactive) { - return; - } - - /** If selected we don't change the format **/ - if (this.args.isEdgeSelected[edgeId] == null) { - this.changeEdgeFormat(edgeId, this.getFormatter().getEdgeById(edgeId).getDefault()); - } -}; - -GraphCanvas.prototype.changeEdgeFormat = function(edgeId, format) { - var svgEdge = DOM.select(this.getSVGEdgeId(edgeId) + "_shadow"); - if (svgEdge != null) { - var properties = format.toJSON(); - for ( var item in properties) { - svgEdge.setAttribute(item, properties[item]); - } - } -}; - -GraphCanvas.prototype.deselectEdge = function(edgeID) { - if (this.args.isEdgeSelected[edgeID] != null) { - this.changeEdgeFormat(edgeID, this.getFormatter().getEdgeById(edgeID).getDefault()); - var index = this.args.isEdgeSelected[edgeID]; - delete this.args.isEdgeSelected[edgeID]; - } -}; - -GraphCanvas.prototype.deselectEdges = function() { - var selected = JSON.parse(JSON.stringify(this.getSelectedEdges())); - for ( var i = 0; i < selected.length; i++) { - this.deselectEdge(selected[i]); - } -}; - -GraphCanvas.prototype.removeSelectedEdges = function() { - var selected = JSON.parse(JSON.stringify(this.getSelectedEdges())); - this.deselectEdges(); - for ( var i = 0; i < selected.length; i++) { - if (this.getDataset().getEdgeById(selected[i]) != null) { - this.getDataset().getEdgeById(selected[i]).remove(); - } - } -}; - -GraphCanvas.prototype.renderEdge = function(edgeId) { - var svgAttributesEdge = this.getFormatter().getEdgeById(edgeId).getDefault().toJSON(); - var edge = this.getDataset().getEdgeById(edgeId); - - var svgNodeTarget = this.getVertexById(edge.getNodeTarget().getId()); - var svgNodeSource = this.getVertexById(edge.getNodeSource().getId()); - svgAttributesEdge.id = this.getSVGEdgeId(edge.getId()) + "_shadow"; - - var svgEdge = null; - - if (this.getFormatter().getEdgeById(edgeId) instanceof LineEdgeGraphFormatter) { - var coordenateSourceX = svgNodeSource.getAttribute("dragx"); - var coordenateSourceY = svgNodeSource.getAttribute("dragy"); - var coordenateTargetX = svgNodeTarget.getAttribute("dragx"); - var coordenateTargetY = svgNodeTarget.getAttribute("dragy"); - - SVG.drawLine(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, this.GraphEdgeGroup, svgAttributesEdge); - var attributesShadow = {}; - attributesShadow.id = this.getSVGEdgeId(edge.getId()); - attributesShadow["stroke-opacity"] = 0; - attributesShadow["stroke-width"] = 4; - attributesShadow["stroke"] = "black"; - svgEdge = SVG.drawLine(svgNodeSource.getAttribute("dragx"), svgNodeSource.getAttribute("dragy"), svgNodeTarget.getAttribute("dragx"), - svgNodeTarget.getAttribute("dragy"), this.GraphEdgeGroup, attributesShadow); - } - - if (this.getFormatter().getEdgeById(edgeId) instanceof BezierEdgeGraphFormatter) { - var nodeId = edge.getNodeTarget().getId(); - var nodeSize = this.formatter.getVertexById(nodeId).getDefault().getSize() * this.getFormatter().getNodesMaxSize(); - svgAttributesEdge.fill = "none"; - svgAttributesEdge.id = this.getSVGEdgeId(edgeId); - var d = this.calculateCoordenatesBezier(nodeSize, svgNodeSource.getAttribute("dragx"), svgNodeSource.getAttribute("dragy")); - svgEdge = SVG.drawPath(d, this.GraphEdgeGroup, svgAttributesEdge); - } - ; - - if ((this.getFormatter().getEdgeById(edgeId) instanceof DirectedLineEdgeGraphFormatter) - || (this.getFormatter().getEdgeById(edgeId) instanceof CutDirectedLineEdgeGraphFormatter) - || (this.getFormatter().getEdgeById(edgeId) instanceof DotDirectedLineEdgeGraphFormatter) - || (this.getFormatter().getEdgeById(edgeId) instanceof OdotDirectedLineEdgeGraphFormatter) - || (this.getFormatter().getEdgeById(edgeId) instanceof OdirectedLineEdgeGraphFormatter)) { - var coordenateSourceX = svgNodeSource.getAttribute("dragx"); - var coordenateSourceY = svgNodeSource.getAttribute("dragy"); - var coordenateTargetX = svgNodeTarget.getAttribute("dragx"); - var coordenateTargetY = svgNodeTarget.getAttribute("dragy"); - - var offset = parseFloat(this.getFormatter().getVertexById(this.getDataset().getEdgeById(edgeId).getNodeTarget().getId()).getDefault() - .getSize() - * this.circleDefaultRadius); - var point = this._calculateEdgePointerPosition(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, offset); - coordenateTargetX = point.x; - coordenateTargetY = point.y; - SVG.drawLine(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, this.GraphEdgeGroup, svgAttributesEdge); - - var attributesShadow = {}; - attributesShadow.id = this.getSVGEdgeId(edge.getId()); - attributesShadow["stroke-opacity"] = 0; - attributesShadow["stroke-width"] = 4; - attributesShadow["stroke"] = "black"; - svgEdge = SVG.drawLine(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, this.GraphEdgeGroup, attributesShadow); - } - - if (this.getFormatter().getEdgeById(edgeId) instanceof DirectedLineEdgeGraphFormatter - || (this.getFormatter().getEdgeById(edgeId) instanceof OdirectedLineEdgeGraphFormatter)) { - var coordenateSourceX = svgNodeSource.getAttribute("dragx"); - var coordenateSourceY = svgNodeSource.getAttribute("dragy"); - var coordenateTargetX = svgNodeTarget.getAttribute("dragx"); - var coordenateTargetY = svgNodeTarget.getAttribute("dragy"); - - var point = this._calculateEdgePointerPosition(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, offset); - coordenateTargetX = point.x; - coordenateTargetY = point.y; - - var angle = Geometry.toDegree(point.angle) + 90; - this.arrowDefaultSize = this.getFormatter().getEdgeById(edgeId).getArrowSize(); //getDefault().getArrowSize(); - var d = "-" + this.arrowDefaultSize + ",0 0,-" + parseFloat(this.arrowDefaultSize) * 2 + " " + this.arrowDefaultSize + ",0"; - - var attributes; - - if (this.getFormatter().getEdgeById(edgeId) instanceof DirectedLineEdgeGraphFormatter) { - attributes = [ - [ "fill", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], - [ "stroke", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], [ "id", this.getSVGArrowEdgeId(edgeId) ] ]; - } else { - attributes = [ - [ "fill", "#FFFFFF" ], [ "stroke", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], - [ "id", this.getSVGArrowEdgeId(edgeId) ] ]; - } - - var flechaSVGNode = SVG.drawPoligon(d, this.GraphEdgeGroup, attributes);//, ["transform", "rotate("+angle+"), translate(0,0)"]]); - flechaSVGNode.setAttribute("transform", " translate(" + coordenateTargetX + ", " + coordenateTargetY + "), rotate(" + angle + ")"); - } - ; - - if (this.getFormatter().getEdgeById(edgeId) instanceof CutDirectedLineEdgeGraphFormatter) { - var coordenateSourceX = svgNodeSource.getAttribute("dragx"); - var coordenateSourceY = svgNodeSource.getAttribute("dragy"); - var coordenateTargetX = svgNodeTarget.getAttribute("dragx"); - var coordenateTargetY = svgNodeTarget.getAttribute("dragy"); - - var point = this._calculateEdgePointerPosition(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, offset); - coordenateTargetX = point.x; - coordenateTargetY = point.y; - - var angle = Geometry.toDegree(point.angle) + 90; - - //this.arrowDefaultSize = 2; //getDefault().getArrowSize(); - var d = "-4,0 4,0 4,-2 -4,-2"; - - var flechaSVGNode = SVG.drawPoligon(d, this.GraphEdgeGroup, [ - [ "fill", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], - [ "stroke", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], [ "id", this.getSVGArrowEdgeId(edgeId) ] ]);//, ["transform", "rotate("+angle+"), translate(0,0)"]]); - flechaSVGNode.setAttribute("transform", " translate(" + coordenateTargetX + ", " + coordenateTargetY + "), rotate(" + angle + ")"); - } - ; - - if ((this.getFormatter().getEdgeById(edgeId) instanceof DotDirectedLineEdgeGraphFormatter) - || (this.getFormatter().getEdgeById(edgeId) instanceof OdotDirectedLineEdgeGraphFormatter)) { - var coordenateSourceX = svgNodeSource.getAttribute("dragx"); - var coordenateSourceY = svgNodeSource.getAttribute("dragy"); - var coordenateTargetX = svgNodeTarget.getAttribute("dragx"); - var coordenateTargetY = svgNodeTarget.getAttribute("dragy"); - var point = this._calculateEdgePointerPosition(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, offset); - coordenateTargetX = point.x; - coordenateTargetY = point.y; - var angle = Geometry.toDegree(point.angle) + 90; - // this.arrowDefaultSize = this.formatter.getEdgeById(edgeId).getArrowSize(); //getDefault().getArrowSize(); - var attributes = []; - if (this.getFormatter().getEdgeById(edgeId) instanceof OdotDirectedLineEdgeGraphFormatter) { - attributes = [ - [ "fill", "#FFFFFF" ], [ "stroke", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], - [ "id", this.getSVGArrowEdgeId(edgeId) ] ]; - } else { - attributes = [ - [ "fill", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], - [ "stroke", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], [ "id", this.getSVGArrowEdgeId(edgeId) ] ]; - } - var flechaSVGNode = SVG.drawCircle(0, 0, 4, this.GraphEdgeGroup, attributes); - flechaSVGNode.setAttribute("transform", " translate(" + coordenateTargetX + ", " + coordenateTargetY + "), rotate(" + angle + ")"); - } - ; - - var _this = this; - /** Events for the SVG edge **/ - if (svgEdge != null) { - if (this.getDataset().getEdgesCount() < this.args.maxNumberEdgesFiringEvents) { - svgEdge.addEventListener("mouseover", function() { - _this.overEdge(edgeId); - }, false); - svgEdge.addEventListener("mouseout", function() { - _this.outEdge(edgeId); - }, false); - } - } -}; - -GraphCanvas.prototype._calculateEdgePointerPosition = function(sourceX, sourceY, targetX, targetY, radius) { - var angle = Geometry.getAngleBetweenTwoPoints(sourceX, sourceY, targetX, targetY); - - /** Suponiendo el node source que este a la derecha **/ - if ((targetX - sourceX) < 0) { - var b = Geometry.getAdjacentSideOfRectangleRight(angle, radius); - targetX = parseFloat(targetX) + parseFloat(b); - arrowX = parseFloat(targetX) + parseFloat(b) + this.arrowDefaultSize / 2; - } else { - var b = Geometry.getAdjacentSideOfRectangleRight(angle, radius); - targetX = parseFloat(targetX) - parseFloat(b); - arrowX = parseFloat(targetX) - parseFloat(b) - this.arrowDefaultSize / 2; - } - - /** Suponiendo el node source que este a la arriba **/ - if ((targetY - sourceY) > 0) { - var a = Geometry.getOppositeSideOfRectangleRight(angle, radius); - targetY = parseFloat(targetY) - parseFloat(a); - arrowY = parseFloat(targetY) - parseFloat(a) - this.arrowDefaultSize / 2; - } else { - var a = Geometry.getOppositeSideOfRectangleRight(angle, radius); - targetY = parseFloat(targetY) + parseFloat(a); - arrowY = parseFloat(targetY) + parseFloat(a) - this.arrowDefaultSize / 2; - - } - - return { - "x" : arrowX, - "y" : arrowY, - "angle" : angle - }; -}; - -GraphCanvas.prototype.calculateCoordenatesBezier = function(nodeSize, x1, y1) { - var x11 = x1 - (nodeSize / 2); - var y11 = y1 - (nodeSize / 2); - - var x12 = parseFloat(x1) + parseFloat(nodeSize / 2); - var y12 = y1 - (nodeSize / 2); - - var curvePointX = (x12 - x11) / 2 + x11; - var curvePointY = y1 - (nodeSize * 2); - var d = "M" + x11 + "," + y11 + " T" + curvePointX + "," + curvePointY + " " + x12 + "," + y12; - return d; - -}; - -GraphCanvas.prototype.renderEdges = function() { - for ( var edge in this.getDataset().getEdges()) { - this.renderEdge(this.getDataset().getEdgeById(edge).getId()); - - } -}; - -GraphCanvas.prototype.getLastSelectedNode = function() { - var node = null; - if (this.getSelectedVertices().length > 0) { - var nodeId = this.getSelectedVertices()[this.getSelectedVertices().length - 1]; - node = this.getDataset().getVertexById(nodeId); - } - return node; -}; -/* - GraphCanvas.prototype.getNodeByNameAndIndex = function(node, index){ - var nodeId = this.getDataset().verticesIndex[node][index]; - var nodeItem = this.getDataset().getVertexById(nodeId); - return nodeItem; - }; - */ - -GraphCanvas.prototype.setDataset = function(dataset) { - this.dataset = dataset; -}; - -GraphCanvas.prototype.setFormatter = function(formatter) { - this.formatter = formatter; -}; - -GraphCanvas.prototype.setLayout = function(layout) { - this.layout = layout; -}; - -/** API **/ -GraphCanvas.prototype.getDataset = function() { - return this.dataset; -}; - -GraphCanvas.prototype.getFormatter = function() { - return this.formatter; -}; - -GraphCanvas.prototype.getLayout = function() { - return this.layout; -}; - -/** API DATASET **/ -GraphCanvas.prototype.addVertex = function(name, args) { - this.getDataset().addNode(name, args); -}; - -GraphCanvas.prototype.removeVertex = function(vertexId) { - this.getDataset().getVertexById(vertexId).remove(); -}; - -GraphCanvas.prototype.addEdge = function(edgeName, nodeSourceId, nodeTargetId, args) { - this.getDataset().addEdge(edgeName, nodeSourceId, nodeTargetId, args); -}; -/* - GraphCanvas.prototype.removeEdge = function(edgeId){ - this.getDataset().getEdgeById(edgeId).remove(); - }; - */ - -/** API FORMATTER **/ -GraphCanvas.prototype.getWidth = function() { - return this.getFormatter().getWidth(); -}; - -GraphCanvas.prototype.getHeight = function() { - return this.getFormatter().getHeight(); -}; - -GraphCanvas.prototype.getBackgroundImage = function() { - return this.getFormatter().getBackgroundImage(); -}; +/** + * Example form + * + * @witdh + * @height + */ +function ExampleForm(args) { + this.id = BUI.id(); + this.width = 700; + this.height = 500; + + if (args != null) { + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + } +} + +ExampleForm.prototype._getItems = function() { + return [{ + fieldLabel : 'First Name', + name : 'first', + allowBlank : false + }, { + fieldLabel : 'Last Name', + name : 'last', + allowBlank : false + } ]; +}; + +ExampleForm.prototype._getItems = function() { + return [ ]; +}; + +ExampleForm.prototype._getButtons = function() { + return [ ]; +}; + +ExampleForm.prototype.getPanel = function() { + this.panel = Ext.create('Ext.form.Panel', { + width : this.width, + height : this.height, + margin : 10, + border : 1, + defaultType : 'textfield', + items : this._getItems(), + buttons : this._getButtons() + }); + return this.panel; +}; + +/** It populates the form **/ +ExampleForm.prototype.refresh = function(macromolecule) { +}; -//GraphCanvas.prototype.setBackgroundImage = function(value){ -// this.getFormatter().setBackgroundImage(value); -//}; +function ExperimentForm(args) { + this.id = BUI.id(); + + if (args != null) { + } + + this.onSaved = new Event(this); +} + +ExperimentForm.prototype._getItems = function(experiment) { + this.experiment = experiment; + var typeCombo = Ext.create('Ext.form.ComboBox', { + id : this.id + 'type', + fieldLabel : 'Type', + store : [ "STATIC", "CALIBRATION", "HPLC" ], + queryMode : 'local', + labelWidth : 120, + displayField : 'name', + valueField : 'name', + value : experiment.json.type, + disabled : (experiment.json.type == 'TEMPLATE') + }); + + var items = []; + + + if (experiment.json.type == "HPLC" ){ + var typeMacromolecule = BIOSAXS_COMBOMANAGER.getComboMacromoleculeByMacromolecules(BIOSAXS.proposal.getMacromolecules(), {labelWidth : 120, width: "120px"}); + if (experiment.getHPLCMacromolecule() != null){ + typeMacromolecule.setValue(experiment.getHPLCMacromolecule().macromoleculeId); + items.push(typeMacromolecule); + } + } + + + items.push(typeCombo, { + id : this.id + 'name', + xtype : 'textfield', + fieldLabel : 'Name', + labelWidth : 120, + width : '100%', + value : experiment.json.name + }, { + id : this.id + 'comments', + xtype : 'textareafield', + name : 'comments', + fieldLabel : 'Comments', + labelWidth : 120, + height : 120, + width : '100%', + value : experiment.json.comments + }); + return items; +}; +ExperimentForm.prototype.getPanel = function(experiment) { + var _this = this; + + this.panel = Ext.createWidget({ + xtype : 'container', + layout : 'vbox', + border : 0, + style : { + padding : '10px' + }, + fieldDefaults : { + labelAlign : 'left', + labelWidth : 50 + }, + items : this._getItems(experiment) + }); + return this.panel; +}; + +ExperimentForm.prototype.input = function() { + return new ExperimentHeaderForm().input(); +}; + +ExperimentForm.prototype.test = function(targetId) { + var experimentForm = new ExperimentForm(); + var panel = experimentForm.getPanel(new Experiment(experimentForm.input().experiment)); + panel.render(targetId); +}; -GraphCanvas.prototype.getBackgroundColor = function() { - return this.getFormatter().getBackgroundColor(); -}; +/** + * Shows the header for the experiments changing the color and parameters depending on experiment type + * + */ +function ExperimentHeaderForm(args) { + this.id = BUI.id(); + this.backgroundColor = '#FFFFFF'; +} + +ExperimentHeaderForm.prototype.getHTMLSource = function(experiment) { + var html = BUI.createFormLabel("Name :", experiment.json.name, 75, 400, this.backgroundColor); + if (experiment.json.type == "HPLC") { + if (experiment.getHPLCMacromolecule() != null){ + html = html + BUI.createFormLabel("Molecule :", experiment.getHPLCMacromolecule().acronym, 75, 400, this.backgroundColor); + } + } + else{ + html = html + BUI.createFormLabel("Type :", experiment.json.type, 75, 400, this.backgroundColor); + } + + html = html + BUI.createFormLabel("Date :", experiment.json.creationDate, 75, 400, this.backgroundColor); + return html; +}; + +ExperimentHeaderForm.prototype.getHTMLDownload = function(experiment) { + var bgcolor = "background-color:" + this.backgroundColor + ";"; + var html = "
"; + if ((experiment.json.type == "CALIBATION") || (experiment.json.type == "STATIC")) { + html = html + " Download Source File
"; + html = html + + ""; + } + if (experiment.json.type == "TEMPLATE") { + html = html + + " Download Source File
"; + } + + if (experiment.json.type == "HPLC") { + html = html + " Download h5 File"; + } + + return html; +}; + +ExperimentHeaderForm.prototype.getTopPanel = function(experiment) { + return { + xtype : 'container', + layout : 'hbox', + items : [ { + margin : "0 0 0 0", + width : 475, + border : 0, + html : this.getHTMLSource(experiment) + }, { + margin : "0 0 0 0", + width : 475, + border : 0, + html : this.getHTMLDownload(experiment) + } ] + }; +}; + +ExperimentHeaderForm.prototype.getButton = function(experiment) { + var _this = this; + return Ext.create('Ext.Button', { + text : 'EDIT', + minWidth : '100', + margin : '10 0 0 30', + handler : function() { + var experimentWindow = new ExperimentWindow(); + experimentWindow.onSaved.attach(function(sender, data) { + _this.experiment.json.name = data.name; + _this.experiment.json.type = data.type; + _this.experiment.json.comments = data.comments; + _this.panel.remove(_this.panel.items.items[0]); + _this.panel.remove(_this.panel.items.items[0]); + _this.panel.insert(_this.getTopPanel(_this.experiment)); + _this.panel.insert(_this.getBottomPanel(_this.experiment)); + }); + experimentWindow.show(experiment); + } + }); +}; + +ExperimentHeaderForm.prototype.getBottomPanel = function(experiment) { + return { + xtype : 'container', + layout : 'hbox', + margin : '10 0 0 0', + items : [ this.getComments(experiment), this.getButton(experiment) ] + }; +}; + +ExperimentHeaderForm.prototype.getComments = function(experiment) { + return { + xtype : 'textareafield', + labelStyle : 'font-weight: bold;', + name : 'comments', + fieldLabel : 'Comments', + labelWidth : 70, + height : 40, + minWidth : '450', + readOnly : true, + value : experiment.json.comments + }; +}; + +ExperimentHeaderForm.prototype.getPanel = function(experiment) { + this.experiment = experiment; + + if (experiment.json.type == 'CALIBRATION') { + this.backgroundColor = '#EFFBFB'; + } + if (experiment.json.type == 'TEMPLATE') { + this.backgroundColor = '#E0F8E6'; + } + + this.panel = Ext.create('Ext.container.Container', { + frame : false, + layout : 'vbox', + padding : 5, + bodyPadding : '5 5 0 0', + width : 890, + margin : '0 0 10 0', + height : 120, + style : { + borderColor : '#99bce8', + borderStyle : 'solid', + borderWidth : '1px', + 'background-color' : this.backgroundColor + }, + fieldDefaults : { + msgTarget : 'side', + labelWidth : 100 + }, + items : [ this.getTopPanel(experiment), this.getBottomPanel(experiment) ] + }); + return this.panel; +}; + +ExperimentHeaderForm.prototype.input = function() { + return { + experiment : DATADOC.getExperiment_10() + }; +}; + +ExperimentHeaderForm.prototype.test = function(targetId) { + var experimentHeaderForm = new ExperimentHeaderForm(); + var panel = experimentHeaderForm.getPanel(new Experiment(experimentHeaderForm.input().experiment)); + panel.render(targetId); + +}; -GraphCanvas.prototype.setBackgroundColor = function() { - this.getFormatter().setBackgroundColor(value); -}; +/** + * Macromolecule form with the general parameters of a macromolecule + * + * @witdh + * @height + * + * #onSave button save has been clicked + * #onClose button close has been clicked + */ +function MacromoleculeForm(args) { + this.id = BUI.id(); + this.width = 700; + this.height = 500; + + if (args != null) { + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + } + + /** Events **/ + this.onSave = new Event(this); + this.onClose = new Event(this); +} + +/** Type : is the Ext type then requiredtext or textfield * */ +MacromoleculeForm.prototype._getFieldTextWithHelp = function(type, fieldLabel, fieldName, help) { + return Ext.create('Ext.container.Container', { + margin : "10 0 0 10", + items : [ { + xtype : type, + fieldLabel : fieldLabel, + name : fieldName, + id : this.id + fieldName + }, { + xtype : 'label', + forId : 'myFieldId', + text : help, + margin : "5 0 0 105", + cls : "inline-help" + } ] + }); +}; + +MacromoleculeForm.prototype._getNumericWithHelp = function(type, fieldLabel, fieldName, help) { + return Ext.create('Ext.container.Container', { + margin : "0 0 0 10", + items : [ { + xtype : type, + fieldLabel : fieldLabel, + name : fieldName, + id : this.id + fieldName, + decimalPrecision : 6, + width : 220 + }, { + xtype : 'label', + forId : 'myFieldId', + text : help, + margin : "5 0 0 10", + cls : "inline-help" + } ] + }); +}; + +MacromoleculeForm.prototype._getButtons = function() { + var _this = this; + return [ { + text : 'Save', + handler : function() { + _this._save(); + } + },{ + text : 'Close', + handler : function() { + _this.onClose.notify(); + + } + } ]; +}; + +/** It persits the macromolecule in the database **/ +MacromoleculeForm.prototype._persist = function(macromoleculeId, acronym, name, molecularMass, extintionCoefficient, comments, refractiveIndex, solventViscosity) { + + /** Checking not duplicated acronym **/ + if (((macromoleculeId == null) && (BIOSAXS.proposal.getMacromoleculeByAcronym(acronym) != null))== true){ + BUI.showError("Duplicated acronym"); + return; + } + + + if (macromoleculeId == null){ + /** new macromolecule **/ + this.macromolecule = {}; + this.macromolecule.macromoleculeId = null; + } + else{ + this.macromolecule.macromoleculeId = macromoleculeId; + } + + this.macromolecule["acronym"] = acronym; + this.macromolecule["name"] = name; + this.macromolecule["molecularMass"] = molecularMass; + this.macromolecule["extintionCoefficient"] = extintionCoefficient; + this.macromolecule["comments"] = comments; + this.macromolecule["symmetry"] = Ext.getCmp(this.id + 'comboSym').getValue(); + this.macromolecule["refractiveIndex"] = refractiveIndex; + this.macromolecule["solventViscosity"] = solventViscosity; + + var _this = this; + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, proposal) { + /** Updating the proposal global object **/ + BIOSAXS.proposal.setItems(proposal); + _this.panel.setLoading(false); + + var saved = BIOSAXS.proposal.getMacromoleculeByAcronym(acronym); + /** Refreshing to check that everything is ok **/ + _this.refresh(saved); + _this.onSave.notify(saved); + }); + + this.panel.setLoading("Saving Macromolecule") + adapter.saveMacromolecule(this.macromolecule); +}; + +/** Save the macromolecule in the DB **/ +MacromoleculeForm.prototype._save = function() { + + var _this = this; + + var acronym = this._getField("acronym"); + var name = this._getField("name"); + var molecularMass = this._getField("molecularMass"); + var extintionCoefficient = this._getField("extintionCoefficient"); + var comments = this._getField("comments"); + + var refractiveIndex = this._getField("refractiveIndex"); + var solventViscosity = this._getField("solventViscosity"); + + /** Checking required fields **/ + if (name == "") { + BUI.showError("Name field is mandatory"); + return; + } + if (acronym == "") { + BUI.showError("Acroynm field is mandatory"); + return; + } + + if (this.macromolecule != null){ + /** Checking if it is a new macromolecule **/ + if (this.macromolecule.macromoleculeId == null){ + /** Check if the acronym exists already **/ + this._persist(null, acronym, name, molecularMass, extintionCoefficient, comments, refractiveIndex, solventViscosity); + } + else{ + /** It is an update **/ + this._persist(this.macromolecule.macromoleculeId, acronym, name, molecularMass, extintionCoefficient, comments, refractiveIndex, solventViscosity); + } + } + else{ + /** It is a new macromolecule **/ + this._persist(null, acronym, name, molecularMass, extintionCoefficient, comments, refractiveIndex, solventViscosity); + } +}; + + + +MacromoleculeForm.prototype._getItems = function() { + var _this = this; + /** Symmetry combo box **/ + var symmetry = Ext.create('Ext.data.Store', { + fields : [ 's' ], + data : this._getSymmetries() + }); + + this.symmetryComboBox = Ext.create('Ext.form.ComboBox', { + fieldLabel : 'Symmetry', + store : symmetry, + id : this.id + 'comboSym', + queryMode : 'local', + displayField : 's', + valueField : 's', + value : "P1", + margin : "0 0 0 30", + width : 220 + }); + + return [this._getFieldTextWithHelp("requiredtext", "Name", "name", "Long name. i.e: Bovine serum albumin"), + this._getFieldTextWithHelp("requiredtext", "Acronym", "acronym", "Acronym will be used in the files and analisys. i.e: BSA"), + this._getFieldTextWithHelp("textfield", "Mol. Mass (Da)", "molecularMass", "Atomic mass estimation measured in Da"), + { + xtype : 'container', + layout : 'hbox', + margin : "10 0 0 0", + items :[ + this._getNumericWithHelp("numberfield", "Extinction coef.", "extintionCoefficient", ""), + this.symmetryComboBox + ] + }, + { + xtype : 'container', + layout : 'hbox', + margin : "5 0 0 0", + items :[ + this._getNumericWithHelp("numberfield", "Refractive Index", "refractiveIndex", "How radiation propagates through the medium"), + this._getNumericWithHelp("numberfield", "Solvent Viscosity", "solventViscosity", "") + ] + }, + { + id : this.id + "comments", + xtype : 'textareafield', + name : 'comments', + margin : '35 0 0 10', + fieldLabel : 'Comments', + width : this.width - 100 + } ]; +}; + +MacromoleculeForm.prototype._getSymmetries = function() { + return [ { + "s" : "P1" + }, { + "s" : "P2" + }, { + "s" : "P3" + }, { + "s" : "P4" + }, { + "s" : "P5" + }, { + "s" : "P6" + }, { + "s" : "P32" + }, { + "s" : "P42" + }, { + "s" : "P52" + }, { + "s" : "P62" + }, { + "s" : "P222" + } ] +}; + +MacromoleculeForm.prototype.getPanel = function() { + this.panel = Ext.create('Ext.form.Panel', { + width : this.width, + height : this.height, + margin : 10, + border : 1, + defaultType : 'textfield', + items : this._getItems(), + buttons : this._getButtons() + }); + return this.panel; +}; + + +/** Populates each text field by field name and value **/ +MacromoleculeForm.prototype._populateField = function(fieldName, value) { + if (value != null){ + Ext.getCmp(this.id + fieldName).setValue(value); + } +}; + +/** Gets the value of a textfield **/ +MacromoleculeForm.prototype._getField = function(fieldName) { + return Ext.getCmp(this.id + fieldName).getValue(); +}; + + +/** It populates the form **/ +MacromoleculeForm.prototype.refresh = function(macromolecule) { + this.macromolecule = macromolecule; + if (macromolecule != null){ + this._populateField("name", macromolecule.name); + this._populateField("acronym", macromolecule.acronym); + this._populateField("extintionCoefficient", macromolecule.extintionCoefficient); + this._populateField("molecularMass", macromolecule.molecularMass); + this._populateField("comments", macromolecule.comments); + this._populateField("refractiveIndex", macromolecule.refractiveIndex); + this._populateField("solventViscosity", macromolecule.solventViscosity); + if (macromolecule.symmetry != null){ + Ext.getCmp(this.id + 'comboSym').setValue(macromolecule.symmetry); + } + } +}; + + +MacromoleculeForm.prototype.input = function() { + return {}; +}; + + +/** It populates the form **/ +MacromoleculeForm.prototype.test = function(targetId) { + var macromoleculeForm = new MacromoleculeForm(); + macromoleculeForm.onClose.attach(function(sender){ + alert("Click on close"); + }); + var panel = macromoleculeForm.getPanel(); + panel.render(targetId); +}; + + -//GraphCanvas.prototype.setEdgeFill = function(edgeId, value){ -// this.getFormatter().getEdgeById(edgeId).getDefault().setFill(value); -//}; -// -//GraphCanvas.prototype.getEdgeFill = function(edgeId){ -// return this.getFormatter().getEdgeById(edgeId).getDefault().getFill(); -//}; + + +function ModelVisualizerForm(args){ + this.id =BUI.id(); + this.width = 600; + this.height = 400; + if (args!= null){ + if (args.width != null){ + this.width = args.width; + } + if (args.height != null){ + this.height = args.height; + } + } +}; + +ModelVisualizerForm.prototype._getFirHTML = function(modelId, width, height, type, desc) { + var html = ""; + html = html + ''; + html = html + ''; + html = html + ''; + html = html + '
dammin.' + type + '
' + desc + '
'; + return html; +}; + +ModelVisualizerForm.prototype.getItems = function(modelPanel){ + _this = this; + var height = _this.height/2 - 60; + var width = _this.width/2 - 10; + + return Ext.create('Ext.container.Container', { + layout: { + type: 'vbox', // Arrange child items vertically + }, + items: [ + modelPanel, + { + xtype : 'container', + layout: { + type: 'hbox', // Arrange child items vertically + }, + items : [{ + html : this._getFirHTML("id", width, height, "fir", "Fit of the simulated scattering curve versus a smoothed experimental data (spline interpolation)"), + height :height, + width : width, + padding: 2 + }, + { + html : this._getFirHTML("id", width, height, "fit", "Fit of the simulated scattering curve versus the experimental data."), + height : height, + width : width, + padding: 2 + }] + } + + ] + }); +}; + +ModelVisualizerForm.prototype.refresh = function(models){ + var input = []; +// var colors = ["008000", "F0A804", "0000FF", "800080", "C0C0C0"]; + for (var i = 0; i < models.length; i++) { + console.log(BUI.rainbow(models.length, i).replace("#", "0x")); + input.push({ + color: BUI.rainbow(models.length, i).replace("#", "0x"), + modelId: models[i].modelId, + opacity: 0.8, + radius: 3, + title: BUI.getFileNameByPath(models[i].pdbFile), + type: "SHAPEDETERMINATIONMODEL" + + }); + } + + this.panel.removeAll(); + this.panel.add( + _this.getItems( + new PDBViewer({ + width : this.width - 10, + height : (this.height/2) - 10, + title : "" + }).draw(input) + ) + ); + + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + var splitted = data.toString().split("\n"); + var array = []; + for ( var i = 0; i < splitted.length; i++) { + var line = splitted[i].trim(); + var line_splited = line.split(/\s*[\s,]\s*/); + if (line_splited.length == 4) { + array.push([ Number(line_splited[0]), BUI.getStvArray(line_splited[1], line_splited[2]), BUI.getStvArray(line_splited[3], 0) ]); + } + } + + var id = (_this.id + "firid"); + var dygraphWidget = new StdDevDyGraph(id, { + width : (_this.width/2) - 10, + height :(_this.height/2) -110, + xlabel : 'q(nm-1)' + }); + dygraphWidget.draw(array, [ "#FF0000", "#0000FF", "#FF00FF" ], [ 's', 'I(exp)', 'I(sim)' ]); + }); + + adapter.getModelFile("FIR", models[0].modelId); + + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + var splitted = data.toString().split("\n"); + var array = []; + for ( var i = 0; i < splitted.length; i++) { + var line = splitted[i].trim(); + var line_splited = line.split(/\s*[\s,]\s*/); + if (line_splited.length == 3) { + array.push([ Number(line_splited[0]), BUI.getStvArray(line_splited[1], 0), BUI.getStvArray(line_splited[2], 0) ]); + } + } + + var id = (_this.id + "fitid"); + + var dygraphWidget = new StdDevDyGraph(id, { + width : (_this.width/2) - 10, + height : (_this.height/2) - 110, + xlabel : 'q(nm-1)' + }); + dygraphWidget.draw(array, [ "#FF0000", "#0000FF" ], [ "s", "I(exp)", "I(sim)" ]); + }); + adapter.getModelFile("FIT", models[0].modelId); +}; + +ModelVisualizerForm.prototype.getPanel = function(modelList){ + _this = this; + this.modelList = modelList; + this.panel = Ext.create('Ext.Panel', { + title: 'Results', + width: this.width, + height: this.height, + layout: { + type: 'vbox', // Arrange child items vertically +// align: 'stretch' // Each takes up full width + }, + items: [ + + ], + listeners : { + afterrender : function(grid, eOpts) { +// alert(_this.modelList) + } + } + }); + + return this.panel; + +}; + -/** VERTICES FORMATTER **/ -GraphCanvas.prototype.setVertexSize = function(vertexId, value) { - this.getFormatter().getVertexById(vertexId).getDefault().setSize(value); -}; +/** + * Example form + * + * @witdh + * @height + */ +function MolarityForm(args) { + this.id = BUI.id(); + this.width = 700; + this.height = 500; + + if (args != null) { + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + } + + this.onSave = new Event(this); + this.onClose = new Event(this); +} + + +MolarityForm.prototype._getNumericWithHelp = function(type, fieldLabel, fieldName, help) { + return Ext.create('Ext.container.Container', { + margin : "10 0 0 10", + items : [ { + xtype : type, + fieldLabel : fieldLabel, + name : fieldName, + id : this.id + fieldName, + decimalPrecision : 6 + }, { + xtype : 'label', + forId : 'myFieldId', + text : help, + margin : "5 0 0 105", + cls : "inline-help" + } ] + }); +}; + + +MolarityForm.prototype._getItems = function() { + this.macromoleculeCombo = BIOSAXS_COMBOMANAGER.getComboMacromoleculeByMacromolecules(this.getMacromuleculesCandidates(this.macromolecule), { + width : 250, + labelWidth : 100, + margin : 10 + }); + + return [ { + xtype : 'container', + flex : 1, + margin : '10 0 0 10', + border : 0, + layout : 'anchor', + defaultType : 'requiredtext', + items : [ this.macromoleculeCombo, + this._getNumericWithHelp("textfield", "Ratio", "ratio", "Number in assymmetric units") + ] + } ]; +}; + +MolarityForm.prototype._persist = function() { + var _this = this; + var macromoleculeId = this.macromoleculeCombo.getValue(); + var ratio = Ext.getCmp(this.id + "ratio").getValue(); + var comments = "Not used yet"; + var dataAdapter = new BiosaxsDataAdapter(); + this.panel.setLoading("Saving"); + dataAdapter.onSuccess.attach(function(sender, args) { + _this.onSave.notify(); + }); + dataAdapter.saveStoichiometry(this.macromolecule.macromoleculeId, macromoleculeId, ratio, comments); +}; + +MolarityForm.prototype._getButtons = function() { + var _this = this; + + function onClose() { + _this.onClose.notify(); + } + + return [ { + text : 'Save', + handler : function() { + _this._persist(); + } + }, { + text : 'Cancel', + handler : function() { + onClose(); + } + } ]; +}; + +MolarityForm.prototype.getPanel = function() { + this.panel = Ext.create('Ext.form.Panel', { +// width : null, + height : this.height, + margin : 2, + border : 1, + defaultType : 'requiredtext', + items : this._getItems(), + buttons : this._getButtons() + }); + return this.panel; +}; + +/** macromolecules contains all macromolecules except this one **/ +MolarityForm.prototype.getMacromuleculesCandidates = function(macromolecule) { + var macromolecules = []; + if ( BIOSAXS.proposal.macromolecules){ + for (var i = 0; i < BIOSAXS.proposal.macromolecules.length; i++) { + var m = BIOSAXS.proposal.macromolecules[i]; + if (this.macromolecule != null){ + if (m.macromoleculeId != this.macromolecule.macromoleculeId) { + macromolecules.push(m); + } + } + } + } + return macromolecules; +}; + + +/** It populates the form **/ +MolarityForm.prototype.refresh = function(macromolecule) { + this.macromolecule = macromolecule; + +}; + + +MolarityForm.prototype.input = function() { + return {}; +}; + + +/** It populates the form **/ +MolarityForm.prototype.test = function(targetId) { + var macromoleculeForm = new MolarityForm(); + var panel = macromoleculeForm.getPanel(); + panel.render(targetId); +}; -GraphCanvas.prototype.getVertexSize = function(vertexId) { - return this.getFormatter().getVertexById(vertexId).getDefault().getSize(); -}; +///** +// * +// * @witdh +// * @height +// */ +//function MacromoleculeForm(args) { +// this.id = BUI.id(); +// this.width = 700; +// this.height = 500; +// +// if (args != null) { +// if (args.width != null) { +// this.width = args.width; +// } +// if (args.height != null) { +// this.height = args.height; +// } +// } +// +// this.onClose = new Event(this); +//} +// +//MacromoleculeForm.prototype.getMacromolecule = function() { +// this.macromolecule.name = Ext.getCmp(this.panel.getItemId()).getValues().name; +// this.macromolecule.acronym = Ext.getCmp(this.panel.getItemId()).getValues().acronym; +// this.macromolecule.comments = Ext.getCmp(this.panel.getItemId()).getValues().comments; +// this.macromolecule.extintionCoefficient = Ext.getCmp(this.panel.getItemId()).getValues().extintionCoefficient; +// this.macromolecule.molecularMass = Ext.getCmp(this.panel.getItemId()).getValues().molecularMass; +// return this.macromolecule; +//}; +// +//MacromoleculeForm.prototype.setMacromolecule = function(macromolecule) { +// this.pdbStore.loadData(macromolecule.structure3VOs); +// +//}; +// +//MacromoleculeForm.prototype.getForm = function(macromolecule) { +// this.panel = Ext.createWidget('form', { +// frame : false, +// border : 0, +// padding : 15, +// width : 550, +// height : 350, +// items : [ { +// xtype : 'container', +// layout : 'hbox', +// items : [ { +// xtype : 'container', +// flex : 1, +// border : false, +// layout : 'anchor', +// defaultType : 'requiredtext', +// items : [ { +// fieldLabel : 'Name', +// name : 'name', +// anchor : '95%', +// tooltip : "Name of the macromolecule", +// value : macromolecule.name +// }, { +// fieldLabel : 'Acronym', +// name : 'acronym', +// anchor : '95%', +// value : macromolecule.acronym +// } ] +// }, { +// xtype : 'container', +// flex : 1, +// layout : 'anchor', +// defaultType : 'textfield', +// items : [ { +// xtype : 'numberfield', +// fieldLabel : 'Mol. Mass (Da)', +// name : 'molecularMass', +// value : macromolecule.molecularMass, +// decimalPrecision : 6 +// }, { +// xtype : 'numberfield', +// fieldLabel : 'Extinction coef.', +// name : 'extintionCoefficient', +// value : macromolecule.extintionCoefficient, +// decimalPrecision : 6 +// } ] +// } ] +// }, { +// xtype : 'textareafield', +// name : 'comments', +// fieldLabel : 'Comments', +// value : macromolecule.comments, +// width : this.width - 10 +// }, +// +// { +// html : BUI.getWarningHTML("The macromolecule is unsaved. Save the macromolecule to get access to other tabs"), +// margin : "150 10 10 10", +// id : this.id + "unsavedWarning", +// hidden : !(!macromolecule.macromoleculeId) +// } +// +// ] +// }); +// return this.panel; +//}; +// +//MacromoleculeForm.prototype.save = function() { +// var _this = this; +// +// var adapter = new BiosaxsDataAdapter(); +// adapter.onSuccess.attach(function(sender, proposal) { +// BIOSAXS.proposal.setItems(proposal); +// _this.panel.setLoading(false); +// +// Ext.getCmp(_this.id + "assembly").enable() +// Ext.getCmp(_this.id + "advanced").enable(); +// Ext.getCmp(_this.id + "unsavedWarning").hide(); +// }); +// +// if (this.getMacromolecule().name == "") { +// BUI.showError("Name field is mandatory"); +// return; +// } +// if (this.getMacromolecule().acronym == "") { +// BUI.showError("Acroynm field is mandatory"); +// return; +// } +// +// /** Check if acronym is unique * */ +// if (this.getMacromolecule().macromoleculeId == null) { +// if (BIOSAXS.proposal.getMacromoleculeByAcronym(this.getMacromolecule().acronym) == null) { +// this.panel.setLoading("ISPyB: Saving Macromolecule") +// adapter.saveMacromolecule(this.getMacromolecule()); +// } else { +// alert("There is already an existing macromolecule with the same acronym"); +// +// } +// } else { +// this.panel.setLoading("ISPyB: Saving Macromolecule") +// adapter.saveMacromolecule(this.getMacromolecule()); +// } +// +//}; +// +//MacromoleculeForm.prototype.getPanel = function(macromolecule) { +// var _this = this; +// this.macromolecule = macromolecule; +// return Ext.createWidget('tabpanel', { +// height : this.height, +// margin : 5, +// plain : true, +// style : { +// padding : 5 +// }, +// items : [ { +// tabConfig : { +// title : "General", +// disabled : false +// }, +// items : [ this.getForm(macromolecule) ], +// bbar : [ "->", { +// text : 'Save', +// cls : 'btn-with-border', +// style : { +// +// border : 1 +// }, +// handler : function() { +// _this.save(); +// } +// }, { +// text : 'Close', +// cls : 'btn-with-border', +// handler : function() { +// _this.onClose.notify(); +// } +// } ] +// }, { +// tabConfig : { +// id : this.id + "assembly", +// title : "Assembly", +// tooltip : 'Description of subunits present in the macromolecule', +// // hidden : (!macromolecule.macromoleculeId), +// disabled : (!macromolecule.macromoleculeId) +// }, +// items : [ this.getMolarityGrid(macromolecule) ] +// }, { +// tabConfig : { +// id : this.id + "advanced", +// title : "Advanced Modeling", +// // hidden : (!macromolecule.macromoleculeId), +// tooltip : 'Definition of the description contacts and symetries', +// disabled : (!macromolecule.macromoleculeId) +// }, +// items : [ this.getRigidBodyForm(macromolecule) ] +// } ] +// }); +//}; +// +//MacromoleculeForm.prototype.getRigidBodyForm = function(macromolecule) { +// var _this = this; +// +// // [P1, P2, P3, P4 ,P5 ,P6 ,32, P42, P52, P62] + P222 +// var symmetry = Ext.create('Ext.data.Store', { +// fields : [ 's' ], +// data : [ { +// "s" : "P1" +// }, { +// "s" : "P2" +// }, { +// "s" : "P3" +// }, { +// "s" : "P4" +// }, { +// "s" : "P5" +// }, { +// "s" : "P6" +// }, { +// "s" : "P32" +// }, { +// "s" : "P42" +// }, { +// "s" : "P52" +// }, { +// "s" : "P62" +// }, { +// "s" : "P222" +// } ] +// }); +// +// if (macromolecule.symmetry == null) { +// macromolecule.symmetry = "P1"; +// } +// var comboBox = Ext.create('Ext.form.ComboBox', { +// fieldLabel : 'Symmetry', +// store : symmetry, +// id : 'comboSym', +// queryMode : 'local', +// displayField : 's', +// valueField : 's', +// value : macromolecule.symmetry, +// margin : "10 0 0 0", +// listeners : { +// change : function(combo, newValue, oldValue, eOpts) { +// macromolecule.symmetry = newValue; +// } +// } +// }); +// +// this.rigidBodyPanel = Ext.createWidget('form', { +// frame : false, +// border : 0, +// padding : 10, +// width : 550, +// height : 400, +// items : [ { +// xtype : 'container', +// layout : 'hbox', +// items : [ { +// xtype : 'container', +// border : false, +// layout : 'hbox', +// items : [ { +// xtype : 'label', +// forId : 'myFieldId', +// text : 'Contact Desc:', +// width : 105, +// margin : '0 0 0 0' +// }, { +// xtype : 'textfield', +// hideLabel : true, +// id : "contactsDescriptionFilePath", +// margin : '0 0 0 0', +// width : 300, +// value : macromolecule.contactsDescriptionFilePath +// }, { +// text : 'Upload', +// xtype : 'button', +// margin : "0 0 0 20", +// width : 100, +// handler : function() { +// _this._openUploadDialog(macromolecule.macromoleculeId, "CONTACTS", "Upload Contact Description File"); +// } +// } ] +// } ] +// }, +// +// comboBox, { +// xtype : 'checkbox', +// margin : '10 0 0 5', +// boxLabel : "I want rigid body modeling run on this stuff", +// checked : true, +// width : 300 +// }, _this.getPDBGrid(macromolecule) ] +// }); +// return this.rigidBodyPanel; +//}; +// +//MacromoleculeForm.prototype.update = function() { +// var _this = this; +// BIOSAXS.proposal.onInitialized.attach(function() { +// if (BIOSAXS.proposal != null) { +// var macromolecules = BIOSAXS.proposal.macromolecules; +// for (var i = 0; i < macromolecules.length; i++) { +// if (macromolecules[i].macromoleculeId == _this.macromolecule.macromoleculeId) { +// _this.macromolecule = macromolecules[i]; +// _this.setMacromolecule(_this.macromolecule); +// _this.molarityStore.loadData(_this.parseMolarityData(_this.macromolecule)); +// _this.pdbGrid.setLoading(false); +// Ext.getCmp("contactsDescriptionFilePath").setValue(_this.macromolecule.contactsDescriptionFilePath) +// _this.molarityGrid.setLoading(false); +// +// } +// } +// } +// }); +// this.molarityGrid.setLoading("Updating"); +// this.pdbGrid.setLoading("Updating"); +// BIOSAXS.proposal.init(); +//}; +// +///******************************************************************************* +// * MOLARITY GRID +// ******************************************************************************/ +// +//MacromoleculeForm.prototype.parseMolarityData = function(macromolecule) { +// var data = []; +// if (macromolecule.stoichiometry != null) { +// for (var i = 0; i < macromolecule.stoichiometry.length; i++) { +// data.push({ +// ratio : macromolecule.stoichiometry[i].ratio, +// acronym : macromolecule.stoichiometry[i].macromolecule3VO.acronym, +// comments : macromolecule.stoichiometry[i].macromolecule3VO.comments, +// stoichiometryId : macromolecule.stoichiometry[i].stoichiometryId, +// name : macromolecule.stoichiometry[i].macromolecule3VO.name +// }); +// } +// } +// return data; +//}; +// +//MacromoleculeForm.prototype.getMolarityGrid = function(macromolecule) { +// var _this = this; +// +// this.molarityStore = Ext.create('Ext.data.Store', { +// fields : [ 'acronym', 'ratio', 'comments', 'stoichiometryId', 'name' ], +// data : this.parseMolarityData(macromolecule), +// sorters : { +// property : 'ratio', +// direction : 'DESC' +// } +// }); +// +// this.molarityGrid = Ext.create('Ext.grid.Panel', { +// store : this.molarityStore, +// height : 350, +// padding : 5, +// columns : [ +// +// { +// text : 'Subunit', +// columns : [ { +// text : "Acronym", +// width : 100, +// hidden : false, +// dataIndex : 'acronym', +// sortable : true +// }, { +// text : "Name", +// width : 100, +// hidden : false, +// dataIndex : 'name', +// sortable : true +// }, { +// text : "Comments", +// width : 100, +// dataIndex : 'comments', +// sortable : true +// } ] +// }, { +// text : "Number
in assymmetric units", +// width : 150, +// dataIndex : 'ratio', +// tooltip : 'Number of times this subunit is present in the macromolecule', +// sortable : true +// }, { +// id : this.id + 'MOLARITY_REMOVE', +// flex : 0.1, +// sortable : false, +// renderer : function(value, metaData, record, rowIndex, colIndex, store) { +// return BUI.getRedButton('REMOVE'); +// } +// } ], +// listeners : { +// cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { +// if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'MOLARITY_REMOVE') { +// var dataAdapter = new BiosaxsDataAdapter(); +// dataAdapter.onSuccess.attach(function() { +// _this.molarityGrid.setLoading(false); +// _this.update(); +// }); +// dataAdapter.removeStoichiometry(record.data.stoichiometryId); +// _this.molarityGrid.setLoading("Removing Structure"); +// } +// } +// }, +// buttons : [ { +// text : 'Add molarity', +// handler : function() { +// +// function onClose() { +// w.destroy(); +// _this.update(); +// } +// var w = Ext.create('Ext.window.Window', { +// title : 'Molarity', +// height : 300, +// width : 500, +// modal : true, +// buttons : [ { +// text : 'Save', +// handler : function() { +// var macromoleculeId = (_this.macromoleculeCombo.getValue()); +// var ratio = Ext.getCmp(_this.id + "ratio").getValue(); +// var comments = ""; +// var dataAdapter = new BiosaxsDataAdapter(); +// dataAdapter.onSuccess.attach(function(sender, args) { +// _this.update(); +// w.destroy(); +// }); +// dataAdapter.saveStoichiometry(_this.macromolecule.macromoleculeId, macromoleculeId, ratio, comments); +// } +// }, { +// text : 'Cancel', +// handler : function() { +// onClose(); +// } +// } ], +// items : [ _this.getMolarityForm(macromolecule) ], +// listeners : { +// onEsc : function() { +// onClose(); +// }, +// close : function() { +// onClose(); +// } +// } +// }).show(); +// } +// } ] +// }); +// return this.molarityGrid; +//}; +// +///******************************************************************************* +// * PDB GRID +// ******************************************************************************/ +// +//MacromoleculeForm.prototype._openUploadDialog = function(macromoleculeId, type, title) { +// var _this = this; +// function onClose() { +// w.destroy(); +// _this.update(); +// } +// +// var w = Ext.create('Ext.window.Window', { +// title : title, +// height : 200, +// width : 400, +// modal : true, +// buttons : [ { +// text : 'Close', +// handler : function() { +// onClose(); +// } +// } ], +// layout : 'fit', +// items : { +// html : "" +// }, +// listeners : { +// onEsc : function() { +// onClose(); +// }, +// close : function() { +// onClose(); +// } +// } +// }).show(); +//}; +// +//MacromoleculeForm.prototype._getPlugins = function() { +// var _this = this; +// var plugins = []; +// // if (this.updateRowEnabled) { +// plugins.push(Ext.create('Ext.grid.plugin.RowEditing', { +// clicksToEdit : 1, +// listeners : { +// validateedit : function(grid, e) { +// /** Comments are always updatable* */ +// e.record.raw.symmetry = e.newValues.symmetry; +// e.record.raw.multiplicity = e.newValues.multiplicity; +// +// var adapter = new BiosaxsDataAdapter(); +// adapter.onSuccess.attach(function(sender, measurement) { +// // _this.grid.setLoading(false); +// }); +// adapter.onError.attach(function() { +// alert("Error"); +// // _this.grid.setLoading(false); +// }); +// +// // _this.grid.setLoading(); +// adapter.saveStructure(e.record.raw); +// } +// } +// })); +// // } +// return plugins; +//}; +// +//MacromoleculeForm.prototype.getPDBGrid = function(macromolecule) { +// var _this = this; +// +// var data = macromolecule.structure3VOs; +// +// // /** Getting PDB from subunits **/ +// // if (macromolecule != null){ +// // if (macromolecule.stoichiometry != null){ +// // for (var i =0; i < macromolecule.stoichiometry.length; i++){ +// // var stoichiometry = macromolecule.stoichiometry[i]; +// // if (stoichiometry.macromolecule3VO != null){ +// // if (stoichiometry.macromolecule3VO.structure3VOs != null){ +// // for (var j = 0; j < stoichiometry.macromolecule3VO.structure3VOs.length; +// // j++) { +// // var structure = stoichiometry.macromolecule3VO.structure3VOs[j]; +// // structure["isSubunit"] = stoichiometry.macromolecule3VO.acronym; +// // data.push(structure) +// // } +// // } +// // } +// // } +// // } +// // } +// +// this.pdbStore = Ext.create('Ext.data.Store', { +// fields : [ 'filePath', 'structureId', 'structureType', 'symmetry', 'structureId', 'name', 'multiplicity' ], +// data : macromolecule.structure3VOs, +// groupField : 'structureType', +// sorters : { +// property : 'structureId', +// direction : 'DESC' +// } +// }); +// +// var groupingFeature = Ext.create('Ext.grid.feature.Grouping', { +// groupHeaderTpl : Ext.create('Ext.XTemplate', +// "
{name:this.formatName}
", { +// formatName : function(name) { +// return name; +// } +// }), +// hideGroupedHeader : true, +// startCollapsed : false +// }); +// +// this.pdbGrid = Ext.create('Ext.grid.Panel', { +// margin : "15 0 0 5", +// height : 250, +// store : this.pdbStore, +// plugins : _this._getPlugins(), +// buttons : [ { +// // text : 'Add PDB file', +// text : 'Add Modeling Option', +// handler : function() { +// _this._openUploadDialog(macromolecule.macromoleculeId, "PDB", 'Upload PDB File'); +// } +// } +// +// ], +// columns : [ +// { +// text : "structureId", +// flex : 0.2, +// hidden : true, +// dataIndex : 'structureId', +// sortable : true +// }, +// { +// text : "File", +// flex : 0.5, +// dataIndex : 'filePath', +// sortable : true, +// hidden : true +// }, +// { +// text : "PDB", +// flex : 0.4, +// dataIndex : 'name', +// sortable : true +// }, +// { +// text : "Symmetry", +// flex : 0.4, +// dataIndex : 'symmetry', +// sortable : true, +// editor : { +// xtype : 'combobox', +// typeAhead : true, +// triggerAction : 'all', +// selectOnTab : true, +// store : [ [ "P1", "P1" ], [ "P2", "P2" ], [ "P3", "P3" ], [ "P4", "P4" ], [ "P5", "P5" ], [ "P6", "P6" ], [ "P32", "P32" ], [ "P42", "P42" ], +// [ "P52", "P52" ], [ "P62", "P62" ], [ "P222", "P222" ] ], +// } +// }, { +// text : "Multiplicity", +// flex : 0.4, +// dataIndex : 'multiplicity', +// sortable : true, +// editor : { +// xtype : 'textfield' +// } +// +// }, { +// text : "Subunit", +// flex : 0.2, +// dataIndex : 'isSubunit', +// sortable : true, +// hidden : true +// }, { +// text : "Type", +// flex : 0.2, +// dataIndex : 'structureType', +// sortable : true, +// hidden : true +// }, +// +// { +// id : this.id + 'REMOVE', +// flex : 0.2, +// hidden : true, +// sortable : false, +// renderer : function(value, metaData, record, rowIndex, colIndex, store) { +// return BUI.getRedButton('REMOVE'); +// } +// }, ], +// +// listeners : { +// itemdblclick : function(dataview, record, item, e) { +// _this._editExperiment(record.raw.experimentId); +// }, +// cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { +// +// if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'REMOVE') { +// var dataAdapter = new BiosaxsDataAdapter(); +// dataAdapter.onSuccess.attach(function() { +// _this.pdbGrid.setLoading(false); +// _this.update(); +// }); +// dataAdapter.removeStructure(record.data.structureId); +// _this.pdbGrid.setLoading("Removing PDB file"); +// } +// +// } +// }, +// viewConfig : { +// getRowClass : function(record, rowIdx, params, store) { +// if (record.raw.isSubunit != null) { +// return "blue-row"; +// } +// } +// } +// }); +// +// return this.pdbGrid; +//}; +// +//MacromoleculeForm.prototype.getMolarityForm = function(macromolecule) { +// var _this = this; +// var data = []; +// for (var i = 0; i < BIOSAXS.proposal.macromolecules.length; i++) { +// var m = BIOSAXS.proposal.macromolecules[i]; +// if (m.macromoleculeId != macromolecule.macromoleculeId) { +// data.push(m); +// } +// +// } +// this.macromoleculeCombo = BIOSAXS_COMBOMANAGER.getComboMacromoleculeByMacromolecules(data, { +// width : 250, +// labelWidth : 100, +// margin : 10 +// }); +// +// return Ext.createWidget('form', { +// +// frame : false, +// border : 0, +// // padding : 15, +// width : 550, +// height : 350, +// items : [ { +// xtype : 'container', +// flex : 1, +// border : false, +// layout : 'anchor', +// defaultType : 'requiredtext', +// items : [ this.macromoleculeCombo, { +// xtype : 'numberfield', +// name : 'Ratio', +// id : _this.id + "ratio", +// fieldLabel : 'Number in assymmetric units', +// value : 1, +// decimalPrecision : 6, +// margin : 10 +// }, { +// xtype : 'textareafield', +// name : 'comments', +// fieldLabel : 'Comments', +// margin : 10, +// width : 400, +// value : "" +// +// } ] +// } ] +// }); +// +//}; +// +///******************************************************************************* +// * JAVASCRIPT DOC +// ******************************************************************************/ +//MacromoleculeForm.prototype.input = function() { +// return { +// macromolecule : DATADOC.getMacromolecule_10() +// }; +//}; +// +//MacromoleculeForm.prototype.test = function(targetId) { +// var macromoleculeForm = new MacromoleculeForm(); +// var panel = macromoleculeForm.getPanel(macromoleculeForm.input().macromolecule); +// panel.render(targetId); +//}; -GraphCanvas.prototype.setVertexStroke = function(vertexId, value) { - this.getFormatter().getVertexById(vertexId).getDefault().setStroke(value); -}; +function ResultSummaryForm() { + this.radiationDamageThreshold = BUI.getRadiationDamageThreshold(); + this.qualityThreshold = BUI.getQualityThreshold(); + + /** Data clusters with bufers **/ + this.clusterByBuffers = false; + + /** Visualization are groupeb by concenttrations. Ex: 4.5mg/ml and 4.7mg/ml will be clusterized together **/ + this.collapseConcentrations = true; + + this.summaryHeight = 350; + this.id = BUI.id(); + + var _this = this; + + this.qualityControlResultsWidget = new QualityControlResultsWidget({ + qualityThreshold : this.radiationDamageThreshold, + radiationDamageThreshold : this.qualityThreshold + + }); + this.qualityControlResultsWidget.onQualityChanged.attach(function(sender, value) { + _this.qualityThreshold = value; + _this.thresholdsChanged(); + }); + + this.qualityControlResultsWidget.onRadiationDatamageChanged.attach(function(sender, value) { + _this.radiationDamageThreshold = value; + _this.thresholdsChanged(); + + }); + this.concentrationHTMLTableWidget = new ConcentrationHTMLTableWidget({ + height : 250, + showBufferColumns : this.clusterByBuffers + }); + + this.plot = new BoxWhiskerGraph({ + targetId : _this.id + '_boxPlot', + height : 350, + width : 450, + maxBoxWidth : 25 + }); + + this.rangePlot = new RangeWhiskerGraph({ + targetId : _this.id + '_rangePlot', + height : 350, + width : 450, + maxBoxWidth : 25 + }); +} + +ResultSummaryForm.prototype.thresholdsChanged = function() { + var parsedData = this.prepareData(this.rawData); + + var filtered = JSON.parse(JSON.stringify(parsedData)); + filtered.concentration.concentrations = []; + for ( var conc in parsedData.concentration.concentrations) { + if (parsedData.concentration.concentrations[conc].calculation.rgGnom.validNumber > 0) { + filtered.concentration.concentrations.push(parsedData.concentration.concentrations[conc]); + } + } + + this.plotWhisker(filtered); + this.plotRange(filtered); + + this.concentrationHTMLTableWidget.refresh(parsedData); +}; + +/** Given a frame object (object returned by analyzeFrames()) and depending of the threshold indicates if a datacollection has radiation damage **/ +ResultSummaryForm.prototype.hasRadiationDamage = function(frameObject) { + var bb = frameObject.bufferBeforeFramesMerged / frameObject.framesCount; + var ba = frameObject.bufferAfterFramesMerged / frameObject.framesCount; + var mol = frameObject.framesMerge / frameObject.framesCount; + return !((bb >= this.radiationDamageThreshold) && (ba >= this.radiationDamageThreshold) && (mol >= this.radiationDamageThreshold)); +}; + +/** Return (frameObject) an object with the information about the frames for a data collection**/ +ResultSummaryForm.prototype.analyzeFrames = function(dataCollectionRow) { + return { + bufferAfterFramesMerged : dataCollectionRow.bufferAfterFramesMerged, + bufferBeforeFramesMerged : dataCollectionRow.bufferBeforeFramesMerged, + framesCount : dataCollectionRow.framesCount, + framesMerge : dataCollectionRow.framesMerge + }; +}; + +ResultSummaryForm.prototype.detectDataCollectionWarnings = function(dataCollectionRow) { + var frameObject = this.analyzeFrames(dataCollectionRow); + var warnings = { + count : 0, + type : [] + }; + + if (this.hasRadiationDamage(frameObject)) { + warnings.count = warnings.count + 1; + warnings.type.push("RADIATION DAMAGE"); + } + + if (Number(dataCollectionRow.quality) < this.qualityThreshold) { + warnings.count = 1;//warnings.count + 1; + warnings.type.push("Quality <" + this.qualityThreshold); + } + return warnings; +}; + +/** Return array composed by {concentration} objects **/ +ResultSummaryForm.prototype.getConcentrations = function(data) { + var concentrationsId = {}; + + for ( var i = 0; i < data.length; i++) { + var warning = this.detectDataCollectionWarnings(data[i]); + var id = data[i].conc;// + "_" + data[i].bufferId; + if (this.clusterByBuffers) { + id = data[i].conc + "_" + data[i].bufferId; + } + + if (concentrationsId[id] == null) { + concentrationsId[id] = { + id : id, + concentration : Number(data[i].conc).toFixed(2), + bufferId : data[i].bufferId, + bufferAcronym : data[i].bufferAcronym, + rgGuinier : [], + i0Guinier : [], + rgGnom : [], + dMax : [], + quality : [], + frames : [], + frames_warning : warning.count + }; + } else { + concentrationsId[id].frames_warning = concentrationsId[id].frames_warning + warning.count; + } + + concentrationsId[id].frames.push(data[i]); + + if (warning.count == 0) { + concentrationsId[id].rgGuinier.push(data[i].rgGuinier); + concentrationsId[id].i0Guinier.push(data[i].I0); + concentrationsId[id].quality.push(data[i].quality); + concentrationsId[id].rgGnom.push(data[i].rgGnom); + concentrationsId[id].dMax.push(data[i].dmax); + } + + } + var concentrations = []; + for ( var item in concentrationsId) { + if (concentrationsId.hasOwnProperty(item)) { + concentrations.push({ + concentration : concentrationsId[item].concentration, + id : item, + bufferId : Number(concentrationsId[item].bufferId).toFixed(2), + bufferAcronym : concentrationsId[item].bufferAcronym, + rgGuinier : concentrationsId[item].rgGuinier, + /** Frames **/ + frames : concentrationsId[item].frames, + frames_warning : concentrationsId[item].frames_warning, + /** Calculation **/ + calculation : { + rgGuinier : BUI.getStandardDeviation(concentrationsId[item].rgGuinier), + i0Guinier : BUI.getStandardDeviation(concentrationsId[item].i0Guinier), + quality : BUI.getStandardDeviation(concentrationsId[item].quality), + rgGnom : BUI.getStandardDeviation(concentrationsId[item].rgGnom), + dMax : BUI.getStandardDeviation(concentrationsId[item].dMax) + + } + }); + } + } + + return { + concentrations : concentrations + }; +}; + +ResultSummaryForm.prototype.prepareData = function(data) { + /** Return array composed by {acronym, bufferId} objects **/ + function getBuffers(data) { + var buffersId = {}; + for ( var i = 0; i < data.length; i++) { + buffersId[data[i].bufferId] = data[i].acronym; + } + var buffers = []; + for ( var id in buffersId) { + if (buffersId.hasOwnProperty(id)) { + buffers.push({ + acronym : buffersId[id], + bufferId : id + }); + } + } + return buffers; + } + + /** Get a string with all the concentrations **/ + function getConcentrationString(parseConcentrations) { + var concentrations = []; + for ( var i = 0; i < parseConcentrations.concentrations.length; i++) { + concentrations.push(parseConcentrations.concentrations[i].concentration + " mg/ml "); + } + return concentrations.toString(); + } + + var parseConcentrations = this.getConcentrations(data); + + return { + dataCollectionCount : data.length, + buffers : getBuffers(data), + concentration : parseConcentrations, + concentrationLabel : getConcentrationString(parseConcentrations) + }; +}; + +ResultSummaryForm.prototype.getDataForWhisker = function(data) { + var clusters = []; + + var concentrations = {}; + var i = 0; + var conc = 0; + if (this.collapseConcentrations) { + for (i = 0; i < data.concentration.concentrations.length; i++) { + conc = data.concentration.concentrations[i]; + var concentration = Number(conc.concentration).toFixed(0); + if (concentrations[concentration] == null) { + concentrations[concentration] = {}; + concentrations[concentration].concentration = concentration; + concentrations[concentration].calculation = {}; + concentrations[concentration].calculation.rgGuinier = {}; + concentrations[concentration].calculation.rgGuinier.values = []; + concentrations[concentration].calculation.rgGuinier.values = conc.calculation.rgGuinier.values; + concentrations[concentration].calculation.rgGnom = {}; + concentrations[concentration].calculation.rgGnom.values = []; + concentrations[concentration].calculation.rgGnom.values = conc.calculation.rgGnom.values; + } else { + concentrations[concentration].calculation.rgGuinier.values = concentrations[concentration].calculation.rgGuinier.values + .concat(conc.calculation.rgGuinier.values); + concentrations[concentration].calculation.rgGnom.values = concentrations[concentration].calculation.rgGnom.values + .concat(conc.calculation.rgGnom.values); + } + } + + /** From object to array **/ + var array = []; + for ( var key in concentrations) { + if (concentrations.hasOwnProperty(key)) { + array.push(concentrations[key]); + } + } + data.concentration.concentrations = array; + } + + for (i = 0; i < data.concentration.concentrations.length; i++) { + conc = data.concentration.concentrations[i]; + clusters.push({ + name : conc.concentration + "mg/ml", + concentration : Number(conc.concentration), + x : Number(conc.concentration), + classes : [] + }); + clusters[clusters.length - 1].classes.push({ + name : "Guinier", + color : '#9A2EFE', + values : conc.calculation.rgGuinier.values + + }); + clusters[clusters.length - 1].classes.push({ + name : "P(r)", + color : '#2E64FE', + values : conc.calculation.rgGnom.values + + }); + } + return { + clusters : clusters.sort(function(a, b) { + return a.concentration - b.concentration; + }) + }; +}; + +ResultSummaryForm.prototype.getDataForWhiskerQuality = function(data) { + var clusters = []; + + for ( var i = 0; i < data.concentration.concentrations.length; i++) { + var conc = data.concentration.concentrations[i]; + clusters.push({ + name : conc.concentration + "mg/ml", + classes : [] + }); + clusters[clusters.length - 1].classes.push({ + name : "Quality", + values : conc.calculation.quality.values + + }); + } + + return { + clusters : clusters + }; +}; + +ResultSummaryForm.prototype.plotQualityWhisker = function(parsedData) { + this.qualityPlot.refresh(this.getDataForWhiskerQuality(parsedData)); +}; + +ResultSummaryForm.prototype.plotWhisker = function(parsedData) { + this.plot.refresh(this.getDataForWhisker(parsedData)); +}; + +ResultSummaryForm.prototype.plotRange = function(parsedData) { + this.rangePlot.refresh(this.getDataForWhisker(parsedData)); +}; + +ResultSummaryForm.prototype.getPanel = function(data) { + var _this = this; + _this.rawData = data; + var parsedData = this.prepareData(data); + + this.panel = Ext + .createWidget( + 'form', + { + bodyPadding : 20, + frame : false, + border : 0, + width : this.width, + height : this.summaryHeight + 1000, + items : [ { + xtype : 'container', + layout : 'hbox', + items : [ { + xtype : 'container', + flex : 1, + border : false, + layout : 'anchor', + defaultType : 'textfield', + items : [ + _this.qualityControlResultsWidget.getPanel(), + { + xtype : 'fieldset', + width : 950, + margin : "20, 0 0 0", + height : this.summaryHeight + 500, + items : [ + { + html : "
Concentration Analysis
", + border : 0, + width : 900 + + }, + { + html : this.concentrationHTMLTableWidget.getPanel(parsedData), + border : 0, + width : 900, + margin : "10, 0 0 10" + + }, + { + xtype : 'container', + layout : 'vbox', + border : 5, + items : [ + { + html : "
Rg based on Guinier and Gnom
", + border : 8, + width : 900, + margin : "20 0 0 10" + + }, { + xtype : 'container', + layout : 'hbox', + items : [ { + xtype : 'container', + layout : 'vbox', + items : [ { + html : "
", + border : 0, + width : this.plot.width, + padding : "10 0 0 20", + listeners : { + afterrender : function() { + _this.plotWhisker(parsedData); + + } + } + }, { + html : "
Concentration (mg/ml)
", + width : 450, + border : 0, + margin : "-50 0 0 0" + + } ] + }, { + xtype : 'container', + layout : 'vbox', + items : [ { + html : "
", + border : 0, + width : this.rangePlot.width, + padding : "10 0 0 10", + listeners : { + afterrender : function() { + _this.plotRange(parsedData); + } + } + }, { + html : "
Concentration (mg/ml)
", + width : 450, + border : 0, + margin : "-50 0 0 0" + + } ] + } ] + } ] + } ] + } ] + } + + ] + } ] + }); + return this.panel; + +}; + +ResultSummaryForm.prototype.input = function() { + return { + data : DATADOC.getData_3367() + }; +}; + +ResultSummaryForm.prototype.test = function(targetId) { + var resultSummaryForm = new ResultSummaryForm(); + var panel = resultSummaryForm.getPanel(resultSummaryForm.input().data); + panel.render(targetId); + +}; -GraphCanvas.prototype.getVertexStroke = function(vertexId) { - return this.getFormatter().getVertexById(vertexId).getDefault().getStroke(); -}; +/** + * Example form + * + * @witdh + * @height + */ +function RigibBodyModelingForm(args) { + this.id = BUI.id(); + this.width = 700; + this.height = 500; + + if (args != null) { + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + } + + var _this = this; + this.rigidBodyGrid = new AprioriRigidBodyGrid(); + + this.rigidBodyGrid.onUploadFile.attach(function(sender, type, title){ + _this._openUploadDialog(_this.macromolecule.macromoleculeId, type, title); + }); + + this.rigidBodyGrid.onRemove.attach(function(sender, type, title){ + _this._update(); + }); + + this.onSave = new Event(this); + +} + +RigibBodyModelingForm.prototype._getItems = function() { + var _this = this; + + + return [ { + xtype : 'label', + forId : 'myFieldId', + text : 'Information for model fit, mixture analysis and rigid body modeling', + margin : '15 0 20 10', + cls : "inline-help" + }, + this.rigidBodyGrid.getPanel(), + { + xtype : 'label', + forId : 'myFieldId', + text : 'Distance restraints may be imposed on the model using contacts conditions file (OPTIONAL)', + margin : '25 0 5 10', + cls : "inline-help" + }, + { + xtype : 'container', + layout : 'hbox', + items : [ { + xtype : 'container', + border : false, + layout : 'hbox', + items : [ { + xtype : 'label', + forId : 'myFieldId', + text : 'Contact Description File: (Optional)', + width : 150, + margin : '10 0 0 10' + }, { + id : this.id + "contactsDescriptionFilePath", + xtype : 'textfield', + hideLabel : true, + margin : '10 0 0 0', + width : 200, + disabled: true + }, { + text : 'Upload', + xtype : 'button', + margin : "10 0 0 10", + width : 80, + handler : function() { + + _this._openUploadDialog(_this.macromolecule.macromoleculeId, "CONTACTS", "Upload Contact Description File"); + } + }, { + text : 'Remove', + id : _this.id + "_remove", + xtype : 'button', + margin : "10 0 0 10", + width : 80, + handler : function() { + _this.macromolecule.contactsDescriptionFilePath = null; + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, proposal) { + /** Updating the proposal global object **/ + BIOSAXS.proposal.setItems(proposal); + _this.panel.setLoading(false); + + var saved = BIOSAXS.proposal.getMacromoleculeByAcronym(_this.macromolecule.acronym); + /** Refreshing to check that everything is ok **/ + _this.refresh(saved); + _this.onSave.notify(saved); + }); + + _this.panel.setLoading("Saving Macromolecule") + adapter.saveMacromolecule(_this.macromolecule); + } + } ] + } ] + }, { + xtype : 'panel', + html : "Go to SASREF manual for further information", + margin : "10 0 0 160", + border : 0 + + }, + { + xtype : 'checkbox', + margin : '10 0 0 5', + boxLabel : "I want rigid body modeling run on this stuff", + checked : true, + width : 300 + } ] + +}; + +/** Because update is a jsp page we don't know if the user has uploaded a file or not then we need to refresh **/ +RigibBodyModelingForm.prototype._update = function(macromoleculeId, type, title) { + var _this = this; + BIOSAXS.proposal.onInitialized.attach(function() { + if (BIOSAXS.proposal != null) { + _this.refresh(BIOSAXS.proposal.getMacromoleculeById(_this.macromolecule.macromoleculeId)); + _this.panel.setLoading(false); + } + }); + this.panel.setLoading(); + BIOSAXS.proposal.init(); +}; + +RigibBodyModelingForm.prototype._openUploadDialog = function(macromoleculeId, type, title) { + var _this = this; + function onClose() { + w.destroy(); + _this._update(); + + } + + var w = Ext.create('Ext.window.Window', { + title : title, + height : 200, + width : 400, + modal : true, + buttons : [ { + text : 'Close', + handler : function() { + onClose(); + } + } ], + layout : 'fit', + items : { + html : "" + }, + listeners : { + onEsc : function() { + onClose(); + }, + close : function() { + onClose(); + } + } + }).show(); +}; + +RigibBodyModelingForm.prototype._getButtons = function() { + return []; +}; + +RigibBodyModelingForm.prototype.getPanel = function() { + var _this = this; + this.panel = Ext.create('Ext.form.Panel', { + width : this.width, + height : this.height, + margin : 10, + border : 1, + defaultType : 'textfield', + items : this._getItems(), + buttons : this._getButtons(), + listeners : { + afterrender : function(){ + _this._populate(); + + } + } + }); + return this.panel; +}; + +/** Populates could be call when the DOM is not filled yet **/ +RigibBodyModelingForm.prototype._populate = function() { + if (this.macromolecule != null){ + if (Ext.getCmp(this.id + "contactsDescriptionFilePath") != null){ + if (this.macromolecule.contactsDescriptionFilePath != null){ + Ext.getCmp(this.id + "contactsDescriptionFilePath").setValue(this.macromolecule.contactsDescriptionFilePath); + Ext.getCmp(this.id + "_remove").enable(); + } + else{ + Ext.getCmp(this.id + "_remove").disable(); + Ext.getCmp(this.id + "contactsDescriptionFilePath").setValue(""); + + } + } + } +}; + +/** It populates the form * */ +RigibBodyModelingForm.prototype.refresh = function(macromolecule) { + this.macromolecule = macromolecule; + this.rigidBodyGrid.refresh(macromolecule); + this._populate(); +}; + +RigibBodyModelingForm.prototype.input = function() { + return {}; +}; + + +/** It populates the form **/ +RigibBodyModelingForm.prototype.test = function(targetId) { + var macromoleculeForm = new RigibBodyModelingForm(); + var panel = macromoleculeForm.getPanel(); + panel.render(targetId); +}; + -GraphCanvas.prototype.setVertexStrokeOpacity = function(vertexId, value) { - this.getFormatter().getVertexById(vertexId).getDefault().setStrokeOpacity(value); -}; +/** + * Same form as MX part + * + * @creationMode if true a create button appears instead of save + * @showTitle true or false + */ +function ShipmentForm(args) { + this.id = BUI.id(); + + this.creationMode = false; + this.showTitle = true; + if (args != null) { + if (args.creationMode != null) { + this.creationMode = args.creationMode; + } + if (args.showTitle != null) { + this.showTitle = args.showTitle; + } + } + + this.onSaved = new Event(this); +} + +ShipmentForm.prototype.fillStores = function() { + this.panel.setLoading("Loading Labcontacts from database"); + this.labContactForSendingStore.loadData(BIOSAXS.proposal.getLabcontacts(), false); + this.labContactForReturnStore.loadData(BIOSAXS.proposal.getLabcontacts(), false); + this.panel.setLoading(false); + if (this.shipment != null) { + this.setShipment(this.shipment); + } +}; + +ShipmentForm.prototype.draw = function(targetId) { + this.getPanel().render(targetId); +}; + +ShipmentForm.prototype.setShipment = function(shipment) { + this.shipment = shipment; + var _this = this; + Ext.getCmp(_this.id + "shippingName").setValue(shipment.json.shippingName); + Ext.getCmp(_this.id + "shippingStatus").setValue(shipment.json.shippingStatus); + Ext.getCmp(_this.id + "comments").setValue(shipment.json.comments); + if (shipment.json.sendingLabContactVO != null) { + this.labContactsSendingCombo.setValue(shipment.json.sendingLabContactVO.labContactId); + } + if (shipment.json.returnLabContactVO != null) { + this.labContactsReturnCombo.setValue(shipment.json.returnLabContactVO.labContactId); + } + +}; + +ShipmentForm.prototype._saveShipment = function() { + var _this = this; + var shippingId = null; + if (this.shipment != null) { + shippingId = this.shipment.json.shippingId; + } + var json = { + shippingId : shippingId, + name : Ext.getCmp(_this.id + "shippingName").getValue(), + status : Ext.getCmp(_this.id + "shippingStatus").getValue(), + sendingLabContactId : Ext.getCmp(_this.id + "shipmentform_sendingLabContactId").getValue(), + returnLabContactId : Ext.getCmp(_this.id + "returnLabContactId").getValue(), + returnCourier : Ext.getCmp(_this.id + "returnCourier").getValue(), + courierAccount : Ext.getCmp(_this.id + "courierAccount").getValue(), + BillingReference : Ext.getCmp(_this.id + "BillingReference").getValue(), + dewarAvgCustomsValue : Ext.getCmp(_this.id + "dewarAvgCustomsValue").getValue(), + dewarAvgTransportValue : Ext.getCmp(_this.id + "dewarAvgTransportValue").getValue(), + comments : Ext.getCmp(_this.id + "comments").getValue() + }; + + var dataAdapter = new BiosaxsDataAdapter(); + dataAdapter.onSuccess.attach(function(sender, shipment) { + window.location = BUI.getShippingURL(shipment.shippingId); + }); + + dataAdapter.onError.attach(function(sender, error) { + _this.onError.notify(error); + }); + + /** Cheking params **/ + if (json.name == "") { + BUI.showError("Name field is mandatory"); + return; + } + + if (json.sendingLabContactId == null) { + BUI.showError("Lab contact for sending field is mandatory"); + return; + } + + if (json.returnLabContactId == null) { + BUI.showError("Lab contact for return field is mandatory"); + return; + } + + dataAdapter.createShipment(json.shippingId, json.name, json.status, json.comments, json.sendingLabContactId, json.returnLabContactId, + json.returnCourier, json.courierAccount, json.BillingReference, json.dewarAvgCustomsValue, json.dewarAvgTransportValue); + +}; + +ShipmentForm.prototype.getPanel = function(shipment) { + var _this = this; + this.shipment = shipment; + var required = '*'; + var buttons = []; + + if (_this.creationMode) { + buttons.push({ + text : 'Create', + scope : this, + handler : function() { + _this._saveShipment(); + } + }); + } else { + buttons.push({ + text : 'Save', + scope : this, + handler : function() { + _this._saveShipment(); + } + }); + + } + + this.labContactForSendingStore = Ext.create('Ext.data.Store', { + fields : [ 'cardName', 'labContactId' ] + }); + + this.labContactForReturnStore = Ext.create('Ext.data.Store', { + fields : [ 'cardName', 'labContactId' ] + }); + + // Create the combo box, attached to the states data store + this.labContactsSendingCombo = Ext.create('Ext.form.ComboBox', { + id : _this.id + "shipmentform_sendingLabContactId", + fieldLabel : 'Lab contact for sending', + afterLabelTextTpl : required, + store : this.labContactForSendingStore, + queryMode : 'local', + labelWidth : 200, + displayField : 'cardName', + valueField : 'labContactId' + }); + + this.labContactsReturnCombo = Ext.create('Ext.form.ComboBox', { + id : _this.id + "returnLabContactId", + fieldLabel : 'If No, Lab-Contact for Return', + afterLabelTextTpl : required, + store : this.labContactForReturnStore, + queryMode : 'local', + labelWidth : 200, + displayField : 'cardName', + valueField : 'labContactId', + listeners : { + change : function(x, newValue) { + for ( var i = 0; i < x.getStore().data.items.length; i++) { + if (x.getStore().data.items[i].raw.labContactId == newValue) { + Ext.getCmp(_this.id + "returnCourier").setValue(x.getStore().data.items[i].raw.defaultCourrierCompany); + Ext.getCmp(_this.id + "courierAccount").setValue(x.getStore().data.items[i].raw.courierAccount); + Ext.getCmp(_this.id + "BillingReference").setValue(x.getStore().data.items[i].raw.billingReference); + Ext.getCmp(_this.id + "dewarAvgCustomsValue").setValue(x.getStore().data.items[i].raw.dewarAvgCustomsValue); + Ext.getCmp(_this.id + "dewarAvgTransportValue").setValue(x.getStore().data.items[i].raw.dewarAvgTransportValue); + } + } + } + } + }); + + if (this.panel == null) { + this.panel = Ext.create('Ext.form.Panel', { + bodyPadding : 5, + width : 600, + border : 1, + items : [ { + xtype : 'fieldset', + title : 'Details', + collapsible : false, + defaultType : 'textfield', + layout : 'anchor', + defaults : { + anchor : '100%' + }, + items : [ { + xtype : 'requiredtext', + fieldLabel : 'Shipment Label', + allowBlank : false, + name : 'shippingName', + id : _this.id + 'shippingName', + value : '', + anchor : '50%' + }, { + + xtype : 'textareafield', + name : 'comments', + id : _this.id + 'comments', + fieldLabel : 'Comments', + value : '' + }, { + fieldLabel : 'Status', + readOnly : true, + id : _this.id + 'shippingStatus', + value : 'Opened', + anchor : '50%' + } ] + }, { + xtype : 'fieldset', + title : 'Lab-Contacts', + collapsible : false, + defaultType : 'textfield', + layout : 'anchor', + defaults : { + anchor : '100%' + }, + items : [ this.labContactsSendingCombo, this.labContactsReturnCombo ] + }, { + border : 0, + html : BUI.getWarningHTML("These informations are relevant for all shipments") + }, { + xtype : 'fieldset', + title : 'Courier accounts details for return', + collapsible : false, + layout : 'anchor', + defaults : { + anchor : '100%' + }, + items : [ { + xtype : 'textfield', + labelWidth : 400, + fieldLabel : 'Courier company for return (if ESRF sends a dewar back)', + id : _this.id + 'returnCourier', + value : '' + }, { + xtype : 'textfield', + labelWidth : 400, + fieldLabel : 'Courier account', + id : _this.id + 'courierAccount', + value : '' + }, { + xtype : 'textfield', + labelWidth : 400, + fieldLabel : 'Billing reference', + id : _this.id + 'BillingReference', + value : '' + }, { + xtype : 'numberfield', + labelWidth : 400, + fieldLabel : 'Average Customs value of a dewar (Euro)', + id : _this.id + 'dewarAvgCustomsValue', + value : '' + }, { + xtype : 'numberfield', + labelWidth : 400, + fieldLabel : 'Average Transport value of a dewar (Euro)', + id : _this.id + 'dewarAvgTransportValue', + value : '' + } ] + } ], + buttons : buttons + }); + } + this.fillStores(); + if (this.showTitle) { + this.panel.setTitle('Create a new Shipment'); + } + return this.panel; +}; + +ShipmentForm.prototype.input = function() { + return { + proposal : DATADOC.getProposal_10() + + }; +}; + +ShipmentForm.prototype.test = function(targetId) { + var shipmentForm = new ShipmentForm({ + creationMode : true + + }); + BIOSAXS.proposal = new Proposal(shipmentForm.input().proposal); + shipmentForm.getPanel().render(targetId); +}; -GraphCanvas.prototype.getVertexStrokeOpacity = function(vertexId) { - return this.getFormatter().getVertexById(vertexId).getDefault().getStrokeOpacity(); -}; +/** + * #onSaved + */ +function StockSolutionForm(args) { + this.id = BUI.id(); + this.actions = []; + + if (args != null) { + if (args.actions != null) { + this.actions = args.actions; + } + } + this.onSaved = new Event(this); +} + +StockSolutionForm.prototype.getStockSolution = function() { + if (this.stockSolution != null) { + this.stockSolution.concentration = Ext.getCmp(this.id + "stockSolution_concentration").getValue(); + this.stockSolution.storageTemperature = Ext.getCmp(this.id + "stockSolution_storageTemperature").getValue(); + this.stockSolution.volume = Ext.getCmp(this.id + "stockSolution_volume").getValue(); + this.stockSolution.comments = Ext.getCmp(this.id + "stockSolution_comments").getValue(); + this.stockSolution.name = Ext.getCmp(this.id + "stockSolution_name").getValue(); + this.stockSolution.bufferId = this.bufferCombo.getValue(); + + if (this.macromoleculeCombo.getValue() != null) { + this.stockSolution.macromoleculeId = this.macromoleculeCombo.getValue(); + } else { + this.stockSolution.macromolecule3VO = null; + } + + } else { + return { + concentration : Ext.getCmp(this.id + "stockSolution_concentration").getValue(), + storageTemperature : Ext.getCmp(this.id + "stockSolution_storageTemperature").getValue(), + volume : Ext.getCmp(this.id + "stockSolution_volume").getValue(), + comments : Ext.getCmp(this.id + "stockSolution_comments").getValue(), + name : Ext.getCmp(this.id + "stockSolution_name").getValue(), + bufferId : this.bufferCombo.getValue(), + macromoleculeId : this.macromoleculeCombo.getValue() + }; + } + return this.stockSolution; +}; + +StockSolutionForm.prototype.setStockSolution = function(stockSolution) { + if (stockSolution != null) { + if (stockSolution.macromoleculeId != null) { + this.macromoleculeCombo.setValue(stockSolution.macromoleculeId); + } + this.bufferCombo.setValue(stockSolution.bufferId); + Ext.getCmp(this.id + "stockSolution_concentration").setValue(this.stockSolution.concentration); + Ext.getCmp(this.id + "stockSolution_storageTemperature").setValue(this.stockSolution.storageTemperature); + Ext.getCmp(this.id + "stockSolution_volume").setValue(this.stockSolution.volume); + Ext.getCmp(this.id + "stockSolution_name").setValue(this.stockSolution.name); + Ext.getCmp(this.id + "stockSolution_comments").setValue(this.stockSolution.comments); + } +}; + +StockSolutionForm.prototype.getBufferCombo = function() { + this.bufferCombo = BIOSAXS_COMBOMANAGER.getComboBuffers(BIOSAXS.proposal.getBuffers(), { + labelWidth : 120, + margin : '0 0 10 0', + width : 220 + + }); + return this.bufferCombo; +}; + +StockSolutionForm.prototype.getMacromoleculeCombo = function() { + this.macromoleculeCombo = BIOSAXS_COMBOMANAGER.getComboMacromoleculeByMacromolecules(BIOSAXS.proposal.getMacromolecules(), { + labelWidth : 120, + margin : '0 0 10 0', + width : 220 + + }); + return this.macromoleculeCombo; +}; + +StockSolutionForm.prototype.refresh = function() { +}; + +StockSolutionForm.prototype._getTopPanel = function() { + return { + xtype : 'container', + layout : 'hbox', + border : 0, + items : [ { + xtype : 'container', + layout : 'hbox', + items : [ { + xtype : 'container', + flex : 1, + border : false, + layout : 'anchor', + defaultType : 'textfield', + items : [ + + this.getMacromoleculeCombo(), { + xtype : 'requiredtext', + id : this.id + 'stockSolution_name', + fieldLabel : 'Acronym', + labelWidth : 120, + width : 250 + }, { + xtype : 'requiredtext', + id : this.id + 'stockSolution_concentration', + fieldLabel : 'Conc. (mg/ml)', + labelWidth : 120, + width : 250 + }, + + { + id : this.id + 'stockSolution_storageTemperature', + fieldLabel : 'Storage Temp.(C)', + labelWidth : 120, + width : 250 + }, { + xtype : 'requiredtext', + id : this.id + 'stockSolution_volume', + fieldLabel : 'Volume in Well (µl)', + labelWidth : 120, + width : 250 + } ] + } ] + }, { + xtype : 'container', + flex : 1, + layout : 'anchor', + defaultType : 'textfield', + margin : '0 0 0 10', + items : [ this.getBufferCombo() ] + } ] + }; + +}; + +StockSolutionForm.prototype.getPanel = function(stockSolution) { + this.stockSolution = stockSolution; + this.panel = Ext.createWidget({ + xtype : 'container', + layout : 'vbox', + border : 0, + style : { + padding : '10px' + }, + fieldDefaults : { + labelAlign : 'left', + labelWidth : 50 + }, + items : [ this._getTopPanel(stockSolution), { + id : this.id + 'stockSolution_comments', + xtype : 'textareafield', + name : 'comments', + fieldLabel : 'Comments', + labelWidth : 120, + width : '100%' + } ] + }); + + this.setStockSolution(stockSolution); + return this.panel; +}; + +StockSolutionForm.prototype.input = function() { + return { + stock : { + "stockSolutionId" : 6, + "proposalId" : 3124, + "macromoleculeId" : 5933, + "bufferId" : 811, + "instructionSet3VO" : null, + "boxId" : 305861, + "storageTemperature" : "20", + "volume" : "300", + "concentration" : "1.2", + "comments" : "Buffer EDTA with A", + "name" : "A_EDTA_1.2", + "samples" : [], + "buffer" : "EDTA", + "macromolecule" : "A" + }, + proposal : new MeasurementGrid().input().proposal + }; +}; + +StockSolutionForm.prototype.test = function(targetId) { + var stockSolutionForm = new StockSolutionForm(); + BIOSAXS.proposal = new Proposal(stockSolutionForm.input().proposal); + var panel = stockSolutionForm.getPanel(new Shipment(stockSolutionForm.input().stock)); + panel.render(targetId); +}; -GraphCanvas.prototype.setVertexOpacity = function(vertexId, value) { - this.getFormatter().getVertexById(vertexId).getDefault().setOpacity(value); -}; + +BoxWhiskerGraph.prototype.cleanArray = GenericGraph.prototype.cleanArray; +BoxWhiskerGraph.prototype.plotAxes = GenericGraph.prototype.plotAxes; +BoxWhiskerGraph.prototype.plotRuler = GenericGraph.prototype.plotRuler; +BoxWhiskerGraph.prototype.drawSVGVerticalText = GenericGraph.prototype.drawSVGVerticalText; +BoxWhiskerGraph.prototype.getClassColor = GenericGraph.prototype.getClassColor; +BoxWhiskerGraph.prototype.getDimensions = GenericGraph.prototype.getDimensions; +BoxWhiskerGraph.prototype.calculate = GenericGraph.prototype.calculate; +BoxWhiskerGraph.prototype.getMedian = GenericGraph.prototype.getMedian; +BoxWhiskerGraph.prototype.pointToPixel = GenericGraph.prototype.pointToPixel; +BoxWhiskerGraph.prototype.maxValueWhisker = GenericGraph.prototype.maxValueWhisker; +BoxWhiskerGraph.prototype.refresh = GenericGraph.prototype.refresh; + +/** + * Subclass of GenericGraph + * + * @maxBoxWidth + */ +function BoxWhiskerGraph(args){ + this.maxBoxWidth = 25; + + if (args == null){ + args = new Object(); + } + args["plotHorizontalByCluster"] = true; + + GenericGraph.call(this, args); + + if (args.maxBoxWidth != null){ + this.maxBoxWidth = args.maxBoxWidth; + } +}; + + + +/** +There are several different methods for calculating quartiles.[1] This calculator uses a method described by Moore and McCabe to find quartile values. +The same method also used by The TI-83 to calculate quartile values. +With this method, the first quartile is the median of the numbers below the median, the third quartile is the median of the numbers above the median. + +http://www.miniwebtool.com/quartile-calculator/ +http://www.alcula.com/calculators/statistics/box-plot/ +**/ +BoxWhiskerGraph.prototype.getQ1 = function(array){ + array = array.slice(0, array.length/2); + return this.getMedian(array); +}; + +BoxWhiskerGraph.prototype.getQ3 = function(array){ + array = array.slice((array.length + 1)/2); + return this.getMedian(array); + +}; + +BoxWhiskerGraph.prototype.getQ2 = function(array){ + return this.getMedian(array); +}; + +BoxWhiskerGraph.prototype.getBelowOutliers = function(belowLimit, array){ + var points = new Array(); + for (var i = 0; i < array.length; i++){ + if (array[i] <= belowLimit){ + points.push(array[i]); + } + } + return points; +}; + +BoxWhiskerGraph.prototype.getAboveOutliers = function(aboveLimit, array){ + var points = new Array(); + for (var i = 0; i < array.length; i++){ + if (array[i] >= aboveLimit){ + points.push(array[i]); + } + } + return points; +}; + + +BoxWhiskerGraph.prototype.minValueWhisker = function(belowLimit, q1, array){ + var points = new Array(); + + for (var i = 0; i < array.length; i++){ + if ((array[i] < q1) && (array[i]) > belowLimit){ + points.push(array[i]); + } + } + + if (points.length > 0){ + points.sort(function(a, b){return a - b;}); + return points[0]; + } + return null; +}; + +BoxWhiskerGraph.prototype.isNumber = function(value){ + if (value=="") return false; + + var d = parseInt(value); + if (!isNaN(d)) return true; else return false; + +}; + +BoxWhiskerGraph.prototype.plotBoxWhisker = function(boxProperties){ + if (this.maxBoxWidth != null){ + if (boxProperties.width > this.maxBoxWidth){ + boxProperties.x = boxProperties.x + (boxProperties.width/2) - (this.maxBoxWidth/2); + boxProperties.width = this.maxBoxWidth; + } + + } + + if (this.plotPoints){ + for(var i = 0; i < boxProperties.values.length; i++){ + var value = boxProperties.values[i]; + var toPixel = this.pointToPixel(value, boxProperties); + SVG.drawCircle(boxProperties.x + (boxProperties.width/2) + 2, toPixel, this.pointRadius, this.svg, [["fill", "green"], ["fill-opacity", this.fillOpacityPoint],['stroke-opacity', this.strokeOpacityPoint], ["stroke", "black"]]); + } + } + + + var boxColor = this.getClassColor(boxProperties.name); + var result = this.calculate(boxProperties.values); + /** Q1 **/ + + if (this.isNumber(result.Q1)){ + SVG.drawLine(boxProperties.x, this.pointToPixel(result.Q1, boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result.Q1, boxProperties), this.svg, [["stroke", boxColor]]); + } + /** Q2 **/ + if (this.isNumber(result.Q2)){ + SVG.drawLine(boxProperties.x, this.pointToPixel(result.Q2, boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result.Q2, boxProperties), this.svg, [["stroke", "blue"], ["stroke-width", "2"]]); + } + + /** Q3 **/ + if (this.isNumber(result.Q3)){ + SVG.drawLine(boxProperties.x, this.pointToPixel(result.Q3, boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result.Q3, boxProperties), this.svg, [["stroke", boxColor]]); + } + + /** Concenting Q1 and Q3 **/ + if (this.isNumber(result.Q1)&&this.isNumber(result.Q3)){ + SVG.drawLine(boxProperties.x, this.pointToPixel(result.Q1, boxProperties), boxProperties.x, this.pointToPixel(result.Q3, boxProperties), this.svg, [["stroke", boxColor]]); + SVG.drawLine(boxProperties.x + boxProperties.width, this.pointToPixel(result.Q1, boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result.Q3, boxProperties), this.svg, [["stroke", boxColor]]); + } + + /** min-whisker **/ + if (result["min-whisker"] != null){ + if (this.isNumber(result.Q1)){ + SVG.drawLine(boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result.Q1, boxProperties), boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result["min-whisker"], boxProperties), this.svg, [["stroke", boxColor]]); + } + SVG.drawLine(boxProperties.x,this.pointToPixel(result["min-whisker"], boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result["min-whisker"], boxProperties) , this.svg, [["stroke", boxColor]]); + + } + + /** max-whisker **/ + if (result["max-whisker"] != null){ + if (this.isNumber(result.Q3)){ + SVG.drawLine(boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result.Q3, boxProperties), boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result["max-whisker"], boxProperties), this.svg, [["stroke", boxColor]]); + } + SVG.drawLine(boxProperties.x , this.pointToPixel(result["max-whisker"], boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result["max-whisker"], boxProperties), this.svg, [["stroke", boxColor]]); + + } + + /** outliners **/ + if (result["above-outliers"] != null){ + for (var point in result["above-outliers"]){ + SVG.drawCircle(boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result["above-outliers"][point], boxProperties), this.pointRadius, this.svg, [["fill", "red"], ["fill-opacity", "1"]]); + //SVG.drawText(boxProperties.x + (boxProperties.width/2) - 2, this.pointToPixel(result["above-outliers"][point], boxProperties) + 2, "x",this.svg, [["fill", "black"], ["font-size", "x-small"]]); + } + } + if (result["below-outliers"] != null){ + for (var point in result["below-outliers"]){ + SVG.drawCircle(boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result["below-outliers"][point], boxProperties), this.pointRadius, this.svg, [["fill", "red"], ["fill-opacity", "1"]]); + //SVG.drawText(boxProperties.x + (boxProperties.width/2) - 2, this.pointToPixel(result["below-outliers"][point], boxProperties) + 2, "x",this.svg, [["fill", "black"], ["font-size", "x-small"]]); + } + } +}; + + + +BoxWhiskerGraph.prototype.plotClusterTitles = function(properties){ + /** Cluster Titles **/ + var posX = this.left + this.rulerWidth; + var data = this.data; + for(var i = 0; i < data.clusters.length; i++ ){ + /** title for the clusters **/ + posX = posX + this.interClustersSpace; + + /** Drawing title of classes **/ + var cluster = data.clusters[i]; + var posXClasses = posX; + for(var j = 0; j < cluster.classes.length; j++){ + //SVG.drawRectangle(posXClasses, this.height - (this.bottom + this.clusterTitleHeight + this.rulerHeight), properties.classWidth, this.rulerHeight, this.svg, [["fill", "green"]]); +// SVG.drawText(posXClasses + 1/6*properties.classWidth, this.height - (this.bottom + this.clusterTitleHeight + (this.rulerHeight*1/4)), cluster.classes[j].name, this.svg, [["style", "font-size:xx-small"]]); + var color = cluster.classes[j].color; + this.drawSVGVerticalText(posXClasses + 1/2*(properties.classWidth), this.height - (this.bottom - this.clusterTitleHeight + (this.rulerHeight)), cluster.classes[j].name , [["style", "font-size:x-small;"], ["fill", color]]); + + // SVG.drawRectangle(posXClasses, this.height - (this.bottom + this.clusterTitleHeight), properties.classWidth, 2, this.svg, [["fill", "black"]]); + posXClasses = posXClasses + properties.classWidth + this.interClassesSpace; + } + + var clusterTitleSpace = (data.clusters[i].classes.length * properties.classWidth) + ((data.clusters[i].classes.length - 1) * this.interClassesSpace); + //SVG.drawRectangle(posX, this.height - (this.bottom + this.clusterTitleHeight), clusterTitleSpace, this.clusterTitleHeight, this.svg, [["fill", "pink"]]); + SVG.drawRectangle(posX, this.height - (this.clusterTitleHeight+this.bottom), clusterTitleSpace, 1, this.svg, []); + +// var transform = ["translate", "(" + posX + 1/3*clusterTitleSpace +", " + this.height - (this.bottom + (this.clusterTitleHeight*1/4)) +")"], ["transform", "rotate(180)"]; +// var transform = ["transform", "translate(" + (posX + 1/3*clusterTitleSpace) +", " + (this.height - (this.bottom + (this.clusterTitleHeight*1/4))) + "), rotate(-90) "]; +// this.drawSVGVerticalText(posX + 1/3*clusterTitleSpace, this.height - (this.bottom + (this.clusterTitleHeight*1/4)),data.clusters[i].name, [["style", "font-size:x-small"]]); + SVG.drawText(posX , this.height - (this.bottom + (this.clusterTitleHeight*1/4)),data.clusters[i].name ,this.svg, [["style", "font-size:x-small"]]); + posX = posX + clusterTitleSpace; + } +}; + +BoxWhiskerGraph.prototype.plotWhisters = function(data, properties){ + var colors = ["yellow", "orange", "green"]; + var posX = this.left + this.rulerWidth; + for(var i = 0; i < data.clusters.length; i++ ){ + var cluster = data.clusters[i]; + /** inter cluster space **/ + //SVG.drawRectangle(posX, this.top, this.interClustersSpace, this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight, this.svg, [["fill", "black"]]); + posX = posX + this.interClustersSpace; + + for (var j = 0; j < cluster.classes.length; j ++){ + + //SVG.drawRectangle(posX, this.top, properties.classWidth, this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight, this.svg, [["fill", colors[j]]]); + this.plotBoxWhisker( + { + name : cluster.classes[j].name, + values : cluster.classes[j].values, + minPoint : properties.minPoint, + maxPoint : properties.maxPoint, + x : posX, + y : this.top, + width : properties.classWidth, + height : this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight + + + } + ); + posX = posX + properties.classWidth; + //SVG.drawRectangle(posX, this.top, this.interClassesSpace, this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight, this.svg, [["fill", "black"]]); + if (j < cluster.classes.length - 1){ + posX = posX + this.interClassesSpace; + } + } + } +}; + +BoxWhiskerGraph.prototype.draw = function(targetId, data){ + this.targetId = targetId; + var properties = (this.getDimensions(data)); + this.svg = SVG.createSVGCanvas(document.getElementById(this.targetId), [["width", this.width], ["height", this.height]]); + this.plotAxes(properties); + this.plotClusterTitles(properties); + this.plotWhisters(data,properties); +}; + +BoxWhiskerGraph.prototype.input = function(){ + return DATADOC.getBoxWhikerData(); +}; + +BoxWhiskerGraph.prototype.test = function(targetId){ + var plot = new BoxWhiskerGraph( + { + targetId : targetId, + height : 350, + width : 450, + maxBoxWidth : 25 + } + ); + plot.refresh(this.input()); +}; + + + + + -GraphCanvas.prototype.getVertexOpacity = function(vertexId) { - return this.getFormatter().getVertexById(vertexId).getDefault().getOpacity(); -}; + +function DataSet(){ + this.json = null; + +}; + + +DataSet.prototype.loadFromJSON = function(json){ + if(json != null) { + if(this.validate(json)) { + this.json = json; + } + } +}; + + +DataSet.prototype.toJSON = function(json){ + return this.json; +}; + + +/** Abstract method to be override on childs classes **/ +DataSet.prototype.validate = function(json){ + if (true){ + return true; + } + /*else{ + throw "Data validation failed"; + }*/ +}; + + -GraphCanvas.prototype.setVertexFill = function(vertexId, color) { - this.getFormatter().getVertexById(vertexId).getDefault().setFill(color); -}; + +Edge.prototype.getName = GraphItem.prototype.getName; +Edge.prototype.setName = GraphItem.prototype.setName; +Edge.prototype.getId = GraphItem.prototype.getId; + +function Edge(id, name, nodeSource, nodeTarget, args){ + GraphItem.prototype.constructor.call(this, id, name, args); + + this.sourceNode = nodeSource; + this.targetNode = nodeTarget; + +}; + +Edge.prototype.toJSON = function(){ + return {"index": this.id,"sourceIndex":this.sourceNode.getId(),"targetIndex":this.targetNode.getId(),"args":this.args}; +}; + +Edge.prototype.getNodeSource = function(){ + return this.sourceNode; +}; + +Edge.prototype.getNodeTarget = function(){ + return this.targetNode; +}; + +Edge.prototype.remove = function(){ + //Remove edge object in the nodes + this.getNodeSource().removeEdge(this); + this.getNodeTarget().removeEdge(this); + + this.deleted.notify(this); +}; -GraphCanvas.prototype.getVertexFill = function(vertexId) { - return this.getFormatter().getVertexById(vertexId).getDefault().getFill(); -}; + +EdgeGraphFormatter.prototype.setProperties = ItemGraphFormatter.prototype.setProperties; +EdgeGraphFormatter.prototype.getDefault = ItemGraphFormatter.prototype.getDefault; +EdgeGraphFormatter.prototype.getSelected = ItemGraphFormatter.prototype.getSelected; +EdgeGraphFormatter.prototype.getOver = ItemGraphFormatter.prototype.getOver; +EdgeGraphFormatter.prototype.getDragging = ItemGraphFormatter.prototype.getDragging; +EdgeGraphFormatter.prototype.getId = ItemGraphFormatter.prototype.getId; +EdgeGraphFormatter.prototype.toJSON = ItemGraphFormatter.prototype.toJSON; +EdgeGraphFormatter.prototype.loadFromJSON = ItemGraphFormatter.prototype.loadFromJSON; +EdgeGraphFormatter.prototype._setEvents = ItemGraphFormatter.prototype._setEvents; + +function EdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ + ItemGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); + + this.getDefault().args.type = "EdgeGraphFormatter"; +}; + + + + +LineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; +LineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; +LineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; +LineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; +LineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; +LineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; +LineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; +LineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; +LineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; + +function LineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ + EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); + this.args.type = "LineEdgeGraphFormatter"; +}; + +/** DIRECTED **/ +DirectedLineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; +DirectedLineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; +DirectedLineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; +DirectedLineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; +DirectedLineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; +DirectedLineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; +DirectedLineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; +DirectedLineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; +DirectedLineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; + +function DirectedLineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ + EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); + this.args.type = "DirectedLineEdgeGraphFormatter"; + this.args.arrowSize = "3"; +}; +DirectedLineEdgeGraphFormatter.prototype.getArrowSize = function(){ + return this.args.arrowSize; +}; + +OdirectedLineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; +OdirectedLineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; +OdirectedLineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; +OdirectedLineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; +OdirectedLineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; +OdirectedLineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; +OdirectedLineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; +OdirectedLineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; +OdirectedLineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; + +function OdirectedLineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ + EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); + this.args.type = "DirectedLineEdgeGraphFormatter"; + this.args.arrowSize = "3"; +}; + +OdirectedLineEdgeGraphFormatter.prototype.getArrowSize = function(){ + return this.args.arrowSize; +}; + + +/** CUT (inhibition) **/ +CutDirectedLineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; +CutDirectedLineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; +CutDirectedLineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; +CutDirectedLineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; +CutDirectedLineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; +CutDirectedLineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; +CutDirectedLineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; +CutDirectedLineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; +CutDirectedLineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; + +function CutDirectedLineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ + EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); + this.args.type = "CutDirectedLineEdgeGraphFormatter"; +}; + + + + +BezierEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; +BezierEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; +BezierEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; +BezierEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; +BezierEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; +BezierEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; +BezierEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; +BezierEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; +BezierEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; +BezierEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; + +function BezierEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ + EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); + this.args.type = "BezierEdgeGraphFormatter"; +}; + + + +DotDirectedLineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; +DotDirectedLineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; +DotDirectedLineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; +DotDirectedLineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; +DotDirectedLineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; +DotDirectedLineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; +DotDirectedLineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; +DotDirectedLineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; +DotDirectedLineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; + +function DotDirectedLineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ + EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); + this.args.type = "DotDirectedLineEdgeGraphFormatter"; +}; + + +OdotDirectedLineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; +OdotDirectedLineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; +OdotDirectedLineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; +OdotDirectedLineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; +OdotDirectedLineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; +OdotDirectedLineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; +OdotDirectedLineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; +OdotDirectedLineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; +OdotDirectedLineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; + +function OdotDirectedLineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ + EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); + this.args.type = "OdotDirectedLineEdgeGraphFormatter"; +}; + + -/** EDGES FORMATTER **/ -GraphCanvas.prototype.setEdgeSize = function(edgeId, value) { - this.getFormatter().getEdgeById(edgeId).getDefault().setSize(value); -}; +function GraphDataset(){ + DataSet.prototype.constructor.call(this); + this.edges = new Object(); + this.vertices = new Object(); + this.verticesIndex = new Object(); + + //Events + this.newVertex = new Event(this); + this.vertexNameChanged = new Event(this); + this.vertexDeleted = new Event(this); + + this.newEdge = new Event(this); + this.edgeNameChanged = new Event(this); + this.edgeDeleted = new Event(this); + + this.json = new Object(); + this.json.vertices = new Array(); + this.json.edges = new Array(); + this.json.relations = new Array(); +}; + +GraphDataset.prototype.loadFromJSON = DataSet.prototype.loadFromJSON; +GraphDataset.prototype.toJSON = DataSet.prototype.toJSON; +GraphDataset.prototype.validate = DataSet.prototype.validate; + +/** Devuelve el numero de edges incidentes sobre el nodo con mas edges **/ +GraphDataset.prototype.getMaxClass = function(){ + var maxClassNode = 0; + for ( var node in this.vertices) { + if (this.vertices[node].getEdgesCount() > maxClassNode){ + maxClassNode = this.vertices[node].getEdgesCount(); + } + } + return maxClassNode; +}; + +/** Devuelve el numero de edges incidentes sobre el nodo con mas edges **/ +GraphDataset.prototype.getMinClass = function(){ + var minClassNode = Math.min(); + for ( var node in this.vertices) { + if (this.vertices[node].getEdgesCount() < minClassNode){ + minClassNode = this.vertices[node].getEdgesCount(); + } + } + return minClassNode; +}; + +GraphDataset.prototype.getVertexByName = function(nodeName){ + var results = new Array(); + + for (var vertexId in this.verticesIndex[nodeName]){ + var vertexByid = this.getVertexById(this.verticesIndex[nodeName][vertexId]); + results.push(vertexByid); + //* añadido nuevo porque fallaba el anterior codigo + return vertexByid + } + + if (results <= 1){ + return this.getVertexById(this.verticesIndex[nodeName]); + } + else{ + return results; + } +}; + +GraphDataset.prototype.getVertexById = function(id){ + return this.vertices[id]; +}; + +GraphDataset.prototype.toSIF = function(){ + var sifDataAdapter = new SifFileDataAdapter(); + return sifDataAdapter.toSIF(this); +}; + +GraphDataset.prototype.toSIFID = function(){ + var sifDataAdapter = new SifFileDataAdapter(); + return sifDataAdapter.toSIFID(this); +}; + +GraphDataset.prototype.toDOT = function(){ + var dotFileDataAdapter = new DotFileDataAdapter(); + return dotFileDataAdapter.toDOT(this); +}; + +GraphDataset.prototype.toDOTID = function(){ + var dotFileDataAdapter = new DotFileDataAdapter(); + return dotFileDataAdapter.toDOTID(this); +}; + +GraphDataset.prototype._addNode = function(nodeName, args){ + return new Vertex(this._getVerticesCount()-1, nodeName, args); +}; + +GraphDataset.prototype.addNode = function(nodeName, args){ + this.json.vertices.push(nodeName); + this._addVerticesIndex(nodeName, this._getVerticesCount() - 1); + var vertex = this._addNode(nodeName, args); + this.vertices[this._getVerticesCount()-1] = vertex; + this._setNodeEvents(vertex); + this.newVertex.notify(vertex); +}; + +GraphDataset.prototype._addVerticesIndex = function(nodeName, id){ + if (this.verticesIndex[nodeName] == null){ + this.verticesIndex[nodeName] = new Array(); + } + this.verticesIndex[nodeName].push(id); +}; + +GraphDataset.prototype.addEdge = function(edgeName, nodeSourceId, nodeTargetId, args){ + this.json.edges.push(edgeName); + var nodeSource = this.getVertexById(nodeSourceId); + var nodeTarget = this.getVertexById(nodeTargetId); + var index = this.getEdgesCount() - 1; + this.edges[index] = new Edge(index, edgeName, nodeSource, nodeTarget, args); + this.json.relations.push({"index": index, "sourceIndex": nodeSourceId, "targetIndex": nodeTargetId, "args": args }); + + nodeSource.addEdge(this.edges[index]); + nodeTarget.addEdge(this.edges[index]); + this._setEdgeEvents(this.edges[index]); + this.newEdge.notify(this.edges[index]); +}; + +GraphDataset.prototype.getVertices = function(){ + return this.vertices; +}; + +GraphDataset.prototype.getEdges = function(){ + return this.edges; +}; + +GraphDataset.prototype.getEdgeById = function(edgeId){ + return this.edges[edgeId]; +}; + +GraphDataset.prototype._getVerticesCount = function(){ + return this.json.vertices.length; +}; + + +GraphDataset.prototype.getVerticesCount = function(){ + var count = 0; + for ( var vertex in this.getVertices()) { + count ++; + } + return count; +}; + + +GraphDataset.prototype.getEdgesCount = function(){ + return this.json.edges.length; +}; + +GraphDataset.prototype.init = function(){ + this.edges = new Object(); + this.vertices = new Object(); +}; + +GraphDataset.prototype._setNodeEvents = function(node){ + var _this = this; + //NODE EVENTS + node.deleted.attach(function (sender, node){ + _this._removeNode(node); + }); + + node.nameChanged.attach(function (sender, args){ + var item = args.item; + var newName = item.name; + var indexes = _this.verticesIndex[args.previousName]; + for(var i = 0; i < indexes.length; i++){ + if(indexes[i] == item.id) + indexes.splice(i,1); + } + if(indexes.length == 0){ + delete _this.verticesIndex[args.previousName]; + } + _this._addVerticesIndex(newName, item.id); + _this.json.vertices[item.id] = newName; + _this.vertexNameChanged.notify(args); + }); +}; + +GraphDataset.prototype._setEdgeEvents = function(edge){ + var _this = this; + //EDGE EVENTS + edge.nameChanged.attach(function (sender, edge){ + _this.edgeNameChanged.notify(edge); + + }); + + edge.deleted.attach(function (sender, edge){ + _this._removeEdge(edge); + }); +}; + +GraphDataset.prototype._connectVerticesByName = function(nodeNameSource, nodeNameTarget){ + var source = this.getVertexByName(nodeNameSource); + var target = this.getVertexByName(nodeNameTarget); + + if ((source != null)&&(target!=null)){ + this.addEdge(source.getName() +"_" + target.getName(), source.getId(), target.getId(), {}); + } + else{ + if (source == null){ + console.log("No encontrado: " + nodeNameSource) + } + if (target == null){ + console.log("No encontrado: " + nodeNameTarget) + } + } +}; + +GraphDataset.prototype.loadFromJSON = function(json){ + var json = json; + this.init(); + this.json = new Object(); + this.json.vertices = new Array(); + this.json.edges = new Array(); + this.json.relations = new Array(); + + for ( var i = 0; i < json.nodes.length; i++) { + if (json.nodes[i] != null){ + var name = json.nodes[i]; + this.addNode(name); + } + else{ + this.json.vertices.push(null); + } + } + + for ( var i = 0; i < json.edges.length; i++) { + if (json.edges[i] != null){ + if (json.relations[i] != null){ + var name = json.edges[i]; + this.addEdge(name, json.relations[i].sourceIndex, json.relations[i].targetIndex, json.relations[i].args); + } + } + else{ + this.json.edges.push(null); + this.json.relations.push(null); + } + } +}; + +GraphDataset.prototype.prettyPrint = function(){ + for ( var node in this.vertices) { + console.log(this.vertices[node].getName() ); + for ( var j = 0; j < this.vertices[node].getEdgesIn().length; j++) { + console.log(" --> " + this.vertices[node].getEdgesIn()[j].getNodeTarget().getName() ); + } + } +}; + +GraphDataset.prototype._removeEdge = function(edge){ + this.json.edges[edge.getId()] = null; + this.json.relations[edge.getId()] = null; + + delete this.edges[edge.getId()]; + this.edgeDeleted.notify(edge); + + +}; + +GraphDataset.prototype._removeNode = function(node){ + this.json.vertices[node.getId()] = null; + delete this.vertices[node.getId()]; + this.vertexDeleted.notify(node); +}; + +GraphDataset.prototype.toJSON = function(){ + var json = new Object(); + var nodes = new Array(); + json.nodes = this.json.vertices; //nodes; + json.edges = this.json.edges; //edges; + json.relations = this.json.relations; + return json; +}; + +GraphDataset.prototype.clone = function(){ + var dsDataset = new GraphDataset(); + dsDataset.loadFromJSON(this.toJSON()); + return dsDataset; +}; +//GraphDataset.prototype.test = function(){ +// this.loadFromJSON(this.toJSON()); +//}; + +function labels(){ + var names = new Array(); + + var dataset = interactomeViewer.graphEditorWidget.dataset; + var layout = interactomeViewer.graphEditorWidget.layout; + + for ( var vertexId in interactomeViewer.graphEditorWidget.dataset.getVertices()) { + names.push(interactomeViewer.graphEditorWidget.dataset.getVertexById(vertexId).getName()); + } + + var sorted = (names.sort()); + console.log(sorted) + var distance = 0.01; + var altura = 0.6; + for ( var i = 0; i < names.length; i++) { + var id =dataset.getVertexByName(names[i]).getId(); + + layout.getNodeById(id).setCoordenates(distance, altura); + + + distance = parseFloat(distance) + parseFloat(0.03); + + altura = parseFloat(altura) + parseFloat(0.02); + + if (parseFloat(altura) == 0.9800000000000003){ + + altura = 0.6; + distance = distance - 0.51; + } + + } + + +}; -GraphCanvas.prototype.getEdgeSize = function(edgeId) { - return this.getFormatter().getEdgeById(edgeId).getDefault().getSize(); -}; +function GraphItem(id, name, args){ + this.id = id; + this.name = name; + this.type = "NONE"; + + this.args = new Object(); + + + if (args!=null){ + this.args = args; + if (args.type !=null){ + this.type = args.type; + } + } + + //Events + this.nameChanged = new Event(this); + this.deleted = new Event(this); +} + +GraphItem.prototype.getName = function(){ + return this.name; +}; + +GraphItem.prototype.getId = function(){ + return this.id; +}; + +GraphItem.prototype.setName = function(name){ + var oldName = this.getName(); + this.name = name; + this.nameChanged.notify({"item": this, "previousName" : oldName}); +}; + + + + -GraphCanvas.prototype.setEdgeStroke = function(edgeId, value) { - this.getFormatter().getEdgeById(edgeId).getDefault().setStroke(value); -}; +function LayoutDataset(){ + this.dataset = null; + this.vertices = new Object(); + this.changed = new Event(this); + + + this.args = new Object(); + + //RANDOM, CIRCLE + this.args.type = "CIRCLE"; +}; + +LayoutDataset.prototype.loadFromJSON = function(dataset, json){ + var _this = this; + this.vertices = new Object(); + this.dataset = dataset; //new GraphDataset(); + for ( var vertex in json) { + this.vertices[vertex] = new NodeLayout(vertex, json[vertex].x, json[vertex].y); + this.vertices[vertex].changed.attach(function (sender, item){ + _this.changed.notify(item); + }); + } + this._attachDatasetEvents(); +}; + + +LayoutDataset.prototype.toJSON = function(){ + var serialize = new Object(); + for ( var vertex in this.vertices) { + serialize[vertex] = new Object(); + serialize[vertex].x = this.vertices[vertex].x; + serialize[vertex].y = this.vertices[vertex].y; + } + serialize.dataset = new Object(); + serialize.dataset =this.dataset.toJSON(); + return serialize; +}; + +LayoutDataset.prototype.dataBind = function(graphDataset){ + this.dataset = graphDataset; + this._attachDatasetEvents(); + this._calculateLayout(); +}; + +LayoutDataset.prototype._removeVertex = function(vertexId){ + delete this.vertices[vertexId]; +}; + +LayoutDataset.prototype._attachDatasetEvents = function(){ + var _this = this; + + this.dataset.vertexDeleted.attach(function (sender, item){ + _this._removeVertex(item.getId()); + }); + + this.dataset.newVertex.attach(function (sender, item){ + _this.vertices[item.getId()] = new NodeLayout(item.getId(), 0.5, 0.5); + _this.vertices[item.getId()].changed.attach(function (sender, item){ + _this.changed.notify(item); + }); + }); +}; + +LayoutDataset.prototype.getType = function(){ + return this.args.type; +}; + +LayoutDataset.prototype._calculateLayoutVertices = function(type, count){ + + if (type == "CIRCLE"){ + var radius = 0.4; + var centerX = 0.5; + var centerY = 0.5; + var verticesCoordinates = new Array(); + for(var i = 0; i < count; i++){ + x = centerX + radius * Math.sin(i * 2 * Math.PI/count); + y = centerY + radius * Math.cos(i * 2 * Math.PI/count); + verticesCoordinates.push({'x':x,'y':y}); + } + return verticesCoordinates; + } +}; + + +LayoutDataset.prototype._calculateLayout = function(){ + var _this = this; + if (this.getType() == "RANDOM"){ + for ( var vertex in this.dataset.getVertices()) { + if (this.vertices[vertex] == null){ + this.vertices[vertex] = new NodeLayout(vertex, 0, 0); + } + this.vertices[vertex].setCoordinates(Math.random(), Math.random()); + this.vertices[vertex].changed.attach(function (sender, item){ + _this.changed.notify(item); + }); + } + } + + if ( this.getType() == "CIRCLE"){ + + var count = this.dataset._getVerticesCount(); + var verticesCoordinates = this._calculateLayoutVertices(this.getType(), count); + + var aux = 0; + for ( var vertex in this.dataset.getVertices()) { + if (this.vertices[vertex] == null){ + this.vertices[vertex] = new NodeLayout(vertex, 0, 0); + } + this.vertices[vertex].setCoordinates(verticesCoordinates[aux].x, verticesCoordinates[aux].y);//{"x":, "y":}; + aux++; + this.vertices[vertex].changed.attach(function (sender, item){ + _this.changed.notify(item); + }); + } + } + + + if (this.getType() == "SQUARE"){ + + var count = this.dataset._getVerticesCount(); + var xMin = 0.1; + var xMax = 0.9; + var yMin = 0.1; + var yMax = 0.9; + + var rows = Math.sqrt(count); + var step = (xMax - xMin) / rows; + + var verticesCoordinates = new Array(); + for(var i = 0; i < rows; i ++){ + for ( var j = 0; j < rows; j++) { + x = i * step + xMin; + y = j * step + yMin; + verticesCoordinates.push({'x':x,'y':y}); + } + } + + var aux = 0; + for ( var vertex in this.dataset.getVertices()) { + if (this.vertices[vertex] == null){ + this.vertices[vertex] = new NodeLayout(vertex, 0, 0); + } + this.vertices[vertex].setCoordinates(verticesCoordinates[aux].x, verticesCoordinates[aux].y);//{"x":, "y":}; + aux++; + this.vertices[vertex].changed.attach(function (sender, item){ + _this.changed.notify(item); + }); + } + } + +}; + +LayoutDataset.prototype.getNodeById = function(id){ + return this.vertices[id]; +}; + +LayoutDataset.prototype.getVerticesByArea = function(x1, y1, x2, y2){ + var vertices = new Array(); + for ( var vertex in this.dataset.getVertices()) { + if ((this.vertices[vertex].x >= x1)&&(this.vertices[vertex].x <= x2)){ + if ((this.vertices[vertex].y >= y1)&&(this.vertices[vertex].y <= y2)){ + vertices.push(this.vertices[vertex]); + } + } + } + return vertices; +}; + + + + +LayoutDataset.prototype.getLayout = function(type){ + + if (type == "CIRCLE"){ + this.args.type = "CIRCLE"; + this._calculateLayout(); + return; + } + + if (type == "SQUARE"){ + this.args.type = "SQUARE"; + this._calculateLayout(); + return; + } + + if (type == "RANDOM"){ + this.args.type = "RANDOM"; + this._calculateLayout(); + return; + } + + + var dotText = this.dataset.toDOTID(); + var url = "http://bioinfo.cipf.es/utils/ws/rest/network/layout/"+type+".coords"; + var _this = this; + + $.ajax({ + async: true, + type: "POST", + url: url, + dataType: "text", + data: { + dot :dotText + }, + cache: false, + success: function(data){ + var response = JSON.parse(data); + for ( var vertexId in response) { + _this.vertices[vertexId].setCoordinates(response[vertexId].x, response[vertexId].y); + } + } + }); + +// $.ajax({ +// async: true, +// type: "POST", +// url: url, +// dataType: "script", +// data: { +// dot :dotText +// }, +// cache: false, +// success: function(data){ +// var response = JSON.parse(data); +// for ( var vertexId in response) { +// _this.vertices[vertexId].setCoordinates(response[vertexId].x, response[vertexId].y); +// } +// } +// }); + +}; + +function NodeLayout(id, x, y, args){ + this.id = id; + this.x = x; + this.y = y; + this.changed = new Event(this); +}; + +NodeLayout.prototype.getId = function(id){ + return this.id; +}; + +NodeLayout.prototype.setCoordinates = function(x, y){ + this.x = x; + this.y = y; + this.changed.notify(this); +}; + -GraphCanvas.prototype.getEdgeStroke = function(edgeId) { - return this.getFormatter().getEdgeById(edgeId).getDefault().getStroke(); -}; + +function NetworkDataSetFormatter(vertexFormatProperties, defaultEdgeProperties, args){ + DataSet.prototype.constructor.call(this); + + this.args = new Object(); + + this.vertices = new Object(); + this.edges = new Object(); + this.dataset = null; + this.maxClass = 0; + this.minClass = 0; + + /** Coordenates with default Setting */ + this.args.width = 1100; + this.args.height = 500; + + /** Optional parameters */ + this.args.backgroundColor = "#FFFFFF"; + this.args.backgroundImage = null; + this.args.backgroundImageHeight = null; + this.args.backgroundImageWidth = null; + this.args.backgroundImageX = null; + this.args.backgroundImageY = null; + + + this.args.balanceNodes = false; + this.args.nodesMaxSize = 3; + this.args.nodesMinSize = 0.5; + + + /** Zoom **/ + this.args.zoomScale = 1; + this.args.zoomScaleStepFactor = 0.4; + + if (args != null){ + if (args.backgroundImage != null){ + this.args.backgroundImage = args.backgroundImage; + } + + if (args.width != null){ + this.args.width = args.width; + } + + if (args.height != null){ + this.args.height = args.height; + this.args.svgHeight = args.height; + } + + if (args.svgHeight != null){ + this.args.svgHeight = args.svgHeight; + } + + if (args.backgroundColor != null){ + this.args.backgroundColor = args.backgroundColor; + } + + if(args.balanceNodes != null){ + this.args.balanceNodes = args.balanceNodes; + } + + if(args.nodesMaxSize != null){ + this.args.nodesMaxSize = args.nodesMaxSize; + } + if(args.nodesMinSize != null){ + this.args.nodesMinSize = args.nodesMinSize; + } + } + + this.args.defaultEdgeProperties = {"fill":"#000000", "radius":"1", "stroke":"#000000", "size":1, "title":{"fontSize":10, "fontColor":"#000000"}}; + this.args.vertexFormatProperties = { "fill":"#000000", "stroke":"#000000", "stroke-opacity":"#000000"}; + + if (vertexFormatProperties!= null){ + this.args.vertexFormatProperties = vertexFormatProperties; + } + if (defaultEdgeProperties!= null){ + this.args.defaultEdgeProperties = defaultEdgeProperties; + } + + /** Events **/ + this.changed = new Event(this); + this.edgeChanged = new Event(this); + this.resized = new Event(this); + this.backgroundImageChanged= new Event(this); + this.backgroundColorChanged= new Event(this); +}; + +NetworkDataSetFormatter.prototype.loadFromJSON = function(dataset, json){ + this.args = new Object(); + this.vertices = new Object(); + this.args = json; + this._setDataset(dataset); + var _this = this; + + for ( var vertex in json.vertices) { + this.addVertex(vertex, json.vertices[vertex]); + } + + for ( var edgeId in json.edges) { + this.addEdge(edgeId, json.edges[edgeId]); + } +}; + + +NetworkDataSetFormatter.prototype.toJSON = function(){ + + +// this.args.vertices = new Object(); +// this.args.edges = new Object(); +// +// for ( var vertex in this.vertices) { +// this.args.vertices[vertex] = this.getVertexById(vertex).toJSON(); +// } +// for ( var edge in this.edges) { +// this.args.edges[edge] = this.getEdgeById(edge).toJSON(); +// } +// +// return (this.args); + + + var serialize = new Object(); + serialize = JSON.parse(JSON.stringify(this.args)); + serialize.vertices = new Object(); + serialize.edges = new Object(); + + for ( var vertex in this.vertices) { + serialize.vertices[vertex] = this.getVertexById(vertex).toJSON(); + } + for ( var edge in this.edges) { + serialize.edges[edge] = this.getEdgeById(edge).toJSON(); + } + + return (serialize); +}; + + + +NetworkDataSetFormatter.prototype._getNodeSize = function(nodeId){ + if (this.isVerticesBalanced()){ + var total = this.maxClass - this.minClass; + if (total == 0){ total = 1;} + var nodeConnection = this.dataset.getVertexById(nodeId).getEdges().length; + return ((nodeConnection*this.args.nodesMaxSize)/total) + this.args.nodesMinSize; + } + return this.getVertexById(nodeId).getDefault().getSize(); +}; + +NetworkDataSetFormatter.prototype._recalculateSize = function(){ + if (this.isVerticesBalanced()){ + this.maxClass = this.dataset.getMaxClass(); + this.minClass = this.dataset.getMinClass(); + for ( var vertexIdAll in this.vertices) { + var size = this._getNodeSize(vertexIdAll); + this.vertices[vertexIdAll].getDefault().setSize(size); + this.vertices[vertexIdAll].getSelected().setSize(size); + this.vertices[vertexIdAll].getOver().setSize(size); + } + } +}; + + +NetworkDataSetFormatter.prototype.addVertex = function(vertexId, json){ + + + if (json == null){ + this.vertices[vertexId] = new CircleVertexGraphFormatter(vertexId, this.args.vertexFormatProperties.defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); + } + else{ + + /** Cargo los attributos desde el json **/ + if (json.type == null){ + this.vertices[vertexId] = new CircleVertexGraphFormatter(vertexId, this.args.vertexFormatProperties.defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); + } + + if ((json.type == "SquareVertexGraphFormatter")||(json.type == "SquareVertexNetworkFormatter")){ + this.vertices[vertexId] = new SquareVertexGraphFormatter(vertexId); + this.vertices[vertexId].loadFromJSON(json); + } + + if ((json.type == "CircleVertexGraphFormatter")||(json.type == "CircleVertexNetworkFormatter")){ + this.vertices[vertexId] = new CircleVertexGraphFormatter(vertexId); + this.vertices[vertexId].loadFromJSON(json); + } + + if ((json.type == "EllipseVertexGraphFormatter")||(json.type == "EllipseVertexNetworkFormatter")){ + this.vertices[vertexId] = new EllipseVertexGraphFormatter(vertexId); + this.vertices[vertexId].loadFromJSON(json); + } + + if ((json.type == "RectangleVertexGraphFormatter")||(json.type == "RectangleVertexNetworkFormatter")){ + this.vertices[vertexId] = new RectangleVertexGraphFormatter(vertexId); + this.vertices[vertexId].loadFromJSON(json); + } + + if ((json.type == "RoundedVertexGraphFormatter")||(json.type == "RoundedVertexNetworkFormatter")){ + this.vertices[vertexId] = new RoundedVertexGraphFormatter(vertexId); + this.vertices[vertexId].loadFromJSON(json); + } + + } + + + var _this = this; + this.vertices[vertexId].stateChanged.attach(function (sender, item){ + _this.changed.notify(item); + }); + + var size = this._getNodeSize(vertexId); + this.vertices[vertexId].defaultFormat.args.size = size; + this.vertices[vertexId].selected.args.size = size; + this.vertices[vertexId].over.args.size = size; + +}; + +NetworkDataSetFormatter.prototype.addEdge = function(edgeId, json){ + + /** Es un edge nuevo que le doy los atributos por defecto **/ + if (json == null){ + if (this.dataset.getEdgeById(edgeId).getNodeSource().getId() == this.dataset.getEdgeById(edgeId).getNodeTarget().getId()){ + this.edges[edgeId] = new BezierEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); + }else{ + this.edges[edgeId] = new DirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); + } + } + else{ + /** Cargo los attributos desde el json **/ + if (json.type == null){ + this.edges[edgeId] = new LineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); + } + + if ((json.type == "LineEdgeGraphFormatter")||(json.type == "LineEdgeNetworkFormatter")){ + this.edges[edgeId] = new LineEdgeGraphFormatter(edgeId); + this.edges[edgeId].loadFromJSON(json); + } + if ((json.type == "DirectedLineEdgeGraphFormatter")||(json.type == "DirectedLineEdgeNetworkFormatter")){ + this.edges[edgeId] = new DirectedLineEdgeGraphFormatter(edgeId); + this.edges[edgeId].loadFromJSON(json); + } + + if ((json.type == "BezierEdgeGraphFormatter")||(json.type == "BezierEdgeNetworkFormatter")){ + this.edges[edgeId] = new BezierEdgeGraphFormatter(edgeId); + this.edges[edgeId].loadFromJSON(json); + } + + + if ((json.type == "CutDirectedLineEdgeGraphFormatter")||(json.type == "CutDirectedLineEdgeNetworkFormatter")){ + this.edges[edgeId] = new CutDirectedLineEdgeGraphFormatter(edgeId); + this.edges[edgeId].loadFromJSON(json); + } + + if ((json.type == "DotDirectedLineEdgeGraphFormatter")||(json.type == "DotDirectedLineEdgeNetworkFormatter")){ + this.edges[edgeId] = new DotDirectedLineEdgeGraphFormatter(edgeId); + this.edges[edgeId].loadFromJSON(json); + } + if ((json.type == "OdotDirectedLineEdgeGraphFormatter")||(json.type == "OdotDirectedLineEdgeNetworkFormatter")){ + this.edges[edgeId] = new OdotDirectedLineEdgeGraphFormatter(edgeId); + this.edges[edgeId].loadFromJSON(json); + } + + if ((json.type == "OdirectedLineEdgeGraphFormatter")||(json.type == "OdirectedLineEdgeNetworkFormatter")){ + this.edges[edgeId] = new OdirectedLineEdgeGraphFormatter(edgeId); + this.edges[edgeId].loadFromJSON(json); + } + } + + var _this = this; + this.edges[edgeId].stateChanged.attach(function (sender, item){ + _this.edgeChanged.notify(item); + }); + + this._recalculateSize(); +}; + +NetworkDataSetFormatter.prototype._setDataset = function(dataset){ + this.dataset = dataset; + this.maxClass = dataset.getMaxClass(); + this.minClass = dataset.getMinClass(); + this._attachDatasetEvents(); +}; + +NetworkDataSetFormatter.prototype.changeEdgeType = function(edgeId, type){ + if ((type == "LineEdgeGraphFormatter")||(type == "LineEdgeNetworkFormatter")){ + this.edges[edgeId] = new LineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); + + } + if ((type == "DirectedLineEdgeGraphFormatter")||(type == "DirectedLineEdgeNetworkFormatter")){ + this.edges[edgeId] = new DirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); + } + + if ((type == "CutDirectedLineEdgeGraphFormatter")||(type == "CutDirectedLineEdgeNetworkFormatter")){ + this.edges[edgeId] = new CutDirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); + } + + if ((type == "DotDirectedLineEdgeGraphFormatter")||(type == "DotDirectedLineEdgeNetworkFormatter")){ + this.edges[edgeId] = new DotDirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); + } + + if ((type == "OdotDirectedLineEdgeGraphFormatter")||(type == "OdotDirectedLineEdgeNetworkFormatter")){ + this.edges[edgeId] = new OdotDirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); + } + + if ((type == "OdirectedLineEdgeGraphFormatter")||(type == "OdirectedLineEdgeNetworkFormatter")){ + this.edges[edgeId] = new OdirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); + } + + + + var _this = this; + this.edges[edgeId].stateChanged.attach(function (sender, item){ + _this.edgeChanged.notify(item); + }); + _this.edgeChanged.notify(this.edges[edgeId]); +}; +/* +classe = "SquareNetworkNodeFormatter"; +} +if (value == "circle"){ + classe = "CircleNetworkNodeFormatter"; + **/ +NetworkDataSetFormatter.prototype.changeNodeType = function(vertexId, type){ + var defaultFormat = JSON.parse(JSON.stringify(this.vertices[vertexId].getDefault())); + var selectedFormat = JSON.parse(JSON.stringify(this.vertices[vertexId].getSelected())); + var defaultFormat = JSON.parse(JSON.stringify(this.vertices[vertexId].getDefault())); + var defaultFormat = JSON.parse(JSON.stringify(this.vertices[vertexId].getDefault())); + + if ((type == "SquareVertexGraphFormatter")||(type == "SquareVertexNetworkFormatter")){ + this.vertices[vertexId] = new SquareVertexGraphFormatter(vertexId,defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); + } + + if ((type == "CircleVertexGraphFormatter")||(type == "CircleVertexNetworkFormatter")){ + this.vertices[vertexId] = new CircleVertexGraphFormatter(vertexId, defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); + } + + if ((type == "EllipseVertexGraphFormatter")||(type == "EllipseVertexNetworkFormatter")){ + this.vertices[vertexId] = new EllipseVertexGraphFormatter(vertexId, defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); + } + + if ((type == "RectangleVertexGraphFormatter")||(type == "RectangleVertexNetworkFormatter")){ + this.vertices[vertexId] = new RectangleVertexGraphFormatter(vertexId, defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); + } + + if ((type == "RoundedVertexGraphFormatter")||(type == "RoundedVertexNetworkFormatter")){ + this.vertices[vertexId] = new RoundedVertexGraphFormatter(vertexId, defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); + } + + if ((type == "OctagonVertexGraphFormatter")||(type == "OctagonVertexNetworkhFormatter")){ + this.vertices[vertexId] = new OctagonVertexGraphFormatter(vertexId, defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); + } + + + var _this = this; + this.vertices[vertexId].stateChanged.attach(function (sender, item){ + _this.changed.notify(item); + }); + _this.changed.notify(this.vertices[vertexId]); +}; + + + +NetworkDataSetFormatter.prototype.dataBind = function(networkDataSet){ + var _this = this; + this._setDataset(networkDataSet); + + for ( var vertex in this.dataset.getVertices()) { + this.addVertex(vertex); + } + + for ( var edge in this.dataset.getEdges()) { + this.addEdge(edge); + } +}; + +NetworkDataSetFormatter.prototype._removeEdge = function(edgeId){ + delete this.edges[edgeId]; +}; + +NetworkDataSetFormatter.prototype._removeVertex = function(vertexId){ + delete this.vertices[vertexId]; +}; + +NetworkDataSetFormatter.prototype._attachDatasetEvents = function(id){ + var _this = this; + this.dataset.vertexDeleted.attach(function (sender, item){ + _this._removeVertex(item.getId()); + }); + + this.dataset.edgeDeleted.attach(function (sender, item){ + _this._removeEdge(item.getId()); + }); + + this.dataset.newVertex.attach(function (sender, item){ + _this.addVertex(item.getId()); + }); + + this.dataset.newEdge.attach(function (sender, item){ + _this.addEdge(item.getId()); + }); +}; + + +NetworkDataSetFormatter.prototype.getVertexById = function(id){ + return this.vertices[id]; +}; + +NetworkDataSetFormatter.prototype.getEdgeById = function(id){ + return this.edges[id]; +}; + +NetworkDataSetFormatter.prototype.makeLabelsBigger = function(){ +for ( var vertexId in this.vertices) { + var fontSize = this.vertices[vertexId].getDefault().getFontSize() + 2; + this.vertices[vertexId].getDefault().setFontSize(fontSize); + } +}; + +NetworkDataSetFormatter.prototype.makeLabelsSmaller = function(){ + for ( var vertexId in this.vertices) { + var fontSize = this.vertices[vertexId].getDefault().getFontSize() - 2; + this.vertices[vertexId].getDefault().setFontSize(fontSize); + } +}; + + +NetworkDataSetFormatter.prototype.resize = function(width, height){ + this.args.width = width; + this.args.height = height; + this.resized.notify(); +}; + +/** ZOOM GETTERS **/ +NetworkDataSetFormatter.prototype.getZoomScaleStepFactor = function(){return this.args.zoomScaleStepFactor;}; +NetworkDataSetFormatter.prototype.setZoomScaleStepFactor = function(scaleFactor){this.args.zoomScaleStepFactor = scaleFactor;}; +NetworkDataSetFormatter.prototype.getZoomScale = function(){return this.args.zoomScale;}; +NetworkDataSetFormatter.prototype.setZoomScale = function(scale){this.args.zoomScale = scale;}; + +NetworkDataSetFormatter.prototype.getNodesMaxSize = function(){return this.args.nodesMaxSize;}; +NetworkDataSetFormatter.prototype.getNodesMinSize = function(){return this.args.nodesMinSize;}; + +/** SIZE SETTERS AND GETTERS **/ +NetworkDataSetFormatter.prototype.isVerticesBalanced = function(){return this.args.balanceNodes;}; +NetworkDataSetFormatter.prototype.getWidth = function(){return this.args.width;}; +NetworkDataSetFormatter.prototype.getHeight = function(){return this.args.height;}; + +/** OPTIONAL PARAMETERS GETTERS AND SETTERS **/ +NetworkDataSetFormatter.prototype.getBackgroundImage = function(){return this.args.backgroundImage;}; +NetworkDataSetFormatter.prototype.setBackgroundImage = function(value){this.args.backgroundImage = value; this.backgroundImageChanged.notify(this);}; + + +NetworkDataSetFormatter.prototype.getBackgroundImageWidth = function(){return this.args.backgroundImageWidth;}; +NetworkDataSetFormatter.prototype.setBackgroundImageWidth = function(value){this.args.backgroundImageWidth = value; this.backgroundImageChanged.notify(this);}; + +NetworkDataSetFormatter.prototype.getBackgroundImageHeight = function(){return this.args.backgroundImageHeight;}; +NetworkDataSetFormatter.prototype.setBackgroundImageHeight = function(value){this.args.backgroundImageHeight = value; this.backgroundImageChanged.notify(this);}; + +NetworkDataSetFormatter.prototype.getBackgroundImageX = function(){return this.args.backgroundImageX;}; +NetworkDataSetFormatter.prototype.setBackgroundImageX = function(value){this.args.backgroundImageX = value; this.backgroundImageChanged.notify(this);}; + +NetworkDataSetFormatter.prototype.getBackgroundImageY = function(){return this.args.backgroundImageX;}; +NetworkDataSetFormatter.prototype.setBackgroundImageY = function(value){this.args.backgroundImageY = value; this.backgroundImageChanged.notify(this);}; + + + +NetworkDataSetFormatter.prototype.getBackgroundColor = function(){return this.args.backgroundColor;}; +NetworkDataSetFormatter.prototype.setBackgroundColor = function(value){this.args.backgroundColor = value; this.backgroundColorChanged.notify(this);}; + +NetworkDataSetFormatter.prototype.getWidth = function(){return this.args.width;}; +NetworkDataSetFormatter.prototype.setWidth = function(value){this.args.width = value;}; + +NetworkDataSetFormatter.prototype.getHeight = function(){return this.args.height;}; +NetworkDataSetFormatter.prototype.setHeight = function(value){this.args.height = value;}; + + -GraphCanvas.prototype.setEdgeStrokeOpacity = function(edgeId, value) { - this.getFormatter().getEdgeById(edgeId).getDefault().setStrokeOpacity(value); -}; + +Vertex.prototype.getName = GraphItem.prototype.getName; +Vertex.prototype.setName = GraphItem.prototype.setName; +Vertex.prototype.getId = GraphItem.prototype.getId; + +function Vertex(id, name, args){ + GraphItem.prototype.constructor.call(this, id, name, args); + this.edgesIn= new Array(); + this.edgesOut= new Array(); +}; + +Vertex.prototype.getEdges = function(){ + return this.edgesIn.concat(this.edgesOut); +}; + +Vertex.prototype.getEdgesCount = function(){ + return this.getEdges().length; +}; + +Vertex.prototype.getEdgesIn = function(){ + return this.edgesIn; +}; + +Vertex.prototype.getEdgesOut = function(){ + return this.edgesOut; +}; + +Vertex.prototype.addEdge = function(edge){ + if (edge.getNodeSource().getId() == this.id){ + this.edgesIn.push(edge); + } + else{ + this.edgesOut.push(edge); + } +}; + +Vertex.prototype.removeEdge = function(edge){ + for ( var i = 0; i < this.getEdgesIn().length; i++) { + var edgeIn = this.edgesIn[i]; + if (edgeIn.getId() == edge.getId()){ + this.edgesIn.splice(i, 1); + } + } + for ( var i = 0; i < this.getEdgesOut().length; i++) { + var edgeIn = this.edgesOut[i]; + if (edgeIn.getId() == edge.getId()){ + this.edgesOut.splice(i, 1); + } + } +}; + +Vertex.prototype.remove = function(){ + var edges = this.getEdges(); + for ( var i = 0; i < edges.length; i++) { + var edge = edges[i]; + edge.remove(); + } + this.deleted.notify(this); +}; + + + + -GraphCanvas.prototype.getEdgeStrokeOpacity = function(edgeId) { - return this.getFormatter().getEdgeById(edgeId).getDefault().getStrokeOpacity(); -}; +VertexGraphFormatter.prototype.getDefault = ItemGraphFormatter.prototype.getDefault; +VertexGraphFormatter.prototype.getSelected = ItemGraphFormatter.prototype.getSelected; +VertexGraphFormatter.prototype.getOver = ItemGraphFormatter.prototype.getOver; +VertexGraphFormatter.prototype.getDragging = ItemGraphFormatter.prototype.getDragging; +VertexGraphFormatter.prototype.getId = ItemGraphFormatter.prototype.getId; +VertexGraphFormatter.prototype.toJSON = ItemGraphFormatter.prototype.toJSON; +VertexGraphFormatter.prototype.loadFromJSON = ItemGraphFormatter.prototype.loadFromJSON; +VertexGraphFormatter.prototype._setEvents = ItemGraphFormatter.prototype._setEvents; + + +function VertexGraphFormatter(defaultFormat, selectedFormat, overFormat, draggingFormat){ + ItemGraphFormatter.prototype.constructor.call(this, defaultFormat, selectedFormat, overFormat, draggingFormat); +}; + + +CircleVertexGraphFormatter.prototype.getDefault = VertexGraphFormatter.prototype.getDefault; +CircleVertexGraphFormatter.prototype.getSelected = VertexGraphFormatter.prototype.getSelected; +CircleVertexGraphFormatter.prototype.getOver = VertexGraphFormatter.prototype.getOver; +CircleVertexGraphFormatter.prototype.getDragging = VertexGraphFormatter.prototype.getDragging; +CircleVertexGraphFormatter.prototype.getId = VertexGraphFormatter.prototype.getId; +CircleVertexGraphFormatter.prototype.toJSON = VertexGraphFormatter.prototype.toJSON; +CircleVertexGraphFormatter.prototype.loadFromJSON = VertexGraphFormatter.prototype.loadFromJSON; +CircleVertexGraphFormatter.prototype._setEvents = VertexGraphFormatter.prototype._setEvents; + +function CircleVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ + VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); + this.args.type = "CircleVertexGraphFormatter"; + if (defaultFormat != null){ + if (defaultFormat.radius != null){ + this.defaultFormat.args.radius = defaultFormat.radius; + } + } + + if (selectedFormat != null){ + if (selectedFormat.radius != null){ + this.selected.args.radius = selectedFormat.radius; + } + } + + if (overFormat != null){ + if (overFormat.radius != null){ + this.over.args.radius = overFormat.radius; + } + } + + if (draggingFormat != null){ + if (draggingFormat.radius != null){ + this.dragging.args.draggingFormat = draggingFormat.radius; + } + } +}; + + + +SquareVertexGraphFormatter.prototype.getDefault = VertexGraphFormatter.prototype.getDefault; +SquareVertexGraphFormatter.prototype.getSelected = VertexGraphFormatter.prototype.getSelected; +SquareVertexGraphFormatter.prototype.getOver = VertexGraphFormatter.prototype.getOver; +SquareVertexGraphFormatter.prototype.getDragging = VertexGraphFormatter.prototype.getDragging; +SquareVertexGraphFormatter.prototype.getId = VertexGraphFormatter.prototype.getId; +SquareVertexGraphFormatter.prototype.toJSON = VertexGraphFormatter.prototype.toJSON; +SquareVertexGraphFormatter.prototype.loadFromJSON = VertexGraphFormatter.prototype.loadFromJSON; +SquareVertexGraphFormatter.prototype._setEvents = VertexGraphFormatter.prototype._setEvents; + +function SquareVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ + VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); + this.args.type = "SquareVertexGraphFormatter"; + if (defaultFormat != null){ + if (defaultFormat.radius != null){ + this.defaultFormat.args.radius = defaultFormat.radius; + } + } + + if (selectedFormat != null){ + if (selectedFormat.radius != null){ + this.selected.args.radius = selectedFormat.radius; + } + } + + if (overFormat != null){ + if (overFormat.radius != null){ + this.over.args.radius = overFormat.radius; + } + } + + if (draggingFormat != null){ + if (draggingFormat.radius != null){ + this.dragging.args.draggingFormat = draggingFormat.radius; + } + } +}; + + +EllipseVertexGraphFormatter.prototype.getDefault = VertexGraphFormatter.prototype.getDefault; +EllipseVertexGraphFormatter.prototype.getSelected = VertexGraphFormatter.prototype.getSelected; +EllipseVertexGraphFormatter.prototype.getOver = VertexGraphFormatter.prototype.getOver; +EllipseVertexGraphFormatter.prototype.getDragging = VertexGraphFormatter.prototype.getDragging; +EllipseVertexGraphFormatter.prototype.getId = VertexGraphFormatter.prototype.getId; +EllipseVertexGraphFormatter.prototype.toJSON = VertexGraphFormatter.prototype.toJSON; +EllipseVertexGraphFormatter.prototype.loadFromJSON = VertexGraphFormatter.prototype.loadFromJSON; +EllipseVertexGraphFormatter.prototype._setEvents = VertexGraphFormatter.prototype._setEvents; + +function EllipseVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ + VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); + this.args.type = "EllipseVertexGraphFormatter"; + if (defaultFormat != null){ + if (defaultFormat.radius != null){ + this.defaultFormat.args.radius = defaultFormat.radius; + } + } + + if (selectedFormat != null){ + if (selectedFormat.radius != null){ + this.selected.args.radius = selectedFormat.radius; + } + } + + if (overFormat != null){ + if (overFormat.radius != null){ + this.over.args.radius = overFormat.radius; + } + } + + if (draggingFormat != null){ + if (draggingFormat.radius != null){ + this.dragging.args.draggingFormat = draggingFormat.radius; + } + } +}; + + + +RectangleVertexGraphFormatter.prototype.getDefault = ItemGraphFormatter.prototype.getDefault; +RectangleVertexGraphFormatter.prototype.getSelected = ItemGraphFormatter.prototype.getSelected; +RectangleVertexGraphFormatter.prototype.getOver = ItemGraphFormatter.prototype.getOver; +RectangleVertexGraphFormatter.prototype.getDragging = ItemGraphFormatter.prototype.getDragging; +RectangleVertexGraphFormatter.prototype.getId = ItemGraphFormatter.prototype.getId; +RectangleVertexGraphFormatter.prototype.toJSON = ItemGraphFormatter.prototype.toJSON; +RectangleVertexGraphFormatter.prototype.loadFromJSON = ItemGraphFormatter.prototype.loadFromJSON; +RectangleVertexGraphFormatter.prototype._setEvents = ItemGraphFormatter.prototype._setEvents; + +function RectangleVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ + VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); + this.args.type = "RectangleVertexGraphFormatter"; + if (defaultFormat != null){ + if (defaultFormat.radius != null){ + this.defaultFormat.args.radius = defaultFormat.radius; + } + } + + if (selectedFormat != null){ + if (selectedFormat.radius != null){ + this.selected.args.radius = selectedFormat.radius; + } + } + + if (overFormat != null){ + if (overFormat.radius != null){ + this.over.args.radius = overFormat.radius; + } + } + + if (draggingFormat != null){ + if (draggingFormat.radius != null){ + this.dragging.args.draggingFormat = draggingFormat.radius; + } + } +}; + + + +RoundedVertexGraphFormatter.prototype.getDefault = ItemGraphFormatter.prototype.getDefault; +RoundedVertexGraphFormatter.prototype.getSelected = ItemGraphFormatter.prototype.getSelected; +RoundedVertexGraphFormatter.prototype.getOver = ItemGraphFormatter.prototype.getOver; +RoundedVertexGraphFormatter.prototype.getDragging = ItemGraphFormatter.prototype.getDragging; +RoundedVertexGraphFormatter.prototype.getId = ItemGraphFormatter.prototype.getId; +RoundedVertexGraphFormatter.prototype.toJSON = ItemGraphFormatter.prototype.toJSON; +RoundedVertexGraphFormatter.prototype.loadFromJSON = ItemGraphFormatter.prototype.loadFromJSON; +RoundedVertexGraphFormatter.prototype._setEvents = ItemGraphFormatter.prototype._setEvents; + +function RoundedVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ + VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); + this.args.type = "RoundedVertexGraphFormatter"; + if (defaultFormat != null){ + if (defaultFormat.radius != null){ + this.defaultFormat.args.radius = defaultFormat.radius; + } + } + + if (selectedFormat != null){ + if (selectedFormat.radius != null){ + this.selected.args.radius = selectedFormat.radius; + } + } + + if (overFormat != null){ + if (overFormat.radius != null){ + this.over.args.radius = overFormat.radius; + } + } + + if (draggingFormat != null){ + if (draggingFormat.radius != null){ + this.dragging.args.draggingFormat = draggingFormat.radius; + } + } +}; + + + +OctagonVertexGraphFormatter.prototype.getDefault = ItemGraphFormatter.prototype.getDefault; +OctagonVertexGraphFormatter.prototype.getSelected = ItemGraphFormatter.prototype.getSelected; +OctagonVertexGraphFormatter.prototype.getOver = ItemGraphFormatter.prototype.getOver; +OctagonVertexGraphFormatter.prototype.getDragging = ItemGraphFormatter.prototype.getDragging; +OctagonVertexGraphFormatter.prototype.getId = ItemGraphFormatter.prototype.getId; +OctagonVertexGraphFormatter.prototype.toJSON = ItemGraphFormatter.prototype.toJSON; +OctagonVertexGraphFormatter.prototype.loadFromJSON = ItemGraphFormatter.prototype.loadFromJSON; +OctagonVertexGraphFormatter.prototype._setEvents = ItemGraphFormatter.prototype._setEvents; + +function OctagonVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ + VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); + this.args.type = "OctagonVertexGraphFormatter"; + if (defaultFormat != null){ + if (defaultFormat.radius != null){ + this.defaultFormat.args.radius = defaultFormat.radius; + } + } + + if (selectedFormat != null){ + if (selectedFormat.radius != null){ + this.selected.args.radius = selectedFormat.radius; + } + } + + if (overFormat != null){ + if (overFormat.radius != null){ + this.over.args.radius = overFormat.radius; + } + } + + if (draggingFormat != null){ + if (draggingFormat.radius != null){ + this.dragging.args.draggingFormat = draggingFormat.radius; + } + } +}; + -GraphCanvas.prototype.setEdgeFill = function(edgeId, color) { - this.getFormatter().getEdgeById(edgeId).getDefault().setFill(color); + +var Colors = new function() +{ + this.hashColor = []; + this.getColorByScoreArrayValue = function (arrayScore) + { + var array = new Array(); + + for (var i = 0; i< arrayScore.length; i++) + { + + var color = this.getColorByScoreValue(arrayScore[i]) + array.push( color); + + } + return array; + }; + + this.getHexStringByScoreArrayValue = function (arrayScore) + { + var arrayColor = this.getColorByScoreArrayValue(arrayScore); + var arrayHex = new Array(); + for (var i = 0; i< arrayColor.length; i++) + { + arrayHex.push( arrayColor[i].HexString()); + } + return arrayHex; + }; + + this.getColorByScoreValue = function (score) + { + + var truncate = score.toString().substr(0,4); + if (this.hashColor[truncate]!=null) + { + return this.hashColor[truncate]; + } + + + if(isNaN(score)) { + return Colors.ColorFromRGB(0,0,0); + } + var value; + + var from, to; + if(score < 0.5) { + from = Colors.ColorFromRGB(0,0,255); + to = Colors.ColorFromRGB(255,255,255); + value = (score * 2); + } else { + from = Colors.ColorFromRGB(255,255,255); + to = Colors.ColorFromRGB(255,0,0); + value = (score * 2) - 1; + } + + var x = value; + var y = 1.0 - value; + var color = Colors.ColorFromRGB(y * from.Red() + x * to.Red(), y * from.Green() + x * to.Green(), y * from.Blue() + x * to.Blue()); + + this.hashColor[truncate] = color; + + return color; + }; + + this.ColorFromHSV = function(hue, sat, val) + { + var color = new Color(); + color.SetHSV(hue,sat,val); + return color; + }; + + this.ColorFromRGB = function(r, g, b) + { + var color = new Color(); + color.SetRGB(r,g,b); + return color; + }; + + this.ColorFromHex = function(hexStr) + { + var color = new Color(); + color.SetHexString(hexStr); + return color; + }; + + function Color() { + //Stored as values between 0 and 1 + var red = 0; + var green = 0; + var blue = 0; + + //Stored as values between 0 and 360 + var hue = 0; + + //Strored as values between 0 and 1 + var saturation = 0; + var value = 0; + + this.SetRGB = function(r, g, b) + { + red = r/255.0; + green = g/255.0; + blue = b/255.0; + calculateHSV(); + }; + + this.Red = function() { return Math.round(red*255); }; + + this.Green = function() { return Math.round(green*255); }; + + this.Blue = function() { return Math.round(blue*255); }; + + this.SetHSV = function(h, s, v) + { + hue = h; + saturation = s; + value = v; + calculateRGB(); + }; + + this.Hue = function() + { return hue; }; + + this.Saturation = function() + { return saturation; }; + + this.Value = function() + { return value; }; + + this.SetHexString = function(hexString) + { + if(hexString == null || typeof(hexString) != "string") + { + this.SetRGB(0,0,0); + return; + } + + if (hexString.substr(0, 1) == '#') + hexString = hexString.substr(1); + + if(hexString.length != 6) + { + this.SetRGB(0,0,0); + return; + } + + var r = parseInt(hexString.substr(0, 2), 16); + var g = parseInt(hexString.substr(2, 2), 16); + var b = parseInt(hexString.substr(4, 2), 16); + if (isNaN(r) || isNaN(g) || isNaN(b)) + { + this.SetRGB(0,0,0); + return; + } + + this.SetRGB(r,g,b); + }; + + this.HexString = function() + { + + var rStr = this.Red().toString(16); + if (rStr.length == 1) + rStr = '0' + rStr; + var gStr = this.Green().toString(16); + if (gStr.length == 1) + gStr = '0' + gStr; + var bStr = this.Blue().toString(16); + if (bStr.length == 1) + bStr = '0' + bStr; + return ('#' + rStr + gStr + bStr).toUpperCase(); + }; + + this.Complement = function() + { + var newHue = (hue >= 180) ? hue - 180 : hue + 180; + var newVal = (value * (saturation - 1) + 1); + var newSat = (value*saturation) / newVal; + var newColor = new Color(); + newColor.SetHSV(newHue, newSat, newVal); + return newColor; + } ; + + function calculateHSV() + { + var max = Math.max(Math.max(red, green), blue); + var min = Math.min(Math.min(red, green), blue); + + value = max; + + saturation = 0; + if(max != 0) + saturation = 1 - min/max; + + hue = 0; + if(min == max) + return; + + var delta = (max - min); + if (red == max) + hue = (green - blue) / delta; + else if (green == max) + hue = 2 + ((blue - red) / delta); + else + hue = 4 + ((red - green) / delta); + hue = hue * 60; + if(hue < 0) + hue += 360; + } + + function calculateRGB() + { + red = value; + green = value; + blue = value; + + if(value == 0 || saturation == 0) + return; + + var tHue = (hue / 60); + var i = Math.floor(tHue); + var f = tHue - i; + var p = value * (1 - saturation); + var q = value * (1 - saturation * f); + var t = value * (1 - saturation * (1 - f)); + switch(i) + { + case 0: + red = value; green = t; blue = p; + break; + case 1: + red = q; green = value; blue = p; + break; + case 2: + red = p; green = value; blue = t; + break; + case 3: + red = p; green = q; blue = value; + break; + case 4: + red = t; green = p; blue = value; + break; + default: + red = value; green = p; blue = q; + break; + } + } + } +} +(); +/* + * Clase gestiona la insercción, eliminación de los elementos en el DOM + * + * Vital hacerla SIEMPRE compatible hacia atrás + * + * Last update: 28-10-2010 + * + */ + + +var DOM = {}; + +DOM.createNewElement = function(type, nodeParent, attributes) +{ + + var node = document.createElement(type); + for (var i=0; i0) + { + parent.removeChild(parent.childNodes[0]); + + } +}; + +DOM.select = function(targetID) +{ + return document.getElementById(targetID); +// return $("#"+targetID); }; +var Geometry = +{ + + /** From tow points obtains the angles formed with the cartesian side **/ + getAngleBetweenTwoPoints : function(x1, y1, x2, y2){ + //var m = (y1 - y2)/ (x1 - x2); + return Math.atan2(y2-y1, x2-x1); + }, + + getAdjacentSideOfRectangleRight : function(angle, hypotenuse){ + return Math.abs(Math.cos(angle)*hypotenuse); + }, + + getOppositeSideOfRectangleRight : function(angle, hypotenuse){ + return Math.abs(Math.sin(angle)*hypotenuse); + }, + + toDegree: function(radian){ + return radian*180/Math.PI; + + } + + +}; -GraphCanvas.prototype.getEdgeFill = function(edgeId) { - return this.getFormatter().getEdgeById(edgeId).getDefault().getFill(); -}; +var SVG = +{ + svgns : 'http://www.w3.org/2000/svg', + xlinkns : "http://www.w3.org/1999/xlink", + + createSVGCanvas: function(parentNode, attributes) + { + + attributes.push( ['xmlns', SVG.svgns], ['xmlns:xlink', 'http://www.w3.org/1999/xlink']); + var svg = document.createElementNS("http://www.w3.org/2000/svg", "svg"); + this._setProperties(svg, attributes); + parentNode.appendChild( svg); + return svg; + + }, + + createRectangle : function (x, y, width, height, attributes){ + var rect = document.createElementNS(this.svgns, "rect"); + rect.setAttribute("x",x); + rect.setAttribute("y",y); + rect.setAttribute("width",width); + rect.setAttribute("height",height); + SVG._setProperties(rect, attributes); + return rect; + }, + + drawImage64 : function (x, y, width, height, base64, svgNode, attributes) { + var node = SVG.createImage64(x, y, width, height, base64, attributes); + svgNode.appendChild(node); + return node; + }, + + createImage64 : function (x, y, width, height, base64, attributes) { + var img = document.createElementNS(this.svgns, "image"); + img.setAttribute("x",x); + img.setAttribute("y",y); + img.setAttribute("width",width); + img.setAttribute("height",height); + img.setAttribute("xlink:href",base64); + SVG._setProperties(img, attributes); + return img; + }, + + createLine: function (x1, y1, x2, y2, attributes){ + var line = document.createElementNS(this.svgns,"line"); + line.setAttribute("x1",x1); + line.setAttribute("y1",y1); + line.setAttribute("x2", x2); + line.setAttribute("y2", y2); + SVG._setProperties(line, attributes); + return line; + }, + + createClip: function (id, nodeToClip, attributes){ + var clip = document.createElementNS(this.svgns,"clipPath"); + clip.setAttribute("id",id); + clip.appendChild(nodeToClip); + return clip; + }, + + drawClip : function (id, nodeToClip, svgNode) { + var node = SVG.createClip(id, nodeToClip); + svgNode.appendChild(node); + return node; + }, + + drawRectangle : function (cx, cy, width, height, svgNode, attributes) { + try{ + var node = SVG.createRectangle(cx, cy, width, height, attributes); + svgNode.appendChild(node); + } + catch(e){ + + console.log("-------------------- "); + console.log("Error on drawRectangle " + e); + console.log(attributes); + console.log("-------------------- "); + } + return node; + }, + + createEllipse : function (x, y, rx, ry, attributes){ + var rect = document.createElementNS(this.svgns, "ellipse"); + rect.setAttribute("cx",x); + rect.setAttribute("cy",y); + rect.setAttribute("rx",rx); + rect.setAttribute("ry",ry); + SVG._setProperties(rect, attributes); + return rect; + }, + + drawEllipse : function (cx, cy, rx, ry, svgNode, attributes) { + var node = SVG.createEllipse(cx, cy, rx, ry, attributes); + svgNode.appendChild(node); + return node; + }, + + drawImage : function (x, y, canvasSVG, attributes) { + var image = document.createElementNS(this.svgns, "image"); + image.setAttribute("x",x); + image.setAttribute("y",y); + canvasSVG.appendChild(image); + SVG._setProperties(image, attributes); + }, + + drawLine : function (x1, y1, x2, y2, nodeSVG, attributes) { + try{ + var line = SVG.createLine(x1, y1, x2, y2, attributes); + nodeSVG.appendChild(line); + }catch(e){ + } + return line; + }, + + + drawPath: function (d, nodeSVG, attributes) { + var path = SVG.createPath(d, attributes); + nodeSVG.appendChild(path); + return path; + }, + + createPoligon : function (points, attributes){ + var poligon = document.createElementNS(this.svgns, "polygon"); + poligon.setAttribute("points",points); + SVG._setProperties(poligon, attributes); + return poligon; + }, + + drawPoligon : function (points, canvasSVG, attributes){ + var poligon = SVG.createPoligon(points, attributes); + canvasSVG.appendChild(poligon); + return poligon; + }, + // + + createPath : function (d, attributes){ + var path = document.createElementNS(this.svgns, "path"); + path.setAttribute("d",d); + SVG._setProperties(path, attributes); + return path; + }, + + drawCircle : function (x, y, radio, canvasSVG, attributes) { + + var newText = document.createElementNS(this.svgns,"circle"); + newText.setAttribute("cx",x); + newText.setAttribute("cy",y); + newText.setAttribute("r",radio); + + canvasSVG.appendChild(newText); + attributes["cursor"] = "pointer"; + this._setProperties(newText, attributes); + return newText; + }, + + + _setProperties: function(node, attributes) + { + if (attributes instanceof Array){ + for (var i=0; i< attributes.length; i++) + { + node.setAttribute(attributes[i][0], attributes[i][1]); + } + } + else{ + for ( var key in attributes){ + node.setAttribute(key, attributes[key]); + } + } + }, + +/* drawPath: function(pointsArray, canvasSVG, attributes){ + var path = document.createElementNS(this.svgns,"polyline"); + path.setAttribute ('id', id); + + var d= pointsArray[0].x+ " "+ pointsArray[0].y; + for (var i=1; i< pointsArray.length; i++) + { + d=d+" "+pointsArray[i].x+" "+pointsArray[i].y; + } + path.setAttribute ('points', d); + canvasSVG.appendChild(path); + },*/ + + createText : function (x, y, text, attributes) { + var node = document.createElementNS(this.svgns,"text"); + node.setAttributeNS(null , "x",x); + node.setAttributeNS(null, "y",y); + + var textNode = document.createTextNode(text); + node.appendChild(textNode); + + this._setProperties(node, attributes); + return node; + }, + + drawText : function (x, y, text, canvasSVG, attributes) { + var text = SVG.createText(x, y, text, attributes); + canvasSVG.appendChild(text); + return text; + }, + + + + drawGroup: function(svgNode, attributes) + { + var group = SVG.createGroup(attributes); + svgNode.appendChild(group); + return group; + }, + + createGroup: function(attributes){ + var group = document.createElementNS(this.svgns,"g"); + this._setProperties(group, attributes); + return group; + } + +}; + + + +var CanvasToSVG = { + + convert: function(sourceCanvas, targetSVG, x, y, id, attributes) { + + var img = this._convert(sourceCanvas, targetSVG, x, y, id); + + for (var i=0; i< attributes.length; i++) + { + img.setAttribute(attributes[i][0], attributes[i][1]); + } + }, + + _convert: function(sourceCanvas, targetSVG, x, y, id) { + var svgNS = "http://www.w3.org/2000/svg"; + var xlinkNS = "http://www.w3.org/1999/xlink"; + // get base64 encoded png from Canvas + var image = sourceCanvas.toDataURL(); + + // must be careful with the namespaces + var svgimg = document.createElementNS(svgNS, "image"); + + svgimg.setAttribute('id', id); + + //svgimg.setAttribute('class', class); + //svgimg.setAttribute('xlink:href', image); + svgimg.setAttributeNS(xlinkNS, 'xlink:href', image); + + + + + svgimg.setAttribute('x', x ? x : 0); + svgimg.setAttribute('y', y ? y : 0); + svgimg.setAttribute('width', sourceCanvas.width); + svgimg.setAttribute('height', sourceCanvas.height); + //svgimg.setAttribute('cursor', 'pointer'); + svgimg.imageData = image; + + targetSVG.appendChild(svgimg); + return svgimg; + }, + + importSVG: function(sourceSVG, targetCanvas) { + svg_xml = sourceSVG;//(new XMLSerializer()).serializeToString(sourceSVG); + var ctx = targetCanvas.getContext('2d'); + + var img = new Image(); + img.src = "data:image/svg+xml;base64," + btoa(svg_xml); +// img.onload = function() { + ctx.drawImage(img, 0, 0); +// }; + } + +}; +/* +Graph.prototype.importSVG = function(sourceSVG, targetCanvas) { + sourceSVG = this._svg; + targetCanvas = document.createElementNS('canvas'); + // https://developer.mozilla.org/en/XMLSerializer + svg_xml = (new XMLSerializer()).serializeToString(sourceSVG); + var ctx = targetCanvas.getContext('2d'); + // this is just a JavaScript (HTML) image + var img = new Image(); + // http://en.wikipedia.org/wiki/SVG#Native_support + // https://developer.mozilla.org/en/DOM/window.btoa + img.src = "data:image/svg+xml;base64," + btoa(svg_xml); + img.onload = function() { + // after this, Canvas’ origin-clean is DIRTY + ctx.drawImage(img, 0, 0); + } +}; +*/ -/** API LAYOUT **/ -GraphCanvas.prototype.setCoordinates = function(vertexId, x, y) { - return this.getLayout().getEdgeById(vertexId).setCoordinates(x, y); -}; +/* + +Normalizacion de datos para dibujar colores +Issues: + No sé como debería llamarse esta libreria + No sé si ya existe una funciçon en javascript que lo haga + + +*/ + + +var Normalizer = new function() +{ + this.normalizeArray = function (arrayData) + { + + return this.standardizeArray(this.normal(arrayData)); + +// var result = this._getMaxAndMin(arrayData); +// var min =result[0]; +// var max = result[1]; +// +// +// //los hacemos todos positivos +// for (var i = 0; i< arrayData.length; i++) +// { +// arrayData[i]= Math.abs(min) + parseFloat(arrayData[i]); +// } +// +// var result = this._getMaxAndMin(arrayData); +// var min =result[0]; +// var max = result[1]; +// +// +// var resultArray = new Array(); +// for (var i = 0; i< arrayData.length; i++) +// { +// resultArray.push(arrayData[i]*1/max); +// } +// return resultArray; + }; + + this.normal = function(arrayData){ + var mean = this._getMean(arrayData); + var deviation = this._getStdDeviation(arrayData); + var result = this._getMaxAndMin(arrayData); + var min = result[0]; + var max = result[1]; + + var resultArray = new Array(); + for (var i = 0; i< arrayData.length; i++) { + if (deviation!=0){ + resultArray.push((arrayData[i]-mean)/deviation); + }else{ + resultArray.push(arrayData[i]); + } + } + return resultArray; + }; + + this.standardizeArray = function(arrayData) + { + var result = this._getMaxAndMin(arrayData); + var min = result[0]; + var max = result[1]; + + var offset = ( min <= 0 ) ? Math.abs(min) : (-1 * min); + var resultArray = new Array(); + for (var i = 0; i< arrayData.length; i++) { + if(max + offset!=0){ + resultArray.push((arrayData[i] + offset) / (max + offset)); + }else{ + resultArray.push(arrayData[i]+offset); + } + } + return resultArray; + }; + + + this._getMean = function(arrayData) { + var sum = 0; + for (var i = 0; i< arrayData.length; i++) { + sum = sum + parseFloat(arrayData[i]); + } + return sum/arrayData.length; + }; + + this._getStdDeviation = function(arrayData) { + var mean = this._getMean(arrayData); + var acum = 0.0; + for(var i=0; i max) max = parseFloat(arrayData[i]); + } + + return [min, max]; + }; +}; +function GraphCanvas(componentID, targetNode, args) { + this.args = {}; + /** target */ + this.targetID = targetNode.id; + + /** id manage */ + this.id = componentID; + this.args.idGraph = this.id + "main"; + this.args.idBackgroundNode = this.id + "background"; + + this.args.idEdgesGraph = this.id + "edges"; + this.args.idNodesGraph = this.id + "vertices"; + this.args.idLabelGraph = this.id + "label"; + this.args.idBackground = this.id + "background"; + + /** Objects Graph **/ + this.dataset = null; + this.formatter = null; + this.layout = null; + + /** Drawing **/ + this.circleDefaultRadius = 2; + this.squareDefaultSide = this.circleDefaultRadius * 1.5; + + /** Directed Arrow **/ + this.arrowDefaultSize = this.circleDefaultRadius; + + /** Groups **/ + this.GraphGroup = null; + this.GraphNodeGroup = null; + this.GraphLabelGroup = null; + this.GraphBackground = null; + + /** SETTINGS FLAGS **/ + this.args.draggingCanvasEnabled = false; //Flag to set if the canvas can be dragged + this.args.multipleSelectionEnabled = false; + this.args.interactive = false; + this.args.labeled = false; + this.args.linkEnabled = false; + + /** If numberEdge > maxNumberEdgesMoving then only it will move edges when mouse up **/ + this.args.maxNumberEdgesMoving = 3; + this.args.maxNumberEdgesFiringEvents = 50; + + /** Linking edges **/ + this.args.linking = false; + this.linkStartX = 0; + this.linkStartY = 0; + this.linkSVGNode = null; + this.linkNodeSource = null; + this.linkNodeTarget = null; + + /** Dragging Control **/ + this.draggingElement = null; + this.dragging = false; + this.nMouseOffsetX = 0; + this.nMouseOffsetY = 0; + this.dragStartX = 0; + this.dragStartY = 0; + this.desplazamientoX = 0; + this.desplazamientoY = 0; + + /** Selection Control **/ + this.selecting = false; + this.selectorX = null; + this.selectorY = null; + this.selectorSVGNode = null; + + /** Node status **/ + this.args.isVertexSelected = {}; + this.args.selectedVertices = []; + + /** Edges status **/ + this.args.isEdgeSelected = {}; + //this.args.selectedEdges = []; + + if (args != null) { + if (args.multipleSelectionEnabled != null) { + this.args.multipleSelectionEnabled = args.multipleSelectionEnabled; + this.args.draggingCanvasEnabled = !(this.args.multipleSelectionEnabled); + } + if (args.draggingCanvasEnabled != null) { + this.args.draggingCanvasEnabled = args.draggingCanvasEnabled; + this.args.multipleSelectionEnabled = !(this.args.draggingCanvasEnabled); + } + if (args.interactive != null) { + this.args.interactive = args.interactive; + } + if (args.labeled != null) { + this.args.labeled = args.labeled; + } + + } + + /** Hashmap with the svg node labels **/ + this.svgLabels = {}; + + /** EVENTS **/ + this.onVertexOut = new Event(this); + this.onVertexOver = new Event(this); + this.onVertexSelect = new Event(this); + this.onEdgeSelect = new Event(this); + this.onCanvasClicked = new Event(this); + this.onVertexUp = new Event(this); +} + +GraphCanvas.prototype.showLabels = function(value) { + this.args.labeled = value; + this.removeLabels(); + if (value) { + this.renderLabels(); + } +}; + +GraphCanvas.prototype.getSelectedVertices = function() { + return this.args.selectedVertices; +}; + +GraphCanvas.prototype.getSelectedEdges = function() { + var selected = []; + for ( var selectedEdge in this.args.isEdgeSelected) { + selected.push(selectedEdge); + } + return selected; +}; + +GraphCanvas.prototype.createSVGDom = function(targetID, id, width, height, backgroundColor) { + var container = document.getElementById(targetID); + this._svg = SVG.createSVGCanvas(container, [ + [ "style", "background-color:" + backgroundColor + ";" ], [ "id", id ], [ "dragx", 0 ], [ "dragy", 0 ], + [ "height", this.getFormatter().getHeight() ], [ "width", this.getFormatter().getWidth() ] ]); + return this._svg; +}; + +/** MULTIPLE SELECTION **/ +GraphCanvas.prototype.isMultipleSelectionEnabled = function() { + return this.args.multipleSelectionEnabled; +}; + +GraphCanvas.prototype.setMultipleSelection = function(value) { + this.args.multipleSelectionEnabled = value; + this.args.draggingCanvasEnabled = (!value); +}; + +GraphCanvas.prototype.setSelecting = function(value) { + this.selecting = value; +}; + +/** linking **/ +GraphCanvas.prototype.setLinking = function(value) { + this.args.linkEnabled = value; + this.selecting = !value; + this.dragging = !value; +}; + +/** CANVAS MOVING **/ +GraphCanvas.prototype.setDraggingCanvas = function(value) { + this.args.draggingCanvasEnabled = value; + this.args.multipleSelectionEnabled = !value; +}; + +GraphCanvas.prototype.isDraggingCanvasEnabled = function() { + return this.args.draggingCanvasEnabled; +}; +/** ZOOM **/ +GraphCanvas.prototype.getScale = function() { + return this.getFormatter().getZoomScale(); +}; + +GraphCanvas.prototype.setScale = function(scale) { + var graphNode = document.getElementById(this.args.idGraph); + graphNode.setAttribute("transform", graphNode.getAttribute("transform").replace("scale(" + this.getScale() + ")", "scale(" + scale + ")")); + this.getFormatter().setZoomScale(scale); +}; + +GraphCanvas.prototype.zoomIn = function() { + this.setScale(this.getScale() + this.getFormatter().getZoomScaleStepFactor()); +}; + +GraphCanvas.prototype.zoomOut = function() { + this.setScale(this.getScale() - this.getFormatter().getZoomScaleStepFactor()); + +}; + +/** SVG COORDENATES **/ +GraphCanvas.prototype.getSVGCoordenates = function(evt) { + var p = this._svg.createSVGPoint(); + p.x = evt.clientX; + p.y = evt.clientY; + + var m = this._svg.getScreenCTM(document.documentElement); + p = p.matrixTransform(m.inverse()); + return p; +}; + +/** SVG EVENTS **/ +GraphCanvas.prototype.mouseClick = function(event) { + if (event.button == 0) { + if (!this.args.interactive) { + return; + } + + if (this.isVertex(event.target)) { + this.clickNode(this.getVertexIdFromSVGId(event.target.id)); + } + /** Como el evento mouseClick viene despues del mouse up es aqui donde manejo el tema de deseccionar los elementos que estoy dragging **/ + if (this.dragging) { + this.dragging = false; + } + } +}; + +GraphCanvas.prototype.mouseMove = function(evt) { + if (this.selecting) { + this.clearLabels(); + + var width = (this.getSVGCoordenates(evt).x - this.selectorX); + var height = (this.getSVGCoordenates(evt).y - this.selectorY); + if ((width > 0) && (height > 0)) { + this.displaySelection(this.selectorX, this.selectorY, width, height); + } + if ((width > 0) && (height < 0)) { + this.displaySelection(this.selectorX, this.getSVGCoordenates(evt).y, width, Math.abs(height)); + } + if ((width < 0) && (height < 0)) { + this.displaySelection(this.getSVGCoordenates(evt).x, this.getSVGCoordenates(evt).y, Math.abs(width), Math.abs(height)); + } + if ((width < 0) && (height > 0)) { + this.displaySelection(this.selectorX + width, this.selectorY, Math.abs(width), Math.abs(height)); + } + + var x1 = (parseFloat(this.selectorSVGNode.getAttribute("x")) - DOM.select(this.id).getAttribute("dragx")) / this.getFormatter().getWidth(); + var y1 = (parseFloat(this.selectorSVGNode.getAttribute("y")) - DOM.select(this.id).getAttribute("dragy")) / this.getFormatter().getHeight(); + var x2 = (x1 + parseFloat(this.selectorSVGNode.getAttribute("width") / this.getFormatter().getWidth())); + var y2 = (y1 + parseFloat(this.selectorSVGNode.getAttribute("height") / this.getFormatter().getHeight())); + + this.deselectNodes(this.getLayout()); + var verticesSelected = this.getLayout().getVerticesByArea(x1 / this.getFormatter().getZoomScale(), y1 / this.getFormatter().getZoomScale(), + x2 / this.getFormatter().getZoomScale(), y2 / this.getFormatter().getZoomScale()); + for ( var i = 0; i < verticesSelected.length; i++) { + this.selectNode(verticesSelected[i].getId()); + this.renderLabel(verticesSelected[i].getId()); + } + + } + var p = null; + if (this.args.linking) { + p = this.getSVGCoordenates(evt); + if (this.linkSVGNode != null) { + this.linkSVGNode.setAttribute("x2", p.x - 2); + this.linkSVGNode.setAttribute("y2", p.y - 2); + } + } + + if (this.dragging) { + p = this.getSVGCoordenates(evt); + p.x -= this.nMouseOffsetX; + p.y -= this.nMouseOffsetY; + this.desplazamientoX = (this.getSVGCoordenates(evt).x - this.dragStartX);// + parseFloat(DOM.select(this.id).getAttribute("dragx")); + this.desplazamientoY = (this.getSVGCoordenates(evt).y - this.dragStartY);// + parseFloat(DOM.select(this.id).getAttribute("dragy")); + + if (this.draggingElement != null) { + /** Click sobre el recct del banground que provoca que mueva todo el canvas **/ + if (this.isNodeCanvas(this.draggingElement)) { + + p = this.getSVGCoordenates(evt); + p.x = this.desplazamientoX; + p.y = this.desplazamientoY; + + this.draggingElement.setAttribute("dragx", p.x); + this.draggingElement.setAttribute("dragy", p.y); + this.draggingElement = document.getElementById(this.args.idGraph); + this.draggingElement.setAttribute("transform", "translate(" + p.x + "," + p.y + "), scale(" + this.getScale() + ")"); + + DOM.select(this.id).setAttribute("dragx", p.x); + DOM.select(this.id).setAttribute("dragy", p.y); + + if (this.NodeSVGbackgroundImage != null) { + this.NodeSVGbackgroundImage.setAttribute("dragx", p.x); + this.NodeSVGbackgroundImage.setAttribute("dragy", p.y); + } + } else { + if (this.isVertex(this.draggingElement)) { + this.selectNode(this.getVertexIdFromSVGId(this.draggingElement.id)); + this.desplazamientoX = this.desplazamientoX / this.getFormatter().getZoomScale(); + this.desplazamientoY = this.desplazamientoY / this.getFormatter().getZoomScale(); + this.moveSelectedNodes(this.desplazamientoX, this.desplazamientoY); + + this.dragStartX = this.getSVGCoordenates(evt).x; + this.dragStartY = this.getSVGCoordenates(evt).y; + } else { + if (this.isNodeBackground(this.draggingElement)) { + + this.draggingElement.setAttribute("dragx", p.x); + this.draggingElement.setAttribute("dragy", p.y); + this.draggingElement = document.getElementById(this.args.idGraph); + this.draggingElement.setAttribute("transform", "translate(" + p.x + "," + p.y + "), scale(" + this.getScale() + ")"); + } else { + this.draggingElement.setAttribute("transform", "translate(" + p.x + "," + p.y + ")"); + } + } + } + } + } +}; + +GraphCanvas.prototype.moveSelectedNodes = function(offsetX, offsetY) { + for ( var i = 0; i < this.getSelectedVertices().length; i++) { + + var nodeId = this.getSelectedVertices()[i]; + var svgNodeId = this.getSVGNodeId(nodeId); + + var x = parseFloat(DOM.select(svgNodeId).getAttribute("dragx")) + parseFloat(offsetX);// - parseFloat(DOM.select(this.id).getAttribute("dragx")); + var y = parseFloat(DOM.select(svgNodeId).getAttribute("dragy")) + parseFloat(offsetY);// + parseFloat(DOM.select(this.id).getAttribute("dragy")); + + this._movingNode(DOM.select(svgNodeId), x, y); + } +}; + +GraphCanvas.prototype.mouseDown = function(evt) { + if (event.button == 0) { + + /** if !no interactive mouse events do anything **/ + if (!this.args.interactive) { + return; + } + + var p = this.getSVGCoordenates(evt); + + /** When click on canvas or background deselect all **/ + if (this.isNodeCanvas(evt.target) || this.isNodeBackground(evt.target)) { + this.deselectNodes(); + this.deselectEdges(); + this.onCanvasClicked.notify(); + } + + /** if I am linking vertices **/ + if (this.args.linkEnabled) { + + if (!this.args.linking) { + this.args.linking = true; + if (this.isVertex(evt.target)) { + this.linkStartX = p.x; + this.linkStartY = p.y; + this.linkSVGNode = SVG.drawLine(p.x, p.y, p.x, p.y, this._svg, { + "stroke" : "#FF0000" + }); + this.linkNodeSource = this.getVertexIdFromSVGId(evt.target.id); + } + } else { + this.linkNodeTarget = this.getVertexIdFromSVGId(evt.target.id); + this.args.linking = false; + this.args.linkEnabled = false; + if (this.isVertex(evt.target)) { + this.getDataset().addEdge(this.linkNodeSource + "_" + this.linkNodeTarget, this.linkNodeSource, this.linkNodeTarget, {}); + } + this.linkSVGNode.parentNode.removeChild(this.linkSVGNode); + } + return; + } + + /** Id is a vertex or the canvas **/ + if (this.isVertex(evt.target) || this.isNodeCanvas(evt.target) || this.isNodeBackground(evt.target)) { + this._startDragging(evt); + } + /** if i is edge **/ + if (this.isEdge(evt.target)) { + this.selectEdge(this.getEdgeIdFromSVGId(evt.target.getAttribute("id"))); + } + + if (this.args.multipleSelectionEnabled) { + if (!this.dragging) { + this.setSelecting(true); + this.selectorX = p.x; + this.selectorY = p.y; + this.displaySelection(p.x, p.y, 1, 1); + } + } + + } + if (event.button == 1) { + this.setLinking(false); + this.setMultipleSelection(false); + this.selecting = false; + + /** Id is a vertex or the canvas **/ + if (this.isVertex(evt.target) || this.isNodeCanvas(evt.target) || this.isNodeBackground(evt.target)) { + this._startDragging(evt); + } + } +}; + +GraphCanvas.prototype.mouseUp = function(event) { + if (!this.args.interactive) { + return; + } + + if (this.dragging) { + this._stopDragging(event); + if (this.isVertex(event.target)) { + var vertexId = this.getVertexIdFromSVGId(event.target.id); + if (this.getDataset().getVertexById(vertexId).getEdges().length >= this.args.maxNumberEdgesMoving) { + this.moveEdge(vertexId); + } + } + } + + if (this.selecting) { + this.setSelecting(false); + + var x1 = (parseFloat(this.selectorSVGNode.getAttribute("x")) - DOM.select(this.id).getAttribute("dragx")) / this.getFormatter().getWidth(); + var y1 = (parseFloat(this.selectorSVGNode.getAttribute("y")) - DOM.select(this.id).getAttribute("dragy")) / this.getFormatter().getHeight(); + var x2 = (x1 + parseFloat(this.selectorSVGNode.getAttribute("width") / this.formatter.getWidth())); + var y2 = (y1 + parseFloat(this.selectorSVGNode.getAttribute("height") / this.formatter.getHeight())); + + var verticesSelected = this.getLayout().getVerticesByArea(x1 / this.getFormatter().getZoomScale, y1 / this.getFormatter().getZoomScale, + x2 / this.getFormatter().getZoomScale, y2 / this.getFormatter().getZoomScale); + + for ( var i = 0; i < verticesSelected.length; i++) { + this.selectNode(verticesSelected[i].getId()); + } + + if (this.selectorSVGNode != null) { + this._svg.removeChild(this.selectorSVGNode); + } + + if (this.args.labeled) { + this.clearLabels(); + this.renderLabels(); + } + + this.selectorSVGNode = null; + // this.renderLabels(); + } +}; + +/** SELECTION **/ +GraphCanvas.prototype.displaySelection = function(x, y, width, height) { + if (this.selectorSVGNode != null) { + this.selectorSVGNode.setAttribute("x", x); + this.selectorSVGNode.setAttribute("y", y); + this.selectorSVGNode.setAttribute("width", width); + this.selectorSVGNode.setAttribute("height", height); + } else { + this.selectorSVGNode = SVG.drawRectangle(x, y, width, height, this._svg, { + "fill" : "red", + "stroke" : "black", + "opacity" : "0.2", + "stroke-opacity" : "1" + }); + } +}; + +/** DRAGGING **/ +GraphCanvas.prototype._startDragging = function(evt) { + if (!this.isDraggingCanvasEnabled()) { + if (this.isNodeCanvas(evt.target)) { + this.draggingElement = null; + } + } + + if (this.isVertex(evt.target) || (this.isNodeBackground(evt.target) && (this.isDraggingCanvasEnabled()))|| (this.isNodeCanvas(evt.target) && (this.isDraggingCanvasEnabled()))) { + this.clearLabels(); + this.draggingElement = evt.target; + this.dragging = true; + var p = this.getSVGCoordenates(evt); + + this.nMouseOffsetX = p.x - parseInt(evt.target.getAttribute("dragx")); + this.nMouseOffsetY = p.y - parseInt(evt.target.getAttribute("dragy")); + + if (this.isVertex(evt.target)) { + this.dragStartX = parseInt(this.draggingElement.getAttribute("dragx")) * this.getFormatter().getZoomScale() + + parseFloat(DOM.select(this.id).getAttribute("dragx")); + this.dragStartY = parseInt(this.draggingElement.getAttribute("dragy")) * this.getFormatter().getZoomScale() + + parseFloat(DOM.select(this.id).getAttribute("dragy")); + } else { + this.dragStartX = p.x - parseInt(this.draggingElement.getAttribute("dragx"));// + parseFloat(DOM.select(this.id).getAttribute("dragx")); + this.dragStartY = p.y - parseInt(this.draggingElement.getAttribute("dragy"));// + parseFloat(DOM.select(this.id).getAttribute("dragy")); + } + } +}; + +GraphCanvas.prototype._stopDragging = function(event) { + this.nMouseOffsetX = 0; + this.nMouseOffsetX = 0; + /** despues del evento up viene el evento click entonces acabo el dragging en el mouseclick **/ + this.dragging = false; + this.draggingElement = null; + this.renderLabels(); + + this.setLinking(false); + this.setMultipleSelection(true); + this.selecting = false; + +}; + +/** Move the edges of the vertex with the vertexId indicado **/ +GraphCanvas.prototype.moveEdge = function(vertexId) { + var x = this.getLayout().getNodeById(vertexId).x * this.getFormatter().getWidth(); + var y = this.getLayout().getNodeById(vertexId).y * this.getFormatter().getHeight(); + + /** Moving edges out **/ + for ( var i = 0; i < this.getDataset().getVertexById(vertexId).getEdgesOut().length; i++) { + var edgeId = this.getDataset().getVertexById(vertexId).getEdgesOut()[i].getId(); + var svgEdgeId = this.getSVGEdgeId(edgeId); + var edgeFormatter = this.getFormatter().getEdgeById(edgeId); + if (edgeFormatter instanceof LineEdgeGraphFormatter) { + DOM.select(svgEdgeId + "_shadow").setAttribute("x2", x); + DOM.select(svgEdgeId + "_shadow").setAttribute("y2", y); + DOM.select(svgEdgeId).setAttribute("x2", x); + DOM.select(svgEdgeId).setAttribute("y2", y); + } + + if ((edgeFormatter instanceof DirectedLineEdgeGraphFormatter) || (edgeFormatter instanceof OdirectedLineEdgeGraphFormatter) + || (edgeFormatter instanceof OdotDirectedLineEdgeGraphFormatter) || (edgeFormatter instanceof DotDirectedLineEdgeGraphFormatter) + || (edgeFormatter instanceof CutDirectedLineEdgeGraphFormatter)) { + this.removeEdge(edgeId); + this.renderEdge(edgeId); + } + } + + /** Moving edges in **/ + for ( var i = 0; i < this.getDataset().getVertexById(vertexId).getEdgesIn().length; i++) { + var edgeId = this.getDataset().getVertexById(vertexId).getEdgesIn()[i].getId(); + var svgEdgeId = this.getSVGEdgeId(edgeId); + var edgeFormatter = this.getFormatter().getEdgeById(edgeId); + if (edgeFormatter instanceof LineEdgeGraphFormatter) { + DOM.select(svgEdgeId).setAttribute("x1", x); + DOM.select(svgEdgeId).setAttribute("y1", y); + DOM.select(svgEdgeId + "_shadow").setAttribute("x1", x); + DOM.select(svgEdgeId + "_shadow").setAttribute("y1", y); + } + + if ((edgeFormatter instanceof DirectedLineEdgeGraphFormatter) || (edgeFormatter instanceof OdirectedLineEdgeGraphFormatter) + || (edgeFormatter instanceof OdotDirectedLineEdgeGraphFormatter) || (edgeFormatter instanceof DotDirectedLineEdgeGraphFormatter) + || (edgeFormatter instanceof CutDirectedLineEdgeGraphFormatter)) { + this.removeEdge(edgeId); + this.renderEdge(edgeId); + } + + if (edgeFormatter instanceof BezierEdgeGraphFormatter) { + var radius = this.getFormatter().getVertexById(vertexId).getDefault().getSize() * this.getFormatter().getNodesMaxSize(); + var d = this.calculateCoordenatesBezier(radius, x, y); + DOM.select(svgEdgeId).setAttribute("d", d); + } + } +}; + +GraphCanvas.prototype.moveNode = function(vertexId) { + var x = this.getLayout().getNodeById(vertexId).x * this.getFormatter().getWidth(); + var y = this.getLayout().getNodeById(vertexId).y * this.getFormatter().getHeight(); + var svgNodeElement = DOM.select(this.getSVGNodeId(vertexId)); + + svgNodeElement.setAttribute("dragx", x); + svgNodeElement.setAttribute("dragy", y); + svgNodeElement.setAttribute("transform", "translate(" + x + "," + y + ")"); + + if (this.getDataset().getVertexById(vertexId).getEdges().length < this.args.maxNumberEdgesMoving) { + this.moveEdge(vertexId); + } +}; + +GraphCanvas.prototype._movingNode = function(svgNodeElement, x, y) { + var vertexId = this.getVertexIdFromSVGId(svgNodeElement.getAttribute("id")); + this.getLayout().getNodeById(vertexId).setCoordinates(x / this.getFormatter().getWidth(), y / this.getFormatter().getHeight()); + this.desplazamientoX = 0; + this.desplazamientoY = 0; + this.removeLabel(vertexId); + this.renderLabel(vertexId); +}; + +/** INIT **/ +GraphCanvas.prototype.init = function() { + + this._svg = this.createSVGDom(this.targetID, this.id, this.getFormatter().getWidth(), this.getFormatter().getHeight(), this.getFormatter() + .getBackgroundColor()); + this.GraphGroup = SVG.drawGroup(this._svg, [ [ "id", this.args.idGraph ], [ "transform", "translate(0,0), scale(1)" ] ]); + this.GraphBackground = SVG.drawGroup(this.GraphGroup, [ [ "id", this.args.idBackground ] ]); + this.GraphEdgeGroup = SVG.drawGroup(this.GraphGroup, [ [ "id", this.args.idEdgesGraph ] ]); + this.GraphNodeGroup = SVG.drawGroup(this.GraphGroup, [ [ "id", this.args.idNodesGraph ] ]); + this.GraphLabelGroup = SVG.drawGroup(this.GraphGroup, [ [ "id", this.args.idLabelGraph ] ]); + + if ((this.getFormatter().getBackgroundImage() != null) && (this.getFormatter().getBackgroundImage() != "")) { + this.setBackgroundImage(this.getFormatter().getBackgroundImage()); + } + /** SVG Events listener */ + var _this = this; + this._svg.addEventListener("click", function(event) { + _this.mouseClick(event); + }, false); + this._svg.addEventListener("mousemove", function(event) { + _this.mouseMove(event, _this); + }, false); + this._svg.addEventListener("mousedown", function(event) { + _this.mouseDown(event, _this); + }, false); + this._svg.addEventListener("mouseup", function(event) { + _this.mouseUp(event, _this); + }, false); +}; + +/* + GraphCanvas.prototype.backgroungToSVG = function(){ + var _this = this; + var canvas = document.createElement('canvas'); + canvas.setAttribute("id", "canvas"); + canvas.width = this.formatter.getWidth(); + canvas.height = this.formatter.getHeight(); + + this._svg.parentNode.parentNode.appendChild(canvas); + var ctx = document.getElementById('canvas').getContext('2d'); + var img = new Image(); + + img.src = this.formatter.getBackgroundImage(); + ctx.drawImage(img,0,0 ,_this.formatter.getWidth(), _this.formatter.getHeight()); + + + img.onload = function() { + canvas.parentNode.removeChild(canvas); + } + + this.NodeSVGbackgroundImage.setAttribute("xlink:href", document.getElementById("canvas").toDataURL()); + this.NodeSVGbackgroundImage.removeAttribute("href"); + + // + + };*/ + +GraphCanvas.prototype.setBackgroundImage = function() { + if (this.NodeSVGbackgroundImage != null) { + this.NodeSVGbackgroundImage.parentNode.removeChild(this.NodeSVGbackgroundImage); + } + $('#' + this.targetID).svg(); + $('#' + this.targetID).svg("get"); + + $('#' + this.targetID).svg("get")._svg = document.getElementById(this.id); + + var svg = $('#' + this.targetID).svg("get"); + this.NodeSVGbackgroundImage = svg.image(0, 0, this.getFormatter().getWidth(), this.getFormatter().getHeight(), this.getFormatter() + .getBackgroundImage()); + this.NodeSVGbackgroundImage.setAttribute("id", this.args.idBackgroundNode); + + this.NodeSVGbackgroundImage.setAttribute("x", 0); + this.NodeSVGbackgroundImage.setAttribute("y", 0); + + this.NodeSVGbackgroundImage.setAttribute("dragx", 0); + this.NodeSVGbackgroundImage.setAttribute("dragy", 0); + + if (this.getFormatter().args.backgroundImageHeight != null) { + this.NodeSVGbackgroundImage.setAttribute("height", this.getFormatter().args.backgroundImageHeight); + } + if (this.getFormatter().args.backgroundImageWidth != null) { + this.NodeSVGbackgroundImage.setAttribute("width", this.getFormatter().args.backgroundImageWidth); + } + + if (this.getFormatter().args.backgroundImageX != null) { + this.NodeSVGbackgroundImage.setAttribute("x", this.getFormatter().args.backgroundImageX); + } + if (this.getFormatter().args.backgroundImageY != null) { + this.NodeSVGbackgroundImage.setAttribute("y", this.getFormatter().args.backgroundImageY); + } + + this.GraphBackground.appendChild(this.NodeSVGbackgroundImage); + this.NodeSVGbackgroundImage.removeAttribute("href"); + this.NodeSVGbackgroundImage.setAttribute("xlink:href", this.getFormatter().getBackgroundImage()); +}; + +GraphCanvas.prototype.removeBackgroundImage = function() { + if (this.NodeSVGbackgroundImage != null) { + this.NodeSVGbackgroundImage.parentNode.removeChild(this.NodeSVGbackgroundImage); + } +}; + +GraphCanvas.prototype._setBackgroundColor = function(color) { + var attributes = [ [ "fill", color ] ]; + SVG.drawRectangle(0, 0, this.getFormatter().getWidth(), this.getFormatter().getHeight(), this.GraphBackground, attributes); +}; + +/** Serialize **/ +GraphCanvas.prototype.toJSON = function() { + var json = {}; + json.dataset = {}; + json.formatter = {}; + json.layout = {}; + json.dataset = this.getDataset().toJSON(); + json.formatter = this.getFormatter().toJSON(); + json.layout = this.getLayout().toJSON(); + return json; +}; + +GraphCanvas.prototype.toHTML = function() { + //this.backgroungToSVG(); + var html = this._svg.parentElement.innerHTML; + + var start = html.indexOf("") + 6; + + return html.substr(start, end); +}; + +/** DRAW **/ +GraphCanvas.prototype.draw = function(graphdataset, graphformatter, graphlayout) { + this.setDataset(graphdataset); + this.setFormatter(graphformatter); + this.setLayout(graphlayout); + + var _this = this; + this.getFormatter().changed.attach(function(sender, item) { + _this.removeNode(item.getId()); + _this.renderNode(item.getId()); + if (_this.args.labeled) { + _this.removeLabel(item.getId()); + _this.renderLabel(item.getId()); + } + + }); + //TODO + this.getFormatter().edgeChanged.attach(function(sender, item) { + _this.removeEdge(item.getId()); + _this.renderEdge(item.getId()); + }); + + this.getFormatter().resized.attach(function(sender, item) { + _this.resize(_this.getFormatter().getWidth(), _this.getFormatter().getHeight()); + }); + + this.getFormatter().backgroundImageChanged.attach(function(sender, item) { + _this.setBackgroundImage(_this.getFormatter().getBackgroundImage()); + }); + + this.getFormatter().backgroundColorChanged.attach(function(sender, item) { + _this._setBackgroundColor(_this.getFormatter().getBackgroundColor()); + }); + + this.getLayout().changed.attach(function(sender, item) { + _this.moveNode(item.getId()); + _this.moveEdge(item.getId()); + if (_this.args.labeled) { + _this.removeLabel(item.getId()); + _this.renderLabel(item.getId()); + } + }); + + this.getDataset().newVertex.attach(function(sender, item) { + + _this.renderNode(item.getId()); + if (_this.args.labeled) { + _this.renderLabel(item.getId()); + } + }); + + this.getDataset().newEdge.attach(function(sender, item) { + _this.renderEdge(item.getId()); + }); + + this.getDataset().vertexDeleted.attach(function(sender, item) { + _this.removeNode(item.getId()); + if (_this.args.labeled) { + _this.removeLabel(item.getId()); + } + }); + + this.getDataset().edgeDeleted.attach(function(sender, item) { + _this.removeEdge(item.getId()); + }); + + this.getDataset().vertexNameChanged.attach(function(sender, args) { + if (_this.args.labeled) { + _this.removeLabel(args.item.getId()); + _this.removeLabel(args.item.getId()); + _this.renderLabel(args.item.getId()); + } + }); + this.init(); + this.render(); +}; + +GraphCanvas.prototype.render = function() { + for ( var id in this.getDataset().getVertices()) { + this.renderNode(id); + } + this.renderLabels(); + this.renderEdges(); +}; + +GraphCanvas.prototype.renderLabels = function() { + if (this.args.labeled) { + for ( var id in this.getDataset().getVertices()) { + this.renderLabel(id); + } + } +}; + +GraphCanvas.prototype.removeLabels = function() { + for ( var id in this.getDataset().getVertices()) { + this.removeLabel(id); + } +}; + +/** Utilities method for nodes **/ +GraphCanvas.prototype.isNodeCanvas = function(node) { + return ((node.id == this.args.idGraph) || (node.id == this.id)); +}; + +GraphCanvas.prototype.isNodeBackground = function(node) { + return ((node.id == this.args.idBackgroundNode)); +}; + +GraphCanvas.prototype.isVertex = function(node) { + if (node.getAttribute("id") != null) { + if (node.getAttribute("id").indexOf("_v_") != -1) { + return true; + } + } + return false; +}; + +GraphCanvas.prototype.isLabel = function(node) { + if (node.getAttribute("id") != null) { + if (node.getAttribute("id").indexOf("_l_") != -1) { + return true; + } + } + return false; +}; + +GraphCanvas.prototype.isEdge = function(node) { + if (node.getAttribute("id") != null) { + if (node.getAttribute("id").indexOf("_e_") != -1) { + return true; + } + } + return false; +}; + +/** Resize **/ +GraphCanvas.prototype.resize = function(width, height) { + // this._svg.setAttribute("width", width); + // this._svg.setAttribute("height", height); + if (this.NodeSVGbackgroundImage != null) { + this.NodeSVGbackgroundImage.setAttribute("width", width); + this.NodeSVGbackgroundImage.setAttribute("height", height); + } + + this._svg.setAttribute("width", width); + this._svg.setAttribute("height", height); + + this.clearCanvas(); + this.render(); +}; + +GraphCanvas.prototype.clearCanvas = function() { + DOM.removeChilds(this.GraphEdgeGroup.getAttribute("id")); + DOM.removeChilds(this.GraphNodeGroup.getAttribute("id")); + this.clearLabels(); +}; + +GraphCanvas.prototype.clearLabels = function() { + DOM.removeChilds(this.GraphLabelGroup.getAttribute("id")); +}; + +/** ID'S converter **/ +GraphCanvas.prototype.getSVGNodeId = function(nodeId) { + return this.id + "_v_" + nodeId; +}; + +GraphCanvas.prototype.getSVGEdgeId = function(edgeId) { + return this.id + "_e_" + edgeId; +}; + +GraphCanvas.prototype.getSVGArrowEdgeId = function(edgeId) { + return this.id + "_arrow_" + edgeId; +}; + +GraphCanvas.prototype.getSVGLabelId = function(edgeId) { + return this.id + "_l_" + edgeId; +}; + +GraphCanvas.prototype.blinkVertexById = function(vertexId) { + $("#" + this.getSVGNodeId(vertexId)).fadeIn().fadeOut().fadeIn().fadeOut().fadeIn().fadeOut(); +}; + +GraphCanvas.prototype.getVertexIdFromSVGId = function(svgVertexId) { + return svgVertexId.replace(this.id, "").replace("_v_", ""); +}; + +GraphCanvas.prototype.getEdgeIdFromSVGId = function(svgEdgeId) { + return svgEdgeId.replace(this.id, "").replace("_e_", ""); +}; + +/** VERTEX **/ +GraphCanvas.prototype.getVertexById = function(id) { + return document.getElementById(this.getSVGNodeId(id)); +}; + +GraphCanvas.prototype.renderNodes = function() { + for ( var id in this.getDataset().getVertices()) { + this.renderNode(id); + } +}; + +GraphCanvas.prototype.overNode = function(nodeId) { + if (!this.args.interactive) { + return; + } + /** If selected we don't change the format **/ + if (this.args.isVertexSelected[nodeId] == null) { + var args = this.getFormatter().getVertexById(nodeId).getOver(); + args.args["cursor"] = 'pointer'; + this.changeVertexFormat(nodeId, args); + } +}; + +GraphCanvas.prototype.outNode = function(nodeId) { + if (!this.args.interactive) { + return; + } + + /** If selected we don't change the format **/ + if (this.args.isVertexSelected[nodeId] == null) { + this.changeVertexFormat(nodeId, this.getFormatter().getVertexById(nodeId).getDefault()); + } +}; + +GraphCanvas.prototype.overLabel = function(nodeId) { + this.overNode(nodeId); + // this.svgLabels[nodeId].setAttribute("cursor", "pointer"); +}; + +GraphCanvas.prototype.outLabel = function(nodeId) { + this.outNode(nodeId); + // this.svgLabels[nodeId].setAttribute("cursor", ""); +}; + +GraphCanvas.prototype.clickNode = function(nodeId) { + if (!this.args.interactive) { + return; + } + + /** si el evento se dispara oprque estaba dragging entonces no activo nada **/ + if (this.args.isVertexSelected[nodeId] == null) { + this.selectNode(nodeId); + } else { + this.deselectNode(nodeId); + } +}; + +GraphCanvas.prototype.selectNode = function(nodeId) { + for ( var i = 0; i < this.args.selectedVertices.length; i++) { + var format = this.getFormatter().getVertexById(nodeId).getSelected(); + format.opacity = 0.2; + this.changeVertexFormat(nodeId, this.getFormatter().getVertexById(nodeId).getSelected()); + } + + if (this.args.isVertexSelected[nodeId] == null) { + var format = this.getFormatter().getVertexById(nodeId).getSelected(); + format.opacity = 1; + this.changeVertexFormat(nodeId, this.getFormatter().getVertexById(nodeId).getSelected()); + this.args.selectedVertices.push(nodeId); + this.args.isVertexSelected[nodeId] = this.args.selectedVertices.length - 1; + this.onVertexSelect.notify(nodeId); + } +}; + +GraphCanvas.prototype.selectAllEdges = function() { + this.deselectNodes(); + this.deselectEdges(); + + for ( var edgesId in this.getDataset().edges) { + this.selectEdge(edgesId); + } +}; + +GraphCanvas.prototype.selectAllNodes = function() { + this.deselectNodes(); + this.deselectEdges(); + + for ( var vertexId in this.getDataset().vertices) { + this.selectNode(vertexId); + } +}; + +GraphCanvas.prototype.selectAll = function() { + this.deselectNodes(); + this.deselectEdges(); + + for ( var vertexId in this.getDataset().vertices) { + this.selectNode(vertexId); + } + + for ( var edgesId in this.getDataset().edges) { + this.selectEdge(edgesId); + } +}; + +GraphCanvas.prototype.selectEdge = function(edgeId) { + if (this.args.isEdgeSelected[edgeId] == null) { + this.changeEdgeFormat(edgeId, this.getFormatter().getEdgeById(edgeId).getSelected()); + //this.args.selectedEdges.push(edgeId); + this.args.isEdgeSelected[edgeId] = true; //this.args.selectedEdges.length - 1; + this.onEdgeSelect.notify(edgeId); + } +}; + +GraphCanvas.prototype.selectEdges = function(edges) { + + for ( var i = 0; i < edges.length; i++) { + this.selectEdge(edges[i]); + } +}; + +GraphCanvas.prototype.deselectNode = function(nodeId) { + if (this.args.isVertexSelected[nodeId] != null) { + this.changeVertexFormat(nodeId, this.getFormatter().getVertexById(nodeId).getDefault()); + this.args.selectedVertices.splice(this.args.isVertexSelected[nodeId], 1); + var index = this.args.isVertexSelected[nodeId]; + delete this.args.isVertexSelected[nodeId]; + + for ( var vertex in this.args.isVertexSelected) { + if (this.args.isVertexSelected[vertex] > index) { + this.args.isVertexSelected[vertex] = this.args.isVertexSelected[vertex] - 1; + } + } + } +}; + +GraphCanvas.prototype.deselectNodes = function() { + var selected = JSON.parse(JSON.stringify(this.getSelectedVertices())); + for ( var i = 0; i < selected.length; i++) { + this.deselectNode(selected[i]); + } +}; +GraphCanvas.prototype.selectNodes = function(idNodes) { + + for ( var i = 0; i < idNodes.length; i++) { + this.selectNode(idNodes[i]); + } + + // for ( var vertex in this.args.isVertexSelected) { + // if (this.args.isVertexSelected[vertex] > index){ + // this.args.isVertexSelected[vertex] = this.args.isVertexSelected[vertex] - 1; + // } + // } + +}; + +GraphCanvas.prototype.changeVertexFormat = function(nodeId, format) { + var svgNode = DOM.select(this.getSVGNodeId(nodeId)); + if (svgNode != null) { + var properties = format.toJSON(); + for ( var item in properties) { + svgNode.setAttribute(item, properties[item]); + } + + if (this.getFormatter().getVertexById(nodeId) instanceof CircleVertexGraphFormatter) { + var transform = "translate(" + svgNode.getAttribute("dragx") + "," + svgNode.getAttribute("dragy") + "), scale(" + format.getSize() + ")"; + svgNode.setAttribute("transform", transform); + } + } +}; + +GraphCanvas.prototype.renderLabel = function(nodeId) { + var x = Math.ceil(this.getLayout().getNodeById(nodeId).x * this.getFormatter().getWidth()); + var y = Math.ceil(this.getLayout().getNodeById(nodeId).y * this.getFormatter().getHeight()); + + var svgAttributesNode = JSON.parse(JSON.stringify(this.getFormatter().getVertexById(nodeId).getDefault().toJSON().title)); + svgAttributesNode.id = this.getSVGLabelId(this.getDataset().getVertexById(nodeId).getId()); + svgAttributesNode.dx = (-1) * (this.getDataset().getVertexById(nodeId).getName().length * svgAttributesNode["font-size"]) / 4 - 4; + + svgAttributesNode.dy = parseFloat((this.getFormatter().getVertexById(nodeId).getDefault().getSize())) + + parseFloat(svgAttributesNode["font-size"]) + parseFloat(this.getFormatter().getVertexById(nodeId).getDefault().getStrokeWidth()) - 4; + svgAttributesNode.dragx = Math.ceil(this.getLayout().getNodeById(nodeId).x * this.getFormatter().getWidth()); + + var gragy = parseFloat(this.getFormatter().getVertexById(nodeId).getDefault().getSize()) + + Math.ceil(this.getLayout().getNodeById(nodeId).y * this.getFormatter().getHeight()); + svgAttributesNode.dragy = gragy; + svgAttributesNode.transform = "translate(" + svgAttributesNode.dragx + "," + svgAttributesNode.dragy + ")";//, scale("+this.formatter.getVertexById(nodeId).getDefault().getSize()+")"; + + var nodeSVG = SVG.drawText(0, 0, this.getDataset().getVertexById(nodeId).getName(), this.GraphLabelGroup, svgAttributesNode); + + this.svgLabels[nodeId] = nodeSVG; + + /** Events for the SVG node **/ + var _this = this; + if (nodeSVG != null) { + nodeSVG.addEventListener("mouseover", function() { + _this.overLabel(nodeId); + }, false); + nodeSVG.addEventListener("mouseout", function() { + _this.outLabel(nodeId); + }, false); + } + +}; + +GraphCanvas.prototype.removeLabel = function(labelId) { + if (DOM.select(this.getSVGLabelId(labelId)) != null) { + DOM.select(this.getSVGLabelId(labelId)).parentNode.removeChild(DOM.select(this.getSVGLabelId(labelId))); + } +}; + +GraphCanvas.prototype.renderNode = function(nodeId) { + var svgAttributesNode = JSON.parse(JSON.stringify(this.getFormatter().getVertexById(nodeId).getDefault().toJSON())); + svgAttributesNode.dragx = Math.ceil(this.getLayout().getNodeById(nodeId).x * this.getFormatter().getWidth()); + svgAttributesNode.dragy = Math.ceil(this.getLayout().getNodeById(nodeId).y * this.getFormatter().getHeight()); + svgAttributesNode.transform = "translate(" + svgAttributesNode.dragx + "," + svgAttributesNode.dragy + ")"; + svgAttributesNode.id = this.getSVGNodeId(nodeId); + /*svgAttributesNode["stroke-width"] = 3 ; + svgAttributesNode["stroke-opacity"] = 1 ; + svgAttributesNode["fill-opacity"] = svgAttributesNode["opacity"] ; + svgAttributesNode["opacity"] = 1 ;*/ + this.circleDefaultRadius = this.getFormatter().getVertexById(nodeId).getDefault().getSize(); + var nodeSVG; + + if (this.getFormatter().getVertexById(nodeId) instanceof CircleVertexGraphFormatter) { + nodeSVG = SVG.drawCircle(0, 0, this.circleDefaultRadius, this.GraphNodeGroup, svgAttributesNode); + } + + if (this.getFormatter().getVertexById(nodeId) instanceof SquareVertexGraphFormatter) { + //nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius) ,0 - (this.formatter.getVertexById(nodeId).getDefault().getSize()) , (this.getFormatter().getVertexById(nodeId).getDefault().getSize()*2), (this.getFormatter().getVertexById(nodeId).getDefault().getSize()*2), this.GraphNodeGroup, svgAttributesNode); + nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius), 0 - (this.circleDefaultRadius), (this.circleDefaultRadius * 2), + (this.circleDefaultRadius * 2), this.GraphNodeGroup, svgAttributesNode); + } + + if (this.getFormatter().getVertexById(nodeId) instanceof EllipseVertexGraphFormatter) { + nodeSVG = SVG.drawEllipse(0, 0, this.circleDefaultRadius * 1.5, this.circleDefaultRadius, this.GraphNodeGroup, svgAttributesNode); + } + + if (this.getFormatter().getVertexById(nodeId) instanceof RectangleVertexGraphFormatter) { + //nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius) ,0 - ((this.circleDefaultRadius*2)/2) , (this.circleDefaultRadius*2), (this.circleDefaultRadius), this.GraphNodeGroup, svgAttributesNode); + nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius * 1.5), 0 - (this.circleDefaultRadius), (this.circleDefaultRadius * 2 * 1.5), + (this.circleDefaultRadius * 2), this.GraphNodeGroup, svgAttributesNode); + + } + + if (this.getFormatter().getVertexById(nodeId) instanceof RoundedVertexGraphFormatter) { + svgAttributesNode.ry = 2;// this.formatter.getVertexById(nodeId).getDefault().getSize()/4; + svgAttributesNode.rx = 2;// this.formatter.getVertexById(nodeId).getDefault().getSize()/4; + nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius * 1.5), 0 - (this.circleDefaultRadius), (this.circleDefaultRadius * 2 * 1.5), + (this.circleDefaultRadius * 2), this.GraphNodeGroup, svgAttributesNode); + } + + // + + if (this.getFormatter().getVertexById(nodeId) instanceof OctagonVertexGraphFormatter) { + svgAttributesNode.ry = 2; + svgAttributesNode.rx = 2; + nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius * 1.5), 0 - (this.circleDefaultRadius), (this.circleDefaultRadius * 2 * 1.5), + (this.circleDefaultRadius * 2), this.GraphNodeGroup, svgAttributesNode); + } + + nodeSVG.internalId = nodeId; + // + var _this = this; + + /** Events for the SVG node **/ + if (nodeSVG != null) { + nodeSVG.addEventListener("mouseover", function() { + _this.onVertexOver.notify(nodeId); + _this.overNode(nodeId); + }, false); + nodeSVG.addEventListener("mouseout", function() { + _this.onVertexOut.notify(nodeId); + _this.outNode(nodeId); + }, false); + //nodeSVG.addEventListener("click", function(){_this.clickNode(nodeId);}, false); + // + nodeSVG.addEventListener("mouseup", function() { + _this.onVertexUp.notify(nodeId); + }, false); + } +}; + +GraphCanvas.prototype.removeNode = function(nodeId) { + DOM.select(this.getSVGNodeId(nodeId)).parentNode.removeChild(DOM.select(this.getSVGNodeId(nodeId))); + if (this.args.labeled) { + this.removeLabel(nodeId); + } +}; + +/** REMOVING **/ +GraphCanvas.prototype.removeSelected = function() { + /** El orden importa **/ + this.removeSelectedEdges(); + this.removeSelectedNode(); + +}; + +GraphCanvas.prototype.removeSelectedNode = function() { + var selected = JSON.parse(JSON.stringify(this.getSelectedVertices())); + this.deselectNodes(); + var sorted = selected.sort(function(a, b) { + return a - b + }); + for ( var i = 0; i < sorted.length; i++) { + if (this.getDataset().getVertexById(sorted[i]) != null) { + this.getDataset().getVertexById(sorted[i]).remove(); + } + } +}; + +/** EDGES **/ +GraphCanvas.prototype.removeEdge = function(edgeId) { + if (DOM.select(this.getSVGEdgeId(edgeId)) != null) { + DOM.select(this.getSVGEdgeId(edgeId)).parentNode.removeChild(DOM.select(this.getSVGEdgeId(edgeId))); + } + + if (DOM.select(this.getSVGEdgeId(edgeId) + "_shadow") != null) { + DOM.select(this.getSVGEdgeId(edgeId) + "_shadow").parentNode.removeChild(DOM.select(this.getSVGEdgeId(edgeId) + "_shadow")); + } + + if (DOM.select(this.getSVGArrowEdgeId(edgeId)) != null) { + DOM.select(this.getSVGArrowEdgeId(edgeId)).parentNode.removeChild(DOM.select(this.getSVGArrowEdgeId(edgeId))); + } +}; + +GraphCanvas.prototype.overEdge = function(edgeId) { + if ((!this.args.interactive) || this.dragging || this.selecting) { + return; + } + + /** If selected we don't change the format **/ + if (this.args.isEdgeSelected[edgeId] == null) { + var format = this.getFormatter().getEdgeById(edgeId).getOver(); + format.args["cursor"] = "pointer"; + this.changeEdgeFormat(edgeId, format); + } +}; + +GraphCanvas.prototype.outEdge = function(edgeId) { + if (!this.args.interactive) { + return; + } + + /** If selected we don't change the format **/ + if (this.args.isEdgeSelected[edgeId] == null) { + this.changeEdgeFormat(edgeId, this.getFormatter().getEdgeById(edgeId).getDefault()); + } +}; + +GraphCanvas.prototype.changeEdgeFormat = function(edgeId, format) { + var svgEdge = DOM.select(this.getSVGEdgeId(edgeId) + "_shadow"); + if (svgEdge != null) { + var properties = format.toJSON(); + for ( var item in properties) { + svgEdge.setAttribute(item, properties[item]); + } + } +}; + +GraphCanvas.prototype.deselectEdge = function(edgeID) { + if (this.args.isEdgeSelected[edgeID] != null) { + this.changeEdgeFormat(edgeID, this.getFormatter().getEdgeById(edgeID).getDefault()); + var index = this.args.isEdgeSelected[edgeID]; + delete this.args.isEdgeSelected[edgeID]; + } +}; + +GraphCanvas.prototype.deselectEdges = function() { + var selected = JSON.parse(JSON.stringify(this.getSelectedEdges())); + for ( var i = 0; i < selected.length; i++) { + this.deselectEdge(selected[i]); + } +}; + +GraphCanvas.prototype.removeSelectedEdges = function() { + var selected = JSON.parse(JSON.stringify(this.getSelectedEdges())); + this.deselectEdges(); + for ( var i = 0; i < selected.length; i++) { + if (this.getDataset().getEdgeById(selected[i]) != null) { + this.getDataset().getEdgeById(selected[i]).remove(); + } + } +}; + +GraphCanvas.prototype.renderEdge = function(edgeId) { + var svgAttributesEdge = this.getFormatter().getEdgeById(edgeId).getDefault().toJSON(); + var edge = this.getDataset().getEdgeById(edgeId); + + var svgNodeTarget = this.getVertexById(edge.getNodeTarget().getId()); + var svgNodeSource = this.getVertexById(edge.getNodeSource().getId()); + svgAttributesEdge.id = this.getSVGEdgeId(edge.getId()) + "_shadow"; + + var svgEdge = null; + + if (this.getFormatter().getEdgeById(edgeId) instanceof LineEdgeGraphFormatter) { + var coordenateSourceX = svgNodeSource.getAttribute("dragx"); + var coordenateSourceY = svgNodeSource.getAttribute("dragy"); + var coordenateTargetX = svgNodeTarget.getAttribute("dragx"); + var coordenateTargetY = svgNodeTarget.getAttribute("dragy"); + + SVG.drawLine(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, this.GraphEdgeGroup, svgAttributesEdge); + var attributesShadow = {}; + attributesShadow.id = this.getSVGEdgeId(edge.getId()); + attributesShadow["stroke-opacity"] = 0; + attributesShadow["stroke-width"] = 4; + attributesShadow["stroke"] = "black"; + svgEdge = SVG.drawLine(svgNodeSource.getAttribute("dragx"), svgNodeSource.getAttribute("dragy"), svgNodeTarget.getAttribute("dragx"), + svgNodeTarget.getAttribute("dragy"), this.GraphEdgeGroup, attributesShadow); + } + + if (this.getFormatter().getEdgeById(edgeId) instanceof BezierEdgeGraphFormatter) { + var nodeId = edge.getNodeTarget().getId(); + var nodeSize = this.formatter.getVertexById(nodeId).getDefault().getSize() * this.getFormatter().getNodesMaxSize(); + svgAttributesEdge.fill = "none"; + svgAttributesEdge.id = this.getSVGEdgeId(edgeId); + var d = this.calculateCoordenatesBezier(nodeSize, svgNodeSource.getAttribute("dragx"), svgNodeSource.getAttribute("dragy")); + svgEdge = SVG.drawPath(d, this.GraphEdgeGroup, svgAttributesEdge); + } + ; + + if ((this.getFormatter().getEdgeById(edgeId) instanceof DirectedLineEdgeGraphFormatter) + || (this.getFormatter().getEdgeById(edgeId) instanceof CutDirectedLineEdgeGraphFormatter) + || (this.getFormatter().getEdgeById(edgeId) instanceof DotDirectedLineEdgeGraphFormatter) + || (this.getFormatter().getEdgeById(edgeId) instanceof OdotDirectedLineEdgeGraphFormatter) + || (this.getFormatter().getEdgeById(edgeId) instanceof OdirectedLineEdgeGraphFormatter)) { + var coordenateSourceX = svgNodeSource.getAttribute("dragx"); + var coordenateSourceY = svgNodeSource.getAttribute("dragy"); + var coordenateTargetX = svgNodeTarget.getAttribute("dragx"); + var coordenateTargetY = svgNodeTarget.getAttribute("dragy"); + + var offset = parseFloat(this.getFormatter().getVertexById(this.getDataset().getEdgeById(edgeId).getNodeTarget().getId()).getDefault() + .getSize() + * this.circleDefaultRadius); + var point = this._calculateEdgePointerPosition(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, offset); + coordenateTargetX = point.x; + coordenateTargetY = point.y; + SVG.drawLine(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, this.GraphEdgeGroup, svgAttributesEdge); + + var attributesShadow = {}; + attributesShadow.id = this.getSVGEdgeId(edge.getId()); + attributesShadow["stroke-opacity"] = 0; + attributesShadow["stroke-width"] = 4; + attributesShadow["stroke"] = "black"; + svgEdge = SVG.drawLine(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, this.GraphEdgeGroup, attributesShadow); + } + + if (this.getFormatter().getEdgeById(edgeId) instanceof DirectedLineEdgeGraphFormatter + || (this.getFormatter().getEdgeById(edgeId) instanceof OdirectedLineEdgeGraphFormatter)) { + var coordenateSourceX = svgNodeSource.getAttribute("dragx"); + var coordenateSourceY = svgNodeSource.getAttribute("dragy"); + var coordenateTargetX = svgNodeTarget.getAttribute("dragx"); + var coordenateTargetY = svgNodeTarget.getAttribute("dragy"); + + var point = this._calculateEdgePointerPosition(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, offset); + coordenateTargetX = point.x; + coordenateTargetY = point.y; + + var angle = Geometry.toDegree(point.angle) + 90; + this.arrowDefaultSize = this.getFormatter().getEdgeById(edgeId).getArrowSize(); //getDefault().getArrowSize(); + var d = "-" + this.arrowDefaultSize + ",0 0,-" + parseFloat(this.arrowDefaultSize) * 2 + " " + this.arrowDefaultSize + ",0"; + + var attributes; + + if (this.getFormatter().getEdgeById(edgeId) instanceof DirectedLineEdgeGraphFormatter) { + attributes = [ + [ "fill", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], + [ "stroke", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], [ "id", this.getSVGArrowEdgeId(edgeId) ] ]; + } else { + attributes = [ + [ "fill", "#FFFFFF" ], [ "stroke", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], + [ "id", this.getSVGArrowEdgeId(edgeId) ] ]; + } + + var flechaSVGNode = SVG.drawPoligon(d, this.GraphEdgeGroup, attributes);//, ["transform", "rotate("+angle+"), translate(0,0)"]]); + flechaSVGNode.setAttribute("transform", " translate(" + coordenateTargetX + ", " + coordenateTargetY + "), rotate(" + angle + ")"); + } + ; + + if (this.getFormatter().getEdgeById(edgeId) instanceof CutDirectedLineEdgeGraphFormatter) { + var coordenateSourceX = svgNodeSource.getAttribute("dragx"); + var coordenateSourceY = svgNodeSource.getAttribute("dragy"); + var coordenateTargetX = svgNodeTarget.getAttribute("dragx"); + var coordenateTargetY = svgNodeTarget.getAttribute("dragy"); + + var point = this._calculateEdgePointerPosition(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, offset); + coordenateTargetX = point.x; + coordenateTargetY = point.y; + + var angle = Geometry.toDegree(point.angle) + 90; + + //this.arrowDefaultSize = 2; //getDefault().getArrowSize(); + var d = "-4,0 4,0 4,-2 -4,-2"; + + var flechaSVGNode = SVG.drawPoligon(d, this.GraphEdgeGroup, [ + [ "fill", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], + [ "stroke", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], [ "id", this.getSVGArrowEdgeId(edgeId) ] ]);//, ["transform", "rotate("+angle+"), translate(0,0)"]]); + flechaSVGNode.setAttribute("transform", " translate(" + coordenateTargetX + ", " + coordenateTargetY + "), rotate(" + angle + ")"); + } + ; + + if ((this.getFormatter().getEdgeById(edgeId) instanceof DotDirectedLineEdgeGraphFormatter) + || (this.getFormatter().getEdgeById(edgeId) instanceof OdotDirectedLineEdgeGraphFormatter)) { + var coordenateSourceX = svgNodeSource.getAttribute("dragx"); + var coordenateSourceY = svgNodeSource.getAttribute("dragy"); + var coordenateTargetX = svgNodeTarget.getAttribute("dragx"); + var coordenateTargetY = svgNodeTarget.getAttribute("dragy"); + var point = this._calculateEdgePointerPosition(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, offset); + coordenateTargetX = point.x; + coordenateTargetY = point.y; + var angle = Geometry.toDegree(point.angle) + 90; + // this.arrowDefaultSize = this.formatter.getEdgeById(edgeId).getArrowSize(); //getDefault().getArrowSize(); + var attributes = []; + if (this.getFormatter().getEdgeById(edgeId) instanceof OdotDirectedLineEdgeGraphFormatter) { + attributes = [ + [ "fill", "#FFFFFF" ], [ "stroke", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], + [ "id", this.getSVGArrowEdgeId(edgeId) ] ]; + } else { + attributes = [ + [ "fill", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], + [ "stroke", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], [ "id", this.getSVGArrowEdgeId(edgeId) ] ]; + } + var flechaSVGNode = SVG.drawCircle(0, 0, 4, this.GraphEdgeGroup, attributes); + flechaSVGNode.setAttribute("transform", " translate(" + coordenateTargetX + ", " + coordenateTargetY + "), rotate(" + angle + ")"); + } + ; + + var _this = this; + /** Events for the SVG edge **/ + if (svgEdge != null) { + if (this.getDataset().getEdgesCount() < this.args.maxNumberEdgesFiringEvents) { + svgEdge.addEventListener("mouseover", function() { + _this.overEdge(edgeId); + }, false); + svgEdge.addEventListener("mouseout", function() { + _this.outEdge(edgeId); + }, false); + } + } +}; + +GraphCanvas.prototype._calculateEdgePointerPosition = function(sourceX, sourceY, targetX, targetY, radius) { + var angle = Geometry.getAngleBetweenTwoPoints(sourceX, sourceY, targetX, targetY); + + /** Suponiendo el node source que este a la derecha **/ + if ((targetX - sourceX) < 0) { + var b = Geometry.getAdjacentSideOfRectangleRight(angle, radius); + targetX = parseFloat(targetX) + parseFloat(b); + arrowX = parseFloat(targetX) + parseFloat(b) + this.arrowDefaultSize / 2; + } else { + var b = Geometry.getAdjacentSideOfRectangleRight(angle, radius); + targetX = parseFloat(targetX) - parseFloat(b); + arrowX = parseFloat(targetX) - parseFloat(b) - this.arrowDefaultSize / 2; + } + + /** Suponiendo el node source que este a la arriba **/ + if ((targetY - sourceY) > 0) { + var a = Geometry.getOppositeSideOfRectangleRight(angle, radius); + targetY = parseFloat(targetY) - parseFloat(a); + arrowY = parseFloat(targetY) - parseFloat(a) - this.arrowDefaultSize / 2; + } else { + var a = Geometry.getOppositeSideOfRectangleRight(angle, radius); + targetY = parseFloat(targetY) + parseFloat(a); + arrowY = parseFloat(targetY) + parseFloat(a) - this.arrowDefaultSize / 2; + + } + + return { + "x" : arrowX, + "y" : arrowY, + "angle" : angle + }; +}; + +GraphCanvas.prototype.calculateCoordenatesBezier = function(nodeSize, x1, y1) { + var x11 = x1 - (nodeSize / 2); + var y11 = y1 - (nodeSize / 2); + + var x12 = parseFloat(x1) + parseFloat(nodeSize / 2); + var y12 = y1 - (nodeSize / 2); + + var curvePointX = (x12 - x11) / 2 + x11; + var curvePointY = y1 - (nodeSize * 2); + var d = "M" + x11 + "," + y11 + " T" + curvePointX + "," + curvePointY + " " + x12 + "," + y12; + return d; + +}; + +GraphCanvas.prototype.renderEdges = function() { + for ( var edge in this.getDataset().getEdges()) { + this.renderEdge(this.getDataset().getEdgeById(edge).getId()); + + } +}; + +GraphCanvas.prototype.getLastSelectedNode = function() { + var node = null; + if (this.getSelectedVertices().length > 0) { + var nodeId = this.getSelectedVertices()[this.getSelectedVertices().length - 1]; + node = this.getDataset().getVertexById(nodeId); + } + return node; +}; +/* + GraphCanvas.prototype.getNodeByNameAndIndex = function(node, index){ + var nodeId = this.getDataset().verticesIndex[node][index]; + var nodeItem = this.getDataset().getVertexById(nodeId); + return nodeItem; + }; + */ + +GraphCanvas.prototype.setDataset = function(dataset) { + this.dataset = dataset; +}; + +GraphCanvas.prototype.setFormatter = function(formatter) { + this.formatter = formatter; +}; + +GraphCanvas.prototype.setLayout = function(layout) { + this.layout = layout; +}; + +/** API **/ +GraphCanvas.prototype.getDataset = function() { + return this.dataset; +}; + +GraphCanvas.prototype.getFormatter = function() { + return this.formatter; +}; + +GraphCanvas.prototype.getLayout = function() { + return this.layout; +}; + +/** API DATASET **/ +GraphCanvas.prototype.addVertex = function(name, args) { + this.getDataset().addNode(name, args); +}; + +GraphCanvas.prototype.removeVertex = function(vertexId) { + this.getDataset().getVertexById(vertexId).remove(); +}; + +GraphCanvas.prototype.addEdge = function(edgeName, nodeSourceId, nodeTargetId, args) { + this.getDataset().addEdge(edgeName, nodeSourceId, nodeTargetId, args); +}; +/* + GraphCanvas.prototype.removeEdge = function(edgeId){ + this.getDataset().getEdgeById(edgeId).remove(); + }; + */ + +/** API FORMATTER **/ +GraphCanvas.prototype.getWidth = function() { + return this.getFormatter().getWidth(); +}; + +GraphCanvas.prototype.getHeight = function() { + return this.getFormatter().getHeight(); +}; + +GraphCanvas.prototype.getBackgroundImage = function() { + return this.getFormatter().getBackgroundImage(); +}; + +//GraphCanvas.prototype.setBackgroundImage = function(value){ +// this.getFormatter().setBackgroundImage(value); +//}; + +GraphCanvas.prototype.getBackgroundColor = function() { + return this.getFormatter().getBackgroundColor(); +}; + +GraphCanvas.prototype.setBackgroundColor = function() { + this.getFormatter().setBackgroundColor(value); +}; + +//GraphCanvas.prototype.setEdgeFill = function(edgeId, value){ +// this.getFormatter().getEdgeById(edgeId).getDefault().setFill(value); +//}; +// +//GraphCanvas.prototype.getEdgeFill = function(edgeId){ +// return this.getFormatter().getEdgeById(edgeId).getDefault().getFill(); +//}; + +/** VERTICES FORMATTER **/ +GraphCanvas.prototype.setVertexSize = function(vertexId, value) { + this.getFormatter().getVertexById(vertexId).getDefault().setSize(value); +}; + +GraphCanvas.prototype.getVertexSize = function(vertexId) { + return this.getFormatter().getVertexById(vertexId).getDefault().getSize(); +}; + +GraphCanvas.prototype.setVertexStroke = function(vertexId, value) { + this.getFormatter().getVertexById(vertexId).getDefault().setStroke(value); +}; + +GraphCanvas.prototype.getVertexStroke = function(vertexId) { + return this.getFormatter().getVertexById(vertexId).getDefault().getStroke(); +}; + +GraphCanvas.prototype.setVertexStrokeOpacity = function(vertexId, value) { + this.getFormatter().getVertexById(vertexId).getDefault().setStrokeOpacity(value); +}; + +GraphCanvas.prototype.getVertexStrokeOpacity = function(vertexId) { + return this.getFormatter().getVertexById(vertexId).getDefault().getStrokeOpacity(); +}; + +GraphCanvas.prototype.setVertexOpacity = function(vertexId, value) { + this.getFormatter().getVertexById(vertexId).getDefault().setOpacity(value); +}; + +GraphCanvas.prototype.getVertexOpacity = function(vertexId) { + return this.getFormatter().getVertexById(vertexId).getDefault().getOpacity(); +}; + +GraphCanvas.prototype.setVertexFill = function(vertexId, color) { + this.getFormatter().getVertexById(vertexId).getDefault().setFill(color); +}; + +GraphCanvas.prototype.getVertexFill = function(vertexId) { + return this.getFormatter().getVertexById(vertexId).getDefault().getFill(); +}; + +/** EDGES FORMATTER **/ +GraphCanvas.prototype.setEdgeSize = function(edgeId, value) { + this.getFormatter().getEdgeById(edgeId).getDefault().setSize(value); +}; + +GraphCanvas.prototype.getEdgeSize = function(edgeId) { + return this.getFormatter().getEdgeById(edgeId).getDefault().getSize(); +}; + +GraphCanvas.prototype.setEdgeStroke = function(edgeId, value) { + this.getFormatter().getEdgeById(edgeId).getDefault().setStroke(value); +}; + +GraphCanvas.prototype.getEdgeStroke = function(edgeId) { + return this.getFormatter().getEdgeById(edgeId).getDefault().getStroke(); +}; + +GraphCanvas.prototype.setEdgeStrokeOpacity = function(edgeId, value) { + this.getFormatter().getEdgeById(edgeId).getDefault().setStrokeOpacity(value); +}; + +GraphCanvas.prototype.getEdgeStrokeOpacity = function(edgeId) { + return this.getFormatter().getEdgeById(edgeId).getDefault().getStrokeOpacity(); +}; + +GraphCanvas.prototype.setEdgeFill = function(edgeId, color) { + this.getFormatter().getEdgeById(edgeId).getDefault().setFill(color); +}; + +GraphCanvas.prototype.getEdgeFill = function(edgeId) { + return this.getFormatter().getEdgeById(edgeId).getDefault().getFill(); +}; + +/** API LAYOUT **/ +GraphCanvas.prototype.setCoordinates = function(vertexId, x, y) { + return this.getLayout().getEdgeById(vertexId).setCoordinates(x, y); +}; @@ -14339,283 +14339,283 @@ MergesHPLCGraph.prototype.getMenu = function () { } }); - return actions; + return actions; +}; + + +MergesHPLCGraph.prototype.input = function () { + return DATADOC.getScatteringHPLCFrameData(); +}; + +MergesHPLCGraph.prototype.test = function (targetId) { + var mainPlotPanel = new MergesHPLCGraph({ + title : 'Scattering', + width : this.plotWidth, + height : 500, + showRangeSelector : false, + xParam : 0, + xlabel : "scattering_I", + plots : { + "scattering_I" : true, + "subtracted_I" : true, + "buffer_I" : true + } + }); + mainPlotPanel.getPanel().render(targetId); + mainPlotPanel.loadData(mainPlotPanel.input()); +}; + + +function NetworkWidget(args) { + this.id = "NetworkViewer_" + Math.random().toString().replace(".", "_"); + + this.label = true; + if (args != null) { + if (args.targetId != null) { + this.targetId = args.targetId; + } + if (args.label != null) { + this.label = args.label; + } + } + + this.onVertexOver = new Event(this); + this.onVertexOut = new Event(this); +} + +NetworkWidget.prototype.draw = function(dataset, formatter, layout) { + + this.graphCanvas = new GraphCanvas(this.id, document.getElementById(this.targetId), { + "labeled" : this.label, + "multipleSelectionEnabled" : false, + "draggingCanvasEnabled" : false + }); + this.graphCanvas.draw(dataset, formatter, layout); + + var _this = this; + this.graphCanvas.onVertexOver.attach(function(sender, nodeId) { + _this.onVertexOver.notify(nodeId); + }); + + this.graphCanvas.onVertexOut.attach(function(sender, nodeId) { + _this.onVertexOut.notify(nodeId); + }); +}; + +/** SELECT VERTICES BY NAME * */ +NetworkWidget.prototype.selectVertexByName = function(vertexName) { + var vertices = this.getDataset().getVertexByName(vertexName); + if (vertices != null) { + for ( var nodeId in vertices) { + if (vertices.hasOwnProperty(nodeId)) { + var vertexId = vertices[nodeId].getId(); + this.selectVertexById(vertexId); + } + } + } +}; + +NetworkWidget.prototype.selectVerticesByName = function(verticesName) { + for ( var i = 0; i < verticesName.length; i++) { + this.selectVertexByName(verticesName[i]); + } +}; + +/** SELECT VERTICES BY ID * */ +NetworkWidget.prototype.selectVertexById = function(vertexId) { + this.graphCanvas.selectNode(vertexId); + this.blinkVertexById(vertexId); +}; + +NetworkWidget.prototype.selectVerticesById = function(verticesId) { + for ( var i = 0; i < verticesId.length; i++) { + this.selectVertexById(verticesId[i]); + } +}; + +/** VECINDARIO * */ +NetworkWidget.prototype.selectNeighbourhood = function() { + this.selectEdgesFromVertices(); + this.selectAdjacent(); +}; + +/** DESELECT * */ +NetworkWidget.prototype.deselectNodes = function() { + this.graphCanvas.deselectNodes(); +}; + +/** SELECT ALL NODES * */ +NetworkWidget.prototype.selectAllNodes = function() { + this.getGraphCanvas().selectAllNodes(); +}; + +/** SELECT EVERYTHING * */ +NetworkWidget.prototype.selectAll = function() { + this.getGraphCanvas().selectAll(); +}; + +/** SELECT ALL EDGES * */ +NetworkWidget.prototype.selectAllEdges = function() { + this.getGraphCanvas().selectAllEdges(); +}; + +/** ZOOM * */ +NetworkWidget.prototype.setScale = function(value) { + this.graphCanvas.setScale(value); +}; + +NetworkWidget.prototype.getScale = function() { + return this.graphCanvas.getScale(value); +}; + +/** SELECT ADJACENT VERTICES FROM SELECTED VERTICES * */ +NetworkWidget.prototype.selectAdjacent = function() { + var selectedVertices = this.getGraphCanvas().getSelectedVertices(); + var edges = []; + for ( var i = 0; i < selectedVertices.length; i++) { + edges = edges.concat(this.getGraphCanvas().getDataset().getVertexById(selectedVertices[i]).getEdges()); + } + var vertices = []; + for ( i = 0; i < edges.length; i++) { + vertices.push(edges[i].getNodeSource().getId()); + vertices.push(edges[i].getNodeTarget().getId()); + } + + this.selectVerticesById(vertices); +}; + +/** SELECT EDGES FROM SELECTED VERTICES * */ +NetworkWidget.prototype.selectEdgesFromVertices = function() { + var selectedVertices = this.getGraphCanvas().getSelectedVertices(); + var edges = []; + for ( var i = 0; i < selectedVertices.length; i++) { + edges = edges.concat(this.getGraphCanvas().getDataset().getVertexById(selectedVertices[i]).getEdges()); + } + var edgesId = []; + for ( i = 0; i < edges.length; i++) { + edgesId.push(edges[i].getId()); + } + this.getGraphCanvas().selectEdges(edgesId); +}; + +/** BLINKING * */ +NetworkWidget.prototype.blinkVertexById = function(vertexId) { + this.graphCanvas.blinkVertexById(vertexId); +}; + +/** COMPONENTE CONEXA DE LOS NODOS SELECCIONADOS * */ +NetworkWidget.prototype.selectConnectedComponent = function() { + var elements = this.getConnectedComponent(); + this.selectVerticesById(elements.nodes); + this.graphCanvas.selectEdges(elements.edges); +}; + +NetworkWidget.prototype.getConnectedComponent = function() { + var nodosVisitados = {}; + var aristasVisitadas = {}; + var arrNodos = []; + var arrAristas = []; + var selectedGraphNodesId = this.getGraphCanvas().getSelectedVertices(); + for ( var i = 0; i < selectedGraphNodesId.length; i++) { + this.visitNode(selectedGraphNodesId[i], nodosVisitados, aristasVisitadas, arrNodos, arrAristas); + } + return { + nodes : arrNodos, + edges : arrAristas + }; +}; + +NetworkWidget.prototype.visitNode = function(nodeId, nodosVisitados, aristasVisitadas, arrNodos, arrAristas) { + nodosVisitados[nodeId] = true; + arrNodos.push(nodeId); + var nodeEdges = this.getDataset().getVertexById(nodeId).getEdges(); + for ( var j = 0; j < nodeEdges.length; j++) { + var edge = nodeEdges[j]; + var edgeId = edge.getId(); + if (aristasVisitadas[edgeId] == null) { + aristasVisitadas[edgeId] = true; + arrAristas.push(edgeId); + var nodeTargetId = edge.getNodeTarget().getId(); + if (nodosVisitados[nodeTargetId] == null) { + this.visitNode(nodeTargetId, nodosVisitados, aristasVisitadas, arrNodos, arrAristas); + } + var nodeSourceId = edge.getNodeSource().getId(); + if (nodosVisitados[nodeSourceId] == null) { + this.visitNode(nodeSourceId, nodosVisitados, aristasVisitadas, arrNodos, arrAristas); + } + } + } +}; + +/** COLLAPSE SELECTED VERTICES * */ +NetworkWidget.prototype.collapse = function() { + var selectedVertices = this.getGraphCanvas().getSelectedVertices(); + var xMin = -Infinity; + var xMax = Infinity; + var yMin = -Infinity; + var yMax = Infinity; + + for ( var i = 0; i < selectedVertices.length; i++) { + var vertex = this.getGraphCanvas().getLayout().getNodeById(selectedVertices[i]); + if (xMin < vertex.x) { + xMin = vertex.x; + } + if (xMax > vertex.x) { + xMax = vertex.x; + } + if (yMin < vertex.y) { + yMin = vertex.y; + } + if (yMax > vertex.y) { + yMax = vertex.y; + } + } + + var centerX = xMin - xMax; + var centerY = yMin - yMax; + var radius = (xMax - xMin) / 4; + + var count = selectedVertices.length; + var verticesCoordinates = []; + + for ( i = 0; i < selectedVertices.length; i++) { + x = centerX + radius * Math.sin(i * 2 * Math.PI / count); + y = centerY + radius * Math.cos(i * 2 * Math.PI / count); + verticesCoordinates.push({ + 'x' : x, + 'y' : y + }); + } + + for ( i = 0; i < selectedVertices.length; i++) { + this.getGraphCanvas().getLayout().getNodeById(selectedVertices[i]).setCoordinates(verticesCoordinates[i].x, verticesCoordinates[i].y); + } }; +/** SETTER FONT SIZE * */ +NetworkWidget.prototype.setVerticesFontSize = function(value) { + for ( var nodeId in this.getDataset().getVertices()) { + if (this.getDataset().getVertices().hasOwnProperty(nodeId)) { + this.getFormatter().getVertexById(nodeId).getDefault().setFontSize(value); + } + } +}; -MergesHPLCGraph.prototype.input = function () { - return DATADOC.getScatteringHPLCFrameData(); +/** GETTERS * */ +NetworkWidget.prototype.getFormatter = function() { + return this.getGraphCanvas().getFormatter(); +}; +NetworkWidget.prototype.getLayout = function() { + return this.getGraphCanvas().getLayout(); }; -MergesHPLCGraph.prototype.test = function (targetId) { - var mainPlotPanel = new MergesHPLCGraph({ - title : 'Scattering', - width : this.plotWidth, - height : 500, - showRangeSelector : false, - xParam : 0, - xlabel : "scattering_I", - plots : { - "scattering_I" : true, - "subtracted_I" : true, - "buffer_I" : true - } - }); - mainPlotPanel.getPanel().render(targetId); - mainPlotPanel.loadData(mainPlotPanel.input()); +NetworkWidget.prototype.getDataset = function() { + return this.getGraphCanvas().getDataset(); }; - -function NetworkWidget(args) { - this.id = "NetworkViewer_" + Math.random().toString().replace(".", "_"); - - this.label = true; - if (args != null) { - if (args.targetId != null) { - this.targetId = args.targetId; - } - if (args.label != null) { - this.label = args.label; - } - } - - this.onVertexOver = new Event(this); - this.onVertexOut = new Event(this); -} - -NetworkWidget.prototype.draw = function(dataset, formatter, layout) { - - this.graphCanvas = new GraphCanvas(this.id, document.getElementById(this.targetId), { - "labeled" : this.label, - "multipleSelectionEnabled" : false, - "draggingCanvasEnabled" : false - }); - this.graphCanvas.draw(dataset, formatter, layout); - - var _this = this; - this.graphCanvas.onVertexOver.attach(function(sender, nodeId) { - _this.onVertexOver.notify(nodeId); - }); - - this.graphCanvas.onVertexOut.attach(function(sender, nodeId) { - _this.onVertexOut.notify(nodeId); - }); -}; - -/** SELECT VERTICES BY NAME * */ -NetworkWidget.prototype.selectVertexByName = function(vertexName) { - var vertices = this.getDataset().getVertexByName(vertexName); - if (vertices != null) { - for ( var nodeId in vertices) { - if (vertices.hasOwnProperty(nodeId)) { - var vertexId = vertices[nodeId].getId(); - this.selectVertexById(vertexId); - } - } - } -}; - -NetworkWidget.prototype.selectVerticesByName = function(verticesName) { - for ( var i = 0; i < verticesName.length; i++) { - this.selectVertexByName(verticesName[i]); - } -}; - -/** SELECT VERTICES BY ID * */ -NetworkWidget.prototype.selectVertexById = function(vertexId) { - this.graphCanvas.selectNode(vertexId); - this.blinkVertexById(vertexId); -}; - -NetworkWidget.prototype.selectVerticesById = function(verticesId) { - for ( var i = 0; i < verticesId.length; i++) { - this.selectVertexById(verticesId[i]); - } -}; - -/** VECINDARIO * */ -NetworkWidget.prototype.selectNeighbourhood = function() { - this.selectEdgesFromVertices(); - this.selectAdjacent(); -}; - -/** DESELECT * */ -NetworkWidget.prototype.deselectNodes = function() { - this.graphCanvas.deselectNodes(); -}; - -/** SELECT ALL NODES * */ -NetworkWidget.prototype.selectAllNodes = function() { - this.getGraphCanvas().selectAllNodes(); -}; - -/** SELECT EVERYTHING * */ -NetworkWidget.prototype.selectAll = function() { - this.getGraphCanvas().selectAll(); -}; - -/** SELECT ALL EDGES * */ -NetworkWidget.prototype.selectAllEdges = function() { - this.getGraphCanvas().selectAllEdges(); -}; - -/** ZOOM * */ -NetworkWidget.prototype.setScale = function(value) { - this.graphCanvas.setScale(value); -}; - -NetworkWidget.prototype.getScale = function() { - return this.graphCanvas.getScale(value); -}; - -/** SELECT ADJACENT VERTICES FROM SELECTED VERTICES * */ -NetworkWidget.prototype.selectAdjacent = function() { - var selectedVertices = this.getGraphCanvas().getSelectedVertices(); - var edges = []; - for ( var i = 0; i < selectedVertices.length; i++) { - edges = edges.concat(this.getGraphCanvas().getDataset().getVertexById(selectedVertices[i]).getEdges()); - } - var vertices = []; - for ( i = 0; i < edges.length; i++) { - vertices.push(edges[i].getNodeSource().getId()); - vertices.push(edges[i].getNodeTarget().getId()); - } - - this.selectVerticesById(vertices); -}; - -/** SELECT EDGES FROM SELECTED VERTICES * */ -NetworkWidget.prototype.selectEdgesFromVertices = function() { - var selectedVertices = this.getGraphCanvas().getSelectedVertices(); - var edges = []; - for ( var i = 0; i < selectedVertices.length; i++) { - edges = edges.concat(this.getGraphCanvas().getDataset().getVertexById(selectedVertices[i]).getEdges()); - } - var edgesId = []; - for ( i = 0; i < edges.length; i++) { - edgesId.push(edges[i].getId()); - } - this.getGraphCanvas().selectEdges(edgesId); -}; - -/** BLINKING * */ -NetworkWidget.prototype.blinkVertexById = function(vertexId) { - this.graphCanvas.blinkVertexById(vertexId); -}; - -/** COMPONENTE CONEXA DE LOS NODOS SELECCIONADOS * */ -NetworkWidget.prototype.selectConnectedComponent = function() { - var elements = this.getConnectedComponent(); - this.selectVerticesById(elements.nodes); - this.graphCanvas.selectEdges(elements.edges); -}; - -NetworkWidget.prototype.getConnectedComponent = function() { - var nodosVisitados = {}; - var aristasVisitadas = {}; - var arrNodos = []; - var arrAristas = []; - var selectedGraphNodesId = this.getGraphCanvas().getSelectedVertices(); - for ( var i = 0; i < selectedGraphNodesId.length; i++) { - this.visitNode(selectedGraphNodesId[i], nodosVisitados, aristasVisitadas, arrNodos, arrAristas); - } - return { - nodes : arrNodos, - edges : arrAristas - }; -}; - -NetworkWidget.prototype.visitNode = function(nodeId, nodosVisitados, aristasVisitadas, arrNodos, arrAristas) { - nodosVisitados[nodeId] = true; - arrNodos.push(nodeId); - var nodeEdges = this.getDataset().getVertexById(nodeId).getEdges(); - for ( var j = 0; j < nodeEdges.length; j++) { - var edge = nodeEdges[j]; - var edgeId = edge.getId(); - if (aristasVisitadas[edgeId] == null) { - aristasVisitadas[edgeId] = true; - arrAristas.push(edgeId); - var nodeTargetId = edge.getNodeTarget().getId(); - if (nodosVisitados[nodeTargetId] == null) { - this.visitNode(nodeTargetId, nodosVisitados, aristasVisitadas, arrNodos, arrAristas); - } - var nodeSourceId = edge.getNodeSource().getId(); - if (nodosVisitados[nodeSourceId] == null) { - this.visitNode(nodeSourceId, nodosVisitados, aristasVisitadas, arrNodos, arrAristas); - } - } - } -}; - -/** COLLAPSE SELECTED VERTICES * */ -NetworkWidget.prototype.collapse = function() { - var selectedVertices = this.getGraphCanvas().getSelectedVertices(); - var xMin = -Infinity; - var xMax = Infinity; - var yMin = -Infinity; - var yMax = Infinity; - - for ( var i = 0; i < selectedVertices.length; i++) { - var vertex = this.getGraphCanvas().getLayout().getNodeById(selectedVertices[i]); - if (xMin < vertex.x) { - xMin = vertex.x; - } - if (xMax > vertex.x) { - xMax = vertex.x; - } - if (yMin < vertex.y) { - yMin = vertex.y; - } - if (yMax > vertex.y) { - yMax = vertex.y; - } - } - - var centerX = xMin - xMax; - var centerY = yMin - yMax; - var radius = (xMax - xMin) / 4; - - var count = selectedVertices.length; - var verticesCoordinates = []; - - for ( i = 0; i < selectedVertices.length; i++) { - x = centerX + radius * Math.sin(i * 2 * Math.PI / count); - y = centerY + radius * Math.cos(i * 2 * Math.PI / count); - verticesCoordinates.push({ - 'x' : x, - 'y' : y - }); - } - - for ( i = 0; i < selectedVertices.length; i++) { - this.getGraphCanvas().getLayout().getNodeById(selectedVertices[i]).setCoordinates(verticesCoordinates[i].x, verticesCoordinates[i].y); - } -}; - -/** SETTER FONT SIZE * */ -NetworkWidget.prototype.setVerticesFontSize = function(value) { - for ( var nodeId in this.getDataset().getVertices()) { - if (this.getDataset().getVertices().hasOwnProperty(nodeId)) { - this.getFormatter().getVertexById(nodeId).getDefault().setFontSize(value); - } - } -}; - -/** GETTERS * */ -NetworkWidget.prototype.getFormatter = function() { - return this.getGraphCanvas().getFormatter(); -}; -NetworkWidget.prototype.getLayout = function() { - return this.getGraphCanvas().getLayout(); -}; - -NetworkWidget.prototype.getDataset = function() { - return this.getGraphCanvas().getDataset(); -}; - -NetworkWidget.prototype.getGraphCanvas = function() { - return this.graphCanvas; -}; +NetworkWidget.prototype.getGraphCanvas = function() { + return this.graphCanvas; +}; RangeWhiskerGraph.prototype.cleanArray = GenericGraph.prototype.cleanArray; RangeWhiskerGraph.prototype.plotAxes = GenericGraph.prototype.plotAxes; @@ -14883,280 +14883,280 @@ RangeWhiskerGraph.prototype.plotWhisters = function(data, properties) { } } } - } - -}; - -RangeWhiskerGraph.prototype.draw = function(targetId, data) { - //this.calculate(data); - this.targetId = targetId; - var properties = (this.getDimensions(data)); - this.svg = SVG.createSVGCanvas(document.getElementById(this.targetId), [ [ "width", this.width ], [ "height", this.height ] ]); - this.plotAxes(properties); - this.plotWhisters(data, properties); -}; - -RangeWhiskerGraph.prototype.input = function() { - return DATADOC.getBoxWhikerData(); -}; - -RangeWhiskerGraph.prototype.test = function(targetId) { - var plot = new RangeWhiskerGraph({ - targetId : targetId, - height : 350, - width : 450, - maxBoxWidth : 25 - }); - plot.refresh(this.input()); -}; - -StdDevDyGraph.prototype.dblclick = DygraphWidget.prototype.dblclick; -StdDevDyGraph.prototype._createHTLMWrapper = DygraphWidget.prototype._createHTLMWrapper; -StdDevDyGraph.prototype.draw = DygraphWidget.prototype.draw; - -function StdDevDyGraph(targetId, args) { - this.scaled = false; - if (args == null) { - args = {}; - } - args.customBars = true; - DygraphWidget.prototype.constructor.call(this, targetId, args); -} - -StdDevDyGraph.prototype.input = function () { - return { - data : [ [ 1, [ 2, 3, 3.5 ], [ 4, 4.2, 5 ] ], [ 2, [ 5, 5.5, 5.7 ], [ 4, 4.2, 5 ] ] ], - colors : [ "blue", "red" ], - labels : [ "", 'data1', 'data2' ] - }; -}; - -StdDevDyGraph.prototype.test = function (targetId) { - var dygraphObject = new StdDevDyGraph(targetId, { - width : 500, - height : 400, - xlabel : "xLabel", - showRangeSelector : false + } + +}; + +RangeWhiskerGraph.prototype.draw = function(targetId, data) { + //this.calculate(data); + this.targetId = targetId; + var properties = (this.getDimensions(data)); + this.svg = SVG.createSVGCanvas(document.getElementById(this.targetId), [ [ "width", this.width ], [ "height", this.height ] ]); + this.plotAxes(properties); + this.plotWhisters(data, properties); +}; + +RangeWhiskerGraph.prototype.input = function() { + return DATADOC.getBoxWhikerData(); +}; + +RangeWhiskerGraph.prototype.test = function(targetId) { + var plot = new RangeWhiskerGraph({ + targetId : targetId, + height : 350, + width : 450, + maxBoxWidth : 25 + }); + plot.refresh(this.input()); +}; + +StdDevDyGraph.prototype.dblclick = DygraphWidget.prototype.dblclick; +StdDevDyGraph.prototype._createHTLMWrapper = DygraphWidget.prototype._createHTLMWrapper; +StdDevDyGraph.prototype.draw = DygraphWidget.prototype.draw; + +function StdDevDyGraph(targetId, args) { + this.scaled = false; + if (args == null) { + args = {}; + } + args.customBars = true; + DygraphWidget.prototype.constructor.call(this, targetId, args); +} + +StdDevDyGraph.prototype.input = function () { + return { + data : [ [ 1, [ 2, 3, 3.5 ], [ 4, 4.2, 5 ] ], [ 2, [ 5, 5.5, 5.7 ], [ 4, 4.2, 5 ] ] ], + colors : [ "blue", "red" ], + labels : [ "", 'data1', 'data2' ] + }; +}; + +StdDevDyGraph.prototype.test = function (targetId) { + var dygraphObject = new StdDevDyGraph(targetId, { + width : 500, + height : 400, + xlabel : "xLabel", + showRangeSelector : false + }); + + dygraphObject.draw(dygraphObject.input().data, dygraphObject.input().colors, dygraphObject.input().labels); +}; + + + +function AbinitioGrid(args) { + this.height = null; + this.width = null; + this.id = BUI.id(); + + if (args != null) { + if (args.height != null) { + this.height = args.height; + + if (args.width != null) { + this.width = args.width; + } + } + } + + this.onSelected = new Event(this); +}; + + +AbinitioGrid.prototype.refresh = function(subtractions){ + this.store.loadData(this._prepareData(subtractions)); +}; + +AbinitioGrid.prototype._prepareData = function(subtractions){ + /** Parsing data * */ + var models = []; + for (var l = 0; l < subtractions.length; l++) { + var subtraction = subtractions[l]; + for (var k = 0; k < subtraction.substractionToAbInitioModel3VOs.length; k++) { + var data = subtraction.substractionToAbInitioModel3VOs[k].abinitiomodel3VO; + if (data.averagedModel != null) { + models.push(data.averagedModel); + models[models.length - 1].type = "Reference"; + } + + if (data.shapeDeterminationModel != null) { + models.push(data.shapeDeterminationModel); + models[models.length - 1].type = "Refined"; + } + + if (data.modelList3VO != null) { + if (data.modelList3VO.modeltolist3VOs != null) { + for (var i = 0; i < data.modelList3VO.modeltolist3VOs.length; i++) { + models.push(data.modelList3VO.modeltolist3VOs[i].model3VO); + models[models.length - 1].type = "Model"; + } + } + } + } + } + return models; +}; + +AbinitioGrid.prototype.getPanel = function(){ + var _this = this; + + + var modelFields = [ "modelId", "type", "chiSqrt", "dmax", "firFile", "logFile", "fitFile", "pdbFile", "rfactor", "rg", "volume" ]; + Ext.define('AbinitioModel', { + extend : 'Ext.data.Model', + fields : modelFields + + }); + + /** + * Store in Memory + */ + this.store = Ext.create('Ext.data.Store', { + model : 'AbinitioModel', + autoload : true, + groupField : 'type' + }); + + + var groupingFeature = Ext.create('Ext.grid.feature.Grouping',{ + groupHeaderTpl: '{name} ({rows.length} model{[values.rows.length > 1 ? "s" : ""]})', + startCollapsed: true, + collapsible : true + }); + + this.grid = Ext.create('Ext.grid.Panel', { + collapsible : false, + resizable : true, + features: [groupingFeature], + autoscroll : true, + multiSelect : true, + store : this.store, + height : this.height, + width : this.width, + margin : 10, + columns : [ { + text : "Type", + dataindex : "type", + hidden : true, + renderer : function(a, b, record) { + return record.data.type; + }, + flex : 1 + }, + { + text : "ModelId", + dataindex : "modelId", + hidden : true, + renderer : function(a, b, record) { + return record.data.modelId; + + }, + flex : 1 + }, + + { + text : "chiSqrt", + dataindex : "chiSqrt", + renderer : function(a, b, record) { + if (record.data.dmax != null) { + return BUI.formatValuesUnits(record.data.chiSqrt, "", 12, this.decimals); + } + + }, + flex : 1 + }, + { + text : "Dmax", + dataindex : "dmax", + renderer : function(a, b, record) { + if (record.data.dmax != null) { + return BUI.formatValuesUnits(record.data.dmax, "nm", 12, this.decimals); + } + + }, + flex : 1 + }, { + text : "rFactor", + dataindex : "rfactor", + hidden : true, + renderer : function(a, b, record) { + if (record.data.rfactor != null) { + return record.data.rfactor; + } + }, + flex : 1 + }, { + text : "Rg", + dataindex : "rg", + renderer : function(a, b, record) { + if (record.data.rg != null) { + return BUI.formatValuesUnits(record.data.rg, "nm", 12, this.decimals); + } + + }, + flex : 1 + }, + { + text : "Volume", + dataindex : "volume", + renderer : function(a, b, record) { + if (record.raw.volume != null){ + return BUI.formatValuesUnits(record.raw.volume, '') + " nm3"; + } + }, + flex : 1 + }, + { + text : "PDB", + dataindex : "pdbFile", + renderer : function(a, b, record) { + if (record.data.pdbFile != null){ + return record.data.pdbFile.split("/")[record.data.pdbFile.split("/").length - 1]; + } + }, + flex : 1 + }, { + text : "Fir", + dataindex : "firFile", + renderer : function(a, b, record) { + if (record.data.firFile != null){ + return record.data.firFile.split("/")[record.data.firFile.split("/").length - 1]; + } + }, + flex : 1 + }, { + text : "LOG", + dataindex : "logFile", + hidden : true, + renderer : function(a, b, record) { + if (record.data.logFile != null){ + return record.data.logFile.split("/")[record.data.logFile.split("/").length - 1]; + } + }, + flex : 1 + } + ], + viewConfig : { + enableTextSelection : true, + preserveScrollOnRefresh : true, + stripeRows : true, + listeners : { + 'celldblclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + }, + 'cellclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + var models = []; + for (var i = 0; i < grid.getSelectionModel().selected.items.length; i++) { + models.push(grid.getSelectionModel().selected.items[i].raw); + } + _this.onSelected.notify(models); + } + } + } }); - - dygraphObject.draw(dygraphObject.input().data, dygraphObject.input().colors, dygraphObject.input().labels); + return this.grid; + }; - - -function AbinitioGrid(args) { - this.height = null; - this.width = null; - this.id = BUI.id(); - - if (args != null) { - if (args.height != null) { - this.height = args.height; - - if (args.width != null) { - this.width = args.width; - } - } - } - - this.onSelected = new Event(this); -}; - - -AbinitioGrid.prototype.refresh = function(subtractions){ - this.store.loadData(this._prepareData(subtractions)); -}; - -AbinitioGrid.prototype._prepareData = function(subtractions){ - /** Parsing data * */ - var models = []; - for (var l = 0; l < subtractions.length; l++) { - var subtraction = subtractions[l]; - for (var k = 0; k < subtraction.substractionToAbInitioModel3VOs.length; k++) { - var data = subtraction.substractionToAbInitioModel3VOs[k].abinitiomodel3VO; - if (data.averagedModel != null) { - models.push(data.averagedModel); - models[models.length - 1].type = "Reference"; - } - - if (data.shapeDeterminationModel != null) { - models.push(data.shapeDeterminationModel); - models[models.length - 1].type = "Refined"; - } - - if (data.modelList3VO != null) { - if (data.modelList3VO.modeltolist3VOs != null) { - for (var i = 0; i < data.modelList3VO.modeltolist3VOs.length; i++) { - models.push(data.modelList3VO.modeltolist3VOs[i].model3VO); - models[models.length - 1].type = "Model"; - } - } - } - } - } - return models; -}; - -AbinitioGrid.prototype.getPanel = function(){ - var _this = this; - - - var modelFields = [ "modelId", "type", "chiSqrt", "dmax", "firFile", "logFile", "fitFile", "pdbFile", "rfactor", "rg", "volume" ]; - Ext.define('AbinitioModel', { - extend : 'Ext.data.Model', - fields : modelFields - - }); - - /** - * Store in Memory - */ - this.store = Ext.create('Ext.data.Store', { - model : 'AbinitioModel', - autoload : true, - groupField : 'type' - }); - - - var groupingFeature = Ext.create('Ext.grid.feature.Grouping',{ - groupHeaderTpl: '{name} ({rows.length} model{[values.rows.length > 1 ? "s" : ""]})', - startCollapsed: true, - collapsible : true - }); - - this.grid = Ext.create('Ext.grid.Panel', { - collapsible : false, - resizable : true, - features: [groupingFeature], - autoscroll : true, - multiSelect : true, - store : this.store, - height : this.height, - width : this.width, - margin : 10, - columns : [ { - text : "Type", - dataindex : "type", - hidden : true, - renderer : function(a, b, record) { - return record.data.type; - }, - flex : 1 - }, - { - text : "ModelId", - dataindex : "modelId", - hidden : true, - renderer : function(a, b, record) { - return record.data.modelId; - - }, - flex : 1 - }, - - { - text : "chiSqrt", - dataindex : "chiSqrt", - renderer : function(a, b, record) { - if (record.data.dmax != null) { - return BUI.formatValuesUnits(record.data.chiSqrt, "", 12, this.decimals); - } - - }, - flex : 1 - }, - { - text : "Dmax", - dataindex : "dmax", - renderer : function(a, b, record) { - if (record.data.dmax != null) { - return BUI.formatValuesUnits(record.data.dmax, "nm", 12, this.decimals); - } - - }, - flex : 1 - }, { - text : "rFactor", - dataindex : "rfactor", - hidden : true, - renderer : function(a, b, record) { - if (record.data.rfactor != null) { - return record.data.rfactor; - } - }, - flex : 1 - }, { - text : "Rg", - dataindex : "rg", - renderer : function(a, b, record) { - if (record.data.rg != null) { - return BUI.formatValuesUnits(record.data.rg, "nm", 12, this.decimals); - } - - }, - flex : 1 - }, - { - text : "Volume", - dataindex : "volume", - renderer : function(a, b, record) { - if (record.raw.volume != null){ - return BUI.formatValuesUnits(record.raw.volume, '') + " nm3"; - } - }, - flex : 1 - }, - { - text : "PDB", - dataindex : "pdbFile", - renderer : function(a, b, record) { - if (record.data.pdbFile != null){ - return record.data.pdbFile.split("/")[record.data.pdbFile.split("/").length - 1]; - } - }, - flex : 1 - }, { - text : "Fir", - dataindex : "firFile", - renderer : function(a, b, record) { - if (record.data.firFile != null){ - return record.data.firFile.split("/")[record.data.firFile.split("/").length - 1]; - } - }, - flex : 1 - }, { - text : "LOG", - dataindex : "logFile", - hidden : true, - renderer : function(a, b, record) { - if (record.data.logFile != null){ - return record.data.logFile.split("/")[record.data.logFile.split("/").length - 1]; - } - }, - flex : 1 - } - ], - viewConfig : { - enableTextSelection : true, - preserveScrollOnRefresh : true, - stripeRows : true, - listeners : { - 'celldblclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - }, - 'cellclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - var models = []; - for (var i = 0; i < grid.getSelectionModel().selected.items.length; i++) { - models.push(grid.getSelectionModel().selected.items[i].raw); - } - _this.onSelected.notify(models); - } - } - } - }); - return this.grid; - -}; - function AdditiveGrid(args) { this.onRemoveButtonClicked = new Event(this); @@ -16236,255 +16236,255 @@ HPLCAnalysisGrid.prototype._getFramesColumn = function() { }; - - -/** - * Rigid body grid to show PDB, symmetry and multiplicity - * - * - * #onUploadFile click on upload file - */ -function AprioriRigidBodyGrid(args) { - - this.height = 250; - this.btnEditVisible = true; - this.btnRemoveVisible = true; - - if (args != null) { - if (args.height != null) { - this.height = args.height; - } - if (args.btnEditVisible != null) { - this.btnEditVisible = args.btnEditVisible; - } - if (args.btnRemoveVisible != null) { - this.btnRemoveVisible = args.btnRemoveVisible; - } - } - - /** Events **/ - this.onUploadFile = new Event(this); - this.onRemove = new Event(this); -} - -AprioriRigidBodyGrid.prototype._getColumns = function() { -}; - -AprioriRigidBodyGrid.prototype._getTopButtons = function() { - var _this = this; - /** Actions buttons **/ - var actions = []; - - /** ADD BUTTON **/ - actions.push(Ext.create('Ext.Action', { - icon : '../images/add.png', - text : 'Add', - disabled : false, - handler : function(widget, event) { - _this.onAddButtonClicked.notify(); - } - })); - - return actions; -}; - -AprioriRigidBodyGrid.prototype.refresh = function(macromolecule) { - this.macromolecule = macromolecule; - if (macromolecule != null){ - this.pdbStore.loadData(macromolecule.structure3VOs); - } -}; - -AprioriRigidBodyGrid.prototype._prepareData = function() { - var data = []; - for ( var i = 0; i < this.features.length; i++) { - data.push(this.features[i]); - } - return data; -}; - -AprioriRigidBodyGrid.prototype._getPlugins = function() { - var _this = this; - var plugins = []; - plugins.push(Ext.create('Ext.grid.plugin.RowEditing', { - clicksToEdit : 1, - listeners : { - validateedit : function(grid, e) { - /** Comments are always updatable* */ - e.record.raw.symmetry = e.newValues.symmetry; - e.record.raw.multiplicity = e.newValues.multiplicity; - - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, proposal) { - BIOSAXS.proposal.setItems(proposal); - _this.refresh(BIOSAXS.proposal.getMacromoleculeById(_this.macromolecule.macromoleculeId)); - _this.panel.setLoading(false); - }); - adapter.onError.attach(function() { - alert("Error"); - }); - - _this.panel.setLoading(); - adapter.saveStructure(e.record.raw); - } - } - })); - return plugins; -}; - -AprioriRigidBodyGrid.prototype.getPanel = function() { - var _this = this; - - this.pdbStore = Ext.create('Ext.data.Store', { - fields : [ 'filePath', 'structureId', 'structureType', 'symmetry', 'structureId', 'name', 'multiplicity' ], - groupField : 'structureType', - sorters : { - property : 'structureId', - direction : 'DESC' - } - }); - - var groupingFeature = Ext.create('Ext.grid.feature.Grouping', { - groupHeaderTpl : Ext.create('Ext.XTemplate', - "
{name:this.formatName}
", { - formatName : function(name) { - return name; - } - }), - hideGroupedHeader : true, - startCollapsed : false - }); - - this.panel = Ext.create('Ext.grid.Panel', { - margin : "15 10 0 10", - height : this.height, - store : this.pdbStore, - plugins : _this._getPlugins(), - tbar : [ { - text : 'Add Modeling Option (PDB)', - icon : '../images/add.png', - handler : function() { - _this.onUploadFile.notify('PDB', 'Upload PDB File'); - } - } - - ], - columns : [ - { - text : "structureId", - flex : 0.2, - hidden : true, - dataIndex : 'structureId', - sortable : true - }, - { - text : "File", - flex : 0.5, - dataIndex : 'filePath', - sortable : true, - hidden : true - }, - { - text : "PDB", - flex : 0.4, - dataIndex : 'name', - sortable : true - }, - { - text : "Symmetry", - flex : 0.2, - dataIndex : 'symmetry', - sortable : true, - editor : { - xtype : 'combobox', - typeAhead : true, - triggerAction : 'all', - selectOnTab : true, - store : [ [ "P1", "P1" ], [ "P2", "P2" ], [ "P3", "P3" ], [ "P4", "P4" ], [ "P5", "P5" ], [ "P6", "P6" ], [ "P32", "P32" ], [ "P42", "P42" ], - [ "P52", "P52" ], [ "P62", "P62" ], [ "P222", "P222" ] ], - } - }, { - text : "Multiplicity", - flex : 0.2, - dataIndex : 'multiplicity', - sortable : true, - editor : { - xtype : 'textfield' - } - - }, { - text : "Subunit", - flex : 0.2, - dataIndex : 'isSubunit', - sortable : true, - hidden : true - }, { - text : "Type", - flex : 0.2, - dataIndex : 'structureType', - sortable : true, - hidden : true - }, - - { - id : this.id + 'REMOVE', - flex : 0.2, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - return BUI.getRedButton('REMOVE'); - } - }, ], - - listeners : { - itemdblclick : function(dataview, record, item, e) { - _this._editExperiment(record.raw.experimentId); - }, - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'REMOVE') { - var dataAdapter = new BiosaxsDataAdapter(); - dataAdapter.onSuccess.attach(function() { - _this.panel.setLoading(false); - _this.onRemove.notify(); - }); - _this.panel.setLoading("Removing PDB file"); - dataAdapter.removeStructure(record.data.structureId); - } - - } - }, - viewConfig : { - getRowClass : function(record, rowIdx, params, store) { - if (record.raw.isSubunit != null) { - return "blue-row"; - } - } - } - }); - - return this.panel; -}; - - - - -AprioriRigidBodyGrid.prototype.input = function() { - return { - proposal : DATADOC.getProposal_10(), - dewars : DATADOC.getDewars_10() - - }; -}; - -AprioriRigidBodyGrid.prototype.test = function(targetId) { - var AprioriRigidBodyGrid = new AprioriRigidBodyGrid({ - height : 150 - }); - BIOSAXS.proposal = new Proposal(AprioriRigidBodyGrid.input().proposal); - var panel = AprioriRigidBodyGrid.getPanel(AprioriRigidBodyGrid.input().dewars); - panel.render(targetId); - -}; + + +/** + * Rigid body grid to show PDB, symmetry and multiplicity + * + * + * #onUploadFile click on upload file + */ +function AprioriRigidBodyGrid(args) { + + this.height = 250; + this.btnEditVisible = true; + this.btnRemoveVisible = true; + + if (args != null) { + if (args.height != null) { + this.height = args.height; + } + if (args.btnEditVisible != null) { + this.btnEditVisible = args.btnEditVisible; + } + if (args.btnRemoveVisible != null) { + this.btnRemoveVisible = args.btnRemoveVisible; + } + } + + /** Events **/ + this.onUploadFile = new Event(this); + this.onRemove = new Event(this); +} + +AprioriRigidBodyGrid.prototype._getColumns = function() { +}; + +AprioriRigidBodyGrid.prototype._getTopButtons = function() { + var _this = this; + /** Actions buttons **/ + var actions = []; + + /** ADD BUTTON **/ + actions.push(Ext.create('Ext.Action', { + icon : '../images/add.png', + text : 'Add', + disabled : false, + handler : function(widget, event) { + _this.onAddButtonClicked.notify(); + } + })); + + return actions; +}; + +AprioriRigidBodyGrid.prototype.refresh = function(macromolecule) { + this.macromolecule = macromolecule; + if (macromolecule != null){ + this.pdbStore.loadData(macromolecule.structure3VOs); + } +}; + +AprioriRigidBodyGrid.prototype._prepareData = function() { + var data = []; + for ( var i = 0; i < this.features.length; i++) { + data.push(this.features[i]); + } + return data; +}; + +AprioriRigidBodyGrid.prototype._getPlugins = function() { + var _this = this; + var plugins = []; + plugins.push(Ext.create('Ext.grid.plugin.RowEditing', { + clicksToEdit : 1, + listeners : { + validateedit : function(grid, e) { + /** Comments are always updatable* */ + e.record.raw.symmetry = e.newValues.symmetry; + e.record.raw.multiplicity = e.newValues.multiplicity; + + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, proposal) { + BIOSAXS.proposal.setItems(proposal); + _this.refresh(BIOSAXS.proposal.getMacromoleculeById(_this.macromolecule.macromoleculeId)); + _this.panel.setLoading(false); + }); + adapter.onError.attach(function() { + alert("Error"); + }); + + _this.panel.setLoading(); + adapter.saveStructure(e.record.raw); + } + } + })); + return plugins; +}; + +AprioriRigidBodyGrid.prototype.getPanel = function() { + var _this = this; + + this.pdbStore = Ext.create('Ext.data.Store', { + fields : [ 'filePath', 'structureId', 'structureType', 'symmetry', 'structureId', 'name', 'multiplicity' ], + groupField : 'structureType', + sorters : { + property : 'structureId', + direction : 'DESC' + } + }); + + var groupingFeature = Ext.create('Ext.grid.feature.Grouping', { + groupHeaderTpl : Ext.create('Ext.XTemplate', + "
{name:this.formatName}
", { + formatName : function(name) { + return name; + } + }), + hideGroupedHeader : true, + startCollapsed : false + }); + + this.panel = Ext.create('Ext.grid.Panel', { + margin : "15 10 0 10", + height : this.height, + store : this.pdbStore, + plugins : _this._getPlugins(), + tbar : [ { + text : 'Add Modeling Option (PDB)', + icon : '../images/add.png', + handler : function() { + _this.onUploadFile.notify('PDB', 'Upload PDB File'); + } + } + + ], + columns : [ + { + text : "structureId", + flex : 0.2, + hidden : true, + dataIndex : 'structureId', + sortable : true + }, + { + text : "File", + flex : 0.5, + dataIndex : 'filePath', + sortable : true, + hidden : true + }, + { + text : "PDB", + flex : 0.4, + dataIndex : 'name', + sortable : true + }, + { + text : "Symmetry", + flex : 0.2, + dataIndex : 'symmetry', + sortable : true, + editor : { + xtype : 'combobox', + typeAhead : true, + triggerAction : 'all', + selectOnTab : true, + store : [ [ "P1", "P1" ], [ "P2", "P2" ], [ "P3", "P3" ], [ "P4", "P4" ], [ "P5", "P5" ], [ "P6", "P6" ], [ "P32", "P32" ], [ "P42", "P42" ], + [ "P52", "P52" ], [ "P62", "P62" ], [ "P222", "P222" ] ], + } + }, { + text : "Multiplicity", + flex : 0.2, + dataIndex : 'multiplicity', + sortable : true, + editor : { + xtype : 'textfield' + } + + }, { + text : "Subunit", + flex : 0.2, + dataIndex : 'isSubunit', + sortable : true, + hidden : true + }, { + text : "Type", + flex : 0.2, + dataIndex : 'structureType', + sortable : true, + hidden : true + }, + + { + id : this.id + 'REMOVE', + flex : 0.2, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + return BUI.getRedButton('REMOVE'); + } + }, ], + + listeners : { + itemdblclick : function(dataview, record, item, e) { + _this._editExperiment(record.raw.experimentId); + }, + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'REMOVE') { + var dataAdapter = new BiosaxsDataAdapter(); + dataAdapter.onSuccess.attach(function() { + _this.panel.setLoading(false); + _this.onRemove.notify(); + }); + _this.panel.setLoading("Removing PDB file"); + dataAdapter.removeStructure(record.data.structureId); + } + + } + }, + viewConfig : { + getRowClass : function(record, rowIdx, params, store) { + if (record.raw.isSubunit != null) { + return "blue-row"; + } + } + } + }); + + return this.panel; +}; + + + + +AprioriRigidBodyGrid.prototype.input = function() { + return { + proposal : DATADOC.getProposal_10(), + dewars : DATADOC.getDewars_10() + + }; +}; + +AprioriRigidBodyGrid.prototype.test = function(targetId) { + var AprioriRigidBodyGrid = new AprioriRigidBodyGrid({ + height : 150 + }); + BIOSAXS.proposal = new Proposal(AprioriRigidBodyGrid.input().proposal); + var panel = AprioriRigidBodyGrid.getPanel(AprioriRigidBodyGrid.input().dewars); + panel.render(targetId); + +}; /** * It shows buffer grid with a top bar with "Add" button @@ -16513,159 +16513,552 @@ function BufferGrid(args) { this.tbar = args.tbar; } - if (args.collapsed != null) { - this.collapsed = args.collapsed; - } + if (args.collapsed != null) { + this.collapsed = args.collapsed; + } + + if (args.width != null) { + this.width = args.width; + } + } +} + +BufferGrid.prototype._edit = function(bufferId) { + var _this = this; + var window = new BufferWindow(); + window.onSuccess.attach(function(sender, proposal) { + _this.store.loadData(BIOSAXS.proposal.getBuffers()); + }); + window.draw(BIOSAXS.proposal.getBufferById(bufferId)); +}; + +BufferGrid.prototype.refresh = function(buffers) { + this.store.loadData(this._prepareData(buffers), false); +}; + +BufferGrid.prototype._prepareData = function(buffers) { + return buffers; +}; + +BufferGrid.prototype._getTbar = function() { + var _this = this; + var actions = []; + + actions.push(Ext.create('Ext.Action', { + icon : '../images/add.png', + text : 'Add buffer', + disabled : false, + handler : function(widget, event) { + var window = new BufferWindow(); + window.onSuccess.attach(function(sender) { + _this.store.loadData(BIOSAXS.proposal.getBuffers()); + }); + window.draw({}); + } + })); + return actions; +}; + +BufferGrid.prototype.getPanel = function(buffers) { + var _this = this; + + this.store = Ext.create('Ext.data.Store', { + fields : [ 'bufferId', 'acronym', 'name', 'composition' ], + data : buffers + }); + + this.store.sort('acronym'); + + var type = 'Ext.grid.Panel'; + if (this.searchBar == true) { + type = 'Ext.ux.LiveSearchGridPanel'; + } + + this.grid = Ext.create(type, { + title : 'Buffers', + collapsible : true, + collapsed : this.collapsed, + store : this.store, + height : this.height, + width : this.width, + columns : [ + /*{ + text : '', + dataIndex : 'bufferId', + width : 20, + renderer : function(val, y, sample) { + return BUI.getRectangleColorDIV(BIOSAXS.proposal.bufferColors[val], 10, 10); + } + },*/ + { + text : 'Acronym', + dataIndex : 'acronym', + flex : 1 + }, { + text : 'Name', + dataIndex : 'name', + flex : 1, + hidden : true + }, { + text : 'Composition', + dataIndex : 'composition', + flex : 1, + hidden : true + }, { + id : _this.id + 'buttonEditBuffer', + width : 80, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + return BUI.getGreenButton('EDIT'); + } + }, { + id : _this.id + 'buttonRemoveBuffer', + width : 85, + hidden : true, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + return BUI.getRedButton('REMOVE'); + } + } ], + flex : 1, + viewConfig : { + stripeRows : true, + listeners : { + 'celldblclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + _this._edit(record.data.bufferId); + }, + 'cellclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEditBuffer') { + _this._edit(record.data.bufferId); + } + + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemoveBuffer') { + BUI.showBetaWarning(); + } + } + + } + } + }); + + /** Adding the tbar **/ + if (this.tbar) { + this.grid.addDocked({ + xtype : 'toolbar', + items : this._getTbar() + }); + } + return this.grid; +}; + +BufferGrid.prototype.input = function() { + return new MacromoleculeGrid().input(); +}; + +BufferGrid.prototype.test = function(targetId) { + var bufferGrid = new BufferGrid({ + width : 800, + height : 350, + collapsed : false, + tbar : true + }); + + BIOSAXS.proposal = new Proposal(bufferGrid.input().proposal); + var panel = bufferGrid.getPanel(BIOSAXS.proposal.macromolecules); + panel.render(targetId); +}; + +/** + * A shipment may contains one or more cases where stock solutions and sample plates are stored + * + * @height + * @btnEditVisible + * @btnRemoveVisible + * + * #onEditButtonClicked + * #onAddButtonClicked + * #onRemoveButtonClicked + * #onDuplicateButtonClicked + */ +function CaseGrid(args) { + + this.height = 100; + this.btnEditVisible = true; + this.btnRemoveVisible = true; + + if (args != null) { + if (args.height != null) { + this.height = args.height; + } + if (args.btnEditVisible != null) { + this.btnEditVisible = args.btnEditVisible; + } + if (args.btnRemoveVisible != null) { + this.btnRemoveVisible = args.btnRemoveVisible; + } + } + + /** Events **/ + this.onEditButtonClicked = new Event(this); + this.onAddButtonClicked = new Event(this); + this.onRemoveButtonClicked = new Event(this); + this.onDuplicateButtonClicked = new Event(this); +} + +CaseGrid.prototype._getColumns = function() { + var _this = this; + + function actionItemRenderer(value, meta, record, rowIx, ColIx, store) { + /*if (record.raw.specimen3VOs.length > 0){ + return 'x-hide-display'; + }*/ + } + + var columns = [ + { + header : 'Code', + dataIndex : 'code', + name : 'code', + type : 'string', + flex : 1 + }, + { + header : 'Bar Code', + dataIndex : 'barCode', + name : 'barCode', + type : 'string', + flex : 1, + hidden : true + }, + { + header : 'BeamLine', + dataIndex : 'barCode', + type : 'string', + flex : 1, + renderer : function(comp, val, record) { + if (record.raw.sessionVO != null) { + return "" + record.raw.sessionVO.beamlineName + ""; + } + } + }, + { + header : 'Session', + dataIndex : 'barCode', + type : 'string', + flex : 1, + renderer : function(comp, val, record) { + if (record.raw.sessionVO != null) { + return "" + moment(record.raw.sessionVO.startDate).format("MMM Do YY") + ""; + } + } + }, + { + header : 'Status', + dataIndex : 'dewarStatus', + name : 'dewarStatus', + type : 'string', + flex : 1, + renderer : function(comp, val, record) { + if (new String(record.raw.dewarStatus).toUpperCase() == 'OPENED') { + return "" + new String(record.raw.dewarStatus).toUpperCase() + ""; + } + return "" + new String(record.raw.dewarStatus).toUpperCase() + ""; + } + }, + { + header : 'Type', + dataIndex : 'type', + name : 'type', + type : 'string', + flex : 1, + hidden : true + }, + { + header : 'Sample Plates', + dataIndex : 'plates', + name : 'plates', + type : 'string', + flex : 1, + hidden : true + }, + { + header : 'Stock Solutions', + dataIndex : 'plates', + name : 'plates', + type : 'string', + width : 100, + renderer : function(comp, val, record) { + var html = "
"; + var stockSolutions = BIOSAXS.proposal.getStockSolutionsByDewarId(record.raw.dewarId); + html = html + "" + stockSolutions.length + " x"; + return html + "
"; + } + }, { + header : 'isStorageDewar', + dataIndex : 'isStorageDewar', + name : 'isStorageDewar', + type : 'string', + flex : 1, + hidden : true + }, { + header : 'Tracking Number From Synchrotron', + dataIndex : 'trackingNumberFromSynchrotron', + name : 'trackingNumberFromSynchrotron', + type : 'string', + flex : 1, + hidden : true + }, { + header : 'Tracking Number To Synchrotron', + dataIndex : 'trackingNumberToSynchrotron', + name : 'trackingNumberToSynchrotron', + type : 'string', + flex : 1, + hidden : true + }, { + header : 'Storage Location', + dataIndex : 'storageLocation', + name : 'storageLocation', + type : 'string', + flex : 1, + hidden : false + }, { + header : 'Comments', + dataIndex : 'comments', + name : 'comments', + type : 'string', + flex : 1, + hidden : false + } + ]; + + if (this.btnEditVisible) { + columns.push({ + id : _this.id + 'buttonEdit', + text : '', + hidden : !_this.btnEditVisible, + width : 85, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + return BUI.getGreenButton('EDIT'); + } + }); + } - if (args.width != null) { - this.width = args.width; - } + if (this.btnRemoveVisible) { + columns.push({ + id : _this.id + 'buttonRemove', + width : 85, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + if (_this.btnRemoveVisible) { + return BUI.getRedButton('REMOVE'); + } + } + }); } -} -BufferGrid.prototype._edit = function(bufferId) { - var _this = this; - var window = new BufferWindow(); - window.onSuccess.attach(function(sender, proposal) { - _this.store.loadData(BIOSAXS.proposal.getBuffers()); + columns.push({ + dataIndex : 'comments', + type : 'string', + width : 85, + hidden : false, + renderer : function(comp, val, record) { + return BUI.getBlueButton("LABELS", { + href : BUI.getPrintcomponentURL(record.raw.dewarId) + }); + } }); - window.draw(BIOSAXS.proposal.getBufferById(bufferId)); -}; - -BufferGrid.prototype.refresh = function(buffers) { - this.store.loadData(this._prepareData(buffers), false); -}; -BufferGrid.prototype._prepareData = function(buffers) { - return buffers; + return columns; }; -BufferGrid.prototype._getTbar = function() { +CaseGrid.prototype._getTopButtons = function() { var _this = this; + /** Actions buttons **/ var actions = []; + /** ADD BUTTON **/ actions.push(Ext.create('Ext.Action', { icon : '../images/add.png', - text : 'Add buffer', + text : 'Add', disabled : false, handler : function(widget, event) { - var window = new BufferWindow(); - window.onSuccess.attach(function(sender) { - _this.store.loadData(BIOSAXS.proposal.getBuffers()); - }); - window.draw({}); + _this.onAddButtonClicked.notify(); } })); + return actions; }; -BufferGrid.prototype.getPanel = function(buffers) { - var _this = this; +CaseGrid.prototype.refresh = function(dewars) { + this.features = dewars; + this.store.loadData(this._prepareData(dewars), false); +}; - this.store = Ext.create('Ext.data.Store', { - fields : [ 'bufferId', 'acronym', 'name', 'composition' ], - data : buffers - }); +CaseGrid.prototype._sort = function(store) { + store.sort('dewarId', 'DESC'); +}; - this.store.sort('acronym'); +CaseGrid.prototype._prepareData = function() { + var data = []; + for ( var i = 0; i < this.features.length; i++) { + data.push(this.features[i]); + } + return data; +}; - var type = 'Ext.grid.Panel'; - if (this.searchBar == true) { - type = 'Ext.ux.LiveSearchGridPanel'; +CaseGrid.prototype.getPanel = function(dewars, plates) { + this.features = dewars; + this.plates = plates; + return this._renderGrid(); +}; + +CaseGrid.prototype._edit = function(dewar) { + var _this = this; + var caseWindow = new CaseWindow(); + /**SAVED **/ + caseWindow.onSaved.attach(function(sender, dewar) { + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, shipment) { + _this.refresh(shipment.dewarVOs); + }); + adapter.saveCase(BIOSAXS.proposal.getShipmentByDewarId(dewar.dewarId).shippingId, dewar); + }); + caseWindow.draw(dewar); +}; + +CaseGrid.prototype._getStoreFields = function(data) { + return [ { + name : 'dewarId', + type : 'string' + }, { + name : 'barCode', + type : 'string' + }, { + name : 'code', + type : 'string' + }, { + name : 'comments', + type : 'string' + }, { + name : 'dewarStatus', + type : 'string' + }, { + name : 'isStorageDewar', + type : 'string' + }, { + name : 'plates', + type : 'string' + }, { + name : 'transportValue', + type : 'string' + }, { + name : 'trackingNumberFromSynchrotron', + type : 'string' + }, { + name : 'trackingNumberToSynchrotron', + type : 'string' + }, { + name : 'timeStamp', + type : 'string' + }, { + name : 'storageLocation', + type : 'string' + }, { + name : 'type', + type : 'string' } - this.grid = Ext.create(type, { - title : 'Buffers', - collapsible : true, - collapsed : this.collapsed, - store : this.store, + ]; +}; + +CaseGrid.prototype._renderGrid = function() { + var _this = this; + + /** Store **/ + var data = this._prepareData(); + this.store = Ext.create('Ext.data.Store', { + fields : this._getStoreFields(data), + autoload : true, + data : data + }); + this._sort(this.store); + + this.store.loadData(data, false); + + this.grid = Ext.create('Ext.grid.Panel', { + style : { + padding : 5 + }, height : this.height, - width : this.width, - columns : [ - /*{ - text : '', - dataIndex : 'bufferId', - width : 20, - renderer : function(val, y, sample) { - return BUI.getRectangleColorDIV(BIOSAXS.proposal.bufferColors[val], 10, 10); - } - },*/ - { - text : 'Acronym', - dataIndex : 'acronym', - flex : 1 - }, { - text : 'Name', - dataIndex : 'name', - flex : 1, - hidden : true - }, { - text : 'Composition', - dataIndex : 'composition', - flex : 1, - hidden : true - }, { - id : _this.id + 'buttonEditBuffer', - width : 80, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - return BUI.getGreenButton('EDIT'); - } - }, { - id : _this.id + 'buttonRemoveBuffer', - width : 85, - hidden : true, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - return BUI.getRedButton('REMOVE'); - } - } ], - flex : 1, + store : this.store, + columns : this._getColumns(), viewConfig : { stripeRows : true, listeners : { - 'celldblclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - _this._edit(record.data.bufferId); + itemdblclick : function(dataview, record, item, e) { + _this._edit(record.raw); }, - 'cellclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEditBuffer') { - _this._edit(record.data.bufferId); + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEdit') { + _this._edit(record.raw); } - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemoveBuffer') { - BUI.showBetaWarning(); + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemove') { + _this.onRemoveButtonClicked.notify(_this.store.getAt(rowIndex).raw.dewarId); } } - } + }, + selModel : { + mode : 'SINGLE' } }); - /** Adding the tbar **/ - if (this.tbar) { - this.grid.addDocked({ - xtype : 'toolbar', - items : this._getTbar() - }); - } + var actions = _this._getTopButtons(); + this.grid.addDocked({ + xtype : 'toolbar', + items : actions + }); + + this.grid.getSelectionModel().on({ + selectionchange : function(sm, selections) { + if (selections.length) { + for ( var i = 0; i < actions.length; i++) { + if (actions[i].enable) { + actions[i].enable(); + } + } + } else { + for ( var i = 0; i < actions.length; i++) { + if (actions[i].alwaysEnabled == false) { + if (actions[i].disable) { + actions[i].disable(); + } + } + } + } + } + }); return this.grid; }; -BufferGrid.prototype.input = function() { - return new MacromoleculeGrid().input(); +CaseGrid.prototype.input = function() { + return { + proposal : DATADOC.getProposal_10(), + dewars : DATADOC.getDewars_10() + + }; }; -BufferGrid.prototype.test = function(targetId) { - var bufferGrid = new BufferGrid({ - width : 800, - height : 350, - collapsed : false, - tbar : true +CaseGrid.prototype.test = function(targetId) { + var CaseGrid = new CaseGrid({ + height : 150 }); - - BIOSAXS.proposal = new Proposal(bufferGrid.input().proposal); - var panel = bufferGrid.getPanel(BIOSAXS.proposal.macromolecules); + BIOSAXS.proposal = new Proposal(CaseGrid.input().proposal); + var panel = CaseGrid.getPanel(CaseGrid.input().dewars); panel.render(targetId); + }; /** @@ -16680,7 +17073,7 @@ BufferGrid.prototype.test = function(targetId) { * #onRemoveButtonClicked * #onDuplicateButtonClicked */ -function CaseGrid(args) { +function ExampleGrid(args) { this.height = 100; this.btnEditVisible = true; @@ -16705,7 +17098,7 @@ function CaseGrid(args) { this.onDuplicateButtonClicked = new Event(this); } -CaseGrid.prototype._getColumns = function() { +ExampleGrid.prototype._getColumns = function() { var _this = this; function actionItemRenderer(value, meta, record, rowIx, ColIx, store) { @@ -16872,7 +17265,7 @@ CaseGrid.prototype._getColumns = function() { return columns; }; -CaseGrid.prototype._getTopButtons = function() { +ExampleGrid.prototype._getTopButtons = function() { var _this = this; /** Actions buttons **/ var actions = []; @@ -16890,16 +17283,16 @@ CaseGrid.prototype._getTopButtons = function() { return actions; }; -CaseGrid.prototype.refresh = function(dewars) { +ExampleGrid.prototype.refresh = function(dewars) { this.features = dewars; this.store.loadData(this._prepareData(dewars), false); }; -CaseGrid.prototype._sort = function(store) { +ExampleGrid.prototype._sort = function(store) { store.sort('dewarId', 'DESC'); }; -CaseGrid.prototype._prepareData = function() { +ExampleGrid.prototype._prepareData = function() { var data = []; for ( var i = 0; i < this.features.length; i++) { data.push(this.features[i]); @@ -16907,27 +17300,66 @@ CaseGrid.prototype._prepareData = function() { return data; }; -CaseGrid.prototype.getPanel = function(dewars, plates) { - this.features = dewars; - this.plates = plates; - return this._renderGrid(); -}; +ExampleGrid.prototype.getPanel = function() { + this.grid = Ext.create('Ext.grid.Panel', { + style : { + padding : 5 + }, + height : this.height, + store : this.store, + columns : this._getColumns(), + viewConfig : { + stripeRows : true, + listeners : { + itemdblclick : function(dataview, record, item, e) { + _this._edit(record.raw); + }, + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEdit') { + _this._edit(record.raw); + } -CaseGrid.prototype._edit = function(dewar) { - var _this = this; - var caseWindow = new CaseWindow(); - /**SAVED **/ - caseWindow.onSaved.attach(function(sender, dewar) { - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, shipment) { - _this.refresh(shipment.dewarVOs); - }); - adapter.saveCase(BIOSAXS.proposal.getShipmentByDewarId(dewar.dewarId).shippingId, dewar); + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemove') { + _this.onRemoveButtonClicked.notify(_this.store.getAt(rowIndex).raw.dewarId); + } + } + } + }, + selModel : { + mode : 'SINGLE' + } }); - caseWindow.draw(dewar); + + var actions = _this._getTopButtons(); + this.grid.addDocked({ + xtype : 'toolbar', + items : actions + }); + + this.grid.getSelectionModel().on({ + selectionchange : function(sm, selections) { + if (selections.length) { + for ( var i = 0; i < actions.length; i++) { + if (actions[i].enable) { + actions[i].enable(); + } + } + } else { + for ( var i = 0; i < actions.length; i++) { + if (actions[i].alwaysEnabled == false) { + if (actions[i].disable) { + actions[i].disable(); + } + } + } + } + } + }); + return this.grid; }; -CaseGrid.prototype._getStoreFields = function(data) { + +ExampleGrid.prototype._getStoreFields = function(data) { return [ { name : 'dewarId', type : 'string' @@ -16972,7 +17404,7 @@ CaseGrid.prototype._getStoreFields = function(data) { ]; }; -CaseGrid.prototype._renderGrid = function() { +ExampleGrid.prototype._renderGrid = function() { var _this = this; /** Store **/ @@ -17043,7 +17475,7 @@ CaseGrid.prototype._renderGrid = function() { return this.grid; }; -CaseGrid.prototype.input = function() { +ExampleGrid.prototype.input = function() { return { proposal : DATADOC.getProposal_10(), dewars : DATADOC.getDewars_10() @@ -17051,447 +17483,15 @@ CaseGrid.prototype.input = function() { }; }; -CaseGrid.prototype.test = function(targetId) { - var CaseGrid = new CaseGrid({ +ExampleGrid.prototype.test = function(targetId) { + var ExampleGrid = new ExampleGrid({ height : 150 }); - BIOSAXS.proposal = new Proposal(CaseGrid.input().proposal); - var panel = CaseGrid.getPanel(CaseGrid.input().dewars); - panel.render(targetId); - -}; - -/** - * A shipment may contains one or more cases where stock solutions and sample plates are stored - * - * @height - * @btnEditVisible - * @btnRemoveVisible - * - * #onEditButtonClicked - * #onAddButtonClicked - * #onRemoveButtonClicked - * #onDuplicateButtonClicked - */ -function ExampleGrid(args) { - - this.height = 100; - this.btnEditVisible = true; - this.btnRemoveVisible = true; - - if (args != null) { - if (args.height != null) { - this.height = args.height; - } - if (args.btnEditVisible != null) { - this.btnEditVisible = args.btnEditVisible; - } - if (args.btnRemoveVisible != null) { - this.btnRemoveVisible = args.btnRemoveVisible; - } - } - - /** Events **/ - this.onEditButtonClicked = new Event(this); - this.onAddButtonClicked = new Event(this); - this.onRemoveButtonClicked = new Event(this); - this.onDuplicateButtonClicked = new Event(this); -} - -ExampleGrid.prototype._getColumns = function() { - var _this = this; - - function actionItemRenderer(value, meta, record, rowIx, ColIx, store) { - /*if (record.raw.specimen3VOs.length > 0){ - return 'x-hide-display'; - }*/ - } - - var columns = [ - { - header : 'Code', - dataIndex : 'code', - name : 'code', - type : 'string', - flex : 1 - }, - { - header : 'Bar Code', - dataIndex : 'barCode', - name : 'barCode', - type : 'string', - flex : 1, - hidden : true - }, - { - header : 'BeamLine', - dataIndex : 'barCode', - type : 'string', - flex : 1, - renderer : function(comp, val, record) { - if (record.raw.sessionVO != null) { - return "" + record.raw.sessionVO.beamlineName + ""; - } - } - }, - { - header : 'Session', - dataIndex : 'barCode', - type : 'string', - flex : 1, - renderer : function(comp, val, record) { - if (record.raw.sessionVO != null) { - return "" + moment(record.raw.sessionVO.startDate).format("MMM Do YY") + ""; - } - } - }, - { - header : 'Status', - dataIndex : 'dewarStatus', - name : 'dewarStatus', - type : 'string', - flex : 1, - renderer : function(comp, val, record) { - if (new String(record.raw.dewarStatus).toUpperCase() == 'OPENED') { - return "" + new String(record.raw.dewarStatus).toUpperCase() + ""; - } - return "" + new String(record.raw.dewarStatus).toUpperCase() + ""; - } - }, - { - header : 'Type', - dataIndex : 'type', - name : 'type', - type : 'string', - flex : 1, - hidden : true - }, - { - header : 'Sample Plates', - dataIndex : 'plates', - name : 'plates', - type : 'string', - flex : 1, - hidden : true - }, - { - header : 'Stock Solutions', - dataIndex : 'plates', - name : 'plates', - type : 'string', - width : 100, - renderer : function(comp, val, record) { - var html = "
"; - var stockSolutions = BIOSAXS.proposal.getStockSolutionsByDewarId(record.raw.dewarId); - html = html + "" + stockSolutions.length + " x"; - return html + "
"; - } - }, { - header : 'isStorageDewar', - dataIndex : 'isStorageDewar', - name : 'isStorageDewar', - type : 'string', - flex : 1, - hidden : true - }, { - header : 'Tracking Number From Synchrotron', - dataIndex : 'trackingNumberFromSynchrotron', - name : 'trackingNumberFromSynchrotron', - type : 'string', - flex : 1, - hidden : true - }, { - header : 'Tracking Number To Synchrotron', - dataIndex : 'trackingNumberToSynchrotron', - name : 'trackingNumberToSynchrotron', - type : 'string', - flex : 1, - hidden : true - }, { - header : 'Storage Location', - dataIndex : 'storageLocation', - name : 'storageLocation', - type : 'string', - flex : 1, - hidden : false - }, { - header : 'Comments', - dataIndex : 'comments', - name : 'comments', - type : 'string', - flex : 1, - hidden : false - } - ]; - - if (this.btnEditVisible) { - columns.push({ - id : _this.id + 'buttonEdit', - text : '', - hidden : !_this.btnEditVisible, - width : 85, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - return BUI.getGreenButton('EDIT'); - } - }); - } - - if (this.btnRemoveVisible) { - columns.push({ - id : _this.id + 'buttonRemove', - width : 85, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - if (_this.btnRemoveVisible) { - return BUI.getRedButton('REMOVE'); - } - } - }); - } - - columns.push({ - dataIndex : 'comments', - type : 'string', - width : 85, - hidden : false, - renderer : function(comp, val, record) { - return BUI.getBlueButton("LABELS", { - href : BUI.getPrintcomponentURL(record.raw.dewarId) - }); - } - }); - - return columns; -}; - -ExampleGrid.prototype._getTopButtons = function() { - var _this = this; - /** Actions buttons **/ - var actions = []; - - /** ADD BUTTON **/ - actions.push(Ext.create('Ext.Action', { - icon : '../images/add.png', - text : 'Add', - disabled : false, - handler : function(widget, event) { - _this.onAddButtonClicked.notify(); - } - })); - - return actions; -}; - -ExampleGrid.prototype.refresh = function(dewars) { - this.features = dewars; - this.store.loadData(this._prepareData(dewars), false); -}; - -ExampleGrid.prototype._sort = function(store) { - store.sort('dewarId', 'DESC'); -}; - -ExampleGrid.prototype._prepareData = function() { - var data = []; - for ( var i = 0; i < this.features.length; i++) { - data.push(this.features[i]); - } - return data; -}; - -ExampleGrid.prototype.getPanel = function() { - this.grid = Ext.create('Ext.grid.Panel', { - style : { - padding : 5 - }, - height : this.height, - store : this.store, - columns : this._getColumns(), - viewConfig : { - stripeRows : true, - listeners : { - itemdblclick : function(dataview, record, item, e) { - _this._edit(record.raw); - }, - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEdit') { - _this._edit(record.raw); - } - - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemove') { - _this.onRemoveButtonClicked.notify(_this.store.getAt(rowIndex).raw.dewarId); - } - } - } - }, - selModel : { - mode : 'SINGLE' - } - }); - - var actions = _this._getTopButtons(); - this.grid.addDocked({ - xtype : 'toolbar', - items : actions - }); - - this.grid.getSelectionModel().on({ - selectionchange : function(sm, selections) { - if (selections.length) { - for ( var i = 0; i < actions.length; i++) { - if (actions[i].enable) { - actions[i].enable(); - } - } - } else { - for ( var i = 0; i < actions.length; i++) { - if (actions[i].alwaysEnabled == false) { - if (actions[i].disable) { - actions[i].disable(); - } - } - } - } - } - }); - return this.grid; -}; - - -ExampleGrid.prototype._getStoreFields = function(data) { - return [ { - name : 'dewarId', - type : 'string' - }, { - name : 'barCode', - type : 'string' - }, { - name : 'code', - type : 'string' - }, { - name : 'comments', - type : 'string' - }, { - name : 'dewarStatus', - type : 'string' - }, { - name : 'isStorageDewar', - type : 'string' - }, { - name : 'plates', - type : 'string' - }, { - name : 'transportValue', - type : 'string' - }, { - name : 'trackingNumberFromSynchrotron', - type : 'string' - }, { - name : 'trackingNumberToSynchrotron', - type : 'string' - }, { - name : 'timeStamp', - type : 'string' - }, { - name : 'storageLocation', - type : 'string' - }, { - name : 'type', - type : 'string' - } - - ]; -}; - -ExampleGrid.prototype._renderGrid = function() { - var _this = this; - - /** Store **/ - var data = this._prepareData(); - this.store = Ext.create('Ext.data.Store', { - fields : this._getStoreFields(data), - autoload : true, - data : data - }); - this._sort(this.store); - - this.store.loadData(data, false); - - this.grid = Ext.create('Ext.grid.Panel', { - style : { - padding : 5 - }, - height : this.height, - store : this.store, - columns : this._getColumns(), - viewConfig : { - stripeRows : true, - listeners : { - itemdblclick : function(dataview, record, item, e) { - _this._edit(record.raw); - }, - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEdit') { - _this._edit(record.raw); - } - - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemove') { - _this.onRemoveButtonClicked.notify(_this.store.getAt(rowIndex).raw.dewarId); - } - } - } - }, - selModel : { - mode : 'SINGLE' - } - }); - - var actions = _this._getTopButtons(); - this.grid.addDocked({ - xtype : 'toolbar', - items : actions - }); - - this.grid.getSelectionModel().on({ - selectionchange : function(sm, selections) { - if (selections.length) { - for ( var i = 0; i < actions.length; i++) { - if (actions[i].enable) { - actions[i].enable(); - } - } - } else { - for ( var i = 0; i < actions.length; i++) { - if (actions[i].alwaysEnabled == false) { - if (actions[i].disable) { - actions[i].disable(); - } - } - } - } - } - }); - return this.grid; -}; - -ExampleGrid.prototype.input = function() { - return { - proposal : DATADOC.getProposal_10(), - dewars : DATADOC.getDewars_10() - - }; -}; - -ExampleGrid.prototype.test = function(targetId) { - var ExampleGrid = new ExampleGrid({ - height : 150 - }); - BIOSAXS.proposal = new Proposal(ExampleGrid.input().proposal); - var panel = ExampleGrid.getPanel(ExampleGrid.input().dewars); - panel.render(targetId); - -}; + BIOSAXS.proposal = new Proposal(ExampleGrid.input().proposal); + var panel = ExampleGrid.getPanel(ExampleGrid.input().dewars); + panel.render(targetId); + +}; /** @@ -18106,188 +18106,188 @@ ExperimentGrid.prototype.test = function(targetId) { panel.render(targetId); }; - -function FitStructureToExperimentDataGrid(args) { - this.height = null; - this.width = null; - this.id = BUI.id(); - - if (args != null) { - if (args.height != null) { - this.height = args.height; - - if (args.width != null) { - this.width = args.width; - } - } - } - - this.onSelected = new Event(this); -} - -FitStructureToExperimentDataGrid.prototype.getStructuresByMacromolecule = function(macromolecule) { - var structures = []; - if (macromolecule.structure3VOs != null) { - if (macromolecule.structure3VOs.length > 0) { - for (var i = 0; i < macromolecule.structure3VOs.length; i++) { - structures.push(macromolecule.structure3VOs[i]); - } - } - } - return structures; -}; - -FitStructureToExperimentDataGrid.prototype._prepareData = function(subtractions) { - var data = []; - for (var i = 0; i < subtractions.length; i++) { - - for (var j = 0; j < subtractions[i].fitStructureToExperimentalData3VOs.length; j++) { - var fit = subtractions[i].fitStructureToExperimentalData3VOs[j]; - data.push({ - fit : fit.fitFilePath, - fitStructureToExperimentalDataId : fit.fitStructureToExperimentalDataId, - mixtureToStructure3VOs : fit.mixtureToStructure3VOs, - subtractedFile : subtractions[i].substractedFilePath - }); - } - } - return data; - -}; - -FitStructureToExperimentDataGrid.prototype.refresh = function(subtractions) { - this.store.loadData(this._prepareData(subtractions), false); -}; - -FitStructureToExperimentDataGrid.prototype.getPanel = function() { - var _this = this; - this.store = Ext.create('Ext.data.Store', { - fields : [ 'fit', 'subtractedFile', 'structureId', 'fitFilePath', 'mixtureToStructure3VOs' ], - data : [] - }); - - this.store.sort([ { - property : 'name', - direction : 'ASC' - } ]); - - this.selModel = Ext.create('Ext.selection.RowModel', { - allowDeselect : true, - mode : 'MULTI', - listeners : { - selectionchange : function(sm, selections) { - var selected = []; - for (var i = 0; i < selections.length; i++) { - selected.push(selections[i].raw); - } - _this.onSelected.notify(selected); - } - } - }); - - this.panel = Ext.create('Ext.grid.Panel', { - store : this.store, - deferredRender : false, - width : this.width, - height : this.height, - margin : 10, - selModel : this.selModel, - columns : [ { - text : 'Name', - dataIndex : 'fit', - flex : 1, - renderer : function(val, b, record) { - return BUI.getFileName(val); - } - }, { - text : 'PDB', - dataIndex : 'mixtureToStructure3VOs', - flex : 1, - renderer : function(values, b, record) { - var html = ""; - for (var i = 0; i < values.length; i++) { - var structure = BIOSAXS.proposal.getStructuresById(values[i].structureId); - html = html + ""; - if (structure != null){ - html = html + ""; - } - html = html + ""; - } - return html + "
" + structure.name + "
"; - } - }, { - text : 'Volume Fraction', - dataIndex : 'mixtureToStructure3VOs', - flex : 1, - renderer : function(values, b, record) { - var html = ""; - for (var i = 0; i < values.length; i++) { - html = html + ""; - html = html + ""; - html = html + ""; - } - - return html + "
" + values[i].volumeFraction + "
"; - } - },{ - text : 'Subtraction', - dataIndex : 'subtractedFile', - flex : 1, - renderer : function(values, b, record) { - return values.split("/")[values.split("/").length - 1]; - } - },], - - viewConfig : { - enableTextSelection : true, - preserveScrollOnRefresh : true - }, - listeners : { - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - }, - afterrender : function() { - } - } - }); - return this.panel; -}; - -/** Static method **/ -FitStructureToExperimentDataGrid.prototype.RUNFitScattering = function(subtractionId, structureId) { - var _this = this; - /** Add to Workflow **/ - var adapter = new BiosaxsDataAdapter(); - var workflow = { - 'workflowTitle' : 'FitExperimentalDatatoStructure', - 'comments' : 'FitExperimentalDatatoStructure run from ISPyB for subtractionId: ' + subtractionId + ' and structureId ' + structureId - } - - var inputs = [ { - name : 'subtractionId', - value : subtractionId - }, { - name : 'structureId', - value : structureId - } ]; - - adapter.onSuccess.attach(function(sender, data) { - /** Add to Fit **/ - var adapter2 = new BiosaxsDataAdapter(); - var fit = { - 'workflowId' : data.workflowId, - 'subtractionId' : subtractionId, - 'structureId' : structureId, - 'comments' : 'Sent to workflow engine' - } - adapter2.onSuccess.attach(function(sender, fit) { - _this.refresh(_this.subtractionId, _this.macromolecule); - }); - adapter2.addFitStructureData(fit); - - }); - adapter.addWorkflow(workflow, inputs); - -}; + +function FitStructureToExperimentDataGrid(args) { + this.height = null; + this.width = null; + this.id = BUI.id(); + + if (args != null) { + if (args.height != null) { + this.height = args.height; + + if (args.width != null) { + this.width = args.width; + } + } + } + + this.onSelected = new Event(this); +} + +FitStructureToExperimentDataGrid.prototype.getStructuresByMacromolecule = function(macromolecule) { + var structures = []; + if (macromolecule.structure3VOs != null) { + if (macromolecule.structure3VOs.length > 0) { + for (var i = 0; i < macromolecule.structure3VOs.length; i++) { + structures.push(macromolecule.structure3VOs[i]); + } + } + } + return structures; +}; + +FitStructureToExperimentDataGrid.prototype._prepareData = function(subtractions) { + var data = []; + for (var i = 0; i < subtractions.length; i++) { + + for (var j = 0; j < subtractions[i].fitStructureToExperimentalData3VOs.length; j++) { + var fit = subtractions[i].fitStructureToExperimentalData3VOs[j]; + data.push({ + fit : fit.fitFilePath, + fitStructureToExperimentalDataId : fit.fitStructureToExperimentalDataId, + mixtureToStructure3VOs : fit.mixtureToStructure3VOs, + subtractedFile : subtractions[i].substractedFilePath + }); + } + } + return data; + +}; + +FitStructureToExperimentDataGrid.prototype.refresh = function(subtractions) { + this.store.loadData(this._prepareData(subtractions), false); +}; + +FitStructureToExperimentDataGrid.prototype.getPanel = function() { + var _this = this; + this.store = Ext.create('Ext.data.Store', { + fields : [ 'fit', 'subtractedFile', 'structureId', 'fitFilePath', 'mixtureToStructure3VOs' ], + data : [] + }); + + this.store.sort([ { + property : 'name', + direction : 'ASC' + } ]); + + this.selModel = Ext.create('Ext.selection.RowModel', { + allowDeselect : true, + mode : 'MULTI', + listeners : { + selectionchange : function(sm, selections) { + var selected = []; + for (var i = 0; i < selections.length; i++) { + selected.push(selections[i].raw); + } + _this.onSelected.notify(selected); + } + } + }); + + this.panel = Ext.create('Ext.grid.Panel', { + store : this.store, + deferredRender : false, + width : this.width, + height : this.height, + margin : 10, + selModel : this.selModel, + columns : [ { + text : 'Name', + dataIndex : 'fit', + flex : 1, + renderer : function(val, b, record) { + return BUI.getFileName(val); + } + }, { + text : 'PDB', + dataIndex : 'mixtureToStructure3VOs', + flex : 1, + renderer : function(values, b, record) { + var html = ""; + for (var i = 0; i < values.length; i++) { + var structure = BIOSAXS.proposal.getStructuresById(values[i].structureId); + html = html + ""; + if (structure != null){ + html = html + ""; + } + html = html + ""; + } + return html + "
" + structure.name + "
"; + } + }, { + text : 'Volume Fraction', + dataIndex : 'mixtureToStructure3VOs', + flex : 1, + renderer : function(values, b, record) { + var html = ""; + for (var i = 0; i < values.length; i++) { + html = html + ""; + html = html + ""; + html = html + ""; + } + + return html + "
" + values[i].volumeFraction + "
"; + } + },{ + text : 'Subtraction', + dataIndex : 'subtractedFile', + flex : 1, + renderer : function(values, b, record) { + return values.split("/")[values.split("/").length - 1]; + } + },], + + viewConfig : { + enableTextSelection : true, + preserveScrollOnRefresh : true + }, + listeners : { + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + }, + afterrender : function() { + } + } + }); + return this.panel; +}; + +/** Static method **/ +FitStructureToExperimentDataGrid.prototype.RUNFitScattering = function(subtractionId, structureId) { + var _this = this; + /** Add to Workflow **/ + var adapter = new BiosaxsDataAdapter(); + var workflow = { + 'workflowTitle' : 'FitExperimentalDatatoStructure', + 'comments' : 'FitExperimentalDatatoStructure run from ISPyB for subtractionId: ' + subtractionId + ' and structureId ' + structureId + } + + var inputs = [ { + name : 'subtractionId', + value : subtractionId + }, { + name : 'structureId', + value : structureId + } ]; + + adapter.onSuccess.attach(function(sender, data) { + /** Add to Fit **/ + var adapter2 = new BiosaxsDataAdapter(); + var fit = { + 'workflowId' : data.workflowId, + 'subtractionId' : subtractionId, + 'structureId' : structureId, + 'comments' : 'Sent to workflow engine' + } + adapter2.onSuccess.attach(function(sender, fit) { + _this.refresh(_this.subtractionId, _this.macromolecule); + }); + adapter2.addFitStructureData(fit); + + }); + adapter.addWorkflow(workflow, inputs); + +}; /** * It shows buffer grid with a top bar with "Add" button @@ -19893,244 +19893,244 @@ MeasurementGrid.prototype.getPanel = function(measurements, experiments) { }, 1000); } - } catch (e) { - } + } catch (e) { + } + } + } + } + }); + + return this.grid; +}; + +/** Method for testing * */ +MeasurementGrid.prototype.input = function() { + var experiment = DATADOC.getExperiment_10(); + var measurements = DATADOC.getMeasurements_10(); + var proposal = DATADOC.getProposal_10(); + return { + experiment : experiment, + measurements : measurements, + proposal : proposal + }; +}; + +MeasurementGrid.prototype.test = function(targetId) { + var measurementGrid = new MeasurementGrid({ + tbar : true + + }); + BIOSAXS.proposal = new Proposal(measurementGrid.input().proposal); + var panel = measurementGrid.getPanel(measurementGrid.input().measurements, new ExperimentList([ new Experiment(measurementGrid.input().experiment) ])); + panel.render(targetId); +}; + +/** + * A shipment may contains one or more cases where stock solutions and sample + * plates are stored + * + * @height + * @btnEditVisible + * @btnRemoveVisible + * + * #onEditButtonClicked + */ +function MolarityGrid(args) { + this.height = 100; + this.width = 100; + + if (args != null) { + if (args.height != null) { + this.height = args.height; + } + if (args.width != null) { + this.width = args.width; + } + } + + var _this = this; + + this.molarityForm = new MolarityForm({height : 180, width : 455}); + + this.molarityForm.onSave.attach(function(sender){ + _this.molarityWindow.destroy(); + _this.updateProposal(); + + }); + + this.molarityForm.onClose.attach(function(sender){ + _this.molarityWindow.destroy(); + + }); + + /** Events * */ + this.onEditButtonClicked = new Event(this); +} + +MolarityGrid.prototype._getColumns = function() { + return [ { + text : 'Subunit', + columns : [ { + text : "Acronym", + width : 100, + hidden : false, + dataIndex : 'acronym', + sortable : true + }, { + text : "Name", + width : 125, + hidden : false, + dataIndex : 'name', + sortable : true + }, { + text : "MM Est.", + width : 100, + dataIndex : 'molecularMass', + sortable : true, + renderer : function(grid, cls, record){ + return BUI.formatValuesUnits(record.data.molecularMass , "Da", 10, 2); + + } + } ] + }, { +// text : "Number
in assymmetric units", + text : "Ratio", + width : 100, + dataIndex : 'ratio', + tooltip : 'Number of times the subunit is present in the macromolecule', + sortable : true + }, { + id : this.id + 'MOLARITY_REMOVE', + flex : 0.1, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + return BUI.getRedButton('REMOVE'); + } + } ]; +}; + +MolarityGrid.prototype._openMolarityWindow = function() { + this.molarityWindow = Ext.create('Ext.window.Window', { + title : 'Molarity', + height : 220, + width : 500, + modal : true, + items : [this.molarityForm.getPanel() ] + }).show(); +}; + +MolarityGrid.prototype._getButtons = function() { + var _this = this; + return [ { + text : 'Add subunit', + icon : '../images/add.png', + handler : function() { + _this._openMolarityWindow(); + } + }]; +}; + + +MolarityGrid.prototype.updateProposal = function() { + var _this = this; + this.panel.setLoading(); + BIOSAXS.proposal.onInitialized.attach(function() { + if (BIOSAXS.proposal != null) { + var macromolecules = BIOSAXS.proposal.macromolecules; + for (var i = 0; i < macromolecules.length; i++) { + + if (macromolecules[i].macromoleculeId == _this.macromolecule.macromoleculeId) { + _this.refresh(macromolecules[i]); + _this.panel.setLoading(false); + } + } + } + }); + BIOSAXS.proposal.init(); +}; + + +MolarityGrid.prototype.getPanel = function() { + var _this = this; + + this.molarityStore = Ext.create('Ext.data.Store', { + fields : [ 'acronym', 'ratio', 'comments', 'stoichiometryId', 'name', 'molecularMass' ], + sorters : { + property : 'ratio', + direction : 'DESC' + } + }); + + this.panel = Ext.create('Ext.grid.Panel', { + store : this.molarityStore, + height : this.height, + padding : 5, + columns : this._getColumns(), + listeners : { + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + + /** Remove entry * */ + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'MOLARITY_REMOVE') { + var dataAdapter = new BiosaxsDataAdapter(); + dataAdapter.onSuccess.attach(function(sender) { + _this.updateProposal(); + + }); + dataAdapter.removeStoichiometry(record.data.stoichiometryId); + _this.panel.setLoading("Removing Structure"); } } - } + }, + tbar : this._getButtons() }); + return this.panel; +}; - return this.grid; +MolarityGrid.prototype._prepareData = function(macromolecule) { + /** Return an array of [{ratio,acronym, stoichiometryId, name}] **/ + var data = []; + if (macromolecule.stoichiometry != null) { + for (var i = 0; i < macromolecule.stoichiometry.length; i++) { + var hostMacromolecule = BIOSAXS.proposal.getMacromoleculeById(macromolecule.stoichiometry[i].macromoleculeId); + data.push({ + ratio : macromolecule.stoichiometry[i].ratio, + acronym : hostMacromolecule.acronym, + comments : hostMacromolecule.comments, + molecularMass : hostMacromolecule.molecularMass, + stoichiometryId : macromolecule.stoichiometry[i].stoichiometryId, + name : hostMacromolecule.name + }); + } + } + return data; }; -/** Method for testing * */ -MeasurementGrid.prototype.input = function() { - var experiment = DATADOC.getExperiment_10(); - var measurements = DATADOC.getMeasurements_10(); - var proposal = DATADOC.getProposal_10(); +MolarityGrid.prototype.refresh = function(macromolecule) { + if (macromolecule != null){ + this.molarityStore.loadData(this._prepareData(macromolecule)); + this.molarityForm.refresh(macromolecule); + this.macromolecule = macromolecule; + } +}; + +MolarityGrid.prototype.input = function() { return { - experiment : experiment, - measurements : measurements, - proposal : proposal + proposal : DATADOC.getProposal_10(), + dewars : DATADOC.getDewars_10() + }; }; -MeasurementGrid.prototype.test = function(targetId) { - var measurementGrid = new MeasurementGrid({ - tbar : true - +MolarityGrid.prototype.test = function(targetId) { + var MolarityGrid = new MolarityGrid({ + height : 150 }); - BIOSAXS.proposal = new Proposal(measurementGrid.input().proposal); - var panel = measurementGrid.getPanel(measurementGrid.input().measurements, new ExperimentList([ new Experiment(measurementGrid.input().experiment) ])); + BIOSAXS.proposal = new Proposal(MolarityGrid.input().proposal); + var panel = MolarityGrid.getPanel(MolarityGrid.input().dewars); panel.render(targetId); + }; -/** - * A shipment may contains one or more cases where stock solutions and sample - * plates are stored - * - * @height - * @btnEditVisible - * @btnRemoveVisible - * - * #onEditButtonClicked - */ -function MolarityGrid(args) { - this.height = 100; - this.width = 100; - - if (args != null) { - if (args.height != null) { - this.height = args.height; - } - if (args.width != null) { - this.width = args.width; - } - } - - var _this = this; - - this.molarityForm = new MolarityForm({height : 180, width : 455}); - - this.molarityForm.onSave.attach(function(sender){ - _this.molarityWindow.destroy(); - _this.updateProposal(); - - }); - - this.molarityForm.onClose.attach(function(sender){ - _this.molarityWindow.destroy(); - - }); - - /** Events * */ - this.onEditButtonClicked = new Event(this); -} - -MolarityGrid.prototype._getColumns = function() { - return [ { - text : 'Subunit', - columns : [ { - text : "Acronym", - width : 100, - hidden : false, - dataIndex : 'acronym', - sortable : true - }, { - text : "Name", - width : 125, - hidden : false, - dataIndex : 'name', - sortable : true - }, { - text : "MM Est.", - width : 100, - dataIndex : 'molecularMass', - sortable : true, - renderer : function(grid, cls, record){ - return BUI.formatValuesUnits(record.data.molecularMass , "Da", 10, 2); - - } - } ] - }, { -// text : "Number
in assymmetric units", - text : "Ratio", - width : 100, - dataIndex : 'ratio', - tooltip : 'Number of times the subunit is present in the macromolecule', - sortable : true - }, { - id : this.id + 'MOLARITY_REMOVE', - flex : 0.1, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - return BUI.getRedButton('REMOVE'); - } - } ]; -}; - -MolarityGrid.prototype._openMolarityWindow = function() { - this.molarityWindow = Ext.create('Ext.window.Window', { - title : 'Molarity', - height : 220, - width : 500, - modal : true, - items : [this.molarityForm.getPanel() ] - }).show(); -}; - -MolarityGrid.prototype._getButtons = function() { - var _this = this; - return [ { - text : 'Add subunit', - icon : '../images/add.png', - handler : function() { - _this._openMolarityWindow(); - } - }]; -}; - - -MolarityGrid.prototype.updateProposal = function() { - var _this = this; - this.panel.setLoading(); - BIOSAXS.proposal.onInitialized.attach(function() { - if (BIOSAXS.proposal != null) { - var macromolecules = BIOSAXS.proposal.macromolecules; - for (var i = 0; i < macromolecules.length; i++) { - - if (macromolecules[i].macromoleculeId == _this.macromolecule.macromoleculeId) { - _this.refresh(macromolecules[i]); - _this.panel.setLoading(false); - } - } - } - }); - BIOSAXS.proposal.init(); -}; - - -MolarityGrid.prototype.getPanel = function() { - var _this = this; - - this.molarityStore = Ext.create('Ext.data.Store', { - fields : [ 'acronym', 'ratio', 'comments', 'stoichiometryId', 'name', 'molecularMass' ], - sorters : { - property : 'ratio', - direction : 'DESC' - } - }); - - this.panel = Ext.create('Ext.grid.Panel', { - store : this.molarityStore, - height : this.height, - padding : 5, - columns : this._getColumns(), - listeners : { - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - - /** Remove entry * */ - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'MOLARITY_REMOVE') { - var dataAdapter = new BiosaxsDataAdapter(); - dataAdapter.onSuccess.attach(function(sender) { - _this.updateProposal(); - - }); - dataAdapter.removeStoichiometry(record.data.stoichiometryId); - _this.panel.setLoading("Removing Structure"); - } - } - }, - tbar : this._getButtons() - }); - return this.panel; -}; - -MolarityGrid.prototype._prepareData = function(macromolecule) { - /** Return an array of [{ratio,acronym, stoichiometryId, name}] **/ - var data = []; - if (macromolecule.stoichiometry != null) { - for (var i = 0; i < macromolecule.stoichiometry.length; i++) { - var hostMacromolecule = BIOSAXS.proposal.getMacromoleculeById(macromolecule.stoichiometry[i].macromoleculeId); - data.push({ - ratio : macromolecule.stoichiometry[i].ratio, - acronym : hostMacromolecule.acronym, - comments : hostMacromolecule.comments, - molecularMass : hostMacromolecule.molecularMass, - stoichiometryId : macromolecule.stoichiometry[i].stoichiometryId, - name : hostMacromolecule.name - }); - } - } - return data; -}; - -MolarityGrid.prototype.refresh = function(macromolecule) { - if (macromolecule != null){ - this.molarityStore.loadData(this._prepareData(macromolecule)); - this.molarityForm.refresh(macromolecule); - this.macromolecule = macromolecule; - } -}; - -MolarityGrid.prototype.input = function() { - return { - proposal : DATADOC.getProposal_10(), - dewars : DATADOC.getDewars_10() - - }; -}; - -MolarityGrid.prototype.test = function(targetId) { - var MolarityGrid = new MolarityGrid({ - height : 150 - }); - BIOSAXS.proposal = new Proposal(MolarityGrid.input().proposal); - var panel = MolarityGrid.getPanel(MolarityGrid.input().dewars); - panel.render(targetId); - -}; - /** * Given data analysis parsed with ResultsAssemblyWidget makes a selector grid with buffer/protein @@ -20815,135 +20815,135 @@ ResultsAssemblyGrid.prototype.test = function(targetId) { }; - -function RigidModelGrid(args) { - this.height = null; - this.width = null; - this.id = BUI.id(); - - if (args != null) { - if (args.height != null) { - this.height = args.height; - - if (args.width != null) { - this.width = args.width; - } - } - } - - this.onSelected = new Event(this); -} - - -RigidModelGrid.prototype.refresh = function(subtractions) { - var data = []; - if (subtractions != null){ - if (subtractions.length > 0){ - for (j in subtractions){ - var subtraction = subtractions[j]; - if (subtraction.rigidBodyModeling3VOs != null){ - for (i in subtraction.rigidBodyModeling3VOs){ - data.push(subtraction.rigidBodyModeling3VOs[i]); - } - } - } - } - } - this.store.loadData(data); -}; - -RigidModelGrid.prototype.getPanel = function() { - var _this = this; - this.store = Ext.create('Ext.data.Store', { - fields : [ 'symmetry', 'subtractionId', 'subUnitConfigFilePath', 'rigidBodyModelingId', 'rigidBodyModelFilePath', 'logFilePath', 'fitFilePath', 'curveConfigFilePath', - 'crossCorrConfigFilePath', 'contactDescriptionFilePath' ], - data : [] - }); - - this.store.sort([ { - property : 'name', - direction : 'ASC' - } ]); - - this.panel = Ext.create('Ext.grid.Panel', { - store : this.store, - width : this.width, - height : this.height, - margin : 10, - deferredRender : false, - columns : [ { - text : 'RBM', - dataIndex : 'rigidBodyModelFilePath', - hidden : false, - flex : 1, - renderer : function(val){ - return BUI.getFileName(val); - } - }, { - text : 'Sub Unit Conf.', - dataIndex : 'subUnitConfigFilePath', - hidden : true, - flex : 1, - renderer : function(val){ - return BUI.getFileName(val); - } - }, { - text : 'Log', - dataIndex : 'logFilePath', - hidden : true, - flex : 1, - renderer : function(val){ - return BUI.getFileName(val); - } - }, { - text : 'Fit', - dataIndex : 'fitFilePath', - hidden : false, - flex : 1, - renderer : function(val){ - return BUI.getFileName(val); - } - }, { - text : 'Curve Conf.', - dataIndex : 'curveConfigFilePath', - hidden : false, - flex : 1, - renderer : function(val){ - return BUI.getFileName(val); - } - }, { - text : 'Cross Corr.', - dataIndex : 'crossCorrConfigFilePath', - hidden : false, - flex : 1, - renderer : function(val){ - return BUI.getFileName(val); - } - }, { - text : 'Contact Desc.', - dataIndex : 'contactDescriptionFilePath', - hidden : true, - flex : 1, - renderer : function(val){ - return BUI.getFileName(val); - } - } ], - - viewConfig : { - enableTextSelection : true, - preserveScrollOnRefresh : true - }, - listeners : { - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - - }, - afterrender : function() { - } - } - }); - return this.panel; -}; - + +function RigidModelGrid(args) { + this.height = null; + this.width = null; + this.id = BUI.id(); + + if (args != null) { + if (args.height != null) { + this.height = args.height; + + if (args.width != null) { + this.width = args.width; + } + } + } + + this.onSelected = new Event(this); +} + + +RigidModelGrid.prototype.refresh = function(subtractions) { + var data = []; + if (subtractions != null){ + if (subtractions.length > 0){ + for (j in subtractions){ + var subtraction = subtractions[j]; + if (subtraction.rigidBodyModeling3VOs != null){ + for (i in subtraction.rigidBodyModeling3VOs){ + data.push(subtraction.rigidBodyModeling3VOs[i]); + } + } + } + } + } + this.store.loadData(data); +}; + +RigidModelGrid.prototype.getPanel = function() { + var _this = this; + this.store = Ext.create('Ext.data.Store', { + fields : [ 'symmetry', 'subtractionId', 'subUnitConfigFilePath', 'rigidBodyModelingId', 'rigidBodyModelFilePath', 'logFilePath', 'fitFilePath', 'curveConfigFilePath', + 'crossCorrConfigFilePath', 'contactDescriptionFilePath' ], + data : [] + }); + + this.store.sort([ { + property : 'name', + direction : 'ASC' + } ]); + + this.panel = Ext.create('Ext.grid.Panel', { + store : this.store, + width : this.width, + height : this.height, + margin : 10, + deferredRender : false, + columns : [ { + text : 'RBM', + dataIndex : 'rigidBodyModelFilePath', + hidden : false, + flex : 1, + renderer : function(val){ + return BUI.getFileName(val); + } + }, { + text : 'Sub Unit Conf.', + dataIndex : 'subUnitConfigFilePath', + hidden : true, + flex : 1, + renderer : function(val){ + return BUI.getFileName(val); + } + }, { + text : 'Log', + dataIndex : 'logFilePath', + hidden : true, + flex : 1, + renderer : function(val){ + return BUI.getFileName(val); + } + }, { + text : 'Fit', + dataIndex : 'fitFilePath', + hidden : false, + flex : 1, + renderer : function(val){ + return BUI.getFileName(val); + } + }, { + text : 'Curve Conf.', + dataIndex : 'curveConfigFilePath', + hidden : false, + flex : 1, + renderer : function(val){ + return BUI.getFileName(val); + } + }, { + text : 'Cross Corr.', + dataIndex : 'crossCorrConfigFilePath', + hidden : false, + flex : 1, + renderer : function(val){ + return BUI.getFileName(val); + } + }, { + text : 'Contact Desc.', + dataIndex : 'contactDescriptionFilePath', + hidden : true, + flex : 1, + renderer : function(val){ + return BUI.getFileName(val); + } + } ], + + viewConfig : { + enableTextSelection : true, + preserveScrollOnRefresh : true + }, + listeners : { + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + + }, + afterrender : function() { + } + } + }); + return this.panel; +}; + /** * shows shipments @@ -22309,119 +22309,119 @@ StockSolutionGrid.prototype.test = function(targetId) { panel.render(targetId); }; - -function SuperpositionGrid(args) { - this.height = null; - this.width = null; - this.id = BUI.id(); - - if (args != null) { - if (args.height != null) { - this.height = args.height; - - if (args.width != null) { - this.width = args.width; - } - } - } - - this.onSelected = new Event(this); -} - -SuperpositionGrid.prototype._prepareData = function(data) { - return data; -}; - -SuperpositionGrid.prototype.refresh = function(subtractions) { - var data = []; - if (subtractions != null){ - if (subtractions.length > 0){ - for (j in subtractions){ - var subtraction = subtractions[j]; - if (subtraction.superposition3VOs != null){ - for (i in subtraction.superposition3VOs){ - data.push(subtraction.superposition3VOs[i]); - } - } - } - } - } - this.store.loadData(data); -}; - -SuperpositionGrid.prototype.getPanel = function() { - var _this = this; - this.store = Ext.create('Ext.data.Store', { - fields : [ 'abinitioModelPdbFilePath', 'aprioriPdbFilePath', 'alignedPdbFilePath' ], - data : [] - }); - - this.selModel = Ext.create('Ext.selection.RowModel', { - allowDeselect : true, - mode : 'MULTI', - listeners : { - selectionchange : function(sm, selections) { - var selected = []; - for (var i = 0; i < selections.length; i++) { - selected.push(selections[i].raw); - } - _this.onSelected.notify(selected); - } - } - }); - - this.store.sort([ { - property : 'name', - direction : 'ASC' - } ]); - - this.panel = Ext.create('Ext.grid.Panel', { - store : this.store, - selModel : this.selModel, - width : this.width, - height : this.height, - margin : 10, - deferredRender : false, - columns : [ { - text : 'Abinitio', - dataIndex : 'abinitioModelPdbFilePath', - hidden : false, - flex : 1, - renderer : function(val){ - return BUI.getFileName(val); - } - }, { - text : 'Apriori', - dataIndex : 'aprioriPdbFilePath', - hidden : false, - flex : 1, - renderer : function(val){ - return BUI.getFileName(val); - } - }, { - text : 'Aligned', - dataIndex : 'alignedPdbFilePath', - hidden : false, - flex : 1, - renderer : function(val){ - return BUI.getFileName(val); - } - } ], - - viewConfig : { - enableTextSelection : true, - preserveScrollOnRefresh : true - }, - listeners : { - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - - }, - afterrender : function() { - } - } - }); - return this.panel; -}; + +function SuperpositionGrid(args) { + this.height = null; + this.width = null; + this.id = BUI.id(); + + if (args != null) { + if (args.height != null) { + this.height = args.height; + + if (args.width != null) { + this.width = args.width; + } + } + } + + this.onSelected = new Event(this); +} + +SuperpositionGrid.prototype._prepareData = function(data) { + return data; +}; + +SuperpositionGrid.prototype.refresh = function(subtractions) { + var data = []; + if (subtractions != null){ + if (subtractions.length > 0){ + for (j in subtractions){ + var subtraction = subtractions[j]; + if (subtraction.superposition3VOs != null){ + for (i in subtraction.superposition3VOs){ + data.push(subtraction.superposition3VOs[i]); + } + } + } + } + } + this.store.loadData(data); +}; + +SuperpositionGrid.prototype.getPanel = function() { + var _this = this; + this.store = Ext.create('Ext.data.Store', { + fields : [ 'abinitioModelPdbFilePath', 'aprioriPdbFilePath', 'alignedPdbFilePath' ], + data : [] + }); + + this.selModel = Ext.create('Ext.selection.RowModel', { + allowDeselect : true, + mode : 'MULTI', + listeners : { + selectionchange : function(sm, selections) { + var selected = []; + for (var i = 0; i < selections.length; i++) { + selected.push(selections[i].raw); + } + _this.onSelected.notify(selected); + } + } + }); + + this.store.sort([ { + property : 'name', + direction : 'ASC' + } ]); + + this.panel = Ext.create('Ext.grid.Panel', { + store : this.store, + selModel : this.selModel, + width : this.width, + height : this.height, + margin : 10, + deferredRender : false, + columns : [ { + text : 'Abinitio', + dataIndex : 'abinitioModelPdbFilePath', + hidden : false, + flex : 1, + renderer : function(val){ + return BUI.getFileName(val); + } + }, { + text : 'Apriori', + dataIndex : 'aprioriPdbFilePath', + hidden : false, + flex : 1, + renderer : function(val){ + return BUI.getFileName(val); + } + }, { + text : 'Aligned', + dataIndex : 'alignedPdbFilePath', + hidden : false, + flex : 1, + renderer : function(val){ + return BUI.getFileName(val); + } + } ], + + viewConfig : { + enableTextSelection : true, + preserveScrollOnRefresh : true + }, + listeners : { + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + + }, + afterrender : function() { + } + } + }); + return this.panel; +}; /** * See ExperimentGrid @@ -26158,502 +26158,502 @@ ConcentrationHTMLTableWidget.prototype.input = function() { "values" : [] } } - } ] - }, - "concentrationLabel" : "7.17 mg/ml ,3.53 mg/ml ,1.75 mg/ml ,0.91 mg/ml " + } ] + }, + "concentrationLabel" : "7.17 mg/ml ,3.53 mg/ml ,1.75 mg/ml ,0.91 mg/ml " + } + }; +}; + +ConcentrationHTMLTableWidget.prototype.test = function(targetId) { + var concentrationHTMLTableWidget = new ConcentrationHTMLTableWidget(); + document.getElementById(targetId).innerHTML = concentrationHTMLTableWidget.getPanel(concentrationHTMLTableWidget.input().data); +}; + +function DataCollectionWidget() { + +}; + +DataCollectionWidget.prototype.refresh = function(subtractionId) { + +}; + +DataCollectionWidget.prototype.getMacromolecule = function(data) { + for (var i = 0; i < data.length; i++) { + if (data[i].macromoleculeId != null) { + return BIOSAXS.proposal.getMacromoleculeById(data[i].macromoleculeId); + } + } + return null; +}; + +DataCollectionWidget.prototype.getMacromoleculeContainer = function(data) { + var macromolecule = this.getMacromolecule(data); + + var disabled = false; + if (macromolecule == null) { + disabled = true; + } + + var acronym = (macromolecule == null ? "" : macromolecule.acronym); + var mm = (macromolecule == null ? "" : macromolecule.molecularMass); + var comments = (macromolecule == null ? "" : macromolecule.comments); + + return Ext.create('Ext.Panel', { + width : 500, + height : 200, + disabled : disabled, + title : "Macromolecule", + layout : 'form', + bodyPadding : 5, + defaultType : 'textfield', + tbar : { + defaultButtonUI : 'default', + items : [ { + xtype : 'button', + text : 'Edit', + cls : 'btn-with-border', + handler : function() { + var macromoleculeWindow = new MacromoleculeWindow(); + macromoleculeWindow.draw(macromolecule); + /** TODO: update when save **/ + } + } ] + }, + items : [ { + fieldLabel : 'Acronym', + name : 'first', + readOnly : true, + value : acronym + }, { + fieldLabel : 'Molecular Mass', + name : 'last', + readOnly : true, + value : mm + }, { + xtype : 'textareafield', + fieldLabel : 'Comments', + value : '', + name : 'last', + readOnly : true, + value : comments + } ] + }); +}; + +DataCollectionWidget.prototype.getBufferContainer = function(data) { + var _this = this; + var buffer = BIOSAXS.proposal.getBufferById(data[0].bufferId); + + return Ext.create('Ext.Panel', { + width : 500, + height : 200, + title : "Buffer", + layout : 'form', + // collapsed : true, + // collapsible : true, + bodyPadding : 5, + defaultType : 'textfield', + style : { + padding : '0px 0px 0px 2px' + }, + tbar : { + defaultButtonUI : 'default', + items : [ { + xtype : 'button', + text : 'Edit', + cls : 'btn-with-border', + handler : function() { + var bufferWindow = new BufferWindow(); + bufferWindow.draw(BIOSAXS.proposal.getBufferById(data[0].bufferId)); + /** TODO: update when save **/ + } + + } ] + }, + items : [ { + fieldLabel : 'Buffer', + name : 'acronym', + readOnly : true, + value : buffer.acronym + }, { + fieldLabel : 'Composition', + name : 'last', + readOnly : true, + value : buffer.composition + }, { + xtype : 'textareafield', + fieldLabel : 'Comments', + value : buffer.comments, + name : 'last', + readOnly : true + + } ] + }); +}; + +DataCollectionWidget.prototype.getSpecimenContainer = function(data) { + return Ext.create('Ext.container.Container', { + layout : { + type : 'hbox' + }, + style : { + margin : '10px 10px 10px 10px' + }, + border : 0, + style : { + borderColor : '#000000', + borderStyle : 'solid', + borderWidth : '1px' + }, + defaults : { + labelWidth : 80, + // implicitly create Container by specifying xtype + xtype : 'datefield', + flex : 1, + + }, + items : [ this.getMacromoleculeContainer(data), this.getBufferContainer(data) ] + }); +}; + +DataCollectionWidget.prototype.getSeparator = function() { + return { + html : "
", + border : 0 + } +}; + +DataCollectionWidget.prototype.getFitStructurePanel = function(data) { + var _this = this; + + return Ext.create('Ext.container.Container', { + layout : { + type : 'hbox' + }, + style : { + margin : '10px 10px 10px 10px' + }, + border : 0, + style : { + borderColor : '#000000', + borderStyle : 'solid', + borderWidth : '1px' + }, + defaults : { + labelWidth : 80, + xtype : 'datefield', + flex : 1 + }, + items : [ + + ] + }); +}; + +DataCollectionWidget.prototype.getFitStructurePanelWorkflow = function(data) { + var _this = this; + var macromolecule = this.getMacromolecule(data); + + var items = []; + + /** Adding all the pdb files linked to the macromolecule **/ + // if (macromolecule.structure3VOs != null) { + // if (macromolecule.structure3VOs.length > 0) { + // + // items.push(); + // } + // } else { + // items.push({ + // html : "No apriori information added to this macromolecule. Apriori information needed for further analysis", + // margin : "5 5 5 5" + // }); + // } + var fitStructureToExperimentDataGrid = new FitStructureToExperimentDataGrid(); + + fitStructureToExperimentDataGrid.refresh(_this.data[0].subtractionId, _this.getMacromolecule(data)); + return Ext.create('Ext.container.Container', { + style : { + margin : '10px 10px 10px 10px' + }, + border : 0, + + style : { + borderColor : '#000000', + borderStyle : 'solid', + borderWidth : '1px' + }, + defaults : { + labelWidth : 80, + xtype : 'datefield', + flex : 1 + }, + items : [ fitStructureToExperimentDataGrid.getPanel() ], + listeners : { + afterrender : function() { + } + } + }); +}; +/** Static method **/ +DataCollectionWidget.prototype.RUNFitScattering = function(subtractionId, structureId) { + var _this = this; + /** Add to Workflow **/ + var adapter = new BiosaxsDataAdapter(); + var workflow = { + 'workflowTitle' : 'FitExperimentalDatatoStructure', + 'comments' : 'FitExperimentalDatatoStructure run from ISPyB for subtractionId: ' + subtractionId + ' and structureId ' + structureId + } + + var inputs = [ { + name : 'subtractionId', + value : subtractionId + }, { + name : 'structureId', + value : structureId + } ]; + + adapter.onSuccess.attach(function(sender, data) { + /** Add to Fit **/ + var adapter2 = new BiosaxsDataAdapter(); + var fit = { + 'workflowId' : data.workflowId, + 'subtractionId' : subtractionId, + 'structureId' : structureId, + 'comments' : 'Sent to workflow engine' + } + adapter2.onSuccess.attach(function(sender, fit) { + + }); + adapter2.addFitStructureData(fit); + + }); + adapter.addWorkflow(workflow, inputs); + +}; + +DataCollectionWidget.prototype.getSuperpositionTab = function(data) { + var _this = this; + + this.superpositionGrid = new SuperpositionGrid(); + + return Ext.create('Ext.container.Container', { + style : { + margin : '10px 10px 10px 10px' + }, + border : 0, + style : { + borderColor : '#000000', + borderStyle : 'solid', + borderWidth : '1px' + }, + items : [ _this.superpositionGrid.getPanel() ], + listeners : { + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + + }, + afterrender : function() { + /** Getting Rigid bodies **/ + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, result) { + _this.superpositionGrid.refresh(result); + }); + adapter.getSuperpositionBySubtractionId(data[1].subtractionId); + } + } + }); +}; + +DataCollectionWidget.prototype.getAdvancedTab = function(data) { + var _this = this; + return Ext.create('Ext.container.Container', { + style : { + margin : '10px 10px 10px 10px' + }, + border : 0, + style : { + borderColor : '#000000', + borderStyle : 'solid', + borderWidth : '1px' + }, + items : [ _this.getFitStructurePanel(data), _this.getFitStructurePanelWorkflow(data) ] + }); +}; + +DataCollectionWidget.prototype.getRigiBodyForm = function(data) { + var _this = this; + _this.rigiBodyGrid = new RigidModelGrid(); + return _this.rigiBodyGrid.getPanel(); + +}; + +DataCollectionWidget.prototype.getRigidBodyModelingTab = function(data) { + var _this = this; + return Ext.create('Ext.container.Container', { + style : { + margin : '10px 10px 10px 10px' + }, + border : 0, + style : { + borderColor : '#000000', + borderStyle : 'solid', + borderWidth : '1px' + }, + items : [ _this.getRigiBodyForm(data) ], + listeners : { + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + + }, + afterrender : function() { + /** Getting Rigid bodies **/ + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, result) { + _this.rigiBodyGrid.refresh(result); + }); + adapter.getRigidBodyModelingBySubtractionId(data[1].subtractionId); + } + } + }); +}; + +DataCollectionWidget.prototype.getTabs = function(data) { + var _this = this; + + this.subtractionCurveVisualizer = new SubtractionCurveVisualizer(); + + this.tabs = Ext.createWidget('tabpanel', { + activeTab : 1, + plain : true, + defaults : { + autoScroll : true, + bodyPadding : 10 + }, + items : [ { + title : 'Solution', + items : [ _this.getSpecimenContainer(data) ] + }, { + title : 'Primary Data Reduction', + active : true, + tabConfig : { + xtype : 'tab', + margins : '0 0 0 20', + }, + items : [ _this.subtractionCurveVisualizer.getPanel() ] + }, { + title : 'Abinitio', + items : [ _this.getAbinitioModellingContainer(data), _this.getSeparator(), _this.getModelViz(data) ] + }, { + title : 'Mixtures', + items : [ _this.getAdvancedTab(data) ] + }, { + title : 'Superpositions', + items : [ _this.getSuperpositionTab(data) ] + }, { + title : 'Rigid Body Modeling', + items : [ _this.getRigidBodyModelingTab(data) ] + } ] + }); + return this.tabs; +}; + +DataCollectionWidget.prototype.getPanel = function(data) { + var _this = this; + _this.data = data; + this.panel = Ext.create('Ext.container.Container', { + width : 1000, + layout : { + type : 'vbox', + align : 'stretch', + padding : 5 + }, + items : [ _this.getTabs(data) + + ] + }); + + this.panel.on("afterrender", function() { + _this.subtractionCurveVisualizer.refresh([ _this.data[1].mergeId ], [ _this.data[1].subtractionId ]); + }); + return this.panel; +}; + +DataCollectionWidget.prototype.getModelViz = function(data) { + this.modelViz = new ModelVisualizerForm({ + height : 800, + width : 1000 + }); + return this.modelViz.getPanel(); +}; + +/** + * PRIMARY DATA PROCESSING + */ +DataCollectionWidget.prototype.getPrimaryDataProcessingContainer = function(data) { + var _this = this; + this.primaryDataProcessingGrid = new PrimaryDataProcessingGrid({ + height : 250, + width : 1000, + title : 'Primary Data Processing' + }); + + this.primaryDataProcessingGrid.onSelected.attach(function(sender, selected) { + /** Refresh tabs **/ + var averagesId = []; + var subtractionIds = []; + + var subtractionKeys = {}; + for (var i = 0; i < selected.length; i++) { + if (selected[i].mergeId != null) { + averagesId.push(selected[i].mergeId); + } + + if (selected[i].subtractionId != null) { + if (selected[i].macromoleculeId != null) { + if (subtractionKeys[selected[i].subtractionId] == null) { + subtractionIds.push(selected[i].subtractionId); + } + subtractionKeys[selected[i].subtractionId] = true; + } + } } - }; + + /** Refreshing Primary Data Reduction **/ + _this.subtractionCurveVisualizer.refresh(averagesId, subtractionIds); + + }); + return this.primaryDataProcessingGrid.getPanel(data); }; +/** + * getAbinitioModellingContainer + */ +DataCollectionWidget.prototype.getAbinitioModellingContainer = function(data) { + var _this = this; -ConcentrationHTMLTableWidget.prototype.test = function(targetId) { - var concentrationHTMLTableWidget = new ConcentrationHTMLTableWidget(); - document.getElementById(targetId).innerHTML = concentrationHTMLTableWidget.getPanel(concentrationHTMLTableWidget.input().data); + this.abinitioGrid = new AbinitioGrid(); + this.abinitioGrid.onSelected.attach(function(sender, models) { + _this.modelViz.refresh(models); + + }); + /** It may be abinitio models linked to the buffers **/ + var abinitioIdList = []; + for (var i = 0; i < data.length; i++) { + abinitioIdList.push(data[i].abInitioId); + } + + var uniqueIds = []; + $.each(abinitioIdList, function(i, el) { + if ($.inArray(el, uniqueIds) === -1) + uniqueIds.push(el); + }); + + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + _this.abinitioGrid.refresh(data); + }); + adapter.getAbinitioByIdsList(uniqueIds); + return this.abinitioGrid.getPanel([]); }; -function DataCollectionWidget() { - -}; - -DataCollectionWidget.prototype.refresh = function(subtractionId) { - -}; - -DataCollectionWidget.prototype.getMacromolecule = function(data) { - for (var i = 0; i < data.length; i++) { - if (data[i].macromoleculeId != null) { - return BIOSAXS.proposal.getMacromoleculeById(data[i].macromoleculeId); - } - } - return null; -}; - -DataCollectionWidget.prototype.getMacromoleculeContainer = function(data) { - var macromolecule = this.getMacromolecule(data); - - var disabled = false; - if (macromolecule == null) { - disabled = true; - } - - var acronym = (macromolecule == null ? "" : macromolecule.acronym); - var mm = (macromolecule == null ? "" : macromolecule.molecularMass); - var comments = (macromolecule == null ? "" : macromolecule.comments); - - return Ext.create('Ext.Panel', { - width : 500, - height : 200, - disabled : disabled, - title : "Macromolecule", - layout : 'form', - bodyPadding : 5, - defaultType : 'textfield', - tbar : { - defaultButtonUI : 'default', - items : [ { - xtype : 'button', - text : 'Edit', - cls : 'btn-with-border', - handler : function() { - var macromoleculeWindow = new MacromoleculeWindow(); - macromoleculeWindow.draw(macromolecule); - /** TODO: update when save **/ - } - } ] - }, - items : [ { - fieldLabel : 'Acronym', - name : 'first', - readOnly : true, - value : acronym - }, { - fieldLabel : 'Molecular Mass', - name : 'last', - readOnly : true, - value : mm - }, { - xtype : 'textareafield', - fieldLabel : 'Comments', - value : '', - name : 'last', - readOnly : true, - value : comments - } ] - }); -}; - -DataCollectionWidget.prototype.getBufferContainer = function(data) { - var _this = this; - var buffer = BIOSAXS.proposal.getBufferById(data[0].bufferId); - - return Ext.create('Ext.Panel', { - width : 500, - height : 200, - title : "Buffer", - layout : 'form', - // collapsed : true, - // collapsible : true, - bodyPadding : 5, - defaultType : 'textfield', - style : { - padding : '0px 0px 0px 2px' - }, - tbar : { - defaultButtonUI : 'default', - items : [ { - xtype : 'button', - text : 'Edit', - cls : 'btn-with-border', - handler : function() { - var bufferWindow = new BufferWindow(); - bufferWindow.draw(BIOSAXS.proposal.getBufferById(data[0].bufferId)); - /** TODO: update when save **/ - } - - } ] - }, - items : [ { - fieldLabel : 'Buffer', - name : 'acronym', - readOnly : true, - value : buffer.acronym - }, { - fieldLabel : 'Composition', - name : 'last', - readOnly : true, - value : buffer.composition - }, { - xtype : 'textareafield', - fieldLabel : 'Comments', - value : buffer.comments, - name : 'last', - readOnly : true - - } ] - }); -}; - -DataCollectionWidget.prototype.getSpecimenContainer = function(data) { - return Ext.create('Ext.container.Container', { - layout : { - type : 'hbox' - }, - style : { - margin : '10px 10px 10px 10px' - }, - border : 0, - style : { - borderColor : '#000000', - borderStyle : 'solid', - borderWidth : '1px' - }, - defaults : { - labelWidth : 80, - // implicitly create Container by specifying xtype - xtype : 'datefield', - flex : 1, - - }, - items : [ this.getMacromoleculeContainer(data), this.getBufferContainer(data) ] - }); -}; - -DataCollectionWidget.prototype.getSeparator = function() { - return { - html : "
", - border : 0 - } -}; - -DataCollectionWidget.prototype.getFitStructurePanel = function(data) { - var _this = this; - - return Ext.create('Ext.container.Container', { - layout : { - type : 'hbox' - }, - style : { - margin : '10px 10px 10px 10px' - }, - border : 0, - style : { - borderColor : '#000000', - borderStyle : 'solid', - borderWidth : '1px' - }, - defaults : { - labelWidth : 80, - xtype : 'datefield', - flex : 1 - }, - items : [ - - ] - }); -}; - -DataCollectionWidget.prototype.getFitStructurePanelWorkflow = function(data) { - var _this = this; - var macromolecule = this.getMacromolecule(data); - - var items = []; - - /** Adding all the pdb files linked to the macromolecule **/ - // if (macromolecule.structure3VOs != null) { - // if (macromolecule.structure3VOs.length > 0) { - // - // items.push(); - // } - // } else { - // items.push({ - // html : "No apriori information added to this macromolecule. Apriori information needed for further analysis", - // margin : "5 5 5 5" - // }); - // } - var fitStructureToExperimentDataGrid = new FitStructureToExperimentDataGrid(); - - fitStructureToExperimentDataGrid.refresh(_this.data[0].subtractionId, _this.getMacromolecule(data)); - return Ext.create('Ext.container.Container', { - style : { - margin : '10px 10px 10px 10px' - }, - border : 0, - - style : { - borderColor : '#000000', - borderStyle : 'solid', - borderWidth : '1px' - }, - defaults : { - labelWidth : 80, - xtype : 'datefield', - flex : 1 - }, - items : [ fitStructureToExperimentDataGrid.getPanel() ], - listeners : { - afterrender : function() { - } - } - }); -}; -/** Static method **/ -DataCollectionWidget.prototype.RUNFitScattering = function(subtractionId, structureId) { - var _this = this; - /** Add to Workflow **/ - var adapter = new BiosaxsDataAdapter(); - var workflow = { - 'workflowTitle' : 'FitExperimentalDatatoStructure', - 'comments' : 'FitExperimentalDatatoStructure run from ISPyB for subtractionId: ' + subtractionId + ' and structureId ' + structureId - } - - var inputs = [ { - name : 'subtractionId', - value : subtractionId - }, { - name : 'structureId', - value : structureId - } ]; - - adapter.onSuccess.attach(function(sender, data) { - /** Add to Fit **/ - var adapter2 = new BiosaxsDataAdapter(); - var fit = { - 'workflowId' : data.workflowId, - 'subtractionId' : subtractionId, - 'structureId' : structureId, - 'comments' : 'Sent to workflow engine' - } - adapter2.onSuccess.attach(function(sender, fit) { - - }); - adapter2.addFitStructureData(fit); - - }); - adapter.addWorkflow(workflow, inputs); - -}; - -DataCollectionWidget.prototype.getSuperpositionTab = function(data) { - var _this = this; - - this.superpositionGrid = new SuperpositionGrid(); - - return Ext.create('Ext.container.Container', { - style : { - margin : '10px 10px 10px 10px' - }, - border : 0, - style : { - borderColor : '#000000', - borderStyle : 'solid', - borderWidth : '1px' - }, - items : [ _this.superpositionGrid.getPanel() ], - listeners : { - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - - }, - afterrender : function() { - /** Getting Rigid bodies **/ - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, result) { - _this.superpositionGrid.refresh(result); - }); - adapter.getSuperpositionBySubtractionId(data[1].subtractionId); - } - } - }); -}; - -DataCollectionWidget.prototype.getAdvancedTab = function(data) { - var _this = this; - return Ext.create('Ext.container.Container', { - style : { - margin : '10px 10px 10px 10px' - }, - border : 0, - style : { - borderColor : '#000000', - borderStyle : 'solid', - borderWidth : '1px' - }, - items : [ _this.getFitStructurePanel(data), _this.getFitStructurePanelWorkflow(data) ] - }); -}; - -DataCollectionWidget.prototype.getRigiBodyForm = function(data) { - var _this = this; - _this.rigiBodyGrid = new RigidModelGrid(); - return _this.rigiBodyGrid.getPanel(); - -}; - -DataCollectionWidget.prototype.getRigidBodyModelingTab = function(data) { - var _this = this; - return Ext.create('Ext.container.Container', { - style : { - margin : '10px 10px 10px 10px' - }, - border : 0, - style : { - borderColor : '#000000', - borderStyle : 'solid', - borderWidth : '1px' - }, - items : [ _this.getRigiBodyForm(data) ], - listeners : { - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - - }, - afterrender : function() { - /** Getting Rigid bodies **/ - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, result) { - _this.rigiBodyGrid.refresh(result); - }); - adapter.getRigidBodyModelingBySubtractionId(data[1].subtractionId); - } - } - }); -}; - -DataCollectionWidget.prototype.getTabs = function(data) { - var _this = this; - - this.subtractionCurveVisualizer = new SubtractionCurveVisualizer(); - - this.tabs = Ext.createWidget('tabpanel', { - activeTab : 1, - plain : true, - defaults : { - autoScroll : true, - bodyPadding : 10 - }, - items : [ { - title : 'Solution', - items : [ _this.getSpecimenContainer(data) ] - }, { - title : 'Primary Data Reduction', - active : true, - tabConfig : { - xtype : 'tab', - margins : '0 0 0 20', - }, - items : [ _this.subtractionCurveVisualizer.getPanel() ] - }, { - title : 'Abinitio', - items : [ _this.getAbinitioModellingContainer(data), _this.getSeparator(), _this.getModelViz(data) ] - }, { - title : 'Mixtures', - items : [ _this.getAdvancedTab(data) ] - }, { - title : 'Superpositions', - items : [ _this.getSuperpositionTab(data) ] - }, { - title : 'Rigid Body Modeling', - items : [ _this.getRigidBodyModelingTab(data) ] - } ] - }); - return this.tabs; -}; - -DataCollectionWidget.prototype.getPanel = function(data) { - var _this = this; - _this.data = data; - this.panel = Ext.create('Ext.container.Container', { - width : 1000, - layout : { - type : 'vbox', - align : 'stretch', - padding : 5 - }, - items : [ _this.getTabs(data) - - ] - }); - - this.panel.on("afterrender", function() { - _this.subtractionCurveVisualizer.refresh([ _this.data[1].mergeId ], [ _this.data[1].subtractionId ]); - }); - return this.panel; -}; - -DataCollectionWidget.prototype.getModelViz = function(data) { - this.modelViz = new ModelVisualizerForm({ - height : 800, - width : 1000 - }); - return this.modelViz.getPanel(); -}; - -/** - * PRIMARY DATA PROCESSING - */ -DataCollectionWidget.prototype.getPrimaryDataProcessingContainer = function(data) { - var _this = this; - this.primaryDataProcessingGrid = new PrimaryDataProcessingGrid({ - height : 250, - width : 1000, - title : 'Primary Data Processing' - }); - - this.primaryDataProcessingGrid.onSelected.attach(function(sender, selected) { - /** Refresh tabs **/ - var averagesId = []; - var subtractionIds = []; - - var subtractionKeys = {}; - for (var i = 0; i < selected.length; i++) { - if (selected[i].mergeId != null) { - averagesId.push(selected[i].mergeId); - } - - if (selected[i].subtractionId != null) { - if (selected[i].macromoleculeId != null) { - if (subtractionKeys[selected[i].subtractionId] == null) { - subtractionIds.push(selected[i].subtractionId); - } - subtractionKeys[selected[i].subtractionId] = true; - } - } - } - - /** Refreshing Primary Data Reduction **/ - _this.subtractionCurveVisualizer.refresh(averagesId, subtractionIds); - - }); - return this.primaryDataProcessingGrid.getPanel(data); -}; -/** - * getAbinitioModellingContainer - */ -DataCollectionWidget.prototype.getAbinitioModellingContainer = function(data) { - var _this = this; - - this.abinitioGrid = new AbinitioGrid(); - this.abinitioGrid.onSelected.attach(function(sender, models) { - _this.modelViz.refresh(models); - - }); - /** It may be abinitio models linked to the buffers **/ - var abinitioIdList = []; - for (var i = 0; i < data.length; i++) { - abinitioIdList.push(data[i].abInitioId); - } - - var uniqueIds = []; - $.each(abinitioIdList, function(i, el) { - if ($.inArray(el, uniqueIds) === -1) - uniqueIds.push(el); - }); - - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - _this.abinitioGrid.refresh(data); - }); - adapter.getAbinitioByIdsList(uniqueIds); - return this.abinitioGrid.getPanel([]); -}; - /** * Edit the information of a buffer * @@ -29163,258 +29163,258 @@ ShippingWidget.prototype.refresh = function() { }; -/** - * Widget container of Specimen grid and samplePlate widget - * Depending of the sample changer layout it may be displayed vertically or horizontally - * - * @param args - * - * #onExperimentChanged It happens when specimen are modified - */ -function SpecimenWidget(args){ - - this.width = 1000; - this.height = 600; - - if (args != null){ - if (args.width != null){ - this.width = args.width; - } - if (args.height != null){ - this.height = args.height; - } - } - - var _this = this; - - /** Specimen Grid **/ - this.specimenGrid = new SpecimenGrid({ - minHeight : 425, - selectionMode : "SINGLE", - editEnabled : false, - updateRowEnabled : true, - width : 900, - showTitle : false - }); - - - this.specimenGrid.onSpecimenChanged.attach(function(sender, specimen) { - _this.experiment.setSpecimenById(specimen); - _this.refresh(_this.experiment); - }); - - this.specimenGrid.onSelected.attach(function(sender, specimens) { - if (specimens.length > 0) { - _this.specimenSelected = specimens[0]; - } else { - _this.specimenSelected = null; - } - _this.samplePlateGroupWidget.selectSpecimens(specimens); - }); - - - /** Sample plate Widget **/ - this.samplePlateGroupWidget = new SamplePlateGroupWidget({ - showTitle : false, - height : 250, - margin : 5, - bbar : true - }); - - - this.samplePlateGroupWidget.onExperimentChanged.attach(function(sender, json) { - _this.refresh(new Experiment(json)); - }); - - this.samplePlateGroupWidget.onClick.attach(function(sender, args) { - /** Clicking on a plate * */ - var row = args.row; - var column = args.column; - var samplePlateId = args.samplePlate.samplePlateId; - - /** is specimen selected on the grid? * */ - if (_this.specimenSelected != null) { - /** Is position target empty * */ - if (_this.experiment.getSampleByPosition(args.samplePlate.samplePlateId, args.row, args.column).length == 0) { - var specimen = _this.experiment.getSampleById(_this.specimenSelected.specimenId); - if (specimen.sampleplateposition3VO == null) { - specimen.sampleplateposition3VO = {}; - } - - specimen.sampleplateposition3VO = { - columnNumber : column, - rowNumber : row, - samplePlateId : samplePlateId - }; - - _this.samplePlateGroupWidget.panel.setLoading("ISPyB: Saving specimen"); - var adapter = new BiosaxsDataAdapter(); - /** If success * */ - adapter.onSuccess.attach(function(sender, experiment) { - _this.samplePlateGroupWidget.panel.setLoading(false); - }); - - adapter.onError.attach(function(sender, error) { - _this.samplePlateGroupWidget.panel.setLoading(false); - showError(error); - }); - - adapter.saveSpecimen(specimen, _this.experiment); - - _this.samplePlateGroupWidget.refresh(_this.experiment); - _this.specimenGrid.refresh(_this.experiment); - //_this.refresh(_this.experiment); - _this.specimenGrid.deselectAll(); - - } else { - /** - * Can we merge? We can merge when specimen are the - * same. So, same buffer, macromolecule, concentration * - */ - var target = _this.experiment.getSampleByPosition(args.samplePlate.samplePlateId, args.row, args.column)[0]; - var specimen = _this.experiment.getSampleById(_this.specimenSelected.specimenId); - - if ((specimen.bufferId == target.bufferId) && (specimen.concentration == target.concentration)) { - if (((specimen.macromolecule3VO != null) && (target.macromolecule3VO != null) && (specimen.macromolecule3VO.macromoleculeId == target.macromolecule3VO.macromoleculeId)) || - ((specimen.macromolecule3VO == null) && (target.macromolecule3VO == null))) { - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - _this.refresh(new Experiment(data)); - _this.samplePlateGroupWidget.panel.setLoading(false); - - _this.onExperimentChanged.notify(experiment); - }); - adapter.onError.attach(function(sender, error) { - _this.samplePlateGroupWidget.panel.setLoading(false); - showError(error); - }); - _this.samplePlateGroupWidget.panel.setLoading("ISPyB: Merging specimens"); - adapter.mergeSpecimens(specimen.specimenId, target.specimenId); - } - } else { - alert("Well is not empty. Select another well!"); - } - } - } else { - var specimen = _this.experiment.getSampleByPosition(args.samplePlate.samplePlateId, args.row, args.column)[0]; - if (specimen != null) { - _this.specimenGrid.selectById(specimen.specimenId); - } - } - }); - - /** Events **/ - this.onExperimentChanged = new Event(this); -}; - -/** - * Return vbox or hbox depending on the slot positions of the plates - */ -SpecimenWidget.prototype.getContainerLayoutConfiguration = function(experiment){ - var dimensions = this.samplePlateGroupWidget.getDimensions(experiment.getSamplePlates()); - if (dimensions.maxSlotPositionRow < dimensions.maxSlotPositionColumn){ - return { - layout : "vbox", - specimenGridWidth : this.width - 10, - specimenGridHeight : this.height - 260, - samplePlateGroupWidth : this.width - 10, - samplePlateGroupHeight : 250 - }; - } - return { - layout : "hbox", - samplePlateGroupWidth : this.width*1/3 -10, - samplePlateGroupHeight : this.height - 10, - specimenGridWidth : this.width*2/3, - specimenGridHeight : this.height - 10 - }; - -}; - - -SpecimenWidget.prototype.refresh = function(experiment){ - this.experiment = experiment; - - /** Removing all components **/ - this.panel.removeAll(); - - var layoutConfiguration = this.getContainerLayoutConfiguration(experiment); - - /** Setting new width and height for layout vbox and hbox **/ - this.specimenGrid.width = layoutConfiguration.specimenGridWidth; - this.specimenGrid.height = layoutConfiguration.specimenGridHeight; - - this.samplePlateGroupWidget.width = layoutConfiguration.samplePlateGroupWidth; - this.samplePlateGroupWidget.height = layoutConfiguration.samplePlateGroupHeight; - - if (layoutConfiguration.layout == "hbox"){ - this.specimenGrid.margin = "0 0 0 5"; - this.specimenGrid.width =this.specimenGrid.width - 5; - } - /** Insert container depending on layout [vertical|horizontal] */ - var container = Ext.create('Ext.container.Container', { - layout : layoutConfiguration.layout, - height : this.height, - width : this.width, - padding : '2px', - items : [ ] - }); - if (layoutConfiguration.layout == "vbox"){ - container.insert(this.specimenGrid.getPanel()); - container.insert(this.samplePlateGroupWidget.getPanel()); - } - else{ - container.insert(this.samplePlateGroupWidget.getPanel()); - container.insert(this.specimenGrid.getPanel()); - } - - /** Insert Widget **/ - this.panel.insert(container); - - /** Load data **/ - this.specimenGrid.refresh(experiment); - this.samplePlateGroupWidget.refresh(experiment); - - -}; - -/** It creates a dummy container to be inserted the plates once the method refresh has been called - * This is necessay because we can not know the sample changer layout before hand - * **/ -SpecimenWidget.prototype.getPanel = function(){ - this.panel = Ext.create('Ext.container.Container', { - layout : 'vbox', - height : this.height, - border : 0, - margin : 5, - width : this.width, - items : [] - }); - return this.panel; -}; - - -SpecimenWidget.prototype.input = function() { - return { - experiment : DATADOC.getExperiment_10(), - proposal : DATADOC.getProposal_10() - }; -}; - -SpecimenWidget.prototype.test = function(targetId) { - var specimenWidget = new SpecimenWidget({ - height : 500, - width : 1000 - }); - BIOSAXS.proposal = new Proposal(specimenWidget.input().proposal); - var experiment = new Experiment(specimenWidget.input().experiment); - var panel = specimenWidget.getPanel(); - panel.render(targetId); - specimenWidget.refresh(experiment); - -}; - - +/** + * Widget container of Specimen grid and samplePlate widget + * Depending of the sample changer layout it may be displayed vertically or horizontally + * + * @param args + * + * #onExperimentChanged It happens when specimen are modified + */ +function SpecimenWidget(args){ + + this.width = 1000; + this.height = 600; + + if (args != null){ + if (args.width != null){ + this.width = args.width; + } + if (args.height != null){ + this.height = args.height; + } + } + + var _this = this; + + /** Specimen Grid **/ + this.specimenGrid = new SpecimenGrid({ + minHeight : 425, + selectionMode : "SINGLE", + editEnabled : false, + updateRowEnabled : true, + width : 900, + showTitle : false + }); + + + this.specimenGrid.onSpecimenChanged.attach(function(sender, specimen) { + _this.experiment.setSpecimenById(specimen); + _this.refresh(_this.experiment); + }); + + this.specimenGrid.onSelected.attach(function(sender, specimens) { + if (specimens.length > 0) { + _this.specimenSelected = specimens[0]; + } else { + _this.specimenSelected = null; + } + _this.samplePlateGroupWidget.selectSpecimens(specimens); + }); + + + /** Sample plate Widget **/ + this.samplePlateGroupWidget = new SamplePlateGroupWidget({ + showTitle : false, + height : 250, + margin : 5, + bbar : true + }); + + + this.samplePlateGroupWidget.onExperimentChanged.attach(function(sender, json) { + _this.refresh(new Experiment(json)); + }); + + this.samplePlateGroupWidget.onClick.attach(function(sender, args) { + /** Clicking on a plate * */ + var row = args.row; + var column = args.column; + var samplePlateId = args.samplePlate.samplePlateId; + + /** is specimen selected on the grid? * */ + if (_this.specimenSelected != null) { + /** Is position target empty * */ + if (_this.experiment.getSampleByPosition(args.samplePlate.samplePlateId, args.row, args.column).length == 0) { + var specimen = _this.experiment.getSampleById(_this.specimenSelected.specimenId); + if (specimen.sampleplateposition3VO == null) { + specimen.sampleplateposition3VO = {}; + } + + specimen.sampleplateposition3VO = { + columnNumber : column, + rowNumber : row, + samplePlateId : samplePlateId + }; + + _this.samplePlateGroupWidget.panel.setLoading("ISPyB: Saving specimen"); + var adapter = new BiosaxsDataAdapter(); + /** If success * */ + adapter.onSuccess.attach(function(sender, experiment) { + _this.samplePlateGroupWidget.panel.setLoading(false); + }); + + adapter.onError.attach(function(sender, error) { + _this.samplePlateGroupWidget.panel.setLoading(false); + showError(error); + }); + + adapter.saveSpecimen(specimen, _this.experiment); + + _this.samplePlateGroupWidget.refresh(_this.experiment); + _this.specimenGrid.refresh(_this.experiment); + //_this.refresh(_this.experiment); + _this.specimenGrid.deselectAll(); + + } else { + /** + * Can we merge? We can merge when specimen are the + * same. So, same buffer, macromolecule, concentration * + */ + var target = _this.experiment.getSampleByPosition(args.samplePlate.samplePlateId, args.row, args.column)[0]; + var specimen = _this.experiment.getSampleById(_this.specimenSelected.specimenId); + + if ((specimen.bufferId == target.bufferId) && (specimen.concentration == target.concentration)) { + if (((specimen.macromolecule3VO != null) && (target.macromolecule3VO != null) && (specimen.macromolecule3VO.macromoleculeId == target.macromolecule3VO.macromoleculeId)) || + ((specimen.macromolecule3VO == null) && (target.macromolecule3VO == null))) { + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + _this.refresh(new Experiment(data)); + _this.samplePlateGroupWidget.panel.setLoading(false); + + _this.onExperimentChanged.notify(experiment); + }); + adapter.onError.attach(function(sender, error) { + _this.samplePlateGroupWidget.panel.setLoading(false); + showError(error); + }); + _this.samplePlateGroupWidget.panel.setLoading("ISPyB: Merging specimens"); + adapter.mergeSpecimens(specimen.specimenId, target.specimenId); + } + } else { + alert("Well is not empty. Select another well!"); + } + } + } else { + var specimen = _this.experiment.getSampleByPosition(args.samplePlate.samplePlateId, args.row, args.column)[0]; + if (specimen != null) { + _this.specimenGrid.selectById(specimen.specimenId); + } + } + }); + + /** Events **/ + this.onExperimentChanged = new Event(this); +}; + +/** + * Return vbox or hbox depending on the slot positions of the plates + */ +SpecimenWidget.prototype.getContainerLayoutConfiguration = function(experiment){ + var dimensions = this.samplePlateGroupWidget.getDimensions(experiment.getSamplePlates()); + if (dimensions.maxSlotPositionRow < dimensions.maxSlotPositionColumn){ + return { + layout : "vbox", + specimenGridWidth : this.width - 10, + specimenGridHeight : this.height - 260, + samplePlateGroupWidth : this.width - 10, + samplePlateGroupHeight : 250 + }; + } + return { + layout : "hbox", + samplePlateGroupWidth : this.width*1/3 -10, + samplePlateGroupHeight : this.height - 10, + specimenGridWidth : this.width*2/3, + specimenGridHeight : this.height - 10 + }; + +}; + + +SpecimenWidget.prototype.refresh = function(experiment){ + this.experiment = experiment; + + /** Removing all components **/ + this.panel.removeAll(); + + var layoutConfiguration = this.getContainerLayoutConfiguration(experiment); + + /** Setting new width and height for layout vbox and hbox **/ + this.specimenGrid.width = layoutConfiguration.specimenGridWidth; + this.specimenGrid.height = layoutConfiguration.specimenGridHeight; + + this.samplePlateGroupWidget.width = layoutConfiguration.samplePlateGroupWidth; + this.samplePlateGroupWidget.height = layoutConfiguration.samplePlateGroupHeight; + + if (layoutConfiguration.layout == "hbox"){ + this.specimenGrid.margin = "0 0 0 5"; + this.specimenGrid.width =this.specimenGrid.width - 5; + } + /** Insert container depending on layout [vertical|horizontal] */ + var container = Ext.create('Ext.container.Container', { + layout : layoutConfiguration.layout, + height : this.height, + width : this.width, + padding : '2px', + items : [ ] + }); + if (layoutConfiguration.layout == "vbox"){ + container.insert(this.specimenGrid.getPanel()); + container.insert(this.samplePlateGroupWidget.getPanel()); + } + else{ + container.insert(this.samplePlateGroupWidget.getPanel()); + container.insert(this.specimenGrid.getPanel()); + } + + /** Insert Widget **/ + this.panel.insert(container); + + /** Load data **/ + this.specimenGrid.refresh(experiment); + this.samplePlateGroupWidget.refresh(experiment); + + +}; + +/** It creates a dummy container to be inserted the plates once the method refresh has been called + * This is necessay because we can not know the sample changer layout before hand + * **/ +SpecimenWidget.prototype.getPanel = function(){ + this.panel = Ext.create('Ext.container.Container', { + layout : 'vbox', + height : this.height, + border : 0, + margin : 5, + width : this.width, + items : [] + }); + return this.panel; +}; + + +SpecimenWidget.prototype.input = function() { + return { + experiment : DATADOC.getExperiment_10(), + proposal : DATADOC.getProposal_10() + }; +}; + +SpecimenWidget.prototype.test = function(targetId) { + var specimenWidget = new SpecimenWidget({ + height : 500, + width : 1000 + }); + BIOSAXS.proposal = new Proposal(specimenWidget.input().proposal); + var experiment = new Experiment(specimenWidget.input().experiment); + var panel = specimenWidget.getPanel(); + panel.render(targetId); + specimenWidget.refresh(experiment); + +}; + + function WarningWidget(args) { this.actions = []; diff --git a/ispyb-ws/src/main/java/ispyb/ws/rest/mx/AutoprocintegrationRestWebService.java b/ispyb-ws/src/main/java/ispyb/ws/rest/mx/AutoprocintegrationRestWebService.java index cdfe38b5e..4de80758b 100644 --- a/ispyb-ws/src/main/java/ispyb/ws/rest/mx/AutoprocintegrationRestWebService.java +++ b/ispyb-ws/src/main/java/ispyb/ws/rest/mx/AutoprocintegrationRestWebService.java @@ -8,6 +8,8 @@ import ispyb.server.mx.vos.autoproc.AutoProcIntegration3VO; import ispyb.server.mx.vos.autoproc.AutoProcProgram3VO; import ispyb.server.mx.vos.autoproc.AutoProcProgramAttachment3VO; +import ispyb.server.mx.vos.collections.DataCollection3VO; +import ispyb.server.mx.vos.collections.Session3VO; import java.io.File; import java.util.ArrayList; @@ -32,6 +34,7 @@ public class AutoprocintegrationRestWebService extends MXRestWebService { private final static Logger logger = Logger.getLogger(AutoprocintegrationRestWebService.class); + private static final String NOT_ALLOWED = "You don't have access to this resource"; @RolesAllowed({ "User", "Manager", "Industrial", "Localcontact" }) @GET @@ -126,6 +129,13 @@ public Response getAttachments(@PathParam("token") String token, @PathParam("pro } + + + private boolean checkProposalByAutoProcProgramId(int proposalId, int autoProcProgramId) throws NamingException, Exception{ + return this.getSession3Service().findByAutoProcProgramId(autoProcProgramId).getProposalVOId().equals(proposalId); + } + + /** * AutoProcProgramAttachment has not AutoProcProgramId mapped in the EJB object * so it is necessary to keep separately the possible list of ids in order @@ -147,13 +157,19 @@ public Response downloadAttachments( String methodName = "downloadAttachments"; long start = this.logInit(methodName, logger, token, proposal); try { - List ids = this.parseToInteger(autoprocattachmentids); + List autoProcProgramIds = this.parseToInteger(autoprocattachmentids); List> list = new ArrayList>(); HashMap filePaths = new HashMap(); String filename = "download.zip"; - for (Integer id : ids) { - AutoProcProgram3VO autoProcProgram3VO = this.getAutoProcProgram3Service().findByPk(id, true); + for (Integer autoProcProgramId : autoProcProgramIds) { + /** Check that id correspond to the proposal **/ + if (!this.checkProposalByAutoProcProgramId(this.getProposalId(proposal), autoProcProgramId)){ + throw new Exception(NOT_ALLOWED); + } + + + AutoProcProgram3VO autoProcProgram3VO = this.getAutoProcProgram3Service().findByPk(autoProcProgramId, true); /** Prefix for the name of the file and the internal structure if many results are retrieved **/ String prefix = String.format("%s_%s", autoProcProgram3VO.getProcessingPrograms(), autoProcProgram3VO.getAutoProcProgramId()); @@ -164,7 +180,7 @@ public Response downloadAttachments( String filePath = auto.getFilePath() + "/" + auto.getFileName(); if (new File(filePath).exists()){ if (new File(filePath).isFile()){ - if (ids.size() > 1){ + if (autoProcProgramIds.size() > 1){ String zipNameFile = prefix + "/" + auto.getFileName(); filePaths.put(zipNameFile, filePath); } @@ -176,7 +192,7 @@ public Response downloadAttachments( } /** If it is a single result then filename is the name of the program and the ID **/ - if (ids.size() == 1){ + if (autoProcProgramIds.size() == 1){ filename = prefix + ".zip"; } @@ -333,6 +349,10 @@ public Response getXScaleWilson(@PathParam("token") String token, @PathParam("pr } } + private boolean checkProposalByAutoProcProgramAttachmentId(int proposalId, int autoProcProgramAttachmentId) throws NamingException, Exception{ + return this.getSession3Service().findByAutoProcProgramAttachmentId(autoProcProgramAttachmentId).getProposalVOId().equals(proposalId); + } + @RolesAllowed({ "User", "Manager", "Industrial", "Localcontact" }) @GET @Path("{token}/proposal/{proposal}/mx/autoprocintegration/autoprocattachmentid/{autoProcAttachmentId}/download") @@ -343,11 +363,17 @@ public Response downloadAutoProcAttachment(@PathParam("token") String token, @Pa String methodName = "downloadAutoProcAttachment"; long start = this.logInit(methodName, logger, token, proposal); try { - AutoProcProgramAttachment3VO attachment = this.getAutoProcProgramAttachment3Service().findByPk(autoProcAttachmentId); - this.logFinish(methodName, start, logger); - File file = new File(attachment.getFilePath() + "/" + attachment.getFileName()); - this.logFinish(methodName, start, logger); - return this.downloadFileAsAttachment(file.getAbsolutePath()); + /** Checking that attachment is linked to the proposal **/ + if (this.checkProposalByAutoProcProgramAttachmentId(this.getProposalId(proposal), autoProcAttachmentId)){ + AutoProcProgramAttachment3VO attachment = this.getAutoProcProgramAttachment3Service().findByPk(autoProcAttachmentId); + this.logFinish(methodName, start, logger); + File file = new File(attachment.getFilePath() + "/" + attachment.getFileName()); + this.logFinish(methodName, start, logger); + return this.downloadFileAsAttachment(file.getAbsolutePath()); + } + else{ + throw new Exception(NOT_ALLOWED); + } } catch (Exception e) { return this.logError(methodName, e, start, logger); } @@ -360,13 +386,19 @@ public Response downloadAutoProcAttachment(@PathParam("token") String token, @Pa public Response getAutoProcAttachment(@PathParam("token") String token, @PathParam("proposal") String proposal, @PathParam("autoProcAttachmentId") int autoProcAttachmentId) { - String methodName = "downloadAutoProcAttachment"; + String methodName = "getAutoProcAttachment"; long start = this.logInit(methodName, logger, token, proposal); try { - AutoProcProgramAttachment3VO attachment = this.getAutoProcProgramAttachment3Service().findByPk(autoProcAttachmentId); - File file = new File(attachment.getFilePath() + "/" + attachment.getFileName()); - this.logFinish(methodName, start, logger); - return this.downloadFile(file.getAbsolutePath()); + /** Checking that attachment is linked to the proposal **/ + if (this.checkProposalByAutoProcProgramAttachmentId(this.getProposalId(proposal), autoProcAttachmentId)){ + AutoProcProgramAttachment3VO attachment = this.getAutoProcProgramAttachment3Service().findByPk(autoProcAttachmentId); + File file = new File(attachment.getFilePath() + "/" + attachment.getFileName()); + this.logFinish(methodName, start, logger); + return this.downloadFile(file.getAbsolutePath()); + } + else{ + throw new Exception(NOT_ALLOWED); + } } catch (Exception e) { return this.logError(methodName, e, start, logger); } From d1bac5a11316574f68c705aad350230ab52784c4 Mon Sep 17 00:00:00 2001 From: Alejandro De Maria Antolinos Date: Tue, 31 Oct 2017 10:24:22 +0100 Subject: [PATCH 30/38] Added security cheks for downloads. It references #185 --- .../services/sessions/Session3Service.java | 4 + .../sessions/Session3ServiceBean.java | 41 + .../src/main/webapp/js/ispyb/min/ispyb-bx.js | 24046 ++++++++-------- .../mx/AutoprocintegrationRestWebService.java | 62 +- 4 files changed, 12115 insertions(+), 12038 deletions(-) diff --git a/ispyb-ejb/src/main/java/ispyb/server/common/services/sessions/Session3Service.java b/ispyb-ejb/src/main/java/ispyb/server/common/services/sessions/Session3Service.java index a3fe103c2..472d285e6 100644 --- a/ispyb-ejb/src/main/java/ispyb/server/common/services/sessions/Session3Service.java +++ b/ispyb-ejb/src/main/java/ispyb/server/common/services/sessions/Session3Service.java @@ -175,6 +175,8 @@ public List findByStartDateAndBeamLineNameAndNbShifts(final Integer */ public Session3VO findByAutoProcScalingId(final Integer autoProcScalingId) throws Exception; + public Session3VO findByAutoProcProgramAttachmentId(final Integer autoProcProgramAttachmentId) throws Exception; + public void protectSession(Integer sessionId) throws Exception; /** @@ -195,6 +197,8 @@ public List findByStartDateAndBeamLineNameAndNbShifts(final Integer */ public Integer getNbOfTests(final Integer sesId) throws Exception; + public Session3VO findByAutoProcProgramId(int autoProcProgramId); + } \ No newline at end of file diff --git a/ispyb-ejb/src/main/java/ispyb/server/common/services/sessions/Session3ServiceBean.java b/ispyb-ejb/src/main/java/ispyb/server/common/services/sessions/Session3ServiceBean.java index 401f24495..27b4debdc 100644 --- a/ispyb-ejb/src/main/java/ispyb/server/common/services/sessions/Session3ServiceBean.java +++ b/ispyb-ejb/src/main/java/ispyb/server/common/services/sessions/Session3ServiceBean.java @@ -111,6 +111,19 @@ private static final String FIND_ALL(boolean fetchDataCollectionGroup, boolean f + " where s.sessionId = g.sessionId and " + " g.dataCollectionGroupId = c.dataCollectionGroupId and " + " c.dataCollectionId = api.dataCollectionId and " + " api.autoProcIntegrationId = apshi.autoProcIntegrationId and " + " apshi.autoProcScalingId = aps.autoProcScalingId and " + " aps.autoProcScalingId = :autoProcScalingId "; + + private static final String FIND_BY_AUTOPROCPROGRAMATTACHMENT_ID = "select s.* from BLSession s, " + + " DataCollectionGroup g, DataCollection c, AutoProcIntegration api, AutoProcProgram autoprocProgram, AutoProcProgramAttachment autoProcProgramAttachment" + + " where s.sessionId = g.sessionId and g.dataCollectionGroupId = c.dataCollectionGroupId and autoprocProgram.autoProcProgramId = api.autoProcProgramId" + + " and c.dataCollectionId = api.dataCollectionId and autoprocProgram.autoProcProgramId = autoProcProgramAttachment.autoProcProgramId " + + " and autoProcProgramAttachment.autoProcProgramAttachmentId = :autoProcProgramAttachmentId "; + + + private static final String FIND_BY_AUTOPROCPROGRAM_ID = "select s.* from BLSession s, " + + " DataCollectionGroup g, DataCollection c, AutoProcIntegration api, AutoProcProgram autoprocProgram " + + " where s.sessionId = g.sessionId and g.dataCollectionGroupId = c.dataCollectionGroupId and autoprocProgram.autoProcProgramId = api.autoProcProgramId" + + " and c.dataCollectionId = api.dataCollectionId and autoprocProgram.autoProcProgramId = :autoProcProgramId "; + private static String getProposalCodeNumberQuery() { String query = "select * " + " FROM BLSession ses, Proposal pro " @@ -525,6 +538,32 @@ public Session3VO findByAutoProcScalingId(final Integer autoProcScalingId) throw } return null; } + + + @SuppressWarnings("unchecked") + public Session3VO findByAutoProcProgramAttachmentId(final Integer autoProcProgramAttachmentId) throws Exception { + String query = FIND_BY_AUTOPROCPROGRAMATTACHMENT_ID; + List col = this.entityManager.createNativeQuery(query, "sessionNativeQuery") + .setParameter("autoProcProgramAttachmentId", autoProcProgramAttachmentId).getResultList(); + if (col != null && col.size() > 0) { + return col.get(0); + } + return null; + } + + + @Override + public Session3VO findByAutoProcProgramId(int autoProcProgramId) { + String query = FIND_BY_AUTOPROCPROGRAM_ID; + @SuppressWarnings("unchecked") + List col = this.entityManager.createNativeQuery(query, "sessionNativeQuery") + .setParameter("autoProcProgramId", autoProcProgramId).getResultList(); + if (col != null && col.size() > 0) { + return col.get(0); + } + return null; + } + /** @@ -818,4 +857,6 @@ private void checkChangeRemoveAccess(Session3VO vo) throws AccessDeniedException + + } \ No newline at end of file diff --git a/ispyb-ui/src/main/webapp/js/ispyb/min/ispyb-bx.js b/ispyb-ui/src/main/webapp/js/ispyb/min/ispyb-bx.js index 23e07209a..a98a06520 100644 --- a/ispyb-ui/src/main/webapp/js/ispyb/min/ispyb-bx.js +++ b/ispyb-ui/src/main/webapp/js/ispyb/min/ispyb-bx.js @@ -38,321 +38,321 @@ Event.prototype = { } }; -function GenericGraph(args) { - this.width = 600; - this.height = 400; - - this.targetId = null; - /** Free spaces in the borders * */ - this.top = 10; - this.left = 10; - this.bottom = 50; - this.right = 40; - - /** Ruler * */ - this.rulerHeight = 50; - this.rulerWidth = 50; - this.rulerStroke = 2; - this.rulerVerticalMarksNumber = 5; - - this.rulerMaxValue = null; - this.rulerMinValue = null; - - /** plot options * */ - this.plotPoints = true; - this.pointRadius = 2; - this.fillOpacityPoint = 0.2; - this.strokeOpacityPoint = 0.2; - - /** Cluster titles * */ - this.clusterTitleHeight = 20; - this.interClassesSpace = 2; - this.interClustersSpace = 4; - this.fontSize = 7; - - /** - * If true classes and title will be rendender in the rule otherwise will be - * integer values - */ - this.plotHorizontalByCluster = true; - - if (args != null) { - if (args.targetId != null) { - this.targetId = args.targetId; - } - if (args.plotHorizontalByCluster != null) { - this.plotHorizontalByCluster = args.plotHorizontalByCluster; - } - if (args.height != null) { - this.height = args.height; - } - if (args.width != null) { - this.width = args.width; - } - if (args.rulerMinValue != null) { - this.rulerMinValue = args.rulerMinValue; - } - if (args.rulerMaxValue != null) { - this.rulerMaxValue = args.rulerMaxValue; - } - if (args.rulerHeight != null) { - this.rulerHeight = args.rulerHeight; - } - - } -} - -GenericGraph.prototype.calculate = function(data) { - var result = {}; - - var checked = this.cleanArray(data); - - /** sorting array * */ - checked.sort(function(a, b) { - return a - b; - }); - - var median = this.getMedian(checked); - - result.median = median; - result.Q1 = Number(this.getQ1(checked)); - result.Q2 = Number(this.getQ2(checked)); - result.Q3 = Number(this.getQ3(checked)); - result.population = checked; - - result.IQR = Number(result.Q3 - result.Q1); - result.outlier_below_limit = result.Q1 - (1.5 * result.IQR); - result.outlier_above_limit = result.Q3 + (1.5 * result.IQR); - result.below_outliers = this.getBelowOutliers(result.outlier_below_limit, checked); - result.above_outliers = this.getAboveOutliers(result.outlier_above_limit, checked); - - result.min_whisker = this.minValueWhisker(result.outlier_below_limit, result.Q1, checked); - result.max_whisker = this.maxValueWhisker(result.outlier_above_limit, result.Q3, checked); - - return result; -}; - -GenericGraph.prototype.drawSVGVerticalText = function(x, y, text, properties) { - var transform = [ "transform", "translate(" + x + ", " + y + "), rotate(-90) " ]; - properties.push(transform); - SVG.drawText(0, 0, text, this.svg, properties); -}; - -/** Plot the numbers on the axis * */ -GenericGraph.prototype.plotRuler = function(rulerProperties) { - - SVG.drawRectangle(rulerProperties.vertical.x, rulerProperties.vertical.y, rulerProperties.vertical.width, rulerProperties.vertical.height, - this.svg, [ [ "fill", "black" ] ]); - var distance = rulerProperties.vertical.height / (this.rulerVerticalMarksNumber + 1); - for ( var i = 0; i <= this.rulerVerticalMarksNumber + 1; i++) { - var deltaHeight = distance * i; - var aux = rulerProperties.vertical.height - deltaHeight; - - var text = Number((aux / rulerProperties.vertical.height) * (rulerProperties.maxPoint - rulerProperties.minPoint) + rulerProperties.minPoint) - .toFixed(3); - - SVG.drawLine(rulerProperties.horizontal.x, this.top + deltaHeight, rulerProperties.horizontal.x - rulerProperties.markWidth, - this.top + deltaHeight, this.svg, [ [ "stroke", "black" ] ]); - SVG.drawText(this.left, this.top + distance * i + 5, text, this.svg, [ [ "style", "font-size:xx-small" ] ]); - /** Drawing the mark up to the end * */ - SVG.drawLine(rulerProperties.horizontal.x, this.top + deltaHeight, this.width - this.right, this.top + deltaHeight, this.svg, [ - [ "stroke", rulerProperties.markColor ], [ "stroke-width", "0.3" ] ]); - - if (i == this.rulerVerticalMarksNumber + 1) { - SVG.drawLine(rulerProperties.horizontal.x, this.top + deltaHeight, this.width - this.right, this.top + deltaHeight, this.svg, [ [ - "stroke", rulerProperties.markColor ] ]); - } - } - - /** Drawing horizontal rulers * */ - if (!this.plotHorizontalByCluster) { - var width = rulerProperties.horizontal.width; - var ratio = width / (rulerProperties.horizontal.xValues.range); - for ( i = 0; i < rulerProperties.horizontal.xValues.values.length; i++) { - var coorX = rulerProperties.horizontal.xValues.values[i] - rulerProperties.horizontal.xValues.min; - SVG.drawText(rulerProperties.horizontal.x + coorX * ratio, this.height - (this.bottom + (this.clusterTitleHeight)), - rulerProperties.horizontal.xValues.values[i], this.svg, [ [ "style", "font-size:small" ] ]); - } - } -}; - -GenericGraph.prototype.plotAxes = function(properties) { - /** - * Drawing canvas plot-free spaces SVG.drawRectangle(0, this.top, this.left, - * this.height, this.svg, [["fill", "pink"]]); SVG.drawRectangle(this.width - - * this.right, this.top, plot.width, plot.height, this.svg, [["fill", - * "pink"]]); SVG.drawRectangle(0, 0, this.width, this.top, this.svg, - * [["fill", "red"]]); SVG.drawRectangle(0, this.height - this.bottom, - * this.width, this.bottom, this.svg, [["fill", "red"]]); - */ - - /** Drawing ruler Space * */ - this.plotRuler({ - minPoint : Number(properties.minPoint), - maxPoint : Number(properties.maxPoint), - markColor : "black", - markWidth : 20, - vertical : { - x : this.left + this.rulerWidth - this.rulerStroke, - y : this.top, - width : this.rulerStroke, - height : this.height - (this.top + this.bottom + this.clusterTitleHeight) - this.rulerHeight - }, - horizontal : { - x : this.left + this.rulerWidth - this.rulerStroke, - y : this.height - (this.bottom + this.clusterTitleHeight + this.rulerHeight), - width : properties.width, - height : this.rulerStroke, - xValues : properties.xValues - } - }); - -}; - -/** Remove nulls and NaN elements in the array * */ -GenericGraph.prototype.cleanArray = function(data) { - var checked = []; - - /** checking data are numbers * */ - for ( var i = 0; i < data.length; i++) { - if (data[i] != null) { - if (!isNaN(data[i])) { - checked.push(data[i]); - } - } - } - return checked; -}; - -GenericGraph.prototype.refresh = function(data) { - document.getElementById(this.targetId).innerHTML = ""; - this.draw(this.targetId, data); -}; - -GenericGraph.prototype.getClassColor = function(className) { - for ( var i = 0; i < this.data.clusters.length; i++) { - var cluster = this.data.clusters[i]; - for ( var j = 0; j < cluster.classes.length; j++) { - var classes = cluster.classes[j]; - if (classes.name == className) { - if (classes.color != null) { - return classes.color; - } - } - } - } - return "black"; -}; - -GenericGraph.prototype.getDimensions = function(data) { - var results = {}; - var points = []; - - this.data = data; - var classesNumber = 0; - var xValues = []; - - for ( var i = 0; i < data.clusters.length; i++) { - var cluster = data.clusters[i]; - if (!this.plotHorizontalByCluster) { - xValues.push(data.clusters[i].x); - } - for ( var j = 0; j < cluster.classes.length; j++) { - var classes = cluster.classes[j]; - points = points.concat(classes.values); - classesNumber = classesNumber + 1; - } - } - - var checked = this.cleanArray(points); - - checked.sort(function(a, b) { - return a - b; - }); - - results.minPoint = checked[0]; - if (this.rulerMinValue != null) { - results.minPoint = this.rulerMinValue; - } - results.maxPoint = checked[checked.length - 1]; - if (this.rulerMaxValue != null) { - results.maxPoint = this.rulerMaxValue; - } - - results.classesNumber = classesNumber; - results.clusterNumber = data.clusters.length; - - var totalInterClassesFreeSpace = (classesNumber - data.clusters.length) * this.interClassesSpace; - var totalInterClusterFreeSpace = (data.clusters.length) * this.interClustersSpace; - results.classWidth = (this.width - (this.rulerWidth + this.left + this.right + totalInterClassesFreeSpace + totalInterClusterFreeSpace))/ classesNumber; - results.width = this.width - (this.right + this.left) - this.rulerWidth + this.rulerStroke; - - results.xValues = {}; - - xValues.sort(function(a, b) { - return a - b; - }); - results.xValues.values = xValues; - if (xValues.length > 0) { - results.xValues.min = xValues[0]; - results.xValues.max = xValues[xValues.length - 1]; - results.xValues.range = results.xValues.max - results.xValues.min; - } - return results; - -}; - -GenericGraph.prototype.draw = function(targetId, data) { - this.targetId = targetId; - var properties = (this.getDimensions(data)); - this.svg = SVG.createSVGCanvas(document.getElementById(this.targetId), [ [ "width", this.width ], [ "height", this.height ] ]); - this.plotAxes(properties); -}; - -GenericGraph.prototype.getMedian = function(checked) { - /** Calculating median * */ - if (checked.length % 2 == 1) { - return checked[Math.floor(checked.length / 2)]; - } else { - return (Number(checked[(checked.length / 2) - 1]) + Number(checked[checked.length / 2])) / 2; - } -}; - -GenericGraph.prototype.pointToPixel = function(value, boxProperties) { - var ratio = (value - boxProperties.minPoint) / (boxProperties.maxPoint - boxProperties.minPoint); - var pixelLength = boxProperties.height - boxProperties.y + this.top; - return (-1 * ratio) * (pixelLength) + (boxProperties.y + boxProperties.height); -}; - -GenericGraph.prototype.maxValueWhisker = function(aboveLimit, q3, array) { - var points = []; - for ( var i = 0; i < array.length; i++) { - if ((array[i] > q3) && (array[i]) <= aboveLimit) { - points.push(array[i]); - } - } - if (points.length > 0) { - points.sort(function(a, b) { - return a - b; - }); - return points[points.length - 1]; - } - return null; -}; - -GenericGraph.prototype.input = function() { - return DATADOC.getBoxWhikerData(); -}; - -GenericGraph.prototype.test = function(targetId) { - var plot = new GenericGraph({ - targetId : targetId, - height : 350, - width : 450, - maxBoxWidth : 25 - }); - plot.refresh(this.input()); -}; +function GenericGraph(args) { + this.width = 600; + this.height = 400; + + this.targetId = null; + /** Free spaces in the borders * */ + this.top = 10; + this.left = 10; + this.bottom = 50; + this.right = 40; + + /** Ruler * */ + this.rulerHeight = 50; + this.rulerWidth = 50; + this.rulerStroke = 2; + this.rulerVerticalMarksNumber = 5; + + this.rulerMaxValue = null; + this.rulerMinValue = null; + + /** plot options * */ + this.plotPoints = true; + this.pointRadius = 2; + this.fillOpacityPoint = 0.2; + this.strokeOpacityPoint = 0.2; + + /** Cluster titles * */ + this.clusterTitleHeight = 20; + this.interClassesSpace = 2; + this.interClustersSpace = 4; + this.fontSize = 7; + + /** + * If true classes and title will be rendender in the rule otherwise will be + * integer values + */ + this.plotHorizontalByCluster = true; + + if (args != null) { + if (args.targetId != null) { + this.targetId = args.targetId; + } + if (args.plotHorizontalByCluster != null) { + this.plotHorizontalByCluster = args.plotHorizontalByCluster; + } + if (args.height != null) { + this.height = args.height; + } + if (args.width != null) { + this.width = args.width; + } + if (args.rulerMinValue != null) { + this.rulerMinValue = args.rulerMinValue; + } + if (args.rulerMaxValue != null) { + this.rulerMaxValue = args.rulerMaxValue; + } + if (args.rulerHeight != null) { + this.rulerHeight = args.rulerHeight; + } + + } +} + +GenericGraph.prototype.calculate = function(data) { + var result = {}; + + var checked = this.cleanArray(data); + + /** sorting array * */ + checked.sort(function(a, b) { + return a - b; + }); + + var median = this.getMedian(checked); + + result.median = median; + result.Q1 = Number(this.getQ1(checked)); + result.Q2 = Number(this.getQ2(checked)); + result.Q3 = Number(this.getQ3(checked)); + result.population = checked; + + result.IQR = Number(result.Q3 - result.Q1); + result.outlier_below_limit = result.Q1 - (1.5 * result.IQR); + result.outlier_above_limit = result.Q3 + (1.5 * result.IQR); + result.below_outliers = this.getBelowOutliers(result.outlier_below_limit, checked); + result.above_outliers = this.getAboveOutliers(result.outlier_above_limit, checked); + + result.min_whisker = this.minValueWhisker(result.outlier_below_limit, result.Q1, checked); + result.max_whisker = this.maxValueWhisker(result.outlier_above_limit, result.Q3, checked); + + return result; +}; + +GenericGraph.prototype.drawSVGVerticalText = function(x, y, text, properties) { + var transform = [ "transform", "translate(" + x + ", " + y + "), rotate(-90) " ]; + properties.push(transform); + SVG.drawText(0, 0, text, this.svg, properties); +}; + +/** Plot the numbers on the axis * */ +GenericGraph.prototype.plotRuler = function(rulerProperties) { + + SVG.drawRectangle(rulerProperties.vertical.x, rulerProperties.vertical.y, rulerProperties.vertical.width, rulerProperties.vertical.height, + this.svg, [ [ "fill", "black" ] ]); + var distance = rulerProperties.vertical.height / (this.rulerVerticalMarksNumber + 1); + for ( var i = 0; i <= this.rulerVerticalMarksNumber + 1; i++) { + var deltaHeight = distance * i; + var aux = rulerProperties.vertical.height - deltaHeight; + + var text = Number((aux / rulerProperties.vertical.height) * (rulerProperties.maxPoint - rulerProperties.minPoint) + rulerProperties.minPoint) + .toFixed(3); + + SVG.drawLine(rulerProperties.horizontal.x, this.top + deltaHeight, rulerProperties.horizontal.x - rulerProperties.markWidth, + this.top + deltaHeight, this.svg, [ [ "stroke", "black" ] ]); + SVG.drawText(this.left, this.top + distance * i + 5, text, this.svg, [ [ "style", "font-size:xx-small" ] ]); + /** Drawing the mark up to the end * */ + SVG.drawLine(rulerProperties.horizontal.x, this.top + deltaHeight, this.width - this.right, this.top + deltaHeight, this.svg, [ + [ "stroke", rulerProperties.markColor ], [ "stroke-width", "0.3" ] ]); + + if (i == this.rulerVerticalMarksNumber + 1) { + SVG.drawLine(rulerProperties.horizontal.x, this.top + deltaHeight, this.width - this.right, this.top + deltaHeight, this.svg, [ [ + "stroke", rulerProperties.markColor ] ]); + } + } + + /** Drawing horizontal rulers * */ + if (!this.plotHorizontalByCluster) { + var width = rulerProperties.horizontal.width; + var ratio = width / (rulerProperties.horizontal.xValues.range); + for ( i = 0; i < rulerProperties.horizontal.xValues.values.length; i++) { + var coorX = rulerProperties.horizontal.xValues.values[i] - rulerProperties.horizontal.xValues.min; + SVG.drawText(rulerProperties.horizontal.x + coorX * ratio, this.height - (this.bottom + (this.clusterTitleHeight)), + rulerProperties.horizontal.xValues.values[i], this.svg, [ [ "style", "font-size:small" ] ]); + } + } +}; + +GenericGraph.prototype.plotAxes = function(properties) { + /** + * Drawing canvas plot-free spaces SVG.drawRectangle(0, this.top, this.left, + * this.height, this.svg, [["fill", "pink"]]); SVG.drawRectangle(this.width - + * this.right, this.top, plot.width, plot.height, this.svg, [["fill", + * "pink"]]); SVG.drawRectangle(0, 0, this.width, this.top, this.svg, + * [["fill", "red"]]); SVG.drawRectangle(0, this.height - this.bottom, + * this.width, this.bottom, this.svg, [["fill", "red"]]); + */ + + /** Drawing ruler Space * */ + this.plotRuler({ + minPoint : Number(properties.minPoint), + maxPoint : Number(properties.maxPoint), + markColor : "black", + markWidth : 20, + vertical : { + x : this.left + this.rulerWidth - this.rulerStroke, + y : this.top, + width : this.rulerStroke, + height : this.height - (this.top + this.bottom + this.clusterTitleHeight) - this.rulerHeight + }, + horizontal : { + x : this.left + this.rulerWidth - this.rulerStroke, + y : this.height - (this.bottom + this.clusterTitleHeight + this.rulerHeight), + width : properties.width, + height : this.rulerStroke, + xValues : properties.xValues + } + }); + +}; + +/** Remove nulls and NaN elements in the array * */ +GenericGraph.prototype.cleanArray = function(data) { + var checked = []; + + /** checking data are numbers * */ + for ( var i = 0; i < data.length; i++) { + if (data[i] != null) { + if (!isNaN(data[i])) { + checked.push(data[i]); + } + } + } + return checked; +}; + +GenericGraph.prototype.refresh = function(data) { + document.getElementById(this.targetId).innerHTML = ""; + this.draw(this.targetId, data); +}; + +GenericGraph.prototype.getClassColor = function(className) { + for ( var i = 0; i < this.data.clusters.length; i++) { + var cluster = this.data.clusters[i]; + for ( var j = 0; j < cluster.classes.length; j++) { + var classes = cluster.classes[j]; + if (classes.name == className) { + if (classes.color != null) { + return classes.color; + } + } + } + } + return "black"; +}; + +GenericGraph.prototype.getDimensions = function(data) { + var results = {}; + var points = []; + + this.data = data; + var classesNumber = 0; + var xValues = []; + + for ( var i = 0; i < data.clusters.length; i++) { + var cluster = data.clusters[i]; + if (!this.plotHorizontalByCluster) { + xValues.push(data.clusters[i].x); + } + for ( var j = 0; j < cluster.classes.length; j++) { + var classes = cluster.classes[j]; + points = points.concat(classes.values); + classesNumber = classesNumber + 1; + } + } + + var checked = this.cleanArray(points); + + checked.sort(function(a, b) { + return a - b; + }); + + results.minPoint = checked[0]; + if (this.rulerMinValue != null) { + results.minPoint = this.rulerMinValue; + } + results.maxPoint = checked[checked.length - 1]; + if (this.rulerMaxValue != null) { + results.maxPoint = this.rulerMaxValue; + } + + results.classesNumber = classesNumber; + results.clusterNumber = data.clusters.length; + + var totalInterClassesFreeSpace = (classesNumber - data.clusters.length) * this.interClassesSpace; + var totalInterClusterFreeSpace = (data.clusters.length) * this.interClustersSpace; + results.classWidth = (this.width - (this.rulerWidth + this.left + this.right + totalInterClassesFreeSpace + totalInterClusterFreeSpace))/ classesNumber; + results.width = this.width - (this.right + this.left) - this.rulerWidth + this.rulerStroke; + + results.xValues = {}; + + xValues.sort(function(a, b) { + return a - b; + }); + results.xValues.values = xValues; + if (xValues.length > 0) { + results.xValues.min = xValues[0]; + results.xValues.max = xValues[xValues.length - 1]; + results.xValues.range = results.xValues.max - results.xValues.min; + } + return results; + +}; + +GenericGraph.prototype.draw = function(targetId, data) { + this.targetId = targetId; + var properties = (this.getDimensions(data)); + this.svg = SVG.createSVGCanvas(document.getElementById(this.targetId), [ [ "width", this.width ], [ "height", this.height ] ]); + this.plotAxes(properties); +}; + +GenericGraph.prototype.getMedian = function(checked) { + /** Calculating median * */ + if (checked.length % 2 == 1) { + return checked[Math.floor(checked.length / 2)]; + } else { + return (Number(checked[(checked.length / 2) - 1]) + Number(checked[checked.length / 2])) / 2; + } +}; + +GenericGraph.prototype.pointToPixel = function(value, boxProperties) { + var ratio = (value - boxProperties.minPoint) / (boxProperties.maxPoint - boxProperties.minPoint); + var pixelLength = boxProperties.height - boxProperties.y + this.top; + return (-1 * ratio) * (pixelLength) + (boxProperties.y + boxProperties.height); +}; + +GenericGraph.prototype.maxValueWhisker = function(aboveLimit, q3, array) { + var points = []; + for ( var i = 0; i < array.length; i++) { + if ((array[i] > q3) && (array[i]) <= aboveLimit) { + points.push(array[i]); + } + } + if (points.length > 0) { + points.sort(function(a, b) { + return a - b; + }); + return points[points.length - 1]; + } + return null; +}; + +GenericGraph.prototype.input = function() { + return DATADOC.getBoxWhikerData(); +}; + +GenericGraph.prototype.test = function(targetId) { + var plot = new GenericGraph({ + targetId : targetId, + height : 350, + width : 450, + maxBoxWidth : 25 + }); + plot.refresh(this.input()); +}; /** * Using dygraph it plots a chart. Params: targetId, labelsContainerId, args @@ -2087,338 +2087,338 @@ MacromoleculeConditionGrid.prototype.test = function(targetId) { panel.render(targetId); }; - -function ItemGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ - this.id = id; - this.args = new Object(); - - this.defaultFormat = new ItemFormat(defaultFormat); - - if(selectedFormat != null){ - this.selected = new ItemFormat(selectedFormat); - } - else{ - this.selected = new ItemFormat(defaultFormat); - } - - if(overFormat != null){ - this.over = new ItemFormat(overFormat); - } - else{ - this.over = new ItemFormat(defaultFormat); - } - - if(draggingFormat != null){ - this.dragging = new ItemFormat(draggingFormat); - } - else{ - this.dragging = new ItemFormat(defaultFormat); - } - - //Events - this.stateChanged = new Event(this); - - - //Attaching events - var _this = this; - this._setEvents(); -}; - -ItemGraphFormatter.prototype.getType = function(){ - return this.args.type; -}; - - -ItemGraphFormatter.prototype.toJSON = function(){ - var json = this.args; - json.defaultFormat = this.getDefault().toJSON(); - json.over = this.getOver().toJSON(); - json.selected = this.getSelected().toJSON(); - json.dragging = this.getDragging().toJSON(); - json.id = this.id; - return json; -}; - -ItemGraphFormatter.prototype.loadFromJSON = function(json){ - this.args = json; - this.defaultFormat = new ItemFormat(json.defaultFormat); - this.over = new ItemFormat(json.over); - this.selected = new ItemFormat(json.selected); - this.dragging = new ItemFormat(json.dragging); - this._setEvents(); -}; - -ItemGraphFormatter.prototype._setEvents = function(){ - //Attaching events - var _this = this; - - this.defaultFormat.changed.attach(function (sender, item){ - _this.over.setSize(_this.defaultFormat.getSize()); - _this.selected.setSize(_this.defaultFormat.getSize()); - _this.dragging.setSize(_this.defaultFormat.getSize()); - _this.stateChanged.notify(_this); - }); - - this.selected.changed.attach(function (sender, item){ - _this.stateChanged.notify(_this); - }); - - this.over.changed.attach(function (sender, item){ - _this.stateChanged.notify(_this); - }); - - this.dragging.changed.attach(function (sender, item){ - _this.stateChanged.notify(_this); - }); -}; - -/** Getters **/ -ItemGraphFormatter.prototype.getId = function(){return this.id;}; -ItemGraphFormatter.prototype.getDefault = function(){return this.defaultFormat;}; -ItemGraphFormatter.prototype.getSelected = function(){return this.selected;}; -ItemGraphFormatter.prototype.getOver = function(){return this.over;}; -ItemGraphFormatter.prototype.getDragging = function(){return this.dragging;}; - -function ItemFormat(args){ - this.defaultFormat = new Object(); - this.args = new Object(); - this.args.title = new Object(); - //Defult properties - this.args.visible = true; - this.args.hidden = false; - this.args.stroke = "#000000"; - this.args.strokeOpacity = 0.8; - this.args["stroke-width"] = 1; - this.args.fill = "#000000"; - this.args["fill-opacity"] = 1; - this.args.size = 1; - this.args.opacity = 1; - this.args.fontSize = "8"; - this.args.fontColor = "#000000"; - - /** For directed edge with arrow **/ - //this.args.arrowSize = 1; - - - if (args != null){ - if (args.visible != null){ - this.args.visible = args.visible; - } - if (args.opacity != null){ - this.args.opacity = args.opacity; - } - if (args.size != null){ - this.args.size = args.size; - } - if (args.hidden != null){ - this.args.hidden = args.hidden; - } - if (args.stroke != null){ - this.args.stroke = this._fixColor(args.stroke); - } - if (args.strokeOpacity != null){ - this.args.strokeOpacity = args.strokeOpacity; - } - if (args["stroke-width"]!=null){ - this.args["stroke-width"] = args["stroke-width"]; - } - if (args["fill-opacity"]!=null){ - this.args["fill-opacity"] = args["fill-opacity"]; - } - if (args.shape!=null){ - this.args.shape = args.shape; - } - if (args.fill!=null){ - this.args.fill = this._fixColor(args.fill); - } - - - if (args.title!=null){ - if (args.title.fontSize!=null){ - this.args.title.fontSize = args.title.fontSize; - } - if (args.title.fill!=null){ - this.args.title.fill = this._fixColor(args.title.fill); - } - } - - /** For directed edge with arrow **/ - /*if (args.arrowSize!=null){ - this.args.arrowSize = args.arrowSize; - }*/ - - } - - this.changed = new Event(); -}; - -ItemFormat.prototype._fixColor = function(color){ - var fixed = color; - if (color.indexOf("green") != -1){ - fixed = '#04B431'; - } - - if (color.indexOf("blue") != -1){ - fixed = '#045FB4'; - } - - if (color.indexOf("red") != -1){ - fixed = '#DF0101'; - } - - if (color.indexOf("black") != -1){ - fixed = '#000000'; - } - - if (color.indexOf("white") != -1){ - fixed = '#FFFFFF'; - } - - if (color.indexOf("#") == -1){ - fixed = "#" + color; - } - return fixed; -}; - -ItemFormat.prototype.toJSON = function(){ - if(this.args.strokeOpacity != null){ - this.args["stroke-opacity"] = this.args.strokeOpacity; - delete this.args.strokeOpacity; - } - -// if(this.args.strokeWidth != null){ -// this.args["stroke-width"] = this.args.strokeWidth; -// delete this.args["stroke-width"]; -// } - - if(this.args.title.fontColor != null){ - this.args.title["font-color"] = this.args.title.fontColor; - } - else{ - this.args.title["font-color"] = this.args.fontColor;//;this.args.title.fontColor; - } - - if(this.args.title.fontSize != null){ - this.args.title["font-size"] = this.args.title.fontSize;//;this.args.title.fontColor; - } - else{ - this.args.title["font-size"] = this.args.fontSize;//;this.args.title.fontColor; - } - //return this.args; - return this.args; -}; - -ItemFormat.prototype.getAttribute = function(name){return this.args[name];}; - -//Getters and Setters -ItemFormat.prototype.setVisible = function(visible){ - if (this.args.visible != visible){ - this.args.visible = visible; - this.changed.notify(this); - } -}; - -ItemFormat.prototype.getVisible = function(){return this.args.visible;}; - -ItemFormat.prototype.setHidden = function(hidden){ - if (this.args.hidden != hidden){ - this.args.hidden = hidden; - this.changed.notify(this); - } -}; - -ItemFormat.prototype.getHidden = function(){return this.args.hidden;}; - - -ItemFormat.prototype.setStroke = function(stroke){ - if (this.args.stroke != stroke){ - this.args.stroke = stroke; - this.changed.notify(this); - } -}; - -ItemFormat.prototype.getStroke = function(){return this.args.stroke;}; - -ItemFormat.prototype.setStrokeOpacity = function(strokeOpacity){ - if (this.args.strokeOpacity != strokeOpacity){ - this.args.strokeOpacity = strokeOpacity; - this.changed.notify(this); - } -}; - -ItemFormat.prototype.getStrokeOpacity = function(){return this.args["stroke-opacity"];}; - -ItemFormat.prototype.setStrokeWidth = function(strokeWidth){ - if (this.args["stroke-width"] != strokeWidth){ - this.args["stroke-width"] = strokeWidth; - this.changed.notify(this); - } -}; - - -ItemFormat.prototype.getFillOpacity = function(){return this.args["fill-opacity"];}; - -ItemFormat.prototype.setfillOpacity = function(strokeWidth){ - if (this.args["fill-opacity"] != strokeWidth){ - this.args["fill-opacity"] = strokeWidth; - this.changed.notify(this); - } -}; - - -ItemFormat.prototype.getStrokeWidth = function(){ - return this.args["stroke-width"]; -}; - -ItemFormat.prototype.setFill = function(fill){ - if (this.args.fill != fill){ - this.args.fill = fill; - this.changed.notify(this); - } -}; - -ItemFormat.prototype.getFill = function(){return this.args.fill;}; - -ItemFormat.prototype.setSize = function(size){ - if (this.args.size != size){ - this.args.size = size; - this.changed.notify(this); - } -}; - -ItemFormat.prototype.getSize = function(){return this.args.size;}; - -ItemFormat.prototype.setOpacity = function(opacity){ - if (this.args.opacity != opacity){ - this.args.opacity = opacity; - this.changed.notify(this); - } -}; - -ItemFormat.prototype.getOpacity = function(){return this.args.opacity;}; - -ItemFormat.prototype.getArrowSize = function(){return this.args.arrowSize;}; - -ItemFormat.prototype.setArrowSize = function(arrowSize){ - if (this.args.arrowSize != arrowSize){ - this.args.arrowSize = arrowSize; - this.changed.notify(this); - } -}; - -ItemFormat.prototype.getFontSize = function(){return this.args.title.fontSize;}; - -ItemFormat.prototype.setFontSize = function(fontSize){ - - if (this.args.title.fontSize != fontSize){ - this.args.title.fontSize = fontSize; - this.changed.notify(this); - } -}; - - - - + +function ItemGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ + this.id = id; + this.args = new Object(); + + this.defaultFormat = new ItemFormat(defaultFormat); + + if(selectedFormat != null){ + this.selected = new ItemFormat(selectedFormat); + } + else{ + this.selected = new ItemFormat(defaultFormat); + } + + if(overFormat != null){ + this.over = new ItemFormat(overFormat); + } + else{ + this.over = new ItemFormat(defaultFormat); + } + + if(draggingFormat != null){ + this.dragging = new ItemFormat(draggingFormat); + } + else{ + this.dragging = new ItemFormat(defaultFormat); + } + + //Events + this.stateChanged = new Event(this); + + + //Attaching events + var _this = this; + this._setEvents(); +}; + +ItemGraphFormatter.prototype.getType = function(){ + return this.args.type; +}; + + +ItemGraphFormatter.prototype.toJSON = function(){ + var json = this.args; + json.defaultFormat = this.getDefault().toJSON(); + json.over = this.getOver().toJSON(); + json.selected = this.getSelected().toJSON(); + json.dragging = this.getDragging().toJSON(); + json.id = this.id; + return json; +}; + +ItemGraphFormatter.prototype.loadFromJSON = function(json){ + this.args = json; + this.defaultFormat = new ItemFormat(json.defaultFormat); + this.over = new ItemFormat(json.over); + this.selected = new ItemFormat(json.selected); + this.dragging = new ItemFormat(json.dragging); + this._setEvents(); +}; + +ItemGraphFormatter.prototype._setEvents = function(){ + //Attaching events + var _this = this; + + this.defaultFormat.changed.attach(function (sender, item){ + _this.over.setSize(_this.defaultFormat.getSize()); + _this.selected.setSize(_this.defaultFormat.getSize()); + _this.dragging.setSize(_this.defaultFormat.getSize()); + _this.stateChanged.notify(_this); + }); + + this.selected.changed.attach(function (sender, item){ + _this.stateChanged.notify(_this); + }); + + this.over.changed.attach(function (sender, item){ + _this.stateChanged.notify(_this); + }); + + this.dragging.changed.attach(function (sender, item){ + _this.stateChanged.notify(_this); + }); +}; + +/** Getters **/ +ItemGraphFormatter.prototype.getId = function(){return this.id;}; +ItemGraphFormatter.prototype.getDefault = function(){return this.defaultFormat;}; +ItemGraphFormatter.prototype.getSelected = function(){return this.selected;}; +ItemGraphFormatter.prototype.getOver = function(){return this.over;}; +ItemGraphFormatter.prototype.getDragging = function(){return this.dragging;}; + +function ItemFormat(args){ + this.defaultFormat = new Object(); + this.args = new Object(); + this.args.title = new Object(); + //Defult properties + this.args.visible = true; + this.args.hidden = false; + this.args.stroke = "#000000"; + this.args.strokeOpacity = 0.8; + this.args["stroke-width"] = 1; + this.args.fill = "#000000"; + this.args["fill-opacity"] = 1; + this.args.size = 1; + this.args.opacity = 1; + this.args.fontSize = "8"; + this.args.fontColor = "#000000"; + + /** For directed edge with arrow **/ + //this.args.arrowSize = 1; + + + if (args != null){ + if (args.visible != null){ + this.args.visible = args.visible; + } + if (args.opacity != null){ + this.args.opacity = args.opacity; + } + if (args.size != null){ + this.args.size = args.size; + } + if (args.hidden != null){ + this.args.hidden = args.hidden; + } + if (args.stroke != null){ + this.args.stroke = this._fixColor(args.stroke); + } + if (args.strokeOpacity != null){ + this.args.strokeOpacity = args.strokeOpacity; + } + if (args["stroke-width"]!=null){ + this.args["stroke-width"] = args["stroke-width"]; + } + if (args["fill-opacity"]!=null){ + this.args["fill-opacity"] = args["fill-opacity"]; + } + if (args.shape!=null){ + this.args.shape = args.shape; + } + if (args.fill!=null){ + this.args.fill = this._fixColor(args.fill); + } + + + if (args.title!=null){ + if (args.title.fontSize!=null){ + this.args.title.fontSize = args.title.fontSize; + } + if (args.title.fill!=null){ + this.args.title.fill = this._fixColor(args.title.fill); + } + } + + /** For directed edge with arrow **/ + /*if (args.arrowSize!=null){ + this.args.arrowSize = args.arrowSize; + }*/ + + } + + this.changed = new Event(); +}; + +ItemFormat.prototype._fixColor = function(color){ + var fixed = color; + if (color.indexOf("green") != -1){ + fixed = '#04B431'; + } + + if (color.indexOf("blue") != -1){ + fixed = '#045FB4'; + } + + if (color.indexOf("red") != -1){ + fixed = '#DF0101'; + } + + if (color.indexOf("black") != -1){ + fixed = '#000000'; + } + + if (color.indexOf("white") != -1){ + fixed = '#FFFFFF'; + } + + if (color.indexOf("#") == -1){ + fixed = "#" + color; + } + return fixed; +}; + +ItemFormat.prototype.toJSON = function(){ + if(this.args.strokeOpacity != null){ + this.args["stroke-opacity"] = this.args.strokeOpacity; + delete this.args.strokeOpacity; + } + +// if(this.args.strokeWidth != null){ +// this.args["stroke-width"] = this.args.strokeWidth; +// delete this.args["stroke-width"]; +// } + + if(this.args.title.fontColor != null){ + this.args.title["font-color"] = this.args.title.fontColor; + } + else{ + this.args.title["font-color"] = this.args.fontColor;//;this.args.title.fontColor; + } + + if(this.args.title.fontSize != null){ + this.args.title["font-size"] = this.args.title.fontSize;//;this.args.title.fontColor; + } + else{ + this.args.title["font-size"] = this.args.fontSize;//;this.args.title.fontColor; + } + //return this.args; + return this.args; +}; + +ItemFormat.prototype.getAttribute = function(name){return this.args[name];}; + +//Getters and Setters +ItemFormat.prototype.setVisible = function(visible){ + if (this.args.visible != visible){ + this.args.visible = visible; + this.changed.notify(this); + } +}; + +ItemFormat.prototype.getVisible = function(){return this.args.visible;}; + +ItemFormat.prototype.setHidden = function(hidden){ + if (this.args.hidden != hidden){ + this.args.hidden = hidden; + this.changed.notify(this); + } +}; + +ItemFormat.prototype.getHidden = function(){return this.args.hidden;}; + + +ItemFormat.prototype.setStroke = function(stroke){ + if (this.args.stroke != stroke){ + this.args.stroke = stroke; + this.changed.notify(this); + } +}; + +ItemFormat.prototype.getStroke = function(){return this.args.stroke;}; + +ItemFormat.prototype.setStrokeOpacity = function(strokeOpacity){ + if (this.args.strokeOpacity != strokeOpacity){ + this.args.strokeOpacity = strokeOpacity; + this.changed.notify(this); + } +}; + +ItemFormat.prototype.getStrokeOpacity = function(){return this.args["stroke-opacity"];}; + +ItemFormat.prototype.setStrokeWidth = function(strokeWidth){ + if (this.args["stroke-width"] != strokeWidth){ + this.args["stroke-width"] = strokeWidth; + this.changed.notify(this); + } +}; + + +ItemFormat.prototype.getFillOpacity = function(){return this.args["fill-opacity"];}; + +ItemFormat.prototype.setfillOpacity = function(strokeWidth){ + if (this.args["fill-opacity"] != strokeWidth){ + this.args["fill-opacity"] = strokeWidth; + this.changed.notify(this); + } +}; + + +ItemFormat.prototype.getStrokeWidth = function(){ + return this.args["stroke-width"]; +}; + +ItemFormat.prototype.setFill = function(fill){ + if (this.args.fill != fill){ + this.args.fill = fill; + this.changed.notify(this); + } +}; + +ItemFormat.prototype.getFill = function(){return this.args.fill;}; + +ItemFormat.prototype.setSize = function(size){ + if (this.args.size != size){ + this.args.size = size; + this.changed.notify(this); + } +}; + +ItemFormat.prototype.getSize = function(){return this.args.size;}; + +ItemFormat.prototype.setOpacity = function(opacity){ + if (this.args.opacity != opacity){ + this.args.opacity = opacity; + this.changed.notify(this); + } +}; + +ItemFormat.prototype.getOpacity = function(){return this.args.opacity;}; + +ItemFormat.prototype.getArrowSize = function(){return this.args.arrowSize;}; + +ItemFormat.prototype.setArrowSize = function(arrowSize){ + if (this.args.arrowSize != arrowSize){ + this.args.arrowSize = arrowSize; + this.changed.notify(this); + } +}; + +ItemFormat.prototype.getFontSize = function(){return this.args.title.fontSize;}; + +ItemFormat.prototype.setFontSize = function(fontSize){ + + if (this.args.title.fontSize != fontSize){ + this.args.title.fontSize = fontSize; + this.changed.notify(this); + } +}; + + + + /** * This class executes the actions @@ -4952,2095 +4952,1101 @@ function openExperiment(experimentId) { BIOSAXS.openExperiment(experimentId); } -var SITE_CONF = { - SAMPLE_CHANGER_CONFIGURATION : { - "3":{ - "platetype3VO": {"plateTypeId":4,"name":"96 Well plate","rowCount":8,"columnCount":12,"shape":"REC"}, - "name":"96 Well plate", - "slotPositionRow":"1", - "slotPositionColumn":"3", - "storageTemperature":"0", - "sampleplateposition3VOs":[], - "experimentId":0 - }, - "2":{ - "platetype3VO":{"plateTypeId":2,"name":" 4 x ( 8 + 3 ) Block","rowCount":4,"columnCount":11,"shape":"REC"}, - "name":" 4 x ( 8 + 3 ) Block", - "slotPositionRow":"1", - "slotPositionColumn":"2", - "storageTemperature":"0", - "sampleplateposition3VOs":[],"experimentId":0 - }, - "1":{ - "platetype3VO":{"plateTypeId":1,"name":"Deep Well","rowCount":8,"columnCount":12,"shape":"REC"}, - "name":"Deep Well", - "slotPositionRow":"1", - "slotPositionColumn":"1", - "storageTemperature":"0", - "sampleplateposition3VOs":[], - "experimentId":0 - } - } +var SITE_CONF = { + SAMPLE_CHANGER_CONFIGURATION : { + "3":{ + "platetype3VO": {"plateTypeId":4,"name":"96 Well plate","rowCount":8,"columnCount":12,"shape":"REC"}, + "name":"96 Well plate", + "slotPositionRow":"1", + "slotPositionColumn":"3", + "storageTemperature":"0", + "sampleplateposition3VOs":[], + "experimentId":0 + }, + "2":{ + "platetype3VO":{"plateTypeId":2,"name":" 4 x ( 8 + 3 ) Block","rowCount":4,"columnCount":11,"shape":"REC"}, + "name":" 4 x ( 8 + 3 ) Block", + "slotPositionRow":"1", + "slotPositionColumn":"2", + "storageTemperature":"0", + "sampleplateposition3VOs":[],"experimentId":0 + }, + "1":{ + "platetype3VO":{"plateTypeId":1,"name":"Deep Well","rowCount":8,"columnCount":12,"shape":"REC"}, + "name":"Deep Well", + "slotPositionRow":"1", + "slotPositionColumn":"1", + "storageTemperature":"0", + "sampleplateposition3VOs":[], + "experimentId":0 + } + } }; - -var ISPYB_CONF = { - load : function(config) { - for (var key in config) { - ISPYB_CONF[key] = config[key]; - } - }, - SAMPLE_CHANGER_CONFIGURATION : { - "1": { - "platetype3VO": {"plateTypeId": 1, "name": "Deep Well", "rowCount": 8, "columnCount": 12, "shape": "REC"}, - "name": "Deep Well", - "slotPositionRow": "1", - "slotPositionColumn": "1", - "storageTemperature": "0", - "sampleplateposition3VOs": [], - "experimentId": 0 - } - } + +var ISPYB_CONF = { + load : function(config) { + for (var key in config) { + ISPYB_CONF[key] = config[key]; + } + }, + SAMPLE_CHANGER_CONFIGURATION : { + "1": { + "platetype3VO": {"plateTypeId": 1, "name": "Deep Well", "rowCount": 8, "columnCount": 12, "shape": "REC"}, + "name": "Deep Well", + "slotPositionRow": "1", + "slotPositionColumn": "1", + "storageTemperature": "0", + "sampleplateposition3VOs": [], + "experimentId": 0 + } + } }; -var SITE_CONF = { - -}; - -/** - * Example form - * - * @witdh - * @height - */ -function AbinitioForm(args) { - this.id = BUI.id(); - this.width = null; - this.height = null; - - if (args != null) { - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; - } - } - - var _this = this; - /** Widgets **/ - this.abinitioGrid = new AbinitioGrid({ - width : null, - height : 200 - }); - - this.abinitioGrid.onSelected.attach(function(sender, models) { - var modelsIdList = []; - for ( var i in models) { - modelsIdList.push(models[i].modelId); - } - _this._renderPlot(_this.subtractions[0].subtractionId, modelsIdList); - _this._renderPDB(modelsIdList); - }); - - /** Dygraph Widget that plots fir files**/ - this.plotWidget = new PlotWidget({ - width : 745 / 2, - height : 300, - margin : "10 0 5 10" - }); - - /** PDB viewer **/ - this.viewer = new PDBViewer({ - width : 745 / 2, - height : 300 - }); - -} - -AbinitioForm.prototype._renderPlot = function(subtractionId, modelsIdList) { - /** Trying to plot tje subtraction and the models **/ - try { - var colors = [ "#669900", "#0000FF" ]; - this.plotWidget.refresh([], [ ], modelsIdList, [], [], colors); - } catch (e) { - console.log(e); - } -}; - -AbinitioForm.prototype._renderPDB = function(modelsIdList) { - /** Trying to plot the PDB file **/ - try { - var viz = []; - for (var i = 0; i < modelsIdList.length; i++) { - viz.push({ - modelId : modelsIdList[i], - color : "0xFF6600", - opacity : 0.8 - }); - } - this.viewer.refresh(viz); - } catch (e) { - console.log(e); - } -}; - -AbinitioForm.prototype._getItems = function() { - var _this = this; - return [ { - xtype : 'label', - forId : 'myFieldId', - text : 'INLINE HELP: To be updated', - margin : '15 0 20 10', - cls : "inline-help" - }, this.abinitioGrid.getPanel(), { - xtype : 'container', - layout : 'hbox', - items : [ this.plotWidget.getPanel(), this.viewer.getPanel() ] - } ] -}; - -AbinitioForm.prototype._getButtons = function() { - return []; -}; - -AbinitioForm.prototype.getPanel = function() { - var _this = this; - this.panel = Ext.create('Ext.form.Panel', { - width : this.width, - height : this.height, - margin : 10, - border : 1, - defaultType : 'textfield', - items : this._getItems(), - buttons : this._getButtons(), - listeners : { - afterrender : function() { - _this._populate(); +var SITE_CONF = { + +}; - } - } - }); - return this.panel; -}; +/** + * Example form + * + * @witdh + * @height + */ +function AbinitioForm(args) { + this.id = BUI.id(); + this.width = null; + this.height = null; + + if (args != null) { + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + } + + var _this = this; + /** Widgets **/ + this.abinitioGrid = new AbinitioGrid({ + width : null, + height : 200 + }); + + this.abinitioGrid.onSelected.attach(function(sender, models) { + var modelsIdList = []; + for ( var i in models) { + modelsIdList.push(models[i].modelId); + } + _this._renderPlot(_this.subtractions[0].subtractionId, modelsIdList); + _this._renderPDB(modelsIdList); + }); + + /** Dygraph Widget that plots fir files**/ + this.plotWidget = new PlotWidget({ + width : 745 / 2, + height : 300, + margin : "10 0 5 10" + }); + + /** PDB viewer **/ + this.viewer = new PDBViewer({ + width : 745 / 2, + height : 300 + }); + +} + +AbinitioForm.prototype._renderPlot = function(subtractionId, modelsIdList) { + /** Trying to plot tje subtraction and the models **/ + try { + var colors = [ "#669900", "#0000FF" ]; + this.plotWidget.refresh([], [ ], modelsIdList, [], [], colors); + } catch (e) { + console.log(e); + } +}; + +AbinitioForm.prototype._renderPDB = function(modelsIdList) { + /** Trying to plot the PDB file **/ + try { + var viz = []; + for (var i = 0; i < modelsIdList.length; i++) { + viz.push({ + modelId : modelsIdList[i], + color : "0xFF6600", + opacity : 0.8 + }); + } + this.viewer.refresh(viz); + } catch (e) { + console.log(e); + } +}; + +AbinitioForm.prototype._getItems = function() { + var _this = this; + return [ { + xtype : 'label', + forId : 'myFieldId', + text : 'INLINE HELP: To be updated', + margin : '15 0 20 10', + cls : "inline-help" + }, this.abinitioGrid.getPanel(), { + xtype : 'container', + layout : 'hbox', + items : [ this.plotWidget.getPanel(), this.viewer.getPanel() ] + } ] +}; + +AbinitioForm.prototype._getButtons = function() { + return []; +}; + +AbinitioForm.prototype.getPanel = function() { + var _this = this; + this.panel = Ext.create('Ext.form.Panel', { + width : this.width, + height : this.height, + margin : 10, + border : 1, + defaultType : 'textfield', + items : this._getItems(), + buttons : this._getButtons(), + listeners : { + afterrender : function() { + _this._populate(); + + } + } + }); + return this.panel; +}; + +/** Populates could be call when the DOM is not filled yet **/ +AbinitioForm.prototype._populate = function() { +}; + +/** It populates the form * */ +AbinitioForm.prototype.refresh = function(subtractions) { + this.subtractions = subtractions; + this.abinitioGrid.refresh(subtractions); +}; + +AbinitioForm.prototype.input = function() { + return {}; +}; + +/** It populates the form **/ +AbinitioForm.prototype.test = function(targetId) { + var macromoleculeForm = new AbinitioForm(); + var panel = macromoleculeForm.getPanel(); + panel.render(targetId); +}; -/** Populates could be call when the DOM is not filled yet **/ -AbinitioForm.prototype._populate = function() { -}; - -/** It populates the form * */ -AbinitioForm.prototype.refresh = function(subtractions) { - this.subtractions = subtractions; - this.abinitioGrid.refresh(subtractions); -}; - -AbinitioForm.prototype.input = function() { - return {}; -}; - -/** It populates the form **/ -AbinitioForm.prototype.test = function(targetId) { - var macromoleculeForm = new AbinitioForm(); - var panel = macromoleculeForm.getPanel(); - panel.render(targetId); -}; - -/** - * Example form - * - * @witdh - * @height - */ -function DataReductionForm(args) { - this.id = BUI.id(); - this.width = null; - this.height = null; - - if (args != null) { - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; - } - } - - var _this = this; - - /** Widgets **/ - this.plotWidget = new PlotWidget({ - width : 650, - height : 490 - }); - - /** Selected frames to be displayed **/ - this.selectedItems = { - frames : [], - averages : [], - subtractions : [] - }; - -} - -DataReductionForm.prototype._parseSelectedItemsToIds = function(selectedArray) { - var ids = []; - if (selectedArray != null) { - for (var i = 0; i < selectedArray.length; i++) { - ids.push(selectedArray[i].id); - } - } - return ids; -}; - -DataReductionForm.prototype.onSelectionChanged = function(columnName, selected) { - if (selected != null) { - if (columnName == "Frames") { - this.selectedItems.frames = selected; - this.selectedItems.subtractions = []; - } - if (columnName == "Averages") { - this.selectedItems.averages = selected; - } - if (columnName == "Subtractions") { - this.selectedItems.frames = []; - this.selectedItems.subtractions = selected; - } - } - this.plotWidget.refresh(this._parseSelectedItemsToIds(this.selectedItems.frames), this._parseSelectedItemsToIds(this.selectedItems.subtractions)); -}; - -DataReductionForm.prototype._getFramesExtPanel = function(store, columnName, height) { - var _this = this; - - var selModel = Ext.create('Ext.selection.RowModel', { - allowDeselect : true, - mode : 'MULTI', - listeners : { - selectionchange : function(sm, selections) { - var selected = []; - for (var i = 0; i < selections.length; i++) { - selected.push(selections[i].raw); - } - _this.onSelectionChanged(columnName, selected); - } - } - }); - - return Ext.create('Ext.grid.Panel', { - store : store, - margin : 10, - height : height, - width : 200, - selModel : selModel, - columns : [ { - text : columnName, - dataIndex : 'fileName', - flex : 1 - } ], - viewConfig : { - } - }); -}; - -DataReductionForm.prototype._getFramesPanel = function() { - var fields = [ 'fileName', 'type', 'id' ]; - - this.framesStore = Ext.create('Ext.data.Store', { - fields : fields, - sorters : 'fileName' - }); - - this.averagesStore = Ext.create('Ext.data.Store', { - fields : fields - }); - - this.subtractionStore = Ext.create('Ext.data.Store', { - fields : fields - }); - - var gridFrames = this._getFramesExtPanel(this.framesStore, "Frames", 375); - var gridAvgs = this._getFramesExtPanel(this.averagesStore, "Averages", 125); - var subtractionAvgs = this._getFramesExtPanel(this.subtractionStore, "Subtractions", 75); - - return { - xtype : 'container', - layout : 'vbox', - items : [ gridFrames, subtractionAvgs ] - }; -}; - -DataReductionForm.prototype._getImageContainer = function(name, help) { - var html = "
" + name + "
" - return { - xtype : 'container', - layout : 'vbox', - items : [ { - html : html, - margin : "5 0 0 0", - height : 95, - width : 100 - }, { - xtype : 'label', - forId : 'myFieldId', - text : help, - margin : '5 0 0 0', - cls : "inline-help" - } ] - } -}; - -DataReductionForm.prototype._getItems = function() { - var _this = this; - return [ { - xtype : 'container', - layout : 'hbox', - items : [ - this._getFramesPanel(), - this.plotWidget.getPanel(), - { - xtype : 'panel', - width : 110, - frame : true, - margin : "10 5 5 5", - border : 0, - layout : 'vbox', - items : [ this._getImageContainer("scattering", "Scattering"), this._getImageContainer("guinier", "Guinier Region"), - this._getImageContainer("kratky", "Kratky Plot"), this._getImageContainer("gnom", "P(r) distribution") ] - } ] - } ] -}; - -DataReductionForm.prototype._getButtons = function() { - return []; -}; - -DataReductionForm.prototype.getPanel = function() { - var _this = this; - this.panel = Ext.create('Ext.form.Panel', { - width : this.width, - height : this.height, - border : 0, - items : this._getItems(), - buttons : this._getButtons(), - listeners : { - afterrender : function() { - _this._populate(); - } - } - }); - return this.panel; -}; - -/** Populates could be call when the DOM is not filled yet **/ -DataReductionForm.prototype._populate = function() { -}; - -/** It populates the form * */ -DataReductionForm.prototype.refresh = function(subtractions) { - if (subtractions != null) { - for (var i = 0; i < subtractions.length; i++) { - /** Loading frame grids **/ - var subtraction = subtractions[i]; - var averages = [ { - fileName : BUI.getFileName(subtraction.bufferAverageFilePath), - type : 'bufferAvg', - id : subtraction.subtractionId - }, { - fileName : BUI.getFileName(subtraction.sampleAverageFilePath), - type : 'sampleAvg', - id : subtraction.subtractionId - } - - ]; - this.averagesStore.loadData(averages, true); - this.subtractionStore.loadData([ { - fileName : BUI.getFileName(subtraction.substractedFilePath), - type : 'SUBTRACTION', - id : subtraction.subtractionId - } ], true); - - var frames = []; - /** Buffers **/ - if (subtraction.bufferOneDimensionalFiles != null) { - if (subtraction.bufferOneDimensionalFiles.frametolist3VOs != null) { - for (var j = 0; j < subtraction.bufferOneDimensionalFiles.frametolist3VOs.length; j++) { - var frametolist3VO = subtraction.bufferOneDimensionalFiles.frametolist3VOs[j]; - if (frametolist3VO.frame3VO != null) { - frames.push({ - fileName : BUI.getFileName(frametolist3VO.frame3VO.filePath), - type : 'BUFFER', - id : frametolist3VO.frame3VO.frameId - }); - } - } - } - } - /** Samples **/ - if (subtraction.sampleOneDimensionalFiles != null) { - if (subtraction.sampleOneDimensionalFiles.frametolist3VOs != null) { - for (var j = 0; j < subtraction.sampleOneDimensionalFiles.frametolist3VOs.length; j++) { - var frametolist3VO = subtraction.sampleOneDimensionalFiles.frametolist3VOs[j]; - if (frametolist3VO.frame3VO != null) { - frames.push({ - fileName : BUI.getFileName(frametolist3VO.frame3VO.filePath), - type : 'SAMPLE', - id : frametolist3VO.frame3VO.frameId - }); - } - } - } - } - - this.framesStore.loadData(frames, true); - - /** Loading images **/ - this._displayImage("scattering", subtraction.subtractionId); - this._displayImage("kratky", subtraction.subtractionId); - this._displayImage("guinier", subtraction.subtractionId); - this._displayImage("gnom", subtraction.subtractionId); - } - } -}; - -DataReductionForm.prototype._displayImage = function(name, subtractionId) { - var url = BUI.getURL() + '&type=' + name + '&subtractionId=' + subtractionId; - var event = "OnClick= window.open('" + url + "')"; - document.getElementById(this.id + "_" + name).innerHTML = ''; -}; - -DataReductionForm.prototype.input = function() { - return {}; -}; - -/** It populates the form **/ -DataReductionForm.prototype.test = function(targetId) { - var macromoleculeForm = new DataReductionForm(); - var panel = macromoleculeForm.getPanel(); - panel.render(targetId); -}; - -function PlotWidget(args) { - this.width = 600; - this.height = 600; - this.id = BUI.id(); - - this.linear = false; - - this.margin = "10 0 0 0"; - /** for each stat the max and minimum value when it is scaled in order to show correctly in the legend **/ - this.ranges = {}; - if (args != null) { - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; - } - if (args.margin != null) { - this.margin = args.margin; - } - } - -} - -PlotWidget.prototype.getMenu = function() { - var _this = this; - /** Actions buttons **/ - var actions = []; - actions.push("->"); - actions.push({ - text : "Export as Image", - scope : this, - icon : '../images/save.gif', - handler : function(item, pressed) { - var largeImage = document.createElement("img"); - largeImage.style.display = 'block'; - largeImage.style.width = 200 + "px"; - largeImage.style.height = 200 + "px"; - largeImage.setAttribute('src', Dygraph.Export.asCanvas(this.dygraphObject.dygraph).toDataURL()); - window.open(Dygraph.Export.asCanvas(this.dygraphObject.dygraph).toDataURL(), 'Image', ''); - } - }); - - return actions; -}; - -/** Looks for the maximum value and then divide everything but that value **/ -PlotWidget.prototype.scaledData = function(data) { - for (var i = 0; i < data.length; i++) { - var values = this.getMaxAndMinValue(data[i]); - data[i] = this.divideValuesByMax(data[i], values.max); - this.ranges[data[i].label] = values; - } - return data; -}; - -/** Given a stat float[] and a max number it will divide each value by max **/ -PlotWidget.prototype.divideValuesByMax = function(stat, max) { - for (var j = 0; j < stat.data.length; j++) { - if (max != 0) { - stat.data[j] = Number(stat.data[j]) / max; - stat.std[j] = Number(stat.std[j]) / max; - } - } - return stat; -}; - -/** returns max value of a stat **/ -PlotWidget.prototype.getMaxAndMinValue = function(stat) { - var max = 0; - var min = stat.data[0]; - for (var j = 0; j < stat.data.length; j++) { - if (Number(stat.data[j]) > max) { - max = Number(stat.data[j]); - } - if (Number(stat.std[j]) > max) { - max = Number(stat.std[j]); - } - if (Number(stat.data[j]) < min) { - min = Number(stat.data[j]); - } - } - return { - max : Number(max), - min : Number(min) - }; -}; - -PlotWidget.prototype._renderDygraph = function(parsed, colors, labels) { - this.dygraphObject = new StdDevDyGraph(this.id, { - width : this.width - 20, - height : this.height - 40, - xlabel : "", - }); - - this.dygraphObject.draw(parsed, colors, labels); - -}; - -PlotWidget.prototype.getPanel = function() { - this.panel = Ext.create('Ext.panel.Panel', { - width : this.width, - height : this.height, - margin : this.margin, - tbar : this.getMenu(), - items : [ { - html : "", - id : this.id, - width : this.width, - height : this.height, - padding : 10, - margin : "0 0 0 -30", - border : 0 - } ] - }); - - return this.panel; -}; - -PlotWidget.prototype.getPoint = function(y, error) { - var minus = y - error; - var max = y + error; - - if (this.linear) { - return [ Math.abs(minus), y, Math.abs(max) ]; - } - if ((minus != 0) && (max != 0)) { - return [ Math.log(Math.abs(minus)), Math.log(y), Math.log(Math.abs(max)) ]; - } else { - return [ Math.log(y), Math.log(y), Math.log(y) ]; - } - -}; - -PlotWidget.prototype.getDataPlot = function(frames, subtractions, models, fits, rbms) { - var files = []; - var labels = [ "Intensity" ]; - if (frames != null) { - for (var i = 0; i < frames.length; i++) { - files.push(frames[i].data); - labels.push(frames[i].fileName); - } - } - function splitData(data, column, errorColumn, name){ - var result = [] - for (var j = 0; j < data.length; j++) { - console.log(data[j][column]); - result.push([j,data[j][column],data[j][errorColumn]]);//[0, data[i][column],0]]); - } - files.push(result); - labels.push(name); - } - - if (subtractions != null) { - for (var i = 0; i < subtractions.length; i++) { - /** For subtraction **/ - files.push(subtractions[i].subtraction.data); - labels.push(subtractions[i].subtraction.fileName); - /** For sample average **/ -// files.push(subtractions[i].sampleAvg.data); -// labels.push(subtractions[i].sampleAvg.fileName); - /** For buffer average **/ -// files.push(subtractions[i].bufferAvg.data); -// labels.push(subtractions[i].bufferAvg.fileName); - } - } - - if (models != null) { - for (var i = 0; i < models.length; i++) { - for ( var key in models[i]) { - splitData(models[i][key].fir.data, 1, 2, "Intensity"); - splitData(models[i][key].fir.data, 3, 3, "Fit"); - } - } - } - - if (fits != null) { - for (var i = 0; i < fits.length; i++) { - for ( var key in fits[i]) { - - /** adding fit file to be plotted **/ - if (fits[i][key].fit.data[0].length == 3){ - splitData(fits[i][key].fit.data, 1, 1, "Intensity"); - splitData(fits[i][key].fit.data, 2, 2, "Fit"); - } - - /** s, Iexp(s), err, Ifit(s). **/ - if (fits[i][key].fit.data[0].length == 4){ - splitData(fits[i][key].fit.data, 1, 2, "Intensity"); - splitData(fits[i][key].fit.data, 3, 3, "Fit"); - } - - if (fits[i][key].fit.data[0].length == 5){ - /** X Intensity Fit Error Residues **/ - - splitData(fits[i][key].fit.data, 1, 3, "Intensity"); - splitData(fits[i][key].fit.data, 2, 2, "Fit"); - } - } - } - } - - var dataPoints = []; - if (files.length > 0) { - for (var i = 0; i < files[0].length; i++) { - dataPoints.push([ files[0][i][0], this.getPoint(files[0][i][1], files[0][i][2]) ]); - } - if (files.length > 1) { - for (var i = 1; i < files.length; i++) { - for (var j = 0; j < dataPoints.length; j++) { - if (files[i][j] != null){ - dataPoints[j].push(this.getPoint(files[i][j][1], files[i][j][2])); - } - else{ - dataPoints[j].push([0,0,0]); - } - } - } - } - } - - return { - dataPoints : dataPoints, - labels : labels - } -}; - -PlotWidget.prototype.refresh = function(frames, subtractions, models, fits, rbms, colors) { - - var _this = this; - this.panel.setLoading("Reading Files"); - - var dataAdapter = new BiosaxsDataAdapter(); - dataAdapter.onSuccess.attach(function(sender, data) { - _this.panel.setLoading("Rendering"); - var parsed = _this.getDataPlot(data.frames, data.subtractions, data.models, data.fits, rbms); - _this._renderDygraph(parsed.dataPoints, colors, parsed.labels); - _this.panel.setLoading(false); - }); - dataAdapter.onError.attach(function(sender, data) { - _this.panel.setLoading(false); - }); - dataAdapter.getDataPlot(frames, subtractions, models, fits, rbms); -}; - -PlotWidget.prototype.input = function() { - return DATADOC.getHPLCData(); -}; - - -/** - * Fit form - * - * @witdh - * @height - */ -function FitForm(args) { - this.id = BUI.id(); - this.width = null; - this.height = null; - - if (args != null) { - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; - } - } - - var _this = this; - - /** Widgets **/ - this.fitGrid = new FitStructureToExperimentDataGrid({ - width : null, - height : 200 - }); - - this.fitGrid.onSelected.attach(function(sender, fits) { - var modelsIdList = []; - for ( var i in fits) { - modelsIdList.push(fits[i].fitStructureToExperimentalDataId); - } - _this._renderPlot(_this.subtractions[0].subtractionId, modelsIdList); -// var adapter = new BiosaxsDataAdapter(); -// adapter.onSuccess.attach(function(sender, data) { -// -// }); -// adapter.getScatteringCurveByFrameIdsList([], [], [], ids); - }); - - - /** Dygraph Widget that plots fir files**/ - this.plotWidget = new PlotWidget({ - width : 745, - height : 300, - margin : "10 0 10 10" - }); -} - -FitForm.prototype._renderPlot = function(subtractionId, modelsIdList) { - /** Trying to plot tje subtraction and the models **/ - try { - var colors = [ "#669900", "#0000FF" ]; - - this.plotWidget.refresh([], [ ], [], modelsIdList, [], colors); - } catch (e) { - console.log(e); - } -}; - -FitForm.prototype._getItems = function() { - var _this = this; - return [ { - xtype : 'label', - forId : 'myFieldId', - text : 'INLINE HELP: To be updated', - margin : '15 0 20 10', - cls : "inline-help" - }, this.fitGrid.getPanel(), this.plotWidget.getPanel() ] - -}; - -FitForm.prototype._getButtons = function() { - return []; -}; - -FitForm.prototype.getPanel = function() { - var _this = this; - this.panel = Ext.create('Ext.form.Panel', { - width : this.width, - height : this.height, - margin : 10, - border : 1, - defaultType : 'textfield', - items : this._getItems(), - buttons : this._getButtons(), - listeners : { - afterrender : function() { - _this._populate(); - - } - } - }); - return this.panel; -}; - -/** Populates could be call when the DOM is not filled yet **/ -FitForm.prototype._populate = function() { -}; - -/** It populates the form * */ -FitForm.prototype.refresh = function(subtractions) { - this.subtractions = subtractions; - this.fitGrid.refresh(subtractions); -}; - -FitForm.prototype.input = function() { - return {}; -}; - -/** It populates the form **/ -FitForm.prototype.test = function(targetId) { - var macromoleculeForm = new FitForm(); - var panel = macromoleculeForm.getPanel(); - panel.render(targetId); -}; - -/** - * Example form - * - * @witdh - * @height - */ -function RigidBodyModelingResultForm(args) { - this.id = BUI.id(); - this.width = null; - this.height = null; - - if (args != null) { - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; - } - } - - var _this = this; - /** Widgets **/ - this.rigidModelGrid = new RigidModelGrid({ - width : null, - height : 200 - }); - - this.rigidModelGrid.onSelected.attach(function(sender, fits){ - var ids = []; - for ( var i in fits) { - ids.push(fits[i].fitStructureToExperimentalDataId); - } - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data){ -// debugger - - }); - - adapter.getScatteringCurveByFrameIdsList([], [], [], ids); - }); - -} - -RigidBodyModelingResultForm.prototype._getItems = function() { - var _this = this; - return [ { - xtype : 'label', - forId : 'myFieldId', - text : 'INLINE HELP: To be updated', - margin : '15 0 20 10', - cls : "inline-help" - }, this.rigidModelGrid.getPanel() ] - -}; - -RigidBodyModelingResultForm.prototype._getButtons = function() { - return []; -}; - -RigidBodyModelingResultForm.prototype.getPanel = function() { - var _this = this; - this.panel = Ext.create('Ext.form.Panel', { - width : this.width, - height : this.height, - margin : 10, - border : 1, - defaultType : 'textfield', - items : this._getItems(), - buttons : this._getButtons(), - listeners : { - afterrender : function() { - _this._populate(); - - } - } - }); - return this.panel; -}; - -/** Populates could be call when the DOM is not filled yet **/ -RigidBodyModelingResultForm.prototype._populate = function() { -}; - -/** It populates the form * */ -RigidBodyModelingResultForm.prototype.refresh = function(subtractions) { - this.rigidModelGrid.refresh(subtractions); -}; - -RigidBodyModelingResultForm.prototype.input = function() { - return {}; -}; - -/** It populates the form **/ -RigidBodyModelingResultForm.prototype.test = function(targetId) { - var macromoleculeForm = new RigidBodyModelingResultForm(); - var panel = macromoleculeForm.getPanel(); - panel.render(targetId); -}; - -/** - * Example form - * - * @witdh - * @height - */ -function SuperpositionForm(args) { - this.id = BUI.id(); - this.width = null; - this.height = null; - - if (args != null) { - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; - } - } - - var _this = this; - - /** Widgets **/ - this.superpositionGrid = new SuperpositionGrid({ - width : null, - height : 200 - }); - - this.superpositionGrid.onSelected.attach(function(sender, superpositions) { - var ids = []; - for ( var i in superpositions) { - ids.push(superpositions[i].superpositionId); - } -// _this._renderAbinitio(ids); -// _this.aprioriPDBViewer.refresh(); - _this._renderAligned(ids); - // getAlignedPDBContentBySuperpositionList - }); - - /** PDB viewer **/ -// this.abinitioPDBViewer = new PDBViewer({ -// width : 860 / 2, -// height : 300 / 2, -// margin : 0 -// }); -// -// /** PDB viewer **/ -// this.aprioriPDBViewer = new StructurePDBViewer({ -// width : 860 / 2, -// height : 300 / 2, -// margin : 0 -// }); - - this.alignedPDBViewer = new AlignedSuperpositionPDBViewer({ - width : 860 , - height : 300 - }); - -} - -SuperpositionForm.prototype._renderAligned = function(modelsIdList) { - /** Trying to plot the PDB file **/ - try { - this.alignedPDBViewer.refresh(modelsIdList); - } catch (e) { - console.log(e); - } -}; - -SuperpositionForm.prototype._renderAbinitio = function(modelsIdList) { - /** Trying to plot the PDB file **/ - try { - var viz = []; - for (var i = 0; i < modelsIdList.length; i++) { - viz.push({ - modelId : modelsIdList[i], - color : "0xFF6600", - opacity : 0.8 - }); - } - this.abinitioPDBViewer.refresh(viz); - } catch (e) { - console.log(e); - } -}; - -SuperpositionForm.prototype._getItems = function() { - var _this = this; - return [ { - xtype : 'label', - forId : 'myFieldId', - text : 'INLINE HELP: To be updated', - margin : '15 0 20 10', - cls : "inline-help" - }, this.superpositionGrid.getPanel(), { - xtype : 'container', - layout : 'hbox', - items : [ -// { -// xtype : 'container', -// layout : 'vbox', -// items : [ this.abinitioPDBViewer.getPanel(), this.aprioriPDBViewer.getPanel() -// -// ] -// }, - - this.alignedPDBViewer.getPanel() ] - } ] - -}; - -SuperpositionForm.prototype._getButtons = function() { - return []; -}; - -SuperpositionForm.prototype.getPanel = function() { - var _this = this; - this.panel = Ext.create('Ext.form.Panel', { - width : this.width, - height : this.height, - margin : 10, - border : 1, - defaultType : 'textfield', - items : this._getItems(), - buttons : this._getButtons(), - listeners : { - afterrender : function() { - _this._populate(); - - } - } - }); - return this.panel; -}; - -/** Populates could be call when the DOM is not filled yet **/ -SuperpositionForm.prototype._populate = function() { -}; - -/** It populates the form * */ -SuperpositionForm.prototype.refresh = function(subtractions) { - this.subtractions = subtractions; - this.superpositionGrid.refresh(subtractions); -}; - -SuperpositionForm.prototype.input = function() { - return {}; -}; - -/** It populates the form **/ -SuperpositionForm.prototype.test = function(targetId) { - var macromoleculeForm = new SuperpositionForm(); - var panel = macromoleculeForm.getPanel(); - panel.render(targetId); -}; - -/** - * Example form - * - * @witdh - * @height - */ -function AssemblyForm(args) { - this.id = BUI.id(); - this.width = 700; - this.height = 500; - - if (args != null) { - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; - } - } - - this.molarityGrid = new MolarityGrid({height : this.height - 50}); -} - -AssemblyForm.prototype._getItems = function() { - return [ { - xtype : 'label', - forId : 'myFieldId', - text : 'List of previously defined macromolecules present in the assembly. This information will be used for additional cross-checks where possible', - margin : '15 0 20 10', - cls : "inline-help" - }, this.molarityGrid.getPanel() ]; -}; - -AssemblyForm.prototype._getButtons = function() { - return []; -}; - -AssemblyForm.prototype.getPanel = function() { - this.panel = Ext.create('Ext.form.Panel', { - width : this.width, - height : this.height, - margin : 10, - border : 0, - defaultType : 'textfield', - items : this._getItems(), - buttons : this._getButtons() - }); - return this.panel; -}; - - -/** It populates the form **/ -AssemblyForm.prototype.refresh = function(macromolecule) { - this.macromolecule = macromolecule; - this.molarityGrid.refresh(macromolecule); -}; - -AssemblyForm.prototype.input = function() { - return {}; -}; - - -AssemblyForm.prototype.test = function(targetId) { - var assemblyForm = new AssemblyForm(); - - var panel = assemblyForm.getPanel(); - panel.render(targetId); -}; /** - * Edit the information of a buffer + * Example form * - * #onSaved - * #onRemoveAdditive + * @witdh + * @height */ -function BufferForm() { +function DataReductionForm(args) { + this.id = BUI.id(); + this.width = null; + this.height = null; + + if (args != null) { + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + } + var _this = this; - this.additiveGrid = new AdditiveGrid(); - this.additiveGrid.onRemoveButtonClicked.attach(function(sender, args) { - _this.onRemoveAdditive.notify(args); + /** Widgets **/ + this.plotWidget = new PlotWidget({ + width : 650, + height : 490 }); - this.onSaved = new Event(this); - this.onRemoveAdditive = new Event(this); + /** Selected frames to be displayed **/ + this.selectedItems = { + frames : [], + averages : [], + subtractions : [] + }; + } -BufferForm.prototype.getBuffer = function() { - this.buffer.name = Ext.getCmp("buffer_name").getValue(); - this.buffer.acronym = Ext.getCmp("buffer_acronym").getValue(); - this.buffer.comments = Ext.getCmp("buffer_comments").getValue(); - this.buffer.ph = Ext.getCmp("buffer_ph").getValue(); - this.buffer.composition = Ext.getCmp("buffer_composition").getValue(); - this.buffer.bufferhasadditive3VOs = this.additiveGrid.getAdditives(); - return this.buffer; +DataReductionForm.prototype._parseSelectedItemsToIds = function(selectedArray) { + var ids = []; + if (selectedArray != null) { + for (var i = 0; i < selectedArray.length; i++) { + ids.push(selectedArray[i].id); + } + } + return ids; }; -BufferForm.prototype._getTopPanel = function() { +DataReductionForm.prototype.onSelectionChanged = function(columnName, selected) { + if (selected != null) { + if (columnName == "Frames") { + this.selectedItems.frames = selected; + this.selectedItems.subtractions = []; + } + if (columnName == "Averages") { + this.selectedItems.averages = selected; + } + if (columnName == "Subtractions") { + this.selectedItems.frames = []; + this.selectedItems.subtractions = selected; + } + } + this.plotWidget.refresh(this._parseSelectedItemsToIds(this.selectedItems.frames), this._parseSelectedItemsToIds(this.selectedItems.subtractions)); +}; + +DataReductionForm.prototype._getFramesExtPanel = function(store, columnName, height) { + var _this = this; + + var selModel = Ext.create('Ext.selection.RowModel', { + allowDeselect : true, + mode : 'MULTI', + listeners : { + selectionchange : function(sm, selections) { + var selected = []; + for (var i = 0; i < selections.length; i++) { + selected.push(selections[i].raw); + } + _this.onSelectionChanged(columnName, selected); + } + } + }); + + return Ext.create('Ext.grid.Panel', { + store : store, + margin : 10, + height : height, + width : 200, + selModel : selModel, + columns : [ { + text : columnName, + dataIndex : 'fileName', + flex : 1 + } ], + viewConfig : { + } + }); +}; + +DataReductionForm.prototype._getFramesPanel = function() { + var fields = [ 'fileName', 'type', 'id' ]; + + this.framesStore = Ext.create('Ext.data.Store', { + fields : fields, + sorters : 'fileName' + }); + + this.averagesStore = Ext.create('Ext.data.Store', { + fields : fields + }); + + this.subtractionStore = Ext.create('Ext.data.Store', { + fields : fields + }); + + var gridFrames = this._getFramesExtPanel(this.framesStore, "Frames", 375); + var gridAvgs = this._getFramesExtPanel(this.averagesStore, "Averages", 125); + var subtractionAvgs = this._getFramesExtPanel(this.subtractionStore, "Subtractions", 75); + return { xtype : 'container', - layout : 'hbox', - border : 0, - frame : true, + layout : 'vbox', + items : [ gridFrames, subtractionAvgs ] + }; +}; + +DataReductionForm.prototype._getImageContainer = function(name, help) { + var html = "
" + name + "
" + return { + xtype : 'container', + layout : 'vbox', items : [ { - xtype : 'container', - layout : 'hbox', - items : [ { - xtype : 'container', - flex : 1, - border : false, - layout : 'anchor', - defaultType : 'textfield', - items : [ { - xtype : 'requiredtext', - id : 'buffer_name', - fieldLabel : 'Name', - name : 'name', - width : '200px', - value : this.buffer.name - }, { - xtype : 'requiredtext', - id : 'buffer_acronym', - fieldLabel : 'Acronym', - name : 'acronym', - width : '200px', - value : this.buffer.acronym - } ] - } ] + html : html, + margin : "5 0 0 0", + height : 95, + width : 100 }, { - xtype : 'container', - flex : 1, - layout : 'anchor', - defaultType : 'textfield', - margin : '0 0 0 10', - items : [ { - id : 'buffer_ph', - fieldLabel : 'pH', - name : 'ph', - value : this.buffer.ph, - xtype : 'numberfield', - width : 200, - minValue : 0, - maxValue : 15 - }, { - xtype : 'requiredtext', - id : 'buffer_composition', - fieldLabel : 'Composition', - name : 'composition', - width : 200, - value : this.buffer.composition - } ] + xtype : 'label', + forId : 'myFieldId', + text : help, + margin : '5 0 0 0', + cls : "inline-help" } ] - }; + } }; -BufferForm.prototype.getPanel = function(buffer) { - this.buffer = buffer; - this.panel = Ext.createWidget({ +DataReductionForm.prototype._getItems = function() { + var _this = this; + return [ { xtype : 'container', - layout : 'vbox', - style : { - padding : '10px' - }, - fieldDefaults : { - labelAlign : 'left', - labelWidth : 50 + layout : 'hbox', + items : [ + this._getFramesPanel(), + this.plotWidget.getPanel(), + { + xtype : 'panel', + width : 110, + frame : true, + margin : "10 5 5 5", + border : 0, + layout : 'vbox', + items : [ this._getImageContainer("scattering", "Scattering"), this._getImageContainer("guinier", "Guinier Region"), + this._getImageContainer("kratky", "Kratky Plot"), this._getImageContainer("gnom", "P(r) distribution") ] + } ] + } ] +}; - }, - items : [ this._getTopPanel(), { - id : 'buffer_comments', - xtype : 'textareafield', - name : 'comments', - fieldLabel : 'Comments', - width : '100%', - value : buffer.comments - }, this.additiveGrid.getPanel(buffer) ] +DataReductionForm.prototype._getButtons = function() { + return []; +}; + +DataReductionForm.prototype.getPanel = function() { + var _this = this; + this.panel = Ext.create('Ext.form.Panel', { + width : this.width, + height : this.height, + border : 0, + items : this._getItems(), + buttons : this._getButtons(), + listeners : { + afterrender : function() { + _this._populate(); + } + } }); return this.panel; }; -BufferForm.prototype.input = function() { - return { - buffer : { - "bufferId" : 422, - "proposalId" : 10, - "safetyLevelId" : null, - "name" : "B1", - "acronym" : "B1", - "ph" : null, - "composition" : null, - "bufferhasadditive3VOs" : [], - "comments" : null +/** Populates could be call when the DOM is not filled yet **/ +DataReductionForm.prototype._populate = function() { +}; + +/** It populates the form * */ +DataReductionForm.prototype.refresh = function(subtractions) { + if (subtractions != null) { + for (var i = 0; i < subtractions.length; i++) { + /** Loading frame grids **/ + var subtraction = subtractions[i]; + var averages = [ { + fileName : BUI.getFileName(subtraction.bufferAverageFilePath), + type : 'bufferAvg', + id : subtraction.subtractionId + }, { + fileName : BUI.getFileName(subtraction.sampleAverageFilePath), + type : 'sampleAvg', + id : subtraction.subtractionId + } + + ]; + this.averagesStore.loadData(averages, true); + this.subtractionStore.loadData([ { + fileName : BUI.getFileName(subtraction.substractedFilePath), + type : 'SUBTRACTION', + id : subtraction.subtractionId + } ], true); + + var frames = []; + /** Buffers **/ + if (subtraction.bufferOneDimensionalFiles != null) { + if (subtraction.bufferOneDimensionalFiles.frametolist3VOs != null) { + for (var j = 0; j < subtraction.bufferOneDimensionalFiles.frametolist3VOs.length; j++) { + var frametolist3VO = subtraction.bufferOneDimensionalFiles.frametolist3VOs[j]; + if (frametolist3VO.frame3VO != null) { + frames.push({ + fileName : BUI.getFileName(frametolist3VO.frame3VO.filePath), + type : 'BUFFER', + id : frametolist3VO.frame3VO.frameId + }); + } + } + } + } + /** Samples **/ + if (subtraction.sampleOneDimensionalFiles != null) { + if (subtraction.sampleOneDimensionalFiles.frametolist3VOs != null) { + for (var j = 0; j < subtraction.sampleOneDimensionalFiles.frametolist3VOs.length; j++) { + var frametolist3VO = subtraction.sampleOneDimensionalFiles.frametolist3VOs[j]; + if (frametolist3VO.frame3VO != null) { + frames.push({ + fileName : BUI.getFileName(frametolist3VO.frame3VO.filePath), + type : 'SAMPLE', + id : frametolist3VO.frame3VO.frameId + }); + } + } + } + } + + this.framesStore.loadData(frames, true); + + /** Loading images **/ + this._displayImage("scattering", subtraction.subtractionId); + this._displayImage("kratky", subtraction.subtractionId); + this._displayImage("guinier", subtraction.subtractionId); + this._displayImage("gnom", subtraction.subtractionId); } - }; + } }; -BufferForm.prototype.test = function(targetId) { - var bufferForm = new BufferForm(); - var panel = bufferForm.getPanel(bufferForm.input().buffer); +DataReductionForm.prototype._displayImage = function(name, subtractionId) { + var url = BUI.getURL() + '&type=' + name + '&subtractionId=' + subtractionId; + var event = "OnClick= window.open('" + url + "')"; + document.getElementById(this.id + "_" + name).innerHTML = ''; +}; + +DataReductionForm.prototype.input = function() { + return {}; +}; + +/** It populates the form **/ +DataReductionForm.prototype.test = function(targetId) { + var macromoleculeForm = new DataReductionForm(); + var panel = macromoleculeForm.getPanel(); panel.render(targetId); }; - -/** - * @showTitle - * - * #onSaved - * #onAddPlates - * #onRemovePlates - **/ -function CaseForm(args) { - this.width = 700; - this.showTitle = true; + +function PlotWidget(args) { + this.width = 600; + this.height = 600; + this.id = BUI.id(); + + this.linear = false; + + this.margin = "10 0 0 0"; + /** for each stat the max and minimum value when it is scaled in order to show correctly in the legend **/ + this.ranges = {}; if (args != null) { - if (args.showTitle != null) { - this.showTitle = args.showTitle; + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + if (args.margin != null) { + this.margin = args.margin; } } - var _this = this; - this.stockSolutionGrid = new StockSolutionGrid({ - width : this.width - 10, - minHeight : 300, - height : 300, - tbar : true, - showTitle : true, - isPackedVisible : false, - btnAddExisting : true, - btnRemoveVisible : false, - btnUnpackVisible : true - }); +} - /** When selecting existing stock solutions **/ - this.stockSolutionGrid.onStockSolutionSelected.attach(function(sender, stockSolutions) { - if (stockSolutions != null) { - for ( var i = 0; i < stockSolutions.length; i++) { - _this.saveStockSolution(stockSolutions[i]); - } +PlotWidget.prototype.getMenu = function() { + var _this = this; + /** Actions buttons **/ + var actions = []; + actions.push("->"); + actions.push({ + text : "Export as Image", + scope : this, + icon : '../images/save.gif', + handler : function(item, pressed) { + var largeImage = document.createElement("img"); + largeImage.style.display = 'block'; + largeImage.style.width = 200 + "px"; + largeImage.style.height = 200 + "px"; + largeImage.setAttribute('src', Dygraph.Export.asCanvas(this.dygraphObject.dygraph).toDataURL()); + window.open(Dygraph.Export.asCanvas(this.dygraphObject.dygraph).toDataURL(), 'Image', ''); } }); - /** it can be because it has been added a new one or removed **/ - this.stockSolutionGrid.onProposalChanged.attach(function(sender, stockSolution) { - if (stockSolution != null) { - _this.saveStockSolution(stockSolution); - } else { - BIOSAXS.proposal.onInitialized.attach(function() { - _this.stockSolutionGrid.refresh(BIOSAXS.proposal.getStockSolutionsByDewarId(_this.dewar.dewarId)); + return actions; +}; - _this.stockSolutionGrid.grid.setLoading(false); - }); - BIOSAXS.proposal.init(); +/** Looks for the maximum value and then divide everything but that value **/ +PlotWidget.prototype.scaledData = function(data) { + for (var i = 0; i < data.length; i++) { + var values = this.getMaxAndMinValue(data[i]); + data[i] = this.divideValuesByMax(data[i], values.max); + this.ranges[data[i].label] = values; + } + return data; +}; + +/** Given a stat float[] and a max number it will divide each value by max **/ +PlotWidget.prototype.divideValuesByMax = function(stat, max) { + for (var j = 0; j < stat.data.length; j++) { + if (max != 0) { + stat.data[j] = Number(stat.data[j]) / max; + stat.std[j] = Number(stat.std[j]) / max; + } + } + return stat; +}; +/** returns max value of a stat **/ +PlotWidget.prototype.getMaxAndMinValue = function(stat) { + var max = 0; + var min = stat.data[0]; + for (var j = 0; j < stat.data.length; j++) { + if (Number(stat.data[j]) > max) { + max = Number(stat.data[j]); + } + if (Number(stat.std[j]) > max) { + max = Number(stat.std[j]); + } + if (Number(stat.data[j]) < min) { + min = Number(stat.data[j]); } + } + return { + max : Number(max), + min : Number(min) + }; +}; +PlotWidget.prototype._renderDygraph = function(parsed, colors, labels) { + this.dygraphObject = new StdDevDyGraph(this.id, { + width : this.width - 20, + height : this.height - 40, + xlabel : "", }); - this.onSaved = new Event(this); - this.onAddPlates = new Event(this); - this.onRemovePlates = new Event(this); -} + this.dygraphObject.draw(parsed, colors, labels); -CaseForm.prototype.saveStockSolution = function(stockSolution) { - var _this = this; - var adapter = new BiosaxsDataAdapter(); - this.stockSolutionGrid.grid.setLoading("ISPyB: setting case to Stock solution"); - adapter.onSuccess.attach(function(sender, stockSolution) { - BIOSAXS.proposal.onInitialized.attach(function() { - _this.stockSolutionGrid.refresh(BIOSAXS.proposal.getStockSolutionsByDewarId(_this.dewar.dewarId)); - _this.stockSolutionGrid.grid.setLoading(false); - }); - BIOSAXS.proposal.init(); - }); - adapter.onError.attach(function(sender, data) { - _this.stockSolutionGrid.grid.setLoading(false); - BUI.showError(data); - }); - stockSolution.boxId = _this.dewar.dewarId; - adapter.saveStockSolution(stockSolution); }; -CaseForm.prototype.fillStores = function() { - var _this = this; - this.panel.setLoading("Loading Labcontacts from database"); - - var proposal = BUI.getProposal(); - proposal.onDataRetrieved.attach(function(sender, data) { - _this.labContactForSendingStore.loadData(data, false); - _this.labContactForReturnStore.loadData(data, false); - _this.panel.setLoading(false); +PlotWidget.prototype.getPanel = function() { + this.panel = Ext.create('Ext.panel.Panel', { + width : this.width, + height : this.height, + margin : this.margin, + tbar : this.getMenu(), + items : [ { + html : "", + id : this.id, + width : this.width, + height : this.height, + padding : 10, + margin : "0 0 0 -30", + border : 0 + } ] }); - proposal.getLabContactsByProposalId(); - -}; -CaseForm.prototype.refresh = function(dewar) { - this.setDewar(dewar); - this.stockSolutionGrid.refresh(BIOSAXS.proposal.getStockSolutionsByDewarId(dewar.dewarId)); + return this.panel; }; -CaseForm.prototype.getDewar = function() { - this.dewar.code = Ext.getCmp("dewar_code").getValue(); - this.dewar.comments = Ext.getCmp("dewar_comments").getValue(); - this.dewar.trackingNumberFromSynchrotron = Ext.getCmp("dewar_trackingNumberFromSynchrotron").getValue(); - this.dewar.trackingNumberToSynchrotron = Ext.getCmp("dewar_trackingNumberToSynchrotron").getValue(); - this.dewar.transportValue = Ext.getCmp("dewar_transportValue").getValue(); - this.dewar.storageLocation = Ext.getCmp("dewar_storageLocation").getValue(); - this.dewar.firstExperimentId = this.macromoleculeCombo.getValue(); - return this.dewar; -}; +PlotWidget.prototype.getPoint = function(y, error) { + var minus = y - error; + var max = y + error; -CaseForm.prototype.setDewar = function(dewar) { - this.dewar = dewar; - Ext.getCmp("dewar_code").setValue(this.dewar.code); - Ext.getCmp("dewar_dewarStatus").setText(new String(this.dewar.dewarStatus).toUpperCase()); - Ext.getCmp("dewar_comments").setValue(this.dewar.comments); - Ext.getCmp("dewar_trackingNumberFromSynchrotron").setValue(this.dewar.trackingNumberFromSynchrotron); - Ext.getCmp("dewar_trackingNumberToSynchrotron").setValue(this.dewar.trackingNumberToSynchrotron); - Ext.getCmp("dewar_transportValue").setValue(this.dewar.transportValue); - Ext.getCmp("dewar_storageLocation").setValue(this.dewar.storageLocation); - if (dewar.sessionVO != null) { - this.macromoleculeCombo.setValue(dewar.sessionVO.sessionId); + if (this.linear) { + return [ Math.abs(minus), y, Math.abs(max) ]; + } + if ((minus != 0) && (max != 0)) { + return [ Math.log(Math.abs(minus)), Math.log(y), Math.log(Math.abs(max)) ]; + } else { + return [ Math.log(y), Math.log(y), Math.log(y) ]; } -}; -CaseForm.prototype.getSessionCombo = function() { - this.macromoleculeCombo = BIOSAXS_COMBOMANAGER.getComboSessions(BIOSAXS.proposal.getSessions(), { - labelWidth : 100, - margin : '5 0 00 0', - width : 250 - }); - return this.macromoleculeCombo; }; -CaseForm.prototype.getInformationPanel = function() { - if (this.panel == null) { - this.informationPanel = Ext.create('Ext.form.Panel', { - width : this.width - 10, - border : 0, - items : [ { - xtype : 'container', - margin : "2 2 2 2", - collapsible : false, - defaultType : 'textfield', - layout : 'anchor', - items : [ { - xtype : 'container', - layout : 'hbox', - items : [ { - xtype : 'requiredtext', - fieldLabel : 'Code', - allowBlank : false, - name : 'code', - id : 'dewar_code', - anchor : '50%' - }, { - xtype : 'label', - margin : '0 0 0 20', - readOnly : true, - id : 'dewar_dewarStatus', - anchor : '50%' - } ] - }, this.getSessionCombo(), { - margin : '5 0 0 0', - xtype : 'textareafield', - name : 'comments', - id : 'dewar_comments', - width : this.width - 50, - fieldLabel : 'Comments' - } ] - }, { - xtype : 'fieldset', - title : 'Courier Accounts Details for Return', - collapsible : false, - layout : 'anchor', - defaults : { - anchor : '100%' - }, - items : [ { - xtype : 'container', - layout : 'hbox', - items : [ { - xtype : 'textfield', - labelWidth : 200, - width : 280, - fieldLabel : 'Track Number From Synchrotron', - id : 'dewar_trackingNumberFromSynchrotron' - }, { - xtype : 'numberfield', - width : 190, - labelWidth : 110, - margin : '0 0 0 30', - fieldLabel : 'Transport Value', - id : 'dewar_transportValue' +PlotWidget.prototype.getDataPlot = function(frames, subtractions, models, fits, rbms) { + var files = []; + var labels = [ "Intensity" ]; + if (frames != null) { + for (var i = 0; i < frames.length; i++) { + files.push(frames[i].data); + labels.push(frames[i].fileName); + } + } + function splitData(data, column, errorColumn, name){ + var result = [] + for (var j = 0; j < data.length; j++) { + console.log(data[j][column]); + result.push([j,data[j][column],data[j][errorColumn]]);//[0, data[i][column],0]]); + } + files.push(result); + labels.push(name); + } + + if (subtractions != null) { + for (var i = 0; i < subtractions.length; i++) { + /** For subtraction **/ + files.push(subtractions[i].subtraction.data); + labels.push(subtractions[i].subtraction.fileName); + /** For sample average **/ +// files.push(subtractions[i].sampleAvg.data); +// labels.push(subtractions[i].sampleAvg.fileName); + /** For buffer average **/ +// files.push(subtractions[i].bufferAvg.data); +// labels.push(subtractions[i].bufferAvg.fileName); + } + } + + if (models != null) { + for (var i = 0; i < models.length; i++) { + for ( var key in models[i]) { + splitData(models[i][key].fir.data, 1, 2, "Intensity"); + splitData(models[i][key].fir.data, 3, 3, "Fit"); + } + } + } + + if (fits != null) { + for (var i = 0; i < fits.length; i++) { + for ( var key in fits[i]) { + + /** adding fit file to be plotted **/ + if (fits[i][key].fit.data[0].length == 3){ + splitData(fits[i][key].fit.data, 1, 1, "Intensity"); + splitData(fits[i][key].fit.data, 2, 2, "Fit"); + } + + /** s, Iexp(s), err, Ifit(s). **/ + if (fits[i][key].fit.data[0].length == 4){ + splitData(fits[i][key].fit.data, 1, 2, "Intensity"); + splitData(fits[i][key].fit.data, 3, 3, "Fit"); + } + + if (fits[i][key].fit.data[0].length == 5){ + /** X Intensity Fit Error Residues **/ + + splitData(fits[i][key].fit.data, 1, 3, "Intensity"); + splitData(fits[i][key].fit.data, 2, 2, "Fit"); + } + } + } + } + + var dataPoints = []; + if (files.length > 0) { + for (var i = 0; i < files[0].length; i++) { + dataPoints.push([ files[0][i][0], this.getPoint(files[0][i][1], files[0][i][2]) ]); + } + if (files.length > 1) { + for (var i = 1; i < files.length; i++) { + for (var j = 0; j < dataPoints.length; j++) { + if (files[i][j] != null){ + dataPoints[j].push(this.getPoint(files[i][j][1], files[i][j][2])); } - - ] - }, { - xtype : 'container', - layout : 'hbox', - margin : '10 0 0 0', - items : [ - - { - xtype : 'textfield', - labelWidth : 200, - width : 280, - fieldLabel : 'Track Number To Synchrotron', - id : 'dewar_trackingNumberToSynchrotron' - }, { - xtype : 'textfield', - margin : '0 0 0 30', - width : 190, - labelWidth : 110, - fieldLabel : 'Storage Location', - id : 'dewar_storageLocation' + else{ + dataPoints[j].push([0,0,0]); } + } + } + } + } - ] - } ] - } ] - }); + return { + dataPoints : dataPoints, + labels : labels } +}; - return this.informationPanel; +PlotWidget.prototype.refresh = function(frames, subtractions, models, fits, rbms, colors) { + + var _this = this; + this.panel.setLoading("Reading Files"); + + var dataAdapter = new BiosaxsDataAdapter(); + dataAdapter.onSuccess.attach(function(sender, data) { + _this.panel.setLoading("Rendering"); + var parsed = _this.getDataPlot(data.frames, data.subtractions, data.models, data.fits, rbms); + _this._renderDygraph(parsed.dataPoints, colors, parsed.labels); + _this.panel.setLoading(false); + }); + dataAdapter.onError.attach(function(sender, data) { + _this.panel.setLoading(false); + }); + dataAdapter.getDataPlot(frames, subtractions, models, fits, rbms); }; -CaseForm.prototype.getPanel = function(dewar) { - this.dewar = dewar; - this.panel = Ext.createWidget({ - xtype : 'container', - layout : 'vbox', - width : this.width, - border : 0, - items : [ { - items : { - xtype : "container", - layout : "vbox", - margin : "5 5 5 5", - items : [ this.getInformationPanel(dewar), this.stockSolutionGrid.getPanel() ] +PlotWidget.prototype.input = function() { + return DATADOC.getHPLCData(); +}; - } - } ] + +/** + * Fit form + * + * @witdh + * @height + */ +function FitForm(args) { + this.id = BUI.id(); + this.width = null; + this.height = null; + + if (args != null) { + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + } + + var _this = this; + + /** Widgets **/ + this.fitGrid = new FitStructureToExperimentDataGrid({ + width : null, + height : 200 }); - this.refresh(dewar); - return this.panel; + this.fitGrid.onSelected.attach(function(sender, fits) { + var modelsIdList = []; + for ( var i in fits) { + modelsIdList.push(fits[i].fitStructureToExperimentalDataId); + } + _this._renderPlot(_this.subtractions[0].subtractionId, modelsIdList); +// var adapter = new BiosaxsDataAdapter(); +// adapter.onSuccess.attach(function(sender, data) { +// +// }); +// adapter.getScatteringCurveByFrameIdsList([], [], [], ids); + }); + + + /** Dygraph Widget that plots fir files**/ + this.plotWidget = new PlotWidget({ + width : 745, + height : 300, + margin : "10 0 10 10" + }); +} +FitForm.prototype._renderPlot = function(subtractionId, modelsIdList) { + /** Trying to plot tje subtraction and the models **/ + try { + var colors = [ "#669900", "#0000FF" ]; + + this.plotWidget.refresh([], [ ], [], modelsIdList, [], colors); + } catch (e) { + console.log(e); + } }; -CaseForm.prototype.input = function() { - return { - dewar : { - "dewarId" : 305861, - "code" : "ESRF-TEST", - "comments" : "comments", - "storageLocation" : "FRIDGE", - "dewarStatus" : "opened", - "timeStamp" : null, - "isStorageDewar" : null, - "barCode" : "ESRF305861", - "customsValue" : null, - "transportValue" : null, - "trackingNumberToSynchrotron" : "3333", - "trackingNumberFromSynchrotron" : "224466", - "type" : "Dewar", - "sessionVO" : { - "sessionId" : 31697, - "expSessionPk" : null, - "projectCode" : null, - "startDate" : "2012 07 21", - "endDate" : "2012 07 23", - "beamlineName" : "BM29", - "scheduled" : 1, - "nbShifts" : 2, - "comments" : null, - "beamlineOperator" : "PERNOT P", - "usedFlag" : null, - "sessionTitle" : null, - "structureDeterminations" : null, - "dewarTransport" : null, - "databackupFrance" : null, - "databackupEurope" : null, - "visit_number" : null, - "operatorSiteNumber" : "14061", - "timeStamp" : "2012 04 25" +FitForm.prototype._getItems = function() { + var _this = this; + return [ { + xtype : 'label', + forId : 'myFieldId', + text : 'INLINE HELP: To be updated', + margin : '15 0 20 10', + cls : "inline-help" + }, this.fitGrid.getPanel(), this.plotWidget.getPanel() ] + +}; + +FitForm.prototype._getButtons = function() { + return []; +}; + +FitForm.prototype.getPanel = function() { + var _this = this; + this.panel = Ext.create('Ext.form.Panel', { + width : this.width, + height : this.height, + margin : 10, + border : 1, + defaultType : 'textfield', + items : this._getItems(), + buttons : this._getButtons(), + listeners : { + afterrender : function() { + _this._populate(); + } - }, - proposal : { - "assemblies" : [], - "sessions" : [ { - "sessionId" : 31697, - "expSessionPk" : null, - "projectCode" : null, - "startDate" : "2012 07 21", - "endDate" : "2012 07 23", - "beamlineName" : "BM29", - "scheduled" : 1, - "nbShifts" : 2, - "comments" : null, - "beamlineOperator" : "PERNOT P", - "usedFlag" : null, - "sessionTitle" : null, - "structureDeterminations" : null, - "dewarTransport" : null, - "databackupFrance" : null, - "databackupEurope" : null, - "visit_number" : null, - "operatorSiteNumber" : "14061", - "timeStamp" : "2012 04 25" - } ], - "labcontacts" : [ { - "labContactId" : 787, - "personVO" : { - "personId" : 304252, - "personUUID" : null, - "familyName" : "KIM", - "givenName" : "Henry", - "title" : null, - "emailAddress" : "henry-sung.kim@ibs.fr", - "phoneNumber" : "", - "login" : "", - "passwd" : "", - "faxNumber" : "" - }, - "cardName" : "KIM-Institut de Bio", - "defaultCourrierCompany" : "22", - "courierAccount" : "", - "billingReference" : "", - "dewarAvgCustomsValue" : 0, - "dewarAvgTransportValue" : 0 - } ], - "buffers" : [ { - "bufferId" : 811, - "proposalId" : 3124, - "safetyLevelId" : null, - "name" : "EDTA", - "acronym" : "EDTA", - "ph" : null, - "composition" : "", - "bufferhasadditive3VOs" : [], - "comments" : "" - }, { - "bufferId" : 810, - "proposalId" : 3124, - "safetyLevelId" : null, - "name" : "HEPES", - "acronym" : "HEPES", - "ph" : null, - "composition" : "", - "bufferhasadditive3VOs" : [], - "comments" : "" - } ], - "shippings" : [ { - "shippingId" : 304107, - "shippingName" : "TEST", - "deliveryAgentAgentName" : null, - "deliveryAgentShippingDate" : null, - "deliveryAgentDeliveryDate" : null, - "deliveryAgentAgentCode" : null, - "deliveryAgentFlightCode" : null, - "shippingStatus" : "opened", - "timeStamp" : "2013 09 25", - "laboratoryId" : null, - "isStorageShipping" : null, - "creationDate" : "2013 09 25", - "comments" : "test", - "sendingLabContactVO" : { - "labContactId" : 787, - "personVO" : { - "personId" : 304252, - "personUUID" : null, - "familyName" : "KIM", - "givenName" : "Henry", - "title" : null, - "emailAddress" : "henry-sung.kim@ibs.fr", - "phoneNumber" : "", - "login" : "", - "passwd" : "", - "faxNumber" : "" - }, - "cardName" : "KIM-Institut de Bio", - "defaultCourrierCompany" : "22", - "courierAccount" : "", - "billingReference" : "", - "dewarAvgCustomsValue" : 0, - "dewarAvgTransportValue" : 0 - }, - "returnLabContactVO" : { - "labContactId" : 787, - "personVO" : { - "personId" : 304252, - "personUUID" : null, - "familyName" : "KIM", - "givenName" : "Henry", - "title" : null, - "emailAddress" : "henry-sung.kim@ibs.fr", - "phoneNumber" : "", - "login" : "", - "passwd" : "", - "faxNumber" : "" - }, - "cardName" : "KIM-Institut de Bio", - "defaultCourrierCompany" : "22", - "courierAccount" : "", - "billingReference" : "", - "dewarAvgCustomsValue" : 0, - "dewarAvgTransportValue" : 0 - }, - "returnCourier" : null, - "dateOfShippingToUser" : null, - "shippingType" : "DewarTracking", - "dewarVOs" : [ { - "dewarId" : 305861, - "code" : "ESRF-TEST", - "comments" : "comments", - "storageLocation" : "FRIDGE", - "dewarStatus" : "opened", - "timeStamp" : null, - "isStorageDewar" : null, - "barCode" : "ESRF305861", - "customsValue" : null, - "transportValue" : null, - "trackingNumberToSynchrotron" : "3333", - "trackingNumberFromSynchrotron" : "224466", - "type" : "Dewar", - "sessionVO" : { - "sessionId" : 31697, - "expSessionPk" : null, - "projectCode" : null, - "startDate" : "2012 07 21", - "endDate" : "2012 07 23", - "beamlineName" : "BM29", - "scheduled" : 1, - "nbShifts" : 2, - "comments" : null, - "beamlineOperator" : "PERNOT P", - "usedFlag" : null, - "sessionTitle" : null, - "structureDeterminations" : null, - "dewarTransport" : null, - "databackupFrance" : null, - "databackupEurope" : null, - "visit_number" : null, - "operatorSiteNumber" : "14061", - "timeStamp" : "2012 04 25" - } - } ] - } ], - "macromolecules" : [ { - "macromoleculeId" : 5933, - "safetylevelId" : null, - "proposalId" : 3124, - "name" : "A", - "acronym" : "A", - "molecularMass" : "", - "extintionCoefficient" : "", - "sequence" : null, - "creationDate" : null, - "comments" : "", - "macromoleculeregion3VOs" : [], - "stoichiometry3VOsForHostMacromoleculeId" : [], - "structure3VOs" : [] - } ], - "stockSolutions" : [ { - "stockSolutionId" : 6, - "proposalId" : 3124, - "macromoleculeId" : 5933, - "bufferId" : 811, - "instructionSet3VO" : null, - "boxId" : 305861, - "storageTemperature" : "20", - "volume" : "300", - "concentration" : "1.2", - "comments" : "Buffer EDTA with A", - "name" : "A_EDTA_1.2", - "samples" : [] - } ] } + }); + return this.panel; +}; - }; +/** Populates could be call when the DOM is not filled yet **/ +FitForm.prototype._populate = function() { }; -CaseForm.prototype.test = function(targetId) { - var caseForm = new CaseForm(); - BIOSAXS.proposal = new Proposal(caseForm.input().proposal); - var panel = caseForm.getPanel(caseForm.input().dewar); - panel.render(targetId); +/** It populates the form * */ +FitForm.prototype.refresh = function(subtractions) { + this.subtractions = subtractions; + this.fitGrid.refresh(subtractions); +}; + +FitForm.prototype.input = function() { + return {}; +}; + +/** It populates the form **/ +FitForm.prototype.test = function(targetId) { + var macromoleculeForm = new FitForm(); + var panel = macromoleculeForm.getPanel(); + panel.render(targetId); }; -/** - * Example form - * - * @witdh - * @height - */ -function ExampleForm(args) { - this.id = BUI.id(); - this.width = 700; - this.height = 500; - - if (args != null) { - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; - } - } -} - -ExampleForm.prototype._getItems = function() { - return [{ - fieldLabel : 'First Name', - name : 'first', - allowBlank : false - }, { - fieldLabel : 'Last Name', - name : 'last', - allowBlank : false - } ]; -}; - -ExampleForm.prototype._getItems = function() { - return [ ]; -}; - -ExampleForm.prototype._getButtons = function() { - return [ ]; -}; - -ExampleForm.prototype.getPanel = function() { - this.panel = Ext.create('Ext.form.Panel', { - width : this.width, - height : this.height, - margin : 10, - border : 1, - defaultType : 'textfield', - items : this._getItems(), - buttons : this._getButtons() - }); - return this.panel; -}; - -/** It populates the form **/ -ExampleForm.prototype.refresh = function(macromolecule) { -}; - -function ExperimentForm(args) { +/** + * Example form + * + * @witdh + * @height + */ +function RigidBodyModelingResultForm(args) { this.id = BUI.id(); + this.width = null; + this.height = null; if (args != null) { + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } } - this.onSaved = new Event(this); -} - -ExperimentForm.prototype._getItems = function(experiment) { - this.experiment = experiment; - var typeCombo = Ext.create('Ext.form.ComboBox', { - id : this.id + 'type', - fieldLabel : 'Type', - store : [ "STATIC", "CALIBRATION", "HPLC" ], - queryMode : 'local', - labelWidth : 120, - displayField : 'name', - valueField : 'name', - value : experiment.json.type, - disabled : (experiment.json.type == 'TEMPLATE') + var _this = this; + /** Widgets **/ + this.rigidModelGrid = new RigidModelGrid({ + width : null, + height : 200 }); - var items = []; - - - if (experiment.json.type == "HPLC" ){ - var typeMacromolecule = BIOSAXS_COMBOMANAGER.getComboMacromoleculeByMacromolecules(BIOSAXS.proposal.getMacromolecules(), {labelWidth : 120, width: "120px"}); - if (experiment.getHPLCMacromolecule() != null){ - typeMacromolecule.setValue(experiment.getHPLCMacromolecule().macromoleculeId); - items.push(typeMacromolecule); + this.rigidModelGrid.onSelected.attach(function(sender, fits){ + var ids = []; + for ( var i in fits) { + ids.push(fits[i].fitStructureToExperimentalDataId); } - } - - - items.push(typeCombo, { - id : this.id + 'name', - xtype : 'textfield', - fieldLabel : 'Name', - labelWidth : 120, - width : '100%', - value : experiment.json.name - }, { - id : this.id + 'comments', - xtype : 'textareafield', - name : 'comments', - fieldLabel : 'Comments', - labelWidth : 120, - height : 120, - width : '100%', - value : experiment.json.comments + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data){ +// debugger + + }); + + adapter.getScatteringCurveByFrameIdsList([], [], [], ids); }); - return items; + +} + +RigidBodyModelingResultForm.prototype._getItems = function() { + var _this = this; + return [ { + xtype : 'label', + forId : 'myFieldId', + text : 'INLINE HELP: To be updated', + margin : '15 0 20 10', + cls : "inline-help" + }, this.rigidModelGrid.getPanel() ] + }; -ExperimentForm.prototype.getPanel = function(experiment) { + +RigidBodyModelingResultForm.prototype._getButtons = function() { + return []; +}; + +RigidBodyModelingResultForm.prototype.getPanel = function() { var _this = this; - - this.panel = Ext.createWidget({ - xtype : 'container', - layout : 'vbox', - border : 0, - style : { - padding : '10px' - }, - fieldDefaults : { - labelAlign : 'left', - labelWidth : 50 - }, - items : this._getItems(experiment) + this.panel = Ext.create('Ext.form.Panel', { + width : this.width, + height : this.height, + margin : 10, + border : 1, + defaultType : 'textfield', + items : this._getItems(), + buttons : this._getButtons(), + listeners : { + afterrender : function() { + _this._populate(); + + } + } }); return this.panel; }; -ExperimentForm.prototype.input = function() { - return new ExperimentHeaderForm().input(); +/** Populates could be call when the DOM is not filled yet **/ +RigidBodyModelingResultForm.prototype._populate = function() { }; -ExperimentForm.prototype.test = function(targetId) { - var experimentForm = new ExperimentForm(); - var panel = experimentForm.getPanel(new Experiment(experimentForm.input().experiment)); +/** It populates the form * */ +RigidBodyModelingResultForm.prototype.refresh = function(subtractions) { + this.rigidModelGrid.refresh(subtractions); +}; + +RigidBodyModelingResultForm.prototype.input = function() { + return {}; +}; + +/** It populates the form **/ +RigidBodyModelingResultForm.prototype.test = function(targetId) { + var macromoleculeForm = new RigidBodyModelingResultForm(); + var panel = macromoleculeForm.getPanel(); panel.render(targetId); }; /** - * Shows the header for the experiments changing the color and parameters depending on experiment type + * Example form * + * @witdh + * @height */ -function ExperimentHeaderForm(args) { +function SuperpositionForm(args) { this.id = BUI.id(); - this.backgroundColor = '#FFFFFF'; -} + this.width = null; + this.height = null; -ExperimentHeaderForm.prototype.getHTMLSource = function(experiment) { - var html = BUI.createFormLabel("Name :", experiment.json.name, 75, 400, this.backgroundColor); - if (experiment.json.type == "HPLC") { - if (experiment.getHPLCMacromolecule() != null){ - html = html + BUI.createFormLabel("Molecule :", experiment.getHPLCMacromolecule().acronym, 75, 400, this.backgroundColor); + if (args != null) { + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; } } - else{ - html = html + BUI.createFormLabel("Type :", experiment.json.type, 75, 400, this.backgroundColor); - } - - html = html + BUI.createFormLabel("Date :", experiment.json.creationDate, 75, 400, this.backgroundColor); - return html; -}; -ExperimentHeaderForm.prototype.getHTMLDownload = function(experiment) { - var bgcolor = "background-color:" + this.backgroundColor + ";"; - var html = "
"; - if ((experiment.json.type == "CALIBATION") || (experiment.json.type == "STATIC")) { - html = html + " Download Source File
"; - html = html - + ""; - } - if (experiment.json.type == "TEMPLATE") { - html = html - + " Download Source File"; - } + var _this = this; - if (experiment.json.type == "HPLC") { - html = html + " Download h5 File"; - } + /** Widgets **/ + this.superpositionGrid = new SuperpositionGrid({ + width : null, + height : 200 + }); - return html; -}; + this.superpositionGrid.onSelected.attach(function(sender, superpositions) { + var ids = []; + for ( var i in superpositions) { + ids.push(superpositions[i].superpositionId); + } +// _this._renderAbinitio(ids); +// _this.aprioriPDBViewer.refresh(); + _this._renderAligned(ids); + // getAlignedPDBContentBySuperpositionList + }); -ExperimentHeaderForm.prototype.getTopPanel = function(experiment) { - return { - xtype : 'container', - layout : 'hbox', - items : [ { - margin : "0 0 0 0", - width : 475, - border : 0, - html : this.getHTMLSource(experiment) - }, { - margin : "0 0 0 0", - width : 475, - border : 0, - html : this.getHTMLDownload(experiment) - } ] - }; + /** PDB viewer **/ +// this.abinitioPDBViewer = new PDBViewer({ +// width : 860 / 2, +// height : 300 / 2, +// margin : 0 +// }); +// +// /** PDB viewer **/ +// this.aprioriPDBViewer = new StructurePDBViewer({ +// width : 860 / 2, +// height : 300 / 2, +// margin : 0 +// }); + + this.alignedPDBViewer = new AlignedSuperpositionPDBViewer({ + width : 860 , + height : 300 + }); + +} + +SuperpositionForm.prototype._renderAligned = function(modelsIdList) { + /** Trying to plot the PDB file **/ + try { + this.alignedPDBViewer.refresh(modelsIdList); + } catch (e) { + console.log(e); + } }; -ExperimentHeaderForm.prototype.getButton = function(experiment) { - var _this = this; - return Ext.create('Ext.Button', { - text : 'EDIT', - minWidth : '100', - margin : '10 0 0 30', - handler : function() { - var experimentWindow = new ExperimentWindow(); - experimentWindow.onSaved.attach(function(sender, data) { - _this.experiment.json.name = data.name; - _this.experiment.json.type = data.type; - _this.experiment.json.comments = data.comments; - _this.panel.remove(_this.panel.items.items[0]); - _this.panel.remove(_this.panel.items.items[0]); - _this.panel.insert(_this.getTopPanel(_this.experiment)); - _this.panel.insert(_this.getBottomPanel(_this.experiment)); +SuperpositionForm.prototype._renderAbinitio = function(modelsIdList) { + /** Trying to plot the PDB file **/ + try { + var viz = []; + for (var i = 0; i < modelsIdList.length; i++) { + viz.push({ + modelId : modelsIdList[i], + color : "0xFF6600", + opacity : 0.8 }); - experimentWindow.show(experiment); } - }); + this.abinitioPDBViewer.refresh(viz); + } catch (e) { + console.log(e); + } }; -ExperimentHeaderForm.prototype.getBottomPanel = function(experiment) { - return { +SuperpositionForm.prototype._getItems = function() { + var _this = this; + return [ { + xtype : 'label', + forId : 'myFieldId', + text : 'INLINE HELP: To be updated', + margin : '15 0 20 10', + cls : "inline-help" + }, this.superpositionGrid.getPanel(), { xtype : 'container', layout : 'hbox', - margin : '10 0 0 0', - items : [ this.getComments(experiment), this.getButton(experiment) ] - }; + items : [ +// { +// xtype : 'container', +// layout : 'vbox', +// items : [ this.abinitioPDBViewer.getPanel(), this.aprioriPDBViewer.getPanel() +// +// ] +// }, + + this.alignedPDBViewer.getPanel() ] + } ] + }; -ExperimentHeaderForm.prototype.getComments = function(experiment) { - return { - xtype : 'textareafield', - labelStyle : 'font-weight: bold;', - name : 'comments', - fieldLabel : 'Comments', - labelWidth : 70, - height : 40, - minWidth : '450', - readOnly : true, - value : experiment.json.comments - }; +SuperpositionForm.prototype._getButtons = function() { + return []; }; -ExperimentHeaderForm.prototype.getPanel = function(experiment) { - this.experiment = experiment; - - if (experiment.json.type == 'CALIBRATION') { - this.backgroundColor = '#EFFBFB'; - } - if (experiment.json.type == 'TEMPLATE') { - this.backgroundColor = '#E0F8E6'; - } +SuperpositionForm.prototype.getPanel = function() { + var _this = this; + this.panel = Ext.create('Ext.form.Panel', { + width : this.width, + height : this.height, + margin : 10, + border : 1, + defaultType : 'textfield', + items : this._getItems(), + buttons : this._getButtons(), + listeners : { + afterrender : function() { + _this._populate(); - this.panel = Ext.create('Ext.container.Container', { - frame : false, - layout : 'vbox', - padding : 5, - bodyPadding : '5 5 0 0', - width : 890, - margin : '0 0 10 0', - height : 120, - style : { - borderColor : '#99bce8', - borderStyle : 'solid', - borderWidth : '1px', - 'background-color' : this.backgroundColor - }, - fieldDefaults : { - msgTarget : 'side', - labelWidth : 100 - }, - items : [ this.getTopPanel(experiment), this.getBottomPanel(experiment) ] + } + } }); return this.panel; }; -ExperimentHeaderForm.prototype.input = function() { - return { - experiment : DATADOC.getExperiment_10() - }; +/** Populates could be call when the DOM is not filled yet **/ +SuperpositionForm.prototype._populate = function() { }; -ExperimentHeaderForm.prototype.test = function(targetId) { - var experimentHeaderForm = new ExperimentHeaderForm(); - var panel = experimentHeaderForm.getPanel(new Experiment(experimentHeaderForm.input().experiment)); - panel.render(targetId); +/** It populates the form * */ +SuperpositionForm.prototype.refresh = function(subtractions) { + this.subtractions = subtractions; + this.superpositionGrid.refresh(subtractions); +}; + +SuperpositionForm.prototype.input = function() { + return {}; +}; +/** It populates the form **/ +SuperpositionForm.prototype.test = function(targetId) { + var macromoleculeForm = new SuperpositionForm(); + var panel = macromoleculeForm.getPanel(); + panel.render(targetId); }; /** - * Macromolecule form with the general parameters of a macromolecule + * Example form * * @witdh * @height - * - * #onSave button save has been clicked - * #onClose button close has been clicked */ -function MacromoleculeForm(args) { +function AssemblyForm(args) { this.id = BUI.id(); this.width = 700; this.height = 500; @@ -7053,6751 +6059,7745 @@ function MacromoleculeForm(args) { this.height = args.height; } } - - /** Events **/ - this.onSave = new Event(this); - this.onClose = new Event(this); -} -/** Type : is the Ext type then requiredtext or textfield * */ -MacromoleculeForm.prototype._getFieldTextWithHelp = function(type, fieldLabel, fieldName, help) { - return Ext.create('Ext.container.Container', { - margin : "10 0 0 10", - items : [ { - xtype : type, - fieldLabel : fieldLabel, - name : fieldName, - id : this.id + fieldName - }, { - xtype : 'label', - forId : 'myFieldId', - text : help, - margin : "5 0 0 105", - cls : "inline-help" - } ] - }); -}; + this.molarityGrid = new MolarityGrid({height : this.height - 50}); +} -MacromoleculeForm.prototype._getNumericWithHelp = function(type, fieldLabel, fieldName, help) { - return Ext.create('Ext.container.Container', { - margin : "0 0 0 10", - items : [ { - xtype : type, - fieldLabel : fieldLabel, - name : fieldName, - id : this.id + fieldName, - decimalPrecision : 6, - width : 220 - }, { - xtype : 'label', - forId : 'myFieldId', - text : help, - margin : "5 0 0 10", - cls : "inline-help" - } ] - }); +AssemblyForm.prototype._getItems = function() { + return [ { + xtype : 'label', + forId : 'myFieldId', + text : 'List of previously defined macromolecules present in the assembly. This information will be used for additional cross-checks where possible', + margin : '15 0 20 10', + cls : "inline-help" + }, this.molarityGrid.getPanel() ]; }; -MacromoleculeForm.prototype._getButtons = function() { - var _this = this; - return [ { - text : 'Save', - handler : function() { - _this._save(); - } - },{ - text : 'Close', - handler : function() { - _this.onClose.notify(); - - } - } ]; +AssemblyForm.prototype._getButtons = function() { + return []; }; -/** It persits the macromolecule in the database **/ -MacromoleculeForm.prototype._persist = function(macromoleculeId, acronym, name, molecularMass, extintionCoefficient, comments, refractiveIndex, solventViscosity) { - - /** Checking not duplicated acronym **/ - if (((macromoleculeId == null) && (BIOSAXS.proposal.getMacromoleculeByAcronym(acronym) != null))== true){ - BUI.showError("Duplicated acronym"); - return; - } - - - if (macromoleculeId == null){ - /** new macromolecule **/ - this.macromolecule = {}; - this.macromolecule.macromoleculeId = null; - } - else{ - this.macromolecule.macromoleculeId = macromoleculeId; - } - - this.macromolecule["acronym"] = acronym; - this.macromolecule["name"] = name; - this.macromolecule["molecularMass"] = molecularMass; - this.macromolecule["extintionCoefficient"] = extintionCoefficient; - this.macromolecule["comments"] = comments; - this.macromolecule["symmetry"] = Ext.getCmp(this.id + 'comboSym').getValue(); - this.macromolecule["refractiveIndex"] = refractiveIndex; - this.macromolecule["solventViscosity"] = solventViscosity; - - var _this = this; - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, proposal) { - /** Updating the proposal global object **/ - BIOSAXS.proposal.setItems(proposal); - _this.panel.setLoading(false); - - var saved = BIOSAXS.proposal.getMacromoleculeByAcronym(acronym); - /** Refreshing to check that everything is ok **/ - _this.refresh(saved); - _this.onSave.notify(saved); +AssemblyForm.prototype.getPanel = function() { + this.panel = Ext.create('Ext.form.Panel', { + width : this.width, + height : this.height, + margin : 10, + border : 0, + defaultType : 'textfield', + items : this._getItems(), + buttons : this._getButtons() }); - - this.panel.setLoading("Saving Macromolecule") - adapter.saveMacromolecule(this.macromolecule); + return this.panel; }; -/** Save the macromolecule in the DB **/ -MacromoleculeForm.prototype._save = function() { - - var _this = this; - - var acronym = this._getField("acronym"); - var name = this._getField("name"); - var molecularMass = this._getField("molecularMass"); - var extintionCoefficient = this._getField("extintionCoefficient"); - var comments = this._getField("comments"); - - var refractiveIndex = this._getField("refractiveIndex"); - var solventViscosity = this._getField("solventViscosity"); - - /** Checking required fields **/ - if (name == "") { - BUI.showError("Name field is mandatory"); - return; - } - if (acronym == "") { - BUI.showError("Acroynm field is mandatory"); - return; - } - if (this.macromolecule != null){ - /** Checking if it is a new macromolecule **/ - if (this.macromolecule.macromoleculeId == null){ - /** Check if the acronym exists already **/ - this._persist(null, acronym, name, molecularMass, extintionCoefficient, comments, refractiveIndex, solventViscosity); - } - else{ - /** It is an update **/ - this._persist(this.macromolecule.macromoleculeId, acronym, name, molecularMass, extintionCoefficient, comments, refractiveIndex, solventViscosity); - } - } - else{ - /** It is a new macromolecule **/ - this._persist(null, acronym, name, molecularMass, extintionCoefficient, comments, refractiveIndex, solventViscosity); - } +/** It populates the form **/ +AssemblyForm.prototype.refresh = function(macromolecule) { + this.macromolecule = macromolecule; + this.molarityGrid.refresh(macromolecule); }; +AssemblyForm.prototype.input = function() { + return {}; +}; -MacromoleculeForm.prototype._getItems = function() { +AssemblyForm.prototype.test = function(targetId) { + var assemblyForm = new AssemblyForm(); + + var panel = assemblyForm.getPanel(); + panel.render(targetId); +}; +/** + * Edit the information of a buffer + * + * #onSaved + * #onRemoveAdditive + */ +function BufferForm() { var _this = this; - /** Symmetry combo box **/ - var symmetry = Ext.create('Ext.data.Store', { - fields : [ 's' ], - data : this._getSymmetries() - }); - this.symmetryComboBox = Ext.create('Ext.form.ComboBox', { - fieldLabel : 'Symmetry', - store : symmetry, - id : this.id + 'comboSym', - queryMode : 'local', - displayField : 's', - valueField : 's', - value : "P1", - margin : "0 0 0 30", - width : 220 + this.additiveGrid = new AdditiveGrid(); + this.additiveGrid.onRemoveButtonClicked.attach(function(sender, args) { + _this.onRemoveAdditive.notify(args); }); - - return [this._getFieldTextWithHelp("requiredtext", "Name", "name", "Long name. i.e: Bovine serum albumin"), - this._getFieldTextWithHelp("requiredtext", "Acronym", "acronym", "Acronym will be used in the files and analisys. i.e: BSA"), - this._getFieldTextWithHelp("textfield", "Mol. Mass (Da)", "molecularMass", "Atomic mass estimation measured in Da"), - { - xtype : 'container', - layout : 'hbox', - margin : "10 0 0 0", - items :[ - this._getNumericWithHelp("numberfield", "Extinction coef.", "extintionCoefficient", ""), - this.symmetryComboBox - ] - }, - { - xtype : 'container', - layout : 'hbox', - margin : "5 0 0 0", - items :[ - this._getNumericWithHelp("numberfield", "Refractive Index", "refractiveIndex", "How radiation propagates through the medium"), - this._getNumericWithHelp("numberfield", "Solvent Viscosity", "solventViscosity", "") - ] - }, - { - id : this.id + "comments", - xtype : 'textareafield', - name : 'comments', - margin : '35 0 0 10', - fieldLabel : 'Comments', - width : this.width - 100 - } ]; + + this.onSaved = new Event(this); + this.onRemoveAdditive = new Event(this); +} + +BufferForm.prototype.getBuffer = function() { + this.buffer.name = Ext.getCmp("buffer_name").getValue(); + this.buffer.acronym = Ext.getCmp("buffer_acronym").getValue(); + this.buffer.comments = Ext.getCmp("buffer_comments").getValue(); + this.buffer.ph = Ext.getCmp("buffer_ph").getValue(); + this.buffer.composition = Ext.getCmp("buffer_composition").getValue(); + this.buffer.bufferhasadditive3VOs = this.additiveGrid.getAdditives(); + return this.buffer; }; -MacromoleculeForm.prototype._getSymmetries = function() { - return [ { - "s" : "P1" - }, { - "s" : "P2" - }, { - "s" : "P3" - }, { - "s" : "P4" - }, { - "s" : "P5" - }, { - "s" : "P6" - }, { - "s" : "P32" - }, { - "s" : "P42" - }, { - "s" : "P52" - }, { - "s" : "P62" - }, { - "s" : "P222" - } ] +BufferForm.prototype._getTopPanel = function() { + return { + xtype : 'container', + layout : 'hbox', + border : 0, + frame : true, + items : [ { + xtype : 'container', + layout : 'hbox', + items : [ { + xtype : 'container', + flex : 1, + border : false, + layout : 'anchor', + defaultType : 'textfield', + items : [ { + xtype : 'requiredtext', + id : 'buffer_name', + fieldLabel : 'Name', + name : 'name', + width : '200px', + value : this.buffer.name + }, { + xtype : 'requiredtext', + id : 'buffer_acronym', + fieldLabel : 'Acronym', + name : 'acronym', + width : '200px', + value : this.buffer.acronym + } ] + } ] + }, { + xtype : 'container', + flex : 1, + layout : 'anchor', + defaultType : 'textfield', + margin : '0 0 0 10', + items : [ { + id : 'buffer_ph', + fieldLabel : 'pH', + name : 'ph', + value : this.buffer.ph, + xtype : 'numberfield', + width : 200, + minValue : 0, + maxValue : 15 + }, { + xtype : 'requiredtext', + id : 'buffer_composition', + fieldLabel : 'Composition', + name : 'composition', + width : 200, + value : this.buffer.composition + } ] + } ] + }; }; -MacromoleculeForm.prototype.getPanel = function() { - this.panel = Ext.create('Ext.form.Panel', { - width : this.width, - height : this.height, - margin : 10, - border : 1, - defaultType : 'textfield', - items : this._getItems(), - buttons : this._getButtons() +BufferForm.prototype.getPanel = function(buffer) { + this.buffer = buffer; + this.panel = Ext.createWidget({ + xtype : 'container', + layout : 'vbox', + style : { + padding : '10px' + }, + fieldDefaults : { + labelAlign : 'left', + labelWidth : 50 + + }, + items : [ this._getTopPanel(), { + id : 'buffer_comments', + xtype : 'textareafield', + name : 'comments', + fieldLabel : 'Comments', + width : '100%', + value : buffer.comments + }, this.additiveGrid.getPanel(buffer) ] }); return this.panel; }; - -/** Populates each text field by field name and value **/ -MacromoleculeForm.prototype._populateField = function(fieldName, value) { - if (value != null){ - Ext.getCmp(this.id + fieldName).setValue(value); - } +BufferForm.prototype.input = function() { + return { + buffer : { + "bufferId" : 422, + "proposalId" : 10, + "safetyLevelId" : null, + "name" : "B1", + "acronym" : "B1", + "ph" : null, + "composition" : null, + "bufferhasadditive3VOs" : [], + "comments" : null + } + }; }; -/** Gets the value of a textfield **/ -MacromoleculeForm.prototype._getField = function(fieldName) { - return Ext.getCmp(this.id + fieldName).getValue(); +BufferForm.prototype.test = function(targetId) { + var bufferForm = new BufferForm(); + var panel = bufferForm.getPanel(bufferForm.input().buffer); + panel.render(targetId); }; - - -/** It populates the form **/ -MacromoleculeForm.prototype.refresh = function(macromolecule) { - this.macromolecule = macromolecule; - if (macromolecule != null){ - this._populateField("name", macromolecule.name); - this._populateField("acronym", macromolecule.acronym); - this._populateField("extintionCoefficient", macromolecule.extintionCoefficient); - this._populateField("molecularMass", macromolecule.molecularMass); - this._populateField("comments", macromolecule.comments); - this._populateField("refractiveIndex", macromolecule.refractiveIndex); - this._populateField("solventViscosity", macromolecule.solventViscosity); - if (macromolecule.symmetry != null){ - Ext.getCmp(this.id + 'comboSym').setValue(macromolecule.symmetry); + +/** + * @showTitle + * + * #onSaved + * #onAddPlates + * #onRemovePlates + **/ +function CaseForm(args) { + this.width = 700; + this.showTitle = true; + if (args != null) { + if (args.showTitle != null) { + this.showTitle = args.showTitle; } } -}; - -MacromoleculeForm.prototype.input = function() { - return {}; -}; - - -/** It populates the form **/ -MacromoleculeForm.prototype.test = function(targetId) { - var macromoleculeForm = new MacromoleculeForm(); - macromoleculeForm.onClose.attach(function(sender){ - alert("Click on close"); + var _this = this; + this.stockSolutionGrid = new StockSolutionGrid({ + width : this.width - 10, + minHeight : 300, + height : 300, + tbar : true, + showTitle : true, + isPackedVisible : false, + btnAddExisting : true, + btnRemoveVisible : false, + btnUnpackVisible : true }); - var panel = macromoleculeForm.getPanel(); - panel.render(targetId); -}; + /** When selecting existing stock solutions **/ + this.stockSolutionGrid.onStockSolutionSelected.attach(function(sender, stockSolutions) { + if (stockSolutions != null) { + for ( var i = 0; i < stockSolutions.length; i++) { + _this.saveStockSolution(stockSolutions[i]); + } + } + }); - + /** it can be because it has been added a new one or removed **/ + this.stockSolutionGrid.onProposalChanged.attach(function(sender, stockSolution) { + if (stockSolution != null) { + _this.saveStockSolution(stockSolution); + } else { + BIOSAXS.proposal.onInitialized.attach(function() { + _this.stockSolutionGrid.refresh(BIOSAXS.proposal.getStockSolutionsByDewarId(_this.dewar.dewarId)); + _this.stockSolutionGrid.grid.setLoading(false); + }); + BIOSAXS.proposal.init(); -function ModelVisualizerForm(args){ - this.id =BUI.id(); - this.width = 600; - this.height = 400; - if (args!= null){ - if (args.width != null){ - this.width = args.width; - } - if (args.height != null){ - this.height = args.height; } - } -}; -ModelVisualizerForm.prototype._getFirHTML = function(modelId, width, height, type, desc) { - var html = ""; - html = html + ''; - html = html + ''; - html = html + ''; - html = html + '
dammin.' + type + '
' + desc + '
'; - return html; -}; - -ModelVisualizerForm.prototype.getItems = function(modelPanel){ - _this = this; - var height = _this.height/2 - 60; - var width = _this.width/2 - 10; - - return Ext.create('Ext.container.Container', { - layout: { - type: 'vbox', // Arrange child items vertically - }, - items: [ - modelPanel, - { - xtype : 'container', - layout: { - type: 'hbox', // Arrange child items vertically - }, - items : [{ - html : this._getFirHTML("id", width, height, "fir", "Fit of the simulated scattering curve versus a smoothed experimental data (spline interpolation)"), - height :height, - width : width, - padding: 2 - }, - { - html : this._getFirHTML("id", width, height, "fit", "Fit of the simulated scattering curve versus the experimental data."), - height : height, - width : width, - padding: 2 - }] - } - - ] }); -}; -ModelVisualizerForm.prototype.refresh = function(models){ - var input = []; -// var colors = ["008000", "F0A804", "0000FF", "800080", "C0C0C0"]; - for (var i = 0; i < models.length; i++) { - console.log(BUI.rainbow(models.length, i).replace("#", "0x")); - input.push({ - color: BUI.rainbow(models.length, i).replace("#", "0x"), - modelId: models[i].modelId, - opacity: 0.8, - radius: 3, - title: BUI.getFileNameByPath(models[i].pdbFile), - type: "SHAPEDETERMINATIONMODEL" - - }); - } - - this.panel.removeAll(); - this.panel.add( - _this.getItems( - new PDBViewer({ - width : this.width - 10, - height : (this.height/2) - 10, - title : "" - }).draw(input) - ) - ); - + this.onSaved = new Event(this); + this.onAddPlates = new Event(this); + this.onRemovePlates = new Event(this); +} + +CaseForm.prototype.saveStockSolution = function(stockSolution) { + var _this = this; var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - var splitted = data.toString().split("\n"); - var array = []; - for ( var i = 0; i < splitted.length; i++) { - var line = splitted[i].trim(); - var line_splited = line.split(/\s*[\s,]\s*/); - if (line_splited.length == 4) { - array.push([ Number(line_splited[0]), BUI.getStvArray(line_splited[1], line_splited[2]), BUI.getStvArray(line_splited[3], 0) ]); - } - } - - var id = (_this.id + "firid"); - var dygraphWidget = new StdDevDyGraph(id, { - width : (_this.width/2) - 10, - height :(_this.height/2) -110, - xlabel : 'q(nm-1)' + this.stockSolutionGrid.grid.setLoading("ISPyB: setting case to Stock solution"); + adapter.onSuccess.attach(function(sender, stockSolution) { + BIOSAXS.proposal.onInitialized.attach(function() { + _this.stockSolutionGrid.refresh(BIOSAXS.proposal.getStockSolutionsByDewarId(_this.dewar.dewarId)); + _this.stockSolutionGrid.grid.setLoading(false); }); - dygraphWidget.draw(array, [ "#FF0000", "#0000FF", "#FF00FF" ], [ 's', 'I(exp)', 'I(sim)' ]); + BIOSAXS.proposal.init(); }); - - adapter.getModelFile("FIR", models[0].modelId); - - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - var splitted = data.toString().split("\n"); - var array = []; - for ( var i = 0; i < splitted.length; i++) { - var line = splitted[i].trim(); - var line_splited = line.split(/\s*[\s,]\s*/); - if (line_splited.length == 3) { - array.push([ Number(line_splited[0]), BUI.getStvArray(line_splited[1], 0), BUI.getStvArray(line_splited[2], 0) ]); - } - } - - var id = (_this.id + "fitid"); - - var dygraphWidget = new StdDevDyGraph(id, { - width : (_this.width/2) - 10, - height : (_this.height/2) - 110, - xlabel : 'q(nm-1)' - }); - dygraphWidget.draw(array, [ "#FF0000", "#0000FF" ], [ "s", "I(exp)", "I(sim)" ]); + adapter.onError.attach(function(sender, data) { + _this.stockSolutionGrid.grid.setLoading(false); + BUI.showError(data); }); - adapter.getModelFile("FIT", models[0].modelId); + stockSolution.boxId = _this.dewar.dewarId; + adapter.saveStockSolution(stockSolution); }; -ModelVisualizerForm.prototype.getPanel = function(modelList){ - _this = this; - this.modelList = modelList; - this.panel = Ext.create('Ext.Panel', { - title: 'Results', - width: this.width, - height: this.height, - layout: { - type: 'vbox', // Arrange child items vertically -// align: 'stretch' // Each takes up full width - }, - items: [ - - ], - listeners : { - afterrender : function(grid, eOpts) { -// alert(_this.modelList) - } - } +CaseForm.prototype.fillStores = function() { + var _this = this; + this.panel.setLoading("Loading Labcontacts from database"); + + var proposal = BUI.getProposal(); + proposal.onDataRetrieved.attach(function(sender, data) { + _this.labContactForSendingStore.loadData(data, false); + _this.labContactForReturnStore.loadData(data, false); + _this.panel.setLoading(false); }); - - return this.panel; + proposal.getLabContactsByProposalId(); }; +CaseForm.prototype.refresh = function(dewar) { + this.setDewar(dewar); + this.stockSolutionGrid.refresh(BIOSAXS.proposal.getStockSolutionsByDewarId(dewar.dewarId)); +}; + +CaseForm.prototype.getDewar = function() { + this.dewar.code = Ext.getCmp("dewar_code").getValue(); + this.dewar.comments = Ext.getCmp("dewar_comments").getValue(); + this.dewar.trackingNumberFromSynchrotron = Ext.getCmp("dewar_trackingNumberFromSynchrotron").getValue(); + this.dewar.trackingNumberToSynchrotron = Ext.getCmp("dewar_trackingNumberToSynchrotron").getValue(); + this.dewar.transportValue = Ext.getCmp("dewar_transportValue").getValue(); + this.dewar.storageLocation = Ext.getCmp("dewar_storageLocation").getValue(); + this.dewar.firstExperimentId = this.macromoleculeCombo.getValue(); + return this.dewar; +}; + +CaseForm.prototype.setDewar = function(dewar) { + this.dewar = dewar; + Ext.getCmp("dewar_code").setValue(this.dewar.code); + Ext.getCmp("dewar_dewarStatus").setText(new String(this.dewar.dewarStatus).toUpperCase()); + Ext.getCmp("dewar_comments").setValue(this.dewar.comments); + Ext.getCmp("dewar_trackingNumberFromSynchrotron").setValue(this.dewar.trackingNumberFromSynchrotron); + Ext.getCmp("dewar_trackingNumberToSynchrotron").setValue(this.dewar.trackingNumberToSynchrotron); + Ext.getCmp("dewar_transportValue").setValue(this.dewar.transportValue); + Ext.getCmp("dewar_storageLocation").setValue(this.dewar.storageLocation); + if (dewar.sessionVO != null) { + this.macromoleculeCombo.setValue(dewar.sessionVO.sessionId); + } +}; + +CaseForm.prototype.getSessionCombo = function() { + this.macromoleculeCombo = BIOSAXS_COMBOMANAGER.getComboSessions(BIOSAXS.proposal.getSessions(), { + labelWidth : 100, + margin : '5 0 00 0', + width : 250 + }); + return this.macromoleculeCombo; +}; + +CaseForm.prototype.getInformationPanel = function() { + if (this.panel == null) { + this.informationPanel = Ext.create('Ext.form.Panel', { + width : this.width - 10, + border : 0, + items : [ { + xtype : 'container', + margin : "2 2 2 2", + collapsible : false, + defaultType : 'textfield', + layout : 'anchor', + items : [ { + xtype : 'container', + layout : 'hbox', + items : [ { + xtype : 'requiredtext', + fieldLabel : 'Code', + allowBlank : false, + name : 'code', + id : 'dewar_code', + anchor : '50%' + }, { + xtype : 'label', + margin : '0 0 0 20', + readOnly : true, + id : 'dewar_dewarStatus', + anchor : '50%' + } ] + }, this.getSessionCombo(), { + margin : '5 0 0 0', + xtype : 'textareafield', + name : 'comments', + id : 'dewar_comments', + width : this.width - 50, + fieldLabel : 'Comments' + } ] + }, { + xtype : 'fieldset', + title : 'Courier Accounts Details for Return', + collapsible : false, + layout : 'anchor', + defaults : { + anchor : '100%' + }, + items : [ { + xtype : 'container', + layout : 'hbox', + items : [ { + xtype : 'textfield', + labelWidth : 200, + width : 280, + fieldLabel : 'Track Number From Synchrotron', + id : 'dewar_trackingNumberFromSynchrotron' + }, { + xtype : 'numberfield', + width : 190, + labelWidth : 110, + margin : '0 0 0 30', + fieldLabel : 'Transport Value', + id : 'dewar_transportValue' + } + + ] + }, { + xtype : 'container', + layout : 'hbox', + margin : '10 0 0 0', + items : [ + + { + xtype : 'textfield', + labelWidth : 200, + width : 280, + fieldLabel : 'Track Number To Synchrotron', + id : 'dewar_trackingNumberToSynchrotron' + }, { + xtype : 'textfield', + margin : '0 0 0 30', + width : 190, + labelWidth : 110, + fieldLabel : 'Storage Location', + id : 'dewar_storageLocation' + } + + ] + } ] + } ] + }); + } + + return this.informationPanel; +}; + +CaseForm.prototype.getPanel = function(dewar) { + this.dewar = dewar; + this.panel = Ext.createWidget({ + xtype : 'container', + layout : 'vbox', + width : this.width, + border : 0, + items : [ { + items : { + xtype : "container", + layout : "vbox", + margin : "5 5 5 5", + items : [ this.getInformationPanel(dewar), this.stockSolutionGrid.getPanel() ] + + } + } ] + }); + + this.refresh(dewar); + return this.panel; + +}; + +CaseForm.prototype.input = function() { + return { + dewar : { + "dewarId" : 305861, + "code" : "ESRF-TEST", + "comments" : "comments", + "storageLocation" : "FRIDGE", + "dewarStatus" : "opened", + "timeStamp" : null, + "isStorageDewar" : null, + "barCode" : "ESRF305861", + "customsValue" : null, + "transportValue" : null, + "trackingNumberToSynchrotron" : "3333", + "trackingNumberFromSynchrotron" : "224466", + "type" : "Dewar", + "sessionVO" : { + "sessionId" : 31697, + "expSessionPk" : null, + "projectCode" : null, + "startDate" : "2012 07 21", + "endDate" : "2012 07 23", + "beamlineName" : "BM29", + "scheduled" : 1, + "nbShifts" : 2, + "comments" : null, + "beamlineOperator" : "PERNOT P", + "usedFlag" : null, + "sessionTitle" : null, + "structureDeterminations" : null, + "dewarTransport" : null, + "databackupFrance" : null, + "databackupEurope" : null, + "visit_number" : null, + "operatorSiteNumber" : "14061", + "timeStamp" : "2012 04 25" + } + }, + proposal : { + "assemblies" : [], + "sessions" : [ { + "sessionId" : 31697, + "expSessionPk" : null, + "projectCode" : null, + "startDate" : "2012 07 21", + "endDate" : "2012 07 23", + "beamlineName" : "BM29", + "scheduled" : 1, + "nbShifts" : 2, + "comments" : null, + "beamlineOperator" : "PERNOT P", + "usedFlag" : null, + "sessionTitle" : null, + "structureDeterminations" : null, + "dewarTransport" : null, + "databackupFrance" : null, + "databackupEurope" : null, + "visit_number" : null, + "operatorSiteNumber" : "14061", + "timeStamp" : "2012 04 25" + } ], + "labcontacts" : [ { + "labContactId" : 787, + "personVO" : { + "personId" : 304252, + "personUUID" : null, + "familyName" : "KIM", + "givenName" : "Henry", + "title" : null, + "emailAddress" : "henry-sung.kim@ibs.fr", + "phoneNumber" : "", + "login" : "", + "passwd" : "", + "faxNumber" : "" + }, + "cardName" : "KIM-Institut de Bio", + "defaultCourrierCompany" : "22", + "courierAccount" : "", + "billingReference" : "", + "dewarAvgCustomsValue" : 0, + "dewarAvgTransportValue" : 0 + } ], + "buffers" : [ { + "bufferId" : 811, + "proposalId" : 3124, + "safetyLevelId" : null, + "name" : "EDTA", + "acronym" : "EDTA", + "ph" : null, + "composition" : "", + "bufferhasadditive3VOs" : [], + "comments" : "" + }, { + "bufferId" : 810, + "proposalId" : 3124, + "safetyLevelId" : null, + "name" : "HEPES", + "acronym" : "HEPES", + "ph" : null, + "composition" : "", + "bufferhasadditive3VOs" : [], + "comments" : "" + } ], + "shippings" : [ { + "shippingId" : 304107, + "shippingName" : "TEST", + "deliveryAgentAgentName" : null, + "deliveryAgentShippingDate" : null, + "deliveryAgentDeliveryDate" : null, + "deliveryAgentAgentCode" : null, + "deliveryAgentFlightCode" : null, + "shippingStatus" : "opened", + "timeStamp" : "2013 09 25", + "laboratoryId" : null, + "isStorageShipping" : null, + "creationDate" : "2013 09 25", + "comments" : "test", + "sendingLabContactVO" : { + "labContactId" : 787, + "personVO" : { + "personId" : 304252, + "personUUID" : null, + "familyName" : "KIM", + "givenName" : "Henry", + "title" : null, + "emailAddress" : "henry-sung.kim@ibs.fr", + "phoneNumber" : "", + "login" : "", + "passwd" : "", + "faxNumber" : "" + }, + "cardName" : "KIM-Institut de Bio", + "defaultCourrierCompany" : "22", + "courierAccount" : "", + "billingReference" : "", + "dewarAvgCustomsValue" : 0, + "dewarAvgTransportValue" : 0 + }, + "returnLabContactVO" : { + "labContactId" : 787, + "personVO" : { + "personId" : 304252, + "personUUID" : null, + "familyName" : "KIM", + "givenName" : "Henry", + "title" : null, + "emailAddress" : "henry-sung.kim@ibs.fr", + "phoneNumber" : "", + "login" : "", + "passwd" : "", + "faxNumber" : "" + }, + "cardName" : "KIM-Institut de Bio", + "defaultCourrierCompany" : "22", + "courierAccount" : "", + "billingReference" : "", + "dewarAvgCustomsValue" : 0, + "dewarAvgTransportValue" : 0 + }, + "returnCourier" : null, + "dateOfShippingToUser" : null, + "shippingType" : "DewarTracking", + "dewarVOs" : [ { + "dewarId" : 305861, + "code" : "ESRF-TEST", + "comments" : "comments", + "storageLocation" : "FRIDGE", + "dewarStatus" : "opened", + "timeStamp" : null, + "isStorageDewar" : null, + "barCode" : "ESRF305861", + "customsValue" : null, + "transportValue" : null, + "trackingNumberToSynchrotron" : "3333", + "trackingNumberFromSynchrotron" : "224466", + "type" : "Dewar", + "sessionVO" : { + "sessionId" : 31697, + "expSessionPk" : null, + "projectCode" : null, + "startDate" : "2012 07 21", + "endDate" : "2012 07 23", + "beamlineName" : "BM29", + "scheduled" : 1, + "nbShifts" : 2, + "comments" : null, + "beamlineOperator" : "PERNOT P", + "usedFlag" : null, + "sessionTitle" : null, + "structureDeterminations" : null, + "dewarTransport" : null, + "databackupFrance" : null, + "databackupEurope" : null, + "visit_number" : null, + "operatorSiteNumber" : "14061", + "timeStamp" : "2012 04 25" + } + } ] + } ], + "macromolecules" : [ { + "macromoleculeId" : 5933, + "safetylevelId" : null, + "proposalId" : 3124, + "name" : "A", + "acronym" : "A", + "molecularMass" : "", + "extintionCoefficient" : "", + "sequence" : null, + "creationDate" : null, + "comments" : "", + "macromoleculeregion3VOs" : [], + "stoichiometry3VOsForHostMacromoleculeId" : [], + "structure3VOs" : [] + } ], + "stockSolutions" : [ { + "stockSolutionId" : 6, + "proposalId" : 3124, + "macromoleculeId" : 5933, + "bufferId" : 811, + "instructionSet3VO" : null, + "boxId" : 305861, + "storageTemperature" : "20", + "volume" : "300", + "concentration" : "1.2", + "comments" : "Buffer EDTA with A", + "name" : "A_EDTA_1.2", + "samples" : [] + } ] + } + + }; +}; + +CaseForm.prototype.test = function(targetId) { + var caseForm = new CaseForm(); + BIOSAXS.proposal = new Proposal(caseForm.input().proposal); + var panel = caseForm.getPanel(caseForm.input().dewar); + panel.render(targetId); +}; -/** - * Example form - * - * @witdh - * @height - */ -function MolarityForm(args) { - this.id = BUI.id(); - this.width = 700; - this.height = 500; - - if (args != null) { - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; - } - } - - this.onSave = new Event(this); - this.onClose = new Event(this); -} - - -MolarityForm.prototype._getNumericWithHelp = function(type, fieldLabel, fieldName, help) { - return Ext.create('Ext.container.Container', { - margin : "10 0 0 10", - items : [ { - xtype : type, - fieldLabel : fieldLabel, - name : fieldName, - id : this.id + fieldName, - decimalPrecision : 6 - }, { - xtype : 'label', - forId : 'myFieldId', - text : help, - margin : "5 0 0 105", - cls : "inline-help" - } ] - }); -}; - - -MolarityForm.prototype._getItems = function() { - this.macromoleculeCombo = BIOSAXS_COMBOMANAGER.getComboMacromoleculeByMacromolecules(this.getMacromuleculesCandidates(this.macromolecule), { - width : 250, - labelWidth : 100, - margin : 10 - }); - - return [ { - xtype : 'container', - flex : 1, - margin : '10 0 0 10', - border : 0, - layout : 'anchor', - defaultType : 'requiredtext', - items : [ this.macromoleculeCombo, - this._getNumericWithHelp("textfield", "Ratio", "ratio", "Number in assymmetric units") - ] - } ]; -}; - -MolarityForm.prototype._persist = function() { - var _this = this; - var macromoleculeId = this.macromoleculeCombo.getValue(); - var ratio = Ext.getCmp(this.id + "ratio").getValue(); - var comments = "Not used yet"; - var dataAdapter = new BiosaxsDataAdapter(); - this.panel.setLoading("Saving"); - dataAdapter.onSuccess.attach(function(sender, args) { - _this.onSave.notify(); - }); - dataAdapter.saveStoichiometry(this.macromolecule.macromoleculeId, macromoleculeId, ratio, comments); -}; - -MolarityForm.prototype._getButtons = function() { - var _this = this; - - function onClose() { - _this.onClose.notify(); - } - - return [ { - text : 'Save', - handler : function() { - _this._persist(); - } - }, { - text : 'Cancel', - handler : function() { - onClose(); - } - } ]; -}; - -MolarityForm.prototype.getPanel = function() { - this.panel = Ext.create('Ext.form.Panel', { -// width : null, - height : this.height, - margin : 2, - border : 1, - defaultType : 'requiredtext', - items : this._getItems(), - buttons : this._getButtons() - }); - return this.panel; -}; - -/** macromolecules contains all macromolecules except this one **/ -MolarityForm.prototype.getMacromuleculesCandidates = function(macromolecule) { - var macromolecules = []; - if ( BIOSAXS.proposal.macromolecules){ - for (var i = 0; i < BIOSAXS.proposal.macromolecules.length; i++) { - var m = BIOSAXS.proposal.macromolecules[i]; - if (this.macromolecule != null){ - if (m.macromoleculeId != this.macromolecule.macromoleculeId) { - macromolecules.push(m); - } - } - } - } - return macromolecules; -}; - - -/** It populates the form **/ -MolarityForm.prototype.refresh = function(macromolecule) { - this.macromolecule = macromolecule; - -}; - - -MolarityForm.prototype.input = function() { - return {}; -}; - - -/** It populates the form **/ -MolarityForm.prototype.test = function(targetId) { - var macromoleculeForm = new MolarityForm(); - var panel = macromoleculeForm.getPanel(); - panel.render(targetId); -}; - -///** -// * -// * @witdh -// * @height -// */ -//function MacromoleculeForm(args) { -// this.id = BUI.id(); -// this.width = 700; -// this.height = 500; -// -// if (args != null) { -// if (args.width != null) { -// this.width = args.width; -// } -// if (args.height != null) { -// this.height = args.height; -// } -// } -// -// this.onClose = new Event(this); -//} -// -//MacromoleculeForm.prototype.getMacromolecule = function() { -// this.macromolecule.name = Ext.getCmp(this.panel.getItemId()).getValues().name; -// this.macromolecule.acronym = Ext.getCmp(this.panel.getItemId()).getValues().acronym; -// this.macromolecule.comments = Ext.getCmp(this.panel.getItemId()).getValues().comments; -// this.macromolecule.extintionCoefficient = Ext.getCmp(this.panel.getItemId()).getValues().extintionCoefficient; -// this.macromolecule.molecularMass = Ext.getCmp(this.panel.getItemId()).getValues().molecularMass; -// return this.macromolecule; -//}; -// -//MacromoleculeForm.prototype.setMacromolecule = function(macromolecule) { -// this.pdbStore.loadData(macromolecule.structure3VOs); -// -//}; -// -//MacromoleculeForm.prototype.getForm = function(macromolecule) { -// this.panel = Ext.createWidget('form', { -// frame : false, -// border : 0, -// padding : 15, -// width : 550, -// height : 350, -// items : [ { -// xtype : 'container', -// layout : 'hbox', -// items : [ { -// xtype : 'container', -// flex : 1, -// border : false, -// layout : 'anchor', -// defaultType : 'requiredtext', -// items : [ { -// fieldLabel : 'Name', -// name : 'name', -// anchor : '95%', -// tooltip : "Name of the macromolecule", -// value : macromolecule.name -// }, { -// fieldLabel : 'Acronym', -// name : 'acronym', -// anchor : '95%', -// value : macromolecule.acronym -// } ] -// }, { -// xtype : 'container', -// flex : 1, -// layout : 'anchor', -// defaultType : 'textfield', -// items : [ { -// xtype : 'numberfield', -// fieldLabel : 'Mol. Mass (Da)', -// name : 'molecularMass', -// value : macromolecule.molecularMass, -// decimalPrecision : 6 -// }, { -// xtype : 'numberfield', -// fieldLabel : 'Extinction coef.', -// name : 'extintionCoefficient', -// value : macromolecule.extintionCoefficient, -// decimalPrecision : 6 -// } ] -// } ] -// }, { -// xtype : 'textareafield', -// name : 'comments', -// fieldLabel : 'Comments', -// value : macromolecule.comments, -// width : this.width - 10 -// }, -// -// { -// html : BUI.getWarningHTML("The macromolecule is unsaved. Save the macromolecule to get access to other tabs"), -// margin : "150 10 10 10", -// id : this.id + "unsavedWarning", -// hidden : !(!macromolecule.macromoleculeId) -// } -// -// ] -// }); -// return this.panel; -//}; -// -//MacromoleculeForm.prototype.save = function() { -// var _this = this; -// -// var adapter = new BiosaxsDataAdapter(); -// adapter.onSuccess.attach(function(sender, proposal) { -// BIOSAXS.proposal.setItems(proposal); -// _this.panel.setLoading(false); -// -// Ext.getCmp(_this.id + "assembly").enable() -// Ext.getCmp(_this.id + "advanced").enable(); -// Ext.getCmp(_this.id + "unsavedWarning").hide(); -// }); -// -// if (this.getMacromolecule().name == "") { -// BUI.showError("Name field is mandatory"); -// return; -// } -// if (this.getMacromolecule().acronym == "") { -// BUI.showError("Acroynm field is mandatory"); -// return; -// } -// -// /** Check if acronym is unique * */ -// if (this.getMacromolecule().macromoleculeId == null) { -// if (BIOSAXS.proposal.getMacromoleculeByAcronym(this.getMacromolecule().acronym) == null) { -// this.panel.setLoading("ISPyB: Saving Macromolecule") -// adapter.saveMacromolecule(this.getMacromolecule()); -// } else { -// alert("There is already an existing macromolecule with the same acronym"); -// -// } -// } else { -// this.panel.setLoading("ISPyB: Saving Macromolecule") -// adapter.saveMacromolecule(this.getMacromolecule()); -// } -// -//}; -// -//MacromoleculeForm.prototype.getPanel = function(macromolecule) { -// var _this = this; -// this.macromolecule = macromolecule; -// return Ext.createWidget('tabpanel', { -// height : this.height, -// margin : 5, -// plain : true, -// style : { -// padding : 5 -// }, -// items : [ { -// tabConfig : { -// title : "General", -// disabled : false -// }, -// items : [ this.getForm(macromolecule) ], -// bbar : [ "->", { -// text : 'Save', -// cls : 'btn-with-border', -// style : { -// -// border : 1 -// }, -// handler : function() { -// _this.save(); -// } -// }, { -// text : 'Close', -// cls : 'btn-with-border', -// handler : function() { -// _this.onClose.notify(); -// } -// } ] -// }, { -// tabConfig : { -// id : this.id + "assembly", -// title : "Assembly", -// tooltip : 'Description of subunits present in the macromolecule', -// // hidden : (!macromolecule.macromoleculeId), -// disabled : (!macromolecule.macromoleculeId) -// }, -// items : [ this.getMolarityGrid(macromolecule) ] -// }, { -// tabConfig : { -// id : this.id + "advanced", -// title : "Advanced Modeling", -// // hidden : (!macromolecule.macromoleculeId), -// tooltip : 'Definition of the description contacts and symetries', -// disabled : (!macromolecule.macromoleculeId) -// }, -// items : [ this.getRigidBodyForm(macromolecule) ] -// } ] -// }); -//}; -// -//MacromoleculeForm.prototype.getRigidBodyForm = function(macromolecule) { -// var _this = this; -// -// // [P1, P2, P3, P4 ,P5 ,P6 ,32, P42, P52, P62] + P222 -// var symmetry = Ext.create('Ext.data.Store', { -// fields : [ 's' ], -// data : [ { -// "s" : "P1" -// }, { -// "s" : "P2" -// }, { -// "s" : "P3" -// }, { -// "s" : "P4" -// }, { -// "s" : "P5" -// }, { -// "s" : "P6" -// }, { -// "s" : "P32" -// }, { -// "s" : "P42" -// }, { -// "s" : "P52" -// }, { -// "s" : "P62" -// }, { -// "s" : "P222" -// } ] -// }); -// -// if (macromolecule.symmetry == null) { -// macromolecule.symmetry = "P1"; -// } -// var comboBox = Ext.create('Ext.form.ComboBox', { -// fieldLabel : 'Symmetry', -// store : symmetry, -// id : 'comboSym', -// queryMode : 'local', -// displayField : 's', -// valueField : 's', -// value : macromolecule.symmetry, -// margin : "10 0 0 0", -// listeners : { -// change : function(combo, newValue, oldValue, eOpts) { -// macromolecule.symmetry = newValue; -// } -// } -// }); -// -// this.rigidBodyPanel = Ext.createWidget('form', { -// frame : false, -// border : 0, -// padding : 10, -// width : 550, -// height : 400, -// items : [ { -// xtype : 'container', -// layout : 'hbox', -// items : [ { -// xtype : 'container', -// border : false, -// layout : 'hbox', -// items : [ { -// xtype : 'label', -// forId : 'myFieldId', -// text : 'Contact Desc:', -// width : 105, -// margin : '0 0 0 0' -// }, { -// xtype : 'textfield', -// hideLabel : true, -// id : "contactsDescriptionFilePath", -// margin : '0 0 0 0', -// width : 300, -// value : macromolecule.contactsDescriptionFilePath -// }, { -// text : 'Upload', -// xtype : 'button', -// margin : "0 0 0 20", -// width : 100, -// handler : function() { -// _this._openUploadDialog(macromolecule.macromoleculeId, "CONTACTS", "Upload Contact Description File"); -// } -// } ] -// } ] -// }, -// -// comboBox, { -// xtype : 'checkbox', -// margin : '10 0 0 5', -// boxLabel : "I want rigid body modeling run on this stuff", -// checked : true, -// width : 300 -// }, _this.getPDBGrid(macromolecule) ] -// }); -// return this.rigidBodyPanel; -//}; -// -//MacromoleculeForm.prototype.update = function() { -// var _this = this; -// BIOSAXS.proposal.onInitialized.attach(function() { -// if (BIOSAXS.proposal != null) { -// var macromolecules = BIOSAXS.proposal.macromolecules; -// for (var i = 0; i < macromolecules.length; i++) { -// if (macromolecules[i].macromoleculeId == _this.macromolecule.macromoleculeId) { -// _this.macromolecule = macromolecules[i]; -// _this.setMacromolecule(_this.macromolecule); -// _this.molarityStore.loadData(_this.parseMolarityData(_this.macromolecule)); -// _this.pdbGrid.setLoading(false); -// Ext.getCmp("contactsDescriptionFilePath").setValue(_this.macromolecule.contactsDescriptionFilePath) -// _this.molarityGrid.setLoading(false); -// -// } -// } -// } -// }); -// this.molarityGrid.setLoading("Updating"); -// this.pdbGrid.setLoading("Updating"); -// BIOSAXS.proposal.init(); -//}; -// -///******************************************************************************* -// * MOLARITY GRID -// ******************************************************************************/ -// -//MacromoleculeForm.prototype.parseMolarityData = function(macromolecule) { -// var data = []; -// if (macromolecule.stoichiometry != null) { -// for (var i = 0; i < macromolecule.stoichiometry.length; i++) { -// data.push({ -// ratio : macromolecule.stoichiometry[i].ratio, -// acronym : macromolecule.stoichiometry[i].macromolecule3VO.acronym, -// comments : macromolecule.stoichiometry[i].macromolecule3VO.comments, -// stoichiometryId : macromolecule.stoichiometry[i].stoichiometryId, -// name : macromolecule.stoichiometry[i].macromolecule3VO.name -// }); -// } -// } -// return data; -//}; -// -//MacromoleculeForm.prototype.getMolarityGrid = function(macromolecule) { -// var _this = this; -// -// this.molarityStore = Ext.create('Ext.data.Store', { -// fields : [ 'acronym', 'ratio', 'comments', 'stoichiometryId', 'name' ], -// data : this.parseMolarityData(macromolecule), -// sorters : { -// property : 'ratio', -// direction : 'DESC' -// } -// }); -// -// this.molarityGrid = Ext.create('Ext.grid.Panel', { -// store : this.molarityStore, -// height : 350, -// padding : 5, -// columns : [ -// -// { -// text : 'Subunit', -// columns : [ { -// text : "Acronym", -// width : 100, -// hidden : false, -// dataIndex : 'acronym', -// sortable : true -// }, { -// text : "Name", -// width : 100, -// hidden : false, -// dataIndex : 'name', -// sortable : true -// }, { -// text : "Comments", -// width : 100, -// dataIndex : 'comments', -// sortable : true -// } ] -// }, { -// text : "Number
in assymmetric units", -// width : 150, -// dataIndex : 'ratio', -// tooltip : 'Number of times this subunit is present in the macromolecule', -// sortable : true -// }, { -// id : this.id + 'MOLARITY_REMOVE', -// flex : 0.1, -// sortable : false, -// renderer : function(value, metaData, record, rowIndex, colIndex, store) { -// return BUI.getRedButton('REMOVE'); -// } -// } ], -// listeners : { -// cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { -// if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'MOLARITY_REMOVE') { -// var dataAdapter = new BiosaxsDataAdapter(); -// dataAdapter.onSuccess.attach(function() { -// _this.molarityGrid.setLoading(false); -// _this.update(); -// }); -// dataAdapter.removeStoichiometry(record.data.stoichiometryId); -// _this.molarityGrid.setLoading("Removing Structure"); -// } -// } -// }, -// buttons : [ { -// text : 'Add molarity', -// handler : function() { -// -// function onClose() { -// w.destroy(); -// _this.update(); -// } -// var w = Ext.create('Ext.window.Window', { -// title : 'Molarity', -// height : 300, -// width : 500, -// modal : true, -// buttons : [ { -// text : 'Save', -// handler : function() { -// var macromoleculeId = (_this.macromoleculeCombo.getValue()); -// var ratio = Ext.getCmp(_this.id + "ratio").getValue(); -// var comments = ""; -// var dataAdapter = new BiosaxsDataAdapter(); -// dataAdapter.onSuccess.attach(function(sender, args) { -// _this.update(); -// w.destroy(); -// }); -// dataAdapter.saveStoichiometry(_this.macromolecule.macromoleculeId, macromoleculeId, ratio, comments); -// } -// }, { -// text : 'Cancel', -// handler : function() { -// onClose(); -// } -// } ], -// items : [ _this.getMolarityForm(macromolecule) ], -// listeners : { -// onEsc : function() { -// onClose(); -// }, -// close : function() { -// onClose(); -// } -// } -// }).show(); -// } -// } ] -// }); -// return this.molarityGrid; -//}; -// -///******************************************************************************* -// * PDB GRID -// ******************************************************************************/ -// -//MacromoleculeForm.prototype._openUploadDialog = function(macromoleculeId, type, title) { -// var _this = this; -// function onClose() { -// w.destroy(); -// _this.update(); -// } -// -// var w = Ext.create('Ext.window.Window', { -// title : title, -// height : 200, -// width : 400, -// modal : true, -// buttons : [ { -// text : 'Close', -// handler : function() { -// onClose(); -// } -// } ], -// layout : 'fit', -// items : { -// html : "" -// }, -// listeners : { -// onEsc : function() { -// onClose(); -// }, -// close : function() { -// onClose(); -// } -// } -// }).show(); -//}; -// -//MacromoleculeForm.prototype._getPlugins = function() { -// var _this = this; -// var plugins = []; -// // if (this.updateRowEnabled) { -// plugins.push(Ext.create('Ext.grid.plugin.RowEditing', { -// clicksToEdit : 1, -// listeners : { -// validateedit : function(grid, e) { -// /** Comments are always updatable* */ -// e.record.raw.symmetry = e.newValues.symmetry; -// e.record.raw.multiplicity = e.newValues.multiplicity; -// -// var adapter = new BiosaxsDataAdapter(); -// adapter.onSuccess.attach(function(sender, measurement) { -// // _this.grid.setLoading(false); -// }); -// adapter.onError.attach(function() { -// alert("Error"); -// // _this.grid.setLoading(false); -// }); -// -// // _this.grid.setLoading(); -// adapter.saveStructure(e.record.raw); -// } -// } -// })); -// // } -// return plugins; -//}; -// -//MacromoleculeForm.prototype.getPDBGrid = function(macromolecule) { -// var _this = this; -// -// var data = macromolecule.structure3VOs; -// -// // /** Getting PDB from subunits **/ -// // if (macromolecule != null){ -// // if (macromolecule.stoichiometry != null){ -// // for (var i =0; i < macromolecule.stoichiometry.length; i++){ -// // var stoichiometry = macromolecule.stoichiometry[i]; -// // if (stoichiometry.macromolecule3VO != null){ -// // if (stoichiometry.macromolecule3VO.structure3VOs != null){ -// // for (var j = 0; j < stoichiometry.macromolecule3VO.structure3VOs.length; -// // j++) { -// // var structure = stoichiometry.macromolecule3VO.structure3VOs[j]; -// // structure["isSubunit"] = stoichiometry.macromolecule3VO.acronym; -// // data.push(structure) -// // } -// // } -// // } -// // } -// // } -// // } -// -// this.pdbStore = Ext.create('Ext.data.Store', { -// fields : [ 'filePath', 'structureId', 'structureType', 'symmetry', 'structureId', 'name', 'multiplicity' ], -// data : macromolecule.structure3VOs, -// groupField : 'structureType', -// sorters : { -// property : 'structureId', -// direction : 'DESC' -// } -// }); -// -// var groupingFeature = Ext.create('Ext.grid.feature.Grouping', { -// groupHeaderTpl : Ext.create('Ext.XTemplate', -// "
{name:this.formatName}
", { -// formatName : function(name) { -// return name; -// } -// }), -// hideGroupedHeader : true, -// startCollapsed : false -// }); -// -// this.pdbGrid = Ext.create('Ext.grid.Panel', { -// margin : "15 0 0 5", -// height : 250, -// store : this.pdbStore, -// plugins : _this._getPlugins(), -// buttons : [ { -// // text : 'Add PDB file', -// text : 'Add Modeling Option', -// handler : function() { -// _this._openUploadDialog(macromolecule.macromoleculeId, "PDB", 'Upload PDB File'); -// } -// } -// -// ], -// columns : [ -// { -// text : "structureId", -// flex : 0.2, -// hidden : true, -// dataIndex : 'structureId', -// sortable : true -// }, -// { -// text : "File", -// flex : 0.5, -// dataIndex : 'filePath', -// sortable : true, -// hidden : true -// }, -// { -// text : "PDB", -// flex : 0.4, -// dataIndex : 'name', -// sortable : true -// }, -// { -// text : "Symmetry", -// flex : 0.4, -// dataIndex : 'symmetry', -// sortable : true, -// editor : { -// xtype : 'combobox', -// typeAhead : true, -// triggerAction : 'all', -// selectOnTab : true, -// store : [ [ "P1", "P1" ], [ "P2", "P2" ], [ "P3", "P3" ], [ "P4", "P4" ], [ "P5", "P5" ], [ "P6", "P6" ], [ "P32", "P32" ], [ "P42", "P42" ], -// [ "P52", "P52" ], [ "P62", "P62" ], [ "P222", "P222" ] ], -// } -// }, { -// text : "Multiplicity", -// flex : 0.4, -// dataIndex : 'multiplicity', -// sortable : true, -// editor : { -// xtype : 'textfield' -// } -// -// }, { -// text : "Subunit", -// flex : 0.2, -// dataIndex : 'isSubunit', -// sortable : true, -// hidden : true -// }, { -// text : "Type", -// flex : 0.2, -// dataIndex : 'structureType', -// sortable : true, -// hidden : true -// }, -// -// { -// id : this.id + 'REMOVE', -// flex : 0.2, -// hidden : true, -// sortable : false, -// renderer : function(value, metaData, record, rowIndex, colIndex, store) { -// return BUI.getRedButton('REMOVE'); -// } -// }, ], -// -// listeners : { -// itemdblclick : function(dataview, record, item, e) { -// _this._editExperiment(record.raw.experimentId); -// }, -// cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { -// -// if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'REMOVE') { -// var dataAdapter = new BiosaxsDataAdapter(); -// dataAdapter.onSuccess.attach(function() { -// _this.pdbGrid.setLoading(false); -// _this.update(); -// }); -// dataAdapter.removeStructure(record.data.structureId); -// _this.pdbGrid.setLoading("Removing PDB file"); -// } -// -// } -// }, -// viewConfig : { -// getRowClass : function(record, rowIdx, params, store) { -// if (record.raw.isSubunit != null) { -// return "blue-row"; -// } -// } -// } -// }); -// -// return this.pdbGrid; -//}; -// -//MacromoleculeForm.prototype.getMolarityForm = function(macromolecule) { -// var _this = this; -// var data = []; -// for (var i = 0; i < BIOSAXS.proposal.macromolecules.length; i++) { -// var m = BIOSAXS.proposal.macromolecules[i]; -// if (m.macromoleculeId != macromolecule.macromoleculeId) { -// data.push(m); -// } -// -// } -// this.macromoleculeCombo = BIOSAXS_COMBOMANAGER.getComboMacromoleculeByMacromolecules(data, { -// width : 250, -// labelWidth : 100, -// margin : 10 -// }); -// -// return Ext.createWidget('form', { -// -// frame : false, -// border : 0, -// // padding : 15, -// width : 550, -// height : 350, -// items : [ { -// xtype : 'container', -// flex : 1, -// border : false, -// layout : 'anchor', -// defaultType : 'requiredtext', -// items : [ this.macromoleculeCombo, { -// xtype : 'numberfield', -// name : 'Ratio', -// id : _this.id + "ratio", -// fieldLabel : 'Number in assymmetric units', -// value : 1, -// decimalPrecision : 6, -// margin : 10 -// }, { -// xtype : 'textareafield', -// name : 'comments', -// fieldLabel : 'Comments', -// margin : 10, -// width : 400, -// value : "" -// -// } ] -// } ] -// }); -// -//}; -// -///******************************************************************************* -// * JAVASCRIPT DOC -// ******************************************************************************/ -//MacromoleculeForm.prototype.input = function() { -// return { -// macromolecule : DATADOC.getMacromolecule_10() -// }; -//}; -// -//MacromoleculeForm.prototype.test = function(targetId) { -// var macromoleculeForm = new MacromoleculeForm(); -// var panel = macromoleculeForm.getPanel(macromoleculeForm.input().macromolecule); -// panel.render(targetId); -//}; - -function ResultSummaryForm() { - this.radiationDamageThreshold = BUI.getRadiationDamageThreshold(); - this.qualityThreshold = BUI.getQualityThreshold(); - - /** Data clusters with bufers **/ - this.clusterByBuffers = false; - - /** Visualization are groupeb by concenttrations. Ex: 4.5mg/ml and 4.7mg/ml will be clusterized together **/ - this.collapseConcentrations = true; - - this.summaryHeight = 350; - this.id = BUI.id(); - - var _this = this; - - this.qualityControlResultsWidget = new QualityControlResultsWidget({ - qualityThreshold : this.radiationDamageThreshold, - radiationDamageThreshold : this.qualityThreshold - - }); - this.qualityControlResultsWidget.onQualityChanged.attach(function(sender, value) { - _this.qualityThreshold = value; - _this.thresholdsChanged(); - }); - - this.qualityControlResultsWidget.onRadiationDatamageChanged.attach(function(sender, value) { - _this.radiationDamageThreshold = value; - _this.thresholdsChanged(); - - }); - this.concentrationHTMLTableWidget = new ConcentrationHTMLTableWidget({ - height : 250, - showBufferColumns : this.clusterByBuffers - }); - - this.plot = new BoxWhiskerGraph({ - targetId : _this.id + '_boxPlot', - height : 350, - width : 450, - maxBoxWidth : 25 - }); - - this.rangePlot = new RangeWhiskerGraph({ - targetId : _this.id + '_rangePlot', - height : 350, - width : 450, - maxBoxWidth : 25 - }); -} - -ResultSummaryForm.prototype.thresholdsChanged = function() { - var parsedData = this.prepareData(this.rawData); - - var filtered = JSON.parse(JSON.stringify(parsedData)); - filtered.concentration.concentrations = []; - for ( var conc in parsedData.concentration.concentrations) { - if (parsedData.concentration.concentrations[conc].calculation.rgGnom.validNumber > 0) { - filtered.concentration.concentrations.push(parsedData.concentration.concentrations[conc]); - } - } - - this.plotWhisker(filtered); - this.plotRange(filtered); - - this.concentrationHTMLTableWidget.refresh(parsedData); -}; - -/** Given a frame object (object returned by analyzeFrames()) and depending of the threshold indicates if a datacollection has radiation damage **/ -ResultSummaryForm.prototype.hasRadiationDamage = function(frameObject) { - var bb = frameObject.bufferBeforeFramesMerged / frameObject.framesCount; - var ba = frameObject.bufferAfterFramesMerged / frameObject.framesCount; - var mol = frameObject.framesMerge / frameObject.framesCount; - return !((bb >= this.radiationDamageThreshold) && (ba >= this.radiationDamageThreshold) && (mol >= this.radiationDamageThreshold)); -}; - -/** Return (frameObject) an object with the information about the frames for a data collection**/ -ResultSummaryForm.prototype.analyzeFrames = function(dataCollectionRow) { - return { - bufferAfterFramesMerged : dataCollectionRow.bufferAfterFramesMerged, - bufferBeforeFramesMerged : dataCollectionRow.bufferBeforeFramesMerged, - framesCount : dataCollectionRow.framesCount, - framesMerge : dataCollectionRow.framesMerge - }; -}; - -ResultSummaryForm.prototype.detectDataCollectionWarnings = function(dataCollectionRow) { - var frameObject = this.analyzeFrames(dataCollectionRow); - var warnings = { - count : 0, - type : [] - }; - - if (this.hasRadiationDamage(frameObject)) { - warnings.count = warnings.count + 1; - warnings.type.push("RADIATION DAMAGE"); - } - - if (Number(dataCollectionRow.quality) < this.qualityThreshold) { - warnings.count = 1;//warnings.count + 1; - warnings.type.push("Quality <" + this.qualityThreshold); - } - return warnings; -}; - -/** Return array composed by {concentration} objects **/ -ResultSummaryForm.prototype.getConcentrations = function(data) { - var concentrationsId = {}; - - for ( var i = 0; i < data.length; i++) { - var warning = this.detectDataCollectionWarnings(data[i]); - var id = data[i].conc;// + "_" + data[i].bufferId; - if (this.clusterByBuffers) { - id = data[i].conc + "_" + data[i].bufferId; - } - - if (concentrationsId[id] == null) { - concentrationsId[id] = { - id : id, - concentration : Number(data[i].conc).toFixed(2), - bufferId : data[i].bufferId, - bufferAcronym : data[i].bufferAcronym, - rgGuinier : [], - i0Guinier : [], - rgGnom : [], - dMax : [], - quality : [], - frames : [], - frames_warning : warning.count - }; - } else { - concentrationsId[id].frames_warning = concentrationsId[id].frames_warning + warning.count; - } - - concentrationsId[id].frames.push(data[i]); - - if (warning.count == 0) { - concentrationsId[id].rgGuinier.push(data[i].rgGuinier); - concentrationsId[id].i0Guinier.push(data[i].I0); - concentrationsId[id].quality.push(data[i].quality); - concentrationsId[id].rgGnom.push(data[i].rgGnom); - concentrationsId[id].dMax.push(data[i].dmax); - } - - } - var concentrations = []; - for ( var item in concentrationsId) { - if (concentrationsId.hasOwnProperty(item)) { - concentrations.push({ - concentration : concentrationsId[item].concentration, - id : item, - bufferId : Number(concentrationsId[item].bufferId).toFixed(2), - bufferAcronym : concentrationsId[item].bufferAcronym, - rgGuinier : concentrationsId[item].rgGuinier, - /** Frames **/ - frames : concentrationsId[item].frames, - frames_warning : concentrationsId[item].frames_warning, - /** Calculation **/ - calculation : { - rgGuinier : BUI.getStandardDeviation(concentrationsId[item].rgGuinier), - i0Guinier : BUI.getStandardDeviation(concentrationsId[item].i0Guinier), - quality : BUI.getStandardDeviation(concentrationsId[item].quality), - rgGnom : BUI.getStandardDeviation(concentrationsId[item].rgGnom), - dMax : BUI.getStandardDeviation(concentrationsId[item].dMax) - - } - }); - } - } - - return { - concentrations : concentrations - }; -}; - -ResultSummaryForm.prototype.prepareData = function(data) { - /** Return array composed by {acronym, bufferId} objects **/ - function getBuffers(data) { - var buffersId = {}; - for ( var i = 0; i < data.length; i++) { - buffersId[data[i].bufferId] = data[i].acronym; - } - var buffers = []; - for ( var id in buffersId) { - if (buffersId.hasOwnProperty(id)) { - buffers.push({ - acronym : buffersId[id], - bufferId : id - }); - } - } - return buffers; - } - - /** Get a string with all the concentrations **/ - function getConcentrationString(parseConcentrations) { - var concentrations = []; - for ( var i = 0; i < parseConcentrations.concentrations.length; i++) { - concentrations.push(parseConcentrations.concentrations[i].concentration + " mg/ml "); - } - return concentrations.toString(); - } - - var parseConcentrations = this.getConcentrations(data); - - return { - dataCollectionCount : data.length, - buffers : getBuffers(data), - concentration : parseConcentrations, - concentrationLabel : getConcentrationString(parseConcentrations) - }; -}; - -ResultSummaryForm.prototype.getDataForWhisker = function(data) { - var clusters = []; - - var concentrations = {}; - var i = 0; - var conc = 0; - if (this.collapseConcentrations) { - for (i = 0; i < data.concentration.concentrations.length; i++) { - conc = data.concentration.concentrations[i]; - var concentration = Number(conc.concentration).toFixed(0); - if (concentrations[concentration] == null) { - concentrations[concentration] = {}; - concentrations[concentration].concentration = concentration; - concentrations[concentration].calculation = {}; - concentrations[concentration].calculation.rgGuinier = {}; - concentrations[concentration].calculation.rgGuinier.values = []; - concentrations[concentration].calculation.rgGuinier.values = conc.calculation.rgGuinier.values; - concentrations[concentration].calculation.rgGnom = {}; - concentrations[concentration].calculation.rgGnom.values = []; - concentrations[concentration].calculation.rgGnom.values = conc.calculation.rgGnom.values; - } else { - concentrations[concentration].calculation.rgGuinier.values = concentrations[concentration].calculation.rgGuinier.values - .concat(conc.calculation.rgGuinier.values); - concentrations[concentration].calculation.rgGnom.values = concentrations[concentration].calculation.rgGnom.values - .concat(conc.calculation.rgGnom.values); - } - } - - /** From object to array **/ - var array = []; - for ( var key in concentrations) { - if (concentrations.hasOwnProperty(key)) { - array.push(concentrations[key]); - } - } - data.concentration.concentrations = array; - } - - for (i = 0; i < data.concentration.concentrations.length; i++) { - conc = data.concentration.concentrations[i]; - clusters.push({ - name : conc.concentration + "mg/ml", - concentration : Number(conc.concentration), - x : Number(conc.concentration), - classes : [] - }); - clusters[clusters.length - 1].classes.push({ - name : "Guinier", - color : '#9A2EFE', - values : conc.calculation.rgGuinier.values - - }); - clusters[clusters.length - 1].classes.push({ - name : "P(r)", - color : '#2E64FE', - values : conc.calculation.rgGnom.values - - }); - } - return { - clusters : clusters.sort(function(a, b) { - return a.concentration - b.concentration; - }) - }; -}; - -ResultSummaryForm.prototype.getDataForWhiskerQuality = function(data) { - var clusters = []; - - for ( var i = 0; i < data.concentration.concentrations.length; i++) { - var conc = data.concentration.concentrations[i]; - clusters.push({ - name : conc.concentration + "mg/ml", - classes : [] - }); - clusters[clusters.length - 1].classes.push({ - name : "Quality", - values : conc.calculation.quality.values - - }); - } - - return { - clusters : clusters - }; -}; - -ResultSummaryForm.prototype.plotQualityWhisker = function(parsedData) { - this.qualityPlot.refresh(this.getDataForWhiskerQuality(parsedData)); -}; - -ResultSummaryForm.prototype.plotWhisker = function(parsedData) { - this.plot.refresh(this.getDataForWhisker(parsedData)); -}; - -ResultSummaryForm.prototype.plotRange = function(parsedData) { - this.rangePlot.refresh(this.getDataForWhisker(parsedData)); -}; - -ResultSummaryForm.prototype.getPanel = function(data) { - var _this = this; - _this.rawData = data; - var parsedData = this.prepareData(data); - - this.panel = Ext - .createWidget( - 'form', - { - bodyPadding : 20, - frame : false, - border : 0, - width : this.width, - height : this.summaryHeight + 1000, - items : [ { - xtype : 'container', - layout : 'hbox', - items : [ { - xtype : 'container', - flex : 1, - border : false, - layout : 'anchor', - defaultType : 'textfield', - items : [ - _this.qualityControlResultsWidget.getPanel(), - { - xtype : 'fieldset', - width : 950, - margin : "20, 0 0 0", - height : this.summaryHeight + 500, - items : [ - { - html : "
Concentration Analysis
", - border : 0, - width : 900 - - }, - { - html : this.concentrationHTMLTableWidget.getPanel(parsedData), - border : 0, - width : 900, - margin : "10, 0 0 10" - - }, - { - xtype : 'container', - layout : 'vbox', - border : 5, - items : [ - { - html : "
Rg based on Guinier and Gnom
", - border : 8, - width : 900, - margin : "20 0 0 10" - - }, { - xtype : 'container', - layout : 'hbox', - items : [ { - xtype : 'container', - layout : 'vbox', - items : [ { - html : "
", - border : 0, - width : this.plot.width, - padding : "10 0 0 20", - listeners : { - afterrender : function() { - _this.plotWhisker(parsedData); - - } - } - }, { - html : "
Concentration (mg/ml)
", - width : 450, - border : 0, - margin : "-50 0 0 0" - - } ] - }, { - xtype : 'container', - layout : 'vbox', - items : [ { - html : "
", - border : 0, - width : this.rangePlot.width, - padding : "10 0 0 10", - listeners : { - afterrender : function() { - _this.plotRange(parsedData); - } - } - }, { - html : "
Concentration (mg/ml)
", - width : 450, - border : 0, - margin : "-50 0 0 0" - - } ] - } ] - } ] - } ] - } ] - } - - ] - } ] - }); - return this.panel; - -}; - -ResultSummaryForm.prototype.input = function() { - return { - data : DATADOC.getData_3367() - }; -}; - -ResultSummaryForm.prototype.test = function(targetId) { - var resultSummaryForm = new ResultSummaryForm(); - var panel = resultSummaryForm.getPanel(resultSummaryForm.input().data); - panel.render(targetId); - -}; - -/** - * Example form - * - * @witdh - * @height - */ -function RigibBodyModelingForm(args) { - this.id = BUI.id(); - this.width = 700; - this.height = 500; - - if (args != null) { - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; - } - } - - var _this = this; - this.rigidBodyGrid = new AprioriRigidBodyGrid(); - - this.rigidBodyGrid.onUploadFile.attach(function(sender, type, title){ - _this._openUploadDialog(_this.macromolecule.macromoleculeId, type, title); - }); - - this.rigidBodyGrid.onRemove.attach(function(sender, type, title){ - _this._update(); - }); - - this.onSave = new Event(this); - -} - -RigibBodyModelingForm.prototype._getItems = function() { - var _this = this; - - - return [ { - xtype : 'label', - forId : 'myFieldId', - text : 'Information for model fit, mixture analysis and rigid body modeling', - margin : '15 0 20 10', - cls : "inline-help" - }, - this.rigidBodyGrid.getPanel(), - { - xtype : 'label', - forId : 'myFieldId', - text : 'Distance restraints may be imposed on the model using contacts conditions file (OPTIONAL)', - margin : '25 0 5 10', - cls : "inline-help" - }, - { - xtype : 'container', - layout : 'hbox', - items : [ { - xtype : 'container', - border : false, - layout : 'hbox', - items : [ { - xtype : 'label', - forId : 'myFieldId', - text : 'Contact Description File: (Optional)', - width : 150, - margin : '10 0 0 10' - }, { - id : this.id + "contactsDescriptionFilePath", - xtype : 'textfield', - hideLabel : true, - margin : '10 0 0 0', - width : 200, - disabled: true - }, { - text : 'Upload', - xtype : 'button', - margin : "10 0 0 10", - width : 80, - handler : function() { - - _this._openUploadDialog(_this.macromolecule.macromoleculeId, "CONTACTS", "Upload Contact Description File"); - } - }, { - text : 'Remove', - id : _this.id + "_remove", - xtype : 'button', - margin : "10 0 0 10", - width : 80, - handler : function() { - _this.macromolecule.contactsDescriptionFilePath = null; - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, proposal) { - /** Updating the proposal global object **/ - BIOSAXS.proposal.setItems(proposal); - _this.panel.setLoading(false); - - var saved = BIOSAXS.proposal.getMacromoleculeByAcronym(_this.macromolecule.acronym); - /** Refreshing to check that everything is ok **/ - _this.refresh(saved); - _this.onSave.notify(saved); - }); - - _this.panel.setLoading("Saving Macromolecule") - adapter.saveMacromolecule(_this.macromolecule); - } - } ] - } ] - }, { - xtype : 'panel', - html : "Go to SASREF manual for further information", - margin : "10 0 0 160", - border : 0 - - }, - { - xtype : 'checkbox', - margin : '10 0 0 5', - boxLabel : "I want rigid body modeling run on this stuff", - checked : true, - width : 300 - } ] - -}; - -/** Because update is a jsp page we don't know if the user has uploaded a file or not then we need to refresh **/ -RigibBodyModelingForm.prototype._update = function(macromoleculeId, type, title) { - var _this = this; - BIOSAXS.proposal.onInitialized.attach(function() { - if (BIOSAXS.proposal != null) { - _this.refresh(BIOSAXS.proposal.getMacromoleculeById(_this.macromolecule.macromoleculeId)); - _this.panel.setLoading(false); - } - }); - this.panel.setLoading(); - BIOSAXS.proposal.init(); -}; - -RigibBodyModelingForm.prototype._openUploadDialog = function(macromoleculeId, type, title) { - var _this = this; - function onClose() { - w.destroy(); - _this._update(); - - } - - var w = Ext.create('Ext.window.Window', { - title : title, - height : 200, - width : 400, - modal : true, - buttons : [ { - text : 'Close', - handler : function() { - onClose(); - } - } ], - layout : 'fit', - items : { - html : "" - }, - listeners : { - onEsc : function() { - onClose(); - }, - close : function() { - onClose(); - } - } - }).show(); -}; - -RigibBodyModelingForm.prototype._getButtons = function() { - return []; -}; - -RigibBodyModelingForm.prototype.getPanel = function() { - var _this = this; - this.panel = Ext.create('Ext.form.Panel', { - width : this.width, - height : this.height, - margin : 10, - border : 1, - defaultType : 'textfield', - items : this._getItems(), - buttons : this._getButtons(), - listeners : { - afterrender : function(){ - _this._populate(); - - } - } - }); - return this.panel; -}; - -/** Populates could be call when the DOM is not filled yet **/ -RigibBodyModelingForm.prototype._populate = function() { - if (this.macromolecule != null){ - if (Ext.getCmp(this.id + "contactsDescriptionFilePath") != null){ - if (this.macromolecule.contactsDescriptionFilePath != null){ - Ext.getCmp(this.id + "contactsDescriptionFilePath").setValue(this.macromolecule.contactsDescriptionFilePath); - Ext.getCmp(this.id + "_remove").enable(); - } - else{ - Ext.getCmp(this.id + "_remove").disable(); - Ext.getCmp(this.id + "contactsDescriptionFilePath").setValue(""); - - } - } - } -}; - -/** It populates the form * */ -RigibBodyModelingForm.prototype.refresh = function(macromolecule) { - this.macromolecule = macromolecule; - this.rigidBodyGrid.refresh(macromolecule); - this._populate(); -}; - -RigibBodyModelingForm.prototype.input = function() { - return {}; -}; - - -/** It populates the form **/ -RigibBodyModelingForm.prototype.test = function(targetId) { - var macromoleculeForm = new RigibBodyModelingForm(); - var panel = macromoleculeForm.getPanel(); - panel.render(targetId); -}; - - -/** - * Same form as MX part - * - * @creationMode if true a create button appears instead of save - * @showTitle true or false - */ -function ShipmentForm(args) { - this.id = BUI.id(); - - this.creationMode = false; - this.showTitle = true; - if (args != null) { - if (args.creationMode != null) { - this.creationMode = args.creationMode; - } - if (args.showTitle != null) { - this.showTitle = args.showTitle; - } - } - - this.onSaved = new Event(this); -} - -ShipmentForm.prototype.fillStores = function() { - this.panel.setLoading("Loading Labcontacts from database"); - this.labContactForSendingStore.loadData(BIOSAXS.proposal.getLabcontacts(), false); - this.labContactForReturnStore.loadData(BIOSAXS.proposal.getLabcontacts(), false); - this.panel.setLoading(false); - if (this.shipment != null) { - this.setShipment(this.shipment); - } -}; - -ShipmentForm.prototype.draw = function(targetId) { - this.getPanel().render(targetId); -}; - -ShipmentForm.prototype.setShipment = function(shipment) { - this.shipment = shipment; - var _this = this; - Ext.getCmp(_this.id + "shippingName").setValue(shipment.json.shippingName); - Ext.getCmp(_this.id + "shippingStatus").setValue(shipment.json.shippingStatus); - Ext.getCmp(_this.id + "comments").setValue(shipment.json.comments); - if (shipment.json.sendingLabContactVO != null) { - this.labContactsSendingCombo.setValue(shipment.json.sendingLabContactVO.labContactId); - } - if (shipment.json.returnLabContactVO != null) { - this.labContactsReturnCombo.setValue(shipment.json.returnLabContactVO.labContactId); - } - -}; - -ShipmentForm.prototype._saveShipment = function() { - var _this = this; - var shippingId = null; - if (this.shipment != null) { - shippingId = this.shipment.json.shippingId; - } - var json = { - shippingId : shippingId, - name : Ext.getCmp(_this.id + "shippingName").getValue(), - status : Ext.getCmp(_this.id + "shippingStatus").getValue(), - sendingLabContactId : Ext.getCmp(_this.id + "shipmentform_sendingLabContactId").getValue(), - returnLabContactId : Ext.getCmp(_this.id + "returnLabContactId").getValue(), - returnCourier : Ext.getCmp(_this.id + "returnCourier").getValue(), - courierAccount : Ext.getCmp(_this.id + "courierAccount").getValue(), - BillingReference : Ext.getCmp(_this.id + "BillingReference").getValue(), - dewarAvgCustomsValue : Ext.getCmp(_this.id + "dewarAvgCustomsValue").getValue(), - dewarAvgTransportValue : Ext.getCmp(_this.id + "dewarAvgTransportValue").getValue(), - comments : Ext.getCmp(_this.id + "comments").getValue() - }; - - var dataAdapter = new BiosaxsDataAdapter(); - dataAdapter.onSuccess.attach(function(sender, shipment) { - window.location = BUI.getShippingURL(shipment.shippingId); - }); - - dataAdapter.onError.attach(function(sender, error) { - _this.onError.notify(error); - }); - - /** Cheking params **/ - if (json.name == "") { - BUI.showError("Name field is mandatory"); - return; - } - - if (json.sendingLabContactId == null) { - BUI.showError("Lab contact for sending field is mandatory"); - return; - } - - if (json.returnLabContactId == null) { - BUI.showError("Lab contact for return field is mandatory"); - return; - } - - dataAdapter.createShipment(json.shippingId, json.name, json.status, json.comments, json.sendingLabContactId, json.returnLabContactId, - json.returnCourier, json.courierAccount, json.BillingReference, json.dewarAvgCustomsValue, json.dewarAvgTransportValue); - -}; - -ShipmentForm.prototype.getPanel = function(shipment) { - var _this = this; - this.shipment = shipment; - var required = '*'; - var buttons = []; - - if (_this.creationMode) { - buttons.push({ - text : 'Create', - scope : this, - handler : function() { - _this._saveShipment(); - } - }); - } else { - buttons.push({ - text : 'Save', - scope : this, - handler : function() { - _this._saveShipment(); - } - }); - - } - - this.labContactForSendingStore = Ext.create('Ext.data.Store', { - fields : [ 'cardName', 'labContactId' ] - }); - - this.labContactForReturnStore = Ext.create('Ext.data.Store', { - fields : [ 'cardName', 'labContactId' ] - }); - - // Create the combo box, attached to the states data store - this.labContactsSendingCombo = Ext.create('Ext.form.ComboBox', { - id : _this.id + "shipmentform_sendingLabContactId", - fieldLabel : 'Lab contact for sending', - afterLabelTextTpl : required, - store : this.labContactForSendingStore, - queryMode : 'local', - labelWidth : 200, - displayField : 'cardName', - valueField : 'labContactId' - }); - - this.labContactsReturnCombo = Ext.create('Ext.form.ComboBox', { - id : _this.id + "returnLabContactId", - fieldLabel : 'If No, Lab-Contact for Return', - afterLabelTextTpl : required, - store : this.labContactForReturnStore, - queryMode : 'local', - labelWidth : 200, - displayField : 'cardName', - valueField : 'labContactId', - listeners : { - change : function(x, newValue) { - for ( var i = 0; i < x.getStore().data.items.length; i++) { - if (x.getStore().data.items[i].raw.labContactId == newValue) { - Ext.getCmp(_this.id + "returnCourier").setValue(x.getStore().data.items[i].raw.defaultCourrierCompany); - Ext.getCmp(_this.id + "courierAccount").setValue(x.getStore().data.items[i].raw.courierAccount); - Ext.getCmp(_this.id + "BillingReference").setValue(x.getStore().data.items[i].raw.billingReference); - Ext.getCmp(_this.id + "dewarAvgCustomsValue").setValue(x.getStore().data.items[i].raw.dewarAvgCustomsValue); - Ext.getCmp(_this.id + "dewarAvgTransportValue").setValue(x.getStore().data.items[i].raw.dewarAvgTransportValue); - } - } - } - } - }); - - if (this.panel == null) { - this.panel = Ext.create('Ext.form.Panel', { - bodyPadding : 5, - width : 600, - border : 1, - items : [ { - xtype : 'fieldset', - title : 'Details', - collapsible : false, - defaultType : 'textfield', - layout : 'anchor', - defaults : { - anchor : '100%' - }, - items : [ { - xtype : 'requiredtext', - fieldLabel : 'Shipment Label', - allowBlank : false, - name : 'shippingName', - id : _this.id + 'shippingName', - value : '', - anchor : '50%' - }, { - - xtype : 'textareafield', - name : 'comments', - id : _this.id + 'comments', - fieldLabel : 'Comments', - value : '' - }, { - fieldLabel : 'Status', - readOnly : true, - id : _this.id + 'shippingStatus', - value : 'Opened', - anchor : '50%' - } ] - }, { - xtype : 'fieldset', - title : 'Lab-Contacts', - collapsible : false, - defaultType : 'textfield', - layout : 'anchor', - defaults : { - anchor : '100%' - }, - items : [ this.labContactsSendingCombo, this.labContactsReturnCombo ] - }, { - border : 0, - html : BUI.getWarningHTML("These informations are relevant for all shipments") - }, { - xtype : 'fieldset', - title : 'Courier accounts details for return', - collapsible : false, - layout : 'anchor', - defaults : { - anchor : '100%' - }, - items : [ { - xtype : 'textfield', - labelWidth : 400, - fieldLabel : 'Courier company for return (if ESRF sends a dewar back)', - id : _this.id + 'returnCourier', - value : '' - }, { - xtype : 'textfield', - labelWidth : 400, - fieldLabel : 'Courier account', - id : _this.id + 'courierAccount', - value : '' - }, { - xtype : 'textfield', - labelWidth : 400, - fieldLabel : 'Billing reference', - id : _this.id + 'BillingReference', - value : '' - }, { - xtype : 'numberfield', - labelWidth : 400, - fieldLabel : 'Average Customs value of a dewar (Euro)', - id : _this.id + 'dewarAvgCustomsValue', - value : '' - }, { - xtype : 'numberfield', - labelWidth : 400, - fieldLabel : 'Average Transport value of a dewar (Euro)', - id : _this.id + 'dewarAvgTransportValue', - value : '' - } ] - } ], - buttons : buttons - }); - } - this.fillStores(); - if (this.showTitle) { - this.panel.setTitle('Create a new Shipment'); - } - return this.panel; -}; - -ShipmentForm.prototype.input = function() { - return { - proposal : DATADOC.getProposal_10() - - }; -}; - -ShipmentForm.prototype.test = function(targetId) { - var shipmentForm = new ShipmentForm({ - creationMode : true - - }); - BIOSAXS.proposal = new Proposal(shipmentForm.input().proposal); - shipmentForm.getPanel().render(targetId); -}; - -/** - * #onSaved - */ -function StockSolutionForm(args) { - this.id = BUI.id(); - this.actions = []; - - if (args != null) { - if (args.actions != null) { - this.actions = args.actions; - } - } - this.onSaved = new Event(this); -} - -StockSolutionForm.prototype.getStockSolution = function() { - if (this.stockSolution != null) { - this.stockSolution.concentration = Ext.getCmp(this.id + "stockSolution_concentration").getValue(); - this.stockSolution.storageTemperature = Ext.getCmp(this.id + "stockSolution_storageTemperature").getValue(); - this.stockSolution.volume = Ext.getCmp(this.id + "stockSolution_volume").getValue(); - this.stockSolution.comments = Ext.getCmp(this.id + "stockSolution_comments").getValue(); - this.stockSolution.name = Ext.getCmp(this.id + "stockSolution_name").getValue(); - this.stockSolution.bufferId = this.bufferCombo.getValue(); - - if (this.macromoleculeCombo.getValue() != null) { - this.stockSolution.macromoleculeId = this.macromoleculeCombo.getValue(); - } else { - this.stockSolution.macromolecule3VO = null; - } - - } else { - return { - concentration : Ext.getCmp(this.id + "stockSolution_concentration").getValue(), - storageTemperature : Ext.getCmp(this.id + "stockSolution_storageTemperature").getValue(), - volume : Ext.getCmp(this.id + "stockSolution_volume").getValue(), - comments : Ext.getCmp(this.id + "stockSolution_comments").getValue(), - name : Ext.getCmp(this.id + "stockSolution_name").getValue(), - bufferId : this.bufferCombo.getValue(), - macromoleculeId : this.macromoleculeCombo.getValue() - }; - } - return this.stockSolution; -}; - -StockSolutionForm.prototype.setStockSolution = function(stockSolution) { - if (stockSolution != null) { - if (stockSolution.macromoleculeId != null) { - this.macromoleculeCombo.setValue(stockSolution.macromoleculeId); - } - this.bufferCombo.setValue(stockSolution.bufferId); - Ext.getCmp(this.id + "stockSolution_concentration").setValue(this.stockSolution.concentration); - Ext.getCmp(this.id + "stockSolution_storageTemperature").setValue(this.stockSolution.storageTemperature); - Ext.getCmp(this.id + "stockSolution_volume").setValue(this.stockSolution.volume); - Ext.getCmp(this.id + "stockSolution_name").setValue(this.stockSolution.name); - Ext.getCmp(this.id + "stockSolution_comments").setValue(this.stockSolution.comments); - } -}; - -StockSolutionForm.prototype.getBufferCombo = function() { - this.bufferCombo = BIOSAXS_COMBOMANAGER.getComboBuffers(BIOSAXS.proposal.getBuffers(), { - labelWidth : 120, - margin : '0 0 10 0', - width : 220 - - }); - return this.bufferCombo; -}; - -StockSolutionForm.prototype.getMacromoleculeCombo = function() { - this.macromoleculeCombo = BIOSAXS_COMBOMANAGER.getComboMacromoleculeByMacromolecules(BIOSAXS.proposal.getMacromolecules(), { - labelWidth : 120, - margin : '0 0 10 0', - width : 220 - - }); - return this.macromoleculeCombo; -}; - -StockSolutionForm.prototype.refresh = function() { -}; - -StockSolutionForm.prototype._getTopPanel = function() { - return { - xtype : 'container', - layout : 'hbox', - border : 0, - items : [ { - xtype : 'container', - layout : 'hbox', - items : [ { - xtype : 'container', - flex : 1, - border : false, - layout : 'anchor', - defaultType : 'textfield', - items : [ - - this.getMacromoleculeCombo(), { - xtype : 'requiredtext', - id : this.id + 'stockSolution_name', - fieldLabel : 'Acronym', - labelWidth : 120, - width : 250 - }, { - xtype : 'requiredtext', - id : this.id + 'stockSolution_concentration', - fieldLabel : 'Conc. (mg/ml)', - labelWidth : 120, - width : 250 - }, - - { - id : this.id + 'stockSolution_storageTemperature', - fieldLabel : 'Storage Temp.(C)', - labelWidth : 120, - width : 250 - }, { - xtype : 'requiredtext', - id : this.id + 'stockSolution_volume', - fieldLabel : 'Volume in Well (µl)', - labelWidth : 120, - width : 250 - } ] - } ] - }, { - xtype : 'container', - flex : 1, - layout : 'anchor', - defaultType : 'textfield', - margin : '0 0 0 10', - items : [ this.getBufferCombo() ] - } ] - }; - -}; - -StockSolutionForm.prototype.getPanel = function(stockSolution) { - this.stockSolution = stockSolution; - this.panel = Ext.createWidget({ - xtype : 'container', - layout : 'vbox', - border : 0, - style : { - padding : '10px' - }, - fieldDefaults : { - labelAlign : 'left', - labelWidth : 50 - }, - items : [ this._getTopPanel(stockSolution), { - id : this.id + 'stockSolution_comments', - xtype : 'textareafield', - name : 'comments', - fieldLabel : 'Comments', - labelWidth : 120, - width : '100%' - } ] - }); - - this.setStockSolution(stockSolution); - return this.panel; -}; - -StockSolutionForm.prototype.input = function() { - return { - stock : { - "stockSolutionId" : 6, - "proposalId" : 3124, - "macromoleculeId" : 5933, - "bufferId" : 811, - "instructionSet3VO" : null, - "boxId" : 305861, - "storageTemperature" : "20", - "volume" : "300", - "concentration" : "1.2", - "comments" : "Buffer EDTA with A", - "name" : "A_EDTA_1.2", - "samples" : [], - "buffer" : "EDTA", - "macromolecule" : "A" - }, - proposal : new MeasurementGrid().input().proposal - }; -}; - -StockSolutionForm.prototype.test = function(targetId) { - var stockSolutionForm = new StockSolutionForm(); - BIOSAXS.proposal = new Proposal(stockSolutionForm.input().proposal); - var panel = stockSolutionForm.getPanel(new Shipment(stockSolutionForm.input().stock)); - panel.render(targetId); -}; - - -BoxWhiskerGraph.prototype.cleanArray = GenericGraph.prototype.cleanArray; -BoxWhiskerGraph.prototype.plotAxes = GenericGraph.prototype.plotAxes; -BoxWhiskerGraph.prototype.plotRuler = GenericGraph.prototype.plotRuler; -BoxWhiskerGraph.prototype.drawSVGVerticalText = GenericGraph.prototype.drawSVGVerticalText; -BoxWhiskerGraph.prototype.getClassColor = GenericGraph.prototype.getClassColor; -BoxWhiskerGraph.prototype.getDimensions = GenericGraph.prototype.getDimensions; -BoxWhiskerGraph.prototype.calculate = GenericGraph.prototype.calculate; -BoxWhiskerGraph.prototype.getMedian = GenericGraph.prototype.getMedian; -BoxWhiskerGraph.prototype.pointToPixel = GenericGraph.prototype.pointToPixel; -BoxWhiskerGraph.prototype.maxValueWhisker = GenericGraph.prototype.maxValueWhisker; -BoxWhiskerGraph.prototype.refresh = GenericGraph.prototype.refresh; - -/** - * Subclass of GenericGraph - * - * @maxBoxWidth - */ -function BoxWhiskerGraph(args){ - this.maxBoxWidth = 25; - - if (args == null){ - args = new Object(); - } - args["plotHorizontalByCluster"] = true; - - GenericGraph.call(this, args); - - if (args.maxBoxWidth != null){ - this.maxBoxWidth = args.maxBoxWidth; - } -}; - - - -/** -There are several different methods for calculating quartiles.[1] This calculator uses a method described by Moore and McCabe to find quartile values. -The same method also used by The TI-83 to calculate quartile values. -With this method, the first quartile is the median of the numbers below the median, the third quartile is the median of the numbers above the median. - -http://www.miniwebtool.com/quartile-calculator/ -http://www.alcula.com/calculators/statistics/box-plot/ -**/ -BoxWhiskerGraph.prototype.getQ1 = function(array){ - array = array.slice(0, array.length/2); - return this.getMedian(array); -}; - -BoxWhiskerGraph.prototype.getQ3 = function(array){ - array = array.slice((array.length + 1)/2); - return this.getMedian(array); - -}; - -BoxWhiskerGraph.prototype.getQ2 = function(array){ - return this.getMedian(array); -}; - -BoxWhiskerGraph.prototype.getBelowOutliers = function(belowLimit, array){ - var points = new Array(); - for (var i = 0; i < array.length; i++){ - if (array[i] <= belowLimit){ - points.push(array[i]); - } - } - return points; -}; - -BoxWhiskerGraph.prototype.getAboveOutliers = function(aboveLimit, array){ - var points = new Array(); - for (var i = 0; i < array.length; i++){ - if (array[i] >= aboveLimit){ - points.push(array[i]); - } - } - return points; -}; - - -BoxWhiskerGraph.prototype.minValueWhisker = function(belowLimit, q1, array){ - var points = new Array(); - - for (var i = 0; i < array.length; i++){ - if ((array[i] < q1) && (array[i]) > belowLimit){ - points.push(array[i]); - } - } - - if (points.length > 0){ - points.sort(function(a, b){return a - b;}); - return points[0]; - } - return null; -}; - -BoxWhiskerGraph.prototype.isNumber = function(value){ - if (value=="") return false; - - var d = parseInt(value); - if (!isNaN(d)) return true; else return false; - -}; - -BoxWhiskerGraph.prototype.plotBoxWhisker = function(boxProperties){ - if (this.maxBoxWidth != null){ - if (boxProperties.width > this.maxBoxWidth){ - boxProperties.x = boxProperties.x + (boxProperties.width/2) - (this.maxBoxWidth/2); - boxProperties.width = this.maxBoxWidth; - } - - } - - if (this.plotPoints){ - for(var i = 0; i < boxProperties.values.length; i++){ - var value = boxProperties.values[i]; - var toPixel = this.pointToPixel(value, boxProperties); - SVG.drawCircle(boxProperties.x + (boxProperties.width/2) + 2, toPixel, this.pointRadius, this.svg, [["fill", "green"], ["fill-opacity", this.fillOpacityPoint],['stroke-opacity', this.strokeOpacityPoint], ["stroke", "black"]]); - } - } - - - var boxColor = this.getClassColor(boxProperties.name); - var result = this.calculate(boxProperties.values); - /** Q1 **/ - - if (this.isNumber(result.Q1)){ - SVG.drawLine(boxProperties.x, this.pointToPixel(result.Q1, boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result.Q1, boxProperties), this.svg, [["stroke", boxColor]]); - } - /** Q2 **/ - if (this.isNumber(result.Q2)){ - SVG.drawLine(boxProperties.x, this.pointToPixel(result.Q2, boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result.Q2, boxProperties), this.svg, [["stroke", "blue"], ["stroke-width", "2"]]); - } - - /** Q3 **/ - if (this.isNumber(result.Q3)){ - SVG.drawLine(boxProperties.x, this.pointToPixel(result.Q3, boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result.Q3, boxProperties), this.svg, [["stroke", boxColor]]); - } - - /** Concenting Q1 and Q3 **/ - if (this.isNumber(result.Q1)&&this.isNumber(result.Q3)){ - SVG.drawLine(boxProperties.x, this.pointToPixel(result.Q1, boxProperties), boxProperties.x, this.pointToPixel(result.Q3, boxProperties), this.svg, [["stroke", boxColor]]); - SVG.drawLine(boxProperties.x + boxProperties.width, this.pointToPixel(result.Q1, boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result.Q3, boxProperties), this.svg, [["stroke", boxColor]]); - } - - /** min-whisker **/ - if (result["min-whisker"] != null){ - if (this.isNumber(result.Q1)){ - SVG.drawLine(boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result.Q1, boxProperties), boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result["min-whisker"], boxProperties), this.svg, [["stroke", boxColor]]); - } - SVG.drawLine(boxProperties.x,this.pointToPixel(result["min-whisker"], boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result["min-whisker"], boxProperties) , this.svg, [["stroke", boxColor]]); - - } - - /** max-whisker **/ - if (result["max-whisker"] != null){ - if (this.isNumber(result.Q3)){ - SVG.drawLine(boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result.Q3, boxProperties), boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result["max-whisker"], boxProperties), this.svg, [["stroke", boxColor]]); - } - SVG.drawLine(boxProperties.x , this.pointToPixel(result["max-whisker"], boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result["max-whisker"], boxProperties), this.svg, [["stroke", boxColor]]); - - } - - /** outliners **/ - if (result["above-outliers"] != null){ - for (var point in result["above-outliers"]){ - SVG.drawCircle(boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result["above-outliers"][point], boxProperties), this.pointRadius, this.svg, [["fill", "red"], ["fill-opacity", "1"]]); - //SVG.drawText(boxProperties.x + (boxProperties.width/2) - 2, this.pointToPixel(result["above-outliers"][point], boxProperties) + 2, "x",this.svg, [["fill", "black"], ["font-size", "x-small"]]); - } - } - if (result["below-outliers"] != null){ - for (var point in result["below-outliers"]){ - SVG.drawCircle(boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result["below-outliers"][point], boxProperties), this.pointRadius, this.svg, [["fill", "red"], ["fill-opacity", "1"]]); - //SVG.drawText(boxProperties.x + (boxProperties.width/2) - 2, this.pointToPixel(result["below-outliers"][point], boxProperties) + 2, "x",this.svg, [["fill", "black"], ["font-size", "x-small"]]); - } - } -}; - - - -BoxWhiskerGraph.prototype.plotClusterTitles = function(properties){ - /** Cluster Titles **/ - var posX = this.left + this.rulerWidth; - var data = this.data; - for(var i = 0; i < data.clusters.length; i++ ){ - /** title for the clusters **/ - posX = posX + this.interClustersSpace; - - /** Drawing title of classes **/ - var cluster = data.clusters[i]; - var posXClasses = posX; - for(var j = 0; j < cluster.classes.length; j++){ - //SVG.drawRectangle(posXClasses, this.height - (this.bottom + this.clusterTitleHeight + this.rulerHeight), properties.classWidth, this.rulerHeight, this.svg, [["fill", "green"]]); -// SVG.drawText(posXClasses + 1/6*properties.classWidth, this.height - (this.bottom + this.clusterTitleHeight + (this.rulerHeight*1/4)), cluster.classes[j].name, this.svg, [["style", "font-size:xx-small"]]); - var color = cluster.classes[j].color; - this.drawSVGVerticalText(posXClasses + 1/2*(properties.classWidth), this.height - (this.bottom - this.clusterTitleHeight + (this.rulerHeight)), cluster.classes[j].name , [["style", "font-size:x-small;"], ["fill", color]]); - - // SVG.drawRectangle(posXClasses, this.height - (this.bottom + this.clusterTitleHeight), properties.classWidth, 2, this.svg, [["fill", "black"]]); - posXClasses = posXClasses + properties.classWidth + this.interClassesSpace; - } - - var clusterTitleSpace = (data.clusters[i].classes.length * properties.classWidth) + ((data.clusters[i].classes.length - 1) * this.interClassesSpace); - //SVG.drawRectangle(posX, this.height - (this.bottom + this.clusterTitleHeight), clusterTitleSpace, this.clusterTitleHeight, this.svg, [["fill", "pink"]]); - SVG.drawRectangle(posX, this.height - (this.clusterTitleHeight+this.bottom), clusterTitleSpace, 1, this.svg, []); - -// var transform = ["translate", "(" + posX + 1/3*clusterTitleSpace +", " + this.height - (this.bottom + (this.clusterTitleHeight*1/4)) +")"], ["transform", "rotate(180)"]; -// var transform = ["transform", "translate(" + (posX + 1/3*clusterTitleSpace) +", " + (this.height - (this.bottom + (this.clusterTitleHeight*1/4))) + "), rotate(-90) "]; -// this.drawSVGVerticalText(posX + 1/3*clusterTitleSpace, this.height - (this.bottom + (this.clusterTitleHeight*1/4)),data.clusters[i].name, [["style", "font-size:x-small"]]); - SVG.drawText(posX , this.height - (this.bottom + (this.clusterTitleHeight*1/4)),data.clusters[i].name ,this.svg, [["style", "font-size:x-small"]]); - posX = posX + clusterTitleSpace; - } -}; - -BoxWhiskerGraph.prototype.plotWhisters = function(data, properties){ - var colors = ["yellow", "orange", "green"]; - var posX = this.left + this.rulerWidth; - for(var i = 0; i < data.clusters.length; i++ ){ - var cluster = data.clusters[i]; - /** inter cluster space **/ - //SVG.drawRectangle(posX, this.top, this.interClustersSpace, this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight, this.svg, [["fill", "black"]]); - posX = posX + this.interClustersSpace; - - for (var j = 0; j < cluster.classes.length; j ++){ - - //SVG.drawRectangle(posX, this.top, properties.classWidth, this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight, this.svg, [["fill", colors[j]]]); - this.plotBoxWhisker( - { - name : cluster.classes[j].name, - values : cluster.classes[j].values, - minPoint : properties.minPoint, - maxPoint : properties.maxPoint, - x : posX, - y : this.top, - width : properties.classWidth, - height : this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight - - - } - ); - posX = posX + properties.classWidth; - //SVG.drawRectangle(posX, this.top, this.interClassesSpace, this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight, this.svg, [["fill", "black"]]); - if (j < cluster.classes.length - 1){ - posX = posX + this.interClassesSpace; - } - } - } -}; - -BoxWhiskerGraph.prototype.draw = function(targetId, data){ - this.targetId = targetId; - var properties = (this.getDimensions(data)); - this.svg = SVG.createSVGCanvas(document.getElementById(this.targetId), [["width", this.width], ["height", this.height]]); - this.plotAxes(properties); - this.plotClusterTitles(properties); - this.plotWhisters(data,properties); -}; - -BoxWhiskerGraph.prototype.input = function(){ - return DATADOC.getBoxWhikerData(); -}; - -BoxWhiskerGraph.prototype.test = function(targetId){ - var plot = new BoxWhiskerGraph( - { - targetId : targetId, - height : 350, - width : 450, - maxBoxWidth : 25 - } - ); - plot.refresh(this.input()); -}; - - - - - - - -function DataSet(){ - this.json = null; - -}; - - -DataSet.prototype.loadFromJSON = function(json){ - if(json != null) { - if(this.validate(json)) { - this.json = json; - } - } -}; - - -DataSet.prototype.toJSON = function(json){ - return this.json; -}; - - -/** Abstract method to be override on childs classes **/ -DataSet.prototype.validate = function(json){ - if (true){ - return true; - } - /*else{ - throw "Data validation failed"; - }*/ -}; - - - - -Edge.prototype.getName = GraphItem.prototype.getName; -Edge.prototype.setName = GraphItem.prototype.setName; -Edge.prototype.getId = GraphItem.prototype.getId; - -function Edge(id, name, nodeSource, nodeTarget, args){ - GraphItem.prototype.constructor.call(this, id, name, args); - - this.sourceNode = nodeSource; - this.targetNode = nodeTarget; - -}; - -Edge.prototype.toJSON = function(){ - return {"index": this.id,"sourceIndex":this.sourceNode.getId(),"targetIndex":this.targetNode.getId(),"args":this.args}; -}; - -Edge.prototype.getNodeSource = function(){ - return this.sourceNode; -}; - -Edge.prototype.getNodeTarget = function(){ - return this.targetNode; -}; - -Edge.prototype.remove = function(){ - //Remove edge object in the nodes - this.getNodeSource().removeEdge(this); - this.getNodeTarget().removeEdge(this); - - this.deleted.notify(this); -}; - - -EdgeGraphFormatter.prototype.setProperties = ItemGraphFormatter.prototype.setProperties; -EdgeGraphFormatter.prototype.getDefault = ItemGraphFormatter.prototype.getDefault; -EdgeGraphFormatter.prototype.getSelected = ItemGraphFormatter.prototype.getSelected; -EdgeGraphFormatter.prototype.getOver = ItemGraphFormatter.prototype.getOver; -EdgeGraphFormatter.prototype.getDragging = ItemGraphFormatter.prototype.getDragging; -EdgeGraphFormatter.prototype.getId = ItemGraphFormatter.prototype.getId; -EdgeGraphFormatter.prototype.toJSON = ItemGraphFormatter.prototype.toJSON; -EdgeGraphFormatter.prototype.loadFromJSON = ItemGraphFormatter.prototype.loadFromJSON; -EdgeGraphFormatter.prototype._setEvents = ItemGraphFormatter.prototype._setEvents; - -function EdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ - ItemGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); - - this.getDefault().args.type = "EdgeGraphFormatter"; -}; - - - - -LineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; -LineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; -LineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; -LineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; -LineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; -LineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; -LineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; -LineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; -LineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; - -function LineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ - EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); - this.args.type = "LineEdgeGraphFormatter"; -}; - -/** DIRECTED **/ -DirectedLineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; -DirectedLineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; -DirectedLineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; -DirectedLineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; -DirectedLineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; -DirectedLineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; -DirectedLineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; -DirectedLineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; -DirectedLineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; - -function DirectedLineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ - EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); - this.args.type = "DirectedLineEdgeGraphFormatter"; - this.args.arrowSize = "3"; -}; -DirectedLineEdgeGraphFormatter.prototype.getArrowSize = function(){ - return this.args.arrowSize; -}; - -OdirectedLineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; -OdirectedLineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; -OdirectedLineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; -OdirectedLineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; -OdirectedLineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; -OdirectedLineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; -OdirectedLineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; -OdirectedLineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; -OdirectedLineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; - -function OdirectedLineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ - EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); - this.args.type = "DirectedLineEdgeGraphFormatter"; - this.args.arrowSize = "3"; -}; - -OdirectedLineEdgeGraphFormatter.prototype.getArrowSize = function(){ - return this.args.arrowSize; -}; - - -/** CUT (inhibition) **/ -CutDirectedLineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; -CutDirectedLineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; -CutDirectedLineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; -CutDirectedLineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; -CutDirectedLineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; -CutDirectedLineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; -CutDirectedLineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; -CutDirectedLineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; -CutDirectedLineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; - -function CutDirectedLineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ - EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); - this.args.type = "CutDirectedLineEdgeGraphFormatter"; -}; - - - - -BezierEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; -BezierEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; -BezierEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; -BezierEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; -BezierEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; -BezierEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; -BezierEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; -BezierEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; -BezierEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; -BezierEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; - -function BezierEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ - EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); - this.args.type = "BezierEdgeGraphFormatter"; -}; - - - -DotDirectedLineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; -DotDirectedLineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; -DotDirectedLineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; -DotDirectedLineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; -DotDirectedLineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; -DotDirectedLineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; -DotDirectedLineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; -DotDirectedLineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; -DotDirectedLineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; - -function DotDirectedLineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ - EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); - this.args.type = "DotDirectedLineEdgeGraphFormatter"; -}; - - -OdotDirectedLineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; -OdotDirectedLineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; -OdotDirectedLineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; -OdotDirectedLineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; -OdotDirectedLineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; -OdotDirectedLineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; -OdotDirectedLineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; -OdotDirectedLineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; -OdotDirectedLineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; - -function OdotDirectedLineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ - EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); - this.args.type = "OdotDirectedLineEdgeGraphFormatter"; -}; - - - -function GraphDataset(){ - DataSet.prototype.constructor.call(this); - this.edges = new Object(); - this.vertices = new Object(); - this.verticesIndex = new Object(); - - //Events - this.newVertex = new Event(this); - this.vertexNameChanged = new Event(this); - this.vertexDeleted = new Event(this); - - this.newEdge = new Event(this); - this.edgeNameChanged = new Event(this); - this.edgeDeleted = new Event(this); - - this.json = new Object(); - this.json.vertices = new Array(); - this.json.edges = new Array(); - this.json.relations = new Array(); -}; - -GraphDataset.prototype.loadFromJSON = DataSet.prototype.loadFromJSON; -GraphDataset.prototype.toJSON = DataSet.prototype.toJSON; -GraphDataset.prototype.validate = DataSet.prototype.validate; - -/** Devuelve el numero de edges incidentes sobre el nodo con mas edges **/ -GraphDataset.prototype.getMaxClass = function(){ - var maxClassNode = 0; - for ( var node in this.vertices) { - if (this.vertices[node].getEdgesCount() > maxClassNode){ - maxClassNode = this.vertices[node].getEdgesCount(); - } - } - return maxClassNode; -}; - -/** Devuelve el numero de edges incidentes sobre el nodo con mas edges **/ -GraphDataset.prototype.getMinClass = function(){ - var minClassNode = Math.min(); - for ( var node in this.vertices) { - if (this.vertices[node].getEdgesCount() < minClassNode){ - minClassNode = this.vertices[node].getEdgesCount(); - } - } - return minClassNode; -}; - -GraphDataset.prototype.getVertexByName = function(nodeName){ - var results = new Array(); - - for (var vertexId in this.verticesIndex[nodeName]){ - var vertexByid = this.getVertexById(this.verticesIndex[nodeName][vertexId]); - results.push(vertexByid); - //* añadido nuevo porque fallaba el anterior codigo - return vertexByid - } - - if (results <= 1){ - return this.getVertexById(this.verticesIndex[nodeName]); - } - else{ - return results; - } -}; - -GraphDataset.prototype.getVertexById = function(id){ - return this.vertices[id]; -}; - -GraphDataset.prototype.toSIF = function(){ - var sifDataAdapter = new SifFileDataAdapter(); - return sifDataAdapter.toSIF(this); -}; - -GraphDataset.prototype.toSIFID = function(){ - var sifDataAdapter = new SifFileDataAdapter(); - return sifDataAdapter.toSIFID(this); -}; - -GraphDataset.prototype.toDOT = function(){ - var dotFileDataAdapter = new DotFileDataAdapter(); - return dotFileDataAdapter.toDOT(this); -}; - -GraphDataset.prototype.toDOTID = function(){ - var dotFileDataAdapter = new DotFileDataAdapter(); - return dotFileDataAdapter.toDOTID(this); -}; - -GraphDataset.prototype._addNode = function(nodeName, args){ - return new Vertex(this._getVerticesCount()-1, nodeName, args); -}; - -GraphDataset.prototype.addNode = function(nodeName, args){ - this.json.vertices.push(nodeName); - this._addVerticesIndex(nodeName, this._getVerticesCount() - 1); - var vertex = this._addNode(nodeName, args); - this.vertices[this._getVerticesCount()-1] = vertex; - this._setNodeEvents(vertex); - this.newVertex.notify(vertex); -}; - -GraphDataset.prototype._addVerticesIndex = function(nodeName, id){ - if (this.verticesIndex[nodeName] == null){ - this.verticesIndex[nodeName] = new Array(); - } - this.verticesIndex[nodeName].push(id); -}; - -GraphDataset.prototype.addEdge = function(edgeName, nodeSourceId, nodeTargetId, args){ - this.json.edges.push(edgeName); - var nodeSource = this.getVertexById(nodeSourceId); - var nodeTarget = this.getVertexById(nodeTargetId); - var index = this.getEdgesCount() - 1; - this.edges[index] = new Edge(index, edgeName, nodeSource, nodeTarget, args); - this.json.relations.push({"index": index, "sourceIndex": nodeSourceId, "targetIndex": nodeTargetId, "args": args }); - - nodeSource.addEdge(this.edges[index]); - nodeTarget.addEdge(this.edges[index]); - this._setEdgeEvents(this.edges[index]); - this.newEdge.notify(this.edges[index]); -}; - -GraphDataset.prototype.getVertices = function(){ - return this.vertices; -}; - -GraphDataset.prototype.getEdges = function(){ - return this.edges; -}; - -GraphDataset.prototype.getEdgeById = function(edgeId){ - return this.edges[edgeId]; -}; - -GraphDataset.prototype._getVerticesCount = function(){ - return this.json.vertices.length; -}; - - -GraphDataset.prototype.getVerticesCount = function(){ - var count = 0; - for ( var vertex in this.getVertices()) { - count ++; - } - return count; -}; - - -GraphDataset.prototype.getEdgesCount = function(){ - return this.json.edges.length; -}; - -GraphDataset.prototype.init = function(){ - this.edges = new Object(); - this.vertices = new Object(); -}; - -GraphDataset.prototype._setNodeEvents = function(node){ - var _this = this; - //NODE EVENTS - node.deleted.attach(function (sender, node){ - _this._removeNode(node); - }); - - node.nameChanged.attach(function (sender, args){ - var item = args.item; - var newName = item.name; - var indexes = _this.verticesIndex[args.previousName]; - for(var i = 0; i < indexes.length; i++){ - if(indexes[i] == item.id) - indexes.splice(i,1); - } - if(indexes.length == 0){ - delete _this.verticesIndex[args.previousName]; - } - _this._addVerticesIndex(newName, item.id); - _this.json.vertices[item.id] = newName; - _this.vertexNameChanged.notify(args); - }); -}; - -GraphDataset.prototype._setEdgeEvents = function(edge){ - var _this = this; - //EDGE EVENTS - edge.nameChanged.attach(function (sender, edge){ - _this.edgeNameChanged.notify(edge); - - }); - - edge.deleted.attach(function (sender, edge){ - _this._removeEdge(edge); - }); -}; - -GraphDataset.prototype._connectVerticesByName = function(nodeNameSource, nodeNameTarget){ - var source = this.getVertexByName(nodeNameSource); - var target = this.getVertexByName(nodeNameTarget); - - if ((source != null)&&(target!=null)){ - this.addEdge(source.getName() +"_" + target.getName(), source.getId(), target.getId(), {}); - } - else{ - if (source == null){ - console.log("No encontrado: " + nodeNameSource) - } - if (target == null){ - console.log("No encontrado: " + nodeNameTarget) - } - } -}; - -GraphDataset.prototype.loadFromJSON = function(json){ - var json = json; - this.init(); - this.json = new Object(); - this.json.vertices = new Array(); - this.json.edges = new Array(); - this.json.relations = new Array(); - - for ( var i = 0; i < json.nodes.length; i++) { - if (json.nodes[i] != null){ - var name = json.nodes[i]; - this.addNode(name); - } - else{ - this.json.vertices.push(null); - } - } - - for ( var i = 0; i < json.edges.length; i++) { - if (json.edges[i] != null){ - if (json.relations[i] != null){ - var name = json.edges[i]; - this.addEdge(name, json.relations[i].sourceIndex, json.relations[i].targetIndex, json.relations[i].args); - } - } - else{ - this.json.edges.push(null); - this.json.relations.push(null); - } - } -}; - -GraphDataset.prototype.prettyPrint = function(){ - for ( var node in this.vertices) { - console.log(this.vertices[node].getName() ); - for ( var j = 0; j < this.vertices[node].getEdgesIn().length; j++) { - console.log(" --> " + this.vertices[node].getEdgesIn()[j].getNodeTarget().getName() ); - } - } -}; - -GraphDataset.prototype._removeEdge = function(edge){ - this.json.edges[edge.getId()] = null; - this.json.relations[edge.getId()] = null; - - delete this.edges[edge.getId()]; - this.edgeDeleted.notify(edge); - - -}; - -GraphDataset.prototype._removeNode = function(node){ - this.json.vertices[node.getId()] = null; - delete this.vertices[node.getId()]; - this.vertexDeleted.notify(node); -}; - -GraphDataset.prototype.toJSON = function(){ - var json = new Object(); - var nodes = new Array(); - json.nodes = this.json.vertices; //nodes; - json.edges = this.json.edges; //edges; - json.relations = this.json.relations; - return json; -}; - -GraphDataset.prototype.clone = function(){ - var dsDataset = new GraphDataset(); - dsDataset.loadFromJSON(this.toJSON()); - return dsDataset; -}; -//GraphDataset.prototype.test = function(){ -// this.loadFromJSON(this.toJSON()); -//}; - -function labels(){ - var names = new Array(); - - var dataset = interactomeViewer.graphEditorWidget.dataset; - var layout = interactomeViewer.graphEditorWidget.layout; - - for ( var vertexId in interactomeViewer.graphEditorWidget.dataset.getVertices()) { - names.push(interactomeViewer.graphEditorWidget.dataset.getVertexById(vertexId).getName()); - } - - var sorted = (names.sort()); - console.log(sorted) - var distance = 0.01; - var altura = 0.6; - for ( var i = 0; i < names.length; i++) { - var id =dataset.getVertexByName(names[i]).getId(); - - layout.getNodeById(id).setCoordenates(distance, altura); - - - distance = parseFloat(distance) + parseFloat(0.03); - - altura = parseFloat(altura) + parseFloat(0.02); - - if (parseFloat(altura) == 0.9800000000000003){ - - altura = 0.6; - distance = distance - 0.51; - } - - } - - -}; - -function GraphItem(id, name, args){ - this.id = id; - this.name = name; - this.type = "NONE"; - - this.args = new Object(); - - - if (args!=null){ - this.args = args; - if (args.type !=null){ - this.type = args.type; - } - } - - //Events - this.nameChanged = new Event(this); - this.deleted = new Event(this); -} - -GraphItem.prototype.getName = function(){ - return this.name; -}; - -GraphItem.prototype.getId = function(){ - return this.id; -}; - -GraphItem.prototype.setName = function(name){ - var oldName = this.getName(); - this.name = name; - this.nameChanged.notify({"item": this, "previousName" : oldName}); -}; - - - - - -function LayoutDataset(){ - this.dataset = null; - this.vertices = new Object(); - this.changed = new Event(this); - - - this.args = new Object(); - - //RANDOM, CIRCLE - this.args.type = "CIRCLE"; -}; - -LayoutDataset.prototype.loadFromJSON = function(dataset, json){ - var _this = this; - this.vertices = new Object(); - this.dataset = dataset; //new GraphDataset(); - for ( var vertex in json) { - this.vertices[vertex] = new NodeLayout(vertex, json[vertex].x, json[vertex].y); - this.vertices[vertex].changed.attach(function (sender, item){ - _this.changed.notify(item); - }); - } - this._attachDatasetEvents(); -}; - - -LayoutDataset.prototype.toJSON = function(){ - var serialize = new Object(); - for ( var vertex in this.vertices) { - serialize[vertex] = new Object(); - serialize[vertex].x = this.vertices[vertex].x; - serialize[vertex].y = this.vertices[vertex].y; - } - serialize.dataset = new Object(); - serialize.dataset =this.dataset.toJSON(); - return serialize; -}; - -LayoutDataset.prototype.dataBind = function(graphDataset){ - this.dataset = graphDataset; - this._attachDatasetEvents(); - this._calculateLayout(); -}; - -LayoutDataset.prototype._removeVertex = function(vertexId){ - delete this.vertices[vertexId]; -}; - -LayoutDataset.prototype._attachDatasetEvents = function(){ - var _this = this; - - this.dataset.vertexDeleted.attach(function (sender, item){ - _this._removeVertex(item.getId()); - }); - - this.dataset.newVertex.attach(function (sender, item){ - _this.vertices[item.getId()] = new NodeLayout(item.getId(), 0.5, 0.5); - _this.vertices[item.getId()].changed.attach(function (sender, item){ - _this.changed.notify(item); - }); - }); -}; - -LayoutDataset.prototype.getType = function(){ - return this.args.type; -}; - -LayoutDataset.prototype._calculateLayoutVertices = function(type, count){ - - if (type == "CIRCLE"){ - var radius = 0.4; - var centerX = 0.5; - var centerY = 0.5; - var verticesCoordinates = new Array(); - for(var i = 0; i < count; i++){ - x = centerX + radius * Math.sin(i * 2 * Math.PI/count); - y = centerY + radius * Math.cos(i * 2 * Math.PI/count); - verticesCoordinates.push({'x':x,'y':y}); - } - return verticesCoordinates; - } -}; - - -LayoutDataset.prototype._calculateLayout = function(){ - var _this = this; - if (this.getType() == "RANDOM"){ - for ( var vertex in this.dataset.getVertices()) { - if (this.vertices[vertex] == null){ - this.vertices[vertex] = new NodeLayout(vertex, 0, 0); - } - this.vertices[vertex].setCoordinates(Math.random(), Math.random()); - this.vertices[vertex].changed.attach(function (sender, item){ - _this.changed.notify(item); - }); - } - } - - if ( this.getType() == "CIRCLE"){ - - var count = this.dataset._getVerticesCount(); - var verticesCoordinates = this._calculateLayoutVertices(this.getType(), count); - - var aux = 0; - for ( var vertex in this.dataset.getVertices()) { - if (this.vertices[vertex] == null){ - this.vertices[vertex] = new NodeLayout(vertex, 0, 0); - } - this.vertices[vertex].setCoordinates(verticesCoordinates[aux].x, verticesCoordinates[aux].y);//{"x":, "y":}; - aux++; - this.vertices[vertex].changed.attach(function (sender, item){ - _this.changed.notify(item); - }); - } - } - - - if (this.getType() == "SQUARE"){ - - var count = this.dataset._getVerticesCount(); - var xMin = 0.1; - var xMax = 0.9; - var yMin = 0.1; - var yMax = 0.9; - - var rows = Math.sqrt(count); - var step = (xMax - xMin) / rows; - - var verticesCoordinates = new Array(); - for(var i = 0; i < rows; i ++){ - for ( var j = 0; j < rows; j++) { - x = i * step + xMin; - y = j * step + yMin; - verticesCoordinates.push({'x':x,'y':y}); - } - } - - var aux = 0; - for ( var vertex in this.dataset.getVertices()) { - if (this.vertices[vertex] == null){ - this.vertices[vertex] = new NodeLayout(vertex, 0, 0); - } - this.vertices[vertex].setCoordinates(verticesCoordinates[aux].x, verticesCoordinates[aux].y);//{"x":, "y":}; - aux++; - this.vertices[vertex].changed.attach(function (sender, item){ - _this.changed.notify(item); - }); - } - } - -}; - -LayoutDataset.prototype.getNodeById = function(id){ - return this.vertices[id]; -}; - -LayoutDataset.prototype.getVerticesByArea = function(x1, y1, x2, y2){ - var vertices = new Array(); - for ( var vertex in this.dataset.getVertices()) { - if ((this.vertices[vertex].x >= x1)&&(this.vertices[vertex].x <= x2)){ - if ((this.vertices[vertex].y >= y1)&&(this.vertices[vertex].y <= y2)){ - vertices.push(this.vertices[vertex]); - } - } - } - return vertices; -}; - - - - -LayoutDataset.prototype.getLayout = function(type){ - - if (type == "CIRCLE"){ - this.args.type = "CIRCLE"; - this._calculateLayout(); - return; - } - - if (type == "SQUARE"){ - this.args.type = "SQUARE"; - this._calculateLayout(); - return; - } - - if (type == "RANDOM"){ - this.args.type = "RANDOM"; - this._calculateLayout(); - return; - } - - - var dotText = this.dataset.toDOTID(); - var url = "http://bioinfo.cipf.es/utils/ws/rest/network/layout/"+type+".coords"; - var _this = this; - - $.ajax({ - async: true, - type: "POST", - url: url, - dataType: "text", - data: { - dot :dotText - }, - cache: false, - success: function(data){ - var response = JSON.parse(data); - for ( var vertexId in response) { - _this.vertices[vertexId].setCoordinates(response[vertexId].x, response[vertexId].y); - } - } - }); - -// $.ajax({ -// async: true, -// type: "POST", -// url: url, -// dataType: "script", -// data: { -// dot :dotText -// }, -// cache: false, -// success: function(data){ -// var response = JSON.parse(data); -// for ( var vertexId in response) { -// _this.vertices[vertexId].setCoordinates(response[vertexId].x, response[vertexId].y); -// } -// } -// }); - -}; - -function NodeLayout(id, x, y, args){ - this.id = id; - this.x = x; - this.y = y; - this.changed = new Event(this); -}; - -NodeLayout.prototype.getId = function(id){ - return this.id; -}; - -NodeLayout.prototype.setCoordinates = function(x, y){ - this.x = x; - this.y = y; - this.changed.notify(this); -}; - - - -function NetworkDataSetFormatter(vertexFormatProperties, defaultEdgeProperties, args){ - DataSet.prototype.constructor.call(this); - - this.args = new Object(); - - this.vertices = new Object(); - this.edges = new Object(); - this.dataset = null; - this.maxClass = 0; - this.minClass = 0; - - /** Coordenates with default Setting */ - this.args.width = 1100; - this.args.height = 500; - - /** Optional parameters */ - this.args.backgroundColor = "#FFFFFF"; - this.args.backgroundImage = null; - this.args.backgroundImageHeight = null; - this.args.backgroundImageWidth = null; - this.args.backgroundImageX = null; - this.args.backgroundImageY = null; - - - this.args.balanceNodes = false; - this.args.nodesMaxSize = 3; - this.args.nodesMinSize = 0.5; - - - /** Zoom **/ - this.args.zoomScale = 1; - this.args.zoomScaleStepFactor = 0.4; - - if (args != null){ - if (args.backgroundImage != null){ - this.args.backgroundImage = args.backgroundImage; - } - - if (args.width != null){ - this.args.width = args.width; - } - - if (args.height != null){ - this.args.height = args.height; - this.args.svgHeight = args.height; - } - - if (args.svgHeight != null){ - this.args.svgHeight = args.svgHeight; - } - - if (args.backgroundColor != null){ - this.args.backgroundColor = args.backgroundColor; - } - - if(args.balanceNodes != null){ - this.args.balanceNodes = args.balanceNodes; - } - - if(args.nodesMaxSize != null){ - this.args.nodesMaxSize = args.nodesMaxSize; - } - if(args.nodesMinSize != null){ - this.args.nodesMinSize = args.nodesMinSize; - } - } - - this.args.defaultEdgeProperties = {"fill":"#000000", "radius":"1", "stroke":"#000000", "size":1, "title":{"fontSize":10, "fontColor":"#000000"}}; - this.args.vertexFormatProperties = { "fill":"#000000", "stroke":"#000000", "stroke-opacity":"#000000"}; - - if (vertexFormatProperties!= null){ - this.args.vertexFormatProperties = vertexFormatProperties; - } - if (defaultEdgeProperties!= null){ - this.args.defaultEdgeProperties = defaultEdgeProperties; - } - - /** Events **/ - this.changed = new Event(this); - this.edgeChanged = new Event(this); - this.resized = new Event(this); - this.backgroundImageChanged= new Event(this); - this.backgroundColorChanged= new Event(this); -}; - -NetworkDataSetFormatter.prototype.loadFromJSON = function(dataset, json){ - this.args = new Object(); - this.vertices = new Object(); - this.args = json; - this._setDataset(dataset); - var _this = this; - - for ( var vertex in json.vertices) { - this.addVertex(vertex, json.vertices[vertex]); - } - - for ( var edgeId in json.edges) { - this.addEdge(edgeId, json.edges[edgeId]); - } -}; - - -NetworkDataSetFormatter.prototype.toJSON = function(){ - - -// this.args.vertices = new Object(); -// this.args.edges = new Object(); -// -// for ( var vertex in this.vertices) { -// this.args.vertices[vertex] = this.getVertexById(vertex).toJSON(); -// } -// for ( var edge in this.edges) { -// this.args.edges[edge] = this.getEdgeById(edge).toJSON(); -// } -// -// return (this.args); - - - var serialize = new Object(); - serialize = JSON.parse(JSON.stringify(this.args)); - serialize.vertices = new Object(); - serialize.edges = new Object(); - - for ( var vertex in this.vertices) { - serialize.vertices[vertex] = this.getVertexById(vertex).toJSON(); - } - for ( var edge in this.edges) { - serialize.edges[edge] = this.getEdgeById(edge).toJSON(); - } - - return (serialize); -}; - - - -NetworkDataSetFormatter.prototype._getNodeSize = function(nodeId){ - if (this.isVerticesBalanced()){ - var total = this.maxClass - this.minClass; - if (total == 0){ total = 1;} - var nodeConnection = this.dataset.getVertexById(nodeId).getEdges().length; - return ((nodeConnection*this.args.nodesMaxSize)/total) + this.args.nodesMinSize; - } - return this.getVertexById(nodeId).getDefault().getSize(); -}; - -NetworkDataSetFormatter.prototype._recalculateSize = function(){ - if (this.isVerticesBalanced()){ - this.maxClass = this.dataset.getMaxClass(); - this.minClass = this.dataset.getMinClass(); - for ( var vertexIdAll in this.vertices) { - var size = this._getNodeSize(vertexIdAll); - this.vertices[vertexIdAll].getDefault().setSize(size); - this.vertices[vertexIdAll].getSelected().setSize(size); - this.vertices[vertexIdAll].getOver().setSize(size); - } - } -}; - - -NetworkDataSetFormatter.prototype.addVertex = function(vertexId, json){ - - - if (json == null){ - this.vertices[vertexId] = new CircleVertexGraphFormatter(vertexId, this.args.vertexFormatProperties.defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); - } - else{ - - /** Cargo los attributos desde el json **/ - if (json.type == null){ - this.vertices[vertexId] = new CircleVertexGraphFormatter(vertexId, this.args.vertexFormatProperties.defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); - } - - if ((json.type == "SquareVertexGraphFormatter")||(json.type == "SquareVertexNetworkFormatter")){ - this.vertices[vertexId] = new SquareVertexGraphFormatter(vertexId); - this.vertices[vertexId].loadFromJSON(json); - } - - if ((json.type == "CircleVertexGraphFormatter")||(json.type == "CircleVertexNetworkFormatter")){ - this.vertices[vertexId] = new CircleVertexGraphFormatter(vertexId); - this.vertices[vertexId].loadFromJSON(json); - } - - if ((json.type == "EllipseVertexGraphFormatter")||(json.type == "EllipseVertexNetworkFormatter")){ - this.vertices[vertexId] = new EllipseVertexGraphFormatter(vertexId); - this.vertices[vertexId].loadFromJSON(json); - } - - if ((json.type == "RectangleVertexGraphFormatter")||(json.type == "RectangleVertexNetworkFormatter")){ - this.vertices[vertexId] = new RectangleVertexGraphFormatter(vertexId); - this.vertices[vertexId].loadFromJSON(json); - } - - if ((json.type == "RoundedVertexGraphFormatter")||(json.type == "RoundedVertexNetworkFormatter")){ - this.vertices[vertexId] = new RoundedVertexGraphFormatter(vertexId); - this.vertices[vertexId].loadFromJSON(json); - } - - } - - - var _this = this; - this.vertices[vertexId].stateChanged.attach(function (sender, item){ - _this.changed.notify(item); - }); - - var size = this._getNodeSize(vertexId); - this.vertices[vertexId].defaultFormat.args.size = size; - this.vertices[vertexId].selected.args.size = size; - this.vertices[vertexId].over.args.size = size; - -}; - -NetworkDataSetFormatter.prototype.addEdge = function(edgeId, json){ - - /** Es un edge nuevo que le doy los atributos por defecto **/ - if (json == null){ - if (this.dataset.getEdgeById(edgeId).getNodeSource().getId() == this.dataset.getEdgeById(edgeId).getNodeTarget().getId()){ - this.edges[edgeId] = new BezierEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); - }else{ - this.edges[edgeId] = new DirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); - } - } - else{ - /** Cargo los attributos desde el json **/ - if (json.type == null){ - this.edges[edgeId] = new LineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); - } - - if ((json.type == "LineEdgeGraphFormatter")||(json.type == "LineEdgeNetworkFormatter")){ - this.edges[edgeId] = new LineEdgeGraphFormatter(edgeId); - this.edges[edgeId].loadFromJSON(json); - } - if ((json.type == "DirectedLineEdgeGraphFormatter")||(json.type == "DirectedLineEdgeNetworkFormatter")){ - this.edges[edgeId] = new DirectedLineEdgeGraphFormatter(edgeId); - this.edges[edgeId].loadFromJSON(json); - } - - if ((json.type == "BezierEdgeGraphFormatter")||(json.type == "BezierEdgeNetworkFormatter")){ - this.edges[edgeId] = new BezierEdgeGraphFormatter(edgeId); - this.edges[edgeId].loadFromJSON(json); - } - - - if ((json.type == "CutDirectedLineEdgeGraphFormatter")||(json.type == "CutDirectedLineEdgeNetworkFormatter")){ - this.edges[edgeId] = new CutDirectedLineEdgeGraphFormatter(edgeId); - this.edges[edgeId].loadFromJSON(json); - } - - if ((json.type == "DotDirectedLineEdgeGraphFormatter")||(json.type == "DotDirectedLineEdgeNetworkFormatter")){ - this.edges[edgeId] = new DotDirectedLineEdgeGraphFormatter(edgeId); - this.edges[edgeId].loadFromJSON(json); - } - if ((json.type == "OdotDirectedLineEdgeGraphFormatter")||(json.type == "OdotDirectedLineEdgeNetworkFormatter")){ - this.edges[edgeId] = new OdotDirectedLineEdgeGraphFormatter(edgeId); - this.edges[edgeId].loadFromJSON(json); - } - - if ((json.type == "OdirectedLineEdgeGraphFormatter")||(json.type == "OdirectedLineEdgeNetworkFormatter")){ - this.edges[edgeId] = new OdirectedLineEdgeGraphFormatter(edgeId); - this.edges[edgeId].loadFromJSON(json); - } - } - - var _this = this; - this.edges[edgeId].stateChanged.attach(function (sender, item){ - _this.edgeChanged.notify(item); - }); - - this._recalculateSize(); -}; - -NetworkDataSetFormatter.prototype._setDataset = function(dataset){ - this.dataset = dataset; - this.maxClass = dataset.getMaxClass(); - this.minClass = dataset.getMinClass(); - this._attachDatasetEvents(); -}; - -NetworkDataSetFormatter.prototype.changeEdgeType = function(edgeId, type){ - if ((type == "LineEdgeGraphFormatter")||(type == "LineEdgeNetworkFormatter")){ - this.edges[edgeId] = new LineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); - - } - if ((type == "DirectedLineEdgeGraphFormatter")||(type == "DirectedLineEdgeNetworkFormatter")){ - this.edges[edgeId] = new DirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); - } - - if ((type == "CutDirectedLineEdgeGraphFormatter")||(type == "CutDirectedLineEdgeNetworkFormatter")){ - this.edges[edgeId] = new CutDirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); - } - - if ((type == "DotDirectedLineEdgeGraphFormatter")||(type == "DotDirectedLineEdgeNetworkFormatter")){ - this.edges[edgeId] = new DotDirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); - } - - if ((type == "OdotDirectedLineEdgeGraphFormatter")||(type == "OdotDirectedLineEdgeNetworkFormatter")){ - this.edges[edgeId] = new OdotDirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); - } - - if ((type == "OdirectedLineEdgeGraphFormatter")||(type == "OdirectedLineEdgeNetworkFormatter")){ - this.edges[edgeId] = new OdirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); - } - - - - var _this = this; - this.edges[edgeId].stateChanged.attach(function (sender, item){ - _this.edgeChanged.notify(item); - }); - _this.edgeChanged.notify(this.edges[edgeId]); -}; -/* -classe = "SquareNetworkNodeFormatter"; -} -if (value == "circle"){ - classe = "CircleNetworkNodeFormatter"; - **/ -NetworkDataSetFormatter.prototype.changeNodeType = function(vertexId, type){ - var defaultFormat = JSON.parse(JSON.stringify(this.vertices[vertexId].getDefault())); - var selectedFormat = JSON.parse(JSON.stringify(this.vertices[vertexId].getSelected())); - var defaultFormat = JSON.parse(JSON.stringify(this.vertices[vertexId].getDefault())); - var defaultFormat = JSON.parse(JSON.stringify(this.vertices[vertexId].getDefault())); - - if ((type == "SquareVertexGraphFormatter")||(type == "SquareVertexNetworkFormatter")){ - this.vertices[vertexId] = new SquareVertexGraphFormatter(vertexId,defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); - } - - if ((type == "CircleVertexGraphFormatter")||(type == "CircleVertexNetworkFormatter")){ - this.vertices[vertexId] = new CircleVertexGraphFormatter(vertexId, defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); - } - - if ((type == "EllipseVertexGraphFormatter")||(type == "EllipseVertexNetworkFormatter")){ - this.vertices[vertexId] = new EllipseVertexGraphFormatter(vertexId, defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); - } - - if ((type == "RectangleVertexGraphFormatter")||(type == "RectangleVertexNetworkFormatter")){ - this.vertices[vertexId] = new RectangleVertexGraphFormatter(vertexId, defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); - } - - if ((type == "RoundedVertexGraphFormatter")||(type == "RoundedVertexNetworkFormatter")){ - this.vertices[vertexId] = new RoundedVertexGraphFormatter(vertexId, defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); - } - - if ((type == "OctagonVertexGraphFormatter")||(type == "OctagonVertexNetworkhFormatter")){ - this.vertices[vertexId] = new OctagonVertexGraphFormatter(vertexId, defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); - } - - - var _this = this; - this.vertices[vertexId].stateChanged.attach(function (sender, item){ - _this.changed.notify(item); - }); - _this.changed.notify(this.vertices[vertexId]); -}; - - - -NetworkDataSetFormatter.prototype.dataBind = function(networkDataSet){ - var _this = this; - this._setDataset(networkDataSet); - - for ( var vertex in this.dataset.getVertices()) { - this.addVertex(vertex); - } - - for ( var edge in this.dataset.getEdges()) { - this.addEdge(edge); - } -}; - -NetworkDataSetFormatter.prototype._removeEdge = function(edgeId){ - delete this.edges[edgeId]; -}; - -NetworkDataSetFormatter.prototype._removeVertex = function(vertexId){ - delete this.vertices[vertexId]; -}; - -NetworkDataSetFormatter.prototype._attachDatasetEvents = function(id){ - var _this = this; - this.dataset.vertexDeleted.attach(function (sender, item){ - _this._removeVertex(item.getId()); - }); - - this.dataset.edgeDeleted.attach(function (sender, item){ - _this._removeEdge(item.getId()); - }); - - this.dataset.newVertex.attach(function (sender, item){ - _this.addVertex(item.getId()); - }); - - this.dataset.newEdge.attach(function (sender, item){ - _this.addEdge(item.getId()); - }); -}; - - -NetworkDataSetFormatter.prototype.getVertexById = function(id){ - return this.vertices[id]; -}; - -NetworkDataSetFormatter.prototype.getEdgeById = function(id){ - return this.edges[id]; -}; - -NetworkDataSetFormatter.prototype.makeLabelsBigger = function(){ -for ( var vertexId in this.vertices) { - var fontSize = this.vertices[vertexId].getDefault().getFontSize() + 2; - this.vertices[vertexId].getDefault().setFontSize(fontSize); - } -}; - -NetworkDataSetFormatter.prototype.makeLabelsSmaller = function(){ - for ( var vertexId in this.vertices) { - var fontSize = this.vertices[vertexId].getDefault().getFontSize() - 2; - this.vertices[vertexId].getDefault().setFontSize(fontSize); - } -}; - - -NetworkDataSetFormatter.prototype.resize = function(width, height){ - this.args.width = width; - this.args.height = height; - this.resized.notify(); -}; - -/** ZOOM GETTERS **/ -NetworkDataSetFormatter.prototype.getZoomScaleStepFactor = function(){return this.args.zoomScaleStepFactor;}; -NetworkDataSetFormatter.prototype.setZoomScaleStepFactor = function(scaleFactor){this.args.zoomScaleStepFactor = scaleFactor;}; -NetworkDataSetFormatter.prototype.getZoomScale = function(){return this.args.zoomScale;}; -NetworkDataSetFormatter.prototype.setZoomScale = function(scale){this.args.zoomScale = scale;}; - -NetworkDataSetFormatter.prototype.getNodesMaxSize = function(){return this.args.nodesMaxSize;}; -NetworkDataSetFormatter.prototype.getNodesMinSize = function(){return this.args.nodesMinSize;}; - -/** SIZE SETTERS AND GETTERS **/ -NetworkDataSetFormatter.prototype.isVerticesBalanced = function(){return this.args.balanceNodes;}; -NetworkDataSetFormatter.prototype.getWidth = function(){return this.args.width;}; -NetworkDataSetFormatter.prototype.getHeight = function(){return this.args.height;}; - -/** OPTIONAL PARAMETERS GETTERS AND SETTERS **/ -NetworkDataSetFormatter.prototype.getBackgroundImage = function(){return this.args.backgroundImage;}; -NetworkDataSetFormatter.prototype.setBackgroundImage = function(value){this.args.backgroundImage = value; this.backgroundImageChanged.notify(this);}; - - -NetworkDataSetFormatter.prototype.getBackgroundImageWidth = function(){return this.args.backgroundImageWidth;}; -NetworkDataSetFormatter.prototype.setBackgroundImageWidth = function(value){this.args.backgroundImageWidth = value; this.backgroundImageChanged.notify(this);}; - -NetworkDataSetFormatter.prototype.getBackgroundImageHeight = function(){return this.args.backgroundImageHeight;}; -NetworkDataSetFormatter.prototype.setBackgroundImageHeight = function(value){this.args.backgroundImageHeight = value; this.backgroundImageChanged.notify(this);}; - -NetworkDataSetFormatter.prototype.getBackgroundImageX = function(){return this.args.backgroundImageX;}; -NetworkDataSetFormatter.prototype.setBackgroundImageX = function(value){this.args.backgroundImageX = value; this.backgroundImageChanged.notify(this);}; - -NetworkDataSetFormatter.prototype.getBackgroundImageY = function(){return this.args.backgroundImageX;}; -NetworkDataSetFormatter.prototype.setBackgroundImageY = function(value){this.args.backgroundImageY = value; this.backgroundImageChanged.notify(this);}; - - - -NetworkDataSetFormatter.prototype.getBackgroundColor = function(){return this.args.backgroundColor;}; -NetworkDataSetFormatter.prototype.setBackgroundColor = function(value){this.args.backgroundColor = value; this.backgroundColorChanged.notify(this);}; - -NetworkDataSetFormatter.prototype.getWidth = function(){return this.args.width;}; -NetworkDataSetFormatter.prototype.setWidth = function(value){this.args.width = value;}; - -NetworkDataSetFormatter.prototype.getHeight = function(){return this.args.height;}; -NetworkDataSetFormatter.prototype.setHeight = function(value){this.args.height = value;}; - - - - -Vertex.prototype.getName = GraphItem.prototype.getName; -Vertex.prototype.setName = GraphItem.prototype.setName; -Vertex.prototype.getId = GraphItem.prototype.getId; - -function Vertex(id, name, args){ - GraphItem.prototype.constructor.call(this, id, name, args); - this.edgesIn= new Array(); - this.edgesOut= new Array(); -}; - -Vertex.prototype.getEdges = function(){ - return this.edgesIn.concat(this.edgesOut); -}; - -Vertex.prototype.getEdgesCount = function(){ - return this.getEdges().length; -}; - -Vertex.prototype.getEdgesIn = function(){ - return this.edgesIn; -}; - -Vertex.prototype.getEdgesOut = function(){ - return this.edgesOut; -}; - -Vertex.prototype.addEdge = function(edge){ - if (edge.getNodeSource().getId() == this.id){ - this.edgesIn.push(edge); - } - else{ - this.edgesOut.push(edge); - } -}; - -Vertex.prototype.removeEdge = function(edge){ - for ( var i = 0; i < this.getEdgesIn().length; i++) { - var edgeIn = this.edgesIn[i]; - if (edgeIn.getId() == edge.getId()){ - this.edgesIn.splice(i, 1); - } - } - for ( var i = 0; i < this.getEdgesOut().length; i++) { - var edgeIn = this.edgesOut[i]; - if (edgeIn.getId() == edge.getId()){ - this.edgesOut.splice(i, 1); - } - } -}; - -Vertex.prototype.remove = function(){ - var edges = this.getEdges(); - for ( var i = 0; i < edges.length; i++) { - var edge = edges[i]; - edge.remove(); - } - this.deleted.notify(this); -}; - - - - - -VertexGraphFormatter.prototype.getDefault = ItemGraphFormatter.prototype.getDefault; -VertexGraphFormatter.prototype.getSelected = ItemGraphFormatter.prototype.getSelected; -VertexGraphFormatter.prototype.getOver = ItemGraphFormatter.prototype.getOver; -VertexGraphFormatter.prototype.getDragging = ItemGraphFormatter.prototype.getDragging; -VertexGraphFormatter.prototype.getId = ItemGraphFormatter.prototype.getId; -VertexGraphFormatter.prototype.toJSON = ItemGraphFormatter.prototype.toJSON; -VertexGraphFormatter.prototype.loadFromJSON = ItemGraphFormatter.prototype.loadFromJSON; -VertexGraphFormatter.prototype._setEvents = ItemGraphFormatter.prototype._setEvents; - - -function VertexGraphFormatter(defaultFormat, selectedFormat, overFormat, draggingFormat){ - ItemGraphFormatter.prototype.constructor.call(this, defaultFormat, selectedFormat, overFormat, draggingFormat); -}; - - -CircleVertexGraphFormatter.prototype.getDefault = VertexGraphFormatter.prototype.getDefault; -CircleVertexGraphFormatter.prototype.getSelected = VertexGraphFormatter.prototype.getSelected; -CircleVertexGraphFormatter.prototype.getOver = VertexGraphFormatter.prototype.getOver; -CircleVertexGraphFormatter.prototype.getDragging = VertexGraphFormatter.prototype.getDragging; -CircleVertexGraphFormatter.prototype.getId = VertexGraphFormatter.prototype.getId; -CircleVertexGraphFormatter.prototype.toJSON = VertexGraphFormatter.prototype.toJSON; -CircleVertexGraphFormatter.prototype.loadFromJSON = VertexGraphFormatter.prototype.loadFromJSON; -CircleVertexGraphFormatter.prototype._setEvents = VertexGraphFormatter.prototype._setEvents; - -function CircleVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ - VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); - this.args.type = "CircleVertexGraphFormatter"; - if (defaultFormat != null){ - if (defaultFormat.radius != null){ - this.defaultFormat.args.radius = defaultFormat.radius; - } - } - - if (selectedFormat != null){ - if (selectedFormat.radius != null){ - this.selected.args.radius = selectedFormat.radius; - } - } - - if (overFormat != null){ - if (overFormat.radius != null){ - this.over.args.radius = overFormat.radius; - } - } - - if (draggingFormat != null){ - if (draggingFormat.radius != null){ - this.dragging.args.draggingFormat = draggingFormat.radius; - } - } -}; - - - -SquareVertexGraphFormatter.prototype.getDefault = VertexGraphFormatter.prototype.getDefault; -SquareVertexGraphFormatter.prototype.getSelected = VertexGraphFormatter.prototype.getSelected; -SquareVertexGraphFormatter.prototype.getOver = VertexGraphFormatter.prototype.getOver; -SquareVertexGraphFormatter.prototype.getDragging = VertexGraphFormatter.prototype.getDragging; -SquareVertexGraphFormatter.prototype.getId = VertexGraphFormatter.prototype.getId; -SquareVertexGraphFormatter.prototype.toJSON = VertexGraphFormatter.prototype.toJSON; -SquareVertexGraphFormatter.prototype.loadFromJSON = VertexGraphFormatter.prototype.loadFromJSON; -SquareVertexGraphFormatter.prototype._setEvents = VertexGraphFormatter.prototype._setEvents; - -function SquareVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ - VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); - this.args.type = "SquareVertexGraphFormatter"; - if (defaultFormat != null){ - if (defaultFormat.radius != null){ - this.defaultFormat.args.radius = defaultFormat.radius; - } - } - - if (selectedFormat != null){ - if (selectedFormat.radius != null){ - this.selected.args.radius = selectedFormat.radius; - } - } - - if (overFormat != null){ - if (overFormat.radius != null){ - this.over.args.radius = overFormat.radius; - } - } - - if (draggingFormat != null){ - if (draggingFormat.radius != null){ - this.dragging.args.draggingFormat = draggingFormat.radius; - } - } -}; - - -EllipseVertexGraphFormatter.prototype.getDefault = VertexGraphFormatter.prototype.getDefault; -EllipseVertexGraphFormatter.prototype.getSelected = VertexGraphFormatter.prototype.getSelected; -EllipseVertexGraphFormatter.prototype.getOver = VertexGraphFormatter.prototype.getOver; -EllipseVertexGraphFormatter.prototype.getDragging = VertexGraphFormatter.prototype.getDragging; -EllipseVertexGraphFormatter.prototype.getId = VertexGraphFormatter.prototype.getId; -EllipseVertexGraphFormatter.prototype.toJSON = VertexGraphFormatter.prototype.toJSON; -EllipseVertexGraphFormatter.prototype.loadFromJSON = VertexGraphFormatter.prototype.loadFromJSON; -EllipseVertexGraphFormatter.prototype._setEvents = VertexGraphFormatter.prototype._setEvents; - -function EllipseVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ - VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); - this.args.type = "EllipseVertexGraphFormatter"; - if (defaultFormat != null){ - if (defaultFormat.radius != null){ - this.defaultFormat.args.radius = defaultFormat.radius; - } - } - - if (selectedFormat != null){ - if (selectedFormat.radius != null){ - this.selected.args.radius = selectedFormat.radius; - } - } - - if (overFormat != null){ - if (overFormat.radius != null){ - this.over.args.radius = overFormat.radius; - } - } - - if (draggingFormat != null){ - if (draggingFormat.radius != null){ - this.dragging.args.draggingFormat = draggingFormat.radius; - } - } -}; - - - -RectangleVertexGraphFormatter.prototype.getDefault = ItemGraphFormatter.prototype.getDefault; -RectangleVertexGraphFormatter.prototype.getSelected = ItemGraphFormatter.prototype.getSelected; -RectangleVertexGraphFormatter.prototype.getOver = ItemGraphFormatter.prototype.getOver; -RectangleVertexGraphFormatter.prototype.getDragging = ItemGraphFormatter.prototype.getDragging; -RectangleVertexGraphFormatter.prototype.getId = ItemGraphFormatter.prototype.getId; -RectangleVertexGraphFormatter.prototype.toJSON = ItemGraphFormatter.prototype.toJSON; -RectangleVertexGraphFormatter.prototype.loadFromJSON = ItemGraphFormatter.prototype.loadFromJSON; -RectangleVertexGraphFormatter.prototype._setEvents = ItemGraphFormatter.prototype._setEvents; - -function RectangleVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ - VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); - this.args.type = "RectangleVertexGraphFormatter"; - if (defaultFormat != null){ - if (defaultFormat.radius != null){ - this.defaultFormat.args.radius = defaultFormat.radius; - } - } - - if (selectedFormat != null){ - if (selectedFormat.radius != null){ - this.selected.args.radius = selectedFormat.radius; - } - } - - if (overFormat != null){ - if (overFormat.radius != null){ - this.over.args.radius = overFormat.radius; - } - } - - if (draggingFormat != null){ - if (draggingFormat.radius != null){ - this.dragging.args.draggingFormat = draggingFormat.radius; - } - } -}; - - - -RoundedVertexGraphFormatter.prototype.getDefault = ItemGraphFormatter.prototype.getDefault; -RoundedVertexGraphFormatter.prototype.getSelected = ItemGraphFormatter.prototype.getSelected; -RoundedVertexGraphFormatter.prototype.getOver = ItemGraphFormatter.prototype.getOver; -RoundedVertexGraphFormatter.prototype.getDragging = ItemGraphFormatter.prototype.getDragging; -RoundedVertexGraphFormatter.prototype.getId = ItemGraphFormatter.prototype.getId; -RoundedVertexGraphFormatter.prototype.toJSON = ItemGraphFormatter.prototype.toJSON; -RoundedVertexGraphFormatter.prototype.loadFromJSON = ItemGraphFormatter.prototype.loadFromJSON; -RoundedVertexGraphFormatter.prototype._setEvents = ItemGraphFormatter.prototype._setEvents; - -function RoundedVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ - VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); - this.args.type = "RoundedVertexGraphFormatter"; - if (defaultFormat != null){ - if (defaultFormat.radius != null){ - this.defaultFormat.args.radius = defaultFormat.radius; - } - } - - if (selectedFormat != null){ - if (selectedFormat.radius != null){ - this.selected.args.radius = selectedFormat.radius; - } - } - - if (overFormat != null){ - if (overFormat.radius != null){ - this.over.args.radius = overFormat.radius; - } - } - - if (draggingFormat != null){ - if (draggingFormat.radius != null){ - this.dragging.args.draggingFormat = draggingFormat.radius; - } - } -}; - - - -OctagonVertexGraphFormatter.prototype.getDefault = ItemGraphFormatter.prototype.getDefault; -OctagonVertexGraphFormatter.prototype.getSelected = ItemGraphFormatter.prototype.getSelected; -OctagonVertexGraphFormatter.prototype.getOver = ItemGraphFormatter.prototype.getOver; -OctagonVertexGraphFormatter.prototype.getDragging = ItemGraphFormatter.prototype.getDragging; -OctagonVertexGraphFormatter.prototype.getId = ItemGraphFormatter.prototype.getId; -OctagonVertexGraphFormatter.prototype.toJSON = ItemGraphFormatter.prototype.toJSON; -OctagonVertexGraphFormatter.prototype.loadFromJSON = ItemGraphFormatter.prototype.loadFromJSON; -OctagonVertexGraphFormatter.prototype._setEvents = ItemGraphFormatter.prototype._setEvents; - -function OctagonVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ - VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); - this.args.type = "OctagonVertexGraphFormatter"; - if (defaultFormat != null){ - if (defaultFormat.radius != null){ - this.defaultFormat.args.radius = defaultFormat.radius; - } - } - - if (selectedFormat != null){ - if (selectedFormat.radius != null){ - this.selected.args.radius = selectedFormat.radius; - } - } - - if (overFormat != null){ - if (overFormat.radius != null){ - this.over.args.radius = overFormat.radius; - } - } - - if (draggingFormat != null){ - if (draggingFormat.radius != null){ - this.dragging.args.draggingFormat = draggingFormat.radius; - } - } -}; - - - -var Colors = new function() -{ - this.hashColor = []; - this.getColorByScoreArrayValue = function (arrayScore) - { - var array = new Array(); - - for (var i = 0; i< arrayScore.length; i++) - { - - var color = this.getColorByScoreValue(arrayScore[i]) - array.push( color); - - } - return array; - }; - - this.getHexStringByScoreArrayValue = function (arrayScore) - { - var arrayColor = this.getColorByScoreArrayValue(arrayScore); - var arrayHex = new Array(); - for (var i = 0; i< arrayColor.length; i++) - { - arrayHex.push( arrayColor[i].HexString()); - } - return arrayHex; - }; - - this.getColorByScoreValue = function (score) - { - - var truncate = score.toString().substr(0,4); - if (this.hashColor[truncate]!=null) - { - return this.hashColor[truncate]; - } - - - if(isNaN(score)) { - return Colors.ColorFromRGB(0,0,0); - } - var value; - - var from, to; - if(score < 0.5) { - from = Colors.ColorFromRGB(0,0,255); - to = Colors.ColorFromRGB(255,255,255); - value = (score * 2); - } else { - from = Colors.ColorFromRGB(255,255,255); - to = Colors.ColorFromRGB(255,0,0); - value = (score * 2) - 1; - } - - var x = value; - var y = 1.0 - value; - var color = Colors.ColorFromRGB(y * from.Red() + x * to.Red(), y * from.Green() + x * to.Green(), y * from.Blue() + x * to.Blue()); - - this.hashColor[truncate] = color; - - return color; - }; - - this.ColorFromHSV = function(hue, sat, val) - { - var color = new Color(); - color.SetHSV(hue,sat,val); - return color; - }; - - this.ColorFromRGB = function(r, g, b) - { - var color = new Color(); - color.SetRGB(r,g,b); - return color; - }; - - this.ColorFromHex = function(hexStr) - { - var color = new Color(); - color.SetHexString(hexStr); - return color; - }; - - function Color() { - //Stored as values between 0 and 1 - var red = 0; - var green = 0; - var blue = 0; - - //Stored as values between 0 and 360 - var hue = 0; - - //Strored as values between 0 and 1 - var saturation = 0; - var value = 0; - - this.SetRGB = function(r, g, b) - { - red = r/255.0; - green = g/255.0; - blue = b/255.0; - calculateHSV(); - }; - - this.Red = function() { return Math.round(red*255); }; - - this.Green = function() { return Math.round(green*255); }; - - this.Blue = function() { return Math.round(blue*255); }; - - this.SetHSV = function(h, s, v) - { - hue = h; - saturation = s; - value = v; - calculateRGB(); - }; - - this.Hue = function() - { return hue; }; - - this.Saturation = function() - { return saturation; }; - - this.Value = function() - { return value; }; - - this.SetHexString = function(hexString) - { - if(hexString == null || typeof(hexString) != "string") - { - this.SetRGB(0,0,0); - return; - } - - if (hexString.substr(0, 1) == '#') - hexString = hexString.substr(1); - - if(hexString.length != 6) - { - this.SetRGB(0,0,0); - return; - } - - var r = parseInt(hexString.substr(0, 2), 16); - var g = parseInt(hexString.substr(2, 2), 16); - var b = parseInt(hexString.substr(4, 2), 16); - if (isNaN(r) || isNaN(g) || isNaN(b)) - { - this.SetRGB(0,0,0); - return; - } - - this.SetRGB(r,g,b); - }; - - this.HexString = function() - { - - var rStr = this.Red().toString(16); - if (rStr.length == 1) - rStr = '0' + rStr; - var gStr = this.Green().toString(16); - if (gStr.length == 1) - gStr = '0' + gStr; - var bStr = this.Blue().toString(16); - if (bStr.length == 1) - bStr = '0' + bStr; - return ('#' + rStr + gStr + bStr).toUpperCase(); - }; - - this.Complement = function() - { - var newHue = (hue >= 180) ? hue - 180 : hue + 180; - var newVal = (value * (saturation - 1) + 1); - var newSat = (value*saturation) / newVal; - var newColor = new Color(); - newColor.SetHSV(newHue, newSat, newVal); - return newColor; - } ; - - function calculateHSV() - { - var max = Math.max(Math.max(red, green), blue); - var min = Math.min(Math.min(red, green), blue); - - value = max; - - saturation = 0; - if(max != 0) - saturation = 1 - min/max; - - hue = 0; - if(min == max) - return; - - var delta = (max - min); - if (red == max) - hue = (green - blue) / delta; - else if (green == max) - hue = 2 + ((blue - red) / delta); - else - hue = 4 + ((red - green) / delta); - hue = hue * 60; - if(hue < 0) - hue += 360; - } - - function calculateRGB() - { - red = value; - green = value; - blue = value; - - if(value == 0 || saturation == 0) - return; - - var tHue = (hue / 60); - var i = Math.floor(tHue); - var f = tHue - i; - var p = value * (1 - saturation); - var q = value * (1 - saturation * f); - var t = value * (1 - saturation * (1 - f)); - switch(i) - { - case 0: - red = value; green = t; blue = p; - break; - case 1: - red = q; green = value; blue = p; - break; - case 2: - red = p; green = value; blue = t; - break; - case 3: - red = p; green = q; blue = value; - break; - case 4: - red = t; green = p; blue = value; - break; - default: - red = value; green = p; blue = q; - break; - } - } - } -} -(); -/* - * Clase gestiona la insercción, eliminación de los elementos en el DOM - * - * Vital hacerla SIEMPRE compatible hacia atrás - * - * Last update: 28-10-2010 - * - */ - - -var DOM = {}; - -DOM.createNewElement = function(type, nodeParent, attributes) -{ - - var node = document.createElement(type); - for (var i=0; i0) - { - parent.removeChild(parent.childNodes[0]); - - } -}; - -DOM.select = function(targetID) -{ - return document.getElementById(targetID); -// return $("#"+targetID); -}; -var Geometry = -{ - - /** From tow points obtains the angles formed with the cartesian side **/ - getAngleBetweenTwoPoints : function(x1, y1, x2, y2){ - //var m = (y1 - y2)/ (x1 - x2); - return Math.atan2(y2-y1, x2-x1); - }, - - getAdjacentSideOfRectangleRight : function(angle, hypotenuse){ - return Math.abs(Math.cos(angle)*hypotenuse); - }, - - getOppositeSideOfRectangleRight : function(angle, hypotenuse){ - return Math.abs(Math.sin(angle)*hypotenuse); - }, - - toDegree: function(radian){ - return radian*180/Math.PI; - - } - - -}; - -var SVG = -{ - svgns : 'http://www.w3.org/2000/svg', - xlinkns : "http://www.w3.org/1999/xlink", - - createSVGCanvas: function(parentNode, attributes) - { - - attributes.push( ['xmlns', SVG.svgns], ['xmlns:xlink', 'http://www.w3.org/1999/xlink']); - var svg = document.createElementNS("http://www.w3.org/2000/svg", "svg"); - this._setProperties(svg, attributes); - parentNode.appendChild( svg); - return svg; - - }, - - createRectangle : function (x, y, width, height, attributes){ - var rect = document.createElementNS(this.svgns, "rect"); - rect.setAttribute("x",x); - rect.setAttribute("y",y); - rect.setAttribute("width",width); - rect.setAttribute("height",height); - SVG._setProperties(rect, attributes); - return rect; - }, - - drawImage64 : function (x, y, width, height, base64, svgNode, attributes) { - var node = SVG.createImage64(x, y, width, height, base64, attributes); - svgNode.appendChild(node); - return node; - }, - - createImage64 : function (x, y, width, height, base64, attributes) { - var img = document.createElementNS(this.svgns, "image"); - img.setAttribute("x",x); - img.setAttribute("y",y); - img.setAttribute("width",width); - img.setAttribute("height",height); - img.setAttribute("xlink:href",base64); - SVG._setProperties(img, attributes); - return img; - }, - - createLine: function (x1, y1, x2, y2, attributes){ - var line = document.createElementNS(this.svgns,"line"); - line.setAttribute("x1",x1); - line.setAttribute("y1",y1); - line.setAttribute("x2", x2); - line.setAttribute("y2", y2); - SVG._setProperties(line, attributes); - return line; - }, - - createClip: function (id, nodeToClip, attributes){ - var clip = document.createElementNS(this.svgns,"clipPath"); - clip.setAttribute("id",id); - clip.appendChild(nodeToClip); - return clip; - }, - - drawClip : function (id, nodeToClip, svgNode) { - var node = SVG.createClip(id, nodeToClip); - svgNode.appendChild(node); - return node; - }, - - drawRectangle : function (cx, cy, width, height, svgNode, attributes) { - try{ - var node = SVG.createRectangle(cx, cy, width, height, attributes); - svgNode.appendChild(node); - } - catch(e){ - - console.log("-------------------- "); - console.log("Error on drawRectangle " + e); - console.log(attributes); - console.log("-------------------- "); - } - return node; - }, - - createEllipse : function (x, y, rx, ry, attributes){ - var rect = document.createElementNS(this.svgns, "ellipse"); - rect.setAttribute("cx",x); - rect.setAttribute("cy",y); - rect.setAttribute("rx",rx); - rect.setAttribute("ry",ry); - SVG._setProperties(rect, attributes); - return rect; - }, - - drawEllipse : function (cx, cy, rx, ry, svgNode, attributes) { - var node = SVG.createEllipse(cx, cy, rx, ry, attributes); - svgNode.appendChild(node); - return node; - }, - - drawImage : function (x, y, canvasSVG, attributes) { - var image = document.createElementNS(this.svgns, "image"); - image.setAttribute("x",x); - image.setAttribute("y",y); - canvasSVG.appendChild(image); - SVG._setProperties(image, attributes); - }, - - drawLine : function (x1, y1, x2, y2, nodeSVG, attributes) { - try{ - var line = SVG.createLine(x1, y1, x2, y2, attributes); - nodeSVG.appendChild(line); - }catch(e){ - } - return line; - }, - - - drawPath: function (d, nodeSVG, attributes) { - var path = SVG.createPath(d, attributes); - nodeSVG.appendChild(path); - return path; - }, - - createPoligon : function (points, attributes){ - var poligon = document.createElementNS(this.svgns, "polygon"); - poligon.setAttribute("points",points); - SVG._setProperties(poligon, attributes); - return poligon; - }, - - drawPoligon : function (points, canvasSVG, attributes){ - var poligon = SVG.createPoligon(points, attributes); - canvasSVG.appendChild(poligon); - return poligon; - }, - // - - createPath : function (d, attributes){ - var path = document.createElementNS(this.svgns, "path"); - path.setAttribute("d",d); - SVG._setProperties(path, attributes); - return path; - }, - - drawCircle : function (x, y, radio, canvasSVG, attributes) { - - var newText = document.createElementNS(this.svgns,"circle"); - newText.setAttribute("cx",x); - newText.setAttribute("cy",y); - newText.setAttribute("r",radio); - - canvasSVG.appendChild(newText); - attributes["cursor"] = "pointer"; - this._setProperties(newText, attributes); - return newText; - }, - - - _setProperties: function(node, attributes) - { - if (attributes instanceof Array){ - for (var i=0; i< attributes.length; i++) - { - node.setAttribute(attributes[i][0], attributes[i][1]); - } - } - else{ - for ( var key in attributes){ - node.setAttribute(key, attributes[key]); - } - } - }, - -/* drawPath: function(pointsArray, canvasSVG, attributes){ - var path = document.createElementNS(this.svgns,"polyline"); - path.setAttribute ('id', id); - - var d= pointsArray[0].x+ " "+ pointsArray[0].y; - for (var i=1; i< pointsArray.length; i++) - { - d=d+" "+pointsArray[i].x+" "+pointsArray[i].y; - } - path.setAttribute ('points', d); - canvasSVG.appendChild(path); - },*/ - - createText : function (x, y, text, attributes) { - var node = document.createElementNS(this.svgns,"text"); - node.setAttributeNS(null , "x",x); - node.setAttributeNS(null, "y",y); - - var textNode = document.createTextNode(text); - node.appendChild(textNode); - - this._setProperties(node, attributes); - return node; - }, - - drawText : function (x, y, text, canvasSVG, attributes) { - var text = SVG.createText(x, y, text, attributes); - canvasSVG.appendChild(text); - return text; - }, - - - - drawGroup: function(svgNode, attributes) - { - var group = SVG.createGroup(attributes); - svgNode.appendChild(group); - return group; - }, - - createGroup: function(attributes){ - var group = document.createElementNS(this.svgns,"g"); - this._setProperties(group, attributes); - return group; - } - -}; - - - -var CanvasToSVG = { - - convert: function(sourceCanvas, targetSVG, x, y, id, attributes) { - - var img = this._convert(sourceCanvas, targetSVG, x, y, id); - - for (var i=0; i< attributes.length; i++) - { - img.setAttribute(attributes[i][0], attributes[i][1]); - } - }, - - _convert: function(sourceCanvas, targetSVG, x, y, id) { - var svgNS = "http://www.w3.org/2000/svg"; - var xlinkNS = "http://www.w3.org/1999/xlink"; - // get base64 encoded png from Canvas - var image = sourceCanvas.toDataURL(); - - // must be careful with the namespaces - var svgimg = document.createElementNS(svgNS, "image"); - - svgimg.setAttribute('id', id); - - //svgimg.setAttribute('class', class); - //svgimg.setAttribute('xlink:href', image); - svgimg.setAttributeNS(xlinkNS, 'xlink:href', image); - - - - - svgimg.setAttribute('x', x ? x : 0); - svgimg.setAttribute('y', y ? y : 0); - svgimg.setAttribute('width', sourceCanvas.width); - svgimg.setAttribute('height', sourceCanvas.height); - //svgimg.setAttribute('cursor', 'pointer'); - svgimg.imageData = image; - - targetSVG.appendChild(svgimg); - return svgimg; - }, - - importSVG: function(sourceSVG, targetCanvas) { - svg_xml = sourceSVG;//(new XMLSerializer()).serializeToString(sourceSVG); - var ctx = targetCanvas.getContext('2d'); - - var img = new Image(); - img.src = "data:image/svg+xml;base64," + btoa(svg_xml); -// img.onload = function() { - ctx.drawImage(img, 0, 0); -// }; - } - -}; -/* -Graph.prototype.importSVG = function(sourceSVG, targetCanvas) { - sourceSVG = this._svg; - targetCanvas = document.createElementNS('canvas'); - // https://developer.mozilla.org/en/XMLSerializer - svg_xml = (new XMLSerializer()).serializeToString(sourceSVG); - var ctx = targetCanvas.getContext('2d'); - // this is just a JavaScript (HTML) image - var img = new Image(); - // http://en.wikipedia.org/wiki/SVG#Native_support - // https://developer.mozilla.org/en/DOM/window.btoa - img.src = "data:image/svg+xml;base64," + btoa(svg_xml); - img.onload = function() { - // after this, Canvas’ origin-clean is DIRTY - ctx.drawImage(img, 0, 0); - } -}; -*/ - -/* - -Normalizacion de datos para dibujar colores -Issues: - No sé como debería llamarse esta libreria - No sé si ya existe una funciçon en javascript que lo haga - - -*/ - - -var Normalizer = new function() -{ - this.normalizeArray = function (arrayData) - { - - return this.standardizeArray(this.normal(arrayData)); - -// var result = this._getMaxAndMin(arrayData); -// var min =result[0]; -// var max = result[1]; -// -// -// //los hacemos todos positivos -// for (var i = 0; i< arrayData.length; i++) -// { -// arrayData[i]= Math.abs(min) + parseFloat(arrayData[i]); -// } -// -// var result = this._getMaxAndMin(arrayData); -// var min =result[0]; -// var max = result[1]; -// -// -// var resultArray = new Array(); -// for (var i = 0; i< arrayData.length; i++) -// { -// resultArray.push(arrayData[i]*1/max); -// } -// return resultArray; - }; - - this.normal = function(arrayData){ - var mean = this._getMean(arrayData); - var deviation = this._getStdDeviation(arrayData); - var result = this._getMaxAndMin(arrayData); - var min = result[0]; - var max = result[1]; - - var resultArray = new Array(); - for (var i = 0; i< arrayData.length; i++) { - if (deviation!=0){ - resultArray.push((arrayData[i]-mean)/deviation); - }else{ - resultArray.push(arrayData[i]); - } - } - return resultArray; - }; - - this.standardizeArray = function(arrayData) - { - var result = this._getMaxAndMin(arrayData); - var min = result[0]; - var max = result[1]; - - var offset = ( min <= 0 ) ? Math.abs(min) : (-1 * min); - var resultArray = new Array(); - for (var i = 0; i< arrayData.length; i++) { - if(max + offset!=0){ - resultArray.push((arrayData[i] + offset) / (max + offset)); - }else{ - resultArray.push(arrayData[i]+offset); - } - } - return resultArray; - }; - - - this._getMean = function(arrayData) { - var sum = 0; - for (var i = 0; i< arrayData.length; i++) { - sum = sum + parseFloat(arrayData[i]); - } - return sum/arrayData.length; - }; - - this._getStdDeviation = function(arrayData) { - var mean = this._getMean(arrayData); - var acum = 0.0; - for(var i=0; i max) max = parseFloat(arrayData[i]); - } - - return [min, max]; - }; -}; -function GraphCanvas(componentID, targetNode, args) { - this.args = {}; - /** target */ - this.targetID = targetNode.id; - - /** id manage */ - this.id = componentID; - this.args.idGraph = this.id + "main"; - this.args.idBackgroundNode = this.id + "background"; - - this.args.idEdgesGraph = this.id + "edges"; - this.args.idNodesGraph = this.id + "vertices"; - this.args.idLabelGraph = this.id + "label"; - this.args.idBackground = this.id + "background"; - - /** Objects Graph **/ - this.dataset = null; - this.formatter = null; - this.layout = null; - - /** Drawing **/ - this.circleDefaultRadius = 2; - this.squareDefaultSide = this.circleDefaultRadius * 1.5; - - /** Directed Arrow **/ - this.arrowDefaultSize = this.circleDefaultRadius; - - /** Groups **/ - this.GraphGroup = null; - this.GraphNodeGroup = null; - this.GraphLabelGroup = null; - this.GraphBackground = null; - - /** SETTINGS FLAGS **/ - this.args.draggingCanvasEnabled = false; //Flag to set if the canvas can be dragged - this.args.multipleSelectionEnabled = false; - this.args.interactive = false; - this.args.labeled = false; - this.args.linkEnabled = false; - - /** If numberEdge > maxNumberEdgesMoving then only it will move edges when mouse up **/ - this.args.maxNumberEdgesMoving = 3; - this.args.maxNumberEdgesFiringEvents = 50; - - /** Linking edges **/ - this.args.linking = false; - this.linkStartX = 0; - this.linkStartY = 0; - this.linkSVGNode = null; - this.linkNodeSource = null; - this.linkNodeTarget = null; - - /** Dragging Control **/ - this.draggingElement = null; - this.dragging = false; - this.nMouseOffsetX = 0; - this.nMouseOffsetY = 0; - this.dragStartX = 0; - this.dragStartY = 0; - this.desplazamientoX = 0; - this.desplazamientoY = 0; - - /** Selection Control **/ - this.selecting = false; - this.selectorX = null; - this.selectorY = null; - this.selectorSVGNode = null; - - /** Node status **/ - this.args.isVertexSelected = {}; - this.args.selectedVertices = []; - - /** Edges status **/ - this.args.isEdgeSelected = {}; - //this.args.selectedEdges = []; - - if (args != null) { - if (args.multipleSelectionEnabled != null) { - this.args.multipleSelectionEnabled = args.multipleSelectionEnabled; - this.args.draggingCanvasEnabled = !(this.args.multipleSelectionEnabled); - } - if (args.draggingCanvasEnabled != null) { - this.args.draggingCanvasEnabled = args.draggingCanvasEnabled; - this.args.multipleSelectionEnabled = !(this.args.draggingCanvasEnabled); - } - if (args.interactive != null) { - this.args.interactive = args.interactive; - } - if (args.labeled != null) { - this.args.labeled = args.labeled; - } - - } - - /** Hashmap with the svg node labels **/ - this.svgLabels = {}; - - /** EVENTS **/ - this.onVertexOut = new Event(this); - this.onVertexOver = new Event(this); - this.onVertexSelect = new Event(this); - this.onEdgeSelect = new Event(this); - this.onCanvasClicked = new Event(this); - this.onVertexUp = new Event(this); -} - -GraphCanvas.prototype.showLabels = function(value) { - this.args.labeled = value; - this.removeLabels(); - if (value) { - this.renderLabels(); - } -}; - -GraphCanvas.prototype.getSelectedVertices = function() { - return this.args.selectedVertices; -}; - -GraphCanvas.prototype.getSelectedEdges = function() { - var selected = []; - for ( var selectedEdge in this.args.isEdgeSelected) { - selected.push(selectedEdge); - } - return selected; -}; - -GraphCanvas.prototype.createSVGDom = function(targetID, id, width, height, backgroundColor) { - var container = document.getElementById(targetID); - this._svg = SVG.createSVGCanvas(container, [ - [ "style", "background-color:" + backgroundColor + ";" ], [ "id", id ], [ "dragx", 0 ], [ "dragy", 0 ], - [ "height", this.getFormatter().getHeight() ], [ "width", this.getFormatter().getWidth() ] ]); - return this._svg; -}; - -/** MULTIPLE SELECTION **/ -GraphCanvas.prototype.isMultipleSelectionEnabled = function() { - return this.args.multipleSelectionEnabled; -}; - -GraphCanvas.prototype.setMultipleSelection = function(value) { - this.args.multipleSelectionEnabled = value; - this.args.draggingCanvasEnabled = (!value); -}; - -GraphCanvas.prototype.setSelecting = function(value) { - this.selecting = value; -}; - -/** linking **/ -GraphCanvas.prototype.setLinking = function(value) { - this.args.linkEnabled = value; - this.selecting = !value; - this.dragging = !value; -}; - -/** CANVAS MOVING **/ -GraphCanvas.prototype.setDraggingCanvas = function(value) { - this.args.draggingCanvasEnabled = value; - this.args.multipleSelectionEnabled = !value; -}; - -GraphCanvas.prototype.isDraggingCanvasEnabled = function() { - return this.args.draggingCanvasEnabled; -}; -/** ZOOM **/ -GraphCanvas.prototype.getScale = function() { - return this.getFormatter().getZoomScale(); -}; - -GraphCanvas.prototype.setScale = function(scale) { - var graphNode = document.getElementById(this.args.idGraph); - graphNode.setAttribute("transform", graphNode.getAttribute("transform").replace("scale(" + this.getScale() + ")", "scale(" + scale + ")")); - this.getFormatter().setZoomScale(scale); -}; - -GraphCanvas.prototype.zoomIn = function() { - this.setScale(this.getScale() + this.getFormatter().getZoomScaleStepFactor()); -}; - -GraphCanvas.prototype.zoomOut = function() { - this.setScale(this.getScale() - this.getFormatter().getZoomScaleStepFactor()); - -}; - -/** SVG COORDENATES **/ -GraphCanvas.prototype.getSVGCoordenates = function(evt) { - var p = this._svg.createSVGPoint(); - p.x = evt.clientX; - p.y = evt.clientY; - - var m = this._svg.getScreenCTM(document.documentElement); - p = p.matrixTransform(m.inverse()); - return p; -}; - -/** SVG EVENTS **/ -GraphCanvas.prototype.mouseClick = function(event) { - if (event.button == 0) { - if (!this.args.interactive) { - return; - } - - if (this.isVertex(event.target)) { - this.clickNode(this.getVertexIdFromSVGId(event.target.id)); - } - /** Como el evento mouseClick viene despues del mouse up es aqui donde manejo el tema de deseccionar los elementos que estoy dragging **/ - if (this.dragging) { - this.dragging = false; - } - } -}; - -GraphCanvas.prototype.mouseMove = function(evt) { - if (this.selecting) { - this.clearLabels(); - - var width = (this.getSVGCoordenates(evt).x - this.selectorX); - var height = (this.getSVGCoordenates(evt).y - this.selectorY); - if ((width > 0) && (height > 0)) { - this.displaySelection(this.selectorX, this.selectorY, width, height); - } - if ((width > 0) && (height < 0)) { - this.displaySelection(this.selectorX, this.getSVGCoordenates(evt).y, width, Math.abs(height)); - } - if ((width < 0) && (height < 0)) { - this.displaySelection(this.getSVGCoordenates(evt).x, this.getSVGCoordenates(evt).y, Math.abs(width), Math.abs(height)); - } - if ((width < 0) && (height > 0)) { - this.displaySelection(this.selectorX + width, this.selectorY, Math.abs(width), Math.abs(height)); - } - - var x1 = (parseFloat(this.selectorSVGNode.getAttribute("x")) - DOM.select(this.id).getAttribute("dragx")) / this.getFormatter().getWidth(); - var y1 = (parseFloat(this.selectorSVGNode.getAttribute("y")) - DOM.select(this.id).getAttribute("dragy")) / this.getFormatter().getHeight(); - var x2 = (x1 + parseFloat(this.selectorSVGNode.getAttribute("width") / this.getFormatter().getWidth())); - var y2 = (y1 + parseFloat(this.selectorSVGNode.getAttribute("height") / this.getFormatter().getHeight())); - - this.deselectNodes(this.getLayout()); - var verticesSelected = this.getLayout().getVerticesByArea(x1 / this.getFormatter().getZoomScale(), y1 / this.getFormatter().getZoomScale(), - x2 / this.getFormatter().getZoomScale(), y2 / this.getFormatter().getZoomScale()); - for ( var i = 0; i < verticesSelected.length; i++) { - this.selectNode(verticesSelected[i].getId()); - this.renderLabel(verticesSelected[i].getId()); - } - - } - var p = null; - if (this.args.linking) { - p = this.getSVGCoordenates(evt); - if (this.linkSVGNode != null) { - this.linkSVGNode.setAttribute("x2", p.x - 2); - this.linkSVGNode.setAttribute("y2", p.y - 2); - } - } - - if (this.dragging) { - p = this.getSVGCoordenates(evt); - p.x -= this.nMouseOffsetX; - p.y -= this.nMouseOffsetY; - this.desplazamientoX = (this.getSVGCoordenates(evt).x - this.dragStartX);// + parseFloat(DOM.select(this.id).getAttribute("dragx")); - this.desplazamientoY = (this.getSVGCoordenates(evt).y - this.dragStartY);// + parseFloat(DOM.select(this.id).getAttribute("dragy")); - - if (this.draggingElement != null) { - /** Click sobre el recct del banground que provoca que mueva todo el canvas **/ - if (this.isNodeCanvas(this.draggingElement)) { - - p = this.getSVGCoordenates(evt); - p.x = this.desplazamientoX; - p.y = this.desplazamientoY; - - this.draggingElement.setAttribute("dragx", p.x); - this.draggingElement.setAttribute("dragy", p.y); - this.draggingElement = document.getElementById(this.args.idGraph); - this.draggingElement.setAttribute("transform", "translate(" + p.x + "," + p.y + "), scale(" + this.getScale() + ")"); - - DOM.select(this.id).setAttribute("dragx", p.x); - DOM.select(this.id).setAttribute("dragy", p.y); - - if (this.NodeSVGbackgroundImage != null) { - this.NodeSVGbackgroundImage.setAttribute("dragx", p.x); - this.NodeSVGbackgroundImage.setAttribute("dragy", p.y); - } - } else { - if (this.isVertex(this.draggingElement)) { - this.selectNode(this.getVertexIdFromSVGId(this.draggingElement.id)); - this.desplazamientoX = this.desplazamientoX / this.getFormatter().getZoomScale(); - this.desplazamientoY = this.desplazamientoY / this.getFormatter().getZoomScale(); - this.moveSelectedNodes(this.desplazamientoX, this.desplazamientoY); - - this.dragStartX = this.getSVGCoordenates(evt).x; - this.dragStartY = this.getSVGCoordenates(evt).y; - } else { - if (this.isNodeBackground(this.draggingElement)) { - - this.draggingElement.setAttribute("dragx", p.x); - this.draggingElement.setAttribute("dragy", p.y); - this.draggingElement = document.getElementById(this.args.idGraph); - this.draggingElement.setAttribute("transform", "translate(" + p.x + "," + p.y + "), scale(" + this.getScale() + ")"); - } else { - this.draggingElement.setAttribute("transform", "translate(" + p.x + "," + p.y + ")"); - } - } - } - } - } -}; - -GraphCanvas.prototype.moveSelectedNodes = function(offsetX, offsetY) { - for ( var i = 0; i < this.getSelectedVertices().length; i++) { - - var nodeId = this.getSelectedVertices()[i]; - var svgNodeId = this.getSVGNodeId(nodeId); - - var x = parseFloat(DOM.select(svgNodeId).getAttribute("dragx")) + parseFloat(offsetX);// - parseFloat(DOM.select(this.id).getAttribute("dragx")); - var y = parseFloat(DOM.select(svgNodeId).getAttribute("dragy")) + parseFloat(offsetY);// + parseFloat(DOM.select(this.id).getAttribute("dragy")); - - this._movingNode(DOM.select(svgNodeId), x, y); - } -}; - -GraphCanvas.prototype.mouseDown = function(evt) { - if (event.button == 0) { - - /** if !no interactive mouse events do anything **/ - if (!this.args.interactive) { - return; - } - - var p = this.getSVGCoordenates(evt); - - /** When click on canvas or background deselect all **/ - if (this.isNodeCanvas(evt.target) || this.isNodeBackground(evt.target)) { - this.deselectNodes(); - this.deselectEdges(); - this.onCanvasClicked.notify(); - } - - /** if I am linking vertices **/ - if (this.args.linkEnabled) { - - if (!this.args.linking) { - this.args.linking = true; - if (this.isVertex(evt.target)) { - this.linkStartX = p.x; - this.linkStartY = p.y; - this.linkSVGNode = SVG.drawLine(p.x, p.y, p.x, p.y, this._svg, { - "stroke" : "#FF0000" - }); - this.linkNodeSource = this.getVertexIdFromSVGId(evt.target.id); - } - } else { - this.linkNodeTarget = this.getVertexIdFromSVGId(evt.target.id); - this.args.linking = false; - this.args.linkEnabled = false; - if (this.isVertex(evt.target)) { - this.getDataset().addEdge(this.linkNodeSource + "_" + this.linkNodeTarget, this.linkNodeSource, this.linkNodeTarget, {}); - } - this.linkSVGNode.parentNode.removeChild(this.linkSVGNode); - } - return; - } - - /** Id is a vertex or the canvas **/ - if (this.isVertex(evt.target) || this.isNodeCanvas(evt.target) || this.isNodeBackground(evt.target)) { - this._startDragging(evt); - } - /** if i is edge **/ - if (this.isEdge(evt.target)) { - this.selectEdge(this.getEdgeIdFromSVGId(evt.target.getAttribute("id"))); - } - - if (this.args.multipleSelectionEnabled) { - if (!this.dragging) { - this.setSelecting(true); - this.selectorX = p.x; - this.selectorY = p.y; - this.displaySelection(p.x, p.y, 1, 1); - } - } - - } - if (event.button == 1) { - this.setLinking(false); - this.setMultipleSelection(false); - this.selecting = false; - - /** Id is a vertex or the canvas **/ - if (this.isVertex(evt.target) || this.isNodeCanvas(evt.target) || this.isNodeBackground(evt.target)) { - this._startDragging(evt); - } - } -}; - -GraphCanvas.prototype.mouseUp = function(event) { - if (!this.args.interactive) { - return; - } - - if (this.dragging) { - this._stopDragging(event); - if (this.isVertex(event.target)) { - var vertexId = this.getVertexIdFromSVGId(event.target.id); - if (this.getDataset().getVertexById(vertexId).getEdges().length >= this.args.maxNumberEdgesMoving) { - this.moveEdge(vertexId); - } - } - } - - if (this.selecting) { - this.setSelecting(false); - - var x1 = (parseFloat(this.selectorSVGNode.getAttribute("x")) - DOM.select(this.id).getAttribute("dragx")) / this.getFormatter().getWidth(); - var y1 = (parseFloat(this.selectorSVGNode.getAttribute("y")) - DOM.select(this.id).getAttribute("dragy")) / this.getFormatter().getHeight(); - var x2 = (x1 + parseFloat(this.selectorSVGNode.getAttribute("width") / this.formatter.getWidth())); - var y2 = (y1 + parseFloat(this.selectorSVGNode.getAttribute("height") / this.formatter.getHeight())); - - var verticesSelected = this.getLayout().getVerticesByArea(x1 / this.getFormatter().getZoomScale, y1 / this.getFormatter().getZoomScale, - x2 / this.getFormatter().getZoomScale, y2 / this.getFormatter().getZoomScale); - - for ( var i = 0; i < verticesSelected.length; i++) { - this.selectNode(verticesSelected[i].getId()); - } - - if (this.selectorSVGNode != null) { - this._svg.removeChild(this.selectorSVGNode); - } - - if (this.args.labeled) { - this.clearLabels(); - this.renderLabels(); - } - - this.selectorSVGNode = null; - // this.renderLabels(); - } -}; - -/** SELECTION **/ -GraphCanvas.prototype.displaySelection = function(x, y, width, height) { - if (this.selectorSVGNode != null) { - this.selectorSVGNode.setAttribute("x", x); - this.selectorSVGNode.setAttribute("y", y); - this.selectorSVGNode.setAttribute("width", width); - this.selectorSVGNode.setAttribute("height", height); - } else { - this.selectorSVGNode = SVG.drawRectangle(x, y, width, height, this._svg, { - "fill" : "red", - "stroke" : "black", - "opacity" : "0.2", - "stroke-opacity" : "1" - }); - } -}; - -/** DRAGGING **/ -GraphCanvas.prototype._startDragging = function(evt) { - if (!this.isDraggingCanvasEnabled()) { - if (this.isNodeCanvas(evt.target)) { - this.draggingElement = null; - } - } - - if (this.isVertex(evt.target) || (this.isNodeBackground(evt.target) && (this.isDraggingCanvasEnabled()))|| (this.isNodeCanvas(evt.target) && (this.isDraggingCanvasEnabled()))) { - this.clearLabels(); - this.draggingElement = evt.target; - this.dragging = true; - var p = this.getSVGCoordenates(evt); - - this.nMouseOffsetX = p.x - parseInt(evt.target.getAttribute("dragx")); - this.nMouseOffsetY = p.y - parseInt(evt.target.getAttribute("dragy")); - - if (this.isVertex(evt.target)) { - this.dragStartX = parseInt(this.draggingElement.getAttribute("dragx")) * this.getFormatter().getZoomScale() - + parseFloat(DOM.select(this.id).getAttribute("dragx")); - this.dragStartY = parseInt(this.draggingElement.getAttribute("dragy")) * this.getFormatter().getZoomScale() - + parseFloat(DOM.select(this.id).getAttribute("dragy")); - } else { - this.dragStartX = p.x - parseInt(this.draggingElement.getAttribute("dragx"));// + parseFloat(DOM.select(this.id).getAttribute("dragx")); - this.dragStartY = p.y - parseInt(this.draggingElement.getAttribute("dragy"));// + parseFloat(DOM.select(this.id).getAttribute("dragy")); - } - } -}; - -GraphCanvas.prototype._stopDragging = function(event) { - this.nMouseOffsetX = 0; - this.nMouseOffsetX = 0; - /** despues del evento up viene el evento click entonces acabo el dragging en el mouseclick **/ - this.dragging = false; - this.draggingElement = null; - this.renderLabels(); - - this.setLinking(false); - this.setMultipleSelection(true); - this.selecting = false; - -}; - -/** Move the edges of the vertex with the vertexId indicado **/ -GraphCanvas.prototype.moveEdge = function(vertexId) { - var x = this.getLayout().getNodeById(vertexId).x * this.getFormatter().getWidth(); - var y = this.getLayout().getNodeById(vertexId).y * this.getFormatter().getHeight(); - - /** Moving edges out **/ - for ( var i = 0; i < this.getDataset().getVertexById(vertexId).getEdgesOut().length; i++) { - var edgeId = this.getDataset().getVertexById(vertexId).getEdgesOut()[i].getId(); - var svgEdgeId = this.getSVGEdgeId(edgeId); - var edgeFormatter = this.getFormatter().getEdgeById(edgeId); - if (edgeFormatter instanceof LineEdgeGraphFormatter) { - DOM.select(svgEdgeId + "_shadow").setAttribute("x2", x); - DOM.select(svgEdgeId + "_shadow").setAttribute("y2", y); - DOM.select(svgEdgeId).setAttribute("x2", x); - DOM.select(svgEdgeId).setAttribute("y2", y); - } - - if ((edgeFormatter instanceof DirectedLineEdgeGraphFormatter) || (edgeFormatter instanceof OdirectedLineEdgeGraphFormatter) - || (edgeFormatter instanceof OdotDirectedLineEdgeGraphFormatter) || (edgeFormatter instanceof DotDirectedLineEdgeGraphFormatter) - || (edgeFormatter instanceof CutDirectedLineEdgeGraphFormatter)) { - this.removeEdge(edgeId); - this.renderEdge(edgeId); - } - } - - /** Moving edges in **/ - for ( var i = 0; i < this.getDataset().getVertexById(vertexId).getEdgesIn().length; i++) { - var edgeId = this.getDataset().getVertexById(vertexId).getEdgesIn()[i].getId(); - var svgEdgeId = this.getSVGEdgeId(edgeId); - var edgeFormatter = this.getFormatter().getEdgeById(edgeId); - if (edgeFormatter instanceof LineEdgeGraphFormatter) { - DOM.select(svgEdgeId).setAttribute("x1", x); - DOM.select(svgEdgeId).setAttribute("y1", y); - DOM.select(svgEdgeId + "_shadow").setAttribute("x1", x); - DOM.select(svgEdgeId + "_shadow").setAttribute("y1", y); - } - - if ((edgeFormatter instanceof DirectedLineEdgeGraphFormatter) || (edgeFormatter instanceof OdirectedLineEdgeGraphFormatter) - || (edgeFormatter instanceof OdotDirectedLineEdgeGraphFormatter) || (edgeFormatter instanceof DotDirectedLineEdgeGraphFormatter) - || (edgeFormatter instanceof CutDirectedLineEdgeGraphFormatter)) { - this.removeEdge(edgeId); - this.renderEdge(edgeId); - } - - if (edgeFormatter instanceof BezierEdgeGraphFormatter) { - var radius = this.getFormatter().getVertexById(vertexId).getDefault().getSize() * this.getFormatter().getNodesMaxSize(); - var d = this.calculateCoordenatesBezier(radius, x, y); - DOM.select(svgEdgeId).setAttribute("d", d); - } - } -}; - -GraphCanvas.prototype.moveNode = function(vertexId) { - var x = this.getLayout().getNodeById(vertexId).x * this.getFormatter().getWidth(); - var y = this.getLayout().getNodeById(vertexId).y * this.getFormatter().getHeight(); - var svgNodeElement = DOM.select(this.getSVGNodeId(vertexId)); - - svgNodeElement.setAttribute("dragx", x); - svgNodeElement.setAttribute("dragy", y); - svgNodeElement.setAttribute("transform", "translate(" + x + "," + y + ")"); - - if (this.getDataset().getVertexById(vertexId).getEdges().length < this.args.maxNumberEdgesMoving) { - this.moveEdge(vertexId); - } -}; - -GraphCanvas.prototype._movingNode = function(svgNodeElement, x, y) { - var vertexId = this.getVertexIdFromSVGId(svgNodeElement.getAttribute("id")); - this.getLayout().getNodeById(vertexId).setCoordinates(x / this.getFormatter().getWidth(), y / this.getFormatter().getHeight()); - this.desplazamientoX = 0; - this.desplazamientoY = 0; - this.removeLabel(vertexId); - this.renderLabel(vertexId); -}; - -/** INIT **/ -GraphCanvas.prototype.init = function() { - - this._svg = this.createSVGDom(this.targetID, this.id, this.getFormatter().getWidth(), this.getFormatter().getHeight(), this.getFormatter() - .getBackgroundColor()); - this.GraphGroup = SVG.drawGroup(this._svg, [ [ "id", this.args.idGraph ], [ "transform", "translate(0,0), scale(1)" ] ]); - this.GraphBackground = SVG.drawGroup(this.GraphGroup, [ [ "id", this.args.idBackground ] ]); - this.GraphEdgeGroup = SVG.drawGroup(this.GraphGroup, [ [ "id", this.args.idEdgesGraph ] ]); - this.GraphNodeGroup = SVG.drawGroup(this.GraphGroup, [ [ "id", this.args.idNodesGraph ] ]); - this.GraphLabelGroup = SVG.drawGroup(this.GraphGroup, [ [ "id", this.args.idLabelGraph ] ]); - - if ((this.getFormatter().getBackgroundImage() != null) && (this.getFormatter().getBackgroundImage() != "")) { - this.setBackgroundImage(this.getFormatter().getBackgroundImage()); - } - /** SVG Events listener */ - var _this = this; - this._svg.addEventListener("click", function(event) { - _this.mouseClick(event); - }, false); - this._svg.addEventListener("mousemove", function(event) { - _this.mouseMove(event, _this); - }, false); - this._svg.addEventListener("mousedown", function(event) { - _this.mouseDown(event, _this); - }, false); - this._svg.addEventListener("mouseup", function(event) { - _this.mouseUp(event, _this); - }, false); -}; - -/* - GraphCanvas.prototype.backgroungToSVG = function(){ - var _this = this; - var canvas = document.createElement('canvas'); - canvas.setAttribute("id", "canvas"); - canvas.width = this.formatter.getWidth(); - canvas.height = this.formatter.getHeight(); - - this._svg.parentNode.parentNode.appendChild(canvas); - var ctx = document.getElementById('canvas').getContext('2d'); - var img = new Image(); - - img.src = this.formatter.getBackgroundImage(); - ctx.drawImage(img,0,0 ,_this.formatter.getWidth(), _this.formatter.getHeight()); - - - img.onload = function() { - canvas.parentNode.removeChild(canvas); - } - - this.NodeSVGbackgroundImage.setAttribute("xlink:href", document.getElementById("canvas").toDataURL()); - this.NodeSVGbackgroundImage.removeAttribute("href"); - - // - - };*/ - -GraphCanvas.prototype.setBackgroundImage = function() { - if (this.NodeSVGbackgroundImage != null) { - this.NodeSVGbackgroundImage.parentNode.removeChild(this.NodeSVGbackgroundImage); - } - $('#' + this.targetID).svg(); - $('#' + this.targetID).svg("get"); - - $('#' + this.targetID).svg("get")._svg = document.getElementById(this.id); - - var svg = $('#' + this.targetID).svg("get"); - this.NodeSVGbackgroundImage = svg.image(0, 0, this.getFormatter().getWidth(), this.getFormatter().getHeight(), this.getFormatter() - .getBackgroundImage()); - this.NodeSVGbackgroundImage.setAttribute("id", this.args.idBackgroundNode); - - this.NodeSVGbackgroundImage.setAttribute("x", 0); - this.NodeSVGbackgroundImage.setAttribute("y", 0); - - this.NodeSVGbackgroundImage.setAttribute("dragx", 0); - this.NodeSVGbackgroundImage.setAttribute("dragy", 0); - - if (this.getFormatter().args.backgroundImageHeight != null) { - this.NodeSVGbackgroundImage.setAttribute("height", this.getFormatter().args.backgroundImageHeight); - } - if (this.getFormatter().args.backgroundImageWidth != null) { - this.NodeSVGbackgroundImage.setAttribute("width", this.getFormatter().args.backgroundImageWidth); - } - - if (this.getFormatter().args.backgroundImageX != null) { - this.NodeSVGbackgroundImage.setAttribute("x", this.getFormatter().args.backgroundImageX); - } - if (this.getFormatter().args.backgroundImageY != null) { - this.NodeSVGbackgroundImage.setAttribute("y", this.getFormatter().args.backgroundImageY); - } - - this.GraphBackground.appendChild(this.NodeSVGbackgroundImage); - this.NodeSVGbackgroundImage.removeAttribute("href"); - this.NodeSVGbackgroundImage.setAttribute("xlink:href", this.getFormatter().getBackgroundImage()); -}; - -GraphCanvas.prototype.removeBackgroundImage = function() { - if (this.NodeSVGbackgroundImage != null) { - this.NodeSVGbackgroundImage.parentNode.removeChild(this.NodeSVGbackgroundImage); - } -}; - -GraphCanvas.prototype._setBackgroundColor = function(color) { - var attributes = [ [ "fill", color ] ]; - SVG.drawRectangle(0, 0, this.getFormatter().getWidth(), this.getFormatter().getHeight(), this.GraphBackground, attributes); -}; - -/** Serialize **/ -GraphCanvas.prototype.toJSON = function() { - var json = {}; - json.dataset = {}; - json.formatter = {}; - json.layout = {}; - json.dataset = this.getDataset().toJSON(); - json.formatter = this.getFormatter().toJSON(); - json.layout = this.getLayout().toJSON(); - return json; -}; - -GraphCanvas.prototype.toHTML = function() { - //this.backgroungToSVG(); - var html = this._svg.parentElement.innerHTML; - - var start = html.indexOf("") + 6; - - return html.substr(start, end); -}; - -/** DRAW **/ -GraphCanvas.prototype.draw = function(graphdataset, graphformatter, graphlayout) { - this.setDataset(graphdataset); - this.setFormatter(graphformatter); - this.setLayout(graphlayout); - - var _this = this; - this.getFormatter().changed.attach(function(sender, item) { - _this.removeNode(item.getId()); - _this.renderNode(item.getId()); - if (_this.args.labeled) { - _this.removeLabel(item.getId()); - _this.renderLabel(item.getId()); - } - - }); - //TODO - this.getFormatter().edgeChanged.attach(function(sender, item) { - _this.removeEdge(item.getId()); - _this.renderEdge(item.getId()); - }); - - this.getFormatter().resized.attach(function(sender, item) { - _this.resize(_this.getFormatter().getWidth(), _this.getFormatter().getHeight()); - }); - - this.getFormatter().backgroundImageChanged.attach(function(sender, item) { - _this.setBackgroundImage(_this.getFormatter().getBackgroundImage()); - }); - - this.getFormatter().backgroundColorChanged.attach(function(sender, item) { - _this._setBackgroundColor(_this.getFormatter().getBackgroundColor()); - }); - - this.getLayout().changed.attach(function(sender, item) { - _this.moveNode(item.getId()); - _this.moveEdge(item.getId()); - if (_this.args.labeled) { - _this.removeLabel(item.getId()); - _this.renderLabel(item.getId()); - } - }); - - this.getDataset().newVertex.attach(function(sender, item) { - - _this.renderNode(item.getId()); - if (_this.args.labeled) { - _this.renderLabel(item.getId()); - } - }); - - this.getDataset().newEdge.attach(function(sender, item) { - _this.renderEdge(item.getId()); - }); - - this.getDataset().vertexDeleted.attach(function(sender, item) { - _this.removeNode(item.getId()); - if (_this.args.labeled) { - _this.removeLabel(item.getId()); - } - }); - - this.getDataset().edgeDeleted.attach(function(sender, item) { - _this.removeEdge(item.getId()); - }); - - this.getDataset().vertexNameChanged.attach(function(sender, args) { - if (_this.args.labeled) { - _this.removeLabel(args.item.getId()); - _this.removeLabel(args.item.getId()); - _this.renderLabel(args.item.getId()); - } - }); - this.init(); - this.render(); -}; - -GraphCanvas.prototype.render = function() { - for ( var id in this.getDataset().getVertices()) { - this.renderNode(id); - } - this.renderLabels(); - this.renderEdges(); -}; - -GraphCanvas.prototype.renderLabels = function() { - if (this.args.labeled) { - for ( var id in this.getDataset().getVertices()) { - this.renderLabel(id); - } - } -}; - -GraphCanvas.prototype.removeLabels = function() { - for ( var id in this.getDataset().getVertices()) { - this.removeLabel(id); - } -}; - -/** Utilities method for nodes **/ -GraphCanvas.prototype.isNodeCanvas = function(node) { - return ((node.id == this.args.idGraph) || (node.id == this.id)); -}; - -GraphCanvas.prototype.isNodeBackground = function(node) { - return ((node.id == this.args.idBackgroundNode)); -}; - -GraphCanvas.prototype.isVertex = function(node) { - if (node.getAttribute("id") != null) { - if (node.getAttribute("id").indexOf("_v_") != -1) { - return true; - } - } - return false; -}; - -GraphCanvas.prototype.isLabel = function(node) { - if (node.getAttribute("id") != null) { - if (node.getAttribute("id").indexOf("_l_") != -1) { - return true; - } - } - return false; -}; - -GraphCanvas.prototype.isEdge = function(node) { - if (node.getAttribute("id") != null) { - if (node.getAttribute("id").indexOf("_e_") != -1) { - return true; - } - } - return false; -}; - -/** Resize **/ -GraphCanvas.prototype.resize = function(width, height) { - // this._svg.setAttribute("width", width); - // this._svg.setAttribute("height", height); - if (this.NodeSVGbackgroundImage != null) { - this.NodeSVGbackgroundImage.setAttribute("width", width); - this.NodeSVGbackgroundImage.setAttribute("height", height); - } - - this._svg.setAttribute("width", width); - this._svg.setAttribute("height", height); - - this.clearCanvas(); - this.render(); -}; - -GraphCanvas.prototype.clearCanvas = function() { - DOM.removeChilds(this.GraphEdgeGroup.getAttribute("id")); - DOM.removeChilds(this.GraphNodeGroup.getAttribute("id")); - this.clearLabels(); -}; - -GraphCanvas.prototype.clearLabels = function() { - DOM.removeChilds(this.GraphLabelGroup.getAttribute("id")); -}; - -/** ID'S converter **/ -GraphCanvas.prototype.getSVGNodeId = function(nodeId) { - return this.id + "_v_" + nodeId; -}; - -GraphCanvas.prototype.getSVGEdgeId = function(edgeId) { - return this.id + "_e_" + edgeId; -}; - -GraphCanvas.prototype.getSVGArrowEdgeId = function(edgeId) { - return this.id + "_arrow_" + edgeId; -}; - -GraphCanvas.prototype.getSVGLabelId = function(edgeId) { - return this.id + "_l_" + edgeId; -}; - -GraphCanvas.prototype.blinkVertexById = function(vertexId) { - $("#" + this.getSVGNodeId(vertexId)).fadeIn().fadeOut().fadeIn().fadeOut().fadeIn().fadeOut(); -}; - -GraphCanvas.prototype.getVertexIdFromSVGId = function(svgVertexId) { - return svgVertexId.replace(this.id, "").replace("_v_", ""); -}; - -GraphCanvas.prototype.getEdgeIdFromSVGId = function(svgEdgeId) { - return svgEdgeId.replace(this.id, "").replace("_e_", ""); -}; - -/** VERTEX **/ -GraphCanvas.prototype.getVertexById = function(id) { - return document.getElementById(this.getSVGNodeId(id)); -}; - -GraphCanvas.prototype.renderNodes = function() { - for ( var id in this.getDataset().getVertices()) { - this.renderNode(id); - } -}; - -GraphCanvas.prototype.overNode = function(nodeId) { - if (!this.args.interactive) { - return; - } - /** If selected we don't change the format **/ - if (this.args.isVertexSelected[nodeId] == null) { - var args = this.getFormatter().getVertexById(nodeId).getOver(); - args.args["cursor"] = 'pointer'; - this.changeVertexFormat(nodeId, args); - } -}; - -GraphCanvas.prototype.outNode = function(nodeId) { - if (!this.args.interactive) { - return; - } - - /** If selected we don't change the format **/ - if (this.args.isVertexSelected[nodeId] == null) { - this.changeVertexFormat(nodeId, this.getFormatter().getVertexById(nodeId).getDefault()); - } -}; - -GraphCanvas.prototype.overLabel = function(nodeId) { - this.overNode(nodeId); - // this.svgLabels[nodeId].setAttribute("cursor", "pointer"); -}; - -GraphCanvas.prototype.outLabel = function(nodeId) { - this.outNode(nodeId); - // this.svgLabels[nodeId].setAttribute("cursor", ""); -}; - -GraphCanvas.prototype.clickNode = function(nodeId) { - if (!this.args.interactive) { - return; - } - - /** si el evento se dispara oprque estaba dragging entonces no activo nada **/ - if (this.args.isVertexSelected[nodeId] == null) { - this.selectNode(nodeId); - } else { - this.deselectNode(nodeId); - } -}; - -GraphCanvas.prototype.selectNode = function(nodeId) { - for ( var i = 0; i < this.args.selectedVertices.length; i++) { - var format = this.getFormatter().getVertexById(nodeId).getSelected(); - format.opacity = 0.2; - this.changeVertexFormat(nodeId, this.getFormatter().getVertexById(nodeId).getSelected()); - } - - if (this.args.isVertexSelected[nodeId] == null) { - var format = this.getFormatter().getVertexById(nodeId).getSelected(); - format.opacity = 1; - this.changeVertexFormat(nodeId, this.getFormatter().getVertexById(nodeId).getSelected()); - this.args.selectedVertices.push(nodeId); - this.args.isVertexSelected[nodeId] = this.args.selectedVertices.length - 1; - this.onVertexSelect.notify(nodeId); - } -}; - -GraphCanvas.prototype.selectAllEdges = function() { - this.deselectNodes(); - this.deselectEdges(); - - for ( var edgesId in this.getDataset().edges) { - this.selectEdge(edgesId); - } -}; - -GraphCanvas.prototype.selectAllNodes = function() { - this.deselectNodes(); - this.deselectEdges(); - - for ( var vertexId in this.getDataset().vertices) { - this.selectNode(vertexId); - } -}; - -GraphCanvas.prototype.selectAll = function() { - this.deselectNodes(); - this.deselectEdges(); - - for ( var vertexId in this.getDataset().vertices) { - this.selectNode(vertexId); - } - - for ( var edgesId in this.getDataset().edges) { - this.selectEdge(edgesId); - } -}; - -GraphCanvas.prototype.selectEdge = function(edgeId) { - if (this.args.isEdgeSelected[edgeId] == null) { - this.changeEdgeFormat(edgeId, this.getFormatter().getEdgeById(edgeId).getSelected()); - //this.args.selectedEdges.push(edgeId); - this.args.isEdgeSelected[edgeId] = true; //this.args.selectedEdges.length - 1; - this.onEdgeSelect.notify(edgeId); - } -}; - -GraphCanvas.prototype.selectEdges = function(edges) { - - for ( var i = 0; i < edges.length; i++) { - this.selectEdge(edges[i]); - } -}; - -GraphCanvas.prototype.deselectNode = function(nodeId) { - if (this.args.isVertexSelected[nodeId] != null) { - this.changeVertexFormat(nodeId, this.getFormatter().getVertexById(nodeId).getDefault()); - this.args.selectedVertices.splice(this.args.isVertexSelected[nodeId], 1); - var index = this.args.isVertexSelected[nodeId]; - delete this.args.isVertexSelected[nodeId]; - - for ( var vertex in this.args.isVertexSelected) { - if (this.args.isVertexSelected[vertex] > index) { - this.args.isVertexSelected[vertex] = this.args.isVertexSelected[vertex] - 1; - } - } - } -}; - -GraphCanvas.prototype.deselectNodes = function() { - var selected = JSON.parse(JSON.stringify(this.getSelectedVertices())); - for ( var i = 0; i < selected.length; i++) { - this.deselectNode(selected[i]); - } -}; -GraphCanvas.prototype.selectNodes = function(idNodes) { - - for ( var i = 0; i < idNodes.length; i++) { - this.selectNode(idNodes[i]); - } - - // for ( var vertex in this.args.isVertexSelected) { - // if (this.args.isVertexSelected[vertex] > index){ - // this.args.isVertexSelected[vertex] = this.args.isVertexSelected[vertex] - 1; - // } - // } - -}; - -GraphCanvas.prototype.changeVertexFormat = function(nodeId, format) { - var svgNode = DOM.select(this.getSVGNodeId(nodeId)); - if (svgNode != null) { - var properties = format.toJSON(); - for ( var item in properties) { - svgNode.setAttribute(item, properties[item]); - } - - if (this.getFormatter().getVertexById(nodeId) instanceof CircleVertexGraphFormatter) { - var transform = "translate(" + svgNode.getAttribute("dragx") + "," + svgNode.getAttribute("dragy") + "), scale(" + format.getSize() + ")"; - svgNode.setAttribute("transform", transform); - } - } -}; - -GraphCanvas.prototype.renderLabel = function(nodeId) { - var x = Math.ceil(this.getLayout().getNodeById(nodeId).x * this.getFormatter().getWidth()); - var y = Math.ceil(this.getLayout().getNodeById(nodeId).y * this.getFormatter().getHeight()); - - var svgAttributesNode = JSON.parse(JSON.stringify(this.getFormatter().getVertexById(nodeId).getDefault().toJSON().title)); - svgAttributesNode.id = this.getSVGLabelId(this.getDataset().getVertexById(nodeId).getId()); - svgAttributesNode.dx = (-1) * (this.getDataset().getVertexById(nodeId).getName().length * svgAttributesNode["font-size"]) / 4 - 4; - - svgAttributesNode.dy = parseFloat((this.getFormatter().getVertexById(nodeId).getDefault().getSize())) - + parseFloat(svgAttributesNode["font-size"]) + parseFloat(this.getFormatter().getVertexById(nodeId).getDefault().getStrokeWidth()) - 4; - svgAttributesNode.dragx = Math.ceil(this.getLayout().getNodeById(nodeId).x * this.getFormatter().getWidth()); - - var gragy = parseFloat(this.getFormatter().getVertexById(nodeId).getDefault().getSize()) - + Math.ceil(this.getLayout().getNodeById(nodeId).y * this.getFormatter().getHeight()); - svgAttributesNode.dragy = gragy; - svgAttributesNode.transform = "translate(" + svgAttributesNode.dragx + "," + svgAttributesNode.dragy + ")";//, scale("+this.formatter.getVertexById(nodeId).getDefault().getSize()+")"; - - var nodeSVG = SVG.drawText(0, 0, this.getDataset().getVertexById(nodeId).getName(), this.GraphLabelGroup, svgAttributesNode); - - this.svgLabels[nodeId] = nodeSVG; - - /** Events for the SVG node **/ - var _this = this; - if (nodeSVG != null) { - nodeSVG.addEventListener("mouseover", function() { - _this.overLabel(nodeId); - }, false); - nodeSVG.addEventListener("mouseout", function() { - _this.outLabel(nodeId); - }, false); - } - -}; - -GraphCanvas.prototype.removeLabel = function(labelId) { - if (DOM.select(this.getSVGLabelId(labelId)) != null) { - DOM.select(this.getSVGLabelId(labelId)).parentNode.removeChild(DOM.select(this.getSVGLabelId(labelId))); - } -}; - -GraphCanvas.prototype.renderNode = function(nodeId) { - var svgAttributesNode = JSON.parse(JSON.stringify(this.getFormatter().getVertexById(nodeId).getDefault().toJSON())); - svgAttributesNode.dragx = Math.ceil(this.getLayout().getNodeById(nodeId).x * this.getFormatter().getWidth()); - svgAttributesNode.dragy = Math.ceil(this.getLayout().getNodeById(nodeId).y * this.getFormatter().getHeight()); - svgAttributesNode.transform = "translate(" + svgAttributesNode.dragx + "," + svgAttributesNode.dragy + ")"; - svgAttributesNode.id = this.getSVGNodeId(nodeId); - /*svgAttributesNode["stroke-width"] = 3 ; - svgAttributesNode["stroke-opacity"] = 1 ; - svgAttributesNode["fill-opacity"] = svgAttributesNode["opacity"] ; - svgAttributesNode["opacity"] = 1 ;*/ - this.circleDefaultRadius = this.getFormatter().getVertexById(nodeId).getDefault().getSize(); - var nodeSVG; - - if (this.getFormatter().getVertexById(nodeId) instanceof CircleVertexGraphFormatter) { - nodeSVG = SVG.drawCircle(0, 0, this.circleDefaultRadius, this.GraphNodeGroup, svgAttributesNode); - } - - if (this.getFormatter().getVertexById(nodeId) instanceof SquareVertexGraphFormatter) { - //nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius) ,0 - (this.formatter.getVertexById(nodeId).getDefault().getSize()) , (this.getFormatter().getVertexById(nodeId).getDefault().getSize()*2), (this.getFormatter().getVertexById(nodeId).getDefault().getSize()*2), this.GraphNodeGroup, svgAttributesNode); - nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius), 0 - (this.circleDefaultRadius), (this.circleDefaultRadius * 2), - (this.circleDefaultRadius * 2), this.GraphNodeGroup, svgAttributesNode); - } - - if (this.getFormatter().getVertexById(nodeId) instanceof EllipseVertexGraphFormatter) { - nodeSVG = SVG.drawEllipse(0, 0, this.circleDefaultRadius * 1.5, this.circleDefaultRadius, this.GraphNodeGroup, svgAttributesNode); - } - - if (this.getFormatter().getVertexById(nodeId) instanceof RectangleVertexGraphFormatter) { - //nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius) ,0 - ((this.circleDefaultRadius*2)/2) , (this.circleDefaultRadius*2), (this.circleDefaultRadius), this.GraphNodeGroup, svgAttributesNode); - nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius * 1.5), 0 - (this.circleDefaultRadius), (this.circleDefaultRadius * 2 * 1.5), - (this.circleDefaultRadius * 2), this.GraphNodeGroup, svgAttributesNode); - - } - - if (this.getFormatter().getVertexById(nodeId) instanceof RoundedVertexGraphFormatter) { - svgAttributesNode.ry = 2;// this.formatter.getVertexById(nodeId).getDefault().getSize()/4; - svgAttributesNode.rx = 2;// this.formatter.getVertexById(nodeId).getDefault().getSize()/4; - nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius * 1.5), 0 - (this.circleDefaultRadius), (this.circleDefaultRadius * 2 * 1.5), - (this.circleDefaultRadius * 2), this.GraphNodeGroup, svgAttributesNode); - } - - // - - if (this.getFormatter().getVertexById(nodeId) instanceof OctagonVertexGraphFormatter) { - svgAttributesNode.ry = 2; - svgAttributesNode.rx = 2; - nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius * 1.5), 0 - (this.circleDefaultRadius), (this.circleDefaultRadius * 2 * 1.5), - (this.circleDefaultRadius * 2), this.GraphNodeGroup, svgAttributesNode); - } - - nodeSVG.internalId = nodeId; - // - var _this = this; - - /** Events for the SVG node **/ - if (nodeSVG != null) { - nodeSVG.addEventListener("mouseover", function() { - _this.onVertexOver.notify(nodeId); - _this.overNode(nodeId); - }, false); - nodeSVG.addEventListener("mouseout", function() { - _this.onVertexOut.notify(nodeId); - _this.outNode(nodeId); - }, false); - //nodeSVG.addEventListener("click", function(){_this.clickNode(nodeId);}, false); - // - nodeSVG.addEventListener("mouseup", function() { - _this.onVertexUp.notify(nodeId); - }, false); - } -}; - -GraphCanvas.prototype.removeNode = function(nodeId) { - DOM.select(this.getSVGNodeId(nodeId)).parentNode.removeChild(DOM.select(this.getSVGNodeId(nodeId))); - if (this.args.labeled) { - this.removeLabel(nodeId); - } -}; - -/** REMOVING **/ -GraphCanvas.prototype.removeSelected = function() { - /** El orden importa **/ - this.removeSelectedEdges(); - this.removeSelectedNode(); - -}; - -GraphCanvas.prototype.removeSelectedNode = function() { - var selected = JSON.parse(JSON.stringify(this.getSelectedVertices())); - this.deselectNodes(); - var sorted = selected.sort(function(a, b) { - return a - b - }); - for ( var i = 0; i < sorted.length; i++) { - if (this.getDataset().getVertexById(sorted[i]) != null) { - this.getDataset().getVertexById(sorted[i]).remove(); - } - } -}; - -/** EDGES **/ -GraphCanvas.prototype.removeEdge = function(edgeId) { - if (DOM.select(this.getSVGEdgeId(edgeId)) != null) { - DOM.select(this.getSVGEdgeId(edgeId)).parentNode.removeChild(DOM.select(this.getSVGEdgeId(edgeId))); - } - - if (DOM.select(this.getSVGEdgeId(edgeId) + "_shadow") != null) { - DOM.select(this.getSVGEdgeId(edgeId) + "_shadow").parentNode.removeChild(DOM.select(this.getSVGEdgeId(edgeId) + "_shadow")); - } - - if (DOM.select(this.getSVGArrowEdgeId(edgeId)) != null) { - DOM.select(this.getSVGArrowEdgeId(edgeId)).parentNode.removeChild(DOM.select(this.getSVGArrowEdgeId(edgeId))); - } -}; - -GraphCanvas.prototype.overEdge = function(edgeId) { - if ((!this.args.interactive) || this.dragging || this.selecting) { - return; - } - - /** If selected we don't change the format **/ - if (this.args.isEdgeSelected[edgeId] == null) { - var format = this.getFormatter().getEdgeById(edgeId).getOver(); - format.args["cursor"] = "pointer"; - this.changeEdgeFormat(edgeId, format); - } -}; - -GraphCanvas.prototype.outEdge = function(edgeId) { - if (!this.args.interactive) { - return; - } - - /** If selected we don't change the format **/ - if (this.args.isEdgeSelected[edgeId] == null) { - this.changeEdgeFormat(edgeId, this.getFormatter().getEdgeById(edgeId).getDefault()); - } -}; - -GraphCanvas.prototype.changeEdgeFormat = function(edgeId, format) { - var svgEdge = DOM.select(this.getSVGEdgeId(edgeId) + "_shadow"); - if (svgEdge != null) { - var properties = format.toJSON(); - for ( var item in properties) { - svgEdge.setAttribute(item, properties[item]); - } - } -}; - -GraphCanvas.prototype.deselectEdge = function(edgeID) { - if (this.args.isEdgeSelected[edgeID] != null) { - this.changeEdgeFormat(edgeID, this.getFormatter().getEdgeById(edgeID).getDefault()); - var index = this.args.isEdgeSelected[edgeID]; - delete this.args.isEdgeSelected[edgeID]; - } -}; - -GraphCanvas.prototype.deselectEdges = function() { - var selected = JSON.parse(JSON.stringify(this.getSelectedEdges())); - for ( var i = 0; i < selected.length; i++) { - this.deselectEdge(selected[i]); - } -}; - -GraphCanvas.prototype.removeSelectedEdges = function() { - var selected = JSON.parse(JSON.stringify(this.getSelectedEdges())); - this.deselectEdges(); - for ( var i = 0; i < selected.length; i++) { - if (this.getDataset().getEdgeById(selected[i]) != null) { - this.getDataset().getEdgeById(selected[i]).remove(); - } - } -}; - -GraphCanvas.prototype.renderEdge = function(edgeId) { - var svgAttributesEdge = this.getFormatter().getEdgeById(edgeId).getDefault().toJSON(); - var edge = this.getDataset().getEdgeById(edgeId); - - var svgNodeTarget = this.getVertexById(edge.getNodeTarget().getId()); - var svgNodeSource = this.getVertexById(edge.getNodeSource().getId()); - svgAttributesEdge.id = this.getSVGEdgeId(edge.getId()) + "_shadow"; - - var svgEdge = null; - - if (this.getFormatter().getEdgeById(edgeId) instanceof LineEdgeGraphFormatter) { - var coordenateSourceX = svgNodeSource.getAttribute("dragx"); - var coordenateSourceY = svgNodeSource.getAttribute("dragy"); - var coordenateTargetX = svgNodeTarget.getAttribute("dragx"); - var coordenateTargetY = svgNodeTarget.getAttribute("dragy"); - - SVG.drawLine(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, this.GraphEdgeGroup, svgAttributesEdge); - var attributesShadow = {}; - attributesShadow.id = this.getSVGEdgeId(edge.getId()); - attributesShadow["stroke-opacity"] = 0; - attributesShadow["stroke-width"] = 4; - attributesShadow["stroke"] = "black"; - svgEdge = SVG.drawLine(svgNodeSource.getAttribute("dragx"), svgNodeSource.getAttribute("dragy"), svgNodeTarget.getAttribute("dragx"), - svgNodeTarget.getAttribute("dragy"), this.GraphEdgeGroup, attributesShadow); - } - - if (this.getFormatter().getEdgeById(edgeId) instanceof BezierEdgeGraphFormatter) { - var nodeId = edge.getNodeTarget().getId(); - var nodeSize = this.formatter.getVertexById(nodeId).getDefault().getSize() * this.getFormatter().getNodesMaxSize(); - svgAttributesEdge.fill = "none"; - svgAttributesEdge.id = this.getSVGEdgeId(edgeId); - var d = this.calculateCoordenatesBezier(nodeSize, svgNodeSource.getAttribute("dragx"), svgNodeSource.getAttribute("dragy")); - svgEdge = SVG.drawPath(d, this.GraphEdgeGroup, svgAttributesEdge); - } - ; - - if ((this.getFormatter().getEdgeById(edgeId) instanceof DirectedLineEdgeGraphFormatter) - || (this.getFormatter().getEdgeById(edgeId) instanceof CutDirectedLineEdgeGraphFormatter) - || (this.getFormatter().getEdgeById(edgeId) instanceof DotDirectedLineEdgeGraphFormatter) - || (this.getFormatter().getEdgeById(edgeId) instanceof OdotDirectedLineEdgeGraphFormatter) - || (this.getFormatter().getEdgeById(edgeId) instanceof OdirectedLineEdgeGraphFormatter)) { - var coordenateSourceX = svgNodeSource.getAttribute("dragx"); - var coordenateSourceY = svgNodeSource.getAttribute("dragy"); - var coordenateTargetX = svgNodeTarget.getAttribute("dragx"); - var coordenateTargetY = svgNodeTarget.getAttribute("dragy"); - - var offset = parseFloat(this.getFormatter().getVertexById(this.getDataset().getEdgeById(edgeId).getNodeTarget().getId()).getDefault() - .getSize() - * this.circleDefaultRadius); - var point = this._calculateEdgePointerPosition(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, offset); - coordenateTargetX = point.x; - coordenateTargetY = point.y; - SVG.drawLine(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, this.GraphEdgeGroup, svgAttributesEdge); - - var attributesShadow = {}; - attributesShadow.id = this.getSVGEdgeId(edge.getId()); - attributesShadow["stroke-opacity"] = 0; - attributesShadow["stroke-width"] = 4; - attributesShadow["stroke"] = "black"; - svgEdge = SVG.drawLine(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, this.GraphEdgeGroup, attributesShadow); - } - - if (this.getFormatter().getEdgeById(edgeId) instanceof DirectedLineEdgeGraphFormatter - || (this.getFormatter().getEdgeById(edgeId) instanceof OdirectedLineEdgeGraphFormatter)) { - var coordenateSourceX = svgNodeSource.getAttribute("dragx"); - var coordenateSourceY = svgNodeSource.getAttribute("dragy"); - var coordenateTargetX = svgNodeTarget.getAttribute("dragx"); - var coordenateTargetY = svgNodeTarget.getAttribute("dragy"); - - var point = this._calculateEdgePointerPosition(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, offset); - coordenateTargetX = point.x; - coordenateTargetY = point.y; - - var angle = Geometry.toDegree(point.angle) + 90; - this.arrowDefaultSize = this.getFormatter().getEdgeById(edgeId).getArrowSize(); //getDefault().getArrowSize(); - var d = "-" + this.arrowDefaultSize + ",0 0,-" + parseFloat(this.arrowDefaultSize) * 2 + " " + this.arrowDefaultSize + ",0"; - - var attributes; - - if (this.getFormatter().getEdgeById(edgeId) instanceof DirectedLineEdgeGraphFormatter) { - attributes = [ - [ "fill", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], - [ "stroke", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], [ "id", this.getSVGArrowEdgeId(edgeId) ] ]; - } else { - attributes = [ - [ "fill", "#FFFFFF" ], [ "stroke", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], - [ "id", this.getSVGArrowEdgeId(edgeId) ] ]; - } - - var flechaSVGNode = SVG.drawPoligon(d, this.GraphEdgeGroup, attributes);//, ["transform", "rotate("+angle+"), translate(0,0)"]]); - flechaSVGNode.setAttribute("transform", " translate(" + coordenateTargetX + ", " + coordenateTargetY + "), rotate(" + angle + ")"); - } - ; - - if (this.getFormatter().getEdgeById(edgeId) instanceof CutDirectedLineEdgeGraphFormatter) { - var coordenateSourceX = svgNodeSource.getAttribute("dragx"); - var coordenateSourceY = svgNodeSource.getAttribute("dragy"); - var coordenateTargetX = svgNodeTarget.getAttribute("dragx"); - var coordenateTargetY = svgNodeTarget.getAttribute("dragy"); - - var point = this._calculateEdgePointerPosition(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, offset); - coordenateTargetX = point.x; - coordenateTargetY = point.y; - - var angle = Geometry.toDegree(point.angle) + 90; - - //this.arrowDefaultSize = 2; //getDefault().getArrowSize(); - var d = "-4,0 4,0 4,-2 -4,-2"; - - var flechaSVGNode = SVG.drawPoligon(d, this.GraphEdgeGroup, [ - [ "fill", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], - [ "stroke", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], [ "id", this.getSVGArrowEdgeId(edgeId) ] ]);//, ["transform", "rotate("+angle+"), translate(0,0)"]]); - flechaSVGNode.setAttribute("transform", " translate(" + coordenateTargetX + ", " + coordenateTargetY + "), rotate(" + angle + ")"); - } - ; - - if ((this.getFormatter().getEdgeById(edgeId) instanceof DotDirectedLineEdgeGraphFormatter) - || (this.getFormatter().getEdgeById(edgeId) instanceof OdotDirectedLineEdgeGraphFormatter)) { - var coordenateSourceX = svgNodeSource.getAttribute("dragx"); - var coordenateSourceY = svgNodeSource.getAttribute("dragy"); - var coordenateTargetX = svgNodeTarget.getAttribute("dragx"); - var coordenateTargetY = svgNodeTarget.getAttribute("dragy"); - var point = this._calculateEdgePointerPosition(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, offset); - coordenateTargetX = point.x; - coordenateTargetY = point.y; - var angle = Geometry.toDegree(point.angle) + 90; - // this.arrowDefaultSize = this.formatter.getEdgeById(edgeId).getArrowSize(); //getDefault().getArrowSize(); - var attributes = []; - if (this.getFormatter().getEdgeById(edgeId) instanceof OdotDirectedLineEdgeGraphFormatter) { - attributes = [ - [ "fill", "#FFFFFF" ], [ "stroke", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], - [ "id", this.getSVGArrowEdgeId(edgeId) ] ]; - } else { - attributes = [ - [ "fill", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], - [ "stroke", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], [ "id", this.getSVGArrowEdgeId(edgeId) ] ]; - } - var flechaSVGNode = SVG.drawCircle(0, 0, 4, this.GraphEdgeGroup, attributes); - flechaSVGNode.setAttribute("transform", " translate(" + coordenateTargetX + ", " + coordenateTargetY + "), rotate(" + angle + ")"); - } - ; - - var _this = this; - /** Events for the SVG edge **/ - if (svgEdge != null) { - if (this.getDataset().getEdgesCount() < this.args.maxNumberEdgesFiringEvents) { - svgEdge.addEventListener("mouseover", function() { - _this.overEdge(edgeId); - }, false); - svgEdge.addEventListener("mouseout", function() { - _this.outEdge(edgeId); - }, false); - } - } -}; - -GraphCanvas.prototype._calculateEdgePointerPosition = function(sourceX, sourceY, targetX, targetY, radius) { - var angle = Geometry.getAngleBetweenTwoPoints(sourceX, sourceY, targetX, targetY); - - /** Suponiendo el node source que este a la derecha **/ - if ((targetX - sourceX) < 0) { - var b = Geometry.getAdjacentSideOfRectangleRight(angle, radius); - targetX = parseFloat(targetX) + parseFloat(b); - arrowX = parseFloat(targetX) + parseFloat(b) + this.arrowDefaultSize / 2; - } else { - var b = Geometry.getAdjacentSideOfRectangleRight(angle, radius); - targetX = parseFloat(targetX) - parseFloat(b); - arrowX = parseFloat(targetX) - parseFloat(b) - this.arrowDefaultSize / 2; - } - - /** Suponiendo el node source que este a la arriba **/ - if ((targetY - sourceY) > 0) { - var a = Geometry.getOppositeSideOfRectangleRight(angle, radius); - targetY = parseFloat(targetY) - parseFloat(a); - arrowY = parseFloat(targetY) - parseFloat(a) - this.arrowDefaultSize / 2; - } else { - var a = Geometry.getOppositeSideOfRectangleRight(angle, radius); - targetY = parseFloat(targetY) + parseFloat(a); - arrowY = parseFloat(targetY) + parseFloat(a) - this.arrowDefaultSize / 2; - - } - - return { - "x" : arrowX, - "y" : arrowY, - "angle" : angle - }; -}; - -GraphCanvas.prototype.calculateCoordenatesBezier = function(nodeSize, x1, y1) { - var x11 = x1 - (nodeSize / 2); - var y11 = y1 - (nodeSize / 2); - - var x12 = parseFloat(x1) + parseFloat(nodeSize / 2); - var y12 = y1 - (nodeSize / 2); - - var curvePointX = (x12 - x11) / 2 + x11; - var curvePointY = y1 - (nodeSize * 2); - var d = "M" + x11 + "," + y11 + " T" + curvePointX + "," + curvePointY + " " + x12 + "," + y12; - return d; - -}; - -GraphCanvas.prototype.renderEdges = function() { - for ( var edge in this.getDataset().getEdges()) { - this.renderEdge(this.getDataset().getEdgeById(edge).getId()); - - } -}; - -GraphCanvas.prototype.getLastSelectedNode = function() { - var node = null; - if (this.getSelectedVertices().length > 0) { - var nodeId = this.getSelectedVertices()[this.getSelectedVertices().length - 1]; - node = this.getDataset().getVertexById(nodeId); - } - return node; -}; -/* - GraphCanvas.prototype.getNodeByNameAndIndex = function(node, index){ - var nodeId = this.getDataset().verticesIndex[node][index]; - var nodeItem = this.getDataset().getVertexById(nodeId); - return nodeItem; - }; - */ - -GraphCanvas.prototype.setDataset = function(dataset) { - this.dataset = dataset; -}; - -GraphCanvas.prototype.setFormatter = function(formatter) { - this.formatter = formatter; -}; - -GraphCanvas.prototype.setLayout = function(layout) { - this.layout = layout; -}; - -/** API **/ -GraphCanvas.prototype.getDataset = function() { - return this.dataset; -}; - -GraphCanvas.prototype.getFormatter = function() { - return this.formatter; -}; - -GraphCanvas.prototype.getLayout = function() { - return this.layout; -}; - -/** API DATASET **/ -GraphCanvas.prototype.addVertex = function(name, args) { - this.getDataset().addNode(name, args); -}; - -GraphCanvas.prototype.removeVertex = function(vertexId) { - this.getDataset().getVertexById(vertexId).remove(); -}; - -GraphCanvas.prototype.addEdge = function(edgeName, nodeSourceId, nodeTargetId, args) { - this.getDataset().addEdge(edgeName, nodeSourceId, nodeTargetId, args); -}; -/* - GraphCanvas.prototype.removeEdge = function(edgeId){ - this.getDataset().getEdgeById(edgeId).remove(); - }; - */ - -/** API FORMATTER **/ -GraphCanvas.prototype.getWidth = function() { - return this.getFormatter().getWidth(); -}; - -GraphCanvas.prototype.getHeight = function() { - return this.getFormatter().getHeight(); -}; - -GraphCanvas.prototype.getBackgroundImage = function() { - return this.getFormatter().getBackgroundImage(); -}; +/** + * Example form + * + * @witdh + * @height + */ +function ExampleForm(args) { + this.id = BUI.id(); + this.width = 700; + this.height = 500; + + if (args != null) { + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + } +} + +ExampleForm.prototype._getItems = function() { + return [{ + fieldLabel : 'First Name', + name : 'first', + allowBlank : false + }, { + fieldLabel : 'Last Name', + name : 'last', + allowBlank : false + } ]; +}; + +ExampleForm.prototype._getItems = function() { + return [ ]; +}; + +ExampleForm.prototype._getButtons = function() { + return [ ]; +}; + +ExampleForm.prototype.getPanel = function() { + this.panel = Ext.create('Ext.form.Panel', { + width : this.width, + height : this.height, + margin : 10, + border : 1, + defaultType : 'textfield', + items : this._getItems(), + buttons : this._getButtons() + }); + return this.panel; +}; + +/** It populates the form **/ +ExampleForm.prototype.refresh = function(macromolecule) { +}; -//GraphCanvas.prototype.setBackgroundImage = function(value){ -// this.getFormatter().setBackgroundImage(value); -//}; +function ExperimentForm(args) { + this.id = BUI.id(); + + if (args != null) { + } + + this.onSaved = new Event(this); +} + +ExperimentForm.prototype._getItems = function(experiment) { + this.experiment = experiment; + var typeCombo = Ext.create('Ext.form.ComboBox', { + id : this.id + 'type', + fieldLabel : 'Type', + store : [ "STATIC", "CALIBRATION", "HPLC" ], + queryMode : 'local', + labelWidth : 120, + displayField : 'name', + valueField : 'name', + value : experiment.json.type, + disabled : (experiment.json.type == 'TEMPLATE') + }); + + var items = []; + + + if (experiment.json.type == "HPLC" ){ + var typeMacromolecule = BIOSAXS_COMBOMANAGER.getComboMacromoleculeByMacromolecules(BIOSAXS.proposal.getMacromolecules(), {labelWidth : 120, width: "120px"}); + if (experiment.getHPLCMacromolecule() != null){ + typeMacromolecule.setValue(experiment.getHPLCMacromolecule().macromoleculeId); + items.push(typeMacromolecule); + } + } + + + items.push(typeCombo, { + id : this.id + 'name', + xtype : 'textfield', + fieldLabel : 'Name', + labelWidth : 120, + width : '100%', + value : experiment.json.name + }, { + id : this.id + 'comments', + xtype : 'textareafield', + name : 'comments', + fieldLabel : 'Comments', + labelWidth : 120, + height : 120, + width : '100%', + value : experiment.json.comments + }); + return items; +}; +ExperimentForm.prototype.getPanel = function(experiment) { + var _this = this; + + this.panel = Ext.createWidget({ + xtype : 'container', + layout : 'vbox', + border : 0, + style : { + padding : '10px' + }, + fieldDefaults : { + labelAlign : 'left', + labelWidth : 50 + }, + items : this._getItems(experiment) + }); + return this.panel; +}; + +ExperimentForm.prototype.input = function() { + return new ExperimentHeaderForm().input(); +}; + +ExperimentForm.prototype.test = function(targetId) { + var experimentForm = new ExperimentForm(); + var panel = experimentForm.getPanel(new Experiment(experimentForm.input().experiment)); + panel.render(targetId); +}; -GraphCanvas.prototype.getBackgroundColor = function() { - return this.getFormatter().getBackgroundColor(); -}; +/** + * Shows the header for the experiments changing the color and parameters depending on experiment type + * + */ +function ExperimentHeaderForm(args) { + this.id = BUI.id(); + this.backgroundColor = '#FFFFFF'; +} + +ExperimentHeaderForm.prototype.getHTMLSource = function(experiment) { + var html = BUI.createFormLabel("Name :", experiment.json.name, 75, 400, this.backgroundColor); + if (experiment.json.type == "HPLC") { + if (experiment.getHPLCMacromolecule() != null){ + html = html + BUI.createFormLabel("Molecule :", experiment.getHPLCMacromolecule().acronym, 75, 400, this.backgroundColor); + } + } + else{ + html = html + BUI.createFormLabel("Type :", experiment.json.type, 75, 400, this.backgroundColor); + } + + html = html + BUI.createFormLabel("Date :", experiment.json.creationDate, 75, 400, this.backgroundColor); + return html; +}; + +ExperimentHeaderForm.prototype.getHTMLDownload = function(experiment) { + var bgcolor = "background-color:" + this.backgroundColor + ";"; + var html = "
"; + if ((experiment.json.type == "CALIBATION") || (experiment.json.type == "STATIC")) { + html = html + " Download Source File
"; + html = html + + ""; + } + if (experiment.json.type == "TEMPLATE") { + html = html + + " Download Source File"; + } + + if (experiment.json.type == "HPLC") { + html = html + " Download h5 File"; + } + + return html; +}; + +ExperimentHeaderForm.prototype.getTopPanel = function(experiment) { + return { + xtype : 'container', + layout : 'hbox', + items : [ { + margin : "0 0 0 0", + width : 475, + border : 0, + html : this.getHTMLSource(experiment) + }, { + margin : "0 0 0 0", + width : 475, + border : 0, + html : this.getHTMLDownload(experiment) + } ] + }; +}; + +ExperimentHeaderForm.prototype.getButton = function(experiment) { + var _this = this; + return Ext.create('Ext.Button', { + text : 'EDIT', + minWidth : '100', + margin : '10 0 0 30', + handler : function() { + var experimentWindow = new ExperimentWindow(); + experimentWindow.onSaved.attach(function(sender, data) { + _this.experiment.json.name = data.name; + _this.experiment.json.type = data.type; + _this.experiment.json.comments = data.comments; + _this.panel.remove(_this.panel.items.items[0]); + _this.panel.remove(_this.panel.items.items[0]); + _this.panel.insert(_this.getTopPanel(_this.experiment)); + _this.panel.insert(_this.getBottomPanel(_this.experiment)); + }); + experimentWindow.show(experiment); + } + }); +}; + +ExperimentHeaderForm.prototype.getBottomPanel = function(experiment) { + return { + xtype : 'container', + layout : 'hbox', + margin : '10 0 0 0', + items : [ this.getComments(experiment), this.getButton(experiment) ] + }; +}; + +ExperimentHeaderForm.prototype.getComments = function(experiment) { + return { + xtype : 'textareafield', + labelStyle : 'font-weight: bold;', + name : 'comments', + fieldLabel : 'Comments', + labelWidth : 70, + height : 40, + minWidth : '450', + readOnly : true, + value : experiment.json.comments + }; +}; + +ExperimentHeaderForm.prototype.getPanel = function(experiment) { + this.experiment = experiment; + + if (experiment.json.type == 'CALIBRATION') { + this.backgroundColor = '#EFFBFB'; + } + if (experiment.json.type == 'TEMPLATE') { + this.backgroundColor = '#E0F8E6'; + } + + this.panel = Ext.create('Ext.container.Container', { + frame : false, + layout : 'vbox', + padding : 5, + bodyPadding : '5 5 0 0', + width : 890, + margin : '0 0 10 0', + height : 120, + style : { + borderColor : '#99bce8', + borderStyle : 'solid', + borderWidth : '1px', + 'background-color' : this.backgroundColor + }, + fieldDefaults : { + msgTarget : 'side', + labelWidth : 100 + }, + items : [ this.getTopPanel(experiment), this.getBottomPanel(experiment) ] + }); + return this.panel; +}; + +ExperimentHeaderForm.prototype.input = function() { + return { + experiment : DATADOC.getExperiment_10() + }; +}; + +ExperimentHeaderForm.prototype.test = function(targetId) { + var experimentHeaderForm = new ExperimentHeaderForm(); + var panel = experimentHeaderForm.getPanel(new Experiment(experimentHeaderForm.input().experiment)); + panel.render(targetId); + +}; -GraphCanvas.prototype.setBackgroundColor = function() { - this.getFormatter().setBackgroundColor(value); -}; +/** + * Macromolecule form with the general parameters of a macromolecule + * + * @witdh + * @height + * + * #onSave button save has been clicked + * #onClose button close has been clicked + */ +function MacromoleculeForm(args) { + this.id = BUI.id(); + this.width = 700; + this.height = 500; + + if (args != null) { + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + } + + /** Events **/ + this.onSave = new Event(this); + this.onClose = new Event(this); +} + +/** Type : is the Ext type then requiredtext or textfield * */ +MacromoleculeForm.prototype._getFieldTextWithHelp = function(type, fieldLabel, fieldName, help) { + return Ext.create('Ext.container.Container', { + margin : "10 0 0 10", + items : [ { + xtype : type, + fieldLabel : fieldLabel, + name : fieldName, + id : this.id + fieldName + }, { + xtype : 'label', + forId : 'myFieldId', + text : help, + margin : "5 0 0 105", + cls : "inline-help" + } ] + }); +}; + +MacromoleculeForm.prototype._getNumericWithHelp = function(type, fieldLabel, fieldName, help) { + return Ext.create('Ext.container.Container', { + margin : "0 0 0 10", + items : [ { + xtype : type, + fieldLabel : fieldLabel, + name : fieldName, + id : this.id + fieldName, + decimalPrecision : 6, + width : 220 + }, { + xtype : 'label', + forId : 'myFieldId', + text : help, + margin : "5 0 0 10", + cls : "inline-help" + } ] + }); +}; + +MacromoleculeForm.prototype._getButtons = function() { + var _this = this; + return [ { + text : 'Save', + handler : function() { + _this._save(); + } + },{ + text : 'Close', + handler : function() { + _this.onClose.notify(); + + } + } ]; +}; + +/** It persits the macromolecule in the database **/ +MacromoleculeForm.prototype._persist = function(macromoleculeId, acronym, name, molecularMass, extintionCoefficient, comments, refractiveIndex, solventViscosity) { + + /** Checking not duplicated acronym **/ + if (((macromoleculeId == null) && (BIOSAXS.proposal.getMacromoleculeByAcronym(acronym) != null))== true){ + BUI.showError("Duplicated acronym"); + return; + } + + + if (macromoleculeId == null){ + /** new macromolecule **/ + this.macromolecule = {}; + this.macromolecule.macromoleculeId = null; + } + else{ + this.macromolecule.macromoleculeId = macromoleculeId; + } + + this.macromolecule["acronym"] = acronym; + this.macromolecule["name"] = name; + this.macromolecule["molecularMass"] = molecularMass; + this.macromolecule["extintionCoefficient"] = extintionCoefficient; + this.macromolecule["comments"] = comments; + this.macromolecule["symmetry"] = Ext.getCmp(this.id + 'comboSym').getValue(); + this.macromolecule["refractiveIndex"] = refractiveIndex; + this.macromolecule["solventViscosity"] = solventViscosity; + + var _this = this; + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, proposal) { + /** Updating the proposal global object **/ + BIOSAXS.proposal.setItems(proposal); + _this.panel.setLoading(false); + + var saved = BIOSAXS.proposal.getMacromoleculeByAcronym(acronym); + /** Refreshing to check that everything is ok **/ + _this.refresh(saved); + _this.onSave.notify(saved); + }); + + this.panel.setLoading("Saving Macromolecule") + adapter.saveMacromolecule(this.macromolecule); +}; + +/** Save the macromolecule in the DB **/ +MacromoleculeForm.prototype._save = function() { + + var _this = this; + + var acronym = this._getField("acronym"); + var name = this._getField("name"); + var molecularMass = this._getField("molecularMass"); + var extintionCoefficient = this._getField("extintionCoefficient"); + var comments = this._getField("comments"); + + var refractiveIndex = this._getField("refractiveIndex"); + var solventViscosity = this._getField("solventViscosity"); + + /** Checking required fields **/ + if (name == "") { + BUI.showError("Name field is mandatory"); + return; + } + if (acronym == "") { + BUI.showError("Acroynm field is mandatory"); + return; + } + + if (this.macromolecule != null){ + /** Checking if it is a new macromolecule **/ + if (this.macromolecule.macromoleculeId == null){ + /** Check if the acronym exists already **/ + this._persist(null, acronym, name, molecularMass, extintionCoefficient, comments, refractiveIndex, solventViscosity); + } + else{ + /** It is an update **/ + this._persist(this.macromolecule.macromoleculeId, acronym, name, molecularMass, extintionCoefficient, comments, refractiveIndex, solventViscosity); + } + } + else{ + /** It is a new macromolecule **/ + this._persist(null, acronym, name, molecularMass, extintionCoefficient, comments, refractiveIndex, solventViscosity); + } +}; + + + +MacromoleculeForm.prototype._getItems = function() { + var _this = this; + /** Symmetry combo box **/ + var symmetry = Ext.create('Ext.data.Store', { + fields : [ 's' ], + data : this._getSymmetries() + }); + + this.symmetryComboBox = Ext.create('Ext.form.ComboBox', { + fieldLabel : 'Symmetry', + store : symmetry, + id : this.id + 'comboSym', + queryMode : 'local', + displayField : 's', + valueField : 's', + value : "P1", + margin : "0 0 0 30", + width : 220 + }); + + return [this._getFieldTextWithHelp("requiredtext", "Name", "name", "Long name. i.e: Bovine serum albumin"), + this._getFieldTextWithHelp("requiredtext", "Acronym", "acronym", "Acronym will be used in the files and analisys. i.e: BSA"), + this._getFieldTextWithHelp("textfield", "Mol. Mass (Da)", "molecularMass", "Atomic mass estimation measured in Da"), + { + xtype : 'container', + layout : 'hbox', + margin : "10 0 0 0", + items :[ + this._getNumericWithHelp("numberfield", "Extinction coef.", "extintionCoefficient", ""), + this.symmetryComboBox + ] + }, + { + xtype : 'container', + layout : 'hbox', + margin : "5 0 0 0", + items :[ + this._getNumericWithHelp("numberfield", "Refractive Index", "refractiveIndex", "How radiation propagates through the medium"), + this._getNumericWithHelp("numberfield", "Solvent Viscosity", "solventViscosity", "") + ] + }, + { + id : this.id + "comments", + xtype : 'textareafield', + name : 'comments', + margin : '35 0 0 10', + fieldLabel : 'Comments', + width : this.width - 100 + } ]; +}; + +MacromoleculeForm.prototype._getSymmetries = function() { + return [ { + "s" : "P1" + }, { + "s" : "P2" + }, { + "s" : "P3" + }, { + "s" : "P4" + }, { + "s" : "P5" + }, { + "s" : "P6" + }, { + "s" : "P32" + }, { + "s" : "P42" + }, { + "s" : "P52" + }, { + "s" : "P62" + }, { + "s" : "P222" + } ] +}; + +MacromoleculeForm.prototype.getPanel = function() { + this.panel = Ext.create('Ext.form.Panel', { + width : this.width, + height : this.height, + margin : 10, + border : 1, + defaultType : 'textfield', + items : this._getItems(), + buttons : this._getButtons() + }); + return this.panel; +}; + + +/** Populates each text field by field name and value **/ +MacromoleculeForm.prototype._populateField = function(fieldName, value) { + if (value != null){ + Ext.getCmp(this.id + fieldName).setValue(value); + } +}; + +/** Gets the value of a textfield **/ +MacromoleculeForm.prototype._getField = function(fieldName) { + return Ext.getCmp(this.id + fieldName).getValue(); +}; + + +/** It populates the form **/ +MacromoleculeForm.prototype.refresh = function(macromolecule) { + this.macromolecule = macromolecule; + if (macromolecule != null){ + this._populateField("name", macromolecule.name); + this._populateField("acronym", macromolecule.acronym); + this._populateField("extintionCoefficient", macromolecule.extintionCoefficient); + this._populateField("molecularMass", macromolecule.molecularMass); + this._populateField("comments", macromolecule.comments); + this._populateField("refractiveIndex", macromolecule.refractiveIndex); + this._populateField("solventViscosity", macromolecule.solventViscosity); + if (macromolecule.symmetry != null){ + Ext.getCmp(this.id + 'comboSym').setValue(macromolecule.symmetry); + } + } +}; + + +MacromoleculeForm.prototype.input = function() { + return {}; +}; + + +/** It populates the form **/ +MacromoleculeForm.prototype.test = function(targetId) { + var macromoleculeForm = new MacromoleculeForm(); + macromoleculeForm.onClose.attach(function(sender){ + alert("Click on close"); + }); + var panel = macromoleculeForm.getPanel(); + panel.render(targetId); +}; + + -//GraphCanvas.prototype.setEdgeFill = function(edgeId, value){ -// this.getFormatter().getEdgeById(edgeId).getDefault().setFill(value); -//}; -// -//GraphCanvas.prototype.getEdgeFill = function(edgeId){ -// return this.getFormatter().getEdgeById(edgeId).getDefault().getFill(); -//}; + + +function ModelVisualizerForm(args){ + this.id =BUI.id(); + this.width = 600; + this.height = 400; + if (args!= null){ + if (args.width != null){ + this.width = args.width; + } + if (args.height != null){ + this.height = args.height; + } + } +}; + +ModelVisualizerForm.prototype._getFirHTML = function(modelId, width, height, type, desc) { + var html = ""; + html = html + ''; + html = html + ''; + html = html + ''; + html = html + '
dammin.' + type + '
' + desc + '
'; + return html; +}; + +ModelVisualizerForm.prototype.getItems = function(modelPanel){ + _this = this; + var height = _this.height/2 - 60; + var width = _this.width/2 - 10; + + return Ext.create('Ext.container.Container', { + layout: { + type: 'vbox', // Arrange child items vertically + }, + items: [ + modelPanel, + { + xtype : 'container', + layout: { + type: 'hbox', // Arrange child items vertically + }, + items : [{ + html : this._getFirHTML("id", width, height, "fir", "Fit of the simulated scattering curve versus a smoothed experimental data (spline interpolation)"), + height :height, + width : width, + padding: 2 + }, + { + html : this._getFirHTML("id", width, height, "fit", "Fit of the simulated scattering curve versus the experimental data."), + height : height, + width : width, + padding: 2 + }] + } + + ] + }); +}; + +ModelVisualizerForm.prototype.refresh = function(models){ + var input = []; +// var colors = ["008000", "F0A804", "0000FF", "800080", "C0C0C0"]; + for (var i = 0; i < models.length; i++) { + console.log(BUI.rainbow(models.length, i).replace("#", "0x")); + input.push({ + color: BUI.rainbow(models.length, i).replace("#", "0x"), + modelId: models[i].modelId, + opacity: 0.8, + radius: 3, + title: BUI.getFileNameByPath(models[i].pdbFile), + type: "SHAPEDETERMINATIONMODEL" + + }); + } + + this.panel.removeAll(); + this.panel.add( + _this.getItems( + new PDBViewer({ + width : this.width - 10, + height : (this.height/2) - 10, + title : "" + }).draw(input) + ) + ); + + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + var splitted = data.toString().split("\n"); + var array = []; + for ( var i = 0; i < splitted.length; i++) { + var line = splitted[i].trim(); + var line_splited = line.split(/\s*[\s,]\s*/); + if (line_splited.length == 4) { + array.push([ Number(line_splited[0]), BUI.getStvArray(line_splited[1], line_splited[2]), BUI.getStvArray(line_splited[3], 0) ]); + } + } + + var id = (_this.id + "firid"); + var dygraphWidget = new StdDevDyGraph(id, { + width : (_this.width/2) - 10, + height :(_this.height/2) -110, + xlabel : 'q(nm-1)' + }); + dygraphWidget.draw(array, [ "#FF0000", "#0000FF", "#FF00FF" ], [ 's', 'I(exp)', 'I(sim)' ]); + }); + + adapter.getModelFile("FIR", models[0].modelId); + + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + var splitted = data.toString().split("\n"); + var array = []; + for ( var i = 0; i < splitted.length; i++) { + var line = splitted[i].trim(); + var line_splited = line.split(/\s*[\s,]\s*/); + if (line_splited.length == 3) { + array.push([ Number(line_splited[0]), BUI.getStvArray(line_splited[1], 0), BUI.getStvArray(line_splited[2], 0) ]); + } + } + + var id = (_this.id + "fitid"); + + var dygraphWidget = new StdDevDyGraph(id, { + width : (_this.width/2) - 10, + height : (_this.height/2) - 110, + xlabel : 'q(nm-1)' + }); + dygraphWidget.draw(array, [ "#FF0000", "#0000FF" ], [ "s", "I(exp)", "I(sim)" ]); + }); + adapter.getModelFile("FIT", models[0].modelId); +}; + +ModelVisualizerForm.prototype.getPanel = function(modelList){ + _this = this; + this.modelList = modelList; + this.panel = Ext.create('Ext.Panel', { + title: 'Results', + width: this.width, + height: this.height, + layout: { + type: 'vbox', // Arrange child items vertically +// align: 'stretch' // Each takes up full width + }, + items: [ + + ], + listeners : { + afterrender : function(grid, eOpts) { +// alert(_this.modelList) + } + } + }); + + return this.panel; + +}; + -/** VERTICES FORMATTER **/ -GraphCanvas.prototype.setVertexSize = function(vertexId, value) { - this.getFormatter().getVertexById(vertexId).getDefault().setSize(value); -}; +/** + * Example form + * + * @witdh + * @height + */ +function MolarityForm(args) { + this.id = BUI.id(); + this.width = 700; + this.height = 500; + + if (args != null) { + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + } + + this.onSave = new Event(this); + this.onClose = new Event(this); +} + + +MolarityForm.prototype._getNumericWithHelp = function(type, fieldLabel, fieldName, help) { + return Ext.create('Ext.container.Container', { + margin : "10 0 0 10", + items : [ { + xtype : type, + fieldLabel : fieldLabel, + name : fieldName, + id : this.id + fieldName, + decimalPrecision : 6 + }, { + xtype : 'label', + forId : 'myFieldId', + text : help, + margin : "5 0 0 105", + cls : "inline-help" + } ] + }); +}; + + +MolarityForm.prototype._getItems = function() { + this.macromoleculeCombo = BIOSAXS_COMBOMANAGER.getComboMacromoleculeByMacromolecules(this.getMacromuleculesCandidates(this.macromolecule), { + width : 250, + labelWidth : 100, + margin : 10 + }); + + return [ { + xtype : 'container', + flex : 1, + margin : '10 0 0 10', + border : 0, + layout : 'anchor', + defaultType : 'requiredtext', + items : [ this.macromoleculeCombo, + this._getNumericWithHelp("textfield", "Ratio", "ratio", "Number in assymmetric units") + ] + } ]; +}; + +MolarityForm.prototype._persist = function() { + var _this = this; + var macromoleculeId = this.macromoleculeCombo.getValue(); + var ratio = Ext.getCmp(this.id + "ratio").getValue(); + var comments = "Not used yet"; + var dataAdapter = new BiosaxsDataAdapter(); + this.panel.setLoading("Saving"); + dataAdapter.onSuccess.attach(function(sender, args) { + _this.onSave.notify(); + }); + dataAdapter.saveStoichiometry(this.macromolecule.macromoleculeId, macromoleculeId, ratio, comments); +}; + +MolarityForm.prototype._getButtons = function() { + var _this = this; + + function onClose() { + _this.onClose.notify(); + } + + return [ { + text : 'Save', + handler : function() { + _this._persist(); + } + }, { + text : 'Cancel', + handler : function() { + onClose(); + } + } ]; +}; + +MolarityForm.prototype.getPanel = function() { + this.panel = Ext.create('Ext.form.Panel', { +// width : null, + height : this.height, + margin : 2, + border : 1, + defaultType : 'requiredtext', + items : this._getItems(), + buttons : this._getButtons() + }); + return this.panel; +}; + +/** macromolecules contains all macromolecules except this one **/ +MolarityForm.prototype.getMacromuleculesCandidates = function(macromolecule) { + var macromolecules = []; + if ( BIOSAXS.proposal.macromolecules){ + for (var i = 0; i < BIOSAXS.proposal.macromolecules.length; i++) { + var m = BIOSAXS.proposal.macromolecules[i]; + if (this.macromolecule != null){ + if (m.macromoleculeId != this.macromolecule.macromoleculeId) { + macromolecules.push(m); + } + } + } + } + return macromolecules; +}; + + +/** It populates the form **/ +MolarityForm.prototype.refresh = function(macromolecule) { + this.macromolecule = macromolecule; + +}; + + +MolarityForm.prototype.input = function() { + return {}; +}; + + +/** It populates the form **/ +MolarityForm.prototype.test = function(targetId) { + var macromoleculeForm = new MolarityForm(); + var panel = macromoleculeForm.getPanel(); + panel.render(targetId); +}; -GraphCanvas.prototype.getVertexSize = function(vertexId) { - return this.getFormatter().getVertexById(vertexId).getDefault().getSize(); -}; +///** +// * +// * @witdh +// * @height +// */ +//function MacromoleculeForm(args) { +// this.id = BUI.id(); +// this.width = 700; +// this.height = 500; +// +// if (args != null) { +// if (args.width != null) { +// this.width = args.width; +// } +// if (args.height != null) { +// this.height = args.height; +// } +// } +// +// this.onClose = new Event(this); +//} +// +//MacromoleculeForm.prototype.getMacromolecule = function() { +// this.macromolecule.name = Ext.getCmp(this.panel.getItemId()).getValues().name; +// this.macromolecule.acronym = Ext.getCmp(this.panel.getItemId()).getValues().acronym; +// this.macromolecule.comments = Ext.getCmp(this.panel.getItemId()).getValues().comments; +// this.macromolecule.extintionCoefficient = Ext.getCmp(this.panel.getItemId()).getValues().extintionCoefficient; +// this.macromolecule.molecularMass = Ext.getCmp(this.panel.getItemId()).getValues().molecularMass; +// return this.macromolecule; +//}; +// +//MacromoleculeForm.prototype.setMacromolecule = function(macromolecule) { +// this.pdbStore.loadData(macromolecule.structure3VOs); +// +//}; +// +//MacromoleculeForm.prototype.getForm = function(macromolecule) { +// this.panel = Ext.createWidget('form', { +// frame : false, +// border : 0, +// padding : 15, +// width : 550, +// height : 350, +// items : [ { +// xtype : 'container', +// layout : 'hbox', +// items : [ { +// xtype : 'container', +// flex : 1, +// border : false, +// layout : 'anchor', +// defaultType : 'requiredtext', +// items : [ { +// fieldLabel : 'Name', +// name : 'name', +// anchor : '95%', +// tooltip : "Name of the macromolecule", +// value : macromolecule.name +// }, { +// fieldLabel : 'Acronym', +// name : 'acronym', +// anchor : '95%', +// value : macromolecule.acronym +// } ] +// }, { +// xtype : 'container', +// flex : 1, +// layout : 'anchor', +// defaultType : 'textfield', +// items : [ { +// xtype : 'numberfield', +// fieldLabel : 'Mol. Mass (Da)', +// name : 'molecularMass', +// value : macromolecule.molecularMass, +// decimalPrecision : 6 +// }, { +// xtype : 'numberfield', +// fieldLabel : 'Extinction coef.', +// name : 'extintionCoefficient', +// value : macromolecule.extintionCoefficient, +// decimalPrecision : 6 +// } ] +// } ] +// }, { +// xtype : 'textareafield', +// name : 'comments', +// fieldLabel : 'Comments', +// value : macromolecule.comments, +// width : this.width - 10 +// }, +// +// { +// html : BUI.getWarningHTML("The macromolecule is unsaved. Save the macromolecule to get access to other tabs"), +// margin : "150 10 10 10", +// id : this.id + "unsavedWarning", +// hidden : !(!macromolecule.macromoleculeId) +// } +// +// ] +// }); +// return this.panel; +//}; +// +//MacromoleculeForm.prototype.save = function() { +// var _this = this; +// +// var adapter = new BiosaxsDataAdapter(); +// adapter.onSuccess.attach(function(sender, proposal) { +// BIOSAXS.proposal.setItems(proposal); +// _this.panel.setLoading(false); +// +// Ext.getCmp(_this.id + "assembly").enable() +// Ext.getCmp(_this.id + "advanced").enable(); +// Ext.getCmp(_this.id + "unsavedWarning").hide(); +// }); +// +// if (this.getMacromolecule().name == "") { +// BUI.showError("Name field is mandatory"); +// return; +// } +// if (this.getMacromolecule().acronym == "") { +// BUI.showError("Acroynm field is mandatory"); +// return; +// } +// +// /** Check if acronym is unique * */ +// if (this.getMacromolecule().macromoleculeId == null) { +// if (BIOSAXS.proposal.getMacromoleculeByAcronym(this.getMacromolecule().acronym) == null) { +// this.panel.setLoading("ISPyB: Saving Macromolecule") +// adapter.saveMacromolecule(this.getMacromolecule()); +// } else { +// alert("There is already an existing macromolecule with the same acronym"); +// +// } +// } else { +// this.panel.setLoading("ISPyB: Saving Macromolecule") +// adapter.saveMacromolecule(this.getMacromolecule()); +// } +// +//}; +// +//MacromoleculeForm.prototype.getPanel = function(macromolecule) { +// var _this = this; +// this.macromolecule = macromolecule; +// return Ext.createWidget('tabpanel', { +// height : this.height, +// margin : 5, +// plain : true, +// style : { +// padding : 5 +// }, +// items : [ { +// tabConfig : { +// title : "General", +// disabled : false +// }, +// items : [ this.getForm(macromolecule) ], +// bbar : [ "->", { +// text : 'Save', +// cls : 'btn-with-border', +// style : { +// +// border : 1 +// }, +// handler : function() { +// _this.save(); +// } +// }, { +// text : 'Close', +// cls : 'btn-with-border', +// handler : function() { +// _this.onClose.notify(); +// } +// } ] +// }, { +// tabConfig : { +// id : this.id + "assembly", +// title : "Assembly", +// tooltip : 'Description of subunits present in the macromolecule', +// // hidden : (!macromolecule.macromoleculeId), +// disabled : (!macromolecule.macromoleculeId) +// }, +// items : [ this.getMolarityGrid(macromolecule) ] +// }, { +// tabConfig : { +// id : this.id + "advanced", +// title : "Advanced Modeling", +// // hidden : (!macromolecule.macromoleculeId), +// tooltip : 'Definition of the description contacts and symetries', +// disabled : (!macromolecule.macromoleculeId) +// }, +// items : [ this.getRigidBodyForm(macromolecule) ] +// } ] +// }); +//}; +// +//MacromoleculeForm.prototype.getRigidBodyForm = function(macromolecule) { +// var _this = this; +// +// // [P1, P2, P3, P4 ,P5 ,P6 ,32, P42, P52, P62] + P222 +// var symmetry = Ext.create('Ext.data.Store', { +// fields : [ 's' ], +// data : [ { +// "s" : "P1" +// }, { +// "s" : "P2" +// }, { +// "s" : "P3" +// }, { +// "s" : "P4" +// }, { +// "s" : "P5" +// }, { +// "s" : "P6" +// }, { +// "s" : "P32" +// }, { +// "s" : "P42" +// }, { +// "s" : "P52" +// }, { +// "s" : "P62" +// }, { +// "s" : "P222" +// } ] +// }); +// +// if (macromolecule.symmetry == null) { +// macromolecule.symmetry = "P1"; +// } +// var comboBox = Ext.create('Ext.form.ComboBox', { +// fieldLabel : 'Symmetry', +// store : symmetry, +// id : 'comboSym', +// queryMode : 'local', +// displayField : 's', +// valueField : 's', +// value : macromolecule.symmetry, +// margin : "10 0 0 0", +// listeners : { +// change : function(combo, newValue, oldValue, eOpts) { +// macromolecule.symmetry = newValue; +// } +// } +// }); +// +// this.rigidBodyPanel = Ext.createWidget('form', { +// frame : false, +// border : 0, +// padding : 10, +// width : 550, +// height : 400, +// items : [ { +// xtype : 'container', +// layout : 'hbox', +// items : [ { +// xtype : 'container', +// border : false, +// layout : 'hbox', +// items : [ { +// xtype : 'label', +// forId : 'myFieldId', +// text : 'Contact Desc:', +// width : 105, +// margin : '0 0 0 0' +// }, { +// xtype : 'textfield', +// hideLabel : true, +// id : "contactsDescriptionFilePath", +// margin : '0 0 0 0', +// width : 300, +// value : macromolecule.contactsDescriptionFilePath +// }, { +// text : 'Upload', +// xtype : 'button', +// margin : "0 0 0 20", +// width : 100, +// handler : function() { +// _this._openUploadDialog(macromolecule.macromoleculeId, "CONTACTS", "Upload Contact Description File"); +// } +// } ] +// } ] +// }, +// +// comboBox, { +// xtype : 'checkbox', +// margin : '10 0 0 5', +// boxLabel : "I want rigid body modeling run on this stuff", +// checked : true, +// width : 300 +// }, _this.getPDBGrid(macromolecule) ] +// }); +// return this.rigidBodyPanel; +//}; +// +//MacromoleculeForm.prototype.update = function() { +// var _this = this; +// BIOSAXS.proposal.onInitialized.attach(function() { +// if (BIOSAXS.proposal != null) { +// var macromolecules = BIOSAXS.proposal.macromolecules; +// for (var i = 0; i < macromolecules.length; i++) { +// if (macromolecules[i].macromoleculeId == _this.macromolecule.macromoleculeId) { +// _this.macromolecule = macromolecules[i]; +// _this.setMacromolecule(_this.macromolecule); +// _this.molarityStore.loadData(_this.parseMolarityData(_this.macromolecule)); +// _this.pdbGrid.setLoading(false); +// Ext.getCmp("contactsDescriptionFilePath").setValue(_this.macromolecule.contactsDescriptionFilePath) +// _this.molarityGrid.setLoading(false); +// +// } +// } +// } +// }); +// this.molarityGrid.setLoading("Updating"); +// this.pdbGrid.setLoading("Updating"); +// BIOSAXS.proposal.init(); +//}; +// +///******************************************************************************* +// * MOLARITY GRID +// ******************************************************************************/ +// +//MacromoleculeForm.prototype.parseMolarityData = function(macromolecule) { +// var data = []; +// if (macromolecule.stoichiometry != null) { +// for (var i = 0; i < macromolecule.stoichiometry.length; i++) { +// data.push({ +// ratio : macromolecule.stoichiometry[i].ratio, +// acronym : macromolecule.stoichiometry[i].macromolecule3VO.acronym, +// comments : macromolecule.stoichiometry[i].macromolecule3VO.comments, +// stoichiometryId : macromolecule.stoichiometry[i].stoichiometryId, +// name : macromolecule.stoichiometry[i].macromolecule3VO.name +// }); +// } +// } +// return data; +//}; +// +//MacromoleculeForm.prototype.getMolarityGrid = function(macromolecule) { +// var _this = this; +// +// this.molarityStore = Ext.create('Ext.data.Store', { +// fields : [ 'acronym', 'ratio', 'comments', 'stoichiometryId', 'name' ], +// data : this.parseMolarityData(macromolecule), +// sorters : { +// property : 'ratio', +// direction : 'DESC' +// } +// }); +// +// this.molarityGrid = Ext.create('Ext.grid.Panel', { +// store : this.molarityStore, +// height : 350, +// padding : 5, +// columns : [ +// +// { +// text : 'Subunit', +// columns : [ { +// text : "Acronym", +// width : 100, +// hidden : false, +// dataIndex : 'acronym', +// sortable : true +// }, { +// text : "Name", +// width : 100, +// hidden : false, +// dataIndex : 'name', +// sortable : true +// }, { +// text : "Comments", +// width : 100, +// dataIndex : 'comments', +// sortable : true +// } ] +// }, { +// text : "Number
in assymmetric units", +// width : 150, +// dataIndex : 'ratio', +// tooltip : 'Number of times this subunit is present in the macromolecule', +// sortable : true +// }, { +// id : this.id + 'MOLARITY_REMOVE', +// flex : 0.1, +// sortable : false, +// renderer : function(value, metaData, record, rowIndex, colIndex, store) { +// return BUI.getRedButton('REMOVE'); +// } +// } ], +// listeners : { +// cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { +// if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'MOLARITY_REMOVE') { +// var dataAdapter = new BiosaxsDataAdapter(); +// dataAdapter.onSuccess.attach(function() { +// _this.molarityGrid.setLoading(false); +// _this.update(); +// }); +// dataAdapter.removeStoichiometry(record.data.stoichiometryId); +// _this.molarityGrid.setLoading("Removing Structure"); +// } +// } +// }, +// buttons : [ { +// text : 'Add molarity', +// handler : function() { +// +// function onClose() { +// w.destroy(); +// _this.update(); +// } +// var w = Ext.create('Ext.window.Window', { +// title : 'Molarity', +// height : 300, +// width : 500, +// modal : true, +// buttons : [ { +// text : 'Save', +// handler : function() { +// var macromoleculeId = (_this.macromoleculeCombo.getValue()); +// var ratio = Ext.getCmp(_this.id + "ratio").getValue(); +// var comments = ""; +// var dataAdapter = new BiosaxsDataAdapter(); +// dataAdapter.onSuccess.attach(function(sender, args) { +// _this.update(); +// w.destroy(); +// }); +// dataAdapter.saveStoichiometry(_this.macromolecule.macromoleculeId, macromoleculeId, ratio, comments); +// } +// }, { +// text : 'Cancel', +// handler : function() { +// onClose(); +// } +// } ], +// items : [ _this.getMolarityForm(macromolecule) ], +// listeners : { +// onEsc : function() { +// onClose(); +// }, +// close : function() { +// onClose(); +// } +// } +// }).show(); +// } +// } ] +// }); +// return this.molarityGrid; +//}; +// +///******************************************************************************* +// * PDB GRID +// ******************************************************************************/ +// +//MacromoleculeForm.prototype._openUploadDialog = function(macromoleculeId, type, title) { +// var _this = this; +// function onClose() { +// w.destroy(); +// _this.update(); +// } +// +// var w = Ext.create('Ext.window.Window', { +// title : title, +// height : 200, +// width : 400, +// modal : true, +// buttons : [ { +// text : 'Close', +// handler : function() { +// onClose(); +// } +// } ], +// layout : 'fit', +// items : { +// html : "" +// }, +// listeners : { +// onEsc : function() { +// onClose(); +// }, +// close : function() { +// onClose(); +// } +// } +// }).show(); +//}; +// +//MacromoleculeForm.prototype._getPlugins = function() { +// var _this = this; +// var plugins = []; +// // if (this.updateRowEnabled) { +// plugins.push(Ext.create('Ext.grid.plugin.RowEditing', { +// clicksToEdit : 1, +// listeners : { +// validateedit : function(grid, e) { +// /** Comments are always updatable* */ +// e.record.raw.symmetry = e.newValues.symmetry; +// e.record.raw.multiplicity = e.newValues.multiplicity; +// +// var adapter = new BiosaxsDataAdapter(); +// adapter.onSuccess.attach(function(sender, measurement) { +// // _this.grid.setLoading(false); +// }); +// adapter.onError.attach(function() { +// alert("Error"); +// // _this.grid.setLoading(false); +// }); +// +// // _this.grid.setLoading(); +// adapter.saveStructure(e.record.raw); +// } +// } +// })); +// // } +// return plugins; +//}; +// +//MacromoleculeForm.prototype.getPDBGrid = function(macromolecule) { +// var _this = this; +// +// var data = macromolecule.structure3VOs; +// +// // /** Getting PDB from subunits **/ +// // if (macromolecule != null){ +// // if (macromolecule.stoichiometry != null){ +// // for (var i =0; i < macromolecule.stoichiometry.length; i++){ +// // var stoichiometry = macromolecule.stoichiometry[i]; +// // if (stoichiometry.macromolecule3VO != null){ +// // if (stoichiometry.macromolecule3VO.structure3VOs != null){ +// // for (var j = 0; j < stoichiometry.macromolecule3VO.structure3VOs.length; +// // j++) { +// // var structure = stoichiometry.macromolecule3VO.structure3VOs[j]; +// // structure["isSubunit"] = stoichiometry.macromolecule3VO.acronym; +// // data.push(structure) +// // } +// // } +// // } +// // } +// // } +// // } +// +// this.pdbStore = Ext.create('Ext.data.Store', { +// fields : [ 'filePath', 'structureId', 'structureType', 'symmetry', 'structureId', 'name', 'multiplicity' ], +// data : macromolecule.structure3VOs, +// groupField : 'structureType', +// sorters : { +// property : 'structureId', +// direction : 'DESC' +// } +// }); +// +// var groupingFeature = Ext.create('Ext.grid.feature.Grouping', { +// groupHeaderTpl : Ext.create('Ext.XTemplate', +// "
{name:this.formatName}
", { +// formatName : function(name) { +// return name; +// } +// }), +// hideGroupedHeader : true, +// startCollapsed : false +// }); +// +// this.pdbGrid = Ext.create('Ext.grid.Panel', { +// margin : "15 0 0 5", +// height : 250, +// store : this.pdbStore, +// plugins : _this._getPlugins(), +// buttons : [ { +// // text : 'Add PDB file', +// text : 'Add Modeling Option', +// handler : function() { +// _this._openUploadDialog(macromolecule.macromoleculeId, "PDB", 'Upload PDB File'); +// } +// } +// +// ], +// columns : [ +// { +// text : "structureId", +// flex : 0.2, +// hidden : true, +// dataIndex : 'structureId', +// sortable : true +// }, +// { +// text : "File", +// flex : 0.5, +// dataIndex : 'filePath', +// sortable : true, +// hidden : true +// }, +// { +// text : "PDB", +// flex : 0.4, +// dataIndex : 'name', +// sortable : true +// }, +// { +// text : "Symmetry", +// flex : 0.4, +// dataIndex : 'symmetry', +// sortable : true, +// editor : { +// xtype : 'combobox', +// typeAhead : true, +// triggerAction : 'all', +// selectOnTab : true, +// store : [ [ "P1", "P1" ], [ "P2", "P2" ], [ "P3", "P3" ], [ "P4", "P4" ], [ "P5", "P5" ], [ "P6", "P6" ], [ "P32", "P32" ], [ "P42", "P42" ], +// [ "P52", "P52" ], [ "P62", "P62" ], [ "P222", "P222" ] ], +// } +// }, { +// text : "Multiplicity", +// flex : 0.4, +// dataIndex : 'multiplicity', +// sortable : true, +// editor : { +// xtype : 'textfield' +// } +// +// }, { +// text : "Subunit", +// flex : 0.2, +// dataIndex : 'isSubunit', +// sortable : true, +// hidden : true +// }, { +// text : "Type", +// flex : 0.2, +// dataIndex : 'structureType', +// sortable : true, +// hidden : true +// }, +// +// { +// id : this.id + 'REMOVE', +// flex : 0.2, +// hidden : true, +// sortable : false, +// renderer : function(value, metaData, record, rowIndex, colIndex, store) { +// return BUI.getRedButton('REMOVE'); +// } +// }, ], +// +// listeners : { +// itemdblclick : function(dataview, record, item, e) { +// _this._editExperiment(record.raw.experimentId); +// }, +// cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { +// +// if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'REMOVE') { +// var dataAdapter = new BiosaxsDataAdapter(); +// dataAdapter.onSuccess.attach(function() { +// _this.pdbGrid.setLoading(false); +// _this.update(); +// }); +// dataAdapter.removeStructure(record.data.structureId); +// _this.pdbGrid.setLoading("Removing PDB file"); +// } +// +// } +// }, +// viewConfig : { +// getRowClass : function(record, rowIdx, params, store) { +// if (record.raw.isSubunit != null) { +// return "blue-row"; +// } +// } +// } +// }); +// +// return this.pdbGrid; +//}; +// +//MacromoleculeForm.prototype.getMolarityForm = function(macromolecule) { +// var _this = this; +// var data = []; +// for (var i = 0; i < BIOSAXS.proposal.macromolecules.length; i++) { +// var m = BIOSAXS.proposal.macromolecules[i]; +// if (m.macromoleculeId != macromolecule.macromoleculeId) { +// data.push(m); +// } +// +// } +// this.macromoleculeCombo = BIOSAXS_COMBOMANAGER.getComboMacromoleculeByMacromolecules(data, { +// width : 250, +// labelWidth : 100, +// margin : 10 +// }); +// +// return Ext.createWidget('form', { +// +// frame : false, +// border : 0, +// // padding : 15, +// width : 550, +// height : 350, +// items : [ { +// xtype : 'container', +// flex : 1, +// border : false, +// layout : 'anchor', +// defaultType : 'requiredtext', +// items : [ this.macromoleculeCombo, { +// xtype : 'numberfield', +// name : 'Ratio', +// id : _this.id + "ratio", +// fieldLabel : 'Number in assymmetric units', +// value : 1, +// decimalPrecision : 6, +// margin : 10 +// }, { +// xtype : 'textareafield', +// name : 'comments', +// fieldLabel : 'Comments', +// margin : 10, +// width : 400, +// value : "" +// +// } ] +// } ] +// }); +// +//}; +// +///******************************************************************************* +// * JAVASCRIPT DOC +// ******************************************************************************/ +//MacromoleculeForm.prototype.input = function() { +// return { +// macromolecule : DATADOC.getMacromolecule_10() +// }; +//}; +// +//MacromoleculeForm.prototype.test = function(targetId) { +// var macromoleculeForm = new MacromoleculeForm(); +// var panel = macromoleculeForm.getPanel(macromoleculeForm.input().macromolecule); +// panel.render(targetId); +//}; -GraphCanvas.prototype.setVertexStroke = function(vertexId, value) { - this.getFormatter().getVertexById(vertexId).getDefault().setStroke(value); -}; +function ResultSummaryForm() { + this.radiationDamageThreshold = BUI.getRadiationDamageThreshold(); + this.qualityThreshold = BUI.getQualityThreshold(); + + /** Data clusters with bufers **/ + this.clusterByBuffers = false; + + /** Visualization are groupeb by concenttrations. Ex: 4.5mg/ml and 4.7mg/ml will be clusterized together **/ + this.collapseConcentrations = true; + + this.summaryHeight = 350; + this.id = BUI.id(); + + var _this = this; + + this.qualityControlResultsWidget = new QualityControlResultsWidget({ + qualityThreshold : this.radiationDamageThreshold, + radiationDamageThreshold : this.qualityThreshold + + }); + this.qualityControlResultsWidget.onQualityChanged.attach(function(sender, value) { + _this.qualityThreshold = value; + _this.thresholdsChanged(); + }); + + this.qualityControlResultsWidget.onRadiationDatamageChanged.attach(function(sender, value) { + _this.radiationDamageThreshold = value; + _this.thresholdsChanged(); + + }); + this.concentrationHTMLTableWidget = new ConcentrationHTMLTableWidget({ + height : 250, + showBufferColumns : this.clusterByBuffers + }); + + this.plot = new BoxWhiskerGraph({ + targetId : _this.id + '_boxPlot', + height : 350, + width : 450, + maxBoxWidth : 25 + }); + + this.rangePlot = new RangeWhiskerGraph({ + targetId : _this.id + '_rangePlot', + height : 350, + width : 450, + maxBoxWidth : 25 + }); +} + +ResultSummaryForm.prototype.thresholdsChanged = function() { + var parsedData = this.prepareData(this.rawData); + + var filtered = JSON.parse(JSON.stringify(parsedData)); + filtered.concentration.concentrations = []; + for ( var conc in parsedData.concentration.concentrations) { + if (parsedData.concentration.concentrations[conc].calculation.rgGnom.validNumber > 0) { + filtered.concentration.concentrations.push(parsedData.concentration.concentrations[conc]); + } + } + + this.plotWhisker(filtered); + this.plotRange(filtered); + + this.concentrationHTMLTableWidget.refresh(parsedData); +}; + +/** Given a frame object (object returned by analyzeFrames()) and depending of the threshold indicates if a datacollection has radiation damage **/ +ResultSummaryForm.prototype.hasRadiationDamage = function(frameObject) { + var bb = frameObject.bufferBeforeFramesMerged / frameObject.framesCount; + var ba = frameObject.bufferAfterFramesMerged / frameObject.framesCount; + var mol = frameObject.framesMerge / frameObject.framesCount; + return !((bb >= this.radiationDamageThreshold) && (ba >= this.radiationDamageThreshold) && (mol >= this.radiationDamageThreshold)); +}; + +/** Return (frameObject) an object with the information about the frames for a data collection**/ +ResultSummaryForm.prototype.analyzeFrames = function(dataCollectionRow) { + return { + bufferAfterFramesMerged : dataCollectionRow.bufferAfterFramesMerged, + bufferBeforeFramesMerged : dataCollectionRow.bufferBeforeFramesMerged, + framesCount : dataCollectionRow.framesCount, + framesMerge : dataCollectionRow.framesMerge + }; +}; + +ResultSummaryForm.prototype.detectDataCollectionWarnings = function(dataCollectionRow) { + var frameObject = this.analyzeFrames(dataCollectionRow); + var warnings = { + count : 0, + type : [] + }; + + if (this.hasRadiationDamage(frameObject)) { + warnings.count = warnings.count + 1; + warnings.type.push("RADIATION DAMAGE"); + } + + if (Number(dataCollectionRow.quality) < this.qualityThreshold) { + warnings.count = 1;//warnings.count + 1; + warnings.type.push("Quality <" + this.qualityThreshold); + } + return warnings; +}; + +/** Return array composed by {concentration} objects **/ +ResultSummaryForm.prototype.getConcentrations = function(data) { + var concentrationsId = {}; + + for ( var i = 0; i < data.length; i++) { + var warning = this.detectDataCollectionWarnings(data[i]); + var id = data[i].conc;// + "_" + data[i].bufferId; + if (this.clusterByBuffers) { + id = data[i].conc + "_" + data[i].bufferId; + } + + if (concentrationsId[id] == null) { + concentrationsId[id] = { + id : id, + concentration : Number(data[i].conc).toFixed(2), + bufferId : data[i].bufferId, + bufferAcronym : data[i].bufferAcronym, + rgGuinier : [], + i0Guinier : [], + rgGnom : [], + dMax : [], + quality : [], + frames : [], + frames_warning : warning.count + }; + } else { + concentrationsId[id].frames_warning = concentrationsId[id].frames_warning + warning.count; + } + + concentrationsId[id].frames.push(data[i]); + + if (warning.count == 0) { + concentrationsId[id].rgGuinier.push(data[i].rgGuinier); + concentrationsId[id].i0Guinier.push(data[i].I0); + concentrationsId[id].quality.push(data[i].quality); + concentrationsId[id].rgGnom.push(data[i].rgGnom); + concentrationsId[id].dMax.push(data[i].dmax); + } + + } + var concentrations = []; + for ( var item in concentrationsId) { + if (concentrationsId.hasOwnProperty(item)) { + concentrations.push({ + concentration : concentrationsId[item].concentration, + id : item, + bufferId : Number(concentrationsId[item].bufferId).toFixed(2), + bufferAcronym : concentrationsId[item].bufferAcronym, + rgGuinier : concentrationsId[item].rgGuinier, + /** Frames **/ + frames : concentrationsId[item].frames, + frames_warning : concentrationsId[item].frames_warning, + /** Calculation **/ + calculation : { + rgGuinier : BUI.getStandardDeviation(concentrationsId[item].rgGuinier), + i0Guinier : BUI.getStandardDeviation(concentrationsId[item].i0Guinier), + quality : BUI.getStandardDeviation(concentrationsId[item].quality), + rgGnom : BUI.getStandardDeviation(concentrationsId[item].rgGnom), + dMax : BUI.getStandardDeviation(concentrationsId[item].dMax) + + } + }); + } + } + + return { + concentrations : concentrations + }; +}; + +ResultSummaryForm.prototype.prepareData = function(data) { + /** Return array composed by {acronym, bufferId} objects **/ + function getBuffers(data) { + var buffersId = {}; + for ( var i = 0; i < data.length; i++) { + buffersId[data[i].bufferId] = data[i].acronym; + } + var buffers = []; + for ( var id in buffersId) { + if (buffersId.hasOwnProperty(id)) { + buffers.push({ + acronym : buffersId[id], + bufferId : id + }); + } + } + return buffers; + } + + /** Get a string with all the concentrations **/ + function getConcentrationString(parseConcentrations) { + var concentrations = []; + for ( var i = 0; i < parseConcentrations.concentrations.length; i++) { + concentrations.push(parseConcentrations.concentrations[i].concentration + " mg/ml "); + } + return concentrations.toString(); + } + + var parseConcentrations = this.getConcentrations(data); + + return { + dataCollectionCount : data.length, + buffers : getBuffers(data), + concentration : parseConcentrations, + concentrationLabel : getConcentrationString(parseConcentrations) + }; +}; + +ResultSummaryForm.prototype.getDataForWhisker = function(data) { + var clusters = []; + + var concentrations = {}; + var i = 0; + var conc = 0; + if (this.collapseConcentrations) { + for (i = 0; i < data.concentration.concentrations.length; i++) { + conc = data.concentration.concentrations[i]; + var concentration = Number(conc.concentration).toFixed(0); + if (concentrations[concentration] == null) { + concentrations[concentration] = {}; + concentrations[concentration].concentration = concentration; + concentrations[concentration].calculation = {}; + concentrations[concentration].calculation.rgGuinier = {}; + concentrations[concentration].calculation.rgGuinier.values = []; + concentrations[concentration].calculation.rgGuinier.values = conc.calculation.rgGuinier.values; + concentrations[concentration].calculation.rgGnom = {}; + concentrations[concentration].calculation.rgGnom.values = []; + concentrations[concentration].calculation.rgGnom.values = conc.calculation.rgGnom.values; + } else { + concentrations[concentration].calculation.rgGuinier.values = concentrations[concentration].calculation.rgGuinier.values + .concat(conc.calculation.rgGuinier.values); + concentrations[concentration].calculation.rgGnom.values = concentrations[concentration].calculation.rgGnom.values + .concat(conc.calculation.rgGnom.values); + } + } + + /** From object to array **/ + var array = []; + for ( var key in concentrations) { + if (concentrations.hasOwnProperty(key)) { + array.push(concentrations[key]); + } + } + data.concentration.concentrations = array; + } + + for (i = 0; i < data.concentration.concentrations.length; i++) { + conc = data.concentration.concentrations[i]; + clusters.push({ + name : conc.concentration + "mg/ml", + concentration : Number(conc.concentration), + x : Number(conc.concentration), + classes : [] + }); + clusters[clusters.length - 1].classes.push({ + name : "Guinier", + color : '#9A2EFE', + values : conc.calculation.rgGuinier.values + + }); + clusters[clusters.length - 1].classes.push({ + name : "P(r)", + color : '#2E64FE', + values : conc.calculation.rgGnom.values + + }); + } + return { + clusters : clusters.sort(function(a, b) { + return a.concentration - b.concentration; + }) + }; +}; + +ResultSummaryForm.prototype.getDataForWhiskerQuality = function(data) { + var clusters = []; + + for ( var i = 0; i < data.concentration.concentrations.length; i++) { + var conc = data.concentration.concentrations[i]; + clusters.push({ + name : conc.concentration + "mg/ml", + classes : [] + }); + clusters[clusters.length - 1].classes.push({ + name : "Quality", + values : conc.calculation.quality.values + + }); + } + + return { + clusters : clusters + }; +}; + +ResultSummaryForm.prototype.plotQualityWhisker = function(parsedData) { + this.qualityPlot.refresh(this.getDataForWhiskerQuality(parsedData)); +}; + +ResultSummaryForm.prototype.plotWhisker = function(parsedData) { + this.plot.refresh(this.getDataForWhisker(parsedData)); +}; + +ResultSummaryForm.prototype.plotRange = function(parsedData) { + this.rangePlot.refresh(this.getDataForWhisker(parsedData)); +}; + +ResultSummaryForm.prototype.getPanel = function(data) { + var _this = this; + _this.rawData = data; + var parsedData = this.prepareData(data); + + this.panel = Ext + .createWidget( + 'form', + { + bodyPadding : 20, + frame : false, + border : 0, + width : this.width, + height : this.summaryHeight + 1000, + items : [ { + xtype : 'container', + layout : 'hbox', + items : [ { + xtype : 'container', + flex : 1, + border : false, + layout : 'anchor', + defaultType : 'textfield', + items : [ + _this.qualityControlResultsWidget.getPanel(), + { + xtype : 'fieldset', + width : 950, + margin : "20, 0 0 0", + height : this.summaryHeight + 500, + items : [ + { + html : "
Concentration Analysis
", + border : 0, + width : 900 + + }, + { + html : this.concentrationHTMLTableWidget.getPanel(parsedData), + border : 0, + width : 900, + margin : "10, 0 0 10" + + }, + { + xtype : 'container', + layout : 'vbox', + border : 5, + items : [ + { + html : "
Rg based on Guinier and Gnom
", + border : 8, + width : 900, + margin : "20 0 0 10" + + }, { + xtype : 'container', + layout : 'hbox', + items : [ { + xtype : 'container', + layout : 'vbox', + items : [ { + html : "
", + border : 0, + width : this.plot.width, + padding : "10 0 0 20", + listeners : { + afterrender : function() { + _this.plotWhisker(parsedData); + + } + } + }, { + html : "
Concentration (mg/ml)
", + width : 450, + border : 0, + margin : "-50 0 0 0" + + } ] + }, { + xtype : 'container', + layout : 'vbox', + items : [ { + html : "
", + border : 0, + width : this.rangePlot.width, + padding : "10 0 0 10", + listeners : { + afterrender : function() { + _this.plotRange(parsedData); + } + } + }, { + html : "
Concentration (mg/ml)
", + width : 450, + border : 0, + margin : "-50 0 0 0" + + } ] + } ] + } ] + } ] + } ] + } + + ] + } ] + }); + return this.panel; + +}; + +ResultSummaryForm.prototype.input = function() { + return { + data : DATADOC.getData_3367() + }; +}; + +ResultSummaryForm.prototype.test = function(targetId) { + var resultSummaryForm = new ResultSummaryForm(); + var panel = resultSummaryForm.getPanel(resultSummaryForm.input().data); + panel.render(targetId); + +}; -GraphCanvas.prototype.getVertexStroke = function(vertexId) { - return this.getFormatter().getVertexById(vertexId).getDefault().getStroke(); -}; +/** + * Example form + * + * @witdh + * @height + */ +function RigibBodyModelingForm(args) { + this.id = BUI.id(); + this.width = 700; + this.height = 500; + + if (args != null) { + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + } + + var _this = this; + this.rigidBodyGrid = new AprioriRigidBodyGrid(); + + this.rigidBodyGrid.onUploadFile.attach(function(sender, type, title){ + _this._openUploadDialog(_this.macromolecule.macromoleculeId, type, title); + }); + + this.rigidBodyGrid.onRemove.attach(function(sender, type, title){ + _this._update(); + }); + + this.onSave = new Event(this); + +} + +RigibBodyModelingForm.prototype._getItems = function() { + var _this = this; + + + return [ { + xtype : 'label', + forId : 'myFieldId', + text : 'Information for model fit, mixture analysis and rigid body modeling', + margin : '15 0 20 10', + cls : "inline-help" + }, + this.rigidBodyGrid.getPanel(), + { + xtype : 'label', + forId : 'myFieldId', + text : 'Distance restraints may be imposed on the model using contacts conditions file (OPTIONAL)', + margin : '25 0 5 10', + cls : "inline-help" + }, + { + xtype : 'container', + layout : 'hbox', + items : [ { + xtype : 'container', + border : false, + layout : 'hbox', + items : [ { + xtype : 'label', + forId : 'myFieldId', + text : 'Contact Description File: (Optional)', + width : 150, + margin : '10 0 0 10' + }, { + id : this.id + "contactsDescriptionFilePath", + xtype : 'textfield', + hideLabel : true, + margin : '10 0 0 0', + width : 200, + disabled: true + }, { + text : 'Upload', + xtype : 'button', + margin : "10 0 0 10", + width : 80, + handler : function() { + + _this._openUploadDialog(_this.macromolecule.macromoleculeId, "CONTACTS", "Upload Contact Description File"); + } + }, { + text : 'Remove', + id : _this.id + "_remove", + xtype : 'button', + margin : "10 0 0 10", + width : 80, + handler : function() { + _this.macromolecule.contactsDescriptionFilePath = null; + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, proposal) { + /** Updating the proposal global object **/ + BIOSAXS.proposal.setItems(proposal); + _this.panel.setLoading(false); + + var saved = BIOSAXS.proposal.getMacromoleculeByAcronym(_this.macromolecule.acronym); + /** Refreshing to check that everything is ok **/ + _this.refresh(saved); + _this.onSave.notify(saved); + }); + + _this.panel.setLoading("Saving Macromolecule") + adapter.saveMacromolecule(_this.macromolecule); + } + } ] + } ] + }, { + xtype : 'panel', + html : "Go to SASREF manual for further information", + margin : "10 0 0 160", + border : 0 + + }, + { + xtype : 'checkbox', + margin : '10 0 0 5', + boxLabel : "I want rigid body modeling run on this stuff", + checked : true, + width : 300 + } ] + +}; + +/** Because update is a jsp page we don't know if the user has uploaded a file or not then we need to refresh **/ +RigibBodyModelingForm.prototype._update = function(macromoleculeId, type, title) { + var _this = this; + BIOSAXS.proposal.onInitialized.attach(function() { + if (BIOSAXS.proposal != null) { + _this.refresh(BIOSAXS.proposal.getMacromoleculeById(_this.macromolecule.macromoleculeId)); + _this.panel.setLoading(false); + } + }); + this.panel.setLoading(); + BIOSAXS.proposal.init(); +}; + +RigibBodyModelingForm.prototype._openUploadDialog = function(macromoleculeId, type, title) { + var _this = this; + function onClose() { + w.destroy(); + _this._update(); + + } + + var w = Ext.create('Ext.window.Window', { + title : title, + height : 200, + width : 400, + modal : true, + buttons : [ { + text : 'Close', + handler : function() { + onClose(); + } + } ], + layout : 'fit', + items : { + html : "" + }, + listeners : { + onEsc : function() { + onClose(); + }, + close : function() { + onClose(); + } + } + }).show(); +}; + +RigibBodyModelingForm.prototype._getButtons = function() { + return []; +}; + +RigibBodyModelingForm.prototype.getPanel = function() { + var _this = this; + this.panel = Ext.create('Ext.form.Panel', { + width : this.width, + height : this.height, + margin : 10, + border : 1, + defaultType : 'textfield', + items : this._getItems(), + buttons : this._getButtons(), + listeners : { + afterrender : function(){ + _this._populate(); + + } + } + }); + return this.panel; +}; + +/** Populates could be call when the DOM is not filled yet **/ +RigibBodyModelingForm.prototype._populate = function() { + if (this.macromolecule != null){ + if (Ext.getCmp(this.id + "contactsDescriptionFilePath") != null){ + if (this.macromolecule.contactsDescriptionFilePath != null){ + Ext.getCmp(this.id + "contactsDescriptionFilePath").setValue(this.macromolecule.contactsDescriptionFilePath); + Ext.getCmp(this.id + "_remove").enable(); + } + else{ + Ext.getCmp(this.id + "_remove").disable(); + Ext.getCmp(this.id + "contactsDescriptionFilePath").setValue(""); + + } + } + } +}; + +/** It populates the form * */ +RigibBodyModelingForm.prototype.refresh = function(macromolecule) { + this.macromolecule = macromolecule; + this.rigidBodyGrid.refresh(macromolecule); + this._populate(); +}; + +RigibBodyModelingForm.prototype.input = function() { + return {}; +}; + + +/** It populates the form **/ +RigibBodyModelingForm.prototype.test = function(targetId) { + var macromoleculeForm = new RigibBodyModelingForm(); + var panel = macromoleculeForm.getPanel(); + panel.render(targetId); +}; + -GraphCanvas.prototype.setVertexStrokeOpacity = function(vertexId, value) { - this.getFormatter().getVertexById(vertexId).getDefault().setStrokeOpacity(value); -}; +/** + * Same form as MX part + * + * @creationMode if true a create button appears instead of save + * @showTitle true or false + */ +function ShipmentForm(args) { + this.id = BUI.id(); + + this.creationMode = false; + this.showTitle = true; + if (args != null) { + if (args.creationMode != null) { + this.creationMode = args.creationMode; + } + if (args.showTitle != null) { + this.showTitle = args.showTitle; + } + } + + this.onSaved = new Event(this); +} + +ShipmentForm.prototype.fillStores = function() { + this.panel.setLoading("Loading Labcontacts from database"); + this.labContactForSendingStore.loadData(BIOSAXS.proposal.getLabcontacts(), false); + this.labContactForReturnStore.loadData(BIOSAXS.proposal.getLabcontacts(), false); + this.panel.setLoading(false); + if (this.shipment != null) { + this.setShipment(this.shipment); + } +}; + +ShipmentForm.prototype.draw = function(targetId) { + this.getPanel().render(targetId); +}; + +ShipmentForm.prototype.setShipment = function(shipment) { + this.shipment = shipment; + var _this = this; + Ext.getCmp(_this.id + "shippingName").setValue(shipment.json.shippingName); + Ext.getCmp(_this.id + "shippingStatus").setValue(shipment.json.shippingStatus); + Ext.getCmp(_this.id + "comments").setValue(shipment.json.comments); + if (shipment.json.sendingLabContactVO != null) { + this.labContactsSendingCombo.setValue(shipment.json.sendingLabContactVO.labContactId); + } + if (shipment.json.returnLabContactVO != null) { + this.labContactsReturnCombo.setValue(shipment.json.returnLabContactVO.labContactId); + } + +}; + +ShipmentForm.prototype._saveShipment = function() { + var _this = this; + var shippingId = null; + if (this.shipment != null) { + shippingId = this.shipment.json.shippingId; + } + var json = { + shippingId : shippingId, + name : Ext.getCmp(_this.id + "shippingName").getValue(), + status : Ext.getCmp(_this.id + "shippingStatus").getValue(), + sendingLabContactId : Ext.getCmp(_this.id + "shipmentform_sendingLabContactId").getValue(), + returnLabContactId : Ext.getCmp(_this.id + "returnLabContactId").getValue(), + returnCourier : Ext.getCmp(_this.id + "returnCourier").getValue(), + courierAccount : Ext.getCmp(_this.id + "courierAccount").getValue(), + BillingReference : Ext.getCmp(_this.id + "BillingReference").getValue(), + dewarAvgCustomsValue : Ext.getCmp(_this.id + "dewarAvgCustomsValue").getValue(), + dewarAvgTransportValue : Ext.getCmp(_this.id + "dewarAvgTransportValue").getValue(), + comments : Ext.getCmp(_this.id + "comments").getValue() + }; + + var dataAdapter = new BiosaxsDataAdapter(); + dataAdapter.onSuccess.attach(function(sender, shipment) { + window.location = BUI.getShippingURL(shipment.shippingId); + }); + + dataAdapter.onError.attach(function(sender, error) { + _this.onError.notify(error); + }); + + /** Cheking params **/ + if (json.name == "") { + BUI.showError("Name field is mandatory"); + return; + } + + if (json.sendingLabContactId == null) { + BUI.showError("Lab contact for sending field is mandatory"); + return; + } + + if (json.returnLabContactId == null) { + BUI.showError("Lab contact for return field is mandatory"); + return; + } + + dataAdapter.createShipment(json.shippingId, json.name, json.status, json.comments, json.sendingLabContactId, json.returnLabContactId, + json.returnCourier, json.courierAccount, json.BillingReference, json.dewarAvgCustomsValue, json.dewarAvgTransportValue); + +}; + +ShipmentForm.prototype.getPanel = function(shipment) { + var _this = this; + this.shipment = shipment; + var required = '*'; + var buttons = []; + + if (_this.creationMode) { + buttons.push({ + text : 'Create', + scope : this, + handler : function() { + _this._saveShipment(); + } + }); + } else { + buttons.push({ + text : 'Save', + scope : this, + handler : function() { + _this._saveShipment(); + } + }); + + } + + this.labContactForSendingStore = Ext.create('Ext.data.Store', { + fields : [ 'cardName', 'labContactId' ] + }); + + this.labContactForReturnStore = Ext.create('Ext.data.Store', { + fields : [ 'cardName', 'labContactId' ] + }); + + // Create the combo box, attached to the states data store + this.labContactsSendingCombo = Ext.create('Ext.form.ComboBox', { + id : _this.id + "shipmentform_sendingLabContactId", + fieldLabel : 'Lab contact for sending', + afterLabelTextTpl : required, + store : this.labContactForSendingStore, + queryMode : 'local', + labelWidth : 200, + displayField : 'cardName', + valueField : 'labContactId' + }); + + this.labContactsReturnCombo = Ext.create('Ext.form.ComboBox', { + id : _this.id + "returnLabContactId", + fieldLabel : 'If No, Lab-Contact for Return', + afterLabelTextTpl : required, + store : this.labContactForReturnStore, + queryMode : 'local', + labelWidth : 200, + displayField : 'cardName', + valueField : 'labContactId', + listeners : { + change : function(x, newValue) { + for ( var i = 0; i < x.getStore().data.items.length; i++) { + if (x.getStore().data.items[i].raw.labContactId == newValue) { + Ext.getCmp(_this.id + "returnCourier").setValue(x.getStore().data.items[i].raw.defaultCourrierCompany); + Ext.getCmp(_this.id + "courierAccount").setValue(x.getStore().data.items[i].raw.courierAccount); + Ext.getCmp(_this.id + "BillingReference").setValue(x.getStore().data.items[i].raw.billingReference); + Ext.getCmp(_this.id + "dewarAvgCustomsValue").setValue(x.getStore().data.items[i].raw.dewarAvgCustomsValue); + Ext.getCmp(_this.id + "dewarAvgTransportValue").setValue(x.getStore().data.items[i].raw.dewarAvgTransportValue); + } + } + } + } + }); + + if (this.panel == null) { + this.panel = Ext.create('Ext.form.Panel', { + bodyPadding : 5, + width : 600, + border : 1, + items : [ { + xtype : 'fieldset', + title : 'Details', + collapsible : false, + defaultType : 'textfield', + layout : 'anchor', + defaults : { + anchor : '100%' + }, + items : [ { + xtype : 'requiredtext', + fieldLabel : 'Shipment Label', + allowBlank : false, + name : 'shippingName', + id : _this.id + 'shippingName', + value : '', + anchor : '50%' + }, { + + xtype : 'textareafield', + name : 'comments', + id : _this.id + 'comments', + fieldLabel : 'Comments', + value : '' + }, { + fieldLabel : 'Status', + readOnly : true, + id : _this.id + 'shippingStatus', + value : 'Opened', + anchor : '50%' + } ] + }, { + xtype : 'fieldset', + title : 'Lab-Contacts', + collapsible : false, + defaultType : 'textfield', + layout : 'anchor', + defaults : { + anchor : '100%' + }, + items : [ this.labContactsSendingCombo, this.labContactsReturnCombo ] + }, { + border : 0, + html : BUI.getWarningHTML("These informations are relevant for all shipments") + }, { + xtype : 'fieldset', + title : 'Courier accounts details for return', + collapsible : false, + layout : 'anchor', + defaults : { + anchor : '100%' + }, + items : [ { + xtype : 'textfield', + labelWidth : 400, + fieldLabel : 'Courier company for return (if ESRF sends a dewar back)', + id : _this.id + 'returnCourier', + value : '' + }, { + xtype : 'textfield', + labelWidth : 400, + fieldLabel : 'Courier account', + id : _this.id + 'courierAccount', + value : '' + }, { + xtype : 'textfield', + labelWidth : 400, + fieldLabel : 'Billing reference', + id : _this.id + 'BillingReference', + value : '' + }, { + xtype : 'numberfield', + labelWidth : 400, + fieldLabel : 'Average Customs value of a dewar (Euro)', + id : _this.id + 'dewarAvgCustomsValue', + value : '' + }, { + xtype : 'numberfield', + labelWidth : 400, + fieldLabel : 'Average Transport value of a dewar (Euro)', + id : _this.id + 'dewarAvgTransportValue', + value : '' + } ] + } ], + buttons : buttons + }); + } + this.fillStores(); + if (this.showTitle) { + this.panel.setTitle('Create a new Shipment'); + } + return this.panel; +}; + +ShipmentForm.prototype.input = function() { + return { + proposal : DATADOC.getProposal_10() + + }; +}; + +ShipmentForm.prototype.test = function(targetId) { + var shipmentForm = new ShipmentForm({ + creationMode : true + + }); + BIOSAXS.proposal = new Proposal(shipmentForm.input().proposal); + shipmentForm.getPanel().render(targetId); +}; -GraphCanvas.prototype.getVertexStrokeOpacity = function(vertexId) { - return this.getFormatter().getVertexById(vertexId).getDefault().getStrokeOpacity(); -}; +/** + * #onSaved + */ +function StockSolutionForm(args) { + this.id = BUI.id(); + this.actions = []; + + if (args != null) { + if (args.actions != null) { + this.actions = args.actions; + } + } + this.onSaved = new Event(this); +} + +StockSolutionForm.prototype.getStockSolution = function() { + if (this.stockSolution != null) { + this.stockSolution.concentration = Ext.getCmp(this.id + "stockSolution_concentration").getValue(); + this.stockSolution.storageTemperature = Ext.getCmp(this.id + "stockSolution_storageTemperature").getValue(); + this.stockSolution.volume = Ext.getCmp(this.id + "stockSolution_volume").getValue(); + this.stockSolution.comments = Ext.getCmp(this.id + "stockSolution_comments").getValue(); + this.stockSolution.name = Ext.getCmp(this.id + "stockSolution_name").getValue(); + this.stockSolution.bufferId = this.bufferCombo.getValue(); + + if (this.macromoleculeCombo.getValue() != null) { + this.stockSolution.macromoleculeId = this.macromoleculeCombo.getValue(); + } else { + this.stockSolution.macromolecule3VO = null; + } + + } else { + return { + concentration : Ext.getCmp(this.id + "stockSolution_concentration").getValue(), + storageTemperature : Ext.getCmp(this.id + "stockSolution_storageTemperature").getValue(), + volume : Ext.getCmp(this.id + "stockSolution_volume").getValue(), + comments : Ext.getCmp(this.id + "stockSolution_comments").getValue(), + name : Ext.getCmp(this.id + "stockSolution_name").getValue(), + bufferId : this.bufferCombo.getValue(), + macromoleculeId : this.macromoleculeCombo.getValue() + }; + } + return this.stockSolution; +}; + +StockSolutionForm.prototype.setStockSolution = function(stockSolution) { + if (stockSolution != null) { + if (stockSolution.macromoleculeId != null) { + this.macromoleculeCombo.setValue(stockSolution.macromoleculeId); + } + this.bufferCombo.setValue(stockSolution.bufferId); + Ext.getCmp(this.id + "stockSolution_concentration").setValue(this.stockSolution.concentration); + Ext.getCmp(this.id + "stockSolution_storageTemperature").setValue(this.stockSolution.storageTemperature); + Ext.getCmp(this.id + "stockSolution_volume").setValue(this.stockSolution.volume); + Ext.getCmp(this.id + "stockSolution_name").setValue(this.stockSolution.name); + Ext.getCmp(this.id + "stockSolution_comments").setValue(this.stockSolution.comments); + } +}; + +StockSolutionForm.prototype.getBufferCombo = function() { + this.bufferCombo = BIOSAXS_COMBOMANAGER.getComboBuffers(BIOSAXS.proposal.getBuffers(), { + labelWidth : 120, + margin : '0 0 10 0', + width : 220 + + }); + return this.bufferCombo; +}; + +StockSolutionForm.prototype.getMacromoleculeCombo = function() { + this.macromoleculeCombo = BIOSAXS_COMBOMANAGER.getComboMacromoleculeByMacromolecules(BIOSAXS.proposal.getMacromolecules(), { + labelWidth : 120, + margin : '0 0 10 0', + width : 220 + + }); + return this.macromoleculeCombo; +}; + +StockSolutionForm.prototype.refresh = function() { +}; + +StockSolutionForm.prototype._getTopPanel = function() { + return { + xtype : 'container', + layout : 'hbox', + border : 0, + items : [ { + xtype : 'container', + layout : 'hbox', + items : [ { + xtype : 'container', + flex : 1, + border : false, + layout : 'anchor', + defaultType : 'textfield', + items : [ + + this.getMacromoleculeCombo(), { + xtype : 'requiredtext', + id : this.id + 'stockSolution_name', + fieldLabel : 'Acronym', + labelWidth : 120, + width : 250 + }, { + xtype : 'requiredtext', + id : this.id + 'stockSolution_concentration', + fieldLabel : 'Conc. (mg/ml)', + labelWidth : 120, + width : 250 + }, + + { + id : this.id + 'stockSolution_storageTemperature', + fieldLabel : 'Storage Temp.(C)', + labelWidth : 120, + width : 250 + }, { + xtype : 'requiredtext', + id : this.id + 'stockSolution_volume', + fieldLabel : 'Volume in Well (µl)', + labelWidth : 120, + width : 250 + } ] + } ] + }, { + xtype : 'container', + flex : 1, + layout : 'anchor', + defaultType : 'textfield', + margin : '0 0 0 10', + items : [ this.getBufferCombo() ] + } ] + }; + +}; + +StockSolutionForm.prototype.getPanel = function(stockSolution) { + this.stockSolution = stockSolution; + this.panel = Ext.createWidget({ + xtype : 'container', + layout : 'vbox', + border : 0, + style : { + padding : '10px' + }, + fieldDefaults : { + labelAlign : 'left', + labelWidth : 50 + }, + items : [ this._getTopPanel(stockSolution), { + id : this.id + 'stockSolution_comments', + xtype : 'textareafield', + name : 'comments', + fieldLabel : 'Comments', + labelWidth : 120, + width : '100%' + } ] + }); + + this.setStockSolution(stockSolution); + return this.panel; +}; + +StockSolutionForm.prototype.input = function() { + return { + stock : { + "stockSolutionId" : 6, + "proposalId" : 3124, + "macromoleculeId" : 5933, + "bufferId" : 811, + "instructionSet3VO" : null, + "boxId" : 305861, + "storageTemperature" : "20", + "volume" : "300", + "concentration" : "1.2", + "comments" : "Buffer EDTA with A", + "name" : "A_EDTA_1.2", + "samples" : [], + "buffer" : "EDTA", + "macromolecule" : "A" + }, + proposal : new MeasurementGrid().input().proposal + }; +}; + +StockSolutionForm.prototype.test = function(targetId) { + var stockSolutionForm = new StockSolutionForm(); + BIOSAXS.proposal = new Proposal(stockSolutionForm.input().proposal); + var panel = stockSolutionForm.getPanel(new Shipment(stockSolutionForm.input().stock)); + panel.render(targetId); +}; -GraphCanvas.prototype.setVertexOpacity = function(vertexId, value) { - this.getFormatter().getVertexById(vertexId).getDefault().setOpacity(value); -}; + +BoxWhiskerGraph.prototype.cleanArray = GenericGraph.prototype.cleanArray; +BoxWhiskerGraph.prototype.plotAxes = GenericGraph.prototype.plotAxes; +BoxWhiskerGraph.prototype.plotRuler = GenericGraph.prototype.plotRuler; +BoxWhiskerGraph.prototype.drawSVGVerticalText = GenericGraph.prototype.drawSVGVerticalText; +BoxWhiskerGraph.prototype.getClassColor = GenericGraph.prototype.getClassColor; +BoxWhiskerGraph.prototype.getDimensions = GenericGraph.prototype.getDimensions; +BoxWhiskerGraph.prototype.calculate = GenericGraph.prototype.calculate; +BoxWhiskerGraph.prototype.getMedian = GenericGraph.prototype.getMedian; +BoxWhiskerGraph.prototype.pointToPixel = GenericGraph.prototype.pointToPixel; +BoxWhiskerGraph.prototype.maxValueWhisker = GenericGraph.prototype.maxValueWhisker; +BoxWhiskerGraph.prototype.refresh = GenericGraph.prototype.refresh; + +/** + * Subclass of GenericGraph + * + * @maxBoxWidth + */ +function BoxWhiskerGraph(args){ + this.maxBoxWidth = 25; + + if (args == null){ + args = new Object(); + } + args["plotHorizontalByCluster"] = true; + + GenericGraph.call(this, args); + + if (args.maxBoxWidth != null){ + this.maxBoxWidth = args.maxBoxWidth; + } +}; + + + +/** +There are several different methods for calculating quartiles.[1] This calculator uses a method described by Moore and McCabe to find quartile values. +The same method also used by The TI-83 to calculate quartile values. +With this method, the first quartile is the median of the numbers below the median, the third quartile is the median of the numbers above the median. + +http://www.miniwebtool.com/quartile-calculator/ +http://www.alcula.com/calculators/statistics/box-plot/ +**/ +BoxWhiskerGraph.prototype.getQ1 = function(array){ + array = array.slice(0, array.length/2); + return this.getMedian(array); +}; + +BoxWhiskerGraph.prototype.getQ3 = function(array){ + array = array.slice((array.length + 1)/2); + return this.getMedian(array); + +}; + +BoxWhiskerGraph.prototype.getQ2 = function(array){ + return this.getMedian(array); +}; + +BoxWhiskerGraph.prototype.getBelowOutliers = function(belowLimit, array){ + var points = new Array(); + for (var i = 0; i < array.length; i++){ + if (array[i] <= belowLimit){ + points.push(array[i]); + } + } + return points; +}; + +BoxWhiskerGraph.prototype.getAboveOutliers = function(aboveLimit, array){ + var points = new Array(); + for (var i = 0; i < array.length; i++){ + if (array[i] >= aboveLimit){ + points.push(array[i]); + } + } + return points; +}; + + +BoxWhiskerGraph.prototype.minValueWhisker = function(belowLimit, q1, array){ + var points = new Array(); + + for (var i = 0; i < array.length; i++){ + if ((array[i] < q1) && (array[i]) > belowLimit){ + points.push(array[i]); + } + } + + if (points.length > 0){ + points.sort(function(a, b){return a - b;}); + return points[0]; + } + return null; +}; + +BoxWhiskerGraph.prototype.isNumber = function(value){ + if (value=="") return false; + + var d = parseInt(value); + if (!isNaN(d)) return true; else return false; + +}; + +BoxWhiskerGraph.prototype.plotBoxWhisker = function(boxProperties){ + if (this.maxBoxWidth != null){ + if (boxProperties.width > this.maxBoxWidth){ + boxProperties.x = boxProperties.x + (boxProperties.width/2) - (this.maxBoxWidth/2); + boxProperties.width = this.maxBoxWidth; + } + + } + + if (this.plotPoints){ + for(var i = 0; i < boxProperties.values.length; i++){ + var value = boxProperties.values[i]; + var toPixel = this.pointToPixel(value, boxProperties); + SVG.drawCircle(boxProperties.x + (boxProperties.width/2) + 2, toPixel, this.pointRadius, this.svg, [["fill", "green"], ["fill-opacity", this.fillOpacityPoint],['stroke-opacity', this.strokeOpacityPoint], ["stroke", "black"]]); + } + } + + + var boxColor = this.getClassColor(boxProperties.name); + var result = this.calculate(boxProperties.values); + /** Q1 **/ + + if (this.isNumber(result.Q1)){ + SVG.drawLine(boxProperties.x, this.pointToPixel(result.Q1, boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result.Q1, boxProperties), this.svg, [["stroke", boxColor]]); + } + /** Q2 **/ + if (this.isNumber(result.Q2)){ + SVG.drawLine(boxProperties.x, this.pointToPixel(result.Q2, boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result.Q2, boxProperties), this.svg, [["stroke", "blue"], ["stroke-width", "2"]]); + } + + /** Q3 **/ + if (this.isNumber(result.Q3)){ + SVG.drawLine(boxProperties.x, this.pointToPixel(result.Q3, boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result.Q3, boxProperties), this.svg, [["stroke", boxColor]]); + } + + /** Concenting Q1 and Q3 **/ + if (this.isNumber(result.Q1)&&this.isNumber(result.Q3)){ + SVG.drawLine(boxProperties.x, this.pointToPixel(result.Q1, boxProperties), boxProperties.x, this.pointToPixel(result.Q3, boxProperties), this.svg, [["stroke", boxColor]]); + SVG.drawLine(boxProperties.x + boxProperties.width, this.pointToPixel(result.Q1, boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result.Q3, boxProperties), this.svg, [["stroke", boxColor]]); + } + + /** min-whisker **/ + if (result["min-whisker"] != null){ + if (this.isNumber(result.Q1)){ + SVG.drawLine(boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result.Q1, boxProperties), boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result["min-whisker"], boxProperties), this.svg, [["stroke", boxColor]]); + } + SVG.drawLine(boxProperties.x,this.pointToPixel(result["min-whisker"], boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result["min-whisker"], boxProperties) , this.svg, [["stroke", boxColor]]); + + } + + /** max-whisker **/ + if (result["max-whisker"] != null){ + if (this.isNumber(result.Q3)){ + SVG.drawLine(boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result.Q3, boxProperties), boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result["max-whisker"], boxProperties), this.svg, [["stroke", boxColor]]); + } + SVG.drawLine(boxProperties.x , this.pointToPixel(result["max-whisker"], boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result["max-whisker"], boxProperties), this.svg, [["stroke", boxColor]]); + + } + + /** outliners **/ + if (result["above-outliers"] != null){ + for (var point in result["above-outliers"]){ + SVG.drawCircle(boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result["above-outliers"][point], boxProperties), this.pointRadius, this.svg, [["fill", "red"], ["fill-opacity", "1"]]); + //SVG.drawText(boxProperties.x + (boxProperties.width/2) - 2, this.pointToPixel(result["above-outliers"][point], boxProperties) + 2, "x",this.svg, [["fill", "black"], ["font-size", "x-small"]]); + } + } + if (result["below-outliers"] != null){ + for (var point in result["below-outliers"]){ + SVG.drawCircle(boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result["below-outliers"][point], boxProperties), this.pointRadius, this.svg, [["fill", "red"], ["fill-opacity", "1"]]); + //SVG.drawText(boxProperties.x + (boxProperties.width/2) - 2, this.pointToPixel(result["below-outliers"][point], boxProperties) + 2, "x",this.svg, [["fill", "black"], ["font-size", "x-small"]]); + } + } +}; + + + +BoxWhiskerGraph.prototype.plotClusterTitles = function(properties){ + /** Cluster Titles **/ + var posX = this.left + this.rulerWidth; + var data = this.data; + for(var i = 0; i < data.clusters.length; i++ ){ + /** title for the clusters **/ + posX = posX + this.interClustersSpace; + + /** Drawing title of classes **/ + var cluster = data.clusters[i]; + var posXClasses = posX; + for(var j = 0; j < cluster.classes.length; j++){ + //SVG.drawRectangle(posXClasses, this.height - (this.bottom + this.clusterTitleHeight + this.rulerHeight), properties.classWidth, this.rulerHeight, this.svg, [["fill", "green"]]); +// SVG.drawText(posXClasses + 1/6*properties.classWidth, this.height - (this.bottom + this.clusterTitleHeight + (this.rulerHeight*1/4)), cluster.classes[j].name, this.svg, [["style", "font-size:xx-small"]]); + var color = cluster.classes[j].color; + this.drawSVGVerticalText(posXClasses + 1/2*(properties.classWidth), this.height - (this.bottom - this.clusterTitleHeight + (this.rulerHeight)), cluster.classes[j].name , [["style", "font-size:x-small;"], ["fill", color]]); + + // SVG.drawRectangle(posXClasses, this.height - (this.bottom + this.clusterTitleHeight), properties.classWidth, 2, this.svg, [["fill", "black"]]); + posXClasses = posXClasses + properties.classWidth + this.interClassesSpace; + } + + var clusterTitleSpace = (data.clusters[i].classes.length * properties.classWidth) + ((data.clusters[i].classes.length - 1) * this.interClassesSpace); + //SVG.drawRectangle(posX, this.height - (this.bottom + this.clusterTitleHeight), clusterTitleSpace, this.clusterTitleHeight, this.svg, [["fill", "pink"]]); + SVG.drawRectangle(posX, this.height - (this.clusterTitleHeight+this.bottom), clusterTitleSpace, 1, this.svg, []); + +// var transform = ["translate", "(" + posX + 1/3*clusterTitleSpace +", " + this.height - (this.bottom + (this.clusterTitleHeight*1/4)) +")"], ["transform", "rotate(180)"]; +// var transform = ["transform", "translate(" + (posX + 1/3*clusterTitleSpace) +", " + (this.height - (this.bottom + (this.clusterTitleHeight*1/4))) + "), rotate(-90) "]; +// this.drawSVGVerticalText(posX + 1/3*clusterTitleSpace, this.height - (this.bottom + (this.clusterTitleHeight*1/4)),data.clusters[i].name, [["style", "font-size:x-small"]]); + SVG.drawText(posX , this.height - (this.bottom + (this.clusterTitleHeight*1/4)),data.clusters[i].name ,this.svg, [["style", "font-size:x-small"]]); + posX = posX + clusterTitleSpace; + } +}; + +BoxWhiskerGraph.prototype.plotWhisters = function(data, properties){ + var colors = ["yellow", "orange", "green"]; + var posX = this.left + this.rulerWidth; + for(var i = 0; i < data.clusters.length; i++ ){ + var cluster = data.clusters[i]; + /** inter cluster space **/ + //SVG.drawRectangle(posX, this.top, this.interClustersSpace, this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight, this.svg, [["fill", "black"]]); + posX = posX + this.interClustersSpace; + + for (var j = 0; j < cluster.classes.length; j ++){ + + //SVG.drawRectangle(posX, this.top, properties.classWidth, this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight, this.svg, [["fill", colors[j]]]); + this.plotBoxWhisker( + { + name : cluster.classes[j].name, + values : cluster.classes[j].values, + minPoint : properties.minPoint, + maxPoint : properties.maxPoint, + x : posX, + y : this.top, + width : properties.classWidth, + height : this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight + + + } + ); + posX = posX + properties.classWidth; + //SVG.drawRectangle(posX, this.top, this.interClassesSpace, this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight, this.svg, [["fill", "black"]]); + if (j < cluster.classes.length - 1){ + posX = posX + this.interClassesSpace; + } + } + } +}; + +BoxWhiskerGraph.prototype.draw = function(targetId, data){ + this.targetId = targetId; + var properties = (this.getDimensions(data)); + this.svg = SVG.createSVGCanvas(document.getElementById(this.targetId), [["width", this.width], ["height", this.height]]); + this.plotAxes(properties); + this.plotClusterTitles(properties); + this.plotWhisters(data,properties); +}; + +BoxWhiskerGraph.prototype.input = function(){ + return DATADOC.getBoxWhikerData(); +}; + +BoxWhiskerGraph.prototype.test = function(targetId){ + var plot = new BoxWhiskerGraph( + { + targetId : targetId, + height : 350, + width : 450, + maxBoxWidth : 25 + } + ); + plot.refresh(this.input()); +}; + + + + + -GraphCanvas.prototype.getVertexOpacity = function(vertexId) { - return this.getFormatter().getVertexById(vertexId).getDefault().getOpacity(); -}; + +function DataSet(){ + this.json = null; + +}; + + +DataSet.prototype.loadFromJSON = function(json){ + if(json != null) { + if(this.validate(json)) { + this.json = json; + } + } +}; + + +DataSet.prototype.toJSON = function(json){ + return this.json; +}; + + +/** Abstract method to be override on childs classes **/ +DataSet.prototype.validate = function(json){ + if (true){ + return true; + } + /*else{ + throw "Data validation failed"; + }*/ +}; + + -GraphCanvas.prototype.setVertexFill = function(vertexId, color) { - this.getFormatter().getVertexById(vertexId).getDefault().setFill(color); -}; + +Edge.prototype.getName = GraphItem.prototype.getName; +Edge.prototype.setName = GraphItem.prototype.setName; +Edge.prototype.getId = GraphItem.prototype.getId; + +function Edge(id, name, nodeSource, nodeTarget, args){ + GraphItem.prototype.constructor.call(this, id, name, args); + + this.sourceNode = nodeSource; + this.targetNode = nodeTarget; + +}; + +Edge.prototype.toJSON = function(){ + return {"index": this.id,"sourceIndex":this.sourceNode.getId(),"targetIndex":this.targetNode.getId(),"args":this.args}; +}; + +Edge.prototype.getNodeSource = function(){ + return this.sourceNode; +}; + +Edge.prototype.getNodeTarget = function(){ + return this.targetNode; +}; + +Edge.prototype.remove = function(){ + //Remove edge object in the nodes + this.getNodeSource().removeEdge(this); + this.getNodeTarget().removeEdge(this); + + this.deleted.notify(this); +}; -GraphCanvas.prototype.getVertexFill = function(vertexId) { - return this.getFormatter().getVertexById(vertexId).getDefault().getFill(); -}; + +EdgeGraphFormatter.prototype.setProperties = ItemGraphFormatter.prototype.setProperties; +EdgeGraphFormatter.prototype.getDefault = ItemGraphFormatter.prototype.getDefault; +EdgeGraphFormatter.prototype.getSelected = ItemGraphFormatter.prototype.getSelected; +EdgeGraphFormatter.prototype.getOver = ItemGraphFormatter.prototype.getOver; +EdgeGraphFormatter.prototype.getDragging = ItemGraphFormatter.prototype.getDragging; +EdgeGraphFormatter.prototype.getId = ItemGraphFormatter.prototype.getId; +EdgeGraphFormatter.prototype.toJSON = ItemGraphFormatter.prototype.toJSON; +EdgeGraphFormatter.prototype.loadFromJSON = ItemGraphFormatter.prototype.loadFromJSON; +EdgeGraphFormatter.prototype._setEvents = ItemGraphFormatter.prototype._setEvents; + +function EdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ + ItemGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); + + this.getDefault().args.type = "EdgeGraphFormatter"; +}; + + + + +LineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; +LineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; +LineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; +LineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; +LineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; +LineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; +LineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; +LineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; +LineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; + +function LineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ + EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); + this.args.type = "LineEdgeGraphFormatter"; +}; + +/** DIRECTED **/ +DirectedLineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; +DirectedLineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; +DirectedLineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; +DirectedLineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; +DirectedLineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; +DirectedLineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; +DirectedLineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; +DirectedLineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; +DirectedLineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; + +function DirectedLineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ + EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); + this.args.type = "DirectedLineEdgeGraphFormatter"; + this.args.arrowSize = "3"; +}; +DirectedLineEdgeGraphFormatter.prototype.getArrowSize = function(){ + return this.args.arrowSize; +}; + +OdirectedLineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; +OdirectedLineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; +OdirectedLineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; +OdirectedLineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; +OdirectedLineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; +OdirectedLineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; +OdirectedLineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; +OdirectedLineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; +OdirectedLineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; + +function OdirectedLineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ + EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); + this.args.type = "DirectedLineEdgeGraphFormatter"; + this.args.arrowSize = "3"; +}; + +OdirectedLineEdgeGraphFormatter.prototype.getArrowSize = function(){ + return this.args.arrowSize; +}; + + +/** CUT (inhibition) **/ +CutDirectedLineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; +CutDirectedLineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; +CutDirectedLineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; +CutDirectedLineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; +CutDirectedLineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; +CutDirectedLineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; +CutDirectedLineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; +CutDirectedLineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; +CutDirectedLineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; + +function CutDirectedLineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ + EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); + this.args.type = "CutDirectedLineEdgeGraphFormatter"; +}; + + + + +BezierEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; +BezierEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; +BezierEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; +BezierEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; +BezierEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; +BezierEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; +BezierEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; +BezierEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; +BezierEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; +BezierEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; + +function BezierEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ + EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); + this.args.type = "BezierEdgeGraphFormatter"; +}; + + + +DotDirectedLineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; +DotDirectedLineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; +DotDirectedLineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; +DotDirectedLineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; +DotDirectedLineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; +DotDirectedLineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; +DotDirectedLineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; +DotDirectedLineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; +DotDirectedLineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; + +function DotDirectedLineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ + EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); + this.args.type = "DotDirectedLineEdgeGraphFormatter"; +}; + + +OdotDirectedLineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; +OdotDirectedLineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; +OdotDirectedLineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; +OdotDirectedLineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; +OdotDirectedLineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; +OdotDirectedLineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; +OdotDirectedLineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; +OdotDirectedLineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; +OdotDirectedLineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; + +function OdotDirectedLineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ + EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); + this.args.type = "OdotDirectedLineEdgeGraphFormatter"; +}; + + -/** EDGES FORMATTER **/ -GraphCanvas.prototype.setEdgeSize = function(edgeId, value) { - this.getFormatter().getEdgeById(edgeId).getDefault().setSize(value); -}; +function GraphDataset(){ + DataSet.prototype.constructor.call(this); + this.edges = new Object(); + this.vertices = new Object(); + this.verticesIndex = new Object(); + + //Events + this.newVertex = new Event(this); + this.vertexNameChanged = new Event(this); + this.vertexDeleted = new Event(this); + + this.newEdge = new Event(this); + this.edgeNameChanged = new Event(this); + this.edgeDeleted = new Event(this); + + this.json = new Object(); + this.json.vertices = new Array(); + this.json.edges = new Array(); + this.json.relations = new Array(); +}; + +GraphDataset.prototype.loadFromJSON = DataSet.prototype.loadFromJSON; +GraphDataset.prototype.toJSON = DataSet.prototype.toJSON; +GraphDataset.prototype.validate = DataSet.prototype.validate; + +/** Devuelve el numero de edges incidentes sobre el nodo con mas edges **/ +GraphDataset.prototype.getMaxClass = function(){ + var maxClassNode = 0; + for ( var node in this.vertices) { + if (this.vertices[node].getEdgesCount() > maxClassNode){ + maxClassNode = this.vertices[node].getEdgesCount(); + } + } + return maxClassNode; +}; + +/** Devuelve el numero de edges incidentes sobre el nodo con mas edges **/ +GraphDataset.prototype.getMinClass = function(){ + var minClassNode = Math.min(); + for ( var node in this.vertices) { + if (this.vertices[node].getEdgesCount() < minClassNode){ + minClassNode = this.vertices[node].getEdgesCount(); + } + } + return minClassNode; +}; + +GraphDataset.prototype.getVertexByName = function(nodeName){ + var results = new Array(); + + for (var vertexId in this.verticesIndex[nodeName]){ + var vertexByid = this.getVertexById(this.verticesIndex[nodeName][vertexId]); + results.push(vertexByid); + //* añadido nuevo porque fallaba el anterior codigo + return vertexByid + } + + if (results <= 1){ + return this.getVertexById(this.verticesIndex[nodeName]); + } + else{ + return results; + } +}; + +GraphDataset.prototype.getVertexById = function(id){ + return this.vertices[id]; +}; + +GraphDataset.prototype.toSIF = function(){ + var sifDataAdapter = new SifFileDataAdapter(); + return sifDataAdapter.toSIF(this); +}; + +GraphDataset.prototype.toSIFID = function(){ + var sifDataAdapter = new SifFileDataAdapter(); + return sifDataAdapter.toSIFID(this); +}; + +GraphDataset.prototype.toDOT = function(){ + var dotFileDataAdapter = new DotFileDataAdapter(); + return dotFileDataAdapter.toDOT(this); +}; + +GraphDataset.prototype.toDOTID = function(){ + var dotFileDataAdapter = new DotFileDataAdapter(); + return dotFileDataAdapter.toDOTID(this); +}; + +GraphDataset.prototype._addNode = function(nodeName, args){ + return new Vertex(this._getVerticesCount()-1, nodeName, args); +}; + +GraphDataset.prototype.addNode = function(nodeName, args){ + this.json.vertices.push(nodeName); + this._addVerticesIndex(nodeName, this._getVerticesCount() - 1); + var vertex = this._addNode(nodeName, args); + this.vertices[this._getVerticesCount()-1] = vertex; + this._setNodeEvents(vertex); + this.newVertex.notify(vertex); +}; + +GraphDataset.prototype._addVerticesIndex = function(nodeName, id){ + if (this.verticesIndex[nodeName] == null){ + this.verticesIndex[nodeName] = new Array(); + } + this.verticesIndex[nodeName].push(id); +}; + +GraphDataset.prototype.addEdge = function(edgeName, nodeSourceId, nodeTargetId, args){ + this.json.edges.push(edgeName); + var nodeSource = this.getVertexById(nodeSourceId); + var nodeTarget = this.getVertexById(nodeTargetId); + var index = this.getEdgesCount() - 1; + this.edges[index] = new Edge(index, edgeName, nodeSource, nodeTarget, args); + this.json.relations.push({"index": index, "sourceIndex": nodeSourceId, "targetIndex": nodeTargetId, "args": args }); + + nodeSource.addEdge(this.edges[index]); + nodeTarget.addEdge(this.edges[index]); + this._setEdgeEvents(this.edges[index]); + this.newEdge.notify(this.edges[index]); +}; + +GraphDataset.prototype.getVertices = function(){ + return this.vertices; +}; + +GraphDataset.prototype.getEdges = function(){ + return this.edges; +}; + +GraphDataset.prototype.getEdgeById = function(edgeId){ + return this.edges[edgeId]; +}; + +GraphDataset.prototype._getVerticesCount = function(){ + return this.json.vertices.length; +}; + + +GraphDataset.prototype.getVerticesCount = function(){ + var count = 0; + for ( var vertex in this.getVertices()) { + count ++; + } + return count; +}; + + +GraphDataset.prototype.getEdgesCount = function(){ + return this.json.edges.length; +}; + +GraphDataset.prototype.init = function(){ + this.edges = new Object(); + this.vertices = new Object(); +}; + +GraphDataset.prototype._setNodeEvents = function(node){ + var _this = this; + //NODE EVENTS + node.deleted.attach(function (sender, node){ + _this._removeNode(node); + }); + + node.nameChanged.attach(function (sender, args){ + var item = args.item; + var newName = item.name; + var indexes = _this.verticesIndex[args.previousName]; + for(var i = 0; i < indexes.length; i++){ + if(indexes[i] == item.id) + indexes.splice(i,1); + } + if(indexes.length == 0){ + delete _this.verticesIndex[args.previousName]; + } + _this._addVerticesIndex(newName, item.id); + _this.json.vertices[item.id] = newName; + _this.vertexNameChanged.notify(args); + }); +}; + +GraphDataset.prototype._setEdgeEvents = function(edge){ + var _this = this; + //EDGE EVENTS + edge.nameChanged.attach(function (sender, edge){ + _this.edgeNameChanged.notify(edge); + + }); + + edge.deleted.attach(function (sender, edge){ + _this._removeEdge(edge); + }); +}; + +GraphDataset.prototype._connectVerticesByName = function(nodeNameSource, nodeNameTarget){ + var source = this.getVertexByName(nodeNameSource); + var target = this.getVertexByName(nodeNameTarget); + + if ((source != null)&&(target!=null)){ + this.addEdge(source.getName() +"_" + target.getName(), source.getId(), target.getId(), {}); + } + else{ + if (source == null){ + console.log("No encontrado: " + nodeNameSource) + } + if (target == null){ + console.log("No encontrado: " + nodeNameTarget) + } + } +}; + +GraphDataset.prototype.loadFromJSON = function(json){ + var json = json; + this.init(); + this.json = new Object(); + this.json.vertices = new Array(); + this.json.edges = new Array(); + this.json.relations = new Array(); + + for ( var i = 0; i < json.nodes.length; i++) { + if (json.nodes[i] != null){ + var name = json.nodes[i]; + this.addNode(name); + } + else{ + this.json.vertices.push(null); + } + } + + for ( var i = 0; i < json.edges.length; i++) { + if (json.edges[i] != null){ + if (json.relations[i] != null){ + var name = json.edges[i]; + this.addEdge(name, json.relations[i].sourceIndex, json.relations[i].targetIndex, json.relations[i].args); + } + } + else{ + this.json.edges.push(null); + this.json.relations.push(null); + } + } +}; + +GraphDataset.prototype.prettyPrint = function(){ + for ( var node in this.vertices) { + console.log(this.vertices[node].getName() ); + for ( var j = 0; j < this.vertices[node].getEdgesIn().length; j++) { + console.log(" --> " + this.vertices[node].getEdgesIn()[j].getNodeTarget().getName() ); + } + } +}; + +GraphDataset.prototype._removeEdge = function(edge){ + this.json.edges[edge.getId()] = null; + this.json.relations[edge.getId()] = null; + + delete this.edges[edge.getId()]; + this.edgeDeleted.notify(edge); + + +}; + +GraphDataset.prototype._removeNode = function(node){ + this.json.vertices[node.getId()] = null; + delete this.vertices[node.getId()]; + this.vertexDeleted.notify(node); +}; + +GraphDataset.prototype.toJSON = function(){ + var json = new Object(); + var nodes = new Array(); + json.nodes = this.json.vertices; //nodes; + json.edges = this.json.edges; //edges; + json.relations = this.json.relations; + return json; +}; + +GraphDataset.prototype.clone = function(){ + var dsDataset = new GraphDataset(); + dsDataset.loadFromJSON(this.toJSON()); + return dsDataset; +}; +//GraphDataset.prototype.test = function(){ +// this.loadFromJSON(this.toJSON()); +//}; + +function labels(){ + var names = new Array(); + + var dataset = interactomeViewer.graphEditorWidget.dataset; + var layout = interactomeViewer.graphEditorWidget.layout; + + for ( var vertexId in interactomeViewer.graphEditorWidget.dataset.getVertices()) { + names.push(interactomeViewer.graphEditorWidget.dataset.getVertexById(vertexId).getName()); + } + + var sorted = (names.sort()); + console.log(sorted) + var distance = 0.01; + var altura = 0.6; + for ( var i = 0; i < names.length; i++) { + var id =dataset.getVertexByName(names[i]).getId(); + + layout.getNodeById(id).setCoordenates(distance, altura); + + + distance = parseFloat(distance) + parseFloat(0.03); + + altura = parseFloat(altura) + parseFloat(0.02); + + if (parseFloat(altura) == 0.9800000000000003){ + + altura = 0.6; + distance = distance - 0.51; + } + + } + + +}; -GraphCanvas.prototype.getEdgeSize = function(edgeId) { - return this.getFormatter().getEdgeById(edgeId).getDefault().getSize(); -}; +function GraphItem(id, name, args){ + this.id = id; + this.name = name; + this.type = "NONE"; + + this.args = new Object(); + + + if (args!=null){ + this.args = args; + if (args.type !=null){ + this.type = args.type; + } + } + + //Events + this.nameChanged = new Event(this); + this.deleted = new Event(this); +} + +GraphItem.prototype.getName = function(){ + return this.name; +}; + +GraphItem.prototype.getId = function(){ + return this.id; +}; + +GraphItem.prototype.setName = function(name){ + var oldName = this.getName(); + this.name = name; + this.nameChanged.notify({"item": this, "previousName" : oldName}); +}; + + + + -GraphCanvas.prototype.setEdgeStroke = function(edgeId, value) { - this.getFormatter().getEdgeById(edgeId).getDefault().setStroke(value); -}; +function LayoutDataset(){ + this.dataset = null; + this.vertices = new Object(); + this.changed = new Event(this); + + + this.args = new Object(); + + //RANDOM, CIRCLE + this.args.type = "CIRCLE"; +}; + +LayoutDataset.prototype.loadFromJSON = function(dataset, json){ + var _this = this; + this.vertices = new Object(); + this.dataset = dataset; //new GraphDataset(); + for ( var vertex in json) { + this.vertices[vertex] = new NodeLayout(vertex, json[vertex].x, json[vertex].y); + this.vertices[vertex].changed.attach(function (sender, item){ + _this.changed.notify(item); + }); + } + this._attachDatasetEvents(); +}; + + +LayoutDataset.prototype.toJSON = function(){ + var serialize = new Object(); + for ( var vertex in this.vertices) { + serialize[vertex] = new Object(); + serialize[vertex].x = this.vertices[vertex].x; + serialize[vertex].y = this.vertices[vertex].y; + } + serialize.dataset = new Object(); + serialize.dataset =this.dataset.toJSON(); + return serialize; +}; + +LayoutDataset.prototype.dataBind = function(graphDataset){ + this.dataset = graphDataset; + this._attachDatasetEvents(); + this._calculateLayout(); +}; + +LayoutDataset.prototype._removeVertex = function(vertexId){ + delete this.vertices[vertexId]; +}; + +LayoutDataset.prototype._attachDatasetEvents = function(){ + var _this = this; + + this.dataset.vertexDeleted.attach(function (sender, item){ + _this._removeVertex(item.getId()); + }); + + this.dataset.newVertex.attach(function (sender, item){ + _this.vertices[item.getId()] = new NodeLayout(item.getId(), 0.5, 0.5); + _this.vertices[item.getId()].changed.attach(function (sender, item){ + _this.changed.notify(item); + }); + }); +}; + +LayoutDataset.prototype.getType = function(){ + return this.args.type; +}; + +LayoutDataset.prototype._calculateLayoutVertices = function(type, count){ + + if (type == "CIRCLE"){ + var radius = 0.4; + var centerX = 0.5; + var centerY = 0.5; + var verticesCoordinates = new Array(); + for(var i = 0; i < count; i++){ + x = centerX + radius * Math.sin(i * 2 * Math.PI/count); + y = centerY + radius * Math.cos(i * 2 * Math.PI/count); + verticesCoordinates.push({'x':x,'y':y}); + } + return verticesCoordinates; + } +}; + + +LayoutDataset.prototype._calculateLayout = function(){ + var _this = this; + if (this.getType() == "RANDOM"){ + for ( var vertex in this.dataset.getVertices()) { + if (this.vertices[vertex] == null){ + this.vertices[vertex] = new NodeLayout(vertex, 0, 0); + } + this.vertices[vertex].setCoordinates(Math.random(), Math.random()); + this.vertices[vertex].changed.attach(function (sender, item){ + _this.changed.notify(item); + }); + } + } + + if ( this.getType() == "CIRCLE"){ + + var count = this.dataset._getVerticesCount(); + var verticesCoordinates = this._calculateLayoutVertices(this.getType(), count); + + var aux = 0; + for ( var vertex in this.dataset.getVertices()) { + if (this.vertices[vertex] == null){ + this.vertices[vertex] = new NodeLayout(vertex, 0, 0); + } + this.vertices[vertex].setCoordinates(verticesCoordinates[aux].x, verticesCoordinates[aux].y);//{"x":, "y":}; + aux++; + this.vertices[vertex].changed.attach(function (sender, item){ + _this.changed.notify(item); + }); + } + } + + + if (this.getType() == "SQUARE"){ + + var count = this.dataset._getVerticesCount(); + var xMin = 0.1; + var xMax = 0.9; + var yMin = 0.1; + var yMax = 0.9; + + var rows = Math.sqrt(count); + var step = (xMax - xMin) / rows; + + var verticesCoordinates = new Array(); + for(var i = 0; i < rows; i ++){ + for ( var j = 0; j < rows; j++) { + x = i * step + xMin; + y = j * step + yMin; + verticesCoordinates.push({'x':x,'y':y}); + } + } + + var aux = 0; + for ( var vertex in this.dataset.getVertices()) { + if (this.vertices[vertex] == null){ + this.vertices[vertex] = new NodeLayout(vertex, 0, 0); + } + this.vertices[vertex].setCoordinates(verticesCoordinates[aux].x, verticesCoordinates[aux].y);//{"x":, "y":}; + aux++; + this.vertices[vertex].changed.attach(function (sender, item){ + _this.changed.notify(item); + }); + } + } + +}; + +LayoutDataset.prototype.getNodeById = function(id){ + return this.vertices[id]; +}; + +LayoutDataset.prototype.getVerticesByArea = function(x1, y1, x2, y2){ + var vertices = new Array(); + for ( var vertex in this.dataset.getVertices()) { + if ((this.vertices[vertex].x >= x1)&&(this.vertices[vertex].x <= x2)){ + if ((this.vertices[vertex].y >= y1)&&(this.vertices[vertex].y <= y2)){ + vertices.push(this.vertices[vertex]); + } + } + } + return vertices; +}; + + + + +LayoutDataset.prototype.getLayout = function(type){ + + if (type == "CIRCLE"){ + this.args.type = "CIRCLE"; + this._calculateLayout(); + return; + } + + if (type == "SQUARE"){ + this.args.type = "SQUARE"; + this._calculateLayout(); + return; + } + + if (type == "RANDOM"){ + this.args.type = "RANDOM"; + this._calculateLayout(); + return; + } + + + var dotText = this.dataset.toDOTID(); + var url = "http://bioinfo.cipf.es/utils/ws/rest/network/layout/"+type+".coords"; + var _this = this; + + $.ajax({ + async: true, + type: "POST", + url: url, + dataType: "text", + data: { + dot :dotText + }, + cache: false, + success: function(data){ + var response = JSON.parse(data); + for ( var vertexId in response) { + _this.vertices[vertexId].setCoordinates(response[vertexId].x, response[vertexId].y); + } + } + }); + +// $.ajax({ +// async: true, +// type: "POST", +// url: url, +// dataType: "script", +// data: { +// dot :dotText +// }, +// cache: false, +// success: function(data){ +// var response = JSON.parse(data); +// for ( var vertexId in response) { +// _this.vertices[vertexId].setCoordinates(response[vertexId].x, response[vertexId].y); +// } +// } +// }); + +}; + +function NodeLayout(id, x, y, args){ + this.id = id; + this.x = x; + this.y = y; + this.changed = new Event(this); +}; + +NodeLayout.prototype.getId = function(id){ + return this.id; +}; + +NodeLayout.prototype.setCoordinates = function(x, y){ + this.x = x; + this.y = y; + this.changed.notify(this); +}; + -GraphCanvas.prototype.getEdgeStroke = function(edgeId) { - return this.getFormatter().getEdgeById(edgeId).getDefault().getStroke(); -}; + +function NetworkDataSetFormatter(vertexFormatProperties, defaultEdgeProperties, args){ + DataSet.prototype.constructor.call(this); + + this.args = new Object(); + + this.vertices = new Object(); + this.edges = new Object(); + this.dataset = null; + this.maxClass = 0; + this.minClass = 0; + + /** Coordenates with default Setting */ + this.args.width = 1100; + this.args.height = 500; + + /** Optional parameters */ + this.args.backgroundColor = "#FFFFFF"; + this.args.backgroundImage = null; + this.args.backgroundImageHeight = null; + this.args.backgroundImageWidth = null; + this.args.backgroundImageX = null; + this.args.backgroundImageY = null; + + + this.args.balanceNodes = false; + this.args.nodesMaxSize = 3; + this.args.nodesMinSize = 0.5; + + + /** Zoom **/ + this.args.zoomScale = 1; + this.args.zoomScaleStepFactor = 0.4; + + if (args != null){ + if (args.backgroundImage != null){ + this.args.backgroundImage = args.backgroundImage; + } + + if (args.width != null){ + this.args.width = args.width; + } + + if (args.height != null){ + this.args.height = args.height; + this.args.svgHeight = args.height; + } + + if (args.svgHeight != null){ + this.args.svgHeight = args.svgHeight; + } + + if (args.backgroundColor != null){ + this.args.backgroundColor = args.backgroundColor; + } + + if(args.balanceNodes != null){ + this.args.balanceNodes = args.balanceNodes; + } + + if(args.nodesMaxSize != null){ + this.args.nodesMaxSize = args.nodesMaxSize; + } + if(args.nodesMinSize != null){ + this.args.nodesMinSize = args.nodesMinSize; + } + } + + this.args.defaultEdgeProperties = {"fill":"#000000", "radius":"1", "stroke":"#000000", "size":1, "title":{"fontSize":10, "fontColor":"#000000"}}; + this.args.vertexFormatProperties = { "fill":"#000000", "stroke":"#000000", "stroke-opacity":"#000000"}; + + if (vertexFormatProperties!= null){ + this.args.vertexFormatProperties = vertexFormatProperties; + } + if (defaultEdgeProperties!= null){ + this.args.defaultEdgeProperties = defaultEdgeProperties; + } + + /** Events **/ + this.changed = new Event(this); + this.edgeChanged = new Event(this); + this.resized = new Event(this); + this.backgroundImageChanged= new Event(this); + this.backgroundColorChanged= new Event(this); +}; + +NetworkDataSetFormatter.prototype.loadFromJSON = function(dataset, json){ + this.args = new Object(); + this.vertices = new Object(); + this.args = json; + this._setDataset(dataset); + var _this = this; + + for ( var vertex in json.vertices) { + this.addVertex(vertex, json.vertices[vertex]); + } + + for ( var edgeId in json.edges) { + this.addEdge(edgeId, json.edges[edgeId]); + } +}; + + +NetworkDataSetFormatter.prototype.toJSON = function(){ + + +// this.args.vertices = new Object(); +// this.args.edges = new Object(); +// +// for ( var vertex in this.vertices) { +// this.args.vertices[vertex] = this.getVertexById(vertex).toJSON(); +// } +// for ( var edge in this.edges) { +// this.args.edges[edge] = this.getEdgeById(edge).toJSON(); +// } +// +// return (this.args); + + + var serialize = new Object(); + serialize = JSON.parse(JSON.stringify(this.args)); + serialize.vertices = new Object(); + serialize.edges = new Object(); + + for ( var vertex in this.vertices) { + serialize.vertices[vertex] = this.getVertexById(vertex).toJSON(); + } + for ( var edge in this.edges) { + serialize.edges[edge] = this.getEdgeById(edge).toJSON(); + } + + return (serialize); +}; + + + +NetworkDataSetFormatter.prototype._getNodeSize = function(nodeId){ + if (this.isVerticesBalanced()){ + var total = this.maxClass - this.minClass; + if (total == 0){ total = 1;} + var nodeConnection = this.dataset.getVertexById(nodeId).getEdges().length; + return ((nodeConnection*this.args.nodesMaxSize)/total) + this.args.nodesMinSize; + } + return this.getVertexById(nodeId).getDefault().getSize(); +}; + +NetworkDataSetFormatter.prototype._recalculateSize = function(){ + if (this.isVerticesBalanced()){ + this.maxClass = this.dataset.getMaxClass(); + this.minClass = this.dataset.getMinClass(); + for ( var vertexIdAll in this.vertices) { + var size = this._getNodeSize(vertexIdAll); + this.vertices[vertexIdAll].getDefault().setSize(size); + this.vertices[vertexIdAll].getSelected().setSize(size); + this.vertices[vertexIdAll].getOver().setSize(size); + } + } +}; + + +NetworkDataSetFormatter.prototype.addVertex = function(vertexId, json){ + + + if (json == null){ + this.vertices[vertexId] = new CircleVertexGraphFormatter(vertexId, this.args.vertexFormatProperties.defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); + } + else{ + + /** Cargo los attributos desde el json **/ + if (json.type == null){ + this.vertices[vertexId] = new CircleVertexGraphFormatter(vertexId, this.args.vertexFormatProperties.defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); + } + + if ((json.type == "SquareVertexGraphFormatter")||(json.type == "SquareVertexNetworkFormatter")){ + this.vertices[vertexId] = new SquareVertexGraphFormatter(vertexId); + this.vertices[vertexId].loadFromJSON(json); + } + + if ((json.type == "CircleVertexGraphFormatter")||(json.type == "CircleVertexNetworkFormatter")){ + this.vertices[vertexId] = new CircleVertexGraphFormatter(vertexId); + this.vertices[vertexId].loadFromJSON(json); + } + + if ((json.type == "EllipseVertexGraphFormatter")||(json.type == "EllipseVertexNetworkFormatter")){ + this.vertices[vertexId] = new EllipseVertexGraphFormatter(vertexId); + this.vertices[vertexId].loadFromJSON(json); + } + + if ((json.type == "RectangleVertexGraphFormatter")||(json.type == "RectangleVertexNetworkFormatter")){ + this.vertices[vertexId] = new RectangleVertexGraphFormatter(vertexId); + this.vertices[vertexId].loadFromJSON(json); + } + + if ((json.type == "RoundedVertexGraphFormatter")||(json.type == "RoundedVertexNetworkFormatter")){ + this.vertices[vertexId] = new RoundedVertexGraphFormatter(vertexId); + this.vertices[vertexId].loadFromJSON(json); + } + + } + + + var _this = this; + this.vertices[vertexId].stateChanged.attach(function (sender, item){ + _this.changed.notify(item); + }); + + var size = this._getNodeSize(vertexId); + this.vertices[vertexId].defaultFormat.args.size = size; + this.vertices[vertexId].selected.args.size = size; + this.vertices[vertexId].over.args.size = size; + +}; + +NetworkDataSetFormatter.prototype.addEdge = function(edgeId, json){ + + /** Es un edge nuevo que le doy los atributos por defecto **/ + if (json == null){ + if (this.dataset.getEdgeById(edgeId).getNodeSource().getId() == this.dataset.getEdgeById(edgeId).getNodeTarget().getId()){ + this.edges[edgeId] = new BezierEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); + }else{ + this.edges[edgeId] = new DirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); + } + } + else{ + /** Cargo los attributos desde el json **/ + if (json.type == null){ + this.edges[edgeId] = new LineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); + } + + if ((json.type == "LineEdgeGraphFormatter")||(json.type == "LineEdgeNetworkFormatter")){ + this.edges[edgeId] = new LineEdgeGraphFormatter(edgeId); + this.edges[edgeId].loadFromJSON(json); + } + if ((json.type == "DirectedLineEdgeGraphFormatter")||(json.type == "DirectedLineEdgeNetworkFormatter")){ + this.edges[edgeId] = new DirectedLineEdgeGraphFormatter(edgeId); + this.edges[edgeId].loadFromJSON(json); + } + + if ((json.type == "BezierEdgeGraphFormatter")||(json.type == "BezierEdgeNetworkFormatter")){ + this.edges[edgeId] = new BezierEdgeGraphFormatter(edgeId); + this.edges[edgeId].loadFromJSON(json); + } + + + if ((json.type == "CutDirectedLineEdgeGraphFormatter")||(json.type == "CutDirectedLineEdgeNetworkFormatter")){ + this.edges[edgeId] = new CutDirectedLineEdgeGraphFormatter(edgeId); + this.edges[edgeId].loadFromJSON(json); + } + + if ((json.type == "DotDirectedLineEdgeGraphFormatter")||(json.type == "DotDirectedLineEdgeNetworkFormatter")){ + this.edges[edgeId] = new DotDirectedLineEdgeGraphFormatter(edgeId); + this.edges[edgeId].loadFromJSON(json); + } + if ((json.type == "OdotDirectedLineEdgeGraphFormatter")||(json.type == "OdotDirectedLineEdgeNetworkFormatter")){ + this.edges[edgeId] = new OdotDirectedLineEdgeGraphFormatter(edgeId); + this.edges[edgeId].loadFromJSON(json); + } + + if ((json.type == "OdirectedLineEdgeGraphFormatter")||(json.type == "OdirectedLineEdgeNetworkFormatter")){ + this.edges[edgeId] = new OdirectedLineEdgeGraphFormatter(edgeId); + this.edges[edgeId].loadFromJSON(json); + } + } + + var _this = this; + this.edges[edgeId].stateChanged.attach(function (sender, item){ + _this.edgeChanged.notify(item); + }); + + this._recalculateSize(); +}; + +NetworkDataSetFormatter.prototype._setDataset = function(dataset){ + this.dataset = dataset; + this.maxClass = dataset.getMaxClass(); + this.minClass = dataset.getMinClass(); + this._attachDatasetEvents(); +}; + +NetworkDataSetFormatter.prototype.changeEdgeType = function(edgeId, type){ + if ((type == "LineEdgeGraphFormatter")||(type == "LineEdgeNetworkFormatter")){ + this.edges[edgeId] = new LineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); + + } + if ((type == "DirectedLineEdgeGraphFormatter")||(type == "DirectedLineEdgeNetworkFormatter")){ + this.edges[edgeId] = new DirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); + } + + if ((type == "CutDirectedLineEdgeGraphFormatter")||(type == "CutDirectedLineEdgeNetworkFormatter")){ + this.edges[edgeId] = new CutDirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); + } + + if ((type == "DotDirectedLineEdgeGraphFormatter")||(type == "DotDirectedLineEdgeNetworkFormatter")){ + this.edges[edgeId] = new DotDirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); + } + + if ((type == "OdotDirectedLineEdgeGraphFormatter")||(type == "OdotDirectedLineEdgeNetworkFormatter")){ + this.edges[edgeId] = new OdotDirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); + } + + if ((type == "OdirectedLineEdgeGraphFormatter")||(type == "OdirectedLineEdgeNetworkFormatter")){ + this.edges[edgeId] = new OdirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); + } + + + + var _this = this; + this.edges[edgeId].stateChanged.attach(function (sender, item){ + _this.edgeChanged.notify(item); + }); + _this.edgeChanged.notify(this.edges[edgeId]); +}; +/* +classe = "SquareNetworkNodeFormatter"; +} +if (value == "circle"){ + classe = "CircleNetworkNodeFormatter"; + **/ +NetworkDataSetFormatter.prototype.changeNodeType = function(vertexId, type){ + var defaultFormat = JSON.parse(JSON.stringify(this.vertices[vertexId].getDefault())); + var selectedFormat = JSON.parse(JSON.stringify(this.vertices[vertexId].getSelected())); + var defaultFormat = JSON.parse(JSON.stringify(this.vertices[vertexId].getDefault())); + var defaultFormat = JSON.parse(JSON.stringify(this.vertices[vertexId].getDefault())); + + if ((type == "SquareVertexGraphFormatter")||(type == "SquareVertexNetworkFormatter")){ + this.vertices[vertexId] = new SquareVertexGraphFormatter(vertexId,defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); + } + + if ((type == "CircleVertexGraphFormatter")||(type == "CircleVertexNetworkFormatter")){ + this.vertices[vertexId] = new CircleVertexGraphFormatter(vertexId, defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); + } + + if ((type == "EllipseVertexGraphFormatter")||(type == "EllipseVertexNetworkFormatter")){ + this.vertices[vertexId] = new EllipseVertexGraphFormatter(vertexId, defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); + } + + if ((type == "RectangleVertexGraphFormatter")||(type == "RectangleVertexNetworkFormatter")){ + this.vertices[vertexId] = new RectangleVertexGraphFormatter(vertexId, defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); + } + + if ((type == "RoundedVertexGraphFormatter")||(type == "RoundedVertexNetworkFormatter")){ + this.vertices[vertexId] = new RoundedVertexGraphFormatter(vertexId, defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); + } + + if ((type == "OctagonVertexGraphFormatter")||(type == "OctagonVertexNetworkhFormatter")){ + this.vertices[vertexId] = new OctagonVertexGraphFormatter(vertexId, defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); + } + + + var _this = this; + this.vertices[vertexId].stateChanged.attach(function (sender, item){ + _this.changed.notify(item); + }); + _this.changed.notify(this.vertices[vertexId]); +}; + + + +NetworkDataSetFormatter.prototype.dataBind = function(networkDataSet){ + var _this = this; + this._setDataset(networkDataSet); + + for ( var vertex in this.dataset.getVertices()) { + this.addVertex(vertex); + } + + for ( var edge in this.dataset.getEdges()) { + this.addEdge(edge); + } +}; + +NetworkDataSetFormatter.prototype._removeEdge = function(edgeId){ + delete this.edges[edgeId]; +}; + +NetworkDataSetFormatter.prototype._removeVertex = function(vertexId){ + delete this.vertices[vertexId]; +}; + +NetworkDataSetFormatter.prototype._attachDatasetEvents = function(id){ + var _this = this; + this.dataset.vertexDeleted.attach(function (sender, item){ + _this._removeVertex(item.getId()); + }); + + this.dataset.edgeDeleted.attach(function (sender, item){ + _this._removeEdge(item.getId()); + }); + + this.dataset.newVertex.attach(function (sender, item){ + _this.addVertex(item.getId()); + }); + + this.dataset.newEdge.attach(function (sender, item){ + _this.addEdge(item.getId()); + }); +}; + + +NetworkDataSetFormatter.prototype.getVertexById = function(id){ + return this.vertices[id]; +}; + +NetworkDataSetFormatter.prototype.getEdgeById = function(id){ + return this.edges[id]; +}; + +NetworkDataSetFormatter.prototype.makeLabelsBigger = function(){ +for ( var vertexId in this.vertices) { + var fontSize = this.vertices[vertexId].getDefault().getFontSize() + 2; + this.vertices[vertexId].getDefault().setFontSize(fontSize); + } +}; + +NetworkDataSetFormatter.prototype.makeLabelsSmaller = function(){ + for ( var vertexId in this.vertices) { + var fontSize = this.vertices[vertexId].getDefault().getFontSize() - 2; + this.vertices[vertexId].getDefault().setFontSize(fontSize); + } +}; + + +NetworkDataSetFormatter.prototype.resize = function(width, height){ + this.args.width = width; + this.args.height = height; + this.resized.notify(); +}; + +/** ZOOM GETTERS **/ +NetworkDataSetFormatter.prototype.getZoomScaleStepFactor = function(){return this.args.zoomScaleStepFactor;}; +NetworkDataSetFormatter.prototype.setZoomScaleStepFactor = function(scaleFactor){this.args.zoomScaleStepFactor = scaleFactor;}; +NetworkDataSetFormatter.prototype.getZoomScale = function(){return this.args.zoomScale;}; +NetworkDataSetFormatter.prototype.setZoomScale = function(scale){this.args.zoomScale = scale;}; + +NetworkDataSetFormatter.prototype.getNodesMaxSize = function(){return this.args.nodesMaxSize;}; +NetworkDataSetFormatter.prototype.getNodesMinSize = function(){return this.args.nodesMinSize;}; + +/** SIZE SETTERS AND GETTERS **/ +NetworkDataSetFormatter.prototype.isVerticesBalanced = function(){return this.args.balanceNodes;}; +NetworkDataSetFormatter.prototype.getWidth = function(){return this.args.width;}; +NetworkDataSetFormatter.prototype.getHeight = function(){return this.args.height;}; + +/** OPTIONAL PARAMETERS GETTERS AND SETTERS **/ +NetworkDataSetFormatter.prototype.getBackgroundImage = function(){return this.args.backgroundImage;}; +NetworkDataSetFormatter.prototype.setBackgroundImage = function(value){this.args.backgroundImage = value; this.backgroundImageChanged.notify(this);}; + + +NetworkDataSetFormatter.prototype.getBackgroundImageWidth = function(){return this.args.backgroundImageWidth;}; +NetworkDataSetFormatter.prototype.setBackgroundImageWidth = function(value){this.args.backgroundImageWidth = value; this.backgroundImageChanged.notify(this);}; + +NetworkDataSetFormatter.prototype.getBackgroundImageHeight = function(){return this.args.backgroundImageHeight;}; +NetworkDataSetFormatter.prototype.setBackgroundImageHeight = function(value){this.args.backgroundImageHeight = value; this.backgroundImageChanged.notify(this);}; + +NetworkDataSetFormatter.prototype.getBackgroundImageX = function(){return this.args.backgroundImageX;}; +NetworkDataSetFormatter.prototype.setBackgroundImageX = function(value){this.args.backgroundImageX = value; this.backgroundImageChanged.notify(this);}; + +NetworkDataSetFormatter.prototype.getBackgroundImageY = function(){return this.args.backgroundImageX;}; +NetworkDataSetFormatter.prototype.setBackgroundImageY = function(value){this.args.backgroundImageY = value; this.backgroundImageChanged.notify(this);}; + + + +NetworkDataSetFormatter.prototype.getBackgroundColor = function(){return this.args.backgroundColor;}; +NetworkDataSetFormatter.prototype.setBackgroundColor = function(value){this.args.backgroundColor = value; this.backgroundColorChanged.notify(this);}; + +NetworkDataSetFormatter.prototype.getWidth = function(){return this.args.width;}; +NetworkDataSetFormatter.prototype.setWidth = function(value){this.args.width = value;}; + +NetworkDataSetFormatter.prototype.getHeight = function(){return this.args.height;}; +NetworkDataSetFormatter.prototype.setHeight = function(value){this.args.height = value;}; + + -GraphCanvas.prototype.setEdgeStrokeOpacity = function(edgeId, value) { - this.getFormatter().getEdgeById(edgeId).getDefault().setStrokeOpacity(value); -}; + +Vertex.prototype.getName = GraphItem.prototype.getName; +Vertex.prototype.setName = GraphItem.prototype.setName; +Vertex.prototype.getId = GraphItem.prototype.getId; + +function Vertex(id, name, args){ + GraphItem.prototype.constructor.call(this, id, name, args); + this.edgesIn= new Array(); + this.edgesOut= new Array(); +}; + +Vertex.prototype.getEdges = function(){ + return this.edgesIn.concat(this.edgesOut); +}; + +Vertex.prototype.getEdgesCount = function(){ + return this.getEdges().length; +}; + +Vertex.prototype.getEdgesIn = function(){ + return this.edgesIn; +}; + +Vertex.prototype.getEdgesOut = function(){ + return this.edgesOut; +}; + +Vertex.prototype.addEdge = function(edge){ + if (edge.getNodeSource().getId() == this.id){ + this.edgesIn.push(edge); + } + else{ + this.edgesOut.push(edge); + } +}; + +Vertex.prototype.removeEdge = function(edge){ + for ( var i = 0; i < this.getEdgesIn().length; i++) { + var edgeIn = this.edgesIn[i]; + if (edgeIn.getId() == edge.getId()){ + this.edgesIn.splice(i, 1); + } + } + for ( var i = 0; i < this.getEdgesOut().length; i++) { + var edgeIn = this.edgesOut[i]; + if (edgeIn.getId() == edge.getId()){ + this.edgesOut.splice(i, 1); + } + } +}; + +Vertex.prototype.remove = function(){ + var edges = this.getEdges(); + for ( var i = 0; i < edges.length; i++) { + var edge = edges[i]; + edge.remove(); + } + this.deleted.notify(this); +}; + + + + -GraphCanvas.prototype.getEdgeStrokeOpacity = function(edgeId) { - return this.getFormatter().getEdgeById(edgeId).getDefault().getStrokeOpacity(); -}; +VertexGraphFormatter.prototype.getDefault = ItemGraphFormatter.prototype.getDefault; +VertexGraphFormatter.prototype.getSelected = ItemGraphFormatter.prototype.getSelected; +VertexGraphFormatter.prototype.getOver = ItemGraphFormatter.prototype.getOver; +VertexGraphFormatter.prototype.getDragging = ItemGraphFormatter.prototype.getDragging; +VertexGraphFormatter.prototype.getId = ItemGraphFormatter.prototype.getId; +VertexGraphFormatter.prototype.toJSON = ItemGraphFormatter.prototype.toJSON; +VertexGraphFormatter.prototype.loadFromJSON = ItemGraphFormatter.prototype.loadFromJSON; +VertexGraphFormatter.prototype._setEvents = ItemGraphFormatter.prototype._setEvents; + + +function VertexGraphFormatter(defaultFormat, selectedFormat, overFormat, draggingFormat){ + ItemGraphFormatter.prototype.constructor.call(this, defaultFormat, selectedFormat, overFormat, draggingFormat); +}; + + +CircleVertexGraphFormatter.prototype.getDefault = VertexGraphFormatter.prototype.getDefault; +CircleVertexGraphFormatter.prototype.getSelected = VertexGraphFormatter.prototype.getSelected; +CircleVertexGraphFormatter.prototype.getOver = VertexGraphFormatter.prototype.getOver; +CircleVertexGraphFormatter.prototype.getDragging = VertexGraphFormatter.prototype.getDragging; +CircleVertexGraphFormatter.prototype.getId = VertexGraphFormatter.prototype.getId; +CircleVertexGraphFormatter.prototype.toJSON = VertexGraphFormatter.prototype.toJSON; +CircleVertexGraphFormatter.prototype.loadFromJSON = VertexGraphFormatter.prototype.loadFromJSON; +CircleVertexGraphFormatter.prototype._setEvents = VertexGraphFormatter.prototype._setEvents; + +function CircleVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ + VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); + this.args.type = "CircleVertexGraphFormatter"; + if (defaultFormat != null){ + if (defaultFormat.radius != null){ + this.defaultFormat.args.radius = defaultFormat.radius; + } + } + + if (selectedFormat != null){ + if (selectedFormat.radius != null){ + this.selected.args.radius = selectedFormat.radius; + } + } + + if (overFormat != null){ + if (overFormat.radius != null){ + this.over.args.radius = overFormat.radius; + } + } + + if (draggingFormat != null){ + if (draggingFormat.radius != null){ + this.dragging.args.draggingFormat = draggingFormat.radius; + } + } +}; + + + +SquareVertexGraphFormatter.prototype.getDefault = VertexGraphFormatter.prototype.getDefault; +SquareVertexGraphFormatter.prototype.getSelected = VertexGraphFormatter.prototype.getSelected; +SquareVertexGraphFormatter.prototype.getOver = VertexGraphFormatter.prototype.getOver; +SquareVertexGraphFormatter.prototype.getDragging = VertexGraphFormatter.prototype.getDragging; +SquareVertexGraphFormatter.prototype.getId = VertexGraphFormatter.prototype.getId; +SquareVertexGraphFormatter.prototype.toJSON = VertexGraphFormatter.prototype.toJSON; +SquareVertexGraphFormatter.prototype.loadFromJSON = VertexGraphFormatter.prototype.loadFromJSON; +SquareVertexGraphFormatter.prototype._setEvents = VertexGraphFormatter.prototype._setEvents; + +function SquareVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ + VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); + this.args.type = "SquareVertexGraphFormatter"; + if (defaultFormat != null){ + if (defaultFormat.radius != null){ + this.defaultFormat.args.radius = defaultFormat.radius; + } + } + + if (selectedFormat != null){ + if (selectedFormat.radius != null){ + this.selected.args.radius = selectedFormat.radius; + } + } + + if (overFormat != null){ + if (overFormat.radius != null){ + this.over.args.radius = overFormat.radius; + } + } + + if (draggingFormat != null){ + if (draggingFormat.radius != null){ + this.dragging.args.draggingFormat = draggingFormat.radius; + } + } +}; + + +EllipseVertexGraphFormatter.prototype.getDefault = VertexGraphFormatter.prototype.getDefault; +EllipseVertexGraphFormatter.prototype.getSelected = VertexGraphFormatter.prototype.getSelected; +EllipseVertexGraphFormatter.prototype.getOver = VertexGraphFormatter.prototype.getOver; +EllipseVertexGraphFormatter.prototype.getDragging = VertexGraphFormatter.prototype.getDragging; +EllipseVertexGraphFormatter.prototype.getId = VertexGraphFormatter.prototype.getId; +EllipseVertexGraphFormatter.prototype.toJSON = VertexGraphFormatter.prototype.toJSON; +EllipseVertexGraphFormatter.prototype.loadFromJSON = VertexGraphFormatter.prototype.loadFromJSON; +EllipseVertexGraphFormatter.prototype._setEvents = VertexGraphFormatter.prototype._setEvents; + +function EllipseVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ + VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); + this.args.type = "EllipseVertexGraphFormatter"; + if (defaultFormat != null){ + if (defaultFormat.radius != null){ + this.defaultFormat.args.radius = defaultFormat.radius; + } + } + + if (selectedFormat != null){ + if (selectedFormat.radius != null){ + this.selected.args.radius = selectedFormat.radius; + } + } + + if (overFormat != null){ + if (overFormat.radius != null){ + this.over.args.radius = overFormat.radius; + } + } + + if (draggingFormat != null){ + if (draggingFormat.radius != null){ + this.dragging.args.draggingFormat = draggingFormat.radius; + } + } +}; + + + +RectangleVertexGraphFormatter.prototype.getDefault = ItemGraphFormatter.prototype.getDefault; +RectangleVertexGraphFormatter.prototype.getSelected = ItemGraphFormatter.prototype.getSelected; +RectangleVertexGraphFormatter.prototype.getOver = ItemGraphFormatter.prototype.getOver; +RectangleVertexGraphFormatter.prototype.getDragging = ItemGraphFormatter.prototype.getDragging; +RectangleVertexGraphFormatter.prototype.getId = ItemGraphFormatter.prototype.getId; +RectangleVertexGraphFormatter.prototype.toJSON = ItemGraphFormatter.prototype.toJSON; +RectangleVertexGraphFormatter.prototype.loadFromJSON = ItemGraphFormatter.prototype.loadFromJSON; +RectangleVertexGraphFormatter.prototype._setEvents = ItemGraphFormatter.prototype._setEvents; + +function RectangleVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ + VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); + this.args.type = "RectangleVertexGraphFormatter"; + if (defaultFormat != null){ + if (defaultFormat.radius != null){ + this.defaultFormat.args.radius = defaultFormat.radius; + } + } + + if (selectedFormat != null){ + if (selectedFormat.radius != null){ + this.selected.args.radius = selectedFormat.radius; + } + } + + if (overFormat != null){ + if (overFormat.radius != null){ + this.over.args.radius = overFormat.radius; + } + } + + if (draggingFormat != null){ + if (draggingFormat.radius != null){ + this.dragging.args.draggingFormat = draggingFormat.radius; + } + } +}; + + + +RoundedVertexGraphFormatter.prototype.getDefault = ItemGraphFormatter.prototype.getDefault; +RoundedVertexGraphFormatter.prototype.getSelected = ItemGraphFormatter.prototype.getSelected; +RoundedVertexGraphFormatter.prototype.getOver = ItemGraphFormatter.prototype.getOver; +RoundedVertexGraphFormatter.prototype.getDragging = ItemGraphFormatter.prototype.getDragging; +RoundedVertexGraphFormatter.prototype.getId = ItemGraphFormatter.prototype.getId; +RoundedVertexGraphFormatter.prototype.toJSON = ItemGraphFormatter.prototype.toJSON; +RoundedVertexGraphFormatter.prototype.loadFromJSON = ItemGraphFormatter.prototype.loadFromJSON; +RoundedVertexGraphFormatter.prototype._setEvents = ItemGraphFormatter.prototype._setEvents; + +function RoundedVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ + VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); + this.args.type = "RoundedVertexGraphFormatter"; + if (defaultFormat != null){ + if (defaultFormat.radius != null){ + this.defaultFormat.args.radius = defaultFormat.radius; + } + } + + if (selectedFormat != null){ + if (selectedFormat.radius != null){ + this.selected.args.radius = selectedFormat.radius; + } + } + + if (overFormat != null){ + if (overFormat.radius != null){ + this.over.args.radius = overFormat.radius; + } + } + + if (draggingFormat != null){ + if (draggingFormat.radius != null){ + this.dragging.args.draggingFormat = draggingFormat.radius; + } + } +}; + + + +OctagonVertexGraphFormatter.prototype.getDefault = ItemGraphFormatter.prototype.getDefault; +OctagonVertexGraphFormatter.prototype.getSelected = ItemGraphFormatter.prototype.getSelected; +OctagonVertexGraphFormatter.prototype.getOver = ItemGraphFormatter.prototype.getOver; +OctagonVertexGraphFormatter.prototype.getDragging = ItemGraphFormatter.prototype.getDragging; +OctagonVertexGraphFormatter.prototype.getId = ItemGraphFormatter.prototype.getId; +OctagonVertexGraphFormatter.prototype.toJSON = ItemGraphFormatter.prototype.toJSON; +OctagonVertexGraphFormatter.prototype.loadFromJSON = ItemGraphFormatter.prototype.loadFromJSON; +OctagonVertexGraphFormatter.prototype._setEvents = ItemGraphFormatter.prototype._setEvents; + +function OctagonVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ + VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); + this.args.type = "OctagonVertexGraphFormatter"; + if (defaultFormat != null){ + if (defaultFormat.radius != null){ + this.defaultFormat.args.radius = defaultFormat.radius; + } + } + + if (selectedFormat != null){ + if (selectedFormat.radius != null){ + this.selected.args.radius = selectedFormat.radius; + } + } + + if (overFormat != null){ + if (overFormat.radius != null){ + this.over.args.radius = overFormat.radius; + } + } + + if (draggingFormat != null){ + if (draggingFormat.radius != null){ + this.dragging.args.draggingFormat = draggingFormat.radius; + } + } +}; + -GraphCanvas.prototype.setEdgeFill = function(edgeId, color) { - this.getFormatter().getEdgeById(edgeId).getDefault().setFill(color); + +var Colors = new function() +{ + this.hashColor = []; + this.getColorByScoreArrayValue = function (arrayScore) + { + var array = new Array(); + + for (var i = 0; i< arrayScore.length; i++) + { + + var color = this.getColorByScoreValue(arrayScore[i]) + array.push( color); + + } + return array; + }; + + this.getHexStringByScoreArrayValue = function (arrayScore) + { + var arrayColor = this.getColorByScoreArrayValue(arrayScore); + var arrayHex = new Array(); + for (var i = 0; i< arrayColor.length; i++) + { + arrayHex.push( arrayColor[i].HexString()); + } + return arrayHex; + }; + + this.getColorByScoreValue = function (score) + { + + var truncate = score.toString().substr(0,4); + if (this.hashColor[truncate]!=null) + { + return this.hashColor[truncate]; + } + + + if(isNaN(score)) { + return Colors.ColorFromRGB(0,0,0); + } + var value; + + var from, to; + if(score < 0.5) { + from = Colors.ColorFromRGB(0,0,255); + to = Colors.ColorFromRGB(255,255,255); + value = (score * 2); + } else { + from = Colors.ColorFromRGB(255,255,255); + to = Colors.ColorFromRGB(255,0,0); + value = (score * 2) - 1; + } + + var x = value; + var y = 1.0 - value; + var color = Colors.ColorFromRGB(y * from.Red() + x * to.Red(), y * from.Green() + x * to.Green(), y * from.Blue() + x * to.Blue()); + + this.hashColor[truncate] = color; + + return color; + }; + + this.ColorFromHSV = function(hue, sat, val) + { + var color = new Color(); + color.SetHSV(hue,sat,val); + return color; + }; + + this.ColorFromRGB = function(r, g, b) + { + var color = new Color(); + color.SetRGB(r,g,b); + return color; + }; + + this.ColorFromHex = function(hexStr) + { + var color = new Color(); + color.SetHexString(hexStr); + return color; + }; + + function Color() { + //Stored as values between 0 and 1 + var red = 0; + var green = 0; + var blue = 0; + + //Stored as values between 0 and 360 + var hue = 0; + + //Strored as values between 0 and 1 + var saturation = 0; + var value = 0; + + this.SetRGB = function(r, g, b) + { + red = r/255.0; + green = g/255.0; + blue = b/255.0; + calculateHSV(); + }; + + this.Red = function() { return Math.round(red*255); }; + + this.Green = function() { return Math.round(green*255); }; + + this.Blue = function() { return Math.round(blue*255); }; + + this.SetHSV = function(h, s, v) + { + hue = h; + saturation = s; + value = v; + calculateRGB(); + }; + + this.Hue = function() + { return hue; }; + + this.Saturation = function() + { return saturation; }; + + this.Value = function() + { return value; }; + + this.SetHexString = function(hexString) + { + if(hexString == null || typeof(hexString) != "string") + { + this.SetRGB(0,0,0); + return; + } + + if (hexString.substr(0, 1) == '#') + hexString = hexString.substr(1); + + if(hexString.length != 6) + { + this.SetRGB(0,0,0); + return; + } + + var r = parseInt(hexString.substr(0, 2), 16); + var g = parseInt(hexString.substr(2, 2), 16); + var b = parseInt(hexString.substr(4, 2), 16); + if (isNaN(r) || isNaN(g) || isNaN(b)) + { + this.SetRGB(0,0,0); + return; + } + + this.SetRGB(r,g,b); + }; + + this.HexString = function() + { + + var rStr = this.Red().toString(16); + if (rStr.length == 1) + rStr = '0' + rStr; + var gStr = this.Green().toString(16); + if (gStr.length == 1) + gStr = '0' + gStr; + var bStr = this.Blue().toString(16); + if (bStr.length == 1) + bStr = '0' + bStr; + return ('#' + rStr + gStr + bStr).toUpperCase(); + }; + + this.Complement = function() + { + var newHue = (hue >= 180) ? hue - 180 : hue + 180; + var newVal = (value * (saturation - 1) + 1); + var newSat = (value*saturation) / newVal; + var newColor = new Color(); + newColor.SetHSV(newHue, newSat, newVal); + return newColor; + } ; + + function calculateHSV() + { + var max = Math.max(Math.max(red, green), blue); + var min = Math.min(Math.min(red, green), blue); + + value = max; + + saturation = 0; + if(max != 0) + saturation = 1 - min/max; + + hue = 0; + if(min == max) + return; + + var delta = (max - min); + if (red == max) + hue = (green - blue) / delta; + else if (green == max) + hue = 2 + ((blue - red) / delta); + else + hue = 4 + ((red - green) / delta); + hue = hue * 60; + if(hue < 0) + hue += 360; + } + + function calculateRGB() + { + red = value; + green = value; + blue = value; + + if(value == 0 || saturation == 0) + return; + + var tHue = (hue / 60); + var i = Math.floor(tHue); + var f = tHue - i; + var p = value * (1 - saturation); + var q = value * (1 - saturation * f); + var t = value * (1 - saturation * (1 - f)); + switch(i) + { + case 0: + red = value; green = t; blue = p; + break; + case 1: + red = q; green = value; blue = p; + break; + case 2: + red = p; green = value; blue = t; + break; + case 3: + red = p; green = q; blue = value; + break; + case 4: + red = t; green = p; blue = value; + break; + default: + red = value; green = p; blue = q; + break; + } + } + } +} +(); +/* + * Clase gestiona la insercción, eliminación de los elementos en el DOM + * + * Vital hacerla SIEMPRE compatible hacia atrás + * + * Last update: 28-10-2010 + * + */ + + +var DOM = {}; + +DOM.createNewElement = function(type, nodeParent, attributes) +{ + + var node = document.createElement(type); + for (var i=0; i0) + { + parent.removeChild(parent.childNodes[0]); + + } +}; + +DOM.select = function(targetID) +{ + return document.getElementById(targetID); +// return $("#"+targetID); }; +var Geometry = +{ + + /** From tow points obtains the angles formed with the cartesian side **/ + getAngleBetweenTwoPoints : function(x1, y1, x2, y2){ + //var m = (y1 - y2)/ (x1 - x2); + return Math.atan2(y2-y1, x2-x1); + }, + + getAdjacentSideOfRectangleRight : function(angle, hypotenuse){ + return Math.abs(Math.cos(angle)*hypotenuse); + }, + + getOppositeSideOfRectangleRight : function(angle, hypotenuse){ + return Math.abs(Math.sin(angle)*hypotenuse); + }, + + toDegree: function(radian){ + return radian*180/Math.PI; + + } + + +}; -GraphCanvas.prototype.getEdgeFill = function(edgeId) { - return this.getFormatter().getEdgeById(edgeId).getDefault().getFill(); -}; +var SVG = +{ + svgns : 'http://www.w3.org/2000/svg', + xlinkns : "http://www.w3.org/1999/xlink", + + createSVGCanvas: function(parentNode, attributes) + { + + attributes.push( ['xmlns', SVG.svgns], ['xmlns:xlink', 'http://www.w3.org/1999/xlink']); + var svg = document.createElementNS("http://www.w3.org/2000/svg", "svg"); + this._setProperties(svg, attributes); + parentNode.appendChild( svg); + return svg; + + }, + + createRectangle : function (x, y, width, height, attributes){ + var rect = document.createElementNS(this.svgns, "rect"); + rect.setAttribute("x",x); + rect.setAttribute("y",y); + rect.setAttribute("width",width); + rect.setAttribute("height",height); + SVG._setProperties(rect, attributes); + return rect; + }, + + drawImage64 : function (x, y, width, height, base64, svgNode, attributes) { + var node = SVG.createImage64(x, y, width, height, base64, attributes); + svgNode.appendChild(node); + return node; + }, + + createImage64 : function (x, y, width, height, base64, attributes) { + var img = document.createElementNS(this.svgns, "image"); + img.setAttribute("x",x); + img.setAttribute("y",y); + img.setAttribute("width",width); + img.setAttribute("height",height); + img.setAttribute("xlink:href",base64); + SVG._setProperties(img, attributes); + return img; + }, + + createLine: function (x1, y1, x2, y2, attributes){ + var line = document.createElementNS(this.svgns,"line"); + line.setAttribute("x1",x1); + line.setAttribute("y1",y1); + line.setAttribute("x2", x2); + line.setAttribute("y2", y2); + SVG._setProperties(line, attributes); + return line; + }, + + createClip: function (id, nodeToClip, attributes){ + var clip = document.createElementNS(this.svgns,"clipPath"); + clip.setAttribute("id",id); + clip.appendChild(nodeToClip); + return clip; + }, + + drawClip : function (id, nodeToClip, svgNode) { + var node = SVG.createClip(id, nodeToClip); + svgNode.appendChild(node); + return node; + }, + + drawRectangle : function (cx, cy, width, height, svgNode, attributes) { + try{ + var node = SVG.createRectangle(cx, cy, width, height, attributes); + svgNode.appendChild(node); + } + catch(e){ + + console.log("-------------------- "); + console.log("Error on drawRectangle " + e); + console.log(attributes); + console.log("-------------------- "); + } + return node; + }, + + createEllipse : function (x, y, rx, ry, attributes){ + var rect = document.createElementNS(this.svgns, "ellipse"); + rect.setAttribute("cx",x); + rect.setAttribute("cy",y); + rect.setAttribute("rx",rx); + rect.setAttribute("ry",ry); + SVG._setProperties(rect, attributes); + return rect; + }, + + drawEllipse : function (cx, cy, rx, ry, svgNode, attributes) { + var node = SVG.createEllipse(cx, cy, rx, ry, attributes); + svgNode.appendChild(node); + return node; + }, + + drawImage : function (x, y, canvasSVG, attributes) { + var image = document.createElementNS(this.svgns, "image"); + image.setAttribute("x",x); + image.setAttribute("y",y); + canvasSVG.appendChild(image); + SVG._setProperties(image, attributes); + }, + + drawLine : function (x1, y1, x2, y2, nodeSVG, attributes) { + try{ + var line = SVG.createLine(x1, y1, x2, y2, attributes); + nodeSVG.appendChild(line); + }catch(e){ + } + return line; + }, + + + drawPath: function (d, nodeSVG, attributes) { + var path = SVG.createPath(d, attributes); + nodeSVG.appendChild(path); + return path; + }, + + createPoligon : function (points, attributes){ + var poligon = document.createElementNS(this.svgns, "polygon"); + poligon.setAttribute("points",points); + SVG._setProperties(poligon, attributes); + return poligon; + }, + + drawPoligon : function (points, canvasSVG, attributes){ + var poligon = SVG.createPoligon(points, attributes); + canvasSVG.appendChild(poligon); + return poligon; + }, + // + + createPath : function (d, attributes){ + var path = document.createElementNS(this.svgns, "path"); + path.setAttribute("d",d); + SVG._setProperties(path, attributes); + return path; + }, + + drawCircle : function (x, y, radio, canvasSVG, attributes) { + + var newText = document.createElementNS(this.svgns,"circle"); + newText.setAttribute("cx",x); + newText.setAttribute("cy",y); + newText.setAttribute("r",radio); + + canvasSVG.appendChild(newText); + attributes["cursor"] = "pointer"; + this._setProperties(newText, attributes); + return newText; + }, + + + _setProperties: function(node, attributes) + { + if (attributes instanceof Array){ + for (var i=0; i< attributes.length; i++) + { + node.setAttribute(attributes[i][0], attributes[i][1]); + } + } + else{ + for ( var key in attributes){ + node.setAttribute(key, attributes[key]); + } + } + }, + +/* drawPath: function(pointsArray, canvasSVG, attributes){ + var path = document.createElementNS(this.svgns,"polyline"); + path.setAttribute ('id', id); + + var d= pointsArray[0].x+ " "+ pointsArray[0].y; + for (var i=1; i< pointsArray.length; i++) + { + d=d+" "+pointsArray[i].x+" "+pointsArray[i].y; + } + path.setAttribute ('points', d); + canvasSVG.appendChild(path); + },*/ + + createText : function (x, y, text, attributes) { + var node = document.createElementNS(this.svgns,"text"); + node.setAttributeNS(null , "x",x); + node.setAttributeNS(null, "y",y); + + var textNode = document.createTextNode(text); + node.appendChild(textNode); + + this._setProperties(node, attributes); + return node; + }, + + drawText : function (x, y, text, canvasSVG, attributes) { + var text = SVG.createText(x, y, text, attributes); + canvasSVG.appendChild(text); + return text; + }, + + + + drawGroup: function(svgNode, attributes) + { + var group = SVG.createGroup(attributes); + svgNode.appendChild(group); + return group; + }, + + createGroup: function(attributes){ + var group = document.createElementNS(this.svgns,"g"); + this._setProperties(group, attributes); + return group; + } + +}; + + + +var CanvasToSVG = { + + convert: function(sourceCanvas, targetSVG, x, y, id, attributes) { + + var img = this._convert(sourceCanvas, targetSVG, x, y, id); + + for (var i=0; i< attributes.length; i++) + { + img.setAttribute(attributes[i][0], attributes[i][1]); + } + }, + + _convert: function(sourceCanvas, targetSVG, x, y, id) { + var svgNS = "http://www.w3.org/2000/svg"; + var xlinkNS = "http://www.w3.org/1999/xlink"; + // get base64 encoded png from Canvas + var image = sourceCanvas.toDataURL(); + + // must be careful with the namespaces + var svgimg = document.createElementNS(svgNS, "image"); + + svgimg.setAttribute('id', id); + + //svgimg.setAttribute('class', class); + //svgimg.setAttribute('xlink:href', image); + svgimg.setAttributeNS(xlinkNS, 'xlink:href', image); + + + + + svgimg.setAttribute('x', x ? x : 0); + svgimg.setAttribute('y', y ? y : 0); + svgimg.setAttribute('width', sourceCanvas.width); + svgimg.setAttribute('height', sourceCanvas.height); + //svgimg.setAttribute('cursor', 'pointer'); + svgimg.imageData = image; + + targetSVG.appendChild(svgimg); + return svgimg; + }, + + importSVG: function(sourceSVG, targetCanvas) { + svg_xml = sourceSVG;//(new XMLSerializer()).serializeToString(sourceSVG); + var ctx = targetCanvas.getContext('2d'); + + var img = new Image(); + img.src = "data:image/svg+xml;base64," + btoa(svg_xml); +// img.onload = function() { + ctx.drawImage(img, 0, 0); +// }; + } + +}; +/* +Graph.prototype.importSVG = function(sourceSVG, targetCanvas) { + sourceSVG = this._svg; + targetCanvas = document.createElementNS('canvas'); + // https://developer.mozilla.org/en/XMLSerializer + svg_xml = (new XMLSerializer()).serializeToString(sourceSVG); + var ctx = targetCanvas.getContext('2d'); + // this is just a JavaScript (HTML) image + var img = new Image(); + // http://en.wikipedia.org/wiki/SVG#Native_support + // https://developer.mozilla.org/en/DOM/window.btoa + img.src = "data:image/svg+xml;base64," + btoa(svg_xml); + img.onload = function() { + // after this, Canvas’ origin-clean is DIRTY + ctx.drawImage(img, 0, 0); + } +}; +*/ -/** API LAYOUT **/ -GraphCanvas.prototype.setCoordinates = function(vertexId, x, y) { - return this.getLayout().getEdgeById(vertexId).setCoordinates(x, y); -}; +/* + +Normalizacion de datos para dibujar colores +Issues: + No sé como debería llamarse esta libreria + No sé si ya existe una funciçon en javascript que lo haga + + +*/ + + +var Normalizer = new function() +{ + this.normalizeArray = function (arrayData) + { + + return this.standardizeArray(this.normal(arrayData)); + +// var result = this._getMaxAndMin(arrayData); +// var min =result[0]; +// var max = result[1]; +// +// +// //los hacemos todos positivos +// for (var i = 0; i< arrayData.length; i++) +// { +// arrayData[i]= Math.abs(min) + parseFloat(arrayData[i]); +// } +// +// var result = this._getMaxAndMin(arrayData); +// var min =result[0]; +// var max = result[1]; +// +// +// var resultArray = new Array(); +// for (var i = 0; i< arrayData.length; i++) +// { +// resultArray.push(arrayData[i]*1/max); +// } +// return resultArray; + }; + + this.normal = function(arrayData){ + var mean = this._getMean(arrayData); + var deviation = this._getStdDeviation(arrayData); + var result = this._getMaxAndMin(arrayData); + var min = result[0]; + var max = result[1]; + + var resultArray = new Array(); + for (var i = 0; i< arrayData.length; i++) { + if (deviation!=0){ + resultArray.push((arrayData[i]-mean)/deviation); + }else{ + resultArray.push(arrayData[i]); + } + } + return resultArray; + }; + + this.standardizeArray = function(arrayData) + { + var result = this._getMaxAndMin(arrayData); + var min = result[0]; + var max = result[1]; + + var offset = ( min <= 0 ) ? Math.abs(min) : (-1 * min); + var resultArray = new Array(); + for (var i = 0; i< arrayData.length; i++) { + if(max + offset!=0){ + resultArray.push((arrayData[i] + offset) / (max + offset)); + }else{ + resultArray.push(arrayData[i]+offset); + } + } + return resultArray; + }; + + + this._getMean = function(arrayData) { + var sum = 0; + for (var i = 0; i< arrayData.length; i++) { + sum = sum + parseFloat(arrayData[i]); + } + return sum/arrayData.length; + }; + + this._getStdDeviation = function(arrayData) { + var mean = this._getMean(arrayData); + var acum = 0.0; + for(var i=0; i max) max = parseFloat(arrayData[i]); + } + + return [min, max]; + }; +}; +function GraphCanvas(componentID, targetNode, args) { + this.args = {}; + /** target */ + this.targetID = targetNode.id; + + /** id manage */ + this.id = componentID; + this.args.idGraph = this.id + "main"; + this.args.idBackgroundNode = this.id + "background"; + + this.args.idEdgesGraph = this.id + "edges"; + this.args.idNodesGraph = this.id + "vertices"; + this.args.idLabelGraph = this.id + "label"; + this.args.idBackground = this.id + "background"; + + /** Objects Graph **/ + this.dataset = null; + this.formatter = null; + this.layout = null; + + /** Drawing **/ + this.circleDefaultRadius = 2; + this.squareDefaultSide = this.circleDefaultRadius * 1.5; + + /** Directed Arrow **/ + this.arrowDefaultSize = this.circleDefaultRadius; + + /** Groups **/ + this.GraphGroup = null; + this.GraphNodeGroup = null; + this.GraphLabelGroup = null; + this.GraphBackground = null; + + /** SETTINGS FLAGS **/ + this.args.draggingCanvasEnabled = false; //Flag to set if the canvas can be dragged + this.args.multipleSelectionEnabled = false; + this.args.interactive = false; + this.args.labeled = false; + this.args.linkEnabled = false; + + /** If numberEdge > maxNumberEdgesMoving then only it will move edges when mouse up **/ + this.args.maxNumberEdgesMoving = 3; + this.args.maxNumberEdgesFiringEvents = 50; + + /** Linking edges **/ + this.args.linking = false; + this.linkStartX = 0; + this.linkStartY = 0; + this.linkSVGNode = null; + this.linkNodeSource = null; + this.linkNodeTarget = null; + + /** Dragging Control **/ + this.draggingElement = null; + this.dragging = false; + this.nMouseOffsetX = 0; + this.nMouseOffsetY = 0; + this.dragStartX = 0; + this.dragStartY = 0; + this.desplazamientoX = 0; + this.desplazamientoY = 0; + + /** Selection Control **/ + this.selecting = false; + this.selectorX = null; + this.selectorY = null; + this.selectorSVGNode = null; + + /** Node status **/ + this.args.isVertexSelected = {}; + this.args.selectedVertices = []; + + /** Edges status **/ + this.args.isEdgeSelected = {}; + //this.args.selectedEdges = []; + + if (args != null) { + if (args.multipleSelectionEnabled != null) { + this.args.multipleSelectionEnabled = args.multipleSelectionEnabled; + this.args.draggingCanvasEnabled = !(this.args.multipleSelectionEnabled); + } + if (args.draggingCanvasEnabled != null) { + this.args.draggingCanvasEnabled = args.draggingCanvasEnabled; + this.args.multipleSelectionEnabled = !(this.args.draggingCanvasEnabled); + } + if (args.interactive != null) { + this.args.interactive = args.interactive; + } + if (args.labeled != null) { + this.args.labeled = args.labeled; + } + + } + + /** Hashmap with the svg node labels **/ + this.svgLabels = {}; + + /** EVENTS **/ + this.onVertexOut = new Event(this); + this.onVertexOver = new Event(this); + this.onVertexSelect = new Event(this); + this.onEdgeSelect = new Event(this); + this.onCanvasClicked = new Event(this); + this.onVertexUp = new Event(this); +} + +GraphCanvas.prototype.showLabels = function(value) { + this.args.labeled = value; + this.removeLabels(); + if (value) { + this.renderLabels(); + } +}; + +GraphCanvas.prototype.getSelectedVertices = function() { + return this.args.selectedVertices; +}; + +GraphCanvas.prototype.getSelectedEdges = function() { + var selected = []; + for ( var selectedEdge in this.args.isEdgeSelected) { + selected.push(selectedEdge); + } + return selected; +}; + +GraphCanvas.prototype.createSVGDom = function(targetID, id, width, height, backgroundColor) { + var container = document.getElementById(targetID); + this._svg = SVG.createSVGCanvas(container, [ + [ "style", "background-color:" + backgroundColor + ";" ], [ "id", id ], [ "dragx", 0 ], [ "dragy", 0 ], + [ "height", this.getFormatter().getHeight() ], [ "width", this.getFormatter().getWidth() ] ]); + return this._svg; +}; + +/** MULTIPLE SELECTION **/ +GraphCanvas.prototype.isMultipleSelectionEnabled = function() { + return this.args.multipleSelectionEnabled; +}; + +GraphCanvas.prototype.setMultipleSelection = function(value) { + this.args.multipleSelectionEnabled = value; + this.args.draggingCanvasEnabled = (!value); +}; + +GraphCanvas.prototype.setSelecting = function(value) { + this.selecting = value; +}; + +/** linking **/ +GraphCanvas.prototype.setLinking = function(value) { + this.args.linkEnabled = value; + this.selecting = !value; + this.dragging = !value; +}; + +/** CANVAS MOVING **/ +GraphCanvas.prototype.setDraggingCanvas = function(value) { + this.args.draggingCanvasEnabled = value; + this.args.multipleSelectionEnabled = !value; +}; + +GraphCanvas.prototype.isDraggingCanvasEnabled = function() { + return this.args.draggingCanvasEnabled; +}; +/** ZOOM **/ +GraphCanvas.prototype.getScale = function() { + return this.getFormatter().getZoomScale(); +}; + +GraphCanvas.prototype.setScale = function(scale) { + var graphNode = document.getElementById(this.args.idGraph); + graphNode.setAttribute("transform", graphNode.getAttribute("transform").replace("scale(" + this.getScale() + ")", "scale(" + scale + ")")); + this.getFormatter().setZoomScale(scale); +}; + +GraphCanvas.prototype.zoomIn = function() { + this.setScale(this.getScale() + this.getFormatter().getZoomScaleStepFactor()); +}; + +GraphCanvas.prototype.zoomOut = function() { + this.setScale(this.getScale() - this.getFormatter().getZoomScaleStepFactor()); + +}; + +/** SVG COORDENATES **/ +GraphCanvas.prototype.getSVGCoordenates = function(evt) { + var p = this._svg.createSVGPoint(); + p.x = evt.clientX; + p.y = evt.clientY; + + var m = this._svg.getScreenCTM(document.documentElement); + p = p.matrixTransform(m.inverse()); + return p; +}; + +/** SVG EVENTS **/ +GraphCanvas.prototype.mouseClick = function(event) { + if (event.button == 0) { + if (!this.args.interactive) { + return; + } + + if (this.isVertex(event.target)) { + this.clickNode(this.getVertexIdFromSVGId(event.target.id)); + } + /** Como el evento mouseClick viene despues del mouse up es aqui donde manejo el tema de deseccionar los elementos que estoy dragging **/ + if (this.dragging) { + this.dragging = false; + } + } +}; + +GraphCanvas.prototype.mouseMove = function(evt) { + if (this.selecting) { + this.clearLabels(); + + var width = (this.getSVGCoordenates(evt).x - this.selectorX); + var height = (this.getSVGCoordenates(evt).y - this.selectorY); + if ((width > 0) && (height > 0)) { + this.displaySelection(this.selectorX, this.selectorY, width, height); + } + if ((width > 0) && (height < 0)) { + this.displaySelection(this.selectorX, this.getSVGCoordenates(evt).y, width, Math.abs(height)); + } + if ((width < 0) && (height < 0)) { + this.displaySelection(this.getSVGCoordenates(evt).x, this.getSVGCoordenates(evt).y, Math.abs(width), Math.abs(height)); + } + if ((width < 0) && (height > 0)) { + this.displaySelection(this.selectorX + width, this.selectorY, Math.abs(width), Math.abs(height)); + } + + var x1 = (parseFloat(this.selectorSVGNode.getAttribute("x")) - DOM.select(this.id).getAttribute("dragx")) / this.getFormatter().getWidth(); + var y1 = (parseFloat(this.selectorSVGNode.getAttribute("y")) - DOM.select(this.id).getAttribute("dragy")) / this.getFormatter().getHeight(); + var x2 = (x1 + parseFloat(this.selectorSVGNode.getAttribute("width") / this.getFormatter().getWidth())); + var y2 = (y1 + parseFloat(this.selectorSVGNode.getAttribute("height") / this.getFormatter().getHeight())); + + this.deselectNodes(this.getLayout()); + var verticesSelected = this.getLayout().getVerticesByArea(x1 / this.getFormatter().getZoomScale(), y1 / this.getFormatter().getZoomScale(), + x2 / this.getFormatter().getZoomScale(), y2 / this.getFormatter().getZoomScale()); + for ( var i = 0; i < verticesSelected.length; i++) { + this.selectNode(verticesSelected[i].getId()); + this.renderLabel(verticesSelected[i].getId()); + } + + } + var p = null; + if (this.args.linking) { + p = this.getSVGCoordenates(evt); + if (this.linkSVGNode != null) { + this.linkSVGNode.setAttribute("x2", p.x - 2); + this.linkSVGNode.setAttribute("y2", p.y - 2); + } + } + + if (this.dragging) { + p = this.getSVGCoordenates(evt); + p.x -= this.nMouseOffsetX; + p.y -= this.nMouseOffsetY; + this.desplazamientoX = (this.getSVGCoordenates(evt).x - this.dragStartX);// + parseFloat(DOM.select(this.id).getAttribute("dragx")); + this.desplazamientoY = (this.getSVGCoordenates(evt).y - this.dragStartY);// + parseFloat(DOM.select(this.id).getAttribute("dragy")); + + if (this.draggingElement != null) { + /** Click sobre el recct del banground que provoca que mueva todo el canvas **/ + if (this.isNodeCanvas(this.draggingElement)) { + + p = this.getSVGCoordenates(evt); + p.x = this.desplazamientoX; + p.y = this.desplazamientoY; + + this.draggingElement.setAttribute("dragx", p.x); + this.draggingElement.setAttribute("dragy", p.y); + this.draggingElement = document.getElementById(this.args.idGraph); + this.draggingElement.setAttribute("transform", "translate(" + p.x + "," + p.y + "), scale(" + this.getScale() + ")"); + + DOM.select(this.id).setAttribute("dragx", p.x); + DOM.select(this.id).setAttribute("dragy", p.y); + + if (this.NodeSVGbackgroundImage != null) { + this.NodeSVGbackgroundImage.setAttribute("dragx", p.x); + this.NodeSVGbackgroundImage.setAttribute("dragy", p.y); + } + } else { + if (this.isVertex(this.draggingElement)) { + this.selectNode(this.getVertexIdFromSVGId(this.draggingElement.id)); + this.desplazamientoX = this.desplazamientoX / this.getFormatter().getZoomScale(); + this.desplazamientoY = this.desplazamientoY / this.getFormatter().getZoomScale(); + this.moveSelectedNodes(this.desplazamientoX, this.desplazamientoY); + + this.dragStartX = this.getSVGCoordenates(evt).x; + this.dragStartY = this.getSVGCoordenates(evt).y; + } else { + if (this.isNodeBackground(this.draggingElement)) { + + this.draggingElement.setAttribute("dragx", p.x); + this.draggingElement.setAttribute("dragy", p.y); + this.draggingElement = document.getElementById(this.args.idGraph); + this.draggingElement.setAttribute("transform", "translate(" + p.x + "," + p.y + "), scale(" + this.getScale() + ")"); + } else { + this.draggingElement.setAttribute("transform", "translate(" + p.x + "," + p.y + ")"); + } + } + } + } + } +}; + +GraphCanvas.prototype.moveSelectedNodes = function(offsetX, offsetY) { + for ( var i = 0; i < this.getSelectedVertices().length; i++) { + + var nodeId = this.getSelectedVertices()[i]; + var svgNodeId = this.getSVGNodeId(nodeId); + + var x = parseFloat(DOM.select(svgNodeId).getAttribute("dragx")) + parseFloat(offsetX);// - parseFloat(DOM.select(this.id).getAttribute("dragx")); + var y = parseFloat(DOM.select(svgNodeId).getAttribute("dragy")) + parseFloat(offsetY);// + parseFloat(DOM.select(this.id).getAttribute("dragy")); + + this._movingNode(DOM.select(svgNodeId), x, y); + } +}; + +GraphCanvas.prototype.mouseDown = function(evt) { + if (event.button == 0) { + + /** if !no interactive mouse events do anything **/ + if (!this.args.interactive) { + return; + } + + var p = this.getSVGCoordenates(evt); + + /** When click on canvas or background deselect all **/ + if (this.isNodeCanvas(evt.target) || this.isNodeBackground(evt.target)) { + this.deselectNodes(); + this.deselectEdges(); + this.onCanvasClicked.notify(); + } + + /** if I am linking vertices **/ + if (this.args.linkEnabled) { + + if (!this.args.linking) { + this.args.linking = true; + if (this.isVertex(evt.target)) { + this.linkStartX = p.x; + this.linkStartY = p.y; + this.linkSVGNode = SVG.drawLine(p.x, p.y, p.x, p.y, this._svg, { + "stroke" : "#FF0000" + }); + this.linkNodeSource = this.getVertexIdFromSVGId(evt.target.id); + } + } else { + this.linkNodeTarget = this.getVertexIdFromSVGId(evt.target.id); + this.args.linking = false; + this.args.linkEnabled = false; + if (this.isVertex(evt.target)) { + this.getDataset().addEdge(this.linkNodeSource + "_" + this.linkNodeTarget, this.linkNodeSource, this.linkNodeTarget, {}); + } + this.linkSVGNode.parentNode.removeChild(this.linkSVGNode); + } + return; + } + + /** Id is a vertex or the canvas **/ + if (this.isVertex(evt.target) || this.isNodeCanvas(evt.target) || this.isNodeBackground(evt.target)) { + this._startDragging(evt); + } + /** if i is edge **/ + if (this.isEdge(evt.target)) { + this.selectEdge(this.getEdgeIdFromSVGId(evt.target.getAttribute("id"))); + } + + if (this.args.multipleSelectionEnabled) { + if (!this.dragging) { + this.setSelecting(true); + this.selectorX = p.x; + this.selectorY = p.y; + this.displaySelection(p.x, p.y, 1, 1); + } + } + + } + if (event.button == 1) { + this.setLinking(false); + this.setMultipleSelection(false); + this.selecting = false; + + /** Id is a vertex or the canvas **/ + if (this.isVertex(evt.target) || this.isNodeCanvas(evt.target) || this.isNodeBackground(evt.target)) { + this._startDragging(evt); + } + } +}; + +GraphCanvas.prototype.mouseUp = function(event) { + if (!this.args.interactive) { + return; + } + + if (this.dragging) { + this._stopDragging(event); + if (this.isVertex(event.target)) { + var vertexId = this.getVertexIdFromSVGId(event.target.id); + if (this.getDataset().getVertexById(vertexId).getEdges().length >= this.args.maxNumberEdgesMoving) { + this.moveEdge(vertexId); + } + } + } + + if (this.selecting) { + this.setSelecting(false); + + var x1 = (parseFloat(this.selectorSVGNode.getAttribute("x")) - DOM.select(this.id).getAttribute("dragx")) / this.getFormatter().getWidth(); + var y1 = (parseFloat(this.selectorSVGNode.getAttribute("y")) - DOM.select(this.id).getAttribute("dragy")) / this.getFormatter().getHeight(); + var x2 = (x1 + parseFloat(this.selectorSVGNode.getAttribute("width") / this.formatter.getWidth())); + var y2 = (y1 + parseFloat(this.selectorSVGNode.getAttribute("height") / this.formatter.getHeight())); + + var verticesSelected = this.getLayout().getVerticesByArea(x1 / this.getFormatter().getZoomScale, y1 / this.getFormatter().getZoomScale, + x2 / this.getFormatter().getZoomScale, y2 / this.getFormatter().getZoomScale); + + for ( var i = 0; i < verticesSelected.length; i++) { + this.selectNode(verticesSelected[i].getId()); + } + + if (this.selectorSVGNode != null) { + this._svg.removeChild(this.selectorSVGNode); + } + + if (this.args.labeled) { + this.clearLabels(); + this.renderLabels(); + } + + this.selectorSVGNode = null; + // this.renderLabels(); + } +}; + +/** SELECTION **/ +GraphCanvas.prototype.displaySelection = function(x, y, width, height) { + if (this.selectorSVGNode != null) { + this.selectorSVGNode.setAttribute("x", x); + this.selectorSVGNode.setAttribute("y", y); + this.selectorSVGNode.setAttribute("width", width); + this.selectorSVGNode.setAttribute("height", height); + } else { + this.selectorSVGNode = SVG.drawRectangle(x, y, width, height, this._svg, { + "fill" : "red", + "stroke" : "black", + "opacity" : "0.2", + "stroke-opacity" : "1" + }); + } +}; + +/** DRAGGING **/ +GraphCanvas.prototype._startDragging = function(evt) { + if (!this.isDraggingCanvasEnabled()) { + if (this.isNodeCanvas(evt.target)) { + this.draggingElement = null; + } + } + + if (this.isVertex(evt.target) || (this.isNodeBackground(evt.target) && (this.isDraggingCanvasEnabled()))|| (this.isNodeCanvas(evt.target) && (this.isDraggingCanvasEnabled()))) { + this.clearLabels(); + this.draggingElement = evt.target; + this.dragging = true; + var p = this.getSVGCoordenates(evt); + + this.nMouseOffsetX = p.x - parseInt(evt.target.getAttribute("dragx")); + this.nMouseOffsetY = p.y - parseInt(evt.target.getAttribute("dragy")); + + if (this.isVertex(evt.target)) { + this.dragStartX = parseInt(this.draggingElement.getAttribute("dragx")) * this.getFormatter().getZoomScale() + + parseFloat(DOM.select(this.id).getAttribute("dragx")); + this.dragStartY = parseInt(this.draggingElement.getAttribute("dragy")) * this.getFormatter().getZoomScale() + + parseFloat(DOM.select(this.id).getAttribute("dragy")); + } else { + this.dragStartX = p.x - parseInt(this.draggingElement.getAttribute("dragx"));// + parseFloat(DOM.select(this.id).getAttribute("dragx")); + this.dragStartY = p.y - parseInt(this.draggingElement.getAttribute("dragy"));// + parseFloat(DOM.select(this.id).getAttribute("dragy")); + } + } +}; + +GraphCanvas.prototype._stopDragging = function(event) { + this.nMouseOffsetX = 0; + this.nMouseOffsetX = 0; + /** despues del evento up viene el evento click entonces acabo el dragging en el mouseclick **/ + this.dragging = false; + this.draggingElement = null; + this.renderLabels(); + + this.setLinking(false); + this.setMultipleSelection(true); + this.selecting = false; + +}; + +/** Move the edges of the vertex with the vertexId indicado **/ +GraphCanvas.prototype.moveEdge = function(vertexId) { + var x = this.getLayout().getNodeById(vertexId).x * this.getFormatter().getWidth(); + var y = this.getLayout().getNodeById(vertexId).y * this.getFormatter().getHeight(); + + /** Moving edges out **/ + for ( var i = 0; i < this.getDataset().getVertexById(vertexId).getEdgesOut().length; i++) { + var edgeId = this.getDataset().getVertexById(vertexId).getEdgesOut()[i].getId(); + var svgEdgeId = this.getSVGEdgeId(edgeId); + var edgeFormatter = this.getFormatter().getEdgeById(edgeId); + if (edgeFormatter instanceof LineEdgeGraphFormatter) { + DOM.select(svgEdgeId + "_shadow").setAttribute("x2", x); + DOM.select(svgEdgeId + "_shadow").setAttribute("y2", y); + DOM.select(svgEdgeId).setAttribute("x2", x); + DOM.select(svgEdgeId).setAttribute("y2", y); + } + + if ((edgeFormatter instanceof DirectedLineEdgeGraphFormatter) || (edgeFormatter instanceof OdirectedLineEdgeGraphFormatter) + || (edgeFormatter instanceof OdotDirectedLineEdgeGraphFormatter) || (edgeFormatter instanceof DotDirectedLineEdgeGraphFormatter) + || (edgeFormatter instanceof CutDirectedLineEdgeGraphFormatter)) { + this.removeEdge(edgeId); + this.renderEdge(edgeId); + } + } + + /** Moving edges in **/ + for ( var i = 0; i < this.getDataset().getVertexById(vertexId).getEdgesIn().length; i++) { + var edgeId = this.getDataset().getVertexById(vertexId).getEdgesIn()[i].getId(); + var svgEdgeId = this.getSVGEdgeId(edgeId); + var edgeFormatter = this.getFormatter().getEdgeById(edgeId); + if (edgeFormatter instanceof LineEdgeGraphFormatter) { + DOM.select(svgEdgeId).setAttribute("x1", x); + DOM.select(svgEdgeId).setAttribute("y1", y); + DOM.select(svgEdgeId + "_shadow").setAttribute("x1", x); + DOM.select(svgEdgeId + "_shadow").setAttribute("y1", y); + } + + if ((edgeFormatter instanceof DirectedLineEdgeGraphFormatter) || (edgeFormatter instanceof OdirectedLineEdgeGraphFormatter) + || (edgeFormatter instanceof OdotDirectedLineEdgeGraphFormatter) || (edgeFormatter instanceof DotDirectedLineEdgeGraphFormatter) + || (edgeFormatter instanceof CutDirectedLineEdgeGraphFormatter)) { + this.removeEdge(edgeId); + this.renderEdge(edgeId); + } + + if (edgeFormatter instanceof BezierEdgeGraphFormatter) { + var radius = this.getFormatter().getVertexById(vertexId).getDefault().getSize() * this.getFormatter().getNodesMaxSize(); + var d = this.calculateCoordenatesBezier(radius, x, y); + DOM.select(svgEdgeId).setAttribute("d", d); + } + } +}; + +GraphCanvas.prototype.moveNode = function(vertexId) { + var x = this.getLayout().getNodeById(vertexId).x * this.getFormatter().getWidth(); + var y = this.getLayout().getNodeById(vertexId).y * this.getFormatter().getHeight(); + var svgNodeElement = DOM.select(this.getSVGNodeId(vertexId)); + + svgNodeElement.setAttribute("dragx", x); + svgNodeElement.setAttribute("dragy", y); + svgNodeElement.setAttribute("transform", "translate(" + x + "," + y + ")"); + + if (this.getDataset().getVertexById(vertexId).getEdges().length < this.args.maxNumberEdgesMoving) { + this.moveEdge(vertexId); + } +}; + +GraphCanvas.prototype._movingNode = function(svgNodeElement, x, y) { + var vertexId = this.getVertexIdFromSVGId(svgNodeElement.getAttribute("id")); + this.getLayout().getNodeById(vertexId).setCoordinates(x / this.getFormatter().getWidth(), y / this.getFormatter().getHeight()); + this.desplazamientoX = 0; + this.desplazamientoY = 0; + this.removeLabel(vertexId); + this.renderLabel(vertexId); +}; + +/** INIT **/ +GraphCanvas.prototype.init = function() { + + this._svg = this.createSVGDom(this.targetID, this.id, this.getFormatter().getWidth(), this.getFormatter().getHeight(), this.getFormatter() + .getBackgroundColor()); + this.GraphGroup = SVG.drawGroup(this._svg, [ [ "id", this.args.idGraph ], [ "transform", "translate(0,0), scale(1)" ] ]); + this.GraphBackground = SVG.drawGroup(this.GraphGroup, [ [ "id", this.args.idBackground ] ]); + this.GraphEdgeGroup = SVG.drawGroup(this.GraphGroup, [ [ "id", this.args.idEdgesGraph ] ]); + this.GraphNodeGroup = SVG.drawGroup(this.GraphGroup, [ [ "id", this.args.idNodesGraph ] ]); + this.GraphLabelGroup = SVG.drawGroup(this.GraphGroup, [ [ "id", this.args.idLabelGraph ] ]); + + if ((this.getFormatter().getBackgroundImage() != null) && (this.getFormatter().getBackgroundImage() != "")) { + this.setBackgroundImage(this.getFormatter().getBackgroundImage()); + } + /** SVG Events listener */ + var _this = this; + this._svg.addEventListener("click", function(event) { + _this.mouseClick(event); + }, false); + this._svg.addEventListener("mousemove", function(event) { + _this.mouseMove(event, _this); + }, false); + this._svg.addEventListener("mousedown", function(event) { + _this.mouseDown(event, _this); + }, false); + this._svg.addEventListener("mouseup", function(event) { + _this.mouseUp(event, _this); + }, false); +}; + +/* + GraphCanvas.prototype.backgroungToSVG = function(){ + var _this = this; + var canvas = document.createElement('canvas'); + canvas.setAttribute("id", "canvas"); + canvas.width = this.formatter.getWidth(); + canvas.height = this.formatter.getHeight(); + + this._svg.parentNode.parentNode.appendChild(canvas); + var ctx = document.getElementById('canvas').getContext('2d'); + var img = new Image(); + + img.src = this.formatter.getBackgroundImage(); + ctx.drawImage(img,0,0 ,_this.formatter.getWidth(), _this.formatter.getHeight()); + + + img.onload = function() { + canvas.parentNode.removeChild(canvas); + } + + this.NodeSVGbackgroundImage.setAttribute("xlink:href", document.getElementById("canvas").toDataURL()); + this.NodeSVGbackgroundImage.removeAttribute("href"); + + // + + };*/ + +GraphCanvas.prototype.setBackgroundImage = function() { + if (this.NodeSVGbackgroundImage != null) { + this.NodeSVGbackgroundImage.parentNode.removeChild(this.NodeSVGbackgroundImage); + } + $('#' + this.targetID).svg(); + $('#' + this.targetID).svg("get"); + + $('#' + this.targetID).svg("get")._svg = document.getElementById(this.id); + + var svg = $('#' + this.targetID).svg("get"); + this.NodeSVGbackgroundImage = svg.image(0, 0, this.getFormatter().getWidth(), this.getFormatter().getHeight(), this.getFormatter() + .getBackgroundImage()); + this.NodeSVGbackgroundImage.setAttribute("id", this.args.idBackgroundNode); + + this.NodeSVGbackgroundImage.setAttribute("x", 0); + this.NodeSVGbackgroundImage.setAttribute("y", 0); + + this.NodeSVGbackgroundImage.setAttribute("dragx", 0); + this.NodeSVGbackgroundImage.setAttribute("dragy", 0); + + if (this.getFormatter().args.backgroundImageHeight != null) { + this.NodeSVGbackgroundImage.setAttribute("height", this.getFormatter().args.backgroundImageHeight); + } + if (this.getFormatter().args.backgroundImageWidth != null) { + this.NodeSVGbackgroundImage.setAttribute("width", this.getFormatter().args.backgroundImageWidth); + } + + if (this.getFormatter().args.backgroundImageX != null) { + this.NodeSVGbackgroundImage.setAttribute("x", this.getFormatter().args.backgroundImageX); + } + if (this.getFormatter().args.backgroundImageY != null) { + this.NodeSVGbackgroundImage.setAttribute("y", this.getFormatter().args.backgroundImageY); + } + + this.GraphBackground.appendChild(this.NodeSVGbackgroundImage); + this.NodeSVGbackgroundImage.removeAttribute("href"); + this.NodeSVGbackgroundImage.setAttribute("xlink:href", this.getFormatter().getBackgroundImage()); +}; + +GraphCanvas.prototype.removeBackgroundImage = function() { + if (this.NodeSVGbackgroundImage != null) { + this.NodeSVGbackgroundImage.parentNode.removeChild(this.NodeSVGbackgroundImage); + } +}; + +GraphCanvas.prototype._setBackgroundColor = function(color) { + var attributes = [ [ "fill", color ] ]; + SVG.drawRectangle(0, 0, this.getFormatter().getWidth(), this.getFormatter().getHeight(), this.GraphBackground, attributes); +}; + +/** Serialize **/ +GraphCanvas.prototype.toJSON = function() { + var json = {}; + json.dataset = {}; + json.formatter = {}; + json.layout = {}; + json.dataset = this.getDataset().toJSON(); + json.formatter = this.getFormatter().toJSON(); + json.layout = this.getLayout().toJSON(); + return json; +}; + +GraphCanvas.prototype.toHTML = function() { + //this.backgroungToSVG(); + var html = this._svg.parentElement.innerHTML; + + var start = html.indexOf("") + 6; + + return html.substr(start, end); +}; + +/** DRAW **/ +GraphCanvas.prototype.draw = function(graphdataset, graphformatter, graphlayout) { + this.setDataset(graphdataset); + this.setFormatter(graphformatter); + this.setLayout(graphlayout); + + var _this = this; + this.getFormatter().changed.attach(function(sender, item) { + _this.removeNode(item.getId()); + _this.renderNode(item.getId()); + if (_this.args.labeled) { + _this.removeLabel(item.getId()); + _this.renderLabel(item.getId()); + } + + }); + //TODO + this.getFormatter().edgeChanged.attach(function(sender, item) { + _this.removeEdge(item.getId()); + _this.renderEdge(item.getId()); + }); + + this.getFormatter().resized.attach(function(sender, item) { + _this.resize(_this.getFormatter().getWidth(), _this.getFormatter().getHeight()); + }); + + this.getFormatter().backgroundImageChanged.attach(function(sender, item) { + _this.setBackgroundImage(_this.getFormatter().getBackgroundImage()); + }); + + this.getFormatter().backgroundColorChanged.attach(function(sender, item) { + _this._setBackgroundColor(_this.getFormatter().getBackgroundColor()); + }); + + this.getLayout().changed.attach(function(sender, item) { + _this.moveNode(item.getId()); + _this.moveEdge(item.getId()); + if (_this.args.labeled) { + _this.removeLabel(item.getId()); + _this.renderLabel(item.getId()); + } + }); + + this.getDataset().newVertex.attach(function(sender, item) { + + _this.renderNode(item.getId()); + if (_this.args.labeled) { + _this.renderLabel(item.getId()); + } + }); + + this.getDataset().newEdge.attach(function(sender, item) { + _this.renderEdge(item.getId()); + }); + + this.getDataset().vertexDeleted.attach(function(sender, item) { + _this.removeNode(item.getId()); + if (_this.args.labeled) { + _this.removeLabel(item.getId()); + } + }); + + this.getDataset().edgeDeleted.attach(function(sender, item) { + _this.removeEdge(item.getId()); + }); + + this.getDataset().vertexNameChanged.attach(function(sender, args) { + if (_this.args.labeled) { + _this.removeLabel(args.item.getId()); + _this.removeLabel(args.item.getId()); + _this.renderLabel(args.item.getId()); + } + }); + this.init(); + this.render(); +}; + +GraphCanvas.prototype.render = function() { + for ( var id in this.getDataset().getVertices()) { + this.renderNode(id); + } + this.renderLabels(); + this.renderEdges(); +}; + +GraphCanvas.prototype.renderLabels = function() { + if (this.args.labeled) { + for ( var id in this.getDataset().getVertices()) { + this.renderLabel(id); + } + } +}; + +GraphCanvas.prototype.removeLabels = function() { + for ( var id in this.getDataset().getVertices()) { + this.removeLabel(id); + } +}; + +/** Utilities method for nodes **/ +GraphCanvas.prototype.isNodeCanvas = function(node) { + return ((node.id == this.args.idGraph) || (node.id == this.id)); +}; + +GraphCanvas.prototype.isNodeBackground = function(node) { + return ((node.id == this.args.idBackgroundNode)); +}; + +GraphCanvas.prototype.isVertex = function(node) { + if (node.getAttribute("id") != null) { + if (node.getAttribute("id").indexOf("_v_") != -1) { + return true; + } + } + return false; +}; + +GraphCanvas.prototype.isLabel = function(node) { + if (node.getAttribute("id") != null) { + if (node.getAttribute("id").indexOf("_l_") != -1) { + return true; + } + } + return false; +}; + +GraphCanvas.prototype.isEdge = function(node) { + if (node.getAttribute("id") != null) { + if (node.getAttribute("id").indexOf("_e_") != -1) { + return true; + } + } + return false; +}; + +/** Resize **/ +GraphCanvas.prototype.resize = function(width, height) { + // this._svg.setAttribute("width", width); + // this._svg.setAttribute("height", height); + if (this.NodeSVGbackgroundImage != null) { + this.NodeSVGbackgroundImage.setAttribute("width", width); + this.NodeSVGbackgroundImage.setAttribute("height", height); + } + + this._svg.setAttribute("width", width); + this._svg.setAttribute("height", height); + + this.clearCanvas(); + this.render(); +}; + +GraphCanvas.prototype.clearCanvas = function() { + DOM.removeChilds(this.GraphEdgeGroup.getAttribute("id")); + DOM.removeChilds(this.GraphNodeGroup.getAttribute("id")); + this.clearLabels(); +}; + +GraphCanvas.prototype.clearLabels = function() { + DOM.removeChilds(this.GraphLabelGroup.getAttribute("id")); +}; + +/** ID'S converter **/ +GraphCanvas.prototype.getSVGNodeId = function(nodeId) { + return this.id + "_v_" + nodeId; +}; + +GraphCanvas.prototype.getSVGEdgeId = function(edgeId) { + return this.id + "_e_" + edgeId; +}; + +GraphCanvas.prototype.getSVGArrowEdgeId = function(edgeId) { + return this.id + "_arrow_" + edgeId; +}; + +GraphCanvas.prototype.getSVGLabelId = function(edgeId) { + return this.id + "_l_" + edgeId; +}; + +GraphCanvas.prototype.blinkVertexById = function(vertexId) { + $("#" + this.getSVGNodeId(vertexId)).fadeIn().fadeOut().fadeIn().fadeOut().fadeIn().fadeOut(); +}; + +GraphCanvas.prototype.getVertexIdFromSVGId = function(svgVertexId) { + return svgVertexId.replace(this.id, "").replace("_v_", ""); +}; + +GraphCanvas.prototype.getEdgeIdFromSVGId = function(svgEdgeId) { + return svgEdgeId.replace(this.id, "").replace("_e_", ""); +}; + +/** VERTEX **/ +GraphCanvas.prototype.getVertexById = function(id) { + return document.getElementById(this.getSVGNodeId(id)); +}; + +GraphCanvas.prototype.renderNodes = function() { + for ( var id in this.getDataset().getVertices()) { + this.renderNode(id); + } +}; + +GraphCanvas.prototype.overNode = function(nodeId) { + if (!this.args.interactive) { + return; + } + /** If selected we don't change the format **/ + if (this.args.isVertexSelected[nodeId] == null) { + var args = this.getFormatter().getVertexById(nodeId).getOver(); + args.args["cursor"] = 'pointer'; + this.changeVertexFormat(nodeId, args); + } +}; + +GraphCanvas.prototype.outNode = function(nodeId) { + if (!this.args.interactive) { + return; + } + + /** If selected we don't change the format **/ + if (this.args.isVertexSelected[nodeId] == null) { + this.changeVertexFormat(nodeId, this.getFormatter().getVertexById(nodeId).getDefault()); + } +}; + +GraphCanvas.prototype.overLabel = function(nodeId) { + this.overNode(nodeId); + // this.svgLabels[nodeId].setAttribute("cursor", "pointer"); +}; + +GraphCanvas.prototype.outLabel = function(nodeId) { + this.outNode(nodeId); + // this.svgLabels[nodeId].setAttribute("cursor", ""); +}; + +GraphCanvas.prototype.clickNode = function(nodeId) { + if (!this.args.interactive) { + return; + } + + /** si el evento se dispara oprque estaba dragging entonces no activo nada **/ + if (this.args.isVertexSelected[nodeId] == null) { + this.selectNode(nodeId); + } else { + this.deselectNode(nodeId); + } +}; + +GraphCanvas.prototype.selectNode = function(nodeId) { + for ( var i = 0; i < this.args.selectedVertices.length; i++) { + var format = this.getFormatter().getVertexById(nodeId).getSelected(); + format.opacity = 0.2; + this.changeVertexFormat(nodeId, this.getFormatter().getVertexById(nodeId).getSelected()); + } + + if (this.args.isVertexSelected[nodeId] == null) { + var format = this.getFormatter().getVertexById(nodeId).getSelected(); + format.opacity = 1; + this.changeVertexFormat(nodeId, this.getFormatter().getVertexById(nodeId).getSelected()); + this.args.selectedVertices.push(nodeId); + this.args.isVertexSelected[nodeId] = this.args.selectedVertices.length - 1; + this.onVertexSelect.notify(nodeId); + } +}; + +GraphCanvas.prototype.selectAllEdges = function() { + this.deselectNodes(); + this.deselectEdges(); + + for ( var edgesId in this.getDataset().edges) { + this.selectEdge(edgesId); + } +}; + +GraphCanvas.prototype.selectAllNodes = function() { + this.deselectNodes(); + this.deselectEdges(); + + for ( var vertexId in this.getDataset().vertices) { + this.selectNode(vertexId); + } +}; + +GraphCanvas.prototype.selectAll = function() { + this.deselectNodes(); + this.deselectEdges(); + + for ( var vertexId in this.getDataset().vertices) { + this.selectNode(vertexId); + } + + for ( var edgesId in this.getDataset().edges) { + this.selectEdge(edgesId); + } +}; + +GraphCanvas.prototype.selectEdge = function(edgeId) { + if (this.args.isEdgeSelected[edgeId] == null) { + this.changeEdgeFormat(edgeId, this.getFormatter().getEdgeById(edgeId).getSelected()); + //this.args.selectedEdges.push(edgeId); + this.args.isEdgeSelected[edgeId] = true; //this.args.selectedEdges.length - 1; + this.onEdgeSelect.notify(edgeId); + } +}; + +GraphCanvas.prototype.selectEdges = function(edges) { + + for ( var i = 0; i < edges.length; i++) { + this.selectEdge(edges[i]); + } +}; + +GraphCanvas.prototype.deselectNode = function(nodeId) { + if (this.args.isVertexSelected[nodeId] != null) { + this.changeVertexFormat(nodeId, this.getFormatter().getVertexById(nodeId).getDefault()); + this.args.selectedVertices.splice(this.args.isVertexSelected[nodeId], 1); + var index = this.args.isVertexSelected[nodeId]; + delete this.args.isVertexSelected[nodeId]; + + for ( var vertex in this.args.isVertexSelected) { + if (this.args.isVertexSelected[vertex] > index) { + this.args.isVertexSelected[vertex] = this.args.isVertexSelected[vertex] - 1; + } + } + } +}; + +GraphCanvas.prototype.deselectNodes = function() { + var selected = JSON.parse(JSON.stringify(this.getSelectedVertices())); + for ( var i = 0; i < selected.length; i++) { + this.deselectNode(selected[i]); + } +}; +GraphCanvas.prototype.selectNodes = function(idNodes) { + + for ( var i = 0; i < idNodes.length; i++) { + this.selectNode(idNodes[i]); + } + + // for ( var vertex in this.args.isVertexSelected) { + // if (this.args.isVertexSelected[vertex] > index){ + // this.args.isVertexSelected[vertex] = this.args.isVertexSelected[vertex] - 1; + // } + // } + +}; + +GraphCanvas.prototype.changeVertexFormat = function(nodeId, format) { + var svgNode = DOM.select(this.getSVGNodeId(nodeId)); + if (svgNode != null) { + var properties = format.toJSON(); + for ( var item in properties) { + svgNode.setAttribute(item, properties[item]); + } + + if (this.getFormatter().getVertexById(nodeId) instanceof CircleVertexGraphFormatter) { + var transform = "translate(" + svgNode.getAttribute("dragx") + "," + svgNode.getAttribute("dragy") + "), scale(" + format.getSize() + ")"; + svgNode.setAttribute("transform", transform); + } + } +}; + +GraphCanvas.prototype.renderLabel = function(nodeId) { + var x = Math.ceil(this.getLayout().getNodeById(nodeId).x * this.getFormatter().getWidth()); + var y = Math.ceil(this.getLayout().getNodeById(nodeId).y * this.getFormatter().getHeight()); + + var svgAttributesNode = JSON.parse(JSON.stringify(this.getFormatter().getVertexById(nodeId).getDefault().toJSON().title)); + svgAttributesNode.id = this.getSVGLabelId(this.getDataset().getVertexById(nodeId).getId()); + svgAttributesNode.dx = (-1) * (this.getDataset().getVertexById(nodeId).getName().length * svgAttributesNode["font-size"]) / 4 - 4; + + svgAttributesNode.dy = parseFloat((this.getFormatter().getVertexById(nodeId).getDefault().getSize())) + + parseFloat(svgAttributesNode["font-size"]) + parseFloat(this.getFormatter().getVertexById(nodeId).getDefault().getStrokeWidth()) - 4; + svgAttributesNode.dragx = Math.ceil(this.getLayout().getNodeById(nodeId).x * this.getFormatter().getWidth()); + + var gragy = parseFloat(this.getFormatter().getVertexById(nodeId).getDefault().getSize()) + + Math.ceil(this.getLayout().getNodeById(nodeId).y * this.getFormatter().getHeight()); + svgAttributesNode.dragy = gragy; + svgAttributesNode.transform = "translate(" + svgAttributesNode.dragx + "," + svgAttributesNode.dragy + ")";//, scale("+this.formatter.getVertexById(nodeId).getDefault().getSize()+")"; + + var nodeSVG = SVG.drawText(0, 0, this.getDataset().getVertexById(nodeId).getName(), this.GraphLabelGroup, svgAttributesNode); + + this.svgLabels[nodeId] = nodeSVG; + + /** Events for the SVG node **/ + var _this = this; + if (nodeSVG != null) { + nodeSVG.addEventListener("mouseover", function() { + _this.overLabel(nodeId); + }, false); + nodeSVG.addEventListener("mouseout", function() { + _this.outLabel(nodeId); + }, false); + } + +}; + +GraphCanvas.prototype.removeLabel = function(labelId) { + if (DOM.select(this.getSVGLabelId(labelId)) != null) { + DOM.select(this.getSVGLabelId(labelId)).parentNode.removeChild(DOM.select(this.getSVGLabelId(labelId))); + } +}; + +GraphCanvas.prototype.renderNode = function(nodeId) { + var svgAttributesNode = JSON.parse(JSON.stringify(this.getFormatter().getVertexById(nodeId).getDefault().toJSON())); + svgAttributesNode.dragx = Math.ceil(this.getLayout().getNodeById(nodeId).x * this.getFormatter().getWidth()); + svgAttributesNode.dragy = Math.ceil(this.getLayout().getNodeById(nodeId).y * this.getFormatter().getHeight()); + svgAttributesNode.transform = "translate(" + svgAttributesNode.dragx + "," + svgAttributesNode.dragy + ")"; + svgAttributesNode.id = this.getSVGNodeId(nodeId); + /*svgAttributesNode["stroke-width"] = 3 ; + svgAttributesNode["stroke-opacity"] = 1 ; + svgAttributesNode["fill-opacity"] = svgAttributesNode["opacity"] ; + svgAttributesNode["opacity"] = 1 ;*/ + this.circleDefaultRadius = this.getFormatter().getVertexById(nodeId).getDefault().getSize(); + var nodeSVG; + + if (this.getFormatter().getVertexById(nodeId) instanceof CircleVertexGraphFormatter) { + nodeSVG = SVG.drawCircle(0, 0, this.circleDefaultRadius, this.GraphNodeGroup, svgAttributesNode); + } + + if (this.getFormatter().getVertexById(nodeId) instanceof SquareVertexGraphFormatter) { + //nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius) ,0 - (this.formatter.getVertexById(nodeId).getDefault().getSize()) , (this.getFormatter().getVertexById(nodeId).getDefault().getSize()*2), (this.getFormatter().getVertexById(nodeId).getDefault().getSize()*2), this.GraphNodeGroup, svgAttributesNode); + nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius), 0 - (this.circleDefaultRadius), (this.circleDefaultRadius * 2), + (this.circleDefaultRadius * 2), this.GraphNodeGroup, svgAttributesNode); + } + + if (this.getFormatter().getVertexById(nodeId) instanceof EllipseVertexGraphFormatter) { + nodeSVG = SVG.drawEllipse(0, 0, this.circleDefaultRadius * 1.5, this.circleDefaultRadius, this.GraphNodeGroup, svgAttributesNode); + } + + if (this.getFormatter().getVertexById(nodeId) instanceof RectangleVertexGraphFormatter) { + //nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius) ,0 - ((this.circleDefaultRadius*2)/2) , (this.circleDefaultRadius*2), (this.circleDefaultRadius), this.GraphNodeGroup, svgAttributesNode); + nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius * 1.5), 0 - (this.circleDefaultRadius), (this.circleDefaultRadius * 2 * 1.5), + (this.circleDefaultRadius * 2), this.GraphNodeGroup, svgAttributesNode); + + } + + if (this.getFormatter().getVertexById(nodeId) instanceof RoundedVertexGraphFormatter) { + svgAttributesNode.ry = 2;// this.formatter.getVertexById(nodeId).getDefault().getSize()/4; + svgAttributesNode.rx = 2;// this.formatter.getVertexById(nodeId).getDefault().getSize()/4; + nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius * 1.5), 0 - (this.circleDefaultRadius), (this.circleDefaultRadius * 2 * 1.5), + (this.circleDefaultRadius * 2), this.GraphNodeGroup, svgAttributesNode); + } + + // + + if (this.getFormatter().getVertexById(nodeId) instanceof OctagonVertexGraphFormatter) { + svgAttributesNode.ry = 2; + svgAttributesNode.rx = 2; + nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius * 1.5), 0 - (this.circleDefaultRadius), (this.circleDefaultRadius * 2 * 1.5), + (this.circleDefaultRadius * 2), this.GraphNodeGroup, svgAttributesNode); + } + + nodeSVG.internalId = nodeId; + // + var _this = this; + + /** Events for the SVG node **/ + if (nodeSVG != null) { + nodeSVG.addEventListener("mouseover", function() { + _this.onVertexOver.notify(nodeId); + _this.overNode(nodeId); + }, false); + nodeSVG.addEventListener("mouseout", function() { + _this.onVertexOut.notify(nodeId); + _this.outNode(nodeId); + }, false); + //nodeSVG.addEventListener("click", function(){_this.clickNode(nodeId);}, false); + // + nodeSVG.addEventListener("mouseup", function() { + _this.onVertexUp.notify(nodeId); + }, false); + } +}; + +GraphCanvas.prototype.removeNode = function(nodeId) { + DOM.select(this.getSVGNodeId(nodeId)).parentNode.removeChild(DOM.select(this.getSVGNodeId(nodeId))); + if (this.args.labeled) { + this.removeLabel(nodeId); + } +}; + +/** REMOVING **/ +GraphCanvas.prototype.removeSelected = function() { + /** El orden importa **/ + this.removeSelectedEdges(); + this.removeSelectedNode(); + +}; + +GraphCanvas.prototype.removeSelectedNode = function() { + var selected = JSON.parse(JSON.stringify(this.getSelectedVertices())); + this.deselectNodes(); + var sorted = selected.sort(function(a, b) { + return a - b + }); + for ( var i = 0; i < sorted.length; i++) { + if (this.getDataset().getVertexById(sorted[i]) != null) { + this.getDataset().getVertexById(sorted[i]).remove(); + } + } +}; + +/** EDGES **/ +GraphCanvas.prototype.removeEdge = function(edgeId) { + if (DOM.select(this.getSVGEdgeId(edgeId)) != null) { + DOM.select(this.getSVGEdgeId(edgeId)).parentNode.removeChild(DOM.select(this.getSVGEdgeId(edgeId))); + } + + if (DOM.select(this.getSVGEdgeId(edgeId) + "_shadow") != null) { + DOM.select(this.getSVGEdgeId(edgeId) + "_shadow").parentNode.removeChild(DOM.select(this.getSVGEdgeId(edgeId) + "_shadow")); + } + + if (DOM.select(this.getSVGArrowEdgeId(edgeId)) != null) { + DOM.select(this.getSVGArrowEdgeId(edgeId)).parentNode.removeChild(DOM.select(this.getSVGArrowEdgeId(edgeId))); + } +}; + +GraphCanvas.prototype.overEdge = function(edgeId) { + if ((!this.args.interactive) || this.dragging || this.selecting) { + return; + } + + /** If selected we don't change the format **/ + if (this.args.isEdgeSelected[edgeId] == null) { + var format = this.getFormatter().getEdgeById(edgeId).getOver(); + format.args["cursor"] = "pointer"; + this.changeEdgeFormat(edgeId, format); + } +}; + +GraphCanvas.prototype.outEdge = function(edgeId) { + if (!this.args.interactive) { + return; + } + + /** If selected we don't change the format **/ + if (this.args.isEdgeSelected[edgeId] == null) { + this.changeEdgeFormat(edgeId, this.getFormatter().getEdgeById(edgeId).getDefault()); + } +}; + +GraphCanvas.prototype.changeEdgeFormat = function(edgeId, format) { + var svgEdge = DOM.select(this.getSVGEdgeId(edgeId) + "_shadow"); + if (svgEdge != null) { + var properties = format.toJSON(); + for ( var item in properties) { + svgEdge.setAttribute(item, properties[item]); + } + } +}; + +GraphCanvas.prototype.deselectEdge = function(edgeID) { + if (this.args.isEdgeSelected[edgeID] != null) { + this.changeEdgeFormat(edgeID, this.getFormatter().getEdgeById(edgeID).getDefault()); + var index = this.args.isEdgeSelected[edgeID]; + delete this.args.isEdgeSelected[edgeID]; + } +}; + +GraphCanvas.prototype.deselectEdges = function() { + var selected = JSON.parse(JSON.stringify(this.getSelectedEdges())); + for ( var i = 0; i < selected.length; i++) { + this.deselectEdge(selected[i]); + } +}; + +GraphCanvas.prototype.removeSelectedEdges = function() { + var selected = JSON.parse(JSON.stringify(this.getSelectedEdges())); + this.deselectEdges(); + for ( var i = 0; i < selected.length; i++) { + if (this.getDataset().getEdgeById(selected[i]) != null) { + this.getDataset().getEdgeById(selected[i]).remove(); + } + } +}; + +GraphCanvas.prototype.renderEdge = function(edgeId) { + var svgAttributesEdge = this.getFormatter().getEdgeById(edgeId).getDefault().toJSON(); + var edge = this.getDataset().getEdgeById(edgeId); + + var svgNodeTarget = this.getVertexById(edge.getNodeTarget().getId()); + var svgNodeSource = this.getVertexById(edge.getNodeSource().getId()); + svgAttributesEdge.id = this.getSVGEdgeId(edge.getId()) + "_shadow"; + + var svgEdge = null; + + if (this.getFormatter().getEdgeById(edgeId) instanceof LineEdgeGraphFormatter) { + var coordenateSourceX = svgNodeSource.getAttribute("dragx"); + var coordenateSourceY = svgNodeSource.getAttribute("dragy"); + var coordenateTargetX = svgNodeTarget.getAttribute("dragx"); + var coordenateTargetY = svgNodeTarget.getAttribute("dragy"); + + SVG.drawLine(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, this.GraphEdgeGroup, svgAttributesEdge); + var attributesShadow = {}; + attributesShadow.id = this.getSVGEdgeId(edge.getId()); + attributesShadow["stroke-opacity"] = 0; + attributesShadow["stroke-width"] = 4; + attributesShadow["stroke"] = "black"; + svgEdge = SVG.drawLine(svgNodeSource.getAttribute("dragx"), svgNodeSource.getAttribute("dragy"), svgNodeTarget.getAttribute("dragx"), + svgNodeTarget.getAttribute("dragy"), this.GraphEdgeGroup, attributesShadow); + } + + if (this.getFormatter().getEdgeById(edgeId) instanceof BezierEdgeGraphFormatter) { + var nodeId = edge.getNodeTarget().getId(); + var nodeSize = this.formatter.getVertexById(nodeId).getDefault().getSize() * this.getFormatter().getNodesMaxSize(); + svgAttributesEdge.fill = "none"; + svgAttributesEdge.id = this.getSVGEdgeId(edgeId); + var d = this.calculateCoordenatesBezier(nodeSize, svgNodeSource.getAttribute("dragx"), svgNodeSource.getAttribute("dragy")); + svgEdge = SVG.drawPath(d, this.GraphEdgeGroup, svgAttributesEdge); + } + ; + + if ((this.getFormatter().getEdgeById(edgeId) instanceof DirectedLineEdgeGraphFormatter) + || (this.getFormatter().getEdgeById(edgeId) instanceof CutDirectedLineEdgeGraphFormatter) + || (this.getFormatter().getEdgeById(edgeId) instanceof DotDirectedLineEdgeGraphFormatter) + || (this.getFormatter().getEdgeById(edgeId) instanceof OdotDirectedLineEdgeGraphFormatter) + || (this.getFormatter().getEdgeById(edgeId) instanceof OdirectedLineEdgeGraphFormatter)) { + var coordenateSourceX = svgNodeSource.getAttribute("dragx"); + var coordenateSourceY = svgNodeSource.getAttribute("dragy"); + var coordenateTargetX = svgNodeTarget.getAttribute("dragx"); + var coordenateTargetY = svgNodeTarget.getAttribute("dragy"); + + var offset = parseFloat(this.getFormatter().getVertexById(this.getDataset().getEdgeById(edgeId).getNodeTarget().getId()).getDefault() + .getSize() + * this.circleDefaultRadius); + var point = this._calculateEdgePointerPosition(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, offset); + coordenateTargetX = point.x; + coordenateTargetY = point.y; + SVG.drawLine(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, this.GraphEdgeGroup, svgAttributesEdge); + + var attributesShadow = {}; + attributesShadow.id = this.getSVGEdgeId(edge.getId()); + attributesShadow["stroke-opacity"] = 0; + attributesShadow["stroke-width"] = 4; + attributesShadow["stroke"] = "black"; + svgEdge = SVG.drawLine(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, this.GraphEdgeGroup, attributesShadow); + } + + if (this.getFormatter().getEdgeById(edgeId) instanceof DirectedLineEdgeGraphFormatter + || (this.getFormatter().getEdgeById(edgeId) instanceof OdirectedLineEdgeGraphFormatter)) { + var coordenateSourceX = svgNodeSource.getAttribute("dragx"); + var coordenateSourceY = svgNodeSource.getAttribute("dragy"); + var coordenateTargetX = svgNodeTarget.getAttribute("dragx"); + var coordenateTargetY = svgNodeTarget.getAttribute("dragy"); + + var point = this._calculateEdgePointerPosition(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, offset); + coordenateTargetX = point.x; + coordenateTargetY = point.y; + + var angle = Geometry.toDegree(point.angle) + 90; + this.arrowDefaultSize = this.getFormatter().getEdgeById(edgeId).getArrowSize(); //getDefault().getArrowSize(); + var d = "-" + this.arrowDefaultSize + ",0 0,-" + parseFloat(this.arrowDefaultSize) * 2 + " " + this.arrowDefaultSize + ",0"; + + var attributes; + + if (this.getFormatter().getEdgeById(edgeId) instanceof DirectedLineEdgeGraphFormatter) { + attributes = [ + [ "fill", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], + [ "stroke", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], [ "id", this.getSVGArrowEdgeId(edgeId) ] ]; + } else { + attributes = [ + [ "fill", "#FFFFFF" ], [ "stroke", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], + [ "id", this.getSVGArrowEdgeId(edgeId) ] ]; + } + + var flechaSVGNode = SVG.drawPoligon(d, this.GraphEdgeGroup, attributes);//, ["transform", "rotate("+angle+"), translate(0,0)"]]); + flechaSVGNode.setAttribute("transform", " translate(" + coordenateTargetX + ", " + coordenateTargetY + "), rotate(" + angle + ")"); + } + ; + + if (this.getFormatter().getEdgeById(edgeId) instanceof CutDirectedLineEdgeGraphFormatter) { + var coordenateSourceX = svgNodeSource.getAttribute("dragx"); + var coordenateSourceY = svgNodeSource.getAttribute("dragy"); + var coordenateTargetX = svgNodeTarget.getAttribute("dragx"); + var coordenateTargetY = svgNodeTarget.getAttribute("dragy"); + + var point = this._calculateEdgePointerPosition(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, offset); + coordenateTargetX = point.x; + coordenateTargetY = point.y; + + var angle = Geometry.toDegree(point.angle) + 90; + + //this.arrowDefaultSize = 2; //getDefault().getArrowSize(); + var d = "-4,0 4,0 4,-2 -4,-2"; + + var flechaSVGNode = SVG.drawPoligon(d, this.GraphEdgeGroup, [ + [ "fill", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], + [ "stroke", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], [ "id", this.getSVGArrowEdgeId(edgeId) ] ]);//, ["transform", "rotate("+angle+"), translate(0,0)"]]); + flechaSVGNode.setAttribute("transform", " translate(" + coordenateTargetX + ", " + coordenateTargetY + "), rotate(" + angle + ")"); + } + ; + + if ((this.getFormatter().getEdgeById(edgeId) instanceof DotDirectedLineEdgeGraphFormatter) + || (this.getFormatter().getEdgeById(edgeId) instanceof OdotDirectedLineEdgeGraphFormatter)) { + var coordenateSourceX = svgNodeSource.getAttribute("dragx"); + var coordenateSourceY = svgNodeSource.getAttribute("dragy"); + var coordenateTargetX = svgNodeTarget.getAttribute("dragx"); + var coordenateTargetY = svgNodeTarget.getAttribute("dragy"); + var point = this._calculateEdgePointerPosition(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, offset); + coordenateTargetX = point.x; + coordenateTargetY = point.y; + var angle = Geometry.toDegree(point.angle) + 90; + // this.arrowDefaultSize = this.formatter.getEdgeById(edgeId).getArrowSize(); //getDefault().getArrowSize(); + var attributes = []; + if (this.getFormatter().getEdgeById(edgeId) instanceof OdotDirectedLineEdgeGraphFormatter) { + attributes = [ + [ "fill", "#FFFFFF" ], [ "stroke", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], + [ "id", this.getSVGArrowEdgeId(edgeId) ] ]; + } else { + attributes = [ + [ "fill", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], + [ "stroke", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], [ "id", this.getSVGArrowEdgeId(edgeId) ] ]; + } + var flechaSVGNode = SVG.drawCircle(0, 0, 4, this.GraphEdgeGroup, attributes); + flechaSVGNode.setAttribute("transform", " translate(" + coordenateTargetX + ", " + coordenateTargetY + "), rotate(" + angle + ")"); + } + ; + + var _this = this; + /** Events for the SVG edge **/ + if (svgEdge != null) { + if (this.getDataset().getEdgesCount() < this.args.maxNumberEdgesFiringEvents) { + svgEdge.addEventListener("mouseover", function() { + _this.overEdge(edgeId); + }, false); + svgEdge.addEventListener("mouseout", function() { + _this.outEdge(edgeId); + }, false); + } + } +}; + +GraphCanvas.prototype._calculateEdgePointerPosition = function(sourceX, sourceY, targetX, targetY, radius) { + var angle = Geometry.getAngleBetweenTwoPoints(sourceX, sourceY, targetX, targetY); + + /** Suponiendo el node source que este a la derecha **/ + if ((targetX - sourceX) < 0) { + var b = Geometry.getAdjacentSideOfRectangleRight(angle, radius); + targetX = parseFloat(targetX) + parseFloat(b); + arrowX = parseFloat(targetX) + parseFloat(b) + this.arrowDefaultSize / 2; + } else { + var b = Geometry.getAdjacentSideOfRectangleRight(angle, radius); + targetX = parseFloat(targetX) - parseFloat(b); + arrowX = parseFloat(targetX) - parseFloat(b) - this.arrowDefaultSize / 2; + } + + /** Suponiendo el node source que este a la arriba **/ + if ((targetY - sourceY) > 0) { + var a = Geometry.getOppositeSideOfRectangleRight(angle, radius); + targetY = parseFloat(targetY) - parseFloat(a); + arrowY = parseFloat(targetY) - parseFloat(a) - this.arrowDefaultSize / 2; + } else { + var a = Geometry.getOppositeSideOfRectangleRight(angle, radius); + targetY = parseFloat(targetY) + parseFloat(a); + arrowY = parseFloat(targetY) + parseFloat(a) - this.arrowDefaultSize / 2; + + } + + return { + "x" : arrowX, + "y" : arrowY, + "angle" : angle + }; +}; + +GraphCanvas.prototype.calculateCoordenatesBezier = function(nodeSize, x1, y1) { + var x11 = x1 - (nodeSize / 2); + var y11 = y1 - (nodeSize / 2); + + var x12 = parseFloat(x1) + parseFloat(nodeSize / 2); + var y12 = y1 - (nodeSize / 2); + + var curvePointX = (x12 - x11) / 2 + x11; + var curvePointY = y1 - (nodeSize * 2); + var d = "M" + x11 + "," + y11 + " T" + curvePointX + "," + curvePointY + " " + x12 + "," + y12; + return d; + +}; + +GraphCanvas.prototype.renderEdges = function() { + for ( var edge in this.getDataset().getEdges()) { + this.renderEdge(this.getDataset().getEdgeById(edge).getId()); + + } +}; + +GraphCanvas.prototype.getLastSelectedNode = function() { + var node = null; + if (this.getSelectedVertices().length > 0) { + var nodeId = this.getSelectedVertices()[this.getSelectedVertices().length - 1]; + node = this.getDataset().getVertexById(nodeId); + } + return node; +}; +/* + GraphCanvas.prototype.getNodeByNameAndIndex = function(node, index){ + var nodeId = this.getDataset().verticesIndex[node][index]; + var nodeItem = this.getDataset().getVertexById(nodeId); + return nodeItem; + }; + */ + +GraphCanvas.prototype.setDataset = function(dataset) { + this.dataset = dataset; +}; + +GraphCanvas.prototype.setFormatter = function(formatter) { + this.formatter = formatter; +}; + +GraphCanvas.prototype.setLayout = function(layout) { + this.layout = layout; +}; + +/** API **/ +GraphCanvas.prototype.getDataset = function() { + return this.dataset; +}; + +GraphCanvas.prototype.getFormatter = function() { + return this.formatter; +}; + +GraphCanvas.prototype.getLayout = function() { + return this.layout; +}; + +/** API DATASET **/ +GraphCanvas.prototype.addVertex = function(name, args) { + this.getDataset().addNode(name, args); +}; + +GraphCanvas.prototype.removeVertex = function(vertexId) { + this.getDataset().getVertexById(vertexId).remove(); +}; + +GraphCanvas.prototype.addEdge = function(edgeName, nodeSourceId, nodeTargetId, args) { + this.getDataset().addEdge(edgeName, nodeSourceId, nodeTargetId, args); +}; +/* + GraphCanvas.prototype.removeEdge = function(edgeId){ + this.getDataset().getEdgeById(edgeId).remove(); + }; + */ + +/** API FORMATTER **/ +GraphCanvas.prototype.getWidth = function() { + return this.getFormatter().getWidth(); +}; + +GraphCanvas.prototype.getHeight = function() { + return this.getFormatter().getHeight(); +}; + +GraphCanvas.prototype.getBackgroundImage = function() { + return this.getFormatter().getBackgroundImage(); +}; + +//GraphCanvas.prototype.setBackgroundImage = function(value){ +// this.getFormatter().setBackgroundImage(value); +//}; + +GraphCanvas.prototype.getBackgroundColor = function() { + return this.getFormatter().getBackgroundColor(); +}; + +GraphCanvas.prototype.setBackgroundColor = function() { + this.getFormatter().setBackgroundColor(value); +}; + +//GraphCanvas.prototype.setEdgeFill = function(edgeId, value){ +// this.getFormatter().getEdgeById(edgeId).getDefault().setFill(value); +//}; +// +//GraphCanvas.prototype.getEdgeFill = function(edgeId){ +// return this.getFormatter().getEdgeById(edgeId).getDefault().getFill(); +//}; + +/** VERTICES FORMATTER **/ +GraphCanvas.prototype.setVertexSize = function(vertexId, value) { + this.getFormatter().getVertexById(vertexId).getDefault().setSize(value); +}; + +GraphCanvas.prototype.getVertexSize = function(vertexId) { + return this.getFormatter().getVertexById(vertexId).getDefault().getSize(); +}; + +GraphCanvas.prototype.setVertexStroke = function(vertexId, value) { + this.getFormatter().getVertexById(vertexId).getDefault().setStroke(value); +}; + +GraphCanvas.prototype.getVertexStroke = function(vertexId) { + return this.getFormatter().getVertexById(vertexId).getDefault().getStroke(); +}; + +GraphCanvas.prototype.setVertexStrokeOpacity = function(vertexId, value) { + this.getFormatter().getVertexById(vertexId).getDefault().setStrokeOpacity(value); +}; + +GraphCanvas.prototype.getVertexStrokeOpacity = function(vertexId) { + return this.getFormatter().getVertexById(vertexId).getDefault().getStrokeOpacity(); +}; + +GraphCanvas.prototype.setVertexOpacity = function(vertexId, value) { + this.getFormatter().getVertexById(vertexId).getDefault().setOpacity(value); +}; + +GraphCanvas.prototype.getVertexOpacity = function(vertexId) { + return this.getFormatter().getVertexById(vertexId).getDefault().getOpacity(); +}; + +GraphCanvas.prototype.setVertexFill = function(vertexId, color) { + this.getFormatter().getVertexById(vertexId).getDefault().setFill(color); +}; + +GraphCanvas.prototype.getVertexFill = function(vertexId) { + return this.getFormatter().getVertexById(vertexId).getDefault().getFill(); +}; + +/** EDGES FORMATTER **/ +GraphCanvas.prototype.setEdgeSize = function(edgeId, value) { + this.getFormatter().getEdgeById(edgeId).getDefault().setSize(value); +}; + +GraphCanvas.prototype.getEdgeSize = function(edgeId) { + return this.getFormatter().getEdgeById(edgeId).getDefault().getSize(); +}; + +GraphCanvas.prototype.setEdgeStroke = function(edgeId, value) { + this.getFormatter().getEdgeById(edgeId).getDefault().setStroke(value); +}; + +GraphCanvas.prototype.getEdgeStroke = function(edgeId) { + return this.getFormatter().getEdgeById(edgeId).getDefault().getStroke(); +}; + +GraphCanvas.prototype.setEdgeStrokeOpacity = function(edgeId, value) { + this.getFormatter().getEdgeById(edgeId).getDefault().setStrokeOpacity(value); +}; + +GraphCanvas.prototype.getEdgeStrokeOpacity = function(edgeId) { + return this.getFormatter().getEdgeById(edgeId).getDefault().getStrokeOpacity(); +}; + +GraphCanvas.prototype.setEdgeFill = function(edgeId, color) { + this.getFormatter().getEdgeById(edgeId).getDefault().setFill(color); +}; + +GraphCanvas.prototype.getEdgeFill = function(edgeId) { + return this.getFormatter().getEdgeById(edgeId).getDefault().getFill(); +}; + +/** API LAYOUT **/ +GraphCanvas.prototype.setCoordinates = function(vertexId, x, y) { + return this.getLayout().getEdgeById(vertexId).setCoordinates(x, y); +}; @@ -14339,283 +14339,283 @@ MergesHPLCGraph.prototype.getMenu = function () { } }); - return actions; + return actions; +}; + + +MergesHPLCGraph.prototype.input = function () { + return DATADOC.getScatteringHPLCFrameData(); +}; + +MergesHPLCGraph.prototype.test = function (targetId) { + var mainPlotPanel = new MergesHPLCGraph({ + title : 'Scattering', + width : this.plotWidth, + height : 500, + showRangeSelector : false, + xParam : 0, + xlabel : "scattering_I", + plots : { + "scattering_I" : true, + "subtracted_I" : true, + "buffer_I" : true + } + }); + mainPlotPanel.getPanel().render(targetId); + mainPlotPanel.loadData(mainPlotPanel.input()); +}; + + +function NetworkWidget(args) { + this.id = "NetworkViewer_" + Math.random().toString().replace(".", "_"); + + this.label = true; + if (args != null) { + if (args.targetId != null) { + this.targetId = args.targetId; + } + if (args.label != null) { + this.label = args.label; + } + } + + this.onVertexOver = new Event(this); + this.onVertexOut = new Event(this); +} + +NetworkWidget.prototype.draw = function(dataset, formatter, layout) { + + this.graphCanvas = new GraphCanvas(this.id, document.getElementById(this.targetId), { + "labeled" : this.label, + "multipleSelectionEnabled" : false, + "draggingCanvasEnabled" : false + }); + this.graphCanvas.draw(dataset, formatter, layout); + + var _this = this; + this.graphCanvas.onVertexOver.attach(function(sender, nodeId) { + _this.onVertexOver.notify(nodeId); + }); + + this.graphCanvas.onVertexOut.attach(function(sender, nodeId) { + _this.onVertexOut.notify(nodeId); + }); +}; + +/** SELECT VERTICES BY NAME * */ +NetworkWidget.prototype.selectVertexByName = function(vertexName) { + var vertices = this.getDataset().getVertexByName(vertexName); + if (vertices != null) { + for ( var nodeId in vertices) { + if (vertices.hasOwnProperty(nodeId)) { + var vertexId = vertices[nodeId].getId(); + this.selectVertexById(vertexId); + } + } + } +}; + +NetworkWidget.prototype.selectVerticesByName = function(verticesName) { + for ( var i = 0; i < verticesName.length; i++) { + this.selectVertexByName(verticesName[i]); + } +}; + +/** SELECT VERTICES BY ID * */ +NetworkWidget.prototype.selectVertexById = function(vertexId) { + this.graphCanvas.selectNode(vertexId); + this.blinkVertexById(vertexId); +}; + +NetworkWidget.prototype.selectVerticesById = function(verticesId) { + for ( var i = 0; i < verticesId.length; i++) { + this.selectVertexById(verticesId[i]); + } +}; + +/** VECINDARIO * */ +NetworkWidget.prototype.selectNeighbourhood = function() { + this.selectEdgesFromVertices(); + this.selectAdjacent(); +}; + +/** DESELECT * */ +NetworkWidget.prototype.deselectNodes = function() { + this.graphCanvas.deselectNodes(); +}; + +/** SELECT ALL NODES * */ +NetworkWidget.prototype.selectAllNodes = function() { + this.getGraphCanvas().selectAllNodes(); +}; + +/** SELECT EVERYTHING * */ +NetworkWidget.prototype.selectAll = function() { + this.getGraphCanvas().selectAll(); +}; + +/** SELECT ALL EDGES * */ +NetworkWidget.prototype.selectAllEdges = function() { + this.getGraphCanvas().selectAllEdges(); +}; + +/** ZOOM * */ +NetworkWidget.prototype.setScale = function(value) { + this.graphCanvas.setScale(value); +}; + +NetworkWidget.prototype.getScale = function() { + return this.graphCanvas.getScale(value); +}; + +/** SELECT ADJACENT VERTICES FROM SELECTED VERTICES * */ +NetworkWidget.prototype.selectAdjacent = function() { + var selectedVertices = this.getGraphCanvas().getSelectedVertices(); + var edges = []; + for ( var i = 0; i < selectedVertices.length; i++) { + edges = edges.concat(this.getGraphCanvas().getDataset().getVertexById(selectedVertices[i]).getEdges()); + } + var vertices = []; + for ( i = 0; i < edges.length; i++) { + vertices.push(edges[i].getNodeSource().getId()); + vertices.push(edges[i].getNodeTarget().getId()); + } + + this.selectVerticesById(vertices); +}; + +/** SELECT EDGES FROM SELECTED VERTICES * */ +NetworkWidget.prototype.selectEdgesFromVertices = function() { + var selectedVertices = this.getGraphCanvas().getSelectedVertices(); + var edges = []; + for ( var i = 0; i < selectedVertices.length; i++) { + edges = edges.concat(this.getGraphCanvas().getDataset().getVertexById(selectedVertices[i]).getEdges()); + } + var edgesId = []; + for ( i = 0; i < edges.length; i++) { + edgesId.push(edges[i].getId()); + } + this.getGraphCanvas().selectEdges(edgesId); +}; + +/** BLINKING * */ +NetworkWidget.prototype.blinkVertexById = function(vertexId) { + this.graphCanvas.blinkVertexById(vertexId); +}; + +/** COMPONENTE CONEXA DE LOS NODOS SELECCIONADOS * */ +NetworkWidget.prototype.selectConnectedComponent = function() { + var elements = this.getConnectedComponent(); + this.selectVerticesById(elements.nodes); + this.graphCanvas.selectEdges(elements.edges); +}; + +NetworkWidget.prototype.getConnectedComponent = function() { + var nodosVisitados = {}; + var aristasVisitadas = {}; + var arrNodos = []; + var arrAristas = []; + var selectedGraphNodesId = this.getGraphCanvas().getSelectedVertices(); + for ( var i = 0; i < selectedGraphNodesId.length; i++) { + this.visitNode(selectedGraphNodesId[i], nodosVisitados, aristasVisitadas, arrNodos, arrAristas); + } + return { + nodes : arrNodos, + edges : arrAristas + }; +}; + +NetworkWidget.prototype.visitNode = function(nodeId, nodosVisitados, aristasVisitadas, arrNodos, arrAristas) { + nodosVisitados[nodeId] = true; + arrNodos.push(nodeId); + var nodeEdges = this.getDataset().getVertexById(nodeId).getEdges(); + for ( var j = 0; j < nodeEdges.length; j++) { + var edge = nodeEdges[j]; + var edgeId = edge.getId(); + if (aristasVisitadas[edgeId] == null) { + aristasVisitadas[edgeId] = true; + arrAristas.push(edgeId); + var nodeTargetId = edge.getNodeTarget().getId(); + if (nodosVisitados[nodeTargetId] == null) { + this.visitNode(nodeTargetId, nodosVisitados, aristasVisitadas, arrNodos, arrAristas); + } + var nodeSourceId = edge.getNodeSource().getId(); + if (nodosVisitados[nodeSourceId] == null) { + this.visitNode(nodeSourceId, nodosVisitados, aristasVisitadas, arrNodos, arrAristas); + } + } + } +}; + +/** COLLAPSE SELECTED VERTICES * */ +NetworkWidget.prototype.collapse = function() { + var selectedVertices = this.getGraphCanvas().getSelectedVertices(); + var xMin = -Infinity; + var xMax = Infinity; + var yMin = -Infinity; + var yMax = Infinity; + + for ( var i = 0; i < selectedVertices.length; i++) { + var vertex = this.getGraphCanvas().getLayout().getNodeById(selectedVertices[i]); + if (xMin < vertex.x) { + xMin = vertex.x; + } + if (xMax > vertex.x) { + xMax = vertex.x; + } + if (yMin < vertex.y) { + yMin = vertex.y; + } + if (yMax > vertex.y) { + yMax = vertex.y; + } + } + + var centerX = xMin - xMax; + var centerY = yMin - yMax; + var radius = (xMax - xMin) / 4; + + var count = selectedVertices.length; + var verticesCoordinates = []; + + for ( i = 0; i < selectedVertices.length; i++) { + x = centerX + radius * Math.sin(i * 2 * Math.PI / count); + y = centerY + radius * Math.cos(i * 2 * Math.PI / count); + verticesCoordinates.push({ + 'x' : x, + 'y' : y + }); + } + + for ( i = 0; i < selectedVertices.length; i++) { + this.getGraphCanvas().getLayout().getNodeById(selectedVertices[i]).setCoordinates(verticesCoordinates[i].x, verticesCoordinates[i].y); + } }; +/** SETTER FONT SIZE * */ +NetworkWidget.prototype.setVerticesFontSize = function(value) { + for ( var nodeId in this.getDataset().getVertices()) { + if (this.getDataset().getVertices().hasOwnProperty(nodeId)) { + this.getFormatter().getVertexById(nodeId).getDefault().setFontSize(value); + } + } +}; -MergesHPLCGraph.prototype.input = function () { - return DATADOC.getScatteringHPLCFrameData(); +/** GETTERS * */ +NetworkWidget.prototype.getFormatter = function() { + return this.getGraphCanvas().getFormatter(); +}; +NetworkWidget.prototype.getLayout = function() { + return this.getGraphCanvas().getLayout(); }; -MergesHPLCGraph.prototype.test = function (targetId) { - var mainPlotPanel = new MergesHPLCGraph({ - title : 'Scattering', - width : this.plotWidth, - height : 500, - showRangeSelector : false, - xParam : 0, - xlabel : "scattering_I", - plots : { - "scattering_I" : true, - "subtracted_I" : true, - "buffer_I" : true - } - }); - mainPlotPanel.getPanel().render(targetId); - mainPlotPanel.loadData(mainPlotPanel.input()); +NetworkWidget.prototype.getDataset = function() { + return this.getGraphCanvas().getDataset(); }; - -function NetworkWidget(args) { - this.id = "NetworkViewer_" + Math.random().toString().replace(".", "_"); - - this.label = true; - if (args != null) { - if (args.targetId != null) { - this.targetId = args.targetId; - } - if (args.label != null) { - this.label = args.label; - } - } - - this.onVertexOver = new Event(this); - this.onVertexOut = new Event(this); -} - -NetworkWidget.prototype.draw = function(dataset, formatter, layout) { - - this.graphCanvas = new GraphCanvas(this.id, document.getElementById(this.targetId), { - "labeled" : this.label, - "multipleSelectionEnabled" : false, - "draggingCanvasEnabled" : false - }); - this.graphCanvas.draw(dataset, formatter, layout); - - var _this = this; - this.graphCanvas.onVertexOver.attach(function(sender, nodeId) { - _this.onVertexOver.notify(nodeId); - }); - - this.graphCanvas.onVertexOut.attach(function(sender, nodeId) { - _this.onVertexOut.notify(nodeId); - }); -}; - -/** SELECT VERTICES BY NAME * */ -NetworkWidget.prototype.selectVertexByName = function(vertexName) { - var vertices = this.getDataset().getVertexByName(vertexName); - if (vertices != null) { - for ( var nodeId in vertices) { - if (vertices.hasOwnProperty(nodeId)) { - var vertexId = vertices[nodeId].getId(); - this.selectVertexById(vertexId); - } - } - } -}; - -NetworkWidget.prototype.selectVerticesByName = function(verticesName) { - for ( var i = 0; i < verticesName.length; i++) { - this.selectVertexByName(verticesName[i]); - } -}; - -/** SELECT VERTICES BY ID * */ -NetworkWidget.prototype.selectVertexById = function(vertexId) { - this.graphCanvas.selectNode(vertexId); - this.blinkVertexById(vertexId); -}; - -NetworkWidget.prototype.selectVerticesById = function(verticesId) { - for ( var i = 0; i < verticesId.length; i++) { - this.selectVertexById(verticesId[i]); - } -}; - -/** VECINDARIO * */ -NetworkWidget.prototype.selectNeighbourhood = function() { - this.selectEdgesFromVertices(); - this.selectAdjacent(); -}; - -/** DESELECT * */ -NetworkWidget.prototype.deselectNodes = function() { - this.graphCanvas.deselectNodes(); -}; - -/** SELECT ALL NODES * */ -NetworkWidget.prototype.selectAllNodes = function() { - this.getGraphCanvas().selectAllNodes(); -}; - -/** SELECT EVERYTHING * */ -NetworkWidget.prototype.selectAll = function() { - this.getGraphCanvas().selectAll(); -}; - -/** SELECT ALL EDGES * */ -NetworkWidget.prototype.selectAllEdges = function() { - this.getGraphCanvas().selectAllEdges(); -}; - -/** ZOOM * */ -NetworkWidget.prototype.setScale = function(value) { - this.graphCanvas.setScale(value); -}; - -NetworkWidget.prototype.getScale = function() { - return this.graphCanvas.getScale(value); -}; - -/** SELECT ADJACENT VERTICES FROM SELECTED VERTICES * */ -NetworkWidget.prototype.selectAdjacent = function() { - var selectedVertices = this.getGraphCanvas().getSelectedVertices(); - var edges = []; - for ( var i = 0; i < selectedVertices.length; i++) { - edges = edges.concat(this.getGraphCanvas().getDataset().getVertexById(selectedVertices[i]).getEdges()); - } - var vertices = []; - for ( i = 0; i < edges.length; i++) { - vertices.push(edges[i].getNodeSource().getId()); - vertices.push(edges[i].getNodeTarget().getId()); - } - - this.selectVerticesById(vertices); -}; - -/** SELECT EDGES FROM SELECTED VERTICES * */ -NetworkWidget.prototype.selectEdgesFromVertices = function() { - var selectedVertices = this.getGraphCanvas().getSelectedVertices(); - var edges = []; - for ( var i = 0; i < selectedVertices.length; i++) { - edges = edges.concat(this.getGraphCanvas().getDataset().getVertexById(selectedVertices[i]).getEdges()); - } - var edgesId = []; - for ( i = 0; i < edges.length; i++) { - edgesId.push(edges[i].getId()); - } - this.getGraphCanvas().selectEdges(edgesId); -}; - -/** BLINKING * */ -NetworkWidget.prototype.blinkVertexById = function(vertexId) { - this.graphCanvas.blinkVertexById(vertexId); -}; - -/** COMPONENTE CONEXA DE LOS NODOS SELECCIONADOS * */ -NetworkWidget.prototype.selectConnectedComponent = function() { - var elements = this.getConnectedComponent(); - this.selectVerticesById(elements.nodes); - this.graphCanvas.selectEdges(elements.edges); -}; - -NetworkWidget.prototype.getConnectedComponent = function() { - var nodosVisitados = {}; - var aristasVisitadas = {}; - var arrNodos = []; - var arrAristas = []; - var selectedGraphNodesId = this.getGraphCanvas().getSelectedVertices(); - for ( var i = 0; i < selectedGraphNodesId.length; i++) { - this.visitNode(selectedGraphNodesId[i], nodosVisitados, aristasVisitadas, arrNodos, arrAristas); - } - return { - nodes : arrNodos, - edges : arrAristas - }; -}; - -NetworkWidget.prototype.visitNode = function(nodeId, nodosVisitados, aristasVisitadas, arrNodos, arrAristas) { - nodosVisitados[nodeId] = true; - arrNodos.push(nodeId); - var nodeEdges = this.getDataset().getVertexById(nodeId).getEdges(); - for ( var j = 0; j < nodeEdges.length; j++) { - var edge = nodeEdges[j]; - var edgeId = edge.getId(); - if (aristasVisitadas[edgeId] == null) { - aristasVisitadas[edgeId] = true; - arrAristas.push(edgeId); - var nodeTargetId = edge.getNodeTarget().getId(); - if (nodosVisitados[nodeTargetId] == null) { - this.visitNode(nodeTargetId, nodosVisitados, aristasVisitadas, arrNodos, arrAristas); - } - var nodeSourceId = edge.getNodeSource().getId(); - if (nodosVisitados[nodeSourceId] == null) { - this.visitNode(nodeSourceId, nodosVisitados, aristasVisitadas, arrNodos, arrAristas); - } - } - } -}; - -/** COLLAPSE SELECTED VERTICES * */ -NetworkWidget.prototype.collapse = function() { - var selectedVertices = this.getGraphCanvas().getSelectedVertices(); - var xMin = -Infinity; - var xMax = Infinity; - var yMin = -Infinity; - var yMax = Infinity; - - for ( var i = 0; i < selectedVertices.length; i++) { - var vertex = this.getGraphCanvas().getLayout().getNodeById(selectedVertices[i]); - if (xMin < vertex.x) { - xMin = vertex.x; - } - if (xMax > vertex.x) { - xMax = vertex.x; - } - if (yMin < vertex.y) { - yMin = vertex.y; - } - if (yMax > vertex.y) { - yMax = vertex.y; - } - } - - var centerX = xMin - xMax; - var centerY = yMin - yMax; - var radius = (xMax - xMin) / 4; - - var count = selectedVertices.length; - var verticesCoordinates = []; - - for ( i = 0; i < selectedVertices.length; i++) { - x = centerX + radius * Math.sin(i * 2 * Math.PI / count); - y = centerY + radius * Math.cos(i * 2 * Math.PI / count); - verticesCoordinates.push({ - 'x' : x, - 'y' : y - }); - } - - for ( i = 0; i < selectedVertices.length; i++) { - this.getGraphCanvas().getLayout().getNodeById(selectedVertices[i]).setCoordinates(verticesCoordinates[i].x, verticesCoordinates[i].y); - } -}; - -/** SETTER FONT SIZE * */ -NetworkWidget.prototype.setVerticesFontSize = function(value) { - for ( var nodeId in this.getDataset().getVertices()) { - if (this.getDataset().getVertices().hasOwnProperty(nodeId)) { - this.getFormatter().getVertexById(nodeId).getDefault().setFontSize(value); - } - } -}; - -/** GETTERS * */ -NetworkWidget.prototype.getFormatter = function() { - return this.getGraphCanvas().getFormatter(); -}; -NetworkWidget.prototype.getLayout = function() { - return this.getGraphCanvas().getLayout(); -}; - -NetworkWidget.prototype.getDataset = function() { - return this.getGraphCanvas().getDataset(); -}; - -NetworkWidget.prototype.getGraphCanvas = function() { - return this.graphCanvas; -}; +NetworkWidget.prototype.getGraphCanvas = function() { + return this.graphCanvas; +}; RangeWhiskerGraph.prototype.cleanArray = GenericGraph.prototype.cleanArray; RangeWhiskerGraph.prototype.plotAxes = GenericGraph.prototype.plotAxes; @@ -14883,280 +14883,280 @@ RangeWhiskerGraph.prototype.plotWhisters = function(data, properties) { } } } - } - -}; - -RangeWhiskerGraph.prototype.draw = function(targetId, data) { - //this.calculate(data); - this.targetId = targetId; - var properties = (this.getDimensions(data)); - this.svg = SVG.createSVGCanvas(document.getElementById(this.targetId), [ [ "width", this.width ], [ "height", this.height ] ]); - this.plotAxes(properties); - this.plotWhisters(data, properties); -}; - -RangeWhiskerGraph.prototype.input = function() { - return DATADOC.getBoxWhikerData(); -}; - -RangeWhiskerGraph.prototype.test = function(targetId) { - var plot = new RangeWhiskerGraph({ - targetId : targetId, - height : 350, - width : 450, - maxBoxWidth : 25 - }); - plot.refresh(this.input()); -}; - -StdDevDyGraph.prototype.dblclick = DygraphWidget.prototype.dblclick; -StdDevDyGraph.prototype._createHTLMWrapper = DygraphWidget.prototype._createHTLMWrapper; -StdDevDyGraph.prototype.draw = DygraphWidget.prototype.draw; - -function StdDevDyGraph(targetId, args) { - this.scaled = false; - if (args == null) { - args = {}; - } - args.customBars = true; - DygraphWidget.prototype.constructor.call(this, targetId, args); -} - -StdDevDyGraph.prototype.input = function () { - return { - data : [ [ 1, [ 2, 3, 3.5 ], [ 4, 4.2, 5 ] ], [ 2, [ 5, 5.5, 5.7 ], [ 4, 4.2, 5 ] ] ], - colors : [ "blue", "red" ], - labels : [ "", 'data1', 'data2' ] - }; -}; - -StdDevDyGraph.prototype.test = function (targetId) { - var dygraphObject = new StdDevDyGraph(targetId, { - width : 500, - height : 400, - xlabel : "xLabel", - showRangeSelector : false + } + +}; + +RangeWhiskerGraph.prototype.draw = function(targetId, data) { + //this.calculate(data); + this.targetId = targetId; + var properties = (this.getDimensions(data)); + this.svg = SVG.createSVGCanvas(document.getElementById(this.targetId), [ [ "width", this.width ], [ "height", this.height ] ]); + this.plotAxes(properties); + this.plotWhisters(data, properties); +}; + +RangeWhiskerGraph.prototype.input = function() { + return DATADOC.getBoxWhikerData(); +}; + +RangeWhiskerGraph.prototype.test = function(targetId) { + var plot = new RangeWhiskerGraph({ + targetId : targetId, + height : 350, + width : 450, + maxBoxWidth : 25 + }); + plot.refresh(this.input()); +}; + +StdDevDyGraph.prototype.dblclick = DygraphWidget.prototype.dblclick; +StdDevDyGraph.prototype._createHTLMWrapper = DygraphWidget.prototype._createHTLMWrapper; +StdDevDyGraph.prototype.draw = DygraphWidget.prototype.draw; + +function StdDevDyGraph(targetId, args) { + this.scaled = false; + if (args == null) { + args = {}; + } + args.customBars = true; + DygraphWidget.prototype.constructor.call(this, targetId, args); +} + +StdDevDyGraph.prototype.input = function () { + return { + data : [ [ 1, [ 2, 3, 3.5 ], [ 4, 4.2, 5 ] ], [ 2, [ 5, 5.5, 5.7 ], [ 4, 4.2, 5 ] ] ], + colors : [ "blue", "red" ], + labels : [ "", 'data1', 'data2' ] + }; +}; + +StdDevDyGraph.prototype.test = function (targetId) { + var dygraphObject = new StdDevDyGraph(targetId, { + width : 500, + height : 400, + xlabel : "xLabel", + showRangeSelector : false + }); + + dygraphObject.draw(dygraphObject.input().data, dygraphObject.input().colors, dygraphObject.input().labels); +}; + + + +function AbinitioGrid(args) { + this.height = null; + this.width = null; + this.id = BUI.id(); + + if (args != null) { + if (args.height != null) { + this.height = args.height; + + if (args.width != null) { + this.width = args.width; + } + } + } + + this.onSelected = new Event(this); +}; + + +AbinitioGrid.prototype.refresh = function(subtractions){ + this.store.loadData(this._prepareData(subtractions)); +}; + +AbinitioGrid.prototype._prepareData = function(subtractions){ + /** Parsing data * */ + var models = []; + for (var l = 0; l < subtractions.length; l++) { + var subtraction = subtractions[l]; + for (var k = 0; k < subtraction.substractionToAbInitioModel3VOs.length; k++) { + var data = subtraction.substractionToAbInitioModel3VOs[k].abinitiomodel3VO; + if (data.averagedModel != null) { + models.push(data.averagedModel); + models[models.length - 1].type = "Reference"; + } + + if (data.shapeDeterminationModel != null) { + models.push(data.shapeDeterminationModel); + models[models.length - 1].type = "Refined"; + } + + if (data.modelList3VO != null) { + if (data.modelList3VO.modeltolist3VOs != null) { + for (var i = 0; i < data.modelList3VO.modeltolist3VOs.length; i++) { + models.push(data.modelList3VO.modeltolist3VOs[i].model3VO); + models[models.length - 1].type = "Model"; + } + } + } + } + } + return models; +}; + +AbinitioGrid.prototype.getPanel = function(){ + var _this = this; + + + var modelFields = [ "modelId", "type", "chiSqrt", "dmax", "firFile", "logFile", "fitFile", "pdbFile", "rfactor", "rg", "volume" ]; + Ext.define('AbinitioModel', { + extend : 'Ext.data.Model', + fields : modelFields + + }); + + /** + * Store in Memory + */ + this.store = Ext.create('Ext.data.Store', { + model : 'AbinitioModel', + autoload : true, + groupField : 'type' + }); + + + var groupingFeature = Ext.create('Ext.grid.feature.Grouping',{ + groupHeaderTpl: '{name} ({rows.length} model{[values.rows.length > 1 ? "s" : ""]})', + startCollapsed: true, + collapsible : true + }); + + this.grid = Ext.create('Ext.grid.Panel', { + collapsible : false, + resizable : true, + features: [groupingFeature], + autoscroll : true, + multiSelect : true, + store : this.store, + height : this.height, + width : this.width, + margin : 10, + columns : [ { + text : "Type", + dataindex : "type", + hidden : true, + renderer : function(a, b, record) { + return record.data.type; + }, + flex : 1 + }, + { + text : "ModelId", + dataindex : "modelId", + hidden : true, + renderer : function(a, b, record) { + return record.data.modelId; + + }, + flex : 1 + }, + + { + text : "chiSqrt", + dataindex : "chiSqrt", + renderer : function(a, b, record) { + if (record.data.dmax != null) { + return BUI.formatValuesUnits(record.data.chiSqrt, "", 12, this.decimals); + } + + }, + flex : 1 + }, + { + text : "Dmax", + dataindex : "dmax", + renderer : function(a, b, record) { + if (record.data.dmax != null) { + return BUI.formatValuesUnits(record.data.dmax, "nm", 12, this.decimals); + } + + }, + flex : 1 + }, { + text : "rFactor", + dataindex : "rfactor", + hidden : true, + renderer : function(a, b, record) { + if (record.data.rfactor != null) { + return record.data.rfactor; + } + }, + flex : 1 + }, { + text : "Rg", + dataindex : "rg", + renderer : function(a, b, record) { + if (record.data.rg != null) { + return BUI.formatValuesUnits(record.data.rg, "nm", 12, this.decimals); + } + + }, + flex : 1 + }, + { + text : "Volume", + dataindex : "volume", + renderer : function(a, b, record) { + if (record.raw.volume != null){ + return BUI.formatValuesUnits(record.raw.volume, '') + " nm3"; + } + }, + flex : 1 + }, + { + text : "PDB", + dataindex : "pdbFile", + renderer : function(a, b, record) { + if (record.data.pdbFile != null){ + return record.data.pdbFile.split("/")[record.data.pdbFile.split("/").length - 1]; + } + }, + flex : 1 + }, { + text : "Fir", + dataindex : "firFile", + renderer : function(a, b, record) { + if (record.data.firFile != null){ + return record.data.firFile.split("/")[record.data.firFile.split("/").length - 1]; + } + }, + flex : 1 + }, { + text : "LOG", + dataindex : "logFile", + hidden : true, + renderer : function(a, b, record) { + if (record.data.logFile != null){ + return record.data.logFile.split("/")[record.data.logFile.split("/").length - 1]; + } + }, + flex : 1 + } + ], + viewConfig : { + enableTextSelection : true, + preserveScrollOnRefresh : true, + stripeRows : true, + listeners : { + 'celldblclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + }, + 'cellclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + var models = []; + for (var i = 0; i < grid.getSelectionModel().selected.items.length; i++) { + models.push(grid.getSelectionModel().selected.items[i].raw); + } + _this.onSelected.notify(models); + } + } + } }); - - dygraphObject.draw(dygraphObject.input().data, dygraphObject.input().colors, dygraphObject.input().labels); + return this.grid; + }; - - -function AbinitioGrid(args) { - this.height = null; - this.width = null; - this.id = BUI.id(); - - if (args != null) { - if (args.height != null) { - this.height = args.height; - - if (args.width != null) { - this.width = args.width; - } - } - } - - this.onSelected = new Event(this); -}; - - -AbinitioGrid.prototype.refresh = function(subtractions){ - this.store.loadData(this._prepareData(subtractions)); -}; - -AbinitioGrid.prototype._prepareData = function(subtractions){ - /** Parsing data * */ - var models = []; - for (var l = 0; l < subtractions.length; l++) { - var subtraction = subtractions[l]; - for (var k = 0; k < subtraction.substractionToAbInitioModel3VOs.length; k++) { - var data = subtraction.substractionToAbInitioModel3VOs[k].abinitiomodel3VO; - if (data.averagedModel != null) { - models.push(data.averagedModel); - models[models.length - 1].type = "Reference"; - } - - if (data.shapeDeterminationModel != null) { - models.push(data.shapeDeterminationModel); - models[models.length - 1].type = "Refined"; - } - - if (data.modelList3VO != null) { - if (data.modelList3VO.modeltolist3VOs != null) { - for (var i = 0; i < data.modelList3VO.modeltolist3VOs.length; i++) { - models.push(data.modelList3VO.modeltolist3VOs[i].model3VO); - models[models.length - 1].type = "Model"; - } - } - } - } - } - return models; -}; - -AbinitioGrid.prototype.getPanel = function(){ - var _this = this; - - - var modelFields = [ "modelId", "type", "chiSqrt", "dmax", "firFile", "logFile", "fitFile", "pdbFile", "rfactor", "rg", "volume" ]; - Ext.define('AbinitioModel', { - extend : 'Ext.data.Model', - fields : modelFields - - }); - - /** - * Store in Memory - */ - this.store = Ext.create('Ext.data.Store', { - model : 'AbinitioModel', - autoload : true, - groupField : 'type' - }); - - - var groupingFeature = Ext.create('Ext.grid.feature.Grouping',{ - groupHeaderTpl: '{name} ({rows.length} model{[values.rows.length > 1 ? "s" : ""]})', - startCollapsed: true, - collapsible : true - }); - - this.grid = Ext.create('Ext.grid.Panel', { - collapsible : false, - resizable : true, - features: [groupingFeature], - autoscroll : true, - multiSelect : true, - store : this.store, - height : this.height, - width : this.width, - margin : 10, - columns : [ { - text : "Type", - dataindex : "type", - hidden : true, - renderer : function(a, b, record) { - return record.data.type; - }, - flex : 1 - }, - { - text : "ModelId", - dataindex : "modelId", - hidden : true, - renderer : function(a, b, record) { - return record.data.modelId; - - }, - flex : 1 - }, - - { - text : "chiSqrt", - dataindex : "chiSqrt", - renderer : function(a, b, record) { - if (record.data.dmax != null) { - return BUI.formatValuesUnits(record.data.chiSqrt, "", 12, this.decimals); - } - - }, - flex : 1 - }, - { - text : "Dmax", - dataindex : "dmax", - renderer : function(a, b, record) { - if (record.data.dmax != null) { - return BUI.formatValuesUnits(record.data.dmax, "nm", 12, this.decimals); - } - - }, - flex : 1 - }, { - text : "rFactor", - dataindex : "rfactor", - hidden : true, - renderer : function(a, b, record) { - if (record.data.rfactor != null) { - return record.data.rfactor; - } - }, - flex : 1 - }, { - text : "Rg", - dataindex : "rg", - renderer : function(a, b, record) { - if (record.data.rg != null) { - return BUI.formatValuesUnits(record.data.rg, "nm", 12, this.decimals); - } - - }, - flex : 1 - }, - { - text : "Volume", - dataindex : "volume", - renderer : function(a, b, record) { - if (record.raw.volume != null){ - return BUI.formatValuesUnits(record.raw.volume, '') + " nm3"; - } - }, - flex : 1 - }, - { - text : "PDB", - dataindex : "pdbFile", - renderer : function(a, b, record) { - if (record.data.pdbFile != null){ - return record.data.pdbFile.split("/")[record.data.pdbFile.split("/").length - 1]; - } - }, - flex : 1 - }, { - text : "Fir", - dataindex : "firFile", - renderer : function(a, b, record) { - if (record.data.firFile != null){ - return record.data.firFile.split("/")[record.data.firFile.split("/").length - 1]; - } - }, - flex : 1 - }, { - text : "LOG", - dataindex : "logFile", - hidden : true, - renderer : function(a, b, record) { - if (record.data.logFile != null){ - return record.data.logFile.split("/")[record.data.logFile.split("/").length - 1]; - } - }, - flex : 1 - } - ], - viewConfig : { - enableTextSelection : true, - preserveScrollOnRefresh : true, - stripeRows : true, - listeners : { - 'celldblclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - }, - 'cellclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - var models = []; - for (var i = 0; i < grid.getSelectionModel().selected.items.length; i++) { - models.push(grid.getSelectionModel().selected.items[i].raw); - } - _this.onSelected.notify(models); - } - } - } - }); - return this.grid; - -}; - function AdditiveGrid(args) { this.onRemoveButtonClicked = new Event(this); @@ -16236,255 +16236,255 @@ HPLCAnalysisGrid.prototype._getFramesColumn = function() { }; - - -/** - * Rigid body grid to show PDB, symmetry and multiplicity - * - * - * #onUploadFile click on upload file - */ -function AprioriRigidBodyGrid(args) { - - this.height = 250; - this.btnEditVisible = true; - this.btnRemoveVisible = true; - - if (args != null) { - if (args.height != null) { - this.height = args.height; - } - if (args.btnEditVisible != null) { - this.btnEditVisible = args.btnEditVisible; - } - if (args.btnRemoveVisible != null) { - this.btnRemoveVisible = args.btnRemoveVisible; - } - } - - /** Events **/ - this.onUploadFile = new Event(this); - this.onRemove = new Event(this); -} - -AprioriRigidBodyGrid.prototype._getColumns = function() { -}; - -AprioriRigidBodyGrid.prototype._getTopButtons = function() { - var _this = this; - /** Actions buttons **/ - var actions = []; - - /** ADD BUTTON **/ - actions.push(Ext.create('Ext.Action', { - icon : '../images/add.png', - text : 'Add', - disabled : false, - handler : function(widget, event) { - _this.onAddButtonClicked.notify(); - } - })); - - return actions; -}; - -AprioriRigidBodyGrid.prototype.refresh = function(macromolecule) { - this.macromolecule = macromolecule; - if (macromolecule != null){ - this.pdbStore.loadData(macromolecule.structure3VOs); - } -}; - -AprioriRigidBodyGrid.prototype._prepareData = function() { - var data = []; - for ( var i = 0; i < this.features.length; i++) { - data.push(this.features[i]); - } - return data; -}; - -AprioriRigidBodyGrid.prototype._getPlugins = function() { - var _this = this; - var plugins = []; - plugins.push(Ext.create('Ext.grid.plugin.RowEditing', { - clicksToEdit : 1, - listeners : { - validateedit : function(grid, e) { - /** Comments are always updatable* */ - e.record.raw.symmetry = e.newValues.symmetry; - e.record.raw.multiplicity = e.newValues.multiplicity; - - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, proposal) { - BIOSAXS.proposal.setItems(proposal); - _this.refresh(BIOSAXS.proposal.getMacromoleculeById(_this.macromolecule.macromoleculeId)); - _this.panel.setLoading(false); - }); - adapter.onError.attach(function() { - alert("Error"); - }); - - _this.panel.setLoading(); - adapter.saveStructure(e.record.raw); - } - } - })); - return plugins; -}; - -AprioriRigidBodyGrid.prototype.getPanel = function() { - var _this = this; - - this.pdbStore = Ext.create('Ext.data.Store', { - fields : [ 'filePath', 'structureId', 'structureType', 'symmetry', 'structureId', 'name', 'multiplicity' ], - groupField : 'structureType', - sorters : { - property : 'structureId', - direction : 'DESC' - } - }); - - var groupingFeature = Ext.create('Ext.grid.feature.Grouping', { - groupHeaderTpl : Ext.create('Ext.XTemplate', - "
{name:this.formatName}
", { - formatName : function(name) { - return name; - } - }), - hideGroupedHeader : true, - startCollapsed : false - }); - - this.panel = Ext.create('Ext.grid.Panel', { - margin : "15 10 0 10", - height : this.height, - store : this.pdbStore, - plugins : _this._getPlugins(), - tbar : [ { - text : 'Add Modeling Option (PDB)', - icon : '../images/add.png', - handler : function() { - _this.onUploadFile.notify('PDB', 'Upload PDB File'); - } - } - - ], - columns : [ - { - text : "structureId", - flex : 0.2, - hidden : true, - dataIndex : 'structureId', - sortable : true - }, - { - text : "File", - flex : 0.5, - dataIndex : 'filePath', - sortable : true, - hidden : true - }, - { - text : "PDB", - flex : 0.4, - dataIndex : 'name', - sortable : true - }, - { - text : "Symmetry", - flex : 0.2, - dataIndex : 'symmetry', - sortable : true, - editor : { - xtype : 'combobox', - typeAhead : true, - triggerAction : 'all', - selectOnTab : true, - store : [ [ "P1", "P1" ], [ "P2", "P2" ], [ "P3", "P3" ], [ "P4", "P4" ], [ "P5", "P5" ], [ "P6", "P6" ], [ "P32", "P32" ], [ "P42", "P42" ], - [ "P52", "P52" ], [ "P62", "P62" ], [ "P222", "P222" ] ], - } - }, { - text : "Multiplicity", - flex : 0.2, - dataIndex : 'multiplicity', - sortable : true, - editor : { - xtype : 'textfield' - } - - }, { - text : "Subunit", - flex : 0.2, - dataIndex : 'isSubunit', - sortable : true, - hidden : true - }, { - text : "Type", - flex : 0.2, - dataIndex : 'structureType', - sortable : true, - hidden : true - }, - - { - id : this.id + 'REMOVE', - flex : 0.2, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - return BUI.getRedButton('REMOVE'); - } - }, ], - - listeners : { - itemdblclick : function(dataview, record, item, e) { - _this._editExperiment(record.raw.experimentId); - }, - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'REMOVE') { - var dataAdapter = new BiosaxsDataAdapter(); - dataAdapter.onSuccess.attach(function() { - _this.panel.setLoading(false); - _this.onRemove.notify(); - }); - _this.panel.setLoading("Removing PDB file"); - dataAdapter.removeStructure(record.data.structureId); - } - - } - }, - viewConfig : { - getRowClass : function(record, rowIdx, params, store) { - if (record.raw.isSubunit != null) { - return "blue-row"; - } - } - } - }); - - return this.panel; -}; - - - - -AprioriRigidBodyGrid.prototype.input = function() { - return { - proposal : DATADOC.getProposal_10(), - dewars : DATADOC.getDewars_10() - - }; -}; - -AprioriRigidBodyGrid.prototype.test = function(targetId) { - var AprioriRigidBodyGrid = new AprioriRigidBodyGrid({ - height : 150 - }); - BIOSAXS.proposal = new Proposal(AprioriRigidBodyGrid.input().proposal); - var panel = AprioriRigidBodyGrid.getPanel(AprioriRigidBodyGrid.input().dewars); - panel.render(targetId); - -}; + + +/** + * Rigid body grid to show PDB, symmetry and multiplicity + * + * + * #onUploadFile click on upload file + */ +function AprioriRigidBodyGrid(args) { + + this.height = 250; + this.btnEditVisible = true; + this.btnRemoveVisible = true; + + if (args != null) { + if (args.height != null) { + this.height = args.height; + } + if (args.btnEditVisible != null) { + this.btnEditVisible = args.btnEditVisible; + } + if (args.btnRemoveVisible != null) { + this.btnRemoveVisible = args.btnRemoveVisible; + } + } + + /** Events **/ + this.onUploadFile = new Event(this); + this.onRemove = new Event(this); +} + +AprioriRigidBodyGrid.prototype._getColumns = function() { +}; + +AprioriRigidBodyGrid.prototype._getTopButtons = function() { + var _this = this; + /** Actions buttons **/ + var actions = []; + + /** ADD BUTTON **/ + actions.push(Ext.create('Ext.Action', { + icon : '../images/add.png', + text : 'Add', + disabled : false, + handler : function(widget, event) { + _this.onAddButtonClicked.notify(); + } + })); + + return actions; +}; + +AprioriRigidBodyGrid.prototype.refresh = function(macromolecule) { + this.macromolecule = macromolecule; + if (macromolecule != null){ + this.pdbStore.loadData(macromolecule.structure3VOs); + } +}; + +AprioriRigidBodyGrid.prototype._prepareData = function() { + var data = []; + for ( var i = 0; i < this.features.length; i++) { + data.push(this.features[i]); + } + return data; +}; + +AprioriRigidBodyGrid.prototype._getPlugins = function() { + var _this = this; + var plugins = []; + plugins.push(Ext.create('Ext.grid.plugin.RowEditing', { + clicksToEdit : 1, + listeners : { + validateedit : function(grid, e) { + /** Comments are always updatable* */ + e.record.raw.symmetry = e.newValues.symmetry; + e.record.raw.multiplicity = e.newValues.multiplicity; + + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, proposal) { + BIOSAXS.proposal.setItems(proposal); + _this.refresh(BIOSAXS.proposal.getMacromoleculeById(_this.macromolecule.macromoleculeId)); + _this.panel.setLoading(false); + }); + adapter.onError.attach(function() { + alert("Error"); + }); + + _this.panel.setLoading(); + adapter.saveStructure(e.record.raw); + } + } + })); + return plugins; +}; + +AprioriRigidBodyGrid.prototype.getPanel = function() { + var _this = this; + + this.pdbStore = Ext.create('Ext.data.Store', { + fields : [ 'filePath', 'structureId', 'structureType', 'symmetry', 'structureId', 'name', 'multiplicity' ], + groupField : 'structureType', + sorters : { + property : 'structureId', + direction : 'DESC' + } + }); + + var groupingFeature = Ext.create('Ext.grid.feature.Grouping', { + groupHeaderTpl : Ext.create('Ext.XTemplate', + "
{name:this.formatName}
", { + formatName : function(name) { + return name; + } + }), + hideGroupedHeader : true, + startCollapsed : false + }); + + this.panel = Ext.create('Ext.grid.Panel', { + margin : "15 10 0 10", + height : this.height, + store : this.pdbStore, + plugins : _this._getPlugins(), + tbar : [ { + text : 'Add Modeling Option (PDB)', + icon : '../images/add.png', + handler : function() { + _this.onUploadFile.notify('PDB', 'Upload PDB File'); + } + } + + ], + columns : [ + { + text : "structureId", + flex : 0.2, + hidden : true, + dataIndex : 'structureId', + sortable : true + }, + { + text : "File", + flex : 0.5, + dataIndex : 'filePath', + sortable : true, + hidden : true + }, + { + text : "PDB", + flex : 0.4, + dataIndex : 'name', + sortable : true + }, + { + text : "Symmetry", + flex : 0.2, + dataIndex : 'symmetry', + sortable : true, + editor : { + xtype : 'combobox', + typeAhead : true, + triggerAction : 'all', + selectOnTab : true, + store : [ [ "P1", "P1" ], [ "P2", "P2" ], [ "P3", "P3" ], [ "P4", "P4" ], [ "P5", "P5" ], [ "P6", "P6" ], [ "P32", "P32" ], [ "P42", "P42" ], + [ "P52", "P52" ], [ "P62", "P62" ], [ "P222", "P222" ] ], + } + }, { + text : "Multiplicity", + flex : 0.2, + dataIndex : 'multiplicity', + sortable : true, + editor : { + xtype : 'textfield' + } + + }, { + text : "Subunit", + flex : 0.2, + dataIndex : 'isSubunit', + sortable : true, + hidden : true + }, { + text : "Type", + flex : 0.2, + dataIndex : 'structureType', + sortable : true, + hidden : true + }, + + { + id : this.id + 'REMOVE', + flex : 0.2, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + return BUI.getRedButton('REMOVE'); + } + }, ], + + listeners : { + itemdblclick : function(dataview, record, item, e) { + _this._editExperiment(record.raw.experimentId); + }, + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'REMOVE') { + var dataAdapter = new BiosaxsDataAdapter(); + dataAdapter.onSuccess.attach(function() { + _this.panel.setLoading(false); + _this.onRemove.notify(); + }); + _this.panel.setLoading("Removing PDB file"); + dataAdapter.removeStructure(record.data.structureId); + } + + } + }, + viewConfig : { + getRowClass : function(record, rowIdx, params, store) { + if (record.raw.isSubunit != null) { + return "blue-row"; + } + } + } + }); + + return this.panel; +}; + + + + +AprioriRigidBodyGrid.prototype.input = function() { + return { + proposal : DATADOC.getProposal_10(), + dewars : DATADOC.getDewars_10() + + }; +}; + +AprioriRigidBodyGrid.prototype.test = function(targetId) { + var AprioriRigidBodyGrid = new AprioriRigidBodyGrid({ + height : 150 + }); + BIOSAXS.proposal = new Proposal(AprioriRigidBodyGrid.input().proposal); + var panel = AprioriRigidBodyGrid.getPanel(AprioriRigidBodyGrid.input().dewars); + panel.render(targetId); + +}; /** * It shows buffer grid with a top bar with "Add" button @@ -16513,159 +16513,552 @@ function BufferGrid(args) { this.tbar = args.tbar; } - if (args.collapsed != null) { - this.collapsed = args.collapsed; - } + if (args.collapsed != null) { + this.collapsed = args.collapsed; + } + + if (args.width != null) { + this.width = args.width; + } + } +} + +BufferGrid.prototype._edit = function(bufferId) { + var _this = this; + var window = new BufferWindow(); + window.onSuccess.attach(function(sender, proposal) { + _this.store.loadData(BIOSAXS.proposal.getBuffers()); + }); + window.draw(BIOSAXS.proposal.getBufferById(bufferId)); +}; + +BufferGrid.prototype.refresh = function(buffers) { + this.store.loadData(this._prepareData(buffers), false); +}; + +BufferGrid.prototype._prepareData = function(buffers) { + return buffers; +}; + +BufferGrid.prototype._getTbar = function() { + var _this = this; + var actions = []; + + actions.push(Ext.create('Ext.Action', { + icon : '../images/add.png', + text : 'Add buffer', + disabled : false, + handler : function(widget, event) { + var window = new BufferWindow(); + window.onSuccess.attach(function(sender) { + _this.store.loadData(BIOSAXS.proposal.getBuffers()); + }); + window.draw({}); + } + })); + return actions; +}; + +BufferGrid.prototype.getPanel = function(buffers) { + var _this = this; + + this.store = Ext.create('Ext.data.Store', { + fields : [ 'bufferId', 'acronym', 'name', 'composition' ], + data : buffers + }); + + this.store.sort('acronym'); + + var type = 'Ext.grid.Panel'; + if (this.searchBar == true) { + type = 'Ext.ux.LiveSearchGridPanel'; + } + + this.grid = Ext.create(type, { + title : 'Buffers', + collapsible : true, + collapsed : this.collapsed, + store : this.store, + height : this.height, + width : this.width, + columns : [ + /*{ + text : '', + dataIndex : 'bufferId', + width : 20, + renderer : function(val, y, sample) { + return BUI.getRectangleColorDIV(BIOSAXS.proposal.bufferColors[val], 10, 10); + } + },*/ + { + text : 'Acronym', + dataIndex : 'acronym', + flex : 1 + }, { + text : 'Name', + dataIndex : 'name', + flex : 1, + hidden : true + }, { + text : 'Composition', + dataIndex : 'composition', + flex : 1, + hidden : true + }, { + id : _this.id + 'buttonEditBuffer', + width : 80, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + return BUI.getGreenButton('EDIT'); + } + }, { + id : _this.id + 'buttonRemoveBuffer', + width : 85, + hidden : true, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + return BUI.getRedButton('REMOVE'); + } + } ], + flex : 1, + viewConfig : { + stripeRows : true, + listeners : { + 'celldblclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + _this._edit(record.data.bufferId); + }, + 'cellclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEditBuffer') { + _this._edit(record.data.bufferId); + } + + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemoveBuffer') { + BUI.showBetaWarning(); + } + } + + } + } + }); + + /** Adding the tbar **/ + if (this.tbar) { + this.grid.addDocked({ + xtype : 'toolbar', + items : this._getTbar() + }); + } + return this.grid; +}; + +BufferGrid.prototype.input = function() { + return new MacromoleculeGrid().input(); +}; + +BufferGrid.prototype.test = function(targetId) { + var bufferGrid = new BufferGrid({ + width : 800, + height : 350, + collapsed : false, + tbar : true + }); + + BIOSAXS.proposal = new Proposal(bufferGrid.input().proposal); + var panel = bufferGrid.getPanel(BIOSAXS.proposal.macromolecules); + panel.render(targetId); +}; + +/** + * A shipment may contains one or more cases where stock solutions and sample plates are stored + * + * @height + * @btnEditVisible + * @btnRemoveVisible + * + * #onEditButtonClicked + * #onAddButtonClicked + * #onRemoveButtonClicked + * #onDuplicateButtonClicked + */ +function CaseGrid(args) { + + this.height = 100; + this.btnEditVisible = true; + this.btnRemoveVisible = true; + + if (args != null) { + if (args.height != null) { + this.height = args.height; + } + if (args.btnEditVisible != null) { + this.btnEditVisible = args.btnEditVisible; + } + if (args.btnRemoveVisible != null) { + this.btnRemoveVisible = args.btnRemoveVisible; + } + } + + /** Events **/ + this.onEditButtonClicked = new Event(this); + this.onAddButtonClicked = new Event(this); + this.onRemoveButtonClicked = new Event(this); + this.onDuplicateButtonClicked = new Event(this); +} + +CaseGrid.prototype._getColumns = function() { + var _this = this; + + function actionItemRenderer(value, meta, record, rowIx, ColIx, store) { + /*if (record.raw.specimen3VOs.length > 0){ + return 'x-hide-display'; + }*/ + } + + var columns = [ + { + header : 'Code', + dataIndex : 'code', + name : 'code', + type : 'string', + flex : 1 + }, + { + header : 'Bar Code', + dataIndex : 'barCode', + name : 'barCode', + type : 'string', + flex : 1, + hidden : true + }, + { + header : 'BeamLine', + dataIndex : 'barCode', + type : 'string', + flex : 1, + renderer : function(comp, val, record) { + if (record.raw.sessionVO != null) { + return "" + record.raw.sessionVO.beamlineName + ""; + } + } + }, + { + header : 'Session', + dataIndex : 'barCode', + type : 'string', + flex : 1, + renderer : function(comp, val, record) { + if (record.raw.sessionVO != null) { + return "" + moment(record.raw.sessionVO.startDate).format("MMM Do YY") + ""; + } + } + }, + { + header : 'Status', + dataIndex : 'dewarStatus', + name : 'dewarStatus', + type : 'string', + flex : 1, + renderer : function(comp, val, record) { + if (new String(record.raw.dewarStatus).toUpperCase() == 'OPENED') { + return "" + new String(record.raw.dewarStatus).toUpperCase() + ""; + } + return "" + new String(record.raw.dewarStatus).toUpperCase() + ""; + } + }, + { + header : 'Type', + dataIndex : 'type', + name : 'type', + type : 'string', + flex : 1, + hidden : true + }, + { + header : 'Sample Plates', + dataIndex : 'plates', + name : 'plates', + type : 'string', + flex : 1, + hidden : true + }, + { + header : 'Stock Solutions', + dataIndex : 'plates', + name : 'plates', + type : 'string', + width : 100, + renderer : function(comp, val, record) { + var html = "
"; + var stockSolutions = BIOSAXS.proposal.getStockSolutionsByDewarId(record.raw.dewarId); + html = html + "" + stockSolutions.length + " x"; + return html + "
"; + } + }, { + header : 'isStorageDewar', + dataIndex : 'isStorageDewar', + name : 'isStorageDewar', + type : 'string', + flex : 1, + hidden : true + }, { + header : 'Tracking Number From Synchrotron', + dataIndex : 'trackingNumberFromSynchrotron', + name : 'trackingNumberFromSynchrotron', + type : 'string', + flex : 1, + hidden : true + }, { + header : 'Tracking Number To Synchrotron', + dataIndex : 'trackingNumberToSynchrotron', + name : 'trackingNumberToSynchrotron', + type : 'string', + flex : 1, + hidden : true + }, { + header : 'Storage Location', + dataIndex : 'storageLocation', + name : 'storageLocation', + type : 'string', + flex : 1, + hidden : false + }, { + header : 'Comments', + dataIndex : 'comments', + name : 'comments', + type : 'string', + flex : 1, + hidden : false + } + ]; + + if (this.btnEditVisible) { + columns.push({ + id : _this.id + 'buttonEdit', + text : '', + hidden : !_this.btnEditVisible, + width : 85, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + return BUI.getGreenButton('EDIT'); + } + }); + } - if (args.width != null) { - this.width = args.width; - } + if (this.btnRemoveVisible) { + columns.push({ + id : _this.id + 'buttonRemove', + width : 85, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + if (_this.btnRemoveVisible) { + return BUI.getRedButton('REMOVE'); + } + } + }); } -} -BufferGrid.prototype._edit = function(bufferId) { - var _this = this; - var window = new BufferWindow(); - window.onSuccess.attach(function(sender, proposal) { - _this.store.loadData(BIOSAXS.proposal.getBuffers()); + columns.push({ + dataIndex : 'comments', + type : 'string', + width : 85, + hidden : false, + renderer : function(comp, val, record) { + return BUI.getBlueButton("LABELS", { + href : BUI.getPrintcomponentURL(record.raw.dewarId) + }); + } }); - window.draw(BIOSAXS.proposal.getBufferById(bufferId)); -}; - -BufferGrid.prototype.refresh = function(buffers) { - this.store.loadData(this._prepareData(buffers), false); -}; -BufferGrid.prototype._prepareData = function(buffers) { - return buffers; + return columns; }; -BufferGrid.prototype._getTbar = function() { +CaseGrid.prototype._getTopButtons = function() { var _this = this; + /** Actions buttons **/ var actions = []; + /** ADD BUTTON **/ actions.push(Ext.create('Ext.Action', { icon : '../images/add.png', - text : 'Add buffer', + text : 'Add', disabled : false, handler : function(widget, event) { - var window = new BufferWindow(); - window.onSuccess.attach(function(sender) { - _this.store.loadData(BIOSAXS.proposal.getBuffers()); - }); - window.draw({}); + _this.onAddButtonClicked.notify(); } })); + return actions; }; -BufferGrid.prototype.getPanel = function(buffers) { - var _this = this; +CaseGrid.prototype.refresh = function(dewars) { + this.features = dewars; + this.store.loadData(this._prepareData(dewars), false); +}; - this.store = Ext.create('Ext.data.Store', { - fields : [ 'bufferId', 'acronym', 'name', 'composition' ], - data : buffers - }); +CaseGrid.prototype._sort = function(store) { + store.sort('dewarId', 'DESC'); +}; - this.store.sort('acronym'); +CaseGrid.prototype._prepareData = function() { + var data = []; + for ( var i = 0; i < this.features.length; i++) { + data.push(this.features[i]); + } + return data; +}; - var type = 'Ext.grid.Panel'; - if (this.searchBar == true) { - type = 'Ext.ux.LiveSearchGridPanel'; +CaseGrid.prototype.getPanel = function(dewars, plates) { + this.features = dewars; + this.plates = plates; + return this._renderGrid(); +}; + +CaseGrid.prototype._edit = function(dewar) { + var _this = this; + var caseWindow = new CaseWindow(); + /**SAVED **/ + caseWindow.onSaved.attach(function(sender, dewar) { + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, shipment) { + _this.refresh(shipment.dewarVOs); + }); + adapter.saveCase(BIOSAXS.proposal.getShipmentByDewarId(dewar.dewarId).shippingId, dewar); + }); + caseWindow.draw(dewar); +}; + +CaseGrid.prototype._getStoreFields = function(data) { + return [ { + name : 'dewarId', + type : 'string' + }, { + name : 'barCode', + type : 'string' + }, { + name : 'code', + type : 'string' + }, { + name : 'comments', + type : 'string' + }, { + name : 'dewarStatus', + type : 'string' + }, { + name : 'isStorageDewar', + type : 'string' + }, { + name : 'plates', + type : 'string' + }, { + name : 'transportValue', + type : 'string' + }, { + name : 'trackingNumberFromSynchrotron', + type : 'string' + }, { + name : 'trackingNumberToSynchrotron', + type : 'string' + }, { + name : 'timeStamp', + type : 'string' + }, { + name : 'storageLocation', + type : 'string' + }, { + name : 'type', + type : 'string' } - this.grid = Ext.create(type, { - title : 'Buffers', - collapsible : true, - collapsed : this.collapsed, - store : this.store, + ]; +}; + +CaseGrid.prototype._renderGrid = function() { + var _this = this; + + /** Store **/ + var data = this._prepareData(); + this.store = Ext.create('Ext.data.Store', { + fields : this._getStoreFields(data), + autoload : true, + data : data + }); + this._sort(this.store); + + this.store.loadData(data, false); + + this.grid = Ext.create('Ext.grid.Panel', { + style : { + padding : 5 + }, height : this.height, - width : this.width, - columns : [ - /*{ - text : '', - dataIndex : 'bufferId', - width : 20, - renderer : function(val, y, sample) { - return BUI.getRectangleColorDIV(BIOSAXS.proposal.bufferColors[val], 10, 10); - } - },*/ - { - text : 'Acronym', - dataIndex : 'acronym', - flex : 1 - }, { - text : 'Name', - dataIndex : 'name', - flex : 1, - hidden : true - }, { - text : 'Composition', - dataIndex : 'composition', - flex : 1, - hidden : true - }, { - id : _this.id + 'buttonEditBuffer', - width : 80, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - return BUI.getGreenButton('EDIT'); - } - }, { - id : _this.id + 'buttonRemoveBuffer', - width : 85, - hidden : true, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - return BUI.getRedButton('REMOVE'); - } - } ], - flex : 1, + store : this.store, + columns : this._getColumns(), viewConfig : { stripeRows : true, listeners : { - 'celldblclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - _this._edit(record.data.bufferId); + itemdblclick : function(dataview, record, item, e) { + _this._edit(record.raw); }, - 'cellclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEditBuffer') { - _this._edit(record.data.bufferId); + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEdit') { + _this._edit(record.raw); } - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemoveBuffer') { - BUI.showBetaWarning(); + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemove') { + _this.onRemoveButtonClicked.notify(_this.store.getAt(rowIndex).raw.dewarId); } } - } + }, + selModel : { + mode : 'SINGLE' } }); - /** Adding the tbar **/ - if (this.tbar) { - this.grid.addDocked({ - xtype : 'toolbar', - items : this._getTbar() - }); - } + var actions = _this._getTopButtons(); + this.grid.addDocked({ + xtype : 'toolbar', + items : actions + }); + + this.grid.getSelectionModel().on({ + selectionchange : function(sm, selections) { + if (selections.length) { + for ( var i = 0; i < actions.length; i++) { + if (actions[i].enable) { + actions[i].enable(); + } + } + } else { + for ( var i = 0; i < actions.length; i++) { + if (actions[i].alwaysEnabled == false) { + if (actions[i].disable) { + actions[i].disable(); + } + } + } + } + } + }); return this.grid; }; -BufferGrid.prototype.input = function() { - return new MacromoleculeGrid().input(); +CaseGrid.prototype.input = function() { + return { + proposal : DATADOC.getProposal_10(), + dewars : DATADOC.getDewars_10() + + }; }; -BufferGrid.prototype.test = function(targetId) { - var bufferGrid = new BufferGrid({ - width : 800, - height : 350, - collapsed : false, - tbar : true +CaseGrid.prototype.test = function(targetId) { + var CaseGrid = new CaseGrid({ + height : 150 }); - - BIOSAXS.proposal = new Proposal(bufferGrid.input().proposal); - var panel = bufferGrid.getPanel(BIOSAXS.proposal.macromolecules); + BIOSAXS.proposal = new Proposal(CaseGrid.input().proposal); + var panel = CaseGrid.getPanel(CaseGrid.input().dewars); panel.render(targetId); + }; /** @@ -16680,7 +17073,7 @@ BufferGrid.prototype.test = function(targetId) { * #onRemoveButtonClicked * #onDuplicateButtonClicked */ -function CaseGrid(args) { +function ExampleGrid(args) { this.height = 100; this.btnEditVisible = true; @@ -16705,7 +17098,7 @@ function CaseGrid(args) { this.onDuplicateButtonClicked = new Event(this); } -CaseGrid.prototype._getColumns = function() { +ExampleGrid.prototype._getColumns = function() { var _this = this; function actionItemRenderer(value, meta, record, rowIx, ColIx, store) { @@ -16872,7 +17265,7 @@ CaseGrid.prototype._getColumns = function() { return columns; }; -CaseGrid.prototype._getTopButtons = function() { +ExampleGrid.prototype._getTopButtons = function() { var _this = this; /** Actions buttons **/ var actions = []; @@ -16890,16 +17283,16 @@ CaseGrid.prototype._getTopButtons = function() { return actions; }; -CaseGrid.prototype.refresh = function(dewars) { +ExampleGrid.prototype.refresh = function(dewars) { this.features = dewars; this.store.loadData(this._prepareData(dewars), false); }; -CaseGrid.prototype._sort = function(store) { +ExampleGrid.prototype._sort = function(store) { store.sort('dewarId', 'DESC'); }; -CaseGrid.prototype._prepareData = function() { +ExampleGrid.prototype._prepareData = function() { var data = []; for ( var i = 0; i < this.features.length; i++) { data.push(this.features[i]); @@ -16907,27 +17300,66 @@ CaseGrid.prototype._prepareData = function() { return data; }; -CaseGrid.prototype.getPanel = function(dewars, plates) { - this.features = dewars; - this.plates = plates; - return this._renderGrid(); -}; +ExampleGrid.prototype.getPanel = function() { + this.grid = Ext.create('Ext.grid.Panel', { + style : { + padding : 5 + }, + height : this.height, + store : this.store, + columns : this._getColumns(), + viewConfig : { + stripeRows : true, + listeners : { + itemdblclick : function(dataview, record, item, e) { + _this._edit(record.raw); + }, + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEdit') { + _this._edit(record.raw); + } -CaseGrid.prototype._edit = function(dewar) { - var _this = this; - var caseWindow = new CaseWindow(); - /**SAVED **/ - caseWindow.onSaved.attach(function(sender, dewar) { - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, shipment) { - _this.refresh(shipment.dewarVOs); - }); - adapter.saveCase(BIOSAXS.proposal.getShipmentByDewarId(dewar.dewarId).shippingId, dewar); + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemove') { + _this.onRemoveButtonClicked.notify(_this.store.getAt(rowIndex).raw.dewarId); + } + } + } + }, + selModel : { + mode : 'SINGLE' + } }); - caseWindow.draw(dewar); + + var actions = _this._getTopButtons(); + this.grid.addDocked({ + xtype : 'toolbar', + items : actions + }); + + this.grid.getSelectionModel().on({ + selectionchange : function(sm, selections) { + if (selections.length) { + for ( var i = 0; i < actions.length; i++) { + if (actions[i].enable) { + actions[i].enable(); + } + } + } else { + for ( var i = 0; i < actions.length; i++) { + if (actions[i].alwaysEnabled == false) { + if (actions[i].disable) { + actions[i].disable(); + } + } + } + } + } + }); + return this.grid; }; -CaseGrid.prototype._getStoreFields = function(data) { + +ExampleGrid.prototype._getStoreFields = function(data) { return [ { name : 'dewarId', type : 'string' @@ -16972,7 +17404,7 @@ CaseGrid.prototype._getStoreFields = function(data) { ]; }; -CaseGrid.prototype._renderGrid = function() { +ExampleGrid.prototype._renderGrid = function() { var _this = this; /** Store **/ @@ -17043,7 +17475,7 @@ CaseGrid.prototype._renderGrid = function() { return this.grid; }; -CaseGrid.prototype.input = function() { +ExampleGrid.prototype.input = function() { return { proposal : DATADOC.getProposal_10(), dewars : DATADOC.getDewars_10() @@ -17051,447 +17483,15 @@ CaseGrid.prototype.input = function() { }; }; -CaseGrid.prototype.test = function(targetId) { - var CaseGrid = new CaseGrid({ +ExampleGrid.prototype.test = function(targetId) { + var ExampleGrid = new ExampleGrid({ height : 150 }); - BIOSAXS.proposal = new Proposal(CaseGrid.input().proposal); - var panel = CaseGrid.getPanel(CaseGrid.input().dewars); - panel.render(targetId); - -}; - -/** - * A shipment may contains one or more cases where stock solutions and sample plates are stored - * - * @height - * @btnEditVisible - * @btnRemoveVisible - * - * #onEditButtonClicked - * #onAddButtonClicked - * #onRemoveButtonClicked - * #onDuplicateButtonClicked - */ -function ExampleGrid(args) { - - this.height = 100; - this.btnEditVisible = true; - this.btnRemoveVisible = true; - - if (args != null) { - if (args.height != null) { - this.height = args.height; - } - if (args.btnEditVisible != null) { - this.btnEditVisible = args.btnEditVisible; - } - if (args.btnRemoveVisible != null) { - this.btnRemoveVisible = args.btnRemoveVisible; - } - } - - /** Events **/ - this.onEditButtonClicked = new Event(this); - this.onAddButtonClicked = new Event(this); - this.onRemoveButtonClicked = new Event(this); - this.onDuplicateButtonClicked = new Event(this); -} - -ExampleGrid.prototype._getColumns = function() { - var _this = this; - - function actionItemRenderer(value, meta, record, rowIx, ColIx, store) { - /*if (record.raw.specimen3VOs.length > 0){ - return 'x-hide-display'; - }*/ - } - - var columns = [ - { - header : 'Code', - dataIndex : 'code', - name : 'code', - type : 'string', - flex : 1 - }, - { - header : 'Bar Code', - dataIndex : 'barCode', - name : 'barCode', - type : 'string', - flex : 1, - hidden : true - }, - { - header : 'BeamLine', - dataIndex : 'barCode', - type : 'string', - flex : 1, - renderer : function(comp, val, record) { - if (record.raw.sessionVO != null) { - return "" + record.raw.sessionVO.beamlineName + ""; - } - } - }, - { - header : 'Session', - dataIndex : 'barCode', - type : 'string', - flex : 1, - renderer : function(comp, val, record) { - if (record.raw.sessionVO != null) { - return "" + moment(record.raw.sessionVO.startDate).format("MMM Do YY") + ""; - } - } - }, - { - header : 'Status', - dataIndex : 'dewarStatus', - name : 'dewarStatus', - type : 'string', - flex : 1, - renderer : function(comp, val, record) { - if (new String(record.raw.dewarStatus).toUpperCase() == 'OPENED') { - return "" + new String(record.raw.dewarStatus).toUpperCase() + ""; - } - return "" + new String(record.raw.dewarStatus).toUpperCase() + ""; - } - }, - { - header : 'Type', - dataIndex : 'type', - name : 'type', - type : 'string', - flex : 1, - hidden : true - }, - { - header : 'Sample Plates', - dataIndex : 'plates', - name : 'plates', - type : 'string', - flex : 1, - hidden : true - }, - { - header : 'Stock Solutions', - dataIndex : 'plates', - name : 'plates', - type : 'string', - width : 100, - renderer : function(comp, val, record) { - var html = "
"; - var stockSolutions = BIOSAXS.proposal.getStockSolutionsByDewarId(record.raw.dewarId); - html = html + "" + stockSolutions.length + " x"; - return html + "
"; - } - }, { - header : 'isStorageDewar', - dataIndex : 'isStorageDewar', - name : 'isStorageDewar', - type : 'string', - flex : 1, - hidden : true - }, { - header : 'Tracking Number From Synchrotron', - dataIndex : 'trackingNumberFromSynchrotron', - name : 'trackingNumberFromSynchrotron', - type : 'string', - flex : 1, - hidden : true - }, { - header : 'Tracking Number To Synchrotron', - dataIndex : 'trackingNumberToSynchrotron', - name : 'trackingNumberToSynchrotron', - type : 'string', - flex : 1, - hidden : true - }, { - header : 'Storage Location', - dataIndex : 'storageLocation', - name : 'storageLocation', - type : 'string', - flex : 1, - hidden : false - }, { - header : 'Comments', - dataIndex : 'comments', - name : 'comments', - type : 'string', - flex : 1, - hidden : false - } - ]; - - if (this.btnEditVisible) { - columns.push({ - id : _this.id + 'buttonEdit', - text : '', - hidden : !_this.btnEditVisible, - width : 85, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - return BUI.getGreenButton('EDIT'); - } - }); - } - - if (this.btnRemoveVisible) { - columns.push({ - id : _this.id + 'buttonRemove', - width : 85, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - if (_this.btnRemoveVisible) { - return BUI.getRedButton('REMOVE'); - } - } - }); - } - - columns.push({ - dataIndex : 'comments', - type : 'string', - width : 85, - hidden : false, - renderer : function(comp, val, record) { - return BUI.getBlueButton("LABELS", { - href : BUI.getPrintcomponentURL(record.raw.dewarId) - }); - } - }); - - return columns; -}; - -ExampleGrid.prototype._getTopButtons = function() { - var _this = this; - /** Actions buttons **/ - var actions = []; - - /** ADD BUTTON **/ - actions.push(Ext.create('Ext.Action', { - icon : '../images/add.png', - text : 'Add', - disabled : false, - handler : function(widget, event) { - _this.onAddButtonClicked.notify(); - } - })); - - return actions; -}; - -ExampleGrid.prototype.refresh = function(dewars) { - this.features = dewars; - this.store.loadData(this._prepareData(dewars), false); -}; - -ExampleGrid.prototype._sort = function(store) { - store.sort('dewarId', 'DESC'); -}; - -ExampleGrid.prototype._prepareData = function() { - var data = []; - for ( var i = 0; i < this.features.length; i++) { - data.push(this.features[i]); - } - return data; -}; - -ExampleGrid.prototype.getPanel = function() { - this.grid = Ext.create('Ext.grid.Panel', { - style : { - padding : 5 - }, - height : this.height, - store : this.store, - columns : this._getColumns(), - viewConfig : { - stripeRows : true, - listeners : { - itemdblclick : function(dataview, record, item, e) { - _this._edit(record.raw); - }, - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEdit') { - _this._edit(record.raw); - } - - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemove') { - _this.onRemoveButtonClicked.notify(_this.store.getAt(rowIndex).raw.dewarId); - } - } - } - }, - selModel : { - mode : 'SINGLE' - } - }); - - var actions = _this._getTopButtons(); - this.grid.addDocked({ - xtype : 'toolbar', - items : actions - }); - - this.grid.getSelectionModel().on({ - selectionchange : function(sm, selections) { - if (selections.length) { - for ( var i = 0; i < actions.length; i++) { - if (actions[i].enable) { - actions[i].enable(); - } - } - } else { - for ( var i = 0; i < actions.length; i++) { - if (actions[i].alwaysEnabled == false) { - if (actions[i].disable) { - actions[i].disable(); - } - } - } - } - } - }); - return this.grid; -}; - - -ExampleGrid.prototype._getStoreFields = function(data) { - return [ { - name : 'dewarId', - type : 'string' - }, { - name : 'barCode', - type : 'string' - }, { - name : 'code', - type : 'string' - }, { - name : 'comments', - type : 'string' - }, { - name : 'dewarStatus', - type : 'string' - }, { - name : 'isStorageDewar', - type : 'string' - }, { - name : 'plates', - type : 'string' - }, { - name : 'transportValue', - type : 'string' - }, { - name : 'trackingNumberFromSynchrotron', - type : 'string' - }, { - name : 'trackingNumberToSynchrotron', - type : 'string' - }, { - name : 'timeStamp', - type : 'string' - }, { - name : 'storageLocation', - type : 'string' - }, { - name : 'type', - type : 'string' - } - - ]; -}; - -ExampleGrid.prototype._renderGrid = function() { - var _this = this; - - /** Store **/ - var data = this._prepareData(); - this.store = Ext.create('Ext.data.Store', { - fields : this._getStoreFields(data), - autoload : true, - data : data - }); - this._sort(this.store); - - this.store.loadData(data, false); - - this.grid = Ext.create('Ext.grid.Panel', { - style : { - padding : 5 - }, - height : this.height, - store : this.store, - columns : this._getColumns(), - viewConfig : { - stripeRows : true, - listeners : { - itemdblclick : function(dataview, record, item, e) { - _this._edit(record.raw); - }, - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEdit') { - _this._edit(record.raw); - } - - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemove') { - _this.onRemoveButtonClicked.notify(_this.store.getAt(rowIndex).raw.dewarId); - } - } - } - }, - selModel : { - mode : 'SINGLE' - } - }); - - var actions = _this._getTopButtons(); - this.grid.addDocked({ - xtype : 'toolbar', - items : actions - }); - - this.grid.getSelectionModel().on({ - selectionchange : function(sm, selections) { - if (selections.length) { - for ( var i = 0; i < actions.length; i++) { - if (actions[i].enable) { - actions[i].enable(); - } - } - } else { - for ( var i = 0; i < actions.length; i++) { - if (actions[i].alwaysEnabled == false) { - if (actions[i].disable) { - actions[i].disable(); - } - } - } - } - } - }); - return this.grid; -}; - -ExampleGrid.prototype.input = function() { - return { - proposal : DATADOC.getProposal_10(), - dewars : DATADOC.getDewars_10() - - }; -}; - -ExampleGrid.prototype.test = function(targetId) { - var ExampleGrid = new ExampleGrid({ - height : 150 - }); - BIOSAXS.proposal = new Proposal(ExampleGrid.input().proposal); - var panel = ExampleGrid.getPanel(ExampleGrid.input().dewars); - panel.render(targetId); - -}; + BIOSAXS.proposal = new Proposal(ExampleGrid.input().proposal); + var panel = ExampleGrid.getPanel(ExampleGrid.input().dewars); + panel.render(targetId); + +}; /** @@ -18106,188 +18106,188 @@ ExperimentGrid.prototype.test = function(targetId) { panel.render(targetId); }; - -function FitStructureToExperimentDataGrid(args) { - this.height = null; - this.width = null; - this.id = BUI.id(); - - if (args != null) { - if (args.height != null) { - this.height = args.height; - - if (args.width != null) { - this.width = args.width; - } - } - } - - this.onSelected = new Event(this); -} - -FitStructureToExperimentDataGrid.prototype.getStructuresByMacromolecule = function(macromolecule) { - var structures = []; - if (macromolecule.structure3VOs != null) { - if (macromolecule.structure3VOs.length > 0) { - for (var i = 0; i < macromolecule.structure3VOs.length; i++) { - structures.push(macromolecule.structure3VOs[i]); - } - } - } - return structures; -}; - -FitStructureToExperimentDataGrid.prototype._prepareData = function(subtractions) { - var data = []; - for (var i = 0; i < subtractions.length; i++) { - - for (var j = 0; j < subtractions[i].fitStructureToExperimentalData3VOs.length; j++) { - var fit = subtractions[i].fitStructureToExperimentalData3VOs[j]; - data.push({ - fit : fit.fitFilePath, - fitStructureToExperimentalDataId : fit.fitStructureToExperimentalDataId, - mixtureToStructure3VOs : fit.mixtureToStructure3VOs, - subtractedFile : subtractions[i].substractedFilePath - }); - } - } - return data; - -}; - -FitStructureToExperimentDataGrid.prototype.refresh = function(subtractions) { - this.store.loadData(this._prepareData(subtractions), false); -}; - -FitStructureToExperimentDataGrid.prototype.getPanel = function() { - var _this = this; - this.store = Ext.create('Ext.data.Store', { - fields : [ 'fit', 'subtractedFile', 'structureId', 'fitFilePath', 'mixtureToStructure3VOs' ], - data : [] - }); - - this.store.sort([ { - property : 'name', - direction : 'ASC' - } ]); - - this.selModel = Ext.create('Ext.selection.RowModel', { - allowDeselect : true, - mode : 'MULTI', - listeners : { - selectionchange : function(sm, selections) { - var selected = []; - for (var i = 0; i < selections.length; i++) { - selected.push(selections[i].raw); - } - _this.onSelected.notify(selected); - } - } - }); - - this.panel = Ext.create('Ext.grid.Panel', { - store : this.store, - deferredRender : false, - width : this.width, - height : this.height, - margin : 10, - selModel : this.selModel, - columns : [ { - text : 'Name', - dataIndex : 'fit', - flex : 1, - renderer : function(val, b, record) { - return BUI.getFileName(val); - } - }, { - text : 'PDB', - dataIndex : 'mixtureToStructure3VOs', - flex : 1, - renderer : function(values, b, record) { - var html = ""; - for (var i = 0; i < values.length; i++) { - var structure = BIOSAXS.proposal.getStructuresById(values[i].structureId); - html = html + ""; - if (structure != null){ - html = html + ""; - } - html = html + ""; - } - return html + "
" + structure.name + "
"; - } - }, { - text : 'Volume Fraction', - dataIndex : 'mixtureToStructure3VOs', - flex : 1, - renderer : function(values, b, record) { - var html = ""; - for (var i = 0; i < values.length; i++) { - html = html + ""; - html = html + ""; - html = html + ""; - } - - return html + "
" + values[i].volumeFraction + "
"; - } - },{ - text : 'Subtraction', - dataIndex : 'subtractedFile', - flex : 1, - renderer : function(values, b, record) { - return values.split("/")[values.split("/").length - 1]; - } - },], - - viewConfig : { - enableTextSelection : true, - preserveScrollOnRefresh : true - }, - listeners : { - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - }, - afterrender : function() { - } - } - }); - return this.panel; -}; - -/** Static method **/ -FitStructureToExperimentDataGrid.prototype.RUNFitScattering = function(subtractionId, structureId) { - var _this = this; - /** Add to Workflow **/ - var adapter = new BiosaxsDataAdapter(); - var workflow = { - 'workflowTitle' : 'FitExperimentalDatatoStructure', - 'comments' : 'FitExperimentalDatatoStructure run from ISPyB for subtractionId: ' + subtractionId + ' and structureId ' + structureId - } - - var inputs = [ { - name : 'subtractionId', - value : subtractionId - }, { - name : 'structureId', - value : structureId - } ]; - - adapter.onSuccess.attach(function(sender, data) { - /** Add to Fit **/ - var adapter2 = new BiosaxsDataAdapter(); - var fit = { - 'workflowId' : data.workflowId, - 'subtractionId' : subtractionId, - 'structureId' : structureId, - 'comments' : 'Sent to workflow engine' - } - adapter2.onSuccess.attach(function(sender, fit) { - _this.refresh(_this.subtractionId, _this.macromolecule); - }); - adapter2.addFitStructureData(fit); - - }); - adapter.addWorkflow(workflow, inputs); - -}; + +function FitStructureToExperimentDataGrid(args) { + this.height = null; + this.width = null; + this.id = BUI.id(); + + if (args != null) { + if (args.height != null) { + this.height = args.height; + + if (args.width != null) { + this.width = args.width; + } + } + } + + this.onSelected = new Event(this); +} + +FitStructureToExperimentDataGrid.prototype.getStructuresByMacromolecule = function(macromolecule) { + var structures = []; + if (macromolecule.structure3VOs != null) { + if (macromolecule.structure3VOs.length > 0) { + for (var i = 0; i < macromolecule.structure3VOs.length; i++) { + structures.push(macromolecule.structure3VOs[i]); + } + } + } + return structures; +}; + +FitStructureToExperimentDataGrid.prototype._prepareData = function(subtractions) { + var data = []; + for (var i = 0; i < subtractions.length; i++) { + + for (var j = 0; j < subtractions[i].fitStructureToExperimentalData3VOs.length; j++) { + var fit = subtractions[i].fitStructureToExperimentalData3VOs[j]; + data.push({ + fit : fit.fitFilePath, + fitStructureToExperimentalDataId : fit.fitStructureToExperimentalDataId, + mixtureToStructure3VOs : fit.mixtureToStructure3VOs, + subtractedFile : subtractions[i].substractedFilePath + }); + } + } + return data; + +}; + +FitStructureToExperimentDataGrid.prototype.refresh = function(subtractions) { + this.store.loadData(this._prepareData(subtractions), false); +}; + +FitStructureToExperimentDataGrid.prototype.getPanel = function() { + var _this = this; + this.store = Ext.create('Ext.data.Store', { + fields : [ 'fit', 'subtractedFile', 'structureId', 'fitFilePath', 'mixtureToStructure3VOs' ], + data : [] + }); + + this.store.sort([ { + property : 'name', + direction : 'ASC' + } ]); + + this.selModel = Ext.create('Ext.selection.RowModel', { + allowDeselect : true, + mode : 'MULTI', + listeners : { + selectionchange : function(sm, selections) { + var selected = []; + for (var i = 0; i < selections.length; i++) { + selected.push(selections[i].raw); + } + _this.onSelected.notify(selected); + } + } + }); + + this.panel = Ext.create('Ext.grid.Panel', { + store : this.store, + deferredRender : false, + width : this.width, + height : this.height, + margin : 10, + selModel : this.selModel, + columns : [ { + text : 'Name', + dataIndex : 'fit', + flex : 1, + renderer : function(val, b, record) { + return BUI.getFileName(val); + } + }, { + text : 'PDB', + dataIndex : 'mixtureToStructure3VOs', + flex : 1, + renderer : function(values, b, record) { + var html = ""; + for (var i = 0; i < values.length; i++) { + var structure = BIOSAXS.proposal.getStructuresById(values[i].structureId); + html = html + ""; + if (structure != null){ + html = html + ""; + } + html = html + ""; + } + return html + "
" + structure.name + "
"; + } + }, { + text : 'Volume Fraction', + dataIndex : 'mixtureToStructure3VOs', + flex : 1, + renderer : function(values, b, record) { + var html = ""; + for (var i = 0; i < values.length; i++) { + html = html + ""; + html = html + ""; + html = html + ""; + } + + return html + "
" + values[i].volumeFraction + "
"; + } + },{ + text : 'Subtraction', + dataIndex : 'subtractedFile', + flex : 1, + renderer : function(values, b, record) { + return values.split("/")[values.split("/").length - 1]; + } + },], + + viewConfig : { + enableTextSelection : true, + preserveScrollOnRefresh : true + }, + listeners : { + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + }, + afterrender : function() { + } + } + }); + return this.panel; +}; + +/** Static method **/ +FitStructureToExperimentDataGrid.prototype.RUNFitScattering = function(subtractionId, structureId) { + var _this = this; + /** Add to Workflow **/ + var adapter = new BiosaxsDataAdapter(); + var workflow = { + 'workflowTitle' : 'FitExperimentalDatatoStructure', + 'comments' : 'FitExperimentalDatatoStructure run from ISPyB for subtractionId: ' + subtractionId + ' and structureId ' + structureId + } + + var inputs = [ { + name : 'subtractionId', + value : subtractionId + }, { + name : 'structureId', + value : structureId + } ]; + + adapter.onSuccess.attach(function(sender, data) { + /** Add to Fit **/ + var adapter2 = new BiosaxsDataAdapter(); + var fit = { + 'workflowId' : data.workflowId, + 'subtractionId' : subtractionId, + 'structureId' : structureId, + 'comments' : 'Sent to workflow engine' + } + adapter2.onSuccess.attach(function(sender, fit) { + _this.refresh(_this.subtractionId, _this.macromolecule); + }); + adapter2.addFitStructureData(fit); + + }); + adapter.addWorkflow(workflow, inputs); + +}; /** * It shows buffer grid with a top bar with "Add" button @@ -19893,244 +19893,244 @@ MeasurementGrid.prototype.getPanel = function(measurements, experiments) { }, 1000); } - } catch (e) { - } + } catch (e) { + } + } + } + } + }); + + return this.grid; +}; + +/** Method for testing * */ +MeasurementGrid.prototype.input = function() { + var experiment = DATADOC.getExperiment_10(); + var measurements = DATADOC.getMeasurements_10(); + var proposal = DATADOC.getProposal_10(); + return { + experiment : experiment, + measurements : measurements, + proposal : proposal + }; +}; + +MeasurementGrid.prototype.test = function(targetId) { + var measurementGrid = new MeasurementGrid({ + tbar : true + + }); + BIOSAXS.proposal = new Proposal(measurementGrid.input().proposal); + var panel = measurementGrid.getPanel(measurementGrid.input().measurements, new ExperimentList([ new Experiment(measurementGrid.input().experiment) ])); + panel.render(targetId); +}; + +/** + * A shipment may contains one or more cases where stock solutions and sample + * plates are stored + * + * @height + * @btnEditVisible + * @btnRemoveVisible + * + * #onEditButtonClicked + */ +function MolarityGrid(args) { + this.height = 100; + this.width = 100; + + if (args != null) { + if (args.height != null) { + this.height = args.height; + } + if (args.width != null) { + this.width = args.width; + } + } + + var _this = this; + + this.molarityForm = new MolarityForm({height : 180, width : 455}); + + this.molarityForm.onSave.attach(function(sender){ + _this.molarityWindow.destroy(); + _this.updateProposal(); + + }); + + this.molarityForm.onClose.attach(function(sender){ + _this.molarityWindow.destroy(); + + }); + + /** Events * */ + this.onEditButtonClicked = new Event(this); +} + +MolarityGrid.prototype._getColumns = function() { + return [ { + text : 'Subunit', + columns : [ { + text : "Acronym", + width : 100, + hidden : false, + dataIndex : 'acronym', + sortable : true + }, { + text : "Name", + width : 125, + hidden : false, + dataIndex : 'name', + sortable : true + }, { + text : "MM Est.", + width : 100, + dataIndex : 'molecularMass', + sortable : true, + renderer : function(grid, cls, record){ + return BUI.formatValuesUnits(record.data.molecularMass , "Da", 10, 2); + + } + } ] + }, { +// text : "Number
in assymmetric units", + text : "Ratio", + width : 100, + dataIndex : 'ratio', + tooltip : 'Number of times the subunit is present in the macromolecule', + sortable : true + }, { + id : this.id + 'MOLARITY_REMOVE', + flex : 0.1, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + return BUI.getRedButton('REMOVE'); + } + } ]; +}; + +MolarityGrid.prototype._openMolarityWindow = function() { + this.molarityWindow = Ext.create('Ext.window.Window', { + title : 'Molarity', + height : 220, + width : 500, + modal : true, + items : [this.molarityForm.getPanel() ] + }).show(); +}; + +MolarityGrid.prototype._getButtons = function() { + var _this = this; + return [ { + text : 'Add subunit', + icon : '../images/add.png', + handler : function() { + _this._openMolarityWindow(); + } + }]; +}; + + +MolarityGrid.prototype.updateProposal = function() { + var _this = this; + this.panel.setLoading(); + BIOSAXS.proposal.onInitialized.attach(function() { + if (BIOSAXS.proposal != null) { + var macromolecules = BIOSAXS.proposal.macromolecules; + for (var i = 0; i < macromolecules.length; i++) { + + if (macromolecules[i].macromoleculeId == _this.macromolecule.macromoleculeId) { + _this.refresh(macromolecules[i]); + _this.panel.setLoading(false); + } + } + } + }); + BIOSAXS.proposal.init(); +}; + + +MolarityGrid.prototype.getPanel = function() { + var _this = this; + + this.molarityStore = Ext.create('Ext.data.Store', { + fields : [ 'acronym', 'ratio', 'comments', 'stoichiometryId', 'name', 'molecularMass' ], + sorters : { + property : 'ratio', + direction : 'DESC' + } + }); + + this.panel = Ext.create('Ext.grid.Panel', { + store : this.molarityStore, + height : this.height, + padding : 5, + columns : this._getColumns(), + listeners : { + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + + /** Remove entry * */ + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'MOLARITY_REMOVE') { + var dataAdapter = new BiosaxsDataAdapter(); + dataAdapter.onSuccess.attach(function(sender) { + _this.updateProposal(); + + }); + dataAdapter.removeStoichiometry(record.data.stoichiometryId); + _this.panel.setLoading("Removing Structure"); } } - } + }, + tbar : this._getButtons() }); + return this.panel; +}; - return this.grid; +MolarityGrid.prototype._prepareData = function(macromolecule) { + /** Return an array of [{ratio,acronym, stoichiometryId, name}] **/ + var data = []; + if (macromolecule.stoichiometry != null) { + for (var i = 0; i < macromolecule.stoichiometry.length; i++) { + var hostMacromolecule = BIOSAXS.proposal.getMacromoleculeById(macromolecule.stoichiometry[i].macromoleculeId); + data.push({ + ratio : macromolecule.stoichiometry[i].ratio, + acronym : hostMacromolecule.acronym, + comments : hostMacromolecule.comments, + molecularMass : hostMacromolecule.molecularMass, + stoichiometryId : macromolecule.stoichiometry[i].stoichiometryId, + name : hostMacromolecule.name + }); + } + } + return data; }; -/** Method for testing * */ -MeasurementGrid.prototype.input = function() { - var experiment = DATADOC.getExperiment_10(); - var measurements = DATADOC.getMeasurements_10(); - var proposal = DATADOC.getProposal_10(); +MolarityGrid.prototype.refresh = function(macromolecule) { + if (macromolecule != null){ + this.molarityStore.loadData(this._prepareData(macromolecule)); + this.molarityForm.refresh(macromolecule); + this.macromolecule = macromolecule; + } +}; + +MolarityGrid.prototype.input = function() { return { - experiment : experiment, - measurements : measurements, - proposal : proposal + proposal : DATADOC.getProposal_10(), + dewars : DATADOC.getDewars_10() + }; }; -MeasurementGrid.prototype.test = function(targetId) { - var measurementGrid = new MeasurementGrid({ - tbar : true - +MolarityGrid.prototype.test = function(targetId) { + var MolarityGrid = new MolarityGrid({ + height : 150 }); - BIOSAXS.proposal = new Proposal(measurementGrid.input().proposal); - var panel = measurementGrid.getPanel(measurementGrid.input().measurements, new ExperimentList([ new Experiment(measurementGrid.input().experiment) ])); + BIOSAXS.proposal = new Proposal(MolarityGrid.input().proposal); + var panel = MolarityGrid.getPanel(MolarityGrid.input().dewars); panel.render(targetId); + }; -/** - * A shipment may contains one or more cases where stock solutions and sample - * plates are stored - * - * @height - * @btnEditVisible - * @btnRemoveVisible - * - * #onEditButtonClicked - */ -function MolarityGrid(args) { - this.height = 100; - this.width = 100; - - if (args != null) { - if (args.height != null) { - this.height = args.height; - } - if (args.width != null) { - this.width = args.width; - } - } - - var _this = this; - - this.molarityForm = new MolarityForm({height : 180, width : 455}); - - this.molarityForm.onSave.attach(function(sender){ - _this.molarityWindow.destroy(); - _this.updateProposal(); - - }); - - this.molarityForm.onClose.attach(function(sender){ - _this.molarityWindow.destroy(); - - }); - - /** Events * */ - this.onEditButtonClicked = new Event(this); -} - -MolarityGrid.prototype._getColumns = function() { - return [ { - text : 'Subunit', - columns : [ { - text : "Acronym", - width : 100, - hidden : false, - dataIndex : 'acronym', - sortable : true - }, { - text : "Name", - width : 125, - hidden : false, - dataIndex : 'name', - sortable : true - }, { - text : "MM Est.", - width : 100, - dataIndex : 'molecularMass', - sortable : true, - renderer : function(grid, cls, record){ - return BUI.formatValuesUnits(record.data.molecularMass , "Da", 10, 2); - - } - } ] - }, { -// text : "Number
in assymmetric units", - text : "Ratio", - width : 100, - dataIndex : 'ratio', - tooltip : 'Number of times the subunit is present in the macromolecule', - sortable : true - }, { - id : this.id + 'MOLARITY_REMOVE', - flex : 0.1, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - return BUI.getRedButton('REMOVE'); - } - } ]; -}; - -MolarityGrid.prototype._openMolarityWindow = function() { - this.molarityWindow = Ext.create('Ext.window.Window', { - title : 'Molarity', - height : 220, - width : 500, - modal : true, - items : [this.molarityForm.getPanel() ] - }).show(); -}; - -MolarityGrid.prototype._getButtons = function() { - var _this = this; - return [ { - text : 'Add subunit', - icon : '../images/add.png', - handler : function() { - _this._openMolarityWindow(); - } - }]; -}; - - -MolarityGrid.prototype.updateProposal = function() { - var _this = this; - this.panel.setLoading(); - BIOSAXS.proposal.onInitialized.attach(function() { - if (BIOSAXS.proposal != null) { - var macromolecules = BIOSAXS.proposal.macromolecules; - for (var i = 0; i < macromolecules.length; i++) { - - if (macromolecules[i].macromoleculeId == _this.macromolecule.macromoleculeId) { - _this.refresh(macromolecules[i]); - _this.panel.setLoading(false); - } - } - } - }); - BIOSAXS.proposal.init(); -}; - - -MolarityGrid.prototype.getPanel = function() { - var _this = this; - - this.molarityStore = Ext.create('Ext.data.Store', { - fields : [ 'acronym', 'ratio', 'comments', 'stoichiometryId', 'name', 'molecularMass' ], - sorters : { - property : 'ratio', - direction : 'DESC' - } - }); - - this.panel = Ext.create('Ext.grid.Panel', { - store : this.molarityStore, - height : this.height, - padding : 5, - columns : this._getColumns(), - listeners : { - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - - /** Remove entry * */ - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'MOLARITY_REMOVE') { - var dataAdapter = new BiosaxsDataAdapter(); - dataAdapter.onSuccess.attach(function(sender) { - _this.updateProposal(); - - }); - dataAdapter.removeStoichiometry(record.data.stoichiometryId); - _this.panel.setLoading("Removing Structure"); - } - } - }, - tbar : this._getButtons() - }); - return this.panel; -}; - -MolarityGrid.prototype._prepareData = function(macromolecule) { - /** Return an array of [{ratio,acronym, stoichiometryId, name}] **/ - var data = []; - if (macromolecule.stoichiometry != null) { - for (var i = 0; i < macromolecule.stoichiometry.length; i++) { - var hostMacromolecule = BIOSAXS.proposal.getMacromoleculeById(macromolecule.stoichiometry[i].macromoleculeId); - data.push({ - ratio : macromolecule.stoichiometry[i].ratio, - acronym : hostMacromolecule.acronym, - comments : hostMacromolecule.comments, - molecularMass : hostMacromolecule.molecularMass, - stoichiometryId : macromolecule.stoichiometry[i].stoichiometryId, - name : hostMacromolecule.name - }); - } - } - return data; -}; - -MolarityGrid.prototype.refresh = function(macromolecule) { - if (macromolecule != null){ - this.molarityStore.loadData(this._prepareData(macromolecule)); - this.molarityForm.refresh(macromolecule); - this.macromolecule = macromolecule; - } -}; - -MolarityGrid.prototype.input = function() { - return { - proposal : DATADOC.getProposal_10(), - dewars : DATADOC.getDewars_10() - - }; -}; - -MolarityGrid.prototype.test = function(targetId) { - var MolarityGrid = new MolarityGrid({ - height : 150 - }); - BIOSAXS.proposal = new Proposal(MolarityGrid.input().proposal); - var panel = MolarityGrid.getPanel(MolarityGrid.input().dewars); - panel.render(targetId); - -}; - /** * Given data analysis parsed with ResultsAssemblyWidget makes a selector grid with buffer/protein @@ -20815,135 +20815,135 @@ ResultsAssemblyGrid.prototype.test = function(targetId) { }; - -function RigidModelGrid(args) { - this.height = null; - this.width = null; - this.id = BUI.id(); - - if (args != null) { - if (args.height != null) { - this.height = args.height; - - if (args.width != null) { - this.width = args.width; - } - } - } - - this.onSelected = new Event(this); -} - - -RigidModelGrid.prototype.refresh = function(subtractions) { - var data = []; - if (subtractions != null){ - if (subtractions.length > 0){ - for (j in subtractions){ - var subtraction = subtractions[j]; - if (subtraction.rigidBodyModeling3VOs != null){ - for (i in subtraction.rigidBodyModeling3VOs){ - data.push(subtraction.rigidBodyModeling3VOs[i]); - } - } - } - } - } - this.store.loadData(data); -}; - -RigidModelGrid.prototype.getPanel = function() { - var _this = this; - this.store = Ext.create('Ext.data.Store', { - fields : [ 'symmetry', 'subtractionId', 'subUnitConfigFilePath', 'rigidBodyModelingId', 'rigidBodyModelFilePath', 'logFilePath', 'fitFilePath', 'curveConfigFilePath', - 'crossCorrConfigFilePath', 'contactDescriptionFilePath' ], - data : [] - }); - - this.store.sort([ { - property : 'name', - direction : 'ASC' - } ]); - - this.panel = Ext.create('Ext.grid.Panel', { - store : this.store, - width : this.width, - height : this.height, - margin : 10, - deferredRender : false, - columns : [ { - text : 'RBM', - dataIndex : 'rigidBodyModelFilePath', - hidden : false, - flex : 1, - renderer : function(val){ - return BUI.getFileName(val); - } - }, { - text : 'Sub Unit Conf.', - dataIndex : 'subUnitConfigFilePath', - hidden : true, - flex : 1, - renderer : function(val){ - return BUI.getFileName(val); - } - }, { - text : 'Log', - dataIndex : 'logFilePath', - hidden : true, - flex : 1, - renderer : function(val){ - return BUI.getFileName(val); - } - }, { - text : 'Fit', - dataIndex : 'fitFilePath', - hidden : false, - flex : 1, - renderer : function(val){ - return BUI.getFileName(val); - } - }, { - text : 'Curve Conf.', - dataIndex : 'curveConfigFilePath', - hidden : false, - flex : 1, - renderer : function(val){ - return BUI.getFileName(val); - } - }, { - text : 'Cross Corr.', - dataIndex : 'crossCorrConfigFilePath', - hidden : false, - flex : 1, - renderer : function(val){ - return BUI.getFileName(val); - } - }, { - text : 'Contact Desc.', - dataIndex : 'contactDescriptionFilePath', - hidden : true, - flex : 1, - renderer : function(val){ - return BUI.getFileName(val); - } - } ], - - viewConfig : { - enableTextSelection : true, - preserveScrollOnRefresh : true - }, - listeners : { - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - - }, - afterrender : function() { - } - } - }); - return this.panel; -}; - + +function RigidModelGrid(args) { + this.height = null; + this.width = null; + this.id = BUI.id(); + + if (args != null) { + if (args.height != null) { + this.height = args.height; + + if (args.width != null) { + this.width = args.width; + } + } + } + + this.onSelected = new Event(this); +} + + +RigidModelGrid.prototype.refresh = function(subtractions) { + var data = []; + if (subtractions != null){ + if (subtractions.length > 0){ + for (j in subtractions){ + var subtraction = subtractions[j]; + if (subtraction.rigidBodyModeling3VOs != null){ + for (i in subtraction.rigidBodyModeling3VOs){ + data.push(subtraction.rigidBodyModeling3VOs[i]); + } + } + } + } + } + this.store.loadData(data); +}; + +RigidModelGrid.prototype.getPanel = function() { + var _this = this; + this.store = Ext.create('Ext.data.Store', { + fields : [ 'symmetry', 'subtractionId', 'subUnitConfigFilePath', 'rigidBodyModelingId', 'rigidBodyModelFilePath', 'logFilePath', 'fitFilePath', 'curveConfigFilePath', + 'crossCorrConfigFilePath', 'contactDescriptionFilePath' ], + data : [] + }); + + this.store.sort([ { + property : 'name', + direction : 'ASC' + } ]); + + this.panel = Ext.create('Ext.grid.Panel', { + store : this.store, + width : this.width, + height : this.height, + margin : 10, + deferredRender : false, + columns : [ { + text : 'RBM', + dataIndex : 'rigidBodyModelFilePath', + hidden : false, + flex : 1, + renderer : function(val){ + return BUI.getFileName(val); + } + }, { + text : 'Sub Unit Conf.', + dataIndex : 'subUnitConfigFilePath', + hidden : true, + flex : 1, + renderer : function(val){ + return BUI.getFileName(val); + } + }, { + text : 'Log', + dataIndex : 'logFilePath', + hidden : true, + flex : 1, + renderer : function(val){ + return BUI.getFileName(val); + } + }, { + text : 'Fit', + dataIndex : 'fitFilePath', + hidden : false, + flex : 1, + renderer : function(val){ + return BUI.getFileName(val); + } + }, { + text : 'Curve Conf.', + dataIndex : 'curveConfigFilePath', + hidden : false, + flex : 1, + renderer : function(val){ + return BUI.getFileName(val); + } + }, { + text : 'Cross Corr.', + dataIndex : 'crossCorrConfigFilePath', + hidden : false, + flex : 1, + renderer : function(val){ + return BUI.getFileName(val); + } + }, { + text : 'Contact Desc.', + dataIndex : 'contactDescriptionFilePath', + hidden : true, + flex : 1, + renderer : function(val){ + return BUI.getFileName(val); + } + } ], + + viewConfig : { + enableTextSelection : true, + preserveScrollOnRefresh : true + }, + listeners : { + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + + }, + afterrender : function() { + } + } + }); + return this.panel; +}; + /** * shows shipments @@ -22309,119 +22309,119 @@ StockSolutionGrid.prototype.test = function(targetId) { panel.render(targetId); }; - -function SuperpositionGrid(args) { - this.height = null; - this.width = null; - this.id = BUI.id(); - - if (args != null) { - if (args.height != null) { - this.height = args.height; - - if (args.width != null) { - this.width = args.width; - } - } - } - - this.onSelected = new Event(this); -} - -SuperpositionGrid.prototype._prepareData = function(data) { - return data; -}; - -SuperpositionGrid.prototype.refresh = function(subtractions) { - var data = []; - if (subtractions != null){ - if (subtractions.length > 0){ - for (j in subtractions){ - var subtraction = subtractions[j]; - if (subtraction.superposition3VOs != null){ - for (i in subtraction.superposition3VOs){ - data.push(subtraction.superposition3VOs[i]); - } - } - } - } - } - this.store.loadData(data); -}; - -SuperpositionGrid.prototype.getPanel = function() { - var _this = this; - this.store = Ext.create('Ext.data.Store', { - fields : [ 'abinitioModelPdbFilePath', 'aprioriPdbFilePath', 'alignedPdbFilePath' ], - data : [] - }); - - this.selModel = Ext.create('Ext.selection.RowModel', { - allowDeselect : true, - mode : 'MULTI', - listeners : { - selectionchange : function(sm, selections) { - var selected = []; - for (var i = 0; i < selections.length; i++) { - selected.push(selections[i].raw); - } - _this.onSelected.notify(selected); - } - } - }); - - this.store.sort([ { - property : 'name', - direction : 'ASC' - } ]); - - this.panel = Ext.create('Ext.grid.Panel', { - store : this.store, - selModel : this.selModel, - width : this.width, - height : this.height, - margin : 10, - deferredRender : false, - columns : [ { - text : 'Abinitio', - dataIndex : 'abinitioModelPdbFilePath', - hidden : false, - flex : 1, - renderer : function(val){ - return BUI.getFileName(val); - } - }, { - text : 'Apriori', - dataIndex : 'aprioriPdbFilePath', - hidden : false, - flex : 1, - renderer : function(val){ - return BUI.getFileName(val); - } - }, { - text : 'Aligned', - dataIndex : 'alignedPdbFilePath', - hidden : false, - flex : 1, - renderer : function(val){ - return BUI.getFileName(val); - } - } ], - - viewConfig : { - enableTextSelection : true, - preserveScrollOnRefresh : true - }, - listeners : { - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - - }, - afterrender : function() { - } - } - }); - return this.panel; -}; + +function SuperpositionGrid(args) { + this.height = null; + this.width = null; + this.id = BUI.id(); + + if (args != null) { + if (args.height != null) { + this.height = args.height; + + if (args.width != null) { + this.width = args.width; + } + } + } + + this.onSelected = new Event(this); +} + +SuperpositionGrid.prototype._prepareData = function(data) { + return data; +}; + +SuperpositionGrid.prototype.refresh = function(subtractions) { + var data = []; + if (subtractions != null){ + if (subtractions.length > 0){ + for (j in subtractions){ + var subtraction = subtractions[j]; + if (subtraction.superposition3VOs != null){ + for (i in subtraction.superposition3VOs){ + data.push(subtraction.superposition3VOs[i]); + } + } + } + } + } + this.store.loadData(data); +}; + +SuperpositionGrid.prototype.getPanel = function() { + var _this = this; + this.store = Ext.create('Ext.data.Store', { + fields : [ 'abinitioModelPdbFilePath', 'aprioriPdbFilePath', 'alignedPdbFilePath' ], + data : [] + }); + + this.selModel = Ext.create('Ext.selection.RowModel', { + allowDeselect : true, + mode : 'MULTI', + listeners : { + selectionchange : function(sm, selections) { + var selected = []; + for (var i = 0; i < selections.length; i++) { + selected.push(selections[i].raw); + } + _this.onSelected.notify(selected); + } + } + }); + + this.store.sort([ { + property : 'name', + direction : 'ASC' + } ]); + + this.panel = Ext.create('Ext.grid.Panel', { + store : this.store, + selModel : this.selModel, + width : this.width, + height : this.height, + margin : 10, + deferredRender : false, + columns : [ { + text : 'Abinitio', + dataIndex : 'abinitioModelPdbFilePath', + hidden : false, + flex : 1, + renderer : function(val){ + return BUI.getFileName(val); + } + }, { + text : 'Apriori', + dataIndex : 'aprioriPdbFilePath', + hidden : false, + flex : 1, + renderer : function(val){ + return BUI.getFileName(val); + } + }, { + text : 'Aligned', + dataIndex : 'alignedPdbFilePath', + hidden : false, + flex : 1, + renderer : function(val){ + return BUI.getFileName(val); + } + } ], + + viewConfig : { + enableTextSelection : true, + preserveScrollOnRefresh : true + }, + listeners : { + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + + }, + afterrender : function() { + } + } + }); + return this.panel; +}; /** * See ExperimentGrid @@ -26158,502 +26158,502 @@ ConcentrationHTMLTableWidget.prototype.input = function() { "values" : [] } } - } ] - }, - "concentrationLabel" : "7.17 mg/ml ,3.53 mg/ml ,1.75 mg/ml ,0.91 mg/ml " + } ] + }, + "concentrationLabel" : "7.17 mg/ml ,3.53 mg/ml ,1.75 mg/ml ,0.91 mg/ml " + } + }; +}; + +ConcentrationHTMLTableWidget.prototype.test = function(targetId) { + var concentrationHTMLTableWidget = new ConcentrationHTMLTableWidget(); + document.getElementById(targetId).innerHTML = concentrationHTMLTableWidget.getPanel(concentrationHTMLTableWidget.input().data); +}; + +function DataCollectionWidget() { + +}; + +DataCollectionWidget.prototype.refresh = function(subtractionId) { + +}; + +DataCollectionWidget.prototype.getMacromolecule = function(data) { + for (var i = 0; i < data.length; i++) { + if (data[i].macromoleculeId != null) { + return BIOSAXS.proposal.getMacromoleculeById(data[i].macromoleculeId); + } + } + return null; +}; + +DataCollectionWidget.prototype.getMacromoleculeContainer = function(data) { + var macromolecule = this.getMacromolecule(data); + + var disabled = false; + if (macromolecule == null) { + disabled = true; + } + + var acronym = (macromolecule == null ? "" : macromolecule.acronym); + var mm = (macromolecule == null ? "" : macromolecule.molecularMass); + var comments = (macromolecule == null ? "" : macromolecule.comments); + + return Ext.create('Ext.Panel', { + width : 500, + height : 200, + disabled : disabled, + title : "Macromolecule", + layout : 'form', + bodyPadding : 5, + defaultType : 'textfield', + tbar : { + defaultButtonUI : 'default', + items : [ { + xtype : 'button', + text : 'Edit', + cls : 'btn-with-border', + handler : function() { + var macromoleculeWindow = new MacromoleculeWindow(); + macromoleculeWindow.draw(macromolecule); + /** TODO: update when save **/ + } + } ] + }, + items : [ { + fieldLabel : 'Acronym', + name : 'first', + readOnly : true, + value : acronym + }, { + fieldLabel : 'Molecular Mass', + name : 'last', + readOnly : true, + value : mm + }, { + xtype : 'textareafield', + fieldLabel : 'Comments', + value : '', + name : 'last', + readOnly : true, + value : comments + } ] + }); +}; + +DataCollectionWidget.prototype.getBufferContainer = function(data) { + var _this = this; + var buffer = BIOSAXS.proposal.getBufferById(data[0].bufferId); + + return Ext.create('Ext.Panel', { + width : 500, + height : 200, + title : "Buffer", + layout : 'form', + // collapsed : true, + // collapsible : true, + bodyPadding : 5, + defaultType : 'textfield', + style : { + padding : '0px 0px 0px 2px' + }, + tbar : { + defaultButtonUI : 'default', + items : [ { + xtype : 'button', + text : 'Edit', + cls : 'btn-with-border', + handler : function() { + var bufferWindow = new BufferWindow(); + bufferWindow.draw(BIOSAXS.proposal.getBufferById(data[0].bufferId)); + /** TODO: update when save **/ + } + + } ] + }, + items : [ { + fieldLabel : 'Buffer', + name : 'acronym', + readOnly : true, + value : buffer.acronym + }, { + fieldLabel : 'Composition', + name : 'last', + readOnly : true, + value : buffer.composition + }, { + xtype : 'textareafield', + fieldLabel : 'Comments', + value : buffer.comments, + name : 'last', + readOnly : true + + } ] + }); +}; + +DataCollectionWidget.prototype.getSpecimenContainer = function(data) { + return Ext.create('Ext.container.Container', { + layout : { + type : 'hbox' + }, + style : { + margin : '10px 10px 10px 10px' + }, + border : 0, + style : { + borderColor : '#000000', + borderStyle : 'solid', + borderWidth : '1px' + }, + defaults : { + labelWidth : 80, + // implicitly create Container by specifying xtype + xtype : 'datefield', + flex : 1, + + }, + items : [ this.getMacromoleculeContainer(data), this.getBufferContainer(data) ] + }); +}; + +DataCollectionWidget.prototype.getSeparator = function() { + return { + html : "
", + border : 0 + } +}; + +DataCollectionWidget.prototype.getFitStructurePanel = function(data) { + var _this = this; + + return Ext.create('Ext.container.Container', { + layout : { + type : 'hbox' + }, + style : { + margin : '10px 10px 10px 10px' + }, + border : 0, + style : { + borderColor : '#000000', + borderStyle : 'solid', + borderWidth : '1px' + }, + defaults : { + labelWidth : 80, + xtype : 'datefield', + flex : 1 + }, + items : [ + + ] + }); +}; + +DataCollectionWidget.prototype.getFitStructurePanelWorkflow = function(data) { + var _this = this; + var macromolecule = this.getMacromolecule(data); + + var items = []; + + /** Adding all the pdb files linked to the macromolecule **/ + // if (macromolecule.structure3VOs != null) { + // if (macromolecule.structure3VOs.length > 0) { + // + // items.push(); + // } + // } else { + // items.push({ + // html : "No apriori information added to this macromolecule. Apriori information needed for further analysis", + // margin : "5 5 5 5" + // }); + // } + var fitStructureToExperimentDataGrid = new FitStructureToExperimentDataGrid(); + + fitStructureToExperimentDataGrid.refresh(_this.data[0].subtractionId, _this.getMacromolecule(data)); + return Ext.create('Ext.container.Container', { + style : { + margin : '10px 10px 10px 10px' + }, + border : 0, + + style : { + borderColor : '#000000', + borderStyle : 'solid', + borderWidth : '1px' + }, + defaults : { + labelWidth : 80, + xtype : 'datefield', + flex : 1 + }, + items : [ fitStructureToExperimentDataGrid.getPanel() ], + listeners : { + afterrender : function() { + } + } + }); +}; +/** Static method **/ +DataCollectionWidget.prototype.RUNFitScattering = function(subtractionId, structureId) { + var _this = this; + /** Add to Workflow **/ + var adapter = new BiosaxsDataAdapter(); + var workflow = { + 'workflowTitle' : 'FitExperimentalDatatoStructure', + 'comments' : 'FitExperimentalDatatoStructure run from ISPyB for subtractionId: ' + subtractionId + ' and structureId ' + structureId + } + + var inputs = [ { + name : 'subtractionId', + value : subtractionId + }, { + name : 'structureId', + value : structureId + } ]; + + adapter.onSuccess.attach(function(sender, data) { + /** Add to Fit **/ + var adapter2 = new BiosaxsDataAdapter(); + var fit = { + 'workflowId' : data.workflowId, + 'subtractionId' : subtractionId, + 'structureId' : structureId, + 'comments' : 'Sent to workflow engine' + } + adapter2.onSuccess.attach(function(sender, fit) { + + }); + adapter2.addFitStructureData(fit); + + }); + adapter.addWorkflow(workflow, inputs); + +}; + +DataCollectionWidget.prototype.getSuperpositionTab = function(data) { + var _this = this; + + this.superpositionGrid = new SuperpositionGrid(); + + return Ext.create('Ext.container.Container', { + style : { + margin : '10px 10px 10px 10px' + }, + border : 0, + style : { + borderColor : '#000000', + borderStyle : 'solid', + borderWidth : '1px' + }, + items : [ _this.superpositionGrid.getPanel() ], + listeners : { + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + + }, + afterrender : function() { + /** Getting Rigid bodies **/ + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, result) { + _this.superpositionGrid.refresh(result); + }); + adapter.getSuperpositionBySubtractionId(data[1].subtractionId); + } + } + }); +}; + +DataCollectionWidget.prototype.getAdvancedTab = function(data) { + var _this = this; + return Ext.create('Ext.container.Container', { + style : { + margin : '10px 10px 10px 10px' + }, + border : 0, + style : { + borderColor : '#000000', + borderStyle : 'solid', + borderWidth : '1px' + }, + items : [ _this.getFitStructurePanel(data), _this.getFitStructurePanelWorkflow(data) ] + }); +}; + +DataCollectionWidget.prototype.getRigiBodyForm = function(data) { + var _this = this; + _this.rigiBodyGrid = new RigidModelGrid(); + return _this.rigiBodyGrid.getPanel(); + +}; + +DataCollectionWidget.prototype.getRigidBodyModelingTab = function(data) { + var _this = this; + return Ext.create('Ext.container.Container', { + style : { + margin : '10px 10px 10px 10px' + }, + border : 0, + style : { + borderColor : '#000000', + borderStyle : 'solid', + borderWidth : '1px' + }, + items : [ _this.getRigiBodyForm(data) ], + listeners : { + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + + }, + afterrender : function() { + /** Getting Rigid bodies **/ + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, result) { + _this.rigiBodyGrid.refresh(result); + }); + adapter.getRigidBodyModelingBySubtractionId(data[1].subtractionId); + } + } + }); +}; + +DataCollectionWidget.prototype.getTabs = function(data) { + var _this = this; + + this.subtractionCurveVisualizer = new SubtractionCurveVisualizer(); + + this.tabs = Ext.createWidget('tabpanel', { + activeTab : 1, + plain : true, + defaults : { + autoScroll : true, + bodyPadding : 10 + }, + items : [ { + title : 'Solution', + items : [ _this.getSpecimenContainer(data) ] + }, { + title : 'Primary Data Reduction', + active : true, + tabConfig : { + xtype : 'tab', + margins : '0 0 0 20', + }, + items : [ _this.subtractionCurveVisualizer.getPanel() ] + }, { + title : 'Abinitio', + items : [ _this.getAbinitioModellingContainer(data), _this.getSeparator(), _this.getModelViz(data) ] + }, { + title : 'Mixtures', + items : [ _this.getAdvancedTab(data) ] + }, { + title : 'Superpositions', + items : [ _this.getSuperpositionTab(data) ] + }, { + title : 'Rigid Body Modeling', + items : [ _this.getRigidBodyModelingTab(data) ] + } ] + }); + return this.tabs; +}; + +DataCollectionWidget.prototype.getPanel = function(data) { + var _this = this; + _this.data = data; + this.panel = Ext.create('Ext.container.Container', { + width : 1000, + layout : { + type : 'vbox', + align : 'stretch', + padding : 5 + }, + items : [ _this.getTabs(data) + + ] + }); + + this.panel.on("afterrender", function() { + _this.subtractionCurveVisualizer.refresh([ _this.data[1].mergeId ], [ _this.data[1].subtractionId ]); + }); + return this.panel; +}; + +DataCollectionWidget.prototype.getModelViz = function(data) { + this.modelViz = new ModelVisualizerForm({ + height : 800, + width : 1000 + }); + return this.modelViz.getPanel(); +}; + +/** + * PRIMARY DATA PROCESSING + */ +DataCollectionWidget.prototype.getPrimaryDataProcessingContainer = function(data) { + var _this = this; + this.primaryDataProcessingGrid = new PrimaryDataProcessingGrid({ + height : 250, + width : 1000, + title : 'Primary Data Processing' + }); + + this.primaryDataProcessingGrid.onSelected.attach(function(sender, selected) { + /** Refresh tabs **/ + var averagesId = []; + var subtractionIds = []; + + var subtractionKeys = {}; + for (var i = 0; i < selected.length; i++) { + if (selected[i].mergeId != null) { + averagesId.push(selected[i].mergeId); + } + + if (selected[i].subtractionId != null) { + if (selected[i].macromoleculeId != null) { + if (subtractionKeys[selected[i].subtractionId] == null) { + subtractionIds.push(selected[i].subtractionId); + } + subtractionKeys[selected[i].subtractionId] = true; + } + } } - }; + + /** Refreshing Primary Data Reduction **/ + _this.subtractionCurveVisualizer.refresh(averagesId, subtractionIds); + + }); + return this.primaryDataProcessingGrid.getPanel(data); }; +/** + * getAbinitioModellingContainer + */ +DataCollectionWidget.prototype.getAbinitioModellingContainer = function(data) { + var _this = this; -ConcentrationHTMLTableWidget.prototype.test = function(targetId) { - var concentrationHTMLTableWidget = new ConcentrationHTMLTableWidget(); - document.getElementById(targetId).innerHTML = concentrationHTMLTableWidget.getPanel(concentrationHTMLTableWidget.input().data); + this.abinitioGrid = new AbinitioGrid(); + this.abinitioGrid.onSelected.attach(function(sender, models) { + _this.modelViz.refresh(models); + + }); + /** It may be abinitio models linked to the buffers **/ + var abinitioIdList = []; + for (var i = 0; i < data.length; i++) { + abinitioIdList.push(data[i].abInitioId); + } + + var uniqueIds = []; + $.each(abinitioIdList, function(i, el) { + if ($.inArray(el, uniqueIds) === -1) + uniqueIds.push(el); + }); + + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + _this.abinitioGrid.refresh(data); + }); + adapter.getAbinitioByIdsList(uniqueIds); + return this.abinitioGrid.getPanel([]); }; -function DataCollectionWidget() { - -}; - -DataCollectionWidget.prototype.refresh = function(subtractionId) { - -}; - -DataCollectionWidget.prototype.getMacromolecule = function(data) { - for (var i = 0; i < data.length; i++) { - if (data[i].macromoleculeId != null) { - return BIOSAXS.proposal.getMacromoleculeById(data[i].macromoleculeId); - } - } - return null; -}; - -DataCollectionWidget.prototype.getMacromoleculeContainer = function(data) { - var macromolecule = this.getMacromolecule(data); - - var disabled = false; - if (macromolecule == null) { - disabled = true; - } - - var acronym = (macromolecule == null ? "" : macromolecule.acronym); - var mm = (macromolecule == null ? "" : macromolecule.molecularMass); - var comments = (macromolecule == null ? "" : macromolecule.comments); - - return Ext.create('Ext.Panel', { - width : 500, - height : 200, - disabled : disabled, - title : "Macromolecule", - layout : 'form', - bodyPadding : 5, - defaultType : 'textfield', - tbar : { - defaultButtonUI : 'default', - items : [ { - xtype : 'button', - text : 'Edit', - cls : 'btn-with-border', - handler : function() { - var macromoleculeWindow = new MacromoleculeWindow(); - macromoleculeWindow.draw(macromolecule); - /** TODO: update when save **/ - } - } ] - }, - items : [ { - fieldLabel : 'Acronym', - name : 'first', - readOnly : true, - value : acronym - }, { - fieldLabel : 'Molecular Mass', - name : 'last', - readOnly : true, - value : mm - }, { - xtype : 'textareafield', - fieldLabel : 'Comments', - value : '', - name : 'last', - readOnly : true, - value : comments - } ] - }); -}; - -DataCollectionWidget.prototype.getBufferContainer = function(data) { - var _this = this; - var buffer = BIOSAXS.proposal.getBufferById(data[0].bufferId); - - return Ext.create('Ext.Panel', { - width : 500, - height : 200, - title : "Buffer", - layout : 'form', - // collapsed : true, - // collapsible : true, - bodyPadding : 5, - defaultType : 'textfield', - style : { - padding : '0px 0px 0px 2px' - }, - tbar : { - defaultButtonUI : 'default', - items : [ { - xtype : 'button', - text : 'Edit', - cls : 'btn-with-border', - handler : function() { - var bufferWindow = new BufferWindow(); - bufferWindow.draw(BIOSAXS.proposal.getBufferById(data[0].bufferId)); - /** TODO: update when save **/ - } - - } ] - }, - items : [ { - fieldLabel : 'Buffer', - name : 'acronym', - readOnly : true, - value : buffer.acronym - }, { - fieldLabel : 'Composition', - name : 'last', - readOnly : true, - value : buffer.composition - }, { - xtype : 'textareafield', - fieldLabel : 'Comments', - value : buffer.comments, - name : 'last', - readOnly : true - - } ] - }); -}; - -DataCollectionWidget.prototype.getSpecimenContainer = function(data) { - return Ext.create('Ext.container.Container', { - layout : { - type : 'hbox' - }, - style : { - margin : '10px 10px 10px 10px' - }, - border : 0, - style : { - borderColor : '#000000', - borderStyle : 'solid', - borderWidth : '1px' - }, - defaults : { - labelWidth : 80, - // implicitly create Container by specifying xtype - xtype : 'datefield', - flex : 1, - - }, - items : [ this.getMacromoleculeContainer(data), this.getBufferContainer(data) ] - }); -}; - -DataCollectionWidget.prototype.getSeparator = function() { - return { - html : "
", - border : 0 - } -}; - -DataCollectionWidget.prototype.getFitStructurePanel = function(data) { - var _this = this; - - return Ext.create('Ext.container.Container', { - layout : { - type : 'hbox' - }, - style : { - margin : '10px 10px 10px 10px' - }, - border : 0, - style : { - borderColor : '#000000', - borderStyle : 'solid', - borderWidth : '1px' - }, - defaults : { - labelWidth : 80, - xtype : 'datefield', - flex : 1 - }, - items : [ - - ] - }); -}; - -DataCollectionWidget.prototype.getFitStructurePanelWorkflow = function(data) { - var _this = this; - var macromolecule = this.getMacromolecule(data); - - var items = []; - - /** Adding all the pdb files linked to the macromolecule **/ - // if (macromolecule.structure3VOs != null) { - // if (macromolecule.structure3VOs.length > 0) { - // - // items.push(); - // } - // } else { - // items.push({ - // html : "No apriori information added to this macromolecule. Apriori information needed for further analysis", - // margin : "5 5 5 5" - // }); - // } - var fitStructureToExperimentDataGrid = new FitStructureToExperimentDataGrid(); - - fitStructureToExperimentDataGrid.refresh(_this.data[0].subtractionId, _this.getMacromolecule(data)); - return Ext.create('Ext.container.Container', { - style : { - margin : '10px 10px 10px 10px' - }, - border : 0, - - style : { - borderColor : '#000000', - borderStyle : 'solid', - borderWidth : '1px' - }, - defaults : { - labelWidth : 80, - xtype : 'datefield', - flex : 1 - }, - items : [ fitStructureToExperimentDataGrid.getPanel() ], - listeners : { - afterrender : function() { - } - } - }); -}; -/** Static method **/ -DataCollectionWidget.prototype.RUNFitScattering = function(subtractionId, structureId) { - var _this = this; - /** Add to Workflow **/ - var adapter = new BiosaxsDataAdapter(); - var workflow = { - 'workflowTitle' : 'FitExperimentalDatatoStructure', - 'comments' : 'FitExperimentalDatatoStructure run from ISPyB for subtractionId: ' + subtractionId + ' and structureId ' + structureId - } - - var inputs = [ { - name : 'subtractionId', - value : subtractionId - }, { - name : 'structureId', - value : structureId - } ]; - - adapter.onSuccess.attach(function(sender, data) { - /** Add to Fit **/ - var adapter2 = new BiosaxsDataAdapter(); - var fit = { - 'workflowId' : data.workflowId, - 'subtractionId' : subtractionId, - 'structureId' : structureId, - 'comments' : 'Sent to workflow engine' - } - adapter2.onSuccess.attach(function(sender, fit) { - - }); - adapter2.addFitStructureData(fit); - - }); - adapter.addWorkflow(workflow, inputs); - -}; - -DataCollectionWidget.prototype.getSuperpositionTab = function(data) { - var _this = this; - - this.superpositionGrid = new SuperpositionGrid(); - - return Ext.create('Ext.container.Container', { - style : { - margin : '10px 10px 10px 10px' - }, - border : 0, - style : { - borderColor : '#000000', - borderStyle : 'solid', - borderWidth : '1px' - }, - items : [ _this.superpositionGrid.getPanel() ], - listeners : { - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - - }, - afterrender : function() { - /** Getting Rigid bodies **/ - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, result) { - _this.superpositionGrid.refresh(result); - }); - adapter.getSuperpositionBySubtractionId(data[1].subtractionId); - } - } - }); -}; - -DataCollectionWidget.prototype.getAdvancedTab = function(data) { - var _this = this; - return Ext.create('Ext.container.Container', { - style : { - margin : '10px 10px 10px 10px' - }, - border : 0, - style : { - borderColor : '#000000', - borderStyle : 'solid', - borderWidth : '1px' - }, - items : [ _this.getFitStructurePanel(data), _this.getFitStructurePanelWorkflow(data) ] - }); -}; - -DataCollectionWidget.prototype.getRigiBodyForm = function(data) { - var _this = this; - _this.rigiBodyGrid = new RigidModelGrid(); - return _this.rigiBodyGrid.getPanel(); - -}; - -DataCollectionWidget.prototype.getRigidBodyModelingTab = function(data) { - var _this = this; - return Ext.create('Ext.container.Container', { - style : { - margin : '10px 10px 10px 10px' - }, - border : 0, - style : { - borderColor : '#000000', - borderStyle : 'solid', - borderWidth : '1px' - }, - items : [ _this.getRigiBodyForm(data) ], - listeners : { - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - - }, - afterrender : function() { - /** Getting Rigid bodies **/ - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, result) { - _this.rigiBodyGrid.refresh(result); - }); - adapter.getRigidBodyModelingBySubtractionId(data[1].subtractionId); - } - } - }); -}; - -DataCollectionWidget.prototype.getTabs = function(data) { - var _this = this; - - this.subtractionCurveVisualizer = new SubtractionCurveVisualizer(); - - this.tabs = Ext.createWidget('tabpanel', { - activeTab : 1, - plain : true, - defaults : { - autoScroll : true, - bodyPadding : 10 - }, - items : [ { - title : 'Solution', - items : [ _this.getSpecimenContainer(data) ] - }, { - title : 'Primary Data Reduction', - active : true, - tabConfig : { - xtype : 'tab', - margins : '0 0 0 20', - }, - items : [ _this.subtractionCurveVisualizer.getPanel() ] - }, { - title : 'Abinitio', - items : [ _this.getAbinitioModellingContainer(data), _this.getSeparator(), _this.getModelViz(data) ] - }, { - title : 'Mixtures', - items : [ _this.getAdvancedTab(data) ] - }, { - title : 'Superpositions', - items : [ _this.getSuperpositionTab(data) ] - }, { - title : 'Rigid Body Modeling', - items : [ _this.getRigidBodyModelingTab(data) ] - } ] - }); - return this.tabs; -}; - -DataCollectionWidget.prototype.getPanel = function(data) { - var _this = this; - _this.data = data; - this.panel = Ext.create('Ext.container.Container', { - width : 1000, - layout : { - type : 'vbox', - align : 'stretch', - padding : 5 - }, - items : [ _this.getTabs(data) - - ] - }); - - this.panel.on("afterrender", function() { - _this.subtractionCurveVisualizer.refresh([ _this.data[1].mergeId ], [ _this.data[1].subtractionId ]); - }); - return this.panel; -}; - -DataCollectionWidget.prototype.getModelViz = function(data) { - this.modelViz = new ModelVisualizerForm({ - height : 800, - width : 1000 - }); - return this.modelViz.getPanel(); -}; - -/** - * PRIMARY DATA PROCESSING - */ -DataCollectionWidget.prototype.getPrimaryDataProcessingContainer = function(data) { - var _this = this; - this.primaryDataProcessingGrid = new PrimaryDataProcessingGrid({ - height : 250, - width : 1000, - title : 'Primary Data Processing' - }); - - this.primaryDataProcessingGrid.onSelected.attach(function(sender, selected) { - /** Refresh tabs **/ - var averagesId = []; - var subtractionIds = []; - - var subtractionKeys = {}; - for (var i = 0; i < selected.length; i++) { - if (selected[i].mergeId != null) { - averagesId.push(selected[i].mergeId); - } - - if (selected[i].subtractionId != null) { - if (selected[i].macromoleculeId != null) { - if (subtractionKeys[selected[i].subtractionId] == null) { - subtractionIds.push(selected[i].subtractionId); - } - subtractionKeys[selected[i].subtractionId] = true; - } - } - } - - /** Refreshing Primary Data Reduction **/ - _this.subtractionCurveVisualizer.refresh(averagesId, subtractionIds); - - }); - return this.primaryDataProcessingGrid.getPanel(data); -}; -/** - * getAbinitioModellingContainer - */ -DataCollectionWidget.prototype.getAbinitioModellingContainer = function(data) { - var _this = this; - - this.abinitioGrid = new AbinitioGrid(); - this.abinitioGrid.onSelected.attach(function(sender, models) { - _this.modelViz.refresh(models); - - }); - /** It may be abinitio models linked to the buffers **/ - var abinitioIdList = []; - for (var i = 0; i < data.length; i++) { - abinitioIdList.push(data[i].abInitioId); - } - - var uniqueIds = []; - $.each(abinitioIdList, function(i, el) { - if ($.inArray(el, uniqueIds) === -1) - uniqueIds.push(el); - }); - - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - _this.abinitioGrid.refresh(data); - }); - adapter.getAbinitioByIdsList(uniqueIds); - return this.abinitioGrid.getPanel([]); -}; - /** * Edit the information of a buffer * @@ -29163,258 +29163,258 @@ ShippingWidget.prototype.refresh = function() { }; -/** - * Widget container of Specimen grid and samplePlate widget - * Depending of the sample changer layout it may be displayed vertically or horizontally - * - * @param args - * - * #onExperimentChanged It happens when specimen are modified - */ -function SpecimenWidget(args){ - - this.width = 1000; - this.height = 600; - - if (args != null){ - if (args.width != null){ - this.width = args.width; - } - if (args.height != null){ - this.height = args.height; - } - } - - var _this = this; - - /** Specimen Grid **/ - this.specimenGrid = new SpecimenGrid({ - minHeight : 425, - selectionMode : "SINGLE", - editEnabled : false, - updateRowEnabled : true, - width : 900, - showTitle : false - }); - - - this.specimenGrid.onSpecimenChanged.attach(function(sender, specimen) { - _this.experiment.setSpecimenById(specimen); - _this.refresh(_this.experiment); - }); - - this.specimenGrid.onSelected.attach(function(sender, specimens) { - if (specimens.length > 0) { - _this.specimenSelected = specimens[0]; - } else { - _this.specimenSelected = null; - } - _this.samplePlateGroupWidget.selectSpecimens(specimens); - }); - - - /** Sample plate Widget **/ - this.samplePlateGroupWidget = new SamplePlateGroupWidget({ - showTitle : false, - height : 250, - margin : 5, - bbar : true - }); - - - this.samplePlateGroupWidget.onExperimentChanged.attach(function(sender, json) { - _this.refresh(new Experiment(json)); - }); - - this.samplePlateGroupWidget.onClick.attach(function(sender, args) { - /** Clicking on a plate * */ - var row = args.row; - var column = args.column; - var samplePlateId = args.samplePlate.samplePlateId; - - /** is specimen selected on the grid? * */ - if (_this.specimenSelected != null) { - /** Is position target empty * */ - if (_this.experiment.getSampleByPosition(args.samplePlate.samplePlateId, args.row, args.column).length == 0) { - var specimen = _this.experiment.getSampleById(_this.specimenSelected.specimenId); - if (specimen.sampleplateposition3VO == null) { - specimen.sampleplateposition3VO = {}; - } - - specimen.sampleplateposition3VO = { - columnNumber : column, - rowNumber : row, - samplePlateId : samplePlateId - }; - - _this.samplePlateGroupWidget.panel.setLoading("ISPyB: Saving specimen"); - var adapter = new BiosaxsDataAdapter(); - /** If success * */ - adapter.onSuccess.attach(function(sender, experiment) { - _this.samplePlateGroupWidget.panel.setLoading(false); - }); - - adapter.onError.attach(function(sender, error) { - _this.samplePlateGroupWidget.panel.setLoading(false); - showError(error); - }); - - adapter.saveSpecimen(specimen, _this.experiment); - - _this.samplePlateGroupWidget.refresh(_this.experiment); - _this.specimenGrid.refresh(_this.experiment); - //_this.refresh(_this.experiment); - _this.specimenGrid.deselectAll(); - - } else { - /** - * Can we merge? We can merge when specimen are the - * same. So, same buffer, macromolecule, concentration * - */ - var target = _this.experiment.getSampleByPosition(args.samplePlate.samplePlateId, args.row, args.column)[0]; - var specimen = _this.experiment.getSampleById(_this.specimenSelected.specimenId); - - if ((specimen.bufferId == target.bufferId) && (specimen.concentration == target.concentration)) { - if (((specimen.macromolecule3VO != null) && (target.macromolecule3VO != null) && (specimen.macromolecule3VO.macromoleculeId == target.macromolecule3VO.macromoleculeId)) || - ((specimen.macromolecule3VO == null) && (target.macromolecule3VO == null))) { - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - _this.refresh(new Experiment(data)); - _this.samplePlateGroupWidget.panel.setLoading(false); - - _this.onExperimentChanged.notify(experiment); - }); - adapter.onError.attach(function(sender, error) { - _this.samplePlateGroupWidget.panel.setLoading(false); - showError(error); - }); - _this.samplePlateGroupWidget.panel.setLoading("ISPyB: Merging specimens"); - adapter.mergeSpecimens(specimen.specimenId, target.specimenId); - } - } else { - alert("Well is not empty. Select another well!"); - } - } - } else { - var specimen = _this.experiment.getSampleByPosition(args.samplePlate.samplePlateId, args.row, args.column)[0]; - if (specimen != null) { - _this.specimenGrid.selectById(specimen.specimenId); - } - } - }); - - /** Events **/ - this.onExperimentChanged = new Event(this); -}; - -/** - * Return vbox or hbox depending on the slot positions of the plates - */ -SpecimenWidget.prototype.getContainerLayoutConfiguration = function(experiment){ - var dimensions = this.samplePlateGroupWidget.getDimensions(experiment.getSamplePlates()); - if (dimensions.maxSlotPositionRow < dimensions.maxSlotPositionColumn){ - return { - layout : "vbox", - specimenGridWidth : this.width - 10, - specimenGridHeight : this.height - 260, - samplePlateGroupWidth : this.width - 10, - samplePlateGroupHeight : 250 - }; - } - return { - layout : "hbox", - samplePlateGroupWidth : this.width*1/3 -10, - samplePlateGroupHeight : this.height - 10, - specimenGridWidth : this.width*2/3, - specimenGridHeight : this.height - 10 - }; - -}; - - -SpecimenWidget.prototype.refresh = function(experiment){ - this.experiment = experiment; - - /** Removing all components **/ - this.panel.removeAll(); - - var layoutConfiguration = this.getContainerLayoutConfiguration(experiment); - - /** Setting new width and height for layout vbox and hbox **/ - this.specimenGrid.width = layoutConfiguration.specimenGridWidth; - this.specimenGrid.height = layoutConfiguration.specimenGridHeight; - - this.samplePlateGroupWidget.width = layoutConfiguration.samplePlateGroupWidth; - this.samplePlateGroupWidget.height = layoutConfiguration.samplePlateGroupHeight; - - if (layoutConfiguration.layout == "hbox"){ - this.specimenGrid.margin = "0 0 0 5"; - this.specimenGrid.width =this.specimenGrid.width - 5; - } - /** Insert container depending on layout [vertical|horizontal] */ - var container = Ext.create('Ext.container.Container', { - layout : layoutConfiguration.layout, - height : this.height, - width : this.width, - padding : '2px', - items : [ ] - }); - if (layoutConfiguration.layout == "vbox"){ - container.insert(this.specimenGrid.getPanel()); - container.insert(this.samplePlateGroupWidget.getPanel()); - } - else{ - container.insert(this.samplePlateGroupWidget.getPanel()); - container.insert(this.specimenGrid.getPanel()); - } - - /** Insert Widget **/ - this.panel.insert(container); - - /** Load data **/ - this.specimenGrid.refresh(experiment); - this.samplePlateGroupWidget.refresh(experiment); - - -}; - -/** It creates a dummy container to be inserted the plates once the method refresh has been called - * This is necessay because we can not know the sample changer layout before hand - * **/ -SpecimenWidget.prototype.getPanel = function(){ - this.panel = Ext.create('Ext.container.Container', { - layout : 'vbox', - height : this.height, - border : 0, - margin : 5, - width : this.width, - items : [] - }); - return this.panel; -}; - - -SpecimenWidget.prototype.input = function() { - return { - experiment : DATADOC.getExperiment_10(), - proposal : DATADOC.getProposal_10() - }; -}; - -SpecimenWidget.prototype.test = function(targetId) { - var specimenWidget = new SpecimenWidget({ - height : 500, - width : 1000 - }); - BIOSAXS.proposal = new Proposal(specimenWidget.input().proposal); - var experiment = new Experiment(specimenWidget.input().experiment); - var panel = specimenWidget.getPanel(); - panel.render(targetId); - specimenWidget.refresh(experiment); - -}; - - +/** + * Widget container of Specimen grid and samplePlate widget + * Depending of the sample changer layout it may be displayed vertically or horizontally + * + * @param args + * + * #onExperimentChanged It happens when specimen are modified + */ +function SpecimenWidget(args){ + + this.width = 1000; + this.height = 600; + + if (args != null){ + if (args.width != null){ + this.width = args.width; + } + if (args.height != null){ + this.height = args.height; + } + } + + var _this = this; + + /** Specimen Grid **/ + this.specimenGrid = new SpecimenGrid({ + minHeight : 425, + selectionMode : "SINGLE", + editEnabled : false, + updateRowEnabled : true, + width : 900, + showTitle : false + }); + + + this.specimenGrid.onSpecimenChanged.attach(function(sender, specimen) { + _this.experiment.setSpecimenById(specimen); + _this.refresh(_this.experiment); + }); + + this.specimenGrid.onSelected.attach(function(sender, specimens) { + if (specimens.length > 0) { + _this.specimenSelected = specimens[0]; + } else { + _this.specimenSelected = null; + } + _this.samplePlateGroupWidget.selectSpecimens(specimens); + }); + + + /** Sample plate Widget **/ + this.samplePlateGroupWidget = new SamplePlateGroupWidget({ + showTitle : false, + height : 250, + margin : 5, + bbar : true + }); + + + this.samplePlateGroupWidget.onExperimentChanged.attach(function(sender, json) { + _this.refresh(new Experiment(json)); + }); + + this.samplePlateGroupWidget.onClick.attach(function(sender, args) { + /** Clicking on a plate * */ + var row = args.row; + var column = args.column; + var samplePlateId = args.samplePlate.samplePlateId; + + /** is specimen selected on the grid? * */ + if (_this.specimenSelected != null) { + /** Is position target empty * */ + if (_this.experiment.getSampleByPosition(args.samplePlate.samplePlateId, args.row, args.column).length == 0) { + var specimen = _this.experiment.getSampleById(_this.specimenSelected.specimenId); + if (specimen.sampleplateposition3VO == null) { + specimen.sampleplateposition3VO = {}; + } + + specimen.sampleplateposition3VO = { + columnNumber : column, + rowNumber : row, + samplePlateId : samplePlateId + }; + + _this.samplePlateGroupWidget.panel.setLoading("ISPyB: Saving specimen"); + var adapter = new BiosaxsDataAdapter(); + /** If success * */ + adapter.onSuccess.attach(function(sender, experiment) { + _this.samplePlateGroupWidget.panel.setLoading(false); + }); + + adapter.onError.attach(function(sender, error) { + _this.samplePlateGroupWidget.panel.setLoading(false); + showError(error); + }); + + adapter.saveSpecimen(specimen, _this.experiment); + + _this.samplePlateGroupWidget.refresh(_this.experiment); + _this.specimenGrid.refresh(_this.experiment); + //_this.refresh(_this.experiment); + _this.specimenGrid.deselectAll(); + + } else { + /** + * Can we merge? We can merge when specimen are the + * same. So, same buffer, macromolecule, concentration * + */ + var target = _this.experiment.getSampleByPosition(args.samplePlate.samplePlateId, args.row, args.column)[0]; + var specimen = _this.experiment.getSampleById(_this.specimenSelected.specimenId); + + if ((specimen.bufferId == target.bufferId) && (specimen.concentration == target.concentration)) { + if (((specimen.macromolecule3VO != null) && (target.macromolecule3VO != null) && (specimen.macromolecule3VO.macromoleculeId == target.macromolecule3VO.macromoleculeId)) || + ((specimen.macromolecule3VO == null) && (target.macromolecule3VO == null))) { + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + _this.refresh(new Experiment(data)); + _this.samplePlateGroupWidget.panel.setLoading(false); + + _this.onExperimentChanged.notify(experiment); + }); + adapter.onError.attach(function(sender, error) { + _this.samplePlateGroupWidget.panel.setLoading(false); + showError(error); + }); + _this.samplePlateGroupWidget.panel.setLoading("ISPyB: Merging specimens"); + adapter.mergeSpecimens(specimen.specimenId, target.specimenId); + } + } else { + alert("Well is not empty. Select another well!"); + } + } + } else { + var specimen = _this.experiment.getSampleByPosition(args.samplePlate.samplePlateId, args.row, args.column)[0]; + if (specimen != null) { + _this.specimenGrid.selectById(specimen.specimenId); + } + } + }); + + /** Events **/ + this.onExperimentChanged = new Event(this); +}; + +/** + * Return vbox or hbox depending on the slot positions of the plates + */ +SpecimenWidget.prototype.getContainerLayoutConfiguration = function(experiment){ + var dimensions = this.samplePlateGroupWidget.getDimensions(experiment.getSamplePlates()); + if (dimensions.maxSlotPositionRow < dimensions.maxSlotPositionColumn){ + return { + layout : "vbox", + specimenGridWidth : this.width - 10, + specimenGridHeight : this.height - 260, + samplePlateGroupWidth : this.width - 10, + samplePlateGroupHeight : 250 + }; + } + return { + layout : "hbox", + samplePlateGroupWidth : this.width*1/3 -10, + samplePlateGroupHeight : this.height - 10, + specimenGridWidth : this.width*2/3, + specimenGridHeight : this.height - 10 + }; + +}; + + +SpecimenWidget.prototype.refresh = function(experiment){ + this.experiment = experiment; + + /** Removing all components **/ + this.panel.removeAll(); + + var layoutConfiguration = this.getContainerLayoutConfiguration(experiment); + + /** Setting new width and height for layout vbox and hbox **/ + this.specimenGrid.width = layoutConfiguration.specimenGridWidth; + this.specimenGrid.height = layoutConfiguration.specimenGridHeight; + + this.samplePlateGroupWidget.width = layoutConfiguration.samplePlateGroupWidth; + this.samplePlateGroupWidget.height = layoutConfiguration.samplePlateGroupHeight; + + if (layoutConfiguration.layout == "hbox"){ + this.specimenGrid.margin = "0 0 0 5"; + this.specimenGrid.width =this.specimenGrid.width - 5; + } + /** Insert container depending on layout [vertical|horizontal] */ + var container = Ext.create('Ext.container.Container', { + layout : layoutConfiguration.layout, + height : this.height, + width : this.width, + padding : '2px', + items : [ ] + }); + if (layoutConfiguration.layout == "vbox"){ + container.insert(this.specimenGrid.getPanel()); + container.insert(this.samplePlateGroupWidget.getPanel()); + } + else{ + container.insert(this.samplePlateGroupWidget.getPanel()); + container.insert(this.specimenGrid.getPanel()); + } + + /** Insert Widget **/ + this.panel.insert(container); + + /** Load data **/ + this.specimenGrid.refresh(experiment); + this.samplePlateGroupWidget.refresh(experiment); + + +}; + +/** It creates a dummy container to be inserted the plates once the method refresh has been called + * This is necessay because we can not know the sample changer layout before hand + * **/ +SpecimenWidget.prototype.getPanel = function(){ + this.panel = Ext.create('Ext.container.Container', { + layout : 'vbox', + height : this.height, + border : 0, + margin : 5, + width : this.width, + items : [] + }); + return this.panel; +}; + + +SpecimenWidget.prototype.input = function() { + return { + experiment : DATADOC.getExperiment_10(), + proposal : DATADOC.getProposal_10() + }; +}; + +SpecimenWidget.prototype.test = function(targetId) { + var specimenWidget = new SpecimenWidget({ + height : 500, + width : 1000 + }); + BIOSAXS.proposal = new Proposal(specimenWidget.input().proposal); + var experiment = new Experiment(specimenWidget.input().experiment); + var panel = specimenWidget.getPanel(); + panel.render(targetId); + specimenWidget.refresh(experiment); + +}; + + function WarningWidget(args) { this.actions = []; diff --git a/ispyb-ws/src/main/java/ispyb/ws/rest/mx/AutoprocintegrationRestWebService.java b/ispyb-ws/src/main/java/ispyb/ws/rest/mx/AutoprocintegrationRestWebService.java index cdfe38b5e..4de80758b 100644 --- a/ispyb-ws/src/main/java/ispyb/ws/rest/mx/AutoprocintegrationRestWebService.java +++ b/ispyb-ws/src/main/java/ispyb/ws/rest/mx/AutoprocintegrationRestWebService.java @@ -8,6 +8,8 @@ import ispyb.server.mx.vos.autoproc.AutoProcIntegration3VO; import ispyb.server.mx.vos.autoproc.AutoProcProgram3VO; import ispyb.server.mx.vos.autoproc.AutoProcProgramAttachment3VO; +import ispyb.server.mx.vos.collections.DataCollection3VO; +import ispyb.server.mx.vos.collections.Session3VO; import java.io.File; import java.util.ArrayList; @@ -32,6 +34,7 @@ public class AutoprocintegrationRestWebService extends MXRestWebService { private final static Logger logger = Logger.getLogger(AutoprocintegrationRestWebService.class); + private static final String NOT_ALLOWED = "You don't have access to this resource"; @RolesAllowed({ "User", "Manager", "Industrial", "Localcontact" }) @GET @@ -126,6 +129,13 @@ public Response getAttachments(@PathParam("token") String token, @PathParam("pro } + + + private boolean checkProposalByAutoProcProgramId(int proposalId, int autoProcProgramId) throws NamingException, Exception{ + return this.getSession3Service().findByAutoProcProgramId(autoProcProgramId).getProposalVOId().equals(proposalId); + } + + /** * AutoProcProgramAttachment has not AutoProcProgramId mapped in the EJB object * so it is necessary to keep separately the possible list of ids in order @@ -147,13 +157,19 @@ public Response downloadAttachments( String methodName = "downloadAttachments"; long start = this.logInit(methodName, logger, token, proposal); try { - List ids = this.parseToInteger(autoprocattachmentids); + List autoProcProgramIds = this.parseToInteger(autoprocattachmentids); List> list = new ArrayList>(); HashMap filePaths = new HashMap(); String filename = "download.zip"; - for (Integer id : ids) { - AutoProcProgram3VO autoProcProgram3VO = this.getAutoProcProgram3Service().findByPk(id, true); + for (Integer autoProcProgramId : autoProcProgramIds) { + /** Check that id correspond to the proposal **/ + if (!this.checkProposalByAutoProcProgramId(this.getProposalId(proposal), autoProcProgramId)){ + throw new Exception(NOT_ALLOWED); + } + + + AutoProcProgram3VO autoProcProgram3VO = this.getAutoProcProgram3Service().findByPk(autoProcProgramId, true); /** Prefix for the name of the file and the internal structure if many results are retrieved **/ String prefix = String.format("%s_%s", autoProcProgram3VO.getProcessingPrograms(), autoProcProgram3VO.getAutoProcProgramId()); @@ -164,7 +180,7 @@ public Response downloadAttachments( String filePath = auto.getFilePath() + "/" + auto.getFileName(); if (new File(filePath).exists()){ if (new File(filePath).isFile()){ - if (ids.size() > 1){ + if (autoProcProgramIds.size() > 1){ String zipNameFile = prefix + "/" + auto.getFileName(); filePaths.put(zipNameFile, filePath); } @@ -176,7 +192,7 @@ public Response downloadAttachments( } /** If it is a single result then filename is the name of the program and the ID **/ - if (ids.size() == 1){ + if (autoProcProgramIds.size() == 1){ filename = prefix + ".zip"; } @@ -333,6 +349,10 @@ public Response getXScaleWilson(@PathParam("token") String token, @PathParam("pr } } + private boolean checkProposalByAutoProcProgramAttachmentId(int proposalId, int autoProcProgramAttachmentId) throws NamingException, Exception{ + return this.getSession3Service().findByAutoProcProgramAttachmentId(autoProcProgramAttachmentId).getProposalVOId().equals(proposalId); + } + @RolesAllowed({ "User", "Manager", "Industrial", "Localcontact" }) @GET @Path("{token}/proposal/{proposal}/mx/autoprocintegration/autoprocattachmentid/{autoProcAttachmentId}/download") @@ -343,11 +363,17 @@ public Response downloadAutoProcAttachment(@PathParam("token") String token, @Pa String methodName = "downloadAutoProcAttachment"; long start = this.logInit(methodName, logger, token, proposal); try { - AutoProcProgramAttachment3VO attachment = this.getAutoProcProgramAttachment3Service().findByPk(autoProcAttachmentId); - this.logFinish(methodName, start, logger); - File file = new File(attachment.getFilePath() + "/" + attachment.getFileName()); - this.logFinish(methodName, start, logger); - return this.downloadFileAsAttachment(file.getAbsolutePath()); + /** Checking that attachment is linked to the proposal **/ + if (this.checkProposalByAutoProcProgramAttachmentId(this.getProposalId(proposal), autoProcAttachmentId)){ + AutoProcProgramAttachment3VO attachment = this.getAutoProcProgramAttachment3Service().findByPk(autoProcAttachmentId); + this.logFinish(methodName, start, logger); + File file = new File(attachment.getFilePath() + "/" + attachment.getFileName()); + this.logFinish(methodName, start, logger); + return this.downloadFileAsAttachment(file.getAbsolutePath()); + } + else{ + throw new Exception(NOT_ALLOWED); + } } catch (Exception e) { return this.logError(methodName, e, start, logger); } @@ -360,13 +386,19 @@ public Response downloadAutoProcAttachment(@PathParam("token") String token, @Pa public Response getAutoProcAttachment(@PathParam("token") String token, @PathParam("proposal") String proposal, @PathParam("autoProcAttachmentId") int autoProcAttachmentId) { - String methodName = "downloadAutoProcAttachment"; + String methodName = "getAutoProcAttachment"; long start = this.logInit(methodName, logger, token, proposal); try { - AutoProcProgramAttachment3VO attachment = this.getAutoProcProgramAttachment3Service().findByPk(autoProcAttachmentId); - File file = new File(attachment.getFilePath() + "/" + attachment.getFileName()); - this.logFinish(methodName, start, logger); - return this.downloadFile(file.getAbsolutePath()); + /** Checking that attachment is linked to the proposal **/ + if (this.checkProposalByAutoProcProgramAttachmentId(this.getProposalId(proposal), autoProcAttachmentId)){ + AutoProcProgramAttachment3VO attachment = this.getAutoProcProgramAttachment3Service().findByPk(autoProcAttachmentId); + File file = new File(attachment.getFilePath() + "/" + attachment.getFileName()); + this.logFinish(methodName, start, logger); + return this.downloadFile(file.getAbsolutePath()); + } + else{ + throw new Exception(NOT_ALLOWED); + } } catch (Exception e) { return this.logError(methodName, e, start, logger); } From f0359679e32ddd743ec2150890a4c18a94b0a842 Mon Sep 17 00:00:00 2001 From: delageniere Date: Tue, 31 Oct 2017 15:39:32 +0100 Subject: [PATCH 31/38] analysis report improvement --- .../common/util/export/ExiPdfRtfExporter.java | 82 +- .../src/main/webapp/help/release_notes.txt | 13 +- .../src/main/webapp/js/ispyb/min/ispyb-bx.js | 42726 ++++++++-------- 3 files changed, 21414 insertions(+), 21407 deletions(-) diff --git a/ispyb-ejb/src/main/java/ispyb/common/util/export/ExiPdfRtfExporter.java b/ispyb-ejb/src/main/java/ispyb/common/util/export/ExiPdfRtfExporter.java index 9b3ac7606..347bca985 100644 --- a/ispyb-ejb/src/main/java/ispyb/common/util/export/ExiPdfRtfExporter.java +++ b/ispyb-ejb/src/main/java/ispyb/common/util/export/ExiPdfRtfExporter.java @@ -171,8 +171,9 @@ public class ExiPdfRtfExporter { public final static float CRYSTAL_IMAGE_HEIGHT = 174; //public final static float IMAGE_HEIGHT = 120; - public final static float IMAGE_HEIGHT = 100; + public final static float IMAGE_HEIGHT = 80; public final static float IMAGE_HEIGHT_SMALL = 50; + public final static float IMAGE_HEIGHT_SNAPSHOT = 60; // public final static float CRYSTAL_IMAGE_WIDTH = 160; // public final static float CRYSTAL_IMAGE_HEIGHT = 99; @@ -491,13 +492,16 @@ private void setSessionTable(Document document) throws Exception { * @throws Exception */ private void setDataCollectionTable(Document document) throws Exception { + document.add(new Paragraph("Data Collections:", FONT_TITLE)); document.add(new Paragraph(" ")); + if (dataCollections.isEmpty()) { document.add(new Paragraph("There is no data collection in this report", FONT_DOC)); } else { - document.add(new Paragraph(" ")); + document.add(new Paragraph(" ")); + // need the list of DCgroups for crystal class summary Map mapDataCollectionGroupIdCClass = new HashMap(); @@ -583,15 +587,17 @@ private void setDataCollectionMapData(Document document, Map dat table.getDefaultCell().setHorizontalAlignment(Element.ALIGN_LEFT); table.getDefaultCell().setBorderWidth(0); table.setBorder(0); + table.setCellsFitPage(true); + table.setWidth(90); // 1st Cell - parag = "Workflow: \n" - + "Protein: \n" - + "Sample: \n" - + "Prefix: \n" - + "Run #: \n" - + "Images: \n" - + "Transmission: \n"; + parag = "Workflow:\n" + + "Protein:\n" + + "Sample:\n" + + "Prefix:\n" + + "Run #:\n" + + "Images:\n" + + "Transmission:\n"; LOG.info("parag=" + parag); p = new Paragraph(parag, FONT_DOC); table.addCell(p); @@ -603,7 +609,7 @@ private void setDataCollectionMapData(Document document, Map dat + getCellParam(dataCollectionMapItem, "DataCollection_imagePrefix", null) + "\n" + getCellParam(dataCollectionMapItem, "DataCollection_dataCollectionNumber", null) + "\n" + getCellParam(dataCollectionMapItem, "DataCollection_numberOfImages", null) + "\n" - + getCellParam(dataCollectionMapItem, "DataCollection_transmission", df2) + "\n"; + + getCellParam(dataCollectionMapItem, "transmission", df2) + "%\n"; LOG.info("parag=" + parag); p = new Paragraph(parag, FONT_DOC_BOLD); table.addCell(p); @@ -622,14 +628,14 @@ private void setDataCollectionMapData(Document document, Map dat // Cell 4 - parag = getCellParam(dataCollectionMapItem, "DataCollection_resolution", df2) - + "("+ getCellParam(dataCollectionMapItem, "DataCollection_resolutionAtCorner", df2) + ") \n" - + getCellParam(dataCollectionMapItem, "DataCollection_wavelength", df3) + "\n" - + getCellParam(dataCollectionMapItem, "DataCollection_axisRange", df2) + "\n" - + getCellParam(dataCollectionMapItem, "DataCollection_omegaStart", df2) + "\n" - + getCellParam(dataCollectionMapItem, "DataCollection_exposureTime", df2) + "\n" - + getCellParam(dataCollectionMapItem, "DataCollection_flux", null) + "\n" - + getCellParam(dataCollectionMapItem, "DataCollection_flux_end", null) + "\n" ; + parag = getCellParam(dataCollectionMapItem, "DataCollection_resolution", df2) + Constants.ANGSTROM + + " ("+ getCellParam(dataCollectionMapItem, "DataCollection_resolutionAtCorner", df2) + Constants.ANGSTROM + ") \n" + + getCellParam(dataCollectionMapItem, "DataCollection_wavelength", df3) + Constants.ANGSTROM + "\n" + + getCellParam(dataCollectionMapItem, "DataCollection_axisRange", df2) + Constants.DEGREE + "\n" + + getCellParam(dataCollectionMapItem, "DataCollection_omegaStart", df2) + Constants.DEGREE + "\n" + + getCellParam(dataCollectionMapItem, "DataCollection_exposureTime", df2) + "s \n" + + getCellParam(dataCollectionMapItem, "DataCollection_flux", null) + "ph/sec \n" + + getCellParam(dataCollectionMapItem, "DataCollection_flux_end", null) + "ph/sec \n" ; table.addCell(new Paragraph(parag, FONT_DOC_BOLD)); @@ -643,13 +649,9 @@ private void setDataCollectionMapData(Document document, Map dat } else { table.addCell(" "); } - - //cellThumbnail.setRowspan(nbRows); - - + // 6 Cell : snapshot - Cell cellSnapshot = getCellImage(dataCollectionMapItem,"DataCollection_xtalSnapshotFullPath1", IMAGE_HEIGHT); - //cellSnapshot.setRowspan(nbRows); + Cell cellSnapshot = getCellImage(dataCollectionMapItem,"DataCollection_xtalSnapshotFullPath1", IMAGE_HEIGHT_SNAPSHOT); cellSnapshot.setBorderWidth(0); table.addCell(cellSnapshot); @@ -688,7 +690,13 @@ private void setDataCollectionMapData(Document document, Map dat private void setDataAnalysisMapData(Document document, Map dataCollectionMapItem) throws Exception { //row 1 + String parag = getCellParam(dataCollectionMapItem, "DataCollectionGroup_experimentType", null) + + " " + getCellParam(dataCollectionMapItem, "DataCollection_startTime", null); + Paragraph p = new Paragraph(parag, FONT_DOC_BLUE); + //document.add(p); + Table table = new Table(NB_COL_DATA_ANALYSIS); + table.setWidth(100); table.setCellsFitPage(true); table.setBorder(0); @@ -696,12 +704,12 @@ private void setDataAnalysisMapData(Document document, Map dataC table.getDefaultCell().setBorderWidth(0); // 1st Cell - String parag = "Protein: \n\n" + parag = "Protein: \n\n" + "Prefix: \n\n" + "Images: \n\n" ; LOG.info("parag=" + parag); - Paragraph p = new Paragraph(parag, FONT_DOC_SMALL); + p = new Paragraph(parag, FONT_DOC_SMALL); table.addCell(p); // 2st Cell @@ -723,9 +731,9 @@ private void setDataAnalysisMapData(Document document, Map dataC // Cell 4 parag = getCellParam(dataCollectionMapItem, "Workflow_workflowType", null) + "\n" - + getCellParam(dataCollectionMapItem, "DataCollection_resolution", df2) - + "("+ getCellParam(dataCollectionMapItem, "DataCollection_resolutionAtCorner", df2) + ") \n" - + getCellParam(dataCollectionMapItem, "DataCollection_wavelength", df3) + "\n" ; + + getCellParam(dataCollectionMapItem, "DataCollection_resolution", df2) + Constants.ANGSTROM + + "("+ getCellParam(dataCollectionMapItem, "DataCollection_resolutionAtCorner", df2) + Constants.ANGSTROM + ") \n" + + getCellParam(dataCollectionMapItem, "DataCollection_wavelength", df3) + Constants.ANGSTROM + "\n" ; p = new Paragraph(parag, FONT_DOC_SMALL_BOLD); table.addCell(p); @@ -955,20 +963,8 @@ private Cell getCellValue(String value) { private Cell getCellImage(Map dataCollectionMapItem, String imageParam, float image_size) throws Exception { if (dataCollectionMapItem.get(imageParam) != null && !(dataCollectionMapItem.get(imageParam).toString()).equals("") ) { - String image = dataCollectionMapItem.get(imageParam).toString(); - image = PathUtils.getPath(image); - try { - Image jpg1 = Image.getInstance(image); - jpg1.scaleAbsolute(jpg1.getWidth() * image_size / jpg1.getHeight(), image_size); - Cell cell = new Cell(jpg1); - cell.setLeading(0); - cell.setBorderWidth(0); - cell.setHorizontalAlignment(Element.ALIGN_CENTER); - cell.setVerticalAlignment(Element.ALIGN_CENTER); - return cell; - } catch (IOException e) { - return new Cell(new Paragraph(image + " not found", FONT_DOC)); - } + String imagePath = dataCollectionMapItem.get(imageParam).toString(); + return this.getCellImage(imagePath, image_size); } return new Cell(new Paragraph("", FONT_DOC)); } diff --git a/ispyb-ui/src/main/webapp/help/release_notes.txt b/ispyb-ui/src/main/webapp/help/release_notes.txt index b107e4d6f..9e02aaccc 100644 --- a/ispyb-ui/src/main/webapp/help/release_notes.txt +++ b/ispyb-ui/src/main/webapp/help/release_notes.txt @@ -1,4 +1,15 @@ -New TAG : 5.2.1 +New TAG : 5.3.3 + + +************** +* 31.10.2017 * +************** + +- work in progress: #135 +- fixes issue #176 + + +New TAG : 5.3.2 ************** diff --git a/ispyb-ui/src/main/webapp/js/ispyb/min/ispyb-bx.js b/ispyb-ui/src/main/webapp/js/ispyb/min/ispyb-bx.js index a98a06520..23e07209a 100644 --- a/ispyb-ui/src/main/webapp/js/ispyb/min/ispyb-bx.js +++ b/ispyb-ui/src/main/webapp/js/ispyb/min/ispyb-bx.js @@ -38,321 +38,321 @@ Event.prototype = { } }; -function GenericGraph(args) { - this.width = 600; - this.height = 400; - - this.targetId = null; - /** Free spaces in the borders * */ - this.top = 10; - this.left = 10; - this.bottom = 50; - this.right = 40; - - /** Ruler * */ - this.rulerHeight = 50; - this.rulerWidth = 50; - this.rulerStroke = 2; - this.rulerVerticalMarksNumber = 5; - - this.rulerMaxValue = null; - this.rulerMinValue = null; - - /** plot options * */ - this.plotPoints = true; - this.pointRadius = 2; - this.fillOpacityPoint = 0.2; - this.strokeOpacityPoint = 0.2; - - /** Cluster titles * */ - this.clusterTitleHeight = 20; - this.interClassesSpace = 2; - this.interClustersSpace = 4; - this.fontSize = 7; - - /** - * If true classes and title will be rendender in the rule otherwise will be - * integer values - */ - this.plotHorizontalByCluster = true; - - if (args != null) { - if (args.targetId != null) { - this.targetId = args.targetId; - } - if (args.plotHorizontalByCluster != null) { - this.plotHorizontalByCluster = args.plotHorizontalByCluster; - } - if (args.height != null) { - this.height = args.height; - } - if (args.width != null) { - this.width = args.width; - } - if (args.rulerMinValue != null) { - this.rulerMinValue = args.rulerMinValue; - } - if (args.rulerMaxValue != null) { - this.rulerMaxValue = args.rulerMaxValue; - } - if (args.rulerHeight != null) { - this.rulerHeight = args.rulerHeight; - } - - } -} - -GenericGraph.prototype.calculate = function(data) { - var result = {}; - - var checked = this.cleanArray(data); - - /** sorting array * */ - checked.sort(function(a, b) { - return a - b; - }); - - var median = this.getMedian(checked); - - result.median = median; - result.Q1 = Number(this.getQ1(checked)); - result.Q2 = Number(this.getQ2(checked)); - result.Q3 = Number(this.getQ3(checked)); - result.population = checked; - - result.IQR = Number(result.Q3 - result.Q1); - result.outlier_below_limit = result.Q1 - (1.5 * result.IQR); - result.outlier_above_limit = result.Q3 + (1.5 * result.IQR); - result.below_outliers = this.getBelowOutliers(result.outlier_below_limit, checked); - result.above_outliers = this.getAboveOutliers(result.outlier_above_limit, checked); - - result.min_whisker = this.minValueWhisker(result.outlier_below_limit, result.Q1, checked); - result.max_whisker = this.maxValueWhisker(result.outlier_above_limit, result.Q3, checked); - - return result; -}; - -GenericGraph.prototype.drawSVGVerticalText = function(x, y, text, properties) { - var transform = [ "transform", "translate(" + x + ", " + y + "), rotate(-90) " ]; - properties.push(transform); - SVG.drawText(0, 0, text, this.svg, properties); -}; - -/** Plot the numbers on the axis * */ -GenericGraph.prototype.plotRuler = function(rulerProperties) { - - SVG.drawRectangle(rulerProperties.vertical.x, rulerProperties.vertical.y, rulerProperties.vertical.width, rulerProperties.vertical.height, - this.svg, [ [ "fill", "black" ] ]); - var distance = rulerProperties.vertical.height / (this.rulerVerticalMarksNumber + 1); - for ( var i = 0; i <= this.rulerVerticalMarksNumber + 1; i++) { - var deltaHeight = distance * i; - var aux = rulerProperties.vertical.height - deltaHeight; - - var text = Number((aux / rulerProperties.vertical.height) * (rulerProperties.maxPoint - rulerProperties.minPoint) + rulerProperties.minPoint) - .toFixed(3); - - SVG.drawLine(rulerProperties.horizontal.x, this.top + deltaHeight, rulerProperties.horizontal.x - rulerProperties.markWidth, - this.top + deltaHeight, this.svg, [ [ "stroke", "black" ] ]); - SVG.drawText(this.left, this.top + distance * i + 5, text, this.svg, [ [ "style", "font-size:xx-small" ] ]); - /** Drawing the mark up to the end * */ - SVG.drawLine(rulerProperties.horizontal.x, this.top + deltaHeight, this.width - this.right, this.top + deltaHeight, this.svg, [ - [ "stroke", rulerProperties.markColor ], [ "stroke-width", "0.3" ] ]); - - if (i == this.rulerVerticalMarksNumber + 1) { - SVG.drawLine(rulerProperties.horizontal.x, this.top + deltaHeight, this.width - this.right, this.top + deltaHeight, this.svg, [ [ - "stroke", rulerProperties.markColor ] ]); - } - } - - /** Drawing horizontal rulers * */ - if (!this.plotHorizontalByCluster) { - var width = rulerProperties.horizontal.width; - var ratio = width / (rulerProperties.horizontal.xValues.range); - for ( i = 0; i < rulerProperties.horizontal.xValues.values.length; i++) { - var coorX = rulerProperties.horizontal.xValues.values[i] - rulerProperties.horizontal.xValues.min; - SVG.drawText(rulerProperties.horizontal.x + coorX * ratio, this.height - (this.bottom + (this.clusterTitleHeight)), - rulerProperties.horizontal.xValues.values[i], this.svg, [ [ "style", "font-size:small" ] ]); - } - } -}; - -GenericGraph.prototype.plotAxes = function(properties) { - /** - * Drawing canvas plot-free spaces SVG.drawRectangle(0, this.top, this.left, - * this.height, this.svg, [["fill", "pink"]]); SVG.drawRectangle(this.width - - * this.right, this.top, plot.width, plot.height, this.svg, [["fill", - * "pink"]]); SVG.drawRectangle(0, 0, this.width, this.top, this.svg, - * [["fill", "red"]]); SVG.drawRectangle(0, this.height - this.bottom, - * this.width, this.bottom, this.svg, [["fill", "red"]]); - */ - - /** Drawing ruler Space * */ - this.plotRuler({ - minPoint : Number(properties.minPoint), - maxPoint : Number(properties.maxPoint), - markColor : "black", - markWidth : 20, - vertical : { - x : this.left + this.rulerWidth - this.rulerStroke, - y : this.top, - width : this.rulerStroke, - height : this.height - (this.top + this.bottom + this.clusterTitleHeight) - this.rulerHeight - }, - horizontal : { - x : this.left + this.rulerWidth - this.rulerStroke, - y : this.height - (this.bottom + this.clusterTitleHeight + this.rulerHeight), - width : properties.width, - height : this.rulerStroke, - xValues : properties.xValues - } - }); - -}; - -/** Remove nulls and NaN elements in the array * */ -GenericGraph.prototype.cleanArray = function(data) { - var checked = []; - - /** checking data are numbers * */ - for ( var i = 0; i < data.length; i++) { - if (data[i] != null) { - if (!isNaN(data[i])) { - checked.push(data[i]); - } - } - } - return checked; -}; - -GenericGraph.prototype.refresh = function(data) { - document.getElementById(this.targetId).innerHTML = ""; - this.draw(this.targetId, data); -}; - -GenericGraph.prototype.getClassColor = function(className) { - for ( var i = 0; i < this.data.clusters.length; i++) { - var cluster = this.data.clusters[i]; - for ( var j = 0; j < cluster.classes.length; j++) { - var classes = cluster.classes[j]; - if (classes.name == className) { - if (classes.color != null) { - return classes.color; - } - } - } - } - return "black"; -}; - -GenericGraph.prototype.getDimensions = function(data) { - var results = {}; - var points = []; - - this.data = data; - var classesNumber = 0; - var xValues = []; - - for ( var i = 0; i < data.clusters.length; i++) { - var cluster = data.clusters[i]; - if (!this.plotHorizontalByCluster) { - xValues.push(data.clusters[i].x); - } - for ( var j = 0; j < cluster.classes.length; j++) { - var classes = cluster.classes[j]; - points = points.concat(classes.values); - classesNumber = classesNumber + 1; - } - } - - var checked = this.cleanArray(points); - - checked.sort(function(a, b) { - return a - b; - }); - - results.minPoint = checked[0]; - if (this.rulerMinValue != null) { - results.minPoint = this.rulerMinValue; - } - results.maxPoint = checked[checked.length - 1]; - if (this.rulerMaxValue != null) { - results.maxPoint = this.rulerMaxValue; - } - - results.classesNumber = classesNumber; - results.clusterNumber = data.clusters.length; - - var totalInterClassesFreeSpace = (classesNumber - data.clusters.length) * this.interClassesSpace; - var totalInterClusterFreeSpace = (data.clusters.length) * this.interClustersSpace; - results.classWidth = (this.width - (this.rulerWidth + this.left + this.right + totalInterClassesFreeSpace + totalInterClusterFreeSpace))/ classesNumber; - results.width = this.width - (this.right + this.left) - this.rulerWidth + this.rulerStroke; - - results.xValues = {}; - - xValues.sort(function(a, b) { - return a - b; - }); - results.xValues.values = xValues; - if (xValues.length > 0) { - results.xValues.min = xValues[0]; - results.xValues.max = xValues[xValues.length - 1]; - results.xValues.range = results.xValues.max - results.xValues.min; - } - return results; - -}; - -GenericGraph.prototype.draw = function(targetId, data) { - this.targetId = targetId; - var properties = (this.getDimensions(data)); - this.svg = SVG.createSVGCanvas(document.getElementById(this.targetId), [ [ "width", this.width ], [ "height", this.height ] ]); - this.plotAxes(properties); -}; - -GenericGraph.prototype.getMedian = function(checked) { - /** Calculating median * */ - if (checked.length % 2 == 1) { - return checked[Math.floor(checked.length / 2)]; - } else { - return (Number(checked[(checked.length / 2) - 1]) + Number(checked[checked.length / 2])) / 2; - } -}; - -GenericGraph.prototype.pointToPixel = function(value, boxProperties) { - var ratio = (value - boxProperties.minPoint) / (boxProperties.maxPoint - boxProperties.minPoint); - var pixelLength = boxProperties.height - boxProperties.y + this.top; - return (-1 * ratio) * (pixelLength) + (boxProperties.y + boxProperties.height); -}; - -GenericGraph.prototype.maxValueWhisker = function(aboveLimit, q3, array) { - var points = []; - for ( var i = 0; i < array.length; i++) { - if ((array[i] > q3) && (array[i]) <= aboveLimit) { - points.push(array[i]); - } - } - if (points.length > 0) { - points.sort(function(a, b) { - return a - b; - }); - return points[points.length - 1]; - } - return null; -}; - -GenericGraph.prototype.input = function() { - return DATADOC.getBoxWhikerData(); -}; - -GenericGraph.prototype.test = function(targetId) { - var plot = new GenericGraph({ - targetId : targetId, - height : 350, - width : 450, - maxBoxWidth : 25 - }); - plot.refresh(this.input()); -}; +function GenericGraph(args) { + this.width = 600; + this.height = 400; + + this.targetId = null; + /** Free spaces in the borders * */ + this.top = 10; + this.left = 10; + this.bottom = 50; + this.right = 40; + + /** Ruler * */ + this.rulerHeight = 50; + this.rulerWidth = 50; + this.rulerStroke = 2; + this.rulerVerticalMarksNumber = 5; + + this.rulerMaxValue = null; + this.rulerMinValue = null; + + /** plot options * */ + this.plotPoints = true; + this.pointRadius = 2; + this.fillOpacityPoint = 0.2; + this.strokeOpacityPoint = 0.2; + + /** Cluster titles * */ + this.clusterTitleHeight = 20; + this.interClassesSpace = 2; + this.interClustersSpace = 4; + this.fontSize = 7; + + /** + * If true classes and title will be rendender in the rule otherwise will be + * integer values + */ + this.plotHorizontalByCluster = true; + + if (args != null) { + if (args.targetId != null) { + this.targetId = args.targetId; + } + if (args.plotHorizontalByCluster != null) { + this.plotHorizontalByCluster = args.plotHorizontalByCluster; + } + if (args.height != null) { + this.height = args.height; + } + if (args.width != null) { + this.width = args.width; + } + if (args.rulerMinValue != null) { + this.rulerMinValue = args.rulerMinValue; + } + if (args.rulerMaxValue != null) { + this.rulerMaxValue = args.rulerMaxValue; + } + if (args.rulerHeight != null) { + this.rulerHeight = args.rulerHeight; + } + + } +} + +GenericGraph.prototype.calculate = function(data) { + var result = {}; + + var checked = this.cleanArray(data); + + /** sorting array * */ + checked.sort(function(a, b) { + return a - b; + }); + + var median = this.getMedian(checked); + + result.median = median; + result.Q1 = Number(this.getQ1(checked)); + result.Q2 = Number(this.getQ2(checked)); + result.Q3 = Number(this.getQ3(checked)); + result.population = checked; + + result.IQR = Number(result.Q3 - result.Q1); + result.outlier_below_limit = result.Q1 - (1.5 * result.IQR); + result.outlier_above_limit = result.Q3 + (1.5 * result.IQR); + result.below_outliers = this.getBelowOutliers(result.outlier_below_limit, checked); + result.above_outliers = this.getAboveOutliers(result.outlier_above_limit, checked); + + result.min_whisker = this.minValueWhisker(result.outlier_below_limit, result.Q1, checked); + result.max_whisker = this.maxValueWhisker(result.outlier_above_limit, result.Q3, checked); + + return result; +}; + +GenericGraph.prototype.drawSVGVerticalText = function(x, y, text, properties) { + var transform = [ "transform", "translate(" + x + ", " + y + "), rotate(-90) " ]; + properties.push(transform); + SVG.drawText(0, 0, text, this.svg, properties); +}; + +/** Plot the numbers on the axis * */ +GenericGraph.prototype.plotRuler = function(rulerProperties) { + + SVG.drawRectangle(rulerProperties.vertical.x, rulerProperties.vertical.y, rulerProperties.vertical.width, rulerProperties.vertical.height, + this.svg, [ [ "fill", "black" ] ]); + var distance = rulerProperties.vertical.height / (this.rulerVerticalMarksNumber + 1); + for ( var i = 0; i <= this.rulerVerticalMarksNumber + 1; i++) { + var deltaHeight = distance * i; + var aux = rulerProperties.vertical.height - deltaHeight; + + var text = Number((aux / rulerProperties.vertical.height) * (rulerProperties.maxPoint - rulerProperties.minPoint) + rulerProperties.minPoint) + .toFixed(3); + + SVG.drawLine(rulerProperties.horizontal.x, this.top + deltaHeight, rulerProperties.horizontal.x - rulerProperties.markWidth, + this.top + deltaHeight, this.svg, [ [ "stroke", "black" ] ]); + SVG.drawText(this.left, this.top + distance * i + 5, text, this.svg, [ [ "style", "font-size:xx-small" ] ]); + /** Drawing the mark up to the end * */ + SVG.drawLine(rulerProperties.horizontal.x, this.top + deltaHeight, this.width - this.right, this.top + deltaHeight, this.svg, [ + [ "stroke", rulerProperties.markColor ], [ "stroke-width", "0.3" ] ]); + + if (i == this.rulerVerticalMarksNumber + 1) { + SVG.drawLine(rulerProperties.horizontal.x, this.top + deltaHeight, this.width - this.right, this.top + deltaHeight, this.svg, [ [ + "stroke", rulerProperties.markColor ] ]); + } + } + + /** Drawing horizontal rulers * */ + if (!this.plotHorizontalByCluster) { + var width = rulerProperties.horizontal.width; + var ratio = width / (rulerProperties.horizontal.xValues.range); + for ( i = 0; i < rulerProperties.horizontal.xValues.values.length; i++) { + var coorX = rulerProperties.horizontal.xValues.values[i] - rulerProperties.horizontal.xValues.min; + SVG.drawText(rulerProperties.horizontal.x + coorX * ratio, this.height - (this.bottom + (this.clusterTitleHeight)), + rulerProperties.horizontal.xValues.values[i], this.svg, [ [ "style", "font-size:small" ] ]); + } + } +}; + +GenericGraph.prototype.plotAxes = function(properties) { + /** + * Drawing canvas plot-free spaces SVG.drawRectangle(0, this.top, this.left, + * this.height, this.svg, [["fill", "pink"]]); SVG.drawRectangle(this.width - + * this.right, this.top, plot.width, plot.height, this.svg, [["fill", + * "pink"]]); SVG.drawRectangle(0, 0, this.width, this.top, this.svg, + * [["fill", "red"]]); SVG.drawRectangle(0, this.height - this.bottom, + * this.width, this.bottom, this.svg, [["fill", "red"]]); + */ + + /** Drawing ruler Space * */ + this.plotRuler({ + minPoint : Number(properties.minPoint), + maxPoint : Number(properties.maxPoint), + markColor : "black", + markWidth : 20, + vertical : { + x : this.left + this.rulerWidth - this.rulerStroke, + y : this.top, + width : this.rulerStroke, + height : this.height - (this.top + this.bottom + this.clusterTitleHeight) - this.rulerHeight + }, + horizontal : { + x : this.left + this.rulerWidth - this.rulerStroke, + y : this.height - (this.bottom + this.clusterTitleHeight + this.rulerHeight), + width : properties.width, + height : this.rulerStroke, + xValues : properties.xValues + } + }); + +}; + +/** Remove nulls and NaN elements in the array * */ +GenericGraph.prototype.cleanArray = function(data) { + var checked = []; + + /** checking data are numbers * */ + for ( var i = 0; i < data.length; i++) { + if (data[i] != null) { + if (!isNaN(data[i])) { + checked.push(data[i]); + } + } + } + return checked; +}; + +GenericGraph.prototype.refresh = function(data) { + document.getElementById(this.targetId).innerHTML = ""; + this.draw(this.targetId, data); +}; + +GenericGraph.prototype.getClassColor = function(className) { + for ( var i = 0; i < this.data.clusters.length; i++) { + var cluster = this.data.clusters[i]; + for ( var j = 0; j < cluster.classes.length; j++) { + var classes = cluster.classes[j]; + if (classes.name == className) { + if (classes.color != null) { + return classes.color; + } + } + } + } + return "black"; +}; + +GenericGraph.prototype.getDimensions = function(data) { + var results = {}; + var points = []; + + this.data = data; + var classesNumber = 0; + var xValues = []; + + for ( var i = 0; i < data.clusters.length; i++) { + var cluster = data.clusters[i]; + if (!this.plotHorizontalByCluster) { + xValues.push(data.clusters[i].x); + } + for ( var j = 0; j < cluster.classes.length; j++) { + var classes = cluster.classes[j]; + points = points.concat(classes.values); + classesNumber = classesNumber + 1; + } + } + + var checked = this.cleanArray(points); + + checked.sort(function(a, b) { + return a - b; + }); + + results.minPoint = checked[0]; + if (this.rulerMinValue != null) { + results.minPoint = this.rulerMinValue; + } + results.maxPoint = checked[checked.length - 1]; + if (this.rulerMaxValue != null) { + results.maxPoint = this.rulerMaxValue; + } + + results.classesNumber = classesNumber; + results.clusterNumber = data.clusters.length; + + var totalInterClassesFreeSpace = (classesNumber - data.clusters.length) * this.interClassesSpace; + var totalInterClusterFreeSpace = (data.clusters.length) * this.interClustersSpace; + results.classWidth = (this.width - (this.rulerWidth + this.left + this.right + totalInterClassesFreeSpace + totalInterClusterFreeSpace))/ classesNumber; + results.width = this.width - (this.right + this.left) - this.rulerWidth + this.rulerStroke; + + results.xValues = {}; + + xValues.sort(function(a, b) { + return a - b; + }); + results.xValues.values = xValues; + if (xValues.length > 0) { + results.xValues.min = xValues[0]; + results.xValues.max = xValues[xValues.length - 1]; + results.xValues.range = results.xValues.max - results.xValues.min; + } + return results; + +}; + +GenericGraph.prototype.draw = function(targetId, data) { + this.targetId = targetId; + var properties = (this.getDimensions(data)); + this.svg = SVG.createSVGCanvas(document.getElementById(this.targetId), [ [ "width", this.width ], [ "height", this.height ] ]); + this.plotAxes(properties); +}; + +GenericGraph.prototype.getMedian = function(checked) { + /** Calculating median * */ + if (checked.length % 2 == 1) { + return checked[Math.floor(checked.length / 2)]; + } else { + return (Number(checked[(checked.length / 2) - 1]) + Number(checked[checked.length / 2])) / 2; + } +}; + +GenericGraph.prototype.pointToPixel = function(value, boxProperties) { + var ratio = (value - boxProperties.minPoint) / (boxProperties.maxPoint - boxProperties.minPoint); + var pixelLength = boxProperties.height - boxProperties.y + this.top; + return (-1 * ratio) * (pixelLength) + (boxProperties.y + boxProperties.height); +}; + +GenericGraph.prototype.maxValueWhisker = function(aboveLimit, q3, array) { + var points = []; + for ( var i = 0; i < array.length; i++) { + if ((array[i] > q3) && (array[i]) <= aboveLimit) { + points.push(array[i]); + } + } + if (points.length > 0) { + points.sort(function(a, b) { + return a - b; + }); + return points[points.length - 1]; + } + return null; +}; + +GenericGraph.prototype.input = function() { + return DATADOC.getBoxWhikerData(); +}; + +GenericGraph.prototype.test = function(targetId) { + var plot = new GenericGraph({ + targetId : targetId, + height : 350, + width : 450, + maxBoxWidth : 25 + }); + plot.refresh(this.input()); +}; /** * Using dygraph it plots a chart. Params: targetId, labelsContainerId, args @@ -2087,338 +2087,338 @@ MacromoleculeConditionGrid.prototype.test = function(targetId) { panel.render(targetId); }; - -function ItemGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ - this.id = id; - this.args = new Object(); - - this.defaultFormat = new ItemFormat(defaultFormat); - - if(selectedFormat != null){ - this.selected = new ItemFormat(selectedFormat); - } - else{ - this.selected = new ItemFormat(defaultFormat); - } - - if(overFormat != null){ - this.over = new ItemFormat(overFormat); - } - else{ - this.over = new ItemFormat(defaultFormat); - } - - if(draggingFormat != null){ - this.dragging = new ItemFormat(draggingFormat); - } - else{ - this.dragging = new ItemFormat(defaultFormat); - } - - //Events - this.stateChanged = new Event(this); - - - //Attaching events - var _this = this; - this._setEvents(); -}; - -ItemGraphFormatter.prototype.getType = function(){ - return this.args.type; -}; - - -ItemGraphFormatter.prototype.toJSON = function(){ - var json = this.args; - json.defaultFormat = this.getDefault().toJSON(); - json.over = this.getOver().toJSON(); - json.selected = this.getSelected().toJSON(); - json.dragging = this.getDragging().toJSON(); - json.id = this.id; - return json; -}; - -ItemGraphFormatter.prototype.loadFromJSON = function(json){ - this.args = json; - this.defaultFormat = new ItemFormat(json.defaultFormat); - this.over = new ItemFormat(json.over); - this.selected = new ItemFormat(json.selected); - this.dragging = new ItemFormat(json.dragging); - this._setEvents(); -}; - -ItemGraphFormatter.prototype._setEvents = function(){ - //Attaching events - var _this = this; - - this.defaultFormat.changed.attach(function (sender, item){ - _this.over.setSize(_this.defaultFormat.getSize()); - _this.selected.setSize(_this.defaultFormat.getSize()); - _this.dragging.setSize(_this.defaultFormat.getSize()); - _this.stateChanged.notify(_this); - }); - - this.selected.changed.attach(function (sender, item){ - _this.stateChanged.notify(_this); - }); - - this.over.changed.attach(function (sender, item){ - _this.stateChanged.notify(_this); - }); - - this.dragging.changed.attach(function (sender, item){ - _this.stateChanged.notify(_this); - }); -}; - -/** Getters **/ -ItemGraphFormatter.prototype.getId = function(){return this.id;}; -ItemGraphFormatter.prototype.getDefault = function(){return this.defaultFormat;}; -ItemGraphFormatter.prototype.getSelected = function(){return this.selected;}; -ItemGraphFormatter.prototype.getOver = function(){return this.over;}; -ItemGraphFormatter.prototype.getDragging = function(){return this.dragging;}; - -function ItemFormat(args){ - this.defaultFormat = new Object(); - this.args = new Object(); - this.args.title = new Object(); - //Defult properties - this.args.visible = true; - this.args.hidden = false; - this.args.stroke = "#000000"; - this.args.strokeOpacity = 0.8; - this.args["stroke-width"] = 1; - this.args.fill = "#000000"; - this.args["fill-opacity"] = 1; - this.args.size = 1; - this.args.opacity = 1; - this.args.fontSize = "8"; - this.args.fontColor = "#000000"; - - /** For directed edge with arrow **/ - //this.args.arrowSize = 1; - - - if (args != null){ - if (args.visible != null){ - this.args.visible = args.visible; - } - if (args.opacity != null){ - this.args.opacity = args.opacity; - } - if (args.size != null){ - this.args.size = args.size; - } - if (args.hidden != null){ - this.args.hidden = args.hidden; - } - if (args.stroke != null){ - this.args.stroke = this._fixColor(args.stroke); - } - if (args.strokeOpacity != null){ - this.args.strokeOpacity = args.strokeOpacity; - } - if (args["stroke-width"]!=null){ - this.args["stroke-width"] = args["stroke-width"]; - } - if (args["fill-opacity"]!=null){ - this.args["fill-opacity"] = args["fill-opacity"]; - } - if (args.shape!=null){ - this.args.shape = args.shape; - } - if (args.fill!=null){ - this.args.fill = this._fixColor(args.fill); - } - - - if (args.title!=null){ - if (args.title.fontSize!=null){ - this.args.title.fontSize = args.title.fontSize; - } - if (args.title.fill!=null){ - this.args.title.fill = this._fixColor(args.title.fill); - } - } - - /** For directed edge with arrow **/ - /*if (args.arrowSize!=null){ - this.args.arrowSize = args.arrowSize; - }*/ - - } - - this.changed = new Event(); -}; - -ItemFormat.prototype._fixColor = function(color){ - var fixed = color; - if (color.indexOf("green") != -1){ - fixed = '#04B431'; - } - - if (color.indexOf("blue") != -1){ - fixed = '#045FB4'; - } - - if (color.indexOf("red") != -1){ - fixed = '#DF0101'; - } - - if (color.indexOf("black") != -1){ - fixed = '#000000'; - } - - if (color.indexOf("white") != -1){ - fixed = '#FFFFFF'; - } - - if (color.indexOf("#") == -1){ - fixed = "#" + color; - } - return fixed; -}; - -ItemFormat.prototype.toJSON = function(){ - if(this.args.strokeOpacity != null){ - this.args["stroke-opacity"] = this.args.strokeOpacity; - delete this.args.strokeOpacity; - } - -// if(this.args.strokeWidth != null){ -// this.args["stroke-width"] = this.args.strokeWidth; -// delete this.args["stroke-width"]; -// } - - if(this.args.title.fontColor != null){ - this.args.title["font-color"] = this.args.title.fontColor; - } - else{ - this.args.title["font-color"] = this.args.fontColor;//;this.args.title.fontColor; - } - - if(this.args.title.fontSize != null){ - this.args.title["font-size"] = this.args.title.fontSize;//;this.args.title.fontColor; - } - else{ - this.args.title["font-size"] = this.args.fontSize;//;this.args.title.fontColor; - } - //return this.args; - return this.args; -}; - -ItemFormat.prototype.getAttribute = function(name){return this.args[name];}; - -//Getters and Setters -ItemFormat.prototype.setVisible = function(visible){ - if (this.args.visible != visible){ - this.args.visible = visible; - this.changed.notify(this); - } -}; - -ItemFormat.prototype.getVisible = function(){return this.args.visible;}; - -ItemFormat.prototype.setHidden = function(hidden){ - if (this.args.hidden != hidden){ - this.args.hidden = hidden; - this.changed.notify(this); - } -}; - -ItemFormat.prototype.getHidden = function(){return this.args.hidden;}; - - -ItemFormat.prototype.setStroke = function(stroke){ - if (this.args.stroke != stroke){ - this.args.stroke = stroke; - this.changed.notify(this); - } -}; - -ItemFormat.prototype.getStroke = function(){return this.args.stroke;}; - -ItemFormat.prototype.setStrokeOpacity = function(strokeOpacity){ - if (this.args.strokeOpacity != strokeOpacity){ - this.args.strokeOpacity = strokeOpacity; - this.changed.notify(this); - } -}; - -ItemFormat.prototype.getStrokeOpacity = function(){return this.args["stroke-opacity"];}; - -ItemFormat.prototype.setStrokeWidth = function(strokeWidth){ - if (this.args["stroke-width"] != strokeWidth){ - this.args["stroke-width"] = strokeWidth; - this.changed.notify(this); - } -}; - - -ItemFormat.prototype.getFillOpacity = function(){return this.args["fill-opacity"];}; - -ItemFormat.prototype.setfillOpacity = function(strokeWidth){ - if (this.args["fill-opacity"] != strokeWidth){ - this.args["fill-opacity"] = strokeWidth; - this.changed.notify(this); - } -}; - - -ItemFormat.prototype.getStrokeWidth = function(){ - return this.args["stroke-width"]; -}; - -ItemFormat.prototype.setFill = function(fill){ - if (this.args.fill != fill){ - this.args.fill = fill; - this.changed.notify(this); - } -}; - -ItemFormat.prototype.getFill = function(){return this.args.fill;}; - -ItemFormat.prototype.setSize = function(size){ - if (this.args.size != size){ - this.args.size = size; - this.changed.notify(this); - } -}; - -ItemFormat.prototype.getSize = function(){return this.args.size;}; - -ItemFormat.prototype.setOpacity = function(opacity){ - if (this.args.opacity != opacity){ - this.args.opacity = opacity; - this.changed.notify(this); - } -}; - -ItemFormat.prototype.getOpacity = function(){return this.args.opacity;}; - -ItemFormat.prototype.getArrowSize = function(){return this.args.arrowSize;}; - -ItemFormat.prototype.setArrowSize = function(arrowSize){ - if (this.args.arrowSize != arrowSize){ - this.args.arrowSize = arrowSize; - this.changed.notify(this); - } -}; - -ItemFormat.prototype.getFontSize = function(){return this.args.title.fontSize;}; - -ItemFormat.prototype.setFontSize = function(fontSize){ - - if (this.args.title.fontSize != fontSize){ - this.args.title.fontSize = fontSize; - this.changed.notify(this); - } -}; - - - - + +function ItemGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ + this.id = id; + this.args = new Object(); + + this.defaultFormat = new ItemFormat(defaultFormat); + + if(selectedFormat != null){ + this.selected = new ItemFormat(selectedFormat); + } + else{ + this.selected = new ItemFormat(defaultFormat); + } + + if(overFormat != null){ + this.over = new ItemFormat(overFormat); + } + else{ + this.over = new ItemFormat(defaultFormat); + } + + if(draggingFormat != null){ + this.dragging = new ItemFormat(draggingFormat); + } + else{ + this.dragging = new ItemFormat(defaultFormat); + } + + //Events + this.stateChanged = new Event(this); + + + //Attaching events + var _this = this; + this._setEvents(); +}; + +ItemGraphFormatter.prototype.getType = function(){ + return this.args.type; +}; + + +ItemGraphFormatter.prototype.toJSON = function(){ + var json = this.args; + json.defaultFormat = this.getDefault().toJSON(); + json.over = this.getOver().toJSON(); + json.selected = this.getSelected().toJSON(); + json.dragging = this.getDragging().toJSON(); + json.id = this.id; + return json; +}; + +ItemGraphFormatter.prototype.loadFromJSON = function(json){ + this.args = json; + this.defaultFormat = new ItemFormat(json.defaultFormat); + this.over = new ItemFormat(json.over); + this.selected = new ItemFormat(json.selected); + this.dragging = new ItemFormat(json.dragging); + this._setEvents(); +}; + +ItemGraphFormatter.prototype._setEvents = function(){ + //Attaching events + var _this = this; + + this.defaultFormat.changed.attach(function (sender, item){ + _this.over.setSize(_this.defaultFormat.getSize()); + _this.selected.setSize(_this.defaultFormat.getSize()); + _this.dragging.setSize(_this.defaultFormat.getSize()); + _this.stateChanged.notify(_this); + }); + + this.selected.changed.attach(function (sender, item){ + _this.stateChanged.notify(_this); + }); + + this.over.changed.attach(function (sender, item){ + _this.stateChanged.notify(_this); + }); + + this.dragging.changed.attach(function (sender, item){ + _this.stateChanged.notify(_this); + }); +}; + +/** Getters **/ +ItemGraphFormatter.prototype.getId = function(){return this.id;}; +ItemGraphFormatter.prototype.getDefault = function(){return this.defaultFormat;}; +ItemGraphFormatter.prototype.getSelected = function(){return this.selected;}; +ItemGraphFormatter.prototype.getOver = function(){return this.over;}; +ItemGraphFormatter.prototype.getDragging = function(){return this.dragging;}; + +function ItemFormat(args){ + this.defaultFormat = new Object(); + this.args = new Object(); + this.args.title = new Object(); + //Defult properties + this.args.visible = true; + this.args.hidden = false; + this.args.stroke = "#000000"; + this.args.strokeOpacity = 0.8; + this.args["stroke-width"] = 1; + this.args.fill = "#000000"; + this.args["fill-opacity"] = 1; + this.args.size = 1; + this.args.opacity = 1; + this.args.fontSize = "8"; + this.args.fontColor = "#000000"; + + /** For directed edge with arrow **/ + //this.args.arrowSize = 1; + + + if (args != null){ + if (args.visible != null){ + this.args.visible = args.visible; + } + if (args.opacity != null){ + this.args.opacity = args.opacity; + } + if (args.size != null){ + this.args.size = args.size; + } + if (args.hidden != null){ + this.args.hidden = args.hidden; + } + if (args.stroke != null){ + this.args.stroke = this._fixColor(args.stroke); + } + if (args.strokeOpacity != null){ + this.args.strokeOpacity = args.strokeOpacity; + } + if (args["stroke-width"]!=null){ + this.args["stroke-width"] = args["stroke-width"]; + } + if (args["fill-opacity"]!=null){ + this.args["fill-opacity"] = args["fill-opacity"]; + } + if (args.shape!=null){ + this.args.shape = args.shape; + } + if (args.fill!=null){ + this.args.fill = this._fixColor(args.fill); + } + + + if (args.title!=null){ + if (args.title.fontSize!=null){ + this.args.title.fontSize = args.title.fontSize; + } + if (args.title.fill!=null){ + this.args.title.fill = this._fixColor(args.title.fill); + } + } + + /** For directed edge with arrow **/ + /*if (args.arrowSize!=null){ + this.args.arrowSize = args.arrowSize; + }*/ + + } + + this.changed = new Event(); +}; + +ItemFormat.prototype._fixColor = function(color){ + var fixed = color; + if (color.indexOf("green") != -1){ + fixed = '#04B431'; + } + + if (color.indexOf("blue") != -1){ + fixed = '#045FB4'; + } + + if (color.indexOf("red") != -1){ + fixed = '#DF0101'; + } + + if (color.indexOf("black") != -1){ + fixed = '#000000'; + } + + if (color.indexOf("white") != -1){ + fixed = '#FFFFFF'; + } + + if (color.indexOf("#") == -1){ + fixed = "#" + color; + } + return fixed; +}; + +ItemFormat.prototype.toJSON = function(){ + if(this.args.strokeOpacity != null){ + this.args["stroke-opacity"] = this.args.strokeOpacity; + delete this.args.strokeOpacity; + } + +// if(this.args.strokeWidth != null){ +// this.args["stroke-width"] = this.args.strokeWidth; +// delete this.args["stroke-width"]; +// } + + if(this.args.title.fontColor != null){ + this.args.title["font-color"] = this.args.title.fontColor; + } + else{ + this.args.title["font-color"] = this.args.fontColor;//;this.args.title.fontColor; + } + + if(this.args.title.fontSize != null){ + this.args.title["font-size"] = this.args.title.fontSize;//;this.args.title.fontColor; + } + else{ + this.args.title["font-size"] = this.args.fontSize;//;this.args.title.fontColor; + } + //return this.args; + return this.args; +}; + +ItemFormat.prototype.getAttribute = function(name){return this.args[name];}; + +//Getters and Setters +ItemFormat.prototype.setVisible = function(visible){ + if (this.args.visible != visible){ + this.args.visible = visible; + this.changed.notify(this); + } +}; + +ItemFormat.prototype.getVisible = function(){return this.args.visible;}; + +ItemFormat.prototype.setHidden = function(hidden){ + if (this.args.hidden != hidden){ + this.args.hidden = hidden; + this.changed.notify(this); + } +}; + +ItemFormat.prototype.getHidden = function(){return this.args.hidden;}; + + +ItemFormat.prototype.setStroke = function(stroke){ + if (this.args.stroke != stroke){ + this.args.stroke = stroke; + this.changed.notify(this); + } +}; + +ItemFormat.prototype.getStroke = function(){return this.args.stroke;}; + +ItemFormat.prototype.setStrokeOpacity = function(strokeOpacity){ + if (this.args.strokeOpacity != strokeOpacity){ + this.args.strokeOpacity = strokeOpacity; + this.changed.notify(this); + } +}; + +ItemFormat.prototype.getStrokeOpacity = function(){return this.args["stroke-opacity"];}; + +ItemFormat.prototype.setStrokeWidth = function(strokeWidth){ + if (this.args["stroke-width"] != strokeWidth){ + this.args["stroke-width"] = strokeWidth; + this.changed.notify(this); + } +}; + + +ItemFormat.prototype.getFillOpacity = function(){return this.args["fill-opacity"];}; + +ItemFormat.prototype.setfillOpacity = function(strokeWidth){ + if (this.args["fill-opacity"] != strokeWidth){ + this.args["fill-opacity"] = strokeWidth; + this.changed.notify(this); + } +}; + + +ItemFormat.prototype.getStrokeWidth = function(){ + return this.args["stroke-width"]; +}; + +ItemFormat.prototype.setFill = function(fill){ + if (this.args.fill != fill){ + this.args.fill = fill; + this.changed.notify(this); + } +}; + +ItemFormat.prototype.getFill = function(){return this.args.fill;}; + +ItemFormat.prototype.setSize = function(size){ + if (this.args.size != size){ + this.args.size = size; + this.changed.notify(this); + } +}; + +ItemFormat.prototype.getSize = function(){return this.args.size;}; + +ItemFormat.prototype.setOpacity = function(opacity){ + if (this.args.opacity != opacity){ + this.args.opacity = opacity; + this.changed.notify(this); + } +}; + +ItemFormat.prototype.getOpacity = function(){return this.args.opacity;}; + +ItemFormat.prototype.getArrowSize = function(){return this.args.arrowSize;}; + +ItemFormat.prototype.setArrowSize = function(arrowSize){ + if (this.args.arrowSize != arrowSize){ + this.args.arrowSize = arrowSize; + this.changed.notify(this); + } +}; + +ItemFormat.prototype.getFontSize = function(){return this.args.title.fontSize;}; + +ItemFormat.prototype.setFontSize = function(fontSize){ + + if (this.args.title.fontSize != fontSize){ + this.args.title.fontSize = fontSize; + this.changed.notify(this); + } +}; + + + + /** * This class executes the actions @@ -4952,1101 +4952,2095 @@ function openExperiment(experimentId) { BIOSAXS.openExperiment(experimentId); } -var SITE_CONF = { - SAMPLE_CHANGER_CONFIGURATION : { - "3":{ - "platetype3VO": {"plateTypeId":4,"name":"96 Well plate","rowCount":8,"columnCount":12,"shape":"REC"}, - "name":"96 Well plate", - "slotPositionRow":"1", - "slotPositionColumn":"3", - "storageTemperature":"0", - "sampleplateposition3VOs":[], - "experimentId":0 - }, - "2":{ - "platetype3VO":{"plateTypeId":2,"name":" 4 x ( 8 + 3 ) Block","rowCount":4,"columnCount":11,"shape":"REC"}, - "name":" 4 x ( 8 + 3 ) Block", - "slotPositionRow":"1", - "slotPositionColumn":"2", - "storageTemperature":"0", - "sampleplateposition3VOs":[],"experimentId":0 - }, - "1":{ - "platetype3VO":{"plateTypeId":1,"name":"Deep Well","rowCount":8,"columnCount":12,"shape":"REC"}, - "name":"Deep Well", - "slotPositionRow":"1", - "slotPositionColumn":"1", - "storageTemperature":"0", - "sampleplateposition3VOs":[], - "experimentId":0 - } - } +var SITE_CONF = { + SAMPLE_CHANGER_CONFIGURATION : { + "3":{ + "platetype3VO": {"plateTypeId":4,"name":"96 Well plate","rowCount":8,"columnCount":12,"shape":"REC"}, + "name":"96 Well plate", + "slotPositionRow":"1", + "slotPositionColumn":"3", + "storageTemperature":"0", + "sampleplateposition3VOs":[], + "experimentId":0 + }, + "2":{ + "platetype3VO":{"plateTypeId":2,"name":" 4 x ( 8 + 3 ) Block","rowCount":4,"columnCount":11,"shape":"REC"}, + "name":" 4 x ( 8 + 3 ) Block", + "slotPositionRow":"1", + "slotPositionColumn":"2", + "storageTemperature":"0", + "sampleplateposition3VOs":[],"experimentId":0 + }, + "1":{ + "platetype3VO":{"plateTypeId":1,"name":"Deep Well","rowCount":8,"columnCount":12,"shape":"REC"}, + "name":"Deep Well", + "slotPositionRow":"1", + "slotPositionColumn":"1", + "storageTemperature":"0", + "sampleplateposition3VOs":[], + "experimentId":0 + } + } }; - -var ISPYB_CONF = { - load : function(config) { - for (var key in config) { - ISPYB_CONF[key] = config[key]; - } - }, - SAMPLE_CHANGER_CONFIGURATION : { - "1": { - "platetype3VO": {"plateTypeId": 1, "name": "Deep Well", "rowCount": 8, "columnCount": 12, "shape": "REC"}, - "name": "Deep Well", - "slotPositionRow": "1", - "slotPositionColumn": "1", - "storageTemperature": "0", - "sampleplateposition3VOs": [], - "experimentId": 0 - } - } + +var ISPYB_CONF = { + load : function(config) { + for (var key in config) { + ISPYB_CONF[key] = config[key]; + } + }, + SAMPLE_CHANGER_CONFIGURATION : { + "1": { + "platetype3VO": {"plateTypeId": 1, "name": "Deep Well", "rowCount": 8, "columnCount": 12, "shape": "REC"}, + "name": "Deep Well", + "slotPositionRow": "1", + "slotPositionColumn": "1", + "storageTemperature": "0", + "sampleplateposition3VOs": [], + "experimentId": 0 + } + } }; -var SITE_CONF = { - -}; +var SITE_CONF = { + +}; -/** - * Example form - * - * @witdh - * @height - */ -function AbinitioForm(args) { - this.id = BUI.id(); - this.width = null; - this.height = null; - - if (args != null) { - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; - } - } - - var _this = this; - /** Widgets **/ - this.abinitioGrid = new AbinitioGrid({ - width : null, - height : 200 - }); - - this.abinitioGrid.onSelected.attach(function(sender, models) { - var modelsIdList = []; - for ( var i in models) { - modelsIdList.push(models[i].modelId); - } - _this._renderPlot(_this.subtractions[0].subtractionId, modelsIdList); - _this._renderPDB(modelsIdList); - }); - - /** Dygraph Widget that plots fir files**/ - this.plotWidget = new PlotWidget({ - width : 745 / 2, - height : 300, - margin : "10 0 5 10" - }); - - /** PDB viewer **/ - this.viewer = new PDBViewer({ - width : 745 / 2, - height : 300 - }); - -} - -AbinitioForm.prototype._renderPlot = function(subtractionId, modelsIdList) { - /** Trying to plot tje subtraction and the models **/ - try { - var colors = [ "#669900", "#0000FF" ]; - this.plotWidget.refresh([], [ ], modelsIdList, [], [], colors); - } catch (e) { - console.log(e); - } -}; - -AbinitioForm.prototype._renderPDB = function(modelsIdList) { - /** Trying to plot the PDB file **/ - try { - var viz = []; - for (var i = 0; i < modelsIdList.length; i++) { - viz.push({ - modelId : modelsIdList[i], - color : "0xFF6600", - opacity : 0.8 - }); - } - this.viewer.refresh(viz); - } catch (e) { - console.log(e); - } -}; - -AbinitioForm.prototype._getItems = function() { - var _this = this; - return [ { - xtype : 'label', - forId : 'myFieldId', - text : 'INLINE HELP: To be updated', - margin : '15 0 20 10', - cls : "inline-help" - }, this.abinitioGrid.getPanel(), { - xtype : 'container', - layout : 'hbox', - items : [ this.plotWidget.getPanel(), this.viewer.getPanel() ] - } ] -}; - -AbinitioForm.prototype._getButtons = function() { - return []; -}; - -AbinitioForm.prototype.getPanel = function() { - var _this = this; - this.panel = Ext.create('Ext.form.Panel', { - width : this.width, - height : this.height, - margin : 10, - border : 1, - defaultType : 'textfield', - items : this._getItems(), - buttons : this._getButtons(), - listeners : { - afterrender : function() { - _this._populate(); - - } - } - }); - return this.panel; -}; - -/** Populates could be call when the DOM is not filled yet **/ -AbinitioForm.prototype._populate = function() { -}; - -/** It populates the form * */ -AbinitioForm.prototype.refresh = function(subtractions) { - this.subtractions = subtractions; - this.abinitioGrid.refresh(subtractions); -}; - -AbinitioForm.prototype.input = function() { - return {}; -}; - -/** It populates the form **/ -AbinitioForm.prototype.test = function(targetId) { - var macromoleculeForm = new AbinitioForm(); - var panel = macromoleculeForm.getPanel(); - panel.render(targetId); -}; +/** + * Example form + * + * @witdh + * @height + */ +function AbinitioForm(args) { + this.id = BUI.id(); + this.width = null; + this.height = null; -/** - * Example form - * - * @witdh - * @height - */ -function DataReductionForm(args) { - this.id = BUI.id(); - this.width = null; - this.height = null; - - if (args != null) { - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; - } - } - + if (args != null) { + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + } + + var _this = this; + /** Widgets **/ + this.abinitioGrid = new AbinitioGrid({ + width : null, + height : 200 + }); + + this.abinitioGrid.onSelected.attach(function(sender, models) { + var modelsIdList = []; + for ( var i in models) { + modelsIdList.push(models[i].modelId); + } + _this._renderPlot(_this.subtractions[0].subtractionId, modelsIdList); + _this._renderPDB(modelsIdList); + }); + + /** Dygraph Widget that plots fir files**/ + this.plotWidget = new PlotWidget({ + width : 745 / 2, + height : 300, + margin : "10 0 5 10" + }); + + /** PDB viewer **/ + this.viewer = new PDBViewer({ + width : 745 / 2, + height : 300 + }); + +} + +AbinitioForm.prototype._renderPlot = function(subtractionId, modelsIdList) { + /** Trying to plot tje subtraction and the models **/ + try { + var colors = [ "#669900", "#0000FF" ]; + this.plotWidget.refresh([], [ ], modelsIdList, [], [], colors); + } catch (e) { + console.log(e); + } +}; + +AbinitioForm.prototype._renderPDB = function(modelsIdList) { + /** Trying to plot the PDB file **/ + try { + var viz = []; + for (var i = 0; i < modelsIdList.length; i++) { + viz.push({ + modelId : modelsIdList[i], + color : "0xFF6600", + opacity : 0.8 + }); + } + this.viewer.refresh(viz); + } catch (e) { + console.log(e); + } +}; + +AbinitioForm.prototype._getItems = function() { + var _this = this; + return [ { + xtype : 'label', + forId : 'myFieldId', + text : 'INLINE HELP: To be updated', + margin : '15 0 20 10', + cls : "inline-help" + }, this.abinitioGrid.getPanel(), { + xtype : 'container', + layout : 'hbox', + items : [ this.plotWidget.getPanel(), this.viewer.getPanel() ] + } ] +}; + +AbinitioForm.prototype._getButtons = function() { + return []; +}; + +AbinitioForm.prototype.getPanel = function() { + var _this = this; + this.panel = Ext.create('Ext.form.Panel', { + width : this.width, + height : this.height, + margin : 10, + border : 1, + defaultType : 'textfield', + items : this._getItems(), + buttons : this._getButtons(), + listeners : { + afterrender : function() { + _this._populate(); + + } + } + }); + return this.panel; +}; + +/** Populates could be call when the DOM is not filled yet **/ +AbinitioForm.prototype._populate = function() { +}; + +/** It populates the form * */ +AbinitioForm.prototype.refresh = function(subtractions) { + this.subtractions = subtractions; + this.abinitioGrid.refresh(subtractions); +}; + +AbinitioForm.prototype.input = function() { + return {}; +}; + +/** It populates the form **/ +AbinitioForm.prototype.test = function(targetId) { + var macromoleculeForm = new AbinitioForm(); + var panel = macromoleculeForm.getPanel(); + panel.render(targetId); +}; + +/** + * Example form + * + * @witdh + * @height + */ +function DataReductionForm(args) { + this.id = BUI.id(); + this.width = null; + this.height = null; + + if (args != null) { + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + } + + var _this = this; + + /** Widgets **/ + this.plotWidget = new PlotWidget({ + width : 650, + height : 490 + }); + + /** Selected frames to be displayed **/ + this.selectedItems = { + frames : [], + averages : [], + subtractions : [] + }; + +} + +DataReductionForm.prototype._parseSelectedItemsToIds = function(selectedArray) { + var ids = []; + if (selectedArray != null) { + for (var i = 0; i < selectedArray.length; i++) { + ids.push(selectedArray[i].id); + } + } + return ids; +}; + +DataReductionForm.prototype.onSelectionChanged = function(columnName, selected) { + if (selected != null) { + if (columnName == "Frames") { + this.selectedItems.frames = selected; + this.selectedItems.subtractions = []; + } + if (columnName == "Averages") { + this.selectedItems.averages = selected; + } + if (columnName == "Subtractions") { + this.selectedItems.frames = []; + this.selectedItems.subtractions = selected; + } + } + this.plotWidget.refresh(this._parseSelectedItemsToIds(this.selectedItems.frames), this._parseSelectedItemsToIds(this.selectedItems.subtractions)); +}; + +DataReductionForm.prototype._getFramesExtPanel = function(store, columnName, height) { + var _this = this; + + var selModel = Ext.create('Ext.selection.RowModel', { + allowDeselect : true, + mode : 'MULTI', + listeners : { + selectionchange : function(sm, selections) { + var selected = []; + for (var i = 0; i < selections.length; i++) { + selected.push(selections[i].raw); + } + _this.onSelectionChanged(columnName, selected); + } + } + }); + + return Ext.create('Ext.grid.Panel', { + store : store, + margin : 10, + height : height, + width : 200, + selModel : selModel, + columns : [ { + text : columnName, + dataIndex : 'fileName', + flex : 1 + } ], + viewConfig : { + } + }); +}; + +DataReductionForm.prototype._getFramesPanel = function() { + var fields = [ 'fileName', 'type', 'id' ]; + + this.framesStore = Ext.create('Ext.data.Store', { + fields : fields, + sorters : 'fileName' + }); + + this.averagesStore = Ext.create('Ext.data.Store', { + fields : fields + }); + + this.subtractionStore = Ext.create('Ext.data.Store', { + fields : fields + }); + + var gridFrames = this._getFramesExtPanel(this.framesStore, "Frames", 375); + var gridAvgs = this._getFramesExtPanel(this.averagesStore, "Averages", 125); + var subtractionAvgs = this._getFramesExtPanel(this.subtractionStore, "Subtractions", 75); + + return { + xtype : 'container', + layout : 'vbox', + items : [ gridFrames, subtractionAvgs ] + }; +}; + +DataReductionForm.prototype._getImageContainer = function(name, help) { + var html = "
" + name + "
" + return { + xtype : 'container', + layout : 'vbox', + items : [ { + html : html, + margin : "5 0 0 0", + height : 95, + width : 100 + }, { + xtype : 'label', + forId : 'myFieldId', + text : help, + margin : '5 0 0 0', + cls : "inline-help" + } ] + } +}; + +DataReductionForm.prototype._getItems = function() { + var _this = this; + return [ { + xtype : 'container', + layout : 'hbox', + items : [ + this._getFramesPanel(), + this.plotWidget.getPanel(), + { + xtype : 'panel', + width : 110, + frame : true, + margin : "10 5 5 5", + border : 0, + layout : 'vbox', + items : [ this._getImageContainer("scattering", "Scattering"), this._getImageContainer("guinier", "Guinier Region"), + this._getImageContainer("kratky", "Kratky Plot"), this._getImageContainer("gnom", "P(r) distribution") ] + } ] + } ] +}; + +DataReductionForm.prototype._getButtons = function() { + return []; +}; + +DataReductionForm.prototype.getPanel = function() { + var _this = this; + this.panel = Ext.create('Ext.form.Panel', { + width : this.width, + height : this.height, + border : 0, + items : this._getItems(), + buttons : this._getButtons(), + listeners : { + afterrender : function() { + _this._populate(); + } + } + }); + return this.panel; +}; + +/** Populates could be call when the DOM is not filled yet **/ +DataReductionForm.prototype._populate = function() { +}; + +/** It populates the form * */ +DataReductionForm.prototype.refresh = function(subtractions) { + if (subtractions != null) { + for (var i = 0; i < subtractions.length; i++) { + /** Loading frame grids **/ + var subtraction = subtractions[i]; + var averages = [ { + fileName : BUI.getFileName(subtraction.bufferAverageFilePath), + type : 'bufferAvg', + id : subtraction.subtractionId + }, { + fileName : BUI.getFileName(subtraction.sampleAverageFilePath), + type : 'sampleAvg', + id : subtraction.subtractionId + } + + ]; + this.averagesStore.loadData(averages, true); + this.subtractionStore.loadData([ { + fileName : BUI.getFileName(subtraction.substractedFilePath), + type : 'SUBTRACTION', + id : subtraction.subtractionId + } ], true); + + var frames = []; + /** Buffers **/ + if (subtraction.bufferOneDimensionalFiles != null) { + if (subtraction.bufferOneDimensionalFiles.frametolist3VOs != null) { + for (var j = 0; j < subtraction.bufferOneDimensionalFiles.frametolist3VOs.length; j++) { + var frametolist3VO = subtraction.bufferOneDimensionalFiles.frametolist3VOs[j]; + if (frametolist3VO.frame3VO != null) { + frames.push({ + fileName : BUI.getFileName(frametolist3VO.frame3VO.filePath), + type : 'BUFFER', + id : frametolist3VO.frame3VO.frameId + }); + } + } + } + } + /** Samples **/ + if (subtraction.sampleOneDimensionalFiles != null) { + if (subtraction.sampleOneDimensionalFiles.frametolist3VOs != null) { + for (var j = 0; j < subtraction.sampleOneDimensionalFiles.frametolist3VOs.length; j++) { + var frametolist3VO = subtraction.sampleOneDimensionalFiles.frametolist3VOs[j]; + if (frametolist3VO.frame3VO != null) { + frames.push({ + fileName : BUI.getFileName(frametolist3VO.frame3VO.filePath), + type : 'SAMPLE', + id : frametolist3VO.frame3VO.frameId + }); + } + } + } + } + + this.framesStore.loadData(frames, true); + + /** Loading images **/ + this._displayImage("scattering", subtraction.subtractionId); + this._displayImage("kratky", subtraction.subtractionId); + this._displayImage("guinier", subtraction.subtractionId); + this._displayImage("gnom", subtraction.subtractionId); + } + } +}; + +DataReductionForm.prototype._displayImage = function(name, subtractionId) { + var url = BUI.getURL() + '&type=' + name + '&subtractionId=' + subtractionId; + var event = "OnClick= window.open('" + url + "')"; + document.getElementById(this.id + "_" + name).innerHTML = ''; +}; + +DataReductionForm.prototype.input = function() { + return {}; +}; + +/** It populates the form **/ +DataReductionForm.prototype.test = function(targetId) { + var macromoleculeForm = new DataReductionForm(); + var panel = macromoleculeForm.getPanel(); + panel.render(targetId); +}; + +function PlotWidget(args) { + this.width = 600; + this.height = 600; + this.id = BUI.id(); + + this.linear = false; + + this.margin = "10 0 0 0"; + /** for each stat the max and minimum value when it is scaled in order to show correctly in the legend **/ + this.ranges = {}; + if (args != null) { + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + if (args.margin != null) { + this.margin = args.margin; + } + } + +} + +PlotWidget.prototype.getMenu = function() { + var _this = this; + /** Actions buttons **/ + var actions = []; + actions.push("->"); + actions.push({ + text : "Export as Image", + scope : this, + icon : '../images/save.gif', + handler : function(item, pressed) { + var largeImage = document.createElement("img"); + largeImage.style.display = 'block'; + largeImage.style.width = 200 + "px"; + largeImage.style.height = 200 + "px"; + largeImage.setAttribute('src', Dygraph.Export.asCanvas(this.dygraphObject.dygraph).toDataURL()); + window.open(Dygraph.Export.asCanvas(this.dygraphObject.dygraph).toDataURL(), 'Image', ''); + } + }); + + return actions; +}; + +/** Looks for the maximum value and then divide everything but that value **/ +PlotWidget.prototype.scaledData = function(data) { + for (var i = 0; i < data.length; i++) { + var values = this.getMaxAndMinValue(data[i]); + data[i] = this.divideValuesByMax(data[i], values.max); + this.ranges[data[i].label] = values; + } + return data; +}; + +/** Given a stat float[] and a max number it will divide each value by max **/ +PlotWidget.prototype.divideValuesByMax = function(stat, max) { + for (var j = 0; j < stat.data.length; j++) { + if (max != 0) { + stat.data[j] = Number(stat.data[j]) / max; + stat.std[j] = Number(stat.std[j]) / max; + } + } + return stat; +}; + +/** returns max value of a stat **/ +PlotWidget.prototype.getMaxAndMinValue = function(stat) { + var max = 0; + var min = stat.data[0]; + for (var j = 0; j < stat.data.length; j++) { + if (Number(stat.data[j]) > max) { + max = Number(stat.data[j]); + } + if (Number(stat.std[j]) > max) { + max = Number(stat.std[j]); + } + if (Number(stat.data[j]) < min) { + min = Number(stat.data[j]); + } + } + return { + max : Number(max), + min : Number(min) + }; +}; + +PlotWidget.prototype._renderDygraph = function(parsed, colors, labels) { + this.dygraphObject = new StdDevDyGraph(this.id, { + width : this.width - 20, + height : this.height - 40, + xlabel : "", + }); + + this.dygraphObject.draw(parsed, colors, labels); + +}; + +PlotWidget.prototype.getPanel = function() { + this.panel = Ext.create('Ext.panel.Panel', { + width : this.width, + height : this.height, + margin : this.margin, + tbar : this.getMenu(), + items : [ { + html : "", + id : this.id, + width : this.width, + height : this.height, + padding : 10, + margin : "0 0 0 -30", + border : 0 + } ] + }); + + return this.panel; +}; + +PlotWidget.prototype.getPoint = function(y, error) { + var minus = y - error; + var max = y + error; + + if (this.linear) { + return [ Math.abs(minus), y, Math.abs(max) ]; + } + if ((minus != 0) && (max != 0)) { + return [ Math.log(Math.abs(minus)), Math.log(y), Math.log(Math.abs(max)) ]; + } else { + return [ Math.log(y), Math.log(y), Math.log(y) ]; + } + +}; + +PlotWidget.prototype.getDataPlot = function(frames, subtractions, models, fits, rbms) { + var files = []; + var labels = [ "Intensity" ]; + if (frames != null) { + for (var i = 0; i < frames.length; i++) { + files.push(frames[i].data); + labels.push(frames[i].fileName); + } + } + function splitData(data, column, errorColumn, name){ + var result = [] + for (var j = 0; j < data.length; j++) { + console.log(data[j][column]); + result.push([j,data[j][column],data[j][errorColumn]]);//[0, data[i][column],0]]); + } + files.push(result); + labels.push(name); + } + + if (subtractions != null) { + for (var i = 0; i < subtractions.length; i++) { + /** For subtraction **/ + files.push(subtractions[i].subtraction.data); + labels.push(subtractions[i].subtraction.fileName); + /** For sample average **/ +// files.push(subtractions[i].sampleAvg.data); +// labels.push(subtractions[i].sampleAvg.fileName); + /** For buffer average **/ +// files.push(subtractions[i].bufferAvg.data); +// labels.push(subtractions[i].bufferAvg.fileName); + } + } + + if (models != null) { + for (var i = 0; i < models.length; i++) { + for ( var key in models[i]) { + splitData(models[i][key].fir.data, 1, 2, "Intensity"); + splitData(models[i][key].fir.data, 3, 3, "Fit"); + } + } + } + + if (fits != null) { + for (var i = 0; i < fits.length; i++) { + for ( var key in fits[i]) { + + /** adding fit file to be plotted **/ + if (fits[i][key].fit.data[0].length == 3){ + splitData(fits[i][key].fit.data, 1, 1, "Intensity"); + splitData(fits[i][key].fit.data, 2, 2, "Fit"); + } + + /** s, Iexp(s), err, Ifit(s). **/ + if (fits[i][key].fit.data[0].length == 4){ + splitData(fits[i][key].fit.data, 1, 2, "Intensity"); + splitData(fits[i][key].fit.data, 3, 3, "Fit"); + } + + if (fits[i][key].fit.data[0].length == 5){ + /** X Intensity Fit Error Residues **/ + + splitData(fits[i][key].fit.data, 1, 3, "Intensity"); + splitData(fits[i][key].fit.data, 2, 2, "Fit"); + } + } + } + } + + var dataPoints = []; + if (files.length > 0) { + for (var i = 0; i < files[0].length; i++) { + dataPoints.push([ files[0][i][0], this.getPoint(files[0][i][1], files[0][i][2]) ]); + } + if (files.length > 1) { + for (var i = 1; i < files.length; i++) { + for (var j = 0; j < dataPoints.length; j++) { + if (files[i][j] != null){ + dataPoints[j].push(this.getPoint(files[i][j][1], files[i][j][2])); + } + else{ + dataPoints[j].push([0,0,0]); + } + } + } + } + } + + return { + dataPoints : dataPoints, + labels : labels + } +}; + +PlotWidget.prototype.refresh = function(frames, subtractions, models, fits, rbms, colors) { + + var _this = this; + this.panel.setLoading("Reading Files"); + + var dataAdapter = new BiosaxsDataAdapter(); + dataAdapter.onSuccess.attach(function(sender, data) { + _this.panel.setLoading("Rendering"); + var parsed = _this.getDataPlot(data.frames, data.subtractions, data.models, data.fits, rbms); + _this._renderDygraph(parsed.dataPoints, colors, parsed.labels); + _this.panel.setLoading(false); + }); + dataAdapter.onError.attach(function(sender, data) { + _this.panel.setLoading(false); + }); + dataAdapter.getDataPlot(frames, subtractions, models, fits, rbms); +}; + +PlotWidget.prototype.input = function() { + return DATADOC.getHPLCData(); +}; + + +/** + * Fit form + * + * @witdh + * @height + */ +function FitForm(args) { + this.id = BUI.id(); + this.width = null; + this.height = null; + + if (args != null) { + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + } + + var _this = this; + + /** Widgets **/ + this.fitGrid = new FitStructureToExperimentDataGrid({ + width : null, + height : 200 + }); + + this.fitGrid.onSelected.attach(function(sender, fits) { + var modelsIdList = []; + for ( var i in fits) { + modelsIdList.push(fits[i].fitStructureToExperimentalDataId); + } + _this._renderPlot(_this.subtractions[0].subtractionId, modelsIdList); +// var adapter = new BiosaxsDataAdapter(); +// adapter.onSuccess.attach(function(sender, data) { +// +// }); +// adapter.getScatteringCurveByFrameIdsList([], [], [], ids); + }); + + + /** Dygraph Widget that plots fir files**/ + this.plotWidget = new PlotWidget({ + width : 745, + height : 300, + margin : "10 0 10 10" + }); +} + +FitForm.prototype._renderPlot = function(subtractionId, modelsIdList) { + /** Trying to plot tje subtraction and the models **/ + try { + var colors = [ "#669900", "#0000FF" ]; + + this.plotWidget.refresh([], [ ], [], modelsIdList, [], colors); + } catch (e) { + console.log(e); + } +}; + +FitForm.prototype._getItems = function() { + var _this = this; + return [ { + xtype : 'label', + forId : 'myFieldId', + text : 'INLINE HELP: To be updated', + margin : '15 0 20 10', + cls : "inline-help" + }, this.fitGrid.getPanel(), this.plotWidget.getPanel() ] + +}; + +FitForm.prototype._getButtons = function() { + return []; +}; + +FitForm.prototype.getPanel = function() { + var _this = this; + this.panel = Ext.create('Ext.form.Panel', { + width : this.width, + height : this.height, + margin : 10, + border : 1, + defaultType : 'textfield', + items : this._getItems(), + buttons : this._getButtons(), + listeners : { + afterrender : function() { + _this._populate(); + + } + } + }); + return this.panel; +}; + +/** Populates could be call when the DOM is not filled yet **/ +FitForm.prototype._populate = function() { +}; + +/** It populates the form * */ +FitForm.prototype.refresh = function(subtractions) { + this.subtractions = subtractions; + this.fitGrid.refresh(subtractions); +}; + +FitForm.prototype.input = function() { + return {}; +}; + +/** It populates the form **/ +FitForm.prototype.test = function(targetId) { + var macromoleculeForm = new FitForm(); + var panel = macromoleculeForm.getPanel(); + panel.render(targetId); +}; + +/** + * Example form + * + * @witdh + * @height + */ +function RigidBodyModelingResultForm(args) { + this.id = BUI.id(); + this.width = null; + this.height = null; + + if (args != null) { + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + } + + var _this = this; + /** Widgets **/ + this.rigidModelGrid = new RigidModelGrid({ + width : null, + height : 200 + }); + + this.rigidModelGrid.onSelected.attach(function(sender, fits){ + var ids = []; + for ( var i in fits) { + ids.push(fits[i].fitStructureToExperimentalDataId); + } + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data){ +// debugger + + }); + + adapter.getScatteringCurveByFrameIdsList([], [], [], ids); + }); + +} + +RigidBodyModelingResultForm.prototype._getItems = function() { + var _this = this; + return [ { + xtype : 'label', + forId : 'myFieldId', + text : 'INLINE HELP: To be updated', + margin : '15 0 20 10', + cls : "inline-help" + }, this.rigidModelGrid.getPanel() ] + +}; + +RigidBodyModelingResultForm.prototype._getButtons = function() { + return []; +}; + +RigidBodyModelingResultForm.prototype.getPanel = function() { + var _this = this; + this.panel = Ext.create('Ext.form.Panel', { + width : this.width, + height : this.height, + margin : 10, + border : 1, + defaultType : 'textfield', + items : this._getItems(), + buttons : this._getButtons(), + listeners : { + afterrender : function() { + _this._populate(); + + } + } + }); + return this.panel; +}; + +/** Populates could be call when the DOM is not filled yet **/ +RigidBodyModelingResultForm.prototype._populate = function() { +}; + +/** It populates the form * */ +RigidBodyModelingResultForm.prototype.refresh = function(subtractions) { + this.rigidModelGrid.refresh(subtractions); +}; + +RigidBodyModelingResultForm.prototype.input = function() { + return {}; +}; + +/** It populates the form **/ +RigidBodyModelingResultForm.prototype.test = function(targetId) { + var macromoleculeForm = new RigidBodyModelingResultForm(); + var panel = macromoleculeForm.getPanel(); + panel.render(targetId); +}; + +/** + * Example form + * + * @witdh + * @height + */ +function SuperpositionForm(args) { + this.id = BUI.id(); + this.width = null; + this.height = null; + + if (args != null) { + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + } + + var _this = this; + + /** Widgets **/ + this.superpositionGrid = new SuperpositionGrid({ + width : null, + height : 200 + }); + + this.superpositionGrid.onSelected.attach(function(sender, superpositions) { + var ids = []; + for ( var i in superpositions) { + ids.push(superpositions[i].superpositionId); + } +// _this._renderAbinitio(ids); +// _this.aprioriPDBViewer.refresh(); + _this._renderAligned(ids); + // getAlignedPDBContentBySuperpositionList + }); + + /** PDB viewer **/ +// this.abinitioPDBViewer = new PDBViewer({ +// width : 860 / 2, +// height : 300 / 2, +// margin : 0 +// }); +// +// /** PDB viewer **/ +// this.aprioriPDBViewer = new StructurePDBViewer({ +// width : 860 / 2, +// height : 300 / 2, +// margin : 0 +// }); + + this.alignedPDBViewer = new AlignedSuperpositionPDBViewer({ + width : 860 , + height : 300 + }); + +} + +SuperpositionForm.prototype._renderAligned = function(modelsIdList) { + /** Trying to plot the PDB file **/ + try { + this.alignedPDBViewer.refresh(modelsIdList); + } catch (e) { + console.log(e); + } +}; + +SuperpositionForm.prototype._renderAbinitio = function(modelsIdList) { + /** Trying to plot the PDB file **/ + try { + var viz = []; + for (var i = 0; i < modelsIdList.length; i++) { + viz.push({ + modelId : modelsIdList[i], + color : "0xFF6600", + opacity : 0.8 + }); + } + this.abinitioPDBViewer.refresh(viz); + } catch (e) { + console.log(e); + } +}; + +SuperpositionForm.prototype._getItems = function() { + var _this = this; + return [ { + xtype : 'label', + forId : 'myFieldId', + text : 'INLINE HELP: To be updated', + margin : '15 0 20 10', + cls : "inline-help" + }, this.superpositionGrid.getPanel(), { + xtype : 'container', + layout : 'hbox', + items : [ +// { +// xtype : 'container', +// layout : 'vbox', +// items : [ this.abinitioPDBViewer.getPanel(), this.aprioriPDBViewer.getPanel() +// +// ] +// }, + + this.alignedPDBViewer.getPanel() ] + } ] + +}; + +SuperpositionForm.prototype._getButtons = function() { + return []; +}; + +SuperpositionForm.prototype.getPanel = function() { + var _this = this; + this.panel = Ext.create('Ext.form.Panel', { + width : this.width, + height : this.height, + margin : 10, + border : 1, + defaultType : 'textfield', + items : this._getItems(), + buttons : this._getButtons(), + listeners : { + afterrender : function() { + _this._populate(); + + } + } + }); + return this.panel; +}; + +/** Populates could be call when the DOM is not filled yet **/ +SuperpositionForm.prototype._populate = function() { +}; + +/** It populates the form * */ +SuperpositionForm.prototype.refresh = function(subtractions) { + this.subtractions = subtractions; + this.superpositionGrid.refresh(subtractions); +}; + +SuperpositionForm.prototype.input = function() { + return {}; +}; + +/** It populates the form **/ +SuperpositionForm.prototype.test = function(targetId) { + var macromoleculeForm = new SuperpositionForm(); + var panel = macromoleculeForm.getPanel(); + panel.render(targetId); +}; + +/** + * Example form + * + * @witdh + * @height + */ +function AssemblyForm(args) { + this.id = BUI.id(); + this.width = 700; + this.height = 500; + + if (args != null) { + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + } + + this.molarityGrid = new MolarityGrid({height : this.height - 50}); +} + +AssemblyForm.prototype._getItems = function() { + return [ { + xtype : 'label', + forId : 'myFieldId', + text : 'List of previously defined macromolecules present in the assembly. This information will be used for additional cross-checks where possible', + margin : '15 0 20 10', + cls : "inline-help" + }, this.molarityGrid.getPanel() ]; +}; + +AssemblyForm.prototype._getButtons = function() { + return []; +}; + +AssemblyForm.prototype.getPanel = function() { + this.panel = Ext.create('Ext.form.Panel', { + width : this.width, + height : this.height, + margin : 10, + border : 0, + defaultType : 'textfield', + items : this._getItems(), + buttons : this._getButtons() + }); + return this.panel; +}; + + +/** It populates the form **/ +AssemblyForm.prototype.refresh = function(macromolecule) { + this.macromolecule = macromolecule; + this.molarityGrid.refresh(macromolecule); +}; + +AssemblyForm.prototype.input = function() { + return {}; +}; + + +AssemblyForm.prototype.test = function(targetId) { + var assemblyForm = new AssemblyForm(); + + var panel = assemblyForm.getPanel(); + panel.render(targetId); +}; +/** + * Edit the information of a buffer + * + * #onSaved + * #onRemoveAdditive + */ +function BufferForm() { var _this = this; - /** Widgets **/ - this.plotWidget = new PlotWidget({ - width : 650, - height : 490 + this.additiveGrid = new AdditiveGrid(); + this.additiveGrid.onRemoveButtonClicked.attach(function(sender, args) { + _this.onRemoveAdditive.notify(args); }); - /** Selected frames to be displayed **/ - this.selectedItems = { - frames : [], - averages : [], - subtractions : [] - }; - + this.onSaved = new Event(this); + this.onRemoveAdditive = new Event(this); } -DataReductionForm.prototype._parseSelectedItemsToIds = function(selectedArray) { - var ids = []; - if (selectedArray != null) { - for (var i = 0; i < selectedArray.length; i++) { - ids.push(selectedArray[i].id); - } - } - return ids; -}; - -DataReductionForm.prototype.onSelectionChanged = function(columnName, selected) { - if (selected != null) { - if (columnName == "Frames") { - this.selectedItems.frames = selected; - this.selectedItems.subtractions = []; - } - if (columnName == "Averages") { - this.selectedItems.averages = selected; - } - if (columnName == "Subtractions") { - this.selectedItems.frames = []; - this.selectedItems.subtractions = selected; - } - } - this.plotWidget.refresh(this._parseSelectedItemsToIds(this.selectedItems.frames), this._parseSelectedItemsToIds(this.selectedItems.subtractions)); -}; - -DataReductionForm.prototype._getFramesExtPanel = function(store, columnName, height) { - var _this = this; - - var selModel = Ext.create('Ext.selection.RowModel', { - allowDeselect : true, - mode : 'MULTI', - listeners : { - selectionchange : function(sm, selections) { - var selected = []; - for (var i = 0; i < selections.length; i++) { - selected.push(selections[i].raw); - } - _this.onSelectionChanged(columnName, selected); - } - } - }); - - return Ext.create('Ext.grid.Panel', { - store : store, - margin : 10, - height : height, - width : 200, - selModel : selModel, - columns : [ { - text : columnName, - dataIndex : 'fileName', - flex : 1 - } ], - viewConfig : { - } - }); +BufferForm.prototype.getBuffer = function() { + this.buffer.name = Ext.getCmp("buffer_name").getValue(); + this.buffer.acronym = Ext.getCmp("buffer_acronym").getValue(); + this.buffer.comments = Ext.getCmp("buffer_comments").getValue(); + this.buffer.ph = Ext.getCmp("buffer_ph").getValue(); + this.buffer.composition = Ext.getCmp("buffer_composition").getValue(); + this.buffer.bufferhasadditive3VOs = this.additiveGrid.getAdditives(); + return this.buffer; }; -DataReductionForm.prototype._getFramesPanel = function() { - var fields = [ 'fileName', 'type', 'id' ]; - - this.framesStore = Ext.create('Ext.data.Store', { - fields : fields, - sorters : 'fileName' - }); - - this.averagesStore = Ext.create('Ext.data.Store', { - fields : fields - }); - - this.subtractionStore = Ext.create('Ext.data.Store', { - fields : fields - }); - - var gridFrames = this._getFramesExtPanel(this.framesStore, "Frames", 375); - var gridAvgs = this._getFramesExtPanel(this.averagesStore, "Averages", 125); - var subtractionAvgs = this._getFramesExtPanel(this.subtractionStore, "Subtractions", 75); - - return { - xtype : 'container', - layout : 'vbox', - items : [ gridFrames, subtractionAvgs ] - }; -}; - -DataReductionForm.prototype._getImageContainer = function(name, help) { - var html = "
" + name + "
" +BufferForm.prototype._getTopPanel = function() { return { xtype : 'container', - layout : 'vbox', + layout : 'hbox', + border : 0, + frame : true, items : [ { - html : html, - margin : "5 0 0 0", - height : 95, - width : 100 + xtype : 'container', + layout : 'hbox', + items : [ { + xtype : 'container', + flex : 1, + border : false, + layout : 'anchor', + defaultType : 'textfield', + items : [ { + xtype : 'requiredtext', + id : 'buffer_name', + fieldLabel : 'Name', + name : 'name', + width : '200px', + value : this.buffer.name + }, { + xtype : 'requiredtext', + id : 'buffer_acronym', + fieldLabel : 'Acronym', + name : 'acronym', + width : '200px', + value : this.buffer.acronym + } ] + } ] }, { - xtype : 'label', - forId : 'myFieldId', - text : help, - margin : '5 0 0 0', - cls : "inline-help" + xtype : 'container', + flex : 1, + layout : 'anchor', + defaultType : 'textfield', + margin : '0 0 0 10', + items : [ { + id : 'buffer_ph', + fieldLabel : 'pH', + name : 'ph', + value : this.buffer.ph, + xtype : 'numberfield', + width : 200, + minValue : 0, + maxValue : 15 + }, { + xtype : 'requiredtext', + id : 'buffer_composition', + fieldLabel : 'Composition', + name : 'composition', + width : 200, + value : this.buffer.composition + } ] } ] - } + }; }; -DataReductionForm.prototype._getItems = function() { - var _this = this; - return [ { +BufferForm.prototype.getPanel = function(buffer) { + this.buffer = buffer; + this.panel = Ext.createWidget({ xtype : 'container', - layout : 'hbox', - items : [ - this._getFramesPanel(), - this.plotWidget.getPanel(), - { - xtype : 'panel', - width : 110, - frame : true, - margin : "10 5 5 5", - border : 0, - layout : 'vbox', - items : [ this._getImageContainer("scattering", "Scattering"), this._getImageContainer("guinier", "Guinier Region"), - this._getImageContainer("kratky", "Kratky Plot"), this._getImageContainer("gnom", "P(r) distribution") ] - } ] - } ] -}; - -DataReductionForm.prototype._getButtons = function() { - return []; -}; + layout : 'vbox', + style : { + padding : '10px' + }, + fieldDefaults : { + labelAlign : 'left', + labelWidth : 50 -DataReductionForm.prototype.getPanel = function() { - var _this = this; - this.panel = Ext.create('Ext.form.Panel', { - width : this.width, - height : this.height, - border : 0, - items : this._getItems(), - buttons : this._getButtons(), - listeners : { - afterrender : function() { - _this._populate(); - } - } + }, + items : [ this._getTopPanel(), { + id : 'buffer_comments', + xtype : 'textareafield', + name : 'comments', + fieldLabel : 'Comments', + width : '100%', + value : buffer.comments + }, this.additiveGrid.getPanel(buffer) ] }); return this.panel; }; -/** Populates could be call when the DOM is not filled yet **/ -DataReductionForm.prototype._populate = function() { -}; - -/** It populates the form * */ -DataReductionForm.prototype.refresh = function(subtractions) { - if (subtractions != null) { - for (var i = 0; i < subtractions.length; i++) { - /** Loading frame grids **/ - var subtraction = subtractions[i]; - var averages = [ { - fileName : BUI.getFileName(subtraction.bufferAverageFilePath), - type : 'bufferAvg', - id : subtraction.subtractionId - }, { - fileName : BUI.getFileName(subtraction.sampleAverageFilePath), - type : 'sampleAvg', - id : subtraction.subtractionId - } - - ]; - this.averagesStore.loadData(averages, true); - this.subtractionStore.loadData([ { - fileName : BUI.getFileName(subtraction.substractedFilePath), - type : 'SUBTRACTION', - id : subtraction.subtractionId - } ], true); - - var frames = []; - /** Buffers **/ - if (subtraction.bufferOneDimensionalFiles != null) { - if (subtraction.bufferOneDimensionalFiles.frametolist3VOs != null) { - for (var j = 0; j < subtraction.bufferOneDimensionalFiles.frametolist3VOs.length; j++) { - var frametolist3VO = subtraction.bufferOneDimensionalFiles.frametolist3VOs[j]; - if (frametolist3VO.frame3VO != null) { - frames.push({ - fileName : BUI.getFileName(frametolist3VO.frame3VO.filePath), - type : 'BUFFER', - id : frametolist3VO.frame3VO.frameId - }); - } - } - } - } - /** Samples **/ - if (subtraction.sampleOneDimensionalFiles != null) { - if (subtraction.sampleOneDimensionalFiles.frametolist3VOs != null) { - for (var j = 0; j < subtraction.sampleOneDimensionalFiles.frametolist3VOs.length; j++) { - var frametolist3VO = subtraction.sampleOneDimensionalFiles.frametolist3VOs[j]; - if (frametolist3VO.frame3VO != null) { - frames.push({ - fileName : BUI.getFileName(frametolist3VO.frame3VO.filePath), - type : 'SAMPLE', - id : frametolist3VO.frame3VO.frameId - }); - } - } - } - } - - this.framesStore.loadData(frames, true); - - /** Loading images **/ - this._displayImage("scattering", subtraction.subtractionId); - this._displayImage("kratky", subtraction.subtractionId); - this._displayImage("guinier", subtraction.subtractionId); - this._displayImage("gnom", subtraction.subtractionId); +BufferForm.prototype.input = function() { + return { + buffer : { + "bufferId" : 422, + "proposalId" : 10, + "safetyLevelId" : null, + "name" : "B1", + "acronym" : "B1", + "ph" : null, + "composition" : null, + "bufferhasadditive3VOs" : [], + "comments" : null } - } -}; - -DataReductionForm.prototype._displayImage = function(name, subtractionId) { - var url = BUI.getURL() + '&type=' + name + '&subtractionId=' + subtractionId; - var event = "OnClick= window.open('" + url + "')"; - document.getElementById(this.id + "_" + name).innerHTML = ''; -}; - -DataReductionForm.prototype.input = function() { - return {}; + }; }; -/** It populates the form **/ -DataReductionForm.prototype.test = function(targetId) { - var macromoleculeForm = new DataReductionForm(); - var panel = macromoleculeForm.getPanel(); +BufferForm.prototype.test = function(targetId) { + var bufferForm = new BufferForm(); + var panel = bufferForm.getPanel(bufferForm.input().buffer); panel.render(targetId); }; - -function PlotWidget(args) { - this.width = 600; - this.height = 600; - this.id = BUI.id(); - - this.linear = false; - - this.margin = "10 0 0 0"; - /** for each stat the max and minimum value when it is scaled in order to show correctly in the legend **/ - this.ranges = {}; + +/** + * @showTitle + * + * #onSaved + * #onAddPlates + * #onRemovePlates + **/ +function CaseForm(args) { + this.width = 700; + this.showTitle = true; if (args != null) { - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; - } - if (args.margin != null) { - this.margin = args.margin; + if (args.showTitle != null) { + this.showTitle = args.showTitle; } } -} - -PlotWidget.prototype.getMenu = function() { var _this = this; - /** Actions buttons **/ - var actions = []; - actions.push("->"); - actions.push({ - text : "Export as Image", - scope : this, - icon : '../images/save.gif', - handler : function(item, pressed) { - var largeImage = document.createElement("img"); - largeImage.style.display = 'block'; - largeImage.style.width = 200 + "px"; - largeImage.style.height = 200 + "px"; - largeImage.setAttribute('src', Dygraph.Export.asCanvas(this.dygraphObject.dygraph).toDataURL()); - window.open(Dygraph.Export.asCanvas(this.dygraphObject.dygraph).toDataURL(), 'Image', ''); + this.stockSolutionGrid = new StockSolutionGrid({ + width : this.width - 10, + minHeight : 300, + height : 300, + tbar : true, + showTitle : true, + isPackedVisible : false, + btnAddExisting : true, + btnRemoveVisible : false, + btnUnpackVisible : true + }); + + /** When selecting existing stock solutions **/ + this.stockSolutionGrid.onStockSolutionSelected.attach(function(sender, stockSolutions) { + if (stockSolutions != null) { + for ( var i = 0; i < stockSolutions.length; i++) { + _this.saveStockSolution(stockSolutions[i]); + } } }); - return actions; -}; + /** it can be because it has been added a new one or removed **/ + this.stockSolutionGrid.onProposalChanged.attach(function(sender, stockSolution) { + if (stockSolution != null) { + _this.saveStockSolution(stockSolution); + } else { + BIOSAXS.proposal.onInitialized.attach(function() { + _this.stockSolutionGrid.refresh(BIOSAXS.proposal.getStockSolutionsByDewarId(_this.dewar.dewarId)); -/** Looks for the maximum value and then divide everything but that value **/ -PlotWidget.prototype.scaledData = function(data) { - for (var i = 0; i < data.length; i++) { - var values = this.getMaxAndMinValue(data[i]); - data[i] = this.divideValuesByMax(data[i], values.max); - this.ranges[data[i].label] = values; - } - return data; -}; + _this.stockSolutionGrid.grid.setLoading(false); + }); + BIOSAXS.proposal.init(); -/** Given a stat float[] and a max number it will divide each value by max **/ -PlotWidget.prototype.divideValuesByMax = function(stat, max) { - for (var j = 0; j < stat.data.length; j++) { - if (max != 0) { - stat.data[j] = Number(stat.data[j]) / max; - stat.std[j] = Number(stat.std[j]) / max; } - } - return stat; -}; -/** returns max value of a stat **/ -PlotWidget.prototype.getMaxAndMinValue = function(stat) { - var max = 0; - var min = stat.data[0]; - for (var j = 0; j < stat.data.length; j++) { - if (Number(stat.data[j]) > max) { - max = Number(stat.data[j]); - } - if (Number(stat.std[j]) > max) { - max = Number(stat.std[j]); - } - if (Number(stat.data[j]) < min) { - min = Number(stat.data[j]); - } - } - return { - max : Number(max), - min : Number(min) - }; -}; - -PlotWidget.prototype._renderDygraph = function(parsed, colors, labels) { - this.dygraphObject = new StdDevDyGraph(this.id, { - width : this.width - 20, - height : this.height - 40, - xlabel : "", }); - this.dygraphObject.draw(parsed, colors, labels); + this.onSaved = new Event(this); + this.onAddPlates = new Event(this); + this.onRemovePlates = new Event(this); +} +CaseForm.prototype.saveStockSolution = function(stockSolution) { + var _this = this; + var adapter = new BiosaxsDataAdapter(); + this.stockSolutionGrid.grid.setLoading("ISPyB: setting case to Stock solution"); + adapter.onSuccess.attach(function(sender, stockSolution) { + BIOSAXS.proposal.onInitialized.attach(function() { + _this.stockSolutionGrid.refresh(BIOSAXS.proposal.getStockSolutionsByDewarId(_this.dewar.dewarId)); + _this.stockSolutionGrid.grid.setLoading(false); + }); + BIOSAXS.proposal.init(); + }); + adapter.onError.attach(function(sender, data) { + _this.stockSolutionGrid.grid.setLoading(false); + BUI.showError(data); + }); + stockSolution.boxId = _this.dewar.dewarId; + adapter.saveStockSolution(stockSolution); }; -PlotWidget.prototype.getPanel = function() { - this.panel = Ext.create('Ext.panel.Panel', { - width : this.width, - height : this.height, - margin : this.margin, - tbar : this.getMenu(), - items : [ { - html : "", - id : this.id, - width : this.width, - height : this.height, - padding : 10, - margin : "0 0 0 -30", - border : 0 - } ] +CaseForm.prototype.fillStores = function() { + var _this = this; + this.panel.setLoading("Loading Labcontacts from database"); + + var proposal = BUI.getProposal(); + proposal.onDataRetrieved.attach(function(sender, data) { + _this.labContactForSendingStore.loadData(data, false); + _this.labContactForReturnStore.loadData(data, false); + _this.panel.setLoading(false); }); + proposal.getLabContactsByProposalId(); - return this.panel; }; -PlotWidget.prototype.getPoint = function(y, error) { - var minus = y - error; - var max = y + error; - - if (this.linear) { - return [ Math.abs(minus), y, Math.abs(max) ]; - } - if ((minus != 0) && (max != 0)) { - return [ Math.log(Math.abs(minus)), Math.log(y), Math.log(Math.abs(max)) ]; - } else { - return [ Math.log(y), Math.log(y), Math.log(y) ]; - } - +CaseForm.prototype.refresh = function(dewar) { + this.setDewar(dewar); + this.stockSolutionGrid.refresh(BIOSAXS.proposal.getStockSolutionsByDewarId(dewar.dewarId)); }; -PlotWidget.prototype.getDataPlot = function(frames, subtractions, models, fits, rbms) { - var files = []; - var labels = [ "Intensity" ]; - if (frames != null) { - for (var i = 0; i < frames.length; i++) { - files.push(frames[i].data); - labels.push(frames[i].fileName); - } - } - function splitData(data, column, errorColumn, name){ - var result = [] - for (var j = 0; j < data.length; j++) { - console.log(data[j][column]); - result.push([j,data[j][column],data[j][errorColumn]]);//[0, data[i][column],0]]); - } - files.push(result); - labels.push(name); - } - - if (subtractions != null) { - for (var i = 0; i < subtractions.length; i++) { - /** For subtraction **/ - files.push(subtractions[i].subtraction.data); - labels.push(subtractions[i].subtraction.fileName); - /** For sample average **/ -// files.push(subtractions[i].sampleAvg.data); -// labels.push(subtractions[i].sampleAvg.fileName); - /** For buffer average **/ -// files.push(subtractions[i].bufferAvg.data); -// labels.push(subtractions[i].bufferAvg.fileName); - } - } - - if (models != null) { - for (var i = 0; i < models.length; i++) { - for ( var key in models[i]) { - splitData(models[i][key].fir.data, 1, 2, "Intensity"); - splitData(models[i][key].fir.data, 3, 3, "Fit"); - } - } - } - - if (fits != null) { - for (var i = 0; i < fits.length; i++) { - for ( var key in fits[i]) { - - /** adding fit file to be plotted **/ - if (fits[i][key].fit.data[0].length == 3){ - splitData(fits[i][key].fit.data, 1, 1, "Intensity"); - splitData(fits[i][key].fit.data, 2, 2, "Fit"); - } - - /** s, Iexp(s), err, Ifit(s). **/ - if (fits[i][key].fit.data[0].length == 4){ - splitData(fits[i][key].fit.data, 1, 2, "Intensity"); - splitData(fits[i][key].fit.data, 3, 3, "Fit"); - } - - if (fits[i][key].fit.data[0].length == 5){ - /** X Intensity Fit Error Residues **/ - - splitData(fits[i][key].fit.data, 1, 3, "Intensity"); - splitData(fits[i][key].fit.data, 2, 2, "Fit"); - } - } - } - } - - var dataPoints = []; - if (files.length > 0) { - for (var i = 0; i < files[0].length; i++) { - dataPoints.push([ files[0][i][0], this.getPoint(files[0][i][1], files[0][i][2]) ]); - } - if (files.length > 1) { - for (var i = 1; i < files.length; i++) { - for (var j = 0; j < dataPoints.length; j++) { - if (files[i][j] != null){ - dataPoints[j].push(this.getPoint(files[i][j][1], files[i][j][2])); - } - else{ - dataPoints[j].push([0,0,0]); - } - } - } - } - } +CaseForm.prototype.getDewar = function() { + this.dewar.code = Ext.getCmp("dewar_code").getValue(); + this.dewar.comments = Ext.getCmp("dewar_comments").getValue(); + this.dewar.trackingNumberFromSynchrotron = Ext.getCmp("dewar_trackingNumberFromSynchrotron").getValue(); + this.dewar.trackingNumberToSynchrotron = Ext.getCmp("dewar_trackingNumberToSynchrotron").getValue(); + this.dewar.transportValue = Ext.getCmp("dewar_transportValue").getValue(); + this.dewar.storageLocation = Ext.getCmp("dewar_storageLocation").getValue(); + this.dewar.firstExperimentId = this.macromoleculeCombo.getValue(); + return this.dewar; +}; - return { - dataPoints : dataPoints, - labels : labels +CaseForm.prototype.setDewar = function(dewar) { + this.dewar = dewar; + Ext.getCmp("dewar_code").setValue(this.dewar.code); + Ext.getCmp("dewar_dewarStatus").setText(new String(this.dewar.dewarStatus).toUpperCase()); + Ext.getCmp("dewar_comments").setValue(this.dewar.comments); + Ext.getCmp("dewar_trackingNumberFromSynchrotron").setValue(this.dewar.trackingNumberFromSynchrotron); + Ext.getCmp("dewar_trackingNumberToSynchrotron").setValue(this.dewar.trackingNumberToSynchrotron); + Ext.getCmp("dewar_transportValue").setValue(this.dewar.transportValue); + Ext.getCmp("dewar_storageLocation").setValue(this.dewar.storageLocation); + if (dewar.sessionVO != null) { + this.macromoleculeCombo.setValue(dewar.sessionVO.sessionId); } }; -PlotWidget.prototype.refresh = function(frames, subtractions, models, fits, rbms, colors) { - - var _this = this; - this.panel.setLoading("Reading Files"); - - var dataAdapter = new BiosaxsDataAdapter(); - dataAdapter.onSuccess.attach(function(sender, data) { - _this.panel.setLoading("Rendering"); - var parsed = _this.getDataPlot(data.frames, data.subtractions, data.models, data.fits, rbms); - _this._renderDygraph(parsed.dataPoints, colors, parsed.labels); - _this.panel.setLoading(false); - }); - dataAdapter.onError.attach(function(sender, data) { - _this.panel.setLoading(false); +CaseForm.prototype.getSessionCombo = function() { + this.macromoleculeCombo = BIOSAXS_COMBOMANAGER.getComboSessions(BIOSAXS.proposal.getSessions(), { + labelWidth : 100, + margin : '5 0 00 0', + width : 250 }); - dataAdapter.getDataPlot(frames, subtractions, models, fits, rbms); -}; - -PlotWidget.prototype.input = function() { - return DATADOC.getHPLCData(); + return this.macromoleculeCombo; }; - -/** - * Fit form - * - * @witdh - * @height - */ -function FitForm(args) { - this.id = BUI.id(); - this.width = null; - this.height = null; - - if (args != null) { - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; - } - } +CaseForm.prototype.getInformationPanel = function() { + if (this.panel == null) { + this.informationPanel = Ext.create('Ext.form.Panel', { + width : this.width - 10, + border : 0, + items : [ { + xtype : 'container', + margin : "2 2 2 2", + collapsible : false, + defaultType : 'textfield', + layout : 'anchor', + items : [ { + xtype : 'container', + layout : 'hbox', + items : [ { + xtype : 'requiredtext', + fieldLabel : 'Code', + allowBlank : false, + name : 'code', + id : 'dewar_code', + anchor : '50%' + }, { + xtype : 'label', + margin : '0 0 0 20', + readOnly : true, + id : 'dewar_dewarStatus', + anchor : '50%' + } ] + }, this.getSessionCombo(), { + margin : '5 0 0 0', + xtype : 'textareafield', + name : 'comments', + id : 'dewar_comments', + width : this.width - 50, + fieldLabel : 'Comments' + } ] + }, { + xtype : 'fieldset', + title : 'Courier Accounts Details for Return', + collapsible : false, + layout : 'anchor', + defaults : { + anchor : '100%' + }, + items : [ { + xtype : 'container', + layout : 'hbox', + items : [ { + xtype : 'textfield', + labelWidth : 200, + width : 280, + fieldLabel : 'Track Number From Synchrotron', + id : 'dewar_trackingNumberFromSynchrotron' + }, { + xtype : 'numberfield', + width : 190, + labelWidth : 110, + margin : '0 0 0 30', + fieldLabel : 'Transport Value', + id : 'dewar_transportValue' + } - var _this = this; - - /** Widgets **/ - this.fitGrid = new FitStructureToExperimentDataGrid({ - width : null, - height : 200 - }); + ] + }, { + xtype : 'container', + layout : 'hbox', + margin : '10 0 0 0', + items : [ - this.fitGrid.onSelected.attach(function(sender, fits) { - var modelsIdList = []; - for ( var i in fits) { - modelsIdList.push(fits[i].fitStructureToExperimentalDataId); - } - _this._renderPlot(_this.subtractions[0].subtractionId, modelsIdList); -// var adapter = new BiosaxsDataAdapter(); -// adapter.onSuccess.attach(function(sender, data) { -// -// }); -// adapter.getScatteringCurveByFrameIdsList([], [], [], ids); - }); - - - /** Dygraph Widget that plots fir files**/ - this.plotWidget = new PlotWidget({ - width : 745, - height : 300, - margin : "10 0 10 10" - }); -} + { + xtype : 'textfield', + labelWidth : 200, + width : 280, + fieldLabel : 'Track Number To Synchrotron', + id : 'dewar_trackingNumberToSynchrotron' + }, { + xtype : 'textfield', + margin : '0 0 0 30', + width : 190, + labelWidth : 110, + fieldLabel : 'Storage Location', + id : 'dewar_storageLocation' + } -FitForm.prototype._renderPlot = function(subtractionId, modelsIdList) { - /** Trying to plot tje subtraction and the models **/ - try { - var colors = [ "#669900", "#0000FF" ]; - - this.plotWidget.refresh([], [ ], [], modelsIdList, [], colors); - } catch (e) { - console.log(e); + ] + } ] + } ] + }); } -}; - -FitForm.prototype._getItems = function() { - var _this = this; - return [ { - xtype : 'label', - forId : 'myFieldId', - text : 'INLINE HELP: To be updated', - margin : '15 0 20 10', - cls : "inline-help" - }, this.fitGrid.getPanel(), this.plotWidget.getPanel() ] - -}; -FitForm.prototype._getButtons = function() { - return []; + return this.informationPanel; }; -FitForm.prototype.getPanel = function() { - var _this = this; - this.panel = Ext.create('Ext.form.Panel', { +CaseForm.prototype.getPanel = function(dewar) { + this.dewar = dewar; + this.panel = Ext.createWidget({ + xtype : 'container', + layout : 'vbox', width : this.width, - height : this.height, - margin : 10, - border : 1, - defaultType : 'textfield', - items : this._getItems(), - buttons : this._getButtons(), - listeners : { - afterrender : function() { - _this._populate(); + border : 0, + items : [ { + items : { + xtype : "container", + layout : "vbox", + margin : "5 5 5 5", + items : [ this.getInformationPanel(dewar), this.stockSolutionGrid.getPanel() ] } - } + } ] }); + + this.refresh(dewar); return this.panel; -}; -/** Populates could be call when the DOM is not filled yet **/ -FitForm.prototype._populate = function() { }; -/** It populates the form * */ -FitForm.prototype.refresh = function(subtractions) { - this.subtractions = subtractions; - this.fitGrid.refresh(subtractions); -}; +CaseForm.prototype.input = function() { + return { + dewar : { + "dewarId" : 305861, + "code" : "ESRF-TEST", + "comments" : "comments", + "storageLocation" : "FRIDGE", + "dewarStatus" : "opened", + "timeStamp" : null, + "isStorageDewar" : null, + "barCode" : "ESRF305861", + "customsValue" : null, + "transportValue" : null, + "trackingNumberToSynchrotron" : "3333", + "trackingNumberFromSynchrotron" : "224466", + "type" : "Dewar", + "sessionVO" : { + "sessionId" : 31697, + "expSessionPk" : null, + "projectCode" : null, + "startDate" : "2012 07 21", + "endDate" : "2012 07 23", + "beamlineName" : "BM29", + "scheduled" : 1, + "nbShifts" : 2, + "comments" : null, + "beamlineOperator" : "PERNOT P", + "usedFlag" : null, + "sessionTitle" : null, + "structureDeterminations" : null, + "dewarTransport" : null, + "databackupFrance" : null, + "databackupEurope" : null, + "visit_number" : null, + "operatorSiteNumber" : "14061", + "timeStamp" : "2012 04 25" + } + }, + proposal : { + "assemblies" : [], + "sessions" : [ { + "sessionId" : 31697, + "expSessionPk" : null, + "projectCode" : null, + "startDate" : "2012 07 21", + "endDate" : "2012 07 23", + "beamlineName" : "BM29", + "scheduled" : 1, + "nbShifts" : 2, + "comments" : null, + "beamlineOperator" : "PERNOT P", + "usedFlag" : null, + "sessionTitle" : null, + "structureDeterminations" : null, + "dewarTransport" : null, + "databackupFrance" : null, + "databackupEurope" : null, + "visit_number" : null, + "operatorSiteNumber" : "14061", + "timeStamp" : "2012 04 25" + } ], + "labcontacts" : [ { + "labContactId" : 787, + "personVO" : { + "personId" : 304252, + "personUUID" : null, + "familyName" : "KIM", + "givenName" : "Henry", + "title" : null, + "emailAddress" : "henry-sung.kim@ibs.fr", + "phoneNumber" : "", + "login" : "", + "passwd" : "", + "faxNumber" : "" + }, + "cardName" : "KIM-Institut de Bio", + "defaultCourrierCompany" : "22", + "courierAccount" : "", + "billingReference" : "", + "dewarAvgCustomsValue" : 0, + "dewarAvgTransportValue" : 0 + } ], + "buffers" : [ { + "bufferId" : 811, + "proposalId" : 3124, + "safetyLevelId" : null, + "name" : "EDTA", + "acronym" : "EDTA", + "ph" : null, + "composition" : "", + "bufferhasadditive3VOs" : [], + "comments" : "" + }, { + "bufferId" : 810, + "proposalId" : 3124, + "safetyLevelId" : null, + "name" : "HEPES", + "acronym" : "HEPES", + "ph" : null, + "composition" : "", + "bufferhasadditive3VOs" : [], + "comments" : "" + } ], + "shippings" : [ { + "shippingId" : 304107, + "shippingName" : "TEST", + "deliveryAgentAgentName" : null, + "deliveryAgentShippingDate" : null, + "deliveryAgentDeliveryDate" : null, + "deliveryAgentAgentCode" : null, + "deliveryAgentFlightCode" : null, + "shippingStatus" : "opened", + "timeStamp" : "2013 09 25", + "laboratoryId" : null, + "isStorageShipping" : null, + "creationDate" : "2013 09 25", + "comments" : "test", + "sendingLabContactVO" : { + "labContactId" : 787, + "personVO" : { + "personId" : 304252, + "personUUID" : null, + "familyName" : "KIM", + "givenName" : "Henry", + "title" : null, + "emailAddress" : "henry-sung.kim@ibs.fr", + "phoneNumber" : "", + "login" : "", + "passwd" : "", + "faxNumber" : "" + }, + "cardName" : "KIM-Institut de Bio", + "defaultCourrierCompany" : "22", + "courierAccount" : "", + "billingReference" : "", + "dewarAvgCustomsValue" : 0, + "dewarAvgTransportValue" : 0 + }, + "returnLabContactVO" : { + "labContactId" : 787, + "personVO" : { + "personId" : 304252, + "personUUID" : null, + "familyName" : "KIM", + "givenName" : "Henry", + "title" : null, + "emailAddress" : "henry-sung.kim@ibs.fr", + "phoneNumber" : "", + "login" : "", + "passwd" : "", + "faxNumber" : "" + }, + "cardName" : "KIM-Institut de Bio", + "defaultCourrierCompany" : "22", + "courierAccount" : "", + "billingReference" : "", + "dewarAvgCustomsValue" : 0, + "dewarAvgTransportValue" : 0 + }, + "returnCourier" : null, + "dateOfShippingToUser" : null, + "shippingType" : "DewarTracking", + "dewarVOs" : [ { + "dewarId" : 305861, + "code" : "ESRF-TEST", + "comments" : "comments", + "storageLocation" : "FRIDGE", + "dewarStatus" : "opened", + "timeStamp" : null, + "isStorageDewar" : null, + "barCode" : "ESRF305861", + "customsValue" : null, + "transportValue" : null, + "trackingNumberToSynchrotron" : "3333", + "trackingNumberFromSynchrotron" : "224466", + "type" : "Dewar", + "sessionVO" : { + "sessionId" : 31697, + "expSessionPk" : null, + "projectCode" : null, + "startDate" : "2012 07 21", + "endDate" : "2012 07 23", + "beamlineName" : "BM29", + "scheduled" : 1, + "nbShifts" : 2, + "comments" : null, + "beamlineOperator" : "PERNOT P", + "usedFlag" : null, + "sessionTitle" : null, + "structureDeterminations" : null, + "dewarTransport" : null, + "databackupFrance" : null, + "databackupEurope" : null, + "visit_number" : null, + "operatorSiteNumber" : "14061", + "timeStamp" : "2012 04 25" + } + } ] + } ], + "macromolecules" : [ { + "macromoleculeId" : 5933, + "safetylevelId" : null, + "proposalId" : 3124, + "name" : "A", + "acronym" : "A", + "molecularMass" : "", + "extintionCoefficient" : "", + "sequence" : null, + "creationDate" : null, + "comments" : "", + "macromoleculeregion3VOs" : [], + "stoichiometry3VOsForHostMacromoleculeId" : [], + "structure3VOs" : [] + } ], + "stockSolutions" : [ { + "stockSolutionId" : 6, + "proposalId" : 3124, + "macromoleculeId" : 5933, + "bufferId" : 811, + "instructionSet3VO" : null, + "boxId" : 305861, + "storageTemperature" : "20", + "volume" : "300", + "concentration" : "1.2", + "comments" : "Buffer EDTA with A", + "name" : "A_EDTA_1.2", + "samples" : [] + } ] + } -FitForm.prototype.input = function() { - return {}; + }; }; -/** It populates the form **/ -FitForm.prototype.test = function(targetId) { - var macromoleculeForm = new FitForm(); - var panel = macromoleculeForm.getPanel(); - panel.render(targetId); -}; - -/** - * Example form - * - * @witdh - * @height - */ -function RigidBodyModelingResultForm(args) { +CaseForm.prototype.test = function(targetId) { + var caseForm = new CaseForm(); + BIOSAXS.proposal = new Proposal(caseForm.input().proposal); + var panel = caseForm.getPanel(caseForm.input().dewar); + panel.render(targetId); +}; + +/** + * Example form + * + * @witdh + * @height + */ +function ExampleForm(args) { + this.id = BUI.id(); + this.width = 700; + this.height = 500; + + if (args != null) { + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + } +} + +ExampleForm.prototype._getItems = function() { + return [{ + fieldLabel : 'First Name', + name : 'first', + allowBlank : false + }, { + fieldLabel : 'Last Name', + name : 'last', + allowBlank : false + } ]; +}; + +ExampleForm.prototype._getItems = function() { + return [ ]; +}; + +ExampleForm.prototype._getButtons = function() { + return [ ]; +}; + +ExampleForm.prototype.getPanel = function() { + this.panel = Ext.create('Ext.form.Panel', { + width : this.width, + height : this.height, + margin : 10, + border : 1, + defaultType : 'textfield', + items : this._getItems(), + buttons : this._getButtons() + }); + return this.panel; +}; + +/** It populates the form **/ +ExampleForm.prototype.refresh = function(macromolecule) { +}; + +function ExperimentForm(args) { this.id = BUI.id(); - this.width = null; - this.height = null; if (args != null) { - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; - } } - var _this = this; - /** Widgets **/ - this.rigidModelGrid = new RigidModelGrid({ - width : null, - height : 200 + this.onSaved = new Event(this); +} + +ExperimentForm.prototype._getItems = function(experiment) { + this.experiment = experiment; + var typeCombo = Ext.create('Ext.form.ComboBox', { + id : this.id + 'type', + fieldLabel : 'Type', + store : [ "STATIC", "CALIBRATION", "HPLC" ], + queryMode : 'local', + labelWidth : 120, + displayField : 'name', + valueField : 'name', + value : experiment.json.type, + disabled : (experiment.json.type == 'TEMPLATE') }); - this.rigidModelGrid.onSelected.attach(function(sender, fits){ - var ids = []; - for ( var i in fits) { - ids.push(fits[i].fitStructureToExperimentalDataId); + var items = []; + + + if (experiment.json.type == "HPLC" ){ + var typeMacromolecule = BIOSAXS_COMBOMANAGER.getComboMacromoleculeByMacromolecules(BIOSAXS.proposal.getMacromolecules(), {labelWidth : 120, width: "120px"}); + if (experiment.getHPLCMacromolecule() != null){ + typeMacromolecule.setValue(experiment.getHPLCMacromolecule().macromoleculeId); + items.push(typeMacromolecule); } - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data){ -// debugger - - }); - - adapter.getScatteringCurveByFrameIdsList([], [], [], ids); + } + + + items.push(typeCombo, { + id : this.id + 'name', + xtype : 'textfield', + fieldLabel : 'Name', + labelWidth : 120, + width : '100%', + value : experiment.json.name + }, { + id : this.id + 'comments', + xtype : 'textareafield', + name : 'comments', + fieldLabel : 'Comments', + labelWidth : 120, + height : 120, + width : '100%', + value : experiment.json.comments }); - -} - -RigidBodyModelingResultForm.prototype._getItems = function() { - var _this = this; - return [ { - xtype : 'label', - forId : 'myFieldId', - text : 'INLINE HELP: To be updated', - margin : '15 0 20 10', - cls : "inline-help" - }, this.rigidModelGrid.getPanel() ] - -}; - -RigidBodyModelingResultForm.prototype._getButtons = function() { - return []; + return items; }; - -RigidBodyModelingResultForm.prototype.getPanel = function() { +ExperimentForm.prototype.getPanel = function(experiment) { var _this = this; - this.panel = Ext.create('Ext.form.Panel', { - width : this.width, - height : this.height, - margin : 10, - border : 1, - defaultType : 'textfield', - items : this._getItems(), - buttons : this._getButtons(), - listeners : { - afterrender : function() { - _this._populate(); - - } - } + + this.panel = Ext.createWidget({ + xtype : 'container', + layout : 'vbox', + border : 0, + style : { + padding : '10px' + }, + fieldDefaults : { + labelAlign : 'left', + labelWidth : 50 + }, + items : this._getItems(experiment) }); return this.panel; }; -/** Populates could be call when the DOM is not filled yet **/ -RigidBodyModelingResultForm.prototype._populate = function() { -}; - -/** It populates the form * */ -RigidBodyModelingResultForm.prototype.refresh = function(subtractions) { - this.rigidModelGrid.refresh(subtractions); -}; - -RigidBodyModelingResultForm.prototype.input = function() { - return {}; +ExperimentForm.prototype.input = function() { + return new ExperimentHeaderForm().input(); }; -/** It populates the form **/ -RigidBodyModelingResultForm.prototype.test = function(targetId) { - var macromoleculeForm = new RigidBodyModelingResultForm(); - var panel = macromoleculeForm.getPanel(); +ExperimentForm.prototype.test = function(targetId) { + var experimentForm = new ExperimentForm(); + var panel = experimentForm.getPanel(new Experiment(experimentForm.input().experiment)); panel.render(targetId); }; /** - * Example form + * Shows the header for the experiments changing the color and parameters depending on experiment type * - * @witdh - * @height */ -function SuperpositionForm(args) { +function ExperimentHeaderForm(args) { this.id = BUI.id(); - this.width = null; - this.height = null; + this.backgroundColor = '#FFFFFF'; +} - if (args != null) { - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; +ExperimentHeaderForm.prototype.getHTMLSource = function(experiment) { + var html = BUI.createFormLabel("Name :", experiment.json.name, 75, 400, this.backgroundColor); + if (experiment.json.type == "HPLC") { + if (experiment.getHPLCMacromolecule() != null){ + html = html + BUI.createFormLabel("Molecule :", experiment.getHPLCMacromolecule().acronym, 75, 400, this.backgroundColor); } } + else{ + html = html + BUI.createFormLabel("Type :", experiment.json.type, 75, 400, this.backgroundColor); + } + + html = html + BUI.createFormLabel("Date :", experiment.json.creationDate, 75, 400, this.backgroundColor); + return html; +}; - var _this = this; - - /** Widgets **/ - this.superpositionGrid = new SuperpositionGrid({ - width : null, - height : 200 - }); - - this.superpositionGrid.onSelected.attach(function(sender, superpositions) { - var ids = []; - for ( var i in superpositions) { - ids.push(superpositions[i].superpositionId); - } -// _this._renderAbinitio(ids); -// _this.aprioriPDBViewer.refresh(); - _this._renderAligned(ids); - // getAlignedPDBContentBySuperpositionList - }); - - /** PDB viewer **/ -// this.abinitioPDBViewer = new PDBViewer({ -// width : 860 / 2, -// height : 300 / 2, -// margin : 0 -// }); -// -// /** PDB viewer **/ -// this.aprioriPDBViewer = new StructurePDBViewer({ -// width : 860 / 2, -// height : 300 / 2, -// margin : 0 -// }); +ExperimentHeaderForm.prototype.getHTMLDownload = function(experiment) { + var bgcolor = "background-color:" + this.backgroundColor + ";"; + var html = "
"; + if ((experiment.json.type == "CALIBATION") || (experiment.json.type == "STATIC")) { + html = html + " Download Source File
"; + html = html + + ""; + } + if (experiment.json.type == "TEMPLATE") { + html = html + + " Download Source File"; + } - this.alignedPDBViewer = new AlignedSuperpositionPDBViewer({ - width : 860 , - height : 300 - }); + if (experiment.json.type == "HPLC") { + html = html + " Download h5 File"; + } -} + return html; +}; -SuperpositionForm.prototype._renderAligned = function(modelsIdList) { - /** Trying to plot the PDB file **/ - try { - this.alignedPDBViewer.refresh(modelsIdList); - } catch (e) { - console.log(e); - } +ExperimentHeaderForm.prototype.getTopPanel = function(experiment) { + return { + xtype : 'container', + layout : 'hbox', + items : [ { + margin : "0 0 0 0", + width : 475, + border : 0, + html : this.getHTMLSource(experiment) + }, { + margin : "0 0 0 0", + width : 475, + border : 0, + html : this.getHTMLDownload(experiment) + } ] + }; }; -SuperpositionForm.prototype._renderAbinitio = function(modelsIdList) { - /** Trying to plot the PDB file **/ - try { - var viz = []; - for (var i = 0; i < modelsIdList.length; i++) { - viz.push({ - modelId : modelsIdList[i], - color : "0xFF6600", - opacity : 0.8 +ExperimentHeaderForm.prototype.getButton = function(experiment) { + var _this = this; + return Ext.create('Ext.Button', { + text : 'EDIT', + minWidth : '100', + margin : '10 0 0 30', + handler : function() { + var experimentWindow = new ExperimentWindow(); + experimentWindow.onSaved.attach(function(sender, data) { + _this.experiment.json.name = data.name; + _this.experiment.json.type = data.type; + _this.experiment.json.comments = data.comments; + _this.panel.remove(_this.panel.items.items[0]); + _this.panel.remove(_this.panel.items.items[0]); + _this.panel.insert(_this.getTopPanel(_this.experiment)); + _this.panel.insert(_this.getBottomPanel(_this.experiment)); }); + experimentWindow.show(experiment); } - this.abinitioPDBViewer.refresh(viz); - } catch (e) { - console.log(e); - } + }); }; -SuperpositionForm.prototype._getItems = function() { - var _this = this; - return [ { - xtype : 'label', - forId : 'myFieldId', - text : 'INLINE HELP: To be updated', - margin : '15 0 20 10', - cls : "inline-help" - }, this.superpositionGrid.getPanel(), { +ExperimentHeaderForm.prototype.getBottomPanel = function(experiment) { + return { xtype : 'container', layout : 'hbox', - items : [ -// { -// xtype : 'container', -// layout : 'vbox', -// items : [ this.abinitioPDBViewer.getPanel(), this.aprioriPDBViewer.getPanel() -// -// ] -// }, - - this.alignedPDBViewer.getPanel() ] - } ] - -}; - -SuperpositionForm.prototype._getButtons = function() { - return []; + margin : '10 0 0 0', + items : [ this.getComments(experiment), this.getButton(experiment) ] + }; }; -SuperpositionForm.prototype.getPanel = function() { - var _this = this; - this.panel = Ext.create('Ext.form.Panel', { - width : this.width, - height : this.height, - margin : 10, - border : 1, - defaultType : 'textfield', - items : this._getItems(), - buttons : this._getButtons(), - listeners : { - afterrender : function() { - _this._populate(); - - } - } - }); - return this.panel; +ExperimentHeaderForm.prototype.getComments = function(experiment) { + return { + xtype : 'textareafield', + labelStyle : 'font-weight: bold;', + name : 'comments', + fieldLabel : 'Comments', + labelWidth : 70, + height : 40, + minWidth : '450', + readOnly : true, + value : experiment.json.comments + }; }; -/** Populates could be call when the DOM is not filled yet **/ -SuperpositionForm.prototype._populate = function() { -}; +ExperimentHeaderForm.prototype.getPanel = function(experiment) { + this.experiment = experiment; + + if (experiment.json.type == 'CALIBRATION') { + this.backgroundColor = '#EFFBFB'; + } + if (experiment.json.type == 'TEMPLATE') { + this.backgroundColor = '#E0F8E6'; + } -/** It populates the form * */ -SuperpositionForm.prototype.refresh = function(subtractions) { - this.subtractions = subtractions; - this.superpositionGrid.refresh(subtractions); + this.panel = Ext.create('Ext.container.Container', { + frame : false, + layout : 'vbox', + padding : 5, + bodyPadding : '5 5 0 0', + width : 890, + margin : '0 0 10 0', + height : 120, + style : { + borderColor : '#99bce8', + borderStyle : 'solid', + borderWidth : '1px', + 'background-color' : this.backgroundColor + }, + fieldDefaults : { + msgTarget : 'side', + labelWidth : 100 + }, + items : [ this.getTopPanel(experiment), this.getBottomPanel(experiment) ] + }); + return this.panel; }; -SuperpositionForm.prototype.input = function() { - return {}; +ExperimentHeaderForm.prototype.input = function() { + return { + experiment : DATADOC.getExperiment_10() + }; }; -/** It populates the form **/ -SuperpositionForm.prototype.test = function(targetId) { - var macromoleculeForm = new SuperpositionForm(); - var panel = macromoleculeForm.getPanel(); +ExperimentHeaderForm.prototype.test = function(targetId) { + var experimentHeaderForm = new ExperimentHeaderForm(); + var panel = experimentHeaderForm.getPanel(new Experiment(experimentHeaderForm.input().experiment)); panel.render(targetId); + }; /** - * Example form + * Macromolecule form with the general parameters of a macromolecule * * @witdh * @height + * + * #onSave button save has been clicked + * #onClose button close has been clicked */ -function AssemblyForm(args) { +function MacromoleculeForm(args) { this.id = BUI.id(); this.width = 700; this.height = 500; @@ -6059,15944 +7053,9793 @@ function AssemblyForm(args) { this.height = args.height; } } - - this.molarityGrid = new MolarityGrid({height : this.height - 50}); + + /** Events **/ + this.onSave = new Event(this); + this.onClose = new Event(this); } -AssemblyForm.prototype._getItems = function() { - return [ { - xtype : 'label', - forId : 'myFieldId', - text : 'List of previously defined macromolecules present in the assembly. This information will be used for additional cross-checks where possible', - margin : '15 0 20 10', - cls : "inline-help" - }, this.molarityGrid.getPanel() ]; -}; - -AssemblyForm.prototype._getButtons = function() { - return []; +/** Type : is the Ext type then requiredtext or textfield * */ +MacromoleculeForm.prototype._getFieldTextWithHelp = function(type, fieldLabel, fieldName, help) { + return Ext.create('Ext.container.Container', { + margin : "10 0 0 10", + items : [ { + xtype : type, + fieldLabel : fieldLabel, + name : fieldName, + id : this.id + fieldName + }, { + xtype : 'label', + forId : 'myFieldId', + text : help, + margin : "5 0 0 105", + cls : "inline-help" + } ] + }); }; -AssemblyForm.prototype.getPanel = function() { - this.panel = Ext.create('Ext.form.Panel', { - width : this.width, - height : this.height, - margin : 10, - border : 0, - defaultType : 'textfield', - items : this._getItems(), - buttons : this._getButtons() +MacromoleculeForm.prototype._getNumericWithHelp = function(type, fieldLabel, fieldName, help) { + return Ext.create('Ext.container.Container', { + margin : "0 0 0 10", + items : [ { + xtype : type, + fieldLabel : fieldLabel, + name : fieldName, + id : this.id + fieldName, + decimalPrecision : 6, + width : 220 + }, { + xtype : 'label', + forId : 'myFieldId', + text : help, + margin : "5 0 0 10", + cls : "inline-help" + } ] }); - return this.panel; }; - -/** It populates the form **/ -AssemblyForm.prototype.refresh = function(macromolecule) { - this.macromolecule = macromolecule; - this.molarityGrid.refresh(macromolecule); +MacromoleculeForm.prototype._getButtons = function() { + var _this = this; + return [ { + text : 'Save', + handler : function() { + _this._save(); + } + },{ + text : 'Close', + handler : function() { + _this.onClose.notify(); + + } + } ]; }; -AssemblyForm.prototype.input = function() { - return {}; +/** It persits the macromolecule in the database **/ +MacromoleculeForm.prototype._persist = function(macromoleculeId, acronym, name, molecularMass, extintionCoefficient, comments, refractiveIndex, solventViscosity) { + + /** Checking not duplicated acronym **/ + if (((macromoleculeId == null) && (BIOSAXS.proposal.getMacromoleculeByAcronym(acronym) != null))== true){ + BUI.showError("Duplicated acronym"); + return; + } + + + if (macromoleculeId == null){ + /** new macromolecule **/ + this.macromolecule = {}; + this.macromolecule.macromoleculeId = null; + } + else{ + this.macromolecule.macromoleculeId = macromoleculeId; + } + + this.macromolecule["acronym"] = acronym; + this.macromolecule["name"] = name; + this.macromolecule["molecularMass"] = molecularMass; + this.macromolecule["extintionCoefficient"] = extintionCoefficient; + this.macromolecule["comments"] = comments; + this.macromolecule["symmetry"] = Ext.getCmp(this.id + 'comboSym').getValue(); + this.macromolecule["refractiveIndex"] = refractiveIndex; + this.macromolecule["solventViscosity"] = solventViscosity; + + var _this = this; + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, proposal) { + /** Updating the proposal global object **/ + BIOSAXS.proposal.setItems(proposal); + _this.panel.setLoading(false); + + var saved = BIOSAXS.proposal.getMacromoleculeByAcronym(acronym); + /** Refreshing to check that everything is ok **/ + _this.refresh(saved); + _this.onSave.notify(saved); + }); + + this.panel.setLoading("Saving Macromolecule") + adapter.saveMacromolecule(this.macromolecule); }; - -AssemblyForm.prototype.test = function(targetId) { - var assemblyForm = new AssemblyForm(); +/** Save the macromolecule in the DB **/ +MacromoleculeForm.prototype._save = function() { - var panel = assemblyForm.getPanel(); - panel.render(targetId); -}; -/** - * Edit the information of a buffer - * - * #onSaved - * #onRemoveAdditive - */ -function BufferForm() { var _this = this; + + var acronym = this._getField("acronym"); + var name = this._getField("name"); + var molecularMass = this._getField("molecularMass"); + var extintionCoefficient = this._getField("extintionCoefficient"); + var comments = this._getField("comments"); + + var refractiveIndex = this._getField("refractiveIndex"); + var solventViscosity = this._getField("solventViscosity"); + + /** Checking required fields **/ + if (name == "") { + BUI.showError("Name field is mandatory"); + return; + } + if (acronym == "") { + BUI.showError("Acroynm field is mandatory"); + return; + } - this.additiveGrid = new AdditiveGrid(); - this.additiveGrid.onRemoveButtonClicked.attach(function(sender, args) { - _this.onRemoveAdditive.notify(args); - }); + if (this.macromolecule != null){ + /** Checking if it is a new macromolecule **/ + if (this.macromolecule.macromoleculeId == null){ + /** Check if the acronym exists already **/ + this._persist(null, acronym, name, molecularMass, extintionCoefficient, comments, refractiveIndex, solventViscosity); + } + else{ + /** It is an update **/ + this._persist(this.macromolecule.macromoleculeId, acronym, name, molecularMass, extintionCoefficient, comments, refractiveIndex, solventViscosity); + } + } + else{ + /** It is a new macromolecule **/ + this._persist(null, acronym, name, molecularMass, extintionCoefficient, comments, refractiveIndex, solventViscosity); + } +}; - this.onSaved = new Event(this); - this.onRemoveAdditive = new Event(this); -} -BufferForm.prototype.getBuffer = function() { - this.buffer.name = Ext.getCmp("buffer_name").getValue(); - this.buffer.acronym = Ext.getCmp("buffer_acronym").getValue(); - this.buffer.comments = Ext.getCmp("buffer_comments").getValue(); - this.buffer.ph = Ext.getCmp("buffer_ph").getValue(); - this.buffer.composition = Ext.getCmp("buffer_composition").getValue(); - this.buffer.bufferhasadditive3VOs = this.additiveGrid.getAdditives(); - return this.buffer; -}; -BufferForm.prototype._getTopPanel = function() { - return { - xtype : 'container', - layout : 'hbox', - border : 0, - frame : true, - items : [ { - xtype : 'container', - layout : 'hbox', - items : [ { +MacromoleculeForm.prototype._getItems = function() { + var _this = this; + /** Symmetry combo box **/ + var symmetry = Ext.create('Ext.data.Store', { + fields : [ 's' ], + data : this._getSymmetries() + }); + + this.symmetryComboBox = Ext.create('Ext.form.ComboBox', { + fieldLabel : 'Symmetry', + store : symmetry, + id : this.id + 'comboSym', + queryMode : 'local', + displayField : 's', + valueField : 's', + value : "P1", + margin : "0 0 0 30", + width : 220 + }); + + return [this._getFieldTextWithHelp("requiredtext", "Name", "name", "Long name. i.e: Bovine serum albumin"), + this._getFieldTextWithHelp("requiredtext", "Acronym", "acronym", "Acronym will be used in the files and analisys. i.e: BSA"), + this._getFieldTextWithHelp("textfield", "Mol. Mass (Da)", "molecularMass", "Atomic mass estimation measured in Da"), + { xtype : 'container', - flex : 1, - border : false, - layout : 'anchor', - defaultType : 'textfield', - items : [ { - xtype : 'requiredtext', - id : 'buffer_name', - fieldLabel : 'Name', - name : 'name', - width : '200px', - value : this.buffer.name - }, { - xtype : 'requiredtext', - id : 'buffer_acronym', - fieldLabel : 'Acronym', - name : 'acronym', - width : '200px', - value : this.buffer.acronym - } ] - } ] - }, { - xtype : 'container', - flex : 1, - layout : 'anchor', - defaultType : 'textfield', - margin : '0 0 0 10', - items : [ { - id : 'buffer_ph', - fieldLabel : 'pH', - name : 'ph', - value : this.buffer.ph, - xtype : 'numberfield', - width : 200, - minValue : 0, - maxValue : 15 - }, { - xtype : 'requiredtext', - id : 'buffer_composition', - fieldLabel : 'Composition', - name : 'composition', - width : 200, - value : this.buffer.composition - } ] - } ] - }; + layout : 'hbox', + margin : "10 0 0 0", + items :[ + this._getNumericWithHelp("numberfield", "Extinction coef.", "extintionCoefficient", ""), + this.symmetryComboBox + ] + }, + { + xtype : 'container', + layout : 'hbox', + margin : "5 0 0 0", + items :[ + this._getNumericWithHelp("numberfield", "Refractive Index", "refractiveIndex", "How radiation propagates through the medium"), + this._getNumericWithHelp("numberfield", "Solvent Viscosity", "solventViscosity", "") + ] + }, + { + id : this.id + "comments", + xtype : 'textareafield', + name : 'comments', + margin : '35 0 0 10', + fieldLabel : 'Comments', + width : this.width - 100 + } ]; }; -BufferForm.prototype.getPanel = function(buffer) { - this.buffer = buffer; - this.panel = Ext.createWidget({ - xtype : 'container', - layout : 'vbox', - style : { - padding : '10px' - }, - fieldDefaults : { - labelAlign : 'left', - labelWidth : 50 +MacromoleculeForm.prototype._getSymmetries = function() { + return [ { + "s" : "P1" + }, { + "s" : "P2" + }, { + "s" : "P3" + }, { + "s" : "P4" + }, { + "s" : "P5" + }, { + "s" : "P6" + }, { + "s" : "P32" + }, { + "s" : "P42" + }, { + "s" : "P52" + }, { + "s" : "P62" + }, { + "s" : "P222" + } ] +}; - }, - items : [ this._getTopPanel(), { - id : 'buffer_comments', - xtype : 'textareafield', - name : 'comments', - fieldLabel : 'Comments', - width : '100%', - value : buffer.comments - }, this.additiveGrid.getPanel(buffer) ] +MacromoleculeForm.prototype.getPanel = function() { + this.panel = Ext.create('Ext.form.Panel', { + width : this.width, + height : this.height, + margin : 10, + border : 1, + defaultType : 'textfield', + items : this._getItems(), + buttons : this._getButtons() }); return this.panel; }; -BufferForm.prototype.input = function() { - return { - buffer : { - "bufferId" : 422, - "proposalId" : 10, - "safetyLevelId" : null, - "name" : "B1", - "acronym" : "B1", - "ph" : null, - "composition" : null, - "bufferhasadditive3VOs" : [], - "comments" : null - } - }; + +/** Populates each text field by field name and value **/ +MacromoleculeForm.prototype._populateField = function(fieldName, value) { + if (value != null){ + Ext.getCmp(this.id + fieldName).setValue(value); + } }; -BufferForm.prototype.test = function(targetId) { - var bufferForm = new BufferForm(); - var panel = bufferForm.getPanel(bufferForm.input().buffer); - panel.render(targetId); +/** Gets the value of a textfield **/ +MacromoleculeForm.prototype._getField = function(fieldName) { + return Ext.getCmp(this.id + fieldName).getValue(); }; - -/** - * @showTitle - * - * #onSaved - * #onAddPlates - * #onRemovePlates - **/ -function CaseForm(args) { - this.width = 700; - this.showTitle = true; - if (args != null) { - if (args.showTitle != null) { - this.showTitle = args.showTitle; - } - } - var _this = this; - this.stockSolutionGrid = new StockSolutionGrid({ - width : this.width - 10, - minHeight : 300, - height : 300, - tbar : true, - showTitle : true, - isPackedVisible : false, - btnAddExisting : true, - btnRemoveVisible : false, - btnUnpackVisible : true - }); - /** When selecting existing stock solutions **/ - this.stockSolutionGrid.onStockSolutionSelected.attach(function(sender, stockSolutions) { - if (stockSolutions != null) { - for ( var i = 0; i < stockSolutions.length; i++) { - _this.saveStockSolution(stockSolutions[i]); - } +/** It populates the form **/ +MacromoleculeForm.prototype.refresh = function(macromolecule) { + this.macromolecule = macromolecule; + if (macromolecule != null){ + this._populateField("name", macromolecule.name); + this._populateField("acronym", macromolecule.acronym); + this._populateField("extintionCoefficient", macromolecule.extintionCoefficient); + this._populateField("molecularMass", macromolecule.molecularMass); + this._populateField("comments", macromolecule.comments); + this._populateField("refractiveIndex", macromolecule.refractiveIndex); + this._populateField("solventViscosity", macromolecule.solventViscosity); + if (macromolecule.symmetry != null){ + Ext.getCmp(this.id + 'comboSym').setValue(macromolecule.symmetry); } - }); + } +}; - /** it can be because it has been added a new one or removed **/ - this.stockSolutionGrid.onProposalChanged.attach(function(sender, stockSolution) { - if (stockSolution != null) { - _this.saveStockSolution(stockSolution); - } else { - BIOSAXS.proposal.onInitialized.attach(function() { - _this.stockSolutionGrid.refresh(BIOSAXS.proposal.getStockSolutionsByDewarId(_this.dewar.dewarId)); - _this.stockSolutionGrid.grid.setLoading(false); - }); - BIOSAXS.proposal.init(); +MacromoleculeForm.prototype.input = function() { + return {}; +}; - } +/** It populates the form **/ +MacromoleculeForm.prototype.test = function(targetId) { + var macromoleculeForm = new MacromoleculeForm(); + macromoleculeForm.onClose.attach(function(sender){ + alert("Click on close"); }); + var panel = macromoleculeForm.getPanel(); + panel.render(targetId); +}; - this.onSaved = new Event(this); - this.onAddPlates = new Event(this); - this.onRemovePlates = new Event(this); -} -CaseForm.prototype.saveStockSolution = function(stockSolution) { - var _this = this; - var adapter = new BiosaxsDataAdapter(); - this.stockSolutionGrid.grid.setLoading("ISPyB: setting case to Stock solution"); - adapter.onSuccess.attach(function(sender, stockSolution) { - BIOSAXS.proposal.onInitialized.attach(function() { - _this.stockSolutionGrid.refresh(BIOSAXS.proposal.getStockSolutionsByDewarId(_this.dewar.dewarId)); - _this.stockSolutionGrid.grid.setLoading(false); - }); - BIOSAXS.proposal.init(); - }); - adapter.onError.attach(function(sender, data) { - _this.stockSolutionGrid.grid.setLoading(false); - BUI.showError(data); - }); - stockSolution.boxId = _this.dewar.dewarId; - adapter.saveStockSolution(stockSolution); -}; - -CaseForm.prototype.fillStores = function() { - var _this = this; - this.panel.setLoading("Loading Labcontacts from database"); + - var proposal = BUI.getProposal(); - proposal.onDataRetrieved.attach(function(sender, data) { - _this.labContactForSendingStore.loadData(data, false); - _this.labContactForReturnStore.loadData(data, false); - _this.panel.setLoading(false); - }); - proposal.getLabContactsByProposalId(); +function ModelVisualizerForm(args){ + this.id =BUI.id(); + this.width = 600; + this.height = 400; + if (args!= null){ + if (args.width != null){ + this.width = args.width; + } + if (args.height != null){ + this.height = args.height; + } + } }; -CaseForm.prototype.refresh = function(dewar) { - this.setDewar(dewar); - this.stockSolutionGrid.refresh(BIOSAXS.proposal.getStockSolutionsByDewarId(dewar.dewarId)); +ModelVisualizerForm.prototype._getFirHTML = function(modelId, width, height, type, desc) { + var html = ""; + html = html + ''; + html = html + ''; + html = html + ''; + html = html + '
dammin.' + type + '
' + desc + '
'; + return html; }; -CaseForm.prototype.getDewar = function() { - this.dewar.code = Ext.getCmp("dewar_code").getValue(); - this.dewar.comments = Ext.getCmp("dewar_comments").getValue(); - this.dewar.trackingNumberFromSynchrotron = Ext.getCmp("dewar_trackingNumberFromSynchrotron").getValue(); - this.dewar.trackingNumberToSynchrotron = Ext.getCmp("dewar_trackingNumberToSynchrotron").getValue(); - this.dewar.transportValue = Ext.getCmp("dewar_transportValue").getValue(); - this.dewar.storageLocation = Ext.getCmp("dewar_storageLocation").getValue(); - this.dewar.firstExperimentId = this.macromoleculeCombo.getValue(); - return this.dewar; +ModelVisualizerForm.prototype.getItems = function(modelPanel){ + _this = this; + var height = _this.height/2 - 60; + var width = _this.width/2 - 10; + + return Ext.create('Ext.container.Container', { + layout: { + type: 'vbox', // Arrange child items vertically + }, + items: [ + modelPanel, + { + xtype : 'container', + layout: { + type: 'hbox', // Arrange child items vertically + }, + items : [{ + html : this._getFirHTML("id", width, height, "fir", "Fit of the simulated scattering curve versus a smoothed experimental data (spline interpolation)"), + height :height, + width : width, + padding: 2 + }, + { + html : this._getFirHTML("id", width, height, "fit", "Fit of the simulated scattering curve versus the experimental data."), + height : height, + width : width, + padding: 2 + }] + } + + ] + }); }; -CaseForm.prototype.setDewar = function(dewar) { - this.dewar = dewar; - Ext.getCmp("dewar_code").setValue(this.dewar.code); - Ext.getCmp("dewar_dewarStatus").setText(new String(this.dewar.dewarStatus).toUpperCase()); - Ext.getCmp("dewar_comments").setValue(this.dewar.comments); - Ext.getCmp("dewar_trackingNumberFromSynchrotron").setValue(this.dewar.trackingNumberFromSynchrotron); - Ext.getCmp("dewar_trackingNumberToSynchrotron").setValue(this.dewar.trackingNumberToSynchrotron); - Ext.getCmp("dewar_transportValue").setValue(this.dewar.transportValue); - Ext.getCmp("dewar_storageLocation").setValue(this.dewar.storageLocation); - if (dewar.sessionVO != null) { - this.macromoleculeCombo.setValue(dewar.sessionVO.sessionId); +ModelVisualizerForm.prototype.refresh = function(models){ + var input = []; +// var colors = ["008000", "F0A804", "0000FF", "800080", "C0C0C0"]; + for (var i = 0; i < models.length; i++) { + console.log(BUI.rainbow(models.length, i).replace("#", "0x")); + input.push({ + color: BUI.rainbow(models.length, i).replace("#", "0x"), + modelId: models[i].modelId, + opacity: 0.8, + radius: 3, + title: BUI.getFileNameByPath(models[i].pdbFile), + type: "SHAPEDETERMINATIONMODEL" + + }); } + + this.panel.removeAll(); + this.panel.add( + _this.getItems( + new PDBViewer({ + width : this.width - 10, + height : (this.height/2) - 10, + title : "" + }).draw(input) + ) + ); + + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + var splitted = data.toString().split("\n"); + var array = []; + for ( var i = 0; i < splitted.length; i++) { + var line = splitted[i].trim(); + var line_splited = line.split(/\s*[\s,]\s*/); + if (line_splited.length == 4) { + array.push([ Number(line_splited[0]), BUI.getStvArray(line_splited[1], line_splited[2]), BUI.getStvArray(line_splited[3], 0) ]); + } + } + + var id = (_this.id + "firid"); + var dygraphWidget = new StdDevDyGraph(id, { + width : (_this.width/2) - 10, + height :(_this.height/2) -110, + xlabel : 'q(nm-1)' + }); + dygraphWidget.draw(array, [ "#FF0000", "#0000FF", "#FF00FF" ], [ 's', 'I(exp)', 'I(sim)' ]); + }); + + adapter.getModelFile("FIR", models[0].modelId); + + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + var splitted = data.toString().split("\n"); + var array = []; + for ( var i = 0; i < splitted.length; i++) { + var line = splitted[i].trim(); + var line_splited = line.split(/\s*[\s,]\s*/); + if (line_splited.length == 3) { + array.push([ Number(line_splited[0]), BUI.getStvArray(line_splited[1], 0), BUI.getStvArray(line_splited[2], 0) ]); + } + } + + var id = (_this.id + "fitid"); + + var dygraphWidget = new StdDevDyGraph(id, { + width : (_this.width/2) - 10, + height : (_this.height/2) - 110, + xlabel : 'q(nm-1)' + }); + dygraphWidget.draw(array, [ "#FF0000", "#0000FF" ], [ "s", "I(exp)", "I(sim)" ]); + }); + adapter.getModelFile("FIT", models[0].modelId); }; -CaseForm.prototype.getSessionCombo = function() { - this.macromoleculeCombo = BIOSAXS_COMBOMANAGER.getComboSessions(BIOSAXS.proposal.getSessions(), { - labelWidth : 100, - margin : '5 0 00 0', - width : 250 +ModelVisualizerForm.prototype.getPanel = function(modelList){ + _this = this; + this.modelList = modelList; + this.panel = Ext.create('Ext.Panel', { + title: 'Results', + width: this.width, + height: this.height, + layout: { + type: 'vbox', // Arrange child items vertically +// align: 'stretch' // Each takes up full width + }, + items: [ + + ], + listeners : { + afterrender : function(grid, eOpts) { +// alert(_this.modelList) + } + } }); - return this.macromoleculeCombo; + + return this.panel; + }; -CaseForm.prototype.getInformationPanel = function() { - if (this.panel == null) { - this.informationPanel = Ext.create('Ext.form.Panel', { - width : this.width - 10, - border : 0, - items : [ { - xtype : 'container', - margin : "2 2 2 2", - collapsible : false, - defaultType : 'textfield', - layout : 'anchor', - items : [ { - xtype : 'container', - layout : 'hbox', - items : [ { - xtype : 'requiredtext', - fieldLabel : 'Code', - allowBlank : false, - name : 'code', - id : 'dewar_code', - anchor : '50%' - }, { - xtype : 'label', - margin : '0 0 0 20', - readOnly : true, - id : 'dewar_dewarStatus', - anchor : '50%' - } ] - }, this.getSessionCombo(), { - margin : '5 0 0 0', - xtype : 'textareafield', - name : 'comments', - id : 'dewar_comments', - width : this.width - 50, - fieldLabel : 'Comments' - } ] - }, { - xtype : 'fieldset', - title : 'Courier Accounts Details for Return', - collapsible : false, - layout : 'anchor', - defaults : { - anchor : '100%' - }, - items : [ { - xtype : 'container', - layout : 'hbox', - items : [ { - xtype : 'textfield', - labelWidth : 200, - width : 280, - fieldLabel : 'Track Number From Synchrotron', - id : 'dewar_trackingNumberFromSynchrotron' - }, { - xtype : 'numberfield', - width : 190, - labelWidth : 110, - margin : '0 0 0 30', - fieldLabel : 'Transport Value', - id : 'dewar_transportValue' - } - - ] - }, { - xtype : 'container', - layout : 'hbox', - margin : '10 0 0 0', - items : [ - - { - xtype : 'textfield', - labelWidth : 200, - width : 280, - fieldLabel : 'Track Number To Synchrotron', - id : 'dewar_trackingNumberToSynchrotron' - }, { - xtype : 'textfield', - margin : '0 0 0 30', - width : 190, - labelWidth : 110, - fieldLabel : 'Storage Location', - id : 'dewar_storageLocation' - } - - ] - } ] - } ] - }); - } - - return this.informationPanel; -}; - -CaseForm.prototype.getPanel = function(dewar) { - this.dewar = dewar; - this.panel = Ext.createWidget({ - xtype : 'container', - layout : 'vbox', - width : this.width, - border : 0, - items : [ { - items : { - xtype : "container", - layout : "vbox", - margin : "5 5 5 5", - items : [ this.getInformationPanel(dewar), this.stockSolutionGrid.getPanel() ] - - } - } ] - }); - - this.refresh(dewar); - return this.panel; - -}; - -CaseForm.prototype.input = function() { - return { - dewar : { - "dewarId" : 305861, - "code" : "ESRF-TEST", - "comments" : "comments", - "storageLocation" : "FRIDGE", - "dewarStatus" : "opened", - "timeStamp" : null, - "isStorageDewar" : null, - "barCode" : "ESRF305861", - "customsValue" : null, - "transportValue" : null, - "trackingNumberToSynchrotron" : "3333", - "trackingNumberFromSynchrotron" : "224466", - "type" : "Dewar", - "sessionVO" : { - "sessionId" : 31697, - "expSessionPk" : null, - "projectCode" : null, - "startDate" : "2012 07 21", - "endDate" : "2012 07 23", - "beamlineName" : "BM29", - "scheduled" : 1, - "nbShifts" : 2, - "comments" : null, - "beamlineOperator" : "PERNOT P", - "usedFlag" : null, - "sessionTitle" : null, - "structureDeterminations" : null, - "dewarTransport" : null, - "databackupFrance" : null, - "databackupEurope" : null, - "visit_number" : null, - "operatorSiteNumber" : "14061", - "timeStamp" : "2012 04 25" - } - }, - proposal : { - "assemblies" : [], - "sessions" : [ { - "sessionId" : 31697, - "expSessionPk" : null, - "projectCode" : null, - "startDate" : "2012 07 21", - "endDate" : "2012 07 23", - "beamlineName" : "BM29", - "scheduled" : 1, - "nbShifts" : 2, - "comments" : null, - "beamlineOperator" : "PERNOT P", - "usedFlag" : null, - "sessionTitle" : null, - "structureDeterminations" : null, - "dewarTransport" : null, - "databackupFrance" : null, - "databackupEurope" : null, - "visit_number" : null, - "operatorSiteNumber" : "14061", - "timeStamp" : "2012 04 25" - } ], - "labcontacts" : [ { - "labContactId" : 787, - "personVO" : { - "personId" : 304252, - "personUUID" : null, - "familyName" : "KIM", - "givenName" : "Henry", - "title" : null, - "emailAddress" : "henry-sung.kim@ibs.fr", - "phoneNumber" : "", - "login" : "", - "passwd" : "", - "faxNumber" : "" - }, - "cardName" : "KIM-Institut de Bio", - "defaultCourrierCompany" : "22", - "courierAccount" : "", - "billingReference" : "", - "dewarAvgCustomsValue" : 0, - "dewarAvgTransportValue" : 0 - } ], - "buffers" : [ { - "bufferId" : 811, - "proposalId" : 3124, - "safetyLevelId" : null, - "name" : "EDTA", - "acronym" : "EDTA", - "ph" : null, - "composition" : "", - "bufferhasadditive3VOs" : [], - "comments" : "" - }, { - "bufferId" : 810, - "proposalId" : 3124, - "safetyLevelId" : null, - "name" : "HEPES", - "acronym" : "HEPES", - "ph" : null, - "composition" : "", - "bufferhasadditive3VOs" : [], - "comments" : "" - } ], - "shippings" : [ { - "shippingId" : 304107, - "shippingName" : "TEST", - "deliveryAgentAgentName" : null, - "deliveryAgentShippingDate" : null, - "deliveryAgentDeliveryDate" : null, - "deliveryAgentAgentCode" : null, - "deliveryAgentFlightCode" : null, - "shippingStatus" : "opened", - "timeStamp" : "2013 09 25", - "laboratoryId" : null, - "isStorageShipping" : null, - "creationDate" : "2013 09 25", - "comments" : "test", - "sendingLabContactVO" : { - "labContactId" : 787, - "personVO" : { - "personId" : 304252, - "personUUID" : null, - "familyName" : "KIM", - "givenName" : "Henry", - "title" : null, - "emailAddress" : "henry-sung.kim@ibs.fr", - "phoneNumber" : "", - "login" : "", - "passwd" : "", - "faxNumber" : "" - }, - "cardName" : "KIM-Institut de Bio", - "defaultCourrierCompany" : "22", - "courierAccount" : "", - "billingReference" : "", - "dewarAvgCustomsValue" : 0, - "dewarAvgTransportValue" : 0 - }, - "returnLabContactVO" : { - "labContactId" : 787, - "personVO" : { - "personId" : 304252, - "personUUID" : null, - "familyName" : "KIM", - "givenName" : "Henry", - "title" : null, - "emailAddress" : "henry-sung.kim@ibs.fr", - "phoneNumber" : "", - "login" : "", - "passwd" : "", - "faxNumber" : "" - }, - "cardName" : "KIM-Institut de Bio", - "defaultCourrierCompany" : "22", - "courierAccount" : "", - "billingReference" : "", - "dewarAvgCustomsValue" : 0, - "dewarAvgTransportValue" : 0 - }, - "returnCourier" : null, - "dateOfShippingToUser" : null, - "shippingType" : "DewarTracking", - "dewarVOs" : [ { - "dewarId" : 305861, - "code" : "ESRF-TEST", - "comments" : "comments", - "storageLocation" : "FRIDGE", - "dewarStatus" : "opened", - "timeStamp" : null, - "isStorageDewar" : null, - "barCode" : "ESRF305861", - "customsValue" : null, - "transportValue" : null, - "trackingNumberToSynchrotron" : "3333", - "trackingNumberFromSynchrotron" : "224466", - "type" : "Dewar", - "sessionVO" : { - "sessionId" : 31697, - "expSessionPk" : null, - "projectCode" : null, - "startDate" : "2012 07 21", - "endDate" : "2012 07 23", - "beamlineName" : "BM29", - "scheduled" : 1, - "nbShifts" : 2, - "comments" : null, - "beamlineOperator" : "PERNOT P", - "usedFlag" : null, - "sessionTitle" : null, - "structureDeterminations" : null, - "dewarTransport" : null, - "databackupFrance" : null, - "databackupEurope" : null, - "visit_number" : null, - "operatorSiteNumber" : "14061", - "timeStamp" : "2012 04 25" - } - } ] - } ], - "macromolecules" : [ { - "macromoleculeId" : 5933, - "safetylevelId" : null, - "proposalId" : 3124, - "name" : "A", - "acronym" : "A", - "molecularMass" : "", - "extintionCoefficient" : "", - "sequence" : null, - "creationDate" : null, - "comments" : "", - "macromoleculeregion3VOs" : [], - "stoichiometry3VOsForHostMacromoleculeId" : [], - "structure3VOs" : [] - } ], - "stockSolutions" : [ { - "stockSolutionId" : 6, - "proposalId" : 3124, - "macromoleculeId" : 5933, - "bufferId" : 811, - "instructionSet3VO" : null, - "boxId" : 305861, - "storageTemperature" : "20", - "volume" : "300", - "concentration" : "1.2", - "comments" : "Buffer EDTA with A", - "name" : "A_EDTA_1.2", - "samples" : [] - } ] - } - - }; -}; - -CaseForm.prototype.test = function(targetId) { - var caseForm = new CaseForm(); - BIOSAXS.proposal = new Proposal(caseForm.input().proposal); - var panel = caseForm.getPanel(caseForm.input().dewar); - panel.render(targetId); -}; - -/** - * Example form - * - * @witdh - * @height - */ -function ExampleForm(args) { - this.id = BUI.id(); - this.width = 700; - this.height = 500; - - if (args != null) { - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; - } - } -} - -ExampleForm.prototype._getItems = function() { - return [{ - fieldLabel : 'First Name', - name : 'first', - allowBlank : false - }, { - fieldLabel : 'Last Name', - name : 'last', - allowBlank : false - } ]; -}; - -ExampleForm.prototype._getItems = function() { - return [ ]; -}; - -ExampleForm.prototype._getButtons = function() { - return [ ]; -}; - -ExampleForm.prototype.getPanel = function() { - this.panel = Ext.create('Ext.form.Panel', { - width : this.width, - height : this.height, - margin : 10, - border : 1, - defaultType : 'textfield', - items : this._getItems(), - buttons : this._getButtons() - }); - return this.panel; -}; - -/** It populates the form **/ -ExampleForm.prototype.refresh = function(macromolecule) { -}; - -function ExperimentForm(args) { - this.id = BUI.id(); - - if (args != null) { - } - - this.onSaved = new Event(this); -} - -ExperimentForm.prototype._getItems = function(experiment) { - this.experiment = experiment; - var typeCombo = Ext.create('Ext.form.ComboBox', { - id : this.id + 'type', - fieldLabel : 'Type', - store : [ "STATIC", "CALIBRATION", "HPLC" ], - queryMode : 'local', - labelWidth : 120, - displayField : 'name', - valueField : 'name', - value : experiment.json.type, - disabled : (experiment.json.type == 'TEMPLATE') - }); - - var items = []; - - - if (experiment.json.type == "HPLC" ){ - var typeMacromolecule = BIOSAXS_COMBOMANAGER.getComboMacromoleculeByMacromolecules(BIOSAXS.proposal.getMacromolecules(), {labelWidth : 120, width: "120px"}); - if (experiment.getHPLCMacromolecule() != null){ - typeMacromolecule.setValue(experiment.getHPLCMacromolecule().macromoleculeId); - items.push(typeMacromolecule); - } - } - - - items.push(typeCombo, { - id : this.id + 'name', - xtype : 'textfield', - fieldLabel : 'Name', - labelWidth : 120, - width : '100%', - value : experiment.json.name - }, { - id : this.id + 'comments', - xtype : 'textareafield', - name : 'comments', - fieldLabel : 'Comments', - labelWidth : 120, - height : 120, - width : '100%', - value : experiment.json.comments - }); - return items; -}; -ExperimentForm.prototype.getPanel = function(experiment) { - var _this = this; - - this.panel = Ext.createWidget({ - xtype : 'container', - layout : 'vbox', - border : 0, - style : { - padding : '10px' - }, - fieldDefaults : { - labelAlign : 'left', - labelWidth : 50 - }, - items : this._getItems(experiment) - }); - return this.panel; -}; - -ExperimentForm.prototype.input = function() { - return new ExperimentHeaderForm().input(); -}; - -ExperimentForm.prototype.test = function(targetId) { - var experimentForm = new ExperimentForm(); - var panel = experimentForm.getPanel(new Experiment(experimentForm.input().experiment)); - panel.render(targetId); -}; - -/** - * Shows the header for the experiments changing the color and parameters depending on experiment type - * - */ -function ExperimentHeaderForm(args) { - this.id = BUI.id(); - this.backgroundColor = '#FFFFFF'; -} - -ExperimentHeaderForm.prototype.getHTMLSource = function(experiment) { - var html = BUI.createFormLabel("Name :", experiment.json.name, 75, 400, this.backgroundColor); - if (experiment.json.type == "HPLC") { - if (experiment.getHPLCMacromolecule() != null){ - html = html + BUI.createFormLabel("Molecule :", experiment.getHPLCMacromolecule().acronym, 75, 400, this.backgroundColor); - } - } - else{ - html = html + BUI.createFormLabel("Type :", experiment.json.type, 75, 400, this.backgroundColor); - } - - html = html + BUI.createFormLabel("Date :", experiment.json.creationDate, 75, 400, this.backgroundColor); - return html; -}; - -ExperimentHeaderForm.prototype.getHTMLDownload = function(experiment) { - var bgcolor = "background-color:" + this.backgroundColor + ";"; - var html = "
"; - if ((experiment.json.type == "CALIBATION") || (experiment.json.type == "STATIC")) { - html = html + " Download Source File
"; - html = html - + ""; - } - if (experiment.json.type == "TEMPLATE") { - html = html - + " Download Source File"; - } - - if (experiment.json.type == "HPLC") { - html = html + " Download h5 File"; - } - - return html; -}; - -ExperimentHeaderForm.prototype.getTopPanel = function(experiment) { - return { - xtype : 'container', - layout : 'hbox', - items : [ { - margin : "0 0 0 0", - width : 475, - border : 0, - html : this.getHTMLSource(experiment) - }, { - margin : "0 0 0 0", - width : 475, - border : 0, - html : this.getHTMLDownload(experiment) - } ] - }; -}; - -ExperimentHeaderForm.prototype.getButton = function(experiment) { - var _this = this; - return Ext.create('Ext.Button', { - text : 'EDIT', - minWidth : '100', - margin : '10 0 0 30', - handler : function() { - var experimentWindow = new ExperimentWindow(); - experimentWindow.onSaved.attach(function(sender, data) { - _this.experiment.json.name = data.name; - _this.experiment.json.type = data.type; - _this.experiment.json.comments = data.comments; - _this.panel.remove(_this.panel.items.items[0]); - _this.panel.remove(_this.panel.items.items[0]); - _this.panel.insert(_this.getTopPanel(_this.experiment)); - _this.panel.insert(_this.getBottomPanel(_this.experiment)); - }); - experimentWindow.show(experiment); - } - }); -}; - -ExperimentHeaderForm.prototype.getBottomPanel = function(experiment) { - return { - xtype : 'container', - layout : 'hbox', - margin : '10 0 0 0', - items : [ this.getComments(experiment), this.getButton(experiment) ] - }; -}; - -ExperimentHeaderForm.prototype.getComments = function(experiment) { - return { - xtype : 'textareafield', - labelStyle : 'font-weight: bold;', - name : 'comments', - fieldLabel : 'Comments', - labelWidth : 70, - height : 40, - minWidth : '450', - readOnly : true, - value : experiment.json.comments - }; -}; - -ExperimentHeaderForm.prototype.getPanel = function(experiment) { - this.experiment = experiment; - - if (experiment.json.type == 'CALIBRATION') { - this.backgroundColor = '#EFFBFB'; - } - if (experiment.json.type == 'TEMPLATE') { - this.backgroundColor = '#E0F8E6'; - } - - this.panel = Ext.create('Ext.container.Container', { - frame : false, - layout : 'vbox', - padding : 5, - bodyPadding : '5 5 0 0', - width : 890, - margin : '0 0 10 0', - height : 120, - style : { - borderColor : '#99bce8', - borderStyle : 'solid', - borderWidth : '1px', - 'background-color' : this.backgroundColor - }, - fieldDefaults : { - msgTarget : 'side', - labelWidth : 100 - }, - items : [ this.getTopPanel(experiment), this.getBottomPanel(experiment) ] - }); - return this.panel; -}; - -ExperimentHeaderForm.prototype.input = function() { - return { - experiment : DATADOC.getExperiment_10() - }; -}; - -ExperimentHeaderForm.prototype.test = function(targetId) { - var experimentHeaderForm = new ExperimentHeaderForm(); - var panel = experimentHeaderForm.getPanel(new Experiment(experimentHeaderForm.input().experiment)); - panel.render(targetId); - -}; - -/** - * Macromolecule form with the general parameters of a macromolecule - * - * @witdh - * @height - * - * #onSave button save has been clicked - * #onClose button close has been clicked - */ -function MacromoleculeForm(args) { - this.id = BUI.id(); - this.width = 700; - this.height = 500; - - if (args != null) { - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; - } - } - - /** Events **/ - this.onSave = new Event(this); - this.onClose = new Event(this); -} - -/** Type : is the Ext type then requiredtext or textfield * */ -MacromoleculeForm.prototype._getFieldTextWithHelp = function(type, fieldLabel, fieldName, help) { - return Ext.create('Ext.container.Container', { - margin : "10 0 0 10", - items : [ { - xtype : type, - fieldLabel : fieldLabel, - name : fieldName, - id : this.id + fieldName - }, { - xtype : 'label', - forId : 'myFieldId', - text : help, - margin : "5 0 0 105", - cls : "inline-help" - } ] - }); -}; - -MacromoleculeForm.prototype._getNumericWithHelp = function(type, fieldLabel, fieldName, help) { - return Ext.create('Ext.container.Container', { - margin : "0 0 0 10", - items : [ { - xtype : type, - fieldLabel : fieldLabel, - name : fieldName, - id : this.id + fieldName, - decimalPrecision : 6, - width : 220 - }, { - xtype : 'label', - forId : 'myFieldId', - text : help, - margin : "5 0 0 10", - cls : "inline-help" - } ] - }); -}; - -MacromoleculeForm.prototype._getButtons = function() { - var _this = this; - return [ { - text : 'Save', - handler : function() { - _this._save(); - } - },{ - text : 'Close', - handler : function() { - _this.onClose.notify(); - - } - } ]; -}; - -/** It persits the macromolecule in the database **/ -MacromoleculeForm.prototype._persist = function(macromoleculeId, acronym, name, molecularMass, extintionCoefficient, comments, refractiveIndex, solventViscosity) { - - /** Checking not duplicated acronym **/ - if (((macromoleculeId == null) && (BIOSAXS.proposal.getMacromoleculeByAcronym(acronym) != null))== true){ - BUI.showError("Duplicated acronym"); - return; - } - - - if (macromoleculeId == null){ - /** new macromolecule **/ - this.macromolecule = {}; - this.macromolecule.macromoleculeId = null; - } - else{ - this.macromolecule.macromoleculeId = macromoleculeId; - } - - this.macromolecule["acronym"] = acronym; - this.macromolecule["name"] = name; - this.macromolecule["molecularMass"] = molecularMass; - this.macromolecule["extintionCoefficient"] = extintionCoefficient; - this.macromolecule["comments"] = comments; - this.macromolecule["symmetry"] = Ext.getCmp(this.id + 'comboSym').getValue(); - this.macromolecule["refractiveIndex"] = refractiveIndex; - this.macromolecule["solventViscosity"] = solventViscosity; - - var _this = this; - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, proposal) { - /** Updating the proposal global object **/ - BIOSAXS.proposal.setItems(proposal); - _this.panel.setLoading(false); - - var saved = BIOSAXS.proposal.getMacromoleculeByAcronym(acronym); - /** Refreshing to check that everything is ok **/ - _this.refresh(saved); - _this.onSave.notify(saved); - }); - - this.panel.setLoading("Saving Macromolecule") - adapter.saveMacromolecule(this.macromolecule); -}; - -/** Save the macromolecule in the DB **/ -MacromoleculeForm.prototype._save = function() { - - var _this = this; - - var acronym = this._getField("acronym"); - var name = this._getField("name"); - var molecularMass = this._getField("molecularMass"); - var extintionCoefficient = this._getField("extintionCoefficient"); - var comments = this._getField("comments"); - - var refractiveIndex = this._getField("refractiveIndex"); - var solventViscosity = this._getField("solventViscosity"); - - /** Checking required fields **/ - if (name == "") { - BUI.showError("Name field is mandatory"); - return; - } - if (acronym == "") { - BUI.showError("Acroynm field is mandatory"); - return; - } - - if (this.macromolecule != null){ - /** Checking if it is a new macromolecule **/ - if (this.macromolecule.macromoleculeId == null){ - /** Check if the acronym exists already **/ - this._persist(null, acronym, name, molecularMass, extintionCoefficient, comments, refractiveIndex, solventViscosity); - } - else{ - /** It is an update **/ - this._persist(this.macromolecule.macromoleculeId, acronym, name, molecularMass, extintionCoefficient, comments, refractiveIndex, solventViscosity); - } - } - else{ - /** It is a new macromolecule **/ - this._persist(null, acronym, name, molecularMass, extintionCoefficient, comments, refractiveIndex, solventViscosity); - } -}; - - - -MacromoleculeForm.prototype._getItems = function() { - var _this = this; - /** Symmetry combo box **/ - var symmetry = Ext.create('Ext.data.Store', { - fields : [ 's' ], - data : this._getSymmetries() - }); - - this.symmetryComboBox = Ext.create('Ext.form.ComboBox', { - fieldLabel : 'Symmetry', - store : symmetry, - id : this.id + 'comboSym', - queryMode : 'local', - displayField : 's', - valueField : 's', - value : "P1", - margin : "0 0 0 30", - width : 220 - }); - - return [this._getFieldTextWithHelp("requiredtext", "Name", "name", "Long name. i.e: Bovine serum albumin"), - this._getFieldTextWithHelp("requiredtext", "Acronym", "acronym", "Acronym will be used in the files and analisys. i.e: BSA"), - this._getFieldTextWithHelp("textfield", "Mol. Mass (Da)", "molecularMass", "Atomic mass estimation measured in Da"), - { - xtype : 'container', - layout : 'hbox', - margin : "10 0 0 0", - items :[ - this._getNumericWithHelp("numberfield", "Extinction coef.", "extintionCoefficient", ""), - this.symmetryComboBox - ] - }, - { - xtype : 'container', - layout : 'hbox', - margin : "5 0 0 0", - items :[ - this._getNumericWithHelp("numberfield", "Refractive Index", "refractiveIndex", "How radiation propagates through the medium"), - this._getNumericWithHelp("numberfield", "Solvent Viscosity", "solventViscosity", "") - ] - }, - { - id : this.id + "comments", - xtype : 'textareafield', - name : 'comments', - margin : '35 0 0 10', - fieldLabel : 'Comments', - width : this.width - 100 - } ]; -}; - -MacromoleculeForm.prototype._getSymmetries = function() { - return [ { - "s" : "P1" - }, { - "s" : "P2" - }, { - "s" : "P3" - }, { - "s" : "P4" - }, { - "s" : "P5" - }, { - "s" : "P6" - }, { - "s" : "P32" - }, { - "s" : "P42" - }, { - "s" : "P52" - }, { - "s" : "P62" - }, { - "s" : "P222" - } ] -}; - -MacromoleculeForm.prototype.getPanel = function() { - this.panel = Ext.create('Ext.form.Panel', { - width : this.width, - height : this.height, - margin : 10, - border : 1, - defaultType : 'textfield', - items : this._getItems(), - buttons : this._getButtons() - }); - return this.panel; -}; - - -/** Populates each text field by field name and value **/ -MacromoleculeForm.prototype._populateField = function(fieldName, value) { - if (value != null){ - Ext.getCmp(this.id + fieldName).setValue(value); - } -}; - -/** Gets the value of a textfield **/ -MacromoleculeForm.prototype._getField = function(fieldName) { - return Ext.getCmp(this.id + fieldName).getValue(); -}; - - -/** It populates the form **/ -MacromoleculeForm.prototype.refresh = function(macromolecule) { - this.macromolecule = macromolecule; - if (macromolecule != null){ - this._populateField("name", macromolecule.name); - this._populateField("acronym", macromolecule.acronym); - this._populateField("extintionCoefficient", macromolecule.extintionCoefficient); - this._populateField("molecularMass", macromolecule.molecularMass); - this._populateField("comments", macromolecule.comments); - this._populateField("refractiveIndex", macromolecule.refractiveIndex); - this._populateField("solventViscosity", macromolecule.solventViscosity); - if (macromolecule.symmetry != null){ - Ext.getCmp(this.id + 'comboSym').setValue(macromolecule.symmetry); - } - } -}; - - -MacromoleculeForm.prototype.input = function() { - return {}; -}; - - -/** It populates the form **/ -MacromoleculeForm.prototype.test = function(targetId) { - var macromoleculeForm = new MacromoleculeForm(); - macromoleculeForm.onClose.attach(function(sender){ - alert("Click on close"); - }); - var panel = macromoleculeForm.getPanel(); - panel.render(targetId); -}; - - - - - -function ModelVisualizerForm(args){ - this.id =BUI.id(); - this.width = 600; - this.height = 400; - if (args!= null){ - if (args.width != null){ - this.width = args.width; - } - if (args.height != null){ - this.height = args.height; - } - } -}; - -ModelVisualizerForm.prototype._getFirHTML = function(modelId, width, height, type, desc) { - var html = ""; - html = html + ''; - html = html + ''; - html = html + ''; - html = html + '
dammin.' + type + '
' + desc + '
'; - return html; -}; - -ModelVisualizerForm.prototype.getItems = function(modelPanel){ - _this = this; - var height = _this.height/2 - 60; - var width = _this.width/2 - 10; - - return Ext.create('Ext.container.Container', { - layout: { - type: 'vbox', // Arrange child items vertically - }, - items: [ - modelPanel, - { - xtype : 'container', - layout: { - type: 'hbox', // Arrange child items vertically - }, - items : [{ - html : this._getFirHTML("id", width, height, "fir", "Fit of the simulated scattering curve versus a smoothed experimental data (spline interpolation)"), - height :height, - width : width, - padding: 2 - }, - { - html : this._getFirHTML("id", width, height, "fit", "Fit of the simulated scattering curve versus the experimental data."), - height : height, - width : width, - padding: 2 - }] - } - - ] - }); -}; - -ModelVisualizerForm.prototype.refresh = function(models){ - var input = []; -// var colors = ["008000", "F0A804", "0000FF", "800080", "C0C0C0"]; - for (var i = 0; i < models.length; i++) { - console.log(BUI.rainbow(models.length, i).replace("#", "0x")); - input.push({ - color: BUI.rainbow(models.length, i).replace("#", "0x"), - modelId: models[i].modelId, - opacity: 0.8, - radius: 3, - title: BUI.getFileNameByPath(models[i].pdbFile), - type: "SHAPEDETERMINATIONMODEL" - - }); - } - - this.panel.removeAll(); - this.panel.add( - _this.getItems( - new PDBViewer({ - width : this.width - 10, - height : (this.height/2) - 10, - title : "" - }).draw(input) - ) - ); - - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - var splitted = data.toString().split("\n"); - var array = []; - for ( var i = 0; i < splitted.length; i++) { - var line = splitted[i].trim(); - var line_splited = line.split(/\s*[\s,]\s*/); - if (line_splited.length == 4) { - array.push([ Number(line_splited[0]), BUI.getStvArray(line_splited[1], line_splited[2]), BUI.getStvArray(line_splited[3], 0) ]); - } - } - - var id = (_this.id + "firid"); - var dygraphWidget = new StdDevDyGraph(id, { - width : (_this.width/2) - 10, - height :(_this.height/2) -110, - xlabel : 'q(nm-1)' - }); - dygraphWidget.draw(array, [ "#FF0000", "#0000FF", "#FF00FF" ], [ 's', 'I(exp)', 'I(sim)' ]); - }); - - adapter.getModelFile("FIR", models[0].modelId); - - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - var splitted = data.toString().split("\n"); - var array = []; - for ( var i = 0; i < splitted.length; i++) { - var line = splitted[i].trim(); - var line_splited = line.split(/\s*[\s,]\s*/); - if (line_splited.length == 3) { - array.push([ Number(line_splited[0]), BUI.getStvArray(line_splited[1], 0), BUI.getStvArray(line_splited[2], 0) ]); - } - } - - var id = (_this.id + "fitid"); - - var dygraphWidget = new StdDevDyGraph(id, { - width : (_this.width/2) - 10, - height : (_this.height/2) - 110, - xlabel : 'q(nm-1)' - }); - dygraphWidget.draw(array, [ "#FF0000", "#0000FF" ], [ "s", "I(exp)", "I(sim)" ]); - }); - adapter.getModelFile("FIT", models[0].modelId); -}; - -ModelVisualizerForm.prototype.getPanel = function(modelList){ - _this = this; - this.modelList = modelList; - this.panel = Ext.create('Ext.Panel', { - title: 'Results', - width: this.width, - height: this.height, - layout: { - type: 'vbox', // Arrange child items vertically -// align: 'stretch' // Each takes up full width - }, - items: [ - - ], - listeners : { - afterrender : function(grid, eOpts) { -// alert(_this.modelList) - } - } - }); - - return this.panel; - -}; - - -/** - * Example form - * - * @witdh - * @height - */ -function MolarityForm(args) { - this.id = BUI.id(); - this.width = 700; - this.height = 500; - - if (args != null) { - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; - } - } - - this.onSave = new Event(this); - this.onClose = new Event(this); -} - - -MolarityForm.prototype._getNumericWithHelp = function(type, fieldLabel, fieldName, help) { - return Ext.create('Ext.container.Container', { - margin : "10 0 0 10", - items : [ { - xtype : type, - fieldLabel : fieldLabel, - name : fieldName, - id : this.id + fieldName, - decimalPrecision : 6 - }, { - xtype : 'label', - forId : 'myFieldId', - text : help, - margin : "5 0 0 105", - cls : "inline-help" - } ] - }); -}; - - -MolarityForm.prototype._getItems = function() { - this.macromoleculeCombo = BIOSAXS_COMBOMANAGER.getComboMacromoleculeByMacromolecules(this.getMacromuleculesCandidates(this.macromolecule), { - width : 250, - labelWidth : 100, - margin : 10 - }); - - return [ { - xtype : 'container', - flex : 1, - margin : '10 0 0 10', - border : 0, - layout : 'anchor', - defaultType : 'requiredtext', - items : [ this.macromoleculeCombo, - this._getNumericWithHelp("textfield", "Ratio", "ratio", "Number in assymmetric units") - ] - } ]; -}; - -MolarityForm.prototype._persist = function() { - var _this = this; - var macromoleculeId = this.macromoleculeCombo.getValue(); - var ratio = Ext.getCmp(this.id + "ratio").getValue(); - var comments = "Not used yet"; - var dataAdapter = new BiosaxsDataAdapter(); - this.panel.setLoading("Saving"); - dataAdapter.onSuccess.attach(function(sender, args) { - _this.onSave.notify(); - }); - dataAdapter.saveStoichiometry(this.macromolecule.macromoleculeId, macromoleculeId, ratio, comments); -}; - -MolarityForm.prototype._getButtons = function() { - var _this = this; - - function onClose() { - _this.onClose.notify(); - } - - return [ { - text : 'Save', - handler : function() { - _this._persist(); - } - }, { - text : 'Cancel', - handler : function() { - onClose(); - } - } ]; -}; - -MolarityForm.prototype.getPanel = function() { - this.panel = Ext.create('Ext.form.Panel', { -// width : null, - height : this.height, - margin : 2, - border : 1, - defaultType : 'requiredtext', - items : this._getItems(), - buttons : this._getButtons() - }); - return this.panel; -}; - -/** macromolecules contains all macromolecules except this one **/ -MolarityForm.prototype.getMacromuleculesCandidates = function(macromolecule) { - var macromolecules = []; - if ( BIOSAXS.proposal.macromolecules){ - for (var i = 0; i < BIOSAXS.proposal.macromolecules.length; i++) { - var m = BIOSAXS.proposal.macromolecules[i]; - if (this.macromolecule != null){ - if (m.macromoleculeId != this.macromolecule.macromoleculeId) { - macromolecules.push(m); - } - } - } - } - return macromolecules; -}; - - -/** It populates the form **/ -MolarityForm.prototype.refresh = function(macromolecule) { - this.macromolecule = macromolecule; - -}; - - -MolarityForm.prototype.input = function() { - return {}; -}; - - -/** It populates the form **/ -MolarityForm.prototype.test = function(targetId) { - var macromoleculeForm = new MolarityForm(); - var panel = macromoleculeForm.getPanel(); - panel.render(targetId); -}; - -///** -// * -// * @witdh -// * @height -// */ -//function MacromoleculeForm(args) { -// this.id = BUI.id(); -// this.width = 700; -// this.height = 500; -// -// if (args != null) { -// if (args.width != null) { -// this.width = args.width; -// } -// if (args.height != null) { -// this.height = args.height; -// } -// } -// -// this.onClose = new Event(this); -//} -// -//MacromoleculeForm.prototype.getMacromolecule = function() { -// this.macromolecule.name = Ext.getCmp(this.panel.getItemId()).getValues().name; -// this.macromolecule.acronym = Ext.getCmp(this.panel.getItemId()).getValues().acronym; -// this.macromolecule.comments = Ext.getCmp(this.panel.getItemId()).getValues().comments; -// this.macromolecule.extintionCoefficient = Ext.getCmp(this.panel.getItemId()).getValues().extintionCoefficient; -// this.macromolecule.molecularMass = Ext.getCmp(this.panel.getItemId()).getValues().molecularMass; -// return this.macromolecule; -//}; -// -//MacromoleculeForm.prototype.setMacromolecule = function(macromolecule) { -// this.pdbStore.loadData(macromolecule.structure3VOs); -// -//}; -// -//MacromoleculeForm.prototype.getForm = function(macromolecule) { -// this.panel = Ext.createWidget('form', { -// frame : false, -// border : 0, -// padding : 15, -// width : 550, -// height : 350, -// items : [ { -// xtype : 'container', -// layout : 'hbox', -// items : [ { -// xtype : 'container', -// flex : 1, -// border : false, -// layout : 'anchor', -// defaultType : 'requiredtext', -// items : [ { -// fieldLabel : 'Name', -// name : 'name', -// anchor : '95%', -// tooltip : "Name of the macromolecule", -// value : macromolecule.name -// }, { -// fieldLabel : 'Acronym', -// name : 'acronym', -// anchor : '95%', -// value : macromolecule.acronym -// } ] -// }, { -// xtype : 'container', -// flex : 1, -// layout : 'anchor', -// defaultType : 'textfield', -// items : [ { -// xtype : 'numberfield', -// fieldLabel : 'Mol. Mass (Da)', -// name : 'molecularMass', -// value : macromolecule.molecularMass, -// decimalPrecision : 6 -// }, { -// xtype : 'numberfield', -// fieldLabel : 'Extinction coef.', -// name : 'extintionCoefficient', -// value : macromolecule.extintionCoefficient, -// decimalPrecision : 6 -// } ] -// } ] -// }, { -// xtype : 'textareafield', -// name : 'comments', -// fieldLabel : 'Comments', -// value : macromolecule.comments, -// width : this.width - 10 -// }, -// -// { -// html : BUI.getWarningHTML("The macromolecule is unsaved. Save the macromolecule to get access to other tabs"), -// margin : "150 10 10 10", -// id : this.id + "unsavedWarning", -// hidden : !(!macromolecule.macromoleculeId) -// } -// -// ] -// }); -// return this.panel; -//}; -// -//MacromoleculeForm.prototype.save = function() { -// var _this = this; -// -// var adapter = new BiosaxsDataAdapter(); -// adapter.onSuccess.attach(function(sender, proposal) { -// BIOSAXS.proposal.setItems(proposal); -// _this.panel.setLoading(false); -// -// Ext.getCmp(_this.id + "assembly").enable() -// Ext.getCmp(_this.id + "advanced").enable(); -// Ext.getCmp(_this.id + "unsavedWarning").hide(); -// }); -// -// if (this.getMacromolecule().name == "") { -// BUI.showError("Name field is mandatory"); -// return; -// } -// if (this.getMacromolecule().acronym == "") { -// BUI.showError("Acroynm field is mandatory"); -// return; -// } -// -// /** Check if acronym is unique * */ -// if (this.getMacromolecule().macromoleculeId == null) { -// if (BIOSAXS.proposal.getMacromoleculeByAcronym(this.getMacromolecule().acronym) == null) { -// this.panel.setLoading("ISPyB: Saving Macromolecule") -// adapter.saveMacromolecule(this.getMacromolecule()); -// } else { -// alert("There is already an existing macromolecule with the same acronym"); -// -// } -// } else { -// this.panel.setLoading("ISPyB: Saving Macromolecule") -// adapter.saveMacromolecule(this.getMacromolecule()); -// } -// -//}; -// -//MacromoleculeForm.prototype.getPanel = function(macromolecule) { -// var _this = this; -// this.macromolecule = macromolecule; -// return Ext.createWidget('tabpanel', { -// height : this.height, -// margin : 5, -// plain : true, -// style : { -// padding : 5 -// }, -// items : [ { -// tabConfig : { -// title : "General", -// disabled : false -// }, -// items : [ this.getForm(macromolecule) ], -// bbar : [ "->", { -// text : 'Save', -// cls : 'btn-with-border', -// style : { -// -// border : 1 -// }, -// handler : function() { -// _this.save(); -// } -// }, { -// text : 'Close', -// cls : 'btn-with-border', -// handler : function() { -// _this.onClose.notify(); -// } -// } ] -// }, { -// tabConfig : { -// id : this.id + "assembly", -// title : "Assembly", -// tooltip : 'Description of subunits present in the macromolecule', -// // hidden : (!macromolecule.macromoleculeId), -// disabled : (!macromolecule.macromoleculeId) -// }, -// items : [ this.getMolarityGrid(macromolecule) ] -// }, { -// tabConfig : { -// id : this.id + "advanced", -// title : "Advanced Modeling", -// // hidden : (!macromolecule.macromoleculeId), -// tooltip : 'Definition of the description contacts and symetries', -// disabled : (!macromolecule.macromoleculeId) -// }, -// items : [ this.getRigidBodyForm(macromolecule) ] -// } ] -// }); -//}; -// -//MacromoleculeForm.prototype.getRigidBodyForm = function(macromolecule) { -// var _this = this; -// -// // [P1, P2, P3, P4 ,P5 ,P6 ,32, P42, P52, P62] + P222 -// var symmetry = Ext.create('Ext.data.Store', { -// fields : [ 's' ], -// data : [ { -// "s" : "P1" -// }, { -// "s" : "P2" -// }, { -// "s" : "P3" -// }, { -// "s" : "P4" -// }, { -// "s" : "P5" -// }, { -// "s" : "P6" -// }, { -// "s" : "P32" -// }, { -// "s" : "P42" -// }, { -// "s" : "P52" -// }, { -// "s" : "P62" -// }, { -// "s" : "P222" -// } ] -// }); -// -// if (macromolecule.symmetry == null) { -// macromolecule.symmetry = "P1"; -// } -// var comboBox = Ext.create('Ext.form.ComboBox', { -// fieldLabel : 'Symmetry', -// store : symmetry, -// id : 'comboSym', -// queryMode : 'local', -// displayField : 's', -// valueField : 's', -// value : macromolecule.symmetry, -// margin : "10 0 0 0", -// listeners : { -// change : function(combo, newValue, oldValue, eOpts) { -// macromolecule.symmetry = newValue; -// } -// } -// }); -// -// this.rigidBodyPanel = Ext.createWidget('form', { -// frame : false, -// border : 0, -// padding : 10, -// width : 550, -// height : 400, -// items : [ { -// xtype : 'container', -// layout : 'hbox', -// items : [ { -// xtype : 'container', -// border : false, -// layout : 'hbox', -// items : [ { -// xtype : 'label', -// forId : 'myFieldId', -// text : 'Contact Desc:', -// width : 105, -// margin : '0 0 0 0' -// }, { -// xtype : 'textfield', -// hideLabel : true, -// id : "contactsDescriptionFilePath", -// margin : '0 0 0 0', -// width : 300, -// value : macromolecule.contactsDescriptionFilePath -// }, { -// text : 'Upload', -// xtype : 'button', -// margin : "0 0 0 20", -// width : 100, -// handler : function() { -// _this._openUploadDialog(macromolecule.macromoleculeId, "CONTACTS", "Upload Contact Description File"); -// } -// } ] -// } ] -// }, -// -// comboBox, { -// xtype : 'checkbox', -// margin : '10 0 0 5', -// boxLabel : "I want rigid body modeling run on this stuff", -// checked : true, -// width : 300 -// }, _this.getPDBGrid(macromolecule) ] -// }); -// return this.rigidBodyPanel; -//}; -// -//MacromoleculeForm.prototype.update = function() { -// var _this = this; -// BIOSAXS.proposal.onInitialized.attach(function() { -// if (BIOSAXS.proposal != null) { -// var macromolecules = BIOSAXS.proposal.macromolecules; -// for (var i = 0; i < macromolecules.length; i++) { -// if (macromolecules[i].macromoleculeId == _this.macromolecule.macromoleculeId) { -// _this.macromolecule = macromolecules[i]; -// _this.setMacromolecule(_this.macromolecule); -// _this.molarityStore.loadData(_this.parseMolarityData(_this.macromolecule)); -// _this.pdbGrid.setLoading(false); -// Ext.getCmp("contactsDescriptionFilePath").setValue(_this.macromolecule.contactsDescriptionFilePath) -// _this.molarityGrid.setLoading(false); -// -// } -// } -// } -// }); -// this.molarityGrid.setLoading("Updating"); -// this.pdbGrid.setLoading("Updating"); -// BIOSAXS.proposal.init(); -//}; -// -///******************************************************************************* -// * MOLARITY GRID -// ******************************************************************************/ -// -//MacromoleculeForm.prototype.parseMolarityData = function(macromolecule) { -// var data = []; -// if (macromolecule.stoichiometry != null) { -// for (var i = 0; i < macromolecule.stoichiometry.length; i++) { -// data.push({ -// ratio : macromolecule.stoichiometry[i].ratio, -// acronym : macromolecule.stoichiometry[i].macromolecule3VO.acronym, -// comments : macromolecule.stoichiometry[i].macromolecule3VO.comments, -// stoichiometryId : macromolecule.stoichiometry[i].stoichiometryId, -// name : macromolecule.stoichiometry[i].macromolecule3VO.name -// }); -// } -// } -// return data; -//}; -// -//MacromoleculeForm.prototype.getMolarityGrid = function(macromolecule) { -// var _this = this; -// -// this.molarityStore = Ext.create('Ext.data.Store', { -// fields : [ 'acronym', 'ratio', 'comments', 'stoichiometryId', 'name' ], -// data : this.parseMolarityData(macromolecule), -// sorters : { -// property : 'ratio', -// direction : 'DESC' -// } -// }); -// -// this.molarityGrid = Ext.create('Ext.grid.Panel', { -// store : this.molarityStore, -// height : 350, -// padding : 5, -// columns : [ -// -// { -// text : 'Subunit', -// columns : [ { -// text : "Acronym", -// width : 100, -// hidden : false, -// dataIndex : 'acronym', -// sortable : true -// }, { -// text : "Name", -// width : 100, -// hidden : false, -// dataIndex : 'name', -// sortable : true -// }, { -// text : "Comments", -// width : 100, -// dataIndex : 'comments', -// sortable : true -// } ] -// }, { -// text : "Number
in assymmetric units", -// width : 150, -// dataIndex : 'ratio', -// tooltip : 'Number of times this subunit is present in the macromolecule', -// sortable : true -// }, { -// id : this.id + 'MOLARITY_REMOVE', -// flex : 0.1, -// sortable : false, -// renderer : function(value, metaData, record, rowIndex, colIndex, store) { -// return BUI.getRedButton('REMOVE'); -// } -// } ], -// listeners : { -// cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { -// if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'MOLARITY_REMOVE') { -// var dataAdapter = new BiosaxsDataAdapter(); -// dataAdapter.onSuccess.attach(function() { -// _this.molarityGrid.setLoading(false); -// _this.update(); -// }); -// dataAdapter.removeStoichiometry(record.data.stoichiometryId); -// _this.molarityGrid.setLoading("Removing Structure"); -// } -// } -// }, -// buttons : [ { -// text : 'Add molarity', -// handler : function() { -// -// function onClose() { -// w.destroy(); -// _this.update(); -// } -// var w = Ext.create('Ext.window.Window', { -// title : 'Molarity', -// height : 300, -// width : 500, -// modal : true, -// buttons : [ { -// text : 'Save', -// handler : function() { -// var macromoleculeId = (_this.macromoleculeCombo.getValue()); -// var ratio = Ext.getCmp(_this.id + "ratio").getValue(); -// var comments = ""; -// var dataAdapter = new BiosaxsDataAdapter(); -// dataAdapter.onSuccess.attach(function(sender, args) { -// _this.update(); -// w.destroy(); -// }); -// dataAdapter.saveStoichiometry(_this.macromolecule.macromoleculeId, macromoleculeId, ratio, comments); -// } -// }, { -// text : 'Cancel', -// handler : function() { -// onClose(); -// } -// } ], -// items : [ _this.getMolarityForm(macromolecule) ], -// listeners : { -// onEsc : function() { -// onClose(); -// }, -// close : function() { -// onClose(); -// } -// } -// }).show(); -// } -// } ] -// }); -// return this.molarityGrid; -//}; -// -///******************************************************************************* -// * PDB GRID -// ******************************************************************************/ -// -//MacromoleculeForm.prototype._openUploadDialog = function(macromoleculeId, type, title) { -// var _this = this; -// function onClose() { -// w.destroy(); -// _this.update(); -// } -// -// var w = Ext.create('Ext.window.Window', { -// title : title, -// height : 200, -// width : 400, -// modal : true, -// buttons : [ { -// text : 'Close', -// handler : function() { -// onClose(); -// } -// } ], -// layout : 'fit', -// items : { -// html : "" -// }, -// listeners : { -// onEsc : function() { -// onClose(); -// }, -// close : function() { -// onClose(); -// } -// } -// }).show(); -//}; -// -//MacromoleculeForm.prototype._getPlugins = function() { -// var _this = this; -// var plugins = []; -// // if (this.updateRowEnabled) { -// plugins.push(Ext.create('Ext.grid.plugin.RowEditing', { -// clicksToEdit : 1, -// listeners : { -// validateedit : function(grid, e) { -// /** Comments are always updatable* */ -// e.record.raw.symmetry = e.newValues.symmetry; -// e.record.raw.multiplicity = e.newValues.multiplicity; -// -// var adapter = new BiosaxsDataAdapter(); -// adapter.onSuccess.attach(function(sender, measurement) { -// // _this.grid.setLoading(false); -// }); -// adapter.onError.attach(function() { -// alert("Error"); -// // _this.grid.setLoading(false); -// }); -// -// // _this.grid.setLoading(); -// adapter.saveStructure(e.record.raw); -// } -// } -// })); -// // } -// return plugins; -//}; -// -//MacromoleculeForm.prototype.getPDBGrid = function(macromolecule) { -// var _this = this; -// -// var data = macromolecule.structure3VOs; -// -// // /** Getting PDB from subunits **/ -// // if (macromolecule != null){ -// // if (macromolecule.stoichiometry != null){ -// // for (var i =0; i < macromolecule.stoichiometry.length; i++){ -// // var stoichiometry = macromolecule.stoichiometry[i]; -// // if (stoichiometry.macromolecule3VO != null){ -// // if (stoichiometry.macromolecule3VO.structure3VOs != null){ -// // for (var j = 0; j < stoichiometry.macromolecule3VO.structure3VOs.length; -// // j++) { -// // var structure = stoichiometry.macromolecule3VO.structure3VOs[j]; -// // structure["isSubunit"] = stoichiometry.macromolecule3VO.acronym; -// // data.push(structure) -// // } -// // } -// // } -// // } -// // } -// // } -// -// this.pdbStore = Ext.create('Ext.data.Store', { -// fields : [ 'filePath', 'structureId', 'structureType', 'symmetry', 'structureId', 'name', 'multiplicity' ], -// data : macromolecule.structure3VOs, -// groupField : 'structureType', -// sorters : { -// property : 'structureId', -// direction : 'DESC' -// } -// }); -// -// var groupingFeature = Ext.create('Ext.grid.feature.Grouping', { -// groupHeaderTpl : Ext.create('Ext.XTemplate', -// "
{name:this.formatName}
", { -// formatName : function(name) { -// return name; -// } -// }), -// hideGroupedHeader : true, -// startCollapsed : false -// }); -// -// this.pdbGrid = Ext.create('Ext.grid.Panel', { -// margin : "15 0 0 5", -// height : 250, -// store : this.pdbStore, -// plugins : _this._getPlugins(), -// buttons : [ { -// // text : 'Add PDB file', -// text : 'Add Modeling Option', -// handler : function() { -// _this._openUploadDialog(macromolecule.macromoleculeId, "PDB", 'Upload PDB File'); -// } -// } -// -// ], -// columns : [ -// { -// text : "structureId", -// flex : 0.2, -// hidden : true, -// dataIndex : 'structureId', -// sortable : true -// }, -// { -// text : "File", -// flex : 0.5, -// dataIndex : 'filePath', -// sortable : true, -// hidden : true -// }, -// { -// text : "PDB", -// flex : 0.4, -// dataIndex : 'name', -// sortable : true -// }, -// { -// text : "Symmetry", -// flex : 0.4, -// dataIndex : 'symmetry', -// sortable : true, -// editor : { -// xtype : 'combobox', -// typeAhead : true, -// triggerAction : 'all', -// selectOnTab : true, -// store : [ [ "P1", "P1" ], [ "P2", "P2" ], [ "P3", "P3" ], [ "P4", "P4" ], [ "P5", "P5" ], [ "P6", "P6" ], [ "P32", "P32" ], [ "P42", "P42" ], -// [ "P52", "P52" ], [ "P62", "P62" ], [ "P222", "P222" ] ], -// } -// }, { -// text : "Multiplicity", -// flex : 0.4, -// dataIndex : 'multiplicity', -// sortable : true, -// editor : { -// xtype : 'textfield' -// } -// -// }, { -// text : "Subunit", -// flex : 0.2, -// dataIndex : 'isSubunit', -// sortable : true, -// hidden : true -// }, { -// text : "Type", -// flex : 0.2, -// dataIndex : 'structureType', -// sortable : true, -// hidden : true -// }, -// -// { -// id : this.id + 'REMOVE', -// flex : 0.2, -// hidden : true, -// sortable : false, -// renderer : function(value, metaData, record, rowIndex, colIndex, store) { -// return BUI.getRedButton('REMOVE'); -// } -// }, ], -// -// listeners : { -// itemdblclick : function(dataview, record, item, e) { -// _this._editExperiment(record.raw.experimentId); -// }, -// cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { -// -// if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'REMOVE') { -// var dataAdapter = new BiosaxsDataAdapter(); -// dataAdapter.onSuccess.attach(function() { -// _this.pdbGrid.setLoading(false); -// _this.update(); -// }); -// dataAdapter.removeStructure(record.data.structureId); -// _this.pdbGrid.setLoading("Removing PDB file"); -// } -// -// } -// }, -// viewConfig : { -// getRowClass : function(record, rowIdx, params, store) { -// if (record.raw.isSubunit != null) { -// return "blue-row"; -// } -// } -// } -// }); -// -// return this.pdbGrid; -//}; -// -//MacromoleculeForm.prototype.getMolarityForm = function(macromolecule) { -// var _this = this; -// var data = []; -// for (var i = 0; i < BIOSAXS.proposal.macromolecules.length; i++) { -// var m = BIOSAXS.proposal.macromolecules[i]; -// if (m.macromoleculeId != macromolecule.macromoleculeId) { -// data.push(m); -// } -// -// } -// this.macromoleculeCombo = BIOSAXS_COMBOMANAGER.getComboMacromoleculeByMacromolecules(data, { -// width : 250, -// labelWidth : 100, -// margin : 10 -// }); -// -// return Ext.createWidget('form', { -// -// frame : false, -// border : 0, -// // padding : 15, -// width : 550, -// height : 350, -// items : [ { -// xtype : 'container', -// flex : 1, -// border : false, -// layout : 'anchor', -// defaultType : 'requiredtext', -// items : [ this.macromoleculeCombo, { -// xtype : 'numberfield', -// name : 'Ratio', -// id : _this.id + "ratio", -// fieldLabel : 'Number in assymmetric units', -// value : 1, -// decimalPrecision : 6, -// margin : 10 -// }, { -// xtype : 'textareafield', -// name : 'comments', -// fieldLabel : 'Comments', -// margin : 10, -// width : 400, -// value : "" -// -// } ] -// } ] -// }); -// -//}; -// -///******************************************************************************* -// * JAVASCRIPT DOC -// ******************************************************************************/ -//MacromoleculeForm.prototype.input = function() { -// return { -// macromolecule : DATADOC.getMacromolecule_10() -// }; -//}; -// -//MacromoleculeForm.prototype.test = function(targetId) { -// var macromoleculeForm = new MacromoleculeForm(); -// var panel = macromoleculeForm.getPanel(macromoleculeForm.input().macromolecule); -// panel.render(targetId); -//}; - -function ResultSummaryForm() { - this.radiationDamageThreshold = BUI.getRadiationDamageThreshold(); - this.qualityThreshold = BUI.getQualityThreshold(); - - /** Data clusters with bufers **/ - this.clusterByBuffers = false; - - /** Visualization are groupeb by concenttrations. Ex: 4.5mg/ml and 4.7mg/ml will be clusterized together **/ - this.collapseConcentrations = true; - - this.summaryHeight = 350; - this.id = BUI.id(); - - var _this = this; - - this.qualityControlResultsWidget = new QualityControlResultsWidget({ - qualityThreshold : this.radiationDamageThreshold, - radiationDamageThreshold : this.qualityThreshold - - }); - this.qualityControlResultsWidget.onQualityChanged.attach(function(sender, value) { - _this.qualityThreshold = value; - _this.thresholdsChanged(); - }); - - this.qualityControlResultsWidget.onRadiationDatamageChanged.attach(function(sender, value) { - _this.radiationDamageThreshold = value; - _this.thresholdsChanged(); - - }); - this.concentrationHTMLTableWidget = new ConcentrationHTMLTableWidget({ - height : 250, - showBufferColumns : this.clusterByBuffers - }); - - this.plot = new BoxWhiskerGraph({ - targetId : _this.id + '_boxPlot', - height : 350, - width : 450, - maxBoxWidth : 25 - }); - - this.rangePlot = new RangeWhiskerGraph({ - targetId : _this.id + '_rangePlot', - height : 350, - width : 450, - maxBoxWidth : 25 - }); -} - -ResultSummaryForm.prototype.thresholdsChanged = function() { - var parsedData = this.prepareData(this.rawData); - - var filtered = JSON.parse(JSON.stringify(parsedData)); - filtered.concentration.concentrations = []; - for ( var conc in parsedData.concentration.concentrations) { - if (parsedData.concentration.concentrations[conc].calculation.rgGnom.validNumber > 0) { - filtered.concentration.concentrations.push(parsedData.concentration.concentrations[conc]); - } - } - - this.plotWhisker(filtered); - this.plotRange(filtered); - - this.concentrationHTMLTableWidget.refresh(parsedData); -}; - -/** Given a frame object (object returned by analyzeFrames()) and depending of the threshold indicates if a datacollection has radiation damage **/ -ResultSummaryForm.prototype.hasRadiationDamage = function(frameObject) { - var bb = frameObject.bufferBeforeFramesMerged / frameObject.framesCount; - var ba = frameObject.bufferAfterFramesMerged / frameObject.framesCount; - var mol = frameObject.framesMerge / frameObject.framesCount; - return !((bb >= this.radiationDamageThreshold) && (ba >= this.radiationDamageThreshold) && (mol >= this.radiationDamageThreshold)); -}; - -/** Return (frameObject) an object with the information about the frames for a data collection**/ -ResultSummaryForm.prototype.analyzeFrames = function(dataCollectionRow) { - return { - bufferAfterFramesMerged : dataCollectionRow.bufferAfterFramesMerged, - bufferBeforeFramesMerged : dataCollectionRow.bufferBeforeFramesMerged, - framesCount : dataCollectionRow.framesCount, - framesMerge : dataCollectionRow.framesMerge - }; -}; - -ResultSummaryForm.prototype.detectDataCollectionWarnings = function(dataCollectionRow) { - var frameObject = this.analyzeFrames(dataCollectionRow); - var warnings = { - count : 0, - type : [] - }; - - if (this.hasRadiationDamage(frameObject)) { - warnings.count = warnings.count + 1; - warnings.type.push("RADIATION DAMAGE"); - } - - if (Number(dataCollectionRow.quality) < this.qualityThreshold) { - warnings.count = 1;//warnings.count + 1; - warnings.type.push("Quality <" + this.qualityThreshold); - } - return warnings; -}; - -/** Return array composed by {concentration} objects **/ -ResultSummaryForm.prototype.getConcentrations = function(data) { - var concentrationsId = {}; - - for ( var i = 0; i < data.length; i++) { - var warning = this.detectDataCollectionWarnings(data[i]); - var id = data[i].conc;// + "_" + data[i].bufferId; - if (this.clusterByBuffers) { - id = data[i].conc + "_" + data[i].bufferId; - } - - if (concentrationsId[id] == null) { - concentrationsId[id] = { - id : id, - concentration : Number(data[i].conc).toFixed(2), - bufferId : data[i].bufferId, - bufferAcronym : data[i].bufferAcronym, - rgGuinier : [], - i0Guinier : [], - rgGnom : [], - dMax : [], - quality : [], - frames : [], - frames_warning : warning.count - }; - } else { - concentrationsId[id].frames_warning = concentrationsId[id].frames_warning + warning.count; - } - - concentrationsId[id].frames.push(data[i]); - - if (warning.count == 0) { - concentrationsId[id].rgGuinier.push(data[i].rgGuinier); - concentrationsId[id].i0Guinier.push(data[i].I0); - concentrationsId[id].quality.push(data[i].quality); - concentrationsId[id].rgGnom.push(data[i].rgGnom); - concentrationsId[id].dMax.push(data[i].dmax); - } - - } - var concentrations = []; - for ( var item in concentrationsId) { - if (concentrationsId.hasOwnProperty(item)) { - concentrations.push({ - concentration : concentrationsId[item].concentration, - id : item, - bufferId : Number(concentrationsId[item].bufferId).toFixed(2), - bufferAcronym : concentrationsId[item].bufferAcronym, - rgGuinier : concentrationsId[item].rgGuinier, - /** Frames **/ - frames : concentrationsId[item].frames, - frames_warning : concentrationsId[item].frames_warning, - /** Calculation **/ - calculation : { - rgGuinier : BUI.getStandardDeviation(concentrationsId[item].rgGuinier), - i0Guinier : BUI.getStandardDeviation(concentrationsId[item].i0Guinier), - quality : BUI.getStandardDeviation(concentrationsId[item].quality), - rgGnom : BUI.getStandardDeviation(concentrationsId[item].rgGnom), - dMax : BUI.getStandardDeviation(concentrationsId[item].dMax) - - } - }); - } - } - - return { - concentrations : concentrations - }; -}; - -ResultSummaryForm.prototype.prepareData = function(data) { - /** Return array composed by {acronym, bufferId} objects **/ - function getBuffers(data) { - var buffersId = {}; - for ( var i = 0; i < data.length; i++) { - buffersId[data[i].bufferId] = data[i].acronym; - } - var buffers = []; - for ( var id in buffersId) { - if (buffersId.hasOwnProperty(id)) { - buffers.push({ - acronym : buffersId[id], - bufferId : id - }); - } - } - return buffers; - } - - /** Get a string with all the concentrations **/ - function getConcentrationString(parseConcentrations) { - var concentrations = []; - for ( var i = 0; i < parseConcentrations.concentrations.length; i++) { - concentrations.push(parseConcentrations.concentrations[i].concentration + " mg/ml "); - } - return concentrations.toString(); - } - - var parseConcentrations = this.getConcentrations(data); - - return { - dataCollectionCount : data.length, - buffers : getBuffers(data), - concentration : parseConcentrations, - concentrationLabel : getConcentrationString(parseConcentrations) - }; -}; - -ResultSummaryForm.prototype.getDataForWhisker = function(data) { - var clusters = []; - - var concentrations = {}; - var i = 0; - var conc = 0; - if (this.collapseConcentrations) { - for (i = 0; i < data.concentration.concentrations.length; i++) { - conc = data.concentration.concentrations[i]; - var concentration = Number(conc.concentration).toFixed(0); - if (concentrations[concentration] == null) { - concentrations[concentration] = {}; - concentrations[concentration].concentration = concentration; - concentrations[concentration].calculation = {}; - concentrations[concentration].calculation.rgGuinier = {}; - concentrations[concentration].calculation.rgGuinier.values = []; - concentrations[concentration].calculation.rgGuinier.values = conc.calculation.rgGuinier.values; - concentrations[concentration].calculation.rgGnom = {}; - concentrations[concentration].calculation.rgGnom.values = []; - concentrations[concentration].calculation.rgGnom.values = conc.calculation.rgGnom.values; - } else { - concentrations[concentration].calculation.rgGuinier.values = concentrations[concentration].calculation.rgGuinier.values - .concat(conc.calculation.rgGuinier.values); - concentrations[concentration].calculation.rgGnom.values = concentrations[concentration].calculation.rgGnom.values - .concat(conc.calculation.rgGnom.values); - } - } - - /** From object to array **/ - var array = []; - for ( var key in concentrations) { - if (concentrations.hasOwnProperty(key)) { - array.push(concentrations[key]); - } - } - data.concentration.concentrations = array; - } - - for (i = 0; i < data.concentration.concentrations.length; i++) { - conc = data.concentration.concentrations[i]; - clusters.push({ - name : conc.concentration + "mg/ml", - concentration : Number(conc.concentration), - x : Number(conc.concentration), - classes : [] - }); - clusters[clusters.length - 1].classes.push({ - name : "Guinier", - color : '#9A2EFE', - values : conc.calculation.rgGuinier.values - - }); - clusters[clusters.length - 1].classes.push({ - name : "P(r)", - color : '#2E64FE', - values : conc.calculation.rgGnom.values - - }); - } - return { - clusters : clusters.sort(function(a, b) { - return a.concentration - b.concentration; - }) - }; -}; - -ResultSummaryForm.prototype.getDataForWhiskerQuality = function(data) { - var clusters = []; - - for ( var i = 0; i < data.concentration.concentrations.length; i++) { - var conc = data.concentration.concentrations[i]; - clusters.push({ - name : conc.concentration + "mg/ml", - classes : [] - }); - clusters[clusters.length - 1].classes.push({ - name : "Quality", - values : conc.calculation.quality.values - - }); - } - - return { - clusters : clusters - }; -}; - -ResultSummaryForm.prototype.plotQualityWhisker = function(parsedData) { - this.qualityPlot.refresh(this.getDataForWhiskerQuality(parsedData)); -}; - -ResultSummaryForm.prototype.plotWhisker = function(parsedData) { - this.plot.refresh(this.getDataForWhisker(parsedData)); -}; - -ResultSummaryForm.prototype.plotRange = function(parsedData) { - this.rangePlot.refresh(this.getDataForWhisker(parsedData)); -}; - -ResultSummaryForm.prototype.getPanel = function(data) { - var _this = this; - _this.rawData = data; - var parsedData = this.prepareData(data); - - this.panel = Ext - .createWidget( - 'form', - { - bodyPadding : 20, - frame : false, - border : 0, - width : this.width, - height : this.summaryHeight + 1000, - items : [ { - xtype : 'container', - layout : 'hbox', - items : [ { - xtype : 'container', - flex : 1, - border : false, - layout : 'anchor', - defaultType : 'textfield', - items : [ - _this.qualityControlResultsWidget.getPanel(), - { - xtype : 'fieldset', - width : 950, - margin : "20, 0 0 0", - height : this.summaryHeight + 500, - items : [ - { - html : "
Concentration Analysis
", - border : 0, - width : 900 - - }, - { - html : this.concentrationHTMLTableWidget.getPanel(parsedData), - border : 0, - width : 900, - margin : "10, 0 0 10" - - }, - { - xtype : 'container', - layout : 'vbox', - border : 5, - items : [ - { - html : "
Rg based on Guinier and Gnom
", - border : 8, - width : 900, - margin : "20 0 0 10" - - }, { - xtype : 'container', - layout : 'hbox', - items : [ { - xtype : 'container', - layout : 'vbox', - items : [ { - html : "
", - border : 0, - width : this.plot.width, - padding : "10 0 0 20", - listeners : { - afterrender : function() { - _this.plotWhisker(parsedData); - - } - } - }, { - html : "
Concentration (mg/ml)
", - width : 450, - border : 0, - margin : "-50 0 0 0" - - } ] - }, { - xtype : 'container', - layout : 'vbox', - items : [ { - html : "
", - border : 0, - width : this.rangePlot.width, - padding : "10 0 0 10", - listeners : { - afterrender : function() { - _this.plotRange(parsedData); - } - } - }, { - html : "
Concentration (mg/ml)
", - width : 450, - border : 0, - margin : "-50 0 0 0" - - } ] - } ] - } ] - } ] - } ] - } - - ] - } ] - }); - return this.panel; - -}; - -ResultSummaryForm.prototype.input = function() { - return { - data : DATADOC.getData_3367() - }; -}; - -ResultSummaryForm.prototype.test = function(targetId) { - var resultSummaryForm = new ResultSummaryForm(); - var panel = resultSummaryForm.getPanel(resultSummaryForm.input().data); - panel.render(targetId); - -}; - -/** - * Example form - * - * @witdh - * @height - */ -function RigibBodyModelingForm(args) { - this.id = BUI.id(); - this.width = 700; - this.height = 500; - - if (args != null) { - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; - } - } - - var _this = this; - this.rigidBodyGrid = new AprioriRigidBodyGrid(); - - this.rigidBodyGrid.onUploadFile.attach(function(sender, type, title){ - _this._openUploadDialog(_this.macromolecule.macromoleculeId, type, title); - }); - - this.rigidBodyGrid.onRemove.attach(function(sender, type, title){ - _this._update(); - }); - - this.onSave = new Event(this); - -} - -RigibBodyModelingForm.prototype._getItems = function() { - var _this = this; - - - return [ { - xtype : 'label', - forId : 'myFieldId', - text : 'Information for model fit, mixture analysis and rigid body modeling', - margin : '15 0 20 10', - cls : "inline-help" - }, - this.rigidBodyGrid.getPanel(), - { - xtype : 'label', - forId : 'myFieldId', - text : 'Distance restraints may be imposed on the model using contacts conditions file (OPTIONAL)', - margin : '25 0 5 10', - cls : "inline-help" - }, - { - xtype : 'container', - layout : 'hbox', - items : [ { - xtype : 'container', - border : false, - layout : 'hbox', - items : [ { - xtype : 'label', - forId : 'myFieldId', - text : 'Contact Description File: (Optional)', - width : 150, - margin : '10 0 0 10' - }, { - id : this.id + "contactsDescriptionFilePath", - xtype : 'textfield', - hideLabel : true, - margin : '10 0 0 0', - width : 200, - disabled: true - }, { - text : 'Upload', - xtype : 'button', - margin : "10 0 0 10", - width : 80, - handler : function() { - - _this._openUploadDialog(_this.macromolecule.macromoleculeId, "CONTACTS", "Upload Contact Description File"); - } - }, { - text : 'Remove', - id : _this.id + "_remove", - xtype : 'button', - margin : "10 0 0 10", - width : 80, - handler : function() { - _this.macromolecule.contactsDescriptionFilePath = null; - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, proposal) { - /** Updating the proposal global object **/ - BIOSAXS.proposal.setItems(proposal); - _this.panel.setLoading(false); - - var saved = BIOSAXS.proposal.getMacromoleculeByAcronym(_this.macromolecule.acronym); - /** Refreshing to check that everything is ok **/ - _this.refresh(saved); - _this.onSave.notify(saved); - }); - - _this.panel.setLoading("Saving Macromolecule") - adapter.saveMacromolecule(_this.macromolecule); - } - } ] - } ] - }, { - xtype : 'panel', - html : "Go to SASREF manual for further information", - margin : "10 0 0 160", - border : 0 - - }, - { - xtype : 'checkbox', - margin : '10 0 0 5', - boxLabel : "I want rigid body modeling run on this stuff", - checked : true, - width : 300 - } ] - -}; - -/** Because update is a jsp page we don't know if the user has uploaded a file or not then we need to refresh **/ -RigibBodyModelingForm.prototype._update = function(macromoleculeId, type, title) { - var _this = this; - BIOSAXS.proposal.onInitialized.attach(function() { - if (BIOSAXS.proposal != null) { - _this.refresh(BIOSAXS.proposal.getMacromoleculeById(_this.macromolecule.macromoleculeId)); - _this.panel.setLoading(false); - } - }); - this.panel.setLoading(); - BIOSAXS.proposal.init(); -}; - -RigibBodyModelingForm.prototype._openUploadDialog = function(macromoleculeId, type, title) { - var _this = this; - function onClose() { - w.destroy(); - _this._update(); - - } - - var w = Ext.create('Ext.window.Window', { - title : title, - height : 200, - width : 400, - modal : true, - buttons : [ { - text : 'Close', - handler : function() { - onClose(); - } - } ], - layout : 'fit', - items : { - html : "" - }, - listeners : { - onEsc : function() { - onClose(); - }, - close : function() { - onClose(); - } - } - }).show(); -}; - -RigibBodyModelingForm.prototype._getButtons = function() { - return []; -}; - -RigibBodyModelingForm.prototype.getPanel = function() { - var _this = this; - this.panel = Ext.create('Ext.form.Panel', { - width : this.width, - height : this.height, - margin : 10, - border : 1, - defaultType : 'textfield', - items : this._getItems(), - buttons : this._getButtons(), - listeners : { - afterrender : function(){ - _this._populate(); - - } - } - }); - return this.panel; -}; - -/** Populates could be call when the DOM is not filled yet **/ -RigibBodyModelingForm.prototype._populate = function() { - if (this.macromolecule != null){ - if (Ext.getCmp(this.id + "contactsDescriptionFilePath") != null){ - if (this.macromolecule.contactsDescriptionFilePath != null){ - Ext.getCmp(this.id + "contactsDescriptionFilePath").setValue(this.macromolecule.contactsDescriptionFilePath); - Ext.getCmp(this.id + "_remove").enable(); - } - else{ - Ext.getCmp(this.id + "_remove").disable(); - Ext.getCmp(this.id + "contactsDescriptionFilePath").setValue(""); - - } - } - } -}; - -/** It populates the form * */ -RigibBodyModelingForm.prototype.refresh = function(macromolecule) { - this.macromolecule = macromolecule; - this.rigidBodyGrid.refresh(macromolecule); - this._populate(); -}; - -RigibBodyModelingForm.prototype.input = function() { - return {}; -}; - - -/** It populates the form **/ -RigibBodyModelingForm.prototype.test = function(targetId) { - var macromoleculeForm = new RigibBodyModelingForm(); - var panel = macromoleculeForm.getPanel(); - panel.render(targetId); -}; - - -/** - * Same form as MX part - * - * @creationMode if true a create button appears instead of save - * @showTitle true or false - */ -function ShipmentForm(args) { - this.id = BUI.id(); - - this.creationMode = false; - this.showTitle = true; - if (args != null) { - if (args.creationMode != null) { - this.creationMode = args.creationMode; - } - if (args.showTitle != null) { - this.showTitle = args.showTitle; - } - } - - this.onSaved = new Event(this); -} - -ShipmentForm.prototype.fillStores = function() { - this.panel.setLoading("Loading Labcontacts from database"); - this.labContactForSendingStore.loadData(BIOSAXS.proposal.getLabcontacts(), false); - this.labContactForReturnStore.loadData(BIOSAXS.proposal.getLabcontacts(), false); - this.panel.setLoading(false); - if (this.shipment != null) { - this.setShipment(this.shipment); - } -}; - -ShipmentForm.prototype.draw = function(targetId) { - this.getPanel().render(targetId); -}; - -ShipmentForm.prototype.setShipment = function(shipment) { - this.shipment = shipment; - var _this = this; - Ext.getCmp(_this.id + "shippingName").setValue(shipment.json.shippingName); - Ext.getCmp(_this.id + "shippingStatus").setValue(shipment.json.shippingStatus); - Ext.getCmp(_this.id + "comments").setValue(shipment.json.comments); - if (shipment.json.sendingLabContactVO != null) { - this.labContactsSendingCombo.setValue(shipment.json.sendingLabContactVO.labContactId); - } - if (shipment.json.returnLabContactVO != null) { - this.labContactsReturnCombo.setValue(shipment.json.returnLabContactVO.labContactId); - } - -}; - -ShipmentForm.prototype._saveShipment = function() { - var _this = this; - var shippingId = null; - if (this.shipment != null) { - shippingId = this.shipment.json.shippingId; - } - var json = { - shippingId : shippingId, - name : Ext.getCmp(_this.id + "shippingName").getValue(), - status : Ext.getCmp(_this.id + "shippingStatus").getValue(), - sendingLabContactId : Ext.getCmp(_this.id + "shipmentform_sendingLabContactId").getValue(), - returnLabContactId : Ext.getCmp(_this.id + "returnLabContactId").getValue(), - returnCourier : Ext.getCmp(_this.id + "returnCourier").getValue(), - courierAccount : Ext.getCmp(_this.id + "courierAccount").getValue(), - BillingReference : Ext.getCmp(_this.id + "BillingReference").getValue(), - dewarAvgCustomsValue : Ext.getCmp(_this.id + "dewarAvgCustomsValue").getValue(), - dewarAvgTransportValue : Ext.getCmp(_this.id + "dewarAvgTransportValue").getValue(), - comments : Ext.getCmp(_this.id + "comments").getValue() - }; - - var dataAdapter = new BiosaxsDataAdapter(); - dataAdapter.onSuccess.attach(function(sender, shipment) { - window.location = BUI.getShippingURL(shipment.shippingId); - }); - - dataAdapter.onError.attach(function(sender, error) { - _this.onError.notify(error); - }); - - /** Cheking params **/ - if (json.name == "") { - BUI.showError("Name field is mandatory"); - return; - } - - if (json.sendingLabContactId == null) { - BUI.showError("Lab contact for sending field is mandatory"); - return; - } - - if (json.returnLabContactId == null) { - BUI.showError("Lab contact for return field is mandatory"); - return; - } - - dataAdapter.createShipment(json.shippingId, json.name, json.status, json.comments, json.sendingLabContactId, json.returnLabContactId, - json.returnCourier, json.courierAccount, json.BillingReference, json.dewarAvgCustomsValue, json.dewarAvgTransportValue); - -}; - -ShipmentForm.prototype.getPanel = function(shipment) { - var _this = this; - this.shipment = shipment; - var required = '*'; - var buttons = []; - - if (_this.creationMode) { - buttons.push({ - text : 'Create', - scope : this, - handler : function() { - _this._saveShipment(); - } - }); - } else { - buttons.push({ - text : 'Save', - scope : this, - handler : function() { - _this._saveShipment(); - } - }); - - } - - this.labContactForSendingStore = Ext.create('Ext.data.Store', { - fields : [ 'cardName', 'labContactId' ] - }); - - this.labContactForReturnStore = Ext.create('Ext.data.Store', { - fields : [ 'cardName', 'labContactId' ] - }); - - // Create the combo box, attached to the states data store - this.labContactsSendingCombo = Ext.create('Ext.form.ComboBox', { - id : _this.id + "shipmentform_sendingLabContactId", - fieldLabel : 'Lab contact for sending', - afterLabelTextTpl : required, - store : this.labContactForSendingStore, - queryMode : 'local', - labelWidth : 200, - displayField : 'cardName', - valueField : 'labContactId' - }); - - this.labContactsReturnCombo = Ext.create('Ext.form.ComboBox', { - id : _this.id + "returnLabContactId", - fieldLabel : 'If No, Lab-Contact for Return', - afterLabelTextTpl : required, - store : this.labContactForReturnStore, - queryMode : 'local', - labelWidth : 200, - displayField : 'cardName', - valueField : 'labContactId', - listeners : { - change : function(x, newValue) { - for ( var i = 0; i < x.getStore().data.items.length; i++) { - if (x.getStore().data.items[i].raw.labContactId == newValue) { - Ext.getCmp(_this.id + "returnCourier").setValue(x.getStore().data.items[i].raw.defaultCourrierCompany); - Ext.getCmp(_this.id + "courierAccount").setValue(x.getStore().data.items[i].raw.courierAccount); - Ext.getCmp(_this.id + "BillingReference").setValue(x.getStore().data.items[i].raw.billingReference); - Ext.getCmp(_this.id + "dewarAvgCustomsValue").setValue(x.getStore().data.items[i].raw.dewarAvgCustomsValue); - Ext.getCmp(_this.id + "dewarAvgTransportValue").setValue(x.getStore().data.items[i].raw.dewarAvgTransportValue); - } - } - } - } - }); - - if (this.panel == null) { - this.panel = Ext.create('Ext.form.Panel', { - bodyPadding : 5, - width : 600, - border : 1, - items : [ { - xtype : 'fieldset', - title : 'Details', - collapsible : false, - defaultType : 'textfield', - layout : 'anchor', - defaults : { - anchor : '100%' - }, - items : [ { - xtype : 'requiredtext', - fieldLabel : 'Shipment Label', - allowBlank : false, - name : 'shippingName', - id : _this.id + 'shippingName', - value : '', - anchor : '50%' - }, { - - xtype : 'textareafield', - name : 'comments', - id : _this.id + 'comments', - fieldLabel : 'Comments', - value : '' - }, { - fieldLabel : 'Status', - readOnly : true, - id : _this.id + 'shippingStatus', - value : 'Opened', - anchor : '50%' - } ] - }, { - xtype : 'fieldset', - title : 'Lab-Contacts', - collapsible : false, - defaultType : 'textfield', - layout : 'anchor', - defaults : { - anchor : '100%' - }, - items : [ this.labContactsSendingCombo, this.labContactsReturnCombo ] - }, { - border : 0, - html : BUI.getWarningHTML("These informations are relevant for all shipments") - }, { - xtype : 'fieldset', - title : 'Courier accounts details for return', - collapsible : false, - layout : 'anchor', - defaults : { - anchor : '100%' - }, - items : [ { - xtype : 'textfield', - labelWidth : 400, - fieldLabel : 'Courier company for return (if ESRF sends a dewar back)', - id : _this.id + 'returnCourier', - value : '' - }, { - xtype : 'textfield', - labelWidth : 400, - fieldLabel : 'Courier account', - id : _this.id + 'courierAccount', - value : '' - }, { - xtype : 'textfield', - labelWidth : 400, - fieldLabel : 'Billing reference', - id : _this.id + 'BillingReference', - value : '' - }, { - xtype : 'numberfield', - labelWidth : 400, - fieldLabel : 'Average Customs value of a dewar (Euro)', - id : _this.id + 'dewarAvgCustomsValue', - value : '' - }, { - xtype : 'numberfield', - labelWidth : 400, - fieldLabel : 'Average Transport value of a dewar (Euro)', - id : _this.id + 'dewarAvgTransportValue', - value : '' - } ] - } ], - buttons : buttons - }); - } - this.fillStores(); - if (this.showTitle) { - this.panel.setTitle('Create a new Shipment'); - } - return this.panel; -}; - -ShipmentForm.prototype.input = function() { - return { - proposal : DATADOC.getProposal_10() - - }; -}; - -ShipmentForm.prototype.test = function(targetId) { - var shipmentForm = new ShipmentForm({ - creationMode : true - - }); - BIOSAXS.proposal = new Proposal(shipmentForm.input().proposal); - shipmentForm.getPanel().render(targetId); -}; - -/** - * #onSaved - */ -function StockSolutionForm(args) { - this.id = BUI.id(); - this.actions = []; - - if (args != null) { - if (args.actions != null) { - this.actions = args.actions; - } - } - this.onSaved = new Event(this); -} - -StockSolutionForm.prototype.getStockSolution = function() { - if (this.stockSolution != null) { - this.stockSolution.concentration = Ext.getCmp(this.id + "stockSolution_concentration").getValue(); - this.stockSolution.storageTemperature = Ext.getCmp(this.id + "stockSolution_storageTemperature").getValue(); - this.stockSolution.volume = Ext.getCmp(this.id + "stockSolution_volume").getValue(); - this.stockSolution.comments = Ext.getCmp(this.id + "stockSolution_comments").getValue(); - this.stockSolution.name = Ext.getCmp(this.id + "stockSolution_name").getValue(); - this.stockSolution.bufferId = this.bufferCombo.getValue(); - - if (this.macromoleculeCombo.getValue() != null) { - this.stockSolution.macromoleculeId = this.macromoleculeCombo.getValue(); - } else { - this.stockSolution.macromolecule3VO = null; - } - - } else { - return { - concentration : Ext.getCmp(this.id + "stockSolution_concentration").getValue(), - storageTemperature : Ext.getCmp(this.id + "stockSolution_storageTemperature").getValue(), - volume : Ext.getCmp(this.id + "stockSolution_volume").getValue(), - comments : Ext.getCmp(this.id + "stockSolution_comments").getValue(), - name : Ext.getCmp(this.id + "stockSolution_name").getValue(), - bufferId : this.bufferCombo.getValue(), - macromoleculeId : this.macromoleculeCombo.getValue() - }; - } - return this.stockSolution; -}; - -StockSolutionForm.prototype.setStockSolution = function(stockSolution) { - if (stockSolution != null) { - if (stockSolution.macromoleculeId != null) { - this.macromoleculeCombo.setValue(stockSolution.macromoleculeId); - } - this.bufferCombo.setValue(stockSolution.bufferId); - Ext.getCmp(this.id + "stockSolution_concentration").setValue(this.stockSolution.concentration); - Ext.getCmp(this.id + "stockSolution_storageTemperature").setValue(this.stockSolution.storageTemperature); - Ext.getCmp(this.id + "stockSolution_volume").setValue(this.stockSolution.volume); - Ext.getCmp(this.id + "stockSolution_name").setValue(this.stockSolution.name); - Ext.getCmp(this.id + "stockSolution_comments").setValue(this.stockSolution.comments); - } -}; - -StockSolutionForm.prototype.getBufferCombo = function() { - this.bufferCombo = BIOSAXS_COMBOMANAGER.getComboBuffers(BIOSAXS.proposal.getBuffers(), { - labelWidth : 120, - margin : '0 0 10 0', - width : 220 - - }); - return this.bufferCombo; -}; - -StockSolutionForm.prototype.getMacromoleculeCombo = function() { - this.macromoleculeCombo = BIOSAXS_COMBOMANAGER.getComboMacromoleculeByMacromolecules(BIOSAXS.proposal.getMacromolecules(), { - labelWidth : 120, - margin : '0 0 10 0', - width : 220 - - }); - return this.macromoleculeCombo; -}; - -StockSolutionForm.prototype.refresh = function() { -}; - -StockSolutionForm.prototype._getTopPanel = function() { - return { - xtype : 'container', - layout : 'hbox', - border : 0, - items : [ { - xtype : 'container', - layout : 'hbox', - items : [ { - xtype : 'container', - flex : 1, - border : false, - layout : 'anchor', - defaultType : 'textfield', - items : [ - - this.getMacromoleculeCombo(), { - xtype : 'requiredtext', - id : this.id + 'stockSolution_name', - fieldLabel : 'Acronym', - labelWidth : 120, - width : 250 - }, { - xtype : 'requiredtext', - id : this.id + 'stockSolution_concentration', - fieldLabel : 'Conc. (mg/ml)', - labelWidth : 120, - width : 250 - }, - - { - id : this.id + 'stockSolution_storageTemperature', - fieldLabel : 'Storage Temp.(C)', - labelWidth : 120, - width : 250 - }, { - xtype : 'requiredtext', - id : this.id + 'stockSolution_volume', - fieldLabel : 'Volume in Well (µl)', - labelWidth : 120, - width : 250 - } ] - } ] - }, { - xtype : 'container', - flex : 1, - layout : 'anchor', - defaultType : 'textfield', - margin : '0 0 0 10', - items : [ this.getBufferCombo() ] - } ] - }; - -}; - -StockSolutionForm.prototype.getPanel = function(stockSolution) { - this.stockSolution = stockSolution; - this.panel = Ext.createWidget({ - xtype : 'container', - layout : 'vbox', - border : 0, - style : { - padding : '10px' - }, - fieldDefaults : { - labelAlign : 'left', - labelWidth : 50 - }, - items : [ this._getTopPanel(stockSolution), { - id : this.id + 'stockSolution_comments', - xtype : 'textareafield', - name : 'comments', - fieldLabel : 'Comments', - labelWidth : 120, - width : '100%' - } ] - }); - - this.setStockSolution(stockSolution); - return this.panel; -}; - -StockSolutionForm.prototype.input = function() { - return { - stock : { - "stockSolutionId" : 6, - "proposalId" : 3124, - "macromoleculeId" : 5933, - "bufferId" : 811, - "instructionSet3VO" : null, - "boxId" : 305861, - "storageTemperature" : "20", - "volume" : "300", - "concentration" : "1.2", - "comments" : "Buffer EDTA with A", - "name" : "A_EDTA_1.2", - "samples" : [], - "buffer" : "EDTA", - "macromolecule" : "A" - }, - proposal : new MeasurementGrid().input().proposal - }; -}; - -StockSolutionForm.prototype.test = function(targetId) { - var stockSolutionForm = new StockSolutionForm(); - BIOSAXS.proposal = new Proposal(stockSolutionForm.input().proposal); - var panel = stockSolutionForm.getPanel(new Shipment(stockSolutionForm.input().stock)); - panel.render(targetId); -}; - - -BoxWhiskerGraph.prototype.cleanArray = GenericGraph.prototype.cleanArray; -BoxWhiskerGraph.prototype.plotAxes = GenericGraph.prototype.plotAxes; -BoxWhiskerGraph.prototype.plotRuler = GenericGraph.prototype.plotRuler; -BoxWhiskerGraph.prototype.drawSVGVerticalText = GenericGraph.prototype.drawSVGVerticalText; -BoxWhiskerGraph.prototype.getClassColor = GenericGraph.prototype.getClassColor; -BoxWhiskerGraph.prototype.getDimensions = GenericGraph.prototype.getDimensions; -BoxWhiskerGraph.prototype.calculate = GenericGraph.prototype.calculate; -BoxWhiskerGraph.prototype.getMedian = GenericGraph.prototype.getMedian; -BoxWhiskerGraph.prototype.pointToPixel = GenericGraph.prototype.pointToPixel; -BoxWhiskerGraph.prototype.maxValueWhisker = GenericGraph.prototype.maxValueWhisker; -BoxWhiskerGraph.prototype.refresh = GenericGraph.prototype.refresh; - -/** - * Subclass of GenericGraph - * - * @maxBoxWidth - */ -function BoxWhiskerGraph(args){ - this.maxBoxWidth = 25; - - if (args == null){ - args = new Object(); - } - args["plotHorizontalByCluster"] = true; - - GenericGraph.call(this, args); - - if (args.maxBoxWidth != null){ - this.maxBoxWidth = args.maxBoxWidth; - } -}; - - - -/** -There are several different methods for calculating quartiles.[1] This calculator uses a method described by Moore and McCabe to find quartile values. -The same method also used by The TI-83 to calculate quartile values. -With this method, the first quartile is the median of the numbers below the median, the third quartile is the median of the numbers above the median. - -http://www.miniwebtool.com/quartile-calculator/ -http://www.alcula.com/calculators/statistics/box-plot/ -**/ -BoxWhiskerGraph.prototype.getQ1 = function(array){ - array = array.slice(0, array.length/2); - return this.getMedian(array); -}; - -BoxWhiskerGraph.prototype.getQ3 = function(array){ - array = array.slice((array.length + 1)/2); - return this.getMedian(array); - -}; - -BoxWhiskerGraph.prototype.getQ2 = function(array){ - return this.getMedian(array); -}; - -BoxWhiskerGraph.prototype.getBelowOutliers = function(belowLimit, array){ - var points = new Array(); - for (var i = 0; i < array.length; i++){ - if (array[i] <= belowLimit){ - points.push(array[i]); - } - } - return points; -}; - -BoxWhiskerGraph.prototype.getAboveOutliers = function(aboveLimit, array){ - var points = new Array(); - for (var i = 0; i < array.length; i++){ - if (array[i] >= aboveLimit){ - points.push(array[i]); - } - } - return points; -}; - - -BoxWhiskerGraph.prototype.minValueWhisker = function(belowLimit, q1, array){ - var points = new Array(); - - for (var i = 0; i < array.length; i++){ - if ((array[i] < q1) && (array[i]) > belowLimit){ - points.push(array[i]); - } - } - - if (points.length > 0){ - points.sort(function(a, b){return a - b;}); - return points[0]; - } - return null; -}; - -BoxWhiskerGraph.prototype.isNumber = function(value){ - if (value=="") return false; - - var d = parseInt(value); - if (!isNaN(d)) return true; else return false; - -}; - -BoxWhiskerGraph.prototype.plotBoxWhisker = function(boxProperties){ - if (this.maxBoxWidth != null){ - if (boxProperties.width > this.maxBoxWidth){ - boxProperties.x = boxProperties.x + (boxProperties.width/2) - (this.maxBoxWidth/2); - boxProperties.width = this.maxBoxWidth; - } - - } - - if (this.plotPoints){ - for(var i = 0; i < boxProperties.values.length; i++){ - var value = boxProperties.values[i]; - var toPixel = this.pointToPixel(value, boxProperties); - SVG.drawCircle(boxProperties.x + (boxProperties.width/2) + 2, toPixel, this.pointRadius, this.svg, [["fill", "green"], ["fill-opacity", this.fillOpacityPoint],['stroke-opacity', this.strokeOpacityPoint], ["stroke", "black"]]); - } - } - - - var boxColor = this.getClassColor(boxProperties.name); - var result = this.calculate(boxProperties.values); - /** Q1 **/ - - if (this.isNumber(result.Q1)){ - SVG.drawLine(boxProperties.x, this.pointToPixel(result.Q1, boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result.Q1, boxProperties), this.svg, [["stroke", boxColor]]); - } - /** Q2 **/ - if (this.isNumber(result.Q2)){ - SVG.drawLine(boxProperties.x, this.pointToPixel(result.Q2, boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result.Q2, boxProperties), this.svg, [["stroke", "blue"], ["stroke-width", "2"]]); - } - - /** Q3 **/ - if (this.isNumber(result.Q3)){ - SVG.drawLine(boxProperties.x, this.pointToPixel(result.Q3, boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result.Q3, boxProperties), this.svg, [["stroke", boxColor]]); - } - - /** Concenting Q1 and Q3 **/ - if (this.isNumber(result.Q1)&&this.isNumber(result.Q3)){ - SVG.drawLine(boxProperties.x, this.pointToPixel(result.Q1, boxProperties), boxProperties.x, this.pointToPixel(result.Q3, boxProperties), this.svg, [["stroke", boxColor]]); - SVG.drawLine(boxProperties.x + boxProperties.width, this.pointToPixel(result.Q1, boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result.Q3, boxProperties), this.svg, [["stroke", boxColor]]); - } - - /** min-whisker **/ - if (result["min-whisker"] != null){ - if (this.isNumber(result.Q1)){ - SVG.drawLine(boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result.Q1, boxProperties), boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result["min-whisker"], boxProperties), this.svg, [["stroke", boxColor]]); - } - SVG.drawLine(boxProperties.x,this.pointToPixel(result["min-whisker"], boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result["min-whisker"], boxProperties) , this.svg, [["stroke", boxColor]]); - - } - - /** max-whisker **/ - if (result["max-whisker"] != null){ - if (this.isNumber(result.Q3)){ - SVG.drawLine(boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result.Q3, boxProperties), boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result["max-whisker"], boxProperties), this.svg, [["stroke", boxColor]]); - } - SVG.drawLine(boxProperties.x , this.pointToPixel(result["max-whisker"], boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result["max-whisker"], boxProperties), this.svg, [["stroke", boxColor]]); - - } - - /** outliners **/ - if (result["above-outliers"] != null){ - for (var point in result["above-outliers"]){ - SVG.drawCircle(boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result["above-outliers"][point], boxProperties), this.pointRadius, this.svg, [["fill", "red"], ["fill-opacity", "1"]]); - //SVG.drawText(boxProperties.x + (boxProperties.width/2) - 2, this.pointToPixel(result["above-outliers"][point], boxProperties) + 2, "x",this.svg, [["fill", "black"], ["font-size", "x-small"]]); - } - } - if (result["below-outliers"] != null){ - for (var point in result["below-outliers"]){ - SVG.drawCircle(boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result["below-outliers"][point], boxProperties), this.pointRadius, this.svg, [["fill", "red"], ["fill-opacity", "1"]]); - //SVG.drawText(boxProperties.x + (boxProperties.width/2) - 2, this.pointToPixel(result["below-outliers"][point], boxProperties) + 2, "x",this.svg, [["fill", "black"], ["font-size", "x-small"]]); - } - } -}; - - - -BoxWhiskerGraph.prototype.plotClusterTitles = function(properties){ - /** Cluster Titles **/ - var posX = this.left + this.rulerWidth; - var data = this.data; - for(var i = 0; i < data.clusters.length; i++ ){ - /** title for the clusters **/ - posX = posX + this.interClustersSpace; - - /** Drawing title of classes **/ - var cluster = data.clusters[i]; - var posXClasses = posX; - for(var j = 0; j < cluster.classes.length; j++){ - //SVG.drawRectangle(posXClasses, this.height - (this.bottom + this.clusterTitleHeight + this.rulerHeight), properties.classWidth, this.rulerHeight, this.svg, [["fill", "green"]]); -// SVG.drawText(posXClasses + 1/6*properties.classWidth, this.height - (this.bottom + this.clusterTitleHeight + (this.rulerHeight*1/4)), cluster.classes[j].name, this.svg, [["style", "font-size:xx-small"]]); - var color = cluster.classes[j].color; - this.drawSVGVerticalText(posXClasses + 1/2*(properties.classWidth), this.height - (this.bottom - this.clusterTitleHeight + (this.rulerHeight)), cluster.classes[j].name , [["style", "font-size:x-small;"], ["fill", color]]); - - // SVG.drawRectangle(posXClasses, this.height - (this.bottom + this.clusterTitleHeight), properties.classWidth, 2, this.svg, [["fill", "black"]]); - posXClasses = posXClasses + properties.classWidth + this.interClassesSpace; - } - - var clusterTitleSpace = (data.clusters[i].classes.length * properties.classWidth) + ((data.clusters[i].classes.length - 1) * this.interClassesSpace); - //SVG.drawRectangle(posX, this.height - (this.bottom + this.clusterTitleHeight), clusterTitleSpace, this.clusterTitleHeight, this.svg, [["fill", "pink"]]); - SVG.drawRectangle(posX, this.height - (this.clusterTitleHeight+this.bottom), clusterTitleSpace, 1, this.svg, []); - -// var transform = ["translate", "(" + posX + 1/3*clusterTitleSpace +", " + this.height - (this.bottom + (this.clusterTitleHeight*1/4)) +")"], ["transform", "rotate(180)"]; -// var transform = ["transform", "translate(" + (posX + 1/3*clusterTitleSpace) +", " + (this.height - (this.bottom + (this.clusterTitleHeight*1/4))) + "), rotate(-90) "]; -// this.drawSVGVerticalText(posX + 1/3*clusterTitleSpace, this.height - (this.bottom + (this.clusterTitleHeight*1/4)),data.clusters[i].name, [["style", "font-size:x-small"]]); - SVG.drawText(posX , this.height - (this.bottom + (this.clusterTitleHeight*1/4)),data.clusters[i].name ,this.svg, [["style", "font-size:x-small"]]); - posX = posX + clusterTitleSpace; - } -}; - -BoxWhiskerGraph.prototype.plotWhisters = function(data, properties){ - var colors = ["yellow", "orange", "green"]; - var posX = this.left + this.rulerWidth; - for(var i = 0; i < data.clusters.length; i++ ){ - var cluster = data.clusters[i]; - /** inter cluster space **/ - //SVG.drawRectangle(posX, this.top, this.interClustersSpace, this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight, this.svg, [["fill", "black"]]); - posX = posX + this.interClustersSpace; - - for (var j = 0; j < cluster.classes.length; j ++){ - - //SVG.drawRectangle(posX, this.top, properties.classWidth, this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight, this.svg, [["fill", colors[j]]]); - this.plotBoxWhisker( - { - name : cluster.classes[j].name, - values : cluster.classes[j].values, - minPoint : properties.minPoint, - maxPoint : properties.maxPoint, - x : posX, - y : this.top, - width : properties.classWidth, - height : this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight - - - } - ); - posX = posX + properties.classWidth; - //SVG.drawRectangle(posX, this.top, this.interClassesSpace, this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight, this.svg, [["fill", "black"]]); - if (j < cluster.classes.length - 1){ - posX = posX + this.interClassesSpace; - } - } - } -}; - -BoxWhiskerGraph.prototype.draw = function(targetId, data){ - this.targetId = targetId; - var properties = (this.getDimensions(data)); - this.svg = SVG.createSVGCanvas(document.getElementById(this.targetId), [["width", this.width], ["height", this.height]]); - this.plotAxes(properties); - this.plotClusterTitles(properties); - this.plotWhisters(data,properties); -}; - -BoxWhiskerGraph.prototype.input = function(){ - return DATADOC.getBoxWhikerData(); -}; - -BoxWhiskerGraph.prototype.test = function(targetId){ - var plot = new BoxWhiskerGraph( - { - targetId : targetId, - height : 350, - width : 450, - maxBoxWidth : 25 - } - ); - plot.refresh(this.input()); -}; - - - - - - - -function DataSet(){ - this.json = null; - -}; - - -DataSet.prototype.loadFromJSON = function(json){ - if(json != null) { - if(this.validate(json)) { - this.json = json; - } - } -}; - - -DataSet.prototype.toJSON = function(json){ - return this.json; -}; - - -/** Abstract method to be override on childs classes **/ -DataSet.prototype.validate = function(json){ - if (true){ - return true; - } - /*else{ - throw "Data validation failed"; - }*/ -}; - - - - -Edge.prototype.getName = GraphItem.prototype.getName; -Edge.prototype.setName = GraphItem.prototype.setName; -Edge.prototype.getId = GraphItem.prototype.getId; - -function Edge(id, name, nodeSource, nodeTarget, args){ - GraphItem.prototype.constructor.call(this, id, name, args); - - this.sourceNode = nodeSource; - this.targetNode = nodeTarget; - -}; - -Edge.prototype.toJSON = function(){ - return {"index": this.id,"sourceIndex":this.sourceNode.getId(),"targetIndex":this.targetNode.getId(),"args":this.args}; -}; - -Edge.prototype.getNodeSource = function(){ - return this.sourceNode; -}; - -Edge.prototype.getNodeTarget = function(){ - return this.targetNode; -}; - -Edge.prototype.remove = function(){ - //Remove edge object in the nodes - this.getNodeSource().removeEdge(this); - this.getNodeTarget().removeEdge(this); - - this.deleted.notify(this); -}; - - -EdgeGraphFormatter.prototype.setProperties = ItemGraphFormatter.prototype.setProperties; -EdgeGraphFormatter.prototype.getDefault = ItemGraphFormatter.prototype.getDefault; -EdgeGraphFormatter.prototype.getSelected = ItemGraphFormatter.prototype.getSelected; -EdgeGraphFormatter.prototype.getOver = ItemGraphFormatter.prototype.getOver; -EdgeGraphFormatter.prototype.getDragging = ItemGraphFormatter.prototype.getDragging; -EdgeGraphFormatter.prototype.getId = ItemGraphFormatter.prototype.getId; -EdgeGraphFormatter.prototype.toJSON = ItemGraphFormatter.prototype.toJSON; -EdgeGraphFormatter.prototype.loadFromJSON = ItemGraphFormatter.prototype.loadFromJSON; -EdgeGraphFormatter.prototype._setEvents = ItemGraphFormatter.prototype._setEvents; - -function EdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ - ItemGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); - - this.getDefault().args.type = "EdgeGraphFormatter"; -}; - - - - -LineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; -LineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; -LineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; -LineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; -LineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; -LineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; -LineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; -LineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; -LineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; - -function LineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ - EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); - this.args.type = "LineEdgeGraphFormatter"; -}; - -/** DIRECTED **/ -DirectedLineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; -DirectedLineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; -DirectedLineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; -DirectedLineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; -DirectedLineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; -DirectedLineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; -DirectedLineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; -DirectedLineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; -DirectedLineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; - -function DirectedLineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ - EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); - this.args.type = "DirectedLineEdgeGraphFormatter"; - this.args.arrowSize = "3"; -}; -DirectedLineEdgeGraphFormatter.prototype.getArrowSize = function(){ - return this.args.arrowSize; -}; - -OdirectedLineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; -OdirectedLineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; -OdirectedLineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; -OdirectedLineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; -OdirectedLineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; -OdirectedLineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; -OdirectedLineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; -OdirectedLineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; -OdirectedLineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; - -function OdirectedLineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ - EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); - this.args.type = "DirectedLineEdgeGraphFormatter"; - this.args.arrowSize = "3"; -}; - -OdirectedLineEdgeGraphFormatter.prototype.getArrowSize = function(){ - return this.args.arrowSize; -}; - - -/** CUT (inhibition) **/ -CutDirectedLineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; -CutDirectedLineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; -CutDirectedLineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; -CutDirectedLineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; -CutDirectedLineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; -CutDirectedLineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; -CutDirectedLineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; -CutDirectedLineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; -CutDirectedLineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; - -function CutDirectedLineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ - EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); - this.args.type = "CutDirectedLineEdgeGraphFormatter"; -}; - - - - -BezierEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; -BezierEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; -BezierEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; -BezierEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; -BezierEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; -BezierEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; -BezierEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; -BezierEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; -BezierEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; -BezierEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; - -function BezierEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ - EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); - this.args.type = "BezierEdgeGraphFormatter"; -}; - - - -DotDirectedLineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; -DotDirectedLineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; -DotDirectedLineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; -DotDirectedLineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; -DotDirectedLineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; -DotDirectedLineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; -DotDirectedLineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; -DotDirectedLineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; -DotDirectedLineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; - -function DotDirectedLineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ - EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); - this.args.type = "DotDirectedLineEdgeGraphFormatter"; -}; - - -OdotDirectedLineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; -OdotDirectedLineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; -OdotDirectedLineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; -OdotDirectedLineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; -OdotDirectedLineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; -OdotDirectedLineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; -OdotDirectedLineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; -OdotDirectedLineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; -OdotDirectedLineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; - -function OdotDirectedLineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ - EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); - this.args.type = "OdotDirectedLineEdgeGraphFormatter"; -}; - - - -function GraphDataset(){ - DataSet.prototype.constructor.call(this); - this.edges = new Object(); - this.vertices = new Object(); - this.verticesIndex = new Object(); - - //Events - this.newVertex = new Event(this); - this.vertexNameChanged = new Event(this); - this.vertexDeleted = new Event(this); - - this.newEdge = new Event(this); - this.edgeNameChanged = new Event(this); - this.edgeDeleted = new Event(this); - - this.json = new Object(); - this.json.vertices = new Array(); - this.json.edges = new Array(); - this.json.relations = new Array(); -}; - -GraphDataset.prototype.loadFromJSON = DataSet.prototype.loadFromJSON; -GraphDataset.prototype.toJSON = DataSet.prototype.toJSON; -GraphDataset.prototype.validate = DataSet.prototype.validate; - -/** Devuelve el numero de edges incidentes sobre el nodo con mas edges **/ -GraphDataset.prototype.getMaxClass = function(){ - var maxClassNode = 0; - for ( var node in this.vertices) { - if (this.vertices[node].getEdgesCount() > maxClassNode){ - maxClassNode = this.vertices[node].getEdgesCount(); - } - } - return maxClassNode; -}; - -/** Devuelve el numero de edges incidentes sobre el nodo con mas edges **/ -GraphDataset.prototype.getMinClass = function(){ - var minClassNode = Math.min(); - for ( var node in this.vertices) { - if (this.vertices[node].getEdgesCount() < minClassNode){ - minClassNode = this.vertices[node].getEdgesCount(); - } - } - return minClassNode; -}; - -GraphDataset.prototype.getVertexByName = function(nodeName){ - var results = new Array(); - - for (var vertexId in this.verticesIndex[nodeName]){ - var vertexByid = this.getVertexById(this.verticesIndex[nodeName][vertexId]); - results.push(vertexByid); - //* añadido nuevo porque fallaba el anterior codigo - return vertexByid - } - - if (results <= 1){ - return this.getVertexById(this.verticesIndex[nodeName]); - } - else{ - return results; - } -}; - -GraphDataset.prototype.getVertexById = function(id){ - return this.vertices[id]; -}; - -GraphDataset.prototype.toSIF = function(){ - var sifDataAdapter = new SifFileDataAdapter(); - return sifDataAdapter.toSIF(this); -}; - -GraphDataset.prototype.toSIFID = function(){ - var sifDataAdapter = new SifFileDataAdapter(); - return sifDataAdapter.toSIFID(this); -}; - -GraphDataset.prototype.toDOT = function(){ - var dotFileDataAdapter = new DotFileDataAdapter(); - return dotFileDataAdapter.toDOT(this); -}; - -GraphDataset.prototype.toDOTID = function(){ - var dotFileDataAdapter = new DotFileDataAdapter(); - return dotFileDataAdapter.toDOTID(this); -}; - -GraphDataset.prototype._addNode = function(nodeName, args){ - return new Vertex(this._getVerticesCount()-1, nodeName, args); -}; - -GraphDataset.prototype.addNode = function(nodeName, args){ - this.json.vertices.push(nodeName); - this._addVerticesIndex(nodeName, this._getVerticesCount() - 1); - var vertex = this._addNode(nodeName, args); - this.vertices[this._getVerticesCount()-1] = vertex; - this._setNodeEvents(vertex); - this.newVertex.notify(vertex); -}; - -GraphDataset.prototype._addVerticesIndex = function(nodeName, id){ - if (this.verticesIndex[nodeName] == null){ - this.verticesIndex[nodeName] = new Array(); - } - this.verticesIndex[nodeName].push(id); -}; - -GraphDataset.prototype.addEdge = function(edgeName, nodeSourceId, nodeTargetId, args){ - this.json.edges.push(edgeName); - var nodeSource = this.getVertexById(nodeSourceId); - var nodeTarget = this.getVertexById(nodeTargetId); - var index = this.getEdgesCount() - 1; - this.edges[index] = new Edge(index, edgeName, nodeSource, nodeTarget, args); - this.json.relations.push({"index": index, "sourceIndex": nodeSourceId, "targetIndex": nodeTargetId, "args": args }); - - nodeSource.addEdge(this.edges[index]); - nodeTarget.addEdge(this.edges[index]); - this._setEdgeEvents(this.edges[index]); - this.newEdge.notify(this.edges[index]); -}; - -GraphDataset.prototype.getVertices = function(){ - return this.vertices; -}; - -GraphDataset.prototype.getEdges = function(){ - return this.edges; -}; - -GraphDataset.prototype.getEdgeById = function(edgeId){ - return this.edges[edgeId]; -}; - -GraphDataset.prototype._getVerticesCount = function(){ - return this.json.vertices.length; -}; - - -GraphDataset.prototype.getVerticesCount = function(){ - var count = 0; - for ( var vertex in this.getVertices()) { - count ++; - } - return count; -}; - - -GraphDataset.prototype.getEdgesCount = function(){ - return this.json.edges.length; -}; - -GraphDataset.prototype.init = function(){ - this.edges = new Object(); - this.vertices = new Object(); -}; - -GraphDataset.prototype._setNodeEvents = function(node){ - var _this = this; - //NODE EVENTS - node.deleted.attach(function (sender, node){ - _this._removeNode(node); - }); - - node.nameChanged.attach(function (sender, args){ - var item = args.item; - var newName = item.name; - var indexes = _this.verticesIndex[args.previousName]; - for(var i = 0; i < indexes.length; i++){ - if(indexes[i] == item.id) - indexes.splice(i,1); - } - if(indexes.length == 0){ - delete _this.verticesIndex[args.previousName]; - } - _this._addVerticesIndex(newName, item.id); - _this.json.vertices[item.id] = newName; - _this.vertexNameChanged.notify(args); - }); -}; - -GraphDataset.prototype._setEdgeEvents = function(edge){ - var _this = this; - //EDGE EVENTS - edge.nameChanged.attach(function (sender, edge){ - _this.edgeNameChanged.notify(edge); - - }); - - edge.deleted.attach(function (sender, edge){ - _this._removeEdge(edge); - }); -}; - -GraphDataset.prototype._connectVerticesByName = function(nodeNameSource, nodeNameTarget){ - var source = this.getVertexByName(nodeNameSource); - var target = this.getVertexByName(nodeNameTarget); - - if ((source != null)&&(target!=null)){ - this.addEdge(source.getName() +"_" + target.getName(), source.getId(), target.getId(), {}); - } - else{ - if (source == null){ - console.log("No encontrado: " + nodeNameSource) - } - if (target == null){ - console.log("No encontrado: " + nodeNameTarget) - } - } -}; - -GraphDataset.prototype.loadFromJSON = function(json){ - var json = json; - this.init(); - this.json = new Object(); - this.json.vertices = new Array(); - this.json.edges = new Array(); - this.json.relations = new Array(); - - for ( var i = 0; i < json.nodes.length; i++) { - if (json.nodes[i] != null){ - var name = json.nodes[i]; - this.addNode(name); - } - else{ - this.json.vertices.push(null); - } - } - - for ( var i = 0; i < json.edges.length; i++) { - if (json.edges[i] != null){ - if (json.relations[i] != null){ - var name = json.edges[i]; - this.addEdge(name, json.relations[i].sourceIndex, json.relations[i].targetIndex, json.relations[i].args); - } - } - else{ - this.json.edges.push(null); - this.json.relations.push(null); - } - } -}; - -GraphDataset.prototype.prettyPrint = function(){ - for ( var node in this.vertices) { - console.log(this.vertices[node].getName() ); - for ( var j = 0; j < this.vertices[node].getEdgesIn().length; j++) { - console.log(" --> " + this.vertices[node].getEdgesIn()[j].getNodeTarget().getName() ); - } - } -}; - -GraphDataset.prototype._removeEdge = function(edge){ - this.json.edges[edge.getId()] = null; - this.json.relations[edge.getId()] = null; - - delete this.edges[edge.getId()]; - this.edgeDeleted.notify(edge); - - -}; - -GraphDataset.prototype._removeNode = function(node){ - this.json.vertices[node.getId()] = null; - delete this.vertices[node.getId()]; - this.vertexDeleted.notify(node); -}; - -GraphDataset.prototype.toJSON = function(){ - var json = new Object(); - var nodes = new Array(); - json.nodes = this.json.vertices; //nodes; - json.edges = this.json.edges; //edges; - json.relations = this.json.relations; - return json; -}; - -GraphDataset.prototype.clone = function(){ - var dsDataset = new GraphDataset(); - dsDataset.loadFromJSON(this.toJSON()); - return dsDataset; -}; -//GraphDataset.prototype.test = function(){ -// this.loadFromJSON(this.toJSON()); -//}; - -function labels(){ - var names = new Array(); - - var dataset = interactomeViewer.graphEditorWidget.dataset; - var layout = interactomeViewer.graphEditorWidget.layout; - - for ( var vertexId in interactomeViewer.graphEditorWidget.dataset.getVertices()) { - names.push(interactomeViewer.graphEditorWidget.dataset.getVertexById(vertexId).getName()); - } - - var sorted = (names.sort()); - console.log(sorted) - var distance = 0.01; - var altura = 0.6; - for ( var i = 0; i < names.length; i++) { - var id =dataset.getVertexByName(names[i]).getId(); - - layout.getNodeById(id).setCoordenates(distance, altura); - - - distance = parseFloat(distance) + parseFloat(0.03); - - altura = parseFloat(altura) + parseFloat(0.02); - - if (parseFloat(altura) == 0.9800000000000003){ - - altura = 0.6; - distance = distance - 0.51; - } - - } - - -}; - -function GraphItem(id, name, args){ - this.id = id; - this.name = name; - this.type = "NONE"; - - this.args = new Object(); - - - if (args!=null){ - this.args = args; - if (args.type !=null){ - this.type = args.type; - } - } - - //Events - this.nameChanged = new Event(this); - this.deleted = new Event(this); -} - -GraphItem.prototype.getName = function(){ - return this.name; -}; - -GraphItem.prototype.getId = function(){ - return this.id; -}; - -GraphItem.prototype.setName = function(name){ - var oldName = this.getName(); - this.name = name; - this.nameChanged.notify({"item": this, "previousName" : oldName}); -}; - - - - - -function LayoutDataset(){ - this.dataset = null; - this.vertices = new Object(); - this.changed = new Event(this); - - - this.args = new Object(); - - //RANDOM, CIRCLE - this.args.type = "CIRCLE"; -}; - -LayoutDataset.prototype.loadFromJSON = function(dataset, json){ - var _this = this; - this.vertices = new Object(); - this.dataset = dataset; //new GraphDataset(); - for ( var vertex in json) { - this.vertices[vertex] = new NodeLayout(vertex, json[vertex].x, json[vertex].y); - this.vertices[vertex].changed.attach(function (sender, item){ - _this.changed.notify(item); - }); - } - this._attachDatasetEvents(); -}; - - -LayoutDataset.prototype.toJSON = function(){ - var serialize = new Object(); - for ( var vertex in this.vertices) { - serialize[vertex] = new Object(); - serialize[vertex].x = this.vertices[vertex].x; - serialize[vertex].y = this.vertices[vertex].y; - } - serialize.dataset = new Object(); - serialize.dataset =this.dataset.toJSON(); - return serialize; -}; - -LayoutDataset.prototype.dataBind = function(graphDataset){ - this.dataset = graphDataset; - this._attachDatasetEvents(); - this._calculateLayout(); -}; - -LayoutDataset.prototype._removeVertex = function(vertexId){ - delete this.vertices[vertexId]; -}; - -LayoutDataset.prototype._attachDatasetEvents = function(){ - var _this = this; - - this.dataset.vertexDeleted.attach(function (sender, item){ - _this._removeVertex(item.getId()); - }); - - this.dataset.newVertex.attach(function (sender, item){ - _this.vertices[item.getId()] = new NodeLayout(item.getId(), 0.5, 0.5); - _this.vertices[item.getId()].changed.attach(function (sender, item){ - _this.changed.notify(item); - }); - }); -}; - -LayoutDataset.prototype.getType = function(){ - return this.args.type; -}; - -LayoutDataset.prototype._calculateLayoutVertices = function(type, count){ - - if (type == "CIRCLE"){ - var radius = 0.4; - var centerX = 0.5; - var centerY = 0.5; - var verticesCoordinates = new Array(); - for(var i = 0; i < count; i++){ - x = centerX + radius * Math.sin(i * 2 * Math.PI/count); - y = centerY + radius * Math.cos(i * 2 * Math.PI/count); - verticesCoordinates.push({'x':x,'y':y}); - } - return verticesCoordinates; - } -}; - - -LayoutDataset.prototype._calculateLayout = function(){ - var _this = this; - if (this.getType() == "RANDOM"){ - for ( var vertex in this.dataset.getVertices()) { - if (this.vertices[vertex] == null){ - this.vertices[vertex] = new NodeLayout(vertex, 0, 0); - } - this.vertices[vertex].setCoordinates(Math.random(), Math.random()); - this.vertices[vertex].changed.attach(function (sender, item){ - _this.changed.notify(item); - }); - } - } - - if ( this.getType() == "CIRCLE"){ - - var count = this.dataset._getVerticesCount(); - var verticesCoordinates = this._calculateLayoutVertices(this.getType(), count); - - var aux = 0; - for ( var vertex in this.dataset.getVertices()) { - if (this.vertices[vertex] == null){ - this.vertices[vertex] = new NodeLayout(vertex, 0, 0); - } - this.vertices[vertex].setCoordinates(verticesCoordinates[aux].x, verticesCoordinates[aux].y);//{"x":, "y":}; - aux++; - this.vertices[vertex].changed.attach(function (sender, item){ - _this.changed.notify(item); - }); - } - } - - - if (this.getType() == "SQUARE"){ - - var count = this.dataset._getVerticesCount(); - var xMin = 0.1; - var xMax = 0.9; - var yMin = 0.1; - var yMax = 0.9; - - var rows = Math.sqrt(count); - var step = (xMax - xMin) / rows; - - var verticesCoordinates = new Array(); - for(var i = 0; i < rows; i ++){ - for ( var j = 0; j < rows; j++) { - x = i * step + xMin; - y = j * step + yMin; - verticesCoordinates.push({'x':x,'y':y}); - } - } - - var aux = 0; - for ( var vertex in this.dataset.getVertices()) { - if (this.vertices[vertex] == null){ - this.vertices[vertex] = new NodeLayout(vertex, 0, 0); - } - this.vertices[vertex].setCoordinates(verticesCoordinates[aux].x, verticesCoordinates[aux].y);//{"x":, "y":}; - aux++; - this.vertices[vertex].changed.attach(function (sender, item){ - _this.changed.notify(item); - }); - } - } - -}; - -LayoutDataset.prototype.getNodeById = function(id){ - return this.vertices[id]; -}; - -LayoutDataset.prototype.getVerticesByArea = function(x1, y1, x2, y2){ - var vertices = new Array(); - for ( var vertex in this.dataset.getVertices()) { - if ((this.vertices[vertex].x >= x1)&&(this.vertices[vertex].x <= x2)){ - if ((this.vertices[vertex].y >= y1)&&(this.vertices[vertex].y <= y2)){ - vertices.push(this.vertices[vertex]); - } - } - } - return vertices; -}; - - - - -LayoutDataset.prototype.getLayout = function(type){ - - if (type == "CIRCLE"){ - this.args.type = "CIRCLE"; - this._calculateLayout(); - return; - } - - if (type == "SQUARE"){ - this.args.type = "SQUARE"; - this._calculateLayout(); - return; - } - - if (type == "RANDOM"){ - this.args.type = "RANDOM"; - this._calculateLayout(); - return; - } - - - var dotText = this.dataset.toDOTID(); - var url = "http://bioinfo.cipf.es/utils/ws/rest/network/layout/"+type+".coords"; - var _this = this; - - $.ajax({ - async: true, - type: "POST", - url: url, - dataType: "text", - data: { - dot :dotText - }, - cache: false, - success: function(data){ - var response = JSON.parse(data); - for ( var vertexId in response) { - _this.vertices[vertexId].setCoordinates(response[vertexId].x, response[vertexId].y); - } - } - }); - -// $.ajax({ -// async: true, -// type: "POST", -// url: url, -// dataType: "script", -// data: { -// dot :dotText -// }, -// cache: false, -// success: function(data){ -// var response = JSON.parse(data); -// for ( var vertexId in response) { -// _this.vertices[vertexId].setCoordinates(response[vertexId].x, response[vertexId].y); -// } -// } -// }); - -}; - -function NodeLayout(id, x, y, args){ - this.id = id; - this.x = x; - this.y = y; - this.changed = new Event(this); -}; - -NodeLayout.prototype.getId = function(id){ - return this.id; -}; - -NodeLayout.prototype.setCoordinates = function(x, y){ - this.x = x; - this.y = y; - this.changed.notify(this); -}; - - - -function NetworkDataSetFormatter(vertexFormatProperties, defaultEdgeProperties, args){ - DataSet.prototype.constructor.call(this); - - this.args = new Object(); - - this.vertices = new Object(); - this.edges = new Object(); - this.dataset = null; - this.maxClass = 0; - this.minClass = 0; - - /** Coordenates with default Setting */ - this.args.width = 1100; - this.args.height = 500; - - /** Optional parameters */ - this.args.backgroundColor = "#FFFFFF"; - this.args.backgroundImage = null; - this.args.backgroundImageHeight = null; - this.args.backgroundImageWidth = null; - this.args.backgroundImageX = null; - this.args.backgroundImageY = null; - - - this.args.balanceNodes = false; - this.args.nodesMaxSize = 3; - this.args.nodesMinSize = 0.5; - - - /** Zoom **/ - this.args.zoomScale = 1; - this.args.zoomScaleStepFactor = 0.4; - - if (args != null){ - if (args.backgroundImage != null){ - this.args.backgroundImage = args.backgroundImage; - } - - if (args.width != null){ - this.args.width = args.width; - } - - if (args.height != null){ - this.args.height = args.height; - this.args.svgHeight = args.height; - } - - if (args.svgHeight != null){ - this.args.svgHeight = args.svgHeight; - } - - if (args.backgroundColor != null){ - this.args.backgroundColor = args.backgroundColor; - } - - if(args.balanceNodes != null){ - this.args.balanceNodes = args.balanceNodes; - } - - if(args.nodesMaxSize != null){ - this.args.nodesMaxSize = args.nodesMaxSize; - } - if(args.nodesMinSize != null){ - this.args.nodesMinSize = args.nodesMinSize; - } - } - - this.args.defaultEdgeProperties = {"fill":"#000000", "radius":"1", "stroke":"#000000", "size":1, "title":{"fontSize":10, "fontColor":"#000000"}}; - this.args.vertexFormatProperties = { "fill":"#000000", "stroke":"#000000", "stroke-opacity":"#000000"}; - - if (vertexFormatProperties!= null){ - this.args.vertexFormatProperties = vertexFormatProperties; - } - if (defaultEdgeProperties!= null){ - this.args.defaultEdgeProperties = defaultEdgeProperties; - } - - /** Events **/ - this.changed = new Event(this); - this.edgeChanged = new Event(this); - this.resized = new Event(this); - this.backgroundImageChanged= new Event(this); - this.backgroundColorChanged= new Event(this); -}; - -NetworkDataSetFormatter.prototype.loadFromJSON = function(dataset, json){ - this.args = new Object(); - this.vertices = new Object(); - this.args = json; - this._setDataset(dataset); - var _this = this; - - for ( var vertex in json.vertices) { - this.addVertex(vertex, json.vertices[vertex]); - } - - for ( var edgeId in json.edges) { - this.addEdge(edgeId, json.edges[edgeId]); - } -}; - - -NetworkDataSetFormatter.prototype.toJSON = function(){ - - -// this.args.vertices = new Object(); -// this.args.edges = new Object(); -// -// for ( var vertex in this.vertices) { -// this.args.vertices[vertex] = this.getVertexById(vertex).toJSON(); -// } -// for ( var edge in this.edges) { -// this.args.edges[edge] = this.getEdgeById(edge).toJSON(); -// } -// -// return (this.args); - - - var serialize = new Object(); - serialize = JSON.parse(JSON.stringify(this.args)); - serialize.vertices = new Object(); - serialize.edges = new Object(); - - for ( var vertex in this.vertices) { - serialize.vertices[vertex] = this.getVertexById(vertex).toJSON(); - } - for ( var edge in this.edges) { - serialize.edges[edge] = this.getEdgeById(edge).toJSON(); - } - - return (serialize); -}; - - - -NetworkDataSetFormatter.prototype._getNodeSize = function(nodeId){ - if (this.isVerticesBalanced()){ - var total = this.maxClass - this.minClass; - if (total == 0){ total = 1;} - var nodeConnection = this.dataset.getVertexById(nodeId).getEdges().length; - return ((nodeConnection*this.args.nodesMaxSize)/total) + this.args.nodesMinSize; - } - return this.getVertexById(nodeId).getDefault().getSize(); -}; - -NetworkDataSetFormatter.prototype._recalculateSize = function(){ - if (this.isVerticesBalanced()){ - this.maxClass = this.dataset.getMaxClass(); - this.minClass = this.dataset.getMinClass(); - for ( var vertexIdAll in this.vertices) { - var size = this._getNodeSize(vertexIdAll); - this.vertices[vertexIdAll].getDefault().setSize(size); - this.vertices[vertexIdAll].getSelected().setSize(size); - this.vertices[vertexIdAll].getOver().setSize(size); - } - } -}; - - -NetworkDataSetFormatter.prototype.addVertex = function(vertexId, json){ - - - if (json == null){ - this.vertices[vertexId] = new CircleVertexGraphFormatter(vertexId, this.args.vertexFormatProperties.defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); - } - else{ - - /** Cargo los attributos desde el json **/ - if (json.type == null){ - this.vertices[vertexId] = new CircleVertexGraphFormatter(vertexId, this.args.vertexFormatProperties.defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); - } - - if ((json.type == "SquareVertexGraphFormatter")||(json.type == "SquareVertexNetworkFormatter")){ - this.vertices[vertexId] = new SquareVertexGraphFormatter(vertexId); - this.vertices[vertexId].loadFromJSON(json); - } - - if ((json.type == "CircleVertexGraphFormatter")||(json.type == "CircleVertexNetworkFormatter")){ - this.vertices[vertexId] = new CircleVertexGraphFormatter(vertexId); - this.vertices[vertexId].loadFromJSON(json); - } - - if ((json.type == "EllipseVertexGraphFormatter")||(json.type == "EllipseVertexNetworkFormatter")){ - this.vertices[vertexId] = new EllipseVertexGraphFormatter(vertexId); - this.vertices[vertexId].loadFromJSON(json); - } - - if ((json.type == "RectangleVertexGraphFormatter")||(json.type == "RectangleVertexNetworkFormatter")){ - this.vertices[vertexId] = new RectangleVertexGraphFormatter(vertexId); - this.vertices[vertexId].loadFromJSON(json); - } - - if ((json.type == "RoundedVertexGraphFormatter")||(json.type == "RoundedVertexNetworkFormatter")){ - this.vertices[vertexId] = new RoundedVertexGraphFormatter(vertexId); - this.vertices[vertexId].loadFromJSON(json); - } - - } - - - var _this = this; - this.vertices[vertexId].stateChanged.attach(function (sender, item){ - _this.changed.notify(item); - }); - - var size = this._getNodeSize(vertexId); - this.vertices[vertexId].defaultFormat.args.size = size; - this.vertices[vertexId].selected.args.size = size; - this.vertices[vertexId].over.args.size = size; - -}; - -NetworkDataSetFormatter.prototype.addEdge = function(edgeId, json){ - - /** Es un edge nuevo que le doy los atributos por defecto **/ - if (json == null){ - if (this.dataset.getEdgeById(edgeId).getNodeSource().getId() == this.dataset.getEdgeById(edgeId).getNodeTarget().getId()){ - this.edges[edgeId] = new BezierEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); - }else{ - this.edges[edgeId] = new DirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); - } - } - else{ - /** Cargo los attributos desde el json **/ - if (json.type == null){ - this.edges[edgeId] = new LineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); - } - - if ((json.type == "LineEdgeGraphFormatter")||(json.type == "LineEdgeNetworkFormatter")){ - this.edges[edgeId] = new LineEdgeGraphFormatter(edgeId); - this.edges[edgeId].loadFromJSON(json); - } - if ((json.type == "DirectedLineEdgeGraphFormatter")||(json.type == "DirectedLineEdgeNetworkFormatter")){ - this.edges[edgeId] = new DirectedLineEdgeGraphFormatter(edgeId); - this.edges[edgeId].loadFromJSON(json); - } - - if ((json.type == "BezierEdgeGraphFormatter")||(json.type == "BezierEdgeNetworkFormatter")){ - this.edges[edgeId] = new BezierEdgeGraphFormatter(edgeId); - this.edges[edgeId].loadFromJSON(json); - } - - - if ((json.type == "CutDirectedLineEdgeGraphFormatter")||(json.type == "CutDirectedLineEdgeNetworkFormatter")){ - this.edges[edgeId] = new CutDirectedLineEdgeGraphFormatter(edgeId); - this.edges[edgeId].loadFromJSON(json); - } - - if ((json.type == "DotDirectedLineEdgeGraphFormatter")||(json.type == "DotDirectedLineEdgeNetworkFormatter")){ - this.edges[edgeId] = new DotDirectedLineEdgeGraphFormatter(edgeId); - this.edges[edgeId].loadFromJSON(json); - } - if ((json.type == "OdotDirectedLineEdgeGraphFormatter")||(json.type == "OdotDirectedLineEdgeNetworkFormatter")){ - this.edges[edgeId] = new OdotDirectedLineEdgeGraphFormatter(edgeId); - this.edges[edgeId].loadFromJSON(json); - } - - if ((json.type == "OdirectedLineEdgeGraphFormatter")||(json.type == "OdirectedLineEdgeNetworkFormatter")){ - this.edges[edgeId] = new OdirectedLineEdgeGraphFormatter(edgeId); - this.edges[edgeId].loadFromJSON(json); - } - } - - var _this = this; - this.edges[edgeId].stateChanged.attach(function (sender, item){ - _this.edgeChanged.notify(item); - }); - - this._recalculateSize(); -}; - -NetworkDataSetFormatter.prototype._setDataset = function(dataset){ - this.dataset = dataset; - this.maxClass = dataset.getMaxClass(); - this.minClass = dataset.getMinClass(); - this._attachDatasetEvents(); -}; - -NetworkDataSetFormatter.prototype.changeEdgeType = function(edgeId, type){ - if ((type == "LineEdgeGraphFormatter")||(type == "LineEdgeNetworkFormatter")){ - this.edges[edgeId] = new LineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); - - } - if ((type == "DirectedLineEdgeGraphFormatter")||(type == "DirectedLineEdgeNetworkFormatter")){ - this.edges[edgeId] = new DirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); - } - - if ((type == "CutDirectedLineEdgeGraphFormatter")||(type == "CutDirectedLineEdgeNetworkFormatter")){ - this.edges[edgeId] = new CutDirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); - } - - if ((type == "DotDirectedLineEdgeGraphFormatter")||(type == "DotDirectedLineEdgeNetworkFormatter")){ - this.edges[edgeId] = new DotDirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); - } - - if ((type == "OdotDirectedLineEdgeGraphFormatter")||(type == "OdotDirectedLineEdgeNetworkFormatter")){ - this.edges[edgeId] = new OdotDirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); - } - - if ((type == "OdirectedLineEdgeGraphFormatter")||(type == "OdirectedLineEdgeNetworkFormatter")){ - this.edges[edgeId] = new OdirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); - } - - - - var _this = this; - this.edges[edgeId].stateChanged.attach(function (sender, item){ - _this.edgeChanged.notify(item); - }); - _this.edgeChanged.notify(this.edges[edgeId]); -}; -/* -classe = "SquareNetworkNodeFormatter"; -} -if (value == "circle"){ - classe = "CircleNetworkNodeFormatter"; - **/ -NetworkDataSetFormatter.prototype.changeNodeType = function(vertexId, type){ - var defaultFormat = JSON.parse(JSON.stringify(this.vertices[vertexId].getDefault())); - var selectedFormat = JSON.parse(JSON.stringify(this.vertices[vertexId].getSelected())); - var defaultFormat = JSON.parse(JSON.stringify(this.vertices[vertexId].getDefault())); - var defaultFormat = JSON.parse(JSON.stringify(this.vertices[vertexId].getDefault())); - - if ((type == "SquareVertexGraphFormatter")||(type == "SquareVertexNetworkFormatter")){ - this.vertices[vertexId] = new SquareVertexGraphFormatter(vertexId,defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); - } - - if ((type == "CircleVertexGraphFormatter")||(type == "CircleVertexNetworkFormatter")){ - this.vertices[vertexId] = new CircleVertexGraphFormatter(vertexId, defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); - } - - if ((type == "EllipseVertexGraphFormatter")||(type == "EllipseVertexNetworkFormatter")){ - this.vertices[vertexId] = new EllipseVertexGraphFormatter(vertexId, defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); - } - - if ((type == "RectangleVertexGraphFormatter")||(type == "RectangleVertexNetworkFormatter")){ - this.vertices[vertexId] = new RectangleVertexGraphFormatter(vertexId, defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); - } - - if ((type == "RoundedVertexGraphFormatter")||(type == "RoundedVertexNetworkFormatter")){ - this.vertices[vertexId] = new RoundedVertexGraphFormatter(vertexId, defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); - } - - if ((type == "OctagonVertexGraphFormatter")||(type == "OctagonVertexNetworkhFormatter")){ - this.vertices[vertexId] = new OctagonVertexGraphFormatter(vertexId, defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); - } - - - var _this = this; - this.vertices[vertexId].stateChanged.attach(function (sender, item){ - _this.changed.notify(item); - }); - _this.changed.notify(this.vertices[vertexId]); -}; - - - -NetworkDataSetFormatter.prototype.dataBind = function(networkDataSet){ - var _this = this; - this._setDataset(networkDataSet); - - for ( var vertex in this.dataset.getVertices()) { - this.addVertex(vertex); - } - - for ( var edge in this.dataset.getEdges()) { - this.addEdge(edge); - } -}; - -NetworkDataSetFormatter.prototype._removeEdge = function(edgeId){ - delete this.edges[edgeId]; -}; - -NetworkDataSetFormatter.prototype._removeVertex = function(vertexId){ - delete this.vertices[vertexId]; -}; - -NetworkDataSetFormatter.prototype._attachDatasetEvents = function(id){ - var _this = this; - this.dataset.vertexDeleted.attach(function (sender, item){ - _this._removeVertex(item.getId()); - }); - - this.dataset.edgeDeleted.attach(function (sender, item){ - _this._removeEdge(item.getId()); - }); - - this.dataset.newVertex.attach(function (sender, item){ - _this.addVertex(item.getId()); - }); - - this.dataset.newEdge.attach(function (sender, item){ - _this.addEdge(item.getId()); - }); -}; - - -NetworkDataSetFormatter.prototype.getVertexById = function(id){ - return this.vertices[id]; -}; - -NetworkDataSetFormatter.prototype.getEdgeById = function(id){ - return this.edges[id]; -}; - -NetworkDataSetFormatter.prototype.makeLabelsBigger = function(){ -for ( var vertexId in this.vertices) { - var fontSize = this.vertices[vertexId].getDefault().getFontSize() + 2; - this.vertices[vertexId].getDefault().setFontSize(fontSize); - } -}; - -NetworkDataSetFormatter.prototype.makeLabelsSmaller = function(){ - for ( var vertexId in this.vertices) { - var fontSize = this.vertices[vertexId].getDefault().getFontSize() - 2; - this.vertices[vertexId].getDefault().setFontSize(fontSize); - } -}; - - -NetworkDataSetFormatter.prototype.resize = function(width, height){ - this.args.width = width; - this.args.height = height; - this.resized.notify(); -}; - -/** ZOOM GETTERS **/ -NetworkDataSetFormatter.prototype.getZoomScaleStepFactor = function(){return this.args.zoomScaleStepFactor;}; -NetworkDataSetFormatter.prototype.setZoomScaleStepFactor = function(scaleFactor){this.args.zoomScaleStepFactor = scaleFactor;}; -NetworkDataSetFormatter.prototype.getZoomScale = function(){return this.args.zoomScale;}; -NetworkDataSetFormatter.prototype.setZoomScale = function(scale){this.args.zoomScale = scale;}; - -NetworkDataSetFormatter.prototype.getNodesMaxSize = function(){return this.args.nodesMaxSize;}; -NetworkDataSetFormatter.prototype.getNodesMinSize = function(){return this.args.nodesMinSize;}; - -/** SIZE SETTERS AND GETTERS **/ -NetworkDataSetFormatter.prototype.isVerticesBalanced = function(){return this.args.balanceNodes;}; -NetworkDataSetFormatter.prototype.getWidth = function(){return this.args.width;}; -NetworkDataSetFormatter.prototype.getHeight = function(){return this.args.height;}; - -/** OPTIONAL PARAMETERS GETTERS AND SETTERS **/ -NetworkDataSetFormatter.prototype.getBackgroundImage = function(){return this.args.backgroundImage;}; -NetworkDataSetFormatter.prototype.setBackgroundImage = function(value){this.args.backgroundImage = value; this.backgroundImageChanged.notify(this);}; - - -NetworkDataSetFormatter.prototype.getBackgroundImageWidth = function(){return this.args.backgroundImageWidth;}; -NetworkDataSetFormatter.prototype.setBackgroundImageWidth = function(value){this.args.backgroundImageWidth = value; this.backgroundImageChanged.notify(this);}; - -NetworkDataSetFormatter.prototype.getBackgroundImageHeight = function(){return this.args.backgroundImageHeight;}; -NetworkDataSetFormatter.prototype.setBackgroundImageHeight = function(value){this.args.backgroundImageHeight = value; this.backgroundImageChanged.notify(this);}; - -NetworkDataSetFormatter.prototype.getBackgroundImageX = function(){return this.args.backgroundImageX;}; -NetworkDataSetFormatter.prototype.setBackgroundImageX = function(value){this.args.backgroundImageX = value; this.backgroundImageChanged.notify(this);}; - -NetworkDataSetFormatter.prototype.getBackgroundImageY = function(){return this.args.backgroundImageX;}; -NetworkDataSetFormatter.prototype.setBackgroundImageY = function(value){this.args.backgroundImageY = value; this.backgroundImageChanged.notify(this);}; - - - -NetworkDataSetFormatter.prototype.getBackgroundColor = function(){return this.args.backgroundColor;}; -NetworkDataSetFormatter.prototype.setBackgroundColor = function(value){this.args.backgroundColor = value; this.backgroundColorChanged.notify(this);}; - -NetworkDataSetFormatter.prototype.getWidth = function(){return this.args.width;}; -NetworkDataSetFormatter.prototype.setWidth = function(value){this.args.width = value;}; - -NetworkDataSetFormatter.prototype.getHeight = function(){return this.args.height;}; -NetworkDataSetFormatter.prototype.setHeight = function(value){this.args.height = value;}; - - - - -Vertex.prototype.getName = GraphItem.prototype.getName; -Vertex.prototype.setName = GraphItem.prototype.setName; -Vertex.prototype.getId = GraphItem.prototype.getId; - -function Vertex(id, name, args){ - GraphItem.prototype.constructor.call(this, id, name, args); - this.edgesIn= new Array(); - this.edgesOut= new Array(); -}; - -Vertex.prototype.getEdges = function(){ - return this.edgesIn.concat(this.edgesOut); -}; - -Vertex.prototype.getEdgesCount = function(){ - return this.getEdges().length; -}; - -Vertex.prototype.getEdgesIn = function(){ - return this.edgesIn; -}; - -Vertex.prototype.getEdgesOut = function(){ - return this.edgesOut; -}; - -Vertex.prototype.addEdge = function(edge){ - if (edge.getNodeSource().getId() == this.id){ - this.edgesIn.push(edge); - } - else{ - this.edgesOut.push(edge); - } -}; - -Vertex.prototype.removeEdge = function(edge){ - for ( var i = 0; i < this.getEdgesIn().length; i++) { - var edgeIn = this.edgesIn[i]; - if (edgeIn.getId() == edge.getId()){ - this.edgesIn.splice(i, 1); - } - } - for ( var i = 0; i < this.getEdgesOut().length; i++) { - var edgeIn = this.edgesOut[i]; - if (edgeIn.getId() == edge.getId()){ - this.edgesOut.splice(i, 1); - } - } -}; - -Vertex.prototype.remove = function(){ - var edges = this.getEdges(); - for ( var i = 0; i < edges.length; i++) { - var edge = edges[i]; - edge.remove(); - } - this.deleted.notify(this); -}; - - - - - -VertexGraphFormatter.prototype.getDefault = ItemGraphFormatter.prototype.getDefault; -VertexGraphFormatter.prototype.getSelected = ItemGraphFormatter.prototype.getSelected; -VertexGraphFormatter.prototype.getOver = ItemGraphFormatter.prototype.getOver; -VertexGraphFormatter.prototype.getDragging = ItemGraphFormatter.prototype.getDragging; -VertexGraphFormatter.prototype.getId = ItemGraphFormatter.prototype.getId; -VertexGraphFormatter.prototype.toJSON = ItemGraphFormatter.prototype.toJSON; -VertexGraphFormatter.prototype.loadFromJSON = ItemGraphFormatter.prototype.loadFromJSON; -VertexGraphFormatter.prototype._setEvents = ItemGraphFormatter.prototype._setEvents; - - -function VertexGraphFormatter(defaultFormat, selectedFormat, overFormat, draggingFormat){ - ItemGraphFormatter.prototype.constructor.call(this, defaultFormat, selectedFormat, overFormat, draggingFormat); -}; - - -CircleVertexGraphFormatter.prototype.getDefault = VertexGraphFormatter.prototype.getDefault; -CircleVertexGraphFormatter.prototype.getSelected = VertexGraphFormatter.prototype.getSelected; -CircleVertexGraphFormatter.prototype.getOver = VertexGraphFormatter.prototype.getOver; -CircleVertexGraphFormatter.prototype.getDragging = VertexGraphFormatter.prototype.getDragging; -CircleVertexGraphFormatter.prototype.getId = VertexGraphFormatter.prototype.getId; -CircleVertexGraphFormatter.prototype.toJSON = VertexGraphFormatter.prototype.toJSON; -CircleVertexGraphFormatter.prototype.loadFromJSON = VertexGraphFormatter.prototype.loadFromJSON; -CircleVertexGraphFormatter.prototype._setEvents = VertexGraphFormatter.prototype._setEvents; - -function CircleVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ - VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); - this.args.type = "CircleVertexGraphFormatter"; - if (defaultFormat != null){ - if (defaultFormat.radius != null){ - this.defaultFormat.args.radius = defaultFormat.radius; - } - } - - if (selectedFormat != null){ - if (selectedFormat.radius != null){ - this.selected.args.radius = selectedFormat.radius; - } - } - - if (overFormat != null){ - if (overFormat.radius != null){ - this.over.args.radius = overFormat.radius; - } - } - - if (draggingFormat != null){ - if (draggingFormat.radius != null){ - this.dragging.args.draggingFormat = draggingFormat.radius; - } - } -}; - - - -SquareVertexGraphFormatter.prototype.getDefault = VertexGraphFormatter.prototype.getDefault; -SquareVertexGraphFormatter.prototype.getSelected = VertexGraphFormatter.prototype.getSelected; -SquareVertexGraphFormatter.prototype.getOver = VertexGraphFormatter.prototype.getOver; -SquareVertexGraphFormatter.prototype.getDragging = VertexGraphFormatter.prototype.getDragging; -SquareVertexGraphFormatter.prototype.getId = VertexGraphFormatter.prototype.getId; -SquareVertexGraphFormatter.prototype.toJSON = VertexGraphFormatter.prototype.toJSON; -SquareVertexGraphFormatter.prototype.loadFromJSON = VertexGraphFormatter.prototype.loadFromJSON; -SquareVertexGraphFormatter.prototype._setEvents = VertexGraphFormatter.prototype._setEvents; - -function SquareVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ - VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); - this.args.type = "SquareVertexGraphFormatter"; - if (defaultFormat != null){ - if (defaultFormat.radius != null){ - this.defaultFormat.args.radius = defaultFormat.radius; - } - } - - if (selectedFormat != null){ - if (selectedFormat.radius != null){ - this.selected.args.radius = selectedFormat.radius; - } - } - - if (overFormat != null){ - if (overFormat.radius != null){ - this.over.args.radius = overFormat.radius; - } - } - - if (draggingFormat != null){ - if (draggingFormat.radius != null){ - this.dragging.args.draggingFormat = draggingFormat.radius; - } - } -}; - - -EllipseVertexGraphFormatter.prototype.getDefault = VertexGraphFormatter.prototype.getDefault; -EllipseVertexGraphFormatter.prototype.getSelected = VertexGraphFormatter.prototype.getSelected; -EllipseVertexGraphFormatter.prototype.getOver = VertexGraphFormatter.prototype.getOver; -EllipseVertexGraphFormatter.prototype.getDragging = VertexGraphFormatter.prototype.getDragging; -EllipseVertexGraphFormatter.prototype.getId = VertexGraphFormatter.prototype.getId; -EllipseVertexGraphFormatter.prototype.toJSON = VertexGraphFormatter.prototype.toJSON; -EllipseVertexGraphFormatter.prototype.loadFromJSON = VertexGraphFormatter.prototype.loadFromJSON; -EllipseVertexGraphFormatter.prototype._setEvents = VertexGraphFormatter.prototype._setEvents; - -function EllipseVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ - VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); - this.args.type = "EllipseVertexGraphFormatter"; - if (defaultFormat != null){ - if (defaultFormat.radius != null){ - this.defaultFormat.args.radius = defaultFormat.radius; - } - } - - if (selectedFormat != null){ - if (selectedFormat.radius != null){ - this.selected.args.radius = selectedFormat.radius; - } - } - - if (overFormat != null){ - if (overFormat.radius != null){ - this.over.args.radius = overFormat.radius; - } - } - - if (draggingFormat != null){ - if (draggingFormat.radius != null){ - this.dragging.args.draggingFormat = draggingFormat.radius; - } - } -}; - - - -RectangleVertexGraphFormatter.prototype.getDefault = ItemGraphFormatter.prototype.getDefault; -RectangleVertexGraphFormatter.prototype.getSelected = ItemGraphFormatter.prototype.getSelected; -RectangleVertexGraphFormatter.prototype.getOver = ItemGraphFormatter.prototype.getOver; -RectangleVertexGraphFormatter.prototype.getDragging = ItemGraphFormatter.prototype.getDragging; -RectangleVertexGraphFormatter.prototype.getId = ItemGraphFormatter.prototype.getId; -RectangleVertexGraphFormatter.prototype.toJSON = ItemGraphFormatter.prototype.toJSON; -RectangleVertexGraphFormatter.prototype.loadFromJSON = ItemGraphFormatter.prototype.loadFromJSON; -RectangleVertexGraphFormatter.prototype._setEvents = ItemGraphFormatter.prototype._setEvents; - -function RectangleVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ - VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); - this.args.type = "RectangleVertexGraphFormatter"; - if (defaultFormat != null){ - if (defaultFormat.radius != null){ - this.defaultFormat.args.radius = defaultFormat.radius; - } - } - - if (selectedFormat != null){ - if (selectedFormat.radius != null){ - this.selected.args.radius = selectedFormat.radius; - } - } - - if (overFormat != null){ - if (overFormat.radius != null){ - this.over.args.radius = overFormat.radius; - } - } - - if (draggingFormat != null){ - if (draggingFormat.radius != null){ - this.dragging.args.draggingFormat = draggingFormat.radius; - } - } -}; - - - -RoundedVertexGraphFormatter.prototype.getDefault = ItemGraphFormatter.prototype.getDefault; -RoundedVertexGraphFormatter.prototype.getSelected = ItemGraphFormatter.prototype.getSelected; -RoundedVertexGraphFormatter.prototype.getOver = ItemGraphFormatter.prototype.getOver; -RoundedVertexGraphFormatter.prototype.getDragging = ItemGraphFormatter.prototype.getDragging; -RoundedVertexGraphFormatter.prototype.getId = ItemGraphFormatter.prototype.getId; -RoundedVertexGraphFormatter.prototype.toJSON = ItemGraphFormatter.prototype.toJSON; -RoundedVertexGraphFormatter.prototype.loadFromJSON = ItemGraphFormatter.prototype.loadFromJSON; -RoundedVertexGraphFormatter.prototype._setEvents = ItemGraphFormatter.prototype._setEvents; - -function RoundedVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ - VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); - this.args.type = "RoundedVertexGraphFormatter"; - if (defaultFormat != null){ - if (defaultFormat.radius != null){ - this.defaultFormat.args.radius = defaultFormat.radius; - } - } - - if (selectedFormat != null){ - if (selectedFormat.radius != null){ - this.selected.args.radius = selectedFormat.radius; - } - } - - if (overFormat != null){ - if (overFormat.radius != null){ - this.over.args.radius = overFormat.radius; - } - } - - if (draggingFormat != null){ - if (draggingFormat.radius != null){ - this.dragging.args.draggingFormat = draggingFormat.radius; - } - } -}; - - - -OctagonVertexGraphFormatter.prototype.getDefault = ItemGraphFormatter.prototype.getDefault; -OctagonVertexGraphFormatter.prototype.getSelected = ItemGraphFormatter.prototype.getSelected; -OctagonVertexGraphFormatter.prototype.getOver = ItemGraphFormatter.prototype.getOver; -OctagonVertexGraphFormatter.prototype.getDragging = ItemGraphFormatter.prototype.getDragging; -OctagonVertexGraphFormatter.prototype.getId = ItemGraphFormatter.prototype.getId; -OctagonVertexGraphFormatter.prototype.toJSON = ItemGraphFormatter.prototype.toJSON; -OctagonVertexGraphFormatter.prototype.loadFromJSON = ItemGraphFormatter.prototype.loadFromJSON; -OctagonVertexGraphFormatter.prototype._setEvents = ItemGraphFormatter.prototype._setEvents; - -function OctagonVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ - VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); - this.args.type = "OctagonVertexGraphFormatter"; - if (defaultFormat != null){ - if (defaultFormat.radius != null){ - this.defaultFormat.args.radius = defaultFormat.radius; - } - } - - if (selectedFormat != null){ - if (selectedFormat.radius != null){ - this.selected.args.radius = selectedFormat.radius; - } - } - - if (overFormat != null){ - if (overFormat.radius != null){ - this.over.args.radius = overFormat.radius; - } - } - - if (draggingFormat != null){ - if (draggingFormat.radius != null){ - this.dragging.args.draggingFormat = draggingFormat.radius; - } - } -}; - - - -var Colors = new function() -{ - this.hashColor = []; - this.getColorByScoreArrayValue = function (arrayScore) - { - var array = new Array(); - - for (var i = 0; i< arrayScore.length; i++) - { - - var color = this.getColorByScoreValue(arrayScore[i]) - array.push( color); - - } - return array; - }; - - this.getHexStringByScoreArrayValue = function (arrayScore) - { - var arrayColor = this.getColorByScoreArrayValue(arrayScore); - var arrayHex = new Array(); - for (var i = 0; i< arrayColor.length; i++) - { - arrayHex.push( arrayColor[i].HexString()); - } - return arrayHex; - }; - - this.getColorByScoreValue = function (score) - { - - var truncate = score.toString().substr(0,4); - if (this.hashColor[truncate]!=null) - { - return this.hashColor[truncate]; - } - - - if(isNaN(score)) { - return Colors.ColorFromRGB(0,0,0); - } - var value; - - var from, to; - if(score < 0.5) { - from = Colors.ColorFromRGB(0,0,255); - to = Colors.ColorFromRGB(255,255,255); - value = (score * 2); - } else { - from = Colors.ColorFromRGB(255,255,255); - to = Colors.ColorFromRGB(255,0,0); - value = (score * 2) - 1; - } - - var x = value; - var y = 1.0 - value; - var color = Colors.ColorFromRGB(y * from.Red() + x * to.Red(), y * from.Green() + x * to.Green(), y * from.Blue() + x * to.Blue()); - - this.hashColor[truncate] = color; - - return color; - }; - - this.ColorFromHSV = function(hue, sat, val) - { - var color = new Color(); - color.SetHSV(hue,sat,val); - return color; - }; - - this.ColorFromRGB = function(r, g, b) - { - var color = new Color(); - color.SetRGB(r,g,b); - return color; - }; - - this.ColorFromHex = function(hexStr) - { - var color = new Color(); - color.SetHexString(hexStr); - return color; - }; - - function Color() { - //Stored as values between 0 and 1 - var red = 0; - var green = 0; - var blue = 0; - - //Stored as values between 0 and 360 - var hue = 0; - - //Strored as values between 0 and 1 - var saturation = 0; - var value = 0; - - this.SetRGB = function(r, g, b) - { - red = r/255.0; - green = g/255.0; - blue = b/255.0; - calculateHSV(); - }; - - this.Red = function() { return Math.round(red*255); }; - - this.Green = function() { return Math.round(green*255); }; - - this.Blue = function() { return Math.round(blue*255); }; - - this.SetHSV = function(h, s, v) - { - hue = h; - saturation = s; - value = v; - calculateRGB(); - }; - - this.Hue = function() - { return hue; }; - - this.Saturation = function() - { return saturation; }; - - this.Value = function() - { return value; }; - - this.SetHexString = function(hexString) - { - if(hexString == null || typeof(hexString) != "string") - { - this.SetRGB(0,0,0); - return; - } - - if (hexString.substr(0, 1) == '#') - hexString = hexString.substr(1); - - if(hexString.length != 6) - { - this.SetRGB(0,0,0); - return; - } - - var r = parseInt(hexString.substr(0, 2), 16); - var g = parseInt(hexString.substr(2, 2), 16); - var b = parseInt(hexString.substr(4, 2), 16); - if (isNaN(r) || isNaN(g) || isNaN(b)) - { - this.SetRGB(0,0,0); - return; - } - - this.SetRGB(r,g,b); - }; - - this.HexString = function() - { - - var rStr = this.Red().toString(16); - if (rStr.length == 1) - rStr = '0' + rStr; - var gStr = this.Green().toString(16); - if (gStr.length == 1) - gStr = '0' + gStr; - var bStr = this.Blue().toString(16); - if (bStr.length == 1) - bStr = '0' + bStr; - return ('#' + rStr + gStr + bStr).toUpperCase(); - }; - - this.Complement = function() - { - var newHue = (hue >= 180) ? hue - 180 : hue + 180; - var newVal = (value * (saturation - 1) + 1); - var newSat = (value*saturation) / newVal; - var newColor = new Color(); - newColor.SetHSV(newHue, newSat, newVal); - return newColor; - } ; - - function calculateHSV() - { - var max = Math.max(Math.max(red, green), blue); - var min = Math.min(Math.min(red, green), blue); - - value = max; - - saturation = 0; - if(max != 0) - saturation = 1 - min/max; - - hue = 0; - if(min == max) - return; - - var delta = (max - min); - if (red == max) - hue = (green - blue) / delta; - else if (green == max) - hue = 2 + ((blue - red) / delta); - else - hue = 4 + ((red - green) / delta); - hue = hue * 60; - if(hue < 0) - hue += 360; - } - - function calculateRGB() - { - red = value; - green = value; - blue = value; - - if(value == 0 || saturation == 0) - return; - - var tHue = (hue / 60); - var i = Math.floor(tHue); - var f = tHue - i; - var p = value * (1 - saturation); - var q = value * (1 - saturation * f); - var t = value * (1 - saturation * (1 - f)); - switch(i) - { - case 0: - red = value; green = t; blue = p; - break; - case 1: - red = q; green = value; blue = p; - break; - case 2: - red = p; green = value; blue = t; - break; - case 3: - red = p; green = q; blue = value; - break; - case 4: - red = t; green = p; blue = value; - break; - default: - red = value; green = p; blue = q; - break; - } - } - } -} -(); -/* - * Clase gestiona la insercción, eliminación de los elementos en el DOM - * - * Vital hacerla SIEMPRE compatible hacia atrás - * - * Last update: 28-10-2010 - * - */ - - -var DOM = {}; - -DOM.createNewElement = function(type, nodeParent, attributes) -{ - - var node = document.createElement(type); - for (var i=0; i0) - { - parent.removeChild(parent.childNodes[0]); - - } -}; - -DOM.select = function(targetID) -{ - return document.getElementById(targetID); -// return $("#"+targetID); -}; -var Geometry = -{ - - /** From tow points obtains the angles formed with the cartesian side **/ - getAngleBetweenTwoPoints : function(x1, y1, x2, y2){ - //var m = (y1 - y2)/ (x1 - x2); - return Math.atan2(y2-y1, x2-x1); - }, - - getAdjacentSideOfRectangleRight : function(angle, hypotenuse){ - return Math.abs(Math.cos(angle)*hypotenuse); - }, - - getOppositeSideOfRectangleRight : function(angle, hypotenuse){ - return Math.abs(Math.sin(angle)*hypotenuse); - }, - - toDegree: function(radian){ - return radian*180/Math.PI; - - } - - -}; - -var SVG = -{ - svgns : 'http://www.w3.org/2000/svg', - xlinkns : "http://www.w3.org/1999/xlink", - - createSVGCanvas: function(parentNode, attributes) - { - - attributes.push( ['xmlns', SVG.svgns], ['xmlns:xlink', 'http://www.w3.org/1999/xlink']); - var svg = document.createElementNS("http://www.w3.org/2000/svg", "svg"); - this._setProperties(svg, attributes); - parentNode.appendChild( svg); - return svg; - - }, - - createRectangle : function (x, y, width, height, attributes){ - var rect = document.createElementNS(this.svgns, "rect"); - rect.setAttribute("x",x); - rect.setAttribute("y",y); - rect.setAttribute("width",width); - rect.setAttribute("height",height); - SVG._setProperties(rect, attributes); - return rect; - }, - - drawImage64 : function (x, y, width, height, base64, svgNode, attributes) { - var node = SVG.createImage64(x, y, width, height, base64, attributes); - svgNode.appendChild(node); - return node; - }, - - createImage64 : function (x, y, width, height, base64, attributes) { - var img = document.createElementNS(this.svgns, "image"); - img.setAttribute("x",x); - img.setAttribute("y",y); - img.setAttribute("width",width); - img.setAttribute("height",height); - img.setAttribute("xlink:href",base64); - SVG._setProperties(img, attributes); - return img; - }, - - createLine: function (x1, y1, x2, y2, attributes){ - var line = document.createElementNS(this.svgns,"line"); - line.setAttribute("x1",x1); - line.setAttribute("y1",y1); - line.setAttribute("x2", x2); - line.setAttribute("y2", y2); - SVG._setProperties(line, attributes); - return line; - }, - - createClip: function (id, nodeToClip, attributes){ - var clip = document.createElementNS(this.svgns,"clipPath"); - clip.setAttribute("id",id); - clip.appendChild(nodeToClip); - return clip; - }, - - drawClip : function (id, nodeToClip, svgNode) { - var node = SVG.createClip(id, nodeToClip); - svgNode.appendChild(node); - return node; - }, - - drawRectangle : function (cx, cy, width, height, svgNode, attributes) { - try{ - var node = SVG.createRectangle(cx, cy, width, height, attributes); - svgNode.appendChild(node); - } - catch(e){ - - console.log("-------------------- "); - console.log("Error on drawRectangle " + e); - console.log(attributes); - console.log("-------------------- "); - } - return node; - }, - - createEllipse : function (x, y, rx, ry, attributes){ - var rect = document.createElementNS(this.svgns, "ellipse"); - rect.setAttribute("cx",x); - rect.setAttribute("cy",y); - rect.setAttribute("rx",rx); - rect.setAttribute("ry",ry); - SVG._setProperties(rect, attributes); - return rect; - }, - - drawEllipse : function (cx, cy, rx, ry, svgNode, attributes) { - var node = SVG.createEllipse(cx, cy, rx, ry, attributes); - svgNode.appendChild(node); - return node; - }, - - drawImage : function (x, y, canvasSVG, attributes) { - var image = document.createElementNS(this.svgns, "image"); - image.setAttribute("x",x); - image.setAttribute("y",y); - canvasSVG.appendChild(image); - SVG._setProperties(image, attributes); - }, - - drawLine : function (x1, y1, x2, y2, nodeSVG, attributes) { - try{ - var line = SVG.createLine(x1, y1, x2, y2, attributes); - nodeSVG.appendChild(line); - }catch(e){ - } - return line; - }, - - - drawPath: function (d, nodeSVG, attributes) { - var path = SVG.createPath(d, attributes); - nodeSVG.appendChild(path); - return path; - }, - - createPoligon : function (points, attributes){ - var poligon = document.createElementNS(this.svgns, "polygon"); - poligon.setAttribute("points",points); - SVG._setProperties(poligon, attributes); - return poligon; - }, - - drawPoligon : function (points, canvasSVG, attributes){ - var poligon = SVG.createPoligon(points, attributes); - canvasSVG.appendChild(poligon); - return poligon; - }, - // - - createPath : function (d, attributes){ - var path = document.createElementNS(this.svgns, "path"); - path.setAttribute("d",d); - SVG._setProperties(path, attributes); - return path; - }, - - drawCircle : function (x, y, radio, canvasSVG, attributes) { - - var newText = document.createElementNS(this.svgns,"circle"); - newText.setAttribute("cx",x); - newText.setAttribute("cy",y); - newText.setAttribute("r",radio); - - canvasSVG.appendChild(newText); - attributes["cursor"] = "pointer"; - this._setProperties(newText, attributes); - return newText; - }, - - - _setProperties: function(node, attributes) - { - if (attributes instanceof Array){ - for (var i=0; i< attributes.length; i++) - { - node.setAttribute(attributes[i][0], attributes[i][1]); - } - } - else{ - for ( var key in attributes){ - node.setAttribute(key, attributes[key]); - } - } - }, - -/* drawPath: function(pointsArray, canvasSVG, attributes){ - var path = document.createElementNS(this.svgns,"polyline"); - path.setAttribute ('id', id); - - var d= pointsArray[0].x+ " "+ pointsArray[0].y; - for (var i=1; i< pointsArray.length; i++) - { - d=d+" "+pointsArray[i].x+" "+pointsArray[i].y; - } - path.setAttribute ('points', d); - canvasSVG.appendChild(path); - },*/ - - createText : function (x, y, text, attributes) { - var node = document.createElementNS(this.svgns,"text"); - node.setAttributeNS(null , "x",x); - node.setAttributeNS(null, "y",y); - - var textNode = document.createTextNode(text); - node.appendChild(textNode); - - this._setProperties(node, attributes); - return node; - }, - - drawText : function (x, y, text, canvasSVG, attributes) { - var text = SVG.createText(x, y, text, attributes); - canvasSVG.appendChild(text); - return text; - }, - - - - drawGroup: function(svgNode, attributes) - { - var group = SVG.createGroup(attributes); - svgNode.appendChild(group); - return group; - }, - - createGroup: function(attributes){ - var group = document.createElementNS(this.svgns,"g"); - this._setProperties(group, attributes); - return group; - } - -}; - - - -var CanvasToSVG = { - - convert: function(sourceCanvas, targetSVG, x, y, id, attributes) { - - var img = this._convert(sourceCanvas, targetSVG, x, y, id); - - for (var i=0; i< attributes.length; i++) - { - img.setAttribute(attributes[i][0], attributes[i][1]); - } - }, - - _convert: function(sourceCanvas, targetSVG, x, y, id) { - var svgNS = "http://www.w3.org/2000/svg"; - var xlinkNS = "http://www.w3.org/1999/xlink"; - // get base64 encoded png from Canvas - var image = sourceCanvas.toDataURL(); - - // must be careful with the namespaces - var svgimg = document.createElementNS(svgNS, "image"); - - svgimg.setAttribute('id', id); - - //svgimg.setAttribute('class', class); - //svgimg.setAttribute('xlink:href', image); - svgimg.setAttributeNS(xlinkNS, 'xlink:href', image); - - - - - svgimg.setAttribute('x', x ? x : 0); - svgimg.setAttribute('y', y ? y : 0); - svgimg.setAttribute('width', sourceCanvas.width); - svgimg.setAttribute('height', sourceCanvas.height); - //svgimg.setAttribute('cursor', 'pointer'); - svgimg.imageData = image; - - targetSVG.appendChild(svgimg); - return svgimg; - }, - - importSVG: function(sourceSVG, targetCanvas) { - svg_xml = sourceSVG;//(new XMLSerializer()).serializeToString(sourceSVG); - var ctx = targetCanvas.getContext('2d'); - - var img = new Image(); - img.src = "data:image/svg+xml;base64," + btoa(svg_xml); -// img.onload = function() { - ctx.drawImage(img, 0, 0); -// }; - } - -}; -/* -Graph.prototype.importSVG = function(sourceSVG, targetCanvas) { - sourceSVG = this._svg; - targetCanvas = document.createElementNS('canvas'); - // https://developer.mozilla.org/en/XMLSerializer - svg_xml = (new XMLSerializer()).serializeToString(sourceSVG); - var ctx = targetCanvas.getContext('2d'); - // this is just a JavaScript (HTML) image - var img = new Image(); - // http://en.wikipedia.org/wiki/SVG#Native_support - // https://developer.mozilla.org/en/DOM/window.btoa - img.src = "data:image/svg+xml;base64," + btoa(svg_xml); - img.onload = function() { - // after this, Canvas’ origin-clean is DIRTY - ctx.drawImage(img, 0, 0); - } -}; -*/ - -/* - -Normalizacion de datos para dibujar colores -Issues: - No sé como debería llamarse esta libreria - No sé si ya existe una funciçon en javascript que lo haga - - -*/ - - -var Normalizer = new function() -{ - this.normalizeArray = function (arrayData) - { - - return this.standardizeArray(this.normal(arrayData)); - -// var result = this._getMaxAndMin(arrayData); -// var min =result[0]; -// var max = result[1]; -// -// -// //los hacemos todos positivos -// for (var i = 0; i< arrayData.length; i++) -// { -// arrayData[i]= Math.abs(min) + parseFloat(arrayData[i]); -// } -// -// var result = this._getMaxAndMin(arrayData); -// var min =result[0]; -// var max = result[1]; -// -// -// var resultArray = new Array(); -// for (var i = 0; i< arrayData.length; i++) -// { -// resultArray.push(arrayData[i]*1/max); -// } -// return resultArray; - }; - - this.normal = function(arrayData){ - var mean = this._getMean(arrayData); - var deviation = this._getStdDeviation(arrayData); - var result = this._getMaxAndMin(arrayData); - var min = result[0]; - var max = result[1]; - - var resultArray = new Array(); - for (var i = 0; i< arrayData.length; i++) { - if (deviation!=0){ - resultArray.push((arrayData[i]-mean)/deviation); - }else{ - resultArray.push(arrayData[i]); - } - } - return resultArray; - }; - - this.standardizeArray = function(arrayData) - { - var result = this._getMaxAndMin(arrayData); - var min = result[0]; - var max = result[1]; - - var offset = ( min <= 0 ) ? Math.abs(min) : (-1 * min); - var resultArray = new Array(); - for (var i = 0; i< arrayData.length; i++) { - if(max + offset!=0){ - resultArray.push((arrayData[i] + offset) / (max + offset)); - }else{ - resultArray.push(arrayData[i]+offset); - } - } - return resultArray; - }; - - - this._getMean = function(arrayData) { - var sum = 0; - for (var i = 0; i< arrayData.length; i++) { - sum = sum + parseFloat(arrayData[i]); - } - return sum/arrayData.length; - }; - - this._getStdDeviation = function(arrayData) { - var mean = this._getMean(arrayData); - var acum = 0.0; - for(var i=0; i max) max = parseFloat(arrayData[i]); - } - - return [min, max]; - }; -}; -function GraphCanvas(componentID, targetNode, args) { - this.args = {}; - /** target */ - this.targetID = targetNode.id; - - /** id manage */ - this.id = componentID; - this.args.idGraph = this.id + "main"; - this.args.idBackgroundNode = this.id + "background"; - - this.args.idEdgesGraph = this.id + "edges"; - this.args.idNodesGraph = this.id + "vertices"; - this.args.idLabelGraph = this.id + "label"; - this.args.idBackground = this.id + "background"; - - /** Objects Graph **/ - this.dataset = null; - this.formatter = null; - this.layout = null; - - /** Drawing **/ - this.circleDefaultRadius = 2; - this.squareDefaultSide = this.circleDefaultRadius * 1.5; - - /** Directed Arrow **/ - this.arrowDefaultSize = this.circleDefaultRadius; - - /** Groups **/ - this.GraphGroup = null; - this.GraphNodeGroup = null; - this.GraphLabelGroup = null; - this.GraphBackground = null; - - /** SETTINGS FLAGS **/ - this.args.draggingCanvasEnabled = false; //Flag to set if the canvas can be dragged - this.args.multipleSelectionEnabled = false; - this.args.interactive = false; - this.args.labeled = false; - this.args.linkEnabled = false; - - /** If numberEdge > maxNumberEdgesMoving then only it will move edges when mouse up **/ - this.args.maxNumberEdgesMoving = 3; - this.args.maxNumberEdgesFiringEvents = 50; - - /** Linking edges **/ - this.args.linking = false; - this.linkStartX = 0; - this.linkStartY = 0; - this.linkSVGNode = null; - this.linkNodeSource = null; - this.linkNodeTarget = null; - - /** Dragging Control **/ - this.draggingElement = null; - this.dragging = false; - this.nMouseOffsetX = 0; - this.nMouseOffsetY = 0; - this.dragStartX = 0; - this.dragStartY = 0; - this.desplazamientoX = 0; - this.desplazamientoY = 0; - - /** Selection Control **/ - this.selecting = false; - this.selectorX = null; - this.selectorY = null; - this.selectorSVGNode = null; - - /** Node status **/ - this.args.isVertexSelected = {}; - this.args.selectedVertices = []; - - /** Edges status **/ - this.args.isEdgeSelected = {}; - //this.args.selectedEdges = []; - - if (args != null) { - if (args.multipleSelectionEnabled != null) { - this.args.multipleSelectionEnabled = args.multipleSelectionEnabled; - this.args.draggingCanvasEnabled = !(this.args.multipleSelectionEnabled); - } - if (args.draggingCanvasEnabled != null) { - this.args.draggingCanvasEnabled = args.draggingCanvasEnabled; - this.args.multipleSelectionEnabled = !(this.args.draggingCanvasEnabled); - } - if (args.interactive != null) { - this.args.interactive = args.interactive; - } - if (args.labeled != null) { - this.args.labeled = args.labeled; - } - - } - - /** Hashmap with the svg node labels **/ - this.svgLabels = {}; - - /** EVENTS **/ - this.onVertexOut = new Event(this); - this.onVertexOver = new Event(this); - this.onVertexSelect = new Event(this); - this.onEdgeSelect = new Event(this); - this.onCanvasClicked = new Event(this); - this.onVertexUp = new Event(this); -} - -GraphCanvas.prototype.showLabels = function(value) { - this.args.labeled = value; - this.removeLabels(); - if (value) { - this.renderLabels(); - } -}; - -GraphCanvas.prototype.getSelectedVertices = function() { - return this.args.selectedVertices; -}; - -GraphCanvas.prototype.getSelectedEdges = function() { - var selected = []; - for ( var selectedEdge in this.args.isEdgeSelected) { - selected.push(selectedEdge); - } - return selected; -}; - -GraphCanvas.prototype.createSVGDom = function(targetID, id, width, height, backgroundColor) { - var container = document.getElementById(targetID); - this._svg = SVG.createSVGCanvas(container, [ - [ "style", "background-color:" + backgroundColor + ";" ], [ "id", id ], [ "dragx", 0 ], [ "dragy", 0 ], - [ "height", this.getFormatter().getHeight() ], [ "width", this.getFormatter().getWidth() ] ]); - return this._svg; -}; - -/** MULTIPLE SELECTION **/ -GraphCanvas.prototype.isMultipleSelectionEnabled = function() { - return this.args.multipleSelectionEnabled; -}; - -GraphCanvas.prototype.setMultipleSelection = function(value) { - this.args.multipleSelectionEnabled = value; - this.args.draggingCanvasEnabled = (!value); -}; - -GraphCanvas.prototype.setSelecting = function(value) { - this.selecting = value; -}; - -/** linking **/ -GraphCanvas.prototype.setLinking = function(value) { - this.args.linkEnabled = value; - this.selecting = !value; - this.dragging = !value; -}; - -/** CANVAS MOVING **/ -GraphCanvas.prototype.setDraggingCanvas = function(value) { - this.args.draggingCanvasEnabled = value; - this.args.multipleSelectionEnabled = !value; -}; - -GraphCanvas.prototype.isDraggingCanvasEnabled = function() { - return this.args.draggingCanvasEnabled; -}; -/** ZOOM **/ -GraphCanvas.prototype.getScale = function() { - return this.getFormatter().getZoomScale(); -}; - -GraphCanvas.prototype.setScale = function(scale) { - var graphNode = document.getElementById(this.args.idGraph); - graphNode.setAttribute("transform", graphNode.getAttribute("transform").replace("scale(" + this.getScale() + ")", "scale(" + scale + ")")); - this.getFormatter().setZoomScale(scale); -}; - -GraphCanvas.prototype.zoomIn = function() { - this.setScale(this.getScale() + this.getFormatter().getZoomScaleStepFactor()); -}; - -GraphCanvas.prototype.zoomOut = function() { - this.setScale(this.getScale() - this.getFormatter().getZoomScaleStepFactor()); - -}; - -/** SVG COORDENATES **/ -GraphCanvas.prototype.getSVGCoordenates = function(evt) { - var p = this._svg.createSVGPoint(); - p.x = evt.clientX; - p.y = evt.clientY; - - var m = this._svg.getScreenCTM(document.documentElement); - p = p.matrixTransform(m.inverse()); - return p; -}; - -/** SVG EVENTS **/ -GraphCanvas.prototype.mouseClick = function(event) { - if (event.button == 0) { - if (!this.args.interactive) { - return; - } - - if (this.isVertex(event.target)) { - this.clickNode(this.getVertexIdFromSVGId(event.target.id)); - } - /** Como el evento mouseClick viene despues del mouse up es aqui donde manejo el tema de deseccionar los elementos que estoy dragging **/ - if (this.dragging) { - this.dragging = false; - } - } -}; - -GraphCanvas.prototype.mouseMove = function(evt) { - if (this.selecting) { - this.clearLabels(); - - var width = (this.getSVGCoordenates(evt).x - this.selectorX); - var height = (this.getSVGCoordenates(evt).y - this.selectorY); - if ((width > 0) && (height > 0)) { - this.displaySelection(this.selectorX, this.selectorY, width, height); - } - if ((width > 0) && (height < 0)) { - this.displaySelection(this.selectorX, this.getSVGCoordenates(evt).y, width, Math.abs(height)); - } - if ((width < 0) && (height < 0)) { - this.displaySelection(this.getSVGCoordenates(evt).x, this.getSVGCoordenates(evt).y, Math.abs(width), Math.abs(height)); - } - if ((width < 0) && (height > 0)) { - this.displaySelection(this.selectorX + width, this.selectorY, Math.abs(width), Math.abs(height)); - } - - var x1 = (parseFloat(this.selectorSVGNode.getAttribute("x")) - DOM.select(this.id).getAttribute("dragx")) / this.getFormatter().getWidth(); - var y1 = (parseFloat(this.selectorSVGNode.getAttribute("y")) - DOM.select(this.id).getAttribute("dragy")) / this.getFormatter().getHeight(); - var x2 = (x1 + parseFloat(this.selectorSVGNode.getAttribute("width") / this.getFormatter().getWidth())); - var y2 = (y1 + parseFloat(this.selectorSVGNode.getAttribute("height") / this.getFormatter().getHeight())); - - this.deselectNodes(this.getLayout()); - var verticesSelected = this.getLayout().getVerticesByArea(x1 / this.getFormatter().getZoomScale(), y1 / this.getFormatter().getZoomScale(), - x2 / this.getFormatter().getZoomScale(), y2 / this.getFormatter().getZoomScale()); - for ( var i = 0; i < verticesSelected.length; i++) { - this.selectNode(verticesSelected[i].getId()); - this.renderLabel(verticesSelected[i].getId()); - } - - } - var p = null; - if (this.args.linking) { - p = this.getSVGCoordenates(evt); - if (this.linkSVGNode != null) { - this.linkSVGNode.setAttribute("x2", p.x - 2); - this.linkSVGNode.setAttribute("y2", p.y - 2); - } - } - - if (this.dragging) { - p = this.getSVGCoordenates(evt); - p.x -= this.nMouseOffsetX; - p.y -= this.nMouseOffsetY; - this.desplazamientoX = (this.getSVGCoordenates(evt).x - this.dragStartX);// + parseFloat(DOM.select(this.id).getAttribute("dragx")); - this.desplazamientoY = (this.getSVGCoordenates(evt).y - this.dragStartY);// + parseFloat(DOM.select(this.id).getAttribute("dragy")); - - if (this.draggingElement != null) { - /** Click sobre el recct del banground que provoca que mueva todo el canvas **/ - if (this.isNodeCanvas(this.draggingElement)) { - - p = this.getSVGCoordenates(evt); - p.x = this.desplazamientoX; - p.y = this.desplazamientoY; - - this.draggingElement.setAttribute("dragx", p.x); - this.draggingElement.setAttribute("dragy", p.y); - this.draggingElement = document.getElementById(this.args.idGraph); - this.draggingElement.setAttribute("transform", "translate(" + p.x + "," + p.y + "), scale(" + this.getScale() + ")"); - - DOM.select(this.id).setAttribute("dragx", p.x); - DOM.select(this.id).setAttribute("dragy", p.y); - - if (this.NodeSVGbackgroundImage != null) { - this.NodeSVGbackgroundImage.setAttribute("dragx", p.x); - this.NodeSVGbackgroundImage.setAttribute("dragy", p.y); - } - } else { - if (this.isVertex(this.draggingElement)) { - this.selectNode(this.getVertexIdFromSVGId(this.draggingElement.id)); - this.desplazamientoX = this.desplazamientoX / this.getFormatter().getZoomScale(); - this.desplazamientoY = this.desplazamientoY / this.getFormatter().getZoomScale(); - this.moveSelectedNodes(this.desplazamientoX, this.desplazamientoY); - - this.dragStartX = this.getSVGCoordenates(evt).x; - this.dragStartY = this.getSVGCoordenates(evt).y; - } else { - if (this.isNodeBackground(this.draggingElement)) { - - this.draggingElement.setAttribute("dragx", p.x); - this.draggingElement.setAttribute("dragy", p.y); - this.draggingElement = document.getElementById(this.args.idGraph); - this.draggingElement.setAttribute("transform", "translate(" + p.x + "," + p.y + "), scale(" + this.getScale() + ")"); - } else { - this.draggingElement.setAttribute("transform", "translate(" + p.x + "," + p.y + ")"); - } - } - } - } - } -}; - -GraphCanvas.prototype.moveSelectedNodes = function(offsetX, offsetY) { - for ( var i = 0; i < this.getSelectedVertices().length; i++) { - - var nodeId = this.getSelectedVertices()[i]; - var svgNodeId = this.getSVGNodeId(nodeId); - - var x = parseFloat(DOM.select(svgNodeId).getAttribute("dragx")) + parseFloat(offsetX);// - parseFloat(DOM.select(this.id).getAttribute("dragx")); - var y = parseFloat(DOM.select(svgNodeId).getAttribute("dragy")) + parseFloat(offsetY);// + parseFloat(DOM.select(this.id).getAttribute("dragy")); - - this._movingNode(DOM.select(svgNodeId), x, y); - } -}; - -GraphCanvas.prototype.mouseDown = function(evt) { - if (event.button == 0) { - - /** if !no interactive mouse events do anything **/ - if (!this.args.interactive) { - return; - } - - var p = this.getSVGCoordenates(evt); - - /** When click on canvas or background deselect all **/ - if (this.isNodeCanvas(evt.target) || this.isNodeBackground(evt.target)) { - this.deselectNodes(); - this.deselectEdges(); - this.onCanvasClicked.notify(); - } - - /** if I am linking vertices **/ - if (this.args.linkEnabled) { - - if (!this.args.linking) { - this.args.linking = true; - if (this.isVertex(evt.target)) { - this.linkStartX = p.x; - this.linkStartY = p.y; - this.linkSVGNode = SVG.drawLine(p.x, p.y, p.x, p.y, this._svg, { - "stroke" : "#FF0000" - }); - this.linkNodeSource = this.getVertexIdFromSVGId(evt.target.id); - } - } else { - this.linkNodeTarget = this.getVertexIdFromSVGId(evt.target.id); - this.args.linking = false; - this.args.linkEnabled = false; - if (this.isVertex(evt.target)) { - this.getDataset().addEdge(this.linkNodeSource + "_" + this.linkNodeTarget, this.linkNodeSource, this.linkNodeTarget, {}); - } - this.linkSVGNode.parentNode.removeChild(this.linkSVGNode); - } - return; - } - - /** Id is a vertex or the canvas **/ - if (this.isVertex(evt.target) || this.isNodeCanvas(evt.target) || this.isNodeBackground(evt.target)) { - this._startDragging(evt); - } - /** if i is edge **/ - if (this.isEdge(evt.target)) { - this.selectEdge(this.getEdgeIdFromSVGId(evt.target.getAttribute("id"))); - } - - if (this.args.multipleSelectionEnabled) { - if (!this.dragging) { - this.setSelecting(true); - this.selectorX = p.x; - this.selectorY = p.y; - this.displaySelection(p.x, p.y, 1, 1); - } - } - - } - if (event.button == 1) { - this.setLinking(false); - this.setMultipleSelection(false); - this.selecting = false; - - /** Id is a vertex or the canvas **/ - if (this.isVertex(evt.target) || this.isNodeCanvas(evt.target) || this.isNodeBackground(evt.target)) { - this._startDragging(evt); - } - } -}; - -GraphCanvas.prototype.mouseUp = function(event) { - if (!this.args.interactive) { - return; - } - - if (this.dragging) { - this._stopDragging(event); - if (this.isVertex(event.target)) { - var vertexId = this.getVertexIdFromSVGId(event.target.id); - if (this.getDataset().getVertexById(vertexId).getEdges().length >= this.args.maxNumberEdgesMoving) { - this.moveEdge(vertexId); - } - } - } - - if (this.selecting) { - this.setSelecting(false); - - var x1 = (parseFloat(this.selectorSVGNode.getAttribute("x")) - DOM.select(this.id).getAttribute("dragx")) / this.getFormatter().getWidth(); - var y1 = (parseFloat(this.selectorSVGNode.getAttribute("y")) - DOM.select(this.id).getAttribute("dragy")) / this.getFormatter().getHeight(); - var x2 = (x1 + parseFloat(this.selectorSVGNode.getAttribute("width") / this.formatter.getWidth())); - var y2 = (y1 + parseFloat(this.selectorSVGNode.getAttribute("height") / this.formatter.getHeight())); - - var verticesSelected = this.getLayout().getVerticesByArea(x1 / this.getFormatter().getZoomScale, y1 / this.getFormatter().getZoomScale, - x2 / this.getFormatter().getZoomScale, y2 / this.getFormatter().getZoomScale); - - for ( var i = 0; i < verticesSelected.length; i++) { - this.selectNode(verticesSelected[i].getId()); - } - - if (this.selectorSVGNode != null) { - this._svg.removeChild(this.selectorSVGNode); - } - - if (this.args.labeled) { - this.clearLabels(); - this.renderLabels(); - } - - this.selectorSVGNode = null; - // this.renderLabels(); - } -}; - -/** SELECTION **/ -GraphCanvas.prototype.displaySelection = function(x, y, width, height) { - if (this.selectorSVGNode != null) { - this.selectorSVGNode.setAttribute("x", x); - this.selectorSVGNode.setAttribute("y", y); - this.selectorSVGNode.setAttribute("width", width); - this.selectorSVGNode.setAttribute("height", height); - } else { - this.selectorSVGNode = SVG.drawRectangle(x, y, width, height, this._svg, { - "fill" : "red", - "stroke" : "black", - "opacity" : "0.2", - "stroke-opacity" : "1" - }); - } -}; - -/** DRAGGING **/ -GraphCanvas.prototype._startDragging = function(evt) { - if (!this.isDraggingCanvasEnabled()) { - if (this.isNodeCanvas(evt.target)) { - this.draggingElement = null; - } - } - - if (this.isVertex(evt.target) || (this.isNodeBackground(evt.target) && (this.isDraggingCanvasEnabled()))|| (this.isNodeCanvas(evt.target) && (this.isDraggingCanvasEnabled()))) { - this.clearLabels(); - this.draggingElement = evt.target; - this.dragging = true; - var p = this.getSVGCoordenates(evt); - - this.nMouseOffsetX = p.x - parseInt(evt.target.getAttribute("dragx")); - this.nMouseOffsetY = p.y - parseInt(evt.target.getAttribute("dragy")); - - if (this.isVertex(evt.target)) { - this.dragStartX = parseInt(this.draggingElement.getAttribute("dragx")) * this.getFormatter().getZoomScale() - + parseFloat(DOM.select(this.id).getAttribute("dragx")); - this.dragStartY = parseInt(this.draggingElement.getAttribute("dragy")) * this.getFormatter().getZoomScale() - + parseFloat(DOM.select(this.id).getAttribute("dragy")); - } else { - this.dragStartX = p.x - parseInt(this.draggingElement.getAttribute("dragx"));// + parseFloat(DOM.select(this.id).getAttribute("dragx")); - this.dragStartY = p.y - parseInt(this.draggingElement.getAttribute("dragy"));// + parseFloat(DOM.select(this.id).getAttribute("dragy")); - } - } -}; - -GraphCanvas.prototype._stopDragging = function(event) { - this.nMouseOffsetX = 0; - this.nMouseOffsetX = 0; - /** despues del evento up viene el evento click entonces acabo el dragging en el mouseclick **/ - this.dragging = false; - this.draggingElement = null; - this.renderLabels(); - - this.setLinking(false); - this.setMultipleSelection(true); - this.selecting = false; - -}; - -/** Move the edges of the vertex with the vertexId indicado **/ -GraphCanvas.prototype.moveEdge = function(vertexId) { - var x = this.getLayout().getNodeById(vertexId).x * this.getFormatter().getWidth(); - var y = this.getLayout().getNodeById(vertexId).y * this.getFormatter().getHeight(); - - /** Moving edges out **/ - for ( var i = 0; i < this.getDataset().getVertexById(vertexId).getEdgesOut().length; i++) { - var edgeId = this.getDataset().getVertexById(vertexId).getEdgesOut()[i].getId(); - var svgEdgeId = this.getSVGEdgeId(edgeId); - var edgeFormatter = this.getFormatter().getEdgeById(edgeId); - if (edgeFormatter instanceof LineEdgeGraphFormatter) { - DOM.select(svgEdgeId + "_shadow").setAttribute("x2", x); - DOM.select(svgEdgeId + "_shadow").setAttribute("y2", y); - DOM.select(svgEdgeId).setAttribute("x2", x); - DOM.select(svgEdgeId).setAttribute("y2", y); - } - - if ((edgeFormatter instanceof DirectedLineEdgeGraphFormatter) || (edgeFormatter instanceof OdirectedLineEdgeGraphFormatter) - || (edgeFormatter instanceof OdotDirectedLineEdgeGraphFormatter) || (edgeFormatter instanceof DotDirectedLineEdgeGraphFormatter) - || (edgeFormatter instanceof CutDirectedLineEdgeGraphFormatter)) { - this.removeEdge(edgeId); - this.renderEdge(edgeId); - } - } - - /** Moving edges in **/ - for ( var i = 0; i < this.getDataset().getVertexById(vertexId).getEdgesIn().length; i++) { - var edgeId = this.getDataset().getVertexById(vertexId).getEdgesIn()[i].getId(); - var svgEdgeId = this.getSVGEdgeId(edgeId); - var edgeFormatter = this.getFormatter().getEdgeById(edgeId); - if (edgeFormatter instanceof LineEdgeGraphFormatter) { - DOM.select(svgEdgeId).setAttribute("x1", x); - DOM.select(svgEdgeId).setAttribute("y1", y); - DOM.select(svgEdgeId + "_shadow").setAttribute("x1", x); - DOM.select(svgEdgeId + "_shadow").setAttribute("y1", y); - } - - if ((edgeFormatter instanceof DirectedLineEdgeGraphFormatter) || (edgeFormatter instanceof OdirectedLineEdgeGraphFormatter) - || (edgeFormatter instanceof OdotDirectedLineEdgeGraphFormatter) || (edgeFormatter instanceof DotDirectedLineEdgeGraphFormatter) - || (edgeFormatter instanceof CutDirectedLineEdgeGraphFormatter)) { - this.removeEdge(edgeId); - this.renderEdge(edgeId); - } - - if (edgeFormatter instanceof BezierEdgeGraphFormatter) { - var radius = this.getFormatter().getVertexById(vertexId).getDefault().getSize() * this.getFormatter().getNodesMaxSize(); - var d = this.calculateCoordenatesBezier(radius, x, y); - DOM.select(svgEdgeId).setAttribute("d", d); - } - } -}; - -GraphCanvas.prototype.moveNode = function(vertexId) { - var x = this.getLayout().getNodeById(vertexId).x * this.getFormatter().getWidth(); - var y = this.getLayout().getNodeById(vertexId).y * this.getFormatter().getHeight(); - var svgNodeElement = DOM.select(this.getSVGNodeId(vertexId)); - - svgNodeElement.setAttribute("dragx", x); - svgNodeElement.setAttribute("dragy", y); - svgNodeElement.setAttribute("transform", "translate(" + x + "," + y + ")"); - - if (this.getDataset().getVertexById(vertexId).getEdges().length < this.args.maxNumberEdgesMoving) { - this.moveEdge(vertexId); - } -}; - -GraphCanvas.prototype._movingNode = function(svgNodeElement, x, y) { - var vertexId = this.getVertexIdFromSVGId(svgNodeElement.getAttribute("id")); - this.getLayout().getNodeById(vertexId).setCoordinates(x / this.getFormatter().getWidth(), y / this.getFormatter().getHeight()); - this.desplazamientoX = 0; - this.desplazamientoY = 0; - this.removeLabel(vertexId); - this.renderLabel(vertexId); -}; - -/** INIT **/ -GraphCanvas.prototype.init = function() { - - this._svg = this.createSVGDom(this.targetID, this.id, this.getFormatter().getWidth(), this.getFormatter().getHeight(), this.getFormatter() - .getBackgroundColor()); - this.GraphGroup = SVG.drawGroup(this._svg, [ [ "id", this.args.idGraph ], [ "transform", "translate(0,0), scale(1)" ] ]); - this.GraphBackground = SVG.drawGroup(this.GraphGroup, [ [ "id", this.args.idBackground ] ]); - this.GraphEdgeGroup = SVG.drawGroup(this.GraphGroup, [ [ "id", this.args.idEdgesGraph ] ]); - this.GraphNodeGroup = SVG.drawGroup(this.GraphGroup, [ [ "id", this.args.idNodesGraph ] ]); - this.GraphLabelGroup = SVG.drawGroup(this.GraphGroup, [ [ "id", this.args.idLabelGraph ] ]); - - if ((this.getFormatter().getBackgroundImage() != null) && (this.getFormatter().getBackgroundImage() != "")) { - this.setBackgroundImage(this.getFormatter().getBackgroundImage()); - } - /** SVG Events listener */ - var _this = this; - this._svg.addEventListener("click", function(event) { - _this.mouseClick(event); - }, false); - this._svg.addEventListener("mousemove", function(event) { - _this.mouseMove(event, _this); - }, false); - this._svg.addEventListener("mousedown", function(event) { - _this.mouseDown(event, _this); - }, false); - this._svg.addEventListener("mouseup", function(event) { - _this.mouseUp(event, _this); - }, false); -}; - -/* - GraphCanvas.prototype.backgroungToSVG = function(){ - var _this = this; - var canvas = document.createElement('canvas'); - canvas.setAttribute("id", "canvas"); - canvas.width = this.formatter.getWidth(); - canvas.height = this.formatter.getHeight(); - - this._svg.parentNode.parentNode.appendChild(canvas); - var ctx = document.getElementById('canvas').getContext('2d'); - var img = new Image(); - - img.src = this.formatter.getBackgroundImage(); - ctx.drawImage(img,0,0 ,_this.formatter.getWidth(), _this.formatter.getHeight()); - - - img.onload = function() { - canvas.parentNode.removeChild(canvas); - } - - this.NodeSVGbackgroundImage.setAttribute("xlink:href", document.getElementById("canvas").toDataURL()); - this.NodeSVGbackgroundImage.removeAttribute("href"); - - // - - };*/ - -GraphCanvas.prototype.setBackgroundImage = function() { - if (this.NodeSVGbackgroundImage != null) { - this.NodeSVGbackgroundImage.parentNode.removeChild(this.NodeSVGbackgroundImage); - } - $('#' + this.targetID).svg(); - $('#' + this.targetID).svg("get"); - - $('#' + this.targetID).svg("get")._svg = document.getElementById(this.id); - - var svg = $('#' + this.targetID).svg("get"); - this.NodeSVGbackgroundImage = svg.image(0, 0, this.getFormatter().getWidth(), this.getFormatter().getHeight(), this.getFormatter() - .getBackgroundImage()); - this.NodeSVGbackgroundImage.setAttribute("id", this.args.idBackgroundNode); - - this.NodeSVGbackgroundImage.setAttribute("x", 0); - this.NodeSVGbackgroundImage.setAttribute("y", 0); - - this.NodeSVGbackgroundImage.setAttribute("dragx", 0); - this.NodeSVGbackgroundImage.setAttribute("dragy", 0); - - if (this.getFormatter().args.backgroundImageHeight != null) { - this.NodeSVGbackgroundImage.setAttribute("height", this.getFormatter().args.backgroundImageHeight); - } - if (this.getFormatter().args.backgroundImageWidth != null) { - this.NodeSVGbackgroundImage.setAttribute("width", this.getFormatter().args.backgroundImageWidth); - } - - if (this.getFormatter().args.backgroundImageX != null) { - this.NodeSVGbackgroundImage.setAttribute("x", this.getFormatter().args.backgroundImageX); - } - if (this.getFormatter().args.backgroundImageY != null) { - this.NodeSVGbackgroundImage.setAttribute("y", this.getFormatter().args.backgroundImageY); - } - - this.GraphBackground.appendChild(this.NodeSVGbackgroundImage); - this.NodeSVGbackgroundImage.removeAttribute("href"); - this.NodeSVGbackgroundImage.setAttribute("xlink:href", this.getFormatter().getBackgroundImage()); -}; - -GraphCanvas.prototype.removeBackgroundImage = function() { - if (this.NodeSVGbackgroundImage != null) { - this.NodeSVGbackgroundImage.parentNode.removeChild(this.NodeSVGbackgroundImage); - } -}; - -GraphCanvas.prototype._setBackgroundColor = function(color) { - var attributes = [ [ "fill", color ] ]; - SVG.drawRectangle(0, 0, this.getFormatter().getWidth(), this.getFormatter().getHeight(), this.GraphBackground, attributes); -}; - -/** Serialize **/ -GraphCanvas.prototype.toJSON = function() { - var json = {}; - json.dataset = {}; - json.formatter = {}; - json.layout = {}; - json.dataset = this.getDataset().toJSON(); - json.formatter = this.getFormatter().toJSON(); - json.layout = this.getLayout().toJSON(); - return json; -}; - -GraphCanvas.prototype.toHTML = function() { - //this.backgroungToSVG(); - var html = this._svg.parentElement.innerHTML; - - var start = html.indexOf("") + 6; - - return html.substr(start, end); -}; - -/** DRAW **/ -GraphCanvas.prototype.draw = function(graphdataset, graphformatter, graphlayout) { - this.setDataset(graphdataset); - this.setFormatter(graphformatter); - this.setLayout(graphlayout); - - var _this = this; - this.getFormatter().changed.attach(function(sender, item) { - _this.removeNode(item.getId()); - _this.renderNode(item.getId()); - if (_this.args.labeled) { - _this.removeLabel(item.getId()); - _this.renderLabel(item.getId()); - } - - }); - //TODO - this.getFormatter().edgeChanged.attach(function(sender, item) { - _this.removeEdge(item.getId()); - _this.renderEdge(item.getId()); - }); - - this.getFormatter().resized.attach(function(sender, item) { - _this.resize(_this.getFormatter().getWidth(), _this.getFormatter().getHeight()); - }); - - this.getFormatter().backgroundImageChanged.attach(function(sender, item) { - _this.setBackgroundImage(_this.getFormatter().getBackgroundImage()); - }); - - this.getFormatter().backgroundColorChanged.attach(function(sender, item) { - _this._setBackgroundColor(_this.getFormatter().getBackgroundColor()); - }); - - this.getLayout().changed.attach(function(sender, item) { - _this.moveNode(item.getId()); - _this.moveEdge(item.getId()); - if (_this.args.labeled) { - _this.removeLabel(item.getId()); - _this.renderLabel(item.getId()); - } - }); - - this.getDataset().newVertex.attach(function(sender, item) { - - _this.renderNode(item.getId()); - if (_this.args.labeled) { - _this.renderLabel(item.getId()); - } - }); - - this.getDataset().newEdge.attach(function(sender, item) { - _this.renderEdge(item.getId()); - }); - - this.getDataset().vertexDeleted.attach(function(sender, item) { - _this.removeNode(item.getId()); - if (_this.args.labeled) { - _this.removeLabel(item.getId()); - } - }); - - this.getDataset().edgeDeleted.attach(function(sender, item) { - _this.removeEdge(item.getId()); - }); - - this.getDataset().vertexNameChanged.attach(function(sender, args) { - if (_this.args.labeled) { - _this.removeLabel(args.item.getId()); - _this.removeLabel(args.item.getId()); - _this.renderLabel(args.item.getId()); - } - }); - this.init(); - this.render(); -}; - -GraphCanvas.prototype.render = function() { - for ( var id in this.getDataset().getVertices()) { - this.renderNode(id); - } - this.renderLabels(); - this.renderEdges(); -}; - -GraphCanvas.prototype.renderLabels = function() { - if (this.args.labeled) { - for ( var id in this.getDataset().getVertices()) { - this.renderLabel(id); - } - } -}; - -GraphCanvas.prototype.removeLabels = function() { - for ( var id in this.getDataset().getVertices()) { - this.removeLabel(id); - } -}; - -/** Utilities method for nodes **/ -GraphCanvas.prototype.isNodeCanvas = function(node) { - return ((node.id == this.args.idGraph) || (node.id == this.id)); -}; - -GraphCanvas.prototype.isNodeBackground = function(node) { - return ((node.id == this.args.idBackgroundNode)); -}; - -GraphCanvas.prototype.isVertex = function(node) { - if (node.getAttribute("id") != null) { - if (node.getAttribute("id").indexOf("_v_") != -1) { - return true; - } - } - return false; -}; - -GraphCanvas.prototype.isLabel = function(node) { - if (node.getAttribute("id") != null) { - if (node.getAttribute("id").indexOf("_l_") != -1) { - return true; - } - } - return false; -}; - -GraphCanvas.prototype.isEdge = function(node) { - if (node.getAttribute("id") != null) { - if (node.getAttribute("id").indexOf("_e_") != -1) { - return true; - } - } - return false; -}; - -/** Resize **/ -GraphCanvas.prototype.resize = function(width, height) { - // this._svg.setAttribute("width", width); - // this._svg.setAttribute("height", height); - if (this.NodeSVGbackgroundImage != null) { - this.NodeSVGbackgroundImage.setAttribute("width", width); - this.NodeSVGbackgroundImage.setAttribute("height", height); - } - - this._svg.setAttribute("width", width); - this._svg.setAttribute("height", height); - - this.clearCanvas(); - this.render(); -}; - -GraphCanvas.prototype.clearCanvas = function() { - DOM.removeChilds(this.GraphEdgeGroup.getAttribute("id")); - DOM.removeChilds(this.GraphNodeGroup.getAttribute("id")); - this.clearLabels(); -}; - -GraphCanvas.prototype.clearLabels = function() { - DOM.removeChilds(this.GraphLabelGroup.getAttribute("id")); -}; - -/** ID'S converter **/ -GraphCanvas.prototype.getSVGNodeId = function(nodeId) { - return this.id + "_v_" + nodeId; -}; - -GraphCanvas.prototype.getSVGEdgeId = function(edgeId) { - return this.id + "_e_" + edgeId; -}; - -GraphCanvas.prototype.getSVGArrowEdgeId = function(edgeId) { - return this.id + "_arrow_" + edgeId; -}; - -GraphCanvas.prototype.getSVGLabelId = function(edgeId) { - return this.id + "_l_" + edgeId; -}; - -GraphCanvas.prototype.blinkVertexById = function(vertexId) { - $("#" + this.getSVGNodeId(vertexId)).fadeIn().fadeOut().fadeIn().fadeOut().fadeIn().fadeOut(); -}; - -GraphCanvas.prototype.getVertexIdFromSVGId = function(svgVertexId) { - return svgVertexId.replace(this.id, "").replace("_v_", ""); -}; - -GraphCanvas.prototype.getEdgeIdFromSVGId = function(svgEdgeId) { - return svgEdgeId.replace(this.id, "").replace("_e_", ""); -}; - -/** VERTEX **/ -GraphCanvas.prototype.getVertexById = function(id) { - return document.getElementById(this.getSVGNodeId(id)); -}; - -GraphCanvas.prototype.renderNodes = function() { - for ( var id in this.getDataset().getVertices()) { - this.renderNode(id); - } -}; - -GraphCanvas.prototype.overNode = function(nodeId) { - if (!this.args.interactive) { - return; - } - /** If selected we don't change the format **/ - if (this.args.isVertexSelected[nodeId] == null) { - var args = this.getFormatter().getVertexById(nodeId).getOver(); - args.args["cursor"] = 'pointer'; - this.changeVertexFormat(nodeId, args); - } -}; - -GraphCanvas.prototype.outNode = function(nodeId) { - if (!this.args.interactive) { - return; - } - - /** If selected we don't change the format **/ - if (this.args.isVertexSelected[nodeId] == null) { - this.changeVertexFormat(nodeId, this.getFormatter().getVertexById(nodeId).getDefault()); - } -}; - -GraphCanvas.prototype.overLabel = function(nodeId) { - this.overNode(nodeId); - // this.svgLabels[nodeId].setAttribute("cursor", "pointer"); -}; - -GraphCanvas.prototype.outLabel = function(nodeId) { - this.outNode(nodeId); - // this.svgLabels[nodeId].setAttribute("cursor", ""); -}; - -GraphCanvas.prototype.clickNode = function(nodeId) { - if (!this.args.interactive) { - return; - } - - /** si el evento se dispara oprque estaba dragging entonces no activo nada **/ - if (this.args.isVertexSelected[nodeId] == null) { - this.selectNode(nodeId); - } else { - this.deselectNode(nodeId); - } -}; - -GraphCanvas.prototype.selectNode = function(nodeId) { - for ( var i = 0; i < this.args.selectedVertices.length; i++) { - var format = this.getFormatter().getVertexById(nodeId).getSelected(); - format.opacity = 0.2; - this.changeVertexFormat(nodeId, this.getFormatter().getVertexById(nodeId).getSelected()); - } - - if (this.args.isVertexSelected[nodeId] == null) { - var format = this.getFormatter().getVertexById(nodeId).getSelected(); - format.opacity = 1; - this.changeVertexFormat(nodeId, this.getFormatter().getVertexById(nodeId).getSelected()); - this.args.selectedVertices.push(nodeId); - this.args.isVertexSelected[nodeId] = this.args.selectedVertices.length - 1; - this.onVertexSelect.notify(nodeId); - } -}; - -GraphCanvas.prototype.selectAllEdges = function() { - this.deselectNodes(); - this.deselectEdges(); - - for ( var edgesId in this.getDataset().edges) { - this.selectEdge(edgesId); - } -}; - -GraphCanvas.prototype.selectAllNodes = function() { - this.deselectNodes(); - this.deselectEdges(); - - for ( var vertexId in this.getDataset().vertices) { - this.selectNode(vertexId); - } -}; - -GraphCanvas.prototype.selectAll = function() { - this.deselectNodes(); - this.deselectEdges(); - - for ( var vertexId in this.getDataset().vertices) { - this.selectNode(vertexId); - } - - for ( var edgesId in this.getDataset().edges) { - this.selectEdge(edgesId); - } -}; - -GraphCanvas.prototype.selectEdge = function(edgeId) { - if (this.args.isEdgeSelected[edgeId] == null) { - this.changeEdgeFormat(edgeId, this.getFormatter().getEdgeById(edgeId).getSelected()); - //this.args.selectedEdges.push(edgeId); - this.args.isEdgeSelected[edgeId] = true; //this.args.selectedEdges.length - 1; - this.onEdgeSelect.notify(edgeId); - } -}; - -GraphCanvas.prototype.selectEdges = function(edges) { - - for ( var i = 0; i < edges.length; i++) { - this.selectEdge(edges[i]); - } -}; - -GraphCanvas.prototype.deselectNode = function(nodeId) { - if (this.args.isVertexSelected[nodeId] != null) { - this.changeVertexFormat(nodeId, this.getFormatter().getVertexById(nodeId).getDefault()); - this.args.selectedVertices.splice(this.args.isVertexSelected[nodeId], 1); - var index = this.args.isVertexSelected[nodeId]; - delete this.args.isVertexSelected[nodeId]; - - for ( var vertex in this.args.isVertexSelected) { - if (this.args.isVertexSelected[vertex] > index) { - this.args.isVertexSelected[vertex] = this.args.isVertexSelected[vertex] - 1; - } - } - } -}; - -GraphCanvas.prototype.deselectNodes = function() { - var selected = JSON.parse(JSON.stringify(this.getSelectedVertices())); - for ( var i = 0; i < selected.length; i++) { - this.deselectNode(selected[i]); - } -}; -GraphCanvas.prototype.selectNodes = function(idNodes) { - - for ( var i = 0; i < idNodes.length; i++) { - this.selectNode(idNodes[i]); - } - - // for ( var vertex in this.args.isVertexSelected) { - // if (this.args.isVertexSelected[vertex] > index){ - // this.args.isVertexSelected[vertex] = this.args.isVertexSelected[vertex] - 1; - // } - // } - -}; - -GraphCanvas.prototype.changeVertexFormat = function(nodeId, format) { - var svgNode = DOM.select(this.getSVGNodeId(nodeId)); - if (svgNode != null) { - var properties = format.toJSON(); - for ( var item in properties) { - svgNode.setAttribute(item, properties[item]); - } - - if (this.getFormatter().getVertexById(nodeId) instanceof CircleVertexGraphFormatter) { - var transform = "translate(" + svgNode.getAttribute("dragx") + "," + svgNode.getAttribute("dragy") + "), scale(" + format.getSize() + ")"; - svgNode.setAttribute("transform", transform); - } - } -}; - -GraphCanvas.prototype.renderLabel = function(nodeId) { - var x = Math.ceil(this.getLayout().getNodeById(nodeId).x * this.getFormatter().getWidth()); - var y = Math.ceil(this.getLayout().getNodeById(nodeId).y * this.getFormatter().getHeight()); - - var svgAttributesNode = JSON.parse(JSON.stringify(this.getFormatter().getVertexById(nodeId).getDefault().toJSON().title)); - svgAttributesNode.id = this.getSVGLabelId(this.getDataset().getVertexById(nodeId).getId()); - svgAttributesNode.dx = (-1) * (this.getDataset().getVertexById(nodeId).getName().length * svgAttributesNode["font-size"]) / 4 - 4; - - svgAttributesNode.dy = parseFloat((this.getFormatter().getVertexById(nodeId).getDefault().getSize())) - + parseFloat(svgAttributesNode["font-size"]) + parseFloat(this.getFormatter().getVertexById(nodeId).getDefault().getStrokeWidth()) - 4; - svgAttributesNode.dragx = Math.ceil(this.getLayout().getNodeById(nodeId).x * this.getFormatter().getWidth()); - - var gragy = parseFloat(this.getFormatter().getVertexById(nodeId).getDefault().getSize()) - + Math.ceil(this.getLayout().getNodeById(nodeId).y * this.getFormatter().getHeight()); - svgAttributesNode.dragy = gragy; - svgAttributesNode.transform = "translate(" + svgAttributesNode.dragx + "," + svgAttributesNode.dragy + ")";//, scale("+this.formatter.getVertexById(nodeId).getDefault().getSize()+")"; - - var nodeSVG = SVG.drawText(0, 0, this.getDataset().getVertexById(nodeId).getName(), this.GraphLabelGroup, svgAttributesNode); - - this.svgLabels[nodeId] = nodeSVG; - - /** Events for the SVG node **/ - var _this = this; - if (nodeSVG != null) { - nodeSVG.addEventListener("mouseover", function() { - _this.overLabel(nodeId); - }, false); - nodeSVG.addEventListener("mouseout", function() { - _this.outLabel(nodeId); - }, false); - } - -}; - -GraphCanvas.prototype.removeLabel = function(labelId) { - if (DOM.select(this.getSVGLabelId(labelId)) != null) { - DOM.select(this.getSVGLabelId(labelId)).parentNode.removeChild(DOM.select(this.getSVGLabelId(labelId))); - } -}; - -GraphCanvas.prototype.renderNode = function(nodeId) { - var svgAttributesNode = JSON.parse(JSON.stringify(this.getFormatter().getVertexById(nodeId).getDefault().toJSON())); - svgAttributesNode.dragx = Math.ceil(this.getLayout().getNodeById(nodeId).x * this.getFormatter().getWidth()); - svgAttributesNode.dragy = Math.ceil(this.getLayout().getNodeById(nodeId).y * this.getFormatter().getHeight()); - svgAttributesNode.transform = "translate(" + svgAttributesNode.dragx + "," + svgAttributesNode.dragy + ")"; - svgAttributesNode.id = this.getSVGNodeId(nodeId); - /*svgAttributesNode["stroke-width"] = 3 ; - svgAttributesNode["stroke-opacity"] = 1 ; - svgAttributesNode["fill-opacity"] = svgAttributesNode["opacity"] ; - svgAttributesNode["opacity"] = 1 ;*/ - this.circleDefaultRadius = this.getFormatter().getVertexById(nodeId).getDefault().getSize(); - var nodeSVG; - - if (this.getFormatter().getVertexById(nodeId) instanceof CircleVertexGraphFormatter) { - nodeSVG = SVG.drawCircle(0, 0, this.circleDefaultRadius, this.GraphNodeGroup, svgAttributesNode); - } - - if (this.getFormatter().getVertexById(nodeId) instanceof SquareVertexGraphFormatter) { - //nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius) ,0 - (this.formatter.getVertexById(nodeId).getDefault().getSize()) , (this.getFormatter().getVertexById(nodeId).getDefault().getSize()*2), (this.getFormatter().getVertexById(nodeId).getDefault().getSize()*2), this.GraphNodeGroup, svgAttributesNode); - nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius), 0 - (this.circleDefaultRadius), (this.circleDefaultRadius * 2), - (this.circleDefaultRadius * 2), this.GraphNodeGroup, svgAttributesNode); - } - - if (this.getFormatter().getVertexById(nodeId) instanceof EllipseVertexGraphFormatter) { - nodeSVG = SVG.drawEllipse(0, 0, this.circleDefaultRadius * 1.5, this.circleDefaultRadius, this.GraphNodeGroup, svgAttributesNode); - } - - if (this.getFormatter().getVertexById(nodeId) instanceof RectangleVertexGraphFormatter) { - //nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius) ,0 - ((this.circleDefaultRadius*2)/2) , (this.circleDefaultRadius*2), (this.circleDefaultRadius), this.GraphNodeGroup, svgAttributesNode); - nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius * 1.5), 0 - (this.circleDefaultRadius), (this.circleDefaultRadius * 2 * 1.5), - (this.circleDefaultRadius * 2), this.GraphNodeGroup, svgAttributesNode); - - } - - if (this.getFormatter().getVertexById(nodeId) instanceof RoundedVertexGraphFormatter) { - svgAttributesNode.ry = 2;// this.formatter.getVertexById(nodeId).getDefault().getSize()/4; - svgAttributesNode.rx = 2;// this.formatter.getVertexById(nodeId).getDefault().getSize()/4; - nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius * 1.5), 0 - (this.circleDefaultRadius), (this.circleDefaultRadius * 2 * 1.5), - (this.circleDefaultRadius * 2), this.GraphNodeGroup, svgAttributesNode); - } - - // - - if (this.getFormatter().getVertexById(nodeId) instanceof OctagonVertexGraphFormatter) { - svgAttributesNode.ry = 2; - svgAttributesNode.rx = 2; - nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius * 1.5), 0 - (this.circleDefaultRadius), (this.circleDefaultRadius * 2 * 1.5), - (this.circleDefaultRadius * 2), this.GraphNodeGroup, svgAttributesNode); - } - - nodeSVG.internalId = nodeId; - // - var _this = this; - - /** Events for the SVG node **/ - if (nodeSVG != null) { - nodeSVG.addEventListener("mouseover", function() { - _this.onVertexOver.notify(nodeId); - _this.overNode(nodeId); - }, false); - nodeSVG.addEventListener("mouseout", function() { - _this.onVertexOut.notify(nodeId); - _this.outNode(nodeId); - }, false); - //nodeSVG.addEventListener("click", function(){_this.clickNode(nodeId);}, false); - // - nodeSVG.addEventListener("mouseup", function() { - _this.onVertexUp.notify(nodeId); - }, false); - } -}; - -GraphCanvas.prototype.removeNode = function(nodeId) { - DOM.select(this.getSVGNodeId(nodeId)).parentNode.removeChild(DOM.select(this.getSVGNodeId(nodeId))); - if (this.args.labeled) { - this.removeLabel(nodeId); - } -}; - -/** REMOVING **/ -GraphCanvas.prototype.removeSelected = function() { - /** El orden importa **/ - this.removeSelectedEdges(); - this.removeSelectedNode(); - -}; - -GraphCanvas.prototype.removeSelectedNode = function() { - var selected = JSON.parse(JSON.stringify(this.getSelectedVertices())); - this.deselectNodes(); - var sorted = selected.sort(function(a, b) { - return a - b - }); - for ( var i = 0; i < sorted.length; i++) { - if (this.getDataset().getVertexById(sorted[i]) != null) { - this.getDataset().getVertexById(sorted[i]).remove(); - } - } -}; - -/** EDGES **/ -GraphCanvas.prototype.removeEdge = function(edgeId) { - if (DOM.select(this.getSVGEdgeId(edgeId)) != null) { - DOM.select(this.getSVGEdgeId(edgeId)).parentNode.removeChild(DOM.select(this.getSVGEdgeId(edgeId))); - } - - if (DOM.select(this.getSVGEdgeId(edgeId) + "_shadow") != null) { - DOM.select(this.getSVGEdgeId(edgeId) + "_shadow").parentNode.removeChild(DOM.select(this.getSVGEdgeId(edgeId) + "_shadow")); - } - - if (DOM.select(this.getSVGArrowEdgeId(edgeId)) != null) { - DOM.select(this.getSVGArrowEdgeId(edgeId)).parentNode.removeChild(DOM.select(this.getSVGArrowEdgeId(edgeId))); - } -}; - -GraphCanvas.prototype.overEdge = function(edgeId) { - if ((!this.args.interactive) || this.dragging || this.selecting) { - return; - } - - /** If selected we don't change the format **/ - if (this.args.isEdgeSelected[edgeId] == null) { - var format = this.getFormatter().getEdgeById(edgeId).getOver(); - format.args["cursor"] = "pointer"; - this.changeEdgeFormat(edgeId, format); - } -}; - -GraphCanvas.prototype.outEdge = function(edgeId) { - if (!this.args.interactive) { - return; - } - - /** If selected we don't change the format **/ - if (this.args.isEdgeSelected[edgeId] == null) { - this.changeEdgeFormat(edgeId, this.getFormatter().getEdgeById(edgeId).getDefault()); - } -}; - -GraphCanvas.prototype.changeEdgeFormat = function(edgeId, format) { - var svgEdge = DOM.select(this.getSVGEdgeId(edgeId) + "_shadow"); - if (svgEdge != null) { - var properties = format.toJSON(); - for ( var item in properties) { - svgEdge.setAttribute(item, properties[item]); - } - } -}; - -GraphCanvas.prototype.deselectEdge = function(edgeID) { - if (this.args.isEdgeSelected[edgeID] != null) { - this.changeEdgeFormat(edgeID, this.getFormatter().getEdgeById(edgeID).getDefault()); - var index = this.args.isEdgeSelected[edgeID]; - delete this.args.isEdgeSelected[edgeID]; - } -}; - -GraphCanvas.prototype.deselectEdges = function() { - var selected = JSON.parse(JSON.stringify(this.getSelectedEdges())); - for ( var i = 0; i < selected.length; i++) { - this.deselectEdge(selected[i]); - } -}; - -GraphCanvas.prototype.removeSelectedEdges = function() { - var selected = JSON.parse(JSON.stringify(this.getSelectedEdges())); - this.deselectEdges(); - for ( var i = 0; i < selected.length; i++) { - if (this.getDataset().getEdgeById(selected[i]) != null) { - this.getDataset().getEdgeById(selected[i]).remove(); - } - } -}; - -GraphCanvas.prototype.renderEdge = function(edgeId) { - var svgAttributesEdge = this.getFormatter().getEdgeById(edgeId).getDefault().toJSON(); - var edge = this.getDataset().getEdgeById(edgeId); - - var svgNodeTarget = this.getVertexById(edge.getNodeTarget().getId()); - var svgNodeSource = this.getVertexById(edge.getNodeSource().getId()); - svgAttributesEdge.id = this.getSVGEdgeId(edge.getId()) + "_shadow"; - - var svgEdge = null; - - if (this.getFormatter().getEdgeById(edgeId) instanceof LineEdgeGraphFormatter) { - var coordenateSourceX = svgNodeSource.getAttribute("dragx"); - var coordenateSourceY = svgNodeSource.getAttribute("dragy"); - var coordenateTargetX = svgNodeTarget.getAttribute("dragx"); - var coordenateTargetY = svgNodeTarget.getAttribute("dragy"); - - SVG.drawLine(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, this.GraphEdgeGroup, svgAttributesEdge); - var attributesShadow = {}; - attributesShadow.id = this.getSVGEdgeId(edge.getId()); - attributesShadow["stroke-opacity"] = 0; - attributesShadow["stroke-width"] = 4; - attributesShadow["stroke"] = "black"; - svgEdge = SVG.drawLine(svgNodeSource.getAttribute("dragx"), svgNodeSource.getAttribute("dragy"), svgNodeTarget.getAttribute("dragx"), - svgNodeTarget.getAttribute("dragy"), this.GraphEdgeGroup, attributesShadow); - } - - if (this.getFormatter().getEdgeById(edgeId) instanceof BezierEdgeGraphFormatter) { - var nodeId = edge.getNodeTarget().getId(); - var nodeSize = this.formatter.getVertexById(nodeId).getDefault().getSize() * this.getFormatter().getNodesMaxSize(); - svgAttributesEdge.fill = "none"; - svgAttributesEdge.id = this.getSVGEdgeId(edgeId); - var d = this.calculateCoordenatesBezier(nodeSize, svgNodeSource.getAttribute("dragx"), svgNodeSource.getAttribute("dragy")); - svgEdge = SVG.drawPath(d, this.GraphEdgeGroup, svgAttributesEdge); - } - ; - - if ((this.getFormatter().getEdgeById(edgeId) instanceof DirectedLineEdgeGraphFormatter) - || (this.getFormatter().getEdgeById(edgeId) instanceof CutDirectedLineEdgeGraphFormatter) - || (this.getFormatter().getEdgeById(edgeId) instanceof DotDirectedLineEdgeGraphFormatter) - || (this.getFormatter().getEdgeById(edgeId) instanceof OdotDirectedLineEdgeGraphFormatter) - || (this.getFormatter().getEdgeById(edgeId) instanceof OdirectedLineEdgeGraphFormatter)) { - var coordenateSourceX = svgNodeSource.getAttribute("dragx"); - var coordenateSourceY = svgNodeSource.getAttribute("dragy"); - var coordenateTargetX = svgNodeTarget.getAttribute("dragx"); - var coordenateTargetY = svgNodeTarget.getAttribute("dragy"); - - var offset = parseFloat(this.getFormatter().getVertexById(this.getDataset().getEdgeById(edgeId).getNodeTarget().getId()).getDefault() - .getSize() - * this.circleDefaultRadius); - var point = this._calculateEdgePointerPosition(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, offset); - coordenateTargetX = point.x; - coordenateTargetY = point.y; - SVG.drawLine(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, this.GraphEdgeGroup, svgAttributesEdge); - - var attributesShadow = {}; - attributesShadow.id = this.getSVGEdgeId(edge.getId()); - attributesShadow["stroke-opacity"] = 0; - attributesShadow["stroke-width"] = 4; - attributesShadow["stroke"] = "black"; - svgEdge = SVG.drawLine(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, this.GraphEdgeGroup, attributesShadow); - } - - if (this.getFormatter().getEdgeById(edgeId) instanceof DirectedLineEdgeGraphFormatter - || (this.getFormatter().getEdgeById(edgeId) instanceof OdirectedLineEdgeGraphFormatter)) { - var coordenateSourceX = svgNodeSource.getAttribute("dragx"); - var coordenateSourceY = svgNodeSource.getAttribute("dragy"); - var coordenateTargetX = svgNodeTarget.getAttribute("dragx"); - var coordenateTargetY = svgNodeTarget.getAttribute("dragy"); - - var point = this._calculateEdgePointerPosition(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, offset); - coordenateTargetX = point.x; - coordenateTargetY = point.y; - - var angle = Geometry.toDegree(point.angle) + 90; - this.arrowDefaultSize = this.getFormatter().getEdgeById(edgeId).getArrowSize(); //getDefault().getArrowSize(); - var d = "-" + this.arrowDefaultSize + ",0 0,-" + parseFloat(this.arrowDefaultSize) * 2 + " " + this.arrowDefaultSize + ",0"; - - var attributes; - - if (this.getFormatter().getEdgeById(edgeId) instanceof DirectedLineEdgeGraphFormatter) { - attributes = [ - [ "fill", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], - [ "stroke", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], [ "id", this.getSVGArrowEdgeId(edgeId) ] ]; - } else { - attributes = [ - [ "fill", "#FFFFFF" ], [ "stroke", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], - [ "id", this.getSVGArrowEdgeId(edgeId) ] ]; - } - - var flechaSVGNode = SVG.drawPoligon(d, this.GraphEdgeGroup, attributes);//, ["transform", "rotate("+angle+"), translate(0,0)"]]); - flechaSVGNode.setAttribute("transform", " translate(" + coordenateTargetX + ", " + coordenateTargetY + "), rotate(" + angle + ")"); - } - ; - - if (this.getFormatter().getEdgeById(edgeId) instanceof CutDirectedLineEdgeGraphFormatter) { - var coordenateSourceX = svgNodeSource.getAttribute("dragx"); - var coordenateSourceY = svgNodeSource.getAttribute("dragy"); - var coordenateTargetX = svgNodeTarget.getAttribute("dragx"); - var coordenateTargetY = svgNodeTarget.getAttribute("dragy"); - - var point = this._calculateEdgePointerPosition(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, offset); - coordenateTargetX = point.x; - coordenateTargetY = point.y; - - var angle = Geometry.toDegree(point.angle) + 90; - - //this.arrowDefaultSize = 2; //getDefault().getArrowSize(); - var d = "-4,0 4,0 4,-2 -4,-2"; - - var flechaSVGNode = SVG.drawPoligon(d, this.GraphEdgeGroup, [ - [ "fill", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], - [ "stroke", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], [ "id", this.getSVGArrowEdgeId(edgeId) ] ]);//, ["transform", "rotate("+angle+"), translate(0,0)"]]); - flechaSVGNode.setAttribute("transform", " translate(" + coordenateTargetX + ", " + coordenateTargetY + "), rotate(" + angle + ")"); - } - ; - - if ((this.getFormatter().getEdgeById(edgeId) instanceof DotDirectedLineEdgeGraphFormatter) - || (this.getFormatter().getEdgeById(edgeId) instanceof OdotDirectedLineEdgeGraphFormatter)) { - var coordenateSourceX = svgNodeSource.getAttribute("dragx"); - var coordenateSourceY = svgNodeSource.getAttribute("dragy"); - var coordenateTargetX = svgNodeTarget.getAttribute("dragx"); - var coordenateTargetY = svgNodeTarget.getAttribute("dragy"); - var point = this._calculateEdgePointerPosition(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, offset); - coordenateTargetX = point.x; - coordenateTargetY = point.y; - var angle = Geometry.toDegree(point.angle) + 90; - // this.arrowDefaultSize = this.formatter.getEdgeById(edgeId).getArrowSize(); //getDefault().getArrowSize(); - var attributes = []; - if (this.getFormatter().getEdgeById(edgeId) instanceof OdotDirectedLineEdgeGraphFormatter) { - attributes = [ - [ "fill", "#FFFFFF" ], [ "stroke", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], - [ "id", this.getSVGArrowEdgeId(edgeId) ] ]; - } else { - attributes = [ - [ "fill", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], - [ "stroke", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], [ "id", this.getSVGArrowEdgeId(edgeId) ] ]; - } - var flechaSVGNode = SVG.drawCircle(0, 0, 4, this.GraphEdgeGroup, attributes); - flechaSVGNode.setAttribute("transform", " translate(" + coordenateTargetX + ", " + coordenateTargetY + "), rotate(" + angle + ")"); - } - ; - - var _this = this; - /** Events for the SVG edge **/ - if (svgEdge != null) { - if (this.getDataset().getEdgesCount() < this.args.maxNumberEdgesFiringEvents) { - svgEdge.addEventListener("mouseover", function() { - _this.overEdge(edgeId); - }, false); - svgEdge.addEventListener("mouseout", function() { - _this.outEdge(edgeId); - }, false); - } - } -}; - -GraphCanvas.prototype._calculateEdgePointerPosition = function(sourceX, sourceY, targetX, targetY, radius) { - var angle = Geometry.getAngleBetweenTwoPoints(sourceX, sourceY, targetX, targetY); - - /** Suponiendo el node source que este a la derecha **/ - if ((targetX - sourceX) < 0) { - var b = Geometry.getAdjacentSideOfRectangleRight(angle, radius); - targetX = parseFloat(targetX) + parseFloat(b); - arrowX = parseFloat(targetX) + parseFloat(b) + this.arrowDefaultSize / 2; - } else { - var b = Geometry.getAdjacentSideOfRectangleRight(angle, radius); - targetX = parseFloat(targetX) - parseFloat(b); - arrowX = parseFloat(targetX) - parseFloat(b) - this.arrowDefaultSize / 2; - } - - /** Suponiendo el node source que este a la arriba **/ - if ((targetY - sourceY) > 0) { - var a = Geometry.getOppositeSideOfRectangleRight(angle, radius); - targetY = parseFloat(targetY) - parseFloat(a); - arrowY = parseFloat(targetY) - parseFloat(a) - this.arrowDefaultSize / 2; - } else { - var a = Geometry.getOppositeSideOfRectangleRight(angle, radius); - targetY = parseFloat(targetY) + parseFloat(a); - arrowY = parseFloat(targetY) + parseFloat(a) - this.arrowDefaultSize / 2; - - } - - return { - "x" : arrowX, - "y" : arrowY, - "angle" : angle - }; -}; - -GraphCanvas.prototype.calculateCoordenatesBezier = function(nodeSize, x1, y1) { - var x11 = x1 - (nodeSize / 2); - var y11 = y1 - (nodeSize / 2); - - var x12 = parseFloat(x1) + parseFloat(nodeSize / 2); - var y12 = y1 - (nodeSize / 2); - - var curvePointX = (x12 - x11) / 2 + x11; - var curvePointY = y1 - (nodeSize * 2); - var d = "M" + x11 + "," + y11 + " T" + curvePointX + "," + curvePointY + " " + x12 + "," + y12; - return d; - -}; - -GraphCanvas.prototype.renderEdges = function() { - for ( var edge in this.getDataset().getEdges()) { - this.renderEdge(this.getDataset().getEdgeById(edge).getId()); - - } -}; - -GraphCanvas.prototype.getLastSelectedNode = function() { - var node = null; - if (this.getSelectedVertices().length > 0) { - var nodeId = this.getSelectedVertices()[this.getSelectedVertices().length - 1]; - node = this.getDataset().getVertexById(nodeId); - } - return node; -}; -/* - GraphCanvas.prototype.getNodeByNameAndIndex = function(node, index){ - var nodeId = this.getDataset().verticesIndex[node][index]; - var nodeItem = this.getDataset().getVertexById(nodeId); - return nodeItem; - }; - */ - -GraphCanvas.prototype.setDataset = function(dataset) { - this.dataset = dataset; -}; - -GraphCanvas.prototype.setFormatter = function(formatter) { - this.formatter = formatter; -}; - -GraphCanvas.prototype.setLayout = function(layout) { - this.layout = layout; -}; - -/** API **/ -GraphCanvas.prototype.getDataset = function() { - return this.dataset; -}; - -GraphCanvas.prototype.getFormatter = function() { - return this.formatter; -}; - -GraphCanvas.prototype.getLayout = function() { - return this.layout; -}; - -/** API DATASET **/ -GraphCanvas.prototype.addVertex = function(name, args) { - this.getDataset().addNode(name, args); -}; - -GraphCanvas.prototype.removeVertex = function(vertexId) { - this.getDataset().getVertexById(vertexId).remove(); -}; - -GraphCanvas.prototype.addEdge = function(edgeName, nodeSourceId, nodeTargetId, args) { - this.getDataset().addEdge(edgeName, nodeSourceId, nodeTargetId, args); -}; -/* - GraphCanvas.prototype.removeEdge = function(edgeId){ - this.getDataset().getEdgeById(edgeId).remove(); - }; - */ - -/** API FORMATTER **/ -GraphCanvas.prototype.getWidth = function() { - return this.getFormatter().getWidth(); -}; - -GraphCanvas.prototype.getHeight = function() { - return this.getFormatter().getHeight(); -}; - -GraphCanvas.prototype.getBackgroundImage = function() { - return this.getFormatter().getBackgroundImage(); -}; - -//GraphCanvas.prototype.setBackgroundImage = function(value){ -// this.getFormatter().setBackgroundImage(value); -//}; - -GraphCanvas.prototype.getBackgroundColor = function() { - return this.getFormatter().getBackgroundColor(); -}; - -GraphCanvas.prototype.setBackgroundColor = function() { - this.getFormatter().setBackgroundColor(value); -}; - -//GraphCanvas.prototype.setEdgeFill = function(edgeId, value){ -// this.getFormatter().getEdgeById(edgeId).getDefault().setFill(value); -//}; -// -//GraphCanvas.prototype.getEdgeFill = function(edgeId){ -// return this.getFormatter().getEdgeById(edgeId).getDefault().getFill(); -//}; - -/** VERTICES FORMATTER **/ -GraphCanvas.prototype.setVertexSize = function(vertexId, value) { - this.getFormatter().getVertexById(vertexId).getDefault().setSize(value); -}; - -GraphCanvas.prototype.getVertexSize = function(vertexId) { - return this.getFormatter().getVertexById(vertexId).getDefault().getSize(); -}; - -GraphCanvas.prototype.setVertexStroke = function(vertexId, value) { - this.getFormatter().getVertexById(vertexId).getDefault().setStroke(value); -}; - -GraphCanvas.prototype.getVertexStroke = function(vertexId) { - return this.getFormatter().getVertexById(vertexId).getDefault().getStroke(); -}; - -GraphCanvas.prototype.setVertexStrokeOpacity = function(vertexId, value) { - this.getFormatter().getVertexById(vertexId).getDefault().setStrokeOpacity(value); -}; - -GraphCanvas.prototype.getVertexStrokeOpacity = function(vertexId) { - return this.getFormatter().getVertexById(vertexId).getDefault().getStrokeOpacity(); -}; - -GraphCanvas.prototype.setVertexOpacity = function(vertexId, value) { - this.getFormatter().getVertexById(vertexId).getDefault().setOpacity(value); -}; - -GraphCanvas.prototype.getVertexOpacity = function(vertexId) { - return this.getFormatter().getVertexById(vertexId).getDefault().getOpacity(); -}; - -GraphCanvas.prototype.setVertexFill = function(vertexId, color) { - this.getFormatter().getVertexById(vertexId).getDefault().setFill(color); -}; - -GraphCanvas.prototype.getVertexFill = function(vertexId) { - return this.getFormatter().getVertexById(vertexId).getDefault().getFill(); -}; - -/** EDGES FORMATTER **/ -GraphCanvas.prototype.setEdgeSize = function(edgeId, value) { - this.getFormatter().getEdgeById(edgeId).getDefault().setSize(value); -}; - -GraphCanvas.prototype.getEdgeSize = function(edgeId) { - return this.getFormatter().getEdgeById(edgeId).getDefault().getSize(); -}; - -GraphCanvas.prototype.setEdgeStroke = function(edgeId, value) { - this.getFormatter().getEdgeById(edgeId).getDefault().setStroke(value); -}; - -GraphCanvas.prototype.getEdgeStroke = function(edgeId) { - return this.getFormatter().getEdgeById(edgeId).getDefault().getStroke(); -}; - -GraphCanvas.prototype.setEdgeStrokeOpacity = function(edgeId, value) { - this.getFormatter().getEdgeById(edgeId).getDefault().setStrokeOpacity(value); -}; - -GraphCanvas.prototype.getEdgeStrokeOpacity = function(edgeId) { - return this.getFormatter().getEdgeById(edgeId).getDefault().getStrokeOpacity(); -}; - -GraphCanvas.prototype.setEdgeFill = function(edgeId, color) { - this.getFormatter().getEdgeById(edgeId).getDefault().setFill(color); -}; - -GraphCanvas.prototype.getEdgeFill = function(edgeId) { - return this.getFormatter().getEdgeById(edgeId).getDefault().getFill(); -}; - -/** API LAYOUT **/ -GraphCanvas.prototype.setCoordinates = function(vertexId, x, y) { - return this.getLayout().getEdgeById(vertexId).setCoordinates(x, y); -}; - - - -function HPLCGraph(args) { - this.width = 600; - this.height = 600; - this.title = ''; - this.bbar = false; - this.plotInnerPanelPadding = 10; - this.plotPanelPadding = 5; - this.id = BUI.id(); - - this.hidePlots = null; - this.xlabel = ""; - this.scaled = false; - this.xParam = null; - this.showRangeSelector = true; - this.interactionModel = null; - - /** for each stat the max and minimum value when it is scaled in order to show correctly in the legend **/ - this.ranges = {}; - if (args != null) { - if (args.interactionModel != null) { - this.interactionModel = args.interactionModel; - } - if (args.width != null) { - this.width = args.width; - } - if (args.height != null) { - this.height = args.height; - } - if (args.bbar != null) { - this.bbar = args.bbar; - } - if (args.title != null) { - this.title = args.title; - } - if (args.plots != null) { - this.plots = args.plots; - } - - if (args.scaled != null) { - this.scaled = args.scaled; - } - if (args.xlabel != null) { - this.xlabel = args.xlabel; - } - if (args.xParam != null) { - this.xParam = args.xParam; - } - if (args.showRangeSelector != null) { - this.showRangeSelector = args.showRangeSelector; - } - } - - this.onZoomX = new Event(this); - this.onResetZoom = new Event(this); - this.dblclick = new Event(this); -} - -HPLCGraph.prototype.getMenu = function () { - var _this = this; - /** Actions buttons **/ - var actions = []; - - function toggle(item, pressed) { - if (pressed) { - _this.plots[item.param] = true; - } else { - delete _this.plots[item.param]; - } - _this.reloadData(this.hplcData); - } - - for (var i = 0; i < this.hplcData.length; i++) { - if (this.hplcData[i].showOnMenu != false) { - var param = this.hplcData[i].param; - var style = "style='padding:0 0px 0 5px;'"; - actions.push({ - text : "
" + BUI.getRectangleColorDIV(this.hplcData[i].color, 10, 10) + " " + this.hplcData[i].label + "
", - id : _this.id + param, - param : param, - enableToggle : true, - scope : this, - toggleHandler : toggle, - pressed : (_this.plots[param] != null) - }); - } - } - actions.push("-"); - - actions.push({ - text : "Scale", - enableToggle : true, - scope : this, - pressed : this.scaled, - icon : '../images/icon_graph.png', - toggleHandler : function (item, pressed) { - _this.scaled = pressed; - _this.reloadData(this.hplcData); - } - }); - - actions.push("->"); - actions.push({ - text : "Save", - scope : this, - icon : '../images/save.gif', - handler : function (item, pressed) { - var largeImage = document.createElement("img"); - largeImage.style.display = 'block'; - largeImage.style.width = 200 + "px"; - largeImage.style.height = 200 + "px"; - largeImage.setAttribute('src', Dygraph.Export.asCanvas(this.dygraphObject.dygraph).toDataURL()); - window.open(Dygraph.Export.asCanvas(this.dygraphObject.dygraph).toDataURL(), 'Image', ''); - } - }); - - return actions; -}; - -/** Looks for the maximum value and then divide everything but that value **/ -HPLCGraph.prototype.scaledData = function (data) { - for (var i = 0; i < data.length; i++) { - var values = this.getMaxAndMinValue(data[i]); - data[i] = this.divideValuesByMax(data[i], values.max); - this.ranges[data[i].label] = values; - } - return data; -}; - - -/** Given a stat float[] and a max number it will divide each value by max **/ -HPLCGraph.prototype.divideValuesByMax = function (stat, max) { - for (var j = 0; j < stat.data.length; j++) { - if (max != 0) { - stat.data[j] = Number(stat.data[j]) / max; - stat.std[j] = Number(stat.std[j]) / max; - } - } - return stat; -}; - -/** returns max value of a stat **/ -HPLCGraph.prototype.getMaxAndMinValue = function (stat) { - var max = 0; - var min = stat.data[0]; - for (var j = 0; j < stat.data.length; j++) { - if (Number(stat.data[j]) > max) { - max = Number(stat.data[j]); - } - if (Number(stat.std[j]) > max) { - max = Number(stat.std[j]); - } - if (Number(stat.data[j]) < min) { - min = Number(stat.data[j]); - } - } - return { - max : Number(max), - min : Number(min) - }; -}; - -HPLCGraph.prototype.getPoint = function (data, i) { - var point = [ 10, 10, 10 ]; - var y = parseFloat(data.data[i]); - var error = parseFloat(data.std[i]); - if (data.fdata == null) { - return [ y - error, y, y + error ]; - } else { - if (data.fstd != null) { - return [ data.fstd(y - error), data.fdata(y), data.fstd(y + error) ]; - } - return [ data.fdata(y) - error, data.fdata(y), data.fdata(y) + error ]; - } - return point; -}; - -HPLCGraph.prototype.reloadData = function(hplcData) { - this.panel.setLoading(false); - this.hplcData = hplcData; - - var data = hplcData; - - - /** In case of having peaks **/ - if (this.peaks != null) { - for (var peak in this.peaks) { - var values = []; - var std = []; - for (var i = 0; i < this.peaks[peak].length; i++) { - values.push(this.peaks[peak][i][1]); - std.push(this.peaks[peak][i][2]); - } - data.push({ - param : peak, - data : values, - showOnMenu : false, - fdata : function (a) { - var value = (Math.log(parseFloat(a))); - if (isNumber(value)) { - return value; - } - }, - fstd : function (a) { - var value = Math.log(Math.abs(parseFloat(a))); - if (isNumber(value)) - return value; - }, - std : std, - color : this.colorPeak[peak], - label : peak - }); - - } - } - - - if (this.scaled) { - data = this.scaledData(JSON.parse(JSON.stringify(hplcData))); - } - - var paramIndex = {}; - var parsed = []; - var j = 0; - for (var i = 0; i < data[0].data.length - 1; i++) { - var aux = []; - for (j = 0; j < data.length; j++) { - if (this.plots != null) { - if (this.plots[data[j].param] != null) { - aux.push(this.getPoint(data[j], i)); - paramIndex[data[j].param] = aux.length - 1; - } - } else { - aux.push([ data[j].data[i] - data[j].std[i], data[j].data[i], data[j].data[i] + data[j].std[i] ]); - } - } - parsed.push([]); - - var index = i; - if (this.xParam != null) { - index = parseFloat(data[this.xParam].data[i]); - } - - parsed[parsed.length - 1].push(index); - - for (j = 0; j < data.length; j++) { - if (this.plots != null) { - if (this.plots[data[j].param] != null) { - parsed[parsed.length - 1].push(aux[paramIndex[data[j].param]]); - } - } else { - parsed[parsed.length - 1].push(aux[j]); - } - } - } - - var colors = []; - var labels = [ "" ]; - for (j = 0; j < data.length; j++) { - if (this.plots != null) { - if (this.plots[data[j].param] != null) { - colors.push(data[j].color); - labels.push(data[j].label); - } - } else { - parsed[parsed.length - 1].push(aux[j]); - } - } - - this._renderDygraph(parsed, colors, labels); -}; - -HPLCGraph.prototype._renderDygraph = function (parsed, colors, labels) { - this.dygraphObject = new StdDevDyGraph(this.id, { - width : this.width, - height : this.height - 10, - xlabel : this.xlabel, - showRangeSelector : this.showRangeSelector, - interactionModel : this.interactionModel, - scaled : this.scaled, - ranges : this.ranges - }); - this.dygraphObject.draw(parsed, colors, labels); - - var _this = this; - this.dygraphObject.onZoomX.attach(function (sender, args) { - try { - _this.onZoomX.notify(args); - } catch (e) { - } - }); - - this.dygraphObject.onResetZoom.attach(function (sender, args) { - try { - _this.onResetZoom.notify(args); - } catch (e) { - } - }); - - this.dygraphObject.dblclick.attach(function (sender, args) { - try { - _this.dblclick.notify(args); - } catch (e) { - } - }); - -}; - -HPLCGraph.prototype.loadData = function (data) { - var _this = this; - this.reloadData(data); - this.panel.addDocked({ - xtype : 'toolbar', - items : this.getMenu() - }); - - - if (this.bbar == true){ - this.panel.addDocked({ - xtype : 'toolbar', - dock: 'bottom', - items : [ - { - xtype: 'numberfield', - id: 'main_field_start', - fieldLabel: 'Range from', - width: 170, - labelWidth : 70, - value: 0, - minValue: 0 - }, - { - xtype: 'numberfield', - id: 'main_field_end', - fieldLabel: 'to', - width: 130, - labelWidth : 30, - value: 0, - minValue: 0 - }, - { - xtype: 'button', - text: 'Go', - handler: function () { - var start = parseFloat(Ext.getCmp("main_field_start").getValue()); - var end = parseFloat(Ext.getCmp("main_field_end").getValue()); - - if (start < 0) { - start = 0; - } - if (end < 0) { - end = 0; - } - if (start > end) { - var aux = end; - end = start; - start = aux; - } - - _this.dygraphObject.dygraph.updateOptions({ isZoomedIgnoreProgrammaticZoom: true, dateWindow: [start, end] }); - } - } - ] - }); - } -}; - -HPLCGraph.prototype.getPanel = function () { - this.panel = Ext.create('Ext.panel.Panel', { - padding : this.plotPanelPadding, - width : this.width + 4 * this.plotInnerPanelPadding, - height : this.height + 4 * this.plotInnerPanelPadding, - items : [ { - html : "", - id : this.id, - width : this.width, - height : this.height - } ] - }); - - return this.panel; -}; - -HPLCGraph.prototype.input = function () { - return DATADOC.getHPLCData(); -}; - -HPLCGraph.prototype.getDataByFrameNumber = function (frameNumber) { - var data = {}; - data.frameNumber = frameNumber; - for (var key in this.hplcData){ - data[this.hplcData[key].label] = this.hplcData[key].data[frameNumber]; - } - console.log(data); - return data; -}; - - -HPLCGraph.prototype.test = function (targetId) { - var mainPlotPanel = new HPLCGraph({ - title : 'I0', - width : 800, - height : 400, - plots : { - "I0" : true, - "Rg" : true, - "Mass" : true - }, - xlabel : "HPLC Frames", - scaled : this.scaled, - interactionModel : { - 'dblclick' : function (event, g, context) { - } - } - }); - mainPlotPanel.getPanel().render(targetId); - mainPlotPanel.loadData(mainPlotPanel.input()); - -}; - - -function MergesHPLCGraph(args) { - HPLCGraph.prototype.constructor.call(this, args); - -// this.peakColors = ["#00FB42", "#00BA31", "#007C21", "#003E10"]; - this.peakColors = ["#DEBD00", "#6D9100", "#872900", "#0092CC"]; -} - - -MergesHPLCGraph.prototype.scaledData = HPLCGraph.prototype.scaledData; -MergesHPLCGraph.prototype.divideValuesByMax = HPLCGraph.prototype.divideValuesByMax; -MergesHPLCGraph.prototype.getMaxAndMinValue = HPLCGraph.prototype.getMaxAndMinValue; -MergesHPLCGraph.prototype.getPoint = HPLCGraph.prototype.getPoint; -MergesHPLCGraph.prototype.reloadData = HPLCGraph.prototype.reloadData; -MergesHPLCGraph.prototype._renderDygraph = HPLCGraph.prototype._renderDygraph; -MergesHPLCGraph.prototype.loadData = HPLCGraph.prototype.loadData; -MergesHPLCGraph.prototype.getPanel = HPLCGraph.prototype.getPanel; -MergesHPLCGraph.prototype.getDataByFrameNumber = HPLCGraph.prototype.getDataByFrameNumber; - - -MergesHPLCGraph.prototype.setPeaks = function (data) { - this.peaks = data; - /** get size of peaks **/ - this.peakKeys = []; - this.colorPeak = {}; - var colorCount = 1; - for (var key in this.peaks) { - if (this.peaks.hasOwnProperty(key)) { - var color = this.peakColors[colorCount % this.peakColors.length]; - colorCount = colorCount + 1; - this.peakKeys.push(key); - this.colorPeak[key] = color; - } - } - this.peakKeys.sort(); -}; - - -MergesHPLCGraph.prototype.getMenu = function () { - var _this = this; - /** Actions buttons **/ - var actions = []; - - function toggle(item, pressed) { - if (pressed) { - _this.plots[item.param] = true; - } else { - delete _this.plots[item.param]; - } - _this.reloadData(_this.hplcData); - } - - - /** Toolbar for peaks Average **/ - if (this.peaks != null) { - var items = []; - for (var i = 0; i < this.peakKeys.length; i++) { - var color = this.colorPeak[this.peakKeys[i]]; - items.push({ - text: "Peak #" + i + " " + this.peakKeys[i].replace("- ", " to #").replace(".0", "").replace(".0", "") + "", - peakid : this.peakKeys[i], - checked: false, - checkHandler: function (sender, pressed) { - var item = new Object(); - item.param = sender.peakid; - toggle(item, pressed); - } - }); - } - - var menu = Ext.create('Ext.menu.Menu', { - id: 'mainMenu', - style: { - overflow: 'visible' - }, - items: items - }); - var tb = Ext.create('Ext.toolbar.Toolbar'); - tb.add({ - text: 'Peaks Avg.', - menu: menu - }); - actions.push(tb); - } - - - - for (var i = 0; i < this.hplcData.length; i++) { - if (this.hplcData[i].showOnMenu != false) { - var param = this.hplcData[i].param; - var style = "style='padding:0 0px 0 5px;'"; - actions.push({ - text : "
" + BUI.getRectangleColorDIV(this.hplcData[i].color, 10, 10) + " " + this.hplcData[i].label + "
", - id : _this.id + param, - param : param, - enableToggle : true, - scope : this, - margin : 5, - toggleHandler : toggle, - pressed : (_this.plots[param] != null) - }); - } - } - - actions.push("->"); - actions.push({ - text : "Save", - scope : this, - icon : '../images/save.gif', - handler : function (item, pressed) { - var largeImage = document.createElement("img"); - largeImage.style.display = 'block'; - largeImage.style.width = 200 + "px"; - largeImage.style.height = 200 + "px"; - largeImage.setAttribute('src', Dygraph.Export.asCanvas(this.dygraphObject.dygraph).toDataURL()); - window.open(Dygraph.Export.asCanvas(this.dygraphObject.dygraph).toDataURL(), 'Image', ''); - } - }); - - return actions; -}; - - -MergesHPLCGraph.prototype.input = function () { - return DATADOC.getScatteringHPLCFrameData(); -}; - -MergesHPLCGraph.prototype.test = function (targetId) { - var mainPlotPanel = new MergesHPLCGraph({ - title : 'Scattering', - width : this.plotWidth, - height : 500, - showRangeSelector : false, - xParam : 0, - xlabel : "scattering_I", - plots : { - "scattering_I" : true, - "subtracted_I" : true, - "buffer_I" : true - } - }); - mainPlotPanel.getPanel().render(targetId); - mainPlotPanel.loadData(mainPlotPanel.input()); -}; - - -function NetworkWidget(args) { - this.id = "NetworkViewer_" + Math.random().toString().replace(".", "_"); - - this.label = true; - if (args != null) { - if (args.targetId != null) { - this.targetId = args.targetId; - } - if (args.label != null) { - this.label = args.label; - } - } - - this.onVertexOver = new Event(this); - this.onVertexOut = new Event(this); -} - -NetworkWidget.prototype.draw = function(dataset, formatter, layout) { - - this.graphCanvas = new GraphCanvas(this.id, document.getElementById(this.targetId), { - "labeled" : this.label, - "multipleSelectionEnabled" : false, - "draggingCanvasEnabled" : false - }); - this.graphCanvas.draw(dataset, formatter, layout); - - var _this = this; - this.graphCanvas.onVertexOver.attach(function(sender, nodeId) { - _this.onVertexOver.notify(nodeId); - }); - - this.graphCanvas.onVertexOut.attach(function(sender, nodeId) { - _this.onVertexOut.notify(nodeId); - }); -}; - -/** SELECT VERTICES BY NAME * */ -NetworkWidget.prototype.selectVertexByName = function(vertexName) { - var vertices = this.getDataset().getVertexByName(vertexName); - if (vertices != null) { - for ( var nodeId in vertices) { - if (vertices.hasOwnProperty(nodeId)) { - var vertexId = vertices[nodeId].getId(); - this.selectVertexById(vertexId); - } - } - } -}; - -NetworkWidget.prototype.selectVerticesByName = function(verticesName) { - for ( var i = 0; i < verticesName.length; i++) { - this.selectVertexByName(verticesName[i]); - } -}; - -/** SELECT VERTICES BY ID * */ -NetworkWidget.prototype.selectVertexById = function(vertexId) { - this.graphCanvas.selectNode(vertexId); - this.blinkVertexById(vertexId); -}; - -NetworkWidget.prototype.selectVerticesById = function(verticesId) { - for ( var i = 0; i < verticesId.length; i++) { - this.selectVertexById(verticesId[i]); - } -}; - -/** VECINDARIO * */ -NetworkWidget.prototype.selectNeighbourhood = function() { - this.selectEdgesFromVertices(); - this.selectAdjacent(); -}; - -/** DESELECT * */ -NetworkWidget.prototype.deselectNodes = function() { - this.graphCanvas.deselectNodes(); -}; - -/** SELECT ALL NODES * */ -NetworkWidget.prototype.selectAllNodes = function() { - this.getGraphCanvas().selectAllNodes(); -}; - -/** SELECT EVERYTHING * */ -NetworkWidget.prototype.selectAll = function() { - this.getGraphCanvas().selectAll(); -}; - -/** SELECT ALL EDGES * */ -NetworkWidget.prototype.selectAllEdges = function() { - this.getGraphCanvas().selectAllEdges(); -}; - -/** ZOOM * */ -NetworkWidget.prototype.setScale = function(value) { - this.graphCanvas.setScale(value); -}; - -NetworkWidget.prototype.getScale = function() { - return this.graphCanvas.getScale(value); -}; - -/** SELECT ADJACENT VERTICES FROM SELECTED VERTICES * */ -NetworkWidget.prototype.selectAdjacent = function() { - var selectedVertices = this.getGraphCanvas().getSelectedVertices(); - var edges = []; - for ( var i = 0; i < selectedVertices.length; i++) { - edges = edges.concat(this.getGraphCanvas().getDataset().getVertexById(selectedVertices[i]).getEdges()); - } - var vertices = []; - for ( i = 0; i < edges.length; i++) { - vertices.push(edges[i].getNodeSource().getId()); - vertices.push(edges[i].getNodeTarget().getId()); - } - - this.selectVerticesById(vertices); -}; - -/** SELECT EDGES FROM SELECTED VERTICES * */ -NetworkWidget.prototype.selectEdgesFromVertices = function() { - var selectedVertices = this.getGraphCanvas().getSelectedVertices(); - var edges = []; - for ( var i = 0; i < selectedVertices.length; i++) { - edges = edges.concat(this.getGraphCanvas().getDataset().getVertexById(selectedVertices[i]).getEdges()); - } - var edgesId = []; - for ( i = 0; i < edges.length; i++) { - edgesId.push(edges[i].getId()); - } - this.getGraphCanvas().selectEdges(edgesId); -}; - -/** BLINKING * */ -NetworkWidget.prototype.blinkVertexById = function(vertexId) { - this.graphCanvas.blinkVertexById(vertexId); -}; - -/** COMPONENTE CONEXA DE LOS NODOS SELECCIONADOS * */ -NetworkWidget.prototype.selectConnectedComponent = function() { - var elements = this.getConnectedComponent(); - this.selectVerticesById(elements.nodes); - this.graphCanvas.selectEdges(elements.edges); -}; - -NetworkWidget.prototype.getConnectedComponent = function() { - var nodosVisitados = {}; - var aristasVisitadas = {}; - var arrNodos = []; - var arrAristas = []; - var selectedGraphNodesId = this.getGraphCanvas().getSelectedVertices(); - for ( var i = 0; i < selectedGraphNodesId.length; i++) { - this.visitNode(selectedGraphNodesId[i], nodosVisitados, aristasVisitadas, arrNodos, arrAristas); - } - return { - nodes : arrNodos, - edges : arrAristas - }; -}; - -NetworkWidget.prototype.visitNode = function(nodeId, nodosVisitados, aristasVisitadas, arrNodos, arrAristas) { - nodosVisitados[nodeId] = true; - arrNodos.push(nodeId); - var nodeEdges = this.getDataset().getVertexById(nodeId).getEdges(); - for ( var j = 0; j < nodeEdges.length; j++) { - var edge = nodeEdges[j]; - var edgeId = edge.getId(); - if (aristasVisitadas[edgeId] == null) { - aristasVisitadas[edgeId] = true; - arrAristas.push(edgeId); - var nodeTargetId = edge.getNodeTarget().getId(); - if (nodosVisitados[nodeTargetId] == null) { - this.visitNode(nodeTargetId, nodosVisitados, aristasVisitadas, arrNodos, arrAristas); - } - var nodeSourceId = edge.getNodeSource().getId(); - if (nodosVisitados[nodeSourceId] == null) { - this.visitNode(nodeSourceId, nodosVisitados, aristasVisitadas, arrNodos, arrAristas); - } - } - } -}; - -/** COLLAPSE SELECTED VERTICES * */ -NetworkWidget.prototype.collapse = function() { - var selectedVertices = this.getGraphCanvas().getSelectedVertices(); - var xMin = -Infinity; - var xMax = Infinity; - var yMin = -Infinity; - var yMax = Infinity; - - for ( var i = 0; i < selectedVertices.length; i++) { - var vertex = this.getGraphCanvas().getLayout().getNodeById(selectedVertices[i]); - if (xMin < vertex.x) { - xMin = vertex.x; - } - if (xMax > vertex.x) { - xMax = vertex.x; - } - if (yMin < vertex.y) { - yMin = vertex.y; - } - if (yMax > vertex.y) { - yMax = vertex.y; - } - } - - var centerX = xMin - xMax; - var centerY = yMin - yMax; - var radius = (xMax - xMin) / 4; - - var count = selectedVertices.length; - var verticesCoordinates = []; - - for ( i = 0; i < selectedVertices.length; i++) { - x = centerX + radius * Math.sin(i * 2 * Math.PI / count); - y = centerY + radius * Math.cos(i * 2 * Math.PI / count); - verticesCoordinates.push({ - 'x' : x, - 'y' : y - }); - } - - for ( i = 0; i < selectedVertices.length; i++) { - this.getGraphCanvas().getLayout().getNodeById(selectedVertices[i]).setCoordinates(verticesCoordinates[i].x, verticesCoordinates[i].y); - } -}; - -/** SETTER FONT SIZE * */ -NetworkWidget.prototype.setVerticesFontSize = function(value) { - for ( var nodeId in this.getDataset().getVertices()) { - if (this.getDataset().getVertices().hasOwnProperty(nodeId)) { - this.getFormatter().getVertexById(nodeId).getDefault().setFontSize(value); - } - } -}; - -/** GETTERS * */ -NetworkWidget.prototype.getFormatter = function() { - return this.getGraphCanvas().getFormatter(); -}; -NetworkWidget.prototype.getLayout = function() { - return this.getGraphCanvas().getLayout(); -}; - -NetworkWidget.prototype.getDataset = function() { - return this.getGraphCanvas().getDataset(); -}; - -NetworkWidget.prototype.getGraphCanvas = function() { - return this.graphCanvas; -}; - -RangeWhiskerGraph.prototype.cleanArray = GenericGraph.prototype.cleanArray; -RangeWhiskerGraph.prototype.plotAxes = GenericGraph.prototype.plotAxes; -RangeWhiskerGraph.prototype.plotRuler = GenericGraph.prototype.plotRuler; -RangeWhiskerGraph.prototype.drawSVGVerticalText = GenericGraph.prototype.drawSVGVerticalText; -RangeWhiskerGraph.prototype.getClassColor = GenericGraph.prototype.getClassColor; -RangeWhiskerGraph.prototype.getDimensions = GenericGraph.prototype.getDimensions; -RangeWhiskerGraph.prototype.calculate = GenericGraph.prototype.calculate; -RangeWhiskerGraph.prototype.getMedian = GenericGraph.prototype.getMedian; -RangeWhiskerGraph.prototype.pointToPixel = GenericGraph.prototype.pointToPixel; -RangeWhiskerGraph.prototype.maxValueWhisker = GenericGraph.prototype.maxValueWhisker; -RangeWhiskerGraph.prototype.refresh = GenericGraph.prototype.refresh; - -/** - * Subclass of GenericGraph - * - * @plotHorizontalByCluster - */ -function RangeWhiskerGraph(args) { - this.maxBoxWidth = 25; - - if (args == null) { - args = {}; - } - args.plotHorizontalByCluster = false; - - GenericGraph.call(this, args); - - if (args.maxBoxWidth != null) { - this.maxBoxWidth = args.maxBoxWidth; - } -} - -RangeWhiskerGraph.prototype.refresh = function(data) { - document.getElementById(this.targetId).innerHTML = ""; - this.draw(this.targetId, data); -}; - -RangeWhiskerGraph.prototype.isNumber = function(value) { - if (value == "") - return false; - - var d = parseInt(value); - if (!isNaN(d)) - return true; - else - return false; - -}; - -/** - There are several different methods for calculating quartiles.[1] This calculator uses a method described by Moore and McCabe to find quartile values. - The same method also used by The TI-83 to calculate quartile values. - With this method, the first quartile is the median of the numbers below the median, the third quartile is the median of the numbers above the median. - - http://www.miniwebtool.com/quartile-calculator/ - http://www.alcula.com/calculators/statistics/box-plot/ - - **/ -RangeWhiskerGraph.prototype.getQ1 = function(array) { - array = array.slice(0, array.length / 2); - return this.getMedian(array); -}; - -RangeWhiskerGraph.prototype.getQ3 = function(array) { - array = array.slice((array.length + 1) / 2); - return this.getMedian(array); - -}; - -RangeWhiskerGraph.prototype.getQ2 = function(array) { - return this.getMedian(array); -}; - -RangeWhiskerGraph.prototype.getBelowOutliers = function(belowLimit, array) { - var points = []; - for ( var i = 0; i < array.length; i++) { - if (array[i] <= belowLimit) { - points.push(array[i]); - } - } - return points; -}; - -RangeWhiskerGraph.prototype.getAboveOutliers = function(aboveLimit, array) { - var points = []; - for ( var i = 0; i < array.length; i++) { - if (array[i] >= aboveLimit) { - points.push(array[i]); - } - } - return points; -}; - -RangeWhiskerGraph.prototype.minValueWhisker = function(belowLimit, q1, array) { - var points = []; - - for ( var i = 0; i < array.length; i++) { - if ((array[i] < q1) && (array[i]) > belowLimit) { - points.push(array[i]); - } - } - - if (points.length > 0) { - points.sort(function(a, b) { - return a - b; - }); - return points[0]; - } - return null; -}; - -//RangeWhiskerGraph.prototype.maxValueWhisker = function(aboveLimit, q3, array){ -// var points = []; -// for (var i = 0; i < array.length; i++){ -// if ((array[i] > q3) && (array[i]) <= aboveLimit){ -// points.push(array[i]); -// } -// } -// if (points.length > 0){ -// points.sort(function(a, b){return a - b;}); -// return points[points.length - 1]; -// } -// return null; -//}; - -RangeWhiskerGraph.prototype.drawPoints = function(boxProperties) { - if (this.plotPoints) { - for ( var i = 0; i < boxProperties.values.length; i++) { - var value = boxProperties.values[i]; - var toPixel = this.pointToPixel(value, boxProperties); - SVG.drawCircle(boxProperties.x, toPixel, this.pointRadius, this.svg, - [ - [ "fill", "green" ], [ "fill-opacity", this.fillOpacityPoint ], [ 'stroke-opacity', this.strokeOpacityPoint ], - [ "stroke", "black" ] ]); - } - } -}; - -RangeWhiskerGraph.prototype.plotRangeQ1Q3 = function(data, properties) { - var posX = this.left + this.rulerWidth; - - var boxBordersPointsQ1 = []; - var boxBordersPointsQ3 = []; - var Q2 = []; - - for ( var i = 0; i < data.clusters.length; i++) { - var cluster = data.clusters[i]; - /** inter cluster space **/ - posX = posX + this.interClustersSpace; - - for ( var j = 0; j < cluster.classes.length; j++) { - var ratio = properties.width / (properties.xValues.range); - var coorX = (cluster.x - properties.xValues.min) * ratio + this.rulerWidth; - var boxProperties = { - name : cluster.classes[j].name, - values : cluster.classes[j].values, - minPoint : properties.minPoint, - maxPoint : properties.maxPoint, - x : coorX + this.left, - y : this.top, - width : properties.classWidth, - height : this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight - }; - - var result = this.calculate(boxProperties.values); - var boxColor = this.getClassColor(boxProperties.name); - - if (this.isNumber(result.Q1) && this.isNumber(result.Q3)) { - var x = boxProperties.x; - var y = this.pointToPixel(result.Q1, boxProperties); - if (boxBordersPointsQ1[cluster.classes[j].name] == null) { - boxBordersPointsQ1[cluster.classes[j].name] = []; - } - boxBordersPointsQ1[cluster.classes[j].name].push({ - x : x, - y : y - }); - - x = boxProperties.x; - y = this.pointToPixel(result.Q3, boxProperties); - if (boxBordersPointsQ3[cluster.classes[j].name] == null) { - boxBordersPointsQ3[cluster.classes[j].name] = []; - } - boxBordersPointsQ3[cluster.classes[j].name].push({ - x : x, - y : y - }); - } else { - - if (this.isNumber(result.Q2)) { - - if (boxBordersPointsQ1[cluster.classes[j].name] == null) { - boxBordersPointsQ1[cluster.classes[j].name] = []; - } - - if (boxBordersPointsQ3[cluster.classes[j].name] == null) { - boxBordersPointsQ3[cluster.classes[j].name] = []; - } - - boxBordersPointsQ1[cluster.classes[j].name].push({ - x : boxProperties.x, - y : this.pointToPixel(result.Q2, boxProperties) - }); - boxBordersPointsQ3[cluster.classes[j].name].push({ - x : boxProperties.x, - y : this.pointToPixel(result.Q2, boxProperties) - }); - } - } - } - } - for ( var classe in boxBordersPointsQ1) { - var points = boxBordersPointsQ1[classe]; - var pointsSVG = ""; - for (var k = 0; k < points.length; k++) { - pointsSVG = Number(points[k].x).toFixed(1) + "," + Number(points[k].y).toFixed(1) + " " + pointsSVG; - } - - points = boxBordersPointsQ3[classe]; - for (var z = points.length - 1; z >= 0; z--) { - pointsSVG = Number(points[z].x).toFixed(1) + "," + Number(points[z].y).toFixed(1) + " " + pointsSVG; - } - - SVG.drawPoligon(pointsSVG, this.svg, [ - [ "fill", this.getClassColor(classe) ], [ "opacity", "0.3" ], [ "stroke", "black" ], [ "stroke-width", 1 ] ]); - } -}; - -RangeWhiskerGraph.prototype.plotWhisters = function(data, properties) { - var colors = [ "yellow", "orange", "green" ]; - - this.plotRangeQ1Q3(data, properties); - var Q2 = {}; - - for ( var i = 0; i < data.clusters.length; i++) { - var cluster = data.clusters[i]; - for ( var j = 0; j < cluster.classes.length; j++) { - var ratio = properties.width / (properties.xValues.range); - var coorX = (cluster.x - properties.xValues.min) * ratio + this.left + this.rulerWidth - this.rulerStroke; - var boxProperties = { - name : cluster.classes[j].name, - values : cluster.classes[j].values, - minPoint : properties.minPoint, - maxPoint : properties.maxPoint, - x : coorX, - y : this.top, - width : properties.classWidth, - height : this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight - }; - - this.drawPoints(boxProperties); - - /** PLOTTING Q2 **/ - var result = this.calculate(boxProperties.values); - var boxColor = this.getClassColor(boxProperties.name); - if (this.isNumber(result.Q2)) { - if (Q2[boxProperties.name] != null) { - SVG.drawLine(boxProperties.x, this.pointToPixel(result.Q2, boxProperties), Q2[boxProperties.name].x, Q2[boxProperties.name].y, - this.svg, [ [ "stroke", boxColor ], [ "stroke-width", "2" ] ]); - } - Q2[boxProperties.name] = { - x : boxProperties.x, - y : this.pointToPixel(result.Q2, boxProperties) - } - } - } - } - -}; - -RangeWhiskerGraph.prototype.draw = function(targetId, data) { - //this.calculate(data); - this.targetId = targetId; - var properties = (this.getDimensions(data)); - this.svg = SVG.createSVGCanvas(document.getElementById(this.targetId), [ [ "width", this.width ], [ "height", this.height ] ]); - this.plotAxes(properties); - this.plotWhisters(data, properties); -}; - -RangeWhiskerGraph.prototype.input = function() { - return DATADOC.getBoxWhikerData(); -}; - -RangeWhiskerGraph.prototype.test = function(targetId) { - var plot = new RangeWhiskerGraph({ - targetId : targetId, - height : 350, - width : 450, - maxBoxWidth : 25 - }); - plot.refresh(this.input()); -}; - -StdDevDyGraph.prototype.dblclick = DygraphWidget.prototype.dblclick; -StdDevDyGraph.prototype._createHTLMWrapper = DygraphWidget.prototype._createHTLMWrapper; -StdDevDyGraph.prototype.draw = DygraphWidget.prototype.draw; - -function StdDevDyGraph(targetId, args) { - this.scaled = false; - if (args == null) { - args = {}; - } - args.customBars = true; - DygraphWidget.prototype.constructor.call(this, targetId, args); -} - -StdDevDyGraph.prototype.input = function () { - return { - data : [ [ 1, [ 2, 3, 3.5 ], [ 4, 4.2, 5 ] ], [ 2, [ 5, 5.5, 5.7 ], [ 4, 4.2, 5 ] ] ], - colors : [ "blue", "red" ], - labels : [ "", 'data1', 'data2' ] - }; -}; - -StdDevDyGraph.prototype.test = function (targetId) { - var dygraphObject = new StdDevDyGraph(targetId, { - width : 500, - height : 400, - xlabel : "xLabel", - showRangeSelector : false - }); - - dygraphObject.draw(dygraphObject.input().data, dygraphObject.input().colors, dygraphObject.input().labels); -}; - - - -function AbinitioGrid(args) { - this.height = null; - this.width = null; - this.id = BUI.id(); - - if (args != null) { - if (args.height != null) { - this.height = args.height; - - if (args.width != null) { - this.width = args.width; - } - } - } - - this.onSelected = new Event(this); -}; - - -AbinitioGrid.prototype.refresh = function(subtractions){ - this.store.loadData(this._prepareData(subtractions)); -}; - -AbinitioGrid.prototype._prepareData = function(subtractions){ - /** Parsing data * */ - var models = []; - for (var l = 0; l < subtractions.length; l++) { - var subtraction = subtractions[l]; - for (var k = 0; k < subtraction.substractionToAbInitioModel3VOs.length; k++) { - var data = subtraction.substractionToAbInitioModel3VOs[k].abinitiomodel3VO; - if (data.averagedModel != null) { - models.push(data.averagedModel); - models[models.length - 1].type = "Reference"; - } - - if (data.shapeDeterminationModel != null) { - models.push(data.shapeDeterminationModel); - models[models.length - 1].type = "Refined"; - } - - if (data.modelList3VO != null) { - if (data.modelList3VO.modeltolist3VOs != null) { - for (var i = 0; i < data.modelList3VO.modeltolist3VOs.length; i++) { - models.push(data.modelList3VO.modeltolist3VOs[i].model3VO); - models[models.length - 1].type = "Model"; - } - } - } - } - } - return models; -}; - -AbinitioGrid.prototype.getPanel = function(){ - var _this = this; - - - var modelFields = [ "modelId", "type", "chiSqrt", "dmax", "firFile", "logFile", "fitFile", "pdbFile", "rfactor", "rg", "volume" ]; - Ext.define('AbinitioModel', { - extend : 'Ext.data.Model', - fields : modelFields - - }); - - /** - * Store in Memory - */ - this.store = Ext.create('Ext.data.Store', { - model : 'AbinitioModel', - autoload : true, - groupField : 'type' - }); - - - var groupingFeature = Ext.create('Ext.grid.feature.Grouping',{ - groupHeaderTpl: '{name} ({rows.length} model{[values.rows.length > 1 ? "s" : ""]})', - startCollapsed: true, - collapsible : true - }); - - this.grid = Ext.create('Ext.grid.Panel', { - collapsible : false, - resizable : true, - features: [groupingFeature], - autoscroll : true, - multiSelect : true, - store : this.store, - height : this.height, - width : this.width, - margin : 10, - columns : [ { - text : "Type", - dataindex : "type", - hidden : true, - renderer : function(a, b, record) { - return record.data.type; - }, - flex : 1 - }, - { - text : "ModelId", - dataindex : "modelId", - hidden : true, - renderer : function(a, b, record) { - return record.data.modelId; - - }, - flex : 1 - }, - - { - text : "chiSqrt", - dataindex : "chiSqrt", - renderer : function(a, b, record) { - if (record.data.dmax != null) { - return BUI.formatValuesUnits(record.data.chiSqrt, "", 12, this.decimals); - } - - }, - flex : 1 - }, - { - text : "Dmax", - dataindex : "dmax", - renderer : function(a, b, record) { - if (record.data.dmax != null) { - return BUI.formatValuesUnits(record.data.dmax, "nm", 12, this.decimals); - } - - }, - flex : 1 - }, { - text : "rFactor", - dataindex : "rfactor", - hidden : true, - renderer : function(a, b, record) { - if (record.data.rfactor != null) { - return record.data.rfactor; - } - }, - flex : 1 - }, { - text : "Rg", - dataindex : "rg", - renderer : function(a, b, record) { - if (record.data.rg != null) { - return BUI.formatValuesUnits(record.data.rg, "nm", 12, this.decimals); - } - - }, - flex : 1 - }, - { - text : "Volume", - dataindex : "volume", - renderer : function(a, b, record) { - if (record.raw.volume != null){ - return BUI.formatValuesUnits(record.raw.volume, '') + " nm3"; - } - }, - flex : 1 - }, - { - text : "PDB", - dataindex : "pdbFile", - renderer : function(a, b, record) { - if (record.data.pdbFile != null){ - return record.data.pdbFile.split("/")[record.data.pdbFile.split("/").length - 1]; - } - }, - flex : 1 - }, { - text : "Fir", - dataindex : "firFile", - renderer : function(a, b, record) { - if (record.data.firFile != null){ - return record.data.firFile.split("/")[record.data.firFile.split("/").length - 1]; - } - }, - flex : 1 - }, { - text : "LOG", - dataindex : "logFile", - hidden : true, - renderer : function(a, b, record) { - if (record.data.logFile != null){ - return record.data.logFile.split("/")[record.data.logFile.split("/").length - 1]; - } - }, - flex : 1 - } - ], - viewConfig : { - enableTextSelection : true, - preserveScrollOnRefresh : true, - stripeRows : true, - listeners : { - 'celldblclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - }, - 'cellclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - var models = []; - for (var i = 0; i < grid.getSelectionModel().selected.items.length; i++) { - models.push(grid.getSelectionModel().selected.items[i].raw); - } - _this.onSelected.notify(models); - } - } - } - }); - return this.grid; - -}; - - -function AdditiveGrid(args) { - this.onRemoveButtonClicked = new Event(this); -} - -AdditiveGrid.prototype.getBuffer = function() { - return this.buffer; -}; - -AdditiveGrid.prototype._getActions = function() { - var _this = this; - /** Actions buttons **/ - var actions = []; - - actions.push(Ext.create('Ext.Action', { - icon : '../images/add.png', - text : 'Add', - disabled : true, - alwaysEnabled : true, - handler : function(widget, event) { - _this.buffer.bufferhasadditive3VOs.push(BIOSAXS_BEANS.getBufferhasAdditive3VO()); - _this.refresh(_this.buffer, _this.experiment); - } - })); - - return actions; -}; - -AdditiveGrid.prototype.refresh = function(buffer, experiment) { - this.buffer = buffer; - this.experiment = experiment; - if (buffer) { - if (buffer.bufferhasadditive3VOs) { - this.features = buffer.bufferhasadditive3VOs; - } - } - this.experiment = experiment; - this.store.loadData(this._prepareData(), false); -}; - -AdditiveGrid.prototype.getAdditives = function() { - var additives = []; - for ( var i = 0; i < this.store.getCount(); i++) { - var bufferHasAdditive = BIOSAXS_BEANS.getBufferhasAdditive3VO(); - var data = this.store.getAt(i).getData(); - - bufferHasAdditive.additive3VO.name = data.name; - bufferHasAdditive.additive3VO.comments = data.comments; - bufferHasAdditive.additive3VO.additiveType = data.additiveType; - - bufferHasAdditive.bufferId = this.buffer.bufferId; - bufferHasAdditive.bufferHasAdditiveId = data.bufferHasAdditiveId; - bufferHasAdditive.quantity = data.quantity; - additives.push(bufferHasAdditive); - } - - return additives; -}; - -AdditiveGrid.prototype._getFields = function(buffers) { - var columns = [ - - { - header : 'Name', - dataIndex : 'name', - type : 'string', - editor : { - allowBlank : true - }, - flex : 1 - }, - { - header : 'Type', - name : 'additiveType', - dataIndex : 'additiveType', - editor : { - xtype : 'combobox', - typeAhead : true, - triggerAction : 'all', - selectOnTab : true, - store : BIOSAXS.proposal.getAdditiveTypes(), - lazyRender : true, - listClass : 'x-combo-list-small' - }, - flex : 0.6 - }, - { - header : 'Quantity', - dataIndex : 'quantity', - name : 'quantity', - editor : { - allowBlank : true - }, - type : 'string', - flex : 1 - }, - { - xtype : 'actioncolumn', - items : [ { - icon : '../images/cancel.png', - tooltip : 'Delete additive', - scope : this, - handler : function(grid, rowIndex, colIndex) { - if ((grid.getStore().getAt(rowIndex).data.bufferHasAdditiveId == null)|| (grid.getStore().getAt(rowIndex).data.bufferHasAdditiveId == "")) { - grid.getStore().removeAt(rowIndex); - } else { - this.onRemoveButtonClicked.notify({ - 'bufferId' : this.buffer.bufferId, - 'bufferHasAdditiveId' : this.store.getAt(rowIndex).data.bufferHasAdditiveId - }); - } - } - } ] - } ]; - - return columns; -}; - -AdditiveGrid.prototype._prepareData = function() { - var data = []; - if (this.features == null) { - this.features = []; - } - for (var i = 0; i < this.features.length; i++) { - var object = this.features[i]; - object.name = this.features[i].additive3VO.name; - object.additiveType = this.features[i].additive3VO.additiveType; - object.comments = this.features[i].additive3VO.comments; - object.additiveId = this.features[i].additive3VO.additiveId; - data.push(object); - } - return data; -}; - -AdditiveGrid.prototype.getPanel = function(buffer, experiment) { - this.buffer = buffer; - this.features = buffer.bufferhasadditive3VOs; - this.experiment = experiment; - return this._renderGrid(); -}; - -AdditiveGrid.prototype.getStore = function() { - var _this = this; - var store = Ext.create('Ext.data.Store', { - fields : [ "name", "additiveType", "comments", "additiveId", "bufferHasAdditiveId", "quantity" ], - autoload : false, - data : this._prepareData(), - listeners : { - update : function(store, record) { - record.index = _this.grid.getSelectionModel().getCurrentPosition().row; - _this.buffer.bufferhasadditive3VOs[record.index].additive3VO.name = record.data.name; - _this.buffer.bufferhasadditive3VOs[record.index].additive3VO.additiveType = record.data.additiveType; - _this.buffer.bufferhasadditive3VOs[record.index].additive3VO.comments = record.data.comments; - _this.buffer.bufferhasadditive3VOs[record.index].quantity = record.data.quantity; - } - } - }); - - // store.sort('bufferHasAdditiveId', 'ASC'); - store.loadData(this._prepareData(), false); - return store; -}; - -AdditiveGrid.prototype._renderGrid = function() { - var _this = this; - this.store = this.getStore(); - - var cellEditing = Ext.create('Ext.grid.plugin.CellEditing', { - clicksToEdit : 1 - }); - - this.grid = Ext.create('Ext.grid.Panel', { - dockedItems : [ { - xtype : 'toolbar', - items : this._getActions() - } ], - store : this.store, - height : 230, - title : "Additives", - width : "100%", - columns : _this._getFields(), - plugins : [ cellEditing ], - viewConfig : { - stripeRows : true, - listeners : { - itemcontextmenu : function(view, rec, node, index, e) { - e.stopEvent(); - contextMenu.showAt(e.getXY()); - return false; - } - } - }, - selModel : { - mode : 'SINGLE' - } - }); - - return this.grid; -}; - -AdditiveGrid.prototype.input = function() { -}; - -AdditiveGrid.prototype.test = function(targetId) { - var grid = new AdditiveGrid(); - var panel = grid.getPanel([]); - panel.render(targetId); - -}; - -/** AnalysisGrid **/ -function AnalysisGrid(args) { - var _this = this; - - this.id = BUI.id(); - if (Ext.get("mainPanel")){ - this.width = Ext.get("mainPanel").getWidth(); - } - else{ - this.width = this.maxWidth; - } - this.maxWidth = 1500; - - /** Visibles **/ - this.isGuinierTabVisible = true; - this.isGnomTabVisible = true; - this.isPorodTabVisible = true; - this.isScatteringPlotVisible = true; - this.isAbinitioTabVisible = true; - this.showButtonsVisible = true; - this.isI0Visible = true; - - this.margin = null; - this.grouped = true; - - this.hideNulls = false; - this.decimals = 4; - this.height = null; - this.sorters = [ { - property : 'conc', - direction : 'ASC' - } ]; - - if (args != null) { - if (args.grouped != null) { - this.grouped = args.grouped; - } - - if (args.showButtonsVisible != null) { - this.showButtonsVisible = args.showButtonsVisible; - } - if (args.isI0Visible != null) { - this.isI0Visible = args.isI0Visible; - } - if (args.sorters != null) { - this.sorters = args.sorters; - } - if (args.isScatteringPlotVisible != null) { - this.isScatteringPlotVisible = args.isScatteringPlotVisible; - } - if (args.isGuinierTabVisible != null) { - this.isGuinierTabVisible = args.isGuinierTabVisible; - } - if (args.isGnomTabVisible != null) { - this.isGnomTabVisible = args.isGnomTabVisible; - } - if (args.isPorodTabVisible != null) { - this.isPorodTabVisible = args.isPorodTabVisible; - } - if (args.hideNulls != null) { - this.hideNulls = args.hideNulls; - } - if (args.height != null) { - this.height = args.height; - } - if (args.width != null) { - this.width = args.width; - } - if (args.maxWidth != null) { - this.maxWidth = args.maxWidth; - } - } -} - -AnalysisGrid.prototype.refresh = function(data, args) { - this.store.loadData(this._prepareData(data), false); - if (args != null){ - if (args.experiment != null){ - this.experiment = args.experiment; - } - } -}; - -AnalysisGrid.prototype._getPorod = function() { - return { - text : 'Porod', - name : 'Porod', - columns : [ - { - text : 'Volume', - dataIndex : 'volumeEdna', - width : 75, - sortable : true, - hidden : !this.isPorodTabVisible, - renderer : function(val, y, sample) { - if (sample.raw.volume != null) - return BUI.formatValuesUnits(sample.raw.volume, '') + " nm3"; - } - }, - { - text : 'MM Vol. est.', - dataIndex : 'volumeEdna', - tooltip : '[Volume/2 - Volume/1.5] (Guinier)', - sortable : true, - width : 95, - hidden : !this.isPorodTabVisible, - renderer : function(val, y, sample) { - if (sample.raw.volume != null) - return Number(sample.raw.volume / 2).toFixed(1) + " - " + Number(sample.raw.volume / 1.5).toFixed(1)+ "kD"; - } - } ] - }; -}; - - -AnalysisGrid.prototype._getFramesColumn = function() { - var _this = this; - return { - text : 'Frames (Averaged/Total)', - dataIndex : 'datacollection', - name : 'datacollection', - sortable : true, - width : 150, - renderer : function(dataCollections, y, data) { - /** Bug of Webservices: frames count were swapped with frames averages **/ - if (data.raw.bufferAfterFramesCount){ - if (data.raw.bufferAfterFramesMerged){ - if (parseInt(data.raw.bufferAfterFramesMerged) > parseInt(data.raw.bufferAfterFramesCount)){ - var aux = parseInt(data.raw.bufferAfterFramesCount); - data.raw.bufferAfterFramesCount= data.raw.bufferAfterFramesMerged; - data.raw.bufferAfterFramesMerged = aux; - } - } - } - - if (data.raw.bufferBeforeFramesCount){ - if (data.raw.bufferBeforeFramesMerged){ - if (parseInt(data.raw.bufferBeforeFramesMerged) > parseInt(data.raw.bufferBeforeFramesCount)){ - var aux = parseInt(data.raw.bufferBeforeFramesCount); - data.raw.bufferBeforeFramesCount= data.raw.bufferBeforeFramesMerged; - data.raw.bufferBeforeFramesMerged = aux; - } - } - - } - - var bufferAcronym = data.raw.bufferAcronym; - var macromoleculeAcronym = data.raw.macromoleculeAcronym; - var bbmerges = data.raw.bufferBeforeFramesMerged; - var molmerges = data.raw.framesMerge; - var bamerges = data.raw.bufferAfterFramesMerged; - var totalframes = data.raw.framesCount; - var bufferId = data.raw.bufferId; - var macromoleculeId = data.raw.macromoleculeId; - var macromoleculeColor = null; - if (_this.experiment != null){ - macromoleculeColor = _this.experiment.macromoleculeColors[data.raw.macromoleculeId]; - } - - /** BUG in the database to be fixed **/ - try{ - if (totalframes != null){ - if(molmerges != null){ - if (parseFloat(totalframes) < parseFloat(molmerges)){ - var aux = totalframes; - totalframes = molmerges; - molmerges = aux; - } - } - } - } - catch(e){ - - } - - return BUI.getHTMLTableForFrameAveraged(bufferAcronym, - macromoleculeAcronym, - bbmerges, - molmerges, - bamerges, - totalframes, - bufferId, - macromoleculeId, - macromoleculeColor); - } - }; -}; - -AnalysisGrid.prototype._getColumns = function() { - var _this = this; - return [ - { - name : 'groupeField', - dataIndex : 'groupeField', - hidden : true - - }, - { - "header" : "subtractionId", - hidden : true, - "dataIndex" : "subtractionId", - "name" : "subtractionId" - }, - { - header : "Macromolecule", - dataIndex : "macromoleculeAcronym", - name : "macromoleculeAcronym", - renderer : function(val, y, sample) { - return '
' + val + '
' + - BUI.formatValuesUnits(sample.raw.conc, "mg/ml", 10, this.decimals) + '
' + - BUI.formatValuesUnits(sample.raw.exposureTemperature, "C", 10, this.decimals) + '
' - } - }, - { - header : "Order", - dataIndex : "priorityLevelId", - name : "priorityLevelId", - hidden : true - }, - { - header : "Code", - dataIndex : "code", - name : "code", - hidden : true - }, - { - header : "Conc.", - dataIndex : "conc", - width : 80, - name : "conc", - type : "number", - hidden : true, - renderer : function(val, y, sample) { - return BUI.formatValuesUnits(val, "mg/ml", 10, this.decimals); - } - }, - { - text : 'Scattering', - width : 100, - dataIndex : 'subtractionId', - name : 'subtractionId', - hidden : !this.isScatteringPlotVisible, - renderer : function(val, y, sample) { - var url = BUI.getURL() + '&type=scattering&subtractionId=' + sample.raw.subtractionId; - var event = "OnClick= window.open('" + url + "')"; - return ''; - } - }, - { - text : 'Kratky', - width : 100, - dataIndex : 'subtractionId', - hidden : true, - name : 'subtractionId', - renderer : function(val, y, sample) { - var url = BUI.getURL() + '&type=kratky&subtractionId=' + sample.raw.subtractionId; - var event = "OnClick= window.open('" + url + "')"; - return ''; - } - }, - this._getFramesColumn(), - { - text : 'File Name', - dataIndex : 'averageFilePath', - name : 'averageFilePath', - sortable : true, - width : 150, - hidden : true, - renderer : function(dataCollections, y, data) { - return BUI.getHTMLTableForPrefixes(data.raw.bufferBeforeAverageFilePath, data.raw.averageFilePath, - data.raw.bufferAfterAverageFilePath); - } - }, - - { - text : 'Guinier', - name : 'Guinier', - columns : [ - { - text : 'Rg', - dataIndex : 'rgGuinier', - name : 'rgGuinier', - hidden : !this.isGuinierTabVisible, - width : 75, - tooltip : 'In polymer physics, the radius of gyration is used to describe the dimensions of a polymer chain.', - sortable : true, - renderer : function(val, y, sample) { - if (sample.raw.rgGuinier != null) { - /** Show warning if rgGuinier and rgGnom differ more than 10% **/ - if (Math.abs(sample.raw.rgGuinier - sample.raw.rgGnom) > (sample.raw.rgGuinier * 0.1)) { - return "" + BUI.formatValuesUnits(sample.raw.rgGuinier, "") + ""; - - } - return BUI.formatValuesUnits(sample.raw.rgGuinier, "nm", 12, this.decimals); - } - } - }, - { - text : 'Points', - dataIndex : 'points', - sortable : true, - width : 100, - type : 'string', - hidden : !this.isGuinierTabVisible, - renderer : function(val, y, sample) { - if ((sample.raw.firstPointUsed == "") || (sample.raw.firstPointUsed == null)) - return; - return "" + sample.raw.firstPointUsed + " - " + sample.raw.lastPointUsed + " (" + - (sample.raw.lastPointUsed - sample.raw.firstPointUsed) + " )"; - } - }, - { - text : 'Quality', - dataIndex : 'quality', - hidden : !this.isGuinierTabVisible, - tooltip : 'Estimated data quality. 1.0 - means ideal quality, 0.0 - unusable data. In table format it is given in percent (100% - ideal quality, 0% - unusable data). Please note that this estimation is based only on the Guinier interval (very low angles).', - width : 60, - sortable : true, - renderer : function(val, y, sample) { - if (sample.raw.quality != null) { - val = sample.raw.quality; - if ((val != null) && (val != "")) { - return "" + (Number(val) * 100).toFixed(2) + " %"; - } - } - } - }, { - text : 'I(0)', - dataIndex : 'I0', - sortable : true, - hidden : !this.isI0Visible, - tooltip : 'Extrapolated scattering intensity at zero angle I(0) (forward scattering)', - width : 75, - type : 'string', - renderer : function(val, y, sample) { - if (sample.raw.I0 != null) { - return BUI.formatValuesErrorUnitsScientificFormat(sample.raw.I0, sample.raw.i0stdev, ""); - } - } - }, { - text : 'Aggregated', - tooltip : "If aggregation was detected from the slope of the data curve at low angles the value is '1', otherwise '0'.", - dataIndex : 'isagregated', - hidden : true, - width : 75, - renderer : function(val, y, sample) { - if ((sample.raw.isagregated != null)) { - if (val == true) { - return "Yes"; - } else { - return "No"; - } - } - } - }, { - text : 'Guinier', - sortable : true, - dataIndex : 'subtractionId', - type : 'string', - width : 100, - hidden : true, - renderer : function(val, y, sample) { - - if (sample.raw.subtractionId != null) { - var url = BUI.getURL() + '&type=guinier&subtractionId=' + sample.raw.subtractionId; - var event = "OnClick= window.open('" + url + "')"; - return ''; - } - } - } ] - }, - { - text : 'Gnom', - name : 'Gnom', - - columns : [ { - text : 'Rg', - dataIndex : 'rgGnom', - type : 'string', - width : 65, - hidden : !this.isGnomTabVisible, - sortable : true, - renderer : function(val, y, sample) { - /** Show warning if rgGuinier and rgGnom differ more than 10% **/ - if (sample.raw.rgGnom != null) { - if (Math.abs(sample.raw.rgGuinier - sample.raw.rgGnom) > (sample.raw.rgGuinier * 0.1)) { - return "" + BUI.formatValuesUnits(sample.raw.rgGnom, "") + ""; - - } - return BUI.formatValuesUnits(sample.raw.rgGnom, "nm"); - } - } - }, { - text : 'Total', - dataIndex : 'total', - width : 65, - hidden : !this.isGnomTabVisible, - sortable : true, - renderer : function(val, y, sample) { - if (sample.raw.total != null) - return BUI.formatValuesUnits(sample.raw.total, ''); - } - }, { - text : 'Dmax', - dataIndex : 'dmax', - sortable : true, - width : 75, - hidden : !this.isGnomTabVisible, - renderer : function(val, y, sample) { - if (sample.raw.dmax != null) - return BUI.formatValuesUnits(sample.raw.dmax, "") + " nm"; - } - }, { - text : 'P(r)', - sortable : true, - hidden : true, - width : 100, - dataIndex : 'subtractionId', - type : 'string', - renderer : function(val, y, sample) { - var url = BUI.getURL() + '&type=gnom&subtractionId=' + sample.raw.subtractionId; - var event = "OnClick= window.open('" + url + "')"; - return ''; - } - } ] - }, - this._getPorod(), - { - text : 'AbInitio Modeling', - name : 'AbInitio_modeling', - - columns : [ - { - text : 'NSD', - dataIndex : 'volumeEdna', - width : 100, - sortable : true, - hidden : true, - renderer : function(val, y, sample) { - var url = BUI.getNSDImageURL(sample.raw.modelListId); - var event = "OnClick= window.open('" + url + "')"; - return ''; - } - }, - { - text : 'Chi2', - dataIndex : 'volumeEdna', - sortable : true, - hidden : true, - width : 100, - renderer : function(val, y, sample) { - var url = BUI.getCHI2ImageURL(sample.raw.modelListId); - var event = "OnClick= window.open('" + url + "')"; - return ''; - } - }, - { - text : 'Pdb', - dataIndex : 'volumeEdna', - tooltip : 'Damaver: The program suite DAMAVER is a set of programs to align ab initio models, select the most typical one and build an averaged model. Dammif : Rapid ab initio shape determination by simulated annealing using a single phase dummy atom model. Dammin :Ab initio shape determination by simulated annealing using a single phase dummy atom model', - sortable : true, - width : 125, - hidden : !this.isAbinitioTabVisible, - renderer : function(val, y, sample) { - var html = new String(); - var split = null; - var url = null; - var file = sample.raw.averagedModel; - if (file != null) { - split = file.split("/"); - if (split.length > 0) { - url = BUI.getPdbURL() + '&type=AVERAGED&abInitioModelId=' + sample.raw.abInitioModelId; - html = html + ''+ split[split.length - 1] + '

'; - - } - } - - file = sample.raw.rapidShapeDeterminationModel; - if (file != null) { - split = file.split("/"); - if (split.length > 0) { - url = BUI.getPdbURL() + '&type=RAPIDSHAPEDETERMINATIONMODEL&abInitioModelId=' + sample.raw.abInitioModelId; - html = html + '' + split[split.length - 1] + '

'; - } - } - - file = sample.raw.shapeDeterminationModel; - if (file != null) { - split = file.split("/"); - if (split.length > 0) { - url = BUI.getPdbURL() + '&type=SHAPEDETERMINATIONMODEL&abInitioModelId=' + sample.raw.abInitioModelId; - html = html + ''+ split[split.length - 1] + ''; - } - } - return html; - } - }, - { - text : 'Damaver', - dataIndex : 'volumeEdna', - hidden : true, - tooltip : 'Damaver: The program suite DAMAVER is a set of programs to align ab initio models, select the most typical one and build an averaged model. ', - sortable : true, - width : 125, - renderer : function(val, y, sample) { - var file = sample.raw.averagedModel; - if (file != null) { - var split = file.split("/"); - if (split.length > 0) { - var url = BUI.getPdbURL() + '&type=AVERAGED&abInitioModelId=' + sample.raw.abInitioModelId; - return '' + split[split.length - 1]+ ''; - } - } - return sample.raw.averagedModel; - } - }, - { - text : 'Dammif', - dataIndex : 'volumeEdna', - hidden : true, - tooltip : 'Dammif : Rapid ab initio shape determination by simulated annealing using a single phase dummy atom model', - sortable : true, - width : 125, - renderer : function(val, y, sample) { - var file = sample.raw.rapidShapeDeterminationModel; - if (file != null) { - var split = file.split("/"); - if (split.length > 0) { - var url = BUI.getPdbURL() + '&type=RAPIDSHAPEDETERMINATIONMODEL&abInitioModelId=' + sample.raw.abInitioModelId; - return '' + split[split.length - 1] + ''; - } - } - return sample.raw.averagedModel; - } - }, - { - text : 'Dammin', - dataIndex : 'volumeEdna', - hidden : true, - tooltip : 'Dammin :Ab initio shape determination by simulated annealing using a single phase dummy atom model', - sortable : true, - width : 125, - renderer : function(val, y, sample) { - var file = sample.raw.shapeDeterminationModel; - if (file != null) { - var split = file.split("/"); - if (split.length > 0) { - var url = BUI.getPdbURL() + '&type=SHAPEDETERMINATIONMODEL&abInitioModelId=' + sample.raw.abInitioModelId; - return '' + split[split.length - 1]+ ''; - } - } - return sample.raw.averagedModel; - } - } ] - }, { - text : 'Time', - dataIndex : 'substractionCreationTime', - name : 'substractionCreationTime', - hidden : true, - width : 80, - sortable : true, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - try { - if (record.raw.substractionCreationTime != null) { - return moment(record.raw.substractionCreationTime).format('h:mm:ss a'); - } - } catch (e) { - return "NA"; - } - } - }, { - text : 'Date', - dataIndex : 'substractionCreationTime', - name : 'substractionCreationTime', - hidden : true, - width : 80, - sortable : true, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - try { - if (record.raw.substractionCreationTime != null) { - return moment(record.raw.substractionCreationTime).format("LL"); - } - } catch (e) { - return "NA"; - } - } - }, - this._getButtons()]; -}; - -AnalysisGrid.prototype._getButtons = function() { - return { - id : this.id + 'buttonPlot', - name : 'buttonPlot', - hidden : !this.showButtonsVisible, - width : 110, - sortable : false, - renderer : function(value, metaData, sample, rowIndex, colIndex, store) { - var html = ""; - - if (sample.raw.subtractionId) { - html = html + ""; - if (sample.raw.rapidShapeDeterminationModelId != null) { - html = html + ""; - } - } - return html + "
" + BUI.getGreenButton('Calibration', { - height : 20, - width : 100 - }) + "
" + BUI.getGreenButton('Primary Data Proc.', { - height : 20, - width : 100 - }) + "
" + BUI.getGreenButton('AbInitio Modeling', { - height : 20, - width : 100 - }) + "
"; - } - }; -}; -AnalysisGrid.prototype._prepareData = function(data) { - if (this.hideNulls) { - var result = []; - for ( var i = 0; i < data.length; i++) { - if (data[i].subtractionId != null) { - data[i].groupeField = data[i].macromoleculeAcronym + " " + data[i].bufferAcronym; - result.push(data[i]); - } - } - return result; - } else { - return data; - } -}; - -AnalysisGrid.prototype.getPanel = function(data) { - var _this = this; - var columns = this._getColumns(); - - var fields = JSON.parse(JSON.stringify(columns)); - fields.push({ - name : 'experimentId', - dataIndex : 'experimentId' - - }); - this.store = Ext.create('Ext.data.Store', { - fields : fields, - autoload : true, - data : this._prepareData(data), - groupField : 'groupeField' - }); - - this.store.sort(this.sorters); - - var features = []; - - if (this.grouped) { - features.push({ - ftype : 'grouping', - groupHeaderTpl : '{name}', - hideGroupedHeader : false, - startCollapsed : false - }); - } - - this.grid = Ext.create('Ext.grid.Panel', { - style : { - padding : 5 - }, - maxWidth : this.maxWidth, - width : this.width, - height : this.height, - store : this.store, - columns : columns, - resizable : true, - features : features, - viewConfig : { - preserveScrollOnRefresh : true, - stripeRows : true, - listeners : { - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonPlot') { - if (e.target.defaultValue == 'AbInitio Modeling') { - var url = BUI.getPDBVisualizerURL(record.raw.averagedModelId, record.raw.subtractionId, record.raw.experimentId); - window.open(url, "_blank"); - } - - if (e.target.defaultValue == 'Primary Data Proc.') { - _this._edit(record.raw); - } - - if (e.target.defaultValue == 'Calibration') { - _this._showCalibration(record.raw); - } - } - } - } - }, - selModel : { - mode : 'SINGLE' - } - }); - - return this.grid; - -}; - -AnalysisGrid.prototype._openVisualizarBySubstractionId = function(record) { - //experimentId, subtractionId) { - var experimentId = record.experimentId; - var subtractionId = record.subtractionId; - - var _this = this; - var adapter = new BiosaxsDataAdapter(); - this.subtractionId = subtractionId; - - adapter.onSuccess.attach(function(sender, data) { - var experiment = new Experiment(data); - var experimentList = new ExperimentList([ experiment ]); - var subtraction = experiment.getSubtractionById(_this.subtractionId); - _this.grid.setLoading(false); - _this._openVisualizer(experimentList, subtraction, record); - }); - this.grid.setLoading("ISPyB: Fetching experiment"); - adapter.getExperimentById(experimentId, "MEDIUM"); -}; - -AnalysisGrid.prototype._edit = function(record) { - var experimentId = record.experimentId; - var _this = this; - - if (BIOSAXS.proposal.macromolecules == null) { - this.grid.setLoading("ISPyB: Fetching proposal"); - BIOSAXS.proposal.onInitialized.attach(function(sender, data) { - _this._openVisualizarBySubstractionId(record); - }); - BIOSAXS.proposal.init(); - } else { - this._openVisualizarBySubstractionId(record); - } -}; - - -AnalysisGrid.prototype._showCalibration = function(row) { - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - Ext.create('Ext.window.Window', { - title : 'Calibration', - width : 900, - resizable : true, - height : 400, - modal : true, - frame : false, - draggable : true, - closable : true, - autoscroll : true, - paddin : 5, - layout : { - type : 'vbox', - align : 'stretch' - }, - items : [ new AnalysisGrid({ - isGuinierTabVisible : false, - isGnomTabVisible : false, - isPorodTabVisible : false, - isAbinitioTabVisible : false, - isI0Visible : true, - showButtonsVisible : false, - height : 350, - sorters : [ { - property : 'experimentId', - direction : 'DESC' - } ] - }).getPanel(data) ] - }).show(); - }); - adapter.getAnalysisCalibrationByProposalId(); -}; - -AnalysisGrid.prototype._openVisualizer = function(experimentList, subtraction, record) { - var merges = experimentList.getMergesByDataCollectionId(subtraction.dataCollectionId); - var mergeIdList = []; - for ( var i = 0; i < merges.length; i++) { - mergeIdList.push(merges[i].mergeId); - } - - var dataAdapter = new BiosaxsDataAdapter(); - dataAdapter.onSuccess.attach(function(sender, merges) { - var dataCollectionCurveVisualizer = new DataCollectionCurveVisualizer(); - dataCollectionCurveVisualizer.draw(); - dataCollectionCurveVisualizer.refresh(merges, experimentList, subtraction.dataCollectionId, record); - }); - - dataAdapter.onError.attach(function(sender, error) { - }); - - dataAdapter.getMergesByIdsList(mergeIdList); -}; - -AnalysisGrid.prototype.input = function() { - return { - data : DATADOC.getData_3367().slice(20, 30),//[{"total":"0.447505552082","bufferBeforeMeasurementId":22150,"sampleMergeId":12373,"averagedModelId":43636,"I0":"32.50776","proposalCode":"OPD","averagedModel":"/data/pyarch/bm29/opd29/1137/1d/damaver.pdb","bufferAfterMergeId":12374,"framesCount":"10","bufferBeforeMergeId":12372,"averageFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_016_ave.dat","bufferAfterMeasurementId":22152,"rgGuinier":"2.96883","subtractedFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_016_sub.dat","firstPointUsed":"30","chi2RgFilePath":"/data/pyarch/bm29/opd29/1137/1d/chi2_R.png","abInitioModelId":272,"macromoleculeId":112,"code":"_20.0_1.25","transmission":"100.0","timeStart":"2013-07-17 17:10:25.743734","bufferAcronym":"MES","quality":"0.87091","shapeDeterminationModelId":43638,"expermientComments":"[BsxCube] Generated from BsxCube","bufferId":707,"isagregated":"False","dmax":"10.390905","bufferBeforeAverageFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_015_ave.dat","exposureTemperature":"20.0","subtractionId":5165,"conc":"1.25","rapidShapeDeterminationModel":"/data/pyarch/bm29/opd29/1137/1d/damfilt.pdb","experimentCreationDate":"Jul 17, 2013 5:08:37 PM","lastPointUsed":"92","modelListId":272,"framesMerge":"10","rapidShapeDeterminationModelId":43637,"bufferAfterAverageFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_017_ave.dat","nsdFilePath":"/data/pyarch/bm29/opd29/1137/1d/nsd.png","bufferAfterFramesMerged":"10","experimentId":1137,"macromoleculeAcronym":"MG386","i0stdev":"0.05726128","sampleMeasurementId":22151,"measurementComments":"[1] MES","priorityLevelId":2,"bufferBeforeFramesMerged":"10","substractionCreationTime":"Jul 17, 2013 5:12:32 PM","proposalNumber":"29","rgGnom":"3.05242714339","volume":"44.1406","shapeDeterminationModel":"/data/pyarch/bm29/opd29/1137/1d/dammin.pdb","comments":null},{"total":"0.582641941147","bufferBeforeMeasurementId":22152,"sampleMergeId":12375,"averagedModelId":43809,"I0":"31.4366153846","proposalCode":"OPD","averagedModel":"/data/pyarch/bm29/opd29/1137/1d/damaver.pdb","bufferAfterMergeId":12376,"framesCount":"10","bufferBeforeMergeId":12374,"averageFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_018_ave.dat","bufferAfterMeasurementId":22155,"rgGuinier":"2.95541","subtractedFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_018_sub.dat","firstPointUsed":"21","chi2RgFilePath":"/data/pyarch/bm29/opd29/1137/1d/chi2_R.png","abInitioModelId":273,"macromoleculeId":112,"code":"_20.0_0.65000000000000002","transmission":"100.0","timeStart":"2013-07-17 17:12:55.837462","bufferAcronym":"MES","quality":"0.870164","shapeDeterminationModelId":43811,"expermientComments":"[BsxCube] Generated from BsxCube","bufferId":707,"isagregated":"False","dmax":"10.343935","bufferBeforeAverageFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_017_ave.dat","exposureTemperature":"20.0","subtractionId":5166,"conc":"0.65000000000000002","rapidShapeDeterminationModel":"/data/pyarch/bm29/opd29/1137/1d/damfilt.pdb","experimentCreationDate":"Jul 17, 2013 5:08:37 PM","lastPointUsed":"80","modelListId":273,"framesMerge":"10","rapidShapeDeterminationModelId":43810,"bufferAfterAverageFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_019_ave.dat","nsdFilePath":"/data/pyarch/bm29/opd29/1137/1d/nsd.png","bufferAfterFramesMerged":"10","experimentId":1137,"macromoleculeAcronym":"MG386","i0stdev":"0.100250461538","sampleMeasurementId":22154,"measurementComments":"[2] MES","priorityLevelId":4,"bufferBeforeFramesMerged":"10","substractionCreationTime":"Jul 17, 2013 5:15:02 PM","proposalNumber":"29","rgGnom":"2.9963404542","volume":"42.2255","shapeDeterminationModel":"/data/pyarch/bm29/opd29/1137/1d/dammin.pdb","comments":null}], - proposal : new ResultsAssemblyGrid().input().proposal - }; -}; - -AnalysisGrid.prototype.test = function(targetId) { - var analysisGrid = new AnalysisGrid(); - BIOSAXS.proposal = new Proposal(analysisGrid.input().proposal); - var panel = analysisGrid.getPanel(analysisGrid.input().data); - panel.render(targetId); -}; - - -function HPLCAnalysisGrid(args) { - AnalysisGrid.prototype.constructor.call(this, args); -} - -HPLCAnalysisGrid.prototype._edit = AnalysisGrid.prototype._edit; -HPLCAnalysisGrid.prototype._getColumns = AnalysisGrid.prototype._getColumns; -HPLCAnalysisGrid.prototype._openVisualizarBySubstractionId = AnalysisGrid.prototype._openVisualizarBySubstractionId; -HPLCAnalysisGrid.prototype._openVisualizer = AnalysisGrid.prototype._openVisualizer; -HPLCAnalysisGrid.prototype._prepareData = AnalysisGrid.prototype._prepareData; -HPLCAnalysisGrid.prototype._showCalibration = AnalysisGrid.prototype._showCalibration; -HPLCAnalysisGrid.prototype.getPanel = AnalysisGrid.prototype.getPanel; -HPLCAnalysisGrid.prototype.input = AnalysisGrid.prototype.input; -HPLCAnalysisGrid.prototype.test = AnalysisGrid.prototype.test; -HPLCAnalysisGrid.prototype.refresh = AnalysisGrid.prototype.refresh; -HPLCAnalysisGrid.prototype._getPorod = AnalysisGrid.prototype._getPorod; - -HPLCAnalysisGrid.prototype._getButtons = function() { - return { - id : this.id + 'buttonPlot', - name : 'buttonPlot', - hidden : !this.showButtonsVisible, - width : 110, - sortable : false, - renderer : function(value, metaData, sample, rowIndex, colIndex, store) { - var html = ""; - - if (sample.raw.subtractionId) { - if (sample.raw.rapidShapeDeterminationModelId != null) { - html = html + ""; - } - } - return html + "
" + BUI.getGreenButton('AbInitio Modeling', { - height : 20, - width : 100 - }) + "
"; - } - }; -}; - -HPLCAnalysisGrid.prototype._getFramesColumn = function() { - return { - text : 'Frames', - dataIndex : 'datacollection', - name : 'datacollection', - sortable : true, - width : 150, - renderer : function(dataCollections, y, data) { - molmerges = data.raw.framesMerge; - totalframes = data.raw.framesCount; - return molmerges +" - "+ totalframes; - } - }; -}; - - - - -/** - * Rigid body grid to show PDB, symmetry and multiplicity - * - * - * #onUploadFile click on upload file - */ -function AprioriRigidBodyGrid(args) { - - this.height = 250; - this.btnEditVisible = true; - this.btnRemoveVisible = true; - - if (args != null) { - if (args.height != null) { - this.height = args.height; - } - if (args.btnEditVisible != null) { - this.btnEditVisible = args.btnEditVisible; - } - if (args.btnRemoveVisible != null) { - this.btnRemoveVisible = args.btnRemoveVisible; - } - } - - /** Events **/ - this.onUploadFile = new Event(this); - this.onRemove = new Event(this); -} - -AprioriRigidBodyGrid.prototype._getColumns = function() { -}; - -AprioriRigidBodyGrid.prototype._getTopButtons = function() { - var _this = this; - /** Actions buttons **/ - var actions = []; - - /** ADD BUTTON **/ - actions.push(Ext.create('Ext.Action', { - icon : '../images/add.png', - text : 'Add', - disabled : false, - handler : function(widget, event) { - _this.onAddButtonClicked.notify(); - } - })); - - return actions; -}; - -AprioriRigidBodyGrid.prototype.refresh = function(macromolecule) { - this.macromolecule = macromolecule; - if (macromolecule != null){ - this.pdbStore.loadData(macromolecule.structure3VOs); - } -}; - -AprioriRigidBodyGrid.prototype._prepareData = function() { - var data = []; - for ( var i = 0; i < this.features.length; i++) { - data.push(this.features[i]); - } - return data; -}; - -AprioriRigidBodyGrid.prototype._getPlugins = function() { - var _this = this; - var plugins = []; - plugins.push(Ext.create('Ext.grid.plugin.RowEditing', { - clicksToEdit : 1, - listeners : { - validateedit : function(grid, e) { - /** Comments are always updatable* */ - e.record.raw.symmetry = e.newValues.symmetry; - e.record.raw.multiplicity = e.newValues.multiplicity; - - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, proposal) { - BIOSAXS.proposal.setItems(proposal); - _this.refresh(BIOSAXS.proposal.getMacromoleculeById(_this.macromolecule.macromoleculeId)); - _this.panel.setLoading(false); - }); - adapter.onError.attach(function() { - alert("Error"); - }); - - _this.panel.setLoading(); - adapter.saveStructure(e.record.raw); - } - } - })); - return plugins; -}; - -AprioriRigidBodyGrid.prototype.getPanel = function() { - var _this = this; - - this.pdbStore = Ext.create('Ext.data.Store', { - fields : [ 'filePath', 'structureId', 'structureType', 'symmetry', 'structureId', 'name', 'multiplicity' ], - groupField : 'structureType', - sorters : { - property : 'structureId', - direction : 'DESC' - } - }); - - var groupingFeature = Ext.create('Ext.grid.feature.Grouping', { - groupHeaderTpl : Ext.create('Ext.XTemplate', - "
{name:this.formatName}
", { - formatName : function(name) { - return name; - } - }), - hideGroupedHeader : true, - startCollapsed : false - }); - - this.panel = Ext.create('Ext.grid.Panel', { - margin : "15 10 0 10", - height : this.height, - store : this.pdbStore, - plugins : _this._getPlugins(), - tbar : [ { - text : 'Add Modeling Option (PDB)', - icon : '../images/add.png', - handler : function() { - _this.onUploadFile.notify('PDB', 'Upload PDB File'); - } - } - - ], - columns : [ - { - text : "structureId", - flex : 0.2, - hidden : true, - dataIndex : 'structureId', - sortable : true - }, - { - text : "File", - flex : 0.5, - dataIndex : 'filePath', - sortable : true, - hidden : true - }, - { - text : "PDB", - flex : 0.4, - dataIndex : 'name', - sortable : true - }, - { - text : "Symmetry", - flex : 0.2, - dataIndex : 'symmetry', - sortable : true, - editor : { - xtype : 'combobox', - typeAhead : true, - triggerAction : 'all', - selectOnTab : true, - store : [ [ "P1", "P1" ], [ "P2", "P2" ], [ "P3", "P3" ], [ "P4", "P4" ], [ "P5", "P5" ], [ "P6", "P6" ], [ "P32", "P32" ], [ "P42", "P42" ], - [ "P52", "P52" ], [ "P62", "P62" ], [ "P222", "P222" ] ], - } - }, { - text : "Multiplicity", - flex : 0.2, - dataIndex : 'multiplicity', - sortable : true, - editor : { - xtype : 'textfield' - } - - }, { - text : "Subunit", - flex : 0.2, - dataIndex : 'isSubunit', - sortable : true, - hidden : true - }, { - text : "Type", - flex : 0.2, - dataIndex : 'structureType', - sortable : true, - hidden : true - }, - - { - id : this.id + 'REMOVE', - flex : 0.2, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - return BUI.getRedButton('REMOVE'); - } - }, ], - - listeners : { - itemdblclick : function(dataview, record, item, e) { - _this._editExperiment(record.raw.experimentId); - }, - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'REMOVE') { - var dataAdapter = new BiosaxsDataAdapter(); - dataAdapter.onSuccess.attach(function() { - _this.panel.setLoading(false); - _this.onRemove.notify(); - }); - _this.panel.setLoading("Removing PDB file"); - dataAdapter.removeStructure(record.data.structureId); - } - - } - }, - viewConfig : { - getRowClass : function(record, rowIdx, params, store) { - if (record.raw.isSubunit != null) { - return "blue-row"; - } - } - } - }); - - return this.panel; -}; - - - - -AprioriRigidBodyGrid.prototype.input = function() { - return { - proposal : DATADOC.getProposal_10(), - dewars : DATADOC.getDewars_10() - - }; -}; - -AprioriRigidBodyGrid.prototype.test = function(targetId) { - var AprioriRigidBodyGrid = new AprioriRigidBodyGrid({ - height : 150 - }); - BIOSAXS.proposal = new Proposal(AprioriRigidBodyGrid.input().proposal); - var panel = AprioriRigidBodyGrid.getPanel(AprioriRigidBodyGrid.input().dewars); - panel.render(targetId); - -}; - -/** - * It shows buffer grid with a top bar with "Add" button - * - * @height - * @searchBar - * @collapsed - * @width - */ -function BufferGrid(args) { - this.height = 500; - this.searchBar = false; - this.tbar = false; - this.collapsed = false; - this.id = BUI.id(); - - if (args != null) { - if (args.height != null) { - this.height = args.height; - } - if (args.searchBar != null) { - this.searchBar = args.searchBar; - } - - if (args.tbar != null) { - this.tbar = args.tbar; - } - - if (args.collapsed != null) { - this.collapsed = args.collapsed; - } - - if (args.width != null) { - this.width = args.width; - } - } -} - -BufferGrid.prototype._edit = function(bufferId) { - var _this = this; - var window = new BufferWindow(); - window.onSuccess.attach(function(sender, proposal) { - _this.store.loadData(BIOSAXS.proposal.getBuffers()); - }); - window.draw(BIOSAXS.proposal.getBufferById(bufferId)); -}; - -BufferGrid.prototype.refresh = function(buffers) { - this.store.loadData(this._prepareData(buffers), false); -}; - -BufferGrid.prototype._prepareData = function(buffers) { - return buffers; -}; - -BufferGrid.prototype._getTbar = function() { - var _this = this; - var actions = []; - - actions.push(Ext.create('Ext.Action', { - icon : '../images/add.png', - text : 'Add buffer', - disabled : false, - handler : function(widget, event) { - var window = new BufferWindow(); - window.onSuccess.attach(function(sender) { - _this.store.loadData(BIOSAXS.proposal.getBuffers()); - }); - window.draw({}); - } - })); - return actions; -}; - -BufferGrid.prototype.getPanel = function(buffers) { - var _this = this; - - this.store = Ext.create('Ext.data.Store', { - fields : [ 'bufferId', 'acronym', 'name', 'composition' ], - data : buffers - }); - - this.store.sort('acronym'); - - var type = 'Ext.grid.Panel'; - if (this.searchBar == true) { - type = 'Ext.ux.LiveSearchGridPanel'; - } - - this.grid = Ext.create(type, { - title : 'Buffers', - collapsible : true, - collapsed : this.collapsed, - store : this.store, - height : this.height, - width : this.width, - columns : [ - /*{ - text : '', - dataIndex : 'bufferId', - width : 20, - renderer : function(val, y, sample) { - return BUI.getRectangleColorDIV(BIOSAXS.proposal.bufferColors[val], 10, 10); - } - },*/ - { - text : 'Acronym', - dataIndex : 'acronym', - flex : 1 - }, { - text : 'Name', - dataIndex : 'name', - flex : 1, - hidden : true - }, { - text : 'Composition', - dataIndex : 'composition', - flex : 1, - hidden : true - }, { - id : _this.id + 'buttonEditBuffer', - width : 80, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - return BUI.getGreenButton('EDIT'); - } - }, { - id : _this.id + 'buttonRemoveBuffer', - width : 85, - hidden : true, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - return BUI.getRedButton('REMOVE'); - } - } ], - flex : 1, - viewConfig : { - stripeRows : true, - listeners : { - 'celldblclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - _this._edit(record.data.bufferId); - }, - 'cellclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEditBuffer') { - _this._edit(record.data.bufferId); - } - - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemoveBuffer') { - BUI.showBetaWarning(); - } - } - - } - } - }); - - /** Adding the tbar **/ - if (this.tbar) { - this.grid.addDocked({ - xtype : 'toolbar', - items : this._getTbar() - }); - } - return this.grid; -}; - -BufferGrid.prototype.input = function() { - return new MacromoleculeGrid().input(); -}; - -BufferGrid.prototype.test = function(targetId) { - var bufferGrid = new BufferGrid({ - width : 800, - height : 350, - collapsed : false, - tbar : true - }); - - BIOSAXS.proposal = new Proposal(bufferGrid.input().proposal); - var panel = bufferGrid.getPanel(BIOSAXS.proposal.macromolecules); - panel.render(targetId); -}; - -/** - * A shipment may contains one or more cases where stock solutions and sample plates are stored - * - * @height - * @btnEditVisible - * @btnRemoveVisible - * - * #onEditButtonClicked - * #onAddButtonClicked - * #onRemoveButtonClicked - * #onDuplicateButtonClicked - */ -function CaseGrid(args) { - - this.height = 100; - this.btnEditVisible = true; - this.btnRemoveVisible = true; - - if (args != null) { - if (args.height != null) { - this.height = args.height; - } - if (args.btnEditVisible != null) { - this.btnEditVisible = args.btnEditVisible; - } - if (args.btnRemoveVisible != null) { - this.btnRemoveVisible = args.btnRemoveVisible; - } - } - - /** Events **/ - this.onEditButtonClicked = new Event(this); - this.onAddButtonClicked = new Event(this); - this.onRemoveButtonClicked = new Event(this); - this.onDuplicateButtonClicked = new Event(this); -} - -CaseGrid.prototype._getColumns = function() { - var _this = this; - - function actionItemRenderer(value, meta, record, rowIx, ColIx, store) { - /*if (record.raw.specimen3VOs.length > 0){ - return 'x-hide-display'; - }*/ - } - - var columns = [ - { - header : 'Code', - dataIndex : 'code', - name : 'code', - type : 'string', - flex : 1 - }, - { - header : 'Bar Code', - dataIndex : 'barCode', - name : 'barCode', - type : 'string', - flex : 1, - hidden : true - }, - { - header : 'BeamLine', - dataIndex : 'barCode', - type : 'string', - flex : 1, - renderer : function(comp, val, record) { - if (record.raw.sessionVO != null) { - return "" + record.raw.sessionVO.beamlineName + ""; - } - } - }, - { - header : 'Session', - dataIndex : 'barCode', - type : 'string', - flex : 1, - renderer : function(comp, val, record) { - if (record.raw.sessionVO != null) { - return "" + moment(record.raw.sessionVO.startDate).format("MMM Do YY") + ""; - } - } - }, - { - header : 'Status', - dataIndex : 'dewarStatus', - name : 'dewarStatus', - type : 'string', - flex : 1, - renderer : function(comp, val, record) { - if (new String(record.raw.dewarStatus).toUpperCase() == 'OPENED') { - return "" + new String(record.raw.dewarStatus).toUpperCase() + ""; - } - return "" + new String(record.raw.dewarStatus).toUpperCase() + ""; - } - }, - { - header : 'Type', - dataIndex : 'type', - name : 'type', - type : 'string', - flex : 1, - hidden : true - }, - { - header : 'Sample Plates', - dataIndex : 'plates', - name : 'plates', - type : 'string', - flex : 1, - hidden : true - }, - { - header : 'Stock Solutions', - dataIndex : 'plates', - name : 'plates', - type : 'string', - width : 100, - renderer : function(comp, val, record) { - var html = "
"; - var stockSolutions = BIOSAXS.proposal.getStockSolutionsByDewarId(record.raw.dewarId); - html = html + "" + stockSolutions.length + " x"; - return html + "
"; - } - }, { - header : 'isStorageDewar', - dataIndex : 'isStorageDewar', - name : 'isStorageDewar', - type : 'string', - flex : 1, - hidden : true - }, { - header : 'Tracking Number From Synchrotron', - dataIndex : 'trackingNumberFromSynchrotron', - name : 'trackingNumberFromSynchrotron', - type : 'string', - flex : 1, - hidden : true - }, { - header : 'Tracking Number To Synchrotron', - dataIndex : 'trackingNumberToSynchrotron', - name : 'trackingNumberToSynchrotron', - type : 'string', - flex : 1, - hidden : true - }, { - header : 'Storage Location', - dataIndex : 'storageLocation', - name : 'storageLocation', - type : 'string', - flex : 1, - hidden : false - }, { - header : 'Comments', - dataIndex : 'comments', - name : 'comments', - type : 'string', - flex : 1, - hidden : false - } - ]; - - if (this.btnEditVisible) { - columns.push({ - id : _this.id + 'buttonEdit', - text : '', - hidden : !_this.btnEditVisible, - width : 85, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - return BUI.getGreenButton('EDIT'); - } - }); - } - - if (this.btnRemoveVisible) { - columns.push({ - id : _this.id + 'buttonRemove', - width : 85, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - if (_this.btnRemoveVisible) { - return BUI.getRedButton('REMOVE'); - } - } - }); - } - - columns.push({ - dataIndex : 'comments', - type : 'string', - width : 85, - hidden : false, - renderer : function(comp, val, record) { - return BUI.getBlueButton("LABELS", { - href : BUI.getPrintcomponentURL(record.raw.dewarId) - }); - } - }); - - return columns; -}; - -CaseGrid.prototype._getTopButtons = function() { - var _this = this; - /** Actions buttons **/ - var actions = []; - - /** ADD BUTTON **/ - actions.push(Ext.create('Ext.Action', { - icon : '../images/add.png', - text : 'Add', - disabled : false, - handler : function(widget, event) { - _this.onAddButtonClicked.notify(); - } - })); - - return actions; -}; - -CaseGrid.prototype.refresh = function(dewars) { - this.features = dewars; - this.store.loadData(this._prepareData(dewars), false); -}; - -CaseGrid.prototype._sort = function(store) { - store.sort('dewarId', 'DESC'); -}; - -CaseGrid.prototype._prepareData = function() { - var data = []; - for ( var i = 0; i < this.features.length; i++) { - data.push(this.features[i]); - } - return data; -}; - -CaseGrid.prototype.getPanel = function(dewars, plates) { - this.features = dewars; - this.plates = plates; - return this._renderGrid(); -}; - -CaseGrid.prototype._edit = function(dewar) { - var _this = this; - var caseWindow = new CaseWindow(); - /**SAVED **/ - caseWindow.onSaved.attach(function(sender, dewar) { - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, shipment) { - _this.refresh(shipment.dewarVOs); - }); - adapter.saveCase(BIOSAXS.proposal.getShipmentByDewarId(dewar.dewarId).shippingId, dewar); - }); - caseWindow.draw(dewar); -}; - -CaseGrid.prototype._getStoreFields = function(data) { - return [ { - name : 'dewarId', - type : 'string' - }, { - name : 'barCode', - type : 'string' - }, { - name : 'code', - type : 'string' - }, { - name : 'comments', - type : 'string' - }, { - name : 'dewarStatus', - type : 'string' - }, { - name : 'isStorageDewar', - type : 'string' - }, { - name : 'plates', - type : 'string' - }, { - name : 'transportValue', - type : 'string' - }, { - name : 'trackingNumberFromSynchrotron', - type : 'string' - }, { - name : 'trackingNumberToSynchrotron', - type : 'string' - }, { - name : 'timeStamp', - type : 'string' - }, { - name : 'storageLocation', - type : 'string' - }, { - name : 'type', - type : 'string' - } - - ]; -}; - -CaseGrid.prototype._renderGrid = function() { - var _this = this; - - /** Store **/ - var data = this._prepareData(); - this.store = Ext.create('Ext.data.Store', { - fields : this._getStoreFields(data), - autoload : true, - data : data - }); - this._sort(this.store); - - this.store.loadData(data, false); - - this.grid = Ext.create('Ext.grid.Panel', { - style : { - padding : 5 - }, - height : this.height, - store : this.store, - columns : this._getColumns(), - viewConfig : { - stripeRows : true, - listeners : { - itemdblclick : function(dataview, record, item, e) { - _this._edit(record.raw); - }, - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEdit') { - _this._edit(record.raw); - } - - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemove') { - _this.onRemoveButtonClicked.notify(_this.store.getAt(rowIndex).raw.dewarId); - } - } - } - }, - selModel : { - mode : 'SINGLE' - } - }); - - var actions = _this._getTopButtons(); - this.grid.addDocked({ - xtype : 'toolbar', - items : actions - }); - - this.grid.getSelectionModel().on({ - selectionchange : function(sm, selections) { - if (selections.length) { - for ( var i = 0; i < actions.length; i++) { - if (actions[i].enable) { - actions[i].enable(); - } - } - } else { - for ( var i = 0; i < actions.length; i++) { - if (actions[i].alwaysEnabled == false) { - if (actions[i].disable) { - actions[i].disable(); - } - } - } - } - } - }); - return this.grid; -}; - -CaseGrid.prototype.input = function() { - return { - proposal : DATADOC.getProposal_10(), - dewars : DATADOC.getDewars_10() - - }; -}; - -CaseGrid.prototype.test = function(targetId) { - var CaseGrid = new CaseGrid({ - height : 150 - }); - BIOSAXS.proposal = new Proposal(CaseGrid.input().proposal); - var panel = CaseGrid.getPanel(CaseGrid.input().dewars); - panel.render(targetId); - -}; - -/** - * A shipment may contains one or more cases where stock solutions and sample plates are stored - * - * @height - * @btnEditVisible - * @btnRemoveVisible - * - * #onEditButtonClicked - * #onAddButtonClicked - * #onRemoveButtonClicked - * #onDuplicateButtonClicked - */ -function ExampleGrid(args) { - - this.height = 100; - this.btnEditVisible = true; - this.btnRemoveVisible = true; - - if (args != null) { - if (args.height != null) { - this.height = args.height; - } - if (args.btnEditVisible != null) { - this.btnEditVisible = args.btnEditVisible; - } - if (args.btnRemoveVisible != null) { - this.btnRemoveVisible = args.btnRemoveVisible; - } - } - - /** Events **/ - this.onEditButtonClicked = new Event(this); - this.onAddButtonClicked = new Event(this); - this.onRemoveButtonClicked = new Event(this); - this.onDuplicateButtonClicked = new Event(this); -} - -ExampleGrid.prototype._getColumns = function() { - var _this = this; - - function actionItemRenderer(value, meta, record, rowIx, ColIx, store) { - /*if (record.raw.specimen3VOs.length > 0){ - return 'x-hide-display'; - }*/ - } - - var columns = [ - { - header : 'Code', - dataIndex : 'code', - name : 'code', - type : 'string', - flex : 1 - }, - { - header : 'Bar Code', - dataIndex : 'barCode', - name : 'barCode', - type : 'string', - flex : 1, - hidden : true - }, - { - header : 'BeamLine', - dataIndex : 'barCode', - type : 'string', - flex : 1, - renderer : function(comp, val, record) { - if (record.raw.sessionVO != null) { - return "" + record.raw.sessionVO.beamlineName + ""; - } - } - }, - { - header : 'Session', - dataIndex : 'barCode', - type : 'string', - flex : 1, - renderer : function(comp, val, record) { - if (record.raw.sessionVO != null) { - return "" + moment(record.raw.sessionVO.startDate).format("MMM Do YY") + ""; - } - } - }, - { - header : 'Status', - dataIndex : 'dewarStatus', - name : 'dewarStatus', - type : 'string', - flex : 1, - renderer : function(comp, val, record) { - if (new String(record.raw.dewarStatus).toUpperCase() == 'OPENED') { - return "" + new String(record.raw.dewarStatus).toUpperCase() + ""; - } - return "" + new String(record.raw.dewarStatus).toUpperCase() + ""; - } - }, - { - header : 'Type', - dataIndex : 'type', - name : 'type', - type : 'string', - flex : 1, - hidden : true - }, - { - header : 'Sample Plates', - dataIndex : 'plates', - name : 'plates', - type : 'string', - flex : 1, - hidden : true - }, - { - header : 'Stock Solutions', - dataIndex : 'plates', - name : 'plates', - type : 'string', - width : 100, - renderer : function(comp, val, record) { - var html = "
"; - var stockSolutions = BIOSAXS.proposal.getStockSolutionsByDewarId(record.raw.dewarId); - html = html + "" + stockSolutions.length + " x"; - return html + "
"; - } - }, { - header : 'isStorageDewar', - dataIndex : 'isStorageDewar', - name : 'isStorageDewar', - type : 'string', - flex : 1, - hidden : true - }, { - header : 'Tracking Number From Synchrotron', - dataIndex : 'trackingNumberFromSynchrotron', - name : 'trackingNumberFromSynchrotron', - type : 'string', - flex : 1, - hidden : true - }, { - header : 'Tracking Number To Synchrotron', - dataIndex : 'trackingNumberToSynchrotron', - name : 'trackingNumberToSynchrotron', - type : 'string', - flex : 1, - hidden : true - }, { - header : 'Storage Location', - dataIndex : 'storageLocation', - name : 'storageLocation', - type : 'string', - flex : 1, - hidden : false - }, { - header : 'Comments', - dataIndex : 'comments', - name : 'comments', - type : 'string', - flex : 1, - hidden : false - } - ]; - - if (this.btnEditVisible) { - columns.push({ - id : _this.id + 'buttonEdit', - text : '', - hidden : !_this.btnEditVisible, - width : 85, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - return BUI.getGreenButton('EDIT'); - } - }); - } - - if (this.btnRemoveVisible) { - columns.push({ - id : _this.id + 'buttonRemove', - width : 85, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - if (_this.btnRemoveVisible) { - return BUI.getRedButton('REMOVE'); - } - } - }); - } - - columns.push({ - dataIndex : 'comments', - type : 'string', - width : 85, - hidden : false, - renderer : function(comp, val, record) { - return BUI.getBlueButton("LABELS", { - href : BUI.getPrintcomponentURL(record.raw.dewarId) - }); - } - }); - - return columns; -}; - -ExampleGrid.prototype._getTopButtons = function() { - var _this = this; - /** Actions buttons **/ - var actions = []; - - /** ADD BUTTON **/ - actions.push(Ext.create('Ext.Action', { - icon : '../images/add.png', - text : 'Add', - disabled : false, - handler : function(widget, event) { - _this.onAddButtonClicked.notify(); - } - })); - - return actions; -}; - -ExampleGrid.prototype.refresh = function(dewars) { - this.features = dewars; - this.store.loadData(this._prepareData(dewars), false); -}; - -ExampleGrid.prototype._sort = function(store) { - store.sort('dewarId', 'DESC'); -}; - -ExampleGrid.prototype._prepareData = function() { - var data = []; - for ( var i = 0; i < this.features.length; i++) { - data.push(this.features[i]); - } - return data; -}; - -ExampleGrid.prototype.getPanel = function() { - this.grid = Ext.create('Ext.grid.Panel', { - style : { - padding : 5 - }, - height : this.height, - store : this.store, - columns : this._getColumns(), - viewConfig : { - stripeRows : true, - listeners : { - itemdblclick : function(dataview, record, item, e) { - _this._edit(record.raw); - }, - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEdit') { - _this._edit(record.raw); - } - - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemove') { - _this.onRemoveButtonClicked.notify(_this.store.getAt(rowIndex).raw.dewarId); - } - } - } - }, - selModel : { - mode : 'SINGLE' - } - }); - - var actions = _this._getTopButtons(); - this.grid.addDocked({ - xtype : 'toolbar', - items : actions - }); - - this.grid.getSelectionModel().on({ - selectionchange : function(sm, selections) { - if (selections.length) { - for ( var i = 0; i < actions.length; i++) { - if (actions[i].enable) { - actions[i].enable(); - } - } - } else { - for ( var i = 0; i < actions.length; i++) { - if (actions[i].alwaysEnabled == false) { - if (actions[i].disable) { - actions[i].disable(); - } - } - } - } - } - }); - return this.grid; -}; - - -ExampleGrid.prototype._getStoreFields = function(data) { - return [ { - name : 'dewarId', - type : 'string' - }, { - name : 'barCode', - type : 'string' - }, { - name : 'code', - type : 'string' - }, { - name : 'comments', - type : 'string' - }, { - name : 'dewarStatus', - type : 'string' - }, { - name : 'isStorageDewar', - type : 'string' - }, { - name : 'plates', - type : 'string' - }, { - name : 'transportValue', - type : 'string' - }, { - name : 'trackingNumberFromSynchrotron', - type : 'string' - }, { - name : 'trackingNumberToSynchrotron', - type : 'string' - }, { - name : 'timeStamp', - type : 'string' - }, { - name : 'storageLocation', - type : 'string' - }, { - name : 'type', - type : 'string' - } - - ]; -}; - -ExampleGrid.prototype._renderGrid = function() { - var _this = this; - - /** Store **/ - var data = this._prepareData(); - this.store = Ext.create('Ext.data.Store', { - fields : this._getStoreFields(data), - autoload : true, - data : data - }); - this._sort(this.store); - - this.store.loadData(data, false); - - this.grid = Ext.create('Ext.grid.Panel', { - style : { - padding : 5 - }, - height : this.height, - store : this.store, - columns : this._getColumns(), - viewConfig : { - stripeRows : true, - listeners : { - itemdblclick : function(dataview, record, item, e) { - _this._edit(record.raw); - }, - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEdit') { - _this._edit(record.raw); - } - - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemove') { - _this.onRemoveButtonClicked.notify(_this.store.getAt(rowIndex).raw.dewarId); - } - } - } - }, - selModel : { - mode : 'SINGLE' - } - }); - - var actions = _this._getTopButtons(); - this.grid.addDocked({ - xtype : 'toolbar', - items : actions - }); - - this.grid.getSelectionModel().on({ - selectionchange : function(sm, selections) { - if (selections.length) { - for ( var i = 0; i < actions.length; i++) { - if (actions[i].enable) { - actions[i].enable(); - } - } - } else { - for ( var i = 0; i < actions.length; i++) { - if (actions[i].alwaysEnabled == false) { - if (actions[i].disable) { - actions[i].disable(); - } - } - } - } - } - }); - return this.grid; -}; - -ExampleGrid.prototype.input = function() { - return { - proposal : DATADOC.getProposal_10(), - dewars : DATADOC.getDewars_10() - - }; -}; - -ExampleGrid.prototype.test = function(targetId) { - var ExampleGrid = new ExampleGrid({ - height : 150 - }); - BIOSAXS.proposal = new Proposal(ExampleGrid.input().proposal); - var panel = ExampleGrid.getPanel(ExampleGrid.input().dewars); - panel.render(targetId); - -}; - - -/** - * Shows a list of experiment AKA data acquisitions - * @height - * @sorters - * @minHeight - * @gridType: Ext.ux.LiveSearchGridPanel or Ext.grid.Panel - * @tbar true or false - * @grouping true or false - * @width - * @title - * #onEditButtonClicked - */ -function ExperimentGrid(args) { - this.width = "100%"; - this.height = 700; - this.minHeight = 500; - - this.id = BUI.id(); - this.gridType = 'Ext.grid.Panel'; //'Ext.ux.LiveSearchGridPanel'; - this.tbar = false; - this.hideHeaders = false; - this.grouping = true; - this.title = null; - - this.filtered = null; - - /** maximum row count **/ - this.limit = 100; - - this.sessionIdFilter = null; - - /** if not null filtered by date **/ - this.date = null; - - this.sorters = [ { - property : 'date', - direction : 'DESC' - }, { - property : 'time', - direction : 'DESC' - } ]; - - this.dates = {}; - if (args != null) { - if (args.height != null) { - this.height = args.height; - } - if (args.limit != null) { - this.limit = args.limit; - } - if (args.sorters != null) { - this.sorters = args.sorters; - } - if (args.sessionId != null){ - this.sessionIdFilter = args.sessionId; - } - if (args.filtered != null) { - this.filtered = args.filtered; - } - if (args.minHeight != null) { - this.minHeight = args.minHeight; - } - if (args.gridType != null) { - this.gridType = args.gridType; - } - if (args.tbar != null) { - this.tbar = args.tbar; - } - if (args.grouping != null) { - this.grouping = args.grouping; - } - if (args.width != null) { - this.width = args.width; - } - if (args.title != null) { - this.title = args.title; - } - - } - /** Events **/ - this.onEditButtonClicked = new Event(this); -} - -ExperimentGrid.prototype._getFilterTypes = function() { - return []; -}; - -ExperimentGrid.prototype._prepareData = function(rows) { - var data = []; - var count = 0; - - rows.sort(function(a,b){return b.experimentId - a.experimentId;}); - for ( var i = 0; i < rows.length; i++) { - var row = rows[i]; - this.dates[moment(row.creationDate).format("YYYYMMDD")] = moment(row.creationDate).format("MMM Do YY"); - if ( - ( this.filtered == null || row.experimentType == this.filtered ) && (count < this.limit || this.limit == null ) && (this.sessionIdFilter == null || this.date != null || (this.date == null && this.sessionIdFilter == row.sessionId)) - ){ - - data.push({ - experimentId : row.experimentId, - status : row.status, - dataAcquisitionFilePath : row.dataAcquisitionFilePath, - type : row.experimentType, - name : row.name, - macromolecules_names : row.macromolecules, - percentageAnalysed : { - value : (row.dataCollectionDoneCount / row.dataCollectionCount) * 100, - text : row.dataCollectionDoneCount + " of " + row.dataCollectionCount - }, - percentageCollected : { - value : (row.measurementDoneCount / row.measurementCount) * 100, - text : row.measurementDoneCount + " of " + row.measurementCount - }, - percentageMerged : { - value : (row.measurementAveragedCount / row.measurementCount) * 100, - text : row.measurementAveragedCount + " of " + row.measurementCount - }, - date : moment(row.creationDate).format("YYYYMMDD"), - time : moment(row.creationDate).format("YYYYMMDDHHmmss"), - creationDate : row.creationDate - }); - count ++; - } - } - return data; -}; - -ExperimentGrid.prototype.getPanel = function(experiments) { - this.features = experiments; - return this._renderGrid(experiments); -}; - -ExperimentGrid.prototype.refresh = function(experiments) { - this.experiments = experiments; - var filtered = []; - for ( var i = 0; i < experiments.length; i++) { - if (experiments[i].experimentType != "TEMPLATE") { - filtered.push(experiments[i]); - } - } - - this.parsedData = this._prepareData(filtered); - - var day = {}; - var dates = []; - for ( var i = 0; i < this.experiments.length; i++) { - var date = moment(this.experiments[i].creationDate).format("MMM Do YYYY"); - if (day[date] == null){ - dates.push({ - date : date, - value : moment(this.experiments[i].creationDate) - }); - day[date] = true; - } - } - - this.storeDate.loadData(dates, false); - this.store.loadData(this.parsedData, false); - - /** If it has already been filtered by date we keep the filter **/ - if (this.date != null){ - this._filterByDate(this.date); - } -}; - -ExperimentGrid.prototype._getTopButtons = function() { - var _this = this; - /** Actions buttons **/ - var actions = []; - - actions.push(Ext.create('Ext.Action', { - icon : '../images/calendar_icon.png', - text : 'Show Calendar', - disabled : false, - handler : function(widget, event) { - var window = Ext.create('Ext.window.Window', { - title : 'Calendar', - width : 600, - height : 600, - modal : true, - closable : true, - layout : { - type : 'vbox', - align : 'stretch' - }, - items : [ { - xtype : 'label', - html : 'Click on a data acquisition to select:', - margin : '5 5 5 5' - }, { - html : '
', - margin : '5 5 5 5' - } - - ] - }).show(); - - var calendarWidget = new CalendarWidget({ - height : 450 - }); - var aux = _this.limit; - /** we remove the limit temporarily **/ - _this.limit = null; - _this.sessionIdFilter = null; - calendarWidget.loadData(_this._prepareData(_this.experiments)); - _this.limit = aux; - calendarWidget.draw('calendar'); - calendarWidget.onClick.attach(function(sender, date) { - date = moment(date, "YYYY-MM-DD"); - _this._filterByDate(date); - window.close(); - - }); - - } - })); - this.storeDate = Ext.create('Ext.data.ArrayStore', { - fields: ['date', 'value'], - data : [] - }); - - this.dateMenu = Ext.create('Ext.form.field.ComboBox', { - hideLabel: true, - store: this.storeDate, - displayField: 'date', - typeAhead: true, - queryMode: 'local', - margin : '0 0 0 30', - triggerAction: 'all', - emptyText:'Select a date...', - selectOnFocus:true, - width:135, - listeners:{ - scope: this, - 'select': function (a,b,c){ - _this.limit = null; - _this._filterByDate(moment(b[0].raw.value, "YYYY-MM-DD")); - } - } - }); - - actions.push(this.dateMenu); - - actions.push("->"); - if (_this.filtered != null){ - actions.push({ - html : "Experiment Type: " + _this.filtered +"" - }); - } - else{ - actions.push({ - html : "Experiment Type: ALL" - }); - } - return actions; -}; - -/** - * Date format: "YYYY-MM-DD" - */ -ExperimentGrid.prototype._filterByDate = function(date) { - var experimentsFiltered = []; - /** Getting all the experiments of date**/ - for ( var i = 0; i < this.experiments.length; i++) { - var experiment = this.experiments[i]; - if (experiment.creationDate != null) { - var experimentDate = moment(experiment.creationDate); - if (experimentDate.year() == date.year()) { - if (experimentDate.month() == date.month()) { - if (experimentDate.date() == date.date()) { - experimentsFiltered.push(experiment); - } - } - } - } - } - var parsedData = this._prepareData(experimentsFiltered); - this.store.loadData(parsedData); - this.date = date; -}; - -/** Only for templates **/ -ExperimentGrid.prototype._removeExperimentById = function(experimentId) { - var _this = this; - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(evt, args) { - _this.grid.setLoading(false); - document.getElementById(BIOSAXS.targetId).innerHTML = ""; - BIOSAXS.start(BIOSAXS.targetId); - }); - this.grid.setLoading("Removing experiment "); - adapter.removeExperimentById(experimentId); -}; - -ExperimentGrid.prototype._renderGrid = function() { - var _this = this; - - /** Store **/ - this.store = Ext.create('Ext.data.Store', { - fields : this._getColumns(), - groupField : 'date', - autoload : true, - data : [], - remoteSort: false, - sorters : this.sorters - }); - - - - - var groupingFeature = Ext.create('Ext.grid.feature.Grouping', { - groupHeaderTpl : Ext.create('Ext.XTemplate', - "
{name:this.formatName}
", { - formatName : function(name) { - return _this.dates[name]; - } - }), - hideGroupedHeader : true, - startCollapsed : false - }); - - this.features = []; - if (this.grouping) { - this.features.push(groupingFeature); - } - - /** Grid **/ - this.grid = Ext.create(this.gridType, { - hideHeaders : this.hideHeaders, - resizable : true, - title : this.title, - width : this.width, - minHeight : this.minHeight, - height : this.height, - features : this.features, - store : this.store, - columns : this._getColumns(), - selModel : { - mode : 'SINGLE' - }, - viewConfig : { - stripeRows : true, - getRowClass : function(record, rowIdx, params, store) { - if (record.raw.type == "TEMPLATE") { - return "template-color-row"; - } - if ((record.raw.type == "CALIBRATION") && (record.raw.status == "FINISHED")) { - return "blue-row"; - } - }, - listeners : { - itemdblclick : function(dataview, record, item, e) { - _this._editExperiment(record.raw.experimentId); - }, - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'GO') { - _this._editExperiment(record.raw.experimentId); - } - - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'REMOVE') { - _this._removeExperimentById(record.raw.experimentId); - } - - } - } - } - }); - - var actions = _this._getTopButtons(); - - if (this.tbar) { - this.grid.addDocked({ - xtype : 'toolbar', - items : actions - }); - this.grid.getSelectionModel().on({ - selectionchange : function(sm, selections) { - if (selections.length) { - for ( var i = 0; i < actions.length; i++) { - if (actions[i].enable) { - actions[i].enable(); - } - } - } else { - for ( var i = 0; i < actions.length; i++) { - if (actions[i].alwaysEnabled == false) { - if (actions[i].disable) { - actions[i].disable(); - } - } - } - } - } - }); - } - - return this.grid; -}; - -ExperimentGrid.prototype._getColumns = function() { - var _this = this; - function actionItemRenderer(value, meta, record, rowIx, ColIx, store) { - if (record.raw.buffer3VOs != null) { - if (record.raw.buffer3VOs.length > 0) { - return 'x-hide-display'; - } - } - - if (record.data.platesCount > 0) { - return 'x-hide-display'; - } - } - - return [ - { - text : 'experimentId', - dataIndex : 'experimentId', - name : 'experimentId', - type : 'string', - hidden : true - }, - { - xtype : 'rownumberer', - width : 40 - }, - { - text : 'Name', - dataIndex : 'name', - name : 'name', - type : 'string', - flex : 1 - }, - - { - text : 'Type', - dataIndex : 'type', - name : 'type', - type : 'string', - flex : 1, - renderer : function(val) { - if (val == "CALIBRATION") { - return "" + val + ""; - } - - return val; - } - }, - { - text : 'Macromolecules', - name : 'macromolecules_names', - dataIndex : 'macromolecules_names', - flex : 1, - renderer : function(val) { - if (val != null) { - return " " + val + ""; - } - return " Information not available"; - } - }, - { - text : 'Buffers', - dataIndex : 'buffer_names', - name : 'buffer_names', - flex : 1, - hidden : true, - renderer : function(val) { - return "Buffer/s: " + val + ""; - } - }, - { - text : 'Status', - dataIndex : 'status', - name : 'status', - type : 'string', - flex : 1, - renderer : function(val, x, sample) { - if (sample.raw.type == "TEMPLATE") { - return "READY"; - } - if (sample.raw.status == "ABORTED") { - return "" + val + ""; - } - return "" + val + ""; - } - }, - { - text : 'Download', - dataIndex : 'creationDate', - name : 'creationDate', - renderer : function(val, x, sample) { - if (sample != null) { - if (sample.raw.type == "HPLC") { - return; - } - return BUI.getZipHTMLByExperimentId(sample.raw.experimentId, sample.raw.name); - } - }, - width : 100 - - }, - { - header : 'Measurements', - dataIndex : 'percentageCollected', - name : 'percentageCollected', - type : 'string', - renderer : function(val, y, sample) { - if ((sample.raw.type == "TEMPLATE") || (sample.raw.type == "HPLC")) { - return; - } - return "
" + BUI.getProgessBar(sample.raw.percentageCollected.value, sample.raw.percentageCollected.text) + "
"; - }, - width : 100 - }, - { - header : 'Averaged', - dataIndex : 'percentageMerged', - name : 'percentageMerged', - type : 'string', - renderer : function(val, y, sample) { - if ((sample.raw.type == "TEMPLATE") || (sample.raw.type == "HPLC")) { - return; - } - return "
" + BUI.getProgessBar(sample.raw.percentageMerged.value, sample.raw.percentageMerged.text) + "
"; - }, - width : 100 - }, - { - header : 'Subtractions', - dataIndex : 'percentageAnalysed', - name : 'percentageAnalysed', - type : 'string', - renderer : function(val, y, sample) { - if ((sample.raw.type == "TEMPLATE") || (sample.raw.type == "HPLC")) { - return; - } - return "
" + BUI.getProgessBar(sample.raw.percentageAnalysed.value, sample.raw.percentageAnalysed.text) + "
"; - }, - width : 100 - }, - - { - text : 'time', - dataIndex : 'time', - name : 'time', - hidden : true, - renderer : function(val) { - return val; - }, - width : 100 - - }, { - text : 'Date', - dataIndex : 'date', - name : 'date', - renderer : function(val) { - return val; - }, - width : 100 - - }, - - { - text : 'Time', - dataIndex : 'creationDate', - name : 'creationDate', - renderer : function(val) { - return moment(val).format(" HH:mm:ss"); - }, - width : 100 - - }, { - id : _this.id + 'GO', - width : 80, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - return BUI.getGreenButton('GO'); - } - } ]; -}; - -/** Changes location.href in order to edit the experiment **/ -ExperimentGrid.prototype._editExperiment = function(experimentId) { - if (Ext.urlDecode(window.location.href).sessionId != null) { - location.href = 'viewProjectList.do?reqCode=display&experimentId=' + experimentId + '&sessionId='+ Ext.urlDecode(window.location.href).sessionId; - } else { - location.href = 'viewProjectList.do?reqCode=display&experimentId=' + experimentId; - } -}; - -ExperimentGrid.prototype.input = function() { - var experiments = DATADOC.getExperimentList_10(); - return { - experiments : experiments, - proposal : new MeasurementGrid().input().proposal - - }; -}; - -ExperimentGrid.prototype.test = function(targetId) { - var experimentGrid = new ExperimentGrid({ - height : 350, - minHeight : 350, - width : 1000 - - }); - BIOSAXS.proposal = new Proposal(experimentGrid.input().proposal); - var panel = experimentGrid.getPanel(experimentGrid.input().experiments); - experimentGrid.refresh(experimentGrid.input().experiments); - panel.render(targetId); -}; - -function FitStructureToExperimentDataGrid(args) { - this.height = null; - this.width = null; - this.id = BUI.id(); - - if (args != null) { - if (args.height != null) { - this.height = args.height; - - if (args.width != null) { - this.width = args.width; - } - } - } - - this.onSelected = new Event(this); -} - -FitStructureToExperimentDataGrid.prototype.getStructuresByMacromolecule = function(macromolecule) { - var structures = []; - if (macromolecule.structure3VOs != null) { - if (macromolecule.structure3VOs.length > 0) { - for (var i = 0; i < macromolecule.structure3VOs.length; i++) { - structures.push(macromolecule.structure3VOs[i]); - } - } - } - return structures; -}; - -FitStructureToExperimentDataGrid.prototype._prepareData = function(subtractions) { - var data = []; - for (var i = 0; i < subtractions.length; i++) { - - for (var j = 0; j < subtractions[i].fitStructureToExperimentalData3VOs.length; j++) { - var fit = subtractions[i].fitStructureToExperimentalData3VOs[j]; - data.push({ - fit : fit.fitFilePath, - fitStructureToExperimentalDataId : fit.fitStructureToExperimentalDataId, - mixtureToStructure3VOs : fit.mixtureToStructure3VOs, - subtractedFile : subtractions[i].substractedFilePath - }); - } - } - return data; - -}; - -FitStructureToExperimentDataGrid.prototype.refresh = function(subtractions) { - this.store.loadData(this._prepareData(subtractions), false); -}; - -FitStructureToExperimentDataGrid.prototype.getPanel = function() { - var _this = this; - this.store = Ext.create('Ext.data.Store', { - fields : [ 'fit', 'subtractedFile', 'structureId', 'fitFilePath', 'mixtureToStructure3VOs' ], - data : [] - }); - - this.store.sort([ { - property : 'name', - direction : 'ASC' - } ]); - - this.selModel = Ext.create('Ext.selection.RowModel', { - allowDeselect : true, - mode : 'MULTI', - listeners : { - selectionchange : function(sm, selections) { - var selected = []; - for (var i = 0; i < selections.length; i++) { - selected.push(selections[i].raw); - } - _this.onSelected.notify(selected); - } - } - }); - - this.panel = Ext.create('Ext.grid.Panel', { - store : this.store, - deferredRender : false, - width : this.width, - height : this.height, - margin : 10, - selModel : this.selModel, - columns : [ { - text : 'Name', - dataIndex : 'fit', - flex : 1, - renderer : function(val, b, record) { - return BUI.getFileName(val); - } - }, { - text : 'PDB', - dataIndex : 'mixtureToStructure3VOs', - flex : 1, - renderer : function(values, b, record) { - var html = ""; - for (var i = 0; i < values.length; i++) { - var structure = BIOSAXS.proposal.getStructuresById(values[i].structureId); - html = html + ""; - if (structure != null){ - html = html + ""; - } - html = html + ""; - } - return html + "
" + structure.name + "
"; - } - }, { - text : 'Volume Fraction', - dataIndex : 'mixtureToStructure3VOs', - flex : 1, - renderer : function(values, b, record) { - var html = ""; - for (var i = 0; i < values.length; i++) { - html = html + ""; - html = html + ""; - html = html + ""; - } - - return html + "
" + values[i].volumeFraction + "
"; - } - },{ - text : 'Subtraction', - dataIndex : 'subtractedFile', - flex : 1, - renderer : function(values, b, record) { - return values.split("/")[values.split("/").length - 1]; - } - },], - - viewConfig : { - enableTextSelection : true, - preserveScrollOnRefresh : true - }, - listeners : { - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - }, - afterrender : function() { - } - } - }); - return this.panel; -}; - -/** Static method **/ -FitStructureToExperimentDataGrid.prototype.RUNFitScattering = function(subtractionId, structureId) { - var _this = this; - /** Add to Workflow **/ - var adapter = new BiosaxsDataAdapter(); - var workflow = { - 'workflowTitle' : 'FitExperimentalDatatoStructure', - 'comments' : 'FitExperimentalDatatoStructure run from ISPyB for subtractionId: ' + subtractionId + ' and structureId ' + structureId - } - - var inputs = [ { - name : 'subtractionId', - value : subtractionId - }, { - name : 'structureId', - value : structureId - } ]; - - adapter.onSuccess.attach(function(sender, data) { - /** Add to Fit **/ - var adapter2 = new BiosaxsDataAdapter(); - var fit = { - 'workflowId' : data.workflowId, - 'subtractionId' : subtractionId, - 'structureId' : structureId, - 'comments' : 'Sent to workflow engine' - } - adapter2.onSuccess.attach(function(sender, fit) { - _this.refresh(_this.subtractionId, _this.macromolecule); - }); - adapter2.addFitStructureData(fit); - - }); - adapter.addWorkflow(workflow, inputs); - -}; +/** + * Example form + * + * @witdh + * @height + */ +function MolarityForm(args) { + this.id = BUI.id(); + this.width = 700; + this.height = 500; + + if (args != null) { + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + } + + this.onSave = new Event(this); + this.onClose = new Event(this); +} + -/** - * It shows buffer grid with a top bar with "Add" button - * - * @height - * @searchBar - * @collapsed - * @width - */ -function FrameGrid(args) { - this.height = 500; - this.width = 500; - this.searchBar = false; - this.tbar = false; - this.collapsed = false; - - - if (args != null) { - if (args.height != null) { - this.height = args.height; - } - - if (args.searchBar != null) { - this.searchBar = args.searchBar; - } - - if (args.tbar != null) { - this.tbar = args.tbar; - } - - if (args.collapsed != null) { - this.collapsed = args.collapsed; - } - - if (args.width != null) { - this.width = args.width; - } - } -} - -FrameGrid.prototype._edit = function(bufferId) { - var _this = this; - var window = new BufferWindow(); - window.onSuccess.attach(function(sender, proposal) { - _this.store.loadData(BIOSAXS.proposal.getBuffers()); - }); - window.draw(BIOSAXS.proposal.getBufferById(bufferId)); -}; - -FrameGrid.prototype.refresh = function(buffers, experimentId) { - this.experimentId = experimentId; - this.store.loadData(this._prepareData(buffers), false); -}; - -FrameGrid.prototype._prepareData = function(buffers) { - return buffers; -}; - -FrameGrid.prototype._getTbar = function() { - var _this = this; - var actions = []; - - actions.push(Ext.create('Ext.Action', { - icon : '../images/add.png', - text : 'Add Buffer', - disabled : false, - handler : function(widget, event) { - var window = new BufferWindow(); - window.onSuccess.attach(function(sender) { - _this.store.loadData(BIOSAXS.proposal.getBuffers()); - }); - window.draw({}); - } - })); - return actions; -}; - -FrameGrid.prototype.getPanel = function(buffers) { - var _this = this; - - this.store = Ext.create('Ext.data.Store', { - fields : [ 'frameNumber', 'I0', 'Rg', 'Mass', 'Vc', 'Qr', 'quality'], - data : buffers - }); - - this.store.sort('frameNumber'); - - var type = 'Ext.grid.Panel'; - if (this.searchBar == true) { - type = 'Ext.ux.LiveSearchGridPanel'; - } - - this.grid = Ext.create(type, { - store : this.store, - height : this.height, - width : this.width, - margin : 5, - columns : [{ - text : 'Frame', - dataIndex : 'frameNumber', - flex : 1 - },{ - text : 'I0', - dataIndex : 'I0', - flex : 1, - renderer : function(val, y, sample) { - return BUI.formatValuesUnits(sample.data.I0, "", 12, 3); - } - },{ - text : 'Rg', - dataIndex : 'Rg', - flex : 1, - renderer : function(val, y, sample) { - return BUI.formatValuesUnits(sample.data.Rg, "nm", 12, 3); - } - },{ - text : 'Mass', - dataIndex : 'Mass', - flex : 1, - renderer : function(val, y, sample) { - return BUI.formatValuesUnits(sample.data.Mass, "", 12, 3); - } - },{ - text : 'Vc', - dataIndex : 'Vc', - flex : 1, - renderer : function(val, y, sample) { - return BUI.formatValuesUnits(sample.data.Vc, "", 12, 3); - } - },{ - text : 'Qr', - dataIndex : 'Qr', - flex : 1, - renderer : function(val, y, sample) { - return BUI.formatValuesUnits(sample.data.Qr, "", 12, 3); - } - },{ - text : 'Quality', - dataIndex : 'quality', - flex : 1, - renderer : function(val, y, sample) { - return (Number(sample.data.quality) * 100).toFixed(2) + "%"; - } - }, - { - text : '', - renderer : function(val, x, sample) { - if (sample != null) { - return BUI.getZipHTMLByFrameRangeId(_this.experimentId, sample.raw.frameNumber, sample.raw.frameNumber); - } - }, - width : 100 - }], - flex : 1, - viewConfig : { - stripeRows : true - } - }); - - /** Adding the tbar **/ - if (this.tbar) { - this.grid.addDocked({ - xtype : 'toolbar', - items : this._getTbar() - }); - } - return this.grid; -}; - -FrameGrid.prototype.input = function() { - return []; -}; - -FrameGrid.prototype.test = function(targetId) { - var frameGrid = new FrameGrid({ - width : 800, - height : 350, - collapsed : false, - tbar : true - }); - - var panel = frameGrid.getPanel([]); - panel.render(targetId); -}; - - -function PeakGrid(args) { - this.height = 500; - this.searchBar = false; - this.tbar = false; - this.collapsed = false; - this.width = 500; - this.showExtendedColumns = false; - - if (args != null) { - if (args.showExtendedColumns != null) { - this.showExtendedColumns = args.showExtendedColumns; - } - if (args.height != null) { - this.height = args.height; - } - if (args.searchBar != null) { - this.searchBar = args.searchBar; - } - - if (args.tbar != null) { - this.tbar = args.tbar; - } - - if (args.collapsed != null) { - this.collapsed = args.collapsed; - } - - if (args.width != null) { - this.width = args.width; - } - } -} - - -PeakGrid.prototype.refresh = function(buffers) { - this.store.loadData(this._prepareData(buffers), false); -}; - -PeakGrid.prototype._prepareData = function(buffers) { - -// for ( var i = 0; i < buffers.length; i++) { -// buffers[i].name = "Peak #" + (i+1); +MolarityForm.prototype._getNumericWithHelp = function(type, fieldLabel, fieldName, help) { + return Ext.create('Ext.container.Container', { + margin : "10 0 0 10", + items : [ { + xtype : type, + fieldLabel : fieldLabel, + name : fieldName, + id : this.id + fieldName, + decimalPrecision : 6 + }, { + xtype : 'label', + forId : 'myFieldId', + text : help, + margin : "5 0 0 105", + cls : "inline-help" + } ] + }); +}; + + +MolarityForm.prototype._getItems = function() { + this.macromoleculeCombo = BIOSAXS_COMBOMANAGER.getComboMacromoleculeByMacromolecules(this.getMacromuleculesCandidates(this.macromolecule), { + width : 250, + labelWidth : 100, + margin : 10 + }); + + return [ { + xtype : 'container', + flex : 1, + margin : '10 0 0 10', + border : 0, + layout : 'anchor', + defaultType : 'requiredtext', + items : [ this.macromoleculeCombo, + this._getNumericWithHelp("textfield", "Ratio", "ratio", "Number in assymmetric units") + ] + } ]; +}; + +MolarityForm.prototype._persist = function() { + var _this = this; + var macromoleculeId = this.macromoleculeCombo.getValue(); + var ratio = Ext.getCmp(this.id + "ratio").getValue(); + var comments = "Not used yet"; + var dataAdapter = new BiosaxsDataAdapter(); + this.panel.setLoading("Saving"); + dataAdapter.onSuccess.attach(function(sender, args) { + _this.onSave.notify(); + }); + dataAdapter.saveStoichiometry(this.macromolecule.macromoleculeId, macromoleculeId, ratio, comments); +}; + +MolarityForm.prototype._getButtons = function() { + var _this = this; + + function onClose() { + _this.onClose.notify(); + } + + return [ { + text : 'Save', + handler : function() { + _this._persist(); + } + }, { + text : 'Cancel', + handler : function() { + onClose(); + } + } ]; +}; + +MolarityForm.prototype.getPanel = function() { + this.panel = Ext.create('Ext.form.Panel', { +// width : null, + height : this.height, + margin : 2, + border : 1, + defaultType : 'requiredtext', + items : this._getItems(), + buttons : this._getButtons() + }); + return this.panel; +}; + +/** macromolecules contains all macromolecules except this one **/ +MolarityForm.prototype.getMacromuleculesCandidates = function(macromolecule) { + var macromolecules = []; + if ( BIOSAXS.proposal.macromolecules){ + for (var i = 0; i < BIOSAXS.proposal.macromolecules.length; i++) { + var m = BIOSAXS.proposal.macromolecules[i]; + if (this.macromolecule != null){ + if (m.macromoleculeId != this.macromolecule.macromoleculeId) { + macromolecules.push(m); + } + } + } + } + return macromolecules; +}; + + +/** It populates the form **/ +MolarityForm.prototype.refresh = function(macromolecule) { + this.macromolecule = macromolecule; + +}; + + +MolarityForm.prototype.input = function() { + return {}; +}; + + +/** It populates the form **/ +MolarityForm.prototype.test = function(targetId) { + var macromoleculeForm = new MolarityForm(); + var panel = macromoleculeForm.getPanel(); + panel.render(targetId); +}; + +///** +// * +// * @witdh +// * @height +// */ +//function MacromoleculeForm(args) { +// this.id = BUI.id(); +// this.width = 700; +// this.height = 500; +// +// if (args != null) { +// if (args.width != null) { +// this.width = args.width; +// } +// if (args.height != null) { +// this.height = args.height; +// } +// } +// +// this.onClose = new Event(this); +//} +// +//MacromoleculeForm.prototype.getMacromolecule = function() { +// this.macromolecule.name = Ext.getCmp(this.panel.getItemId()).getValues().name; +// this.macromolecule.acronym = Ext.getCmp(this.panel.getItemId()).getValues().acronym; +// this.macromolecule.comments = Ext.getCmp(this.panel.getItemId()).getValues().comments; +// this.macromolecule.extintionCoefficient = Ext.getCmp(this.panel.getItemId()).getValues().extintionCoefficient; +// this.macromolecule.molecularMass = Ext.getCmp(this.panel.getItemId()).getValues().molecularMass; +// return this.macromolecule; +//}; +// +//MacromoleculeForm.prototype.setMacromolecule = function(macromolecule) { +// this.pdbStore.loadData(macromolecule.structure3VOs); +// +//}; +// +//MacromoleculeForm.prototype.getForm = function(macromolecule) { +// this.panel = Ext.createWidget('form', { +// frame : false, +// border : 0, +// padding : 15, +// width : 550, +// height : 350, +// items : [ { +// xtype : 'container', +// layout : 'hbox', +// items : [ { +// xtype : 'container', +// flex : 1, +// border : false, +// layout : 'anchor', +// defaultType : 'requiredtext', +// items : [ { +// fieldLabel : 'Name', +// name : 'name', +// anchor : '95%', +// tooltip : "Name of the macromolecule", +// value : macromolecule.name +// }, { +// fieldLabel : 'Acronym', +// name : 'acronym', +// anchor : '95%', +// value : macromolecule.acronym +// } ] +// }, { +// xtype : 'container', +// flex : 1, +// layout : 'anchor', +// defaultType : 'textfield', +// items : [ { +// xtype : 'numberfield', +// fieldLabel : 'Mol. Mass (Da)', +// name : 'molecularMass', +// value : macromolecule.molecularMass, +// decimalPrecision : 6 +// }, { +// xtype : 'numberfield', +// fieldLabel : 'Extinction coef.', +// name : 'extintionCoefficient', +// value : macromolecule.extintionCoefficient, +// decimalPrecision : 6 +// } ] +// } ] +// }, { +// xtype : 'textareafield', +// name : 'comments', +// fieldLabel : 'Comments', +// value : macromolecule.comments, +// width : this.width - 10 +// }, +// +// { +// html : BUI.getWarningHTML("The macromolecule is unsaved. Save the macromolecule to get access to other tabs"), +// margin : "150 10 10 10", +// id : this.id + "unsavedWarning", +// hidden : !(!macromolecule.macromoleculeId) +// } +// +// ] +// }); +// return this.panel; +//}; +// +//MacromoleculeForm.prototype.save = function() { +// var _this = this; +// +// var adapter = new BiosaxsDataAdapter(); +// adapter.onSuccess.attach(function(sender, proposal) { +// BIOSAXS.proposal.setItems(proposal); +// _this.panel.setLoading(false); +// +// Ext.getCmp(_this.id + "assembly").enable() +// Ext.getCmp(_this.id + "advanced").enable(); +// Ext.getCmp(_this.id + "unsavedWarning").hide(); +// }); +// +// if (this.getMacromolecule().name == "") { +// BUI.showError("Name field is mandatory"); +// return; +// } +// if (this.getMacromolecule().acronym == "") { +// BUI.showError("Acroynm field is mandatory"); +// return; +// } +// +// /** Check if acronym is unique * */ +// if (this.getMacromolecule().macromoleculeId == null) { +// if (BIOSAXS.proposal.getMacromoleculeByAcronym(this.getMacromolecule().acronym) == null) { +// this.panel.setLoading("ISPyB: Saving Macromolecule") +// adapter.saveMacromolecule(this.getMacromolecule()); +// } else { +// alert("There is already an existing macromolecule with the same acronym"); +// +// } +// } else { +// this.panel.setLoading("ISPyB: Saving Macromolecule") +// adapter.saveMacromolecule(this.getMacromolecule()); +// } +// +//}; +// +//MacromoleculeForm.prototype.getPanel = function(macromolecule) { +// var _this = this; +// this.macromolecule = macromolecule; +// return Ext.createWidget('tabpanel', { +// height : this.height, +// margin : 5, +// plain : true, +// style : { +// padding : 5 +// }, +// items : [ { +// tabConfig : { +// title : "General", +// disabled : false +// }, +// items : [ this.getForm(macromolecule) ], +// bbar : [ "->", { +// text : 'Save', +// cls : 'btn-with-border', +// style : { +// +// border : 1 +// }, +// handler : function() { +// _this.save(); +// } +// }, { +// text : 'Close', +// cls : 'btn-with-border', +// handler : function() { +// _this.onClose.notify(); +// } +// } ] +// }, { +// tabConfig : { +// id : this.id + "assembly", +// title : "Assembly", +// tooltip : 'Description of subunits present in the macromolecule', +// // hidden : (!macromolecule.macromoleculeId), +// disabled : (!macromolecule.macromoleculeId) +// }, +// items : [ this.getMolarityGrid(macromolecule) ] +// }, { +// tabConfig : { +// id : this.id + "advanced", +// title : "Advanced Modeling", +// // hidden : (!macromolecule.macromoleculeId), +// tooltip : 'Definition of the description contacts and symetries', +// disabled : (!macromolecule.macromoleculeId) +// }, +// items : [ this.getRigidBodyForm(macromolecule) ] +// } ] +// }); +//}; +// +//MacromoleculeForm.prototype.getRigidBodyForm = function(macromolecule) { +// var _this = this; +// +// // [P1, P2, P3, P4 ,P5 ,P6 ,32, P42, P52, P62] + P222 +// var symmetry = Ext.create('Ext.data.Store', { +// fields : [ 's' ], +// data : [ { +// "s" : "P1" +// }, { +// "s" : "P2" +// }, { +// "s" : "P3" +// }, { +// "s" : "P4" +// }, { +// "s" : "P5" +// }, { +// "s" : "P6" +// }, { +// "s" : "P32" +// }, { +// "s" : "P42" +// }, { +// "s" : "P52" +// }, { +// "s" : "P62" +// }, { +// "s" : "P222" +// } ] +// }); +// +// if (macromolecule.symmetry == null) { +// macromolecule.symmetry = "P1"; +// } +// var comboBox = Ext.create('Ext.form.ComboBox', { +// fieldLabel : 'Symmetry', +// store : symmetry, +// id : 'comboSym', +// queryMode : 'local', +// displayField : 's', +// valueField : 's', +// value : macromolecule.symmetry, +// margin : "10 0 0 0", +// listeners : { +// change : function(combo, newValue, oldValue, eOpts) { +// macromolecule.symmetry = newValue; +// } +// } +// }); +// +// this.rigidBodyPanel = Ext.createWidget('form', { +// frame : false, +// border : 0, +// padding : 10, +// width : 550, +// height : 400, +// items : [ { +// xtype : 'container', +// layout : 'hbox', +// items : [ { +// xtype : 'container', +// border : false, +// layout : 'hbox', +// items : [ { +// xtype : 'label', +// forId : 'myFieldId', +// text : 'Contact Desc:', +// width : 105, +// margin : '0 0 0 0' +// }, { +// xtype : 'textfield', +// hideLabel : true, +// id : "contactsDescriptionFilePath", +// margin : '0 0 0 0', +// width : 300, +// value : macromolecule.contactsDescriptionFilePath +// }, { +// text : 'Upload', +// xtype : 'button', +// margin : "0 0 0 20", +// width : 100, +// handler : function() { +// _this._openUploadDialog(macromolecule.macromoleculeId, "CONTACTS", "Upload Contact Description File"); +// } +// } ] +// } ] +// }, +// +// comboBox, { +// xtype : 'checkbox', +// margin : '10 0 0 5', +// boxLabel : "I want rigid body modeling run on this stuff", +// checked : true, +// width : 300 +// }, _this.getPDBGrid(macromolecule) ] +// }); +// return this.rigidBodyPanel; +//}; +// +//MacromoleculeForm.prototype.update = function() { +// var _this = this; +// BIOSAXS.proposal.onInitialized.attach(function() { +// if (BIOSAXS.proposal != null) { +// var macromolecules = BIOSAXS.proposal.macromolecules; +// for (var i = 0; i < macromolecules.length; i++) { +// if (macromolecules[i].macromoleculeId == _this.macromolecule.macromoleculeId) { +// _this.macromolecule = macromolecules[i]; +// _this.setMacromolecule(_this.macromolecule); +// _this.molarityStore.loadData(_this.parseMolarityData(_this.macromolecule)); +// _this.pdbGrid.setLoading(false); +// Ext.getCmp("contactsDescriptionFilePath").setValue(_this.macromolecule.contactsDescriptionFilePath) +// _this.molarityGrid.setLoading(false); +// +// } +// } +// } +// }); +// this.molarityGrid.setLoading("Updating"); +// this.pdbGrid.setLoading("Updating"); +// BIOSAXS.proposal.init(); +//}; +// +///******************************************************************************* +// * MOLARITY GRID +// ******************************************************************************/ +// +//MacromoleculeForm.prototype.parseMolarityData = function(macromolecule) { +// var data = []; +// if (macromolecule.stoichiometry != null) { +// for (var i = 0; i < macromolecule.stoichiometry.length; i++) { +// data.push({ +// ratio : macromolecule.stoichiometry[i].ratio, +// acronym : macromolecule.stoichiometry[i].macromolecule3VO.acronym, +// comments : macromolecule.stoichiometry[i].macromolecule3VO.comments, +// stoichiometryId : macromolecule.stoichiometry[i].stoichiometryId, +// name : macromolecule.stoichiometry[i].macromolecule3VO.name +// }); +// } +// } +// return data; +//}; +// +//MacromoleculeForm.prototype.getMolarityGrid = function(macromolecule) { +// var _this = this; +// +// this.molarityStore = Ext.create('Ext.data.Store', { +// fields : [ 'acronym', 'ratio', 'comments', 'stoichiometryId', 'name' ], +// data : this.parseMolarityData(macromolecule), +// sorters : { +// property : 'ratio', +// direction : 'DESC' +// } +// }); +// +// this.molarityGrid = Ext.create('Ext.grid.Panel', { +// store : this.molarityStore, +// height : 350, +// padding : 5, +// columns : [ +// +// { +// text : 'Subunit', +// columns : [ { +// text : "Acronym", +// width : 100, +// hidden : false, +// dataIndex : 'acronym', +// sortable : true +// }, { +// text : "Name", +// width : 100, +// hidden : false, +// dataIndex : 'name', +// sortable : true +// }, { +// text : "Comments", +// width : 100, +// dataIndex : 'comments', +// sortable : true +// } ] +// }, { +// text : "Number
in assymmetric units", +// width : 150, +// dataIndex : 'ratio', +// tooltip : 'Number of times this subunit is present in the macromolecule', +// sortable : true +// }, { +// id : this.id + 'MOLARITY_REMOVE', +// flex : 0.1, +// sortable : false, +// renderer : function(value, metaData, record, rowIndex, colIndex, store) { +// return BUI.getRedButton('REMOVE'); +// } +// } ], +// listeners : { +// cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { +// if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'MOLARITY_REMOVE') { +// var dataAdapter = new BiosaxsDataAdapter(); +// dataAdapter.onSuccess.attach(function() { +// _this.molarityGrid.setLoading(false); +// _this.update(); +// }); +// dataAdapter.removeStoichiometry(record.data.stoichiometryId); +// _this.molarityGrid.setLoading("Removing Structure"); +// } +// } +// }, +// buttons : [ { +// text : 'Add molarity', +// handler : function() { +// +// function onClose() { +// w.destroy(); +// _this.update(); +// } +// var w = Ext.create('Ext.window.Window', { +// title : 'Molarity', +// height : 300, +// width : 500, +// modal : true, +// buttons : [ { +// text : 'Save', +// handler : function() { +// var macromoleculeId = (_this.macromoleculeCombo.getValue()); +// var ratio = Ext.getCmp(_this.id + "ratio").getValue(); +// var comments = ""; +// var dataAdapter = new BiosaxsDataAdapter(); +// dataAdapter.onSuccess.attach(function(sender, args) { +// _this.update(); +// w.destroy(); +// }); +// dataAdapter.saveStoichiometry(_this.macromolecule.macromoleculeId, macromoleculeId, ratio, comments); +// } +// }, { +// text : 'Cancel', +// handler : function() { +// onClose(); +// } +// } ], +// items : [ _this.getMolarityForm(macromolecule) ], +// listeners : { +// onEsc : function() { +// onClose(); +// }, +// close : function() { +// onClose(); +// } +// } +// }).show(); +// } +// } ] +// }); +// return this.molarityGrid; +//}; +// +///******************************************************************************* +// * PDB GRID +// ******************************************************************************/ +// +//MacromoleculeForm.prototype._openUploadDialog = function(macromoleculeId, type, title) { +// var _this = this; +// function onClose() { +// w.destroy(); +// _this.update(); +// } +// +// var w = Ext.create('Ext.window.Window', { +// title : title, +// height : 200, +// width : 400, +// modal : true, +// buttons : [ { +// text : 'Close', +// handler : function() { +// onClose(); +// } +// } ], +// layout : 'fit', +// items : { +// html : "" +// }, +// listeners : { +// onEsc : function() { +// onClose(); +// }, +// close : function() { +// onClose(); +// } +// } +// }).show(); +//}; +// +//MacromoleculeForm.prototype._getPlugins = function() { +// var _this = this; +// var plugins = []; +// // if (this.updateRowEnabled) { +// plugins.push(Ext.create('Ext.grid.plugin.RowEditing', { +// clicksToEdit : 1, +// listeners : { +// validateedit : function(grid, e) { +// /** Comments are always updatable* */ +// e.record.raw.symmetry = e.newValues.symmetry; +// e.record.raw.multiplicity = e.newValues.multiplicity; +// +// var adapter = new BiosaxsDataAdapter(); +// adapter.onSuccess.attach(function(sender, measurement) { +// // _this.grid.setLoading(false); +// }); +// adapter.onError.attach(function() { +// alert("Error"); +// // _this.grid.setLoading(false); +// }); +// +// // _this.grid.setLoading(); +// adapter.saveStructure(e.record.raw); +// } +// } +// })); +// // } +// return plugins; +//}; +// +//MacromoleculeForm.prototype.getPDBGrid = function(macromolecule) { +// var _this = this; +// +// var data = macromolecule.structure3VOs; +// +// // /** Getting PDB from subunits **/ +// // if (macromolecule != null){ +// // if (macromolecule.stoichiometry != null){ +// // for (var i =0; i < macromolecule.stoichiometry.length; i++){ +// // var stoichiometry = macromolecule.stoichiometry[i]; +// // if (stoichiometry.macromolecule3VO != null){ +// // if (stoichiometry.macromolecule3VO.structure3VOs != null){ +// // for (var j = 0; j < stoichiometry.macromolecule3VO.structure3VOs.length; +// // j++) { +// // var structure = stoichiometry.macromolecule3VO.structure3VOs[j]; +// // structure["isSubunit"] = stoichiometry.macromolecule3VO.acronym; +// // data.push(structure) +// // } +// // } +// // } +// // } +// // } +// // } +// +// this.pdbStore = Ext.create('Ext.data.Store', { +// fields : [ 'filePath', 'structureId', 'structureType', 'symmetry', 'structureId', 'name', 'multiplicity' ], +// data : macromolecule.structure3VOs, +// groupField : 'structureType', +// sorters : { +// property : 'structureId', +// direction : 'DESC' +// } +// }); +// +// var groupingFeature = Ext.create('Ext.grid.feature.Grouping', { +// groupHeaderTpl : Ext.create('Ext.XTemplate', +// "
{name:this.formatName}
", { +// formatName : function(name) { +// return name; +// } +// }), +// hideGroupedHeader : true, +// startCollapsed : false +// }); +// +// this.pdbGrid = Ext.create('Ext.grid.Panel', { +// margin : "15 0 0 5", +// height : 250, +// store : this.pdbStore, +// plugins : _this._getPlugins(), +// buttons : [ { +// // text : 'Add PDB file', +// text : 'Add Modeling Option', +// handler : function() { +// _this._openUploadDialog(macromolecule.macromoleculeId, "PDB", 'Upload PDB File'); +// } +// } +// +// ], +// columns : [ +// { +// text : "structureId", +// flex : 0.2, +// hidden : true, +// dataIndex : 'structureId', +// sortable : true +// }, +// { +// text : "File", +// flex : 0.5, +// dataIndex : 'filePath', +// sortable : true, +// hidden : true +// }, +// { +// text : "PDB", +// flex : 0.4, +// dataIndex : 'name', +// sortable : true +// }, +// { +// text : "Symmetry", +// flex : 0.4, +// dataIndex : 'symmetry', +// sortable : true, +// editor : { +// xtype : 'combobox', +// typeAhead : true, +// triggerAction : 'all', +// selectOnTab : true, +// store : [ [ "P1", "P1" ], [ "P2", "P2" ], [ "P3", "P3" ], [ "P4", "P4" ], [ "P5", "P5" ], [ "P6", "P6" ], [ "P32", "P32" ], [ "P42", "P42" ], +// [ "P52", "P52" ], [ "P62", "P62" ], [ "P222", "P222" ] ], +// } +// }, { +// text : "Multiplicity", +// flex : 0.4, +// dataIndex : 'multiplicity', +// sortable : true, +// editor : { +// xtype : 'textfield' +// } +// +// }, { +// text : "Subunit", +// flex : 0.2, +// dataIndex : 'isSubunit', +// sortable : true, +// hidden : true +// }, { +// text : "Type", +// flex : 0.2, +// dataIndex : 'structureType', +// sortable : true, +// hidden : true +// }, +// +// { +// id : this.id + 'REMOVE', +// flex : 0.2, +// hidden : true, +// sortable : false, +// renderer : function(value, metaData, record, rowIndex, colIndex, store) { +// return BUI.getRedButton('REMOVE'); +// } +// }, ], +// +// listeners : { +// itemdblclick : function(dataview, record, item, e) { +// _this._editExperiment(record.raw.experimentId); +// }, +// cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { +// +// if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'REMOVE') { +// var dataAdapter = new BiosaxsDataAdapter(); +// dataAdapter.onSuccess.attach(function() { +// _this.pdbGrid.setLoading(false); +// _this.update(); +// }); +// dataAdapter.removeStructure(record.data.structureId); +// _this.pdbGrid.setLoading("Removing PDB file"); +// } +// +// } +// }, +// viewConfig : { +// getRowClass : function(record, rowIdx, params, store) { +// if (record.raw.isSubunit != null) { +// return "blue-row"; +// } +// } +// } +// }); +// +// return this.pdbGrid; +//}; +// +//MacromoleculeForm.prototype.getMolarityForm = function(macromolecule) { +// var _this = this; +// var data = []; +// for (var i = 0; i < BIOSAXS.proposal.macromolecules.length; i++) { +// var m = BIOSAXS.proposal.macromolecules[i]; +// if (m.macromoleculeId != macromolecule.macromoleculeId) { +// data.push(m); +// } +// // } - /** Adding information of buffer **/ - if (buffers.length > 0){ - buffers.unshift({ - name : "BUFFER", - start : 0, - experimentId : buffers[0].experimentId, - end : buffers[0].start - 1 - }); - } - - - return buffers; -}; - -PeakGrid.prototype._getTbar = function() { - var _this = this; - var actions = []; +// this.macromoleculeCombo = BIOSAXS_COMBOMANAGER.getComboMacromoleculeByMacromolecules(data, { +// width : 250, +// labelWidth : 100, +// margin : 10 +// }); +// +// return Ext.createWidget('form', { +// +// frame : false, +// border : 0, +// // padding : 15, +// width : 550, +// height : 350, +// items : [ { +// xtype : 'container', +// flex : 1, +// border : false, +// layout : 'anchor', +// defaultType : 'requiredtext', +// items : [ this.macromoleculeCombo, { +// xtype : 'numberfield', +// name : 'Ratio', +// id : _this.id + "ratio", +// fieldLabel : 'Number in assymmetric units', +// value : 1, +// decimalPrecision : 6, +// margin : 10 +// }, { +// xtype : 'textareafield', +// name : 'comments', +// fieldLabel : 'Comments', +// margin : 10, +// width : 400, +// value : "" +// +// } ] +// } ] +// }); +// +//}; +// +///******************************************************************************* +// * JAVASCRIPT DOC +// ******************************************************************************/ +//MacromoleculeForm.prototype.input = function() { +// return { +// macromolecule : DATADOC.getMacromolecule_10() +// }; +//}; +// +//MacromoleculeForm.prototype.test = function(targetId) { +// var macromoleculeForm = new MacromoleculeForm(); +// var panel = macromoleculeForm.getPanel(macromoleculeForm.input().macromolecule); +// panel.render(targetId); +//}; + +function ResultSummaryForm() { + this.radiationDamageThreshold = BUI.getRadiationDamageThreshold(); + this.qualityThreshold = BUI.getQualityThreshold(); - actions.push(Ext.create('Ext.Action', { - icon : '../images/add.png', - text : 'Add Buffer', - disabled : false, - handler : function(widget, event) { - var window = new BufferWindow(); - window.onSuccess.attach(function(sender) { - _this.store.loadData(BIOSAXS.proposal.getBuffers()); - }); - window.draw({}); - } - })); - return actions; -}; + /** Data clusters with bufers **/ + this.clusterByBuffers = false; + + /** Visualization are groupeb by concenttrations. Ex: 4.5mg/ml and 4.7mg/ml will be clusterized together **/ + this.collapseConcentrations = true; + + this.summaryHeight = 350; + this.id = BUI.id(); -PeakGrid.prototype.getPanel = function(buffers) { var _this = this; - this.peakCount = 0; - this.store = Ext.create('Ext.data.Store', { - fields : ['name', {name:'start', type : 'int'}, {name:'end', type : 'int'}], - data : buffers - - }); - - this.store.sort('start'); - var type = 'Ext.grid.Panel'; - if (this.searchBar == true) { - type = 'Ext.ux.LiveSearchGridPanel'; - } - this.grid = Ext.create(type, { - store : this.store, - height : this.height, - width : this.width, - margin : 5, - columns : [ - { - text : '', - dataIndex : 'name', - width : 100, - hidden : _this.showExtendedColumns, - renderer : function(val, y, sample) { - if (sample.data.name == "BUFFER") - return "BUFFER"; - _this.peakCount++; - return "Peak #" + _this.peakCount; - } - - - }, - { - text : 'Peaks', - dataIndex : 'start', - sortable : true, - width : 100, - hidden: !_this.showExtendedColumns, - renderer : function(val, y, sample) { - return "From " + Number(sample.raw.start) + " to " + Number(sample.raw.end); - } - }, - { - text : 'Frames', - hidden : _this.showExtendedColumns, - columns : [ - { - text : 'Start', - dataIndex : 'start', - sortable : true, - hidden : _this.showExtendedColumns, - width : 100, - renderer : function(val, y, sample) { - return Number(val); - } - },{ - text : 'End', - dataIndex : 'end', - width : 100, - hidden : _this.showExtendedColumns, - renderer : function(val, y, sample) { - return Number(val); - } - },{ - text : 'Total', - dataIndex : 'end', - width : 100, - hidden : _this.showExtendedColumns, - renderer : function(val, y, sample) { - return "" + (sample.raw.end - sample.raw.start) + " frames"; - } - } - ] - } -// , -// { -// text : '', -// hidden : _this.showExtendedColumns, -// renderer : function(val, x, sample) { -// if (sample != null) { -// return BUI.getZipHTMLByFrameRangeId(sample.raw.experimentId, sample.raw.start, sample.raw.end); -// } -// }, -// width : 100 -// } - ], - flex : 1, - viewConfig : { - stripeRows : true, - getRowClass : function(record, rowIdx, params, store) { - if (record.raw.name == "BUFFER") { - return "blue-row"; - } - } - } + this.qualityControlResultsWidget = new QualityControlResultsWidget({ + qualityThreshold : this.radiationDamageThreshold, + radiationDamageThreshold : this.qualityThreshold + + }); + this.qualityControlResultsWidget.onQualityChanged.attach(function(sender, value) { + _this.qualityThreshold = value; + _this.thresholdsChanged(); }); - /** Adding the tbar **/ - if (this.tbar) { - this.grid.addDocked({ - xtype : 'toolbar', - items : this._getTbar() - }); - } - return this.grid; -}; + this.qualityControlResultsWidget.onRadiationDatamageChanged.attach(function(sender, value) { + _this.radiationDamageThreshold = value; + _this.thresholdsChanged(); -PeakGrid.prototype.input = function() { - return []; -}; + }); + this.concentrationHTMLTableWidget = new ConcentrationHTMLTableWidget({ + height : 250, + showBufferColumns : this.clusterByBuffers + }); -PeakGrid.prototype.test = function(targetId) { - var PeakGrid = new PeakGrid({ - width : 800, + this.plot = new BoxWhiskerGraph({ + targetId : _this.id + '_boxPlot', height : 350, - collapsed : false, - tbar : true + width : 450, + maxBoxWidth : 25 }); - var panel = PeakGrid.getPanel([]); - panel.render(targetId); -}; - -/** - * Macromolecule Grid showing macromolecules and adding anb updating buttons - * - * @height - * @maxHeight - * @width - * @cssFontStyle - * @searchBar makes this grid as Ext.ux.LiveSearchGridPanel - * @tbar top bar containing "Add" and "Update From SMIS" button - * @collapsed - * @collapsible - * @btnEditVisible - * @btnRemoveVisible - * @multiselect makes it multiselect using Ext.selection.CheckboxModel - * - * #onSelected - * #onMacromoleculesChanged - */ -function MacromoleculeGrid(args) { - this.height = 500; - this.width = 500; - this.id = BUI.id(); - this.maxHeight = this.height; + this.rangePlot = new RangeWhiskerGraph({ + targetId : _this.id + '_rangePlot', + height : 350, + width : 450, + maxBoxWidth : 25 + }); +} - this.searchBar = false; - this.tbar = false; +ResultSummaryForm.prototype.thresholdsChanged = function() { + var parsedData = this.prepareData(this.rawData); - this.collapsible = true; - this.collapsed = true; + var filtered = JSON.parse(JSON.stringify(parsedData)); + filtered.concentration.concentrations = []; + for ( var conc in parsedData.concentration.concentrations) { + if (parsedData.concentration.concentrations[conc].calculation.rgGnom.validNumber > 0) { + filtered.concentration.concentrations.push(parsedData.concentration.concentrations[conc]); + } + } - this.btnEditVisible = true; - this.btnRemoveVisible = false; - this.multiselect = false; + this.plotWhisker(filtered); + this.plotRange(filtered); - /** Font style applied to the acronym column **/ - this.cssFontStyle = null; + this.concentrationHTMLTableWidget.refresh(parsedData); +}; - if (args != null) { - if (args.height != null) { - this.height = args.height; - this.maxHeight = this.height; - } - if (args.maxHeight != null) { - this.maxHeight = args.maxHeight; - } - if (args.width != null) { - this.width = args.width; - } - if (args.cssFontStyle != null) { - this.cssFontStyle = args.cssFontStyle; - } +/** Given a frame object (object returned by analyzeFrames()) and depending of the threshold indicates if a datacollection has radiation damage **/ +ResultSummaryForm.prototype.hasRadiationDamage = function(frameObject) { + var bb = frameObject.bufferBeforeFramesMerged / frameObject.framesCount; + var ba = frameObject.bufferAfterFramesMerged / frameObject.framesCount; + var mol = frameObject.framesMerge / frameObject.framesCount; + return !((bb >= this.radiationDamageThreshold) && (ba >= this.radiationDamageThreshold) && (mol >= this.radiationDamageThreshold)); +}; - if (args.searchBar != null) { - this.searchBar = args.searchBar; - } - if (args.tbar != null) { - this.tbar = args.tbar; - } - if (args.collapsible != null) { - this.collapsible = args.collapsible; - } - if (args.collapsed != null) { - this.collapsed = args.collapsed; - } - if (args.btnEditVisible != null) { - this.btnEditVisible = args.btnEditVisible; - } - if (args.btnRemoveVisible != null) { - this.btnRemoveVisible = args.btnRemoveVisible; - } - if (args.multiselect != null) { - this.multiselect = args.multiselect; - } +/** Return (frameObject) an object with the information about the frames for a data collection**/ +ResultSummaryForm.prototype.analyzeFrames = function(dataCollectionRow) { + return { + bufferAfterFramesMerged : dataCollectionRow.bufferAfterFramesMerged, + bufferBeforeFramesMerged : dataCollectionRow.bufferBeforeFramesMerged, + framesCount : dataCollectionRow.framesCount, + framesMerge : dataCollectionRow.framesMerge + }; +}; + +ResultSummaryForm.prototype.detectDataCollectionWarnings = function(dataCollectionRow) { + var frameObject = this.analyzeFrames(dataCollectionRow); + var warnings = { + count : 0, + type : [] + }; + + if (this.hasRadiationDamage(frameObject)) { + warnings.count = warnings.count + 1; + warnings.type.push("RADIATION DAMAGE"); } - this.onSelected = new Event(); - - this.onMacromoleculesChanged = new Event(); -} + if (Number(dataCollectionRow.quality) < this.qualityThreshold) { + warnings.count = 1;//warnings.count + 1; + warnings.type.push("Quality <" + this.qualityThreshold); + } + return warnings; +}; +/** Return array composed by {concentration} objects **/ +ResultSummaryForm.prototype.getConcentrations = function(data) { + var concentrationsId = {}; + for ( var i = 0; i < data.length; i++) { + var warning = this.detectDataCollectionWarnings(data[i]); + var id = data[i].conc;// + "_" + data[i].bufferId; + if (this.clusterByBuffers) { + id = data[i].conc + "_" + data[i].bufferId; + } + if (concentrationsId[id] == null) { + concentrationsId[id] = { + id : id, + concentration : Number(data[i].conc).toFixed(2), + bufferId : data[i].bufferId, + bufferAcronym : data[i].bufferAcronym, + rgGuinier : [], + i0Guinier : [], + rgGnom : [], + dMax : [], + quality : [], + frames : [], + frames_warning : warning.count + }; + } else { + concentrationsId[id].frames_warning = concentrationsId[id].frames_warning + warning.count; + } + concentrationsId[id].frames.push(data[i]); -MacromoleculeGrid.prototype.edit = function(macromolecule) { - var _this = this; - var window = new MacromoleculeWindow(); - window.onSave.attach(function(sender) { - _this.store.loadData(BIOSAXS.proposal.getMacromolecules()); - _this.onMacromoleculesChanged.notify(); - }); - window.draw(macromolecule); -}; + if (warning.count == 0) { + concentrationsId[id].rgGuinier.push(data[i].rgGuinier); + concentrationsId[id].i0Guinier.push(data[i].I0); + concentrationsId[id].quality.push(data[i].quality); + concentrationsId[id].rgGnom.push(data[i].rgGnom); + concentrationsId[id].dMax.push(data[i].dmax); + } -MacromoleculeGrid.prototype.getTbar = function() { - var _this = this; - var actions = []; + } + var concentrations = []; + for ( var item in concentrationsId) { + if (concentrationsId.hasOwnProperty(item)) { + concentrations.push({ + concentration : concentrationsId[item].concentration, + id : item, + bufferId : Number(concentrationsId[item].bufferId).toFixed(2), + bufferAcronym : concentrationsId[item].bufferAcronym, + rgGuinier : concentrationsId[item].rgGuinier, + /** Frames **/ + frames : concentrationsId[item].frames, + frames_warning : concentrationsId[item].frames_warning, + /** Calculation **/ + calculation : { + rgGuinier : BUI.getStandardDeviation(concentrationsId[item].rgGuinier), + i0Guinier : BUI.getStandardDeviation(concentrationsId[item].i0Guinier), + quality : BUI.getStandardDeviation(concentrationsId[item].quality), + rgGnom : BUI.getStandardDeviation(concentrationsId[item].rgGnom), + dMax : BUI.getStandardDeviation(concentrationsId[item].dMax) - actions.push(Ext.create('Ext.Action', { - icon : '../images/add.png', - text : 'Add macromolecule', - disabled : false, - handler : function(widget, event) { - _this.edit(); - } - })); - actions.push("->"); - actions.push(Ext.create('Ext.Action', { - icon : '../images/folder_go.png', - text : 'Update From SMIS', - tooltip : "Retrieve all the macromolecules of your proposal from SMIS database", - disabled : false, - handler : function(widget, event) { - _this.grid.setLoading("Connecting to SMIS"); - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - BIOSAXS.proposal.setMacromolecules(data.macromolecules); - _this.refresh(BIOSAXS.proposal.macromolecules); - _this.grid.setLoading(false); - }); - adapter.onError.attach(function(sender, data) { - _this.grid.setLoading(false); + } }); - adapter.updateDataBaseFromSMIS(); } - })); - return actions; -}; + } -MacromoleculeGrid.prototype.deselectAll = function() { - this.grid.getSelectionModel().deselectAll(); + return { + concentrations : concentrations + }; }; -MacromoleculeGrid.prototype.selectById = function(macromoleculeId) { - this.grid.getSelectionModel().deselectAll(); - for ( var i = 0; i < this.grid.getStore().data.items.length; i++) { - var item = this.grid.getStore().data.items[i].raw; - if (item.macromoleculeId == macromoleculeId) { - this.grid.getSelectionModel().select(i); +ResultSummaryForm.prototype.prepareData = function(data) { + /** Return array composed by {acronym, bufferId} objects **/ + function getBuffers(data) { + var buffersId = {}; + for ( var i = 0; i < data.length; i++) { + buffersId[data[i].bufferId] = data[i].acronym; + } + var buffers = []; + for ( var id in buffersId) { + if (buffersId.hasOwnProperty(id)) { + buffers.push({ + acronym : buffersId[id], + bufferId : id + }); + } } + return buffers; } -}; -MacromoleculeGrid.prototype.refresh = function(macromolecules) { - this.store.loadData(macromolecules, false); + /** Get a string with all the concentrations **/ + function getConcentrationString(parseConcentrations) { + var concentrations = []; + for ( var i = 0; i < parseConcentrations.concentrations.length; i++) { + concentrations.push(parseConcentrations.concentrations[i].concentration + " mg/ml "); + } + return concentrations.toString(); + } + + var parseConcentrations = this.getConcentrations(data); + + return { + dataCollectionCount : data.length, + buffers : getBuffers(data), + concentration : parseConcentrations, + concentrationLabel : getConcentrationString(parseConcentrations) + }; }; -MacromoleculeGrid.prototype.getColumns = function() { - var _this = this; - var columns = [ - { - text : 'Acronym', - dataIndex : 'acronym', - id : this.id + "acronym", - flex : 1, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - if (_this.cssFontStyle != null) { - return "" + value + ""; +ResultSummaryForm.prototype.getDataForWhisker = function(data) { + var clusters = []; + + var concentrations = {}; + var i = 0; + var conc = 0; + if (this.collapseConcentrations) { + for (i = 0; i < data.concentration.concentrations.length; i++) { + conc = data.concentration.concentrations[i]; + var concentration = Number(conc.concentration).toFixed(0); + if (concentrations[concentration] == null) { + concentrations[concentration] = {}; + concentrations[concentration].concentration = concentration; + concentrations[concentration].calculation = {}; + concentrations[concentration].calculation.rgGuinier = {}; + concentrations[concentration].calculation.rgGuinier.values = []; + concentrations[concentration].calculation.rgGuinier.values = conc.calculation.rgGuinier.values; + concentrations[concentration].calculation.rgGnom = {}; + concentrations[concentration].calculation.rgGnom.values = []; + concentrations[concentration].calculation.rgGnom.values = conc.calculation.rgGnom.values; + } else { + concentrations[concentration].calculation.rgGuinier.values = concentrations[concentration].calculation.rgGuinier.values + .concat(conc.calculation.rgGuinier.values); + concentrations[concentration].calculation.rgGnom.values = concentrations[concentration].calculation.rgGnom.values + .concat(conc.calculation.rgGnom.values); } - return value; } - }, { - text : 'Name', - dataIndex : 'name', - id : this.id + "name", - flex : 1, - hidden : true - } ]; - if (this.btnEditVisible) { - columns.push({ - id : _this.id + 'buttonEditMacromolecule', - width : 85, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - if (_this.btnEditVisible) { - return BUI.getGreenButton('EDIT'); - } - return null; + /** From object to array **/ + var array = []; + for ( var key in concentrations) { + if (concentrations.hasOwnProperty(key)) { + array.push(concentrations[key]); } + } + data.concentration.concentrations = array; + } + + for (i = 0; i < data.concentration.concentrations.length; i++) { + conc = data.concentration.concentrations[i]; + clusters.push({ + name : conc.concentration + "mg/ml", + concentration : Number(conc.concentration), + x : Number(conc.concentration), + classes : [] + }); + clusters[clusters.length - 1].classes.push({ + name : "Guinier", + color : '#9A2EFE', + values : conc.calculation.rgGuinier.values + + }); + clusters[clusters.length - 1].classes.push({ + name : "P(r)", + color : '#2E64FE', + values : conc.calculation.rgGnom.values + }); } - if (this.btnRemoveVisible) { - columns.push({ - id : _this.id + 'buttonRemoveMacromolecule', - width : 85, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - if (_this.btnRemoveVisible) { - return BUI.getRedButton('REMOVE'); - } - return null; - } + return { + clusters : clusters.sort(function(a, b) { + return a.concentration - b.concentration; + }) + }; +}; + +ResultSummaryForm.prototype.getDataForWhiskerQuality = function(data) { + var clusters = []; + + for ( var i = 0; i < data.concentration.concentrations.length; i++) { + var conc = data.concentration.concentrations[i]; + clusters.push({ + name : conc.concentration + "mg/ml", + classes : [] + }); + clusters[clusters.length - 1].classes.push({ + name : "Quality", + values : conc.calculation.quality.values + }); } - return columns; + return { + clusters : clusters + }; +}; + +ResultSummaryForm.prototype.plotQualityWhisker = function(parsedData) { + this.qualityPlot.refresh(this.getDataForWhiskerQuality(parsedData)); }; +ResultSummaryForm.prototype.plotWhisker = function(parsedData) { + this.plot.refresh(this.getDataForWhisker(parsedData)); +}; -/** Returns the grid **/ -MacromoleculeGrid.prototype.getPanel = function() { +ResultSummaryForm.prototype.plotRange = function(parsedData) { + this.rangePlot.refresh(this.getDataForWhisker(parsedData)); +}; + +ResultSummaryForm.prototype.getPanel = function(data) { var _this = this; + _this.rawData = data; + var parsedData = this.prepareData(data); - this.store = Ext.create('Ext.data.Store', { - fields : [ 'macromoleculeId', 'name', 'acronym' ] - }); + this.panel = Ext + .createWidget( + 'form', + { + bodyPadding : 20, + frame : false, + border : 0, + width : this.width, + height : this.summaryHeight + 1000, + items : [ { + xtype : 'container', + layout : 'hbox', + items : [ { + xtype : 'container', + flex : 1, + border : false, + layout : 'anchor', + defaultType : 'textfield', + items : [ + _this.qualityControlResultsWidget.getPanel(), + { + xtype : 'fieldset', + width : 950, + margin : "20, 0 0 0", + height : this.summaryHeight + 500, + items : [ + { + html : "
Concentration Analysis
", + border : 0, + width : 900 - var type = 'Ext.grid.Panel'; - if (this.searchBar == true) { - type = 'Ext.ux.LiveSearchGridPanel'; - } + }, + { + html : this.concentrationHTMLTableWidget.getPanel(parsedData), + border : 0, + width : 900, + margin : "10, 0 0 10" - this.selModel = Ext.create('Ext.selection.RowModel', { -// allowDeselect : true, -// mode : 'MULTI', - listeners : { - selectionchange : function(sm, selections) { - var selected = []; - for (var i = 0; i < selections.length; i++) { - selected.push(selections[i].raw); - } - _this.onSelected.notify(selected); - } - } - }); + }, + { + xtype : 'container', + layout : 'vbox', + border : 5, + items : [ + { + html : "
Rg based on Guinier and Gnom
", + border : 8, + width : 900, + margin : "20 0 0 10" - this.grid = Ext.create(type, { - id : this.id, - title : 'Macromolecules', - collapsible : this.collapsible, - collapsed : this.collapsed, - store : this.store, - height : this.height, - maxHeight : this.maxHeight, - selModel : this.selModel, - columns : this.getColumns(), - width : this.width, - viewConfig : { - stripeRows : true, - listeners : { - 'celldblclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - _this.edit(BIOSAXS.proposal.getMacromoleculeById(record.data.macromoleculeId)); - }, - 'cellclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEditMacromolecule') { - _this.edit(BIOSAXS.proposal.getMacromoleculeById(record.data.macromoleculeId)); - } - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemoveMacromolecule') { - BUI.showBetaWarning(); - } - } + }, { + xtype : 'container', + layout : 'hbox', + items : [ { + xtype : 'container', + layout : 'vbox', + items : [ { + html : "
", + border : 0, + width : this.plot.width, + padding : "10 0 0 20", + listeners : { + afterrender : function() { + _this.plotWhisker(parsedData); - } - } - }); + } + } + }, { + html : "
Concentration (mg/ml)
", + width : 450, + border : 0, + margin : "-50 0 0 0" + + } ] + }, { + xtype : 'container', + layout : 'vbox', + items : [ { + html : "
", + border : 0, + width : this.rangePlot.width, + padding : "10 0 0 10", + listeners : { + afterrender : function() { + _this.plotRange(parsedData); + } + } + }, { + html : "
Concentration (mg/ml)
", + width : 450, + border : 0, + margin : "-50 0 0 0" + + } ] + } ] + } ] + } ] + } ] + } + + ] + } ] + }); + return this.panel; - /** Adding the tbar **/ - if (this.tbar) { - this.grid.addDocked({ - xtype : 'toolbar', - items : this.getTbar() - }); - } - return this.grid; }; -MacromoleculeGrid.prototype.input = function() { +ResultSummaryForm.prototype.input = function() { return { - proposal : DATADOC.getProposal_10() + data : DATADOC.getData_3367() }; }; -MacromoleculeGrid.prototype.test = function(targetId) { - var macromoleculeGrid = new MacromoleculeGrid({ - width : 800, - height : 350, - collapsed : false, - tbar : true - }); - - BIOSAXS.proposal = new Proposal(macromoleculeGrid.input().proposal); - var panel = macromoleculeGrid.getPanel(BIOSAXS.proposal.macromolecules); +ResultSummaryForm.prototype.test = function(targetId) { + var resultSummaryForm = new ResultSummaryForm(); + var panel = resultSummaryForm.getPanel(resultSummaryForm.input().data); panel.render(targetId); + }; -/** - * Shows measurements with their attributes as specimen, exposure temperature, - * volume to load, transmission etc... - * - * @addBtnMultipleEdit: if true add a button for changing measurements' - * parameters by choosing multiple measurements. It opens - * MultipleEditMeasurementGridWindow - * @collapsed: if true it doesn't show buffer's measurements - * @editor: hashmap containing columns to be edited. It is an array of a json - * like editor of Ext - * @selModel - * @collapseBtnEnable - * @removeBtnEnabled Ext.selection.RowModel - * @addBtnEnable - * @updateRowEnabled true/false if update plugin is set to the grid - * @showTitle - * @title - * @isStatusColumnHidden - * @isPriorityColumnHidden - * @isTimeColumnHidden - * @estimateTime - * @margin - * @tbar - * @height - * @maxHeight - * @minHeight - * @width - * @maxWidth - * @resizable - * @experimentColorBased when colors for buffers and macromolecules are not - * selected by the proposal but by experiment, so the - * number of colors is smaller +/** + * Example form + * + * @witdh + * @height + */ +function RigibBodyModelingForm(args) { + this.id = BUI.id(); + this.width = 700; + this.height = 500; + + if (args != null) { + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + } + + var _this = this; + this.rigidBodyGrid = new AprioriRigidBodyGrid(); + + this.rigidBodyGrid.onUploadFile.attach(function(sender, type, title){ + _this._openUploadDialog(_this.macromolecule.macromoleculeId, type, title); + }); + + this.rigidBodyGrid.onRemove.attach(function(sender, type, title){ + _this._update(); + }); + + this.onSave = new Event(this); + +} + +RigibBodyModelingForm.prototype._getItems = function() { + var _this = this; + + + return [ { + xtype : 'label', + forId : 'myFieldId', + text : 'Information for model fit, mixture analysis and rigid body modeling', + margin : '15 0 20 10', + cls : "inline-help" + }, + this.rigidBodyGrid.getPanel(), + { + xtype : 'label', + forId : 'myFieldId', + text : 'Distance restraints may be imposed on the model using contacts conditions file (OPTIONAL)', + margin : '25 0 5 10', + cls : "inline-help" + }, + { + xtype : 'container', + layout : 'hbox', + items : [ { + xtype : 'container', + border : false, + layout : 'hbox', + items : [ { + xtype : 'label', + forId : 'myFieldId', + text : 'Contact Description File: (Optional)', + width : 150, + margin : '10 0 0 10' + }, { + id : this.id + "contactsDescriptionFilePath", + xtype : 'textfield', + hideLabel : true, + margin : '10 0 0 0', + width : 200, + disabled: true + }, { + text : 'Upload', + xtype : 'button', + margin : "10 0 0 10", + width : 80, + handler : function() { + + _this._openUploadDialog(_this.macromolecule.macromoleculeId, "CONTACTS", "Upload Contact Description File"); + } + }, { + text : 'Remove', + id : _this.id + "_remove", + xtype : 'button', + margin : "10 0 0 10", + width : 80, + handler : function() { + _this.macromolecule.contactsDescriptionFilePath = null; + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, proposal) { + /** Updating the proposal global object **/ + BIOSAXS.proposal.setItems(proposal); + _this.panel.setLoading(false); + + var saved = BIOSAXS.proposal.getMacromoleculeByAcronym(_this.macromolecule.acronym); + /** Refreshing to check that everything is ok **/ + _this.refresh(saved); + _this.onSave.notify(saved); + }); + + _this.panel.setLoading("Saving Macromolecule") + adapter.saveMacromolecule(_this.macromolecule); + } + } ] + } ] + }, { + xtype : 'panel', + html : "Go to SASREF manual for further information", + margin : "10 0 0 160", + border : 0 + + }, + { + xtype : 'checkbox', + margin : '10 0 0 5', + boxLabel : "I want rigid body modeling run on this stuff", + checked : true, + width : 300 + } ] + +}; + +/** Because update is a jsp page we don't know if the user has uploaded a file or not then we need to refresh **/ +RigibBodyModelingForm.prototype._update = function(macromoleculeId, type, title) { + var _this = this; + BIOSAXS.proposal.onInitialized.attach(function() { + if (BIOSAXS.proposal != null) { + _this.refresh(BIOSAXS.proposal.getMacromoleculeById(_this.macromolecule.macromoleculeId)); + _this.panel.setLoading(false); + } + }); + this.panel.setLoading(); + BIOSAXS.proposal.init(); +}; + +RigibBodyModelingForm.prototype._openUploadDialog = function(macromoleculeId, type, title) { + var _this = this; + function onClose() { + w.destroy(); + _this._update(); + + } + + var w = Ext.create('Ext.window.Window', { + title : title, + height : 200, + width : 400, + modal : true, + buttons : [ { + text : 'Close', + handler : function() { + onClose(); + } + } ], + layout : 'fit', + items : { + html : "" + }, + listeners : { + onEsc : function() { + onClose(); + }, + close : function() { + onClose(); + } + } + }).show(); +}; + +RigibBodyModelingForm.prototype._getButtons = function() { + return []; +}; + +RigibBodyModelingForm.prototype.getPanel = function() { + var _this = this; + this.panel = Ext.create('Ext.form.Panel', { + width : this.width, + height : this.height, + margin : 10, + border : 1, + defaultType : 'textfield', + items : this._getItems(), + buttons : this._getButtons(), + listeners : { + afterrender : function(){ + _this._populate(); + + } + } + }); + return this.panel; +}; + +/** Populates could be call when the DOM is not filled yet **/ +RigibBodyModelingForm.prototype._populate = function() { + if (this.macromolecule != null){ + if (Ext.getCmp(this.id + "contactsDescriptionFilePath") != null){ + if (this.macromolecule.contactsDescriptionFilePath != null){ + Ext.getCmp(this.id + "contactsDescriptionFilePath").setValue(this.macromolecule.contactsDescriptionFilePath); + Ext.getCmp(this.id + "_remove").enable(); + } + else{ + Ext.getCmp(this.id + "_remove").disable(); + Ext.getCmp(this.id + "contactsDescriptionFilePath").setValue(""); + + } + } + } +}; + +/** It populates the form * */ +RigibBodyModelingForm.prototype.refresh = function(macromolecule) { + this.macromolecule = macromolecule; + this.rigidBodyGrid.refresh(macromolecule); + this._populate(); +}; + +RigibBodyModelingForm.prototype.input = function() { + return {}; +}; + + +/** It populates the form **/ +RigibBodyModelingForm.prototype.test = function(targetId) { + var macromoleculeForm = new RigibBodyModelingForm(); + var panel = macromoleculeForm.getPanel(); + panel.render(targetId); +}; + + +/** + * Same form as MX part * - * #onClick #onSelected #onRemoved #onUpdateTime #onMeasurementChanged - * #onExperimentChanged + * @creationMode if true a create button appears instead of save + * @showTitle true or false */ -function MeasurementGrid(args) { +function ShipmentForm(args) { this.id = BUI.id(); - this.height = 500; - this.width = 900; - - this.maxWidth = 1200; - this.maxHeight = 600; - this.minHeight = 500; - - this.unitsFontSize = 9; - this.title = "Measurements"; - this.estimateTime = false; - this.collapsed = true; - this.tbar = true; - + this.creationMode = false; this.showTitle = true; - this.resizable = true; - this.updateRowEnabled = true; - - /** - * Hash map containing the keys of the editable columns. Ex: - * 'exposureTemperature' * - */ - this.editor = { - comments : { - xtype : 'textfield', - allowBlank : true + if (args != null) { + if (args.creationMode != null) { + this.creationMode = args.creationMode; } - }; + if (args.showTitle != null) { + this.showTitle = args.showTitle; + } + } - this.isTimeColumnHidden = false; - this.isStatusColumnHidden = false; - this.isPriorityColumnHidden = true; - this.margin = "0 0 0 0"; + this.onSaved = new Event(this); +} - this.addBtnEnable = true; - this.sorter = [ { - property : 'priority', - direction : 'ASC' - } ]; +ShipmentForm.prototype.fillStores = function() { + this.panel.setLoading("Loading Labcontacts from database"); + this.labContactForSendingStore.loadData(BIOSAXS.proposal.getLabcontacts(), false); + this.labContactForReturnStore.loadData(BIOSAXS.proposal.getLabcontacts(), false); + this.panel.setLoading(false); + if (this.shipment != null) { + this.setShipment(this.shipment); + } +}; - this.removeBtnEnabled = false; - this.collapseBtnEnable = true; - this.addBtnMultipleEdit = false; - this.sortingBtnEnable = false; +ShipmentForm.prototype.draw = function(targetId) { + this.getPanel().render(targetId); +}; +ShipmentForm.prototype.setShipment = function(shipment) { + this.shipment = shipment; var _this = this; - this.selModel = Ext.create('Ext.selection.RowModel', { - allowDeselect : true, - mode : 'MULTI', - listeners : { - selectionchange : function(sm, selections) { - var selected = []; - for (var i = 0; i < selections.length; i++) { - selected.push(selections[i].raw); - } - _this.onSelected.notify(selected); - } - } - }); - - if (args != null) { - - if (args.selModel != null) { - this.selModel = args.selModel; - } + Ext.getCmp(_this.id + "shippingName").setValue(shipment.json.shippingName); + Ext.getCmp(_this.id + "shippingStatus").setValue(shipment.json.shippingStatus); + Ext.getCmp(_this.id + "comments").setValue(shipment.json.comments); + if (shipment.json.sendingLabContactVO != null) { + this.labContactsSendingCombo.setValue(shipment.json.sendingLabContactVO.labContactId); + } + if (shipment.json.returnLabContactVO != null) { + this.labContactsReturnCombo.setValue(shipment.json.returnLabContactVO.labContactId); + } - if (args.removeBtnEnabled != null) { - this.removeBtnEnabled = args.removeBtnEnabled; - } +}; - if (args.addBtnMultipleEdit != null) { - this.addBtnMultipleEdit = args.addBtnMultipleEdit; - } +ShipmentForm.prototype._saveShipment = function() { + var _this = this; + var shippingId = null; + if (this.shipment != null) { + shippingId = this.shipment.json.shippingId; + } + var json = { + shippingId : shippingId, + name : Ext.getCmp(_this.id + "shippingName").getValue(), + status : Ext.getCmp(_this.id + "shippingStatus").getValue(), + sendingLabContactId : Ext.getCmp(_this.id + "shipmentform_sendingLabContactId").getValue(), + returnLabContactId : Ext.getCmp(_this.id + "returnLabContactId").getValue(), + returnCourier : Ext.getCmp(_this.id + "returnCourier").getValue(), + courierAccount : Ext.getCmp(_this.id + "courierAccount").getValue(), + BillingReference : Ext.getCmp(_this.id + "BillingReference").getValue(), + dewarAvgCustomsValue : Ext.getCmp(_this.id + "dewarAvgCustomsValue").getValue(), + dewarAvgTransportValue : Ext.getCmp(_this.id + "dewarAvgTransportValue").getValue(), + comments : Ext.getCmp(_this.id + "comments").getValue() + }; - // if (args.experimentColorBased != null) { - // this.experimentColorBased = args.experimentColorBased; - // } + var dataAdapter = new BiosaxsDataAdapter(); + dataAdapter.onSuccess.attach(function(sender, shipment) { + window.location = BUI.getShippingURL(shipment.shippingId); + }); - if (args.collapsed != null) { - this.collapsed = args.collapsed; - } - if (args.resizable != null) { - this.resizable = args.resizable; - } + dataAdapter.onError.attach(function(sender, error) { + _this.onError.notify(error); + }); - if (args.editor != null) { - this.editor = args.editor; - } + /** Cheking params **/ + if (json.name == "") { + BUI.showError("Name field is mandatory"); + return; + } - if (args.collapseBtnEnable != null) { - this.collapseBtnEnable = args.collapseBtnEnable; - } + if (json.sendingLabContactId == null) { + BUI.showError("Lab contact for sending field is mandatory"); + return; + } - if (args.addBtnEnable != null) { - this.addBtnEnable = args.addBtnEnable; - } - if (args.sortingBtnEnable != null) { - this.sortingBtnEnable = args.sortingBtnEnable; - } + if (json.returnLabContactId == null) { + BUI.showError("Lab contact for return field is mandatory"); + return; + } - if (args.isPriorityColumnHidden != null) { - this.isPriorityColumnHidden = args.isPriorityColumnHidden; - } + dataAdapter.createShipment(json.shippingId, json.name, json.status, json.comments, json.sendingLabContactId, json.returnLabContactId, + json.returnCourier, json.courierAccount, json.BillingReference, json.dewarAvgCustomsValue, json.dewarAvgTransportValue); - if (args.width != null) { - this.width = args.width; - } +}; - if (args.updateRowEnabled != null) { - this.updateRowEnabled = args.updateRowEnabled; - } +ShipmentForm.prototype.getPanel = function(shipment) { + var _this = this; + this.shipment = shipment; + var required = '*'; + var buttons = []; - if (args.showTitle != null) { - this.showTitle = args.showTitle; - if (this.showTitle == false) { - this.title = null; + if (_this.creationMode) { + buttons.push({ + text : 'Create', + scope : this, + handler : function() { + _this._saveShipment(); } - } - - if (args.height != null) { - this.height = args.height; - } - - if (args.maxHeight != null) { - this.maxHeight = args.maxHeight; - } - - if (args.minHeight != null) { - this.minHeight = args.minHeight; - } + }); + } else { + buttons.push({ + text : 'Save', + scope : this, + handler : function() { + _this._saveShipment(); + } + }); - if (args.maxWidth != null) { - this.maxWidth = args.maxWidth; - } + } - if (args.isStatusColumnHidden != null) { - this.isStatusColumnHidden = args.isStatusColumnHidden; - } - if (args.isTimeColumnHidden != null) { - this.isTimeColumnHidden = args.isTimeColumnHidden; - } + this.labContactForSendingStore = Ext.create('Ext.data.Store', { + fields : [ 'cardName', 'labContactId' ] + }); - if (args.title != null) { - this.title = args.title; - } - if (args.estimateTime != null) { - this.estimateTime = args.estimateTime; - } + this.labContactForReturnStore = Ext.create('Ext.data.Store', { + fields : [ 'cardName', 'labContactId' ] + }); - if (args.margin != null) { - this.margin = args.margin; - } + // Create the combo box, attached to the states data store + this.labContactsSendingCombo = Ext.create('Ext.form.ComboBox', { + id : _this.id + "shipmentform_sendingLabContactId", + fieldLabel : 'Lab contact for sending', + afterLabelTextTpl : required, + store : this.labContactForSendingStore, + queryMode : 'local', + labelWidth : 200, + displayField : 'cardName', + valueField : 'labContactId' + }); - if (args.tbar != null) { - this.tbar = args.tbar; + this.labContactsReturnCombo = Ext.create('Ext.form.ComboBox', { + id : _this.id + "returnLabContactId", + fieldLabel : 'If No, Lab-Contact for Return', + afterLabelTextTpl : required, + store : this.labContactForReturnStore, + queryMode : 'local', + labelWidth : 200, + displayField : 'cardName', + valueField : 'labContactId', + listeners : { + change : function(x, newValue) { + for ( var i = 0; i < x.getStore().data.items.length; i++) { + if (x.getStore().data.items[i].raw.labContactId == newValue) { + Ext.getCmp(_this.id + "returnCourier").setValue(x.getStore().data.items[i].raw.defaultCourrierCompany); + Ext.getCmp(_this.id + "courierAccount").setValue(x.getStore().data.items[i].raw.courierAccount); + Ext.getCmp(_this.id + "BillingReference").setValue(x.getStore().data.items[i].raw.billingReference); + Ext.getCmp(_this.id + "dewarAvgCustomsValue").setValue(x.getStore().data.items[i].raw.dewarAvgCustomsValue); + Ext.getCmp(_this.id + "dewarAvgTransportValue").setValue(x.getStore().data.items[i].raw.dewarAvgTransportValue); + } + } + } } + }); - if (args.sorter != null) { - this.sorter = args.sorter; - } + if (this.panel == null) { + this.panel = Ext.create('Ext.form.Panel', { + bodyPadding : 5, + width : 600, + border : 1, + items : [ { + xtype : 'fieldset', + title : 'Details', + collapsible : false, + defaultType : 'textfield', + layout : 'anchor', + defaults : { + anchor : '100%' + }, + items : [ { + xtype : 'requiredtext', + fieldLabel : 'Shipment Label', + allowBlank : false, + name : 'shippingName', + id : _this.id + 'shippingName', + value : '', + anchor : '50%' + }, { + xtype : 'textareafield', + name : 'comments', + id : _this.id + 'comments', + fieldLabel : 'Comments', + value : '' + }, { + fieldLabel : 'Status', + readOnly : true, + id : _this.id + 'shippingStatus', + value : 'Opened', + anchor : '50%' + } ] + }, { + xtype : 'fieldset', + title : 'Lab-Contacts', + collapsible : false, + defaultType : 'textfield', + layout : 'anchor', + defaults : { + anchor : '100%' + }, + items : [ this.labContactsSendingCombo, this.labContactsReturnCombo ] + }, { + border : 0, + html : BUI.getWarningHTML("These informations are relevant for all shipments") + }, { + xtype : 'fieldset', + title : 'Courier accounts details for return', + collapsible : false, + layout : 'anchor', + defaults : { + anchor : '100%' + }, + items : [ { + xtype : 'textfield', + labelWidth : 400, + fieldLabel : 'Courier company for return (if ESRF sends a dewar back)', + id : _this.id + 'returnCourier', + value : '' + }, { + xtype : 'textfield', + labelWidth : 400, + fieldLabel : 'Courier account', + id : _this.id + 'courierAccount', + value : '' + }, { + xtype : 'textfield', + labelWidth : 400, + fieldLabel : 'Billing reference', + id : _this.id + 'BillingReference', + value : '' + }, { + xtype : 'numberfield', + labelWidth : 400, + fieldLabel : 'Average Customs value of a dewar (Euro)', + id : _this.id + 'dewarAvgCustomsValue', + value : '' + }, { + xtype : 'numberfield', + labelWidth : 400, + fieldLabel : 'Average Transport value of a dewar (Euro)', + id : _this.id + 'dewarAvgTransportValue', + value : '' + } ] + } ], + buttons : buttons + }); } - this.onClick = new Event(this); - this.onSelected = new Event(this); - this.onRemoved = new Event(this); - this.onUpdateTime = new Event(this); - this.onMeasurementChanged = new Event(this); - this.onExperimentChanged = new Event(this); -} - -MeasurementGrid.prototype._sortBy = function(sort) { - var _this = this; - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - _this.onExperimentChanged.notify(data); - _this.grid.setLoading(false); - // wizardWidget.window.close(); - }); - adapter.onError.attach(function(sender, data) { - _this.grid.setLoading(false); - alert("Oops, there was a problem"); - }); - _this.grid.setLoading("Sorting"); - adapter.sortMeasurements(this.experiments.experiments[0].experimentId, sort); + this.fillStores(); + if (this.showTitle) { + this.panel.setTitle('Create a new Shipment'); + } + return this.panel; }; -MeasurementGrid.prototype._getMenu = function() { - var _this = this; - if (this.tbar) { +ShipmentForm.prototype.input = function() { + return { + proposal : DATADOC.getProposal_10() - var items = []; - if (_this.addBtnEnable) { - items.push({ - icon : '../images/add.png', - text : 'Add measurements', - handler : function() { - _this._openAddMeasurementWindow(); - } - }); - } + }; +}; - if (_this.addBtnMultipleEdit) { - items.push({ - icon : '../images/Edit_16x16_01.png', - text : 'Multiple Edit', - handler : function() { - var multipleEditMeasurementGridWindow = new MultipleEditMeasurementGridWindow(); - multipleEditMeasurementGridWindow.onExperimentChanged.attach(function(sender, data) { - _this.onExperimentChanged.notify(data); - }); +ShipmentForm.prototype.test = function(targetId) { + var shipmentForm = new ShipmentForm({ + creationMode : true - multipleEditMeasurementGridWindow.draw(_this.measurements, _this.experiments); + }); + BIOSAXS.proposal = new Proposal(shipmentForm.input().proposal); + shipmentForm.getPanel().render(targetId); +}; + +/** + * #onSaved + */ +function StockSolutionForm(args) { + this.id = BUI.id(); + this.actions = []; - } - }); + if (args != null) { + if (args.actions != null) { + this.actions = args.actions; } + } + this.onSaved = new Event(this); +} - items.push("->"); +StockSolutionForm.prototype.getStockSolution = function() { + if (this.stockSolution != null) { + this.stockSolution.concentration = Ext.getCmp(this.id + "stockSolution_concentration").getValue(); + this.stockSolution.storageTemperature = Ext.getCmp(this.id + "stockSolution_storageTemperature").getValue(); + this.stockSolution.volume = Ext.getCmp(this.id + "stockSolution_volume").getValue(); + this.stockSolution.comments = Ext.getCmp(this.id + "stockSolution_comments").getValue(); + this.stockSolution.name = Ext.getCmp(this.id + "stockSolution_name").getValue(); + this.stockSolution.bufferId = this.bufferCombo.getValue(); - if (_this.sortingBtnEnable) { - var split = Ext.create('Ext.button.Split', { - text : 'Sort by', - // handle a click on the button itself - handler : function() { - // alert("The button was clicked"); - }, - menu : new Ext.menu.Menu({ - items : [ - { - text : 'First Created First Measured', - handler : function() { - _this._sortBy("FIFO"); - } - }, "-", { - text : 'Default', - handler : function() { - _this._sortBy("DEFAULT"); - } - } ] - }) - }); - items.push(split); + if (this.macromoleculeCombo.getValue() != null) { + this.stockSolution.macromoleculeId = this.macromoleculeCombo.getValue(); + } else { + this.stockSolution.macromolecule3VO = null; } - if (_this.collapseBtnEnable) { - items.push({ - text : 'Collapse buffers', - enableToggle : true, - scope : this, - toggleHandler : function(item, pressed) { - this.collapsed = pressed; - this.grid.getStore().loadData(this._prepareData(this.measurements, this.experiments), false); - }, - pressed : this.collapsed - }); + } else { + return { + concentration : Ext.getCmp(this.id + "stockSolution_concentration").getValue(), + storageTemperature : Ext.getCmp(this.id + "stockSolution_storageTemperature").getValue(), + volume : Ext.getCmp(this.id + "stockSolution_volume").getValue(), + comments : Ext.getCmp(this.id + "stockSolution_comments").getValue(), + name : Ext.getCmp(this.id + "stockSolution_name").getValue(), + bufferId : this.bufferCombo.getValue(), + macromoleculeId : this.macromoleculeCombo.getValue() + }; + } + return this.stockSolution; +}; + +StockSolutionForm.prototype.setStockSolution = function(stockSolution) { + if (stockSolution != null) { + if (stockSolution.macromoleculeId != null) { + this.macromoleculeCombo.setValue(stockSolution.macromoleculeId); } - var tb = Ext.create('Ext.toolbar.Toolbar', { - items : items - }); - return tb; + this.bufferCombo.setValue(stockSolution.bufferId); + Ext.getCmp(this.id + "stockSolution_concentration").setValue(this.stockSolution.concentration); + Ext.getCmp(this.id + "stockSolution_storageTemperature").setValue(this.stockSolution.storageTemperature); + Ext.getCmp(this.id + "stockSolution_volume").setValue(this.stockSolution.volume); + Ext.getCmp(this.id + "stockSolution_name").setValue(this.stockSolution.name); + Ext.getCmp(this.id + "stockSolution_comments").setValue(this.stockSolution.comments); } - return null; }; -/** Opens WizardWidget for adding new measurements * */ -MeasurementGrid.prototype._openAddMeasurementWindow = function(measurements, experiments) { - var _this = this; - var wizardWidget = new WizardWidget(); - wizardWidget.onFinished.attach(function(sender, result) { - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - _this.onExperimentChanged.notify(data); - _this.grid.setLoading(false); - wizardWidget.window.close(); - }); - wizardWidget.current.setLoading("ISPyB: Adding measurements"); - adapter.addMeasurements(result.name, "comments", result.data, _this.experiments.experiments[0].experimentId); +StockSolutionForm.prototype.getBufferCombo = function() { + this.bufferCombo = BIOSAXS_COMBOMANAGER.getComboBuffers(BIOSAXS.proposal.getBuffers(), { + labelWidth : 120, + margin : '0 0 10 0', + width : 220 + }); + return this.bufferCombo; +}; - wizardWidget.draw(null, new MeasurementCreatorStepWizardForm(BIOSAXS.proposal.getMacromolecules(), { - noNext : true - })); +StockSolutionForm.prototype.getMacromoleculeCombo = function() { + this.macromoleculeCombo = BIOSAXS_COMBOMANAGER.getComboMacromoleculeByMacromolecules(BIOSAXS.proposal.getMacromolecules(), { + labelWidth : 120, + margin : '0 0 10 0', + width : 220 + + }); + return this.macromoleculeCombo; }; -/******************************************************************************* - * Opens WizardWidget for adding new measurements - * - * @Measurements - * @Experiments experimentList Object - ******************************************************************************/ -MeasurementGrid.prototype._prepareData = function(measurements, experiments) { - var data = []; - for (var i = 0; i < measurements.length; i++) { - var measurement = measurements[i]; - var specimen = experiments.getSampleById(measurement.specimenId); - var buffer = experiments.getBufferById(specimen.bufferId); - measurement.buffer_acronym = buffer.acronym; - measurement.bufferId = buffer.bufferId; - measurement.volume = specimen.volume; - if (specimen.macromolecule3VO != null) { - measurement.acronym = specimen.macromolecule3VO.acronym; - measurement.macromoleculeId = specimen.macromolecule3VO.macromoleculeId; - } - measurement.concentration = specimen.concentration; - if (measurement.run3VO != null) { - measurement.energy = measurement.run3VO.energy; - measurement.expExposureTemperature = measurement.run3VO.exposureTemperature; - measurement.storageTemperature = measurement.run3VO.storageTemperature; - measurement.timePerFrame = measurement.run3VO.timePerFrame; - measurement.radiationAbsolute = measurement.run3VO.radiationAbsolute; - measurement.radiationRelative = measurement.run3VO.radiationRelative; - measurement.status = "DONE"; +StockSolutionForm.prototype.refresh = function() { +}; - try { - if (measurement.run3VO.timeStart != null) { - if (measurement.run3VO.timeStart != "") { - measurement.miliseconds = moment(measurement.run3VO.timeStart).format("X"); - } - } - } catch (E) { - console.log(E); - } - } +StockSolutionForm.prototype._getTopPanel = function() { + return { + xtype : 'container', + layout : 'hbox', + border : 0, + items : [ { + xtype : 'container', + layout : 'hbox', + items : [ { + xtype : 'container', + flex : 1, + border : false, + layout : 'anchor', + defaultType : 'textfield', + items : [ - if (experiments.getDataCollectionByMeasurementId(measurement.measurementId).length > 0) { - var measurementtodatacollection3VOs = experiments.getDataCollectionByMeasurementId(measurement.measurementId)[0].measurementtodatacollection3VOs; - for (var k = 0; k < measurementtodatacollection3VOs.length; k++) { - if (measurementtodatacollection3VOs[k].dataCollectionOrder == 1) { - var specimenBuffer = experiments.getSampleById(experiments.getMeasurementById(measurementtodatacollection3VOs[k].measurementId).specimenId); - if (specimenBuffer.sampleplateposition3VO != null) { - measurement.bufferSampleplateposition3VO = specimenBuffer.sampleplateposition3VO; - measurement.bufferSampleplate = (experiments.getSamplePlateById(specimenBuffer.sampleplateposition3VO.samplePlateId)); - } - } - } - } + this.getMacromoleculeCombo(), { + xtype : 'requiredtext', + id : this.id + 'stockSolution_name', + fieldLabel : 'Acronym', + labelWidth : 120, + width : 250 + }, { + xtype : 'requiredtext', + id : this.id + 'stockSolution_concentration', + fieldLabel : 'Conc. (mg/ml)', + labelWidth : 120, + width : 250 + }, - if (this.collapsed) { - /** If collapsed only the samples * */ - if (specimen.macromolecule3VO != null) { - data.push(measurement); - } - } else { - data.push(measurement); - } + { + id : this.id + 'stockSolution_storageTemperature', + fieldLabel : 'Storage Temp.(C)', + labelWidth : 120, + width : 250 + }, { + xtype : 'requiredtext', + id : this.id + 'stockSolution_volume', + fieldLabel : 'Volume in Well (µl)', + labelWidth : 120, + width : 250 + } ] + } ] + }, { + xtype : 'container', + flex : 1, + layout : 'anchor', + defaultType : 'textfield', + margin : '0 0 0 10', + items : [ this.getBufferCombo() ] + } ] + }; - } - return data; }; -/** - * Refresh data grid with the measurements and the experiments - * - * @measurements array with measurement3VO objects - * @experiments array with experiments objects - */ -MeasurementGrid.prototype.refresh = function(measurements, experiments) { - this.experiments = experiments; - this.measurements = measurements; - this.store.loadData(this._prepareData(measurements, experiments), false); +StockSolutionForm.prototype.getPanel = function(stockSolution) { + this.stockSolution = stockSolution; + this.panel = Ext.createWidget({ + xtype : 'container', + layout : 'vbox', + border : 0, + style : { + padding : '10px' + }, + fieldDefaults : { + labelAlign : 'left', + labelWidth : 50 + }, + items : [ this._getTopPanel(stockSolution), { + id : this.id + 'stockSolution_comments', + xtype : 'textareafield', + name : 'comments', + fieldLabel : 'Comments', + labelWidth : 120, + width : '100%' + } ] + }); + + this.setStockSolution(stockSolution); + return this.panel; +}; + +StockSolutionForm.prototype.input = function() { + return { + stock : { + "stockSolutionId" : 6, + "proposalId" : 3124, + "macromoleculeId" : 5933, + "bufferId" : 811, + "instructionSet3VO" : null, + "boxId" : 305861, + "storageTemperature" : "20", + "volume" : "300", + "concentration" : "1.2", + "comments" : "Buffer EDTA with A", + "name" : "A_EDTA_1.2", + "samples" : [], + "buffer" : "EDTA", + "macromolecule" : "A" + }, + proposal : new MeasurementGrid().input().proposal + }; +}; + +StockSolutionForm.prototype.test = function(targetId) { + var stockSolutionForm = new StockSolutionForm(); + BIOSAXS.proposal = new Proposal(stockSolutionForm.input().proposal); + var panel = stockSolutionForm.getPanel(new Shipment(stockSolutionForm.input().stock)); + panel.render(targetId); }; + + +BoxWhiskerGraph.prototype.cleanArray = GenericGraph.prototype.cleanArray; +BoxWhiskerGraph.prototype.plotAxes = GenericGraph.prototype.plotAxes; +BoxWhiskerGraph.prototype.plotRuler = GenericGraph.prototype.plotRuler; +BoxWhiskerGraph.prototype.drawSVGVerticalText = GenericGraph.prototype.drawSVGVerticalText; +BoxWhiskerGraph.prototype.getClassColor = GenericGraph.prototype.getClassColor; +BoxWhiskerGraph.prototype.getDimensions = GenericGraph.prototype.getDimensions; +BoxWhiskerGraph.prototype.calculate = GenericGraph.prototype.calculate; +BoxWhiskerGraph.prototype.getMedian = GenericGraph.prototype.getMedian; +BoxWhiskerGraph.prototype.pointToPixel = GenericGraph.prototype.pointToPixel; +BoxWhiskerGraph.prototype.maxValueWhisker = GenericGraph.prototype.maxValueWhisker; +BoxWhiskerGraph.prototype.refresh = GenericGraph.prototype.refresh; /** - * Set status bar to busy (refreshing icon) + * Subclass of GenericGraph * - * @msg message to be displayed on the bar + * @maxBoxWidth */ -MeasurementGrid.prototype._showStatusBarBusy = function(msg) { - var statusBar = Ext.getCmp(this.id + 'basic-statusbar'); - statusBar.setStatus({ - text : msg, - iconCls : 'x-status-busy', - clear : false - }); +function BoxWhiskerGraph(args){ + this.maxBoxWidth = 25; + + if (args == null){ + args = new Object(); + } + args["plotHorizontalByCluster"] = true; + + GenericGraph.call(this, args); + + if (args.maxBoxWidth != null){ + this.maxBoxWidth = args.maxBoxWidth; + } }; + + /** - * Set status bar to ready (ok icon) - * - * @msg message to be displayed on the bar - */ -MeasurementGrid.prototype._showStatusBarReady = function(msg) { - var statusBar = Ext.getCmp(this.id + 'basic-statusbar'); - statusBar.setStatus({ - text : msg, - iconCls : 'x-status-valid', - clear : false - }); +There are several different methods for calculating quartiles.[1] This calculator uses a method described by Moore and McCabe to find quartile values. +The same method also used by The TI-83 to calculate quartile values. +With this method, the first quartile is the median of the numbers below the median, the third quartile is the median of the numbers above the median. + +http://www.miniwebtool.com/quartile-calculator/ +http://www.alcula.com/calculators/statistics/box-plot/ +**/ +BoxWhiskerGraph.prototype.getQ1 = function(array){ + array = array.slice(0, array.length/2); + return this.getMedian(array); }; -/** - * If updateRowEnabled returns an array with Ext.grid.plugin.RowEditing - */ -MeasurementGrid.prototype._getPlugins = function() { - var _this = this; - var plugins = []; - if (this.updateRowEnabled) { - plugins.push(Ext.create('Ext.grid.plugin.RowEditing', { - clicksToEdit : 1, - listeners : { - validateedit : function(grid, e) { - /** Setting values * */ - for ( var key in _this.editor) { - e.record.raw[key] = e.newValues[key]; - } - /** Comments are always updatable* */ - e.record.raw.comments = e.newValues.comments; +BoxWhiskerGraph.prototype.getQ3 = function(array){ + array = array.slice((array.length + 1)/2); + return this.getMedian(array); + +}; - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, measurement) { - _this.onMeasurementChanged.notify(measurement); - _this.grid.setLoading(false); - }); - adapter.onError.attach(function() { - alert("Error"); - _this.grid.setLoading(false); - }); +BoxWhiskerGraph.prototype.getQ2 = function(array){ + return this.getMedian(array); +}; - _this.grid.setLoading(); - adapter.saveMeasurement(e.record.raw, _this.experiments.experiments[0]); - } - } - })); +BoxWhiskerGraph.prototype.getBelowOutliers = function(belowLimit, array){ + var points = new Array(); + for (var i = 0; i < array.length; i++){ + if (array[i] <= belowLimit){ + points.push(array[i]); + } } - return plugins; + return points; }; -/** - * @key name of the columns mathing the this.editor[key] - */ -MeasurementGrid.prototype._getEditor = function(key) { - if (this.editor[key] != null) { - return this.editor[key]; +BoxWhiskerGraph.prototype.getAboveOutliers = function(aboveLimit, array){ + var points = new Array(); + for (var i = 0; i < array.length; i++){ + if (array[i] >= aboveLimit){ + points.push(array[i]); + } } - return null; + return points; }; -MeasurementGrid.prototype.getPanel = function(measurements, experiments) { - this.experiments = experiments; - this.measurements = measurements; - var _this = this; - this.store = Ext.create('Ext.data.Store', { - fields : [ { - name : 'miliseconds', - type : 'int' - }, 'priority', 'bufferId', { - name : 'exposureTemperature', - type : 'numeric' - }, 'volumeToLoad','code', 'transmission', 'viscosity', 'waitTime', 'flow', 'buffer_acronym', 'macromoleculeId', 'acronym', 'concentration', 'extraFlowTime', 'volume', 'energy', - 'expExposureTemperature', 'storageTemperature', 'timePerFrame', 'radiationAbsolute', 'radiationRelative', 'status', 'comments' ], - data : this._prepareData(measurements, experiments) - }); - this.store.sort(this.sorter); - var bbar = {}; - try { - bbar = Ext.create('Ext.ux.StatusBar', { - id : _this.id + 'basic-statusbar', - defaultText : 'Ready', - text : 'Ready', - iconCls : 'x-status-valid', - items : [] - }); - } catch (exp) { - console.log("bbar error"); + +BoxWhiskerGraph.prototype.minValueWhisker = function(belowLimit, q1, array){ + var points = new Array(); + + for (var i = 0; i < array.length; i++){ + if ((array[i] < q1) && (array[i]) > belowLimit){ + points.push(array[i]); + } + } + + if (points.length > 0){ + points.sort(function(a, b){return a - b;}); + return points[0]; } + return null; +}; - this.grid = Ext - .create( - 'Ext.grid.Panel', - { - id : this.id, - title : this.title, - store : this.store, - selModel : this.selModel, - plugins : this._getPlugins(), - resizable : this.resizable, - margin : this.margin, - maxHeight : this.maxHeight, - minHeight : this.minHeight, - maxWidth : this.maxWidth, - width : this.width, - tbar : this._getMenu(), - columns : [ - { - text : 'Order', - dataIndex : 'priority', - width : 50, - hidden : _this.isPriorityColumnHidden, - sortable : true +BoxWhiskerGraph.prototype.isNumber = function(value){ + if (value=="") return false; - }, - { - text : 'Run Number', - dataIndex : 'code', - width : 50, - hidden : true, - sortable : true + var d = parseInt(value); + if (!isNaN(d)) return true; else return false; - }, +}; - { - text : 'Specimen', - columns : [ +BoxWhiskerGraph.prototype.plotBoxWhisker = function(boxProperties){ + if (this.maxBoxWidth != null){ + if (boxProperties.width > this.maxBoxWidth){ + boxProperties.x = boxProperties.x + (boxProperties.width/2) - (this.maxBoxWidth/2); + boxProperties.width = this.maxBoxWidth; + } + + } - { - text : '', - dataIndex : 'macromoleculeId', - width : 30, - renderer : function(val, y, sample) { - if (val != null) { - if (_this.experiments == null) { - return BUI.getRectangleColorDIV(BIOSAXS.proposal.macromoleculeColors[val], 10, 10); - } else { - return BUI.getRectangleColorDIV(_this.experiments.macromoleculeColors[val], 10, 10); - } - } - }, - sortable : true - }, - { - text : 'Macromo.', - dataIndex : 'acronym', - width : 80, - renderer : function(val, y, sample) { - return val; - }, - sortable : true - }, - { - text : 'Conc. ', - dataIndex : 'concentration', - width : 80, - renderer : function(val, y, sample) { - if (sample.raw.macromoleculeId == null) { - return ""; - } - if (isNaN(val)) - return val; + if (this.plotPoints){ + for(var i = 0; i < boxProperties.values.length; i++){ + var value = boxProperties.values[i]; + var toPixel = this.pointToPixel(value, boxProperties); + SVG.drawCircle(boxProperties.x + (boxProperties.width/2) + 2, toPixel, this.pointRadius, this.svg, [["fill", "green"], ["fill-opacity", this.fillOpacityPoint],['stroke-opacity', this.strokeOpacityPoint], ["stroke", "black"]]); + } + } + - if (val != 0) { - return BUI.formatValuesUnits(val, '', { - fontSize : 16, - decimals : 3, - unitsFontSize : this.unitsFontSize - }); - } else { - return; - } + var boxColor = this.getClassColor(boxProperties.name); + var result = this.calculate(boxProperties.values); + /** Q1 **/ + + if (this.isNumber(result.Q1)){ + SVG.drawLine(boxProperties.x, this.pointToPixel(result.Q1, boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result.Q1, boxProperties), this.svg, [["stroke", boxColor]]); + } + /** Q2 **/ + if (this.isNumber(result.Q2)){ + SVG.drawLine(boxProperties.x, this.pointToPixel(result.Q2, boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result.Q2, boxProperties), this.svg, [["stroke", "blue"], ["stroke-width", "2"]]); + } + + /** Q3 **/ + if (this.isNumber(result.Q3)){ + SVG.drawLine(boxProperties.x, this.pointToPixel(result.Q3, boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result.Q3, boxProperties), this.svg, [["stroke", boxColor]]); + } + + /** Concenting Q1 and Q3 **/ + if (this.isNumber(result.Q1)&&this.isNumber(result.Q3)){ + SVG.drawLine(boxProperties.x, this.pointToPixel(result.Q1, boxProperties), boxProperties.x, this.pointToPixel(result.Q3, boxProperties), this.svg, [["stroke", boxColor]]); + SVG.drawLine(boxProperties.x + boxProperties.width, this.pointToPixel(result.Q1, boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result.Q3, boxProperties), this.svg, [["stroke", boxColor]]); + } + + /** min-whisker **/ + if (result["min-whisker"] != null){ + if (this.isNumber(result.Q1)){ + SVG.drawLine(boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result.Q1, boxProperties), boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result["min-whisker"], boxProperties), this.svg, [["stroke", boxColor]]); + } + SVG.drawLine(boxProperties.x,this.pointToPixel(result["min-whisker"], boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result["min-whisker"], boxProperties) , this.svg, [["stroke", boxColor]]); + + } + + /** max-whisker **/ + if (result["max-whisker"] != null){ + if (this.isNumber(result.Q3)){ + SVG.drawLine(boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result.Q3, boxProperties), boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result["max-whisker"], boxProperties), this.svg, [["stroke", boxColor]]); + } + SVG.drawLine(boxProperties.x , this.pointToPixel(result["max-whisker"], boxProperties), boxProperties.x + boxProperties.width, this.pointToPixel(result["max-whisker"], boxProperties), this.svg, [["stroke", boxColor]]); + + } + + /** outliners **/ + if (result["above-outliers"] != null){ + for (var point in result["above-outliers"]){ + SVG.drawCircle(boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result["above-outliers"][point], boxProperties), this.pointRadius, this.svg, [["fill", "red"], ["fill-opacity", "1"]]); + //SVG.drawText(boxProperties.x + (boxProperties.width/2) - 2, this.pointToPixel(result["above-outliers"][point], boxProperties) + 2, "x",this.svg, [["fill", "black"], ["font-size", "x-small"]]); + } + } + if (result["below-outliers"] != null){ + for (var point in result["below-outliers"]){ + SVG.drawCircle(boxProperties.x + (boxProperties.width/2) + 2, this.pointToPixel(result["below-outliers"][point], boxProperties), this.pointRadius, this.svg, [["fill", "red"], ["fill-opacity", "1"]]); + //SVG.drawText(boxProperties.x + (boxProperties.width/2) - 2, this.pointToPixel(result["below-outliers"][point], boxProperties) + 2, "x",this.svg, [["fill", "black"], ["font-size", "x-small"]]); + } + } +}; - }, - sortable : true - }, - { - text : '', - dataIndex : 'bufferId', - width : 30, - hidden : false, - renderer : function(val, y, sample) { - if (val != null) { - var color = '#FFCCFF'; - if (_this.experiments != null) { - var dc = _this.experiments.getDataCollectionByMeasurementId(sample.raw.measurementId); - if (dc != null) { - if (dc.length > 0) { - color = _this.experiments.getSpecimenColorByBufferId(_this.experiments - .getMeasurementById(dc[0].measurementtodatacollection3VOs[0].measurementId).specimenId); - } - } - } else { - color = BIOSAXS.proposal.bufferColors[val]; - } - return BUI.getRectangleColorDIV(color, 10, 10); - } - }, - sortable : true - }, - { - text : 'Buffer', - dataIndex : 'buffer_acronym', - width : 120, - renderer : function(val, y, sample) { - if (sample.raw.bufferSampleplateposition3VO != null) { - return BIOSAXS.proposal.getBufferById(sample.raw.bufferId).acronym + " Plate: [" - + sample.raw.bufferSampleplate.slotPositionColumn + ", " - + BUI.getSamplePlateLetters()[sample.raw.bufferSampleplateposition3VO.rowNumber - 1] + "-" - + sample.raw.bufferSampleplateposition3VO.columnNumber + "]"; - } - return val; - }, - sortable : true - }, { - text : 'Position', - width : 100, - hidden : true, - renderer : function(val, y, sample) { - if (_this.experiments != null) { - return BUI.getSamplePositionHTML(_this.experiments.getSampleById(sample.raw.specimenId), _this.experiments.experiments[0]); - } - } - } ] - }, - { - text : 'Parameters', - columns : [ - { - text : 'Ex. Flow. time (s)', - dataIndex : 'extraFlowTime', - width : 100, - hidden : true, - renderer : function(val, y, sample) { - return BUI.formatValuesUnits(val, 's', { - fontSize : 12, - decimals : 0, - unitsFontSize : this.unitsFontSize - }); - } - }, - { - text : 'Exp. Temp.', - dataIndex : 'exposureTemperature', - width : 70, - renderer : function(val, y, sample) { - if (Number(val)) { - return BUI.formatValuesUnits(val, 'C', { - fontSize : 12, - decimals : 2, - unitsFontSize : this.unitsFontSize - }); - } - return null; - }, - sortable : true, - editor : this._getEditor("exposureTemperature") - }, - { - text : 'Vol. Load', - dataIndex : 'volumeToLoad', - width : 60, - hidden : false, - editor : this._getEditor("volumeToLoad"), - renderer : function(val, y, sample) { - // return val+ " µl"; - return BUI.formatValuesUnits(val, 'µl', { - fontSize : 12, - decimals : 2, - unitsFontSize : this.unitsFontSize - }); - } - }, - { - text : 'Volume in Well', - dataIndex : 'volume', - hidden : true, - editor : this._getEditor("volume"), - width : 80, - renderer : function(val, y, sample) { - // return val + "(µl)"; - return BUI.formatValuesUnits(val, 'µl', { - fontSize : 12, - decimals : 2, - unitsFontSize : this.unitsFontSize - }); - } - }, - { - text : 'Trans.', - dataIndex : 'transmission', - width : 60, - editor : this._getEditor("transmission"), - renderer : function(val, y, sample) { - return BUI.formatValuesUnits(val, '%', { - fontSize : 12, - decimals : 0, - unitsFontSize : this.unitsFontSize - }); - } - }, - { - text : 'Wait T.', - dataIndex : 'waitTime', - editor : this._getEditor("waitTime"), - width : 50, - renderer : function(val, y, sample) { - // if (val != 0) { - return BUI.formatValuesUnits(val, 's', { - fontSize : 12, - decimals : 0, - unitsFontSize : this.unitsFontSize - }); - // } - } - }, - { - text : 'Flow', - dataIndex : 'flow', - editor : this._getEditor("flow"), - width : 50, - renderer : function(val, y, sample) { - if (val == true) { - return "yes"; - } - return null; - } - }, - { - text : 'Viscosity', - dataIndex : 'viscosity', - tooltip : 'The viscosity of a fluid is a measure of its resistance to gradual deformation by shear stress or tensile stress. For liquids, it corresponds to the informal notion of "thickness"', - editor : this._getEditor("viscosity"), - width : 50, - renderer : function(val, y, sample) { - return val; - } - } ] - }, { - text : 'Status', - dataIndex : 'status', - width : 50, - hidden : _this.isStatusColumnHidden, - renderer : function(val, y, sample) { - if (val != null) { - if (val == 'DONE') { - return "" + val + " "; - } - } - } - }, { - text : 'Time', - dataIndex : 'time', - width : 80, - hidden : _this.isTimeColumnHidden, - renderer : function(val, y, sample) { - if (sample.raw.run3VO != null) { - if (sample.raw.run3VO.timeStart != null) { - if (sample.raw.run3VO.timeStart != "") { - var m = moment(sample.raw.run3VO.timeStart); - return m.format("hh:mm:ss a"); - } - } - } - } - }, { - text : 'Energy', - dataIndex : 'energy', - width : 100, - hidden : true - }, { - text : 'Real Exp. Temp.(C)', - width : 100, - dataIndex : 'expExposureTemperature', - hidden : true - }, { - text : 'Storage Temp.(C)', - width : 100, - dataIndex : 'storageTemperature', - hidden : true - }, { - text : 'Time/Frame (s)', - width : 100, - dataIndex : 'timePerFrame', - hidden : true - }, { - text : 'Radiation Relative', - dataIndex : 'radiationRelative', - width : 100, - hidden : true - }, { - text : 'Radiation Absolute', - dataIndex : 'radiationAbsolute', - width : 100, - hidden : true - }, { - text : 'Comments', - dataIndex : 'comments', - flex : 1, - hidden : false, - editor : this._getEditor("comments") - }, { - id : _this.id + 'buttonRemoveSample', - text : '', - hidden : !_this.removeBtnEnabled, - width : 100, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - if (record.raw.macromoleculeId != null) { - if (_this.removeBtnEnabled) { - return BUI.getRedButton('REMOVE'); - } - } - } - } ], - bbar : bbar, - viewConfig : { - stripeRows : true, - getRowClass : function(record, index, rowParams, store) { - if (record.data.status == "DONE") { - return 'green-row'; - } - }, - listeners : { - 'itemclick' : function(grid, record, item, index, e, eOpts) { - _this.onClick.notify({ - specimen : record.raw - }); - }, - 'cellclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemoveSample') { - grid.getStore().removeAt(rowIndex); +BoxWhiskerGraph.prototype.plotClusterTitles = function(properties){ + /** Cluster Titles **/ + var posX = this.left + this.rulerWidth; + var data = this.data; + for(var i = 0; i < data.clusters.length; i++ ){ + /** title for the clusters **/ + posX = posX + this.interClustersSpace; + + /** Drawing title of classes **/ + var cluster = data.clusters[i]; + var posXClasses = posX; + for(var j = 0; j < cluster.classes.length; j++){ + //SVG.drawRectangle(posXClasses, this.height - (this.bottom + this.clusterTitleHeight + this.rulerHeight), properties.classWidth, this.rulerHeight, this.svg, [["fill", "green"]]); +// SVG.drawText(posXClasses + 1/6*properties.classWidth, this.height - (this.bottom + this.clusterTitleHeight + (this.rulerHeight*1/4)), cluster.classes[j].name, this.svg, [["style", "font-size:xx-small"]]); + var color = cluster.classes[j].color; + this.drawSVGVerticalText(posXClasses + 1/2*(properties.classWidth), this.height - (this.bottom - this.clusterTitleHeight + (this.rulerHeight)), cluster.classes[j].name , [["style", "font-size:x-small;"], ["fill", color]]); + + // SVG.drawRectangle(posXClasses, this.height - (this.bottom + this.clusterTitleHeight), properties.classWidth, 2, this.svg, [["fill", "black"]]); + posXClasses = posXClasses + properties.classWidth + this.interClassesSpace; + } + + var clusterTitleSpace = (data.clusters[i].classes.length * properties.classWidth) + ((data.clusters[i].classes.length - 1) * this.interClassesSpace); + //SVG.drawRectangle(posX, this.height - (this.bottom + this.clusterTitleHeight), clusterTitleSpace, this.clusterTitleHeight, this.svg, [["fill", "pink"]]); + SVG.drawRectangle(posX, this.height - (this.clusterTitleHeight+this.bottom), clusterTitleSpace, 1, this.svg, []); + +// var transform = ["translate", "(" + posX + 1/3*clusterTitleSpace +", " + this.height - (this.bottom + (this.clusterTitleHeight*1/4)) +")"], ["transform", "rotate(180)"]; +// var transform = ["transform", "translate(" + (posX + 1/3*clusterTitleSpace) +", " + (this.height - (this.bottom + (this.clusterTitleHeight*1/4))) + "), rotate(-90) "]; +// this.drawSVGVerticalText(posX + 1/3*clusterTitleSpace, this.height - (this.bottom + (this.clusterTitleHeight*1/4)),data.clusters[i].name, [["style", "font-size:x-small"]]); + SVG.drawText(posX , this.height - (this.bottom + (this.clusterTitleHeight*1/4)),data.clusters[i].name ,this.svg, [["style", "font-size:x-small"]]); + posX = posX + clusterTitleSpace; + } +}; + +BoxWhiskerGraph.prototype.plotWhisters = function(data, properties){ + var colors = ["yellow", "orange", "green"]; + var posX = this.left + this.rulerWidth; + for(var i = 0; i < data.clusters.length; i++ ){ + var cluster = data.clusters[i]; + /** inter cluster space **/ + //SVG.drawRectangle(posX, this.top, this.interClustersSpace, this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight, this.svg, [["fill", "black"]]); + posX = posX + this.interClustersSpace; + + for (var j = 0; j < cluster.classes.length; j ++){ + + //SVG.drawRectangle(posX, this.top, properties.classWidth, this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight, this.svg, [["fill", colors[j]]]); + this.plotBoxWhisker( + { + name : cluster.classes[j].name, + values : cluster.classes[j].values, + minPoint : properties.minPoint, + maxPoint : properties.maxPoint, + x : posX, + y : this.top, + width : properties.classWidth, + height : this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight + + + } + ); + posX = posX + properties.classWidth; + //SVG.drawRectangle(posX, this.top, this.interClassesSpace, this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight, this.svg, [["fill", "black"]]); + if (j < cluster.classes.length - 1){ + posX = posX + this.interClassesSpace; + } + } + } +}; + +BoxWhiskerGraph.prototype.draw = function(targetId, data){ + this.targetId = targetId; + var properties = (this.getDimensions(data)); + this.svg = SVG.createSVGCanvas(document.getElementById(this.targetId), [["width", this.width], ["height", this.height]]); + this.plotAxes(properties); + this.plotClusterTitles(properties); + this.plotWhisters(data,properties); +}; + +BoxWhiskerGraph.prototype.input = function(){ + return DATADOC.getBoxWhikerData(); +}; + +BoxWhiskerGraph.prototype.test = function(targetId){ + var plot = new BoxWhiskerGraph( + { + targetId : targetId, + height : 350, + width : 450, + maxBoxWidth : 25 + } + ); + plot.refresh(this.input()); +}; + + + + + + + +function DataSet(){ + this.json = null; + +}; + + +DataSet.prototype.loadFromJSON = function(json){ + if(json != null) { + if(this.validate(json)) { + this.json = json; + } + } +}; + + +DataSet.prototype.toJSON = function(json){ + return this.json; +}; + + +/** Abstract method to be override on childs classes **/ +DataSet.prototype.validate = function(json){ + if (true){ + return true; + } + /*else{ + throw "Data validation failed"; + }*/ +}; + + + + +Edge.prototype.getName = GraphItem.prototype.getName; +Edge.prototype.setName = GraphItem.prototype.setName; +Edge.prototype.getId = GraphItem.prototype.getId; + +function Edge(id, name, nodeSource, nodeTarget, args){ + GraphItem.prototype.constructor.call(this, id, name, args); + + this.sourceNode = nodeSource; + this.targetNode = nodeTarget; + +}; + +Edge.prototype.toJSON = function(){ + return {"index": this.id,"sourceIndex":this.sourceNode.getId(),"targetIndex":this.targetNode.getId(),"args":this.args}; +}; + +Edge.prototype.getNodeSource = function(){ + return this.sourceNode; +}; + +Edge.prototype.getNodeTarget = function(){ + return this.targetNode; +}; + +Edge.prototype.remove = function(){ + //Remove edge object in the nodes + this.getNodeSource().removeEdge(this); + this.getNodeTarget().removeEdge(this); + + this.deleted.notify(this); +}; + + +EdgeGraphFormatter.prototype.setProperties = ItemGraphFormatter.prototype.setProperties; +EdgeGraphFormatter.prototype.getDefault = ItemGraphFormatter.prototype.getDefault; +EdgeGraphFormatter.prototype.getSelected = ItemGraphFormatter.prototype.getSelected; +EdgeGraphFormatter.prototype.getOver = ItemGraphFormatter.prototype.getOver; +EdgeGraphFormatter.prototype.getDragging = ItemGraphFormatter.prototype.getDragging; +EdgeGraphFormatter.prototype.getId = ItemGraphFormatter.prototype.getId; +EdgeGraphFormatter.prototype.toJSON = ItemGraphFormatter.prototype.toJSON; +EdgeGraphFormatter.prototype.loadFromJSON = ItemGraphFormatter.prototype.loadFromJSON; +EdgeGraphFormatter.prototype._setEvents = ItemGraphFormatter.prototype._setEvents; + +function EdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ + ItemGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); + + this.getDefault().args.type = "EdgeGraphFormatter"; +}; + + + + +LineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; +LineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; +LineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; +LineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; +LineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; +LineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; +LineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; +LineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; +LineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; + +function LineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ + EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); + this.args.type = "LineEdgeGraphFormatter"; +}; + +/** DIRECTED **/ +DirectedLineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; +DirectedLineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; +DirectedLineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; +DirectedLineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; +DirectedLineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; +DirectedLineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; +DirectedLineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; +DirectedLineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; +DirectedLineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; + +function DirectedLineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ + EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); + this.args.type = "DirectedLineEdgeGraphFormatter"; + this.args.arrowSize = "3"; +}; +DirectedLineEdgeGraphFormatter.prototype.getArrowSize = function(){ + return this.args.arrowSize; +}; + +OdirectedLineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; +OdirectedLineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; +OdirectedLineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; +OdirectedLineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; +OdirectedLineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; +OdirectedLineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; +OdirectedLineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; +OdirectedLineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; +OdirectedLineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; + +function OdirectedLineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ + EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); + this.args.type = "DirectedLineEdgeGraphFormatter"; + this.args.arrowSize = "3"; +}; + +OdirectedLineEdgeGraphFormatter.prototype.getArrowSize = function(){ + return this.args.arrowSize; +}; + + +/** CUT (inhibition) **/ +CutDirectedLineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; +CutDirectedLineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; +CutDirectedLineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; +CutDirectedLineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; +CutDirectedLineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; +CutDirectedLineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; +CutDirectedLineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; +CutDirectedLineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; +CutDirectedLineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; + +function CutDirectedLineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ + EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); + this.args.type = "CutDirectedLineEdgeGraphFormatter"; +}; + + + + +BezierEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; +BezierEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; +BezierEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; +BezierEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; +BezierEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; +BezierEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; +BezierEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; +BezierEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; +BezierEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; +BezierEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; + +function BezierEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ + EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); + this.args.type = "BezierEdgeGraphFormatter"; +}; + + + +DotDirectedLineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; +DotDirectedLineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; +DotDirectedLineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; +DotDirectedLineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; +DotDirectedLineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; +DotDirectedLineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; +DotDirectedLineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; +DotDirectedLineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; +DotDirectedLineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; + +function DotDirectedLineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ + EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); + this.args.type = "DotDirectedLineEdgeGraphFormatter"; +}; + + +OdotDirectedLineEdgeGraphFormatter.prototype.setProperties = EdgeGraphFormatter.prototype.setProperties; +OdotDirectedLineEdgeGraphFormatter.prototype.getDefault = EdgeGraphFormatter.prototype.getDefault; +OdotDirectedLineEdgeGraphFormatter.prototype.getSelected = EdgeGraphFormatter.prototype.getSelected; +OdotDirectedLineEdgeGraphFormatter.prototype.getOver = EdgeGraphFormatter.prototype.getOver; +OdotDirectedLineEdgeGraphFormatter.prototype.getDragging = EdgeGraphFormatter.prototype.getDragging; +OdotDirectedLineEdgeGraphFormatter.prototype.getId = EdgeGraphFormatter.prototype.getId; +OdotDirectedLineEdgeGraphFormatter.prototype.toJSON = EdgeGraphFormatter.prototype.toJSON; +OdotDirectedLineEdgeGraphFormatter.prototype.loadFromJSON = EdgeGraphFormatter.prototype.loadFromJSON; +OdotDirectedLineEdgeGraphFormatter.prototype._setEvents = EdgeGraphFormatter.prototype._setEvents; + +function OdotDirectedLineEdgeGraphFormatter(id, defaultFormat, selectedFormat, overFormat, dragginFormat){ + EdgeGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, dragginFormat); + this.args.type = "OdotDirectedLineEdgeGraphFormatter"; +}; + + + +function GraphDataset(){ + DataSet.prototype.constructor.call(this); + this.edges = new Object(); + this.vertices = new Object(); + this.verticesIndex = new Object(); + + //Events + this.newVertex = new Event(this); + this.vertexNameChanged = new Event(this); + this.vertexDeleted = new Event(this); + + this.newEdge = new Event(this); + this.edgeNameChanged = new Event(this); + this.edgeDeleted = new Event(this); + + this.json = new Object(); + this.json.vertices = new Array(); + this.json.edges = new Array(); + this.json.relations = new Array(); +}; + +GraphDataset.prototype.loadFromJSON = DataSet.prototype.loadFromJSON; +GraphDataset.prototype.toJSON = DataSet.prototype.toJSON; +GraphDataset.prototype.validate = DataSet.prototype.validate; + +/** Devuelve el numero de edges incidentes sobre el nodo con mas edges **/ +GraphDataset.prototype.getMaxClass = function(){ + var maxClassNode = 0; + for ( var node in this.vertices) { + if (this.vertices[node].getEdgesCount() > maxClassNode){ + maxClassNode = this.vertices[node].getEdgesCount(); + } + } + return maxClassNode; +}; + +/** Devuelve el numero de edges incidentes sobre el nodo con mas edges **/ +GraphDataset.prototype.getMinClass = function(){ + var minClassNode = Math.min(); + for ( var node in this.vertices) { + if (this.vertices[node].getEdgesCount() < minClassNode){ + minClassNode = this.vertices[node].getEdgesCount(); + } + } + return minClassNode; +}; + +GraphDataset.prototype.getVertexByName = function(nodeName){ + var results = new Array(); + + for (var vertexId in this.verticesIndex[nodeName]){ + var vertexByid = this.getVertexById(this.verticesIndex[nodeName][vertexId]); + results.push(vertexByid); + //* añadido nuevo porque fallaba el anterior codigo + return vertexByid + } + + if (results <= 1){ + return this.getVertexById(this.verticesIndex[nodeName]); + } + else{ + return results; + } +}; + +GraphDataset.prototype.getVertexById = function(id){ + return this.vertices[id]; +}; + +GraphDataset.prototype.toSIF = function(){ + var sifDataAdapter = new SifFileDataAdapter(); + return sifDataAdapter.toSIF(this); +}; + +GraphDataset.prototype.toSIFID = function(){ + var sifDataAdapter = new SifFileDataAdapter(); + return sifDataAdapter.toSIFID(this); +}; + +GraphDataset.prototype.toDOT = function(){ + var dotFileDataAdapter = new DotFileDataAdapter(); + return dotFileDataAdapter.toDOT(this); +}; + +GraphDataset.prototype.toDOTID = function(){ + var dotFileDataAdapter = new DotFileDataAdapter(); + return dotFileDataAdapter.toDOTID(this); +}; + +GraphDataset.prototype._addNode = function(nodeName, args){ + return new Vertex(this._getVerticesCount()-1, nodeName, args); +}; + +GraphDataset.prototype.addNode = function(nodeName, args){ + this.json.vertices.push(nodeName); + this._addVerticesIndex(nodeName, this._getVerticesCount() - 1); + var vertex = this._addNode(nodeName, args); + this.vertices[this._getVerticesCount()-1] = vertex; + this._setNodeEvents(vertex); + this.newVertex.notify(vertex); +}; + +GraphDataset.prototype._addVerticesIndex = function(nodeName, id){ + if (this.verticesIndex[nodeName] == null){ + this.verticesIndex[nodeName] = new Array(); + } + this.verticesIndex[nodeName].push(id); +}; + +GraphDataset.prototype.addEdge = function(edgeName, nodeSourceId, nodeTargetId, args){ + this.json.edges.push(edgeName); + var nodeSource = this.getVertexById(nodeSourceId); + var nodeTarget = this.getVertexById(nodeTargetId); + var index = this.getEdgesCount() - 1; + this.edges[index] = new Edge(index, edgeName, nodeSource, nodeTarget, args); + this.json.relations.push({"index": index, "sourceIndex": nodeSourceId, "targetIndex": nodeTargetId, "args": args }); + + nodeSource.addEdge(this.edges[index]); + nodeTarget.addEdge(this.edges[index]); + this._setEdgeEvents(this.edges[index]); + this.newEdge.notify(this.edges[index]); +}; + +GraphDataset.prototype.getVertices = function(){ + return this.vertices; +}; + +GraphDataset.prototype.getEdges = function(){ + return this.edges; +}; + +GraphDataset.prototype.getEdgeById = function(edgeId){ + return this.edges[edgeId]; +}; + +GraphDataset.prototype._getVerticesCount = function(){ + return this.json.vertices.length; +}; + + +GraphDataset.prototype.getVerticesCount = function(){ + var count = 0; + for ( var vertex in this.getVertices()) { + count ++; + } + return count; +}; + + +GraphDataset.prototype.getEdgesCount = function(){ + return this.json.edges.length; +}; + +GraphDataset.prototype.init = function(){ + this.edges = new Object(); + this.vertices = new Object(); +}; + +GraphDataset.prototype._setNodeEvents = function(node){ + var _this = this; + //NODE EVENTS + node.deleted.attach(function (sender, node){ + _this._removeNode(node); + }); + + node.nameChanged.attach(function (sender, args){ + var item = args.item; + var newName = item.name; + var indexes = _this.verticesIndex[args.previousName]; + for(var i = 0; i < indexes.length; i++){ + if(indexes[i] == item.id) + indexes.splice(i,1); + } + if(indexes.length == 0){ + delete _this.verticesIndex[args.previousName]; + } + _this._addVerticesIndex(newName, item.id); + _this.json.vertices[item.id] = newName; + _this.vertexNameChanged.notify(args); + }); +}; + +GraphDataset.prototype._setEdgeEvents = function(edge){ + var _this = this; + //EDGE EVENTS + edge.nameChanged.attach(function (sender, edge){ + _this.edgeNameChanged.notify(edge); + + }); + + edge.deleted.attach(function (sender, edge){ + _this._removeEdge(edge); + }); +}; + +GraphDataset.prototype._connectVerticesByName = function(nodeNameSource, nodeNameTarget){ + var source = this.getVertexByName(nodeNameSource); + var target = this.getVertexByName(nodeNameTarget); + + if ((source != null)&&(target!=null)){ + this.addEdge(source.getName() +"_" + target.getName(), source.getId(), target.getId(), {}); + } + else{ + if (source == null){ + console.log("No encontrado: " + nodeNameSource) + } + if (target == null){ + console.log("No encontrado: " + nodeNameTarget) + } + } +}; + +GraphDataset.prototype.loadFromJSON = function(json){ + var json = json; + this.init(); + this.json = new Object(); + this.json.vertices = new Array(); + this.json.edges = new Array(); + this.json.relations = new Array(); + + for ( var i = 0; i < json.nodes.length; i++) { + if (json.nodes[i] != null){ + var name = json.nodes[i]; + this.addNode(name); + } + else{ + this.json.vertices.push(null); + } + } + + for ( var i = 0; i < json.edges.length; i++) { + if (json.edges[i] != null){ + if (json.relations[i] != null){ + var name = json.edges[i]; + this.addEdge(name, json.relations[i].sourceIndex, json.relations[i].targetIndex, json.relations[i].args); + } + } + else{ + this.json.edges.push(null); + this.json.relations.push(null); + } + } +}; + +GraphDataset.prototype.prettyPrint = function(){ + for ( var node in this.vertices) { + console.log(this.vertices[node].getName() ); + for ( var j = 0; j < this.vertices[node].getEdgesIn().length; j++) { + console.log(" --> " + this.vertices[node].getEdgesIn()[j].getNodeTarget().getName() ); + } + } +}; + +GraphDataset.prototype._removeEdge = function(edge){ + this.json.edges[edge.getId()] = null; + this.json.relations[edge.getId()] = null; + + delete this.edges[edge.getId()]; + this.edgeDeleted.notify(edge); + + +}; + +GraphDataset.prototype._removeNode = function(node){ + this.json.vertices[node.getId()] = null; + delete this.vertices[node.getId()]; + this.vertexDeleted.notify(node); +}; + +GraphDataset.prototype.toJSON = function(){ + var json = new Object(); + var nodes = new Array(); + json.nodes = this.json.vertices; //nodes; + json.edges = this.json.edges; //edges; + json.relations = this.json.relations; + return json; +}; + +GraphDataset.prototype.clone = function(){ + var dsDataset = new GraphDataset(); + dsDataset.loadFromJSON(this.toJSON()); + return dsDataset; +}; +//GraphDataset.prototype.test = function(){ +// this.loadFromJSON(this.toJSON()); +//}; + +function labels(){ + var names = new Array(); + + var dataset = interactomeViewer.graphEditorWidget.dataset; + var layout = interactomeViewer.graphEditorWidget.layout; + + for ( var vertexId in interactomeViewer.graphEditorWidget.dataset.getVertices()) { + names.push(interactomeViewer.graphEditorWidget.dataset.getVertexById(vertexId).getName()); + } + + var sorted = (names.sort()); + console.log(sorted) + var distance = 0.01; + var altura = 0.6; + for ( var i = 0; i < names.length; i++) { + var id =dataset.getVertexByName(names[i]).getId(); + + layout.getNodeById(id).setCoordenates(distance, altura); + + + distance = parseFloat(distance) + parseFloat(0.03); + + altura = parseFloat(altura) + parseFloat(0.02); + + if (parseFloat(altura) == 0.9800000000000003){ + + altura = 0.6; + distance = distance - 0.51; + } + + } + + +}; + +function GraphItem(id, name, args){ + this.id = id; + this.name = name; + this.type = "NONE"; + + this.args = new Object(); + + + if (args!=null){ + this.args = args; + if (args.type !=null){ + this.type = args.type; + } + } + + //Events + this.nameChanged = new Event(this); + this.deleted = new Event(this); +} + +GraphItem.prototype.getName = function(){ + return this.name; +}; + +GraphItem.prototype.getId = function(){ + return this.id; +}; + +GraphItem.prototype.setName = function(name){ + var oldName = this.getName(); + this.name = name; + this.nameChanged.notify({"item": this, "previousName" : oldName}); +}; + + + + + +function LayoutDataset(){ + this.dataset = null; + this.vertices = new Object(); + this.changed = new Event(this); + + + this.args = new Object(); + + //RANDOM, CIRCLE + this.args.type = "CIRCLE"; +}; + +LayoutDataset.prototype.loadFromJSON = function(dataset, json){ + var _this = this; + this.vertices = new Object(); + this.dataset = dataset; //new GraphDataset(); + for ( var vertex in json) { + this.vertices[vertex] = new NodeLayout(vertex, json[vertex].x, json[vertex].y); + this.vertices[vertex].changed.attach(function (sender, item){ + _this.changed.notify(item); + }); + } + this._attachDatasetEvents(); +}; + + +LayoutDataset.prototype.toJSON = function(){ + var serialize = new Object(); + for ( var vertex in this.vertices) { + serialize[vertex] = new Object(); + serialize[vertex].x = this.vertices[vertex].x; + serialize[vertex].y = this.vertices[vertex].y; + } + serialize.dataset = new Object(); + serialize.dataset =this.dataset.toJSON(); + return serialize; +}; + +LayoutDataset.prototype.dataBind = function(graphDataset){ + this.dataset = graphDataset; + this._attachDatasetEvents(); + this._calculateLayout(); +}; + +LayoutDataset.prototype._removeVertex = function(vertexId){ + delete this.vertices[vertexId]; +}; + +LayoutDataset.prototype._attachDatasetEvents = function(){ + var _this = this; + + this.dataset.vertexDeleted.attach(function (sender, item){ + _this._removeVertex(item.getId()); + }); + + this.dataset.newVertex.attach(function (sender, item){ + _this.vertices[item.getId()] = new NodeLayout(item.getId(), 0.5, 0.5); + _this.vertices[item.getId()].changed.attach(function (sender, item){ + _this.changed.notify(item); + }); + }); +}; + +LayoutDataset.prototype.getType = function(){ + return this.args.type; +}; + +LayoutDataset.prototype._calculateLayoutVertices = function(type, count){ + + if (type == "CIRCLE"){ + var radius = 0.4; + var centerX = 0.5; + var centerY = 0.5; + var verticesCoordinates = new Array(); + for(var i = 0; i < count; i++){ + x = centerX + radius * Math.sin(i * 2 * Math.PI/count); + y = centerY + radius * Math.cos(i * 2 * Math.PI/count); + verticesCoordinates.push({'x':x,'y':y}); + } + return verticesCoordinates; + } +}; + + +LayoutDataset.prototype._calculateLayout = function(){ + var _this = this; + if (this.getType() == "RANDOM"){ + for ( var vertex in this.dataset.getVertices()) { + if (this.vertices[vertex] == null){ + this.vertices[vertex] = new NodeLayout(vertex, 0, 0); + } + this.vertices[vertex].setCoordinates(Math.random(), Math.random()); + this.vertices[vertex].changed.attach(function (sender, item){ + _this.changed.notify(item); + }); + } + } + + if ( this.getType() == "CIRCLE"){ + + var count = this.dataset._getVerticesCount(); + var verticesCoordinates = this._calculateLayoutVertices(this.getType(), count); + + var aux = 0; + for ( var vertex in this.dataset.getVertices()) { + if (this.vertices[vertex] == null){ + this.vertices[vertex] = new NodeLayout(vertex, 0, 0); + } + this.vertices[vertex].setCoordinates(verticesCoordinates[aux].x, verticesCoordinates[aux].y);//{"x":, "y":}; + aux++; + this.vertices[vertex].changed.attach(function (sender, item){ + _this.changed.notify(item); + }); + } + } + + + if (this.getType() == "SQUARE"){ + + var count = this.dataset._getVerticesCount(); + var xMin = 0.1; + var xMax = 0.9; + var yMin = 0.1; + var yMax = 0.9; + + var rows = Math.sqrt(count); + var step = (xMax - xMin) / rows; + + var verticesCoordinates = new Array(); + for(var i = 0; i < rows; i ++){ + for ( var j = 0; j < rows; j++) { + x = i * step + xMin; + y = j * step + yMin; + verticesCoordinates.push({'x':x,'y':y}); + } + } + + var aux = 0; + for ( var vertex in this.dataset.getVertices()) { + if (this.vertices[vertex] == null){ + this.vertices[vertex] = new NodeLayout(vertex, 0, 0); + } + this.vertices[vertex].setCoordinates(verticesCoordinates[aux].x, verticesCoordinates[aux].y);//{"x":, "y":}; + aux++; + this.vertices[vertex].changed.attach(function (sender, item){ + _this.changed.notify(item); + }); + } + } + +}; + +LayoutDataset.prototype.getNodeById = function(id){ + return this.vertices[id]; +}; + +LayoutDataset.prototype.getVerticesByArea = function(x1, y1, x2, y2){ + var vertices = new Array(); + for ( var vertex in this.dataset.getVertices()) { + if ((this.vertices[vertex].x >= x1)&&(this.vertices[vertex].x <= x2)){ + if ((this.vertices[vertex].y >= y1)&&(this.vertices[vertex].y <= y2)){ + vertices.push(this.vertices[vertex]); + } + } + } + return vertices; +}; + + + + +LayoutDataset.prototype.getLayout = function(type){ + + if (type == "CIRCLE"){ + this.args.type = "CIRCLE"; + this._calculateLayout(); + return; + } + + if (type == "SQUARE"){ + this.args.type = "SQUARE"; + this._calculateLayout(); + return; + } + + if (type == "RANDOM"){ + this.args.type = "RANDOM"; + this._calculateLayout(); + return; + } + + + var dotText = this.dataset.toDOTID(); + var url = "http://bioinfo.cipf.es/utils/ws/rest/network/layout/"+type+".coords"; + var _this = this; + + $.ajax({ + async: true, + type: "POST", + url: url, + dataType: "text", + data: { + dot :dotText + }, + cache: false, + success: function(data){ + var response = JSON.parse(data); + for ( var vertexId in response) { + _this.vertices[vertexId].setCoordinates(response[vertexId].x, response[vertexId].y); + } + } + }); + +// $.ajax({ +// async: true, +// type: "POST", +// url: url, +// dataType: "script", +// data: { +// dot :dotText +// }, +// cache: false, +// success: function(data){ +// var response = JSON.parse(data); +// for ( var vertexId in response) { +// _this.vertices[vertexId].setCoordinates(response[vertexId].x, response[vertexId].y); +// } +// } +// }); + +}; + +function NodeLayout(id, x, y, args){ + this.id = id; + this.x = x; + this.y = y; + this.changed = new Event(this); +}; + +NodeLayout.prototype.getId = function(id){ + return this.id; +}; + +NodeLayout.prototype.setCoordinates = function(x, y){ + this.x = x; + this.y = y; + this.changed.notify(this); +}; + + + +function NetworkDataSetFormatter(vertexFormatProperties, defaultEdgeProperties, args){ + DataSet.prototype.constructor.call(this); + + this.args = new Object(); + + this.vertices = new Object(); + this.edges = new Object(); + this.dataset = null; + this.maxClass = 0; + this.minClass = 0; + + /** Coordenates with default Setting */ + this.args.width = 1100; + this.args.height = 500; + + /** Optional parameters */ + this.args.backgroundColor = "#FFFFFF"; + this.args.backgroundImage = null; + this.args.backgroundImageHeight = null; + this.args.backgroundImageWidth = null; + this.args.backgroundImageX = null; + this.args.backgroundImageY = null; + + + this.args.balanceNodes = false; + this.args.nodesMaxSize = 3; + this.args.nodesMinSize = 0.5; + + + /** Zoom **/ + this.args.zoomScale = 1; + this.args.zoomScaleStepFactor = 0.4; + + if (args != null){ + if (args.backgroundImage != null){ + this.args.backgroundImage = args.backgroundImage; + } + + if (args.width != null){ + this.args.width = args.width; + } + + if (args.height != null){ + this.args.height = args.height; + this.args.svgHeight = args.height; + } + + if (args.svgHeight != null){ + this.args.svgHeight = args.svgHeight; + } + + if (args.backgroundColor != null){ + this.args.backgroundColor = args.backgroundColor; + } + + if(args.balanceNodes != null){ + this.args.balanceNodes = args.balanceNodes; + } + + if(args.nodesMaxSize != null){ + this.args.nodesMaxSize = args.nodesMaxSize; + } + if(args.nodesMinSize != null){ + this.args.nodesMinSize = args.nodesMinSize; + } + } + + this.args.defaultEdgeProperties = {"fill":"#000000", "radius":"1", "stroke":"#000000", "size":1, "title":{"fontSize":10, "fontColor":"#000000"}}; + this.args.vertexFormatProperties = { "fill":"#000000", "stroke":"#000000", "stroke-opacity":"#000000"}; + + if (vertexFormatProperties!= null){ + this.args.vertexFormatProperties = vertexFormatProperties; + } + if (defaultEdgeProperties!= null){ + this.args.defaultEdgeProperties = defaultEdgeProperties; + } + + /** Events **/ + this.changed = new Event(this); + this.edgeChanged = new Event(this); + this.resized = new Event(this); + this.backgroundImageChanged= new Event(this); + this.backgroundColorChanged= new Event(this); +}; + +NetworkDataSetFormatter.prototype.loadFromJSON = function(dataset, json){ + this.args = new Object(); + this.vertices = new Object(); + this.args = json; + this._setDataset(dataset); + var _this = this; + + for ( var vertex in json.vertices) { + this.addVertex(vertex, json.vertices[vertex]); + } + + for ( var edgeId in json.edges) { + this.addEdge(edgeId, json.edges[edgeId]); + } +}; + + +NetworkDataSetFormatter.prototype.toJSON = function(){ + + +// this.args.vertices = new Object(); +// this.args.edges = new Object(); +// +// for ( var vertex in this.vertices) { +// this.args.vertices[vertex] = this.getVertexById(vertex).toJSON(); +// } +// for ( var edge in this.edges) { +// this.args.edges[edge] = this.getEdgeById(edge).toJSON(); +// } +// +// return (this.args); + + + var serialize = new Object(); + serialize = JSON.parse(JSON.stringify(this.args)); + serialize.vertices = new Object(); + serialize.edges = new Object(); + + for ( var vertex in this.vertices) { + serialize.vertices[vertex] = this.getVertexById(vertex).toJSON(); + } + for ( var edge in this.edges) { + serialize.edges[edge] = this.getEdgeById(edge).toJSON(); + } + + return (serialize); +}; + + + +NetworkDataSetFormatter.prototype._getNodeSize = function(nodeId){ + if (this.isVerticesBalanced()){ + var total = this.maxClass - this.minClass; + if (total == 0){ total = 1;} + var nodeConnection = this.dataset.getVertexById(nodeId).getEdges().length; + return ((nodeConnection*this.args.nodesMaxSize)/total) + this.args.nodesMinSize; + } + return this.getVertexById(nodeId).getDefault().getSize(); +}; + +NetworkDataSetFormatter.prototype._recalculateSize = function(){ + if (this.isVerticesBalanced()){ + this.maxClass = this.dataset.getMaxClass(); + this.minClass = this.dataset.getMinClass(); + for ( var vertexIdAll in this.vertices) { + var size = this._getNodeSize(vertexIdAll); + this.vertices[vertexIdAll].getDefault().setSize(size); + this.vertices[vertexIdAll].getSelected().setSize(size); + this.vertices[vertexIdAll].getOver().setSize(size); + } + } +}; + + +NetworkDataSetFormatter.prototype.addVertex = function(vertexId, json){ + + + if (json == null){ + this.vertices[vertexId] = new CircleVertexGraphFormatter(vertexId, this.args.vertexFormatProperties.defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); + } + else{ + + /** Cargo los attributos desde el json **/ + if (json.type == null){ + this.vertices[vertexId] = new CircleVertexGraphFormatter(vertexId, this.args.vertexFormatProperties.defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); + } + + if ((json.type == "SquareVertexGraphFormatter")||(json.type == "SquareVertexNetworkFormatter")){ + this.vertices[vertexId] = new SquareVertexGraphFormatter(vertexId); + this.vertices[vertexId].loadFromJSON(json); + } + + if ((json.type == "CircleVertexGraphFormatter")||(json.type == "CircleVertexNetworkFormatter")){ + this.vertices[vertexId] = new CircleVertexGraphFormatter(vertexId); + this.vertices[vertexId].loadFromJSON(json); + } + + if ((json.type == "EllipseVertexGraphFormatter")||(json.type == "EllipseVertexNetworkFormatter")){ + this.vertices[vertexId] = new EllipseVertexGraphFormatter(vertexId); + this.vertices[vertexId].loadFromJSON(json); + } + + if ((json.type == "RectangleVertexGraphFormatter")||(json.type == "RectangleVertexNetworkFormatter")){ + this.vertices[vertexId] = new RectangleVertexGraphFormatter(vertexId); + this.vertices[vertexId].loadFromJSON(json); + } + + if ((json.type == "RoundedVertexGraphFormatter")||(json.type == "RoundedVertexNetworkFormatter")){ + this.vertices[vertexId] = new RoundedVertexGraphFormatter(vertexId); + this.vertices[vertexId].loadFromJSON(json); + } + + } + + + var _this = this; + this.vertices[vertexId].stateChanged.attach(function (sender, item){ + _this.changed.notify(item); + }); + + var size = this._getNodeSize(vertexId); + this.vertices[vertexId].defaultFormat.args.size = size; + this.vertices[vertexId].selected.args.size = size; + this.vertices[vertexId].over.args.size = size; + +}; + +NetworkDataSetFormatter.prototype.addEdge = function(edgeId, json){ + + /** Es un edge nuevo que le doy los atributos por defecto **/ + if (json == null){ + if (this.dataset.getEdgeById(edgeId).getNodeSource().getId() == this.dataset.getEdgeById(edgeId).getNodeTarget().getId()){ + this.edges[edgeId] = new BezierEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); + }else{ + this.edges[edgeId] = new DirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); + } + } + else{ + /** Cargo los attributos desde el json **/ + if (json.type == null){ + this.edges[edgeId] = new LineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); + } + + if ((json.type == "LineEdgeGraphFormatter")||(json.type == "LineEdgeNetworkFormatter")){ + this.edges[edgeId] = new LineEdgeGraphFormatter(edgeId); + this.edges[edgeId].loadFromJSON(json); + } + if ((json.type == "DirectedLineEdgeGraphFormatter")||(json.type == "DirectedLineEdgeNetworkFormatter")){ + this.edges[edgeId] = new DirectedLineEdgeGraphFormatter(edgeId); + this.edges[edgeId].loadFromJSON(json); + } + + if ((json.type == "BezierEdgeGraphFormatter")||(json.type == "BezierEdgeNetworkFormatter")){ + this.edges[edgeId] = new BezierEdgeGraphFormatter(edgeId); + this.edges[edgeId].loadFromJSON(json); + } + + + if ((json.type == "CutDirectedLineEdgeGraphFormatter")||(json.type == "CutDirectedLineEdgeNetworkFormatter")){ + this.edges[edgeId] = new CutDirectedLineEdgeGraphFormatter(edgeId); + this.edges[edgeId].loadFromJSON(json); + } + + if ((json.type == "DotDirectedLineEdgeGraphFormatter")||(json.type == "DotDirectedLineEdgeNetworkFormatter")){ + this.edges[edgeId] = new DotDirectedLineEdgeGraphFormatter(edgeId); + this.edges[edgeId].loadFromJSON(json); + } + if ((json.type == "OdotDirectedLineEdgeGraphFormatter")||(json.type == "OdotDirectedLineEdgeNetworkFormatter")){ + this.edges[edgeId] = new OdotDirectedLineEdgeGraphFormatter(edgeId); + this.edges[edgeId].loadFromJSON(json); + } + + if ((json.type == "OdirectedLineEdgeGraphFormatter")||(json.type == "OdirectedLineEdgeNetworkFormatter")){ + this.edges[edgeId] = new OdirectedLineEdgeGraphFormatter(edgeId); + this.edges[edgeId].loadFromJSON(json); + } + } + + var _this = this; + this.edges[edgeId].stateChanged.attach(function (sender, item){ + _this.edgeChanged.notify(item); + }); + + this._recalculateSize(); +}; + +NetworkDataSetFormatter.prototype._setDataset = function(dataset){ + this.dataset = dataset; + this.maxClass = dataset.getMaxClass(); + this.minClass = dataset.getMinClass(); + this._attachDatasetEvents(); +}; + +NetworkDataSetFormatter.prototype.changeEdgeType = function(edgeId, type){ + if ((type == "LineEdgeGraphFormatter")||(type == "LineEdgeNetworkFormatter")){ + this.edges[edgeId] = new LineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); + + } + if ((type == "DirectedLineEdgeGraphFormatter")||(type == "DirectedLineEdgeNetworkFormatter")){ + this.edges[edgeId] = new DirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); + } + + if ((type == "CutDirectedLineEdgeGraphFormatter")||(type == "CutDirectedLineEdgeNetworkFormatter")){ + this.edges[edgeId] = new CutDirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); + } + + if ((type == "DotDirectedLineEdgeGraphFormatter")||(type == "DotDirectedLineEdgeNetworkFormatter")){ + this.edges[edgeId] = new DotDirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); + } + + if ((type == "OdotDirectedLineEdgeGraphFormatter")||(type == "OdotDirectedLineEdgeNetworkFormatter")){ + this.edges[edgeId] = new OdotDirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); + } + + if ((type == "OdirectedLineEdgeGraphFormatter")||(type == "OdirectedLineEdgeNetworkFormatter")){ + this.edges[edgeId] = new OdirectedLineEdgeGraphFormatter(edgeId, this.args.defaultEdgeProperties.defaultFormat, this.args.defaultEdgeProperties.selected, this.args.defaultEdgeProperties.over, this.args.defaultEdgeProperties.dragging); + } + + + + var _this = this; + this.edges[edgeId].stateChanged.attach(function (sender, item){ + _this.edgeChanged.notify(item); + }); + _this.edgeChanged.notify(this.edges[edgeId]); +}; +/* +classe = "SquareNetworkNodeFormatter"; +} +if (value == "circle"){ + classe = "CircleNetworkNodeFormatter"; + **/ +NetworkDataSetFormatter.prototype.changeNodeType = function(vertexId, type){ + var defaultFormat = JSON.parse(JSON.stringify(this.vertices[vertexId].getDefault())); + var selectedFormat = JSON.parse(JSON.stringify(this.vertices[vertexId].getSelected())); + var defaultFormat = JSON.parse(JSON.stringify(this.vertices[vertexId].getDefault())); + var defaultFormat = JSON.parse(JSON.stringify(this.vertices[vertexId].getDefault())); + + if ((type == "SquareVertexGraphFormatter")||(type == "SquareVertexNetworkFormatter")){ + this.vertices[vertexId] = new SquareVertexGraphFormatter(vertexId,defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); + } + + if ((type == "CircleVertexGraphFormatter")||(type == "CircleVertexNetworkFormatter")){ + this.vertices[vertexId] = new CircleVertexGraphFormatter(vertexId, defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); + } + + if ((type == "EllipseVertexGraphFormatter")||(type == "EllipseVertexNetworkFormatter")){ + this.vertices[vertexId] = new EllipseVertexGraphFormatter(vertexId, defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); + } + + if ((type == "RectangleVertexGraphFormatter")||(type == "RectangleVertexNetworkFormatter")){ + this.vertices[vertexId] = new RectangleVertexGraphFormatter(vertexId, defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); + } + + if ((type == "RoundedVertexGraphFormatter")||(type == "RoundedVertexNetworkFormatter")){ + this.vertices[vertexId] = new RoundedVertexGraphFormatter(vertexId, defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); + } + + if ((type == "OctagonVertexGraphFormatter")||(type == "OctagonVertexNetworkhFormatter")){ + this.vertices[vertexId] = new OctagonVertexGraphFormatter(vertexId, defaultFormat, this.args.vertexFormatProperties.selected, this.args.vertexFormatProperties.over, this.args.vertexFormatProperties.dragging); + } + + + var _this = this; + this.vertices[vertexId].stateChanged.attach(function (sender, item){ + _this.changed.notify(item); + }); + _this.changed.notify(this.vertices[vertexId]); +}; + + + +NetworkDataSetFormatter.prototype.dataBind = function(networkDataSet){ + var _this = this; + this._setDataset(networkDataSet); + + for ( var vertex in this.dataset.getVertices()) { + this.addVertex(vertex); + } + + for ( var edge in this.dataset.getEdges()) { + this.addEdge(edge); + } +}; + +NetworkDataSetFormatter.prototype._removeEdge = function(edgeId){ + delete this.edges[edgeId]; +}; + +NetworkDataSetFormatter.prototype._removeVertex = function(vertexId){ + delete this.vertices[vertexId]; +}; + +NetworkDataSetFormatter.prototype._attachDatasetEvents = function(id){ + var _this = this; + this.dataset.vertexDeleted.attach(function (sender, item){ + _this._removeVertex(item.getId()); + }); + + this.dataset.edgeDeleted.attach(function (sender, item){ + _this._removeEdge(item.getId()); + }); + + this.dataset.newVertex.attach(function (sender, item){ + _this.addVertex(item.getId()); + }); + + this.dataset.newEdge.attach(function (sender, item){ + _this.addEdge(item.getId()); + }); +}; + + +NetworkDataSetFormatter.prototype.getVertexById = function(id){ + return this.vertices[id]; +}; + +NetworkDataSetFormatter.prototype.getEdgeById = function(id){ + return this.edges[id]; +}; + +NetworkDataSetFormatter.prototype.makeLabelsBigger = function(){ +for ( var vertexId in this.vertices) { + var fontSize = this.vertices[vertexId].getDefault().getFontSize() + 2; + this.vertices[vertexId].getDefault().setFontSize(fontSize); + } +}; + +NetworkDataSetFormatter.prototype.makeLabelsSmaller = function(){ + for ( var vertexId in this.vertices) { + var fontSize = this.vertices[vertexId].getDefault().getFontSize() - 2; + this.vertices[vertexId].getDefault().setFontSize(fontSize); + } +}; + + +NetworkDataSetFormatter.prototype.resize = function(width, height){ + this.args.width = width; + this.args.height = height; + this.resized.notify(); +}; + +/** ZOOM GETTERS **/ +NetworkDataSetFormatter.prototype.getZoomScaleStepFactor = function(){return this.args.zoomScaleStepFactor;}; +NetworkDataSetFormatter.prototype.setZoomScaleStepFactor = function(scaleFactor){this.args.zoomScaleStepFactor = scaleFactor;}; +NetworkDataSetFormatter.prototype.getZoomScale = function(){return this.args.zoomScale;}; +NetworkDataSetFormatter.prototype.setZoomScale = function(scale){this.args.zoomScale = scale;}; + +NetworkDataSetFormatter.prototype.getNodesMaxSize = function(){return this.args.nodesMaxSize;}; +NetworkDataSetFormatter.prototype.getNodesMinSize = function(){return this.args.nodesMinSize;}; + +/** SIZE SETTERS AND GETTERS **/ +NetworkDataSetFormatter.prototype.isVerticesBalanced = function(){return this.args.balanceNodes;}; +NetworkDataSetFormatter.prototype.getWidth = function(){return this.args.width;}; +NetworkDataSetFormatter.prototype.getHeight = function(){return this.args.height;}; + +/** OPTIONAL PARAMETERS GETTERS AND SETTERS **/ +NetworkDataSetFormatter.prototype.getBackgroundImage = function(){return this.args.backgroundImage;}; +NetworkDataSetFormatter.prototype.setBackgroundImage = function(value){this.args.backgroundImage = value; this.backgroundImageChanged.notify(this);}; + + +NetworkDataSetFormatter.prototype.getBackgroundImageWidth = function(){return this.args.backgroundImageWidth;}; +NetworkDataSetFormatter.prototype.setBackgroundImageWidth = function(value){this.args.backgroundImageWidth = value; this.backgroundImageChanged.notify(this);}; + +NetworkDataSetFormatter.prototype.getBackgroundImageHeight = function(){return this.args.backgroundImageHeight;}; +NetworkDataSetFormatter.prototype.setBackgroundImageHeight = function(value){this.args.backgroundImageHeight = value; this.backgroundImageChanged.notify(this);}; + +NetworkDataSetFormatter.prototype.getBackgroundImageX = function(){return this.args.backgroundImageX;}; +NetworkDataSetFormatter.prototype.setBackgroundImageX = function(value){this.args.backgroundImageX = value; this.backgroundImageChanged.notify(this);}; + +NetworkDataSetFormatter.prototype.getBackgroundImageY = function(){return this.args.backgroundImageX;}; +NetworkDataSetFormatter.prototype.setBackgroundImageY = function(value){this.args.backgroundImageY = value; this.backgroundImageChanged.notify(this);}; + + + +NetworkDataSetFormatter.prototype.getBackgroundColor = function(){return this.args.backgroundColor;}; +NetworkDataSetFormatter.prototype.setBackgroundColor = function(value){this.args.backgroundColor = value; this.backgroundColorChanged.notify(this);}; + +NetworkDataSetFormatter.prototype.getWidth = function(){return this.args.width;}; +NetworkDataSetFormatter.prototype.setWidth = function(value){this.args.width = value;}; + +NetworkDataSetFormatter.prototype.getHeight = function(){return this.args.height;}; +NetworkDataSetFormatter.prototype.setHeight = function(value){this.args.height = value;}; + + + + +Vertex.prototype.getName = GraphItem.prototype.getName; +Vertex.prototype.setName = GraphItem.prototype.setName; +Vertex.prototype.getId = GraphItem.prototype.getId; + +function Vertex(id, name, args){ + GraphItem.prototype.constructor.call(this, id, name, args); + this.edgesIn= new Array(); + this.edgesOut= new Array(); +}; + +Vertex.prototype.getEdges = function(){ + return this.edgesIn.concat(this.edgesOut); +}; + +Vertex.prototype.getEdgesCount = function(){ + return this.getEdges().length; +}; + +Vertex.prototype.getEdgesIn = function(){ + return this.edgesIn; +}; + +Vertex.prototype.getEdgesOut = function(){ + return this.edgesOut; +}; + +Vertex.prototype.addEdge = function(edge){ + if (edge.getNodeSource().getId() == this.id){ + this.edgesIn.push(edge); + } + else{ + this.edgesOut.push(edge); + } +}; + +Vertex.prototype.removeEdge = function(edge){ + for ( var i = 0; i < this.getEdgesIn().length; i++) { + var edgeIn = this.edgesIn[i]; + if (edgeIn.getId() == edge.getId()){ + this.edgesIn.splice(i, 1); + } + } + for ( var i = 0; i < this.getEdgesOut().length; i++) { + var edgeIn = this.edgesOut[i]; + if (edgeIn.getId() == edge.getId()){ + this.edgesOut.splice(i, 1); + } + } +}; + +Vertex.prototype.remove = function(){ + var edges = this.getEdges(); + for ( var i = 0; i < edges.length; i++) { + var edge = edges[i]; + edge.remove(); + } + this.deleted.notify(this); +}; + + + + + +VertexGraphFormatter.prototype.getDefault = ItemGraphFormatter.prototype.getDefault; +VertexGraphFormatter.prototype.getSelected = ItemGraphFormatter.prototype.getSelected; +VertexGraphFormatter.prototype.getOver = ItemGraphFormatter.prototype.getOver; +VertexGraphFormatter.prototype.getDragging = ItemGraphFormatter.prototype.getDragging; +VertexGraphFormatter.prototype.getId = ItemGraphFormatter.prototype.getId; +VertexGraphFormatter.prototype.toJSON = ItemGraphFormatter.prototype.toJSON; +VertexGraphFormatter.prototype.loadFromJSON = ItemGraphFormatter.prototype.loadFromJSON; +VertexGraphFormatter.prototype._setEvents = ItemGraphFormatter.prototype._setEvents; + + +function VertexGraphFormatter(defaultFormat, selectedFormat, overFormat, draggingFormat){ + ItemGraphFormatter.prototype.constructor.call(this, defaultFormat, selectedFormat, overFormat, draggingFormat); +}; + + +CircleVertexGraphFormatter.prototype.getDefault = VertexGraphFormatter.prototype.getDefault; +CircleVertexGraphFormatter.prototype.getSelected = VertexGraphFormatter.prototype.getSelected; +CircleVertexGraphFormatter.prototype.getOver = VertexGraphFormatter.prototype.getOver; +CircleVertexGraphFormatter.prototype.getDragging = VertexGraphFormatter.prototype.getDragging; +CircleVertexGraphFormatter.prototype.getId = VertexGraphFormatter.prototype.getId; +CircleVertexGraphFormatter.prototype.toJSON = VertexGraphFormatter.prototype.toJSON; +CircleVertexGraphFormatter.prototype.loadFromJSON = VertexGraphFormatter.prototype.loadFromJSON; +CircleVertexGraphFormatter.prototype._setEvents = VertexGraphFormatter.prototype._setEvents; + +function CircleVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ + VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); + this.args.type = "CircleVertexGraphFormatter"; + if (defaultFormat != null){ + if (defaultFormat.radius != null){ + this.defaultFormat.args.radius = defaultFormat.radius; + } + } + + if (selectedFormat != null){ + if (selectedFormat.radius != null){ + this.selected.args.radius = selectedFormat.radius; + } + } + + if (overFormat != null){ + if (overFormat.radius != null){ + this.over.args.radius = overFormat.radius; + } + } + + if (draggingFormat != null){ + if (draggingFormat.radius != null){ + this.dragging.args.draggingFormat = draggingFormat.radius; + } + } +}; + + + +SquareVertexGraphFormatter.prototype.getDefault = VertexGraphFormatter.prototype.getDefault; +SquareVertexGraphFormatter.prototype.getSelected = VertexGraphFormatter.prototype.getSelected; +SquareVertexGraphFormatter.prototype.getOver = VertexGraphFormatter.prototype.getOver; +SquareVertexGraphFormatter.prototype.getDragging = VertexGraphFormatter.prototype.getDragging; +SquareVertexGraphFormatter.prototype.getId = VertexGraphFormatter.prototype.getId; +SquareVertexGraphFormatter.prototype.toJSON = VertexGraphFormatter.prototype.toJSON; +SquareVertexGraphFormatter.prototype.loadFromJSON = VertexGraphFormatter.prototype.loadFromJSON; +SquareVertexGraphFormatter.prototype._setEvents = VertexGraphFormatter.prototype._setEvents; + +function SquareVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ + VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); + this.args.type = "SquareVertexGraphFormatter"; + if (defaultFormat != null){ + if (defaultFormat.radius != null){ + this.defaultFormat.args.radius = defaultFormat.radius; + } + } + + if (selectedFormat != null){ + if (selectedFormat.radius != null){ + this.selected.args.radius = selectedFormat.radius; + } + } + + if (overFormat != null){ + if (overFormat.radius != null){ + this.over.args.radius = overFormat.radius; + } + } + + if (draggingFormat != null){ + if (draggingFormat.radius != null){ + this.dragging.args.draggingFormat = draggingFormat.radius; + } + } +}; + + +EllipseVertexGraphFormatter.prototype.getDefault = VertexGraphFormatter.prototype.getDefault; +EllipseVertexGraphFormatter.prototype.getSelected = VertexGraphFormatter.prototype.getSelected; +EllipseVertexGraphFormatter.prototype.getOver = VertexGraphFormatter.prototype.getOver; +EllipseVertexGraphFormatter.prototype.getDragging = VertexGraphFormatter.prototype.getDragging; +EllipseVertexGraphFormatter.prototype.getId = VertexGraphFormatter.prototype.getId; +EllipseVertexGraphFormatter.prototype.toJSON = VertexGraphFormatter.prototype.toJSON; +EllipseVertexGraphFormatter.prototype.loadFromJSON = VertexGraphFormatter.prototype.loadFromJSON; +EllipseVertexGraphFormatter.prototype._setEvents = VertexGraphFormatter.prototype._setEvents; + +function EllipseVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ + VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); + this.args.type = "EllipseVertexGraphFormatter"; + if (defaultFormat != null){ + if (defaultFormat.radius != null){ + this.defaultFormat.args.radius = defaultFormat.radius; + } + } + + if (selectedFormat != null){ + if (selectedFormat.radius != null){ + this.selected.args.radius = selectedFormat.radius; + } + } + + if (overFormat != null){ + if (overFormat.radius != null){ + this.over.args.radius = overFormat.radius; + } + } + + if (draggingFormat != null){ + if (draggingFormat.radius != null){ + this.dragging.args.draggingFormat = draggingFormat.radius; + } + } +}; + + + +RectangleVertexGraphFormatter.prototype.getDefault = ItemGraphFormatter.prototype.getDefault; +RectangleVertexGraphFormatter.prototype.getSelected = ItemGraphFormatter.prototype.getSelected; +RectangleVertexGraphFormatter.prototype.getOver = ItemGraphFormatter.prototype.getOver; +RectangleVertexGraphFormatter.prototype.getDragging = ItemGraphFormatter.prototype.getDragging; +RectangleVertexGraphFormatter.prototype.getId = ItemGraphFormatter.prototype.getId; +RectangleVertexGraphFormatter.prototype.toJSON = ItemGraphFormatter.prototype.toJSON; +RectangleVertexGraphFormatter.prototype.loadFromJSON = ItemGraphFormatter.prototype.loadFromJSON; +RectangleVertexGraphFormatter.prototype._setEvents = ItemGraphFormatter.prototype._setEvents; + +function RectangleVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ + VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); + this.args.type = "RectangleVertexGraphFormatter"; + if (defaultFormat != null){ + if (defaultFormat.radius != null){ + this.defaultFormat.args.radius = defaultFormat.radius; + } + } + + if (selectedFormat != null){ + if (selectedFormat.radius != null){ + this.selected.args.radius = selectedFormat.radius; + } + } + + if (overFormat != null){ + if (overFormat.radius != null){ + this.over.args.radius = overFormat.radius; + } + } + + if (draggingFormat != null){ + if (draggingFormat.radius != null){ + this.dragging.args.draggingFormat = draggingFormat.radius; + } + } +}; + + + +RoundedVertexGraphFormatter.prototype.getDefault = ItemGraphFormatter.prototype.getDefault; +RoundedVertexGraphFormatter.prototype.getSelected = ItemGraphFormatter.prototype.getSelected; +RoundedVertexGraphFormatter.prototype.getOver = ItemGraphFormatter.prototype.getOver; +RoundedVertexGraphFormatter.prototype.getDragging = ItemGraphFormatter.prototype.getDragging; +RoundedVertexGraphFormatter.prototype.getId = ItemGraphFormatter.prototype.getId; +RoundedVertexGraphFormatter.prototype.toJSON = ItemGraphFormatter.prototype.toJSON; +RoundedVertexGraphFormatter.prototype.loadFromJSON = ItemGraphFormatter.prototype.loadFromJSON; +RoundedVertexGraphFormatter.prototype._setEvents = ItemGraphFormatter.prototype._setEvents; + +function RoundedVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ + VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); + this.args.type = "RoundedVertexGraphFormatter"; + if (defaultFormat != null){ + if (defaultFormat.radius != null){ + this.defaultFormat.args.radius = defaultFormat.radius; + } + } + + if (selectedFormat != null){ + if (selectedFormat.radius != null){ + this.selected.args.radius = selectedFormat.radius; + } + } + + if (overFormat != null){ + if (overFormat.radius != null){ + this.over.args.radius = overFormat.radius; + } + } + + if (draggingFormat != null){ + if (draggingFormat.radius != null){ + this.dragging.args.draggingFormat = draggingFormat.radius; + } + } +}; + + + +OctagonVertexGraphFormatter.prototype.getDefault = ItemGraphFormatter.prototype.getDefault; +OctagonVertexGraphFormatter.prototype.getSelected = ItemGraphFormatter.prototype.getSelected; +OctagonVertexGraphFormatter.prototype.getOver = ItemGraphFormatter.prototype.getOver; +OctagonVertexGraphFormatter.prototype.getDragging = ItemGraphFormatter.prototype.getDragging; +OctagonVertexGraphFormatter.prototype.getId = ItemGraphFormatter.prototype.getId; +OctagonVertexGraphFormatter.prototype.toJSON = ItemGraphFormatter.prototype.toJSON; +OctagonVertexGraphFormatter.prototype.loadFromJSON = ItemGraphFormatter.prototype.loadFromJSON; +OctagonVertexGraphFormatter.prototype._setEvents = ItemGraphFormatter.prototype._setEvents; + +function OctagonVertexGraphFormatter(id, defaultFormat, selectedFormat, overFormat, draggingFormat){ + VertexGraphFormatter.prototype.constructor.call(this, id, defaultFormat, selectedFormat, overFormat, draggingFormat); + this.args.type = "OctagonVertexGraphFormatter"; + if (defaultFormat != null){ + if (defaultFormat.radius != null){ + this.defaultFormat.args.radius = defaultFormat.radius; + } + } + + if (selectedFormat != null){ + if (selectedFormat.radius != null){ + this.selected.args.radius = selectedFormat.radius; + } + } + + if (overFormat != null){ + if (overFormat.radius != null){ + this.over.args.radius = overFormat.radius; + } + } + + if (draggingFormat != null){ + if (draggingFormat.radius != null){ + this.dragging.args.draggingFormat = draggingFormat.radius; + } + } +}; + + + +var Colors = new function() +{ + this.hashColor = []; + this.getColorByScoreArrayValue = function (arrayScore) + { + var array = new Array(); + + for (var i = 0; i< arrayScore.length; i++) + { + + var color = this.getColorByScoreValue(arrayScore[i]) + array.push( color); + + } + return array; + }; + + this.getHexStringByScoreArrayValue = function (arrayScore) + { + var arrayColor = this.getColorByScoreArrayValue(arrayScore); + var arrayHex = new Array(); + for (var i = 0; i< arrayColor.length; i++) + { + arrayHex.push( arrayColor[i].HexString()); + } + return arrayHex; + }; + + this.getColorByScoreValue = function (score) + { + + var truncate = score.toString().substr(0,4); + if (this.hashColor[truncate]!=null) + { + return this.hashColor[truncate]; + } + + + if(isNaN(score)) { + return Colors.ColorFromRGB(0,0,0); + } + var value; + + var from, to; + if(score < 0.5) { + from = Colors.ColorFromRGB(0,0,255); + to = Colors.ColorFromRGB(255,255,255); + value = (score * 2); + } else { + from = Colors.ColorFromRGB(255,255,255); + to = Colors.ColorFromRGB(255,0,0); + value = (score * 2) - 1; + } + + var x = value; + var y = 1.0 - value; + var color = Colors.ColorFromRGB(y * from.Red() + x * to.Red(), y * from.Green() + x * to.Green(), y * from.Blue() + x * to.Blue()); + + this.hashColor[truncate] = color; + + return color; + }; + + this.ColorFromHSV = function(hue, sat, val) + { + var color = new Color(); + color.SetHSV(hue,sat,val); + return color; + }; + + this.ColorFromRGB = function(r, g, b) + { + var color = new Color(); + color.SetRGB(r,g,b); + return color; + }; + + this.ColorFromHex = function(hexStr) + { + var color = new Color(); + color.SetHexString(hexStr); + return color; + }; + + function Color() { + //Stored as values between 0 and 1 + var red = 0; + var green = 0; + var blue = 0; + + //Stored as values between 0 and 360 + var hue = 0; + + //Strored as values between 0 and 1 + var saturation = 0; + var value = 0; + + this.SetRGB = function(r, g, b) + { + red = r/255.0; + green = g/255.0; + blue = b/255.0; + calculateHSV(); + }; + + this.Red = function() { return Math.round(red*255); }; + + this.Green = function() { return Math.round(green*255); }; + + this.Blue = function() { return Math.round(blue*255); }; + + this.SetHSV = function(h, s, v) + { + hue = h; + saturation = s; + value = v; + calculateRGB(); + }; + + this.Hue = function() + { return hue; }; + + this.Saturation = function() + { return saturation; }; + + this.Value = function() + { return value; }; + + this.SetHexString = function(hexString) + { + if(hexString == null || typeof(hexString) != "string") + { + this.SetRGB(0,0,0); + return; + } + + if (hexString.substr(0, 1) == '#') + hexString = hexString.substr(1); + + if(hexString.length != 6) + { + this.SetRGB(0,0,0); + return; + } + + var r = parseInt(hexString.substr(0, 2), 16); + var g = parseInt(hexString.substr(2, 2), 16); + var b = parseInt(hexString.substr(4, 2), 16); + if (isNaN(r) || isNaN(g) || isNaN(b)) + { + this.SetRGB(0,0,0); + return; + } + + this.SetRGB(r,g,b); + }; + + this.HexString = function() + { + + var rStr = this.Red().toString(16); + if (rStr.length == 1) + rStr = '0' + rStr; + var gStr = this.Green().toString(16); + if (gStr.length == 1) + gStr = '0' + gStr; + var bStr = this.Blue().toString(16); + if (bStr.length == 1) + bStr = '0' + bStr; + return ('#' + rStr + gStr + bStr).toUpperCase(); + }; + + this.Complement = function() + { + var newHue = (hue >= 180) ? hue - 180 : hue + 180; + var newVal = (value * (saturation - 1) + 1); + var newSat = (value*saturation) / newVal; + var newColor = new Color(); + newColor.SetHSV(newHue, newSat, newVal); + return newColor; + } ; + + function calculateHSV() + { + var max = Math.max(Math.max(red, green), blue); + var min = Math.min(Math.min(red, green), blue); + + value = max; + + saturation = 0; + if(max != 0) + saturation = 1 - min/max; + + hue = 0; + if(min == max) + return; + + var delta = (max - min); + if (red == max) + hue = (green - blue) / delta; + else if (green == max) + hue = 2 + ((blue - red) / delta); + else + hue = 4 + ((red - green) / delta); + hue = hue * 60; + if(hue < 0) + hue += 360; + } + + function calculateRGB() + { + red = value; + green = value; + blue = value; + + if(value == 0 || saturation == 0) + return; + + var tHue = (hue / 60); + var i = Math.floor(tHue); + var f = tHue - i; + var p = value * (1 - saturation); + var q = value * (1 - saturation * f); + var t = value * (1 - saturation * (1 - f)); + switch(i) + { + case 0: + red = value; green = t; blue = p; + break; + case 1: + red = q; green = value; blue = p; + break; + case 2: + red = p; green = value; blue = t; + break; + case 3: + red = p; green = q; blue = value; + break; + case 4: + red = t; green = p; blue = value; + break; + default: + red = value; green = p; blue = q; + break; + } + } + } +} +(); +/* + * Clase gestiona la insercción, eliminación de los elementos en el DOM + * + * Vital hacerla SIEMPRE compatible hacia atrás + * + * Last update: 28-10-2010 + * + */ + + +var DOM = {}; + +DOM.createNewElement = function(type, nodeParent, attributes) +{ + + var node = document.createElement(type); + for (var i=0; i0) + { + parent.removeChild(parent.childNodes[0]); + + } +}; + +DOM.select = function(targetID) +{ + return document.getElementById(targetID); +// return $("#"+targetID); +}; +var Geometry = +{ + + /** From tow points obtains the angles formed with the cartesian side **/ + getAngleBetweenTwoPoints : function(x1, y1, x2, y2){ + //var m = (y1 - y2)/ (x1 - x2); + return Math.atan2(y2-y1, x2-x1); + }, + + getAdjacentSideOfRectangleRight : function(angle, hypotenuse){ + return Math.abs(Math.cos(angle)*hypotenuse); + }, + + getOppositeSideOfRectangleRight : function(angle, hypotenuse){ + return Math.abs(Math.sin(angle)*hypotenuse); + }, + + toDegree: function(radian){ + return radian*180/Math.PI; + + } + + +}; + +var SVG = +{ + svgns : 'http://www.w3.org/2000/svg', + xlinkns : "http://www.w3.org/1999/xlink", + + createSVGCanvas: function(parentNode, attributes) + { + + attributes.push( ['xmlns', SVG.svgns], ['xmlns:xlink', 'http://www.w3.org/1999/xlink']); + var svg = document.createElementNS("http://www.w3.org/2000/svg", "svg"); + this._setProperties(svg, attributes); + parentNode.appendChild( svg); + return svg; + + }, + + createRectangle : function (x, y, width, height, attributes){ + var rect = document.createElementNS(this.svgns, "rect"); + rect.setAttribute("x",x); + rect.setAttribute("y",y); + rect.setAttribute("width",width); + rect.setAttribute("height",height); + SVG._setProperties(rect, attributes); + return rect; + }, + + drawImage64 : function (x, y, width, height, base64, svgNode, attributes) { + var node = SVG.createImage64(x, y, width, height, base64, attributes); + svgNode.appendChild(node); + return node; + }, + + createImage64 : function (x, y, width, height, base64, attributes) { + var img = document.createElementNS(this.svgns, "image"); + img.setAttribute("x",x); + img.setAttribute("y",y); + img.setAttribute("width",width); + img.setAttribute("height",height); + img.setAttribute("xlink:href",base64); + SVG._setProperties(img, attributes); + return img; + }, + + createLine: function (x1, y1, x2, y2, attributes){ + var line = document.createElementNS(this.svgns,"line"); + line.setAttribute("x1",x1); + line.setAttribute("y1",y1); + line.setAttribute("x2", x2); + line.setAttribute("y2", y2); + SVG._setProperties(line, attributes); + return line; + }, + + createClip: function (id, nodeToClip, attributes){ + var clip = document.createElementNS(this.svgns,"clipPath"); + clip.setAttribute("id",id); + clip.appendChild(nodeToClip); + return clip; + }, + + drawClip : function (id, nodeToClip, svgNode) { + var node = SVG.createClip(id, nodeToClip); + svgNode.appendChild(node); + return node; + }, + + drawRectangle : function (cx, cy, width, height, svgNode, attributes) { + try{ + var node = SVG.createRectangle(cx, cy, width, height, attributes); + svgNode.appendChild(node); + } + catch(e){ + + console.log("-------------------- "); + console.log("Error on drawRectangle " + e); + console.log(attributes); + console.log("-------------------- "); + } + return node; + }, + + createEllipse : function (x, y, rx, ry, attributes){ + var rect = document.createElementNS(this.svgns, "ellipse"); + rect.setAttribute("cx",x); + rect.setAttribute("cy",y); + rect.setAttribute("rx",rx); + rect.setAttribute("ry",ry); + SVG._setProperties(rect, attributes); + return rect; + }, + + drawEllipse : function (cx, cy, rx, ry, svgNode, attributes) { + var node = SVG.createEllipse(cx, cy, rx, ry, attributes); + svgNode.appendChild(node); + return node; + }, + + drawImage : function (x, y, canvasSVG, attributes) { + var image = document.createElementNS(this.svgns, "image"); + image.setAttribute("x",x); + image.setAttribute("y",y); + canvasSVG.appendChild(image); + SVG._setProperties(image, attributes); + }, + + drawLine : function (x1, y1, x2, y2, nodeSVG, attributes) { + try{ + var line = SVG.createLine(x1, y1, x2, y2, attributes); + nodeSVG.appendChild(line); + }catch(e){ + } + return line; + }, + + + drawPath: function (d, nodeSVG, attributes) { + var path = SVG.createPath(d, attributes); + nodeSVG.appendChild(path); + return path; + }, + + createPoligon : function (points, attributes){ + var poligon = document.createElementNS(this.svgns, "polygon"); + poligon.setAttribute("points",points); + SVG._setProperties(poligon, attributes); + return poligon; + }, + + drawPoligon : function (points, canvasSVG, attributes){ + var poligon = SVG.createPoligon(points, attributes); + canvasSVG.appendChild(poligon); + return poligon; + }, + // + + createPath : function (d, attributes){ + var path = document.createElementNS(this.svgns, "path"); + path.setAttribute("d",d); + SVG._setProperties(path, attributes); + return path; + }, + + drawCircle : function (x, y, radio, canvasSVG, attributes) { + + var newText = document.createElementNS(this.svgns,"circle"); + newText.setAttribute("cx",x); + newText.setAttribute("cy",y); + newText.setAttribute("r",radio); + + canvasSVG.appendChild(newText); + attributes["cursor"] = "pointer"; + this._setProperties(newText, attributes); + return newText; + }, + + + _setProperties: function(node, attributes) + { + if (attributes instanceof Array){ + for (var i=0; i< attributes.length; i++) + { + node.setAttribute(attributes[i][0], attributes[i][1]); + } + } + else{ + for ( var key in attributes){ + node.setAttribute(key, attributes[key]); + } + } + }, + +/* drawPath: function(pointsArray, canvasSVG, attributes){ + var path = document.createElementNS(this.svgns,"polyline"); + path.setAttribute ('id', id); + + var d= pointsArray[0].x+ " "+ pointsArray[0].y; + for (var i=1; i< pointsArray.length; i++) + { + d=d+" "+pointsArray[i].x+" "+pointsArray[i].y; + } + path.setAttribute ('points', d); + canvasSVG.appendChild(path); + },*/ + + createText : function (x, y, text, attributes) { + var node = document.createElementNS(this.svgns,"text"); + node.setAttributeNS(null , "x",x); + node.setAttributeNS(null, "y",y); + + var textNode = document.createTextNode(text); + node.appendChild(textNode); + + this._setProperties(node, attributes); + return node; + }, + + drawText : function (x, y, text, canvasSVG, attributes) { + var text = SVG.createText(x, y, text, attributes); + canvasSVG.appendChild(text); + return text; + }, + + + + drawGroup: function(svgNode, attributes) + { + var group = SVG.createGroup(attributes); + svgNode.appendChild(group); + return group; + }, + + createGroup: function(attributes){ + var group = document.createElementNS(this.svgns,"g"); + this._setProperties(group, attributes); + return group; + } + +}; + + + +var CanvasToSVG = { + + convert: function(sourceCanvas, targetSVG, x, y, id, attributes) { + + var img = this._convert(sourceCanvas, targetSVG, x, y, id); + + for (var i=0; i< attributes.length; i++) + { + img.setAttribute(attributes[i][0], attributes[i][1]); + } + }, + + _convert: function(sourceCanvas, targetSVG, x, y, id) { + var svgNS = "http://www.w3.org/2000/svg"; + var xlinkNS = "http://www.w3.org/1999/xlink"; + // get base64 encoded png from Canvas + var image = sourceCanvas.toDataURL(); + + // must be careful with the namespaces + var svgimg = document.createElementNS(svgNS, "image"); + + svgimg.setAttribute('id', id); + + //svgimg.setAttribute('class', class); + //svgimg.setAttribute('xlink:href', image); + svgimg.setAttributeNS(xlinkNS, 'xlink:href', image); + + + + + svgimg.setAttribute('x', x ? x : 0); + svgimg.setAttribute('y', y ? y : 0); + svgimg.setAttribute('width', sourceCanvas.width); + svgimg.setAttribute('height', sourceCanvas.height); + //svgimg.setAttribute('cursor', 'pointer'); + svgimg.imageData = image; + + targetSVG.appendChild(svgimg); + return svgimg; + }, + + importSVG: function(sourceSVG, targetCanvas) { + svg_xml = sourceSVG;//(new XMLSerializer()).serializeToString(sourceSVG); + var ctx = targetCanvas.getContext('2d'); + + var img = new Image(); + img.src = "data:image/svg+xml;base64," + btoa(svg_xml); +// img.onload = function() { + ctx.drawImage(img, 0, 0); +// }; + } + +}; +/* +Graph.prototype.importSVG = function(sourceSVG, targetCanvas) { + sourceSVG = this._svg; + targetCanvas = document.createElementNS('canvas'); + // https://developer.mozilla.org/en/XMLSerializer + svg_xml = (new XMLSerializer()).serializeToString(sourceSVG); + var ctx = targetCanvas.getContext('2d'); + // this is just a JavaScript (HTML) image + var img = new Image(); + // http://en.wikipedia.org/wiki/SVG#Native_support + // https://developer.mozilla.org/en/DOM/window.btoa + img.src = "data:image/svg+xml;base64," + btoa(svg_xml); + img.onload = function() { + // after this, Canvas’ origin-clean is DIRTY + ctx.drawImage(img, 0, 0); + } +}; +*/ + +/* + +Normalizacion de datos para dibujar colores +Issues: + No sé como debería llamarse esta libreria + No sé si ya existe una funciçon en javascript que lo haga + + +*/ + + +var Normalizer = new function() +{ + this.normalizeArray = function (arrayData) + { + + return this.standardizeArray(this.normal(arrayData)); + +// var result = this._getMaxAndMin(arrayData); +// var min =result[0]; +// var max = result[1]; +// +// +// //los hacemos todos positivos +// for (var i = 0; i< arrayData.length; i++) +// { +// arrayData[i]= Math.abs(min) + parseFloat(arrayData[i]); +// } +// +// var result = this._getMaxAndMin(arrayData); +// var min =result[0]; +// var max = result[1]; +// +// +// var resultArray = new Array(); +// for (var i = 0; i< arrayData.length; i++) +// { +// resultArray.push(arrayData[i]*1/max); +// } +// return resultArray; + }; + + this.normal = function(arrayData){ + var mean = this._getMean(arrayData); + var deviation = this._getStdDeviation(arrayData); + var result = this._getMaxAndMin(arrayData); + var min = result[0]; + var max = result[1]; + + var resultArray = new Array(); + for (var i = 0; i< arrayData.length; i++) { + if (deviation!=0){ + resultArray.push((arrayData[i]-mean)/deviation); + }else{ + resultArray.push(arrayData[i]); + } + } + return resultArray; + }; + + this.standardizeArray = function(arrayData) + { + var result = this._getMaxAndMin(arrayData); + var min = result[0]; + var max = result[1]; + + var offset = ( min <= 0 ) ? Math.abs(min) : (-1 * min); + var resultArray = new Array(); + for (var i = 0; i< arrayData.length; i++) { + if(max + offset!=0){ + resultArray.push((arrayData[i] + offset) / (max + offset)); + }else{ + resultArray.push(arrayData[i]+offset); + } + } + return resultArray; + }; + + + this._getMean = function(arrayData) { + var sum = 0; + for (var i = 0; i< arrayData.length; i++) { + sum = sum + parseFloat(arrayData[i]); + } + return sum/arrayData.length; + }; + + this._getStdDeviation = function(arrayData) { + var mean = this._getMean(arrayData); + var acum = 0.0; + for(var i=0; i max) max = parseFloat(arrayData[i]); + } + + return [min, max]; + }; +}; +function GraphCanvas(componentID, targetNode, args) { + this.args = {}; + /** target */ + this.targetID = targetNode.id; + + /** id manage */ + this.id = componentID; + this.args.idGraph = this.id + "main"; + this.args.idBackgroundNode = this.id + "background"; + + this.args.idEdgesGraph = this.id + "edges"; + this.args.idNodesGraph = this.id + "vertices"; + this.args.idLabelGraph = this.id + "label"; + this.args.idBackground = this.id + "background"; + + /** Objects Graph **/ + this.dataset = null; + this.formatter = null; + this.layout = null; + + /** Drawing **/ + this.circleDefaultRadius = 2; + this.squareDefaultSide = this.circleDefaultRadius * 1.5; + + /** Directed Arrow **/ + this.arrowDefaultSize = this.circleDefaultRadius; + + /** Groups **/ + this.GraphGroup = null; + this.GraphNodeGroup = null; + this.GraphLabelGroup = null; + this.GraphBackground = null; + + /** SETTINGS FLAGS **/ + this.args.draggingCanvasEnabled = false; //Flag to set if the canvas can be dragged + this.args.multipleSelectionEnabled = false; + this.args.interactive = false; + this.args.labeled = false; + this.args.linkEnabled = false; + + /** If numberEdge > maxNumberEdgesMoving then only it will move edges when mouse up **/ + this.args.maxNumberEdgesMoving = 3; + this.args.maxNumberEdgesFiringEvents = 50; + + /** Linking edges **/ + this.args.linking = false; + this.linkStartX = 0; + this.linkStartY = 0; + this.linkSVGNode = null; + this.linkNodeSource = null; + this.linkNodeTarget = null; + + /** Dragging Control **/ + this.draggingElement = null; + this.dragging = false; + this.nMouseOffsetX = 0; + this.nMouseOffsetY = 0; + this.dragStartX = 0; + this.dragStartY = 0; + this.desplazamientoX = 0; + this.desplazamientoY = 0; + + /** Selection Control **/ + this.selecting = false; + this.selectorX = null; + this.selectorY = null; + this.selectorSVGNode = null; + + /** Node status **/ + this.args.isVertexSelected = {}; + this.args.selectedVertices = []; + + /** Edges status **/ + this.args.isEdgeSelected = {}; + //this.args.selectedEdges = []; + + if (args != null) { + if (args.multipleSelectionEnabled != null) { + this.args.multipleSelectionEnabled = args.multipleSelectionEnabled; + this.args.draggingCanvasEnabled = !(this.args.multipleSelectionEnabled); + } + if (args.draggingCanvasEnabled != null) { + this.args.draggingCanvasEnabled = args.draggingCanvasEnabled; + this.args.multipleSelectionEnabled = !(this.args.draggingCanvasEnabled); + } + if (args.interactive != null) { + this.args.interactive = args.interactive; + } + if (args.labeled != null) { + this.args.labeled = args.labeled; + } + + } + + /** Hashmap with the svg node labels **/ + this.svgLabels = {}; + + /** EVENTS **/ + this.onVertexOut = new Event(this); + this.onVertexOver = new Event(this); + this.onVertexSelect = new Event(this); + this.onEdgeSelect = new Event(this); + this.onCanvasClicked = new Event(this); + this.onVertexUp = new Event(this); +} + +GraphCanvas.prototype.showLabels = function(value) { + this.args.labeled = value; + this.removeLabels(); + if (value) { + this.renderLabels(); + } +}; + +GraphCanvas.prototype.getSelectedVertices = function() { + return this.args.selectedVertices; +}; + +GraphCanvas.prototype.getSelectedEdges = function() { + var selected = []; + for ( var selectedEdge in this.args.isEdgeSelected) { + selected.push(selectedEdge); + } + return selected; +}; + +GraphCanvas.prototype.createSVGDom = function(targetID, id, width, height, backgroundColor) { + var container = document.getElementById(targetID); + this._svg = SVG.createSVGCanvas(container, [ + [ "style", "background-color:" + backgroundColor + ";" ], [ "id", id ], [ "dragx", 0 ], [ "dragy", 0 ], + [ "height", this.getFormatter().getHeight() ], [ "width", this.getFormatter().getWidth() ] ]); + return this._svg; +}; + +/** MULTIPLE SELECTION **/ +GraphCanvas.prototype.isMultipleSelectionEnabled = function() { + return this.args.multipleSelectionEnabled; +}; + +GraphCanvas.prototype.setMultipleSelection = function(value) { + this.args.multipleSelectionEnabled = value; + this.args.draggingCanvasEnabled = (!value); +}; + +GraphCanvas.prototype.setSelecting = function(value) { + this.selecting = value; +}; + +/** linking **/ +GraphCanvas.prototype.setLinking = function(value) { + this.args.linkEnabled = value; + this.selecting = !value; + this.dragging = !value; +}; + +/** CANVAS MOVING **/ +GraphCanvas.prototype.setDraggingCanvas = function(value) { + this.args.draggingCanvasEnabled = value; + this.args.multipleSelectionEnabled = !value; +}; + +GraphCanvas.prototype.isDraggingCanvasEnabled = function() { + return this.args.draggingCanvasEnabled; +}; +/** ZOOM **/ +GraphCanvas.prototype.getScale = function() { + return this.getFormatter().getZoomScale(); +}; + +GraphCanvas.prototype.setScale = function(scale) { + var graphNode = document.getElementById(this.args.idGraph); + graphNode.setAttribute("transform", graphNode.getAttribute("transform").replace("scale(" + this.getScale() + ")", "scale(" + scale + ")")); + this.getFormatter().setZoomScale(scale); +}; + +GraphCanvas.prototype.zoomIn = function() { + this.setScale(this.getScale() + this.getFormatter().getZoomScaleStepFactor()); +}; + +GraphCanvas.prototype.zoomOut = function() { + this.setScale(this.getScale() - this.getFormatter().getZoomScaleStepFactor()); + +}; + +/** SVG COORDENATES **/ +GraphCanvas.prototype.getSVGCoordenates = function(evt) { + var p = this._svg.createSVGPoint(); + p.x = evt.clientX; + p.y = evt.clientY; + + var m = this._svg.getScreenCTM(document.documentElement); + p = p.matrixTransform(m.inverse()); + return p; +}; + +/** SVG EVENTS **/ +GraphCanvas.prototype.mouseClick = function(event) { + if (event.button == 0) { + if (!this.args.interactive) { + return; + } + + if (this.isVertex(event.target)) { + this.clickNode(this.getVertexIdFromSVGId(event.target.id)); + } + /** Como el evento mouseClick viene despues del mouse up es aqui donde manejo el tema de deseccionar los elementos que estoy dragging **/ + if (this.dragging) { + this.dragging = false; + } + } +}; + +GraphCanvas.prototype.mouseMove = function(evt) { + if (this.selecting) { + this.clearLabels(); + + var width = (this.getSVGCoordenates(evt).x - this.selectorX); + var height = (this.getSVGCoordenates(evt).y - this.selectorY); + if ((width > 0) && (height > 0)) { + this.displaySelection(this.selectorX, this.selectorY, width, height); + } + if ((width > 0) && (height < 0)) { + this.displaySelection(this.selectorX, this.getSVGCoordenates(evt).y, width, Math.abs(height)); + } + if ((width < 0) && (height < 0)) { + this.displaySelection(this.getSVGCoordenates(evt).x, this.getSVGCoordenates(evt).y, Math.abs(width), Math.abs(height)); + } + if ((width < 0) && (height > 0)) { + this.displaySelection(this.selectorX + width, this.selectorY, Math.abs(width), Math.abs(height)); + } + + var x1 = (parseFloat(this.selectorSVGNode.getAttribute("x")) - DOM.select(this.id).getAttribute("dragx")) / this.getFormatter().getWidth(); + var y1 = (parseFloat(this.selectorSVGNode.getAttribute("y")) - DOM.select(this.id).getAttribute("dragy")) / this.getFormatter().getHeight(); + var x2 = (x1 + parseFloat(this.selectorSVGNode.getAttribute("width") / this.getFormatter().getWidth())); + var y2 = (y1 + parseFloat(this.selectorSVGNode.getAttribute("height") / this.getFormatter().getHeight())); + + this.deselectNodes(this.getLayout()); + var verticesSelected = this.getLayout().getVerticesByArea(x1 / this.getFormatter().getZoomScale(), y1 / this.getFormatter().getZoomScale(), + x2 / this.getFormatter().getZoomScale(), y2 / this.getFormatter().getZoomScale()); + for ( var i = 0; i < verticesSelected.length; i++) { + this.selectNode(verticesSelected[i].getId()); + this.renderLabel(verticesSelected[i].getId()); + } + + } + var p = null; + if (this.args.linking) { + p = this.getSVGCoordenates(evt); + if (this.linkSVGNode != null) { + this.linkSVGNode.setAttribute("x2", p.x - 2); + this.linkSVGNode.setAttribute("y2", p.y - 2); + } + } + + if (this.dragging) { + p = this.getSVGCoordenates(evt); + p.x -= this.nMouseOffsetX; + p.y -= this.nMouseOffsetY; + this.desplazamientoX = (this.getSVGCoordenates(evt).x - this.dragStartX);// + parseFloat(DOM.select(this.id).getAttribute("dragx")); + this.desplazamientoY = (this.getSVGCoordenates(evt).y - this.dragStartY);// + parseFloat(DOM.select(this.id).getAttribute("dragy")); + + if (this.draggingElement != null) { + /** Click sobre el recct del banground que provoca que mueva todo el canvas **/ + if (this.isNodeCanvas(this.draggingElement)) { + + p = this.getSVGCoordenates(evt); + p.x = this.desplazamientoX; + p.y = this.desplazamientoY; + + this.draggingElement.setAttribute("dragx", p.x); + this.draggingElement.setAttribute("dragy", p.y); + this.draggingElement = document.getElementById(this.args.idGraph); + this.draggingElement.setAttribute("transform", "translate(" + p.x + "," + p.y + "), scale(" + this.getScale() + ")"); + + DOM.select(this.id).setAttribute("dragx", p.x); + DOM.select(this.id).setAttribute("dragy", p.y); + + if (this.NodeSVGbackgroundImage != null) { + this.NodeSVGbackgroundImage.setAttribute("dragx", p.x); + this.NodeSVGbackgroundImage.setAttribute("dragy", p.y); + } + } else { + if (this.isVertex(this.draggingElement)) { + this.selectNode(this.getVertexIdFromSVGId(this.draggingElement.id)); + this.desplazamientoX = this.desplazamientoX / this.getFormatter().getZoomScale(); + this.desplazamientoY = this.desplazamientoY / this.getFormatter().getZoomScale(); + this.moveSelectedNodes(this.desplazamientoX, this.desplazamientoY); + + this.dragStartX = this.getSVGCoordenates(evt).x; + this.dragStartY = this.getSVGCoordenates(evt).y; + } else { + if (this.isNodeBackground(this.draggingElement)) { + + this.draggingElement.setAttribute("dragx", p.x); + this.draggingElement.setAttribute("dragy", p.y); + this.draggingElement = document.getElementById(this.args.idGraph); + this.draggingElement.setAttribute("transform", "translate(" + p.x + "," + p.y + "), scale(" + this.getScale() + ")"); + } else { + this.draggingElement.setAttribute("transform", "translate(" + p.x + "," + p.y + ")"); + } + } + } + } + } +}; + +GraphCanvas.prototype.moveSelectedNodes = function(offsetX, offsetY) { + for ( var i = 0; i < this.getSelectedVertices().length; i++) { + + var nodeId = this.getSelectedVertices()[i]; + var svgNodeId = this.getSVGNodeId(nodeId); + + var x = parseFloat(DOM.select(svgNodeId).getAttribute("dragx")) + parseFloat(offsetX);// - parseFloat(DOM.select(this.id).getAttribute("dragx")); + var y = parseFloat(DOM.select(svgNodeId).getAttribute("dragy")) + parseFloat(offsetY);// + parseFloat(DOM.select(this.id).getAttribute("dragy")); + + this._movingNode(DOM.select(svgNodeId), x, y); + } +}; + +GraphCanvas.prototype.mouseDown = function(evt) { + if (event.button == 0) { + + /** if !no interactive mouse events do anything **/ + if (!this.args.interactive) { + return; + } + + var p = this.getSVGCoordenates(evt); + + /** When click on canvas or background deselect all **/ + if (this.isNodeCanvas(evt.target) || this.isNodeBackground(evt.target)) { + this.deselectNodes(); + this.deselectEdges(); + this.onCanvasClicked.notify(); + } + + /** if I am linking vertices **/ + if (this.args.linkEnabled) { + + if (!this.args.linking) { + this.args.linking = true; + if (this.isVertex(evt.target)) { + this.linkStartX = p.x; + this.linkStartY = p.y; + this.linkSVGNode = SVG.drawLine(p.x, p.y, p.x, p.y, this._svg, { + "stroke" : "#FF0000" + }); + this.linkNodeSource = this.getVertexIdFromSVGId(evt.target.id); + } + } else { + this.linkNodeTarget = this.getVertexIdFromSVGId(evt.target.id); + this.args.linking = false; + this.args.linkEnabled = false; + if (this.isVertex(evt.target)) { + this.getDataset().addEdge(this.linkNodeSource + "_" + this.linkNodeTarget, this.linkNodeSource, this.linkNodeTarget, {}); + } + this.linkSVGNode.parentNode.removeChild(this.linkSVGNode); + } + return; + } + + /** Id is a vertex or the canvas **/ + if (this.isVertex(evt.target) || this.isNodeCanvas(evt.target) || this.isNodeBackground(evt.target)) { + this._startDragging(evt); + } + /** if i is edge **/ + if (this.isEdge(evt.target)) { + this.selectEdge(this.getEdgeIdFromSVGId(evt.target.getAttribute("id"))); + } + + if (this.args.multipleSelectionEnabled) { + if (!this.dragging) { + this.setSelecting(true); + this.selectorX = p.x; + this.selectorY = p.y; + this.displaySelection(p.x, p.y, 1, 1); + } + } + + } + if (event.button == 1) { + this.setLinking(false); + this.setMultipleSelection(false); + this.selecting = false; + + /** Id is a vertex or the canvas **/ + if (this.isVertex(evt.target) || this.isNodeCanvas(evt.target) || this.isNodeBackground(evt.target)) { + this._startDragging(evt); + } + } +}; + +GraphCanvas.prototype.mouseUp = function(event) { + if (!this.args.interactive) { + return; + } + + if (this.dragging) { + this._stopDragging(event); + if (this.isVertex(event.target)) { + var vertexId = this.getVertexIdFromSVGId(event.target.id); + if (this.getDataset().getVertexById(vertexId).getEdges().length >= this.args.maxNumberEdgesMoving) { + this.moveEdge(vertexId); + } + } + } + + if (this.selecting) { + this.setSelecting(false); + + var x1 = (parseFloat(this.selectorSVGNode.getAttribute("x")) - DOM.select(this.id).getAttribute("dragx")) / this.getFormatter().getWidth(); + var y1 = (parseFloat(this.selectorSVGNode.getAttribute("y")) - DOM.select(this.id).getAttribute("dragy")) / this.getFormatter().getHeight(); + var x2 = (x1 + parseFloat(this.selectorSVGNode.getAttribute("width") / this.formatter.getWidth())); + var y2 = (y1 + parseFloat(this.selectorSVGNode.getAttribute("height") / this.formatter.getHeight())); + + var verticesSelected = this.getLayout().getVerticesByArea(x1 / this.getFormatter().getZoomScale, y1 / this.getFormatter().getZoomScale, + x2 / this.getFormatter().getZoomScale, y2 / this.getFormatter().getZoomScale); + + for ( var i = 0; i < verticesSelected.length; i++) { + this.selectNode(verticesSelected[i].getId()); + } + + if (this.selectorSVGNode != null) { + this._svg.removeChild(this.selectorSVGNode); + } + + if (this.args.labeled) { + this.clearLabels(); + this.renderLabels(); + } + + this.selectorSVGNode = null; + // this.renderLabels(); + } +}; + +/** SELECTION **/ +GraphCanvas.prototype.displaySelection = function(x, y, width, height) { + if (this.selectorSVGNode != null) { + this.selectorSVGNode.setAttribute("x", x); + this.selectorSVGNode.setAttribute("y", y); + this.selectorSVGNode.setAttribute("width", width); + this.selectorSVGNode.setAttribute("height", height); + } else { + this.selectorSVGNode = SVG.drawRectangle(x, y, width, height, this._svg, { + "fill" : "red", + "stroke" : "black", + "opacity" : "0.2", + "stroke-opacity" : "1" + }); + } +}; + +/** DRAGGING **/ +GraphCanvas.prototype._startDragging = function(evt) { + if (!this.isDraggingCanvasEnabled()) { + if (this.isNodeCanvas(evt.target)) { + this.draggingElement = null; + } + } + + if (this.isVertex(evt.target) || (this.isNodeBackground(evt.target) && (this.isDraggingCanvasEnabled()))|| (this.isNodeCanvas(evt.target) && (this.isDraggingCanvasEnabled()))) { + this.clearLabels(); + this.draggingElement = evt.target; + this.dragging = true; + var p = this.getSVGCoordenates(evt); + + this.nMouseOffsetX = p.x - parseInt(evt.target.getAttribute("dragx")); + this.nMouseOffsetY = p.y - parseInt(evt.target.getAttribute("dragy")); + + if (this.isVertex(evt.target)) { + this.dragStartX = parseInt(this.draggingElement.getAttribute("dragx")) * this.getFormatter().getZoomScale() + + parseFloat(DOM.select(this.id).getAttribute("dragx")); + this.dragStartY = parseInt(this.draggingElement.getAttribute("dragy")) * this.getFormatter().getZoomScale() + + parseFloat(DOM.select(this.id).getAttribute("dragy")); + } else { + this.dragStartX = p.x - parseInt(this.draggingElement.getAttribute("dragx"));// + parseFloat(DOM.select(this.id).getAttribute("dragx")); + this.dragStartY = p.y - parseInt(this.draggingElement.getAttribute("dragy"));// + parseFloat(DOM.select(this.id).getAttribute("dragy")); + } + } +}; + +GraphCanvas.prototype._stopDragging = function(event) { + this.nMouseOffsetX = 0; + this.nMouseOffsetX = 0; + /** despues del evento up viene el evento click entonces acabo el dragging en el mouseclick **/ + this.dragging = false; + this.draggingElement = null; + this.renderLabels(); + + this.setLinking(false); + this.setMultipleSelection(true); + this.selecting = false; + +}; + +/** Move the edges of the vertex with the vertexId indicado **/ +GraphCanvas.prototype.moveEdge = function(vertexId) { + var x = this.getLayout().getNodeById(vertexId).x * this.getFormatter().getWidth(); + var y = this.getLayout().getNodeById(vertexId).y * this.getFormatter().getHeight(); + + /** Moving edges out **/ + for ( var i = 0; i < this.getDataset().getVertexById(vertexId).getEdgesOut().length; i++) { + var edgeId = this.getDataset().getVertexById(vertexId).getEdgesOut()[i].getId(); + var svgEdgeId = this.getSVGEdgeId(edgeId); + var edgeFormatter = this.getFormatter().getEdgeById(edgeId); + if (edgeFormatter instanceof LineEdgeGraphFormatter) { + DOM.select(svgEdgeId + "_shadow").setAttribute("x2", x); + DOM.select(svgEdgeId + "_shadow").setAttribute("y2", y); + DOM.select(svgEdgeId).setAttribute("x2", x); + DOM.select(svgEdgeId).setAttribute("y2", y); + } + + if ((edgeFormatter instanceof DirectedLineEdgeGraphFormatter) || (edgeFormatter instanceof OdirectedLineEdgeGraphFormatter) + || (edgeFormatter instanceof OdotDirectedLineEdgeGraphFormatter) || (edgeFormatter instanceof DotDirectedLineEdgeGraphFormatter) + || (edgeFormatter instanceof CutDirectedLineEdgeGraphFormatter)) { + this.removeEdge(edgeId); + this.renderEdge(edgeId); + } + } + + /** Moving edges in **/ + for ( var i = 0; i < this.getDataset().getVertexById(vertexId).getEdgesIn().length; i++) { + var edgeId = this.getDataset().getVertexById(vertexId).getEdgesIn()[i].getId(); + var svgEdgeId = this.getSVGEdgeId(edgeId); + var edgeFormatter = this.getFormatter().getEdgeById(edgeId); + if (edgeFormatter instanceof LineEdgeGraphFormatter) { + DOM.select(svgEdgeId).setAttribute("x1", x); + DOM.select(svgEdgeId).setAttribute("y1", y); + DOM.select(svgEdgeId + "_shadow").setAttribute("x1", x); + DOM.select(svgEdgeId + "_shadow").setAttribute("y1", y); + } + + if ((edgeFormatter instanceof DirectedLineEdgeGraphFormatter) || (edgeFormatter instanceof OdirectedLineEdgeGraphFormatter) + || (edgeFormatter instanceof OdotDirectedLineEdgeGraphFormatter) || (edgeFormatter instanceof DotDirectedLineEdgeGraphFormatter) + || (edgeFormatter instanceof CutDirectedLineEdgeGraphFormatter)) { + this.removeEdge(edgeId); + this.renderEdge(edgeId); + } + + if (edgeFormatter instanceof BezierEdgeGraphFormatter) { + var radius = this.getFormatter().getVertexById(vertexId).getDefault().getSize() * this.getFormatter().getNodesMaxSize(); + var d = this.calculateCoordenatesBezier(radius, x, y); + DOM.select(svgEdgeId).setAttribute("d", d); + } + } +}; + +GraphCanvas.prototype.moveNode = function(vertexId) { + var x = this.getLayout().getNodeById(vertexId).x * this.getFormatter().getWidth(); + var y = this.getLayout().getNodeById(vertexId).y * this.getFormatter().getHeight(); + var svgNodeElement = DOM.select(this.getSVGNodeId(vertexId)); + + svgNodeElement.setAttribute("dragx", x); + svgNodeElement.setAttribute("dragy", y); + svgNodeElement.setAttribute("transform", "translate(" + x + "," + y + ")"); + + if (this.getDataset().getVertexById(vertexId).getEdges().length < this.args.maxNumberEdgesMoving) { + this.moveEdge(vertexId); + } +}; + +GraphCanvas.prototype._movingNode = function(svgNodeElement, x, y) { + var vertexId = this.getVertexIdFromSVGId(svgNodeElement.getAttribute("id")); + this.getLayout().getNodeById(vertexId).setCoordinates(x / this.getFormatter().getWidth(), y / this.getFormatter().getHeight()); + this.desplazamientoX = 0; + this.desplazamientoY = 0; + this.removeLabel(vertexId); + this.renderLabel(vertexId); +}; + +/** INIT **/ +GraphCanvas.prototype.init = function() { + + this._svg = this.createSVGDom(this.targetID, this.id, this.getFormatter().getWidth(), this.getFormatter().getHeight(), this.getFormatter() + .getBackgroundColor()); + this.GraphGroup = SVG.drawGroup(this._svg, [ [ "id", this.args.idGraph ], [ "transform", "translate(0,0), scale(1)" ] ]); + this.GraphBackground = SVG.drawGroup(this.GraphGroup, [ [ "id", this.args.idBackground ] ]); + this.GraphEdgeGroup = SVG.drawGroup(this.GraphGroup, [ [ "id", this.args.idEdgesGraph ] ]); + this.GraphNodeGroup = SVG.drawGroup(this.GraphGroup, [ [ "id", this.args.idNodesGraph ] ]); + this.GraphLabelGroup = SVG.drawGroup(this.GraphGroup, [ [ "id", this.args.idLabelGraph ] ]); + + if ((this.getFormatter().getBackgroundImage() != null) && (this.getFormatter().getBackgroundImage() != "")) { + this.setBackgroundImage(this.getFormatter().getBackgroundImage()); + } + /** SVG Events listener */ + var _this = this; + this._svg.addEventListener("click", function(event) { + _this.mouseClick(event); + }, false); + this._svg.addEventListener("mousemove", function(event) { + _this.mouseMove(event, _this); + }, false); + this._svg.addEventListener("mousedown", function(event) { + _this.mouseDown(event, _this); + }, false); + this._svg.addEventListener("mouseup", function(event) { + _this.mouseUp(event, _this); + }, false); +}; + +/* + GraphCanvas.prototype.backgroungToSVG = function(){ + var _this = this; + var canvas = document.createElement('canvas'); + canvas.setAttribute("id", "canvas"); + canvas.width = this.formatter.getWidth(); + canvas.height = this.formatter.getHeight(); + + this._svg.parentNode.parentNode.appendChild(canvas); + var ctx = document.getElementById('canvas').getContext('2d'); + var img = new Image(); + + img.src = this.formatter.getBackgroundImage(); + ctx.drawImage(img,0,0 ,_this.formatter.getWidth(), _this.formatter.getHeight()); + + + img.onload = function() { + canvas.parentNode.removeChild(canvas); + } + + this.NodeSVGbackgroundImage.setAttribute("xlink:href", document.getElementById("canvas").toDataURL()); + this.NodeSVGbackgroundImage.removeAttribute("href"); + + // + + };*/ + +GraphCanvas.prototype.setBackgroundImage = function() { + if (this.NodeSVGbackgroundImage != null) { + this.NodeSVGbackgroundImage.parentNode.removeChild(this.NodeSVGbackgroundImage); + } + $('#' + this.targetID).svg(); + $('#' + this.targetID).svg("get"); + + $('#' + this.targetID).svg("get")._svg = document.getElementById(this.id); + + var svg = $('#' + this.targetID).svg("get"); + this.NodeSVGbackgroundImage = svg.image(0, 0, this.getFormatter().getWidth(), this.getFormatter().getHeight(), this.getFormatter() + .getBackgroundImage()); + this.NodeSVGbackgroundImage.setAttribute("id", this.args.idBackgroundNode); + + this.NodeSVGbackgroundImage.setAttribute("x", 0); + this.NodeSVGbackgroundImage.setAttribute("y", 0); + + this.NodeSVGbackgroundImage.setAttribute("dragx", 0); + this.NodeSVGbackgroundImage.setAttribute("dragy", 0); + + if (this.getFormatter().args.backgroundImageHeight != null) { + this.NodeSVGbackgroundImage.setAttribute("height", this.getFormatter().args.backgroundImageHeight); + } + if (this.getFormatter().args.backgroundImageWidth != null) { + this.NodeSVGbackgroundImage.setAttribute("width", this.getFormatter().args.backgroundImageWidth); + } + + if (this.getFormatter().args.backgroundImageX != null) { + this.NodeSVGbackgroundImage.setAttribute("x", this.getFormatter().args.backgroundImageX); + } + if (this.getFormatter().args.backgroundImageY != null) { + this.NodeSVGbackgroundImage.setAttribute("y", this.getFormatter().args.backgroundImageY); + } + + this.GraphBackground.appendChild(this.NodeSVGbackgroundImage); + this.NodeSVGbackgroundImage.removeAttribute("href"); + this.NodeSVGbackgroundImage.setAttribute("xlink:href", this.getFormatter().getBackgroundImage()); +}; + +GraphCanvas.prototype.removeBackgroundImage = function() { + if (this.NodeSVGbackgroundImage != null) { + this.NodeSVGbackgroundImage.parentNode.removeChild(this.NodeSVGbackgroundImage); + } +}; + +GraphCanvas.prototype._setBackgroundColor = function(color) { + var attributes = [ [ "fill", color ] ]; + SVG.drawRectangle(0, 0, this.getFormatter().getWidth(), this.getFormatter().getHeight(), this.GraphBackground, attributes); +}; + +/** Serialize **/ +GraphCanvas.prototype.toJSON = function() { + var json = {}; + json.dataset = {}; + json.formatter = {}; + json.layout = {}; + json.dataset = this.getDataset().toJSON(); + json.formatter = this.getFormatter().toJSON(); + json.layout = this.getLayout().toJSON(); + return json; +}; + +GraphCanvas.prototype.toHTML = function() { + //this.backgroungToSVG(); + var html = this._svg.parentElement.innerHTML; + + var start = html.indexOf("") + 6; + + return html.substr(start, end); +}; + +/** DRAW **/ +GraphCanvas.prototype.draw = function(graphdataset, graphformatter, graphlayout) { + this.setDataset(graphdataset); + this.setFormatter(graphformatter); + this.setLayout(graphlayout); + + var _this = this; + this.getFormatter().changed.attach(function(sender, item) { + _this.removeNode(item.getId()); + _this.renderNode(item.getId()); + if (_this.args.labeled) { + _this.removeLabel(item.getId()); + _this.renderLabel(item.getId()); + } + + }); + //TODO + this.getFormatter().edgeChanged.attach(function(sender, item) { + _this.removeEdge(item.getId()); + _this.renderEdge(item.getId()); + }); + + this.getFormatter().resized.attach(function(sender, item) { + _this.resize(_this.getFormatter().getWidth(), _this.getFormatter().getHeight()); + }); + + this.getFormatter().backgroundImageChanged.attach(function(sender, item) { + _this.setBackgroundImage(_this.getFormatter().getBackgroundImage()); + }); + + this.getFormatter().backgroundColorChanged.attach(function(sender, item) { + _this._setBackgroundColor(_this.getFormatter().getBackgroundColor()); + }); + + this.getLayout().changed.attach(function(sender, item) { + _this.moveNode(item.getId()); + _this.moveEdge(item.getId()); + if (_this.args.labeled) { + _this.removeLabel(item.getId()); + _this.renderLabel(item.getId()); + } + }); + + this.getDataset().newVertex.attach(function(sender, item) { + + _this.renderNode(item.getId()); + if (_this.args.labeled) { + _this.renderLabel(item.getId()); + } + }); + + this.getDataset().newEdge.attach(function(sender, item) { + _this.renderEdge(item.getId()); + }); + + this.getDataset().vertexDeleted.attach(function(sender, item) { + _this.removeNode(item.getId()); + if (_this.args.labeled) { + _this.removeLabel(item.getId()); + } + }); + + this.getDataset().edgeDeleted.attach(function(sender, item) { + _this.removeEdge(item.getId()); + }); + + this.getDataset().vertexNameChanged.attach(function(sender, args) { + if (_this.args.labeled) { + _this.removeLabel(args.item.getId()); + _this.removeLabel(args.item.getId()); + _this.renderLabel(args.item.getId()); + } + }); + this.init(); + this.render(); +}; + +GraphCanvas.prototype.render = function() { + for ( var id in this.getDataset().getVertices()) { + this.renderNode(id); + } + this.renderLabels(); + this.renderEdges(); +}; + +GraphCanvas.prototype.renderLabels = function() { + if (this.args.labeled) { + for ( var id in this.getDataset().getVertices()) { + this.renderLabel(id); + } + } +}; + +GraphCanvas.prototype.removeLabels = function() { + for ( var id in this.getDataset().getVertices()) { + this.removeLabel(id); + } +}; + +/** Utilities method for nodes **/ +GraphCanvas.prototype.isNodeCanvas = function(node) { + return ((node.id == this.args.idGraph) || (node.id == this.id)); +}; + +GraphCanvas.prototype.isNodeBackground = function(node) { + return ((node.id == this.args.idBackgroundNode)); +}; + +GraphCanvas.prototype.isVertex = function(node) { + if (node.getAttribute("id") != null) { + if (node.getAttribute("id").indexOf("_v_") != -1) { + return true; + } + } + return false; +}; + +GraphCanvas.prototype.isLabel = function(node) { + if (node.getAttribute("id") != null) { + if (node.getAttribute("id").indexOf("_l_") != -1) { + return true; + } + } + return false; +}; + +GraphCanvas.prototype.isEdge = function(node) { + if (node.getAttribute("id") != null) { + if (node.getAttribute("id").indexOf("_e_") != -1) { + return true; + } + } + return false; +}; + +/** Resize **/ +GraphCanvas.prototype.resize = function(width, height) { + // this._svg.setAttribute("width", width); + // this._svg.setAttribute("height", height); + if (this.NodeSVGbackgroundImage != null) { + this.NodeSVGbackgroundImage.setAttribute("width", width); + this.NodeSVGbackgroundImage.setAttribute("height", height); + } + + this._svg.setAttribute("width", width); + this._svg.setAttribute("height", height); + + this.clearCanvas(); + this.render(); +}; + +GraphCanvas.prototype.clearCanvas = function() { + DOM.removeChilds(this.GraphEdgeGroup.getAttribute("id")); + DOM.removeChilds(this.GraphNodeGroup.getAttribute("id")); + this.clearLabels(); +}; + +GraphCanvas.prototype.clearLabels = function() { + DOM.removeChilds(this.GraphLabelGroup.getAttribute("id")); +}; + +/** ID'S converter **/ +GraphCanvas.prototype.getSVGNodeId = function(nodeId) { + return this.id + "_v_" + nodeId; +}; + +GraphCanvas.prototype.getSVGEdgeId = function(edgeId) { + return this.id + "_e_" + edgeId; +}; + +GraphCanvas.prototype.getSVGArrowEdgeId = function(edgeId) { + return this.id + "_arrow_" + edgeId; +}; + +GraphCanvas.prototype.getSVGLabelId = function(edgeId) { + return this.id + "_l_" + edgeId; +}; + +GraphCanvas.prototype.blinkVertexById = function(vertexId) { + $("#" + this.getSVGNodeId(vertexId)).fadeIn().fadeOut().fadeIn().fadeOut().fadeIn().fadeOut(); +}; + +GraphCanvas.prototype.getVertexIdFromSVGId = function(svgVertexId) { + return svgVertexId.replace(this.id, "").replace("_v_", ""); +}; + +GraphCanvas.prototype.getEdgeIdFromSVGId = function(svgEdgeId) { + return svgEdgeId.replace(this.id, "").replace("_e_", ""); +}; + +/** VERTEX **/ +GraphCanvas.prototype.getVertexById = function(id) { + return document.getElementById(this.getSVGNodeId(id)); +}; + +GraphCanvas.prototype.renderNodes = function() { + for ( var id in this.getDataset().getVertices()) { + this.renderNode(id); + } +}; + +GraphCanvas.prototype.overNode = function(nodeId) { + if (!this.args.interactive) { + return; + } + /** If selected we don't change the format **/ + if (this.args.isVertexSelected[nodeId] == null) { + var args = this.getFormatter().getVertexById(nodeId).getOver(); + args.args["cursor"] = 'pointer'; + this.changeVertexFormat(nodeId, args); + } +}; + +GraphCanvas.prototype.outNode = function(nodeId) { + if (!this.args.interactive) { + return; + } + + /** If selected we don't change the format **/ + if (this.args.isVertexSelected[nodeId] == null) { + this.changeVertexFormat(nodeId, this.getFormatter().getVertexById(nodeId).getDefault()); + } +}; + +GraphCanvas.prototype.overLabel = function(nodeId) { + this.overNode(nodeId); + // this.svgLabels[nodeId].setAttribute("cursor", "pointer"); +}; + +GraphCanvas.prototype.outLabel = function(nodeId) { + this.outNode(nodeId); + // this.svgLabels[nodeId].setAttribute("cursor", ""); +}; + +GraphCanvas.prototype.clickNode = function(nodeId) { + if (!this.args.interactive) { + return; + } + + /** si el evento se dispara oprque estaba dragging entonces no activo nada **/ + if (this.args.isVertexSelected[nodeId] == null) { + this.selectNode(nodeId); + } else { + this.deselectNode(nodeId); + } +}; + +GraphCanvas.prototype.selectNode = function(nodeId) { + for ( var i = 0; i < this.args.selectedVertices.length; i++) { + var format = this.getFormatter().getVertexById(nodeId).getSelected(); + format.opacity = 0.2; + this.changeVertexFormat(nodeId, this.getFormatter().getVertexById(nodeId).getSelected()); + } + + if (this.args.isVertexSelected[nodeId] == null) { + var format = this.getFormatter().getVertexById(nodeId).getSelected(); + format.opacity = 1; + this.changeVertexFormat(nodeId, this.getFormatter().getVertexById(nodeId).getSelected()); + this.args.selectedVertices.push(nodeId); + this.args.isVertexSelected[nodeId] = this.args.selectedVertices.length - 1; + this.onVertexSelect.notify(nodeId); + } +}; + +GraphCanvas.prototype.selectAllEdges = function() { + this.deselectNodes(); + this.deselectEdges(); + + for ( var edgesId in this.getDataset().edges) { + this.selectEdge(edgesId); + } +}; + +GraphCanvas.prototype.selectAllNodes = function() { + this.deselectNodes(); + this.deselectEdges(); + + for ( var vertexId in this.getDataset().vertices) { + this.selectNode(vertexId); + } +}; + +GraphCanvas.prototype.selectAll = function() { + this.deselectNodes(); + this.deselectEdges(); + + for ( var vertexId in this.getDataset().vertices) { + this.selectNode(vertexId); + } + + for ( var edgesId in this.getDataset().edges) { + this.selectEdge(edgesId); + } +}; + +GraphCanvas.prototype.selectEdge = function(edgeId) { + if (this.args.isEdgeSelected[edgeId] == null) { + this.changeEdgeFormat(edgeId, this.getFormatter().getEdgeById(edgeId).getSelected()); + //this.args.selectedEdges.push(edgeId); + this.args.isEdgeSelected[edgeId] = true; //this.args.selectedEdges.length - 1; + this.onEdgeSelect.notify(edgeId); + } +}; + +GraphCanvas.prototype.selectEdges = function(edges) { + + for ( var i = 0; i < edges.length; i++) { + this.selectEdge(edges[i]); + } +}; + +GraphCanvas.prototype.deselectNode = function(nodeId) { + if (this.args.isVertexSelected[nodeId] != null) { + this.changeVertexFormat(nodeId, this.getFormatter().getVertexById(nodeId).getDefault()); + this.args.selectedVertices.splice(this.args.isVertexSelected[nodeId], 1); + var index = this.args.isVertexSelected[nodeId]; + delete this.args.isVertexSelected[nodeId]; + + for ( var vertex in this.args.isVertexSelected) { + if (this.args.isVertexSelected[vertex] > index) { + this.args.isVertexSelected[vertex] = this.args.isVertexSelected[vertex] - 1; + } + } + } +}; + +GraphCanvas.prototype.deselectNodes = function() { + var selected = JSON.parse(JSON.stringify(this.getSelectedVertices())); + for ( var i = 0; i < selected.length; i++) { + this.deselectNode(selected[i]); + } +}; +GraphCanvas.prototype.selectNodes = function(idNodes) { + + for ( var i = 0; i < idNodes.length; i++) { + this.selectNode(idNodes[i]); + } + + // for ( var vertex in this.args.isVertexSelected) { + // if (this.args.isVertexSelected[vertex] > index){ + // this.args.isVertexSelected[vertex] = this.args.isVertexSelected[vertex] - 1; + // } + // } + +}; + +GraphCanvas.prototype.changeVertexFormat = function(nodeId, format) { + var svgNode = DOM.select(this.getSVGNodeId(nodeId)); + if (svgNode != null) { + var properties = format.toJSON(); + for ( var item in properties) { + svgNode.setAttribute(item, properties[item]); + } + + if (this.getFormatter().getVertexById(nodeId) instanceof CircleVertexGraphFormatter) { + var transform = "translate(" + svgNode.getAttribute("dragx") + "," + svgNode.getAttribute("dragy") + "), scale(" + format.getSize() + ")"; + svgNode.setAttribute("transform", transform); + } + } +}; + +GraphCanvas.prototype.renderLabel = function(nodeId) { + var x = Math.ceil(this.getLayout().getNodeById(nodeId).x * this.getFormatter().getWidth()); + var y = Math.ceil(this.getLayout().getNodeById(nodeId).y * this.getFormatter().getHeight()); + + var svgAttributesNode = JSON.parse(JSON.stringify(this.getFormatter().getVertexById(nodeId).getDefault().toJSON().title)); + svgAttributesNode.id = this.getSVGLabelId(this.getDataset().getVertexById(nodeId).getId()); + svgAttributesNode.dx = (-1) * (this.getDataset().getVertexById(nodeId).getName().length * svgAttributesNode["font-size"]) / 4 - 4; + + svgAttributesNode.dy = parseFloat((this.getFormatter().getVertexById(nodeId).getDefault().getSize())) + + parseFloat(svgAttributesNode["font-size"]) + parseFloat(this.getFormatter().getVertexById(nodeId).getDefault().getStrokeWidth()) - 4; + svgAttributesNode.dragx = Math.ceil(this.getLayout().getNodeById(nodeId).x * this.getFormatter().getWidth()); + + var gragy = parseFloat(this.getFormatter().getVertexById(nodeId).getDefault().getSize()) + + Math.ceil(this.getLayout().getNodeById(nodeId).y * this.getFormatter().getHeight()); + svgAttributesNode.dragy = gragy; + svgAttributesNode.transform = "translate(" + svgAttributesNode.dragx + "," + svgAttributesNode.dragy + ")";//, scale("+this.formatter.getVertexById(nodeId).getDefault().getSize()+")"; + + var nodeSVG = SVG.drawText(0, 0, this.getDataset().getVertexById(nodeId).getName(), this.GraphLabelGroup, svgAttributesNode); + + this.svgLabels[nodeId] = nodeSVG; + + /** Events for the SVG node **/ + var _this = this; + if (nodeSVG != null) { + nodeSVG.addEventListener("mouseover", function() { + _this.overLabel(nodeId); + }, false); + nodeSVG.addEventListener("mouseout", function() { + _this.outLabel(nodeId); + }, false); + } + +}; + +GraphCanvas.prototype.removeLabel = function(labelId) { + if (DOM.select(this.getSVGLabelId(labelId)) != null) { + DOM.select(this.getSVGLabelId(labelId)).parentNode.removeChild(DOM.select(this.getSVGLabelId(labelId))); + } +}; + +GraphCanvas.prototype.renderNode = function(nodeId) { + var svgAttributesNode = JSON.parse(JSON.stringify(this.getFormatter().getVertexById(nodeId).getDefault().toJSON())); + svgAttributesNode.dragx = Math.ceil(this.getLayout().getNodeById(nodeId).x * this.getFormatter().getWidth()); + svgAttributesNode.dragy = Math.ceil(this.getLayout().getNodeById(nodeId).y * this.getFormatter().getHeight()); + svgAttributesNode.transform = "translate(" + svgAttributesNode.dragx + "," + svgAttributesNode.dragy + ")"; + svgAttributesNode.id = this.getSVGNodeId(nodeId); + /*svgAttributesNode["stroke-width"] = 3 ; + svgAttributesNode["stroke-opacity"] = 1 ; + svgAttributesNode["fill-opacity"] = svgAttributesNode["opacity"] ; + svgAttributesNode["opacity"] = 1 ;*/ + this.circleDefaultRadius = this.getFormatter().getVertexById(nodeId).getDefault().getSize(); + var nodeSVG; + + if (this.getFormatter().getVertexById(nodeId) instanceof CircleVertexGraphFormatter) { + nodeSVG = SVG.drawCircle(0, 0, this.circleDefaultRadius, this.GraphNodeGroup, svgAttributesNode); + } + + if (this.getFormatter().getVertexById(nodeId) instanceof SquareVertexGraphFormatter) { + //nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius) ,0 - (this.formatter.getVertexById(nodeId).getDefault().getSize()) , (this.getFormatter().getVertexById(nodeId).getDefault().getSize()*2), (this.getFormatter().getVertexById(nodeId).getDefault().getSize()*2), this.GraphNodeGroup, svgAttributesNode); + nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius), 0 - (this.circleDefaultRadius), (this.circleDefaultRadius * 2), + (this.circleDefaultRadius * 2), this.GraphNodeGroup, svgAttributesNode); + } + + if (this.getFormatter().getVertexById(nodeId) instanceof EllipseVertexGraphFormatter) { + nodeSVG = SVG.drawEllipse(0, 0, this.circleDefaultRadius * 1.5, this.circleDefaultRadius, this.GraphNodeGroup, svgAttributesNode); + } + + if (this.getFormatter().getVertexById(nodeId) instanceof RectangleVertexGraphFormatter) { + //nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius) ,0 - ((this.circleDefaultRadius*2)/2) , (this.circleDefaultRadius*2), (this.circleDefaultRadius), this.GraphNodeGroup, svgAttributesNode); + nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius * 1.5), 0 - (this.circleDefaultRadius), (this.circleDefaultRadius * 2 * 1.5), + (this.circleDefaultRadius * 2), this.GraphNodeGroup, svgAttributesNode); + + } + + if (this.getFormatter().getVertexById(nodeId) instanceof RoundedVertexGraphFormatter) { + svgAttributesNode.ry = 2;// this.formatter.getVertexById(nodeId).getDefault().getSize()/4; + svgAttributesNode.rx = 2;// this.formatter.getVertexById(nodeId).getDefault().getSize()/4; + nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius * 1.5), 0 - (this.circleDefaultRadius), (this.circleDefaultRadius * 2 * 1.5), + (this.circleDefaultRadius * 2), this.GraphNodeGroup, svgAttributesNode); + } + + // + + if (this.getFormatter().getVertexById(nodeId) instanceof OctagonVertexGraphFormatter) { + svgAttributesNode.ry = 2; + svgAttributesNode.rx = 2; + nodeSVG = SVG.drawRectangle(0 - (this.circleDefaultRadius * 1.5), 0 - (this.circleDefaultRadius), (this.circleDefaultRadius * 2 * 1.5), + (this.circleDefaultRadius * 2), this.GraphNodeGroup, svgAttributesNode); + } + + nodeSVG.internalId = nodeId; + // + var _this = this; + + /** Events for the SVG node **/ + if (nodeSVG != null) { + nodeSVG.addEventListener("mouseover", function() { + _this.onVertexOver.notify(nodeId); + _this.overNode(nodeId); + }, false); + nodeSVG.addEventListener("mouseout", function() { + _this.onVertexOut.notify(nodeId); + _this.outNode(nodeId); + }, false); + //nodeSVG.addEventListener("click", function(){_this.clickNode(nodeId);}, false); + // + nodeSVG.addEventListener("mouseup", function() { + _this.onVertexUp.notify(nodeId); + }, false); + } +}; + +GraphCanvas.prototype.removeNode = function(nodeId) { + DOM.select(this.getSVGNodeId(nodeId)).parentNode.removeChild(DOM.select(this.getSVGNodeId(nodeId))); + if (this.args.labeled) { + this.removeLabel(nodeId); + } +}; + +/** REMOVING **/ +GraphCanvas.prototype.removeSelected = function() { + /** El orden importa **/ + this.removeSelectedEdges(); + this.removeSelectedNode(); + +}; + +GraphCanvas.prototype.removeSelectedNode = function() { + var selected = JSON.parse(JSON.stringify(this.getSelectedVertices())); + this.deselectNodes(); + var sorted = selected.sort(function(a, b) { + return a - b + }); + for ( var i = 0; i < sorted.length; i++) { + if (this.getDataset().getVertexById(sorted[i]) != null) { + this.getDataset().getVertexById(sorted[i]).remove(); + } + } +}; + +/** EDGES **/ +GraphCanvas.prototype.removeEdge = function(edgeId) { + if (DOM.select(this.getSVGEdgeId(edgeId)) != null) { + DOM.select(this.getSVGEdgeId(edgeId)).parentNode.removeChild(DOM.select(this.getSVGEdgeId(edgeId))); + } + + if (DOM.select(this.getSVGEdgeId(edgeId) + "_shadow") != null) { + DOM.select(this.getSVGEdgeId(edgeId) + "_shadow").parentNode.removeChild(DOM.select(this.getSVGEdgeId(edgeId) + "_shadow")); + } + + if (DOM.select(this.getSVGArrowEdgeId(edgeId)) != null) { + DOM.select(this.getSVGArrowEdgeId(edgeId)).parentNode.removeChild(DOM.select(this.getSVGArrowEdgeId(edgeId))); + } +}; + +GraphCanvas.prototype.overEdge = function(edgeId) { + if ((!this.args.interactive) || this.dragging || this.selecting) { + return; + } + + /** If selected we don't change the format **/ + if (this.args.isEdgeSelected[edgeId] == null) { + var format = this.getFormatter().getEdgeById(edgeId).getOver(); + format.args["cursor"] = "pointer"; + this.changeEdgeFormat(edgeId, format); + } +}; + +GraphCanvas.prototype.outEdge = function(edgeId) { + if (!this.args.interactive) { + return; + } + + /** If selected we don't change the format **/ + if (this.args.isEdgeSelected[edgeId] == null) { + this.changeEdgeFormat(edgeId, this.getFormatter().getEdgeById(edgeId).getDefault()); + } +}; + +GraphCanvas.prototype.changeEdgeFormat = function(edgeId, format) { + var svgEdge = DOM.select(this.getSVGEdgeId(edgeId) + "_shadow"); + if (svgEdge != null) { + var properties = format.toJSON(); + for ( var item in properties) { + svgEdge.setAttribute(item, properties[item]); + } + } +}; + +GraphCanvas.prototype.deselectEdge = function(edgeID) { + if (this.args.isEdgeSelected[edgeID] != null) { + this.changeEdgeFormat(edgeID, this.getFormatter().getEdgeById(edgeID).getDefault()); + var index = this.args.isEdgeSelected[edgeID]; + delete this.args.isEdgeSelected[edgeID]; + } +}; + +GraphCanvas.prototype.deselectEdges = function() { + var selected = JSON.parse(JSON.stringify(this.getSelectedEdges())); + for ( var i = 0; i < selected.length; i++) { + this.deselectEdge(selected[i]); + } +}; + +GraphCanvas.prototype.removeSelectedEdges = function() { + var selected = JSON.parse(JSON.stringify(this.getSelectedEdges())); + this.deselectEdges(); + for ( var i = 0; i < selected.length; i++) { + if (this.getDataset().getEdgeById(selected[i]) != null) { + this.getDataset().getEdgeById(selected[i]).remove(); + } + } +}; + +GraphCanvas.prototype.renderEdge = function(edgeId) { + var svgAttributesEdge = this.getFormatter().getEdgeById(edgeId).getDefault().toJSON(); + var edge = this.getDataset().getEdgeById(edgeId); + + var svgNodeTarget = this.getVertexById(edge.getNodeTarget().getId()); + var svgNodeSource = this.getVertexById(edge.getNodeSource().getId()); + svgAttributesEdge.id = this.getSVGEdgeId(edge.getId()) + "_shadow"; + + var svgEdge = null; + + if (this.getFormatter().getEdgeById(edgeId) instanceof LineEdgeGraphFormatter) { + var coordenateSourceX = svgNodeSource.getAttribute("dragx"); + var coordenateSourceY = svgNodeSource.getAttribute("dragy"); + var coordenateTargetX = svgNodeTarget.getAttribute("dragx"); + var coordenateTargetY = svgNodeTarget.getAttribute("dragy"); + + SVG.drawLine(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, this.GraphEdgeGroup, svgAttributesEdge); + var attributesShadow = {}; + attributesShadow.id = this.getSVGEdgeId(edge.getId()); + attributesShadow["stroke-opacity"] = 0; + attributesShadow["stroke-width"] = 4; + attributesShadow["stroke"] = "black"; + svgEdge = SVG.drawLine(svgNodeSource.getAttribute("dragx"), svgNodeSource.getAttribute("dragy"), svgNodeTarget.getAttribute("dragx"), + svgNodeTarget.getAttribute("dragy"), this.GraphEdgeGroup, attributesShadow); + } + + if (this.getFormatter().getEdgeById(edgeId) instanceof BezierEdgeGraphFormatter) { + var nodeId = edge.getNodeTarget().getId(); + var nodeSize = this.formatter.getVertexById(nodeId).getDefault().getSize() * this.getFormatter().getNodesMaxSize(); + svgAttributesEdge.fill = "none"; + svgAttributesEdge.id = this.getSVGEdgeId(edgeId); + var d = this.calculateCoordenatesBezier(nodeSize, svgNodeSource.getAttribute("dragx"), svgNodeSource.getAttribute("dragy")); + svgEdge = SVG.drawPath(d, this.GraphEdgeGroup, svgAttributesEdge); + } + ; + + if ((this.getFormatter().getEdgeById(edgeId) instanceof DirectedLineEdgeGraphFormatter) + || (this.getFormatter().getEdgeById(edgeId) instanceof CutDirectedLineEdgeGraphFormatter) + || (this.getFormatter().getEdgeById(edgeId) instanceof DotDirectedLineEdgeGraphFormatter) + || (this.getFormatter().getEdgeById(edgeId) instanceof OdotDirectedLineEdgeGraphFormatter) + || (this.getFormatter().getEdgeById(edgeId) instanceof OdirectedLineEdgeGraphFormatter)) { + var coordenateSourceX = svgNodeSource.getAttribute("dragx"); + var coordenateSourceY = svgNodeSource.getAttribute("dragy"); + var coordenateTargetX = svgNodeTarget.getAttribute("dragx"); + var coordenateTargetY = svgNodeTarget.getAttribute("dragy"); + + var offset = parseFloat(this.getFormatter().getVertexById(this.getDataset().getEdgeById(edgeId).getNodeTarget().getId()).getDefault() + .getSize() + * this.circleDefaultRadius); + var point = this._calculateEdgePointerPosition(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, offset); + coordenateTargetX = point.x; + coordenateTargetY = point.y; + SVG.drawLine(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, this.GraphEdgeGroup, svgAttributesEdge); + + var attributesShadow = {}; + attributesShadow.id = this.getSVGEdgeId(edge.getId()); + attributesShadow["stroke-opacity"] = 0; + attributesShadow["stroke-width"] = 4; + attributesShadow["stroke"] = "black"; + svgEdge = SVG.drawLine(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, this.GraphEdgeGroup, attributesShadow); + } + + if (this.getFormatter().getEdgeById(edgeId) instanceof DirectedLineEdgeGraphFormatter + || (this.getFormatter().getEdgeById(edgeId) instanceof OdirectedLineEdgeGraphFormatter)) { + var coordenateSourceX = svgNodeSource.getAttribute("dragx"); + var coordenateSourceY = svgNodeSource.getAttribute("dragy"); + var coordenateTargetX = svgNodeTarget.getAttribute("dragx"); + var coordenateTargetY = svgNodeTarget.getAttribute("dragy"); + + var point = this._calculateEdgePointerPosition(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, offset); + coordenateTargetX = point.x; + coordenateTargetY = point.y; + + var angle = Geometry.toDegree(point.angle) + 90; + this.arrowDefaultSize = this.getFormatter().getEdgeById(edgeId).getArrowSize(); //getDefault().getArrowSize(); + var d = "-" + this.arrowDefaultSize + ",0 0,-" + parseFloat(this.arrowDefaultSize) * 2 + " " + this.arrowDefaultSize + ",0"; + + var attributes; + + if (this.getFormatter().getEdgeById(edgeId) instanceof DirectedLineEdgeGraphFormatter) { + attributes = [ + [ "fill", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], + [ "stroke", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], [ "id", this.getSVGArrowEdgeId(edgeId) ] ]; + } else { + attributes = [ + [ "fill", "#FFFFFF" ], [ "stroke", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], + [ "id", this.getSVGArrowEdgeId(edgeId) ] ]; + } + + var flechaSVGNode = SVG.drawPoligon(d, this.GraphEdgeGroup, attributes);//, ["transform", "rotate("+angle+"), translate(0,0)"]]); + flechaSVGNode.setAttribute("transform", " translate(" + coordenateTargetX + ", " + coordenateTargetY + "), rotate(" + angle + ")"); + } + ; + + if (this.getFormatter().getEdgeById(edgeId) instanceof CutDirectedLineEdgeGraphFormatter) { + var coordenateSourceX = svgNodeSource.getAttribute("dragx"); + var coordenateSourceY = svgNodeSource.getAttribute("dragy"); + var coordenateTargetX = svgNodeTarget.getAttribute("dragx"); + var coordenateTargetY = svgNodeTarget.getAttribute("dragy"); + + var point = this._calculateEdgePointerPosition(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, offset); + coordenateTargetX = point.x; + coordenateTargetY = point.y; + + var angle = Geometry.toDegree(point.angle) + 90; + + //this.arrowDefaultSize = 2; //getDefault().getArrowSize(); + var d = "-4,0 4,0 4,-2 -4,-2"; + + var flechaSVGNode = SVG.drawPoligon(d, this.GraphEdgeGroup, [ + [ "fill", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], + [ "stroke", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], [ "id", this.getSVGArrowEdgeId(edgeId) ] ]);//, ["transform", "rotate("+angle+"), translate(0,0)"]]); + flechaSVGNode.setAttribute("transform", " translate(" + coordenateTargetX + ", " + coordenateTargetY + "), rotate(" + angle + ")"); + } + ; + + if ((this.getFormatter().getEdgeById(edgeId) instanceof DotDirectedLineEdgeGraphFormatter) + || (this.getFormatter().getEdgeById(edgeId) instanceof OdotDirectedLineEdgeGraphFormatter)) { + var coordenateSourceX = svgNodeSource.getAttribute("dragx"); + var coordenateSourceY = svgNodeSource.getAttribute("dragy"); + var coordenateTargetX = svgNodeTarget.getAttribute("dragx"); + var coordenateTargetY = svgNodeTarget.getAttribute("dragy"); + var point = this._calculateEdgePointerPosition(coordenateSourceX, coordenateSourceY, coordenateTargetX, coordenateTargetY, offset); + coordenateTargetX = point.x; + coordenateTargetY = point.y; + var angle = Geometry.toDegree(point.angle) + 90; + // this.arrowDefaultSize = this.formatter.getEdgeById(edgeId).getArrowSize(); //getDefault().getArrowSize(); + var attributes = []; + if (this.getFormatter().getEdgeById(edgeId) instanceof OdotDirectedLineEdgeGraphFormatter) { + attributes = [ + [ "fill", "#FFFFFF" ], [ "stroke", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], + [ "id", this.getSVGArrowEdgeId(edgeId) ] ]; + } else { + attributes = [ + [ "fill", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], + [ "stroke", this.getFormatter().getEdgeById(edgeId).getDefault().getStroke() ], [ "id", this.getSVGArrowEdgeId(edgeId) ] ]; + } + var flechaSVGNode = SVG.drawCircle(0, 0, 4, this.GraphEdgeGroup, attributes); + flechaSVGNode.setAttribute("transform", " translate(" + coordenateTargetX + ", " + coordenateTargetY + "), rotate(" + angle + ")"); + } + ; + + var _this = this; + /** Events for the SVG edge **/ + if (svgEdge != null) { + if (this.getDataset().getEdgesCount() < this.args.maxNumberEdgesFiringEvents) { + svgEdge.addEventListener("mouseover", function() { + _this.overEdge(edgeId); + }, false); + svgEdge.addEventListener("mouseout", function() { + _this.outEdge(edgeId); + }, false); + } + } +}; + +GraphCanvas.prototype._calculateEdgePointerPosition = function(sourceX, sourceY, targetX, targetY, radius) { + var angle = Geometry.getAngleBetweenTwoPoints(sourceX, sourceY, targetX, targetY); + + /** Suponiendo el node source que este a la derecha **/ + if ((targetX - sourceX) < 0) { + var b = Geometry.getAdjacentSideOfRectangleRight(angle, radius); + targetX = parseFloat(targetX) + parseFloat(b); + arrowX = parseFloat(targetX) + parseFloat(b) + this.arrowDefaultSize / 2; + } else { + var b = Geometry.getAdjacentSideOfRectangleRight(angle, radius); + targetX = parseFloat(targetX) - parseFloat(b); + arrowX = parseFloat(targetX) - parseFloat(b) - this.arrowDefaultSize / 2; + } + + /** Suponiendo el node source que este a la arriba **/ + if ((targetY - sourceY) > 0) { + var a = Geometry.getOppositeSideOfRectangleRight(angle, radius); + targetY = parseFloat(targetY) - parseFloat(a); + arrowY = parseFloat(targetY) - parseFloat(a) - this.arrowDefaultSize / 2; + } else { + var a = Geometry.getOppositeSideOfRectangleRight(angle, radius); + targetY = parseFloat(targetY) + parseFloat(a); + arrowY = parseFloat(targetY) + parseFloat(a) - this.arrowDefaultSize / 2; + + } + + return { + "x" : arrowX, + "y" : arrowY, + "angle" : angle + }; +}; + +GraphCanvas.prototype.calculateCoordenatesBezier = function(nodeSize, x1, y1) { + var x11 = x1 - (nodeSize / 2); + var y11 = y1 - (nodeSize / 2); + + var x12 = parseFloat(x1) + parseFloat(nodeSize / 2); + var y12 = y1 - (nodeSize / 2); + + var curvePointX = (x12 - x11) / 2 + x11; + var curvePointY = y1 - (nodeSize * 2); + var d = "M" + x11 + "," + y11 + " T" + curvePointX + "," + curvePointY + " " + x12 + "," + y12; + return d; + +}; + +GraphCanvas.prototype.renderEdges = function() { + for ( var edge in this.getDataset().getEdges()) { + this.renderEdge(this.getDataset().getEdgeById(edge).getId()); + + } +}; + +GraphCanvas.prototype.getLastSelectedNode = function() { + var node = null; + if (this.getSelectedVertices().length > 0) { + var nodeId = this.getSelectedVertices()[this.getSelectedVertices().length - 1]; + node = this.getDataset().getVertexById(nodeId); + } + return node; +}; +/* + GraphCanvas.prototype.getNodeByNameAndIndex = function(node, index){ + var nodeId = this.getDataset().verticesIndex[node][index]; + var nodeItem = this.getDataset().getVertexById(nodeId); + return nodeItem; + }; + */ + +GraphCanvas.prototype.setDataset = function(dataset) { + this.dataset = dataset; +}; + +GraphCanvas.prototype.setFormatter = function(formatter) { + this.formatter = formatter; +}; + +GraphCanvas.prototype.setLayout = function(layout) { + this.layout = layout; +}; + +/** API **/ +GraphCanvas.prototype.getDataset = function() { + return this.dataset; +}; + +GraphCanvas.prototype.getFormatter = function() { + return this.formatter; +}; + +GraphCanvas.prototype.getLayout = function() { + return this.layout; +}; + +/** API DATASET **/ +GraphCanvas.prototype.addVertex = function(name, args) { + this.getDataset().addNode(name, args); +}; + +GraphCanvas.prototype.removeVertex = function(vertexId) { + this.getDataset().getVertexById(vertexId).remove(); +}; + +GraphCanvas.prototype.addEdge = function(edgeName, nodeSourceId, nodeTargetId, args) { + this.getDataset().addEdge(edgeName, nodeSourceId, nodeTargetId, args); +}; +/* + GraphCanvas.prototype.removeEdge = function(edgeId){ + this.getDataset().getEdgeById(edgeId).remove(); + }; + */ + +/** API FORMATTER **/ +GraphCanvas.prototype.getWidth = function() { + return this.getFormatter().getWidth(); +}; + +GraphCanvas.prototype.getHeight = function() { + return this.getFormatter().getHeight(); +}; + +GraphCanvas.prototype.getBackgroundImage = function() { + return this.getFormatter().getBackgroundImage(); +}; + +//GraphCanvas.prototype.setBackgroundImage = function(value){ +// this.getFormatter().setBackgroundImage(value); +//}; + +GraphCanvas.prototype.getBackgroundColor = function() { + return this.getFormatter().getBackgroundColor(); +}; + +GraphCanvas.prototype.setBackgroundColor = function() { + this.getFormatter().setBackgroundColor(value); +}; + +//GraphCanvas.prototype.setEdgeFill = function(edgeId, value){ +// this.getFormatter().getEdgeById(edgeId).getDefault().setFill(value); +//}; +// +//GraphCanvas.prototype.getEdgeFill = function(edgeId){ +// return this.getFormatter().getEdgeById(edgeId).getDefault().getFill(); +//}; + +/** VERTICES FORMATTER **/ +GraphCanvas.prototype.setVertexSize = function(vertexId, value) { + this.getFormatter().getVertexById(vertexId).getDefault().setSize(value); +}; + +GraphCanvas.prototype.getVertexSize = function(vertexId) { + return this.getFormatter().getVertexById(vertexId).getDefault().getSize(); +}; + +GraphCanvas.prototype.setVertexStroke = function(vertexId, value) { + this.getFormatter().getVertexById(vertexId).getDefault().setStroke(value); +}; + +GraphCanvas.prototype.getVertexStroke = function(vertexId) { + return this.getFormatter().getVertexById(vertexId).getDefault().getStroke(); +}; + +GraphCanvas.prototype.setVertexStrokeOpacity = function(vertexId, value) { + this.getFormatter().getVertexById(vertexId).getDefault().setStrokeOpacity(value); +}; + +GraphCanvas.prototype.getVertexStrokeOpacity = function(vertexId) { + return this.getFormatter().getVertexById(vertexId).getDefault().getStrokeOpacity(); +}; + +GraphCanvas.prototype.setVertexOpacity = function(vertexId, value) { + this.getFormatter().getVertexById(vertexId).getDefault().setOpacity(value); +}; + +GraphCanvas.prototype.getVertexOpacity = function(vertexId) { + return this.getFormatter().getVertexById(vertexId).getDefault().getOpacity(); +}; + +GraphCanvas.prototype.setVertexFill = function(vertexId, color) { + this.getFormatter().getVertexById(vertexId).getDefault().setFill(color); +}; + +GraphCanvas.prototype.getVertexFill = function(vertexId) { + return this.getFormatter().getVertexById(vertexId).getDefault().getFill(); +}; + +/** EDGES FORMATTER **/ +GraphCanvas.prototype.setEdgeSize = function(edgeId, value) { + this.getFormatter().getEdgeById(edgeId).getDefault().setSize(value); +}; + +GraphCanvas.prototype.getEdgeSize = function(edgeId) { + return this.getFormatter().getEdgeById(edgeId).getDefault().getSize(); +}; + +GraphCanvas.prototype.setEdgeStroke = function(edgeId, value) { + this.getFormatter().getEdgeById(edgeId).getDefault().setStroke(value); +}; + +GraphCanvas.prototype.getEdgeStroke = function(edgeId) { + return this.getFormatter().getEdgeById(edgeId).getDefault().getStroke(); +}; + +GraphCanvas.prototype.setEdgeStrokeOpacity = function(edgeId, value) { + this.getFormatter().getEdgeById(edgeId).getDefault().setStrokeOpacity(value); +}; + +GraphCanvas.prototype.getEdgeStrokeOpacity = function(edgeId) { + return this.getFormatter().getEdgeById(edgeId).getDefault().getStrokeOpacity(); +}; + +GraphCanvas.prototype.setEdgeFill = function(edgeId, color) { + this.getFormatter().getEdgeById(edgeId).getDefault().setFill(color); +}; + +GraphCanvas.prototype.getEdgeFill = function(edgeId) { + return this.getFormatter().getEdgeById(edgeId).getDefault().getFill(); +}; + +/** API LAYOUT **/ +GraphCanvas.prototype.setCoordinates = function(vertexId, x, y) { + return this.getLayout().getEdgeById(vertexId).setCoordinates(x, y); +}; + + + +function HPLCGraph(args) { + this.width = 600; + this.height = 600; + this.title = ''; + this.bbar = false; + this.plotInnerPanelPadding = 10; + this.plotPanelPadding = 5; + this.id = BUI.id(); - if (record.raw.measurementId != null) { - /** For testing * */ - grid.setLoading("ISPyB: Removing measurement"); - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - grid.setLoading(false); - /** - * We get and refresh experiment - * because specimens has changed * - */ - var adapter2 = new BiosaxsDataAdapter(); - adapter2.onSuccess.attach(function(sender, experiment) { - _this.onRemoved.notify(experiment); - _this._showStatusBarReady('Ready'); - }); - if (_this.experiments.experiments[0].experimentId != null) { - adapter2.getExperimentById(_this.experiments.experiments[0].experimentId, "MEDIUM"); - _this._showStatusBarBusy("ISPyB: Removing Unused Specimens"); - } - }); + this.hidePlots = null; + this.xlabel = ""; + this.scaled = false; + this.xParam = null; + this.showRangeSelector = true; + this.interactionModel = null; + + /** for each stat the max and minimum value when it is scaled in order to show correctly in the legend **/ + this.ranges = {}; + if (args != null) { + if (args.interactionModel != null) { + this.interactionModel = args.interactionModel; + } + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + if (args.bbar != null) { + this.bbar = args.bbar; + } + if (args.title != null) { + this.title = args.title; + } + if (args.plots != null) { + this.plots = args.plots; + } + + if (args.scaled != null) { + this.scaled = args.scaled; + } + if (args.xlabel != null) { + this.xlabel = args.xlabel; + } + if (args.xParam != null) { + this.xParam = args.xParam; + } + if (args.showRangeSelector != null) { + this.showRangeSelector = args.showRangeSelector; + } + } + + this.onZoomX = new Event(this); + this.onResetZoom = new Event(this); + this.dblclick = new Event(this); +} + +HPLCGraph.prototype.getMenu = function () { + var _this = this; + /** Actions buttons **/ + var actions = []; + + function toggle(item, pressed) { + if (pressed) { + _this.plots[item.param] = true; + } else { + delete _this.plots[item.param]; + } + _this.reloadData(this.hplcData); + } + + for (var i = 0; i < this.hplcData.length; i++) { + if (this.hplcData[i].showOnMenu != false) { + var param = this.hplcData[i].param; + var style = "style='padding:0 0px 0 5px;'"; + actions.push({ + text : "
" + BUI.getRectangleColorDIV(this.hplcData[i].color, 10, 10) + " " + this.hplcData[i].label + "
", + id : _this.id + param, + param : param, + enableToggle : true, + scope : this, + toggleHandler : toggle, + pressed : (_this.plots[param] != null) + }); + } + } + actions.push("-"); + + actions.push({ + text : "Scale", + enableToggle : true, + scope : this, + pressed : this.scaled, + icon : '../images/icon_graph.png', + toggleHandler : function (item, pressed) { + _this.scaled = pressed; + _this.reloadData(this.hplcData); + } + }); + + actions.push("->"); + actions.push({ + text : "Save", + scope : this, + icon : '../images/save.gif', + handler : function (item, pressed) { + var largeImage = document.createElement("img"); + largeImage.style.display = 'block'; + largeImage.style.width = 200 + "px"; + largeImage.style.height = 200 + "px"; + largeImage.setAttribute('src', Dygraph.Export.asCanvas(this.dygraphObject.dygraph).toDataURL()); + window.open(Dygraph.Export.asCanvas(this.dygraphObject.dygraph).toDataURL(), 'Image', ''); + } + }); + + return actions; +}; - adapter.onError.attach(function(sender, data) { - alert("Error: " + data); - grid.setLoading(false); - }); +/** Looks for the maximum value and then divide everything but that value **/ +HPLCGraph.prototype.scaledData = function (data) { + for (var i = 0; i < data.length; i++) { + var values = this.getMaxAndMinValue(data[i]); + data[i] = this.divideValuesByMax(data[i], values.max); + this.ranges[data[i].label] = values; + } + return data; +}; - adapter.removeMeasurement(record.raw); - } - } - } +/** Given a stat float[] and a max number it will divide each value by max **/ +HPLCGraph.prototype.divideValuesByMax = function (stat, max) { + for (var j = 0; j < stat.data.length; j++) { + if (max != 0) { + stat.data[j] = Number(stat.data[j]) / max; + stat.std[j] = Number(stat.std[j]) / max; + } + } + return stat; +}; - } - } - }); +/** returns max value of a stat **/ +HPLCGraph.prototype.getMaxAndMinValue = function (stat) { + var max = 0; + var min = stat.data[0]; + for (var j = 0; j < stat.data.length; j++) { + if (Number(stat.data[j]) > max) { + max = Number(stat.data[j]); + } + if (Number(stat.std[j]) > max) { + max = Number(stat.std[j]); + } + if (Number(stat.data[j]) < min) { + min = Number(stat.data[j]); + } + } + return { + max : Number(max), + min : Number(min) + }; +}; - this.grid.on("afterrender", function() { +HPLCGraph.prototype.getPoint = function (data, i) { + var point = [ 10, 10, 10 ]; + var y = parseFloat(data.data[i]); + var error = parseFloat(data.std[i]); + if (data.fdata == null) { + return [ y - error, y, y + error ]; + } else { + if (data.fstd != null) { + return [ data.fstd(y - error), data.fdata(y), data.fstd(y + error) ]; + } + return [ data.fdata(y) - error, data.fdata(y), data.fdata(y) + error ]; + } + return point; +}; - function updateTime() { - try { - _this.estimatedTime = _this.estimatedTime - 1; +HPLCGraph.prototype.reloadData = function(hplcData) { + this.panel.setLoading(false); + this.hplcData = hplcData; - _this.onUpdateTime.notify({ - hours : (Number(_this.estimatedTime / 3600).toFixed()), - minutes : (Number((_this.estimatedTime / 60) % 60).toFixed()), - seconds : (Number(_this.estimatedTime % 60).toFixed()) + var data = hplcData; + - }); + /** In case of having peaks **/ + if (this.peaks != null) { + for (var peak in this.peaks) { + var values = []; + var std = []; + for (var i = 0; i < this.peaks[peak].length; i++) { + values.push(this.peaks[peak][i][1]); + std.push(this.peaks[peak][i][2]); + } + data.push({ + param : peak, + data : values, + showOnMenu : false, + fdata : function (a) { + var value = (Math.log(parseFloat(a))); + if (isNumber(value)) { + return value; + } + }, + fstd : function (a) { + var value = Math.log(Math.abs(parseFloat(a))); + if (isNumber(value)) + return value; + }, + std : std, + color : this.colorPeak[peak], + label : peak + }); + + } + } + + + if (this.scaled) { + data = this.scaledData(JSON.parse(JSON.stringify(hplcData))); + } - if (Number(_this.estimatedTime) < 0) { - _this.timer = null; - grid.setTitle(_this.title); + var paramIndex = {}; + var parsed = []; + var j = 0; + for (var i = 0; i < data[0].data.length - 1; i++) { + var aux = []; + for (j = 0; j < data.length; j++) { + if (this.plots != null) { + if (this.plots[data[j].param] != null) { + aux.push(this.getPoint(data[j], i)); + paramIndex[data[j].param] = aux.length - 1; } + } else { + aux.push([ data[j].data[i] - data[j].std[i], data[j].data[i], data[j].data[i] + data[j].std[i] ]); + } + } + parsed.push([]); - } catch (e) { - console.log(e); - _this.timer = null; + var index = i; + if (this.xParam != null) { + index = parseFloat(data[this.xParam].data[i]); + } + + parsed[parsed.length - 1].push(index); + + for (j = 0; j < data.length; j++) { + if (this.plots != null) { + if (this.plots[data[j].param] != null) { + parsed[parsed.length - 1].push(aux[paramIndex[data[j].param]]); + } + } else { + parsed[parsed.length - 1].push(aux[j]); } } + } - if (_this.estimateTime) { - var experimentList = _this.experiments; - var collected = experimentList.getMeasurementsCollected(); - if (collected.length > 0) { - if (collected[0].run3VO != null) { - try { - var end = collected[0].run3VO.timeEnd; - var start = collected[0].run3VO.timeStart; - var dstart = moment(start); - var dend = moment(end); - var seconds = Number(dend.diff(dstart) / 1000).toFixed(); + var colors = []; + var labels = [ "" ]; + for (j = 0; j < data.length; j++) { + if (this.plots != null) { + if (this.plots[data[j].param] != null) { + colors.push(data[j].color); + labels.push(data[j].label); + } + } else { + parsed[parsed.length - 1].push(aux[j]); + } + } - _this.estimatedTime = (seconds * experimentList.getMeasurementsNotCollected().length); + this._renderDygraph(parsed, colors, labels); +}; - if (_this.estimatedTime > 0) { - updateTime(); - _this.timer = setInterval(function() { - updateTime(); - }, 1000); +HPLCGraph.prototype._renderDygraph = function (parsed, colors, labels) { + this.dygraphObject = new StdDevDyGraph(this.id, { + width : this.width, + height : this.height - 10, + xlabel : this.xlabel, + showRangeSelector : this.showRangeSelector, + interactionModel : this.interactionModel, + scaled : this.scaled, + ranges : this.ranges + }); + this.dygraphObject.draw(parsed, colors, labels); + + var _this = this; + this.dygraphObject.onZoomX.attach(function (sender, args) { + try { + _this.onZoomX.notify(args); + } catch (e) { + } + }); + + this.dygraphObject.onResetZoom.attach(function (sender, args) { + try { + _this.onResetZoom.notify(args); + } catch (e) { + } + }); + + this.dygraphObject.dblclick.attach(function (sender, args) { + try { + _this.dblclick.notify(args); + } catch (e) { + } + }); + +}; + +HPLCGraph.prototype.loadData = function (data) { + var _this = this; + this.reloadData(data); + this.panel.addDocked({ + xtype : 'toolbar', + items : this.getMenu() + }); + + + if (this.bbar == true){ + this.panel.addDocked({ + xtype : 'toolbar', + dock: 'bottom', + items : [ + { + xtype: 'numberfield', + id: 'main_field_start', + fieldLabel: 'Range from', + width: 170, + labelWidth : 70, + value: 0, + minValue: 0 + }, + { + xtype: 'numberfield', + id: 'main_field_end', + fieldLabel: 'to', + width: 130, + labelWidth : 30, + value: 0, + minValue: 0 + }, + { + xtype: 'button', + text: 'Go', + handler: function () { + var start = parseFloat(Ext.getCmp("main_field_start").getValue()); + var end = parseFloat(Ext.getCmp("main_field_end").getValue()); + + if (start < 0) { + start = 0; + } + if (end < 0) { + end = 0; + } + if (start > end) { + var aux = end; + end = start; + start = aux; + } + + _this.dygraphObject.dygraph.updateOptions({ isZoomedIgnoreProgrammaticZoom: true, dateWindow: [start, end] }); + } } + ] + }); + } +}; - } catch (e) { - } - } - } - } +HPLCGraph.prototype.getPanel = function () { + this.panel = Ext.create('Ext.panel.Panel', { + padding : this.plotPanelPadding, + width : this.width + 4 * this.plotInnerPanelPadding, + height : this.height + 4 * this.plotInnerPanelPadding, + items : [ { + html : "", + id : this.id, + width : this.width, + height : this.height + } ] }); - return this.grid; + return this.panel; }; -/** Method for testing * */ -MeasurementGrid.prototype.input = function() { - var experiment = DATADOC.getExperiment_10(); - var measurements = DATADOC.getMeasurements_10(); - var proposal = DATADOC.getProposal_10(); - return { - experiment : experiment, - measurements : measurements, - proposal : proposal - }; +HPLCGraph.prototype.input = function () { + return DATADOC.getHPLCData(); }; -MeasurementGrid.prototype.test = function(targetId) { - var measurementGrid = new MeasurementGrid({ - tbar : true - - }); - BIOSAXS.proposal = new Proposal(measurementGrid.input().proposal); - var panel = measurementGrid.getPanel(measurementGrid.input().measurements, new ExperimentList([ new Experiment(measurementGrid.input().experiment) ])); - panel.render(targetId); +HPLCGraph.prototype.getDataByFrameNumber = function (frameNumber) { + var data = {}; + data.frameNumber = frameNumber; + for (var key in this.hplcData){ + data[this.hplcData[key].label] = this.hplcData[key].data[frameNumber]; + } + console.log(data); + return data; }; - -/** - * A shipment may contains one or more cases where stock solutions and sample - * plates are stored - * - * @height - * @btnEditVisible - * @btnRemoveVisible - * - * #onEditButtonClicked - */ -function MolarityGrid(args) { - this.height = 100; - this.width = 100; - if (args != null) { - if (args.height != null) { - this.height = args.height; - } - if (args.width != null) { - this.width = args.width; + +HPLCGraph.prototype.test = function (targetId) { + var mainPlotPanel = new HPLCGraph({ + title : 'I0', + width : 800, + height : 400, + plots : { + "I0" : true, + "Rg" : true, + "Mass" : true + }, + xlabel : "HPLC Frames", + scaled : this.scaled, + interactionModel : { + 'dblclick' : function (event, g, context) { + } } - } + }); + mainPlotPanel.getPanel().render(targetId); + mainPlotPanel.loadData(mainPlotPanel.input()); - var _this = this; - - this.molarityForm = new MolarityForm({height : 180, width : 455}); +}; - this.molarityForm.onSave.attach(function(sender){ - _this.molarityWindow.destroy(); - _this.updateProposal(); - - }); - - this.molarityForm.onClose.attach(function(sender){ - _this.molarityWindow.destroy(); - - }); + +function MergesHPLCGraph(args) { + HPLCGraph.prototype.constructor.call(this, args); - /** Events * */ - this.onEditButtonClicked = new Event(this); +// this.peakColors = ["#00FB42", "#00BA31", "#007C21", "#003E10"]; + this.peakColors = ["#DEBD00", "#6D9100", "#872900", "#0092CC"]; } -MolarityGrid.prototype._getColumns = function() { - return [ { - text : 'Subunit', - columns : [ { - text : "Acronym", - width : 100, - hidden : false, - dataIndex : 'acronym', - sortable : true - }, { - text : "Name", - width : 125, - hidden : false, - dataIndex : 'name', - sortable : true - }, { - text : "MM Est.", - width : 100, - dataIndex : 'molecularMass', - sortable : true, - renderer : function(grid, cls, record){ - return BUI.formatValuesUnits(record.data.molecularMass , "Da", 10, 2); - - } - } ] - }, { -// text : "Number
in assymmetric units", - text : "Ratio", - width : 100, - dataIndex : 'ratio', - tooltip : 'Number of times the subunit is present in the macromolecule', - sortable : true - }, { - id : this.id + 'MOLARITY_REMOVE', - flex : 0.1, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - return BUI.getRedButton('REMOVE'); - } - } ]; -}; -MolarityGrid.prototype._openMolarityWindow = function() { - this.molarityWindow = Ext.create('Ext.window.Window', { - title : 'Molarity', - height : 220, - width : 500, - modal : true, - items : [this.molarityForm.getPanel() ] - }).show(); -}; +MergesHPLCGraph.prototype.scaledData = HPLCGraph.prototype.scaledData; +MergesHPLCGraph.prototype.divideValuesByMax = HPLCGraph.prototype.divideValuesByMax; +MergesHPLCGraph.prototype.getMaxAndMinValue = HPLCGraph.prototype.getMaxAndMinValue; +MergesHPLCGraph.prototype.getPoint = HPLCGraph.prototype.getPoint; +MergesHPLCGraph.prototype.reloadData = HPLCGraph.prototype.reloadData; +MergesHPLCGraph.prototype._renderDygraph = HPLCGraph.prototype._renderDygraph; +MergesHPLCGraph.prototype.loadData = HPLCGraph.prototype.loadData; +MergesHPLCGraph.prototype.getPanel = HPLCGraph.prototype.getPanel; +MergesHPLCGraph.prototype.getDataByFrameNumber = HPLCGraph.prototype.getDataByFrameNumber; -MolarityGrid.prototype._getButtons = function() { - var _this = this; - return [ { - text : 'Add subunit', - icon : '../images/add.png', - handler : function() { - _this._openMolarityWindow(); + +MergesHPLCGraph.prototype.setPeaks = function (data) { + this.peaks = data; + /** get size of peaks **/ + this.peakKeys = []; + this.colorPeak = {}; + var colorCount = 1; + for (var key in this.peaks) { + if (this.peaks.hasOwnProperty(key)) { + var color = this.peakColors[colorCount % this.peakColors.length]; + colorCount = colorCount + 1; + this.peakKeys.push(key); + this.colorPeak[key] = color; } - }]; + } + this.peakKeys.sort(); }; -MolarityGrid.prototype.updateProposal = function() { +MergesHPLCGraph.prototype.getMenu = function () { var _this = this; - this.panel.setLoading(); - BIOSAXS.proposal.onInitialized.attach(function() { - if (BIOSAXS.proposal != null) { - var macromolecules = BIOSAXS.proposal.macromolecules; - for (var i = 0; i < macromolecules.length; i++) { - - if (macromolecules[i].macromoleculeId == _this.macromolecule.macromoleculeId) { - _this.refresh(macromolecules[i]); - _this.panel.setLoading(false); + /** Actions buttons **/ + var actions = []; + + function toggle(item, pressed) { + if (pressed) { + _this.plots[item.param] = true; + } else { + delete _this.plots[item.param]; + } + _this.reloadData(_this.hplcData); + } + + + /** Toolbar for peaks Average **/ + if (this.peaks != null) { + var items = []; + for (var i = 0; i < this.peakKeys.length; i++) { + var color = this.colorPeak[this.peakKeys[i]]; + items.push({ + text: "Peak #" + i + " " + this.peakKeys[i].replace("- ", " to #").replace(".0", "").replace(".0", "") + "", + peakid : this.peakKeys[i], + checked: false, + checkHandler: function (sender, pressed) { + var item = new Object(); + item.param = sender.peakid; + toggle(item, pressed); } - } + }); } - }); - BIOSAXS.proposal.init(); -}; - + + var menu = Ext.create('Ext.menu.Menu', { + id: 'mainMenu', + style: { + overflow: 'visible' + }, + items: items + }); + var tb = Ext.create('Ext.toolbar.Toolbar'); + tb.add({ + text: 'Peaks Avg.', + menu: menu + }); + actions.push(tb); + } -MolarityGrid.prototype.getPanel = function() { - var _this = this; + - this.molarityStore = Ext.create('Ext.data.Store', { - fields : [ 'acronym', 'ratio', 'comments', 'stoichiometryId', 'name', 'molecularMass' ], - sorters : { - property : 'ratio', - direction : 'DESC' + for (var i = 0; i < this.hplcData.length; i++) { + if (this.hplcData[i].showOnMenu != false) { + var param = this.hplcData[i].param; + var style = "style='padding:0 0px 0 5px;'"; + actions.push({ + text : "
" + BUI.getRectangleColorDIV(this.hplcData[i].color, 10, 10) + " " + this.hplcData[i].label + "
", + id : _this.id + param, + param : param, + enableToggle : true, + scope : this, + margin : 5, + toggleHandler : toggle, + pressed : (_this.plots[param] != null) + }); } - }); - - this.panel = Ext.create('Ext.grid.Panel', { - store : this.molarityStore, - height : this.height, - padding : 5, - columns : this._getColumns(), - listeners : { - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - - /** Remove entry * */ - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'MOLARITY_REMOVE') { - var dataAdapter = new BiosaxsDataAdapter(); - dataAdapter.onSuccess.attach(function(sender) { - _this.updateProposal(); - - }); - dataAdapter.removeStoichiometry(record.data.stoichiometryId); - _this.panel.setLoading("Removing Structure"); - } - } - }, - tbar : this._getButtons() - }); - return this.panel; -}; + } -MolarityGrid.prototype._prepareData = function(macromolecule) { - /** Return an array of [{ratio,acronym, stoichiometryId, name}] **/ - var data = []; - if (macromolecule.stoichiometry != null) { - for (var i = 0; i < macromolecule.stoichiometry.length; i++) { - var hostMacromolecule = BIOSAXS.proposal.getMacromoleculeById(macromolecule.stoichiometry[i].macromoleculeId); - data.push({ - ratio : macromolecule.stoichiometry[i].ratio, - acronym : hostMacromolecule.acronym, - comments : hostMacromolecule.comments, - molecularMass : hostMacromolecule.molecularMass, - stoichiometryId : macromolecule.stoichiometry[i].stoichiometryId, - name : hostMacromolecule.name - }); - } + actions.push("->"); + actions.push({ + text : "Save", + scope : this, + icon : '../images/save.gif', + handler : function (item, pressed) { + var largeImage = document.createElement("img"); + largeImage.style.display = 'block'; + largeImage.style.width = 200 + "px"; + largeImage.style.height = 200 + "px"; + largeImage.setAttribute('src', Dygraph.Export.asCanvas(this.dygraphObject.dygraph).toDataURL()); + window.open(Dygraph.Export.asCanvas(this.dygraphObject.dygraph).toDataURL(), 'Image', ''); } - return data; -}; + }); -MolarityGrid.prototype.refresh = function(macromolecule) { - if (macromolecule != null){ - this.molarityStore.loadData(this._prepareData(macromolecule)); - this.molarityForm.refresh(macromolecule); - this.macromolecule = macromolecule; - } + return actions; }; -MolarityGrid.prototype.input = function() { - return { - proposal : DATADOC.getProposal_10(), - dewars : DATADOC.getDewars_10() - }; +MergesHPLCGraph.prototype.input = function () { + return DATADOC.getScatteringHPLCFrameData(); }; -MolarityGrid.prototype.test = function(targetId) { - var MolarityGrid = new MolarityGrid({ - height : 150 +MergesHPLCGraph.prototype.test = function (targetId) { + var mainPlotPanel = new MergesHPLCGraph({ + title : 'Scattering', + width : this.plotWidth, + height : 500, + showRangeSelector : false, + xParam : 0, + xlabel : "scattering_I", + plots : { + "scattering_I" : true, + "subtracted_I" : true, + "buffer_I" : true + } }); - BIOSAXS.proposal = new Proposal(MolarityGrid.input().proposal); - var panel = MolarityGrid.getPanel(MolarityGrid.input().dewars); - panel.render(targetId); - + mainPlotPanel.getPanel().render(targetId); + mainPlotPanel.loadData(mainPlotPanel.input()); }; + + +function NetworkWidget(args) { + this.id = "NetworkViewer_" + Math.random().toString().replace(".", "_"); + + this.label = true; + if (args != null) { + if (args.targetId != null) { + this.targetId = args.targetId; + } + if (args.label != null) { + this.label = args.label; + } + } + + this.onVertexOver = new Event(this); + this.onVertexOut = new Event(this); +} + +NetworkWidget.prototype.draw = function(dataset, formatter, layout) { + + this.graphCanvas = new GraphCanvas(this.id, document.getElementById(this.targetId), { + "labeled" : this.label, + "multipleSelectionEnabled" : false, + "draggingCanvasEnabled" : false + }); + this.graphCanvas.draw(dataset, formatter, layout); + + var _this = this; + this.graphCanvas.onVertexOver.attach(function(sender, nodeId) { + _this.onVertexOver.notify(nodeId); + }); + + this.graphCanvas.onVertexOut.attach(function(sender, nodeId) { + _this.onVertexOut.notify(nodeId); + }); +}; + +/** SELECT VERTICES BY NAME * */ +NetworkWidget.prototype.selectVertexByName = function(vertexName) { + var vertices = this.getDataset().getVertexByName(vertexName); + if (vertices != null) { + for ( var nodeId in vertices) { + if (vertices.hasOwnProperty(nodeId)) { + var vertexId = vertices[nodeId].getId(); + this.selectVertexById(vertexId); + } + } + } +}; + +NetworkWidget.prototype.selectVerticesByName = function(verticesName) { + for ( var i = 0; i < verticesName.length; i++) { + this.selectVertexByName(verticesName[i]); + } +}; + +/** SELECT VERTICES BY ID * */ +NetworkWidget.prototype.selectVertexById = function(vertexId) { + this.graphCanvas.selectNode(vertexId); + this.blinkVertexById(vertexId); +}; + +NetworkWidget.prototype.selectVerticesById = function(verticesId) { + for ( var i = 0; i < verticesId.length; i++) { + this.selectVertexById(verticesId[i]); + } +}; + +/** VECINDARIO * */ +NetworkWidget.prototype.selectNeighbourhood = function() { + this.selectEdgesFromVertices(); + this.selectAdjacent(); +}; +/** DESELECT * */ +NetworkWidget.prototype.deselectNodes = function() { + this.graphCanvas.deselectNodes(); +}; + +/** SELECT ALL NODES * */ +NetworkWidget.prototype.selectAllNodes = function() { + this.getGraphCanvas().selectAllNodes(); +}; + +/** SELECT EVERYTHING * */ +NetworkWidget.prototype.selectAll = function() { + this.getGraphCanvas().selectAll(); +}; + +/** SELECT ALL EDGES * */ +NetworkWidget.prototype.selectAllEdges = function() { + this.getGraphCanvas().selectAllEdges(); +}; + +/** ZOOM * */ +NetworkWidget.prototype.setScale = function(value) { + this.graphCanvas.setScale(value); +}; + +NetworkWidget.prototype.getScale = function() { + return this.graphCanvas.getScale(value); +}; + +/** SELECT ADJACENT VERTICES FROM SELECTED VERTICES * */ +NetworkWidget.prototype.selectAdjacent = function() { + var selectedVertices = this.getGraphCanvas().getSelectedVertices(); + var edges = []; + for ( var i = 0; i < selectedVertices.length; i++) { + edges = edges.concat(this.getGraphCanvas().getDataset().getVertexById(selectedVertices[i]).getEdges()); + } + var vertices = []; + for ( i = 0; i < edges.length; i++) { + vertices.push(edges[i].getNodeSource().getId()); + vertices.push(edges[i].getNodeTarget().getId()); + } + + this.selectVerticesById(vertices); +}; + +/** SELECT EDGES FROM SELECTED VERTICES * */ +NetworkWidget.prototype.selectEdgesFromVertices = function() { + var selectedVertices = this.getGraphCanvas().getSelectedVertices(); + var edges = []; + for ( var i = 0; i < selectedVertices.length; i++) { + edges = edges.concat(this.getGraphCanvas().getDataset().getVertexById(selectedVertices[i]).getEdges()); + } + var edgesId = []; + for ( i = 0; i < edges.length; i++) { + edgesId.push(edges[i].getId()); + } + this.getGraphCanvas().selectEdges(edgesId); +}; + +/** BLINKING * */ +NetworkWidget.prototype.blinkVertexById = function(vertexId) { + this.graphCanvas.blinkVertexById(vertexId); +}; + +/** COMPONENTE CONEXA DE LOS NODOS SELECCIONADOS * */ +NetworkWidget.prototype.selectConnectedComponent = function() { + var elements = this.getConnectedComponent(); + this.selectVerticesById(elements.nodes); + this.graphCanvas.selectEdges(elements.edges); +}; + +NetworkWidget.prototype.getConnectedComponent = function() { + var nodosVisitados = {}; + var aristasVisitadas = {}; + var arrNodos = []; + var arrAristas = []; + var selectedGraphNodesId = this.getGraphCanvas().getSelectedVertices(); + for ( var i = 0; i < selectedGraphNodesId.length; i++) { + this.visitNode(selectedGraphNodesId[i], nodosVisitados, aristasVisitadas, arrNodos, arrAristas); + } + return { + nodes : arrNodos, + edges : arrAristas + }; +}; + +NetworkWidget.prototype.visitNode = function(nodeId, nodosVisitados, aristasVisitadas, arrNodos, arrAristas) { + nodosVisitados[nodeId] = true; + arrNodos.push(nodeId); + var nodeEdges = this.getDataset().getVertexById(nodeId).getEdges(); + for ( var j = 0; j < nodeEdges.length; j++) { + var edge = nodeEdges[j]; + var edgeId = edge.getId(); + if (aristasVisitadas[edgeId] == null) { + aristasVisitadas[edgeId] = true; + arrAristas.push(edgeId); + var nodeTargetId = edge.getNodeTarget().getId(); + if (nodosVisitados[nodeTargetId] == null) { + this.visitNode(nodeTargetId, nodosVisitados, aristasVisitadas, arrNodos, arrAristas); + } + var nodeSourceId = edge.getNodeSource().getId(); + if (nodosVisitados[nodeSourceId] == null) { + this.visitNode(nodeSourceId, nodosVisitados, aristasVisitadas, arrNodos, arrAristas); + } + } + } +}; + +/** COLLAPSE SELECTED VERTICES * */ +NetworkWidget.prototype.collapse = function() { + var selectedVertices = this.getGraphCanvas().getSelectedVertices(); + var xMin = -Infinity; + var xMax = Infinity; + var yMin = -Infinity; + var yMax = Infinity; + + for ( var i = 0; i < selectedVertices.length; i++) { + var vertex = this.getGraphCanvas().getLayout().getNodeById(selectedVertices[i]); + if (xMin < vertex.x) { + xMin = vertex.x; + } + if (xMax > vertex.x) { + xMax = vertex.x; + } + if (yMin < vertex.y) { + yMin = vertex.y; + } + if (yMax > vertex.y) { + yMax = vertex.y; + } + } + + var centerX = xMin - xMax; + var centerY = yMin - yMax; + var radius = (xMax - xMin) / 4; + + var count = selectedVertices.length; + var verticesCoordinates = []; + + for ( i = 0; i < selectedVertices.length; i++) { + x = centerX + radius * Math.sin(i * 2 * Math.PI / count); + y = centerY + radius * Math.cos(i * 2 * Math.PI / count); + verticesCoordinates.push({ + 'x' : x, + 'y' : y + }); + } + + for ( i = 0; i < selectedVertices.length; i++) { + this.getGraphCanvas().getLayout().getNodeById(selectedVertices[i]).setCoordinates(verticesCoordinates[i].x, verticesCoordinates[i].y); + } +}; +/** SETTER FONT SIZE * */ +NetworkWidget.prototype.setVerticesFontSize = function(value) { + for ( var nodeId in this.getDataset().getVertices()) { + if (this.getDataset().getVertices().hasOwnProperty(nodeId)) { + this.getFormatter().getVertexById(nodeId).getDefault().setFontSize(value); + } + } +}; + +/** GETTERS * */ +NetworkWidget.prototype.getFormatter = function() { + return this.getGraphCanvas().getFormatter(); +}; +NetworkWidget.prototype.getLayout = function() { + return this.getGraphCanvas().getLayout(); +}; + +NetworkWidget.prototype.getDataset = function() { + return this.getGraphCanvas().getDataset(); +}; + +NetworkWidget.prototype.getGraphCanvas = function() { + return this.graphCanvas; +}; + +RangeWhiskerGraph.prototype.cleanArray = GenericGraph.prototype.cleanArray; +RangeWhiskerGraph.prototype.plotAxes = GenericGraph.prototype.plotAxes; +RangeWhiskerGraph.prototype.plotRuler = GenericGraph.prototype.plotRuler; +RangeWhiskerGraph.prototype.drawSVGVerticalText = GenericGraph.prototype.drawSVGVerticalText; +RangeWhiskerGraph.prototype.getClassColor = GenericGraph.prototype.getClassColor; +RangeWhiskerGraph.prototype.getDimensions = GenericGraph.prototype.getDimensions; +RangeWhiskerGraph.prototype.calculate = GenericGraph.prototype.calculate; +RangeWhiskerGraph.prototype.getMedian = GenericGraph.prototype.getMedian; +RangeWhiskerGraph.prototype.pointToPixel = GenericGraph.prototype.pointToPixel; +RangeWhiskerGraph.prototype.maxValueWhisker = GenericGraph.prototype.maxValueWhisker; +RangeWhiskerGraph.prototype.refresh = GenericGraph.prototype.refresh; + /** - * Given data analysis parsed with ResultsAssemblyWidget makes a selector grid with buffer/protein - **/ -function SpecimenSelectorResultGrid() { - this.id = BUI.id(); -} + * Subclass of GenericGraph + * + * @plotHorizontalByCluster + */ +function RangeWhiskerGraph(args) { + this.maxBoxWidth = 25; -SpecimenSelectorResultGrid.prototype._prepareData = function(data) { - var parsed = []; - for ( var i = 0; i < data.length; i++) { - var row = data[i]; - for ( var j = 0; j < row.conditions.length; j++) { - parsed.push({ - bufferId : row.conditions[j].bufferId, - macromoleculeId : row.macromoleculeId, - macromoleculeAcronym : BIOSAXS.proposal.getMacromoleculeById(row.macromoleculeId).acronym, - bufferAcronym : BIOSAXS.proposal.getBufferById(row.conditions[j].bufferId).acronym - }); - } + if (args == null) { + args = {}; } - return parsed; -}; - -SpecimenSelectorResultGrid.prototype.refresh = function(data) { - this.store.loadData(this._prepareData(data)); -}; - -SpecimenSelectorResultGrid.prototype.getPanel = function(data) { - var _this = this; - this.store = Ext.create('Ext.data.Store', { - fields : [ 'macromoleculeId', 'bufferId', 'macromoleculeAcronym', 'bufferAcronym', 'concentration' ], - data : this._prepareData(data), - groupField : 'macromoleculeAcronym' - }); + args.plotHorizontalByCluster = false; - this.store.sort('concentration'); - this.grid = Ext.create('Ext.grid.Panel', { - id : this.id, - store : this.store, - width : this.width, - height : this.height, - maxHeight : this.maxHeight, - border : 1, - features : [ { - ftype : 'grouping', - groupHeaderTpl : '{name}', - hideGroupedHeader : true, - startCollapsed : false - } ], - selModel : Ext.create('Ext.selection.CheckboxModel', { - allowDeselect : true, - mode : 'MULTI', - listeners : { - selectionchange : function(sm, selections) { - _this.selected = []; - for ( var i = 0; i < selections.length; i++) { - _this.selected.push(selections[i].raw); - } - } - } - }), - margin : 10, - sortableColumns : true, - columns : [ { - text : 'Macromolecule', - dataIndex : 'macromoleculeAcronym', - flex : 1 - }, { - text : '', - dataIndex : 'bufferId', - width : 20, - hidden : false, - renderer : function(val, y, sample) { - return BUI.getRectangleColorDIV(BIOSAXS.proposal.bufferColors[val], 10, 10); - } - }, { - text : 'Buffer', - dataIndex : 'bufferAcronym', - flex : 1 - }, { - text : 'Concentration', - dataIndex : 'concentration', - flex : 1, - renderer : function(val, y, sample) { - return val + " mg/ml"; - } - } ] - }); + GenericGraph.call(this, args); - /** Adding the tbar **/ - if (this.tbar) { - this.grid.addDocked({ - xtype : 'toolbar', - items : this.getTbar() - }); + if (args.maxBoxWidth != null) { + this.maxBoxWidth = args.maxBoxWidth; } - return this.grid; -}; +} -SpecimenSelectorResultGrid.prototype.input = function() { - return { - data : new ResultsAssemblyGrid()._prepareData(new ResultsAssemblyGrid().input().data), - proposal : new ResultsAssemblyGrid().input().proposal - }; +RangeWhiskerGraph.prototype.refresh = function(data) { + document.getElementById(this.targetId).innerHTML = ""; + this.draw(this.targetId, data); }; -SpecimenSelectorResultGrid.prototype.test = function(targetId) { - var specimenSelectorResultGrid = new SpecimenSelectorResultGrid(); - BIOSAXS.proposal = new Proposal(specimenSelectorResultGrid.input().proposal); - var panel = specimenSelectorResultGrid.getPanel(specimenSelectorResultGrid.input().data); - panel.render(targetId); -}; +RangeWhiskerGraph.prototype.isNumber = function(value) { + if (value == "") + return false; -/** - * Show all buffer conditions for each macromolecules pointing out the measurements quality - * - * @height - * @maxHeight - * @width - * @searchBar - * @tbar - * @btnResultVisible - * - * #onClick - */ -function ResultsAssemblyGrid(args) { - this.height = 500; - this.id = BUI.id(); - this.maxHeight = this.height; + var d = parseInt(value); + if (!isNaN(d)) + return true; + else + return false; - this.width = 900; - this.searchBar = false; - this.tbar = false; - this.btnResultVisible = false; +}; - /** For processing **/ - this.processed = {}; - this.renderedPlotIndex = 0; +/** + There are several different methods for calculating quartiles.[1] This calculator uses a method described by Moore and McCabe to find quartile values. + The same method also used by The TI-83 to calculate quartile values. + With this method, the first quartile is the median of the numbers below the median, the third quartile is the median of the numbers above the median. - this.plotWidth = 210; - this.plotHeight = 80; + http://www.miniwebtool.com/quartile-calculator/ + http://www.alcula.com/calculators/statistics/box-plot/ - /** Colors **/ - this.validColor = BUI.getValidColor(); - this.warningColor = BUI.getWarningColor(); - this.notValidColor = BUI.getErrorColor(); + **/ +RangeWhiskerGraph.prototype.getQ1 = function(array) { + array = array.slice(0, array.length / 2); + return this.getMedian(array); +}; - /** Show warning if guinier quality less than **/ - this.guinierQuality = BUI.getQualityThreshold(); - this.framePercentageThreshold = BUI.getRadiationDamageThreshold(); +RangeWhiskerGraph.prototype.getQ3 = function(array) { + array = array.slice((array.length + 1) / 2); + return this.getMedian(array); - if (args != null) { - if (args.height != null) { - this.height = args.height; - this.maxHeight = this.height; - } - if (args.maxHeight != null) { - this.maxHeight = args.maxHeight; - } - if (args.width != null) { - this.width = args.width; - } - if (args.searchBar != null) { - this.searchBar = args.searchBar; +}; + +RangeWhiskerGraph.prototype.getQ2 = function(array) { + return this.getMedian(array); +}; + +RangeWhiskerGraph.prototype.getBelowOutliers = function(belowLimit, array) { + var points = []; + for ( var i = 0; i < array.length; i++) { + if (array[i] <= belowLimit) { + points.push(array[i]); } + } + return points; +}; - if (args.tbar != null) { - this.tbar = args.tbar; +RangeWhiskerGraph.prototype.getAboveOutliers = function(aboveLimit, array) { + var points = []; + for ( var i = 0; i < array.length; i++) { + if (array[i] >= aboveLimit) { + points.push(array[i]); } - if (args.btnResultVisible != null) { - this.btnResultVisible = args.btnResultVisible; + } + return points; +}; + +RangeWhiskerGraph.prototype.minValueWhisker = function(belowLimit, q1, array) { + var points = []; + + for ( var i = 0; i < array.length; i++) { + if ((array[i] < q1) && (array[i]) > belowLimit) { + points.push(array[i]); } + } + if (points.length > 0) { + points.sort(function(a, b) { + return a - b; + }); + return points[0]; } + return null; +}; - this.onClick = new Event(); -} +//RangeWhiskerGraph.prototype.maxValueWhisker = function(aboveLimit, q3, array){ +// var points = []; +// for (var i = 0; i < array.length; i++){ +// if ((array[i] > q3) && (array[i]) <= aboveLimit){ +// points.push(array[i]); +// } +// } +// if (points.length > 0){ +// points.sort(function(a, b){return a - b;}); +// return points[points.length - 1]; +// } +// return null; +//}; -ResultsAssemblyGrid.prototype.edit = function(macromoleculeId) { - var _this = this; - var window = new MacromoleculeWindow(); - window.onSuccess.attach(function(sender, proposal) { - _this.store.loadData(_this._prepareData(BIOSAXS.proposal.getMacromolecules())); - }); - window.draw(BIOSAXS.proposal.getMacromoleculeById(macromoleculeId)); +RangeWhiskerGraph.prototype.drawPoints = function(boxProperties) { + if (this.plotPoints) { + for ( var i = 0; i < boxProperties.values.length; i++) { + var value = boxProperties.values[i]; + var toPixel = this.pointToPixel(value, boxProperties); + SVG.drawCircle(boxProperties.x, toPixel, this.pointRadius, this.svg, + [ + [ "fill", "green" ], [ "fill-opacity", this.fillOpacityPoint ], [ 'stroke-opacity', this.strokeOpacityPoint ], + [ "stroke", "black" ] ]); + } + } }; -ResultsAssemblyGrid.prototype.getTbar = function() { - var _this = this; - var actions = []; +RangeWhiskerGraph.prototype.plotRangeQ1Q3 = function(data, properties) { + var posX = this.left + this.rulerWidth; - actions.push(Ext.create('Ext.Action', { - icon : '../images/add.png', - text : 'Add Macromolecule', - disabled : false, - handler : function(widget, event) { - var window = new MacromoleculeWindow(); - window.onSuccess.attach(function(sender) { - _this.refresh(); - }); - window.draw({}); - } - })); + var boxBordersPointsQ1 = []; + var boxBordersPointsQ3 = []; + var Q2 = []; - actions.push(Ext.create('Ext.Action', { - icon : '../images/add.png', - text : 'Define an Assembly', - disabled : false, - handler : function(widget, event) { - var createAssemblywindow = new CreateAssemblyWindow(); - createAssemblywindow.onSaved.attach(function(evt, args) { - if (args.macromoleculeIds.length > 0) { - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, proposal) { - _this.refresh(); - }); - adapter.saveAssembly(args.assemblyId, args.macromoleculeIds); + for ( var i = 0; i < data.clusters.length; i++) { + var cluster = data.clusters[i]; + /** inter cluster space **/ + posX = posX + this.interClustersSpace; - } + for ( var j = 0; j < cluster.classes.length; j++) { + var ratio = properties.width / (properties.xValues.range); + var coorX = (cluster.x - properties.xValues.min) * ratio + this.rulerWidth; + var boxProperties = { + name : cluster.classes[j].name, + values : cluster.classes[j].values, + minPoint : properties.minPoint, + maxPoint : properties.maxPoint, + x : coorX + this.left, + y : this.top, + width : properties.classWidth, + height : this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight + }; - }); - createAssemblywindow.draw(_this.experiment); - } - })); + var result = this.calculate(boxProperties.values); + var boxColor = this.getClassColor(boxProperties.name); - return actions; -}; + if (this.isNumber(result.Q1) && this.isNumber(result.Q3)) { + var x = boxProperties.x; + var y = this.pointToPixel(result.Q1, boxProperties); + if (boxBordersPointsQ1[cluster.classes[j].name] == null) { + boxBordersPointsQ1[cluster.classes[j].name] = []; + } + boxBordersPointsQ1[cluster.classes[j].name].push({ + x : x, + y : y + }); -ResultsAssemblyGrid.prototype.refresh = function() { - this.store.loadData(this._prepareData()); -}; + x = boxProperties.x; + y = this.pointToPixel(result.Q3, boxProperties); + if (boxBordersPointsQ3[cluster.classes[j].name] == null) { + boxBordersPointsQ3[cluster.classes[j].name] = []; + } + boxBordersPointsQ3[cluster.classes[j].name].push({ + x : x, + y : y + }); + } else { -ResultsAssemblyGrid.prototype.addCondition = function(record, data_parsed, i) { - function getCondition(record) { - return { - concentration : record.conc, - quality : record.quality, - bufferBeforeFramesMerged : record.bufferBeforeFramesMerged, - bufferAfterFramesMerged : record.bufferAfterFramesMerged, - framesCount : record.framesCount, - framesMerge : record.framesMerge - }; - } + if (this.isNumber(result.Q2)) { - if (data_parsed[i].conditions != null) { - var bufferFound = false; - for ( var index in data_parsed[i].conditions) { - condition = data_parsed[i].conditions[index]; + if (boxBordersPointsQ1[cluster.classes[j].name] == null) { + boxBordersPointsQ1[cluster.classes[j].name] = []; + } - if ((condition.macromoleculeId == record.macromoleculeId) && (condition.bufferId == record.bufferId)) { - data_parsed[i].conditions[index].concentrations.push(getCondition(record)); - bufferFound = true; + if (boxBordersPointsQ3[cluster.classes[j].name] == null) { + boxBordersPointsQ3[cluster.classes[j].name] = []; + } + + boxBordersPointsQ1[cluster.classes[j].name].push({ + x : boxProperties.x, + y : this.pointToPixel(result.Q2, boxProperties) + }); + boxBordersPointsQ3[cluster.classes[j].name].push({ + x : boxProperties.x, + y : this.pointToPixel(result.Q2, boxProperties) + }); + } } } - if (!bufferFound) { - data_parsed[i].conditions.push({ - macromoleculeId : record.macromoleculeId, - bufferId : record.bufferId, - concentrations : [ getCondition(record) ] - }); + } + for ( var classe in boxBordersPointsQ1) { + var points = boxBordersPointsQ1[classe]; + var pointsSVG = ""; + for (var k = 0; k < points.length; k++) { + pointsSVG = Number(points[k].x).toFixed(1) + "," + Number(points[k].y).toFixed(1) + " " + pointsSVG; + } + + points = boxBordersPointsQ3[classe]; + for (var z = points.length - 1; z >= 0; z--) { + pointsSVG = Number(points[z].x).toFixed(1) + "," + Number(points[z].y).toFixed(1) + " " + pointsSVG; } + + SVG.drawPoligon(pointsSVG, this.svg, [ + [ "fill", this.getClassColor(classe) ], [ "opacity", "0.3" ], [ "stroke", "black" ], [ "stroke-width", 1 ] ]); } }; -ResultsAssemblyGrid.prototype.process = function(record, data_parsed) { - if (this.processed[record.macromoleculeId] == null) { - this.processed[record.macromoleculeId] = true; - record.measurementCount = 1; - record.subtractionCount = 1; - record.averageCount = 1; - record.conditions = []; - data_parsed.push(record); - } +RangeWhiskerGraph.prototype.plotWhisters = function(data, properties) { + var colors = [ "yellow", "orange", "green" ]; - for ( var i = 0; i < data_parsed.length; i++) { - if (data_parsed[i].macromoleculeId == record.macromoleculeId) { - data_parsed[i].measurementCount = data_parsed[i].measurementCount + 1; + this.plotRangeQ1Q3(data, properties); + var Q2 = {}; - if (record.subtractionId != null) { - data_parsed[i].subtractionCount = data_parsed[i].subtractionCount + 1; - this.addCondition(record, data_parsed, i); - } + for ( var i = 0; i < data.clusters.length; i++) { + var cluster = data.clusters[i]; + for ( var j = 0; j < cluster.classes.length; j++) { + var ratio = properties.width / (properties.xValues.range); + var coorX = (cluster.x - properties.xValues.min) * ratio + this.left + this.rulerWidth - this.rulerStroke; + var boxProperties = { + name : cluster.classes[j].name, + values : cluster.classes[j].values, + minPoint : properties.minPoint, + maxPoint : properties.maxPoint, + x : coorX, + y : this.top, + width : properties.classWidth, + height : this.height - this.top - this.bottom - this.clusterTitleHeight - this.rulerHeight + }; - if (record.framesMerge != null) { - data_parsed[i].averageCount = data_parsed[i].averageCount + 1; - } + this.drawPoints(boxProperties); - if (record.timeStart != null) { - if (data_parsed[i].timeStart != null) { - if (moment(data_parsed[i].timeStart).format("X") > moment(record.timeStart).format("X")) { - data_parsed[i].timeStart = record.timeStart; - } + /** PLOTTING Q2 **/ + var result = this.calculate(boxProperties.values); + var boxColor = this.getClassColor(boxProperties.name); + if (this.isNumber(result.Q2)) { + if (Q2[boxProperties.name] != null) { + SVG.drawLine(boxProperties.x, this.pointToPixel(result.Q2, boxProperties), Q2[boxProperties.name].x, Q2[boxProperties.name].y, + this.svg, [ [ "stroke", boxColor ], [ "stroke-width", "2" ] ]); + } + Q2[boxProperties.name] = { + x : boxProperties.x, + y : this.pointToPixel(result.Q2, boxProperties) } } } } - return data_parsed; - }; -ResultsAssemblyGrid.prototype._prepareData = function(data) { - var data_parsed = []; - for ( var i = 0; i < data.length; i++) { - data_parsed = this.process(data[i], data_parsed); - } - this.data = data_parsed; - return data_parsed; +RangeWhiskerGraph.prototype.draw = function(targetId, data) { + //this.calculate(data); + this.targetId = targetId; + var properties = (this.getDimensions(data)); + this.svg = SVG.createSVGCanvas(document.getElementById(this.targetId), [ [ "width", this.width ], [ "height", this.height ] ]); + this.plotAxes(properties); + this.plotWhisters(data, properties); }; -/** Given an array of conditions it returns distinct(concentrations) order by concentration and hash map with number of ocurrences**/ -ResultsAssemblyGrid.prototype.parseConcentrations = function(val, conditions, differentConcentration, quality) { - var conditions = []; - var differentConcentration = {}; - var quality = []; - for ( var i = 0; i < val.length; i++) { - var conc = Number(val[i].concentration).toFixed(1); - var quality = Number(val[i].quality).toFixed(2); - if (differentConcentration[conc] == null) { - differentConcentration[conc] = 0; - conditions.push({ - concentration : conc, - quality : [ quality ], - frames : [ { - bufferAfterFramesMerged : val[i].bufferAfterFramesMerged, - bufferBeforeFramesMerged : val[i].bufferBeforeFramesMerged, - framesMerge : val[i].framesMerge, - framesCount : val[i].framesCount - } ] - }); - } else { - /** Add quality **/ - for ( var j = 0; j < conditions.length; j++) { - if (conditions[j].concentration == conc) { - conditions[j].quality.push(quality); - conditions[j].frames.push({ - bufferAfterFramesMerged : val[i].bufferAfterFramesMerged, - bufferBeforeFramesMerged : val[i].bufferBeforeFramesMerged, - framesMerge : val[i].framesMerge, - framesCount : val[i].framesCount - }); - } - } - } +RangeWhiskerGraph.prototype.input = function() { + return DATADOC.getBoxWhikerData(); +}; - differentConcentration[conc] = differentConcentration[conc] + 1; - } - /** sorting concentrations **/ - conditions.sort(function(a, b) { - return a.concentration - b.concentration; +RangeWhiskerGraph.prototype.test = function(targetId) { + var plot = new RangeWhiskerGraph({ + targetId : targetId, + height : 350, + width : 450, + maxBoxWidth : 25 }); - return { - concentrations : conditions, - differentConcentration : differentConcentration - }; + plot.refresh(this.input()); }; + +StdDevDyGraph.prototype.dblclick = DygraphWidget.prototype.dblclick; +StdDevDyGraph.prototype._createHTLMWrapper = DygraphWidget.prototype._createHTLMWrapper; +StdDevDyGraph.prototype.draw = DygraphWidget.prototype.draw; -ResultsAssemblyGrid.prototype.getConditionWarnings = function(condition) { - - var withWarnings = 0; - - for ( var i = 0; i < condition.frames.length; i++) { - if (condition.quality[i] == null) { - withWarnings = withWarnings + 1; - continue; - } else { - if (Number(condition.quality[i]) < this.guinierQuality) { - withWarnings = withWarnings + 1; - continue; - } - } - - if (condition.frames[i].bufferBeforeFramesMerged / condition.frames[i].framesCount < this.framePercentageThreshold|| condition.frames[i].framesMerged / condition.frames[i].framesCount < this.framePercentageThreshold|| condition.frames[i].bufferAfterFramesMerged / condition.frames[i].framesCount < this.framePercentageThreshold) { - withWarnings = withWarnings + 1; - continue; - } +function StdDevDyGraph(targetId, args) { + this.scaled = false; + if (args == null) { + args = {}; } + args.customBars = true; + DygraphWidget.prototype.constructor.call(this, targetId, args); +} +StdDevDyGraph.prototype.input = function () { return { - withWarnings : withWarnings, - withoutWarnings : condition.frames.length - withWarnings + data : [ [ 1, [ 2, 3, 3.5 ], [ 4, 4.2, 5 ] ], [ 2, [ 5, 5.5, 5.7 ], [ 4, 4.2, 5 ] ] ], + colors : [ "blue", "red" ], + labels : [ "", 'data1', 'data2' ] }; }; -ResultsAssemblyGrid.prototype.getFrameHTMLTable = function(warnings) { - var html = ""; - if (warnings.withWarnings > 0) { - html = html + "
" + warnings.withWarnings + - "x
"; - } - - if (warnings.withoutWarnings > 0) { - html = html + "
" + warnings.withoutWarnings + - "x
"; - } - return html; -}; +StdDevDyGraph.prototype.test = function (targetId) { + var dygraphObject = new StdDevDyGraph(targetId, { + width : 500, + height : 400, + xlabel : "xLabel", + showRangeSelector : false + }); -ResultsAssemblyGrid.prototype.createConcentrationRow = function(numberOcu, condition, warnings){ - var html = ""; - if (numberOcu > 1){ - html = html + "" +numberOcu + "x " + BUI.formatConcentration(condition.concentration); - } - else{ - html = html + BUI.formatConcentration(condition.concentration); - } - html = html + ""; - html = html + this.getFrameHTMLTable(warnings); + ""; - html = html + ""; - return html; + dygraphObject.draw(dygraphObject.input().data, dygraphObject.input().colors, dygraphObject.input().labels); }; + + + +function AbinitioGrid(args) { + this.height = null; + this.width = null; + this.id = BUI.id(); + + if (args != null) { + if (args.height != null) { + this.height = args.height; + + if (args.width != null) { + this.width = args.width; + } + } + } + + this.onSelected = new Event(this); +}; + + +AbinitioGrid.prototype.refresh = function(subtractions){ + this.store.loadData(this._prepareData(subtractions)); +}; + +AbinitioGrid.prototype._prepareData = function(subtractions){ + /** Parsing data * */ + var models = []; + for (var l = 0; l < subtractions.length; l++) { + var subtraction = subtractions[l]; + for (var k = 0; k < subtraction.substractionToAbInitioModel3VOs.length; k++) { + var data = subtraction.substractionToAbInitioModel3VOs[k].abinitiomodel3VO; + if (data.averagedModel != null) { + models.push(data.averagedModel); + models[models.length - 1].type = "Reference"; + } + + if (data.shapeDeterminationModel != null) { + models.push(data.shapeDeterminationModel); + models[models.length - 1].type = "Refined"; + } + + if (data.modelList3VO != null) { + if (data.modelList3VO.modeltolist3VOs != null) { + for (var i = 0; i < data.modelList3VO.modeltolist3VOs.length; i++) { + models.push(data.modelList3VO.modeltolist3VOs[i].model3VO); + models[models.length - 1].type = "Model"; + } + } + } + } + } + return models; +}; + +AbinitioGrid.prototype.getPanel = function(){ + var _this = this; + + + var modelFields = [ "modelId", "type", "chiSqrt", "dmax", "firFile", "logFile", "fitFile", "pdbFile", "rfactor", "rg", "volume" ]; + Ext.define('AbinitioModel', { + extend : 'Ext.data.Model', + fields : modelFields + + }); + + /** + * Store in Memory + */ + this.store = Ext.create('Ext.data.Store', { + model : 'AbinitioModel', + autoload : true, + groupField : 'type' + }); + + + var groupingFeature = Ext.create('Ext.grid.feature.Grouping',{ + groupHeaderTpl: '{name} ({rows.length} model{[values.rows.length > 1 ? "s" : ""]})', + startCollapsed: true, + collapsible : true + }); + + this.grid = Ext.create('Ext.grid.Panel', { + collapsible : false, + resizable : true, + features: [groupingFeature], + autoscroll : true, + multiSelect : true, + store : this.store, + height : this.height, + width : this.width, + margin : 10, + columns : [ { + text : "Type", + dataindex : "type", + hidden : true, + renderer : function(a, b, record) { + return record.data.type; + }, + flex : 1 + }, + { + text : "ModelId", + dataindex : "modelId", + hidden : true, + renderer : function(a, b, record) { + return record.data.modelId; + + }, + flex : 1 + }, + + { + text : "chiSqrt", + dataindex : "chiSqrt", + renderer : function(a, b, record) { + if (record.data.dmax != null) { + return BUI.formatValuesUnits(record.data.chiSqrt, "", 12, this.decimals); + } + + }, + flex : 1 + }, + { + text : "Dmax", + dataindex : "dmax", + renderer : function(a, b, record) { + if (record.data.dmax != null) { + return BUI.formatValuesUnits(record.data.dmax, "nm", 12, this.decimals); + } + + }, + flex : 1 + }, { + text : "rFactor", + dataindex : "rfactor", + hidden : true, + renderer : function(a, b, record) { + if (record.data.rfactor != null) { + return record.data.rfactor; + } + }, + flex : 1 + }, { + text : "Rg", + dataindex : "rg", + renderer : function(a, b, record) { + if (record.data.rg != null) { + return BUI.formatValuesUnits(record.data.rg, "nm", 12, this.decimals); + } + + }, + flex : 1 + }, + { + text : "Volume", + dataindex : "volume", + renderer : function(a, b, record) { + if (record.raw.volume != null){ + return BUI.formatValuesUnits(record.raw.volume, '') + " nm3"; + } + }, + flex : 1 + }, + { + text : "PDB", + dataindex : "pdbFile", + renderer : function(a, b, record) { + if (record.data.pdbFile != null){ + return record.data.pdbFile.split("/")[record.data.pdbFile.split("/").length - 1]; + } + }, + flex : 1 + }, { + text : "Fir", + dataindex : "firFile", + renderer : function(a, b, record) { + if (record.data.firFile != null){ + return record.data.firFile.split("/")[record.data.firFile.split("/").length - 1]; + } + }, + flex : 1 + }, { + text : "LOG", + dataindex : "logFile", + hidden : true, + renderer : function(a, b, record) { + if (record.data.logFile != null){ + return record.data.logFile.split("/")[record.data.logFile.split("/").length - 1]; + } + }, + flex : 1 + } + ], + viewConfig : { + enableTextSelection : true, + preserveScrollOnRefresh : true, + stripeRows : true, + listeners : { + 'celldblclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + }, + 'cellclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + var models = []; + for (var i = 0; i < grid.getSelectionModel().selected.items.length; i++) { + models.push(grid.getSelectionModel().selected.items[i].raw); + } + _this.onSelected.notify(models); + } + } + } + }); + return this.grid; + +}; + +function AdditiveGrid(args) { + this.onRemoveButtonClicked = new Event(this); +} -ResultsAssemblyGrid.prototype.getConditionHTMLTable = function(val, style, record) { - var maxNumberColumns = 2; - var html = "
"; - var nColumns = 0; - for ( var r = 0; r < val.length; r++) { - if (nColumns == maxNumberColumns) { - nColumns = 0; - html = html + ""; - } - html = html + ""; - nColumns = nColumns + 1; - } - html = html + "
"; - var value = val[r]; - - var bufferAcronym = (BIOSAXS.proposal.getBufferById(value.bufferId).acronym); - - var parsed = (this.parseConcentrations(value.concentrations)); - var conditions = parsed.concentrations; - var differentConcentration = parsed.differentConcentration; - - /** Checking warnings **/ - var warnings = []; - var concentrationValidPerconcentration = 0; - var measurements = 0; - for ( var i = 0; i < conditions.length; i++) { - measurements = measurements + conditions[i].frames.length; - var warning = this.getConditionWarnings(conditions[i]); - warnings.push(warning); - if (warning.withoutWarnings > 0) { - concentrationValidPerconcentration = concentrationValidPerconcentration + 1; - } - } - - this.validColor = '#E0F8E0'; - this.warningColor = '#F5DA81'; - this.notValidColor = '#F6CED8'; - - var color = this.warningColor; - if (concentrationValidPerconcentration > 2) { - color = this.validColor; - } - /** More measurement need to be done **/ - if (measurements < 3) { - color = this.notValidColor; - } - - html = html + ""; - html = html + ""; - for ( var i = 0; i < conditions.length; i++) { - html = html + this.createConcentrationRow(differentConcentration[conditions[i].concentration], conditions[i], warnings[i]); - } - - html = html + ""; - html = html + "
" + bufferAcronym.toUpperCase() + - "
"; - - html = html + "
"; - return html; +AdditiveGrid.prototype.getBuffer = function() { + return this.buffer; }; -ResultsAssemblyGrid.prototype._getTbar = function() { - function goTo(url) { - window.location = url; - } - +AdditiveGrid.prototype._getActions = function() { var _this = this; - return [ { - icon : '../images/application_view_list.png', - text : 'Multiple Select', - handler : function() { - var specimenSelectorResultGrid = new SpecimenSelectorResultGrid(); - var window = Ext.create('Ext.window.Window', { - title : 'Multiple select', - height : 600, - width : 600, - layout : 'fit', - items : [ specimenSelectorResultGrid.getPanel(_this.data) ], - buttons : [ { - text : 'Go', - handler : function() { - var array = []; - for ( var i = 0; i < specimenSelectorResultGrid.selected.length; i++) { - var row = specimenSelectorResultGrid.selected[i]; - array.push({ - macromoleculeId : row.macromoleculeId, - bufferId : row.bufferId - }); - } - goTo(BUI.getMacromoleculeResultsURLByMultipleSearch(array)); + /** Actions buttons **/ + var actions = []; - } - }, { - text : 'Cancel', - handler : function() { - window.close(); - } - } ] + actions.push(Ext.create('Ext.Action', { + icon : '../images/add.png', + text : 'Add', + disabled : true, + alwaysEnabled : true, + handler : function(widget, event) { + _this.buffer.bufferhasadditive3VOs.push(BIOSAXS_BEANS.getBufferhasAdditive3VO()); + _this.refresh(_this.buffer, _this.experiment); + } + })); - }).show(); + return actions; +}; +AdditiveGrid.prototype.refresh = function(buffer, experiment) { + this.buffer = buffer; + this.experiment = experiment; + if (buffer) { + if (buffer.bufferhasadditive3VOs) { + this.features = buffer.bufferhasadditive3VOs; } - } ]; + } + this.experiment = experiment; + this.store.loadData(this._prepareData(), false); }; -ResultsAssemblyGrid.prototype.getLegendPanel = function() { - return { - html : '
' + BUI.getRectangleColorDIV(this.validColor, 10, 10) + - 'Good quality measurements' + - BUI.getRectangleColorDIV(this.warningColor, 10, 10) + - 'Probably valid with manual processing' + - BUI.getRectangleColorDIV(this.notValidColor, 10, 10) + - 'More measurements need to be done
' - }; -}; -/** Returns the grid **/ -ResultsAssemblyGrid.prototype.getPanel = function(macromolecules) { - var _this = this; +AdditiveGrid.prototype.getAdditives = function() { + var additives = []; + for ( var i = 0; i < this.store.getCount(); i++) { + var bufferHasAdditive = BIOSAXS_BEANS.getBufferhasAdditive3VO(); + var data = this.store.getAt(i).getData(); - this.store = Ext.create('Ext.data.Store', { - fields : [ - 'macromoleculeId', 'macromoleculeAcronym', 'measurementCount', 'subtractionCount', 'averageCount', 'timeStart', 'concentrationArray', - 'bufferConditions', 'conditions' ], - data : this._prepareData(macromolecules) - }); + bufferHasAdditive.additive3VO.name = data.name; + bufferHasAdditive.additive3VO.comments = data.comments; + bufferHasAdditive.additive3VO.additiveType = data.additiveType; - this.store.sort('macromoleculeAcronym'); + bufferHasAdditive.bufferId = this.buffer.bufferId; + bufferHasAdditive.bufferHasAdditiveId = data.bufferHasAdditiveId; + bufferHasAdditive.quantity = data.quantity; + additives.push(bufferHasAdditive); + } - this.grid = Ext.create('Ext.grid.Panel', { - id : this.id, - title : 'Macromolecules', - store : this.store, - tbar : this._getTbar(), - bbar : [ this.getLegendPanel() ], - width : this.width, - height : this.height, - maxHeight : this.maxHeight, - sortableColumns : true, - columns : [ - { - text : '', - dataIndex : 'macromoleculeId', - width : 20, - hidden : false, - renderer : function(val, y, sample) { - return BUI.getRectangleColorDIV(BIOSAXS.proposal.macromoleculeColors[val], 10, 10); - } - }, - { - text : 'Macromolecule', - dataIndex : 'macromoleculeAcronym', - width : 200 + return additives; +}; + +AdditiveGrid.prototype._getFields = function(buffers) { + var columns = [ + + { + header : 'Name', + dataIndex : 'name', + type : 'string', + editor : { + allowBlank : true }, - { - text : 'Buffer Conditions', - dataIndex : 'conditions', - flex : 1, - renderer : function(val, style, record) { - return _this.getConditionHTMLTable(val, style, record); - } + flex : 1 + }, + { + header : 'Type', + name : 'additiveType', + dataIndex : 'additiveType', + editor : { + xtype : 'combobox', + typeAhead : true, + triggerAction : 'all', + selectOnTab : true, + store : BIOSAXS.proposal.getAdditiveTypes(), + lazyRender : true, + listClass : 'x-combo-list-small' }, - { - header : 'Average', - dataIndex : 'percentageCollected', - name : 'percentageCollected', - type : 'string', - hidden : true, - renderer : function(val, y, sample) { - return "
" + - BUI.getProgessBar((sample.raw.averageCount / sample.raw.measurementCount) * 100, sample.raw.averageCount + "/" + - sample.raw.measurementCount) + "
"; - }, - width : 100, - sorter : false + flex : 0.6 + }, + { + header : 'Quantity', + dataIndex : 'quantity', + name : 'quantity', + editor : { + allowBlank : true }, - { - header : 'Subtractions', - dataIndex : 'percentageCollected', - name : 'percentageCollected', - type : 'string', - hidden : true, - renderer : function(val, y, sample) { - return "
"+ BUI.getProgessBar((sample.raw.subtractionCount / sample.raw.measurementCount) * 100, sample.raw.subtractionCount + "/" + - sample.raw.measurementCount) + "
"; - }, - width : 100 - }, { - header : 'Date', - dataIndex : 'timeStart', - name : 'timeStart', - type : 'string', - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - if (record.raw.timeStart != null) { - return moment(record.raw.timeStart).format("MMM Do YY"); + type : 'string', + flex : 1 + }, + { + xtype : 'actioncolumn', + items : [ { + icon : '../images/cancel.png', + tooltip : 'Delete additive', + scope : this, + handler : function(grid, rowIndex, colIndex) { + if ((grid.getStore().getAt(rowIndex).data.bufferHasAdditiveId == null)|| (grid.getStore().getAt(rowIndex).data.bufferHasAdditiveId == "")) { + grid.getStore().removeAt(rowIndex); + } else { + this.onRemoveButtonClicked.notify({ + 'bufferId' : this.buffer.bufferId, + 'bufferHasAdditiveId' : this.store.getAt(rowIndex).data.bufferHasAdditiveId + }); } } - }, { - header : 'Download', - dataIndex : 'percentageCollected', - name : 'percentageCollected', - type : 'string', - renderer : function(val, y, sample) { - return BUI.getZipHTMLByMacromoleculeId(sample.raw.macromoleculeId); - }, - width : 100 - }, + } ] + } ]; + + return columns; +}; + +AdditiveGrid.prototype._prepareData = function() { + var data = []; + if (this.features == null) { + this.features = []; + } + for (var i = 0; i < this.features.length; i++) { + var object = this.features[i]; + object.name = this.features[i].additive3VO.name; + object.additiveType = this.features[i].additive3VO.additiveType; + object.comments = this.features[i].additive3VO.comments; + object.additiveId = this.features[i].additive3VO.additiveId; + data.push(object); + } + return data; +}; - { - id : 'btnResultVisible', - width : 85, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - return BUI.getGreenButton('GO'); - } - } ], +AdditiveGrid.prototype.getPanel = function(buffer, experiment) { + this.buffer = buffer; + this.features = buffer.bufferhasadditive3VOs; + this.experiment = experiment; + return this._renderGrid(); +}; + +AdditiveGrid.prototype.getStore = function() { + var _this = this; + var store = Ext.create('Ext.data.Store', { + fields : [ "name", "additiveType", "comments", "additiveId", "bufferHasAdditiveId", "quantity" ], + autoload : false, + data : this._prepareData(), + listeners : { + update : function(store, record) { + record.index = _this.grid.getSelectionModel().getCurrentPosition().row; + _this.buffer.bufferhasadditive3VOs[record.index].additive3VO.name = record.data.name; + _this.buffer.bufferhasadditive3VOs[record.index].additive3VO.additiveType = record.data.additiveType; + _this.buffer.bufferhasadditive3VOs[record.index].additive3VO.comments = record.data.comments; + _this.buffer.bufferhasadditive3VOs[record.index].quantity = record.data.quantity; + } + } + }); + + // store.sort('bufferHasAdditiveId', 'ASC'); + store.loadData(this._prepareData(), false); + return store; +}; + +AdditiveGrid.prototype._renderGrid = function() { + var _this = this; + this.store = this.getStore(); + + var cellEditing = Ext.create('Ext.grid.plugin.CellEditing', { + clicksToEdit : 1 + }); + + this.grid = Ext.create('Ext.grid.Panel', { + dockedItems : [ { + xtype : 'toolbar', + items : this._getActions() + } ], + store : this.store, + height : 230, + title : "Additives", + width : "100%", + columns : _this._getFields(), + plugins : [ cellEditing ], viewConfig : { stripeRows : true, listeners : { - afterrender : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - }, - celldblclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - _this.edit(record.data.macromoleculeId); - }, - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - if (grid.getGridColumns()[cellIndex].getId() == 'buttonEditMacromolecule') { - _this.edit(record.data.macromoleculeId); - } - if (grid.getGridColumns()[cellIndex].getId() == 'buttonRemoveMacromolecule') { - BUI.showBetaWarning(); - } - if (grid.getGridColumns()[cellIndex].getId() == 'btnResultVisible') { - window.location = BUI.getMacromoleculeResultsURL(record.data.macromoleculeId); - } + itemcontextmenu : function(view, rec, node, index, e) { + e.stopEvent(); + contextMenu.showAt(e.getXY()); + return false; } } + }, + selModel : { + mode : 'SINGLE' } }); - /** Adding the tbar **/ - if (this.tbar) { - this.grid.addDocked({ - xtype : 'toolbar', - items : this.getTbar() - }); - } return this.grid; }; -ResultsAssemblyGrid.prototype.input = function(targetId) { - return { - data : DATADOC.getData_3367(), - proposal : DATADOC.getProposal_3367() - }; +AdditiveGrid.prototype.input = function() { }; -ResultsAssemblyGrid.prototype.test = function(targetId) { - var grid = new ResultsAssemblyGrid({ - height : 600, - searchBar : false, - tbar : false, - btnResultVisible : true, - width : 1000 - }); - BIOSAXS.proposal = new Proposal(grid.input().proposal); - var panel = grid.getPanel(grid.input().data); +AdditiveGrid.prototype.test = function(targetId) { + var grid = new AdditiveGrid(); + var panel = grid.getPanel([]); panel.render(targetId); }; +/** AnalysisGrid **/ +function AnalysisGrid(args) { + var _this = this; -function RigidModelGrid(args) { - this.height = null; - this.width = null; this.id = BUI.id(); + if (Ext.get("mainPanel")){ + this.width = Ext.get("mainPanel").getWidth(); + } + else{ + this.width = this.maxWidth; + } + this.maxWidth = 1500; + + /** Visibles **/ + this.isGuinierTabVisible = true; + this.isGnomTabVisible = true; + this.isPorodTabVisible = true; + this.isScatteringPlotVisible = true; + this.isAbinitioTabVisible = true; + this.showButtonsVisible = true; + this.isI0Visible = true; + + this.margin = null; + this.grouped = true; + + this.hideNulls = false; + this.decimals = 4; + this.height = null; + this.sorters = [ { + property : 'conc', + direction : 'ASC' + } ]; if (args != null) { + if (args.grouped != null) { + this.grouped = args.grouped; + } + + if (args.showButtonsVisible != null) { + this.showButtonsVisible = args.showButtonsVisible; + } + if (args.isI0Visible != null) { + this.isI0Visible = args.isI0Visible; + } + if (args.sorters != null) { + this.sorters = args.sorters; + } + if (args.isScatteringPlotVisible != null) { + this.isScatteringPlotVisible = args.isScatteringPlotVisible; + } + if (args.isGuinierTabVisible != null) { + this.isGuinierTabVisible = args.isGuinierTabVisible; + } + if (args.isGnomTabVisible != null) { + this.isGnomTabVisible = args.isGnomTabVisible; + } + if (args.isPorodTabVisible != null) { + this.isPorodTabVisible = args.isPorodTabVisible; + } + if (args.hideNulls != null) { + this.hideNulls = args.hideNulls; + } if (args.height != null) { this.height = args.height; + } + if (args.width != null) { + this.width = args.width; + } + if (args.maxWidth != null) { + this.maxWidth = args.maxWidth; + } + } +} - if (args.width != null) { - this.width = args.width; +AnalysisGrid.prototype.refresh = function(data, args) { + this.store.loadData(this._prepareData(data), false); + if (args != null){ + if (args.experiment != null){ + this.experiment = args.experiment; + } + } +}; + +AnalysisGrid.prototype._getPorod = function() { + return { + text : 'Porod', + name : 'Porod', + columns : [ + { + text : 'Volume', + dataIndex : 'volumeEdna', + width : 75, + sortable : true, + hidden : !this.isPorodTabVisible, + renderer : function(val, y, sample) { + if (sample.raw.volume != null) + return BUI.formatValuesUnits(sample.raw.volume, '') + " nm3"; + } + }, + { + text : 'MM Vol. est.', + dataIndex : 'volumeEdna', + tooltip : '[Volume/2 - Volume/1.5] (Guinier)', + sortable : true, + width : 95, + hidden : !this.isPorodTabVisible, + renderer : function(val, y, sample) { + if (sample.raw.volume != null) + return Number(sample.raw.volume / 2).toFixed(1) + " - " + Number(sample.raw.volume / 1.5).toFixed(1)+ "kD"; + } + } ] + }; +}; + + +AnalysisGrid.prototype._getFramesColumn = function() { + var _this = this; + return { + text : 'Frames (Averaged/Total)', + dataIndex : 'datacollection', + name : 'datacollection', + sortable : true, + width : 150, + renderer : function(dataCollections, y, data) { + /** Bug of Webservices: frames count were swapped with frames averages **/ + if (data.raw.bufferAfterFramesCount){ + if (data.raw.bufferAfterFramesMerged){ + if (parseInt(data.raw.bufferAfterFramesMerged) > parseInt(data.raw.bufferAfterFramesCount)){ + var aux = parseInt(data.raw.bufferAfterFramesCount); + data.raw.bufferAfterFramesCount= data.raw.bufferAfterFramesMerged; + data.raw.bufferAfterFramesMerged = aux; + } + } + } + + if (data.raw.bufferBeforeFramesCount){ + if (data.raw.bufferBeforeFramesMerged){ + if (parseInt(data.raw.bufferBeforeFramesMerged) > parseInt(data.raw.bufferBeforeFramesCount)){ + var aux = parseInt(data.raw.bufferBeforeFramesCount); + data.raw.bufferBeforeFramesCount= data.raw.bufferBeforeFramesMerged; + data.raw.bufferBeforeFramesMerged = aux; + } + } + + } + + var bufferAcronym = data.raw.bufferAcronym; + var macromoleculeAcronym = data.raw.macromoleculeAcronym; + var bbmerges = data.raw.bufferBeforeFramesMerged; + var molmerges = data.raw.framesMerge; + var bamerges = data.raw.bufferAfterFramesMerged; + var totalframes = data.raw.framesCount; + var bufferId = data.raw.bufferId; + var macromoleculeId = data.raw.macromoleculeId; + var macromoleculeColor = null; + if (_this.experiment != null){ + macromoleculeColor = _this.experiment.macromoleculeColors[data.raw.macromoleculeId]; } - } - } - - this.onSelected = new Event(this); -} - - -RigidModelGrid.prototype.refresh = function(subtractions) { - var data = []; - if (subtractions != null){ - if (subtractions.length > 0){ - for (j in subtractions){ - var subtraction = subtractions[j]; - if (subtraction.rigidBodyModeling3VOs != null){ - for (i in subtraction.rigidBodyModeling3VOs){ - data.push(subtraction.rigidBodyModeling3VOs[i]); + + /** BUG in the database to be fixed **/ + try{ + if (totalframes != null){ + if(molmerges != null){ + if (parseFloat(totalframes) < parseFloat(molmerges)){ + var aux = totalframes; + totalframes = molmerges; + molmerges = aux; + } } } } + catch(e){ + + } + + return BUI.getHTMLTableForFrameAveraged(bufferAcronym, + macromoleculeAcronym, + bbmerges, + molmerges, + bamerges, + totalframes, + bufferId, + macromoleculeId, + macromoleculeColor); } - } - this.store.loadData(data); + }; }; -RigidModelGrid.prototype.getPanel = function() { +AnalysisGrid.prototype._getColumns = function() { var _this = this; - this.store = Ext.create('Ext.data.Store', { - fields : [ 'symmetry', 'subtractionId', 'subUnitConfigFilePath', 'rigidBodyModelingId', 'rigidBodyModelFilePath', 'logFilePath', 'fitFilePath', 'curveConfigFilePath', - 'crossCorrConfigFilePath', 'contactDescriptionFilePath' ], - data : [] - }); - - this.store.sort([ { - property : 'name', - direction : 'ASC' - } ]); + return [ + { + name : 'groupeField', + dataIndex : 'groupeField', + hidden : true - this.panel = Ext.create('Ext.grid.Panel', { - store : this.store, - width : this.width, - height : this.height, - margin : 10, - deferredRender : false, - columns : [ { - text : 'RBM', - dataIndex : 'rigidBodyModelFilePath', - hidden : false, - flex : 1, - renderer : function(val){ - return BUI.getFileName(val); - } - }, { - text : 'Sub Unit Conf.', - dataIndex : 'subUnitConfigFilePath', + }, + { + "header" : "subtractionId", hidden : true, - flex : 1, - renderer : function(val){ - return BUI.getFileName(val); + "dataIndex" : "subtractionId", + "name" : "subtractionId" + }, + { + header : "Macromolecule", + dataIndex : "macromoleculeAcronym", + name : "macromoleculeAcronym", + renderer : function(val, y, sample) { + return '
' + val + '
' + + BUI.formatValuesUnits(sample.raw.conc, "mg/ml", 10, this.decimals) + '
' + + BUI.formatValuesUnits(sample.raw.exposureTemperature, "C", 10, this.decimals) + '
' } - }, { - text : 'Log', - dataIndex : 'logFilePath', + }, + { + header : "Order", + dataIndex : "priorityLevelId", + name : "priorityLevelId", + hidden : true + }, + { + header : "Code", + dataIndex : "code", + name : "code", + hidden : true + }, + { + header : "Conc.", + dataIndex : "conc", + width : 80, + name : "conc", + type : "number", hidden : true, - flex : 1, - renderer : function(val){ - return BUI.getFileName(val); - } - }, { - text : 'Fit', - dataIndex : 'fitFilePath', - hidden : false, - flex : 1, - renderer : function(val){ - return BUI.getFileName(val); - } - }, { - text : 'Curve Conf.', - dataIndex : 'curveConfigFilePath', - hidden : false, - flex : 1, - renderer : function(val){ - return BUI.getFileName(val); + renderer : function(val, y, sample) { + return BUI.formatValuesUnits(val, "mg/ml", 10, this.decimals); } - }, { - text : 'Cross Corr.', - dataIndex : 'crossCorrConfigFilePath', - hidden : false, - flex : 1, - renderer : function(val){ - return BUI.getFileName(val); + }, + { + text : 'Scattering', + width : 100, + dataIndex : 'subtractionId', + name : 'subtractionId', + hidden : !this.isScatteringPlotVisible, + renderer : function(val, y, sample) { + var url = BUI.getURL() + '&type=scattering&subtractionId=' + sample.raw.subtractionId; + var event = "OnClick= window.open('" + url + "')"; + return ''; } - }, { - text : 'Contact Desc.', - dataIndex : 'contactDescriptionFilePath', + }, + { + text : 'Kratky', + width : 100, + dataIndex : 'subtractionId', hidden : true, - flex : 1, - renderer : function(val){ - return BUI.getFileName(val); + name : 'subtractionId', + renderer : function(val, y, sample) { + var url = BUI.getURL() + '&type=kratky&subtractionId=' + sample.raw.subtractionId; + var event = "OnClick= window.open('" + url + "')"; + return ''; } - } ], - - viewConfig : { - enableTextSelection : true, - preserveScrollOnRefresh : true }, - listeners : { - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - - }, - afterrender : function() { + this._getFramesColumn(), + { + text : 'File Name', + dataIndex : 'averageFilePath', + name : 'averageFilePath', + sortable : true, + width : 150, + hidden : true, + renderer : function(dataCollections, y, data) { + return BUI.getHTMLTableForPrefixes(data.raw.bufferBeforeAverageFilePath, data.raw.averageFilePath, + data.raw.bufferAfterAverageFilePath); } - } - }); - return this.panel; -}; + }, - -/** - * shows shipments - * - * @height - * @width - * @minHeight - * @btnEditVisible - */ -function ShipmentGrid(args) { - this.id = BUI.id(); - this.height = 100; - this.width = null; - this.minHeight = null; - this.btnEditVisible = true; + { + text : 'Guinier', + name : 'Guinier', + columns : [ + { + text : 'Rg', + dataIndex : 'rgGuinier', + name : 'rgGuinier', + hidden : !this.isGuinierTabVisible, + width : 75, + tooltip : 'In polymer physics, the radius of gyration is used to describe the dimensions of a polymer chain.', + sortable : true, + renderer : function(val, y, sample) { + if (sample.raw.rgGuinier != null) { + /** Show warning if rgGuinier and rgGnom differ more than 10% **/ + if (Math.abs(sample.raw.rgGuinier - sample.raw.rgGnom) > (sample.raw.rgGuinier * 0.1)) { + return "" + BUI.formatValuesUnits(sample.raw.rgGuinier, "") + ""; - if (args != null) { - if (args.height != null) { - this.height = args.height; - } - if (args.width != null) { - this.width = args.width; - } - if (args.minHeight != null) { - this.minHeight = args.minHeight; - } - if (args.btnEditVisible != null) { - this.btnEditVisible = args.btnEditVisible; - } - } -} + } + return BUI.formatValuesUnits(sample.raw.rgGuinier, "nm", 12, this.decimals); + } + } + }, + { + text : 'Points', + dataIndex : 'points', + sortable : true, + width : 100, + type : 'string', + hidden : !this.isGuinierTabVisible, + renderer : function(val, y, sample) { + if ((sample.raw.firstPointUsed == "") || (sample.raw.firstPointUsed == null)) + return; + return "" + sample.raw.firstPointUsed + " - " + sample.raw.lastPointUsed + " (" + + (sample.raw.lastPointUsed - sample.raw.firstPointUsed) + " )"; + } + }, + { + text : 'Quality', + dataIndex : 'quality', + hidden : !this.isGuinierTabVisible, + tooltip : 'Estimated data quality. 1.0 - means ideal quality, 0.0 - unusable data. In table format it is given in percent (100% - ideal quality, 0% - unusable data). Please note that this estimation is based only on the Guinier interval (very low angles).', + width : 60, + sortable : true, + renderer : function(val, y, sample) { + if (sample.raw.quality != null) { + val = sample.raw.quality; + if ((val != null) && (val != "")) { + return "" + (Number(val) * 100).toFixed(2) + " %"; + } + } + } + }, { + text : 'I(0)', + dataIndex : 'I0', + sortable : true, + hidden : !this.isI0Visible, + tooltip : 'Extrapolated scattering intensity at zero angle I(0) (forward scattering)', + width : 75, + type : 'string', + renderer : function(val, y, sample) { + if (sample.raw.I0 != null) { + return BUI.formatValuesErrorUnitsScientificFormat(sample.raw.I0, sample.raw.i0stdev, ""); + } + } + }, { + text : 'Aggregated', + tooltip : "If aggregation was detected from the slope of the data curve at low angles the value is '1', otherwise '0'.", + dataIndex : 'isagregated', + hidden : true, + width : 75, + renderer : function(val, y, sample) { + if ((sample.raw.isagregated != null)) { + if (val == true) { + return "Yes"; + } else { + return "No"; + } + } + } + }, { + text : 'Guinier', + sortable : true, + dataIndex : 'subtractionId', + type : 'string', + width : 100, + hidden : true, + renderer : function(val, y, sample) { -ShipmentGrid.prototype._getColumns = function() { - var _this = this; - var columns = [ - { - text : 'Name', - dataIndex : 'shippingName', - flex : 1 + if (sample.raw.subtractionId != null) { + var url = BUI.getURL() + '&type=guinier&subtractionId=' + sample.raw.subtractionId; + var event = "OnClick= window.open('" + url + "')"; + return ''; + } + } + } ] }, { - header : 'Type', - dataIndex : 'shippingType', - flex : 1, - hidden : true, - renderer : function(val, comp, record) { - if (val != null) { - return val.toUpperCase(); - } + text : 'Gnom', + name : 'Gnom', - } - }, - { - header : 'Status', - type : 'string', - flex : 1, - hidden : false, - renderer : function(comp, val, record) { - if (record.raw.shippingStatus != null) { - if (new String(record.raw.shippingStatus).toUpperCase() == 'OPENED') { - return "" + new String(record.raw.shippingStatus).toUpperCase() + ""; + columns : [ { + text : 'Rg', + dataIndex : 'rgGnom', + type : 'string', + width : 65, + hidden : !this.isGnomTabVisible, + sortable : true, + renderer : function(val, y, sample) { + /** Show warning if rgGuinier and rgGnom differ more than 10% **/ + if (sample.raw.rgGnom != null) { + if (Math.abs(sample.raw.rgGuinier - sample.raw.rgGnom) > (sample.raw.rgGuinier * 0.1)) { + return "" + BUI.formatValuesUnits(sample.raw.rgGnom, "") + ""; + + } + return BUI.formatValuesUnits(sample.raw.rgGnom, "nm"); } - return "" + new String(record.raw.shippingStatus).toUpperCase() + ""; } - } + }, { + text : 'Total', + dataIndex : 'total', + width : 65, + hidden : !this.isGnomTabVisible, + sortable : true, + renderer : function(val, y, sample) { + if (sample.raw.total != null) + return BUI.formatValuesUnits(sample.raw.total, ''); + } + }, { + text : 'Dmax', + dataIndex : 'dmax', + sortable : true, + width : 75, + hidden : !this.isGnomTabVisible, + renderer : function(val, y, sample) { + if (sample.raw.dmax != null) + return BUI.formatValuesUnits(sample.raw.dmax, "") + " nm"; + } + }, { + text : 'P(r)', + sortable : true, + hidden : true, + width : 100, + dataIndex : 'subtractionId', + type : 'string', + renderer : function(val, y, sample) { + var url = BUI.getURL() + '&type=gnom&subtractionId=' + sample.raw.subtractionId; + var event = "OnClick= window.open('" + url + "')"; + return ''; + } + } ] }, + this._getPorod(), { - text : 'Cases', - flex : 1, - hidden : false, - renderer : function(comp, val, record) { - var shipment = BIOSAXS.proposal.getShipmentById(record.data.shippingId); - var container = ""; - if (shipment.dewarVOs.length > 0) { - container = container + ""; - } else { - return "Empty"; - } - return container + "
" + shipment.dewarVOs.length + "x
"; - } - }, { - header : 'Comments', - dataIndex : 'comments', - flex : 1, - hidden : false - }, { - header : 'Creation Date', - dataIndex : 'creationDate', - hidden : true - } ]; - - if (this.btnEditVisible) { - columns.push({ - id : _this.id + 'buttonEdit', - text : '', - hidden : !_this.btnEditVisible, - width : 100, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - return BUI.getGreenButton('EDIT'); - } - }); - } - - columns.push({ - id : _this.id + 'buttonRemove', - text : '', - width : 100, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - var shipment = BIOSAXS.proposal.getShipmentById(record.data.shippingId); - if (shipment.dewarVOs.length == 0) { - return BUI.getRedButton('REMOVE'); - } - - } - }); - - return columns; -}; - -ShipmentGrid.prototype._getTopButtons = function() { - var _this = this; - /** Actions buttons **/ - var actions = []; - actions.push(Ext.create('Ext.Action', { - icon : '../images/add.png', - text : 'Add Shipment', - handler : function(widget, event) { - //window.location = BUI.getCreateShipmentURL(); - var _this = this; - - var shipmentForm = new ShipmentForm({ - creationMode : true, - showTitle : false - }); - shipmentForm.onSaved.attach(function(sender, shipment) { - _this.showShipmentTabs(shipment, targetId); - }); - - var window = Ext.create('Ext.window.Window', { - title : 'New Shipment', - height : 600, - width : 800, - layout : 'fit', - items : [ shipmentForm.getPanel() ] - }).show(); - - } - })); - return actions; -}; - -ShipmentGrid.prototype.refresh = function(shippings) { - this.features = shippings; - this.store.loadData(this._prepareData(), false); -}; - -ShipmentGrid.prototype._prepareData = function() { - var data = []; - for ( var i = 0; i < this.features.length; i++) { - data.push(this.features[i]); - } - return data; -}; - -ShipmentGrid.prototype.getPanel = function(shipments) { - this.features = shipments; - return this._renderGrid(); -}; - -ShipmentGrid.prototype.edit = function(shippingId) { - window.location = BUI.getShippingURL(shippingId); -}; - -ShipmentGrid.prototype._getStoreFields = function(data) { - var _this = this; - return [ { - name : 'shippingId' - }, { - name : 'shippingName' - }, { - name : 'shippingStatus' - }, { - name : 'shippingType' - }, { - name : 'creationDate' - }, { - name : 'comments' - } ]; -}; - -ShipmentGrid.prototype._renderGrid = function() { - var _this = this; - - /** Store **/ - var data = this._prepareData(); - this.store = Ext.create('Ext.data.Store', { - fields : this._getStoreFields(data), - autoload : true, - data : data - }); - - this.store.loadData(data, false); + text : 'AbInitio Modeling', + name : 'AbInitio_modeling', - this.grid = Ext.create('Ext.grid.Panel', { - title : "Shipping", - icon : '/ispyb/images/plane.gif', - width : this.width, - minWidth : this.minWidth, - height : this.height, - store : this.store, - columns : this._getColumns(), - viewConfig : { - stripeRows : true, - listeners : { - itemdblclick : function(dataview, record, item, e) { - _this.edit(record.raw.shippingId); + columns : [ + { + text : 'NSD', + dataIndex : 'volumeEdna', + width : 100, + sortable : true, + hidden : true, + renderer : function(val, y, sample) { + var url = BUI.getNSDImageURL(sample.raw.modelListId); + var event = "OnClick= window.open('" + url + "')"; + return ''; + } }, - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEdit') { - _this.edit(record.data.shippingId); + { + text : 'Chi2', + dataIndex : 'volumeEdna', + sortable : true, + hidden : true, + width : 100, + renderer : function(val, y, sample) { + var url = BUI.getCHI2ImageURL(sample.raw.modelListId); + var event = "OnClick= window.open('" + url + "')"; + return ''; } + }, + { + text : 'Pdb', + dataIndex : 'volumeEdna', + tooltip : 'Damaver: The program suite DAMAVER is a set of programs to align ab initio models, select the most typical one and build an averaged model. Dammif : Rapid ab initio shape determination by simulated annealing using a single phase dummy atom model. Dammin :Ab initio shape determination by simulated annealing using a single phase dummy atom model', + sortable : true, + width : 125, + hidden : !this.isAbinitioTabVisible, + renderer : function(val, y, sample) { + var html = new String(); + var split = null; + var url = null; + var file = sample.raw.averagedModel; + if (file != null) { + split = file.split("/"); + if (split.length > 0) { + url = BUI.getPdbURL() + '&type=AVERAGED&abInitioModelId=' + sample.raw.abInitioModelId; + html = html + ''+ split[split.length - 1] + '

'; - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemove') { - var shipment = BIOSAXS.proposal.getShipmentById(record.data.shippingId); - if (shipment.dewarVOs.length == 0) { + } + } - var adapter = new BiosaxsDataAdapter(); - _this.grid.setLoading("ISPyB: Removing shipment"); - adapter.onSuccess.attach(function(sender) { - BIOSAXS.proposal.onInitialized.attach(function(sender) { - _this.refresh(BIOSAXS.proposal.getShipments()); - _this.grid.setLoading(false); - }); - BIOSAXS.proposal.init(); - }); + file = sample.raw.rapidShapeDeterminationModel; + if (file != null) { + split = file.split("/"); + if (split.length > 0) { + url = BUI.getPdbURL() + '&type=RAPIDSHAPEDETERMINATIONMODEL&abInitioModelId=' + sample.raw.abInitioModelId; + html = html + '' + split[split.length - 1] + '

'; + } + } - adapter.onError.attach(function(sender) { - alert("Error"); - _this.grid.setLoading(false); - }); - adapter.removeShipment(record.data.shippingId); + file = sample.raw.shapeDeterminationModel; + if (file != null) { + split = file.split("/"); + if (split.length > 0) { + url = BUI.getPdbURL() + '&type=SHAPEDETERMINATIONMODEL&abInitioModelId=' + sample.raw.abInitioModelId; + html = html + ''+ split[split.length - 1] + ''; + } } + return html; } - } - } - }, - selModel : { - mode : 'SINGLE' - } - }); - - var actions = _this._getTopButtons(); - this.grid.addDocked({ - xtype : 'toolbar', - items : actions - }); - - this.grid.getSelectionModel().on({ - selectionchange : function(sm, selections) { - if (selections.length) { - for ( var i = 0; i < actions.length; i++) { - if (actions[i].enable) { - actions[i].enable(); + }, + { + text : 'Damaver', + dataIndex : 'volumeEdna', + hidden : true, + tooltip : 'Damaver: The program suite DAMAVER is a set of programs to align ab initio models, select the most typical one and build an averaged model. ', + sortable : true, + width : 125, + renderer : function(val, y, sample) { + var file = sample.raw.averagedModel; + if (file != null) { + var split = file.split("/"); + if (split.length > 0) { + var url = BUI.getPdbURL() + '&type=AVERAGED&abInitioModelId=' + sample.raw.abInitioModelId; + return '' + split[split.length - 1]+ ''; + } + } + return sample.raw.averagedModel; } - } - } else { - for ( var i = 0; i < actions.length; i++) { - if (actions[i].alwaysEnabled == false) { - if (actions[i].disable) { - actions[i].disable(); + }, + { + text : 'Dammif', + dataIndex : 'volumeEdna', + hidden : true, + tooltip : 'Dammif : Rapid ab initio shape determination by simulated annealing using a single phase dummy atom model', + sortable : true, + width : 125, + renderer : function(val, y, sample) { + var file = sample.raw.rapidShapeDeterminationModel; + if (file != null) { + var split = file.split("/"); + if (split.length > 0) { + var url = BUI.getPdbURL() + '&type=RAPIDSHAPEDETERMINATIONMODEL&abInitioModelId=' + sample.raw.abInitioModelId; + return '' + split[split.length - 1] + ''; + } } + return sample.raw.averagedModel; } - } - } - } - }); - return this.grid; -}; - -ShipmentGrid.prototype.input = function() { - return { - proposal : new MeasurementGrid().input().proposal, - shippings : DATADOC.getShippings_10() - }; -}; - -ShipmentGrid.prototype.test = function(targetId) { - var shipmentGrid = new ShipmentGrid({ - minHeight : 300, - height : 440 - }); - BIOSAXS.proposal = new Proposal(shipmentGrid.input().proposal); - var panel = shipmentGrid.getPanel(targetId); - panel.render(targetId); - shipmentGrid.refresh(shipmentGrid.input().shippings); -}; - -function SpecimenGrid(args) { - this.id = BUI.id(); - this.height = 500; - this.unitsFontSize = 9; - this.editEnabled = false; - this.isPositionColumnHidden = false; - this.removeBtnEnabled = false; - - this.selectionMode = "MULTI"; - this.updateRowEnabled = false; - this.grouped = true; - this.width = 900; - this.title = 'Specimens'; - - this.margin = "0 0 0 0"; -// this.experimentColorBased = false; - - if (args != null) { - if (args.height != null) { - this.height = args.height; - } - - if (args.showTitle == false) { - this.title = null; - } - - if (args.margin == false) { - this.margin = args.margin; - } - - if (args.grouped == false) { - this.grouped = null; - } - - if (args.width != null) { - this.width = args.width; - } - - - if (args.editEnabled != null) { - this.editEnabled = args.editEnabled; - } - if (args.removeBtnEnabled != null) { - this.removeBtnEnabled = args.removeBtnEnabled; - } - if (args.isPositionColumnHidden != null) { - this.isPositionColumnHidden = args.isPositionColumnHidden; - } - if (args.selectionMode != null) { - this.selectionMode = args.selectionMode; - } - if (args.updateRowEnabled != null) { - this.updateRowEnabled = args.updateRowEnabled; - } - - } - this.onClick = new Event(this); - this.onSelected = new Event(this); - this.onRemoved = new Event(this); - this.onSpecimenChanged = new Event(); -} - -SpecimenGrid.prototype._prepareData = function(experiment) { - var data = []; - - var samples = experiment.getSamples(); - for ( var i = 0; i < samples.length; i++) { - var sample = samples[i]; - if (sample.macromolecule3VO != null) { - sample.macromolecule = sample.macromolecule3VO.acronym; - sample.exposureTemperature = []; - sample.macromoleculeId = sample.macromolecule3VO.macromoleculeId; - } + }, + { + text : 'Dammin', + dataIndex : 'volumeEdna', + hidden : true, + tooltip : 'Dammin :Ab initio shape determination by simulated annealing using a single phase dummy atom model', + sortable : true, + width : 125, + renderer : function(val, y, sample) { + var file = sample.raw.shapeDeterminationModel; + if (file != null) { + var split = file.split("/"); + if (split.length > 0) { + var url = BUI.getPdbURL() + '&type=SHAPEDETERMINATIONMODEL&abInitioModelId=' + sample.raw.abInitioModelId; + return '' + split[split.length - 1]+ ''; + } + } + return sample.raw.averagedModel; + } + } ] + }, { + text : 'Time', + dataIndex : 'substractionCreationTime', + name : 'substractionCreationTime', + hidden : true, + width : 80, + sortable : true, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + try { + if (record.raw.substractionCreationTime != null) { + return moment(record.raw.substractionCreationTime).format('h:mm:ss a'); + } + } catch (e) { + return "NA"; + } + } + }, { + text : 'Date', + dataIndex : 'substractionCreationTime', + name : 'substractionCreationTime', + hidden : true, + width : 80, + sortable : true, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + try { + if (record.raw.substractionCreationTime != null) { + return moment(record.raw.substractionCreationTime).format("LL"); + } + } catch (e) { + return "NA"; + } + } + }, + this._getButtons()]; +}; - if (sample.sampleplateposition3VO != null) { - if (sample.sampleplateposition3VO.samplePlateId != null) { - sample.samplePlateId = sample.sampleplateposition3VO.samplePlateId; - sample.rowNumber = sample.sampleplateposition3VO.rowNumber; - sample.columnNumber = sample.sampleplateposition3VO.columnNumber; - if (experiment.getSamplePlateById(sample.sampleplateposition3VO.samplePlateId).plategroup3VO != null) { - sample.plateGroupName = experiment.getSamplePlateById(sample.sampleplateposition3VO.samplePlateId).plategroup3VO.name; - sample.samplePlateName = experiment.getSamplePlateById(sample.sampleplateposition3VO.samplePlateId).name + " [" + sample.plateGroupName + "]"; - sample.slotPositionColumn = experiment.getSamplePlateById(sample.sampleplateposition3VO.samplePlateId).slotPositionColumn; +AnalysisGrid.prototype._getButtons = function() { + return { + id : this.id + 'buttonPlot', + name : 'buttonPlot', + hidden : !this.showButtonsVisible, + width : 110, + sortable : false, + renderer : function(value, metaData, sample, rowIndex, colIndex, store) { + var html = ""; + + if (sample.raw.subtractionId) { + html = html + ""; + if (sample.raw.rapidShapeDeterminationModelId != null) { + html = html + ""; } } - } else { - sample.samplePlateName = "Unallocated Specimens"; + return html + "
" + BUI.getGreenButton('Calibration', { + height : 20, + width : 100 + }) + "
" + BUI.getGreenButton('Primary Data Proc.', { + height : 20, + width : 100 + }) + "
" + BUI.getGreenButton('AbInitio Modeling', { + height : 20, + width : 100 + }) + "
"; } - - /** For grouping, because sencha has not option for multiple grouping I add a field to your store with a convert function that concatenates these two fields and then group by that field.**/ - sample.groupIndex = sample.bufferId + sample.macromoleculeId; - var macromolecule = BIOSAXS.proposal.getMacromoleculeById(sample.macromoleculeId); - - sample.acronym = "Buffers"; - if (macromolecule != null) { - sample.acronym = BIOSAXS.proposal.getMacromoleculeById(sample.macromoleculeId).acronym; + }; +}; +AnalysisGrid.prototype._prepareData = function(data) { + if (this.hideNulls) { + var result = []; + for ( var i = 0; i < data.length; i++) { + if (data[i].subtractionId != null) { + data[i].groupeField = data[i].macromoleculeAcronym + " " + data[i].bufferAcronym; + result.push(data[i]); + } } - - sample.buffer = experiment.getBufferById(sample.bufferId); - - sample.volumeToLoad = experiment.getVolumeToLoadBySampleId(sample.sampleId); - data.push(sample); + return result; + } else { + return data; } - return data; }; -SpecimenGrid.prototype.deselectAll = function() { - this.grid.getSelectionModel().deselectAll(); -}; +AnalysisGrid.prototype.getPanel = function(data) { + var _this = this; + var columns = this._getColumns(); -SpecimenGrid.prototype.selectById = function(specimenId) { - this.grid.getSelectionModel().deselectAll(); - for ( var i = 0; i < this.grid.getStore().data.items.length; i++) { - var item = this.grid.getStore().data.items[i].raw; - if (item.specimenId == specimenId) { - this.grid.getSelectionModel().select(i); - } - } -}; + var fields = JSON.parse(JSON.stringify(columns)); + fields.push({ + name : 'experimentId', + dataIndex : 'experimentId' -SpecimenGrid.prototype.getStore = function() { - return this.store; -}; + }); + this.store = Ext.create('Ext.data.Store', { + fields : fields, + autoload : true, + data : this._prepareData(data), + groupField : 'groupeField' + }); -SpecimenGrid.prototype.getPlugins = function() { - var _this = this; + this.store.sort(this.sorters); - var plugins = []; + var features = []; - if (this.updateRowEnabled) { - plugins.push(Ext.create('Ext.grid.plugin.RowEditing', { - clicksToEdit : 1, + if (this.grouped) { + features.push({ + ftype : 'grouping', + groupHeaderTpl : '{name}', + hideGroupedHeader : false, + startCollapsed : false + }); + } + + this.grid = Ext.create('Ext.grid.Panel', { + style : { + padding : 5 + }, + maxWidth : this.maxWidth, + width : this.width, + height : this.height, + store : this.store, + columns : columns, + resizable : true, + features : features, + viewConfig : { + preserveScrollOnRefresh : true, + stripeRows : true, listeners : { - validateedit : function(grid, e) { - var measurements = []; + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - if (e.newValues.bufferId != e.record.raw.bufferId) { - /** If buffer has changed we have to change all the specimens sharing same datacollection **/ - var dataCollections = []; - if (e.record.raw.macromoleculeId == null) { - dataCollections = dataCollections.concat(_this.experiment.getDataCollectionsBySpecimenId(e.record.raw.specimenId)); - } else { - var sampleDataCollections = _this.experiment.getDataCollectionsBySpecimenId(e.record.raw.specimenId); - for ( var i = 0; i < sampleDataCollections.length; i++) { - var sampleDataCollection = sampleDataCollections[i]; - if (sampleDataCollection != null) { - for ( var j = 0; j < sampleDataCollection.measurementtodatacollection3VOs.length; j++) { - var measurementTODc = sampleDataCollection.measurementtodatacollection3VOs[j]; - if (measurementTODc.dataCollectionOrder == 1) { - dataCollections = dataCollections.concat(_this.experiment.getDataCollectionsBySpecimenId(_this.experiment - .getMeasurementById(measurementTODc.measurementId).specimenId)); - } - } - } - } - } - var i = null; - for ( i = 0; i < dataCollections.length; i++) { - var dataCollection = dataCollections[i]; - var specimens = _this.experiment.getSpecimenByDataCollectionId(dataCollection.dataCollectionId); - measurements = measurements.concat(specimens); + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonPlot') { + if (e.target.defaultValue == 'AbInitio Modeling') { + var url = BUI.getPDBVisualizerURL(record.raw.averagedModelId, record.raw.subtractionId, record.raw.experimentId); + window.open(url, "_blank"); } - for ( i = 0; i < measurements.length; i++) { - var measurement = measurements[i]; - var specimen = _this.experiment.getSpecimenById(measurement.specimenId); - specimen.bufferId = e.newValues.bufferId; - new BiosaxsDataAdapter().saveSpecimen(specimen, _this.experiment); + if (e.target.defaultValue == 'Primary Data Proc.') { + _this._edit(record.raw); } - } - - /** Setting values **/ - e.record.raw.concentration = e.newValues.concentration; - e.record.raw.volume = e.newValues.volume; - /** Position **/ - if (e.record.raw.sampleplateposition3VO != null) { - var samplePlate = _this.experiment.getSamplePlateBySlotPositionColumn(e.newValues.slotPositionColumn); - if (samplePlate != null) { - e.record.raw.sampleplateposition3VO = { - columnNumber : e.newValues.columnNumber, - rowNumber : e.newValues.rowNumber, - samplePlateId : samplePlate.samplePlateId - }; - } - } else { - if (e.newValues.slotPositionColumn != null) { - var samplePlate = _this.experiment.getSamplePlateBySlotPositionColumn(e.newValues.slotPositionColumn); - if (samplePlate != null) { - e.record.raw.sampleplateposition3VO = { - columnNumber : e.newValues.columnNumber, - rowNumber : e.newValues.rowNumber, - samplePlateId : samplePlate.samplePlateId - }; - } + if (e.target.defaultValue == 'Calibration') { + _this._showCalibration(record.raw); } } - - var macromoleculeId = e.record.data.macromoleculeId; - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, specimen) { - /** Because macromolecule3VO is fecthed LAZY **/ - if (macromoleculeId != null) { - specimen.macromolecule3VO = BIOSAXS.proposal.getMacromoleculeById(macromoleculeId); - } - _this.onSpecimenChanged.notify(specimen); - _this.grid.setLoading(false); - }); - adapter.onError.attach(function() { - alert("Error"); - _this.grid.setLoading(false); - }); - _this.grid.setLoading(); - adapter.saveSpecimen(e.record.raw, _this.experiment); } } - })); - } - return plugins; + }, + selModel : { + mode : 'SINGLE' + } + }); + + return this.grid; + +}; + +AnalysisGrid.prototype._openVisualizarBySubstractionId = function(record) { + //experimentId, subtractionId) { + var experimentId = record.experimentId; + var subtractionId = record.subtractionId; + + var _this = this; + var adapter = new BiosaxsDataAdapter(); + this.subtractionId = subtractionId; + + adapter.onSuccess.attach(function(sender, data) { + var experiment = new Experiment(data); + var experimentList = new ExperimentList([ experiment ]); + var subtraction = experiment.getSubtractionById(_this.subtractionId); + _this.grid.setLoading(false); + _this._openVisualizer(experimentList, subtraction, record); + }); + this.grid.setLoading("ISPyB: Fetching experiment"); + adapter.getExperimentById(experimentId, "MEDIUM"); }; -SpecimenGrid.prototype._getRowCombo = function() { - var data = []; - for ( var i = 1; i <= 8; i++) { - data.push({ - rowNumber : i, - name : BUI.getSamplePlateLetters()[i - 1] +AnalysisGrid.prototype._edit = function(record) { + var experimentId = record.experimentId; + var _this = this; + + if (BIOSAXS.proposal.macromolecules == null) { + this.grid.setLoading("ISPyB: Fetching proposal"); + BIOSAXS.proposal.onInitialized.attach(function(sender, data) { + _this._openVisualizarBySubstractionId(record); }); + BIOSAXS.proposal.init(); + } else { + this._openVisualizarBySubstractionId(record); } +}; - var positionsStore = Ext.create('Ext.data.Store', { - fields : [ 'rowNumber', 'name' ], - data : data - }); - return Ext.create('Ext.form.ComboBox', { - store : positionsStore, - queryMode : 'local', - displayField : 'name', - valueField : 'rowNumber' +AnalysisGrid.prototype._showCalibration = function(row) { + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + Ext.create('Ext.window.Window', { + title : 'Calibration', + width : 900, + resizable : true, + height : 400, + modal : true, + frame : false, + draggable : true, + closable : true, + autoscroll : true, + paddin : 5, + layout : { + type : 'vbox', + align : 'stretch' + }, + items : [ new AnalysisGrid({ + isGuinierTabVisible : false, + isGnomTabVisible : false, + isPorodTabVisible : false, + isAbinitioTabVisible : false, + isI0Visible : true, + showButtonsVisible : false, + height : 350, + sorters : [ { + property : 'experimentId', + direction : 'DESC' + } ] + }).getPanel(data) ] + }).show(); }); + adapter.getAnalysisCalibrationByProposalId(); }; -SpecimenGrid.prototype._getColumnCombo = function() { - var data = []; - for ( var i = 1; i <= 12; i++) { - data.push({ - columnNumber : i - }); +AnalysisGrid.prototype._openVisualizer = function(experimentList, subtraction, record) { + var merges = experimentList.getMergesByDataCollectionId(subtraction.dataCollectionId); + var mergeIdList = []; + for ( var i = 0; i < merges.length; i++) { + mergeIdList.push(merges[i].mergeId); } - var positionsStore = Ext.create('Ext.data.Store', { - fields : [ 'columnNumber' ], - data : data + var dataAdapter = new BiosaxsDataAdapter(); + dataAdapter.onSuccess.attach(function(sender, merges) { + var dataCollectionCurveVisualizer = new DataCollectionCurveVisualizer(); + dataCollectionCurveVisualizer.draw(); + dataCollectionCurveVisualizer.refresh(merges, experimentList, subtraction.dataCollectionId, record); }); - return Ext.create('Ext.form.ComboBox', { - store : positionsStore, - queryMode : 'local', - displayField : 'columnNumber', - valueField : 'columnNumber' + dataAdapter.onError.attach(function(sender, error) { }); + + dataAdapter.getMergesByIdsList(mergeIdList); }; -SpecimenGrid.prototype._getSlotColumBombo = function() { - if (this.experiment){ - var length = this.experiment.getSamplePlates().length; - - var data = []; - for ( var i = 1; i <= length; i++) { - data.push({ - slotPositionColumn : i - }); - } +AnalysisGrid.prototype.input = function() { + return { + data : DATADOC.getData_3367().slice(20, 30),//[{"total":"0.447505552082","bufferBeforeMeasurementId":22150,"sampleMergeId":12373,"averagedModelId":43636,"I0":"32.50776","proposalCode":"OPD","averagedModel":"/data/pyarch/bm29/opd29/1137/1d/damaver.pdb","bufferAfterMergeId":12374,"framesCount":"10","bufferBeforeMergeId":12372,"averageFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_016_ave.dat","bufferAfterMeasurementId":22152,"rgGuinier":"2.96883","subtractedFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_016_sub.dat","firstPointUsed":"30","chi2RgFilePath":"/data/pyarch/bm29/opd29/1137/1d/chi2_R.png","abInitioModelId":272,"macromoleculeId":112,"code":"_20.0_1.25","transmission":"100.0","timeStart":"2013-07-17 17:10:25.743734","bufferAcronym":"MES","quality":"0.87091","shapeDeterminationModelId":43638,"expermientComments":"[BsxCube] Generated from BsxCube","bufferId":707,"isagregated":"False","dmax":"10.390905","bufferBeforeAverageFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_015_ave.dat","exposureTemperature":"20.0","subtractionId":5165,"conc":"1.25","rapidShapeDeterminationModel":"/data/pyarch/bm29/opd29/1137/1d/damfilt.pdb","experimentCreationDate":"Jul 17, 2013 5:08:37 PM","lastPointUsed":"92","modelListId":272,"framesMerge":"10","rapidShapeDeterminationModelId":43637,"bufferAfterAverageFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_017_ave.dat","nsdFilePath":"/data/pyarch/bm29/opd29/1137/1d/nsd.png","bufferAfterFramesMerged":"10","experimentId":1137,"macromoleculeAcronym":"MG386","i0stdev":"0.05726128","sampleMeasurementId":22151,"measurementComments":"[1] MES","priorityLevelId":2,"bufferBeforeFramesMerged":"10","substractionCreationTime":"Jul 17, 2013 5:12:32 PM","proposalNumber":"29","rgGnom":"3.05242714339","volume":"44.1406","shapeDeterminationModel":"/data/pyarch/bm29/opd29/1137/1d/dammin.pdb","comments":null},{"total":"0.582641941147","bufferBeforeMeasurementId":22152,"sampleMergeId":12375,"averagedModelId":43809,"I0":"31.4366153846","proposalCode":"OPD","averagedModel":"/data/pyarch/bm29/opd29/1137/1d/damaver.pdb","bufferAfterMergeId":12376,"framesCount":"10","bufferBeforeMergeId":12374,"averageFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_018_ave.dat","bufferAfterMeasurementId":22155,"rgGuinier":"2.95541","subtractedFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_018_sub.dat","firstPointUsed":"21","chi2RgFilePath":"/data/pyarch/bm29/opd29/1137/1d/chi2_R.png","abInitioModelId":273,"macromoleculeId":112,"code":"_20.0_0.65000000000000002","transmission":"100.0","timeStart":"2013-07-17 17:12:55.837462","bufferAcronym":"MES","quality":"0.870164","shapeDeterminationModelId":43811,"expermientComments":"[BsxCube] Generated from BsxCube","bufferId":707,"isagregated":"False","dmax":"10.343935","bufferBeforeAverageFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_017_ave.dat","exposureTemperature":"20.0","subtractionId":5166,"conc":"0.65000000000000002","rapidShapeDeterminationModel":"/data/pyarch/bm29/opd29/1137/1d/damfilt.pdb","experimentCreationDate":"Jul 17, 2013 5:08:37 PM","lastPointUsed":"80","modelListId":273,"framesMerge":"10","rapidShapeDeterminationModelId":43810,"bufferAfterAverageFilePath":" /data/pyarch/bm29/opd29/1137/1d/MG386_019_ave.dat","nsdFilePath":"/data/pyarch/bm29/opd29/1137/1d/nsd.png","bufferAfterFramesMerged":"10","experimentId":1137,"macromoleculeAcronym":"MG386","i0stdev":"0.100250461538","sampleMeasurementId":22154,"measurementComments":"[2] MES","priorityLevelId":4,"bufferBeforeFramesMerged":"10","substractionCreationTime":"Jul 17, 2013 5:15:02 PM","proposalNumber":"29","rgGnom":"2.9963404542","volume":"42.2255","shapeDeterminationModel":"/data/pyarch/bm29/opd29/1137/1d/dammin.pdb","comments":null}], + proposal : new ResultsAssemblyGrid().input().proposal + }; +}; + +AnalysisGrid.prototype.test = function(targetId) { + var analysisGrid = new AnalysisGrid(); + BIOSAXS.proposal = new Proposal(analysisGrid.input().proposal); + var panel = analysisGrid.getPanel(analysisGrid.input().data); + panel.render(targetId); +}; + + +function HPLCAnalysisGrid(args) { + AnalysisGrid.prototype.constructor.call(this, args); +} - var positionsStore = Ext.create('Ext.data.Store', { - fields : [ 'slotPositionColumn' ], - data : data - }); +HPLCAnalysisGrid.prototype._edit = AnalysisGrid.prototype._edit; +HPLCAnalysisGrid.prototype._getColumns = AnalysisGrid.prototype._getColumns; +HPLCAnalysisGrid.prototype._openVisualizarBySubstractionId = AnalysisGrid.prototype._openVisualizarBySubstractionId; +HPLCAnalysisGrid.prototype._openVisualizer = AnalysisGrid.prototype._openVisualizer; +HPLCAnalysisGrid.prototype._prepareData = AnalysisGrid.prototype._prepareData; +HPLCAnalysisGrid.prototype._showCalibration = AnalysisGrid.prototype._showCalibration; +HPLCAnalysisGrid.prototype.getPanel = AnalysisGrid.prototype.getPanel; +HPLCAnalysisGrid.prototype.input = AnalysisGrid.prototype.input; +HPLCAnalysisGrid.prototype.test = AnalysisGrid.prototype.test; +HPLCAnalysisGrid.prototype.refresh = AnalysisGrid.prototype.refresh; +HPLCAnalysisGrid.prototype._getPorod = AnalysisGrid.prototype._getPorod; + +HPLCAnalysisGrid.prototype._getButtons = function() { + return { + id : this.id + 'buttonPlot', + name : 'buttonPlot', + hidden : !this.showButtonsVisible, + width : 110, + sortable : false, + renderer : function(value, metaData, sample, rowIndex, colIndex, store) { + var html = ""; - return Ext.create('Ext.form.ComboBox', { - store : positionsStore, - queryMode : 'local', - displayField : 'slotPositionColumn', - valueField : 'slotPositionColumn' - }); + if (sample.raw.subtractionId) { + if (sample.raw.rapidShapeDeterminationModelId != null) { + html = html + ""; + } + } + return html + "
" + BUI.getGreenButton('AbInitio Modeling', { + height : 20, + width : 100 + }) + "
"; + } + }; +}; + +HPLCAnalysisGrid.prototype._getFramesColumn = function() { + return { + text : 'Frames', + dataIndex : 'datacollection', + name : 'datacollection', + sortable : true, + width : 150, + renderer : function(dataCollections, y, data) { + molmerges = data.raw.framesMerge; + totalframes = data.raw.framesCount; + return molmerges +" - "+ totalframes; + } + }; +}; + + + + +/** + * Rigid body grid to show PDB, symmetry and multiplicity + * + * + * #onUploadFile click on upload file + */ +function AprioriRigidBodyGrid(args) { + + this.height = 250; + this.btnEditVisible = true; + this.btnRemoveVisible = true; + + if (args != null) { + if (args.height != null) { + this.height = args.height; + } + if (args.btnEditVisible != null) { + this.btnEditVisible = args.btnEditVisible; + } + if (args.btnRemoveVisible != null) { + this.btnRemoveVisible = args.btnRemoveVisible; + } + } + + /** Events **/ + this.onUploadFile = new Event(this); + this.onRemove = new Event(this); +} + +AprioriRigidBodyGrid.prototype._getColumns = function() { +}; + +AprioriRigidBodyGrid.prototype._getTopButtons = function() { + var _this = this; + /** Actions buttons **/ + var actions = []; + + /** ADD BUTTON **/ + actions.push(Ext.create('Ext.Action', { + icon : '../images/add.png', + text : 'Add', + disabled : false, + handler : function(widget, event) { + _this.onAddButtonClicked.notify(); + } + })); + + return actions; +}; + +AprioriRigidBodyGrid.prototype.refresh = function(macromolecule) { + this.macromolecule = macromolecule; + if (macromolecule != null){ + this.pdbStore.loadData(macromolecule.structure3VOs); + } +}; + +AprioriRigidBodyGrid.prototype._prepareData = function() { + var data = []; + for ( var i = 0; i < this.features.length; i++) { + data.push(this.features[i]); + } + return data; +}; + +AprioriRigidBodyGrid.prototype._getPlugins = function() { + var _this = this; + var plugins = []; + plugins.push(Ext.create('Ext.grid.plugin.RowEditing', { + clicksToEdit : 1, + listeners : { + validateedit : function(grid, e) { + /** Comments are always updatable* */ + e.record.raw.symmetry = e.newValues.symmetry; + e.record.raw.multiplicity = e.newValues.multiplicity; + + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, proposal) { + BIOSAXS.proposal.setItems(proposal); + _this.refresh(BIOSAXS.proposal.getMacromoleculeById(_this.macromolecule.macromoleculeId)); + _this.panel.setLoading(false); + }); + adapter.onError.attach(function() { + alert("Error"); + }); + + _this.panel.setLoading(); + adapter.saveStructure(e.record.raw); + } + } + })); + return plugins; +}; + +AprioriRigidBodyGrid.prototype.getPanel = function() { + var _this = this; + + this.pdbStore = Ext.create('Ext.data.Store', { + fields : [ 'filePath', 'structureId', 'structureType', 'symmetry', 'structureId', 'name', 'multiplicity' ], + groupField : 'structureType', + sorters : { + property : 'structureId', + direction : 'DESC' + } + }); + + var groupingFeature = Ext.create('Ext.grid.feature.Grouping', { + groupHeaderTpl : Ext.create('Ext.XTemplate', + "
{name:this.formatName}
", { + formatName : function(name) { + return name; + } + }), + hideGroupedHeader : true, + startCollapsed : false + }); + + this.panel = Ext.create('Ext.grid.Panel', { + margin : "15 10 0 10", + height : this.height, + store : this.pdbStore, + plugins : _this._getPlugins(), + tbar : [ { + text : 'Add Modeling Option (PDB)', + icon : '../images/add.png', + handler : function() { + _this.onUploadFile.notify('PDB', 'Upload PDB File'); + } + } + + ], + columns : [ + { + text : "structureId", + flex : 0.2, + hidden : true, + dataIndex : 'structureId', + sortable : true + }, + { + text : "File", + flex : 0.5, + dataIndex : 'filePath', + sortable : true, + hidden : true + }, + { + text : "PDB", + flex : 0.4, + dataIndex : 'name', + sortable : true + }, + { + text : "Symmetry", + flex : 0.2, + dataIndex : 'symmetry', + sortable : true, + editor : { + xtype : 'combobox', + typeAhead : true, + triggerAction : 'all', + selectOnTab : true, + store : [ [ "P1", "P1" ], [ "P2", "P2" ], [ "P3", "P3" ], [ "P4", "P4" ], [ "P5", "P5" ], [ "P6", "P6" ], [ "P32", "P32" ], [ "P42", "P42" ], + [ "P52", "P52" ], [ "P62", "P62" ], [ "P222", "P222" ] ], + } + }, { + text : "Multiplicity", + flex : 0.2, + dataIndex : 'multiplicity', + sortable : true, + editor : { + xtype : 'textfield' + } + + }, { + text : "Subunit", + flex : 0.2, + dataIndex : 'isSubunit', + sortable : true, + hidden : true + }, { + text : "Type", + flex : 0.2, + dataIndex : 'structureType', + sortable : true, + hidden : true + }, + + { + id : this.id + 'REMOVE', + flex : 0.2, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + return BUI.getRedButton('REMOVE'); + } + }, ], + + listeners : { + itemdblclick : function(dataview, record, item, e) { + _this._editExperiment(record.raw.experimentId); + }, + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'REMOVE') { + var dataAdapter = new BiosaxsDataAdapter(); + dataAdapter.onSuccess.attach(function() { + _this.panel.setLoading(false); + _this.onRemove.notify(); + }); + _this.panel.setLoading("Removing PDB file"); + dataAdapter.removeStructure(record.data.structureId); + } + + } + }, + viewConfig : { + getRowClass : function(record, rowIdx, params, store) { + if (record.raw.isSubunit != null) { + return "blue-row"; + } + } + } + }); + + return this.panel; +}; + + + + +AprioriRigidBodyGrid.prototype.input = function() { + return { + proposal : DATADOC.getProposal_10(), + dewars : DATADOC.getDewars_10() + + }; +}; + +AprioriRigidBodyGrid.prototype.test = function(targetId) { + var AprioriRigidBodyGrid = new AprioriRigidBodyGrid({ + height : 150 + }); + BIOSAXS.proposal = new Proposal(AprioriRigidBodyGrid.input().proposal); + var panel = AprioriRigidBodyGrid.getPanel(AprioriRigidBodyGrid.input().dewars); + panel.render(targetId); + +}; + +/** + * It shows buffer grid with a top bar with "Add" button + * + * @height + * @searchBar + * @collapsed + * @width + */ +function BufferGrid(args) { + this.height = 500; + this.searchBar = false; + this.tbar = false; + this.collapsed = false; + this.id = BUI.id(); + + if (args != null) { + if (args.height != null) { + this.height = args.height; + } + if (args.searchBar != null) { + this.searchBar = args.searchBar; + } + + if (args.tbar != null) { + this.tbar = args.tbar; + } + + if (args.collapsed != null) { + this.collapsed = args.collapsed; + } + + if (args.width != null) { + this.width = args.width; + } } +} + +BufferGrid.prototype._edit = function(bufferId) { + var _this = this; + var window = new BufferWindow(); + window.onSuccess.attach(function(sender, proposal) { + _this.store.loadData(BIOSAXS.proposal.getBuffers()); + }); + window.draw(BIOSAXS.proposal.getBufferById(bufferId)); }; -SpecimenGrid.prototype.getPanelByExperiment = function(experiment) { - this.experiment = experiment; - var data = this._prepareData(experiment); - return this.getPanel(data); +BufferGrid.prototype.refresh = function(buffers) { + this.store.loadData(this._prepareData(buffers), false); }; -SpecimenGrid.prototype.refresh = function(experiment) { - this.experiment = experiment; - var data = this._prepareData(experiment); - this.store.loadData(data); +BufferGrid.prototype._prepareData = function(buffers) { + return buffers; }; -SpecimenGrid.prototype.getPanel = function() { +BufferGrid.prototype._getTbar = function() { var _this = this; - this.store = Ext.create('Ext.data.Store', { - fields : [ - 'buffer', 'bufferId', 'code', 'macromolecule', 'acronym', 'macromoleculeId', 'concentration', 'volume', 'samplePlateId', - 'slotPositionColumn', 'rowNumber', 'columnNumber', 'groupIndex' ], - data : [], - groupField : 'acronym' - }); - this.store.sort([ { - property : 'concentration', - direction : 'ASC' - }, { - property : 'buffer', - direction : 'ASC' - } ]); + var actions = []; - var selModel = Ext.create('Ext.selection.RowModel', { - allowDeselect : true, - mode : this.selectionMode, - listeners : { - selectionchange : function(sm, selections) { - var selected = []; - for ( var i = 0; i < selections.length; i++) { - selected.push(selections[i].raw); - } - _this.onSelected.notify(selected); - } + actions.push(Ext.create('Ext.Action', { + icon : '../images/add.png', + text : 'Add buffer', + disabled : false, + handler : function(widget, event) { + var window = new BufferWindow(); + window.onSuccess.attach(function(sender) { + _this.store.loadData(BIOSAXS.proposal.getBuffers()); + }); + window.draw({}); } - }); - - var features = []; - - if (this.grouped) { - features.push({ - ftype : 'grouping', - groupHeaderTpl : '{name}', - hideGroupedHeader : false, - startCollapsed : false, - id : 'myGroupedStore' - }); - } + })); + return actions; +}; - this.grid = Ext.create( - 'Ext.grid.Panel', - { - title : this.title, - height : this.height, - width : this.width, - selModel : selModel, - store : this.store, - features : features, - margin : this.margin, - plugins : this.getPlugins(), - columns : [ - { - text : '', - dataIndex : 'macromolecule', - width : 20, - renderer : function(val, y, sample) { - var macromoleculeId = null; - if (sample.raw.macromolecule3VO != null) { - macromoleculeId = sample.raw.macromolecule3VO.macromoleculeId; - } - else{ - macromoleculeId = sample.raw.macromoleculeId; - } - - if (macromoleculeId == null) return; - return BUI.getRectangleColorDIV(_this.experiment.macromoleculeColors[macromoleculeId], 10, 10); - } - }, - { - text : 'Macromolecule', - dataIndex : 'macromolecule', - width : 100 - }, - { - text : '', - dataIndex : 'buffer', - width : 20, - renderer : function(val, y, sample) { - var color = "black"; - if (sample.raw.bufferId != null) { - if (_this.experiment.getDataCollectionsBySpecimenId(sample.raw.specimenId)[0] != null){ - color = _this.experiment.getSpecimenColorByBufferId(_this.experiment.getMeasurementById(_this.experiment.getDataCollectionsBySpecimenId(sample.raw.specimenId)[0].measurementtodatacollection3VOs[0].measurementId).specimenId); - } - return BUI.getRectangleColorDIV(color, 10, 10); - } - } - }, { - text : 'Buffer', - dataIndex : 'bufferId', - width : 140, - renderer : function(val, y, sample) { - if (sample.raw.bufferId != null) { - return BIOSAXS.proposal.getBufferById(val).acronym; - } - }, - editor : BIOSAXS_COMBOMANAGER.getComboBuffers(BIOSAXS.proposal.getBuffers(), { - noLabel : true, - width : 300 - }) - }, { - text : 'Conc.', - dataIndex : 'concentration', - width : 100, - editor : { - allowBlank : false - }, - renderer : function(val, meta, sample) { - if (isNaN(val)) { - meta.tdCls = 'yellow-cell'; - return val; - } else { - if (val != 0) { - return BUI.formatValuesUnits(val, 'mg/ml', { - fontSize : 16, - decimals : 3, - unitsFontSize : this.unitsFontSize - }); - } else { - return; - } - } - } - }, { - text : 'Vol. Well', - dataIndex : 'volume', - width : 70, - editor : { - allowBlank : true - }, - renderer : function(val, y, sample) { - return BUI.formatValuesUnits(sample.data.volume, 'µl', { - fontSize : 12, - decimals : 2, - unitsFontSize : this.unitsFontSize - }); - } - }, { - text : 'Position', - hidden : true, - flex : 1, - renderer : function(val, y, sample) { - return BUI.getSamplePositionHTML(sample.raw, _this.experiment); - } - }, { - text : 'samplePlateId', - dataIndex : 'samplePlateId', - hidden : true - }, { - text : 'Plate', - hidden : this.isPositionColumnHidden, - dataIndex : 'slotPositionColumn', - editor : _this._getSlotColumBombo(), - flex : 1, - renderer : function(val, meta, sample) { - if ((val != null) & (val != "")) { - return val; - } else { - meta.tdCls = 'yellow-cell'; - } - } - }, { - text : 'Row', - hidden : this.isPositionColumnHidden, - dataIndex : 'rowNumber', - editor : this._getRowCombo(), - flex : 1, - renderer : function(val, meta, sample) { - if ((val != null) && (val != "")) { - return BUI.getSamplePlateLetters()[val - 1]; - } else { - meta.tdCls = 'yellow-cell'; - } - } - }, { - text : 'Well', - hidden : this.isPositionColumnHidden, - dataIndex : 'columnNumber', - editor : this._getColumnCombo(), - flex : 1, - renderer : function(val, meta, sample) { - if ((val != null) && (val != "")) { - return val; - } else { - meta.tdCls = 'yellow-cell'; - } - } - }, { - id : _this.id + 'buttonEditSample', - text : 'Edit', - width : 80, - sortable : false, - hidden : !_this.editEnabled, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - if (_this.editEnabled) { - return BUI.getGreenButton('EDIT'); - } - } - }, { - id : _this.id + 'buttonRemoveSample', - text : '', - hidden : !_this.removeBtnEnabled, - width : 100, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - if (_this.removeBtnEnabled) { - return BUI.getRedButton('REMOVE'); - } - } - } +BufferGrid.prototype.getPanel = function(buffers) { + var _this = this; - ], - viewConfig : { - preserveScrollOnRefresh : true, - stripeRows : true, - getRowClass : function(record) { - var specimens = _this.experiment.getSampleByPosition(record.data.samplePlateId, record.data.rowNumber, - record.data.columnNumber); - if (specimens.length > 1) { - return 'red-row'; + this.store = Ext.create('Ext.data.Store', { + fields : [ 'bufferId', 'acronym', 'name', 'composition' ], + data : buffers + }); - } - }, - listeners : { - selectionchange : function(grid, selected) { - _this.onClick.notify(record.raw); - }, - cellclick : function(grid, td, cellIndex, record, tr) { - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEditSample') { - } - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemoveSample') { - grid.getStore().removeAt(rowIndex); - _this.onRemoved.notify(); - } + this.store.sort('acronym'); - } + var type = 'Ext.grid.Panel'; + if (this.searchBar == true) { + type = 'Ext.ux.LiveSearchGridPanel'; + } - } - } - }); + this.grid = Ext.create(type, { + title : 'Buffers', + collapsible : true, + collapsed : this.collapsed, + store : this.store, + height : this.height, + width : this.width, + columns : [ + /*{ + text : '', + dataIndex : 'bufferId', + width : 20, + renderer : function(val, y, sample) { + return BUI.getRectangleColorDIV(BIOSAXS.proposal.bufferColors[val], 10, 10); + } + },*/ + { + text : 'Acronym', + dataIndex : 'acronym', + flex : 1 + }, { + text : 'Name', + dataIndex : 'name', + flex : 1, + hidden : true + }, { + text : 'Composition', + dataIndex : 'composition', + flex : 1, + hidden : true + }, { + id : _this.id + 'buttonEditBuffer', + width : 80, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + return BUI.getGreenButton('EDIT'); + } + }, { + id : _this.id + 'buttonRemoveBuffer', + width : 85, + hidden : true, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + return BUI.getRedButton('REMOVE'); + } + } ], + flex : 1, + viewConfig : { + stripeRows : true, + listeners : { + 'celldblclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + _this._edit(record.data.bufferId); + }, + 'cellclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEditBuffer') { + _this._edit(record.data.bufferId); + } + + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemoveBuffer') { + BUI.showBetaWarning(); + } + } + + } + } + }); + + /** Adding the tbar **/ + if (this.tbar) { + this.grid.addDocked({ + xtype : 'toolbar', + items : this._getTbar() + }); + } return this.grid; }; -SpecimenGrid.prototype.input = function() { - return { - experiment : DATADOC.getExperiment_10(), - proposal : DATADOC.getProposal_10() - }; +BufferGrid.prototype.input = function() { + return new MacromoleculeGrid().input(); }; -SpecimenGrid.prototype.test = function(targetId) { - var specimenGrid = new SpecimenGrid({ - height : 400, - maxHeight : 400, - width : 1000 +BufferGrid.prototype.test = function(targetId) { + var bufferGrid = new BufferGrid({ + width : 800, + height : 350, + collapsed : false, + tbar : true }); - BIOSAXS.proposal = new Proposal(specimenGrid.input().proposal); - var experiment = new Experiment(specimenGrid.input().experiment); - var panel = specimenGrid.getPanelByExperiment(experiment); + BIOSAXS.proposal = new Proposal(bufferGrid.input().proposal); + var panel = bufferGrid.getPanel(BIOSAXS.proposal.macromolecules); panel.render(targetId); - }; /** - * Shows a list of stock solutions with macromolecule, buffer, storage temperature, concentration, shipment and comments + * A shipment may contains one or more cases where stock solutions and sample plates are stored * - * @multiselect allows multiple selection - * @height - * @minHeight - * @width - * @tbar - * @showTitle - * @isPackedVisible shows is stock solution is in a box - * @btnEditVisible shows edit button - * @btnAddVisible - * @btnAddExisting - * @btnUnpackVisible allows to unpack a stock solution - * @btnRemoveVisible allow to remove a stock solution + * @height + * @btnEditVisible + * @btnRemoveVisible + * + * #onEditButtonClicked + * #onAddButtonClicked + * #onRemoveButtonClicked + * #onDuplicateButtonClicked */ +function CaseGrid(args) { -function StockSolutionGrid(args) { - this.id = BUI.id(); this.height = 100; - this.width = null; - this.minHeight = null; - this.tbar = true; - - this.title = "Stock Solutions"; - - /** Visible buttons and actions **/ this.btnEditVisible = true; this.btnRemoveVisible = true; - this.btnAddVisible = true; - this.btnAddExisting = false; - this.isPackedVisible = true; - this.btnUnpackVisible = false; - - /** Selectors **/ - this.multiselect = false; - this.selectedStockSolutions = []; if (args != null) { - if (args.btnUnpackVisible != null) { - this.btnUnpackVisible = args.btnUnpackVisible; - } - if (args.multiselect != null) { - this.multiselect = args.multiselect; - } if (args.height != null) { this.height = args.height; } if (args.btnEditVisible != null) { this.btnEditVisible = args.btnEditVisible; } - if (args.btnAddVisible != null) { - this.btnAddVisible = args.btnAddVisible; - } - if (args.btnAddExisting != null) { - this.btnAddExisting = args.btnAddExisting; - } - if (args.width != null) { - this.width = args.width; - } - if (args.minHeight != null) { - this.minHeight = args.minHeight; - } - if (args.tbar != null) { - this.tbar = args.tbar; - } if (args.btnRemoveVisible != null) { this.btnRemoveVisible = args.btnRemoveVisible; } - if (args.isPackedVisible != null) { - this.isPackedVisible = args.isPackedVisible; - } - if (args.showTitle != null) { - this.showTitle = args.showTitle; - if (this.showTitle == false) { - this.title = null; + } + + /** Events **/ + this.onEditButtonClicked = new Event(this); + this.onAddButtonClicked = new Event(this); + this.onRemoveButtonClicked = new Event(this); + this.onDuplicateButtonClicked = new Event(this); +} + +CaseGrid.prototype._getColumns = function() { + var _this = this; + + function actionItemRenderer(value, meta, record, rowIx, ColIx, store) { + /*if (record.raw.specimen3VOs.length > 0){ + return 'x-hide-display'; + }*/ + } + + var columns = [ + { + header : 'Code', + dataIndex : 'code', + name : 'code', + type : 'string', + flex : 1 + }, + { + header : 'Bar Code', + dataIndex : 'barCode', + name : 'barCode', + type : 'string', + flex : 1, + hidden : true + }, + { + header : 'BeamLine', + dataIndex : 'barCode', + type : 'string', + flex : 1, + renderer : function(comp, val, record) { + if (record.raw.sessionVO != null) { + return "" + record.raw.sessionVO.beamlineName + ""; + } + } + }, + { + header : 'Session', + dataIndex : 'barCode', + type : 'string', + flex : 1, + renderer : function(comp, val, record) { + if (record.raw.sessionVO != null) { + return "" + moment(record.raw.sessionVO.startDate).format("MMM Do YY") + ""; + } } - } - - } - - /** Events **/ - this.onProposalChanged = new Event(this); - this.onStockSolutionSelected = new Event(this); -} - -StockSolutionGrid.prototype._getColumns = function() { - var _this = this; - var columns = [ - - { - header : 'Macromolecule', - dataIndex : 'macromolecule', - id : _this.id + 'macromolecule', - type : 'string', - renderer : function(val, y, specimen) { - return '' + val + ''; }, - hidden : false, - flex : 1 - }, { - header : 'Buffer', - dataIndex : 'buffer', - name : 'buffer', - hidden : false, - renderer : function(val, y, specimen) { - return '' + val + ''; + { + header : 'Status', + dataIndex : 'dewarStatus', + name : 'dewarStatus', + type : 'string', + flex : 1, + renderer : function(comp, val, record) { + if (new String(record.raw.dewarStatus).toUpperCase() == 'OPENED') { + return "" + new String(record.raw.dewarStatus).toUpperCase() + ""; + } + return "" + new String(record.raw.dewarStatus).toUpperCase() + ""; + } }, - type : 'string', - flex : 1 - }, { - header : 'Acronym', - dataIndex : 'name', - name : 'name', - type : 'string', - flex : 1, - hidden : true - }, { - header : 'Storage Temp.', - dataIndex : 'storageTemperature', - name : 'storageTemperature', - type : 'string', - flex : 1, - hidden : false, - renderer : function(val) { - return BUI.formatValuesUnits(val, 'C', { - fontSize : 12, - decimals : 2, - unitsFontSize : 10 - }); - } - }, { - header : 'Volume', - dataIndex : 'volume', - type : 'string', - flex : 1, - hidden : false, - renderer : function(val) { - return BUI.formatValuesUnits(val, 'µl', { - fontSize : 12, - decimals : 2, - unitsFontSize : 10 - }); - } - }, { - header : 'Concentration', - dataIndex : 'concentration', - name : 'concentration', - type : 'string', - flex : 1, - renderer : function(val) { - return BUI.formatValuesUnits(val, 'mg/ml', { - fontSize : 12, - decimals : 2, - unitsFontSize : 10 - }); - } - }, { - header : 'Packed', - dataIndex : 'comments', - id : _this.id + "box", - type : 'string', - width : 50, - hidden : !this.isPackedVisible, - renderer : function(val, cmp, a) { - if (a.raw.boxId != null) { - return "
"; + { + header : 'Type', + dataIndex : 'type', + name : 'type', + type : 'string', + flex : 1, + hidden : true + }, + { + header : 'Sample Plates', + dataIndex : 'plates', + name : 'plates', + type : 'string', + flex : 1, + hidden : true + }, + { + header : 'Stock Solutions', + dataIndex : 'plates', + name : 'plates', + type : 'string', + width : 100, + renderer : function(comp, val, record) { + var html = "
"; + var stockSolutions = BIOSAXS.proposal.getStockSolutionsByDewarId(record.raw.dewarId); + html = html + "" + stockSolutions.length + " x"; + return html + "
"; } - + }, { + header : 'isStorageDewar', + dataIndex : 'isStorageDewar', + name : 'isStorageDewar', + type : 'string', + flex : 1, + hidden : true + }, { + header : 'Tracking Number From Synchrotron', + dataIndex : 'trackingNumberFromSynchrotron', + name : 'trackingNumberFromSynchrotron', + type : 'string', + flex : 1, + hidden : true + }, { + header : 'Tracking Number To Synchrotron', + dataIndex : 'trackingNumberToSynchrotron', + name : 'trackingNumberToSynchrotron', + type : 'string', + flex : 1, + hidden : true + }, { + header : 'Storage Location', + dataIndex : 'storageLocation', + name : 'storageLocation', + type : 'string', + flex : 1, + hidden : false + }, { + header : 'Comments', + dataIndex : 'comments', + name : 'comments', + type : 'string', + flex : 1, + hidden : false } - }, { - header : 'Comments', - dataIndex : 'comments', - type : 'string', - flex : 1 - } ]; + ]; if (this.btnEditVisible) { columns.push({ id : _this.id + 'buttonEdit', + text : '', + hidden : !_this.btnEditVisible, width : 85, sortable : false, renderer : function(value, metaData, record, rowIndex, colIndex, store) { - if (_this.btnEditVisible) { - return BUI.getGreenButton('EDIT'); - } + return BUI.getGreenButton('EDIT'); } }); } @@ -22014,4646 +16857,9803 @@ StockSolutionGrid.prototype._getColumns = function() { }); } - if (this.btnUnpackVisible) { - columns.push({ - id : _this.id + 'buttonUnpack', - width : 85, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - if (_this.btnUnpackVisible) { - return BUI.getBlueButton('UNPACK'); - } - } - }); - } + columns.push({ + dataIndex : 'comments', + type : 'string', + width : 85, + hidden : false, + renderer : function(comp, val, record) { + return BUI.getBlueButton("LABELS", { + href : BUI.getPrintcomponentURL(record.raw.dewarId) + }); + } + }); + return columns; }; -StockSolutionGrid.prototype._getTopButtons = function() { - var _this = this; - /** Actions buttons **/ - var actions = []; - - /** ADD BUTTON **/ - if (this.btnAddVisible) { - actions.push(Ext.create('Ext.Action', { - icon : '../images/add.png', - text : 'Add Stock Solution', - tooltip : 'Will create a new stock solution', - disabled : false, - alwaysEnabled : true, - handler : function(widget, event) { - _this.edit(); - } - })); - } - - if (this.btnAddExisting) { - actions.push(Ext.create('Ext.Action', { - icon : '../images/add.png', - text : 'Add Existing', - tooltip : 'Allows to select upacked stock solutions', - disabled : false, - alwaysEnabled : true, - handler : function(widget, event) { - var stockSolutionGrid = new StockSolutionGrid({ - btnAddVisible : false, - btnEditVisible : false, - btnRemoveVisible : false, - btnAddExisting : false, - isPackedVisible : true, - multiselect : true - }); - - var window = Ext.create('Ext.window.Window', { - title : 'Select', - height : 400, - width : 800, - layout : 'fit', - items : [ stockSolutionGrid.getPanel() ], - buttons : [ { - text : 'Pack', - handler : function() { - _this.onStockSolutionSelected.notify(stockSolutionGrid.selectedStockSolutions); - window.close(); - } - }, { - text : 'Cancel', - handler : function() { - window.close(); - } - } ] - - }).show(); +CaseGrid.prototype._getTopButtons = function() { + var _this = this; + /** Actions buttons **/ + var actions = []; - stockSolutionGrid.refresh(BIOSAXS.proposal.getUnpackedStockSolutions()); - } - })); - } + /** ADD BUTTON **/ + actions.push(Ext.create('Ext.Action', { + icon : '../images/add.png', + text : 'Add', + disabled : false, + handler : function(widget, event) { + _this.onAddButtonClicked.notify(); + } + })); return actions; }; -StockSolutionGrid.prototype.refresh = function(stockSolutions) { - this.features = stockSolutions; - this.store.loadData(this._prepareData(), false); +CaseGrid.prototype.refresh = function(dewars) { + this.features = dewars; + this.store.loadData(this._prepareData(dewars), false); }; -StockSolutionGrid.prototype._prepareData = function() { +CaseGrid.prototype._sort = function(store) { + store.sort('dewarId', 'DESC'); +}; + +CaseGrid.prototype._prepareData = function() { var data = []; for ( var i = 0; i < this.features.length; i++) { - var stockSolution = this.features[i]; - stockSolution.buffer = BIOSAXS.proposal.getBufferById(stockSolution.bufferId).acronym; - if (stockSolution.macromoleculeId != null) { - stockSolution.macromolecule = BIOSAXS.proposal.getMacromoleculeById(stockSolution.macromoleculeId).acronym; - } - data.push(stockSolution); + data.push(this.features[i]); } return data; }; -StockSolutionGrid.prototype.getPanel = function() { +CaseGrid.prototype.getPanel = function(dewars, plates) { + this.features = dewars; + this.plates = plates; return this._renderGrid(); }; -StockSolutionGrid.prototype.edit = function(stockSolutionId) { +CaseGrid.prototype._edit = function(dewar) { var _this = this; - var stockSolutionWindow = new StockSolutionWindow(); - /** On stock solution SAVED **/ - stockSolutionWindow.onSaved.attach(function(sender, stockSolution) { - _this.onProposalChanged.notify(stockSolution); + var caseWindow = new CaseWindow(); + /**SAVED **/ + caseWindow.onSaved.attach(function(sender, dewar) { + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, shipment) { + _this.refresh(shipment.dewarVOs); + }); + adapter.saveCase(BIOSAXS.proposal.getShipmentByDewarId(dewar.dewarId).shippingId, dewar); }); - stockSolutionWindow.draw(BIOSAXS.proposal.getStockSolutionById(stockSolutionId)); + caseWindow.draw(dewar); }; -StockSolutionGrid.prototype._getStoreFields = function() { +CaseGrid.prototype._getStoreFields = function(data) { return [ { - name : 'name', + name : 'dewarId', type : 'string' }, { - name : 'stockSolutionId', + name : 'barCode', type : 'string' }, { - name : 'macromolecule', + name : 'code', type : 'string' }, { - name : 'buffer', + name : 'comments', type : 'string' }, { - name : 'storageTemperature', - type : 'numeric' + name : 'dewarStatus', + type : 'string' }, { - name : 'volume', + name : 'isStorageDewar', type : 'string' }, { - name : 'concentration', + name : 'plates', type : 'string' }, { - name : 'buffer', + name : 'transportValue', type : 'string' }, { - name : 'comments', + name : 'trackingNumberFromSynchrotron', type : 'string' - } ]; -}; + }, { + name : 'trackingNumberToSynchrotron', + type : 'string' + }, { + name : 'timeStamp', + type : 'string' + }, { + name : 'storageLocation', + type : 'string' + }, { + name : 'type', + type : 'string' + } -//StockSolutionGrid.prototype.refresh = function() { -// this.proposal.onInitialized.attach(function(sender){ -// -// }); -// this.proposal.init(Ext.urlDecode(window.location.href).sessionId); -//}; + ]; +}; -StockSolutionGrid.prototype._renderGrid = function() { +CaseGrid.prototype._renderGrid = function() { var _this = this; /** Store **/ + var data = this._prepareData(); this.store = Ext.create('Ext.data.Store', { - fields : this._getStoreFields(), //columns, - autoload : true + fields : this._getStoreFields(data), + autoload : true, + data : data }); + this._sort(this.store); - var filters = { - ftype : 'filters', - local : true, - filters : this.filters - }; - - var selModel = null; - - if (this.multiselect) { - selModel = Ext.create('Ext.selection.CheckboxModel', { - //multiSelect : false,//this.multiselect, - mode : 'SINGLE', - listeners : { - selectionchange : function(sm, selections) { - _this.selectedStockSolutions = []; - for ( var i = 0; i < selections.length; i++) { - _this.selectedStockSolutions.push(selections[i].raw); - } - } - } - }); - } else { - selModel = { - mode : 'SINGLE' - }; - } - - this.store.sort("stockSolutionId", "desc"); + this.store.loadData(data, false); this.grid = Ext.create('Ext.grid.Panel', { style : { padding : 5 }, - icon : '/ispyb/images/SampleHolder_24x24_01.png', - title : this.title, height : this.height, - width : this.width, - minWidth : this.minWidth, - selModel : selModel, store : this.store, columns : this._getColumns(), viewConfig : { stripeRows : true, listeners : { itemdblclick : function(dataview, record, item, e) { - _this.edit(record.raw.stockSolutionId); - }, - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - var adapter = null; - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonUnpack') { - _this.grid.setLoading("ISPyB: Unpacking stock solution"); - adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender) { - _this.onProposalChanged.notify(); - _this.grid.setLoading(false); - }); - adapter.onError.attach(function(sender) { - _this.onProposalChanged.notify(); - _this.grid.setLoading(false); - }); - record.raw.boxId = null; - adapter.saveStockSolution(record.raw); - } - - if (grid.getGridColumns()[cellIndex].getId() == _this.id + "box") { - window.location = BUI.getShippingURL(BIOSAXS.proposal.getShipmentByDewarId(record.raw.boxId).shippingId); - } - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEdit') { - _this.edit(record.data.stockSolutionId); - } - - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemove') { - _this.grid.setLoading("ISPyB: Removing stock solution"); - adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender) { - _this.onProposalChanged.notify(); - _this.grid.setLoading(false); - }); - adapter.onError.attach(function(sender) { - _this.onProposalChanged.notify(); - _this.grid.setLoading(false); - }); - adapter.removeStockSolution(record.data.stockSolutionId); - } - } - } - } - - }); - - var actions = _this._getTopButtons(); - this.grid.addDocked({ - xtype : 'toolbar', - items : actions - }); - - var i = null; - this.grid.getSelectionModel().on({ - selectionchange : function(sm, selections) { - if (selections.length) { - for ( i = 0; i < actions.length; i++) { - if (actions[i].enable) { - actions[i].enable(); - } - } - } else { - for ( i = 0; i < actions.length; i++) { - if (actions[i].alwaysEnabled == false) { - if (actions[i].disable) { - actions[i].disable(); - } - } - } - } - } - }); - return this.grid; -}; - -StockSolutionGrid.prototype.input = function() { - return { - proposal : DATADOC.getProposal_10() - }; -}; - -StockSolutionGrid.prototype.test = function(targetId) { - var stockSolutionGrid = new StockSolutionGrid({ - height : 300, - width : 900 - }); - BIOSAXS.proposal = new Proposal(stockSolutionGrid.input().proposal); - var panel = stockSolutionGrid.getPanel(); - stockSolutionGrid.refresh(BIOSAXS.proposal.getStockSolutions()); - panel.render(targetId); -}; - - -function SuperpositionGrid(args) { - this.height = null; - this.width = null; - this.id = BUI.id(); - - if (args != null) { - if (args.height != null) { - this.height = args.height; - - if (args.width != null) { - this.width = args.width; - } - } - } - - this.onSelected = new Event(this); -} - -SuperpositionGrid.prototype._prepareData = function(data) { - return data; -}; + _this._edit(record.raw); + }, + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEdit') { + _this._edit(record.raw); + } -SuperpositionGrid.prototype.refresh = function(subtractions) { - var data = []; - if (subtractions != null){ - if (subtractions.length > 0){ - for (j in subtractions){ - var subtraction = subtractions[j]; - if (subtraction.superposition3VOs != null){ - for (i in subtraction.superposition3VOs){ - data.push(subtraction.superposition3VOs[i]); + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemove') { + _this.onRemoveButtonClicked.notify(_this.store.getAt(rowIndex).raw.dewarId); } } } + }, + selModel : { + mode : 'SINGLE' } - } - this.store.loadData(data); -}; + }); -SuperpositionGrid.prototype.getPanel = function() { - var _this = this; - this.store = Ext.create('Ext.data.Store', { - fields : [ 'abinitioModelPdbFilePath', 'aprioriPdbFilePath', 'alignedPdbFilePath' ], - data : [] + var actions = _this._getTopButtons(); + this.grid.addDocked({ + xtype : 'toolbar', + items : actions }); - this.selModel = Ext.create('Ext.selection.RowModel', { - allowDeselect : true, - mode : 'MULTI', - listeners : { - selectionchange : function(sm, selections) { - var selected = []; - for (var i = 0; i < selections.length; i++) { - selected.push(selections[i].raw); + this.grid.getSelectionModel().on({ + selectionchange : function(sm, selections) { + if (selections.length) { + for ( var i = 0; i < actions.length; i++) { + if (actions[i].enable) { + actions[i].enable(); + } + } + } else { + for ( var i = 0; i < actions.length; i++) { + if (actions[i].alwaysEnabled == false) { + if (actions[i].disable) { + actions[i].disable(); + } + } } - _this.onSelected.notify(selected); } } }); - - this.store.sort([ { - property : 'name', - direction : 'ASC' - } ]); + return this.grid; +}; - this.panel = Ext.create('Ext.grid.Panel', { - store : this.store, - selModel : this.selModel, - width : this.width, - height : this.height, - margin : 10, - deferredRender : false, - columns : [ { - text : 'Abinitio', - dataIndex : 'abinitioModelPdbFilePath', - hidden : false, - flex : 1, - renderer : function(val){ - return BUI.getFileName(val); - } - }, { - text : 'Apriori', - dataIndex : 'aprioriPdbFilePath', - hidden : false, - flex : 1, - renderer : function(val){ - return BUI.getFileName(val); - } - }, { - text : 'Aligned', - dataIndex : 'alignedPdbFilePath', - hidden : false, - flex : 1, - renderer : function(val){ - return BUI.getFileName(val); - } - } ], +CaseGrid.prototype.input = function() { + return { + proposal : DATADOC.getProposal_10(), + dewars : DATADOC.getDewars_10() - viewConfig : { - enableTextSelection : true, - preserveScrollOnRefresh : true - }, - listeners : { - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + }; +}; - }, - afterrender : function() { - } - } +CaseGrid.prototype.test = function(targetId) { + var CaseGrid = new CaseGrid({ + height : 150 }); - return this.panel; + BIOSAXS.proposal = new Proposal(CaseGrid.input().proposal); + var panel = CaseGrid.getPanel(CaseGrid.input().dewars); + panel.render(targetId); + }; +/** + * A shipment may contains one or more cases where stock solutions and sample plates are stored + * + * @height + * @btnEditVisible + * @btnRemoveVisible + * + * #onEditButtonClicked + * #onAddButtonClicked + * #onRemoveButtonClicked + * #onDuplicateButtonClicked + */ +function ExampleGrid(args) { + + this.height = 100; + this.btnEditVisible = true; + this.btnRemoveVisible = true; + + if (args != null) { + if (args.height != null) { + this.height = args.height; + } + if (args.btnEditVisible != null) { + this.btnEditVisible = args.btnEditVisible; + } + if (args.btnRemoveVisible != null) { + this.btnRemoveVisible = args.btnRemoveVisible; + } + } + + /** Events **/ + this.onEditButtonClicked = new Event(this); + this.onAddButtonClicked = new Event(this); + this.onRemoveButtonClicked = new Event(this); + this.onDuplicateButtonClicked = new Event(this); +} + +ExampleGrid.prototype._getColumns = function() { + var _this = this; + + function actionItemRenderer(value, meta, record, rowIx, ColIx, store) { + /*if (record.raw.specimen3VOs.length > 0){ + return 'x-hide-display'; + }*/ + } + + var columns = [ + { + header : 'Code', + dataIndex : 'code', + name : 'code', + type : 'string', + flex : 1 + }, + { + header : 'Bar Code', + dataIndex : 'barCode', + name : 'barCode', + type : 'string', + flex : 1, + hidden : true + }, + { + header : 'BeamLine', + dataIndex : 'barCode', + type : 'string', + flex : 1, + renderer : function(comp, val, record) { + if (record.raw.sessionVO != null) { + return "" + record.raw.sessionVO.beamlineName + ""; + } + } + }, + { + header : 'Session', + dataIndex : 'barCode', + type : 'string', + flex : 1, + renderer : function(comp, val, record) { + if (record.raw.sessionVO != null) { + return "" + moment(record.raw.sessionVO.startDate).format("MMM Do YY") + ""; + } + } + }, + { + header : 'Status', + dataIndex : 'dewarStatus', + name : 'dewarStatus', + type : 'string', + flex : 1, + renderer : function(comp, val, record) { + if (new String(record.raw.dewarStatus).toUpperCase() == 'OPENED') { + return "" + new String(record.raw.dewarStatus).toUpperCase() + ""; + } + return "" + new String(record.raw.dewarStatus).toUpperCase() + ""; + } + }, + { + header : 'Type', + dataIndex : 'type', + name : 'type', + type : 'string', + flex : 1, + hidden : true + }, + { + header : 'Sample Plates', + dataIndex : 'plates', + name : 'plates', + type : 'string', + flex : 1, + hidden : true + }, + { + header : 'Stock Solutions', + dataIndex : 'plates', + name : 'plates', + type : 'string', + width : 100, + renderer : function(comp, val, record) { + var html = "
"; + var stockSolutions = BIOSAXS.proposal.getStockSolutionsByDewarId(record.raw.dewarId); + html = html + "" + stockSolutions.length + " x"; + return html + "
"; + } + }, { + header : 'isStorageDewar', + dataIndex : 'isStorageDewar', + name : 'isStorageDewar', + type : 'string', + flex : 1, + hidden : true + }, { + header : 'Tracking Number From Synchrotron', + dataIndex : 'trackingNumberFromSynchrotron', + name : 'trackingNumberFromSynchrotron', + type : 'string', + flex : 1, + hidden : true + }, { + header : 'Tracking Number To Synchrotron', + dataIndex : 'trackingNumberToSynchrotron', + name : 'trackingNumberToSynchrotron', + type : 'string', + flex : 1, + hidden : true + }, { + header : 'Storage Location', + dataIndex : 'storageLocation', + name : 'storageLocation', + type : 'string', + flex : 1, + hidden : false + }, { + header : 'Comments', + dataIndex : 'comments', + name : 'comments', + type : 'string', + flex : 1, + hidden : false + } + ]; + + if (this.btnEditVisible) { + columns.push({ + id : _this.id + 'buttonEdit', + text : '', + hidden : !_this.btnEditVisible, + width : 85, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + return BUI.getGreenButton('EDIT'); + } + }); + } + + if (this.btnRemoveVisible) { + columns.push({ + id : _this.id + 'buttonRemove', + width : 85, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + if (_this.btnRemoveVisible) { + return BUI.getRedButton('REMOVE'); + } + } + }); + } + + columns.push({ + dataIndex : 'comments', + type : 'string', + width : 85, + hidden : false, + renderer : function(comp, val, record) { + return BUI.getBlueButton("LABELS", { + href : BUI.getPrintcomponentURL(record.raw.dewarId) + }); + } + }); + + return columns; +}; + +ExampleGrid.prototype._getTopButtons = function() { + var _this = this; + /** Actions buttons **/ + var actions = []; + + /** ADD BUTTON **/ + actions.push(Ext.create('Ext.Action', { + icon : '../images/add.png', + text : 'Add', + disabled : false, + handler : function(widget, event) { + _this.onAddButtonClicked.notify(); + } + })); + + return actions; +}; + +ExampleGrid.prototype.refresh = function(dewars) { + this.features = dewars; + this.store.loadData(this._prepareData(dewars), false); +}; + +ExampleGrid.prototype._sort = function(store) { + store.sort('dewarId', 'DESC'); +}; + +ExampleGrid.prototype._prepareData = function() { + var data = []; + for ( var i = 0; i < this.features.length; i++) { + data.push(this.features[i]); + } + return data; +}; + +ExampleGrid.prototype.getPanel = function() { + this.grid = Ext.create('Ext.grid.Panel', { + style : { + padding : 5 + }, + height : this.height, + store : this.store, + columns : this._getColumns(), + viewConfig : { + stripeRows : true, + listeners : { + itemdblclick : function(dataview, record, item, e) { + _this._edit(record.raw); + }, + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEdit') { + _this._edit(record.raw); + } + + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemove') { + _this.onRemoveButtonClicked.notify(_this.store.getAt(rowIndex).raw.dewarId); + } + } + } + }, + selModel : { + mode : 'SINGLE' + } + }); + + var actions = _this._getTopButtons(); + this.grid.addDocked({ + xtype : 'toolbar', + items : actions + }); + + this.grid.getSelectionModel().on({ + selectionchange : function(sm, selections) { + if (selections.length) { + for ( var i = 0; i < actions.length; i++) { + if (actions[i].enable) { + actions[i].enable(); + } + } + } else { + for ( var i = 0; i < actions.length; i++) { + if (actions[i].alwaysEnabled == false) { + if (actions[i].disable) { + actions[i].disable(); + } + } + } + } + } + }); + return this.grid; +}; + + +ExampleGrid.prototype._getStoreFields = function(data) { + return [ { + name : 'dewarId', + type : 'string' + }, { + name : 'barCode', + type : 'string' + }, { + name : 'code', + type : 'string' + }, { + name : 'comments', + type : 'string' + }, { + name : 'dewarStatus', + type : 'string' + }, { + name : 'isStorageDewar', + type : 'string' + }, { + name : 'plates', + type : 'string' + }, { + name : 'transportValue', + type : 'string' + }, { + name : 'trackingNumberFromSynchrotron', + type : 'string' + }, { + name : 'trackingNumberToSynchrotron', + type : 'string' + }, { + name : 'timeStamp', + type : 'string' + }, { + name : 'storageLocation', + type : 'string' + }, { + name : 'type', + type : 'string' + } + + ]; +}; + +ExampleGrid.prototype._renderGrid = function() { + var _this = this; + + /** Store **/ + var data = this._prepareData(); + this.store = Ext.create('Ext.data.Store', { + fields : this._getStoreFields(data), + autoload : true, + data : data + }); + this._sort(this.store); + + this.store.loadData(data, false); + + this.grid = Ext.create('Ext.grid.Panel', { + style : { + padding : 5 + }, + height : this.height, + store : this.store, + columns : this._getColumns(), + viewConfig : { + stripeRows : true, + listeners : { + itemdblclick : function(dataview, record, item, e) { + _this._edit(record.raw); + }, + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEdit') { + _this._edit(record.raw); + } + + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemove') { + _this.onRemoveButtonClicked.notify(_this.store.getAt(rowIndex).raw.dewarId); + } + } + } + }, + selModel : { + mode : 'SINGLE' + } + }); + + var actions = _this._getTopButtons(); + this.grid.addDocked({ + xtype : 'toolbar', + items : actions + }); + + this.grid.getSelectionModel().on({ + selectionchange : function(sm, selections) { + if (selections.length) { + for ( var i = 0; i < actions.length; i++) { + if (actions[i].enable) { + actions[i].enable(); + } + } + } else { + for ( var i = 0; i < actions.length; i++) { + if (actions[i].alwaysEnabled == false) { + if (actions[i].disable) { + actions[i].disable(); + } + } + } + } + } + }); + return this.grid; +}; + +ExampleGrid.prototype.input = function() { + return { + proposal : DATADOC.getProposal_10(), + dewars : DATADOC.getDewars_10() + + }; +}; + +ExampleGrid.prototype.test = function(targetId) { + var ExampleGrid = new ExampleGrid({ + height : 150 + }); + BIOSAXS.proposal = new Proposal(ExampleGrid.input().proposal); + var panel = ExampleGrid.getPanel(ExampleGrid.input().dewars); + panel.render(targetId); + +}; + + /** - * See ExperimentGrid - * + * Shows a list of experiment AKA data acquisitions + * @height + * @sorters + * @minHeight + * @gridType: Ext.ux.LiveSearchGridPanel or Ext.grid.Panel + * @tbar true or false + * @grouping true or false + * @width + * @title + * #onEditButtonClicked */ -function TemplateGrid(args) { - - if (args == null) { - args = {}; - } - args.sorters = [ { - property : 'experimentId', - direction : 'DESC' - } ]; - - ExperimentGrid.prototype.constructor.call(this, args); -} - -TemplateGrid.prototype._getFilterTypes = ExperimentGrid.prototype._getFilterTypes; -TemplateGrid.prototype._prettyPrintMacromolecules = ExperimentGrid.prototype._prettyPrintMacromolecules; -TemplateGrid.prototype._getPercentage = ExperimentGrid.prototype._getPercentage; -TemplateGrid.prototype._getPercentageCollected = ExperimentGrid.prototype._getPercentageCollected; -TemplateGrid.prototype.getPercentageMerged = ExperimentGrid.prototype.getPercentageMerged; -TemplateGrid.prototype._prepareData = ExperimentGrid.prototype._prepareData; -TemplateGrid.prototype.getPanel = ExperimentGrid.prototype.getPanel; -TemplateGrid.prototype._renderGrid = ExperimentGrid.prototype._renderGrid; -TemplateGrid.prototype._editExperiment = ExperimentGrid.prototype._editExperiment; -TemplateGrid.prototype._removeExperimentById = ExperimentGrid.prototype._removeExperimentById; - -TemplateGrid.prototype._getTopButtons = function() { - /** Actions buttons * */ - var actions = []; - - actions.push(Ext.create('Ext.Action', { - icon : '../images/add.png', - text : 'Add experiment', - handler : function(widget, event) { - var wizardWidget = new WizardWidget({ - windowMode : true - }); - - wizardWidget.onFinished.attach(function(sender, result) { - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - var experiment = new Experiment(data); - BIOSAXS.openExperimentByExperiment(experiment); - wizardWidget.window.close(); - }); - wizardWidget.current.setLoading("ISPyB: Creating experiment"); - adapter.createTemplate(result.name, "comments", result.data); - }); - -// wizardWidget.draw(this.targetId, new ExperimentTypeWizardForm()); - wizardWidget.draw(this.targetId, new MeasurementCreatorStepWizardForm(BIOSAXS.proposal.getMacromolecules())); - } - })); - return actions; -}; - -TemplateGrid.prototype.refresh = function(data) { - var filtered = []; - for ( var i = 0; i < data.length; i++) { - if (data[i].experimentType == "TEMPLATE") { - filtered.push(data[i]); - } - } - this.store.loadData(this._prepareData(filtered), false); -}; - -TemplateGrid.prototype._getColumns = function() { - var _this = this; - function actionItemRenderer(value, meta, record, rowIx, ColIx, store) { - if (record.raw.buffer3VOs != null) { - if (record.raw.buffer3VOs.length > 0) { - return 'x-hide-display'; - } - } +function ExperimentGrid(args) { + this.width = "100%"; + this.height = 700; + this.minHeight = 500; - if (record.data.platesCount > 0) { - return 'x-hide-display'; - } - } + this.id = BUI.id(); + this.gridType = 'Ext.grid.Panel'; //'Ext.ux.LiveSearchGridPanel'; + this.tbar = false; + this.hideHeaders = false; + this.grouping = true; + this.title = null; - return [ { - xtype : 'rownumberer', - width : 40 - }, { - text : 'experimentId', - dataIndex : 'experimentId', - name : 'experimentId', - type : 'string', - hidden : true + this.filtered = null; + + /** maximum row count **/ + this.limit = 100; + + this.sessionIdFilter = null; + + /** if not null filtered by date **/ + this.date = null; + + this.sorters = [ { + property : 'date', + direction : 'DESC' }, { - text : 'Name', - dataIndex : 'name', - name : 'name', - type : 'string', - flex : 1 - }, + property : 'time', + direction : 'DESC' + } ]; - { - text : 'Type', - dataIndex : 'type', - name : 'type', - type : 'string', - hidden : true, - flex : 1, - renderer : function(val) { - return val; + this.dates = {}; + if (args != null) { + if (args.height != null) { + this.height = args.height; } - }, { - text : 'Macromolecules', - name : 'macromolecules_names', - dataIndex : 'macromolecules_names', - flex : 1, - renderer : function(val) { - return " " + val + ""; + if (args.limit != null) { + this.limit = args.limit; } - }, { - id : _this.id + 'GO', - width : 80, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - return BUI.getGreenButton('EDIT'); + if (args.sorters != null) { + this.sorters = args.sorters; } - }, { - id : _this.id + 'REMOVE', - width : 100, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - return BUI.getRedButton('REMOVE'); + if (args.sessionId != null){ + this.sessionIdFilter = args.sessionId; + } + if (args.filtered != null) { + this.filtered = args.filtered; + } + if (args.minHeight != null) { + this.minHeight = args.minHeight; + } + if (args.gridType != null) { + this.gridType = args.gridType; + } + if (args.tbar != null) { + this.tbar = args.tbar; + } + if (args.grouping != null) { + this.grouping = args.grouping; + } + if (args.width != null) { + this.width = args.width; + } + if (args.title != null) { + this.title = args.title; } - } ]; -}; - -TemplateGrid.prototype.input = function() { - var experiments = DATADOC.getExperimentList_10(); - return { - experiments : experiments, - proposal : new MeasurementGrid().input().proposal - - }; -}; - -TemplateGrid.prototype.test = function(targetId) { - var experimentGrid = new TemplateGrid({ - height : 350, - minHeight : 350, - width : 1000, - gridType : 'Ext.grid.Panel', - title : 'Experiments', - grouping : false, - tbar : true - }); - BIOSAXS.proposal = new Proposal(experimentGrid.input().proposal); - var panel = experimentGrid.getPanel(experimentGrid.input().experiments); - experimentGrid.refresh(experimentGrid.input().experiments); - panel.render(targetId); -}; - -function VolumeGrid() { - this.id = BUI.id(); + } + /** Events **/ + this.onEditButtonClicked = new Event(this); } -VolumeGrid.prototype.getPanel = function(experiment) { - this.experiment = experiment; - return this.render(); +ExperimentGrid.prototype._getFilterTypes = function() { + return []; }; -VolumeGrid.prototype.getVolumesPanel = function(data, title) { - var _this = this; - var store = Ext.create('Ext.data.Store', { - fields : [ 'name', 'volume', 'macromoleculeId', 'bufferId' ], - data : data - }); - store.sort([ { - property : 'name', - direction : 'ASC' - } ]); - - var grid = Ext.create('Ext.grid.Panel', { - title : title, - height : 400, - maxHeight : 400, - width : 900, - store : store, - margin : '10 0 50 10', - tbar : [ { - text : 'Go to Shipment', - icon : '../images/plane-small.gif', - handler : function() { - window.location = BUI.getCreateShipmentList(); - } - } ], - viewConfig : { - stripeRows : true, - listeners : { - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonCreate') { - var stockSolutionWindow = new StockSolutionWindow(); - /** On stock solution SAVED **/ - stockSolutionWindow.onSaved.attach(function(sender, stockSolution) { - BIOSAXS.proposal.onInitialized.attach(function(sender, data) { - _this.refresh(_this.experiment); - }); - BIOSAXS.proposal.init(); - }); - var acronym = "ST"; - if (record.raw.macromoleculeId != null) { - acronym = acronym + "_" + BIOSAXS.proposal.getMacromoleculeById(record.raw.macromoleculeId).acronym; - } - if (record.raw.bufferId != null) { - acronym = acronym + "_" + BIOSAXS.proposal.getBufferById(record.raw.bufferId).acronym; - } - stockSolutionWindow.draw({ - concentration : record.raw.concentration, - macromoleculeId : record.raw.macromoleculeId, - bufferId : record.raw.bufferId, - name : acronym, - volume : record.raw.volume - }); - } - - if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonStockSolutions') { - var stockSolutionGrid = new StockSolutionGrid({ - btnAddVisible : false, - btnEditVisible : false, - btnRemoveVisible : false, - btnAddExisting : false, - isPackedVisible : true, - multiselect : false - }); - - var window = Ext.create('Ext.window.Window', { - title : 'Stock solutions by specimen', - height : 400, - width : 800, - layout : 'fit', - items : [ stockSolutionGrid.getPanel() ], - buttons : [ { - text : 'Close', - handler : function() { - window.close(); - } - } ] - - }).show(); - stockSolutionGrid.refresh(BIOSAXS.proposal.getStockSolutionsBySpecimen(record.raw.macromoleculeId, record.raw.bufferId)); - } - } - } - }, - columns : [ -// { -// text : '', -// dataIndex : 'macromoleculeId', -// width : 20, -// renderer : function(val, y, sample) { -// if (val != null) { -//// return BUI.getRectangleColorDIV(BIOSAXS.proposal.macromoleculeColors[val], 10, 10); -// return BUI.getRectangleColorDIV(_this.experiment.macromoleculeColors[val], 10, 10); -// } -// } -// }, -// { -// text : '', -// dataIndex : 'bufferId', -// width : 20, -// renderer : function(val, y, sample) { -// if (val != null) { -// return BUI.getRectangleColorDIV(_this.experiment.getSpecimenColorByBufferId(val), 10, 10); -// } -// } -// }, - { - text : 'Specimen', - dataIndex : 'name', - flex : 0.5 - }, - { - text : 'Estimated Volume', - dataIndex : 'volume', - tooltip : 'Estimation of the maximum volume needed for making this experiment', - flex : 0.5, - editor : { - allowBlank : true - }, - renderer : function(val, y, sample) { - return BUI.formatValuesUnits(sample.data.volume, 'µl', { - fontSize : 16, - decimals : 2, - unitsFontSize : this.unitsFontSize - }); - } - }, - { - text : 'Stock Solution', - id : _this.id + 'buttonStockSolutions', - dataIndex : 'name', - flex : 0.5, - tooltip : 'Stock Solutions containing this specimen in this proposal', - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - var macromoleculeId = record.raw.macromoleculeId; - var bufferId = record.raw.bufferId; - var stockSolutions = BIOSAXS.proposal.getStockSolutionsBySpecimen(macromoleculeId, bufferId); - if (stockSolutions.length > 0) { - return "
" + stockSolutions.length + " x
"; - } +ExperimentGrid.prototype._prepareData = function(rows) { + var data = []; + var count = 0; + + rows.sort(function(a,b){return b.experimentId - a.experimentId;}); + for ( var i = 0; i < rows.length; i++) { + var row = rows[i]; + this.dates[moment(row.creationDate).format("YYYYMMDD")] = moment(row.creationDate).format("MMM Do YY"); + if ( + ( this.filtered == null || row.experimentType == this.filtered ) && (count < this.limit || this.limit == null ) && (this.sessionIdFilter == null || this.date != null || (this.date == null && this.sessionIdFilter == row.sessionId)) + ){ - } - }, { - id : _this.id + 'buttonCreate', - text : '', - tooltip : 'Create a new stock solution for shipping', - width : 170, - sortable : false, - renderer : function(value, metaData, record, rowIndex, colIndex, store) { - return BUI.getGreenButton('NEW STOCK SOLUTION', { - width : 160 + data.push({ + experimentId : row.experimentId, + status : row.status, + dataAcquisitionFilePath : row.dataAcquisitionFilePath, + type : row.experimentType, + name : row.name, + macromolecules_names : row.macromolecules, + percentageAnalysed : { + value : (row.dataCollectionDoneCount / row.dataCollectionCount) * 100, + text : row.dataCollectionDoneCount + " of " + row.dataCollectionCount + }, + percentageCollected : { + value : (row.measurementDoneCount / row.measurementCount) * 100, + text : row.measurementDoneCount + " of " + row.measurementCount + }, + percentageMerged : { + value : (row.measurementAveragedCount / row.measurementCount) * 100, + text : row.measurementAveragedCount + " of " + row.measurementCount + }, + date : moment(row.creationDate).format("YYYYMMDD"), + time : moment(row.creationDate).format("YYYYMMDDHHmmss"), + creationDate : row.creationDate }); - } - } ] - }); - return grid; + count ++; + } + } + return data; +}; +ExperimentGrid.prototype.getPanel = function(experiments) { + this.features = experiments; + return this._renderGrid(experiments); }; -VolumeGrid.prototype._prepareData = function(experiment) { - var keys = {}; - for ( var i = 0; i < experiment.getSamples().length; i++) { - var sample = experiment.getSamples()[i]; - var key = ""; - if (sample.macromoleculeId == null) { - key = experiment.getBufferById(sample.bufferId).acronym; - if (keys[key] == null) { - keys[key] = { - macromoleculeId : sample.macromoleculeId, - name : key, - bufferId : sample.bufferId, - volume : 0 - }; - } - keys[key].volume = Number(sample.volume) + Number(keys[key].volume); +ExperimentGrid.prototype.refresh = function(experiments) { + this.experiments = experiments; + var filtered = []; + for ( var i = 0; i < experiments.length; i++) { + if (experiments[i].experimentType != "TEMPLATE") { + filtered.push(experiments[i]); } + } - if ((sample.macromolecule3VO != null) || (sample.macromoleculeId != null)) { - macromoleculeId = sample.macromoleculeId; - if (sample.macromoleculeId == null) { - sample.macromoleculeId = sample.macromolecule3VO.macromoleculeId; - } - key = BIOSAXS.proposal.getMacromoleculeById(sample.macromoleculeId).acronym + " + " + experiment.getBufferById(sample.bufferId).acronym; - if (keys[key] == null) { - keys[key] = { - macromoleculeId : sample.macromoleculeId, - name : key, - bufferId : sample.bufferId, - volume : 0 - }; - } - keys[key].volume = Number(sample.volume) + Number(keys[key].volume); + this.parsedData = this._prepareData(filtered); + + var day = {}; + var dates = []; + for ( var i = 0; i < this.experiments.length; i++) { + var date = moment(this.experiments[i].creationDate).format("MMM Do YYYY"); + if (day[date] == null){ + dates.push({ + date : date, + value : moment(this.experiments[i].creationDate) + }); + day[date] = true; } } - var data = []; - for (var keyId in keys) { - data.push(keys[keyId]); + + this.storeDate.loadData(dates, false); + this.store.loadData(this.parsedData, false); + + /** If it has already been filtered by date we keep the filter **/ + if (this.date != null){ + this._filterByDate(this.date); } - - return data; }; -VolumeGrid.prototype.refresh = function(experiment) { - this.experiment = experiment; - this.macromoleculeGrid.getStore().loadData(this._prepareData(this.experiment), false); -}; +ExperimentGrid.prototype._getTopButtons = function() { + var _this = this; + /** Actions buttons **/ + var actions = []; -VolumeGrid.prototype.render = function() { - this.macromoleculeGrid = this.getVolumesPanel(this._prepareData(this.experiment), "Estimation of required Volume"); + actions.push(Ext.create('Ext.Action', { + icon : '../images/calendar_icon.png', + text : 'Show Calendar', + disabled : false, + handler : function(widget, event) { + var window = Ext.create('Ext.window.Window', { + title : 'Calendar', + width : 600, + height : 600, + modal : true, + closable : true, + layout : { + type : 'vbox', + align : 'stretch' + }, + items : [ { + xtype : 'label', + html : 'Click on a data acquisition to select:', + margin : '5 5 5 5' + }, { + html : '
', + margin : '5 5 5 5' + } - return { - xtype : 'container', - layout : 'vbox', - margin : "0, 0, 0, 5", - items : [ { - xtype : 'container', - layout : 'hbox', - margin : "0, 0, 0, 0", - items : [ this.macromoleculeGrid ] - } ] - }; + ] + }).show(); + + var calendarWidget = new CalendarWidget({ + height : 450 + }); + var aux = _this.limit; + /** we remove the limit temporarily **/ + _this.limit = null; + _this.sessionIdFilter = null; + calendarWidget.loadData(_this._prepareData(_this.experiments)); + _this.limit = aux; + calendarWidget.draw('calendar'); + calendarWidget.onClick.attach(function(sender, date) { + date = moment(date, "YYYY-MM-DD"); + _this._filterByDate(date); + window.close(); + + }); + + } + })); + this.storeDate = Ext.create('Ext.data.ArrayStore', { + fields: ['date', 'value'], + data : [] + }); + + this.dateMenu = Ext.create('Ext.form.field.ComboBox', { + hideLabel: true, + store: this.storeDate, + displayField: 'date', + typeAhead: true, + queryMode: 'local', + margin : '0 0 0 30', + triggerAction: 'all', + emptyText:'Select a date...', + selectOnFocus:true, + width:135, + listeners:{ + scope: this, + 'select': function (a,b,c){ + _this.limit = null; + _this._filterByDate(moment(b[0].raw.value, "YYYY-MM-DD")); + } + } + }); + + actions.push(this.dateMenu); + + actions.push("->"); + if (_this.filtered != null){ + actions.push({ + html : "Experiment Type: " + _this.filtered +"" + }); + } + else{ + actions.push({ + html : "Experiment Type: ALL" + }); + } + return actions; }; -VolumeGrid.prototype.input = function(experiment) { - return { - experiment : DATADOC.getExperiment_10() - }; +/** + * Date format: "YYYY-MM-DD" + */ +ExperimentGrid.prototype._filterByDate = function(date) { + var experimentsFiltered = []; + /** Getting all the experiments of date**/ + for ( var i = 0; i < this.experiments.length; i++) { + var experiment = this.experiments[i]; + if (experiment.creationDate != null) { + var experimentDate = moment(experiment.creationDate); + if (experimentDate.year() == date.year()) { + if (experimentDate.month() == date.month()) { + if (experimentDate.date() == date.date()) { + experimentsFiltered.push(experiment); + } + } + } + } + } + var parsedData = this._prepareData(experimentsFiltered); + this.store.loadData(parsedData); + this.date = date; }; -VolumeGrid.prototype.test = function(targetId) { - var volumeGrid = new VolumeGrid(); - BIOSAXS.proposal = new Proposal(new MeasurementGrid().input().proposal); - var panel = volumeGrid.getPanel(new Experiment(new VolumeGrid().input().experiment)); - Ext.create('Ext.panel.Panel', { - height : 500, - width : 1000, - renderTo : targetId, - items : [ panel ] +/** Only for templates **/ +ExperimentGrid.prototype._removeExperimentById = function(experimentId) { + var _this = this; + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(evt, args) { + _this.grid.setLoading(false); + document.getElementById(BIOSAXS.targetId).innerHTML = ""; + BIOSAXS.start(BIOSAXS.targetId); }); + this.grid.setLoading("Removing experiment "); + adapter.removeExperimentById(experimentId); }; - -/** - * Example of a tab panel to be populated with widgets - * - * @width width in pixels - * @height height in pixels - * - * #myEvent event that this class is supposed to throw - * - **/ -function ExampleTabs(args) { - this.width = 500; - this.height = 500; + +ExperimentGrid.prototype._renderGrid = function() { + var _this = this; + + /** Store **/ + this.store = Ext.create('Ext.data.Store', { + fields : this._getColumns(), + groupField : 'date', + autoload : true, + data : [], + remoteSort: false, + sorters : this.sorters + }); + - if (args != null){ - if (args.width != null){ - this.width= args.width; - } - if (args.height != null){ - this.height= args.height; - } - } - /** Events **/ - this.myEvent = new Event(); -} - -/** Populate the widget **/ -ExampleTabs.prototype.refresh = function(macromolecule) { -}; + var groupingFeature = Ext.create('Ext.grid.feature.Grouping', { + groupHeaderTpl : Ext.create('Ext.XTemplate', + "
{name:this.formatName}
", { + formatName : function(name) { + return _this.dates[name]; + } + }), + hideGroupedHeader : true, + startCollapsed : false + }); -/** It creates a tab panel with the specified with and height **/ -ExampleTabs.prototype.getPanel = function() { - this.panel = Ext.createWidget('tabpanel', { - height : this.height, - width : this.width, - style : { - padding : 2 + this.features = []; + if (this.grouping) { + this.features.push(groupingFeature); + } + + /** Grid **/ + this.grid = Ext.create(this.gridType, { + hideHeaders : this.hideHeaders, + resizable : true, + title : this.title, + width : this.width, + minHeight : this.minHeight, + height : this.height, + features : this.features, + store : this.store, + columns : this._getColumns(), + selModel : { + mode : 'SINGLE' }, - items : [ { - tabConfig : { - title : 'Test', - icon : '/ispyb/images/plane-small.gif' + viewConfig : { + stripeRows : true, + getRowClass : function(record, rowIdx, params, store) { + if (record.raw.type == "TEMPLATE") { + return "template-color-row"; + } + if ((record.raw.type == "CALIBRATION") && (record.raw.status == "FINISHED")) { + return "blue-row"; + } }, - items : [ { - xtype : 'container', - margin : '5 5 5 5', - items : [ ] - } ] - } ] + listeners : { + itemdblclick : function(dataview, record, item, e) { + _this._editExperiment(record.raw.experimentId); + }, + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'GO') { + _this._editExperiment(record.raw.experimentId); + } + + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'REMOVE') { + _this._removeExperimentById(record.raw.experimentId); + } + + } + } + } }); - return this.panel; -}; - -/** - * Shows an experiments with the specimens, measurements, analysis tabs where - * results are shown and the frames widget - * - * @targetId - */ -function ExperimentTabs(targetId) { - this.height = 900; - this.targetId = targetId; + var actions = _this._getTopButtons(); - this.id = BUI.id(); - var _this = this; + if (this.tbar) { + this.grid.addDocked({ + xtype : 'toolbar', + items : actions + }); + this.grid.getSelectionModel().on({ + selectionchange : function(sm, selections) { + if (selections.length) { + for ( var i = 0; i < actions.length; i++) { + if (actions[i].enable) { + actions[i].enable(); + } + } + } else { + for ( var i = 0; i < actions.length; i++) { + if (actions[i].alwaysEnabled == false) { + if (actions[i].disable) { + actions[i].disable(); + } + } + } + } + } + }); + } - this.INTERVAL_UPDATE = BUI.getUpdateInterval(); + return this.grid; +}; - this.gridHeight = 1000; - /** data * */ - this.experiment = null; +ExperimentGrid.prototype._getColumns = function() { + var _this = this; + function actionItemRenderer(value, meta, record, rowIx, ColIx, store) { + if (record.raw.buffer3VOs != null) { + if (record.raw.buffer3VOs.length > 0) { + return 'x-hide-display'; + } + } - - /** Specimen Widget contains a specimenGrid and a sampleChangerWidget than can be displayed with are vertical or horizontal layout **/ - this.specimenWidget = new SpecimenWidget({ - height : 600 - }); - - - /** For Overview * */ - /*this.samplePlateGroupWidget = new SamplePlateGroupWidget({ - showTitle : false, - height : 250, - margin : 5, - border : 0 + if (record.data.platesCount > 0) { + return 'x-hide-display'; + } + } - });*/ + return [ + { + text : 'experimentId', + dataIndex : 'experimentId', + name : 'experimentId', + type : 'string', + hidden : true + }, + { + xtype : 'rownumberer', + width : 40 + }, + { + text : 'Name', + dataIndex : 'name', + name : 'name', + type : 'string', + flex : 1 + }, - /** For Measurements * */ - /*this.measurementSamplePlateGroupWidget = new SamplePlateGroupWidget({ - showTitle : false, - height : 250, - margin : '5 0 0 0', - border : 0 - });*/ + { + text : 'Type', + dataIndex : 'type', + name : 'type', + type : 'string', + flex : 1, + renderer : function(val) { + if (val == "CALIBRATION") { + return "" + val + ""; + } + + return val; + } + }, + { + text : 'Macromolecules', + name : 'macromolecules_names', + dataIndex : 'macromolecules_names', + flex : 1, + renderer : function(val) { + if (val != null) { + return " " + val + ""; + } + return " Information not available"; + } + }, + { + text : 'Buffers', + dataIndex : 'buffer_names', + name : 'buffer_names', + flex : 1, + hidden : true, + renderer : function(val) { + return "Buffer/s: " + val + ""; + } + }, + { + text : 'Status', + dataIndex : 'status', + name : 'status', + type : 'string', + flex : 1, + renderer : function(val, x, sample) { + if (sample.raw.type == "TEMPLATE") { + return "READY"; + } + if (sample.raw.status == "ABORTED") { + return "" + val + ""; + } + return "" + val + ""; + } + }, + { + text : 'Download', + dataIndex : 'creationDate', + name : 'creationDate', + renderer : function(val, x, sample) { + if (sample != null) { + if (sample.raw.type == "HPLC") { + return; + } + return BUI.getZipHTMLByExperimentId(sample.raw.experimentId, sample.raw.name); + } + }, + width : 100 - this.measurementGridDone = new MeasurementGrid({ - height : 600, - minHeight : 400, - maxHeight : 800, - positionColumnsHidden : true, - showTitle : false, - estimateTime : true, - width : 900, - maxWidth : 1500, - addBtnEnable : false, - markDone : true, - removeBtnEnabled : false - }); - this.measurementGridDone.onSelected.attach(function(sender, measurements) { - var specimens = []; - for ( var i = 0; i < measurements.length; i++) { - specimens.push(_this.experiment.getSampleById(measurements[i].specimenId)); - } - //_this.measurementSamplePlateGroupWidget.selectSpecimens(specimens); - }); + }, + { + header : 'Measurements', + dataIndex : 'percentageCollected', + name : 'percentageCollected', + type : 'string', + renderer : function(val, y, sample) { + if ((sample.raw.type == "TEMPLATE") || (sample.raw.type == "HPLC")) { + return; + } + return "
" + BUI.getProgessBar(sample.raw.percentageCollected.value, sample.raw.percentageCollected.text) + "
"; + }, + width : 100 + }, + { + header : 'Averaged', + dataIndex : 'percentageMerged', + name : 'percentageMerged', + type : 'string', + renderer : function(val, y, sample) { + if ((sample.raw.type == "TEMPLATE") || (sample.raw.type == "HPLC")) { + return; + } + return "
" + BUI.getProgessBar(sample.raw.percentageMerged.value, sample.raw.percentageMerged.text) + "
"; + }, + width : 100 + }, + { + header : 'Subtractions', + dataIndex : 'percentageAnalysed', + name : 'percentageAnalysed', + type : 'string', + renderer : function(val, y, sample) { + if ((sample.raw.type == "TEMPLATE") || (sample.raw.type == "HPLC")) { + return; + } + return "
" + BUI.getProgessBar(sample.raw.percentageAnalysed.value, sample.raw.percentageAnalysed.text) + "
"; + }, + width : 100 + }, - /** AnalysisGrid * */ - this.analysisGrid = new AnalysisGrid({ - height : Ext.getBody().getViewSize().height * 0.9 - 300, - positionColumnsHidden : true, - sorters : [ { - property : 'priorityLevelId', - direction : 'ASC' - } ] - }); - - - /** Queue * */ - this.queueGrid = new QueueGrid({ - url : BUI.getQueueUrlByExperiment(), - height : Ext.getBody().getViewSize().height * 0.9 - 300, - width : Ext.getBody().getViewSize().width * 0.9 - 300, - isGrouped : true, - tbar : false, - bbar : false, - sorter : [{ - property: 'measurementId', - direction: 'DESC' - }] - }); + { + text : 'time', + dataIndex : 'time', + name : 'time', + hidden : true, + renderer : function(val) { + return val; + }, + width : 100 -} + }, { + text : 'Date', + dataIndex : 'date', + name : 'date', + renderer : function(val) { + return val; + }, + width : 100 -ExperimentTabs.prototype.error = function(error) { - var e = JSON.parse(error); - showError(e); - this.panel.setLoading(false); -}; + }, -ExperimentTabs.prototype.draw = function(experiment) { - this.renderDataAcquisition(experiment); -}; + { + text : 'Time', + dataIndex : 'creationDate', + name : 'creationDate', + renderer : function(val) { + return moment(val).format(" HH:mm:ss"); + }, + width : 100 -ExperimentTabs.prototype.refreshAnalysisData = function() { - var _this = this; - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - _this.analysisGrid.refresh(data, {experiment : _this.experiment}); - }); - adapter.getAnalysisInformationByExperimentId(this.experiment.experimentId); - - /** Auto load **/ - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - _this.queueGrid.refresh(data); - }); - adapter.getCompactAnalysisByExperimentId(this.experiment.experimentId); - this.queueGrid.store.proxy.url = BUI.getQueueUrlByExperiment(this.experiment.experimentId); - this.queueGrid.refresh(); + }, { + id : _this.id + 'GO', + width : 80, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + return BUI.getGreenButton('GO'); + } + } ]; }; -ExperimentTabs.prototype.getSpecimenContainerHeight = function(experiment) { - var maxItems = 0; - if (maxItems < experiment.getSamples().length + 1) { - maxItems = experiment.getSamples().length + 1; - } - - var height = (maxItems + 1) * 40 + 40; - if (height > 400) { - height = 400; +/** Changes location.href in order to edit the experiment **/ +ExperimentGrid.prototype._editExperiment = function(experimentId) { + if (Ext.urlDecode(window.location.href).sessionId != null) { + location.href = 'viewProjectList.do?reqCode=display&experimentId=' + experimentId + '&sessionId='+ Ext.urlDecode(window.location.href).sessionId; + } else { + location.href = 'viewProjectList.do?reqCode=display&experimentId=' + experimentId; } - return height; -}; - -ExperimentTabs.prototype.getExperimentTitle = function() { - var experimentHeaderForm = new ExperimentHeaderForm(); - return experimentHeaderForm.getPanel(this.experiment); }; -ExperimentTabs.prototype.renderDataAcquisition = function(experiment) { - var _this = this; - this.experiment = experiment; +ExperimentGrid.prototype.input = function() { + var experiments = DATADOC.getExperimentList_10(); + return { + experiments : experiments, + proposal : new MeasurementGrid().input().proposal - var specimenGrid = new SpecimenGrid({ - height : 400, - maxHeight : 500, - width : 890 - }); + }; +}; - specimenGrid.onClick.attach(function(sender, args) { - }); +ExperimentGrid.prototype.test = function(targetId) { + var experimentGrid = new ExperimentGrid({ + height : 350, + minHeight : 350, + width : 1000 - specimenGrid.onSelected.attach(function(sender, specimens) { - //_this.samplePlateGroupWidget.selectSpecimens(specimens); - }); - var specimenContainer = this.specimenWidget.getPanel(); - this.specimenWidget.refresh(experiment); - /* - var specimenContainer = Ext.create('Ext.container.Container', { - layout : 'hbox', - width : 900, - padding : '10 0 0 2', - items : [ specimenGrid.getPanel() ] }); + BIOSAXS.proposal = new Proposal(experimentGrid.input().proposal); + var panel = experimentGrid.getPanel(experimentGrid.input().experiments); + experimentGrid.refresh(experimentGrid.input().experiments); + panel.render(targetId); +}; + + +function FitStructureToExperimentDataGrid(args) { + this.height = null; + this.width = null; + this.id = BUI.id(); + + if (args != null) { + if (args.height != null) { + this.height = args.height; + + if (args.width != null) { + this.width = args.width; + } + } + } + + this.onSelected = new Event(this); +} + +FitStructureToExperimentDataGrid.prototype.getStructuresByMacromolecule = function(macromolecule) { + var structures = []; + if (macromolecule.structure3VOs != null) { + if (macromolecule.structure3VOs.length > 0) { + for (var i = 0; i < macromolecule.structure3VOs.length; i++) { + structures.push(macromolecule.structure3VOs[i]); + } + } + } + return structures; +}; + +FitStructureToExperimentDataGrid.prototype._prepareData = function(subtractions) { + var data = []; + for (var i = 0; i < subtractions.length; i++) { + + for (var j = 0; j < subtractions[i].fitStructureToExperimentalData3VOs.length; j++) { + var fit = subtractions[i].fitStructureToExperimentalData3VOs[j]; + data.push({ + fit : fit.fitFilePath, + fitStructureToExperimentalDataId : fit.fitStructureToExperimentalDataId, + mixtureToStructure3VOs : fit.mixtureToStructure3VOs, + subtractedFile : subtractions[i].substractedFilePath + }); + } + } + return data; + +}; + +FitStructureToExperimentDataGrid.prototype.refresh = function(subtractions) { + this.store.loadData(this._prepareData(subtractions), false); +}; + +FitStructureToExperimentDataGrid.prototype.getPanel = function() { + var _this = this; + this.store = Ext.create('Ext.data.Store', { + fields : [ 'fit', 'subtractedFile', 'structureId', 'fitFilePath', 'mixtureToStructure3VOs' ], + data : [] + }); + + this.store.sort([ { + property : 'name', + direction : 'ASC' + } ]); + + this.selModel = Ext.create('Ext.selection.RowModel', { + allowDeselect : true, + mode : 'MULTI', + listeners : { + selectionchange : function(sm, selections) { + var selected = []; + for (var i = 0; i < selections.length; i++) { + selected.push(selections[i].raw); + } + _this.onSelected.notify(selected); + } + } + }); + + this.panel = Ext.create('Ext.grid.Panel', { + store : this.store, + deferredRender : false, + width : this.width, + height : this.height, + margin : 10, + selModel : this.selModel, + columns : [ { + text : 'Name', + dataIndex : 'fit', + flex : 1, + renderer : function(val, b, record) { + return BUI.getFileName(val); + } + }, { + text : 'PDB', + dataIndex : 'mixtureToStructure3VOs', + flex : 1, + renderer : function(values, b, record) { + var html = ""; + for (var i = 0; i < values.length; i++) { + var structure = BIOSAXS.proposal.getStructuresById(values[i].structureId); + html = html + ""; + if (structure != null){ + html = html + ""; + } + html = html + ""; + } + return html + "
" + structure.name + "
"; + } + }, { + text : 'Volume Fraction', + dataIndex : 'mixtureToStructure3VOs', + flex : 1, + renderer : function(values, b, record) { + var html = ""; + for (var i = 0; i < values.length; i++) { + html = html + ""; + html = html + ""; + html = html + ""; + } + + return html + "
" + values[i].volumeFraction + "
"; + } + },{ + text : 'Subtraction', + dataIndex : 'subtractedFile', + flex : 1, + renderer : function(values, b, record) { + return values.split("/")[values.split("/").length - 1]; + } + },], + + viewConfig : { + enableTextSelection : true, + preserveScrollOnRefresh : true + }, + listeners : { + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + }, + afterrender : function() { + } + } + }); + return this.panel; +}; + +/** Static method **/ +FitStructureToExperimentDataGrid.prototype.RUNFitScattering = function(subtractionId, structureId) { + var _this = this; + /** Add to Workflow **/ + var adapter = new BiosaxsDataAdapter(); + var workflow = { + 'workflowTitle' : 'FitExperimentalDatatoStructure', + 'comments' : 'FitExperimentalDatatoStructure run from ISPyB for subtractionId: ' + subtractionId + ' and structureId ' + structureId + } + + var inputs = [ { + name : 'subtractionId', + value : subtractionId + }, { + name : 'structureId', + value : structureId + } ]; + + adapter.onSuccess.attach(function(sender, data) { + /** Add to Fit **/ + var adapter2 = new BiosaxsDataAdapter(); + var fit = { + 'workflowId' : data.workflowId, + 'subtractionId' : subtractionId, + 'structureId' : structureId, + 'comments' : 'Sent to workflow engine' + } + adapter2.onSuccess.attach(function(sender, fit) { + _this.refresh(_this.subtractionId, _this.macromolecule); + }); + adapter2.addFitStructureData(fit); + + }); + adapter.addWorkflow(workflow, inputs); + +}; + +/** + * It shows buffer grid with a top bar with "Add" button + * + * @height + * @searchBar + * @collapsed + * @width + */ +function FrameGrid(args) { + this.height = 500; + this.width = 500; + this.searchBar = false; + this.tbar = false; + this.collapsed = false; - specimenGrid.refresh(experiment);*/ - var experimentList = new ExperimentList([ _this.experiment ]); - var measurementContainer = Ext.create('Ext.container.Container', { - layout : 'vbox', - padding : '5px 0px 0px 10px', - items : [] - }); - measurementContainer.insert(0, _this.measurementGridDone.getPanel(this.experiment.getMeasurements(), experimentList)); -// measurementContainer.insert(1, _this.measurementSamplePlateGroupWidget.getPanel(experiment)); + if (args != null) { + if (args.height != null) { + this.height = args.height; + } + + if (args.searchBar != null) { + this.searchBar = args.searchBar; + } - // this.dataCollectionCurveVisualizer = new DataCollectionCurveVisualizer(); - // this.dataCollectionCurveVisualizer.experiments = [experiment]; - // this.dataCollectionCurveVisualizer.dataCollectionFrameTree.experiments = - // [experiment]; - // this.dataCollectionCurveVisualizer.dataCollections = - // experiment.getDataCollections(); + if (args.tbar != null) { + this.tbar = args.tbar; + } - this.panel = Ext.createWidget('tabpanel', { - plain : true, - style : { - padding : 2 - }, - items : [ { - tabConfig : { - id : 'genralTabl', - title : "Overview" - }, - items : [ specimenContainer ] - }, { - tabConfig : { - title : 'Measurements' - }, - items : [ measurementContainer] - }, { - tabConfig : { - id : 'SpecimenTab', - title : 'Analysis', - hidden : this.isTemplate() - }, - items : [ { - xtype : 'container', - layout : 'vbox', - padding : '5px 0px 10px 10px', - items : [ _this.analysisGrid.getPanel([]) ] - } ] - }, - { - tabConfig : { - id : 'newAnalysisTab', - title : 'Analysis BETA', - hidden : this.isTemplate() - }, - items : [ { - xtype : 'container', - layout : 'vbox', - padding : '5px 0px 10px 10px', - items : [ _this.queueGrid.getPanel([]) ] - } ] + if (args.collapsed != null) { + this.collapsed = args.collapsed; } - ] + + if (args.width != null) { + this.width = args.width; + } + } +} + +FrameGrid.prototype._edit = function(bufferId) { + var _this = this; + var window = new BufferWindow(); + window.onSuccess.attach(function(sender, proposal) { + _this.store.loadData(BIOSAXS.proposal.getBuffers()); }); + window.draw(BIOSAXS.proposal.getBufferById(bufferId)); +}; - return this.getPanel(this.panel); +FrameGrid.prototype.refresh = function(buffers, experimentId) { + this.experimentId = experimentId; + this.store.loadData(this._prepareData(buffers), false); }; -ExperimentTabs.prototype.isTemplate = function() { - if (this.experiment.json.type == "TEMPLATE") { - return true; - } - return false; +FrameGrid.prototype._prepareData = function(buffers) { + return buffers; }; -ExperimentTabs.prototype.update = function() { +FrameGrid.prototype._getTbar = function() { var _this = this; - var inter; - if (!_this.isTemplate()) { - function updateExperiments() { - _this.refreshAnalysisData(); - window.clearInterval(inter); - inter = setInterval(function() { - updateExperiments(); - }, _this.INTERVAL_UPDATE); - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - var experiment = new Experiment(data); - _this.measurementGridDone.refresh(experiment.getMeasurements(), new ExperimentList([ experiment ])); + var actions = []; + + actions.push(Ext.create('Ext.Action', { + icon : '../images/add.png', + text : 'Add Buffer', + disabled : false, + handler : function(widget, event) { + var window = new BufferWindow(); + window.onSuccess.attach(function(sender) { + _this.store.loadData(BIOSAXS.proposal.getBuffers()); }); - adapter.getExperimentById(_this.experiment.json.experimentId, "MEDIUM"); + window.draw({}); } - inter = setInterval(function() { - updateExperiments(); - }, _this.INTERVAL_UPDATE); - } + })); + return actions; }; -ExperimentTabs.prototype.getPanel = function(panel) { +FrameGrid.prototype.getPanel = function(buffers) { var _this = this; - if (this.experimentPanel == null) { - this.experimentPanel = Ext.create('Ext.container.Container', { - bodyPadding : 2, - width : Ext.getBody().getViewSize().width * 0.9, - renderTo : this.targetId, - style : { - padding : 2 - }, - items : [ this.getExperimentTitle(), this.panel ], - listeners : { - afterrender : function() { - _this.refreshAnalysisData(); - _this.update(); - } - } - }); - } - - return this.experimentPanel; -}; - -ExperimentTabs.prototype.input = function() { - return { - experiment : DATADOC.getExperiment_10(), - proposal : DATADOC.getProposal_10() - }; -}; - -ExperimentTabs.prototype.test = function(targetId) { - var experimentTabs = new ExperimentTabs(targetId); - BIOSAXS.proposal = new Proposal(experimentTabs.input().proposal); - experimentTabs.draw(new Experiment(experimentTabs.input().experiment)); -}; + this.store = Ext.create('Ext.data.Store', { + fields : [ 'frameNumber', 'I0', 'Rg', 'Mass', 'Vc', 'Qr', 'quality'], + data : buffers + }); - -/** - * Shows an experiments with the specimens, measurements, analysis tabs where results are shown and the frames widget - * - * @targetId - */ -function HPLCTabs(targetId) { - this.height = 1400; - this.targetId = targetId; + this.store.sort('frameNumber'); - this.id = BUI.id(); + var type = 'Ext.grid.Panel'; + if (this.searchBar == true) { + type = 'Ext.ux.LiveSearchGridPanel'; + } - this.gridHeight = 600; - this.pointsCount = 1036; - this.plotHeight = 350; - this.plotWidth = 800; - this.plotPanelPadding = 5; + this.grid = Ext.create(type, { + store : this.store, + height : this.height, + width : this.width, + margin : 5, + columns : [{ + text : 'Frame', + dataIndex : 'frameNumber', + flex : 1 + },{ + text : 'I0', + dataIndex : 'I0', + flex : 1, + renderer : function(val, y, sample) { + return BUI.formatValuesUnits(sample.data.I0, "", 12, 3); + } + },{ + text : 'Rg', + dataIndex : 'Rg', + flex : 1, + renderer : function(val, y, sample) { + return BUI.formatValuesUnits(sample.data.Rg, "nm", 12, 3); + } + },{ + text : 'Mass', + dataIndex : 'Mass', + flex : 1, + renderer : function(val, y, sample) { + return BUI.formatValuesUnits(sample.data.Mass, "", 12, 3); + } + },{ + text : 'Vc', + dataIndex : 'Vc', + flex : 1, + renderer : function(val, y, sample) { + return BUI.formatValuesUnits(sample.data.Vc, "", 12, 3); + } + },{ + text : 'Qr', + dataIndex : 'Qr', + flex : 1, + renderer : function(val, y, sample) { + return BUI.formatValuesUnits(sample.data.Qr, "", 12, 3); + } + },{ + text : 'Quality', + dataIndex : 'quality', + flex : 1, + renderer : function(val, y, sample) { + return (Number(sample.data.quality) * 100).toFixed(2) + "%"; + } + }, + { + text : '', + renderer : function(val, x, sample) { + if (sample != null) { + return BUI.getZipHTMLByFrameRangeId(_this.experimentId, sample.raw.frameNumber, sample.raw.frameNumber); + } + }, + width : 100 + }], + flex : 1, + viewConfig : { + stripeRows : true + } + }); - var _this = this; + /** Adding the tbar **/ + if (this.tbar) { + this.grid.addDocked({ + xtype : 'toolbar', + items : this._getTbar() + }); + } + return this.grid; +}; - this.analysisGrid = new HPLCAnalysisGrid({ - height : Ext.getBody().getViewSize().height * 0.9 - 300, - positionColumnsHidden : true, - sorters : [ { - property : 'priorityLevelId', - direction : 'ASC' - } ] - }); +FrameGrid.prototype.input = function() { + return []; +}; - this.frameGrid = new FrameGrid({ - width : 600, - height : 60, - collapsed : false, - tbar : false - }); - - this.peakGrid = new PeakGrid({ - width : 550, - height : 500, - collapsed : false, - tbar : false - }); - - this.peakGrid2 = new PeakGrid({ - width : 102, - height : this.plotHeight, +FrameGrid.prototype.test = function(targetId) { + var frameGrid = new FrameGrid({ + width : 800, + height : 350, collapsed : false, - tbar : false, - showExtendedColumns : true + tbar : true }); - - this.mainPlotPanel = new HPLCGraph({ - title : 'I0', - width : this.plotWidth - 110, - height : this.plotHeight, - bbar : true, - plots : { - "I0" : true, - "Rg" : true - }, - xlabel : "HPLC Frames", - scaled : true, - interactionModel : { - 'dblclick' : function(event, g, context) { - _this._selectFrame(g.lastx_); - var annotations = []; - annotations.push({ - series : g.selPoints_[0].name, - x : g.lastx_, - width : 100, - height : 23, - tickHeight : 4, - shortText : g.lastx_, - text : g.lastx_, - attachAtBottom : true - }); - g.setAnnotations(annotations); - } + var panel = frameGrid.getPanel([]); + panel.render(targetId); +}; + + +function PeakGrid(args) { + this.height = 500; + this.searchBar = false; + this.tbar = false; + this.collapsed = false; + this.width = 500; + this.showExtendedColumns = false; + + if (args != null) { + if (args.showExtendedColumns != null) { + this.showExtendedColumns = args.showExtendedColumns; + } + if (args.height != null) { + this.height = args.height; + } + if (args.searchBar != null) { + this.searchBar = args.searchBar; } - }); - this.intensityPlotPanel = new MergesHPLCGraph({ - title : 'Scattering', - width : this.plotWidth, - height : 500, - showRangeSelector : false, - xParam : 0, - xlabel : "scattering_I", - plots : { - "scattering_I" : true, - "subtracted_I" : true, - "buffer_I" : true + if (args.tbar != null) { + this.tbar = args.tbar; } - }); -} + if (args.collapsed != null) { + this.collapsed = args.collapsed; + } -HPLCTabs.prototype._selectFrame = function(frameNumber) { - try{ - this._renderScatteringCurve(frameNumber); - this.frameGrid.refresh([this.mainPlotPanel.getDataByFrameNumber(frameNumber)], this.experiment.experimentId); - } - catch(e){ - console.log(e); + if (args.width != null) { + this.width = args.width; + } } -}; +} -HPLCTabs.prototype.error = function(error) { - var e = JSON.parse(error); - showError(e); - this.panel.setLoading(false); -}; -HPLCTabs.prototype.loadDataMainPlot = function(data) { - var zeroArray = []; - for ( var i = 0; i < data.I0.length; i++) { - zeroArray.push(0); - } - data = [ { - param : "I0", - data : data.I0, - std : data.I0_Stdev, - color : '#0066CC', - label : "I0" - }, - { - param : "sum_I", - label : "sum_I", - color : "#00FF00", - data : data.sum_I, - std : zeroArray - }, - { - param : "Rg", - label : "Rg", - color : "#21610B", - data : data.Rg, - std : data.Rg_Stdev - }, { - param : "Mass", - data : data.mass, - std : data.mass_Stdev, - color : '#FF9900', - label : "Mass" - }, { - param : "Vc", - data : data.Vc, - std : data.Vc_Stdev, - color : '#990099', - label : "Vc" - }, { - param : "Qr", - data : data.Qr, - std : data.Qr_Stdev, - color : '#FF0066', - label : "Qr" - }, { - param : "quality", - label : "quality", - color : "#FF00FF", - data : data.quality, - std : zeroArray - } ]; - this.data = data; - this.mainPlotPanel.loadData(data); +PeakGrid.prototype.refresh = function(buffers) { + this.store.loadData(this._prepareData(buffers), false); }; -HPLCTabs.prototype._loadIntensityPlotByFrameNumber = function(frameNumber) { - var _this = this; +PeakGrid.prototype._prepareData = function(buffers) { - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - var array = []; - data = [ { - param : "q", - data : data[frameNumber].q, - std : data[frameNumber].q, - fstd : function(a) { - return parseFloat(a); - }, - color : '#green', - label : "q", - showOnMenu : false - }, - { - param : "scattering_I", - data : data[frameNumber].scattering_I, - fdata : function(a) { - return Math.log(parseFloat(a)); - }, - std : data[frameNumber].scattering_Stdev, - fstd : function(a) { - return Math.log(Math.abs(parseFloat(a))); - }, - color : 'green', - label : "Log(I) Sample" - }, - { - param : "buffer_I", - data : data[frameNumber].buffer_I, - fdata : function(a) { - return Math.log(parseFloat(a)); - }, - fstd : function(a) { - return Math.log(Math.abs(parseFloat(a))); - }, - std : data[frameNumber].subtracted_Stdev, - color : '#0000FF', - label : "Log(I) Avg Buf." - }, - { - param : "subtracted_I", - data : data[frameNumber].subtracted_I, - fdata : function(a) { - var value = (Math.log(parseFloat(a))); - if (isNumber(value)) - return value; - }, - fstd : function(a) { - var value = Math.log(Math.abs(parseFloat(a))); - if (isNumber(value)) - return value; - }, - std : data[frameNumber].subtracted_Stdev, - color : 'red', - label : "Log(I) Sub." - } - ]; +// for ( var i = 0; i < buffers.length; i++) { +// buffers[i].name = "Peak #" + (i+1); +// } + /** Adding information of buffer **/ + if (buffers.length > 0){ + buffers.unshift({ + name : "BUFFER", + start : 0, + experimentId : buffers[0].experimentId, + end : buffers[0].start - 1 + }); + } + + + return buffers; +}; - _this.intensityPlotPanel.xlabel = "Frame " + frameNumber + " (q, nm-1)"; +PeakGrid.prototype._getTbar = function() { + var _this = this; + var actions = []; - if (_this.intensityPlotPanel.hplcData == null) { - /** It creates also top bar **/ - _this.intensityPlotPanel.loadData(data); - } else { - _this.intensityPlotPanel.reloadData(data); - + actions.push(Ext.create('Ext.Action', { + icon : '../images/add.png', + text : 'Add Buffer', + disabled : false, + handler : function(widget, event) { + var window = new BufferWindow(); + window.onSuccess.attach(function(sender) { + _this.store.loadData(BIOSAXS.proposal.getBuffers()); + }); + window.draw({}); } - _this.intensityPlotPanel.panel.setLoading(false); - }); - adapter.onError.attach(function(sender, data) { - _this.intensityPlotPanel.panel.setLoading(false); - }); - this.intensityPlotPanel.panel.setLoading("Retrieving Frame " + frameNumber); - adapter.getH5FrameScattering(this.experiment.json.experimentId, frameNumber); + })); + return actions; }; -HPLCTabs.prototype._renderScatteringCurve = function(frameNumber) { +PeakGrid.prototype.getPanel = function(buffers) { var _this = this; + this.peakCount = 0; + this.store = Ext.create('Ext.data.Store', { + fields : ['name', {name:'start', type : 'int'}, {name:'end', type : 'int'}], + data : buffers + + }); - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - _this.intensityPlotPanel.setPeaks(data); - _this._loadIntensityPlotByFrameNumber(frameNumber); - try{ - var peaks = []; - for(key in data){ - peaks.push({ - start : key.split("-")[0], - end : key.split("-")[1], - experimentId : _this.experiment.json.experimentId - }); + this.store.sort('start'); + + var type = 'Ext.grid.Panel'; + if (this.searchBar == true) { + type = 'Ext.ux.LiveSearchGridPanel'; + } + this.grid = Ext.create(type, { + store : this.store, + height : this.height, + width : this.width, + margin : 5, + columns : [ + { + text : '', + dataIndex : 'name', + width : 100, + hidden : _this.showExtendedColumns, + renderer : function(val, y, sample) { + if (sample.data.name == "BUFFER") + return "BUFFER"; + _this.peakCount++; + return "Peak #" + _this.peakCount; + } + + + }, + { + text : 'Peaks', + dataIndex : 'start', + sortable : true, + width : 100, + hidden: !_this.showExtendedColumns, + renderer : function(val, y, sample) { + return "From " + Number(sample.raw.start) + " to " + Number(sample.raw.end); + } + }, + { + text : 'Frames', + hidden : _this.showExtendedColumns, + columns : [ + { + text : 'Start', + dataIndex : 'start', + sortable : true, + hidden : _this.showExtendedColumns, + width : 100, + renderer : function(val, y, sample) { + return Number(val); + } + },{ + text : 'End', + dataIndex : 'end', + width : 100, + hidden : _this.showExtendedColumns, + renderer : function(val, y, sample) { + return Number(val); + } + },{ + text : 'Total', + dataIndex : 'end', + width : 100, + hidden : _this.showExtendedColumns, + renderer : function(val, y, sample) { + return "" + (sample.raw.end - sample.raw.start) + " frames"; + } + } + ] + } +// , +// { +// text : '', +// hidden : _this.showExtendedColumns, +// renderer : function(val, x, sample) { +// if (sample != null) { +// return BUI.getZipHTMLByFrameRangeId(sample.raw.experimentId, sample.raw.start, sample.raw.end); +// } +// }, +// width : 100 +// } + ], + flex : 1, + viewConfig : { + stripeRows : true, + getRowClass : function(record, rowIdx, params, store) { + if (record.raw.name == "BUFFER") { + return "blue-row"; + } } - _this.peakGrid2.refresh(JSON.parse(JSON.stringify(peaks))); - _this.peakGrid.refresh(peaks); -// console.log(peaks); - } - catch(e){ - showError(e); } }); - adapter.onError.attach(function(sender, data) { - _this.intensityPlotPanel.setLoading(false); + + /** Adding the tbar **/ + if (this.tbar) { + this.grid.addDocked({ + xtype : 'toolbar', + items : this._getTbar() + }); + } + return this.grid; +}; + +PeakGrid.prototype.input = function() { + return []; +}; + +PeakGrid.prototype.test = function(targetId) { + var PeakGrid = new PeakGrid({ + width : 800, + height : 350, + collapsed : false, + tbar : true }); - this.intensityPlotPanel.panel.setLoading("Reading HDF5 File "); - adapter.getH5FramesMerge(this.experiment.json.experimentId); + + var panel = PeakGrid.getPanel([]); + panel.render(targetId); }; + +/** + * Macromolecule Grid showing macromolecules and adding anb updating buttons + * + * @height + * @maxHeight + * @width + * @cssFontStyle + * @searchBar makes this grid as Ext.ux.LiveSearchGridPanel + * @tbar top bar containing "Add" and "Update From SMIS" button + * @collapsed + * @collapsible + * @btnEditVisible + * @btnRemoveVisible + * @multiselect makes it multiselect using Ext.selection.CheckboxModel + * + * #onSelected + * #onMacromoleculesChanged + */ +function MacromoleculeGrid(args) { + this.height = 500; + this.width = 500; + this.id = BUI.id(); + this.maxHeight = this.height; -HPLCTabs.prototype._postRenderOverviewPanel = function() { - var _this = this; - var adapter = new BiosaxsDataAdapter(); - adapter.onError.attach(function(sender, data) { - data = data.replace(/NaN/g, '0'); - _this.loadDataMainPlot(JSON.parse(data)); - + this.searchBar = false; + this.tbar = false; + + this.collapsible = true; + this.collapsed = true; + + this.btnEditVisible = true; + this.btnRemoveVisible = false; + this.multiselect = false; + + /** Font style applied to the acronym column **/ + this.cssFontStyle = null; + + if (args != null) { + if (args.height != null) { + this.height = args.height; + this.maxHeight = this.height; + } + if (args.maxHeight != null) { + this.maxHeight = args.maxHeight; + } + if (args.width != null) { + this.width = args.width; + } + if (args.cssFontStyle != null) { + this.cssFontStyle = args.cssFontStyle; + } + + if (args.searchBar != null) { + this.searchBar = args.searchBar; + } + if (args.tbar != null) { + this.tbar = args.tbar; + } + if (args.collapsible != null) { + this.collapsible = args.collapsible; + } + if (args.collapsed != null) { + this.collapsed = args.collapsed; + } + if (args.btnEditVisible != null) { + this.btnEditVisible = args.btnEditVisible; + } + if (args.btnRemoveVisible != null) { + this.btnRemoveVisible = args.btnRemoveVisible; + } + if (args.multiselect != null) { + this.multiselect = args.multiselect; + } + } - }); - adapter.onSuccess.attach(function(sender, data) { - _this.loadDataMainPlot(data); - _this._renderScatteringCurve(0); - }); - adapter.getH5fileParameters(this.experiment.json.experimentId, [ - "I0", "I0_Stdev", "sum_I","Rg", "Rg_Stdev", "Vc", "Vc_Stdev", "Qr", "Qr_Stdev", "mass", "mass_Stdev", "quality" ]); + this.onSelected = new Event(); -}; + this.onMacromoleculesChanged = new Event(); +} -HPLCTabs.prototype._postRenderDetailsPanel = function() { - if (this.data != null) { - this.I0PlotPanel.loadData(this.data); - this.RgPlotPanel.loadData(this.data); - this.MassPlotPanel.loadData(this.data); - this.VcPlotPanel.loadData(this.data); - } -}; -HPLCTabs.prototype.draw = function(experiment) { - var _this = this; - this.renderDataAcquisition(experiment); -}; -HPLCTabs.prototype.getExperimentTitle = function() { - var experimentHeaderForm = new ExperimentHeaderForm(); - return experimentHeaderForm.getPanel(this.experiment); -}; -HPLCTabs.prototype.renderDataAcquisition = function(experiment) { +MacromoleculeGrid.prototype.edit = function(macromolecule) { var _this = this; - this.experiment = experiment; - if (this.experimentPanel == null) { - this.experimentPanel = Ext.create('Ext.container.Container', { - bodyPadding : 2, - height : this.height, - width : Ext.getBody().getViewSize().width * 0.9, - renderTo : this.targetId, - style : { - padding : 2 - }, - items : [ this.getExperimentTitle(), this.getPanel() ], - listeners : { - afterrender : function() { - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - _this.analysisGrid.refresh(data); - }); - adapter.getAnalysisInformationByExperimentId(_this.experiment.experimentId); - } - } - }); - } - return this.experimentPanel; + var window = new MacromoleculeWindow(); + window.onSave.attach(function(sender) { + _this.store.loadData(BIOSAXS.proposal.getMacromolecules()); + _this.onMacromoleculesChanged.notify(); + }); + window.draw(macromolecule); }; -HPLCTabs.prototype.getPanel = function() { +MacromoleculeGrid.prototype.getTbar = function() { var _this = this; - this.panel = Ext.createWidget('tabpanel', - { - plain : true, - height : this.height, -// width : 900, - style : { - padding : 2 - }, - items : [ - { - tabConfig : { - title : "Overview" + var actions = []; - }, - items : [ { - xtype : 'container', - layout : 'hbox', - border : 1, - flex : 1, - items : [ { - xtype : 'container', - layout : 'vbox', - border : 1, - items : [ { - xtype : 'container', - margin : '10px', - border : 1, - items : [ - { - xtype : 'container', - margin : '0px', - layout : 'hbox', - border : 1, - items : [ - this.peakGrid2.getPanel([]), - this.mainPlotPanel.getPanel() - ] - }, - { - xtype : 'container', - layout : 'vbox', - border : 1, - items : [ - { - html: '
Select a frame by double-clicking on the HPLC Frames plot
', - margin: 5, - border : 0 - }, - this.frameGrid.getPanel([]), - this.intensityPlotPanel.getPanel() - ] - } - - ] - }], - listeners : { - afterrender : function() { - _this._postRenderOverviewPanel(); - } - } - } ] - } ] - }, -// { -// tabConfig : { -// title : "Details" -// }, -// items : [ { -// xtype : 'container', -// layout : 'hbox', -// border : 1, -// flex : 1, -// items : [ { -// xtype : 'container', -// layout : 'vbox', -// border : 1, -// items : [ { -// xtype : 'container', -// padding : '1px', -// items : [ -// this.I0PlotPanel.getPanel(), this.RgPlotPanel.getPanel(), this.MassPlotPanel.getPanel(), -// this.VcPlotPanel.getPanel() ] -// } ], -// listeners : { -// afterrender : function() { -// _this._postRenderDetailsPanel(); -// } -// } -// } ] -// } ] -// }, - { - tabConfig : { - title : "Analysis" - }, - items : [ { - xtype : 'container', - layout : 'vbox', - padding : '5px 0px 10px 10px', - items : [ _this.analysisGrid.getPanel([]) ] - } ] - }, - { - tabConfig : { - title : "File Manager" - }, - items : [ { - xtype : 'container', - layout : 'vbox', - padding : '5px 0px 10px 10px', - items : [ - { - html: '
Custom Download
', - margin : '10 0 10 5', - border : 0 - }, - { - html: '
Download has been temporary disabled. Contact your labcontact if you want to extract the frames from the HDF5 file
', - margin : '10 0 10 5', - hidden : _this.experiment.experimentId == 2602, - border : 0 - }, - { - xtype : 'container', - layout : 'hbox', - margin : '0 0 0 20', - flex : 1, - items :[ - { - xtype: 'numberfield', - id: 'field_start', - fieldLabel: 'Frames from', - value: 0, - minValue: 0 - }, - { - xtype: 'numberfield', - id: 'field_end', - fieldLabel: 'to', - labelWidth : 20, - margin : '0 0 0 10', - minValue: 0 - }, - { - xtype: 'button', - /** allowing test account to download frames **/ - disabled : _this.experiment.experimentId != 2602, - text : 'Download', - margin : '0 0 0 10', - handler : function() { - var experimentId = _this.experiment.experimentId; - var start = Ext.getCmp("field_start").getValue(); - var end = Ext.getCmp("field_end").getValue(); - /** Checking if start is bigger than end **/ - if (start > end){ - var aux = end; - end = start; - start = aux; - } - var url = BUI.getZipFrameHPLCUrl(experimentId, start, end); - window.open(url) - } - } - ] - }, - _this.peakGrid.getPanel([]) - - ] - } - ] - } - ] + actions.push(Ext.create('Ext.Action', { + icon : '../images/add.png', + text : 'Add macromolecule', + disabled : false, + handler : function(widget, event) { + _this.edit(); + } + })); + actions.push("->"); + actions.push(Ext.create('Ext.Action', { + icon : '../images/folder_go.png', + text : 'Update From SMIS', + tooltip : "Retrieve all the macromolecules of your proposal from SMIS database", + disabled : false, + handler : function(widget, event) { + _this.grid.setLoading("Connecting to SMIS"); + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + BIOSAXS.proposal.setMacromolecules(data.macromolecules); + _this.refresh(BIOSAXS.proposal.macromolecules); + _this.grid.setLoading(false); + }); + adapter.onError.attach(function(sender, data) { + _this.grid.setLoading(false); }); + adapter.updateDataBaseFromSMIS(); + } + })); + return actions; +}; - return this.panel; +MacromoleculeGrid.prototype.deselectAll = function() { + this.grid.getSelectionModel().deselectAll(); +}; + +MacromoleculeGrid.prototype.selectById = function(macromoleculeId) { + this.grid.getSelectionModel().deselectAll(); + for ( var i = 0; i < this.grid.getStore().data.items.length; i++) { + var item = this.grid.getStore().data.items[i].raw; + if (item.macromoleculeId == macromoleculeId) { + this.grid.getSelectionModel().select(i); + } + } +}; + +MacromoleculeGrid.prototype.refresh = function(macromolecules) { + this.store.loadData(macromolecules, false); +}; + +MacromoleculeGrid.prototype.getColumns = function() { + var _this = this; + var columns = [ + { + text : 'Acronym', + dataIndex : 'acronym', + id : this.id + "acronym", + flex : 1, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + if (_this.cssFontStyle != null) { + return "" + value + ""; + } + return value; + } + }, { + text : 'Name', + dataIndex : 'name', + id : this.id + "name", + flex : 1, + hidden : true + } ]; + + if (this.btnEditVisible) { + columns.push({ + id : _this.id + 'buttonEditMacromolecule', + width : 85, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + if (_this.btnEditVisible) { + return BUI.getGreenButton('EDIT'); + } + return null; + } + }); + } + if (this.btnRemoveVisible) { + columns.push({ + id : _this.id + 'buttonRemoveMacromolecule', + width : 85, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + if (_this.btnRemoveVisible) { + return BUI.getRedButton('REMOVE'); + } + return null; + } + }); + } + + return columns; +}; + + +/** Returns the grid **/ +MacromoleculeGrid.prototype.getPanel = function() { + var _this = this; + + this.store = Ext.create('Ext.data.Store', { + fields : [ 'macromoleculeId', 'name', 'acronym' ] + }); + + var type = 'Ext.grid.Panel'; + if (this.searchBar == true) { + type = 'Ext.ux.LiveSearchGridPanel'; + } + + this.selModel = Ext.create('Ext.selection.RowModel', { +// allowDeselect : true, +// mode : 'MULTI', + listeners : { + selectionchange : function(sm, selections) { + var selected = []; + for (var i = 0; i < selections.length; i++) { + selected.push(selections[i].raw); + } + _this.onSelected.notify(selected); + } + } + }); + + this.grid = Ext.create(type, { + id : this.id, + title : 'Macromolecules', + collapsible : this.collapsible, + collapsed : this.collapsed, + store : this.store, + height : this.height, + maxHeight : this.maxHeight, + selModel : this.selModel, + columns : this.getColumns(), + width : this.width, + viewConfig : { + stripeRows : true, + listeners : { + 'celldblclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + _this.edit(BIOSAXS.proposal.getMacromoleculeById(record.data.macromoleculeId)); + }, + 'cellclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEditMacromolecule') { + _this.edit(BIOSAXS.proposal.getMacromoleculeById(record.data.macromoleculeId)); + } + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemoveMacromolecule') { + BUI.showBetaWarning(); + } + } + + } + } + }); + + /** Adding the tbar **/ + if (this.tbar) { + this.grid.addDocked({ + xtype : 'toolbar', + items : this.getTbar() + }); + } + return this.grid; +}; + +MacromoleculeGrid.prototype.input = function() { + return { + proposal : DATADOC.getProposal_10() + }; +}; + +MacromoleculeGrid.prototype.test = function(targetId) { + var macromoleculeGrid = new MacromoleculeGrid({ + width : 800, + height : 350, + collapsed : false, + tbar : true + }); + + BIOSAXS.proposal = new Proposal(macromoleculeGrid.input().proposal); + var panel = macromoleculeGrid.getPanel(BIOSAXS.proposal.macromolecules); + panel.render(targetId); }; /** - * Main form tab for macromolecule + * Shows measurements with their attributes as specimen, exposure temperature, + * volume to load, transmission etc... * - * @width + * @addBtnMultipleEdit: if true add a button for changing measurements' + * parameters by choosing multiple measurements. It opens + * MultipleEditMeasurementGridWindow + * @collapsed: if true it doesn't show buffer's measurements + * @editor: hashmap containing columns to be edited. It is an array of a json + * like editor of Ext + * @selModel + * @collapseBtnEnable + * @removeBtnEnabled Ext.selection.RowModel + * @addBtnEnable + * @updateRowEnabled true/false if update plugin is set to the grid + * @showTitle + * @title + * @isStatusColumnHidden + * @isPriorityColumnHidden + * @isTimeColumnHidden + * @estimateTime + * @margin + * @tbar * @height + * @maxHeight + * @minHeight + * @width + * @maxWidth + * @resizable + * @experimentColorBased when colors for buffers and macromolecules are not + * selected by the proposal but by experiment, so the + * number of colors is smaller * - * #onClose when user clicks on close button in the MacromoleculeForm - * #onSave when macromole is saved by macromoleculeForm + * #onClick #onSelected #onRemoved #onUpdateTime #onMeasurementChanged + * #onExperimentChanged */ -function MacromoleculeTabs(args) { - this.width = 500; +function MeasurementGrid(args) { + this.id = BUI.id(); + this.height = 500; + this.width = 900; - if (args != null) { - if (args.width != null) { - this.width = args.width; + this.maxWidth = 1200; + this.maxHeight = 600; + this.minHeight = 500; + + this.unitsFontSize = 9; + this.title = "Measurements"; + this.estimateTime = false; + this.collapsed = true; + this.tbar = true; + + this.showTitle = true; + this.resizable = true; + this.updateRowEnabled = true; + + /** + * Hash map containing the keys of the editable columns. Ex: + * 'exposureTemperature' * + */ + this.editor = { + comments : { + xtype : 'textfield', + allowBlank : true } - if (args.height != null) { - this.height = args.height; + }; + + this.isTimeColumnHidden = false; + this.isStatusColumnHidden = false; + this.isPriorityColumnHidden = true; + this.margin = "0 0 0 0"; + + this.addBtnEnable = true; + this.sorter = [ { + property : 'priority', + direction : 'ASC' + } ]; + + this.removeBtnEnabled = false; + this.collapseBtnEnable = true; + this.addBtnMultipleEdit = false; + this.sortingBtnEnable = false; + + var _this = this; + this.selModel = Ext.create('Ext.selection.RowModel', { + allowDeselect : true, + mode : 'MULTI', + listeners : { + selectionchange : function(sm, selections) { + var selected = []; + for (var i = 0; i < selections.length; i++) { + selected.push(selections[i].raw); + } + _this.onSelected.notify(selected); + } } - } + }); - var _this = this; + if (args != null) { - /** Widgets **/ + if (args.selModel != null) { + this.selModel = args.selModel; + } - /** Macromolecule Form **/ - this.macromoleculeForm = new MacromoleculeForm({ - width : this.width - 30, - height : this.height - 50, - }); + if (args.removeBtnEnabled != null) { + this.removeBtnEnabled = args.removeBtnEnabled; + } - this.macromoleculeForm.onClose.attach(function(sender) { - _this.onClose.notify(); - }); + if (args.addBtnMultipleEdit != null) { + this.addBtnMultipleEdit = args.addBtnMultipleEdit; + } - this.macromoleculeForm.onSave.attach(function(sender, macromolecule) { - _this.onSave.notify(macromolecule); - }); + // if (args.experimentColorBased != null) { + // this.experimentColorBased = args.experimentColorBased; + // } - this.assemblyForm = new AssemblyForm({ - width : this.width - 30, - height : this.height - 50, - }); - - this.rigibBodyModelingForm = new RigibBodyModelingForm({ - width : this.width - 30, - height : this.height - 50, - }); - - this.rigibBodyModelingForm.onSave.attach(function(sender, macromolecule) { - _this.onSave.notify(macromolecule); - }); - + if (args.collapsed != null) { + this.collapsed = args.collapsed; + } + if (args.resizable != null) { + this.resizable = args.resizable; + } - /** Events **/ - this.onClose = new Event(this); - this.onSave = new Event(this); -} + if (args.editor != null) { + this.editor = args.editor; + } -/** Populate the widget **/ -MacromoleculeTabs.prototype.refresh = function(macromolecule) { - this.macromoleculeForm.refresh(macromolecule); - this.assemblyForm.refresh(macromolecule); - this.rigibBodyModelingForm.refresh(macromolecule); + if (args.collapseBtnEnable != null) { + this.collapseBtnEnable = args.collapseBtnEnable; + } - if (macromolecule != null){ - if (macromolecule.macromoleculeId == null){ - Ext.getCmp(this.id + "_advancedTab").disable(); - Ext.getCmp(this.id + "_assemblyTab").disable(); + if (args.addBtnEnable != null) { + this.addBtnEnable = args.addBtnEnable; } - else{ - Ext.getCmp(this.id + "_advancedTab").enable(); - Ext.getCmp(this.id + "_assemblyTab").enable(); + if (args.sortingBtnEnable != null) { + this.sortingBtnEnable = args.sortingBtnEnable; } - } - else{ - Ext.getCmp(this.id + "_advancedTab").disable(); - Ext.getCmp(this.id + "_assemblyTab").disable(); - } -}; -MacromoleculeTabs.prototype.getItems = function() { - return [ { - tabConfig : { - title : 'General' - }, - items : [ { - xtype : 'container', - items : [ this.macromoleculeForm.getPanel() ] - } ] - }, { - id : this.id + "_assemblyTab", - tabConfig : { - title : 'Assembly' - }, - items : [ { - xtype : 'container', - items : [ this.assemblyForm.getPanel() ] - } ] - },{ - id : this.id + "_advancedTab", - tabConfig : { - title : 'Advanced' - }, - items : [ this.rigibBodyModelingForm.getPanel() ] - } ]; -}; + if (args.isPriorityColumnHidden != null) { + this.isPriorityColumnHidden = args.isPriorityColumnHidden; + } -MacromoleculeTabs.prototype.getPanel = function() { - this.panel = Ext.createWidget('tabpanel', { - height : this.height, - width : this.width, - plain : true, - margin : 5, - border : 0, - items : this.getItems() - }); - return this.panel; -}; - -function ResultTabs() { -} + if (args.width != null) { + this.width = args.width; + } -ResultTabs.prototype.draw = function(targetId, data, macromoleculeId) { - var panel = this.getPanel(targetId, data, macromoleculeId); - return Ext.create('Ext.container.Container', { - renderTo : targetId, - items : [ BUI.getMacromoleculeHeader(macromoleculeId), panel ] - }); + if (args.updateRowEnabled != null) { + this.updateRowEnabled = args.updateRowEnabled; + } -}; + if (args.showTitle != null) { + this.showTitle = args.showTitle; + if (this.showTitle == false) { + this.title = null; + } + } -ResultTabs.prototype._splitBySpecimen = function(data) { - var splitted = {}; + if (args.height != null) { + this.height = args.height; + } - for ( var i = 0; i < data.length; i++) { - var row = data[i]; - if (splitted[row.macromoleculeId + "_" + row.bufferId] == null) { - splitted[row.macromoleculeId + "_" + row.bufferId] = []; + if (args.maxHeight != null) { + this.maxHeight = args.maxHeight; } - splitted[row.macromoleculeId + "_" + row.bufferId].push(row); - } - return splitted; -}; + if (args.minHeight != null) { + this.minHeight = args.minHeight; + } -ResultTabs.prototype._getTabTitle = function(key, data) { - var macromoleculeId = key.split("_")[0]; - var bufferId = key.split("_")[1]; + if (args.maxWidth != null) { + this.maxWidth = args.maxWidth; + } - return BIOSAXS.proposal.getMacromoleculeById(macromoleculeId).acronym + " + " + BIOSAXS.proposal.getBufferById(bufferId).acronym + "(" + data.length + ")"; -}; + if (args.isStatusColumnHidden != null) { + this.isStatusColumnHidden = args.isStatusColumnHidden; + } + if (args.isTimeColumnHidden != null) { + this.isTimeColumnHidden = args.isTimeColumnHidden; + } -ResultTabs.prototype.getPanel = function(targetId, data, macromoleculeId) { + if (args.title != null) { + this.title = args.title; + } + if (args.estimateTime != null) { + this.estimateTime = args.estimateTime; + } - var dataFiltered = new AnalysisGrid({ - hideNulls : true, - grouped : true, - sorters : [ { - property : 'quality', - direction : 'DESC' - } ] - })._prepareData(data); + if (args.margin != null) { + this.margin = args.margin; + } - var items = [ { - tabConfig : { - title : 'Analysis (' + dataFiltered.length + ')' - }, - items : [ { - xtype : 'container', - layout : 'vbox', - padding : 10, - items : [ new AnalysisGrid({ - isScatteringPlotVisible : false - }).getPanel(dataFiltered) ] - } ] - }, { - tabConfig : { - title : 'Concentration Effects' - }, - items : [ new ResultSummaryForm().getPanel(data) ] - } ]; + if (args.tbar != null) { + this.tbar = args.tbar; + } + + if (args.sorter != null) { + this.sorter = args.sorter; + } - var splitted = this._splitBySpecimen(dataFiltered); - for ( var key in splitted) { - items.push({ - tabConfig : { - title : this._getTabTitle(key, splitted[key]) - }, - items : [ new ResultSummaryForm().getPanel(splitted[key]) ] - }); } + this.onClick = new Event(this); + this.onSelected = new Event(this); + this.onRemoved = new Event(this); + this.onUpdateTime = new Event(this); + this.onMeasurementChanged = new Event(this); + this.onExperimentChanged = new Event(this); +} - this.panel = Ext.createWidget('tabpanel', { - style : { - padding : 2 - }, - items : items +MeasurementGrid.prototype._sortBy = function(sort) { + var _this = this; + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + _this.onExperimentChanged.notify(data); + _this.grid.setLoading(false); + // wizardWidget.window.close(); }); - return this.panel; - + adapter.onError.attach(function(sender, data) { + _this.grid.setLoading(false); + alert("Oops, there was a problem"); + }); + _this.grid.setLoading("Sorting"); + adapter.sortMeasurements(this.experiments.experiments[0].experimentId, sort); }; - - -function ShipmentTabs(targetId) { - this.targetId = targetId; +MeasurementGrid.prototype._getMenu = function() { var _this = this; - this.gridHeight = 500; - /** data **/ - this.shipment = null; - - /** Shipment Form **/ - this.shipmentForm = new ShipmentForm({ - creationMode : false, - showTitle : false - }); - this.shipmentForm.onSaved.attach(function(sender, data) { - _this.refresh(data); + if (this.tbar) { - }); + var items = []; + if (_this.addBtnEnable) { + items.push({ + icon : '../images/add.png', + text : 'Add measurements', + handler : function() { + _this._openAddMeasurementWindow(); + } + }); + } + if (_this.addBtnMultipleEdit) { + items.push({ + icon : '../images/Edit_16x16_01.png', + text : 'Multiple Edit', + handler : function() { + var multipleEditMeasurementGridWindow = new MultipleEditMeasurementGridWindow(); + multipleEditMeasurementGridWindow.onExperimentChanged.attach(function(sender, data) { + _this.onExperimentChanged.notify(data); + }); - /** Cases grid **/ - this.caseGrid = new CaseGrid({ - height : this.gridHeight - }); + multipleEditMeasurementGridWindow.draw(_this.measurements, _this.experiments); - this.caseGrid.onAddButtonClicked.attach(function(sender, dewar) { - _this.caseGrid.grid.setLoading("ISPyB: Creating a new case"); - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, shipment) { - /** updateing shipment on proposal **/ - for ( var i = 0; i < BIOSAXS.proposal.shippings.length; i++) { - if (BIOSAXS.proposal.shippings[i].shippingId == shipment.shippingId) { - BIOSAXS.proposal.shippings[i] = shipment; } - } - _this.refresh(shipment); - }); - adapter.onError.attach(function(sender, shipment) { - _this.caseGrid.grid.setLoading(false); - }); - adapter.addCase(_this.shipment.json.shippingId); - }); + }); + } - this.caseGrid.onRemoveButtonClicked.attach(function(sender, dewarId) { - _this.panel.setLoading("ISPyB: removing case"); - _this.shipment.onSaved.attach(function(sender, shipment) { - _this.refresh(shipment); + items.push("->"); - }); - _this.shipment.removeCase(dewarId); - }); -} + if (_this.sortingBtnEnable) { + var split = Ext.create('Ext.button.Split', { + text : 'Sort by', + // handle a click on the button itself + handler : function() { + // alert("The button was clicked"); + }, + menu : new Ext.menu.Menu({ + items : [ + { + text : 'First Created First Measured', + handler : function() { + _this._sortBy("FIFO"); + } + }, "-", { + text : 'Default', + handler : function() { + _this._sortBy("DEFAULT"); + } + } ] + }) + }); + items.push(split); + } -ShipmentTabs.prototype.refresh = function(shipment) { + if (_this.collapseBtnEnable) { + items.push({ + text : 'Collapse buffers', + enableToggle : true, + scope : this, + toggleHandler : function(item, pressed) { + this.collapsed = pressed; + this.grid.getStore().loadData(this._prepareData(this.measurements, this.experiments), false); + }, + pressed : this.collapsed + }); + } + var tb = Ext.create('Ext.toolbar.Toolbar', { + items : items + }); + return tb; + } + return null; +}; +/** Opens WizardWidget for adding new measurements * */ +MeasurementGrid.prototype._openAddMeasurementWindow = function(measurements, experiments) { var _this = this; - this.shipment = shipment; - var proposal = new Proposal(); - proposal.onDataRetrieved.attach(function(sender, plates) { - - _this.refreshWithPlates(shipment, plates); - _this.caseGrid.grid.setLoading(false); + var wizardWidget = new WizardWidget(); + wizardWidget.onFinished.attach(function(sender, result) { + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + _this.onExperimentChanged.notify(data); + _this.grid.setLoading(false); + wizardWidget.window.close(); + }); + wizardWidget.current.setLoading("ISPyB: Adding measurements"); + adapter.addMeasurements(result.name, "comments", result.data, _this.experiments.experiments[0].experimentId); }); - proposal.getPlatesByProposal(); + + wizardWidget.draw(null, new MeasurementCreatorStepWizardForm(BIOSAXS.proposal.getMacromolecules(), { + noNext : true + })); }; -ShipmentTabs.prototype.refreshWithPlates = function(shipment, plates) { - this.shipment = new Shipment(shipment); +/******************************************************************************* + * Opens WizardWidget for adding new measurements + * + * @Measurements + * @Experiments experimentList Object + ******************************************************************************/ +MeasurementGrid.prototype._prepareData = function(measurements, experiments) { + var data = []; + for (var i = 0; i < measurements.length; i++) { + var measurement = measurements[i]; + var specimen = experiments.getSampleById(measurement.specimenId); + var buffer = experiments.getBufferById(specimen.bufferId); + measurement.buffer_acronym = buffer.acronym; + measurement.bufferId = buffer.bufferId; + measurement.volume = specimen.volume; + if (specimen.macromolecule3VO != null) { + measurement.acronym = specimen.macromolecule3VO.acronym; + measurement.macromoleculeId = specimen.macromolecule3VO.macromoleculeId; + } + measurement.concentration = specimen.concentration; + if (measurement.run3VO != null) { + measurement.energy = measurement.run3VO.energy; + measurement.expExposureTemperature = measurement.run3VO.exposureTemperature; + measurement.storageTemperature = measurement.run3VO.storageTemperature; + measurement.timePerFrame = measurement.run3VO.timePerFrame; + measurement.radiationAbsolute = measurement.run3VO.radiationAbsolute; + measurement.radiationRelative = measurement.run3VO.radiationRelative; + measurement.status = "DONE"; - this.caseGrid.refresh(this.shipment.getDewars(), plates); - this.panel.setLoading(false); + try { + if (measurement.run3VO.timeStart != null) { + if (measurement.run3VO.timeStart != "") { + measurement.miliseconds = moment(measurement.run3VO.timeStart).format("X"); + } + } + } catch (E) { + console.log(E); + } + } + + if (experiments.getDataCollectionByMeasurementId(measurement.measurementId).length > 0) { + var measurementtodatacollection3VOs = experiments.getDataCollectionByMeasurementId(measurement.measurementId)[0].measurementtodatacollection3VOs; + for (var k = 0; k < measurementtodatacollection3VOs.length; k++) { + if (measurementtodatacollection3VOs[k].dataCollectionOrder == 1) { + var specimenBuffer = experiments.getSampleById(experiments.getMeasurementById(measurementtodatacollection3VOs[k].measurementId).specimenId); + if (specimenBuffer.sampleplateposition3VO != null) { + measurement.bufferSampleplateposition3VO = specimenBuffer.sampleplateposition3VO; + measurement.bufferSampleplate = (experiments.getSamplePlateById(specimenBuffer.sampleplateposition3VO.samplePlateId)); + } + } + } + } + + if (this.collapsed) { + /** If collapsed only the samples * */ + if (specimen.macromolecule3VO != null) { + data.push(measurement); + } + } else { + data.push(measurement); + } + + } + return data; }; -ShipmentTabs.prototype.error = function(error) { - var e = JSON.parse(error); - showError(e); - this.panel.setLoading(false); +/** + * Refresh data grid with the measurements and the experiments + * + * @measurements array with measurement3VO objects + * @experiments array with experiments objects + */ +MeasurementGrid.prototype.refresh = function(measurements, experiments) { + this.experiments = experiments; + this.measurements = measurements; + this.store.loadData(this._prepareData(measurements, experiments), false); }; -//ShipmentTabs.prototype.refreshTabTitles = function() { -/*Ext.getCmp("MacromoleculeTab").setText(this.getMacromoleculeTitle()); -Ext.getCmp("BufferTab").setText(this.getBuffersTitle()); -Ext.getCmp("SpecimenTab").setText(this.getSpecimenTitle()); -Ext.getCmp("PlatesTab").setText(this.getPlatesTitle()); -Ext.getCmp("AssembliesTab").setText(this.getShipmentTitle()); -Ext.getCmp("PlateGroupsTab").setText(this.getPlateGroupsTitle());*/ -//}; -ShipmentTabs.prototype.draw = function(shipment) { - var _this = this; - _this.plates = []; - _this.shipment = shipment; - _this.render(shipment); +/** + * Set status bar to busy (refreshing icon) + * + * @msg message to be displayed on the bar + */ +MeasurementGrid.prototype._showStatusBarBusy = function(msg) { + var statusBar = Ext.getCmp(this.id + 'basic-statusbar'); + statusBar.setStatus({ + text : msg, + iconCls : 'x-status-busy', + clear : false + }); +}; - // var proposal = new Proposal(); - // proposal.onDataRetrieved.attach(function(sender, plates){ - // _this.plates = plates; - // _this.shipment = shipment; - // _this.render(shipment); - // - // }); - // proposal.getPlatesByProposal(); +/** + * Set status bar to ready (ok icon) + * + * @msg message to be displayed on the bar + */ +MeasurementGrid.prototype._showStatusBarReady = function(msg) { + var statusBar = Ext.getCmp(this.id + 'basic-statusbar'); + statusBar.setStatus({ + text : msg, + iconCls : 'x-status-valid', + clear : false + }); }; -//ShipmentTabs.prototype.getShipmentTitle = function() { -// return 'Shipment'; -//}; +/** + * If updateRowEnabled returns an array with Ext.grid.plugin.RowEditing + */ +MeasurementGrid.prototype._getPlugins = function() { + var _this = this; + var plugins = []; + if (this.updateRowEnabled) { + plugins.push(Ext.create('Ext.grid.plugin.RowEditing', { + clicksToEdit : 1, + listeners : { + validateedit : function(grid, e) { + /** Setting values * */ + for ( var key in _this.editor) { + e.record.raw[key] = e.newValues[key]; + } + /** Comments are always updatable* */ + e.record.raw.comments = e.newValues.comments; -//ShipmentTabs.prototype.getMacromoleculeTitle = function() { -// return 'Macromolecules (' + this.experiment.getMacromolecules().length + ')'; -//}; + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, measurement) { + _this.onMeasurementChanged.notify(measurement); + _this.grid.setLoading(false); + }); + adapter.onError.attach(function() { + alert("Error"); + _this.grid.setLoading(false); + }); -//ShipmentTabs.prototype.getBuffersTitle = function() { -// return 'Buffers (' + this.experiment.getBuffers().length + ')'; -//}; + _this.grid.setLoading(); + adapter.saveMeasurement(e.record.raw, _this.experiments.experiments[0]); + } + } + })); + } + return plugins; +}; -//ShipmentTabs.prototype.getPlateGroupsTitle = function() { -// return 'Plate Groups (' + this.experiment.getPlateGroups().length + ')'; -//}; +/** + * @key name of the columns mathing the this.editor[key] + */ +MeasurementGrid.prototype._getEditor = function(key) { + if (this.editor[key] != null) { + return this.editor[key]; + } + return null; +}; -//ShipmentTabs.prototype.getSampleChangerTitle = function() { -// return 'Sample Changer'; -//}; +MeasurementGrid.prototype.getPanel = function(measurements, experiments) { + this.experiments = experiments; + this.measurements = measurements; + var _this = this; + this.store = Ext.create('Ext.data.Store', { + fields : [ { + name : 'miliseconds', + type : 'int' + }, 'priority', 'bufferId', { + name : 'exposureTemperature', + type : 'numeric' + }, 'volumeToLoad','code', 'transmission', 'viscosity', 'waitTime', 'flow', 'buffer_acronym', 'macromoleculeId', 'acronym', 'concentration', 'extraFlowTime', 'volume', 'energy', + 'expExposureTemperature', 'storageTemperature', 'timePerFrame', 'radiationAbsolute', 'radiationRelative', 'status', 'comments' ], + data : this._prepareData(measurements, experiments) + }); + this.store.sort(this.sorter); + var bbar = {}; + try { + bbar = Ext.create('Ext.ux.StatusBar', { + id : _this.id + 'basic-statusbar', + defaultText : 'Ready', + text : 'Ready', + iconCls : 'x-status-valid', + items : [] + }); + } catch (exp) { + console.log("bbar error"); + } -//ShipmentTabs.prototype.getSpecimenTitle = function() { -// return 'Specimens(' + this.experiment.getSpecimenCount() + ')'; -//}; + this.grid = Ext + .create( + 'Ext.grid.Panel', + { + id : this.id, + title : this.title, + store : this.store, + selModel : this.selModel, + plugins : this._getPlugins(), + resizable : this.resizable, + margin : this.margin, + maxHeight : this.maxHeight, + minHeight : this.minHeight, + maxWidth : this.maxWidth, + width : this.width, + tbar : this._getMenu(), + columns : [ + { + text : 'Order', + dataIndex : 'priority', + width : 50, + hidden : _this.isPriorityColumnHidden, + sortable : true -//ShipmentTabs.prototype.getPlatesTitle = function() { -// return 'Plates(' + this.experiment.getSamplePlates().length + ')'; -//}; + }, + { + text : 'Run Number', + dataIndex : 'code', + width : 50, + hidden : true, + sortable : true -//ShipmentTabs.prototype.getBuffersTip = function() { -/*if (this.experiment.getBuffers().length == 0){ - return BUI.getWarningHTML("There are no buffers. Click on add to create new ones. Click on edit button or double click to edit them"); - -} -else{ - return BUI.getTipHTML("Click on edit button or double click to edit them. Click on duplicate to create an identical buffer including its additives") -}*/ -//}; + }, -//ShipmentTabs.prototype.refreshTips = function() { -/*Ext.getCmp("BufferTabTip").update(this.getBuffersTip()); -Ext.getCmp("SpecimenTabTip").update(this.getSpecimensTip());*/ -//}; + { + text : 'Specimen', + columns : [ -ShipmentTabs.prototype.render = function(shipment) { - return this.getPanel(shipment); -}; + { + text : '', + dataIndex : 'macromoleculeId', + width : 30, + renderer : function(val, y, sample) { + if (val != null) { + if (_this.experiments == null) { + return BUI.getRectangleColorDIV(BIOSAXS.proposal.macromoleculeColors[val], 10, 10); + } else { + return BUI.getRectangleColorDIV(_this.experiments.macromoleculeColors[val], 10, 10); + } + } + }, + sortable : true + }, + { + text : 'Macromo.', + dataIndex : 'acronym', + width : 80, + renderer : function(val, y, sample) { + return val; + }, + sortable : true + }, + { + text : 'Conc. ', + dataIndex : 'concentration', + width : 80, + renderer : function(val, y, sample) { + if (sample.raw.macromoleculeId == null) { + return ""; + } + if (isNaN(val)) + return val; -ShipmentTabs.prototype.getShipmentHeader = function(shipment) { - var _this = this; - function getHTMLSource() { - var name = shipment.json.shippingName; - var status = shipment.json.shippingStatus; - var creationDate = shipment.json.creationDate; - var html = BUI.createFormLabel("Name :", name, 75, 400); - html = html + BUI.createFormLabel("Status :", status, 75, 400); - html = html + BUI.createFormLabel("Date :", creationDate, 75, 400); - return html; - } + if (val != 0) { + return BUI.formatValuesUnits(val, '', { + fontSize : 16, + decimals : 3, + unitsFontSize : this.unitsFontSize + }); + } else { + return; + } - return Ext.create('Ext.container.Container', { - frame : false, - layout : 'hbox', - title : 'General', - padding : 5, - bodyPadding : '5 5 0 0', - width : 890, - margin : '0 0 10 0', - height : 100, - style : { - borderColor : '#BDBDBD', - borderStyle : 'solid', - borderWidth : '1px' - }, - fieldDefaults : { - msgTarget : 'side', - labelWidth : 100 - }, - items : [ { - margin : "0 0 0 0", - width : 475, - border : 0, - html : getHTMLSource() - } - ] - }); -}; + }, + sortable : true + }, + { + text : '', + dataIndex : 'bufferId', + width : 30, + hidden : false, + renderer : function(val, y, sample) { + if (val != null) { + var color = '#FFCCFF'; + if (_this.experiments != null) { + var dc = _this.experiments.getDataCollectionByMeasurementId(sample.raw.measurementId); + if (dc != null) { + if (dc.length > 0) { + color = _this.experiments.getSpecimenColorByBufferId(_this.experiments + .getMeasurementById(dc[0].measurementtodatacollection3VOs[0].measurementId).specimenId); + } + } + } else { + color = BIOSAXS.proposal.bufferColors[val]; + } + return BUI.getRectangleColorDIV(color, 10, 10); + } + }, + sortable : true + }, + { + text : 'Buffer', + dataIndex : 'buffer_acronym', + width : 120, + renderer : function(val, y, sample) { + if (sample.raw.bufferSampleplateposition3VO != null) { + return BIOSAXS.proposal.getBufferById(sample.raw.bufferId).acronym + " Plate: [" + + sample.raw.bufferSampleplate.slotPositionColumn + ", " + + BUI.getSamplePlateLetters()[sample.raw.bufferSampleplateposition3VO.rowNumber - 1] + "-" + + sample.raw.bufferSampleplateposition3VO.columnNumber + "]"; + } + return val; + }, + sortable : true + }, { + text : 'Position', + width : 100, + hidden : true, + renderer : function(val, y, sample) { + if (_this.experiments != null) { + return BUI.getSamplePositionHTML(_this.experiments.getSampleById(sample.raw.specimenId), _this.experiments.experiments[0]); + } + } + } ] + }, + { + text : 'Parameters', + columns : [ + { + text : 'Ex. Flow. time (s)', + dataIndex : 'extraFlowTime', + width : 100, + hidden : true, + renderer : function(val, y, sample) { + return BUI.formatValuesUnits(val, 's', { + fontSize : 12, + decimals : 0, + unitsFontSize : this.unitsFontSize + }); + } + }, + { + text : 'Exp. Temp.', + dataIndex : 'exposureTemperature', + width : 70, + renderer : function(val, y, sample) { + if (Number(val)) { + return BUI.formatValuesUnits(val, 'C', { + fontSize : 12, + decimals : 2, + unitsFontSize : this.unitsFontSize + }); + } + return null; + }, + sortable : true, + editor : this._getEditor("exposureTemperature") + }, + { + text : 'Vol. Load', + dataIndex : 'volumeToLoad', + width : 60, + hidden : false, + editor : this._getEditor("volumeToLoad"), + renderer : function(val, y, sample) { + // return val+ " µl"; + return BUI.formatValuesUnits(val, 'µl', { + fontSize : 12, + decimals : 2, + unitsFontSize : this.unitsFontSize + }); + } + }, + { + text : 'Volume in Well', + dataIndex : 'volume', + hidden : true, + editor : this._getEditor("volume"), + width : 80, + renderer : function(val, y, sample) { + // return val + "(µl)"; + return BUI.formatValuesUnits(val, 'µl', { + fontSize : 12, + decimals : 2, + unitsFontSize : this.unitsFontSize + }); + } + }, + { + text : 'Trans.', + dataIndex : 'transmission', + width : 60, + editor : this._getEditor("transmission"), + renderer : function(val, y, sample) { + return BUI.formatValuesUnits(val, '%', { + fontSize : 12, + decimals : 0, + unitsFontSize : this.unitsFontSize + }); + } + }, + { + text : 'Wait T.', + dataIndex : 'waitTime', + editor : this._getEditor("waitTime"), + width : 50, + renderer : function(val, y, sample) { + // if (val != 0) { + return BUI.formatValuesUnits(val, 's', { + fontSize : 12, + decimals : 0, + unitsFontSize : this.unitsFontSize + }); + // } + } + }, + { + text : 'Flow', + dataIndex : 'flow', + editor : this._getEditor("flow"), + width : 50, + renderer : function(val, y, sample) { + if (val == true) { + return "yes"; + } + return null; + } + }, + { + text : 'Viscosity', + dataIndex : 'viscosity', + tooltip : 'The viscosity of a fluid is a measure of its resistance to gradual deformation by shear stress or tensile stress. For liquids, it corresponds to the informal notion of "thickness"', + editor : this._getEditor("viscosity"), + width : 50, + renderer : function(val, y, sample) { + return val; + } + } ] + }, { + text : 'Status', + dataIndex : 'status', + width : 50, + hidden : _this.isStatusColumnHidden, + renderer : function(val, y, sample) { + if (val != null) { + if (val == 'DONE') { + return "" + val + " "; + } + } + } + }, { + text : 'Time', + dataIndex : 'time', + width : 80, + hidden : _this.isTimeColumnHidden, + renderer : function(val, y, sample) { + if (sample.raw.run3VO != null) { + if (sample.raw.run3VO.timeStart != null) { + if (sample.raw.run3VO.timeStart != "") { + var m = moment(sample.raw.run3VO.timeStart); + return m.format("hh:mm:ss a"); + } + } + } + } + }, { + text : 'Energy', + dataIndex : 'energy', + width : 100, + hidden : true + }, { + text : 'Real Exp. Temp.(C)', + width : 100, + dataIndex : 'expExposureTemperature', + hidden : true + }, { + text : 'Storage Temp.(C)', + width : 100, + dataIndex : 'storageTemperature', + hidden : true + }, { + text : 'Time/Frame (s)', + width : 100, + dataIndex : 'timePerFrame', + hidden : true + }, { + text : 'Radiation Relative', + dataIndex : 'radiationRelative', + width : 100, + hidden : true + }, { + text : 'Radiation Absolute', + dataIndex : 'radiationAbsolute', + width : 100, + hidden : true + }, { + text : 'Comments', + dataIndex : 'comments', + flex : 1, + hidden : false, + editor : this._getEditor("comments") -ShipmentTabs.prototype.getTabPanel = function(shipment) { - this.panel = Ext.createWidget('tabpanel', { - height : 600, - style : { - padding : 2 - }, - items : [ { - tabConfig : { - id : 'Shipment', - title : 'Shipment', - icon : '/ispyb/images/plane-small.gif' - }, - items : [ { - xtype : 'container', - margin : '5 5 5 5', - items : [ this.shipmentForm.getPanel(shipment) ] - } ] - }, { - tabConfig : { - id : 'Cases', - title : 'Cases', - icon : '../images/box-icon-very-small.png' - }, - items : [ { - xtype : 'container', - margin : '5 5 5 5', - items : [ this.caseGrid.getPanel(shipment.getDewars(), this.plates) ] - } ] - } ] - }); - return this.panel; -}; + }, { + id : _this.id + 'buttonRemoveSample', + text : '', + hidden : !_this.removeBtnEnabled, + width : 100, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + if (record.raw.macromoleculeId != null) { + if (_this.removeBtnEnabled) { + return BUI.getRedButton('REMOVE'); + } + } + } + } ], + bbar : bbar, + viewConfig : { + stripeRows : true, + getRowClass : function(record, index, rowParams, store) { + if (record.data.status == "DONE") { + return 'green-row'; + } -ShipmentTabs.prototype.getPanel = function(shipment) { - var _this = this; - this.shipment = shipment; - if (this.plates == null) { - this.plates = []; - } + }, + listeners : { + 'itemclick' : function(grid, record, item, index, e, eOpts) { + _this.onClick.notify({ + specimen : record.raw + }); + }, + 'cellclick' : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemoveSample') { + grid.getStore().removeAt(rowIndex); - if (this.shipPanel == null) { - this.shipPanel = Ext.create('Ext.container.Container', { - bodyPadding : 2, - width : Ext.getBody().getViewSize().width * 0.9, - renderTo : this.targetId, - style : { - padding : 2 - }, - items : [ this.getShipmentHeader(shipment), this.getTabPanel(shipment) ] - }); - } + if (record.raw.measurementId != null) { + /** For testing * */ + grid.setLoading("ISPyB: Removing measurement"); + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + grid.setLoading(false); + /** + * We get and refresh experiment + * because specimens has changed * + */ + var adapter2 = new BiosaxsDataAdapter(); + adapter2.onSuccess.attach(function(sender, experiment) { + _this.onRemoved.notify(experiment); + _this._showStatusBarReady('Ready'); + }); + if (_this.experiments.experiments[0].experimentId != null) { + adapter2.getExperimentById(_this.experiments.experiments[0].experimentId, "MEDIUM"); + _this._showStatusBarBusy("ISPyB: Removing Unused Specimens"); + } + }); - return this.shipPanel; -}; - -/** - * Shows an template with the specimens, measurements and the experiment's - * requirement - * - * @targetId - */ -function TemplateTabs(targetId) { - this.height = 600; - this.targetId = targetId; + adapter.onError.attach(function(sender, data) { + alert("Error: " + data); + grid.setLoading(false); + }); - this.id = BUI.id(); - var _this = this; + adapter.removeMeasurement(record.raw); + } + } - this.gridHeight = 1000; - /** data * */ - this.experiment = null; + } - this.specimenSelected = null; + } + } + }); - /** Specimen Widget contains a specimenGrid and a sampleChangerWidget than can be displayed with are vertical or horizontal layout **/ - this.specimenWidget = new SpecimenWidget({ - height : this.height - }); - - this.samplePlateGroupWidget = new SamplePlateGroupWidget({ - showTitle : false, - height : 250, - margin : 5, - bbar : true - }); - - this.samplePlateGroupWidget.onExperimentChanged.attach(function(sender, experiment) { - _this.refresh(experiment); - }); + this.grid.on("afterrender", function() { - this.samplePlateGroupWidget.onClick.attach(function(sender, args) { - }); + function updateTime() { + try { + _this.estimatedTime = _this.estimatedTime - 1; - this.volumePlanificator = new VolumeGrid(); + _this.onUpdateTime.notify({ + hours : (Number(_this.estimatedTime / 3600).toFixed()), + minutes : (Number((_this.estimatedTime / 60) % 60).toFixed()), + seconds : (Number(_this.estimatedTime % 60).toFixed()) - /** For Measurements * */ - var storeViscosity = Ext.create('Ext.data.Store', { - fields : [ 'name' ], - data : [ { - "name" : "low" - }, { - "name" : "medium" - }, { - "name" : "high" - } ] - }); + }); - // Create the combo box, attached to the states data store - var viscosityEditor = Ext.create('Ext.form.ComboBox', { - fieldLabel : '', - store : storeViscosity, - queryMode : 'local', - displayField : 'name', - valueField : 'name' - }); + if (Number(_this.estimatedTime) < 0) { + _this.timer = null; + grid.setTitle(_this.title); + } - this.measurementGrid = new MeasurementGrid({ - maxWidth : 1500, - estimateTime : false, - positionColumnsHidden : true, - isPriorityColumnHidden : true, - isStatusColumnHidden : true, - isTimeColumnHidden : true, - updateRowEnabled : true, - collapsed : true, - removeBtnEnabled : true, - showTitle : false, - collapseBtnEnable : false, - addBtnMultipleEdit : true, - sortingBtnEnable : true, - editor : { - exposureTemperature : { - xtype : 'textfield', - allowBlank : true - }, - comments : { - xtype : 'textfield', - allowBlank : true - }, - volumeToLoad : { - xtype : 'numberfield', - allowBlank : true - }, - transmission : { - xtype : 'numberfield', - allowBlank : true - }, - viscosity : viscosityEditor, - waitTime : { - xtype : 'numberfield', - allowBlank : true - }, - flow : { - xtype : 'checkbox', - allowBlank : true + } catch (e) { + console.log(e); + _this.timer = null; } } - }); - - this.measurementGrid.onSelected.attach(function(sender, measurements) { - var specimens = []; - for ( var i = 0; i < measurements.length; i++) { - specimens.push(_this.experiment.getSampleById(measurements[i].specimenId)); - } - }); - this.measurementGrid.onMeasurementChanged.attach(function(sender, measurement) { - _this.experiment.setMeasurement(measurement); - _this.refresh(_this.experiment); - }); + if (_this.estimateTime) { + var experimentList = _this.experiments; + var collected = experimentList.getMeasurementsCollected(); + if (collected.length > 0) { + if (collected[0].run3VO != null) { + try { + var end = collected[0].run3VO.timeEnd; + var start = collected[0].run3VO.timeStart; + var dstart = moment(start); + var dend = moment(end); + var seconds = Number(dend.diff(dstart) / 1000).toFixed(); - this.measurementGrid.onExperimentChanged.attach(function(sender, json) { - _this.refresh(new Experiment(json)); - }); + _this.estimatedTime = (seconds * experimentList.getMeasurementsNotCollected().length); - this.measurementGrid.onRemoved.attach(function(sender, experiment) { - _this.refreshSpecimen(new Experiment(experiment)); - }); + if (_this.estimatedTime > 0) { + updateTime(); + _this.timer = setInterval(function() { + updateTime(); + }, 1000); + } - this.measurementGrid.onUpdateTime.attach(function(sender, args) { - document.getElementById(_this.id + "_counter").innerHTML = args.hours + 'h, ' + args.minutes + 'min and ' + args.seconds + ' seconds'; + } catch (e) { + } + } + } + } }); - -} - -TemplateTabs.prototype.refreshMeasurement = function(experiment) { - this.experiment = experiment; - this.experiment.onSaved = new Event(this); - this.experiment.onSpecimenSaved = new Event(this); - var experimentList = new ExperimentList([ this.experiment ]); - this.measurementGrid.refresh(experimentList.getMeasurementsNotCollected(), experimentList); -}; -TemplateTabs.prototype.refreshSpecimen = function(experiment) { - this.experiment = experiment; - this.experiment.onSaved = new Event(this); - this.experiment.onSpecimenSaved = new Event(this); - this.samplePlateGroupWidget.refresh(this.experiment); - this.specimenWidget.refresh(this.experiment); - this.volumePlanificator.refresh(this.experiment); + return this.grid; }; -TemplateTabs.prototype.refresh = function(experiment) { - // var start = new Date().getTime(); - this.experiment = experiment; - this.experiment.onSaved = new Event(this); - this.experiment.onSpecimenSaved = new Event(this); - - // var experimentList = new ExperimentList([this.experiment]); - this.refreshMeasurement(experiment); - this.refreshSpecimen(experiment); - /** Refreshing grids * */ - this.panel.setLoading(false); - +/** Method for testing * */ +MeasurementGrid.prototype.input = function() { + var experiment = DATADOC.getExperiment_10(); + var measurements = DATADOC.getMeasurements_10(); + var proposal = DATADOC.getProposal_10(); + return { + experiment : experiment, + measurements : measurements, + proposal : proposal + }; }; -TemplateTabs.prototype.error = function(error) { - var e = JSON.parse(error); - showError(e); - this.panel.setLoading(false); +MeasurementGrid.prototype.test = function(targetId) { + var measurementGrid = new MeasurementGrid({ + tbar : true + }); + BIOSAXS.proposal = new Proposal(measurementGrid.input().proposal); + var panel = measurementGrid.getPanel(measurementGrid.input().measurements, new ExperimentList([ new Experiment(measurementGrid.input().experiment) ])); + panel.render(targetId); }; + +/** + * A shipment may contains one or more cases where stock solutions and sample + * plates are stored + * + * @height + * @btnEditVisible + * @btnRemoveVisible + * + * #onEditButtonClicked + */ +function MolarityGrid(args) { + this.height = 100; + this.width = 100; + + if (args != null) { + if (args.height != null) { + this.height = args.height; + } + if (args.width != null) { + this.width = args.width; + } + } + + var _this = this; + + this.molarityForm = new MolarityForm({height : 180, width : 455}); + + this.molarityForm.onSave.attach(function(sender){ + _this.molarityWindow.destroy(); + _this.updateProposal(); + + }); + + this.molarityForm.onClose.attach(function(sender){ + _this.molarityWindow.destroy(); + + }); + + /** Events * */ + this.onEditButtonClicked = new Event(this); +} + +MolarityGrid.prototype._getColumns = function() { + return [ { + text : 'Subunit', + columns : [ { + text : "Acronym", + width : 100, + hidden : false, + dataIndex : 'acronym', + sortable : true + }, { + text : "Name", + width : 125, + hidden : false, + dataIndex : 'name', + sortable : true + }, { + text : "MM Est.", + width : 100, + dataIndex : 'molecularMass', + sortable : true, + renderer : function(grid, cls, record){ + return BUI.formatValuesUnits(record.data.molecularMass , "Da", 10, 2); + + } + } ] + }, { +// text : "Number
in assymmetric units", + text : "Ratio", + width : 100, + dataIndex : 'ratio', + tooltip : 'Number of times the subunit is present in the macromolecule', + sortable : true + }, { + id : this.id + 'MOLARITY_REMOVE', + flex : 0.1, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + return BUI.getRedButton('REMOVE'); + } + } ]; +}; + +MolarityGrid.prototype._openMolarityWindow = function() { + this.molarityWindow = Ext.create('Ext.window.Window', { + title : 'Molarity', + height : 220, + width : 500, + modal : true, + items : [this.molarityForm.getPanel() ] + }).show(); +}; + +MolarityGrid.prototype._getButtons = function() { + var _this = this; + return [ { + text : 'Add subunit', + icon : '../images/add.png', + handler : function() { + _this._openMolarityWindow(); + } + }]; +}; + + +MolarityGrid.prototype.updateProposal = function() { + var _this = this; + this.panel.setLoading(); + BIOSAXS.proposal.onInitialized.attach(function() { + if (BIOSAXS.proposal != null) { + var macromolecules = BIOSAXS.proposal.macromolecules; + for (var i = 0; i < macromolecules.length; i++) { + + if (macromolecules[i].macromoleculeId == _this.macromolecule.macromoleculeId) { + _this.refresh(macromolecules[i]); + _this.panel.setLoading(false); + } + } + } + }); + BIOSAXS.proposal.init(); +}; + + +MolarityGrid.prototype.getPanel = function() { + var _this = this; + + this.molarityStore = Ext.create('Ext.data.Store', { + fields : [ 'acronym', 'ratio', 'comments', 'stoichiometryId', 'name', 'molecularMass' ], + sorters : { + property : 'ratio', + direction : 'DESC' + } + }); + + this.panel = Ext.create('Ext.grid.Panel', { + store : this.molarityStore, + height : this.height, + padding : 5, + columns : this._getColumns(), + listeners : { + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + + /** Remove entry * */ + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'MOLARITY_REMOVE') { + var dataAdapter = new BiosaxsDataAdapter(); + dataAdapter.onSuccess.attach(function(sender) { + _this.updateProposal(); + + }); + dataAdapter.removeStoichiometry(record.data.stoichiometryId); + _this.panel.setLoading("Removing Structure"); + } + } + }, + tbar : this._getButtons() + }); + return this.panel; +}; + +MolarityGrid.prototype._prepareData = function(macromolecule) { + /** Return an array of [{ratio,acronym, stoichiometryId, name}] **/ + var data = []; + if (macromolecule.stoichiometry != null) { + for (var i = 0; i < macromolecule.stoichiometry.length; i++) { + var hostMacromolecule = BIOSAXS.proposal.getMacromoleculeById(macromolecule.stoichiometry[i].macromoleculeId); + data.push({ + ratio : macromolecule.stoichiometry[i].ratio, + acronym : hostMacromolecule.acronym, + comments : hostMacromolecule.comments, + molecularMass : hostMacromolecule.molecularMass, + stoichiometryId : macromolecule.stoichiometry[i].stoichiometryId, + name : hostMacromolecule.name + }); + } + } + return data; +}; + +MolarityGrid.prototype.refresh = function(macromolecule) { + if (macromolecule != null){ + this.molarityStore.loadData(this._prepareData(macromolecule)); + this.molarityForm.refresh(macromolecule); + this.macromolecule = macromolecule; + } +}; + +MolarityGrid.prototype.input = function() { + return { + proposal : DATADOC.getProposal_10(), + dewars : DATADOC.getDewars_10() + + }; +}; + +MolarityGrid.prototype.test = function(targetId) { + var MolarityGrid = new MolarityGrid({ + height : 150 + }); + BIOSAXS.proposal = new Proposal(MolarityGrid.input().proposal); + var panel = MolarityGrid.getPanel(MolarityGrid.input().dewars); + panel.render(targetId); + +}; + + +/** + * Given data analysis parsed with ResultsAssemblyWidget makes a selector grid with buffer/protein + **/ +function SpecimenSelectorResultGrid() { + this.id = BUI.id(); +} -TemplateTabs.prototype.draw = function(experiment) { - this.render(experiment); +SpecimenSelectorResultGrid.prototype._prepareData = function(data) { + var parsed = []; + for ( var i = 0; i < data.length; i++) { + var row = data[i]; + for ( var j = 0; j < row.conditions.length; j++) { + parsed.push({ + bufferId : row.conditions[j].bufferId, + macromoleculeId : row.macromoleculeId, + macromoleculeAcronym : BIOSAXS.proposal.getMacromoleculeById(row.macromoleculeId).acronym, + bufferAcronym : BIOSAXS.proposal.getBufferById(row.conditions[j].bufferId).acronym + }); + } + } + return parsed; }; - -TemplateTabs.prototype.getExperimentTitle = function() { - var _this = this; - var experimentHeaderForm = new ExperimentHeaderForm(); - return experimentHeaderForm.getPanel(this.experiment); +SpecimenSelectorResultGrid.prototype.refresh = function(data) { + this.store.loadData(this._prepareData(data)); }; -TemplateTabs.prototype.render = function(experiment) { +SpecimenSelectorResultGrid.prototype.getPanel = function(data) { var _this = this; - this.experiment = experiment; + this.store = Ext.create('Ext.data.Store', { + fields : [ 'macromoleculeId', 'bufferId', 'macromoleculeAcronym', 'bufferAcronym', 'concentration' ], + data : this._prepareData(data), + groupField : 'macromoleculeAcronym' + }); - /** - * - * Depending on the sample Changer configuration we want to display the plates vertically or horizontally - * Default is vertical - * - * */ - - var specimenContainer = this.specimenWidget.getPanel(); - this.specimenWidget.refresh(experiment); - - var experimentList = new ExperimentList([ _this.experiment ]); - var measurementContainer = Ext.create('Ext.container.Container', { - layout : { - type : 'vbox' - }, - defaults : { - style : { - padding : '5px 0px 0px 10px' + this.store.sort('concentration'); + this.grid = Ext.create('Ext.grid.Panel', { + id : this.id, + store : this.store, + width : this.width, + height : this.height, + maxHeight : this.maxHeight, + border : 1, + features : [ { + ftype : 'grouping', + groupHeaderTpl : '{name}', + hideGroupedHeader : true, + startCollapsed : false + } ], + selModel : Ext.create('Ext.selection.CheckboxModel', { + allowDeselect : true, + mode : 'MULTI', + listeners : { + selectionchange : function(sm, selections) { + _this.selected = []; + for ( var i = 0; i < selections.length; i++) { + _this.selected.push(selections[i].raw); + } + } } - }, - items : [ _this.measurementGrid.getPanel(experimentList.getMeasurementsNotCollected(), experimentList) ] + }), + margin : 10, + sortableColumns : true, + columns : [ { + text : 'Macromolecule', + dataIndex : 'macromoleculeAcronym', + flex : 1 + }, { + text : '', + dataIndex : 'bufferId', + width : 20, + hidden : false, + renderer : function(val, y, sample) { + return BUI.getRectangleColorDIV(BIOSAXS.proposal.bufferColors[val], 10, 10); + } + }, { + text : 'Buffer', + dataIndex : 'bufferAcronym', + flex : 1 + }, { + text : 'Concentration', + dataIndex : 'concentration', + flex : 1, + renderer : function(val, y, sample) { + return val + " mg/ml"; + } + } ] }); - this.panel = Ext - .createWidget( - 'tabpanel', - { - plain : true, - items : [ - { - tabConfig : { - title : 'Measurements' - }, - items : [ { - xtype : 'container', - layout : 'vbox', - border : 1, -// height : _this.gridHeight, - margin : "0 0 10 0", - items : [ measurementContainer ] - } - - ] - }, - { - tabConfig : { - id : 'genralTabl', - title : "Specimens" - // width : 900, - // border : 3 - - }, - items : [ specimenContainer ] - }, - { - tabConfig : { - title : "Requirements" + /** Adding the tbar **/ + if (this.tbar) { + this.grid.addDocked({ + xtype : 'toolbar', + items : this.getTbar() + }); + } + return this.grid; +}; - }, - items : [ - { - html : BUI.getTipHTML("Estimated volume is the maximum volume required. Depending on the order of your measurements you may use less. Click on create stock solutions if you plan to ship these stock solutions"), - margin : "10 10 10 10", - border : 0 - }, this.volumePlanificator.getPanel(experiment) ] - } ] - }); - // ); - return this.getPanel(this.panel); +SpecimenSelectorResultGrid.prototype.input = function() { + return { + data : new ResultsAssemblyGrid()._prepareData(new ResultsAssemblyGrid().input().data), + proposal : new ResultsAssemblyGrid().input().proposal + }; }; -TemplateTabs.prototype.isTemplate = function() { - if (this.experiment.json.type == "TEMPLATE") { - return true; - } - return false; +SpecimenSelectorResultGrid.prototype.test = function(targetId) { + var specimenSelectorResultGrid = new SpecimenSelectorResultGrid(); + BIOSAXS.proposal = new Proposal(specimenSelectorResultGrid.input().proposal); + var panel = specimenSelectorResultGrid.getPanel(specimenSelectorResultGrid.input().data); + panel.render(targetId); }; +/** + * Show all buffer conditions for each macromolecules pointing out the measurements quality + * + * @height + * @maxHeight + * @width + * @searchBar + * @tbar + * @btnResultVisible + * + * #onClick + */ +function ResultsAssemblyGrid(args) { + this.height = 500; + this.id = BUI.id(); + this.maxHeight = this.height; -TemplateTabs.prototype.getPanel = function(panel) { - var _this = this; - if (this.experimentPanel == null) { - this.experimentPanel = Ext.create('Ext.container.Container', { - bodyPadding : 2, - width : 1000,//Ext.getBody().getViewSize().width * 0.9, - renderTo : this.targetId, - height : 500, -// style : { -// padding : 2 -// }, - items : [ - this.getExperimentTitle(), - this.panel - ], - listeners : { - afterrender : function(thisCmp) { - $("#SchemeReport" + _this.experiment.experimentId).click(function() { - $(this).target = "_blank"; - window.open('viewProjectList.do?reqCode=display&menu=platescheme&experimentId=' + _this.experiment.experimentId); - return false; - }); + this.width = 900; + this.searchBar = false; + this.tbar = false; + this.btnResultVisible = false; - } - } - }); - } - return this.experimentPanel; -}; + /** For processing **/ + this.processed = {}; + this.renderedPlotIndex = 0; -TemplateTabs.prototype.input = function(targetId) { - return new ExperimentTabs().input(); -}; + this.plotWidth = 210; + this.plotHeight = 80; -TemplateTabs.prototype.test = function(targetId) { - var experimentTabs = new TemplateTabs(targetId); - BIOSAXS.proposal = new Proposal(experimentTabs.input().proposal); - experimentTabs.draw(new Experiment(experimentTabs.input().experiment)); -}; - -var BUI = { - //interval : 60000, - interval : 40000, - rainbow : function(numOfSteps, step) { - // This function generates vibrant, "evenly spaced" colours (i.e. no clustering). This is ideal for creating easily distinguishable vibrant markers in Google Maps and other apps. - // Adam Cole, 2011-Sept-14 - // HSV to RBG adapted from: http://mjijackson.com/2008/02/rgb-to-hsl-and-rgb-to-hsv-color-model-conversion-algorithms-in-javascript - var r, g, b; - var h = step / numOfSteps; - var i = ~~(h * 6); - var f = h * 6 - i; - var q = 1 - f; - switch (i % 6) { - case 0: - r = 1, g = f, b = 0; - break; - case 1: - r = q, g = 1, b = 0; - break; - case 2: - r = 0, g = 1, b = f; - break; - case 3: - r = 0, g = q, b = 1; - break; - case 4: - r = f, g = 0, b = 1; - break; - case 5: - r = 1, g = 0, b = q; - break; + /** Colors **/ + this.validColor = BUI.getValidColor(); + this.warningColor = BUI.getWarningColor(); + this.notValidColor = BUI.getErrorColor(); + + /** Show warning if guinier quality less than **/ + this.guinierQuality = BUI.getQualityThreshold(); + this.framePercentageThreshold = BUI.getRadiationDamageThreshold(); + + if (args != null) { + if (args.height != null) { + this.height = args.height; + this.maxHeight = this.height; } - var c = "#" + ("00" + (~~(r * 255)).toString(16)).slice(-2) + ("00" + (~~(g * 255)).toString(16)).slice(-2) - + ("00" + (~~(b * 255)).toString(16)).slice(-2); - return (c); - }, - getFileNameByPath : function(filePath) { - if (filePath != null){ - var split = filePath.split("/"); - if (split.length > 0){ - return split[split.length - 1]; - } + if (args.maxHeight != null) { + this.maxHeight = args.maxHeight; + } + if (args.width != null) { + this.width = args.width; + } + if (args.searchBar != null) { + this.searchBar = args.searchBar; } - return "Not file"; - }, - getUpdateInterval : function() { - this.interval = this.interval + 2000; - return this.interval; - }, - getRadiationDamageThreshold : function() { - return 0.7; - }, - getQualityThreshold : function() { - return 0.7; - }, - getCreateShipmentURL : function() { - return '/ispyb/user/viewProjectList.do?reqCode=display&menu=create_shipment'; - }, - getCreateShipmentList : function() { - return '/ispyb/user/viewProjectList.do?reqCode=display&menu=list_shipment'; - }, - getShippingURL : function(shippingId) { - return '/ispyb/user/viewProjectList.do?reqCode=display&menu=shipment&shippingId=' + shippingId; - }, - getMacromoleculeResultsURLByMultipleSearch : function(array) { - return '/ispyb/user/viewProjectList.do?reqCode=display&menu=macromolecule&search=' - + JSON.stringify(array).replace(new RegExp("\"", 'g'), "'"); - }, - getMacromoleculeResultsURL : function(macromoleculeId) { - return '/ispyb/user/viewProjectList.do?reqCode=display&menu=macromolecule¯omoleculeId=' + macromoleculeId; - }, - getMacromoleculeBufferResultsURL : function(macromoleculeId, bufferId) { - return '/ispyb/user/viewProjectList.do?reqCode=display&menu=macromolecule&bufferId=' + bufferId + '¯omoleculeId=' + macromoleculeId; - }, + if (args.tbar != null) { + this.tbar = args.tbar; + } + if (args.btnResultVisible != null) { + this.btnResultVisible = args.btnResultVisible; + } - getMacromoleculeHeader : function(macromoleculeId) { + } - function getHTMLSource(macromoleculeId) { - if (macromoleculeId != null) { - var html = BUI.createFormLabel("Name :", BIOSAXS.proposal.getMacromoleculeById(macromoleculeId).name, 75, 400); - html = html + BUI.createFormLabel("Acronym :", BIOSAXS.proposal.getMacromoleculeById(macromoleculeId).acronym, 75, 400); - if (BIOSAXS.proposal.getMacromoleculeById(macromoleculeId).comments != null) { - html = html + BUI.createFormLabel("Comments :", BIOSAXS.proposal.getMacromoleculeById(macromoleculeId).comments, 75, 400); - } - return html; - } - } + this.onClick = new Event(); +} - return Ext.create('Ext.container.Container', { - frame : false, - layout : 'hbox', - title : 'Macromolecule', - bodyPadding : '5', - width : 890, - margin : '0 0 10 0', - height : 100, - style : { - borderColor : '#BDBDBD', - borderStyle : 'solid', - borderWidth : '1px' - }, - fieldDefaults : { - msgTarget : 'side', - labelWidth : 100 - }, - items : [ { - margin : "10 0 0 10", - width : 475, - border : 0, - html : getHTMLSource(macromoleculeId) - }, { - margin : "10 0 0 10", - width : 475, - border : 0, - html : BUI.getZipHTMLByMacromoleculeId(macromoleculeId) - } - ] - }); - }, +ResultsAssemblyGrid.prototype.edit = function(macromoleculeId) { + var _this = this; + var window = new MacromoleculeWindow(); + window.onSuccess.attach(function(sender, proposal) { + _this.store.loadData(_this._prepareData(BIOSAXS.proposal.getMacromolecules())); + }); + window.draw(BIOSAXS.proposal.getMacromoleculeById(macromoleculeId)); +}; - getZipHTMLByMacromoleculeId : function(macromoleculeId) { - if (macromoleculeId != null) { - var fileName = BIOSAXS.proposal.getMacromoleculeById(macromoleculeId).acronym; - return ""; - } - }, - getZipHTMLByExperimentId : function(experimentId, filename) { - if (filename == null){ - filename = "experiment"; - } - return ""; - }, - - getZipURLByAverageId : function(averageId, filename) { - if (filename == null){ - filename = "experiment"; - } - return "/ispyb/user/dataadapter.do?reqCode=getZipFileByAverageListId&f&mergeIdsList=" + averageId + "&fileName=" + filename; - }, - getZipURLBySubtractionId : function(subtractionId, filename) { - if (filename == null){ - filename = "experiment"; +ResultsAssemblyGrid.prototype.getTbar = function() { + var _this = this; + var actions = []; + + actions.push(Ext.create('Ext.Action', { + icon : '../images/add.png', + text : 'Add Macromolecule', + disabled : false, + handler : function(widget, event) { + var window = new MacromoleculeWindow(); + window.onSuccess.attach(function(sender) { + _this.refresh(); + }); + window.draw({}); } - return "/ispyb/user/dataadapter.do?reqCode=getZipFileByAverageListId&f&subtractionIdList=" + subtractionId + "&fileName=" + filename; - }, - - - getZipHTMLByFrameRangeId : function(experimentId, start, end) { - var fileName = "experiment"; - return ""; - }, - getZipFrameHPLCUrl : function(experimentId, start, end) { - return "/ispyb/user/dataadapter.do?reqCode=getZipFileH5ByFramesRange&f&experimentId=" + experimentId + "&start=" + Number(start) +"&end="+ Number(end); - }, - - getQueueUrl : function() { - return "/ispyb/user/dataadapter.do?reqCode=getPagingCompactAnalysisByProposalId"; - }, - - getQueueUrlByExperiment: function(experimentId) { - return "/ispyb/user/dataadapter.do?reqCode=getPagingCompactAnalysisByExperimentId&f&experimentId=" + experimentId; - }, - getStandardDeviation : function(values) { - var sum = 0; - var count = 0; - var avg = null; + })); + + actions.push(Ext.create('Ext.Action', { + icon : '../images/add.png', + text : 'Define an Assembly', + disabled : false, + handler : function(widget, event) { + var createAssemblywindow = new CreateAssemblyWindow(); + createAssemblywindow.onSaved.attach(function(evt, args) { + if (args.macromoleculeIds.length > 0) { + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, proposal) { + _this.refresh(); + }); + adapter.saveAssembly(args.assemblyId, args.macromoleculeIds); - var curatedValues = new Array(); - for ( var i = 0; i < values.length; i++) { - var value = values[i]; - if (value != null) { - if (!isNaN(value)) { - count = count + 1; - sum = sum + Number(value); - curatedValues.push(Number(value)); } - } - } - if (count > 0) { - avg = sum / count; - } else { - avg = sum; - } - var aux = 0; - for ( var i = 0; i < curatedValues.length; i++) { - var value = curatedValues[i]; - aux = aux + Math.pow(value - avg, 2); + }); + createAssemblywindow.draw(_this.experiment); } - /** std **/ - var std = Math.sqrt(aux / count); + })); + + return actions; +}; + +ResultsAssemblyGrid.prototype.refresh = function() { + this.store.loadData(this._prepareData()); +}; + +ResultsAssemblyGrid.prototype.addCondition = function(record, data_parsed, i) { + function getCondition(record) { return { - std : (std), - sum : (sum), - avg : (avg), - validNumber : count, - totalNumber : values.length, - values : values + concentration : record.conc, + quality : record.quality, + bufferBeforeFramesMerged : record.bufferBeforeFramesMerged, + bufferAfterFramesMerged : record.bufferAfterFramesMerged, + framesCount : record.framesCount, + framesMerge : record.framesMerge }; - }, - - getHTMLTableForFrameAveraged : function(bufferAcronym, macromoleculeAcronym, bbmerges, molmerges, bamerges, totalframes, bufferId,macromoleculeId, macromoleculeColor) { - - function getFrameSpan(framesMerged, total) { - return "(" + framesMerged + " of " + total + ")"; - } + } - function getColorFrame(framesMerged, total) { - if (framesMerged / total < 0.5) { - return "#FA5858"; - } - if ((framesMerged / total >= 0.5) && (framesMerged / total < 0.8)) { - return "#FF9900"; + if (data_parsed[i].conditions != null) { + var bufferFound = false; + for ( var index in data_parsed[i].conditions) { + condition = data_parsed[i].conditions[index]; + + if ((condition.macromoleculeId == record.macromoleculeId) && (condition.bufferId == record.bufferId)) { + data_parsed[i].conditions[index].concentrations.push(getCondition(record)); + bufferFound = true; } - return "white"; } - - function getRow(color, acroynm, framesMerged, totalframes) { - return " " - + BUI.getRectangleColorDIV(color, 10, 10) - + " " + acroynm + "" - + getFrameSpan(framesMerged, totalframes) + ""; + if (!bufferFound) { + data_parsed[i].conditions.push({ + macromoleculeId : record.macromoleculeId, + bufferId : record.bufferId, + concentrations : [ getCondition(record) ] + }); } + } +}; - var html = ""; +ResultsAssemblyGrid.prototype.process = function(record, data_parsed) { + if (this.processed[record.macromoleculeId] == null) { + this.processed[record.macromoleculeId] = true; + record.measurementCount = 1; + record.subtractionCount = 1; + record.averageCount = 1; + record.conditions = []; + data_parsed.push(record); + } - /** Buffer Before **/ - if (bufferAcronym != null) { - if (bbmerges != null) { - color = BIOSAXS.proposal.bufferColors[bufferId]; - html = html + getRow(color, bufferAcronym, bbmerges, totalframes); + for ( var i = 0; i < data_parsed.length; i++) { + if (data_parsed[i].macromoleculeId == record.macromoleculeId) { + data_parsed[i].measurementCount = data_parsed[i].measurementCount + 1; + + if (record.subtractionId != null) { + data_parsed[i].subtractionCount = data_parsed[i].subtractionCount + 1; + this.addCondition(record, data_parsed, i); } - } - /** Molecule **/ - if (macromoleculeAcronym != null) { - if (molmerges != null) { - if (macromoleculeColor == null){ - color = BIOSAXS.proposal.macromoleculeColors[macromoleculeId]; - } - else{ - color = macromoleculeColor; //BIOSAXS.proposal.macromoleculeColors[macromoleculeId]; + if (record.framesMerge != null) { + data_parsed[i].averageCount = data_parsed[i].averageCount + 1; + } + + if (record.timeStart != null) { + if (data_parsed[i].timeStart != null) { + if (moment(data_parsed[i].timeStart).format("X") > moment(record.timeStart).format("X")) { + data_parsed[i].timeStart = record.timeStart; + } } - html = html + getRow(color, macromoleculeAcronym, molmerges, totalframes); } } + } - /** Buffer After **/ - if (bufferAcronym != null) { - if (bamerges != null) { - color = BIOSAXS.proposal.bufferColors[bufferId]; - html = html + getRow(color, bufferAcronym, bamerges, totalframes); + return data_parsed; + +}; + +ResultsAssemblyGrid.prototype._prepareData = function(data) { + var data_parsed = []; + for ( var i = 0; i < data.length; i++) { + data_parsed = this.process(data[i], data_parsed); + } + this.data = data_parsed; + return data_parsed; +}; + +/** Given an array of conditions it returns distinct(concentrations) order by concentration and hash map with number of ocurrences**/ +ResultsAssemblyGrid.prototype.parseConcentrations = function(val, conditions, differentConcentration, quality) { + var conditions = []; + var differentConcentration = {}; + var quality = []; + for ( var i = 0; i < val.length; i++) { + var conc = Number(val[i].concentration).toFixed(1); + var quality = Number(val[i].quality).toFixed(2); + if (differentConcentration[conc] == null) { + differentConcentration[conc] = 0; + conditions.push({ + concentration : conc, + quality : [ quality ], + frames : [ { + bufferAfterFramesMerged : val[i].bufferAfterFramesMerged, + bufferBeforeFramesMerged : val[i].bufferBeforeFramesMerged, + framesMerge : val[i].framesMerge, + framesCount : val[i].framesCount + } ] + }); + } else { + /** Add quality **/ + for ( var j = 0; j < conditions.length; j++) { + if (conditions[j].concentration == conc) { + conditions[j].quality.push(quality); + conditions[j].frames.push({ + bufferAfterFramesMerged : val[i].bufferAfterFramesMerged, + bufferBeforeFramesMerged : val[i].bufferBeforeFramesMerged, + framesMerge : val[i].framesMerge, + framesCount : val[i].framesCount + }); + } } } - return html + "
"; - }, - isWebGLEnabled : function(return_context) { - if (!!window.WebGLRenderingContext) { - var canvas = document.createElement("canvas"); - names = [ "webgl", "experimental-webgl", "moz-webgl", "webkit-3d" ]; - context = false; - for ( var i = 0; i < 4; i++) { - try { - context = canvas.getContext(names[i]); - if (context && typeof context.getParameter == "function") { - // WebGL is enabled - if (return_context) { - // return WebGL object if the function's argument is present - return { - name : names[i], - gl : context - }; - } - // else, return just true - return true; - } - } catch (e) { - } + + differentConcentration[conc] = differentConcentration[conc] + 1; + } + /** sorting concentrations **/ + conditions.sort(function(a, b) { + return a.concentration - b.concentration; + }); + return { + concentrations : conditions, + differentConcentration : differentConcentration + }; +}; + +ResultsAssemblyGrid.prototype.getConditionWarnings = function(condition) { + + var withWarnings = 0; + + for ( var i = 0; i < condition.frames.length; i++) { + if (condition.quality[i] == null) { + withWarnings = withWarnings + 1; + continue; + } else { + if (Number(condition.quality[i]) < this.guinierQuality) { + withWarnings = withWarnings + 1; + continue; } - // WebGL is supported, but disabled - return false; } - // WebGL not supported28. - return false; - }, - getHTMLTableForPrefixes : function(bufferBeforeaverageFilePath, averageFilePath, bufferAfterAverageFilePath) { - function getRow(bufferBeforeaverageFilePath) { - file = bufferBeforeaverageFilePath; - try { - file = bufferBeforeaverageFilePath.split("/")[bufferBeforeaverageFilePath.split("/").length - 1]; - } catch (e) { - file = "NA"; + if (condition.frames[i].bufferBeforeFramesMerged / condition.frames[i].framesCount < this.framePercentageThreshold|| condition.frames[i].framesMerged / condition.frames[i].framesCount < this.framePercentageThreshold|| condition.frames[i].bufferAfterFramesMerged / condition.frames[i].framesCount < this.framePercentageThreshold) { + withWarnings = withWarnings + 1; + continue; + } + } + + return { + withWarnings : withWarnings, + withoutWarnings : condition.frames.length - withWarnings + }; +}; + +ResultsAssemblyGrid.prototype.getFrameHTMLTable = function(warnings) { + var html = ""; + if (warnings.withWarnings > 0) { + html = html + "
" + warnings.withWarnings + + "x
"; + } + + if (warnings.withoutWarnings > 0) { + html = html + "
" + warnings.withoutWarnings + + "x
"; + } + return html; +}; + +ResultsAssemblyGrid.prototype.createConcentrationRow = function(numberOcu, condition, warnings){ + var html = ""; + if (numberOcu > 1){ + html = html + "" +numberOcu + "x " + BUI.formatConcentration(condition.concentration); + } + else{ + html = html + BUI.formatConcentration(condition.concentration); + } + html = html + ""; + html = html + this.getFrameHTMLTable(warnings); + ""; + html = html + ""; + return html; +}; + + +ResultsAssemblyGrid.prototype.getConditionHTMLTable = function(val, style, record) { + var maxNumberColumns = 2; + var html = "
"; + var nColumns = 0; + for ( var r = 0; r < val.length; r++) { + if (nColumns == maxNumberColumns) { + nColumns = 0; + html = html + ""; + } + html = html + ""; } - var html = "
"; + var value = val[r]; + + var bufferAcronym = (BIOSAXS.proposal.getBufferById(value.bufferId).acronym); + + var parsed = (this.parseConcentrations(value.concentrations)); + var conditions = parsed.concentrations; + var differentConcentration = parsed.differentConcentration; + + /** Checking warnings **/ + var warnings = []; + var concentrationValidPerconcentration = 0; + var measurements = 0; + for ( var i = 0; i < conditions.length; i++) { + measurements = measurements + conditions[i].frames.length; + var warning = this.getConditionWarnings(conditions[i]); + warnings.push(warning); + if (warning.withoutWarnings > 0) { + concentrationValidPerconcentration = concentrationValidPerconcentration + 1; } - return "
" + file + "
"; - /** Buffer Before **/ - if (bufferBeforeaverageFilePath != null) { - html = html + getRow(bufferBeforeaverageFilePath); - } + this.validColor = '#E0F8E0'; + this.warningColor = '#F5DA81'; + this.notValidColor = '#F6CED8'; - /** Molecule **/ - if (averageFilePath != null) { - html = html + getRow(averageFilePath); + var color = this.warningColor; + if (concentrationValidPerconcentration > 2) { + color = this.validColor; + } + /** More measurement need to be done **/ + if (measurements < 3) { + color = this.notValidColor; } - /** Buffer After **/ - if (bufferAfterAverageFilePath != null) { - html = html + getRow(bufferAfterAverageFilePath); + html = html + "
"; + html = html + ""; + for ( var i = 0; i < conditions.length; i++) { + html = html + this.createConcentrationRow(differentConcentration[conditions[i].concentration], conditions[i], warnings[i]); } - return html + "
" + bufferAcronym.toUpperCase() + + "
"; - }, - getBaseURL : function() { - return '/ispyb/user/dataadapter.do'; - }, + html = html + ""; + html = html + ""; - getPrintcomponentURL : function(dewarId) { - return '/ispyb/user/viewDewarAction.do?reqCode=generateLabels&dewarId=' + dewarId; + html = html + ""; + nColumns = nColumns + 1; + } + html = html + "
"; + return html; +}; - }, - getPDBVisualizerURL : function(modelId, subtractionId, experimentId) { - return '/ispyb/user/viewProjectList.do?reqCode=display&menu=PDBVisualizer&modelId=' + modelId + '&experimentId=' + experimentId - + '&subtractionId=' + subtractionId; - }, +ResultsAssemblyGrid.prototype._getTbar = function() { + function goTo(url) { + window.location = url; + } - getURL : function() { - return this.getBaseURL() + '?reqCode=getImage'; + var _this = this; + return [ { + icon : '../images/application_view_list.png', + text : 'Multiple Select', + handler : function() { + var specimenSelectorResultGrid = new SpecimenSelectorResultGrid(); + var window = Ext.create('Ext.window.Window', { + title : 'Multiple select', + height : 600, + width : 600, + layout : 'fit', + items : [ specimenSelectorResultGrid.getPanel(_this.data) ], + buttons : [ { + text : 'Go', + handler : function() { + var array = []; + for ( var i = 0; i < specimenSelectorResultGrid.selected.length; i++) { + var row = specimenSelectorResultGrid.selected[i]; + array.push({ + macromoleculeId : row.macromoleculeId, + bufferId : row.bufferId + }); + } + goTo(BUI.getMacromoleculeResultsURLByMultipleSearch(array)); + + } + }, { + text : 'Cancel', + handler : function() { + window.close(); + } + } ] + + }).show(); - }, - getAbinitioImageURL : function() { - return this.getBaseURL() + '?reqCode=getAbinitioImage'; - }, - getNSDImageURL : function(modelListId) { - return BUI.getAbinitioImageURL() + '&type=NSD&modelListId=' + modelListId; - }, - getCHI2ImageURL : function(modelListId) { - return BUI.getAbinitioImageURL() + '&type=CHI2&modelListId=' + modelListId; - }, - getModelFile : function(type, modelId, format) { - return this.getBaseURL() + '?reqCode=getModelFile' + "&type=" + type + "&modelId=" + modelId + "&format=" + format; - }, - getPdbURL : function() { - return this.getBaseURL() + '?reqCode=getPdbFiles'; - }, - getStvArray : function(value, error) { - value = Number(value); - error = Number(error); - return [ value - error, value, value + error ]; - }, - getPointArrayForDygraph : function(x, y, error) { - return [ x, BUI.getStvArray(y, error) ]; - }, - createDIV : function(text, width, className, backgroundColor) { - var nameContainer = document.createElement("div"); - var nameSpan = document.createElement("span"); - if (className != null) { - nameSpan.setAttribute("class", className); - } - if (backgroundColor != null) { - nameSpan.setAttribute("style", "float:left;width:" + width + "px;height:18px;background-color:" + backgroundColor); - } else { - nameSpan.setAttribute("style", "float:left;width:" + width + "px;height:18px;"); } - nameSpan.appendChild(document.createTextNode(text)); - nameContainer.appendChild(nameSpan); - return nameContainer; - }, + } ]; +}; - createFormLabel : function(labelText, text, labelWidth, textWidth, backgroundColor) { - var div = document.createElement("div"); +ResultsAssemblyGrid.prototype.getLegendPanel = function() { + return { + html : '
' + BUI.getRectangleColorDIV(this.validColor, 10, 10) + + 'Good quality measurements' + + BUI.getRectangleColorDIV(this.warningColor, 10, 10) + + 'Probably valid with manual processing' + + BUI.getRectangleColorDIV(this.notValidColor, 10, 10) + + 'More measurements need to be done
' + }; +}; +/** Returns the grid **/ +ResultsAssemblyGrid.prototype.getPanel = function(macromolecules) { + var _this = this; - div.appendChild(BUI.createDIV(labelText, labelWidth, "bLabel", backgroundColor)); - div.appendChild(BUI.createDIV(text, textWidth, "btext", backgroundColor)); - return div.innerHTML; - }, + this.store = Ext.create('Ext.data.Store', { + fields : [ + 'macromoleculeId', 'macromoleculeAcronym', 'measurementCount', 'subtractionCount', 'averageCount', 'timeStart', 'concentrationArray', + 'bufferConditions', 'conditions' ], + data : this._prepareData(macromolecules) + }); - createTextArea : function(labelText, text, labelWidth, rows, cols) { - var div = document.createElement("div"); - div.appendChild(BUI.createDIV(labelText, labelWidth, "bLabel")); - var textArea = document.createElement("textarea"); - textArea.setAttribute("rows", rows); - textArea.setAttribute("cols", cols); - textArea.appendChild(document.createTextNode(text)); - div.appendChild(textArea); - return div.innerHTML; - }, + this.store.sort('macromoleculeAcronym'); - showBetaWarning : function() { - alert("ISPyB for Biosaxs version Beta has not this functionality enabled"); - }, + this.grid = Ext.create('Ext.grid.Panel', { + id : this.id, + title : 'Macromolecules', + store : this.store, + tbar : this._getTbar(), + bbar : [ this.getLegendPanel() ], + width : this.width, + height : this.height, + maxHeight : this.maxHeight, + sortableColumns : true, + columns : [ + { + text : '', + dataIndex : 'macromoleculeId', + width : 20, + hidden : false, + renderer : function(val, y, sample) { + return BUI.getRectangleColorDIV(BIOSAXS.proposal.macromoleculeColors[val], 10, 10); + } + }, + { + text : 'Macromolecule', + dataIndex : 'macromoleculeAcronym', + width : 200 + }, + { + text : 'Buffer Conditions', + dataIndex : 'conditions', + flex : 1, + renderer : function(val, style, record) { + return _this.getConditionHTMLTable(val, style, record); + } + }, + { + header : 'Average', + dataIndex : 'percentageCollected', + name : 'percentageCollected', + type : 'string', + hidden : true, + renderer : function(val, y, sample) { + return "
" + + BUI.getProgessBar((sample.raw.averageCount / sample.raw.measurementCount) * 100, sample.raw.averageCount + "/" + + sample.raw.measurementCount) + "
"; + }, + width : 100, + sorter : false + }, + { + header : 'Subtractions', + dataIndex : 'percentageCollected', + name : 'percentageCollected', + type : 'string', + hidden : true, + renderer : function(val, y, sample) { + return "
"+ BUI.getProgessBar((sample.raw.subtractionCount / sample.raw.measurementCount) * 100, sample.raw.subtractionCount + "/" + + sample.raw.measurementCount) + "
"; + }, + width : 100 + }, { + header : 'Date', + dataIndex : 'timeStart', + name : 'timeStart', + type : 'string', + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + if (record.raw.timeStart != null) { + return moment(record.raw.timeStart).format("MMM Do YY"); + } + } + }, { + header : 'Download', + dataIndex : 'percentageCollected', + name : 'percentageCollected', + type : 'string', + renderer : function(val, y, sample) { + return BUI.getZipHTMLByMacromoleculeId(sample.raw.macromoleculeId); + }, + width : 100 + }, - formatValuesErrorUnitsScientificFormat : function(val, error, unit, args) { - var fontSize = 14; - var decimals = 2; - var errorFontSize = 10; - /** line break **/ - var lineBreak = true; - if (args != null) { - if (args.fontSize != null) { - fontSize = args.fontSize; - } - if (args.decimals != null) { - decimals = args.decimals; - } - if (args.errorFontSize != null) { - errorFontSize = args.errorFontSize; - } - if (args.lineBreak != null) { - lineBreak = args.lineBreak; + { + id : 'btnResultVisible', + width : 85, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + return BUI.getGreenButton('GO'); + } + } ], + viewConfig : { + stripeRows : true, + listeners : { + afterrender : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + }, + celldblclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + _this.edit(record.data.macromoleculeId); + }, + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + if (grid.getGridColumns()[cellIndex].getId() == 'buttonEditMacromolecule') { + _this.edit(record.data.macromoleculeId); + } + if (grid.getGridColumns()[cellIndex].getId() == 'buttonRemoveMacromolecule') { + BUI.showBetaWarning(); + } + if (grid.getGridColumns()[cellIndex].getId() == 'btnResultVisible') { + window.location = BUI.getMacromoleculeResultsURL(record.data.macromoleculeId); + } + } } - } + }); - if (val == "") { - return ""; - } - if (error == null) { - return "" + Number(val).toFixed(decimals) + ""; - } - var html = "" + Number(val).toFixed(decimals) + " " + unit + ""; - if (lineBreak) { - html = html + "
"; - } - return html + " ± " + Number(Number(error).toFixed(3)).toExponential() - + ""; - }, + /** Adding the tbar **/ + if (this.tbar) { + this.grid.addDocked({ + xtype : 'toolbar', + items : this.getTbar() + }); + } + return this.grid; +}; - formatValuesErrorUnits : function(val, error, unit, args) { - var fontSize = 16; - var decimals = 2; - var errorFontSize = 10; - /** line break **/ - var lineBreak = true; - if (args != null) { - if (args.fontSize != null) { - fontSize = args.fontSize; - } - if (args.decimals != null) { - decimals = args.decimals; - } - if (args.errorFontSize != null) { - errorFontSize = args.errorFontSize; - } - if (args.lineBreak != null) { - lineBreak = args.lineBreak; - } +ResultsAssemblyGrid.prototype.input = function(targetId) { + return { + data : DATADOC.getData_3367(), + proposal : DATADOC.getProposal_3367() + }; +}; - } +ResultsAssemblyGrid.prototype.test = function(targetId) { + var grid = new ResultsAssemblyGrid({ + height : 600, + searchBar : false, + tbar : false, + btnResultVisible : true, + width : 1000 + }); + BIOSAXS.proposal = new Proposal(grid.input().proposal); + var panel = grid.getPanel(grid.input().data); + panel.render(targetId); - if (val == "") { - return ""; +}; + + +function RigidModelGrid(args) { + this.height = null; + this.width = null; + this.id = BUI.id(); + + if (args != null) { + if (args.height != null) { + this.height = args.height; + + if (args.width != null) { + this.width = args.width; + } + } + } + + this.onSelected = new Event(this); +} + + +RigidModelGrid.prototype.refresh = function(subtractions) { + var data = []; + if (subtractions != null){ + if (subtractions.length > 0){ + for (j in subtractions){ + var subtraction = subtractions[j]; + if (subtraction.rigidBodyModeling3VOs != null){ + for (i in subtraction.rigidBodyModeling3VOs){ + data.push(subtraction.rigidBodyModeling3VOs[i]); + } + } + } + } + } + this.store.loadData(data); +}; + +RigidModelGrid.prototype.getPanel = function() { + var _this = this; + this.store = Ext.create('Ext.data.Store', { + fields : [ 'symmetry', 'subtractionId', 'subUnitConfigFilePath', 'rigidBodyModelingId', 'rigidBodyModelFilePath', 'logFilePath', 'fitFilePath', 'curveConfigFilePath', + 'crossCorrConfigFilePath', 'contactDescriptionFilePath' ], + data : [] + }); + + this.store.sort([ { + property : 'name', + direction : 'ASC' + } ]); + + this.panel = Ext.create('Ext.grid.Panel', { + store : this.store, + width : this.width, + height : this.height, + margin : 10, + deferredRender : false, + columns : [ { + text : 'RBM', + dataIndex : 'rigidBodyModelFilePath', + hidden : false, + flex : 1, + renderer : function(val){ + return BUI.getFileName(val); + } + }, { + text : 'Sub Unit Conf.', + dataIndex : 'subUnitConfigFilePath', + hidden : true, + flex : 1, + renderer : function(val){ + return BUI.getFileName(val); + } + }, { + text : 'Log', + dataIndex : 'logFilePath', + hidden : true, + flex : 1, + renderer : function(val){ + return BUI.getFileName(val); + } + }, { + text : 'Fit', + dataIndex : 'fitFilePath', + hidden : false, + flex : 1, + renderer : function(val){ + return BUI.getFileName(val); + } + }, { + text : 'Curve Conf.', + dataIndex : 'curveConfigFilePath', + hidden : false, + flex : 1, + renderer : function(val){ + return BUI.getFileName(val); + } + }, { + text : 'Cross Corr.', + dataIndex : 'crossCorrConfigFilePath', + hidden : false, + flex : 1, + renderer : function(val){ + return BUI.getFileName(val); + } + }, { + text : 'Contact Desc.', + dataIndex : 'contactDescriptionFilePath', + hidden : true, + flex : 1, + renderer : function(val){ + return BUI.getFileName(val); + } + } ], + + viewConfig : { + enableTextSelection : true, + preserveScrollOnRefresh : true + }, + listeners : { + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + + }, + afterrender : function() { + } + } + }); + return this.panel; +}; + + +/** + * shows shipments + * + * @height + * @width + * @minHeight + * @btnEditVisible + */ +function ShipmentGrid(args) { + this.id = BUI.id(); + this.height = 100; + this.width = null; + this.minHeight = null; + this.btnEditVisible = true; + + if (args != null) { + if (args.height != null) { + this.height = args.height; } - if (error == null) { - return "" + Number(val).toFixed(decimals) + ""; + if (args.width != null) { + this.width = args.width; } - var html = "" + Number(val).toFixed(decimals) + " " + unit + ""; - if (lineBreak) { - html = html + "
"; + if (args.minHeight != null) { + this.minHeight = args.minHeight; } - return html + " ± " + Number(Number(error).toFixed(8)).toExponential() - + ""; - }, - - formatValuesUnits : function(val, unit, args) { - var fontSize = 12; - var decimals = 2; - var unitsFontSize = 10; - if (args != null) { - if (args.fontSize != null) { - fontSize = args.fontSize; - } - if (args.decimals != null) { - decimals = args.decimals; - } - if (args.unitsFontSize != null) { - unitsFontSize = args.unitsFontSize; - } - + if (args.btnEditVisible != null) { + this.btnEditVisible = args.btnEditVisible; } + } +} - if (val === "") { - return ""; - } - if (unit == null) { - return "" + Number(val).toFixed(decimals) + ""; - } - return "" + Number(val).toFixed(decimals) + " " + unit + ""; - }, +ShipmentGrid.prototype._getColumns = function() { + var _this = this; + var columns = [ + { + text : 'Name', + dataIndex : 'shippingName', + flex : 1 + }, + { + header : 'Type', + dataIndex : 'shippingType', + flex : 1, + hidden : true, + renderer : function(val, comp, record) { + if (val != null) { + return val.toUpperCase(); + } - getGreenButton : function(text, args) { - var width = 70; - var height = 20; - if (args != null) { - if (args.width != null) { - width = args.width; } - if (args.height != null) { - height = args.height; + }, + { + header : 'Status', + type : 'string', + flex : 1, + hidden : false, + renderer : function(comp, val, record) { + if (record.raw.shippingStatus != null) { + if (new String(record.raw.shippingStatus).toUpperCase() == 'OPENED') { + return "" + new String(record.raw.shippingStatus).toUpperCase() + ""; + } + return "" + new String(record.raw.shippingStatus).toUpperCase() + ""; + } + } + }, + { + text : 'Cases', + flex : 1, + hidden : false, + renderer : function(comp, val, record) { + var shipment = BIOSAXS.proposal.getShipmentById(record.data.shippingId); + var container = ""; + if (shipment.dewarVOs.length > 0) { + container = container + ""; + } else { + return "Empty"; + } + return container + "
" + shipment.dewarVOs.length + "x
"; } - } - - return ''; - }, -// getBlueButton : function(text, args) { -// var width = 70; -// var height = 20; -// if (args != null) { -// if (args.width != null) { -// width = args.width; -// } -// if (args.height != null) { -// height = args.height; -// } -// } -// -// return ''; -// }, + }, { + header : 'Comments', + dataIndex : 'comments', + flex : 1, + hidden : false + }, { + header : 'Creation Date', + dataIndex : 'creationDate', + hidden : true + } ]; - getBlueButton : function(text, args) { - var width = 70; - var height = 20; - var href = null; - if (args != null) { - if (args.width != null) { - width = args.width; - } - if (args.height != null) { - height = args.height; + if (this.btnEditVisible) { + columns.push({ + id : _this.id + 'buttonEdit', + text : '', + hidden : !_this.btnEditVisible, + width : 100, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + return BUI.getGreenButton('EDIT'); } - if (args.href != null) { - href = args.href; + }); + } + + columns.push({ + id : _this.id + 'buttonRemove', + text : '', + width : 100, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + var shipment = BIOSAXS.proposal.getShipmentById(record.data.shippingId); + if (shipment.dewarVOs.length == 0) { + return BUI.getRedButton('REMOVE'); } + } - if (href != null) { - return ''; - } else { - return ''; -// return ''; - } - }, - - getSubmitGreenButton : function(text) { - return ''; - }, + }); - getRedButton : function(text) { - return ''; + return columns; +}; - }, - getRectangleColorDIV : function(color, height, width) { - return '
'; - }, +ShipmentGrid.prototype._getTopButtons = function() { + var _this = this; + /** Actions buttons **/ + var actions = []; + actions.push(Ext.create('Ext.Action', { + icon : '../images/add.png', + text : 'Add Shipment', + handler : function(widget, event) { + //window.location = BUI.getCreateShipmentURL(); + var _this = this; - openBufferWindow : function(bufferId) { - var window = new BufferWindow(); - window.draw(tabs.experiment.getBufferById(bufferId), tabs.experiment); - }, + var shipmentForm = new ShipmentForm({ + creationMode : true, + showTitle : false + }); + shipmentForm.onSaved.attach(function(sender, shipment) { + _this.showShipmentTabs(shipment, targetId); + }); + + var window = Ext.create('Ext.window.Window', { + title : 'New Shipment', + height : 600, + width : 800, + layout : 'fit', + items : [ shipmentForm.getPanel() ] + }).show(); - /** Render for safety levels on grids **/ - safetyRenderer : function(val, y, specimen) { - var color = val; - if (val == "YELLOW") { - color = "#E9AB17"; } - return '' + val + ''; - }, + })); + return actions; +}; - getSampleColor : function() { - return '#CB181D'; - }, +ShipmentGrid.prototype.refresh = function(shippings) { + this.features = shippings; + this.store.loadData(this._prepareData(), false); +}; - getLightSampleColor : function() { - return '#FCBBA1'; - }, +ShipmentGrid.prototype._prepareData = function() { + var data = []; + for ( var i = 0; i < this.features.length; i++) { + data.push(this.features[i]); + } + return data; +}; - getBufferColor : function() { - return '#6A51A3'; - }, - getLightBufferColor : function() { - return '#BCBDDC'; - }, +ShipmentGrid.prototype.getPanel = function(shipments) { + this.features = shipments; + return this._renderGrid(); +}; - formatConcentration : function(val) { - if (val != null) { - return "" + Number(val).toFixed(2) + " mg/ml "; - } - return val; - }, +ShipmentGrid.prototype.edit = function(shippingId) { + window.location = BUI.getShippingURL(shippingId); +}; - formatVolume : function(sample, volume) { - if (Number(sample.data.volumeToLoad) > Number(sample.data.volume)) { - return "" + volume + " �l"; - } - if (Number(sample.data.volumeToLoad) == Number(sample.data.volume)) { - return "" + volume + " �l"; - } - return "" + volume + " �l"; - }, +ShipmentGrid.prototype._getStoreFields = function(data) { + var _this = this; + return [ { + name : 'shippingId' + }, { + name : 'shippingName' + }, { + name : 'shippingStatus' + }, { + name : 'shippingType' + }, { + name : 'creationDate' + }, { + name : 'comments' + } ]; +}; - getProposal : function() { - return new Proposal(); - }, +ShipmentGrid.prototype._renderGrid = function() { + var _this = this; - getSampleNameRenderer : function(val, y, record) { - var sample = record.data; - if (record.raw.macromolecule3VO == null) { - return '' + sample.code + ''; - } else { - return '' + sample.code + ''; - } - }, + /** Store **/ + var data = this._prepareData(); + this.store = Ext.create('Ext.data.Store', { + fields : this._getStoreFields(data), + autoload : true, + data : data + }); - getSafetyLevels : function() { - var safetyLevels = new Array(); - safetyLevels.push({ - safetyLevelId : "", - name : "UNKNOWN" - }); - safetyLevels.push({ - safetyLevelId : 1, - name : "GREEN" - }); - safetyLevels.push({ - safetyLevelId : 2, - name : "YELLOW" - }); - safetyLevels.push({ - safetyLevelId : 3, - name : "RED" - }); - return safetyLevels; - }, + this.store.loadData(data, false); + + this.grid = Ext.create('Ext.grid.Panel', { + title : "Shipping", + icon : '/ispyb/images/plane.gif', + width : this.width, + minWidth : this.minWidth, + height : this.height, + store : this.store, + columns : this._getColumns(), + viewConfig : { + stripeRows : true, + listeners : { + itemdblclick : function(dataview, record, item, e) { + _this.edit(record.raw.shippingId); + }, + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEdit') { + _this.edit(record.data.shippingId); + } - getErrorColor : function() { - return '#F6CED8'; - }, - getWarningColor : function() { - return '#F5DA81'; - }, - getValidColor : function() { - return '#E0F8E0'; - }, - getSamplePlateLetters : function() { - return [ "A", "B", "C", "D", "E", "F", "G", "H" ]; - }, - getSamplePositionHTML : function(sample, experiment) { - var plate = ""; - var row = ""; - var column = ""; - var rows = this.getSamplePlateLetters(); - if (sample.sampleplateposition3VO != null) { - var samplePlate = experiment.getSamplePlateById(sample.sampleplateposition3VO.samplePlateId); - if (samplePlate != null) { - plate = (samplePlate.slotPositionColumn); - row = (sample.sampleplateposition3VO.rowNumber); - column = (sample.sampleplateposition3VO.columnNumber); - // var html = "Plate: " + "" + plate + ""; - // html = html + ", Row: " + "" + rows[row - 1] + ""; - // html = html + ", Column: " + "" + column + ""; - var html = "Plate: " + plate - + "-" + rows[row - 1] + "" + column + ""; - return html; + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemove') { + var shipment = BIOSAXS.proposal.getShipmentById(record.data.shippingId); + if (shipment.dewarVOs.length == 0) { + + var adapter = new BiosaxsDataAdapter(); + _this.grid.setLoading("ISPyB: Removing shipment"); + adapter.onSuccess.attach(function(sender) { + BIOSAXS.proposal.onInitialized.attach(function(sender) { + _this.refresh(BIOSAXS.proposal.getShipments()); + _this.grid.setLoading(false); + }); + BIOSAXS.proposal.init(); + }); + + adapter.onError.attach(function(sender) { + alert("Error"); + _this.grid.setLoading(false); + }); + adapter.removeShipment(record.data.shippingId); + } + } + } } + }, + selModel : { + mode : 'SINGLE' } - return ""; - }, + }); - getSafetyLabelName : function(safetyLevelId) { - var safetyLevels = BUI.getSafetyLevels(); - for ( var i = 0; i < safetyLevels.length; i++) { - if (safetyLevels[i].safetyLevelId == safetyLevelId) { - return safetyLevels[i].name; + var actions = _this._getTopButtons(); + this.grid.addDocked({ + xtype : 'toolbar', + items : actions + }); + + this.grid.getSelectionModel().on({ + selectionchange : function(sm, selections) { + if (selections.length) { + for ( var i = 0; i < actions.length; i++) { + if (actions[i].enable) { + actions[i].enable(); + } + } + } else { + for ( var i = 0; i < actions.length; i++) { + if (actions[i].alwaysEnabled == false) { + if (actions[i].disable) { + actions[i].disable(); + } + } + } } } - return "UNKNOWN"; - }, - /** generate random id **/ - id : function() { - var text = ""; - var possible = "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789"; - - for ( var i = 0; i < 5; i++) - text += possible.charAt(Math.floor(Math.random() * possible.length)); + }); + return this.grid; +}; - return text; - }, - showWarning : function(message) { - Ext.Msg.show({ - title : 'Warning', - msg : message, - icon : Ext.Msg.WARNING, - animEl : 'elId' - }); - }, - showError : function(message) { - Ext.Msg.show({ - title : 'Warning', - msg : message, - icon : Ext.Msg.ERROR, - animEl : 'elId' - }); - }, - getTipHTML : function(message) { - //return "
Tip
" - // + message + "
"; - return "
Tip
" - + message + "
"; - }, +ShipmentGrid.prototype.input = function() { + return { + proposal : new MeasurementGrid().input().proposal, + shippings : DATADOC.getShippings_10() + }; +}; - getWarningHTML : function(message) { - return "
Warning
" - + message + "
"; - }, +ShipmentGrid.prototype.test = function(targetId) { + var shipmentGrid = new ShipmentGrid({ + minHeight : 300, + height : 440 + }); + BIOSAXS.proposal = new Proposal(shipmentGrid.input().proposal); + var panel = shipmentGrid.getPanel(targetId); + panel.render(targetId); + shipmentGrid.refresh(shipmentGrid.input().shippings); +}; + +function SpecimenGrid(args) { + this.id = BUI.id(); + this.height = 500; + this.unitsFontSize = 9; + this.editEnabled = false; + this.isPositionColumnHidden = false; + this.removeBtnEnabled = false; - getErrorHTML : function(message) { - return "
Error
" - + message + "
"; - }, + this.selectionMode = "MULTI"; + this.updateRowEnabled = false; + this.grouped = true; + this.width = 900; + this.title = 'Specimens'; + + this.margin = "0 0 0 0"; +// this.experimentColorBased = false; - getProgessBar : function(percentage, text) { - /** percentage 100% green **/ - var color = "#0a0"; + if (args != null) { + if (args.height != null) { + this.height = args.height; + } - color = "#99CC00"; - if (percentage > 100) { - color = "yellow"; - percentage = 100; + if (args.showTitle == false) { + this.title = null; } - if (isNaN(percentage)) { - color = "white"; - percentage = 0; + + if (args.margin == false) { + this.margin = args.margin; } - var defaultText = percentage + "%"; - if (text != null) { - defaultText = text; + if (args.grouped == false) { + this.grouped = null; } - return "
" + defaultText + "
"; - }, - getFileName : function(filePath){ - if (filePath != null){ - return filePath.split("/")[filePath.split("/").length - 1] + if (args.width != null) { + this.width = args.width; } - return ""; - } -}; -Ext.ux.form.RequiredCombo = Ext.extend(Ext.form.ComboBox, { - config : { - cls : 'custom-field-text-required' - }, - initComponent : function() { - Ext.ux.form.RequiredCombo.superclass.initComponent.apply(this, arguments); - }, - checkChange : function() { - if ((this.getValue() == null) || String(this.getValue()).length == 0) { - this.addCls('custom-field-text-required'); - } else { - this.removeCls('custom-field-text-required'); + if (args.editEnabled != null) { + this.editEnabled = args.editEnabled; + } + if (args.removeBtnEnabled != null) { + this.removeBtnEnabled = args.removeBtnEnabled; + } + if (args.isPositionColumnHidden != null) { + this.isPositionColumnHidden = args.isPositionColumnHidden; + } + if (args.selectionMode != null) { + this.selectionMode = args.selectionMode; + } + if (args.updateRowEnabled != null) { + this.updateRowEnabled = args.updateRowEnabled; } + } -}); + this.onClick = new Event(this); + this.onSelected = new Event(this); + this.onRemoved = new Event(this); + this.onSpecimenChanged = new Event(); +} -Ext.define('Ext.form.field.RequiredNumber', { - extend : 'Ext.form.field.Number', - alias : 'widget.requirednumberfield', - alternateClassName : [ 'Ext.form.RequiredNumberField', 'Ext.form.RequiredNumber' ], - config : { - cls : 'custom-field-text-required' - }, +SpecimenGrid.prototype._prepareData = function(experiment) { + var data = []; - initComponent : function() { - var me = this; - me.callParent(); - me.setMinValue(me.minValue); - me.setMaxValue(me.maxValue); - }, + var samples = experiment.getSamples(); + for ( var i = 0; i < samples.length; i++) { + var sample = samples[i]; + if (sample.macromolecule3VO != null) { + sample.macromolecule = sample.macromolecule3VO.acronym; + sample.exposureTemperature = []; + sample.macromoleculeId = sample.macromolecule3VO.macromoleculeId; + } - onChange : function() { - if ((this.getValue() == null) || String(this.getValue()).length == 0) { - this.addCls('custom-field-text-required'); + if (sample.sampleplateposition3VO != null) { + if (sample.sampleplateposition3VO.samplePlateId != null) { + sample.samplePlateId = sample.sampleplateposition3VO.samplePlateId; + sample.rowNumber = sample.sampleplateposition3VO.rowNumber; + sample.columnNumber = sample.sampleplateposition3VO.columnNumber; + if (experiment.getSamplePlateById(sample.sampleplateposition3VO.samplePlateId).plategroup3VO != null) { + sample.plateGroupName = experiment.getSamplePlateById(sample.sampleplateposition3VO.samplePlateId).plategroup3VO.name; + sample.samplePlateName = experiment.getSamplePlateById(sample.sampleplateposition3VO.samplePlateId).name + " [" + sample.plateGroupName + "]"; + sample.slotPositionColumn = experiment.getSamplePlateById(sample.sampleplateposition3VO.samplePlateId).slotPositionColumn; + } + } } else { - this.removeCls('custom-field-text-required'); + sample.samplePlateName = "Unallocated Specimens"; } - this.toggleSpinners(); - this.callParent(arguments); - } -}); -Ext.define('Ext.form.field.RequiredText', { - extend : 'Ext.form.field.Text', - alias : 'widget.requiredtext', - requires : [ 'Ext.form.field.VTypes', 'Ext.layout.component.field.Text' ], - alternateClassName : [ 'Ext.form.RequiredTextField', 'Ext.form.RequiredText' ], - config : { - cls : 'custom-field-text-required' - }, - initComponent : function() { - var me = this; - if (me.allowOnlyWhitespace === false) { - me.allowBlank = false; + /** For grouping, because sencha has not option for multiple grouping I add a field to your store with a convert function that concatenates these two fields and then group by that field.**/ + sample.groupIndex = sample.bufferId + sample.macromoleculeId; + var macromolecule = BIOSAXS.proposal.getMacromoleculeById(sample.macromoleculeId); + + sample.acronym = "Buffers"; + if (macromolecule != null) { + sample.acronym = BIOSAXS.proposal.getMacromoleculeById(sample.macromoleculeId).acronym; } - me.callParent(); - me.addEvents( - /** - * @event autosize - * Fires when the **{@link #autoSize}** function is triggered and the field is resized according to the - * {@link #grow}/{@link #growMin}/{@link #growMax} configs as a result. This event provides a hook for the - * developer to apply additional logic at runtime to resize the field if needed. - * @param {Ext.form.field.Text} this This text field - * @param {Number} width The new field width - */ - 'autosize', - /** - * @event keydown - * Keydown input field event. This event only fires if **{@link #enableKeyEvents}** is set to true. - * @param {Ext.form.field.Text} this This text field - * @param {Ext.EventObject} e - */ - 'keydown', - /** - * @event keyup - * Keyup input field event. This event only fires if **{@link #enableKeyEvents}** is set to true. - * @param {Ext.form.field.Text} this This text field - * @param {Ext.EventObject} e - */ - 'keyup', - /** - * @event keypress - * Keypress input field event. This event only fires if **{@link #enableKeyEvents}** is set to true. - * @param {Ext.form.field.Text} this This text field - * @param {Ext.EventObject} e - */ - 'keypress'); - me.addStateEvents('change'); - me.setGrowSizePolicy(); - }, - checkChange : function() { - if ((this.getValue() == null) || String(this.getValue()).length == 0) { - this.addCls('custom-field-text-required'); - } else { - this.removeCls('custom-field-text-required'); + sample.buffer = experiment.getBufferById(sample.bufferId); + + sample.volumeToLoad = experiment.getVolumeToLoadBySampleId(sample.sampleId); + data.push(sample); + } + return data; +}; + +SpecimenGrid.prototype.deselectAll = function() { + this.grid.getSelectionModel().deselectAll(); +}; + +SpecimenGrid.prototype.selectById = function(specimenId) { + this.grid.getSelectionModel().deselectAll(); + for ( var i = 0; i < this.grid.getStore().data.items.length; i++) { + var item = this.grid.getStore().data.items[i].raw; + if (item.specimenId == specimenId) { + this.grid.getSelectionModel().select(i); } } -}); +}; -var BIOSAXS_COMBOMANAGER = { +SpecimenGrid.prototype.getStore = function() { + return this.store; +}; - getComboMacromoleculeByMacromolecules : function(macromolecules, args) { - var labelWidth = 150; - var margin = "0 0 5 0"; - var width = 300; +SpecimenGrid.prototype.getPlugins = function() { + var _this = this; - if (args != null) { - if (args.labelWidth != null) { - labelWidth = args.labelWidth; - } - if (args.margin != null) { - margin = args.margin; - } - if (args.width != null) { - width = args.width; - } - } + var plugins = []; - var store = Ext.create('Ext.data.Store', { - fields : [ 'macromoleculeId', 'acronym' ], - data : macromolecules, - sorters : [ 'acronym' ] - }); + if (this.updateRowEnabled) { + plugins.push(Ext.create('Ext.grid.plugin.RowEditing', { + clicksToEdit : 1, + listeners : { + validateedit : function(grid, e) { + var measurements = []; - return Ext.create('Ext.form.ComboBox', { - fieldLabel : 'Macromolecules', - labelWidth : labelWidth, - width : width, - margin : margin, - store : store, - editable: false, - queryMode : 'local', - displayField : 'acronym', - valueField : 'macromoleculeId' - }); - }, - getComboBuffers : function(buffers, args) { - var labelWidth = 150; - var margin = "0 0 5 0"; - var width = 300; - var fieldLabel = 'Buffer'; + if (e.newValues.bufferId != e.record.raw.bufferId) { + /** If buffer has changed we have to change all the specimens sharing same datacollection **/ + var dataCollections = []; + if (e.record.raw.macromoleculeId == null) { + dataCollections = dataCollections.concat(_this.experiment.getDataCollectionsBySpecimenId(e.record.raw.specimenId)); + } else { + var sampleDataCollections = _this.experiment.getDataCollectionsBySpecimenId(e.record.raw.specimenId); + for ( var i = 0; i < sampleDataCollections.length; i++) { + var sampleDataCollection = sampleDataCollections[i]; + if (sampleDataCollection != null) { + for ( var j = 0; j < sampleDataCollection.measurementtodatacollection3VOs.length; j++) { + var measurementTODc = sampleDataCollection.measurementtodatacollection3VOs[j]; + if (measurementTODc.dataCollectionOrder == 1) { + dataCollections = dataCollections.concat(_this.experiment.getDataCollectionsBySpecimenId(_this.experiment + .getMeasurementById(measurementTODc.measurementId).specimenId)); + } + } + } + } + } + var i = null; + for ( i = 0; i < dataCollections.length; i++) { + var dataCollection = dataCollections[i]; + var specimens = _this.experiment.getSpecimenByDataCollectionId(dataCollection.dataCollectionId); + measurements = measurements.concat(specimens); + } - if (args != null) { - if (args.labelWidth != null) { - labelWidth = args.labelWidth; - } - if (args.margin != null) { - margin = args.margin; - } - if (args.width != null) { - width = args.width; - } - if (args.noLabel != null) { - fieldLabel = null; - } - } + for ( i = 0; i < measurements.length; i++) { + var measurement = measurements[i]; + var specimen = _this.experiment.getSpecimenById(measurement.specimenId); + specimen.bufferId = e.newValues.bufferId; + new BiosaxsDataAdapter().saveSpecimen(specimen, _this.experiment); + } + } - var store = Ext.create('Ext.data.Store', { - fields : [ 'bufferId', 'acronym' ], - data : buffers, - sorters : [ 'acronym' ] - }); + /** Setting values **/ + e.record.raw.concentration = e.newValues.concentration; + e.record.raw.volume = e.newValues.volume; - return Ext.create('Ext.form.ComboBox', { - fieldLabel : fieldLabel, - labelWidth : labelWidth, - width : width, - margin : margin, - editable: false, - store : store, - queryMode : 'local', - displayField : 'acronym', - valueField : 'bufferId' - }); - }, - getComboSessions : function(sessions, args) { - var labelWidth = 150; - var margin = "0 0 5 0"; - var width = 300; + /** Position **/ + if (e.record.raw.sampleplateposition3VO != null) { + var samplePlate = _this.experiment.getSamplePlateBySlotPositionColumn(e.newValues.slotPositionColumn); + if (samplePlate != null) { + e.record.raw.sampleplateposition3VO = { + columnNumber : e.newValues.columnNumber, + rowNumber : e.newValues.rowNumber, + samplePlateId : samplePlate.samplePlateId + }; + } + } else { + if (e.newValues.slotPositionColumn != null) { + var samplePlate = _this.experiment.getSamplePlateBySlotPositionColumn(e.newValues.slotPositionColumn); + if (samplePlate != null) { + e.record.raw.sampleplateposition3VO = { + columnNumber : e.newValues.columnNumber, + rowNumber : e.newValues.rowNumber, + samplePlateId : samplePlate.samplePlateId + }; + } + } + } - if (args != null) { - if (args.labelWidth != null) { - labelWidth = args.labelWidth; - } - if (args.margin != null) { - margin = args.margin; - } - if (args.width != null) { - width = args.width; + var macromoleculeId = e.record.data.macromoleculeId; + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, specimen) { + /** Because macromolecule3VO is fecthed LAZY **/ + if (macromoleculeId != null) { + specimen.macromolecule3VO = BIOSAXS.proposal.getMacromoleculeById(macromoleculeId); + } + _this.onSpecimenChanged.notify(specimen); + _this.grid.setLoading(false); + }); + adapter.onError.attach(function() { + alert("Error"); + _this.grid.setLoading(false); + }); + _this.grid.setLoading(); + adapter.saveSpecimen(e.record.raw, _this.experiment); + } } - } - - for ( var i = 0; i < sessions.length; i++) { - sessions[i]["startDateFormatted"] = moment(sessions[i].startDate).format("MMM Do YY"); - sessions[i]["sorter"] = moment(sessions[i].startDate).format("YYYYMMDD"); - } + })); + } + return plugins; +}; - var store = Ext.create('Ext.data.Store', { - fields : [ 'sessionId', 'startDateFormatted', 'beamlineName', 'startDate', 'endDate', 'beamlineOperator' ], - data : sessions, - sorters : [ 'sorter' ] +SpecimenGrid.prototype._getRowCombo = function() { + var data = []; + for ( var i = 1; i <= 8; i++) { + data.push({ + rowNumber : i, + name : BUI.getSamplePlateLetters()[i - 1] }); + } - return Ext.create('Ext.form.ComboBox', { - fieldLabel : 'Sessions', - labelWidth : labelWidth, - width : width, - margin : margin, - store : store, - queryMode : 'local', - // displayField : 'startDate', - valueField : 'sessionId', - // Template for the dropdown menu. - // Note the use of "x-boundlist-item" class, - // this is required to make the items selectable. - tpl : Ext.create('Ext.XTemplate', '', - '
{startDateFormatted} {beamlineName}
', ''), - // template for the content inside text field - displayTpl : Ext.create('Ext.XTemplate', '', '{startDateFormatted}', '') + var positionsStore = Ext.create('Ext.data.Store', { + fields : [ 'rowNumber', 'name' ], + data : data + }); - }); - } + return Ext.create('Ext.form.ComboBox', { + store : positionsStore, + queryMode : 'local', + displayField : 'name', + valueField : 'rowNumber' + }); }; - - function GenericWindow(args){ - this.title = "title"; - this.width = 700; - this.height = 500; - this.id = BUI.id(); - - this.close = false; - this.draggable = true; - this.modal = true; - - if (args != null){ - if (args.actions != null){ - this.actions = args.actions; - } - if (args.form != null){ - this.form = args.form; - } - if (args.width != null){ - this.width = args.width; - } - if (args.modal != null){ - this.modal = args.modal; - } - - if (args.height != null){ - this.height = args.height; - } - if (args.title != null){ - this.title = args.title; - } - if (args.form != null){ - this.form = args.form; - } - if (args.close != null){ - this.close = args.close; - } - if (args.draggable != null){ - this.draggable = args.draggable; - } - - } - /** Events **/ - this.onSaved = new Event(this); - }; - - -GenericWindow.prototype.getButtons = function() { - var _this = this; - - if (this.close){ - return [ { - text : 'Close', - handler : function() { - _this.panel.close(); - } - } ]; - } - else{ - return [ { - text : 'Save', - handler : function() { - _this.save(); - - } - }, { - text : 'Cancel', - handler : function() { - _this.panel.close(); - } - } ]; +SpecimenGrid.prototype._getColumnCombo = function() { + var data = []; + for ( var i = 1; i <= 12; i++) { + data.push({ + columnNumber : i + }); } -}; -GenericWindow.prototype.save = function (){ - alert("Method save of GenerciWindow class is abstract"); + var positionsStore = Ext.create('Ext.data.Store', { + fields : [ 'columnNumber' ], + data : data + }); + + return Ext.create('Ext.form.ComboBox', { + store : positionsStore, + queryMode : 'local', + displayField : 'columnNumber', + valueField : 'columnNumber' + }); }; -GenericWindow.prototype._postRender = function(data, experiment){ +SpecimenGrid.prototype._getSlotColumBombo = function() { + if (this.experiment){ + var length = this.experiment.getSamplePlates().length; + + var data = []; + for ( var i = 1; i <= length; i++) { + data.push({ + slotPositionColumn : i + }); + } + + var positionsStore = Ext.create('Ext.data.Store', { + fields : [ 'slotPositionColumn' ], + data : data + }); + return Ext.create('Ext.form.ComboBox', { + store : positionsStore, + queryMode : 'local', + displayField : 'slotPositionColumn', + valueField : 'slotPositionColumn' + }); + } }; - -GenericWindow.prototype.draw = function (data, experiment){ - this._render(data, experiment); +SpecimenGrid.prototype.getPanelByExperiment = function(experiment) { + this.experiment = experiment; + var data = this._prepareData(experiment); + return this.getPanel(data); }; -GenericWindow.prototype.refresh = function(data, experiment){ - this.data = data; - this.experiment = experiment; - this.form.refresh(data, experiment); +SpecimenGrid.prototype.refresh = function(experiment) { + this.experiment = experiment; + var data = this._prepareData(experiment); + this.store.loadData(data); }; -GenericWindow.prototype._render = function(data, experiment){ - this.data = data; - var _this = this; - if (this.panel == null){ - this.panel = Ext.create('Ext.Window', { - id : this.id, - title : this.title, - resizable : true, - constrain : true, - border : 1, - modal : this.modal, - frame : false, - draggable : this.draggable, - closable : true, - autoscroll : true, - layout : { type: 'vbox',align: 'stretch'}, - width : this.width, - height : this.form.height, - buttonAlign :'right', - buttons : this.getButtons(), - items : this.form.getPanel(data, experiment), - listeners: { - scope : this, - minimize : function(){ - this.panel.hide(); - }, - destroy : function(){ - delete this.panel; - } - } - }); - this.panel.setLoading(); - } - - this.panel.show(); - this._postRender(); -}; -function CalendarWidget(args) { - this.height = 740; +SpecimenGrid.prototype.getPanel = function() { + var _this = this; + this.store = Ext.create('Ext.data.Store', { + fields : [ + 'buffer', 'bufferId', 'code', 'macromolecule', 'acronym', 'macromoleculeId', 'concentration', 'volume', 'samplePlateId', + 'slotPositionColumn', 'rowNumber', 'columnNumber', 'groupIndex' ], + data : [], + groupField : 'acronym' + }); + this.store.sort([ { + property : 'concentration', + direction : 'ASC' + }, { + property : 'buffer', + direction : 'ASC' + } ]); - if (args != null) { - if (args.height != null) { - this.height = args.height; + var selModel = Ext.create('Ext.selection.RowModel', { + allowDeselect : true, + mode : this.selectionMode, + listeners : { + selectionchange : function(sm, selections) { + var selected = []; + for ( var i = 0; i < selections.length; i++) { + selected.push(selections[i].raw); + } + _this.onSelected.notify(selected); + } } + }); + + var features = []; + + if (this.grouped) { + features.push({ + ftype : 'grouping', + groupHeaderTpl : '{name}', + hideGroupedHeader : false, + startCollapsed : false, + id : 'myGroupedStore' + }); } - this.onClick = new Event(); -} + this.grid = Ext.create( + 'Ext.grid.Panel', + { + title : this.title, + height : this.height, + width : this.width, + selModel : selModel, + store : this.store, + features : features, + margin : this.margin, + plugins : this.getPlugins(), + columns : [ + { + text : '', + dataIndex : 'macromolecule', + width : 20, + renderer : function(val, y, sample) { + var macromoleculeId = null; + if (sample.raw.macromolecule3VO != null) { + macromoleculeId = sample.raw.macromolecule3VO.macromoleculeId; + } + else{ + macromoleculeId = sample.raw.macromoleculeId; + } + + if (macromoleculeId == null) return; + return BUI.getRectangleColorDIV(_this.experiment.macromoleculeColors[macromoleculeId], 10, 10); + } + }, + { + text : 'Macromolecule', + dataIndex : 'macromolecule', + width : 100 + }, + { + text : '', + dataIndex : 'buffer', + width : 20, + renderer : function(val, y, sample) { + var color = "black"; + if (sample.raw.bufferId != null) { + if (_this.experiment.getDataCollectionsBySpecimenId(sample.raw.specimenId)[0] != null){ + color = _this.experiment.getSpecimenColorByBufferId(_this.experiment.getMeasurementById(_this.experiment.getDataCollectionsBySpecimenId(sample.raw.specimenId)[0].measurementtodatacollection3VOs[0].measurementId).specimenId); + } + return BUI.getRectangleColorDIV(color, 10, 10); + } + } + }, { + text : 'Buffer', + dataIndex : 'bufferId', + width : 140, + renderer : function(val, y, sample) { + if (sample.raw.bufferId != null) { + return BIOSAXS.proposal.getBufferById(val).acronym; + } + }, + editor : BIOSAXS_COMBOMANAGER.getComboBuffers(BIOSAXS.proposal.getBuffers(), { + noLabel : true, + width : 300 + }) + }, { + text : 'Conc.', + dataIndex : 'concentration', + width : 100, + editor : { + allowBlank : false + }, + renderer : function(val, meta, sample) { + if (isNaN(val)) { + meta.tdCls = 'yellow-cell'; + return val; + } else { + if (val != 0) { + return BUI.formatValuesUnits(val, 'mg/ml', { + fontSize : 16, + decimals : 3, + unitsFontSize : this.unitsFontSize + }); + } else { + return; + } + } + } + }, { + text : 'Vol. Well', + dataIndex : 'volume', + width : 70, + editor : { + allowBlank : true + }, + renderer : function(val, y, sample) { + return BUI.formatValuesUnits(sample.data.volume, 'µl', { + fontSize : 12, + decimals : 2, + unitsFontSize : this.unitsFontSize + }); + } + }, { + text : 'Position', + hidden : true, + flex : 1, + renderer : function(val, y, sample) { + return BUI.getSamplePositionHTML(sample.raw, _this.experiment); + } + }, { + text : 'samplePlateId', + dataIndex : 'samplePlateId', + hidden : true + }, { + text : 'Plate', + hidden : this.isPositionColumnHidden, + dataIndex : 'slotPositionColumn', + editor : _this._getSlotColumBombo(), + flex : 1, + renderer : function(val, meta, sample) { + if ((val != null) & (val != "")) { + return val; + } else { + meta.tdCls = 'yellow-cell'; + } + } + }, { + text : 'Row', + hidden : this.isPositionColumnHidden, + dataIndex : 'rowNumber', + editor : this._getRowCombo(), + flex : 1, + renderer : function(val, meta, sample) { + if ((val != null) && (val != "")) { + return BUI.getSamplePlateLetters()[val - 1]; + } else { + meta.tdCls = 'yellow-cell'; + } + } + }, { + text : 'Well', + hidden : this.isPositionColumnHidden, + dataIndex : 'columnNumber', + editor : this._getColumnCombo(), + flex : 1, + renderer : function(val, meta, sample) { + if ((val != null) && (val != "")) { + return val; + } else { + meta.tdCls = 'yellow-cell'; + } + } + }, { + id : _this.id + 'buttonEditSample', + text : 'Edit', + width : 80, + sortable : false, + hidden : !_this.editEnabled, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + if (_this.editEnabled) { + return BUI.getGreenButton('EDIT'); + } + } + }, { + id : _this.id + 'buttonRemoveSample', + text : '', + hidden : !_this.removeBtnEnabled, + width : 100, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + if (_this.removeBtnEnabled) { + return BUI.getRedButton('REMOVE'); + } + } + } -CalendarWidget.prototype.loadData = function(data) { - this.events = []; + ], + viewConfig : { + preserveScrollOnRefresh : true, + stripeRows : true, + getRowClass : function(record) { + var specimens = _this.experiment.getSampleByPosition(record.data.samplePlateId, record.data.rowNumber, + record.data.columnNumber); + if (specimens.length > 1) { + return 'red-row'; - for ( var i = 0; i < data.length; i++) { - var date = moment(data[i].creationDate); - var textColor = 'black'; + } + }, + listeners : { + selectionchange : function(grid, selected) { + _this.onClick.notify(record.raw); + }, + cellclick : function(grid, td, cellIndex, record, tr) { + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEditSample') { + } + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemoveSample') { + grid.getStore().removeAt(rowIndex); + _this.onRemoved.notify(); + } - if (data[i].status == "FINISHED") { - textColor = 'green'; - } - if (data[i].status == "ABORTED") { - textColor = 'red'; - } - this.events.push({ - title : data[i].name, - start : date.format("YYYY-MM-DD HH:mm:ss"), - end : date.format("YYYY-MM-DD HH:mm:ss"), - date : date, - allDay : false, - color : textColor, - className : date.format("YYYY-MM-DD") - }); - } + } + } + } + }); + return this.grid; }; -CalendarWidget.prototype.draw = function(targetId) { - var _this = this; - $('#' + targetId).fullCalendar({ - eventClick : function(calEvent, jsEvent, view) { - _this.onClick.notify(calEvent.className[0]); - - }, - contentHeight : _this.height, - header : { - left : 'prev,next today', - center : 'title', - right : 'month,basicWeek,basicDay' - }, - editable : false, - events : this.events +SpecimenGrid.prototype.input = function() { + return { + experiment : DATADOC.getExperiment_10(), + proposal : DATADOC.getProposal_10() + }; +}; + +SpecimenGrid.prototype.test = function(targetId) { + var specimenGrid = new SpecimenGrid({ + height : 400, + maxHeight : 400, + width : 1000 }); + BIOSAXS.proposal = new Proposal(specimenGrid.input().proposal); + + var experiment = new Experiment(specimenGrid.input().experiment); + var panel = specimenGrid.getPanelByExperiment(experiment); + panel.render(targetId); }; /** - * It shows a table with the guinier and gnom data as well as passed and - * discarded measurements + * Shows a list of stock solutions with macromolecule, buffer, storage temperature, concentration, shipment and comments * - * @height - * @showBufferColumns + * @multiselect allows multiple selection + * @height + * @minHeight + * @width + * @tbar + * @showTitle + * @isPackedVisible shows is stock solution is in a box + * @btnEditVisible shows edit button + * @btnAddVisible + * @btnAddExisting + * @btnUnpackVisible allows to unpack a stock solution + * @btnRemoveVisible allow to remove a stock solution */ -function ConcentrationHTMLTableWidget(args) { + +function StockSolutionGrid(args) { this.id = BUI.id(); + this.height = 100; + this.width = null; + this.minHeight = null; + this.tbar = true; - this.showBufferColumns = true; + this.title = "Stock Solutions"; + + /** Visible buttons and actions **/ + this.btnEditVisible = true; + this.btnRemoveVisible = true; + this.btnAddVisible = true; + this.btnAddExisting = false; + this.isPackedVisible = true; + this.btnUnpackVisible = false; + + /** Selectors **/ + this.multiselect = false; + this.selectedStockSolutions = []; if (args != null) { + if (args.btnUnpackVisible != null) { + this.btnUnpackVisible = args.btnUnpackVisible; + } + if (args.multiselect != null) { + this.multiselect = args.multiselect; + } if (args.height != null) { this.height = args.height; } - if (args.showBufferColumns != null) { - this.showBufferColumns = args.showBufferColumns; + if (args.btnEditVisible != null) { + this.btnEditVisible = args.btnEditVisible; + } + if (args.btnAddVisible != null) { + this.btnAddVisible = args.btnAddVisible; + } + if (args.btnAddExisting != null) { + this.btnAddExisting = args.btnAddExisting; + } + if (args.width != null) { + this.width = args.width; + } + if (args.minHeight != null) { + this.minHeight = args.minHeight; + } + if (args.tbar != null) { + this.tbar = args.tbar; + } + if (args.btnRemoveVisible != null) { + this.btnRemoveVisible = args.btnRemoveVisible; + } + if (args.isPackedVisible != null) { + this.isPackedVisible = args.isPackedVisible; + } + if (args.showTitle != null) { + this.showTitle = args.showTitle; + if (this.showTitle == false) { + this.title = null; + } } - } -} - -ConcentrationHTMLTableWidget.prototype.refresh = function(parsedData) { - document.getElementById(this.id).innerHTML = this.getPanel(parsedData); -}; - -ConcentrationHTMLTableWidget.prototype.getPanel = function(parsedData) { - var html = "
"; - html = html + ""; - /** Title * */ - html = html + ""; - html = html + ""; - if (this.showBufferColumns) { - html = html + ""; } - html = html + ""; - html = html + ""; - html = html + ""; - html = html + ""; - html = html + ""; - html = html + ""; - html = html + ""; - html = html + ""; - html = html + ""; - html = html + ""; - html = html + ""; - html = html + ""; - html = html + ""; + /** Events **/ + this.onProposalChanged = new Event(this); + this.onStockSolutionSelected = new Event(this); +} - parsedData.concentration.concentrations.sort(function(a, b) { - return a.concentration - b.concentration; - }); - /** Row * */ - for ( var i = 0; i < parsedData.concentration.concentrations.length; i++) { - var row = parsedData[i]; +StockSolutionGrid.prototype._getColumns = function() { + var _this = this; + var columns = [ - var tr = ""; - if (i % 2 == 1) { - tr = ""; + { + header : 'Macromolecule', + dataIndex : 'macromolecule', + id : _this.id + 'macromolecule', + type : 'string', + renderer : function(val, y, specimen) { + return '' + val + ''; + }, + hidden : false, + flex : 1 + }, { + header : 'Buffer', + dataIndex : 'buffer', + name : 'buffer', + hidden : false, + renderer : function(val, y, specimen) { + return '' + val + ''; + }, + type : 'string', + flex : 1 + }, { + header : 'Acronym', + dataIndex : 'name', + name : 'name', + type : 'string', + flex : 1, + hidden : true + }, { + header : 'Storage Temp.', + dataIndex : 'storageTemperature', + name : 'storageTemperature', + type : 'string', + flex : 1, + hidden : false, + renderer : function(val) { + return BUI.formatValuesUnits(val, 'C', { + fontSize : 12, + decimals : 2, + unitsFontSize : 10 + }); } - var goodMeasurements = (parsedData.concentration.concentrations[i].frames.length - parsedData.concentration.concentrations[i].frames_warning); - if (goodMeasurements == 0) { - tr = ""; + }, { + header : 'Volume', + dataIndex : 'volume', + type : 'string', + flex : 1, + hidden : false, + renderer : function(val) { + return BUI.formatValuesUnits(val, 'µl', { + fontSize : 12, + decimals : 2, + unitsFontSize : 10 + }); } - html = html + tr; - html = html + ""; - if (this.showBufferColumns) { - html = html + ""; + }, { + header : 'Concentration', + dataIndex : 'concentration', + name : 'concentration', + type : 'string', + flex : 1, + renderer : function(val) { + return BUI.formatValuesUnits(val, 'mg/ml', { + fontSize : 12, + decimals : 2, + unitsFontSize : 10 + }); } - html = html + ""; - html = html + ""; - html = html + ""; - html = html + ""; - html = html + ""; - html = html + ""; - html = html + ""; - html = html + ""; + }, { + header : 'Packed', + dataIndex : 'comments', + id : _this.id + "box", + type : 'string', + width : 50, + hidden : !this.isPackedVisible, + renderer : function(val, cmp, a) { + if (a.raw.boxId != null) { + return "
"; + } + + } + }, { + header : 'Comments', + dataIndex : 'comments', + type : 'string', + flex : 1 + } ]; + + if (this.btnEditVisible) { + columns.push({ + id : _this.id + 'buttonEdit', + width : 85, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + if (_this.btnEditVisible) { + return BUI.getGreenButton('EDIT'); + } + } + }); + } + + if (this.btnRemoveVisible) { + columns.push({ + id : _this.id + 'buttonRemove', + width : 85, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + if (_this.btnRemoveVisible) { + return BUI.getRedButton('REMOVE'); + } + } + }); } - return html + "
ConcentrationBufferMeasurementsGuinierGnom
PassedDiscardedRgI0QualityRgdMax
" + parsedData.concentration.concentrations[i].concentration + "" + parsedData.concentration.concentrations[i].bufferAcronym + "" + goodMeasurements + " of " + parsedData.concentration.concentrations[i].frames.length + "" + parsedData.concentration.concentrations[i].frames_warning + "" + BUI.formatValuesErrorUnits(parsedData.concentration.concentrations[i].calculation.rgGuinier.avg, parsedData.concentration.concentrations[i].calculation.rgGuinier.std, "nm", { - lineBreak : false - }) + "" + BUI.formatValuesErrorUnits(parsedData.concentration.concentrations[i].calculation.i0Guinier.avg, parsedData.concentration.concentrations[i].calculation.i0Guinier.std, " ", { - lineBreak : false - }) + "" + BUI.formatValuesErrorUnits(parsedData.concentration.concentrations[i].calculation.quality.avg, parsedData.concentration.concentrations[i].calculation.quality.std, " ", { - lineBreak : false - }) + "" + BUI.formatValuesErrorUnits(parsedData.concentration.concentrations[i].calculation.rgGnom.avg, parsedData.concentration.concentrations[i].calculation.rgGnom.std, " ", { - lineBreak : false - }) + "" + BUI.formatValuesErrorUnits(parsedData.concentration.concentrations[i].calculation.dMax.avg, parsedData.concentration.concentrations[i].calculation.dMax.std, " ", { - lineBreak : false - }) + "
"; + + if (this.btnUnpackVisible) { + columns.push({ + id : _this.id + 'buttonUnpack', + width : 85, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + if (_this.btnUnpackVisible) { + return BUI.getBlueButton('UNPACK'); + } + } + }); + } + return columns; }; -ConcentrationHTMLTableWidget.prototype.input = function() { - return { - data : { - "dataCollectionCount" : 4, - "buffers" : [ { - "bufferId" : "422" - } ], - "concentration" : { - "concentrations" : [ { - "concentration" : "7.17", - "id" : "7.1699999999999999", - "bufferId" : "422.00", - "bufferAcronym" : "B1", - "rgGuinier" : [ "5.12723" ], - "frames" : [ { - "total" : "0.515705406286", - "bufferBeforeMeasurementId" : 15045, - "sampleMergeId" : 8176, - "averagedModelId" : null, - "I0" : "183.457461646", - "proposalCode" : "OPD", - "averagedModel" : null, - "bufferAfterMergeId" : 8177, - "framesCount" : "10", - "bufferBeforeMergeId" : 8175, - "averageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_065_ave.dat", - "bufferAfterMeasurementId" : 15048, - "rgGuinier" : "5.12723", - "subtractedFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_065_sub.dat", - "firstPointUsed" : "17", - "chi2RgFilePath" : null, - "abInitioModelId" : null, - "macromoleculeId" : 649, - "code" : "_4.0_7.17", - "transmission" : "100.0", - "timeStart" : "2013-06-05 15:43:54.348723", - "bufferAcronym" : "B1", - "quality" : "0.853011", - "shapeDeterminationModelId" : null, - "expermientComments" : "[BsxCube] Generated from BsxCube", - "bufferId" : 422, - "isagregated" : "False", - "dmax" : "25.63615", - "bufferBeforeAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_064_ave.dat", - "exposureTemperature" : "4.0", - "subtractionId" : 3377, - "conc" : "7.1699999999999999", - "rapidShapeDeterminationModel" : null, - "experimentCreationDate" : "Jun 5, 2013 3:30:30 PM", - "lastPointUsed" : "36", - "modelListId" : null, - "framesMerge" : "9", - "rapidShapeDeterminationModelId" : null, - "bufferAfterAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_066_ave.dat", - "nsdFilePath" : null, - "bufferAfterFramesMerged" : "10", - "experimentId" : 700, - "macromoleculeAcronym" : "L9", - "i0stdev" : "0.139364435146", - "sampleMeasurementId" : 15047, - "measurementComments" : "[5]", - "priorityLevelId" : 10, - "bufferBeforeFramesMerged" : "10", - "substractionCreationTime" : "Jun 5, 2013 3:46:31 PM", - "proposalNumber" : "29", - "rgGnom" : "5.40297914939", - "volume" : "475.302", - "shapeDeterminationModel" : null, - "comments" : null, - "groupeField" : "L9 B1" - } ], - "frames_warning" : 0, - "calculation" : { - "rgGuinier" : { - "std" : 0, - "sum" : 5.12723, - "avg" : 5.12723, - "validNumber" : 1, - "totalNumber" : 1, - "values" : [ "5.12723" ] - }, - "i0Guinier" : { - "std" : 0, - "sum" : 183.457461646, - "avg" : 183.457461646, - "validNumber" : 1, - "totalNumber" : 1, - "values" : [ "183.457461646" ] - }, - "quality" : { - "std" : 0, - "sum" : 0.853011, - "avg" : 0.853011, - "validNumber" : 1, - "totalNumber" : 1, - "values" : [ "0.853011" ] - }, - "rgGnom" : { - "std" : 0, - "sum" : 5.40297914939, - "avg" : 5.40297914939, - "validNumber" : 1, - "totalNumber" : 1, - "values" : [ "5.40297914939" ] - }, - "dMax" : { - "std" : 0, - "sum" : 25.63615, - "avg" : 25.63615, - "validNumber" : 1, - "totalNumber" : 1, - "values" : [ "25.63615" ] - } - } - }, { - "concentration" : "3.53", - "id" : "3.5299999999999998", - "bufferId" : "422.00", - "bufferAcronym" : "B1", - "rgGuinier" : [ "4.38278" ], - "frames" : [ { - "total" : "0.497164741078", - "bufferBeforeMeasurementId" : 15048, - "sampleMergeId" : 8178, - "averagedModelId" : null, - "I0" : "160.023229462", - "proposalCode" : "OPD", - "averagedModel" : null, - "bufferAfterMergeId" : 8179, - "framesCount" : "10", - "bufferBeforeMergeId" : 8177, - "averageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_067_ave.dat", - "bufferAfterMeasurementId" : 15051, - "rgGuinier" : "4.38278", - "subtractedFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_067_sub.dat", - "firstPointUsed" : "36", - "chi2RgFilePath" : null, - "abInitioModelId" : null, - "macromoleculeId" : 649, - "code" : "_4.0_3.53", - "transmission" : "100.0", - "timeStart" : "2013-06-05 15:47:04.630129", - "bufferAcronym" : "B1", - "quality" : "0.742825", - "shapeDeterminationModelId" : null, - "expermientComments" : "[BsxCube] Generated from BsxCube", - "bufferId" : 422, - "isagregated" : "False", - "dmax" : "15.33973", - "bufferBeforeAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_066_ave.dat", - "exposureTemperature" : "4.0", - "subtractionId" : 3378, - "conc" : "3.5299999999999998", - "rapidShapeDeterminationModel" : null, - "experimentCreationDate" : "Jun 5, 2013 3:30:30 PM", - "lastPointUsed" : "61", - "modelListId" : null, - "framesMerge" : "10", - "rapidShapeDeterminationModelId" : null, - "bufferAfterAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_068_ave.dat", - "nsdFilePath" : null, - "bufferAfterFramesMerged" : "10", - "experimentId" : 700, - "macromoleculeAcronym" : "L9", - "i0stdev" : "0.1499898017", - "sampleMeasurementId" : 15050, - "measurementComments" : "[6]", - "priorityLevelId" : 12, - "bufferBeforeFramesMerged" : "10", - "substractionCreationTime" : "Jun 5, 2013 3:49:42 PM", - "proposalNumber" : "29", - "rgGnom" : "4.40615474861", - "volume" : "372.656", - "shapeDeterminationModel" : null, - "comments" : null, - "groupeField" : "L9 B1" - } ], - "frames_warning" : 0, - "calculation" : { - "rgGuinier" : { - "std" : 0, - "sum" : 4.38278, - "avg" : 4.38278, - "validNumber" : 1, - "totalNumber" : 1, - "values" : [ "4.38278" ] - }, - "i0Guinier" : { - "std" : 0, - "sum" : 160.023229462, - "avg" : 160.023229462, - "validNumber" : 1, - "totalNumber" : 1, - "values" : [ "160.023229462" ] - }, - "quality" : { - "std" : 0, - "sum" : 0.742825, - "avg" : 0.742825, - "validNumber" : 1, - "totalNumber" : 1, - "values" : [ "0.742825" ] - }, - "rgGnom" : { - "std" : 0, - "sum" : 4.40615474861, - "avg" : 4.40615474861, - "validNumber" : 1, - "totalNumber" : 1, - "values" : [ "4.40615474861" ] - }, - "dMax" : { - "std" : 0, - "sum" : 15.33973, - "avg" : 15.33973, - "validNumber" : 1, - "totalNumber" : 1, - "values" : [ "15.33973" ] +StockSolutionGrid.prototype._getTopButtons = function() { + var _this = this; + /** Actions buttons **/ + var actions = []; + + /** ADD BUTTON **/ + if (this.btnAddVisible) { + actions.push(Ext.create('Ext.Action', { + icon : '../images/add.png', + text : 'Add Stock Solution', + tooltip : 'Will create a new stock solution', + disabled : false, + alwaysEnabled : true, + handler : function(widget, event) { + _this.edit(); + } + })); + } + + if (this.btnAddExisting) { + actions.push(Ext.create('Ext.Action', { + icon : '../images/add.png', + text : 'Add Existing', + tooltip : 'Allows to select upacked stock solutions', + disabled : false, + alwaysEnabled : true, + handler : function(widget, event) { + var stockSolutionGrid = new StockSolutionGrid({ + btnAddVisible : false, + btnEditVisible : false, + btnRemoveVisible : false, + btnAddExisting : false, + isPackedVisible : true, + multiselect : true + }); + + var window = Ext.create('Ext.window.Window', { + title : 'Select', + height : 400, + width : 800, + layout : 'fit', + items : [ stockSolutionGrid.getPanel() ], + buttons : [ { + text : 'Pack', + handler : function() { + _this.onStockSolutionSelected.notify(stockSolutionGrid.selectedStockSolutions); + window.close(); + } + }, { + text : 'Cancel', + handler : function() { + window.close(); } + } ] + + }).show(); + + stockSolutionGrid.refresh(BIOSAXS.proposal.getUnpackedStockSolutions()); + } + })); + } + + return actions; +}; + +StockSolutionGrid.prototype.refresh = function(stockSolutions) { + this.features = stockSolutions; + this.store.loadData(this._prepareData(), false); +}; + +StockSolutionGrid.prototype._prepareData = function() { + var data = []; + for ( var i = 0; i < this.features.length; i++) { + var stockSolution = this.features[i]; + stockSolution.buffer = BIOSAXS.proposal.getBufferById(stockSolution.bufferId).acronym; + if (stockSolution.macromoleculeId != null) { + stockSolution.macromolecule = BIOSAXS.proposal.getMacromoleculeById(stockSolution.macromoleculeId).acronym; + } + data.push(stockSolution); + } + return data; +}; + +StockSolutionGrid.prototype.getPanel = function() { + return this._renderGrid(); +}; + +StockSolutionGrid.prototype.edit = function(stockSolutionId) { + var _this = this; + var stockSolutionWindow = new StockSolutionWindow(); + /** On stock solution SAVED **/ + stockSolutionWindow.onSaved.attach(function(sender, stockSolution) { + _this.onProposalChanged.notify(stockSolution); + }); + stockSolutionWindow.draw(BIOSAXS.proposal.getStockSolutionById(stockSolutionId)); +}; + +StockSolutionGrid.prototype._getStoreFields = function() { + return [ { + name : 'name', + type : 'string' + }, { + name : 'stockSolutionId', + type : 'string' + }, { + name : 'macromolecule', + type : 'string' + }, { + name : 'buffer', + type : 'string' + }, { + name : 'storageTemperature', + type : 'numeric' + }, { + name : 'volume', + type : 'string' + }, { + name : 'concentration', + type : 'string' + }, { + name : 'buffer', + type : 'string' + }, { + name : 'comments', + type : 'string' + } ]; +}; + +//StockSolutionGrid.prototype.refresh = function() { +// this.proposal.onInitialized.attach(function(sender){ +// +// }); +// this.proposal.init(Ext.urlDecode(window.location.href).sessionId); +//}; + +StockSolutionGrid.prototype._renderGrid = function() { + var _this = this; + + /** Store **/ + this.store = Ext.create('Ext.data.Store', { + fields : this._getStoreFields(), //columns, + autoload : true + }); + + var filters = { + ftype : 'filters', + local : true, + filters : this.filters + }; + + var selModel = null; + + if (this.multiselect) { + selModel = Ext.create('Ext.selection.CheckboxModel', { + //multiSelect : false,//this.multiselect, + mode : 'SINGLE', + listeners : { + selectionchange : function(sm, selections) { + _this.selectedStockSolutions = []; + for ( var i = 0; i < selections.length; i++) { + _this.selectedStockSolutions.push(selections[i].raw); } - }, { - "concentration" : "1.75", - "id" : "1.75", - "bufferId" : "422.00", - "bufferAcronym" : "B1", - "rgGuinier" : [], - "frames" : [ { - "total" : "0.5538035065", - "bufferBeforeMeasurementId" : 15051, - "sampleMergeId" : 8180, - "averagedModelId" : null, - "I0" : "146.927428571", - "proposalCode" : "OPD", - "averagedModel" : null, - "bufferAfterMergeId" : 8181, - "framesCount" : "10", - "bufferBeforeMergeId" : 8179, - "averageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_069_ave.dat", - "bufferAfterMeasurementId" : 15054, - "rgGuinier" : "4.27139", - "subtractedFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_069_sub.dat", - "firstPointUsed" : "33", - "chi2RgFilePath" : null, - "abInitioModelId" : null, - "macromoleculeId" : 649, - "code" : "_4.0_1.75", - "transmission" : "100.0", - "timeStart" : "2013-06-05 15:50:09.395824", - "bufferAcronym" : "B1", - "quality" : "0.765999", - "shapeDeterminationModelId" : null, - "expermientComments" : "[BsxCube] Generated from BsxCube", - "bufferId" : 422, - "isagregated" : "False", - "dmax" : "14.949865", - "bufferBeforeAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_068_ave.dat", - "exposureTemperature" : "4.0", - "subtractionId" : 3379, - "conc" : "1.75", - "rapidShapeDeterminationModel" : null, - "experimentCreationDate" : "Jun 5, 2013 3:30:30 PM", - "lastPointUsed" : "62", - "modelListId" : null, - "framesMerge" : "6", - "rapidShapeDeterminationModelId" : null, - "bufferAfterAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_070_ave.dat", - "nsdFilePath" : null, - "bufferAfterFramesMerged" : "10", - "experimentId" : 700, - "macromoleculeAcronym" : "L9", - "i0stdev" : "0.191914285714", - "sampleMeasurementId" : 15053, - "measurementComments" : "[7]", - "priorityLevelId" : 14, - "bufferBeforeFramesMerged" : "10", - "substractionCreationTime" : "Jun 5, 2013 3:52:31 PM", - "proposalNumber" : "29", - "rgGnom" : "4.28379338749", - "volume" : "356.326", - "shapeDeterminationModel" : null, - "comments" : null, - "groupeField" : "L9 B1" - } ], - "frames_warning" : 1, - "calculation" : { - "rgGuinier" : { - "std" : null, - "sum" : 0, - "avg" : 0, - "validNumber" : 0, - "totalNumber" : 0, - "values" : [] - }, - "i0Guinier" : { - "std" : null, - "sum" : 0, - "avg" : 0, - "validNumber" : 0, - "totalNumber" : 0, - "values" : [] - }, - "quality" : { - "std" : null, - "sum" : 0, - "avg" : 0, - "validNumber" : 0, - "totalNumber" : 0, - "values" : [] - }, - "rgGnom" : { - "std" : null, - "sum" : 0, - "avg" : 0, - "validNumber" : 0, - "totalNumber" : 0, - "values" : [] - }, - "dMax" : { - "std" : null, - "sum" : 0, - "avg" : 0, - "validNumber" : 0, - "totalNumber" : 0, - "values" : [] + } + } + }); + } else { + selModel = { + mode : 'SINGLE' + }; + } + + this.store.sort("stockSolutionId", "desc"); + + this.grid = Ext.create('Ext.grid.Panel', { + style : { + padding : 5 + }, + icon : '/ispyb/images/SampleHolder_24x24_01.png', + title : this.title, + height : this.height, + width : this.width, + minWidth : this.minWidth, + selModel : selModel, + store : this.store, + columns : this._getColumns(), + viewConfig : { + stripeRows : true, + listeners : { + itemdblclick : function(dataview, record, item, e) { + _this.edit(record.raw.stockSolutionId); + }, + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + var adapter = null; + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonUnpack') { + _this.grid.setLoading("ISPyB: Unpacking stock solution"); + adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender) { + _this.onProposalChanged.notify(); + _this.grid.setLoading(false); + }); + adapter.onError.attach(function(sender) { + _this.onProposalChanged.notify(); + _this.grid.setLoading(false); + }); + record.raw.boxId = null; + adapter.saveStockSolution(record.raw); + } + + if (grid.getGridColumns()[cellIndex].getId() == _this.id + "box") { + window.location = BUI.getShippingURL(BIOSAXS.proposal.getShipmentByDewarId(record.raw.boxId).shippingId); + } + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonEdit') { + _this.edit(record.data.stockSolutionId); + } + + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonRemove') { + _this.grid.setLoading("ISPyB: Removing stock solution"); + adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender) { + _this.onProposalChanged.notify(); + _this.grid.setLoading(false); + }); + adapter.onError.attach(function(sender) { + _this.onProposalChanged.notify(); + _this.grid.setLoading(false); + }); + adapter.removeStockSolution(record.data.stockSolutionId); + } + } + } + } + + }); + + var actions = _this._getTopButtons(); + this.grid.addDocked({ + xtype : 'toolbar', + items : actions + }); + + var i = null; + this.grid.getSelectionModel().on({ + selectionchange : function(sm, selections) { + if (selections.length) { + for ( i = 0; i < actions.length; i++) { + if (actions[i].enable) { + actions[i].enable(); + } + } + } else { + for ( i = 0; i < actions.length; i++) { + if (actions[i].alwaysEnabled == false) { + if (actions[i].disable) { + actions[i].disable(); + } + } + } + } + } + }); + return this.grid; +}; + +StockSolutionGrid.prototype.input = function() { + return { + proposal : DATADOC.getProposal_10() + }; +}; + +StockSolutionGrid.prototype.test = function(targetId) { + var stockSolutionGrid = new StockSolutionGrid({ + height : 300, + width : 900 + }); + BIOSAXS.proposal = new Proposal(stockSolutionGrid.input().proposal); + var panel = stockSolutionGrid.getPanel(); + stockSolutionGrid.refresh(BIOSAXS.proposal.getStockSolutions()); + panel.render(targetId); +}; + + +function SuperpositionGrid(args) { + this.height = null; + this.width = null; + this.id = BUI.id(); + + if (args != null) { + if (args.height != null) { + this.height = args.height; + + if (args.width != null) { + this.width = args.width; + } + } + } + + this.onSelected = new Event(this); +} + +SuperpositionGrid.prototype._prepareData = function(data) { + return data; +}; + +SuperpositionGrid.prototype.refresh = function(subtractions) { + var data = []; + if (subtractions != null){ + if (subtractions.length > 0){ + for (j in subtractions){ + var subtraction = subtractions[j]; + if (subtraction.superposition3VOs != null){ + for (i in subtraction.superposition3VOs){ + data.push(subtraction.superposition3VOs[i]); + } + } + } + } + } + this.store.loadData(data); +}; + +SuperpositionGrid.prototype.getPanel = function() { + var _this = this; + this.store = Ext.create('Ext.data.Store', { + fields : [ 'abinitioModelPdbFilePath', 'aprioriPdbFilePath', 'alignedPdbFilePath' ], + data : [] + }); + + this.selModel = Ext.create('Ext.selection.RowModel', { + allowDeselect : true, + mode : 'MULTI', + listeners : { + selectionchange : function(sm, selections) { + var selected = []; + for (var i = 0; i < selections.length; i++) { + selected.push(selections[i].raw); + } + _this.onSelected.notify(selected); + } + } + }); + + this.store.sort([ { + property : 'name', + direction : 'ASC' + } ]); + + this.panel = Ext.create('Ext.grid.Panel', { + store : this.store, + selModel : this.selModel, + width : this.width, + height : this.height, + margin : 10, + deferredRender : false, + columns : [ { + text : 'Abinitio', + dataIndex : 'abinitioModelPdbFilePath', + hidden : false, + flex : 1, + renderer : function(val){ + return BUI.getFileName(val); + } + }, { + text : 'Apriori', + dataIndex : 'aprioriPdbFilePath', + hidden : false, + flex : 1, + renderer : function(val){ + return BUI.getFileName(val); + } + }, { + text : 'Aligned', + dataIndex : 'alignedPdbFilePath', + hidden : false, + flex : 1, + renderer : function(val){ + return BUI.getFileName(val); + } + } ], + + viewConfig : { + enableTextSelection : true, + preserveScrollOnRefresh : true + }, + listeners : { + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + + }, + afterrender : function() { + } + } + }); + return this.panel; +}; + +/** + * See ExperimentGrid + * + */ +function TemplateGrid(args) { + + if (args == null) { + args = {}; + } + args.sorters = [ { + property : 'experimentId', + direction : 'DESC' + } ]; + + ExperimentGrid.prototype.constructor.call(this, args); +} + +TemplateGrid.prototype._getFilterTypes = ExperimentGrid.prototype._getFilterTypes; +TemplateGrid.prototype._prettyPrintMacromolecules = ExperimentGrid.prototype._prettyPrintMacromolecules; +TemplateGrid.prototype._getPercentage = ExperimentGrid.prototype._getPercentage; +TemplateGrid.prototype._getPercentageCollected = ExperimentGrid.prototype._getPercentageCollected; +TemplateGrid.prototype.getPercentageMerged = ExperimentGrid.prototype.getPercentageMerged; +TemplateGrid.prototype._prepareData = ExperimentGrid.prototype._prepareData; +TemplateGrid.prototype.getPanel = ExperimentGrid.prototype.getPanel; +TemplateGrid.prototype._renderGrid = ExperimentGrid.prototype._renderGrid; +TemplateGrid.prototype._editExperiment = ExperimentGrid.prototype._editExperiment; +TemplateGrid.prototype._removeExperimentById = ExperimentGrid.prototype._removeExperimentById; + +TemplateGrid.prototype._getTopButtons = function() { + /** Actions buttons * */ + var actions = []; + + actions.push(Ext.create('Ext.Action', { + icon : '../images/add.png', + text : 'Add experiment', + handler : function(widget, event) { + var wizardWidget = new WizardWidget({ + windowMode : true + }); + + wizardWidget.onFinished.attach(function(sender, result) { + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + var experiment = new Experiment(data); + BIOSAXS.openExperimentByExperiment(experiment); + wizardWidget.window.close(); + }); + wizardWidget.current.setLoading("ISPyB: Creating experiment"); + adapter.createTemplate(result.name, "comments", result.data); + }); + +// wizardWidget.draw(this.targetId, new ExperimentTypeWizardForm()); + wizardWidget.draw(this.targetId, new MeasurementCreatorStepWizardForm(BIOSAXS.proposal.getMacromolecules())); + } + })); + return actions; +}; + +TemplateGrid.prototype.refresh = function(data) { + var filtered = []; + for ( var i = 0; i < data.length; i++) { + if (data[i].experimentType == "TEMPLATE") { + filtered.push(data[i]); + } + } + this.store.loadData(this._prepareData(filtered), false); +}; + +TemplateGrid.prototype._getColumns = function() { + var _this = this; + function actionItemRenderer(value, meta, record, rowIx, ColIx, store) { + if (record.raw.buffer3VOs != null) { + if (record.raw.buffer3VOs.length > 0) { + return 'x-hide-display'; + } + } + + if (record.data.platesCount > 0) { + return 'x-hide-display'; + } + } + + return [ { + xtype : 'rownumberer', + width : 40 + }, { + text : 'experimentId', + dataIndex : 'experimentId', + name : 'experimentId', + type : 'string', + hidden : true + }, { + text : 'Name', + dataIndex : 'name', + name : 'name', + type : 'string', + flex : 1 + }, + + { + text : 'Type', + dataIndex : 'type', + name : 'type', + type : 'string', + hidden : true, + flex : 1, + renderer : function(val) { + return val; + } + }, { + text : 'Macromolecules', + name : 'macromolecules_names', + dataIndex : 'macromolecules_names', + flex : 1, + renderer : function(val) { + return " " + val + ""; + } + }, { + id : _this.id + 'GO', + width : 80, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + return BUI.getGreenButton('EDIT'); + } + }, { + id : _this.id + 'REMOVE', + width : 100, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + return BUI.getRedButton('REMOVE'); + } + } ]; +}; + +TemplateGrid.prototype.input = function() { + var experiments = DATADOC.getExperimentList_10(); + return { + experiments : experiments, + proposal : new MeasurementGrid().input().proposal + + }; +}; + +TemplateGrid.prototype.test = function(targetId) { + var experimentGrid = new TemplateGrid({ + height : 350, + minHeight : 350, + width : 1000, + gridType : 'Ext.grid.Panel', + title : 'Experiments', + grouping : false, + tbar : true + + }); + BIOSAXS.proposal = new Proposal(experimentGrid.input().proposal); + var panel = experimentGrid.getPanel(experimentGrid.input().experiments); + experimentGrid.refresh(experimentGrid.input().experiments); + panel.render(targetId); +}; + +function VolumeGrid() { + this.id = BUI.id(); +} + +VolumeGrid.prototype.getPanel = function(experiment) { + this.experiment = experiment; + return this.render(); +}; + +VolumeGrid.prototype.getVolumesPanel = function(data, title) { + var _this = this; + var store = Ext.create('Ext.data.Store', { + fields : [ 'name', 'volume', 'macromoleculeId', 'bufferId' ], + data : data + }); + store.sort([ { + property : 'name', + direction : 'ASC' + } ]); + + var grid = Ext.create('Ext.grid.Panel', { + title : title, + height : 400, + maxHeight : 400, + width : 900, + store : store, + margin : '10 0 50 10', + tbar : [ { + text : 'Go to Shipment', + icon : '../images/plane-small.gif', + handler : function() { + window.location = BUI.getCreateShipmentList(); + } + } ], + viewConfig : { + stripeRows : true, + listeners : { + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonCreate') { + var stockSolutionWindow = new StockSolutionWindow(); + /** On stock solution SAVED **/ + stockSolutionWindow.onSaved.attach(function(sender, stockSolution) { + BIOSAXS.proposal.onInitialized.attach(function(sender, data) { + _this.refresh(_this.experiment); + }); + BIOSAXS.proposal.init(); + }); + var acronym = "ST"; + if (record.raw.macromoleculeId != null) { + acronym = acronym + "_" + BIOSAXS.proposal.getMacromoleculeById(record.raw.macromoleculeId).acronym; + } + if (record.raw.bufferId != null) { + acronym = acronym + "_" + BIOSAXS.proposal.getBufferById(record.raw.bufferId).acronym; } + stockSolutionWindow.draw({ + concentration : record.raw.concentration, + macromoleculeId : record.raw.macromoleculeId, + bufferId : record.raw.bufferId, + name : acronym, + volume : record.raw.volume + }); } - }, { - "concentration" : "0.91", - "id" : "0.91000000000000003", - "bufferId" : "422.00", - "bufferAcronym" : "B1", - "rgGuinier" : [], - "frames" : [ { - "total" : null, - "bufferBeforeMeasurementId" : 15054, - "sampleMergeId" : 8182, - "averagedModelId" : null, - "I0" : "0.0", - "proposalCode" : "OPD", - "averagedModel" : null, - "bufferAfterMergeId" : 8183, - "framesCount" : "10", - "bufferBeforeMergeId" : 8181, - "averageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_071_ave.dat", - "bufferAfterMeasurementId" : 15057, - "rgGuinier" : null, - "subtractedFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_071_sub.dat", - "firstPointUsed" : "0", - "chi2RgFilePath" : null, - "abInitioModelId" : null, - "macromoleculeId" : 649, - "code" : "_4.0_.91", - "transmission" : "100.0", - "timeStart" : "2013-06-05 15:52:58.133705", - "bufferAcronym" : "B1", - "quality" : "0.0", - "shapeDeterminationModelId" : null, - "expermientComments" : "[BsxCube] Generated from BsxCube", - "bufferId" : 422, - "isagregated" : "False", - "dmax" : null, - "bufferBeforeAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_070_ave.dat", - "exposureTemperature" : "4.0", - "subtractionId" : 3380, - "conc" : "0.91000000000000003", - "rapidShapeDeterminationModel" : null, - "experimentCreationDate" : "Jun 5, 2013 3:30:30 PM", - "lastPointUsed" : "0", - "modelListId" : null, - "framesMerge" : "10", - "rapidShapeDeterminationModelId" : null, - "bufferAfterAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_072_ave.dat", - "nsdFilePath" : null, - "bufferAfterFramesMerged" : "10", - "experimentId" : 700, - "macromoleculeAcronym" : "L9", - "i0stdev" : "0.0", - "sampleMeasurementId" : 15056, - "measurementComments" : "[8]", - "priorityLevelId" : 16, - "bufferBeforeFramesMerged" : "10", - "substractionCreationTime" : "Jun 5, 2013 3:55:35 PM", - "proposalNumber" : "29", - "rgGnom" : null, - "volume" : null, - "shapeDeterminationModel" : null, - "comments" : null, - "groupeField" : "L9 B1" - } ], - "frames_warning" : 1, - "calculation" : { - "rgGuinier" : { - "std" : null, - "sum" : 0, - "avg" : 0, - "validNumber" : 0, - "totalNumber" : 0, - "values" : [] - }, - "i0Guinier" : { - "std" : null, - "sum" : 0, - "avg" : 0, - "validNumber" : 0, - "totalNumber" : 0, - "values" : [] + + if (grid.getGridColumns()[cellIndex].getId() == _this.id + 'buttonStockSolutions') { + var stockSolutionGrid = new StockSolutionGrid({ + btnAddVisible : false, + btnEditVisible : false, + btnRemoveVisible : false, + btnAddExisting : false, + isPackedVisible : true, + multiselect : false + }); + + var window = Ext.create('Ext.window.Window', { + title : 'Stock solutions by specimen', + height : 400, + width : 800, + layout : 'fit', + items : [ stockSolutionGrid.getPanel() ], + buttons : [ { + text : 'Close', + handler : function() { + window.close(); + } + } ] + + }).show(); + stockSolutionGrid.refresh(BIOSAXS.proposal.getStockSolutionsBySpecimen(record.raw.macromoleculeId, record.raw.bufferId)); + } + } + } + }, + columns : [ +// { +// text : '', +// dataIndex : 'macromoleculeId', +// width : 20, +// renderer : function(val, y, sample) { +// if (val != null) { +//// return BUI.getRectangleColorDIV(BIOSAXS.proposal.macromoleculeColors[val], 10, 10); +// return BUI.getRectangleColorDIV(_this.experiment.macromoleculeColors[val], 10, 10); +// } +// } +// }, +// { +// text : '', +// dataIndex : 'bufferId', +// width : 20, +// renderer : function(val, y, sample) { +// if (val != null) { +// return BUI.getRectangleColorDIV(_this.experiment.getSpecimenColorByBufferId(val), 10, 10); +// } +// } +// }, + { + text : 'Specimen', + dataIndex : 'name', + flex : 0.5 + }, + { + text : 'Estimated Volume', + dataIndex : 'volume', + tooltip : 'Estimation of the maximum volume needed for making this experiment', + flex : 0.5, + editor : { + allowBlank : true + }, + renderer : function(val, y, sample) { + return BUI.formatValuesUnits(sample.data.volume, 'µl', { + fontSize : 16, + decimals : 2, + unitsFontSize : this.unitsFontSize + }); + } + }, + { + text : 'Stock Solution', + id : _this.id + 'buttonStockSolutions', + dataIndex : 'name', + flex : 0.5, + tooltip : 'Stock Solutions containing this specimen in this proposal', + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + var macromoleculeId = record.raw.macromoleculeId; + var bufferId = record.raw.bufferId; + var stockSolutions = BIOSAXS.proposal.getStockSolutionsBySpecimen(macromoleculeId, bufferId); + if (stockSolutions.length > 0) { + return "
" + stockSolutions.length + " x
"; + } + + } + }, { + id : _this.id + 'buttonCreate', + text : '', + tooltip : 'Create a new stock solution for shipping', + width : 170, + sortable : false, + renderer : function(value, metaData, record, rowIndex, colIndex, store) { + return BUI.getGreenButton('NEW STOCK SOLUTION', { + width : 160 + }); + } + } ] + }); + return grid; + +}; + +VolumeGrid.prototype._prepareData = function(experiment) { + var keys = {}; + for ( var i = 0; i < experiment.getSamples().length; i++) { + var sample = experiment.getSamples()[i]; + var key = ""; + if (sample.macromoleculeId == null) { + key = experiment.getBufferById(sample.bufferId).acronym; + if (keys[key] == null) { + keys[key] = { + macromoleculeId : sample.macromoleculeId, + name : key, + bufferId : sample.bufferId, + volume : 0 + }; + } + keys[key].volume = Number(sample.volume) + Number(keys[key].volume); + } + + if ((sample.macromolecule3VO != null) || (sample.macromoleculeId != null)) { + macromoleculeId = sample.macromoleculeId; + if (sample.macromoleculeId == null) { + sample.macromoleculeId = sample.macromolecule3VO.macromoleculeId; + } + key = BIOSAXS.proposal.getMacromoleculeById(sample.macromoleculeId).acronym + " + " + experiment.getBufferById(sample.bufferId).acronym; + if (keys[key] == null) { + keys[key] = { + macromoleculeId : sample.macromoleculeId, + name : key, + bufferId : sample.bufferId, + volume : 0 + }; + } + keys[key].volume = Number(sample.volume) + Number(keys[key].volume); + } + } + var data = []; + for (var keyId in keys) { + data.push(keys[keyId]); + } + + return data; +}; + +VolumeGrid.prototype.refresh = function(experiment) { + this.experiment = experiment; + this.macromoleculeGrid.getStore().loadData(this._prepareData(this.experiment), false); +}; + +VolumeGrid.prototype.render = function() { + this.macromoleculeGrid = this.getVolumesPanel(this._prepareData(this.experiment), "Estimation of required Volume"); + + return { + xtype : 'container', + layout : 'vbox', + margin : "0, 0, 0, 5", + items : [ { + xtype : 'container', + layout : 'hbox', + margin : "0, 0, 0, 0", + items : [ this.macromoleculeGrid ] + } ] + }; +}; + +VolumeGrid.prototype.input = function(experiment) { + return { + experiment : DATADOC.getExperiment_10() + }; +}; + +VolumeGrid.prototype.test = function(targetId) { + var volumeGrid = new VolumeGrid(); + BIOSAXS.proposal = new Proposal(new MeasurementGrid().input().proposal); + var panel = volumeGrid.getPanel(new Experiment(new VolumeGrid().input().experiment)); + Ext.create('Ext.panel.Panel', { + height : 500, + width : 1000, + renderTo : targetId, + items : [ panel ] + }); +}; + +/** + * Example of a tab panel to be populated with widgets + * + * @width width in pixels + * @height height in pixels + * + * #myEvent event that this class is supposed to throw + * + **/ +function ExampleTabs(args) { + this.width = 500; + this.height = 500; + + if (args != null){ + if (args.width != null){ + this.width= args.width; + } + if (args.height != null){ + this.height= args.height; + } + } + + /** Events **/ + this.myEvent = new Event(); +} + +/** Populate the widget **/ +ExampleTabs.prototype.refresh = function(macromolecule) { + +}; + +/** It creates a tab panel with the specified with and height **/ +ExampleTabs.prototype.getPanel = function() { + this.panel = Ext.createWidget('tabpanel', { + height : this.height, + width : this.width, + style : { + padding : 2 + }, + items : [ { + tabConfig : { + title : 'Test', + icon : '/ispyb/images/plane-small.gif' + }, + items : [ { + xtype : 'container', + margin : '5 5 5 5', + items : [ ] + } ] + } ] + }); + return this.panel; +}; + + +/** + * Shows an experiments with the specimens, measurements, analysis tabs where + * results are shown and the frames widget + * + * @targetId + */ +function ExperimentTabs(targetId) { + this.height = 900; + this.targetId = targetId; + + this.id = BUI.id(); + var _this = this; + + this.INTERVAL_UPDATE = BUI.getUpdateInterval(); + + this.gridHeight = 1000; + /** data * */ + this.experiment = null; + + + /** Specimen Widget contains a specimenGrid and a sampleChangerWidget than can be displayed with are vertical or horizontal layout **/ + this.specimenWidget = new SpecimenWidget({ + height : 600 + }); + + + /** For Overview * */ + /*this.samplePlateGroupWidget = new SamplePlateGroupWidget({ + showTitle : false, + height : 250, + margin : 5, + border : 0 + + });*/ + + /** For Measurements * */ + /*this.measurementSamplePlateGroupWidget = new SamplePlateGroupWidget({ + showTitle : false, + height : 250, + margin : '5 0 0 0', + border : 0 + });*/ + + this.measurementGridDone = new MeasurementGrid({ + height : 600, + minHeight : 400, + maxHeight : 800, + positionColumnsHidden : true, + showTitle : false, + estimateTime : true, + width : 900, + maxWidth : 1500, + addBtnEnable : false, + markDone : true, + removeBtnEnabled : false + }); + this.measurementGridDone.onSelected.attach(function(sender, measurements) { + var specimens = []; + for ( var i = 0; i < measurements.length; i++) { + specimens.push(_this.experiment.getSampleById(measurements[i].specimenId)); + } + //_this.measurementSamplePlateGroupWidget.selectSpecimens(specimens); + }); + + /** AnalysisGrid * */ + this.analysisGrid = new AnalysisGrid({ + height : Ext.getBody().getViewSize().height * 0.9 - 300, + positionColumnsHidden : true, + sorters : [ { + property : 'priorityLevelId', + direction : 'ASC' + } ] + }); + + + /** Queue * */ + this.queueGrid = new QueueGrid({ + url : BUI.getQueueUrlByExperiment(), + height : Ext.getBody().getViewSize().height * 0.9 - 300, + width : Ext.getBody().getViewSize().width * 0.9 - 300, + isGrouped : true, + tbar : false, + bbar : false, + sorter : [{ + property: 'measurementId', + direction: 'DESC' + }] + }); + +} + +ExperimentTabs.prototype.error = function(error) { + var e = JSON.parse(error); + showError(e); + this.panel.setLoading(false); +}; + +ExperimentTabs.prototype.draw = function(experiment) { + this.renderDataAcquisition(experiment); +}; + +ExperimentTabs.prototype.refreshAnalysisData = function() { + var _this = this; + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + _this.analysisGrid.refresh(data, {experiment : _this.experiment}); + }); + adapter.getAnalysisInformationByExperimentId(this.experiment.experimentId); + + /** Auto load **/ + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + _this.queueGrid.refresh(data); + }); + adapter.getCompactAnalysisByExperimentId(this.experiment.experimentId); + this.queueGrid.store.proxy.url = BUI.getQueueUrlByExperiment(this.experiment.experimentId); + this.queueGrid.refresh(); +}; + +ExperimentTabs.prototype.getSpecimenContainerHeight = function(experiment) { + var maxItems = 0; + if (maxItems < experiment.getSamples().length + 1) { + maxItems = experiment.getSamples().length + 1; + } + + var height = (maxItems + 1) * 40 + 40; + if (height > 400) { + height = 400; + } + return height; +}; + +ExperimentTabs.prototype.getExperimentTitle = function() { + var experimentHeaderForm = new ExperimentHeaderForm(); + return experimentHeaderForm.getPanel(this.experiment); +}; + +ExperimentTabs.prototype.renderDataAcquisition = function(experiment) { + var _this = this; + this.experiment = experiment; + + var specimenGrid = new SpecimenGrid({ + height : 400, + maxHeight : 500, + width : 890 + }); + + specimenGrid.onClick.attach(function(sender, args) { + }); + + specimenGrid.onSelected.attach(function(sender, specimens) { + //_this.samplePlateGroupWidget.selectSpecimens(specimens); + }); + var specimenContainer = this.specimenWidget.getPanel(); + this.specimenWidget.refresh(experiment); + /* + var specimenContainer = Ext.create('Ext.container.Container', { + layout : 'hbox', + width : 900, + padding : '10 0 0 2', + items : [ specimenGrid.getPanel() ] + }); + + specimenGrid.refresh(experiment);*/ + + var experimentList = new ExperimentList([ _this.experiment ]); + var measurementContainer = Ext.create('Ext.container.Container', { + layout : 'vbox', + padding : '5px 0px 0px 10px', + items : [] + }); + measurementContainer.insert(0, _this.measurementGridDone.getPanel(this.experiment.getMeasurements(), experimentList)); +// measurementContainer.insert(1, _this.measurementSamplePlateGroupWidget.getPanel(experiment)); + + // this.dataCollectionCurveVisualizer = new DataCollectionCurveVisualizer(); + // this.dataCollectionCurveVisualizer.experiments = [experiment]; + // this.dataCollectionCurveVisualizer.dataCollectionFrameTree.experiments = + // [experiment]; + // this.dataCollectionCurveVisualizer.dataCollections = + // experiment.getDataCollections(); + + this.panel = Ext.createWidget('tabpanel', { + plain : true, + style : { + padding : 2 + }, + items : [ { + tabConfig : { + id : 'genralTabl', + title : "Overview" + }, + items : [ specimenContainer ] + }, { + tabConfig : { + title : 'Measurements' + }, + items : [ measurementContainer] + }, { + tabConfig : { + id : 'SpecimenTab', + title : 'Analysis', + hidden : this.isTemplate() + }, + items : [ { + xtype : 'container', + layout : 'vbox', + padding : '5px 0px 10px 10px', + items : [ _this.analysisGrid.getPanel([]) ] + } ] + }, + { + tabConfig : { + id : 'newAnalysisTab', + title : 'Analysis BETA', + hidden : this.isTemplate() + }, + items : [ { + xtype : 'container', + layout : 'vbox', + padding : '5px 0px 10px 10px', + items : [ _this.queueGrid.getPanel([]) ] + } ] + } + ] + }); + + return this.getPanel(this.panel); +}; + +ExperimentTabs.prototype.isTemplate = function() { + if (this.experiment.json.type == "TEMPLATE") { + return true; + } + return false; +}; + +ExperimentTabs.prototype.update = function() { + var _this = this; + var inter; + if (!_this.isTemplate()) { + function updateExperiments() { + _this.refreshAnalysisData(); + window.clearInterval(inter); + inter = setInterval(function() { + updateExperiments(); + }, _this.INTERVAL_UPDATE); + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + var experiment = new Experiment(data); + _this.measurementGridDone.refresh(experiment.getMeasurements(), new ExperimentList([ experiment ])); + }); + adapter.getExperimentById(_this.experiment.json.experimentId, "MEDIUM"); + } + inter = setInterval(function() { + updateExperiments(); + }, _this.INTERVAL_UPDATE); + } +}; + +ExperimentTabs.prototype.getPanel = function(panel) { + var _this = this; + if (this.experimentPanel == null) { + this.experimentPanel = Ext.create('Ext.container.Container', { + bodyPadding : 2, + width : Ext.getBody().getViewSize().width * 0.9, + renderTo : this.targetId, + style : { + padding : 2 + }, + items : [ this.getExperimentTitle(), this.panel ], + listeners : { + afterrender : function() { + _this.refreshAnalysisData(); + _this.update(); + } + } + }); + } + + return this.experimentPanel; +}; + +ExperimentTabs.prototype.input = function() { + return { + experiment : DATADOC.getExperiment_10(), + proposal : DATADOC.getProposal_10() + }; +}; + +ExperimentTabs.prototype.test = function(targetId) { + var experimentTabs = new ExperimentTabs(targetId); + BIOSAXS.proposal = new Proposal(experimentTabs.input().proposal); + experimentTabs.draw(new Experiment(experimentTabs.input().experiment)); +}; + + + +/** + * Shows an experiments with the specimens, measurements, analysis tabs where results are shown and the frames widget + * + * @targetId + */ +function HPLCTabs(targetId) { + this.height = 1400; + this.targetId = targetId; + + this.id = BUI.id(); + + this.gridHeight = 600; + this.pointsCount = 1036; + this.plotHeight = 350; + this.plotWidth = 800; + this.plotPanelPadding = 5; + + var _this = this; + + this.analysisGrid = new HPLCAnalysisGrid({ + height : Ext.getBody().getViewSize().height * 0.9 - 300, + positionColumnsHidden : true, + sorters : [ { + property : 'priorityLevelId', + direction : 'ASC' + } ] + }); + + this.frameGrid = new FrameGrid({ + width : 600, + height : 60, + collapsed : false, + tbar : false + }); + + this.peakGrid = new PeakGrid({ + width : 550, + height : 500, + collapsed : false, + tbar : false + }); + + this.peakGrid2 = new PeakGrid({ + width : 102, + height : this.plotHeight, + collapsed : false, + tbar : false, + showExtendedColumns : true + }); + + this.mainPlotPanel = new HPLCGraph({ + title : 'I0', + width : this.plotWidth - 110, + height : this.plotHeight, + bbar : true, + plots : { + "I0" : true, + "Rg" : true + }, + xlabel : "HPLC Frames", + scaled : true, + interactionModel : { + 'dblclick' : function(event, g, context) { + _this._selectFrame(g.lastx_); + var annotations = []; + annotations.push({ + series : g.selPoints_[0].name, + x : g.lastx_, + width : 100, + height : 23, + tickHeight : 4, + shortText : g.lastx_, + text : g.lastx_, + attachAtBottom : true + }); + g.setAnnotations(annotations); + + } + } + }); + + this.intensityPlotPanel = new MergesHPLCGraph({ + title : 'Scattering', + width : this.plotWidth, + height : 500, + showRangeSelector : false, + xParam : 0, + xlabel : "scattering_I", + plots : { + "scattering_I" : true, + "subtracted_I" : true, + "buffer_I" : true + } + }); + +} + +HPLCTabs.prototype._selectFrame = function(frameNumber) { + try{ + this._renderScatteringCurve(frameNumber); + this.frameGrid.refresh([this.mainPlotPanel.getDataByFrameNumber(frameNumber)], this.experiment.experimentId); + } + catch(e){ + console.log(e); + } +}; + +HPLCTabs.prototype.error = function(error) { + var e = JSON.parse(error); + showError(e); + this.panel.setLoading(false); +}; + +HPLCTabs.prototype.loadDataMainPlot = function(data) { + var zeroArray = []; + for ( var i = 0; i < data.I0.length; i++) { + zeroArray.push(0); + } + data = [ { + param : "I0", + data : data.I0, + std : data.I0_Stdev, + color : '#0066CC', + label : "I0" + }, + { + param : "sum_I", + label : "sum_I", + color : "#00FF00", + data : data.sum_I, + std : zeroArray + }, + { + param : "Rg", + label : "Rg", + color : "#21610B", + data : data.Rg, + std : data.Rg_Stdev + }, { + param : "Mass", + data : data.mass, + std : data.mass_Stdev, + color : '#FF9900', + label : "Mass" + }, { + param : "Vc", + data : data.Vc, + std : data.Vc_Stdev, + color : '#990099', + label : "Vc" + }, { + param : "Qr", + data : data.Qr, + std : data.Qr_Stdev, + color : '#FF0066', + label : "Qr" + }, { + param : "quality", + label : "quality", + color : "#FF00FF", + data : data.quality, + std : zeroArray + } ]; + this.data = data; + this.mainPlotPanel.loadData(data); +}; + +HPLCTabs.prototype._loadIntensityPlotByFrameNumber = function(frameNumber) { + var _this = this; + + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + var array = []; + data = [ { + param : "q", + data : data[frameNumber].q, + std : data[frameNumber].q, + fstd : function(a) { + return parseFloat(a); + }, + color : '#green', + label : "q", + showOnMenu : false + }, + { + param : "scattering_I", + data : data[frameNumber].scattering_I, + fdata : function(a) { + return Math.log(parseFloat(a)); + }, + std : data[frameNumber].scattering_Stdev, + fstd : function(a) { + return Math.log(Math.abs(parseFloat(a))); + }, + color : 'green', + label : "Log(I) Sample" + }, + { + param : "buffer_I", + data : data[frameNumber].buffer_I, + fdata : function(a) { + return Math.log(parseFloat(a)); + }, + fstd : function(a) { + return Math.log(Math.abs(parseFloat(a))); + }, + std : data[frameNumber].subtracted_Stdev, + color : '#0000FF', + label : "Log(I) Avg Buf." + }, + { + param : "subtracted_I", + data : data[frameNumber].subtracted_I, + fdata : function(a) { + var value = (Math.log(parseFloat(a))); + if (isNumber(value)) + return value; + }, + fstd : function(a) { + var value = Math.log(Math.abs(parseFloat(a))); + if (isNumber(value)) + return value; + }, + std : data[frameNumber].subtracted_Stdev, + color : 'red', + label : "Log(I) Sub." + } + ]; + + _this.intensityPlotPanel.xlabel = "Frame " + frameNumber + " (q, nm-1)"; + + if (_this.intensityPlotPanel.hplcData == null) { + /** It creates also top bar **/ + _this.intensityPlotPanel.loadData(data); + } else { + _this.intensityPlotPanel.reloadData(data); + + } + _this.intensityPlotPanel.panel.setLoading(false); + }); + adapter.onError.attach(function(sender, data) { + _this.intensityPlotPanel.panel.setLoading(false); + }); + this.intensityPlotPanel.panel.setLoading("Retrieving Frame " + frameNumber); + adapter.getH5FrameScattering(this.experiment.json.experimentId, frameNumber); +}; + +HPLCTabs.prototype._renderScatteringCurve = function(frameNumber) { + var _this = this; + + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + _this.intensityPlotPanel.setPeaks(data); + _this._loadIntensityPlotByFrameNumber(frameNumber); + try{ + var peaks = []; + for(key in data){ + peaks.push({ + start : key.split("-")[0], + end : key.split("-")[1], + experimentId : _this.experiment.json.experimentId + }); + } + _this.peakGrid2.refresh(JSON.parse(JSON.stringify(peaks))); + _this.peakGrid.refresh(peaks); +// console.log(peaks); + } + catch(e){ + showError(e); + } + }); + adapter.onError.attach(function(sender, data) { + _this.intensityPlotPanel.setLoading(false); + }); + this.intensityPlotPanel.panel.setLoading("Reading HDF5 File "); + adapter.getH5FramesMerge(this.experiment.json.experimentId); +}; + +HPLCTabs.prototype._postRenderOverviewPanel = function() { + var _this = this; + var adapter = new BiosaxsDataAdapter(); + adapter.onError.attach(function(sender, data) { + data = data.replace(/NaN/g, '0'); + _this.loadDataMainPlot(JSON.parse(data)); + + + }); + adapter.onSuccess.attach(function(sender, data) { + _this.loadDataMainPlot(data); + _this._renderScatteringCurve(0); + }); + adapter.getH5fileParameters(this.experiment.json.experimentId, [ + "I0", "I0_Stdev", "sum_I","Rg", "Rg_Stdev", "Vc", "Vc_Stdev", "Qr", "Qr_Stdev", "mass", "mass_Stdev", "quality" ]); + +}; + +HPLCTabs.prototype._postRenderDetailsPanel = function() { + if (this.data != null) { + this.I0PlotPanel.loadData(this.data); + this.RgPlotPanel.loadData(this.data); + this.MassPlotPanel.loadData(this.data); + this.VcPlotPanel.loadData(this.data); + } + +}; + +HPLCTabs.prototype.draw = function(experiment) { + var _this = this; + this.renderDataAcquisition(experiment); +}; + +HPLCTabs.prototype.getExperimentTitle = function() { + var experimentHeaderForm = new ExperimentHeaderForm(); + return experimentHeaderForm.getPanel(this.experiment); +}; + +HPLCTabs.prototype.renderDataAcquisition = function(experiment) { + var _this = this; + this.experiment = experiment; + if (this.experimentPanel == null) { + this.experimentPanel = Ext.create('Ext.container.Container', { + bodyPadding : 2, + height : this.height, + width : Ext.getBody().getViewSize().width * 0.9, + renderTo : this.targetId, + style : { + padding : 2 + }, + items : [ this.getExperimentTitle(), this.getPanel() ], + listeners : { + afterrender : function() { + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + _this.analysisGrid.refresh(data); + }); + adapter.getAnalysisInformationByExperimentId(_this.experiment.experimentId); + } + } + }); + } + return this.experimentPanel; +}; + +HPLCTabs.prototype.getPanel = function() { + var _this = this; + this.panel = Ext.createWidget('tabpanel', + { + plain : true, + height : this.height, +// width : 900, + style : { + padding : 2 + }, + items : [ + { + tabConfig : { + title : "Overview" + }, - "quality" : { - "std" : null, - "sum" : 0, - "avg" : 0, - "validNumber" : 0, - "totalNumber" : 0, - "values" : [] + items : [ { + xtype : 'container', + layout : 'hbox', + border : 1, + flex : 1, + items : [ { + xtype : 'container', + layout : 'vbox', + border : 1, + items : [ { + xtype : 'container', + margin : '10px', + border : 1, + items : [ + { + xtype : 'container', + margin : '0px', + layout : 'hbox', + border : 1, + items : [ + this.peakGrid2.getPanel([]), + this.mainPlotPanel.getPanel() + ] + }, + { + xtype : 'container', + layout : 'vbox', + border : 1, + items : [ + { + html: '
Select a frame by double-clicking on the HPLC Frames plot
', + margin: 5, + border : 0 + }, + this.frameGrid.getPanel([]), + this.intensityPlotPanel.getPanel() + ] + } + + ] + }], + listeners : { + afterrender : function() { + _this._postRenderOverviewPanel(); + } + } + } ] + } ] + }, +// { +// tabConfig : { +// title : "Details" +// }, +// items : [ { +// xtype : 'container', +// layout : 'hbox', +// border : 1, +// flex : 1, +// items : [ { +// xtype : 'container', +// layout : 'vbox', +// border : 1, +// items : [ { +// xtype : 'container', +// padding : '1px', +// items : [ +// this.I0PlotPanel.getPanel(), this.RgPlotPanel.getPanel(), this.MassPlotPanel.getPanel(), +// this.VcPlotPanel.getPanel() ] +// } ], +// listeners : { +// afterrender : function() { +// _this._postRenderDetailsPanel(); +// } +// } +// } ] +// } ] +// }, + { + tabConfig : { + title : "Analysis" }, - "rgGnom" : { - "std" : null, - "sum" : 0, - "avg" : 0, - "validNumber" : 0, - "totalNumber" : 0, - "values" : [] + items : [ { + xtype : 'container', + layout : 'vbox', + padding : '5px 0px 10px 10px', + items : [ _this.analysisGrid.getPanel([]) ] + } ] + }, + { + tabConfig : { + title : "File Manager" }, - "dMax" : { - "std" : null, - "sum" : 0, - "avg" : 0, - "validNumber" : 0, - "totalNumber" : 0, - "values" : [] + items : [ { + xtype : 'container', + layout : 'vbox', + padding : '5px 0px 10px 10px', + items : [ + { + html: '
Custom Download
', + margin : '10 0 10 5', + border : 0 + }, + { + html: '
Download has been temporary disabled. Contact your labcontact if you want to extract the frames from the HDF5 file
', + margin : '10 0 10 5', + hidden : _this.experiment.experimentId == 2602, + border : 0 + }, + { + xtype : 'container', + layout : 'hbox', + margin : '0 0 0 20', + flex : 1, + items :[ + { + xtype: 'numberfield', + id: 'field_start', + fieldLabel: 'Frames from', + value: 0, + minValue: 0 + }, + { + xtype: 'numberfield', + id: 'field_end', + fieldLabel: 'to', + labelWidth : 20, + margin : '0 0 0 10', + minValue: 0 + }, + { + xtype: 'button', + /** allowing test account to download frames **/ + disabled : _this.experiment.experimentId != 2602, + text : 'Download', + margin : '0 0 0 10', + handler : function() { + var experimentId = _this.experiment.experimentId; + var start = Ext.getCmp("field_start").getValue(); + var end = Ext.getCmp("field_end").getValue(); + /** Checking if start is bigger than end **/ + if (start > end){ + var aux = end; + end = start; + start = aux; + } + var url = BUI.getZipFrameHPLCUrl(experimentId, start, end); + window.open(url) + } + } + ] + }, + _this.peakGrid.getPanel([]) + + ] + } + ] + } + ] + }); + + return this.panel; +}; + +/** + * Main form tab for macromolecule + * + * @width + * @height + * + * #onClose when user clicks on close button in the MacromoleculeForm + * #onSave when macromole is saved by macromoleculeForm + */ +function MacromoleculeTabs(args) { + this.width = 500; + this.height = 500; + + if (args != null) { + if (args.width != null) { + this.width = args.width; + } + if (args.height != null) { + this.height = args.height; + } + } + + var _this = this; + + /** Widgets **/ + + /** Macromolecule Form **/ + this.macromoleculeForm = new MacromoleculeForm({ + width : this.width - 30, + height : this.height - 50, + }); + + this.macromoleculeForm.onClose.attach(function(sender) { + _this.onClose.notify(); + }); + + this.macromoleculeForm.onSave.attach(function(sender, macromolecule) { + _this.onSave.notify(macromolecule); + }); + + this.assemblyForm = new AssemblyForm({ + width : this.width - 30, + height : this.height - 50, + }); + + this.rigibBodyModelingForm = new RigibBodyModelingForm({ + width : this.width - 30, + height : this.height - 50, + }); + + this.rigibBodyModelingForm.onSave.attach(function(sender, macromolecule) { + _this.onSave.notify(macromolecule); + }); + + + /** Events **/ + this.onClose = new Event(this); + this.onSave = new Event(this); +} + +/** Populate the widget **/ +MacromoleculeTabs.prototype.refresh = function(macromolecule) { + this.macromoleculeForm.refresh(macromolecule); + this.assemblyForm.refresh(macromolecule); + this.rigibBodyModelingForm.refresh(macromolecule); + + if (macromolecule != null){ + if (macromolecule.macromoleculeId == null){ + Ext.getCmp(this.id + "_advancedTab").disable(); + Ext.getCmp(this.id + "_assemblyTab").disable(); + } + else{ + Ext.getCmp(this.id + "_advancedTab").enable(); + Ext.getCmp(this.id + "_assemblyTab").enable(); + } + } + else{ + Ext.getCmp(this.id + "_advancedTab").disable(); + Ext.getCmp(this.id + "_assemblyTab").disable(); + } +}; + +MacromoleculeTabs.prototype.getItems = function() { + return [ { + tabConfig : { + title : 'General' + }, + items : [ { + xtype : 'container', + items : [ this.macromoleculeForm.getPanel() ] + } ] + }, { + id : this.id + "_assemblyTab", + tabConfig : { + title : 'Assembly' + }, + items : [ { + xtype : 'container', + items : [ this.assemblyForm.getPanel() ] + } ] + },{ + id : this.id + "_advancedTab", + tabConfig : { + title : 'Advanced' + }, + items : [ this.rigibBodyModelingForm.getPanel() ] + } ]; +}; + +MacromoleculeTabs.prototype.getPanel = function() { + this.panel = Ext.createWidget('tabpanel', { + height : this.height, + width : this.width, + plain : true, + margin : 5, + border : 0, + items : this.getItems() + }); + return this.panel; +}; + +function ResultTabs() { +} + +ResultTabs.prototype.draw = function(targetId, data, macromoleculeId) { + var panel = this.getPanel(targetId, data, macromoleculeId); + return Ext.create('Ext.container.Container', { + renderTo : targetId, + items : [ BUI.getMacromoleculeHeader(macromoleculeId), panel ] + }); + +}; + +ResultTabs.prototype._splitBySpecimen = function(data) { + var splitted = {}; + + for ( var i = 0; i < data.length; i++) { + var row = data[i]; + if (splitted[row.macromoleculeId + "_" + row.bufferId] == null) { + splitted[row.macromoleculeId + "_" + row.bufferId] = []; + } + splitted[row.macromoleculeId + "_" + row.bufferId].push(row); + } + return splitted; + +}; + +ResultTabs.prototype._getTabTitle = function(key, data) { + var macromoleculeId = key.split("_")[0]; + var bufferId = key.split("_")[1]; + + return BIOSAXS.proposal.getMacromoleculeById(macromoleculeId).acronym + " + " + BIOSAXS.proposal.getBufferById(bufferId).acronym + "(" + data.length + ")"; +}; + +ResultTabs.prototype.getPanel = function(targetId, data, macromoleculeId) { + + var dataFiltered = new AnalysisGrid({ + hideNulls : true, + grouped : true, + sorters : [ { + property : 'quality', + direction : 'DESC' + } ] + })._prepareData(data); + + var items = [ { + tabConfig : { + title : 'Analysis (' + dataFiltered.length + ')' + }, + items : [ { + xtype : 'container', + layout : 'vbox', + padding : 10, + items : [ new AnalysisGrid({ + isScatteringPlotVisible : false + }).getPanel(dataFiltered) ] + } ] + }, { + tabConfig : { + title : 'Concentration Effects' + }, + items : [ new ResultSummaryForm().getPanel(data) ] + } ]; + + var splitted = this._splitBySpecimen(dataFiltered); + for ( var key in splitted) { + items.push({ + tabConfig : { + title : this._getTabTitle(key, splitted[key]) + }, + items : [ new ResultSummaryForm().getPanel(splitted[key]) ] + }); + } + + this.panel = Ext.createWidget('tabpanel', { + style : { + padding : 2 + }, + items : items + }); + return this.panel; + +}; + + +function ShipmentTabs(targetId) { + this.targetId = targetId; + + var _this = this; + this.gridHeight = 500; + /** data **/ + this.shipment = null; + + /** Shipment Form **/ + this.shipmentForm = new ShipmentForm({ + creationMode : false, + showTitle : false + }); + this.shipmentForm.onSaved.attach(function(sender, data) { + _this.refresh(data); + + }); + + + /** Cases grid **/ + this.caseGrid = new CaseGrid({ + height : this.gridHeight + }); + + this.caseGrid.onAddButtonClicked.attach(function(sender, dewar) { + _this.caseGrid.grid.setLoading("ISPyB: Creating a new case"); + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, shipment) { + /** updateing shipment on proposal **/ + for ( var i = 0; i < BIOSAXS.proposal.shippings.length; i++) { + if (BIOSAXS.proposal.shippings[i].shippingId == shipment.shippingId) { + BIOSAXS.proposal.shippings[i] = shipment; + } + } + _this.refresh(shipment); + }); + adapter.onError.attach(function(sender, shipment) { + _this.caseGrid.grid.setLoading(false); + }); + adapter.addCase(_this.shipment.json.shippingId); + }); + + this.caseGrid.onRemoveButtonClicked.attach(function(sender, dewarId) { + _this.panel.setLoading("ISPyB: removing case"); + _this.shipment.onSaved.attach(function(sender, shipment) { + _this.refresh(shipment); + + }); + _this.shipment.removeCase(dewarId); + }); +} + +ShipmentTabs.prototype.refresh = function(shipment) { + + var _this = this; + this.shipment = shipment; + var proposal = new Proposal(); + proposal.onDataRetrieved.attach(function(sender, plates) { + + _this.refreshWithPlates(shipment, plates); + _this.caseGrid.grid.setLoading(false); + }); + proposal.getPlatesByProposal(); +}; + +ShipmentTabs.prototype.refreshWithPlates = function(shipment, plates) { + this.shipment = new Shipment(shipment); + + this.caseGrid.refresh(this.shipment.getDewars(), plates); + this.panel.setLoading(false); +}; + +ShipmentTabs.prototype.error = function(error) { + var e = JSON.parse(error); + showError(e); + this.panel.setLoading(false); +}; + +//ShipmentTabs.prototype.refreshTabTitles = function() { +/*Ext.getCmp("MacromoleculeTab").setText(this.getMacromoleculeTitle()); +Ext.getCmp("BufferTab").setText(this.getBuffersTitle()); +Ext.getCmp("SpecimenTab").setText(this.getSpecimenTitle()); +Ext.getCmp("PlatesTab").setText(this.getPlatesTitle()); +Ext.getCmp("AssembliesTab").setText(this.getShipmentTitle()); +Ext.getCmp("PlateGroupsTab").setText(this.getPlateGroupsTitle());*/ +//}; +ShipmentTabs.prototype.draw = function(shipment) { + var _this = this; + _this.plates = []; + _this.shipment = shipment; + _this.render(shipment); + + // var proposal = new Proposal(); + // proposal.onDataRetrieved.attach(function(sender, plates){ + // _this.plates = plates; + // _this.shipment = shipment; + // _this.render(shipment); + // + // }); + // proposal.getPlatesByProposal(); +}; + +//ShipmentTabs.prototype.getShipmentTitle = function() { +// return 'Shipment'; +//}; + +//ShipmentTabs.prototype.getMacromoleculeTitle = function() { +// return 'Macromolecules (' + this.experiment.getMacromolecules().length + ')'; +//}; + +//ShipmentTabs.prototype.getBuffersTitle = function() { +// return 'Buffers (' + this.experiment.getBuffers().length + ')'; +//}; + +//ShipmentTabs.prototype.getPlateGroupsTitle = function() { +// return 'Plate Groups (' + this.experiment.getPlateGroups().length + ')'; +//}; + +//ShipmentTabs.prototype.getSampleChangerTitle = function() { +// return 'Sample Changer'; +//}; + +//ShipmentTabs.prototype.getSpecimenTitle = function() { +// return 'Specimens(' + this.experiment.getSpecimenCount() + ')'; +//}; + +//ShipmentTabs.prototype.getPlatesTitle = function() { +// return 'Plates(' + this.experiment.getSamplePlates().length + ')'; +//}; + +//ShipmentTabs.prototype.getBuffersTip = function() { +/*if (this.experiment.getBuffers().length == 0){ + return BUI.getWarningHTML("There are no buffers. Click on add to create new ones. Click on edit button or double click to edit them"); + +} +else{ + return BUI.getTipHTML("Click on edit button or double click to edit them. Click on duplicate to create an identical buffer including its additives") +}*/ +//}; + +//ShipmentTabs.prototype.refreshTips = function() { +/*Ext.getCmp("BufferTabTip").update(this.getBuffersTip()); +Ext.getCmp("SpecimenTabTip").update(this.getSpecimensTip());*/ +//}; + +ShipmentTabs.prototype.render = function(shipment) { + return this.getPanel(shipment); +}; + +ShipmentTabs.prototype.getShipmentHeader = function(shipment) { + var _this = this; + function getHTMLSource() { + var name = shipment.json.shippingName; + var status = shipment.json.shippingStatus; + var creationDate = shipment.json.creationDate; + var html = BUI.createFormLabel("Name :", name, 75, 400); + html = html + BUI.createFormLabel("Status :", status, 75, 400); + html = html + BUI.createFormLabel("Date :", creationDate, 75, 400); + return html; + } + + return Ext.create('Ext.container.Container', { + frame : false, + layout : 'hbox', + title : 'General', + padding : 5, + bodyPadding : '5 5 0 0', + width : 890, + margin : '0 0 10 0', + height : 100, + style : { + borderColor : '#BDBDBD', + borderStyle : 'solid', + borderWidth : '1px' + }, + fieldDefaults : { + msgTarget : 'side', + labelWidth : 100 + }, + items : [ { + margin : "0 0 0 0", + width : 475, + border : 0, + html : getHTMLSource() + } + ] + }); +}; + +ShipmentTabs.prototype.getTabPanel = function(shipment) { + this.panel = Ext.createWidget('tabpanel', { + height : 600, + style : { + padding : 2 + }, + items : [ { + tabConfig : { + id : 'Shipment', + title : 'Shipment', + icon : '/ispyb/images/plane-small.gif' + }, + items : [ { + xtype : 'container', + margin : '5 5 5 5', + items : [ this.shipmentForm.getPanel(shipment) ] + } ] + }, { + tabConfig : { + id : 'Cases', + title : 'Cases', + icon : '../images/box-icon-very-small.png' + }, + items : [ { + xtype : 'container', + margin : '5 5 5 5', + items : [ this.caseGrid.getPanel(shipment.getDewars(), this.plates) ] + } ] + } ] + }); + return this.panel; +}; + +ShipmentTabs.prototype.getPanel = function(shipment) { + var _this = this; + this.shipment = shipment; + if (this.plates == null) { + this.plates = []; + } + + if (this.shipPanel == null) { + this.shipPanel = Ext.create('Ext.container.Container', { + bodyPadding : 2, + width : Ext.getBody().getViewSize().width * 0.9, + renderTo : this.targetId, + style : { + padding : 2 + }, + items : [ this.getShipmentHeader(shipment), this.getTabPanel(shipment) ] + }); + } + + return this.shipPanel; +}; + +/** + * Shows an template with the specimens, measurements and the experiment's + * requirement + * + * @targetId + */ +function TemplateTabs(targetId) { + this.height = 600; + this.targetId = targetId; + + this.id = BUI.id(); + var _this = this; + + this.gridHeight = 1000; + /** data * */ + this.experiment = null; + + this.specimenSelected = null; + + /** Specimen Widget contains a specimenGrid and a sampleChangerWidget than can be displayed with are vertical or horizontal layout **/ + this.specimenWidget = new SpecimenWidget({ + height : this.height + }); + + this.samplePlateGroupWidget = new SamplePlateGroupWidget({ + showTitle : false, + height : 250, + margin : 5, + bbar : true + }); + + this.samplePlateGroupWidget.onExperimentChanged.attach(function(sender, experiment) { + _this.refresh(experiment); + }); + + this.samplePlateGroupWidget.onClick.attach(function(sender, args) { + }); + + this.volumePlanificator = new VolumeGrid(); + + /** For Measurements * */ + var storeViscosity = Ext.create('Ext.data.Store', { + fields : [ 'name' ], + data : [ { + "name" : "low" + }, { + "name" : "medium" + }, { + "name" : "high" + } ] + }); + + // Create the combo box, attached to the states data store + var viscosityEditor = Ext.create('Ext.form.ComboBox', { + fieldLabel : '', + store : storeViscosity, + queryMode : 'local', + displayField : 'name', + valueField : 'name' + }); + + this.measurementGrid = new MeasurementGrid({ + maxWidth : 1500, + estimateTime : false, + positionColumnsHidden : true, + isPriorityColumnHidden : true, + isStatusColumnHidden : true, + isTimeColumnHidden : true, + updateRowEnabled : true, + collapsed : true, + removeBtnEnabled : true, + showTitle : false, + collapseBtnEnable : false, + addBtnMultipleEdit : true, + sortingBtnEnable : true, + editor : { + exposureTemperature : { + xtype : 'textfield', + allowBlank : true + }, + comments : { + xtype : 'textfield', + allowBlank : true + }, + volumeToLoad : { + xtype : 'numberfield', + allowBlank : true + }, + transmission : { + xtype : 'numberfield', + allowBlank : true + }, + viscosity : viscosityEditor, + waitTime : { + xtype : 'numberfield', + allowBlank : true + }, + flow : { + xtype : 'checkbox', + allowBlank : true + } + } + }); + + this.measurementGrid.onSelected.attach(function(sender, measurements) { + var specimens = []; + for ( var i = 0; i < measurements.length; i++) { + specimens.push(_this.experiment.getSampleById(measurements[i].specimenId)); + } + }); + + this.measurementGrid.onMeasurementChanged.attach(function(sender, measurement) { + _this.experiment.setMeasurement(measurement); + _this.refresh(_this.experiment); + }); + + this.measurementGrid.onExperimentChanged.attach(function(sender, json) { + _this.refresh(new Experiment(json)); + }); + + this.measurementGrid.onRemoved.attach(function(sender, experiment) { + _this.refreshSpecimen(new Experiment(experiment)); + }); + + this.measurementGrid.onUpdateTime.attach(function(sender, args) { + document.getElementById(_this.id + "_counter").innerHTML = args.hours + 'h, ' + args.minutes + 'min and ' + args.seconds + ' seconds'; + }); + +} + +TemplateTabs.prototype.refreshMeasurement = function(experiment) { + this.experiment = experiment; + this.experiment.onSaved = new Event(this); + this.experiment.onSpecimenSaved = new Event(this); + var experimentList = new ExperimentList([ this.experiment ]); + this.measurementGrid.refresh(experimentList.getMeasurementsNotCollected(), experimentList); +}; + +TemplateTabs.prototype.refreshSpecimen = function(experiment) { + this.experiment = experiment; + this.experiment.onSaved = new Event(this); + this.experiment.onSpecimenSaved = new Event(this); + this.samplePlateGroupWidget.refresh(this.experiment); + this.specimenWidget.refresh(this.experiment); + this.volumePlanificator.refresh(this.experiment); +}; + +TemplateTabs.prototype.refresh = function(experiment) { + // var start = new Date().getTime(); + this.experiment = experiment; + this.experiment.onSaved = new Event(this); + this.experiment.onSpecimenSaved = new Event(this); + + // var experimentList = new ExperimentList([this.experiment]); + this.refreshMeasurement(experiment); + this.refreshSpecimen(experiment); + /** Refreshing grids * */ + this.panel.setLoading(false); + +}; + +TemplateTabs.prototype.error = function(error) { + var e = JSON.parse(error); + showError(e); + this.panel.setLoading(false); + +}; + +TemplateTabs.prototype.draw = function(experiment) { + this.render(experiment); +}; + + +TemplateTabs.prototype.getExperimentTitle = function() { + var _this = this; + var experimentHeaderForm = new ExperimentHeaderForm(); + return experimentHeaderForm.getPanel(this.experiment); +}; + +TemplateTabs.prototype.render = function(experiment) { + var _this = this; + this.experiment = experiment; + + /** + * + * Depending on the sample Changer configuration we want to display the plates vertically or horizontally + * Default is vertical + * + * */ + + var specimenContainer = this.specimenWidget.getPanel(); + this.specimenWidget.refresh(experiment); + + var experimentList = new ExperimentList([ _this.experiment ]); + var measurementContainer = Ext.create('Ext.container.Container', { + layout : { + type : 'vbox' + }, + defaults : { + style : { + padding : '5px 0px 0px 10px' + } + }, + items : [ _this.measurementGrid.getPanel(experimentList.getMeasurementsNotCollected(), experimentList) ] + }); + + this.panel = Ext + .createWidget( + 'tabpanel', + { + plain : true, + items : [ + { + tabConfig : { + title : 'Measurements' + }, + items : [ { + xtype : 'container', + layout : 'vbox', + border : 1, +// height : _this.gridHeight, + margin : "0 0 10 0", + items : [ measurementContainer ] + } + + ] + }, + { + tabConfig : { + id : 'genralTabl', + title : "Specimens" + // width : 900, + // border : 3 + + }, + items : [ specimenContainer ] + }, + { + tabConfig : { + title : "Requirements" + + }, + items : [ + { + html : BUI.getTipHTML("Estimated volume is the maximum volume required. Depending on the order of your measurements you may use less. Click on create stock solutions if you plan to ship these stock solutions"), + margin : "10 10 10 10", + border : 0 + }, this.volumePlanificator.getPanel(experiment) ] + } ] + }); + // ); + return this.getPanel(this.panel); +}; + +TemplateTabs.prototype.isTemplate = function() { + if (this.experiment.json.type == "TEMPLATE") { + return true; + } + return false; +}; + + +TemplateTabs.prototype.getPanel = function(panel) { + var _this = this; + if (this.experimentPanel == null) { + this.experimentPanel = Ext.create('Ext.container.Container', { + bodyPadding : 2, + width : 1000,//Ext.getBody().getViewSize().width * 0.9, + renderTo : this.targetId, + height : 500, +// style : { +// padding : 2 +// }, + items : [ + this.getExperimentTitle(), + this.panel + ], + listeners : { + afterrender : function(thisCmp) { + $("#SchemeReport" + _this.experiment.experimentId).click(function() { + $(this).target = "_blank"; + window.open('viewProjectList.do?reqCode=display&menu=platescheme&experimentId=' + _this.experiment.experimentId); + return false; + }); + + } + } + }); + } + return this.experimentPanel; +}; + +TemplateTabs.prototype.input = function(targetId) { + return new ExperimentTabs().input(); +}; + +TemplateTabs.prototype.test = function(targetId) { + var experimentTabs = new TemplateTabs(targetId); + BIOSAXS.proposal = new Proposal(experimentTabs.input().proposal); + experimentTabs.draw(new Experiment(experimentTabs.input().experiment)); +}; + +var BUI = { + //interval : 60000, + interval : 40000, + rainbow : function(numOfSteps, step) { + // This function generates vibrant, "evenly spaced" colours (i.e. no clustering). This is ideal for creating easily distinguishable vibrant markers in Google Maps and other apps. + // Adam Cole, 2011-Sept-14 + // HSV to RBG adapted from: http://mjijackson.com/2008/02/rgb-to-hsl-and-rgb-to-hsv-color-model-conversion-algorithms-in-javascript + var r, g, b; + var h = step / numOfSteps; + var i = ~~(h * 6); + var f = h * 6 - i; + var q = 1 - f; + switch (i % 6) { + case 0: + r = 1, g = f, b = 0; + break; + case 1: + r = q, g = 1, b = 0; + break; + case 2: + r = 0, g = 1, b = f; + break; + case 3: + r = 0, g = q, b = 1; + break; + case 4: + r = f, g = 0, b = 1; + break; + case 5: + r = 1, g = 0, b = q; + break; + } + var c = "#" + ("00" + (~~(r * 255)).toString(16)).slice(-2) + ("00" + (~~(g * 255)).toString(16)).slice(-2) + + ("00" + (~~(b * 255)).toString(16)).slice(-2); + return (c); + }, + getFileNameByPath : function(filePath) { + if (filePath != null){ + var split = filePath.split("/"); + if (split.length > 0){ + return split[split.length - 1]; + } + } + return "Not file"; + }, + getUpdateInterval : function() { + this.interval = this.interval + 2000; + return this.interval; + }, + getRadiationDamageThreshold : function() { + return 0.7; + }, + getQualityThreshold : function() { + return 0.7; + }, + getCreateShipmentURL : function() { + return '/ispyb/user/viewProjectList.do?reqCode=display&menu=create_shipment'; + }, + getCreateShipmentList : function() { + return '/ispyb/user/viewProjectList.do?reqCode=display&menu=list_shipment'; + }, + getShippingURL : function(shippingId) { + return '/ispyb/user/viewProjectList.do?reqCode=display&menu=shipment&shippingId=' + shippingId; + }, + + getMacromoleculeResultsURLByMultipleSearch : function(array) { + return '/ispyb/user/viewProjectList.do?reqCode=display&menu=macromolecule&search=' + + JSON.stringify(array).replace(new RegExp("\"", 'g'), "'"); + }, + getMacromoleculeResultsURL : function(macromoleculeId) { + return '/ispyb/user/viewProjectList.do?reqCode=display&menu=macromolecule¯omoleculeId=' + macromoleculeId; + }, + getMacromoleculeBufferResultsURL : function(macromoleculeId, bufferId) { + return '/ispyb/user/viewProjectList.do?reqCode=display&menu=macromolecule&bufferId=' + bufferId + '¯omoleculeId=' + macromoleculeId; + }, + + getMacromoleculeHeader : function(macromoleculeId) { + + function getHTMLSource(macromoleculeId) { + if (macromoleculeId != null) { + var html = BUI.createFormLabel("Name :", BIOSAXS.proposal.getMacromoleculeById(macromoleculeId).name, 75, 400); + html = html + BUI.createFormLabel("Acronym :", BIOSAXS.proposal.getMacromoleculeById(macromoleculeId).acronym, 75, 400); + if (BIOSAXS.proposal.getMacromoleculeById(macromoleculeId).comments != null) { + html = html + BUI.createFormLabel("Comments :", BIOSAXS.proposal.getMacromoleculeById(macromoleculeId).comments, 75, 400); + } + return html; + } + } + + return Ext.create('Ext.container.Container', { + frame : false, + layout : 'hbox', + title : 'Macromolecule', + bodyPadding : '5', + width : 890, + margin : '0 0 10 0', + height : 100, + style : { + borderColor : '#BDBDBD', + borderStyle : 'solid', + borderWidth : '1px' + }, + fieldDefaults : { + msgTarget : 'side', + labelWidth : 100 + }, + items : [ { + margin : "10 0 0 10", + width : 475, + border : 0, + html : getHTMLSource(macromoleculeId) + }, { + margin : "10 0 0 10", + width : 475, + border : 0, + html : BUI.getZipHTMLByMacromoleculeId(macromoleculeId) + } + ] + }); + }, + + getZipHTMLByMacromoleculeId : function(macromoleculeId) { + if (macromoleculeId != null) { + var fileName = BIOSAXS.proposal.getMacromoleculeById(macromoleculeId).acronym; + return ""; + } + }, + getZipHTMLByExperimentId : function(experimentId, filename) { + if (filename == null){ + filename = "experiment"; + } + return ""; + }, + + getZipURLByAverageId : function(averageId, filename) { + if (filename == null){ + filename = "experiment"; + } + return "/ispyb/user/dataadapter.do?reqCode=getZipFileByAverageListId&f&mergeIdsList=" + averageId + "&fileName=" + filename; + }, + getZipURLBySubtractionId : function(subtractionId, filename) { + if (filename == null){ + filename = "experiment"; + } + return "/ispyb/user/dataadapter.do?reqCode=getZipFileByAverageListId&f&subtractionIdList=" + subtractionId + "&fileName=" + filename; + }, + + + getZipHTMLByFrameRangeId : function(experimentId, start, end) { + var fileName = "experiment"; + return ""; + }, + getZipFrameHPLCUrl : function(experimentId, start, end) { + return "/ispyb/user/dataadapter.do?reqCode=getZipFileH5ByFramesRange&f&experimentId=" + experimentId + "&start=" + Number(start) +"&end="+ Number(end); + }, + + getQueueUrl : function() { + return "/ispyb/user/dataadapter.do?reqCode=getPagingCompactAnalysisByProposalId"; + }, + + getQueueUrlByExperiment: function(experimentId) { + return "/ispyb/user/dataadapter.do?reqCode=getPagingCompactAnalysisByExperimentId&f&experimentId=" + experimentId; + }, + getStandardDeviation : function(values) { + var sum = 0; + var count = 0; + var avg = null; + + var curatedValues = new Array(); + for ( var i = 0; i < values.length; i++) { + var value = values[i]; + if (value != null) { + if (!isNaN(value)) { + count = count + 1; + sum = sum + Number(value); + curatedValues.push(Number(value)); + } + } + } + + if (count > 0) { + avg = sum / count; + } else { + avg = sum; + } + var aux = 0; + for ( var i = 0; i < curatedValues.length; i++) { + var value = curatedValues[i]; + aux = aux + Math.pow(value - avg, 2); + } + /** std **/ + var std = Math.sqrt(aux / count); + return { + std : (std), + sum : (sum), + avg : (avg), + validNumber : count, + totalNumber : values.length, + values : values + }; + }, + + getHTMLTableForFrameAveraged : function(bufferAcronym, macromoleculeAcronym, bbmerges, molmerges, bamerges, totalframes, bufferId,macromoleculeId, macromoleculeColor) { + + function getFrameSpan(framesMerged, total) { + return "(" + framesMerged + " of " + total + ")"; + } + + function getColorFrame(framesMerged, total) { + if (framesMerged / total < 0.5) { + return "#FA5858"; + } + if ((framesMerged / total >= 0.5) && (framesMerged / total < 0.8)) { + return "#FF9900"; + } + return "white"; + } + + function getRow(color, acroynm, framesMerged, totalframes) { + return " " + + BUI.getRectangleColorDIV(color, 10, 10) + + " " + acroynm + "" + + getFrameSpan(framesMerged, totalframes) + ""; + } + + var html = ""; + + /** Buffer Before **/ + if (bufferAcronym != null) { + if (bbmerges != null) { + color = BIOSAXS.proposal.bufferColors[bufferId]; + html = html + getRow(color, bufferAcronym, bbmerges, totalframes); + } + } + + /** Molecule **/ + if (macromoleculeAcronym != null) { + if (molmerges != null) { + if (macromoleculeColor == null){ + color = BIOSAXS.proposal.macromoleculeColors[macromoleculeId]; + } + else{ + color = macromoleculeColor; //BIOSAXS.proposal.macromoleculeColors[macromoleculeId]; + } + html = html + getRow(color, macromoleculeAcronym, molmerges, totalframes); + } + } + + /** Buffer After **/ + if (bufferAcronym != null) { + if (bamerges != null) { + color = BIOSAXS.proposal.bufferColors[bufferId]; + html = html + getRow(color, bufferAcronym, bamerges, totalframes); + } + } + return html + "
"; + }, + isWebGLEnabled : function(return_context) { + if (!!window.WebGLRenderingContext) { + var canvas = document.createElement("canvas"); + names = [ "webgl", "experimental-webgl", "moz-webgl", "webkit-3d" ]; + context = false; + for ( var i = 0; i < 4; i++) { + try { + context = canvas.getContext(names[i]); + if (context && typeof context.getParameter == "function") { + // WebGL is enabled + if (return_context) { + // return WebGL object if the function's argument is present + return { + name : names[i], + gl : context + }; } + // else, return just true + return true; } - } ] - }, - "concentrationLabel" : "7.17 mg/ml ,3.53 mg/ml ,1.75 mg/ml ,0.91 mg/ml " + } catch (e) { + } + } + // WebGL is supported, but disabled + return false; + } + // WebGL not supported28. + return false; + }, + getHTMLTableForPrefixes : function(bufferBeforeaverageFilePath, averageFilePath, bufferAfterAverageFilePath) { + + function getRow(bufferBeforeaverageFilePath) { + file = bufferBeforeaverageFilePath; + try { + file = bufferBeforeaverageFilePath.split("/")[bufferBeforeaverageFilePath.split("/").length - 1]; + } catch (e) { + file = "NA"; + } + return "" + file + ""; + } + var html = ""; + + /** Buffer Before **/ + if (bufferBeforeaverageFilePath != null) { + html = html + getRow(bufferBeforeaverageFilePath); + } + + /** Molecule **/ + if (averageFilePath != null) { + html = html + getRow(averageFilePath); + } + + /** Buffer After **/ + if (bufferAfterAverageFilePath != null) { + html = html + getRow(bufferAfterAverageFilePath); + } + return html + "
"; + }, + + getBaseURL : function() { + return '/ispyb/user/dataadapter.do'; + }, + + getPrintcomponentURL : function(dewarId) { + return '/ispyb/user/viewDewarAction.do?reqCode=generateLabels&dewarId=' + dewarId; + + }, + getPDBVisualizerURL : function(modelId, subtractionId, experimentId) { + return '/ispyb/user/viewProjectList.do?reqCode=display&menu=PDBVisualizer&modelId=' + modelId + '&experimentId=' + experimentId + + '&subtractionId=' + subtractionId; + }, + + getURL : function() { + return this.getBaseURL() + '?reqCode=getImage'; + + }, + getAbinitioImageURL : function() { + return this.getBaseURL() + '?reqCode=getAbinitioImage'; + }, + getNSDImageURL : function(modelListId) { + return BUI.getAbinitioImageURL() + '&type=NSD&modelListId=' + modelListId; + }, + getCHI2ImageURL : function(modelListId) { + return BUI.getAbinitioImageURL() + '&type=CHI2&modelListId=' + modelListId; + }, + getModelFile : function(type, modelId, format) { + return this.getBaseURL() + '?reqCode=getModelFile' + "&type=" + type + "&modelId=" + modelId + "&format=" + format; + }, + getPdbURL : function() { + return this.getBaseURL() + '?reqCode=getPdbFiles'; + }, + getStvArray : function(value, error) { + value = Number(value); + error = Number(error); + return [ value - error, value, value + error ]; + }, + getPointArrayForDygraph : function(x, y, error) { + return [ x, BUI.getStvArray(y, error) ]; + }, + createDIV : function(text, width, className, backgroundColor) { + var nameContainer = document.createElement("div"); + var nameSpan = document.createElement("span"); + if (className != null) { + nameSpan.setAttribute("class", className); + } + if (backgroundColor != null) { + nameSpan.setAttribute("style", "float:left;width:" + width + "px;height:18px;background-color:" + backgroundColor); + } else { + nameSpan.setAttribute("style", "float:left;width:" + width + "px;height:18px;"); + } + nameSpan.appendChild(document.createTextNode(text)); + nameContainer.appendChild(nameSpan); + return nameContainer; + }, + + createFormLabel : function(labelText, text, labelWidth, textWidth, backgroundColor) { + var div = document.createElement("div"); + + div.appendChild(BUI.createDIV(labelText, labelWidth, "bLabel", backgroundColor)); + div.appendChild(BUI.createDIV(text, textWidth, "btext", backgroundColor)); + return div.innerHTML; + }, + + createTextArea : function(labelText, text, labelWidth, rows, cols) { + var div = document.createElement("div"); + div.appendChild(BUI.createDIV(labelText, labelWidth, "bLabel")); + var textArea = document.createElement("textarea"); + textArea.setAttribute("rows", rows); + textArea.setAttribute("cols", cols); + textArea.appendChild(document.createTextNode(text)); + div.appendChild(textArea); + return div.innerHTML; + }, + + showBetaWarning : function() { + alert("ISPyB for Biosaxs version Beta has not this functionality enabled"); + }, + + formatValuesErrorUnitsScientificFormat : function(val, error, unit, args) { + var fontSize = 14; + var decimals = 2; + var errorFontSize = 10; + /** line break **/ + var lineBreak = true; + if (args != null) { + if (args.fontSize != null) { + fontSize = args.fontSize; + } + if (args.decimals != null) { + decimals = args.decimals; + } + if (args.errorFontSize != null) { + errorFontSize = args.errorFontSize; + } + if (args.lineBreak != null) { + lineBreak = args.lineBreak; + } + + } + + if (val == "") { + return ""; + } + if (error == null) { + return "" + Number(val).toFixed(decimals) + ""; + } + var html = "" + Number(val).toFixed(decimals) + " " + unit + ""; + if (lineBreak) { + html = html + "
"; + } + return html + " ± " + Number(Number(error).toFixed(3)).toExponential() + + ""; + }, + + formatValuesErrorUnits : function(val, error, unit, args) { + var fontSize = 16; + var decimals = 2; + var errorFontSize = 10; + /** line break **/ + var lineBreak = true; + if (args != null) { + if (args.fontSize != null) { + fontSize = args.fontSize; + } + if (args.decimals != null) { + decimals = args.decimals; + } + if (args.errorFontSize != null) { + errorFontSize = args.errorFontSize; + } + if (args.lineBreak != null) { + lineBreak = args.lineBreak; + } + + } + + if (val == "") { + return ""; + } + if (error == null) { + return "" + Number(val).toFixed(decimals) + ""; + } + var html = "" + Number(val).toFixed(decimals) + " " + unit + ""; + if (lineBreak) { + html = html + "
"; + } + return html + " ± " + Number(Number(error).toFixed(8)).toExponential() + + ""; + }, + + formatValuesUnits : function(val, unit, args) { + var fontSize = 12; + var decimals = 2; + var unitsFontSize = 10; + if (args != null) { + if (args.fontSize != null) { + fontSize = args.fontSize; + } + if (args.decimals != null) { + decimals = args.decimals; + } + if (args.unitsFontSize != null) { + unitsFontSize = args.unitsFontSize; + } + + } + + if (val === "") { + return ""; + } + if (unit == null) { + return "" + Number(val).toFixed(decimals) + ""; + } + return "" + Number(val).toFixed(decimals) + " " + unit + ""; + }, + + getGreenButton : function(text, args) { + var width = 70; + var height = 20; + if (args != null) { + if (args.width != null) { + width = args.width; + } + if (args.height != null) { + height = args.height; + } + } + + return ''; + }, +// getBlueButton : function(text, args) { +// var width = 70; +// var height = 20; +// if (args != null) { +// if (args.width != null) { +// width = args.width; +// } +// if (args.height != null) { +// height = args.height; +// } +// } +// +// return ''; +// }, + + getBlueButton : function(text, args) { + var width = 70; + var height = 20; + var href = null; + if (args != null) { + if (args.width != null) { + width = args.width; + } + if (args.height != null) { + height = args.height; + } + if (args.href != null) { + href = args.href; + } + } + if (href != null) { + return ''; + } else { + return ''; +// return ''; + } + }, + + getSubmitGreenButton : function(text) { + return ''; + }, + + getRedButton : function(text) { + return ''; + + }, + getRectangleColorDIV : function(color, height, width) { + return '
'; + }, + + openBufferWindow : function(bufferId) { + var window = new BufferWindow(); + window.draw(tabs.experiment.getBufferById(bufferId), tabs.experiment); + }, + + /** Render for safety levels on grids **/ + safetyRenderer : function(val, y, specimen) { + var color = val; + if (val == "YELLOW") { + color = "#E9AB17"; + } + return '' + val + ''; + }, + + getSampleColor : function() { + return '#CB181D'; + }, + + getLightSampleColor : function() { + return '#FCBBA1'; + }, + + getBufferColor : function() { + return '#6A51A3'; + }, + getLightBufferColor : function() { + return '#BCBDDC'; + }, + + formatConcentration : function(val) { + if (val != null) { + return "" + Number(val).toFixed(2) + " mg/ml "; + } + return val; + }, + + formatVolume : function(sample, volume) { + if (Number(sample.data.volumeToLoad) > Number(sample.data.volume)) { + return "" + volume + " �l"; + } + if (Number(sample.data.volumeToLoad) == Number(sample.data.volume)) { + return "" + volume + " �l"; + } + return "" + volume + " �l"; + }, + + getProposal : function() { + return new Proposal(); + }, + + getSampleNameRenderer : function(val, y, record) { + var sample = record.data; + if (record.raw.macromolecule3VO == null) { + return '' + sample.code + ''; + } else { + return '' + sample.code + ''; + } + }, + + getSafetyLevels : function() { + var safetyLevels = new Array(); + safetyLevels.push({ + safetyLevelId : "", + name : "UNKNOWN" + }); + safetyLevels.push({ + safetyLevelId : 1, + name : "GREEN" + }); + safetyLevels.push({ + safetyLevelId : 2, + name : "YELLOW" + }); + safetyLevels.push({ + safetyLevelId : 3, + name : "RED" + }); + return safetyLevels; + }, + + getErrorColor : function() { + return '#F6CED8'; + }, + getWarningColor : function() { + return '#F5DA81'; + }, + getValidColor : function() { + return '#E0F8E0'; + }, + getSamplePlateLetters : function() { + return [ "A", "B", "C", "D", "E", "F", "G", "H" ]; + }, + getSamplePositionHTML : function(sample, experiment) { + var plate = ""; + var row = ""; + var column = ""; + var rows = this.getSamplePlateLetters(); + if (sample.sampleplateposition3VO != null) { + var samplePlate = experiment.getSamplePlateById(sample.sampleplateposition3VO.samplePlateId); + if (samplePlate != null) { + plate = (samplePlate.slotPositionColumn); + row = (sample.sampleplateposition3VO.rowNumber); + column = (sample.sampleplateposition3VO.columnNumber); + // var html = "Plate: " + "" + plate + ""; + // html = html + ", Row: " + "" + rows[row - 1] + ""; + // html = html + ", Column: " + "" + column + ""; + var html = "Plate: " + plate + + "-" + rows[row - 1] + "" + column + ""; + return html; + } + } + return ""; + }, + + getSafetyLabelName : function(safetyLevelId) { + var safetyLevels = BUI.getSafetyLevels(); + for ( var i = 0; i < safetyLevels.length; i++) { + if (safetyLevels[i].safetyLevelId == safetyLevelId) { + return safetyLevels[i].name; + } + } + return "UNKNOWN"; + }, + /** generate random id **/ + id : function() { + var text = ""; + var possible = "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789"; + + for ( var i = 0; i < 5; i++) + text += possible.charAt(Math.floor(Math.random() * possible.length)); + + return text; + }, + showWarning : function(message) { + Ext.Msg.show({ + title : 'Warning', + msg : message, + icon : Ext.Msg.WARNING, + animEl : 'elId' + }); + }, + showError : function(message) { + Ext.Msg.show({ + title : 'Warning', + msg : message, + icon : Ext.Msg.ERROR, + animEl : 'elId' + }); + }, + getTipHTML : function(message) { + //return "
Tip
" + // + message + "
"; + return "
Tip
" + + message + "
"; + }, + + getWarningHTML : function(message) { + return "
Warning
" + + message + "
"; + }, + + getErrorHTML : function(message) { + return "
Error
" + + message + "
"; + }, + + getProgessBar : function(percentage, text) { + /** percentage 100% green **/ + var color = "#0a0"; + + color = "#99CC00"; + if (percentage > 100) { + color = "yellow"; + percentage = 100; + } + if (isNaN(percentage)) { + color = "white"; + percentage = 0; + } + + var defaultText = percentage + "%"; + if (text != null) { + defaultText = text; + } + + return "
" + defaultText + "
"; + }, + getFileName : function(filePath){ + if (filePath != null){ + return filePath.split("/")[filePath.split("/").length - 1] + } + return ""; + } + +}; + +Ext.ux.form.RequiredCombo = Ext.extend(Ext.form.ComboBox, { + config : { + cls : 'custom-field-text-required' + }, + initComponent : function() { + Ext.ux.form.RequiredCombo.superclass.initComponent.apply(this, arguments); + }, + checkChange : function() { + if ((this.getValue() == null) || String(this.getValue()).length == 0) { + this.addCls('custom-field-text-required'); + } else { + this.removeCls('custom-field-text-required'); + } + } +}); + +Ext.define('Ext.form.field.RequiredNumber', { + extend : 'Ext.form.field.Number', + alias : 'widget.requirednumberfield', + alternateClassName : [ 'Ext.form.RequiredNumberField', 'Ext.form.RequiredNumber' ], + config : { + cls : 'custom-field-text-required' + }, + + initComponent : function() { + var me = this; + me.callParent(); + me.setMinValue(me.minValue); + me.setMaxValue(me.maxValue); + }, + + onChange : function() { + if ((this.getValue() == null) || String(this.getValue()).length == 0) { + this.addCls('custom-field-text-required'); + } else { + this.removeCls('custom-field-text-required'); + } + this.toggleSpinners(); + this.callParent(arguments); + } +}); + +Ext.define('Ext.form.field.RequiredText', { + extend : 'Ext.form.field.Text', + alias : 'widget.requiredtext', + requires : [ 'Ext.form.field.VTypes', 'Ext.layout.component.field.Text' ], + alternateClassName : [ 'Ext.form.RequiredTextField', 'Ext.form.RequiredText' ], + config : { + cls : 'custom-field-text-required' + }, + initComponent : function() { + var me = this; + if (me.allowOnlyWhitespace === false) { + me.allowBlank = false; } - }; -}; + me.callParent(); + me.addEvents( + /** + * @event autosize + * Fires when the **{@link #autoSize}** function is triggered and the field is resized according to the + * {@link #grow}/{@link #growMin}/{@link #growMax} configs as a result. This event provides a hook for the + * developer to apply additional logic at runtime to resize the field if needed. + * @param {Ext.form.field.Text} this This text field + * @param {Number} width The new field width + */ + 'autosize', -ConcentrationHTMLTableWidget.prototype.test = function(targetId) { - var concentrationHTMLTableWidget = new ConcentrationHTMLTableWidget(); - document.getElementById(targetId).innerHTML = concentrationHTMLTableWidget.getPanel(concentrationHTMLTableWidget.input().data); -}; - -function DataCollectionWidget() { + /** + * @event keydown + * Keydown input field event. This event only fires if **{@link #enableKeyEvents}** is set to true. + * @param {Ext.form.field.Text} this This text field + * @param {Ext.EventObject} e + */ + 'keydown', + /** + * @event keyup + * Keyup input field event. This event only fires if **{@link #enableKeyEvents}** is set to true. + * @param {Ext.form.field.Text} this This text field + * @param {Ext.EventObject} e + */ + 'keyup', + /** + * @event keypress + * Keypress input field event. This event only fires if **{@link #enableKeyEvents}** is set to true. + * @param {Ext.form.field.Text} this This text field + * @param {Ext.EventObject} e + */ + 'keypress'); + me.addStateEvents('change'); + me.setGrowSizePolicy(); + }, + checkChange : function() { + if ((this.getValue() == null) || String(this.getValue()).length == 0) { + this.addCls('custom-field-text-required'); + } else { + this.removeCls('custom-field-text-required'); + } + } +}); -}; +var BIOSAXS_COMBOMANAGER = { -DataCollectionWidget.prototype.refresh = function(subtractionId) { + getComboMacromoleculeByMacromolecules : function(macromolecules, args) { + var labelWidth = 150; + var margin = "0 0 5 0"; + var width = 300; -}; + if (args != null) { + if (args.labelWidth != null) { + labelWidth = args.labelWidth; + } + if (args.margin != null) { + margin = args.margin; + } + if (args.width != null) { + width = args.width; + } + } -DataCollectionWidget.prototype.getMacromolecule = function(data) { - for (var i = 0; i < data.length; i++) { - if (data[i].macromoleculeId != null) { - return BIOSAXS.proposal.getMacromoleculeById(data[i].macromoleculeId); + var store = Ext.create('Ext.data.Store', { + fields : [ 'macromoleculeId', 'acronym' ], + data : macromolecules, + sorters : [ 'acronym' ] + }); + + return Ext.create('Ext.form.ComboBox', { + fieldLabel : 'Macromolecules', + labelWidth : labelWidth, + width : width, + margin : margin, + store : store, + editable: false, + queryMode : 'local', + displayField : 'acronym', + valueField : 'macromoleculeId' + }); + }, + getComboBuffers : function(buffers, args) { + var labelWidth = 150; + var margin = "0 0 5 0"; + var width = 300; + var fieldLabel = 'Buffer'; + + if (args != null) { + if (args.labelWidth != null) { + labelWidth = args.labelWidth; + } + if (args.margin != null) { + margin = args.margin; + } + if (args.width != null) { + width = args.width; + } + if (args.noLabel != null) { + fieldLabel = null; + } } - } - return null; -}; -DataCollectionWidget.prototype.getMacromoleculeContainer = function(data) { - var macromolecule = this.getMacromolecule(data); + var store = Ext.create('Ext.data.Store', { + fields : [ 'bufferId', 'acronym' ], + data : buffers, + sorters : [ 'acronym' ] + }); - var disabled = false; - if (macromolecule == null) { - disabled = true; - } + return Ext.create('Ext.form.ComboBox', { + fieldLabel : fieldLabel, + labelWidth : labelWidth, + width : width, + margin : margin, + editable: false, + store : store, + queryMode : 'local', + displayField : 'acronym', + valueField : 'bufferId' + }); + }, + getComboSessions : function(sessions, args) { + var labelWidth = 150; + var margin = "0 0 5 0"; + var width = 300; - var acronym = (macromolecule == null ? "" : macromolecule.acronym); - var mm = (macromolecule == null ? "" : macromolecule.molecularMass); - var comments = (macromolecule == null ? "" : macromolecule.comments); + if (args != null) { + if (args.labelWidth != null) { + labelWidth = args.labelWidth; + } + if (args.margin != null) { + margin = args.margin; + } + if (args.width != null) { + width = args.width; + } + } - return Ext.create('Ext.Panel', { - width : 500, - height : 200, - disabled : disabled, - title : "Macromolecule", - layout : 'form', - bodyPadding : 5, - defaultType : 'textfield', - tbar : { - defaultButtonUI : 'default', - items : [ { - xtype : 'button', - text : 'Edit', - cls : 'btn-with-border', - handler : function() { - var macromoleculeWindow = new MacromoleculeWindow(); - macromoleculeWindow.draw(macromolecule); - /** TODO: update when save **/ - } - } ] - }, - items : [ { - fieldLabel : 'Acronym', - name : 'first', - readOnly : true, - value : acronym - }, { - fieldLabel : 'Molecular Mass', - name : 'last', - readOnly : true, - value : mm - }, { - xtype : 'textareafield', - fieldLabel : 'Comments', - value : '', - name : 'last', - readOnly : true, - value : comments - } ] - }); -}; + for ( var i = 0; i < sessions.length; i++) { + sessions[i]["startDateFormatted"] = moment(sessions[i].startDate).format("MMM Do YY"); + sessions[i]["sorter"] = moment(sessions[i].startDate).format("YYYYMMDD"); + } -DataCollectionWidget.prototype.getBufferContainer = function(data) { - var _this = this; - var buffer = BIOSAXS.proposal.getBufferById(data[0].bufferId); + var store = Ext.create('Ext.data.Store', { + fields : [ 'sessionId', 'startDateFormatted', 'beamlineName', 'startDate', 'endDate', 'beamlineOperator' ], + data : sessions, + sorters : [ 'sorter' ] + }); - return Ext.create('Ext.Panel', { - width : 500, - height : 200, - title : "Buffer", - layout : 'form', - // collapsed : true, - // collapsible : true, - bodyPadding : 5, - defaultType : 'textfield', - style : { - padding : '0px 0px 0px 2px' - }, - tbar : { - defaultButtonUI : 'default', - items : [ { - xtype : 'button', - text : 'Edit', - cls : 'btn-with-border', - handler : function() { - var bufferWindow = new BufferWindow(); - bufferWindow.draw(BIOSAXS.proposal.getBufferById(data[0].bufferId)); - /** TODO: update when save **/ - } + return Ext.create('Ext.form.ComboBox', { + fieldLabel : 'Sessions', + labelWidth : labelWidth, + width : width, + margin : margin, + store : store, + queryMode : 'local', + // displayField : 'startDate', + valueField : 'sessionId', + // Template for the dropdown menu. + // Note the use of "x-boundlist-item" class, + // this is required to make the items selectable. + tpl : Ext.create('Ext.XTemplate', '', + '
{startDateFormatted} {beamlineName}
', ''), + // template for the content inside text field + displayTpl : Ext.create('Ext.XTemplate', '', '{startDateFormatted}', '') - } ] - }, - items : [ { - fieldLabel : 'Buffer', - name : 'acronym', - readOnly : true, - value : buffer.acronym - }, { - fieldLabel : 'Composition', - name : 'last', - readOnly : true, - value : buffer.composition + }); + } +}; + + function GenericWindow(args){ + this.title = "title"; + this.width = 700; + this.height = 500; + this.id = BUI.id(); + + this.close = false; + this.draggable = true; + this.modal = true; + + if (args != null){ + if (args.actions != null){ + this.actions = args.actions; + } + if (args.form != null){ + this.form = args.form; + } + if (args.width != null){ + this.width = args.width; + } + if (args.modal != null){ + this.modal = args.modal; + } + + if (args.height != null){ + this.height = args.height; + } + if (args.title != null){ + this.title = args.title; + } + if (args.form != null){ + this.form = args.form; + } + if (args.close != null){ + this.close = args.close; + } + if (args.draggable != null){ + this.draggable = args.draggable; + } + + } + /** Events **/ + this.onSaved = new Event(this); + }; + + + +GenericWindow.prototype.getButtons = function() { + var _this = this; + + if (this.close){ + return [ { + text : 'Close', + handler : function() { + _this.panel.close(); + } + } ]; + } + else{ + return [ { + text : 'Save', + handler : function() { + _this.save(); + + } }, { - xtype : 'textareafield', - fieldLabel : 'Comments', - value : buffer.comments, - name : 'last', - readOnly : true - - } ] - }); + text : 'Cancel', + handler : function() { + _this.panel.close(); + } + } ]; + } }; -DataCollectionWidget.prototype.getSpecimenContainer = function(data) { - return Ext.create('Ext.container.Container', { - layout : { - type : 'hbox' - }, - style : { - margin : '10px 10px 10px 10px' - }, - border : 0, - style : { - borderColor : '#000000', - borderStyle : 'solid', - borderWidth : '1px' - }, - defaults : { - labelWidth : 80, - // implicitly create Container by specifying xtype - xtype : 'datefield', - flex : 1, - - }, - items : [ this.getMacromoleculeContainer(data), this.getBufferContainer(data) ] - }); +GenericWindow.prototype.save = function (){ + alert("Method save of GenerciWindow class is abstract"); }; -DataCollectionWidget.prototype.getSeparator = function() { - return { - html : "
", - border : 0 - } +GenericWindow.prototype._postRender = function(data, experiment){ + }; -DataCollectionWidget.prototype.getFitStructurePanel = function(data) { - var _this = this; - - return Ext.create('Ext.container.Container', { - layout : { - type : 'hbox' - }, - style : { - margin : '10px 10px 10px 10px' - }, - border : 0, - style : { - borderColor : '#000000', - borderStyle : 'solid', - borderWidth : '1px' - }, - defaults : { - labelWidth : 80, - xtype : 'datefield', - flex : 1 - }, - items : [ - ] - }); +GenericWindow.prototype.draw = function (data, experiment){ + this._render(data, experiment); }; -DataCollectionWidget.prototype.getFitStructurePanelWorkflow = function(data) { - var _this = this; - var macromolecule = this.getMacromolecule(data); - - var items = []; +GenericWindow.prototype.refresh = function(data, experiment){ + this.data = data; + this.experiment = experiment; + this.form.refresh(data, experiment); +}; - /** Adding all the pdb files linked to the macromolecule **/ - // if (macromolecule.structure3VOs != null) { - // if (macromolecule.structure3VOs.length > 0) { - // - // items.push(); - // } - // } else { - // items.push({ - // html : "No apriori information added to this macromolecule. Apriori information needed for further analysis", - // margin : "5 5 5 5" - // }); - // } - var fitStructureToExperimentDataGrid = new FitStructureToExperimentDataGrid(); - - fitStructureToExperimentDataGrid.refresh(_this.data[0].subtractionId, _this.getMacromolecule(data)); - return Ext.create('Ext.container.Container', { - style : { - margin : '10px 10px 10px 10px' - }, - border : 0, +GenericWindow.prototype._render = function(data, experiment){ + this.data = data; + var _this = this; + if (this.panel == null){ + this.panel = Ext.create('Ext.Window', { + id : this.id, + title : this.title, + resizable : true, + constrain : true, + border : 1, + modal : this.modal, + frame : false, + draggable : this.draggable, + closable : true, + autoscroll : true, + layout : { type: 'vbox',align: 'stretch'}, + width : this.width, + height : this.form.height, + buttonAlign :'right', + buttons : this.getButtons(), + items : this.form.getPanel(data, experiment), + listeners: { + scope : this, + minimize : function(){ + this.panel.hide(); + }, + destroy : function(){ + delete this.panel; + } + } + }); + this.panel.setLoading(); + } + + this.panel.show(); + this._postRender(); +}; +function CalendarWidget(args) { + this.height = 740; - style : { - borderColor : '#000000', - borderStyle : 'solid', - borderWidth : '1px' - }, - defaults : { - labelWidth : 80, - xtype : 'datefield', - flex : 1 - }, - items : [ fitStructureToExperimentDataGrid.getPanel() ], - listeners : { - afterrender : function() { - } + if (args != null) { + if (args.height != null) { + this.height = args.height; } - }); -}; -/** Static method **/ -DataCollectionWidget.prototype.RUNFitScattering = function(subtractionId, structureId) { - var _this = this; - /** Add to Workflow **/ - var adapter = new BiosaxsDataAdapter(); - var workflow = { - 'workflowTitle' : 'FitExperimentalDatatoStructure', - 'comments' : 'FitExperimentalDatatoStructure run from ISPyB for subtractionId: ' + subtractionId + ' and structureId ' + structureId } - var inputs = [ { - name : 'subtractionId', - value : subtractionId - }, { - name : 'structureId', - value : structureId - } ]; + this.onClick = new Event(); +} - adapter.onSuccess.attach(function(sender, data) { - /** Add to Fit **/ - var adapter2 = new BiosaxsDataAdapter(); - var fit = { - 'workflowId' : data.workflowId, - 'subtractionId' : subtractionId, - 'structureId' : structureId, - 'comments' : 'Sent to workflow engine' - } - adapter2.onSuccess.attach(function(sender, fit) { +CalendarWidget.prototype.loadData = function(data) { + this.events = []; - }); - adapter2.addFitStructureData(fit); + for ( var i = 0; i < data.length; i++) { + var date = moment(data[i].creationDate); + var textColor = 'black'; - }); - adapter.addWorkflow(workflow, inputs); + if (data[i].status == "FINISHED") { + textColor = 'green'; + } + if (data[i].status == "ABORTED") { + textColor = 'red'; + } + this.events.push({ + title : data[i].name, + start : date.format("YYYY-MM-DD HH:mm:ss"), + end : date.format("YYYY-MM-DD HH:mm:ss"), + date : date, + allDay : false, + color : textColor, + className : date.format("YYYY-MM-DD") + }); + } }; -DataCollectionWidget.prototype.getSuperpositionTab = function(data) { +CalendarWidget.prototype.draw = function(targetId) { var _this = this; + $('#' + targetId).fullCalendar({ + eventClick : function(calEvent, jsEvent, view) { + _this.onClick.notify(calEvent.className[0]); - this.superpositionGrid = new SuperpositionGrid(); - - return Ext.create('Ext.container.Container', { - style : { - margin : '10px 10px 10px 10px' - }, - border : 0, - style : { - borderColor : '#000000', - borderStyle : 'solid', - borderWidth : '1px' - }, - items : [ _this.superpositionGrid.getPanel() ], - listeners : { - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { - - }, - afterrender : function() { - /** Getting Rigid bodies **/ - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, result) { - _this.superpositionGrid.refresh(result); - }); - adapter.getSuperpositionBySubtractionId(data[1].subtractionId); - } - } - }); -}; - -DataCollectionWidget.prototype.getAdvancedTab = function(data) { - var _this = this; - return Ext.create('Ext.container.Container', { - style : { - margin : '10px 10px 10px 10px' }, - border : 0, - style : { - borderColor : '#000000', - borderStyle : 'solid', - borderWidth : '1px' + contentHeight : _this.height, + header : { + left : 'prev,next today', + center : 'title', + right : 'month,basicWeek,basicDay' }, - items : [ _this.getFitStructurePanel(data), _this.getFitStructurePanelWorkflow(data) ] + editable : false, + events : this.events }); -}; - -DataCollectionWidget.prototype.getRigiBodyForm = function(data) { - var _this = this; - _this.rigiBodyGrid = new RigidModelGrid(); - return _this.rigiBodyGrid.getPanel(); }; + +/** + * It shows a table with the guinier and gnom data as well as passed and + * discarded measurements + * + * @height + * @showBufferColumns + */ +function ConcentrationHTMLTableWidget(args) { + this.id = BUI.id(); -DataCollectionWidget.prototype.getRigidBodyModelingTab = function(data) { - var _this = this; - return Ext.create('Ext.container.Container', { - style : { - margin : '10px 10px 10px 10px' - }, - border : 0, - style : { - borderColor : '#000000', - borderStyle : 'solid', - borderWidth : '1px' - }, - items : [ _this.getRigiBodyForm(data) ], - listeners : { - cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + this.showBufferColumns = true; - }, - afterrender : function() { - /** Getting Rigid bodies **/ - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, result) { - _this.rigiBodyGrid.refresh(result); - }); - adapter.getRigidBodyModelingBySubtractionId(data[1].subtractionId); - } + if (args != null) { + if (args.height != null) { + this.height = args.height; } - }); -}; - -DataCollectionWidget.prototype.getTabs = function(data) { - var _this = this; - - this.subtractionCurveVisualizer = new SubtractionCurveVisualizer(); - - this.tabs = Ext.createWidget('tabpanel', { - activeTab : 1, - plain : true, - defaults : { - autoScroll : true, - bodyPadding : 10 - }, - items : [ { - title : 'Solution', - items : [ _this.getSpecimenContainer(data) ] - }, { - title : 'Primary Data Reduction', - active : true, - tabConfig : { - xtype : 'tab', - margins : '0 0 0 20', - }, - items : [ _this.subtractionCurveVisualizer.getPanel() ] - }, { - title : 'Abinitio', - items : [ _this.getAbinitioModellingContainer(data), _this.getSeparator(), _this.getModelViz(data) ] - }, { - title : 'Mixtures', - items : [ _this.getAdvancedTab(data) ] - }, { - title : 'Superpositions', - items : [ _this.getSuperpositionTab(data) ] - }, { - title : 'Rigid Body Modeling', - items : [ _this.getRigidBodyModelingTab(data) ] - } ] - }); - return this.tabs; -}; + if (args.showBufferColumns != null) { + this.showBufferColumns = args.showBufferColumns; + } + } +} -DataCollectionWidget.prototype.getPanel = function(data) { - var _this = this; - _this.data = data; - this.panel = Ext.create('Ext.container.Container', { - width : 1000, - layout : { - type : 'vbox', - align : 'stretch', - padding : 5 - }, - items : [ _this.getTabs(data) +ConcentrationHTMLTableWidget.prototype.refresh = function(parsedData) { + document.getElementById(this.id).innerHTML = this.getPanel(parsedData); +}; - ] - }); +ConcentrationHTMLTableWidget.prototype.getPanel = function(parsedData) { + var html = "
"; + html = html + ""; - this.panel.on("afterrender", function() { - _this.subtractionCurveVisualizer.refresh([ _this.data[1].mergeId ], [ _this.data[1].subtractionId ]); - }); - return this.panel; -}; + /** Title * */ + html = html + ""; + html = html + ""; + if (this.showBufferColumns) { + html = html + ""; + } + html = html + ""; + html = html + ""; + html = html + ""; + html = html + ""; -DataCollectionWidget.prototype.getModelViz = function(data) { - this.modelViz = new ModelVisualizerForm({ - height : 800, - width : 1000 - }); - return this.modelViz.getPanel(); -}; + html = html + ""; + html = html + ""; + html = html + ""; + html = html + ""; + html = html + ""; + html = html + ""; + html = html + ""; + html = html + ""; + html = html + ""; -/** - * PRIMARY DATA PROCESSING - */ -DataCollectionWidget.prototype.getPrimaryDataProcessingContainer = function(data) { - var _this = this; - this.primaryDataProcessingGrid = new PrimaryDataProcessingGrid({ - height : 250, - width : 1000, - title : 'Primary Data Processing' + parsedData.concentration.concentrations.sort(function(a, b) { + return a.concentration - b.concentration; }); + /** Row * */ + for ( var i = 0; i < parsedData.concentration.concentrations.length; i++) { + var row = parsedData[i]; - this.primaryDataProcessingGrid.onSelected.attach(function(sender, selected) { - /** Refresh tabs **/ - var averagesId = []; - var subtractionIds = []; - - var subtractionKeys = {}; - for (var i = 0; i < selected.length; i++) { - if (selected[i].mergeId != null) { - averagesId.push(selected[i].mergeId); - } + var tr = ""; + if (i % 2 == 1) { + tr = ""; + } + var goodMeasurements = (parsedData.concentration.concentrations[i].frames.length - parsedData.concentration.concentrations[i].frames_warning); + if (goodMeasurements == 0) { + tr = ""; + } + html = html + tr; + html = html + ""; + if (this.showBufferColumns) { + html = html + ""; + } + html = html + ""; + html = html + ""; + html = html + ""; + html = html + ""; + html = html + ""; + html = html + ""; + html = html + ""; + html = html + ""; + } + return html + "
ConcentrationBufferMeasurementsGuinierGnom
PassedDiscardedRgI0QualityRgdMax
" + parsedData.concentration.concentrations[i].concentration + "" + parsedData.concentration.concentrations[i].bufferAcronym + "" + goodMeasurements + " of " + parsedData.concentration.concentrations[i].frames.length + "" + parsedData.concentration.concentrations[i].frames_warning + "" + BUI.formatValuesErrorUnits(parsedData.concentration.concentrations[i].calculation.rgGuinier.avg, parsedData.concentration.concentrations[i].calculation.rgGuinier.std, "nm", { + lineBreak : false + }) + "" + BUI.formatValuesErrorUnits(parsedData.concentration.concentrations[i].calculation.i0Guinier.avg, parsedData.concentration.concentrations[i].calculation.i0Guinier.std, " ", { + lineBreak : false + }) + "" + BUI.formatValuesErrorUnits(parsedData.concentration.concentrations[i].calculation.quality.avg, parsedData.concentration.concentrations[i].calculation.quality.std, " ", { + lineBreak : false + }) + "" + BUI.formatValuesErrorUnits(parsedData.concentration.concentrations[i].calculation.rgGnom.avg, parsedData.concentration.concentrations[i].calculation.rgGnom.std, " ", { + lineBreak : false + }) + "" + BUI.formatValuesErrorUnits(parsedData.concentration.concentrations[i].calculation.dMax.avg, parsedData.concentration.concentrations[i].calculation.dMax.std, " ", { + lineBreak : false + }) + "
"; +}; - if (selected[i].subtractionId != null) { - if (selected[i].macromoleculeId != null) { - if (subtractionKeys[selected[i].subtractionId] == null) { - subtractionIds.push(selected[i].subtractionId); +ConcentrationHTMLTableWidget.prototype.input = function() { + return { + data : { + "dataCollectionCount" : 4, + "buffers" : [ { + "bufferId" : "422" + } ], + "concentration" : { + "concentrations" : [ { + "concentration" : "7.17", + "id" : "7.1699999999999999", + "bufferId" : "422.00", + "bufferAcronym" : "B1", + "rgGuinier" : [ "5.12723" ], + "frames" : [ { + "total" : "0.515705406286", + "bufferBeforeMeasurementId" : 15045, + "sampleMergeId" : 8176, + "averagedModelId" : null, + "I0" : "183.457461646", + "proposalCode" : "OPD", + "averagedModel" : null, + "bufferAfterMergeId" : 8177, + "framesCount" : "10", + "bufferBeforeMergeId" : 8175, + "averageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_065_ave.dat", + "bufferAfterMeasurementId" : 15048, + "rgGuinier" : "5.12723", + "subtractedFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_065_sub.dat", + "firstPointUsed" : "17", + "chi2RgFilePath" : null, + "abInitioModelId" : null, + "macromoleculeId" : 649, + "code" : "_4.0_7.17", + "transmission" : "100.0", + "timeStart" : "2013-06-05 15:43:54.348723", + "bufferAcronym" : "B1", + "quality" : "0.853011", + "shapeDeterminationModelId" : null, + "expermientComments" : "[BsxCube] Generated from BsxCube", + "bufferId" : 422, + "isagregated" : "False", + "dmax" : "25.63615", + "bufferBeforeAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_064_ave.dat", + "exposureTemperature" : "4.0", + "subtractionId" : 3377, + "conc" : "7.1699999999999999", + "rapidShapeDeterminationModel" : null, + "experimentCreationDate" : "Jun 5, 2013 3:30:30 PM", + "lastPointUsed" : "36", + "modelListId" : null, + "framesMerge" : "9", + "rapidShapeDeterminationModelId" : null, + "bufferAfterAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_066_ave.dat", + "nsdFilePath" : null, + "bufferAfterFramesMerged" : "10", + "experimentId" : 700, + "macromoleculeAcronym" : "L9", + "i0stdev" : "0.139364435146", + "sampleMeasurementId" : 15047, + "measurementComments" : "[5]", + "priorityLevelId" : 10, + "bufferBeforeFramesMerged" : "10", + "substractionCreationTime" : "Jun 5, 2013 3:46:31 PM", + "proposalNumber" : "29", + "rgGnom" : "5.40297914939", + "volume" : "475.302", + "shapeDeterminationModel" : null, + "comments" : null, + "groupeField" : "L9 B1" + } ], + "frames_warning" : 0, + "calculation" : { + "rgGuinier" : { + "std" : 0, + "sum" : 5.12723, + "avg" : 5.12723, + "validNumber" : 1, + "totalNumber" : 1, + "values" : [ "5.12723" ] + }, + "i0Guinier" : { + "std" : 0, + "sum" : 183.457461646, + "avg" : 183.457461646, + "validNumber" : 1, + "totalNumber" : 1, + "values" : [ "183.457461646" ] + }, + "quality" : { + "std" : 0, + "sum" : 0.853011, + "avg" : 0.853011, + "validNumber" : 1, + "totalNumber" : 1, + "values" : [ "0.853011" ] + }, + "rgGnom" : { + "std" : 0, + "sum" : 5.40297914939, + "avg" : 5.40297914939, + "validNumber" : 1, + "totalNumber" : 1, + "values" : [ "5.40297914939" ] + }, + "dMax" : { + "std" : 0, + "sum" : 25.63615, + "avg" : 25.63615, + "validNumber" : 1, + "totalNumber" : 1, + "values" : [ "25.63615" ] + } + } + }, { + "concentration" : "3.53", + "id" : "3.5299999999999998", + "bufferId" : "422.00", + "bufferAcronym" : "B1", + "rgGuinier" : [ "4.38278" ], + "frames" : [ { + "total" : "0.497164741078", + "bufferBeforeMeasurementId" : 15048, + "sampleMergeId" : 8178, + "averagedModelId" : null, + "I0" : "160.023229462", + "proposalCode" : "OPD", + "averagedModel" : null, + "bufferAfterMergeId" : 8179, + "framesCount" : "10", + "bufferBeforeMergeId" : 8177, + "averageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_067_ave.dat", + "bufferAfterMeasurementId" : 15051, + "rgGuinier" : "4.38278", + "subtractedFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_067_sub.dat", + "firstPointUsed" : "36", + "chi2RgFilePath" : null, + "abInitioModelId" : null, + "macromoleculeId" : 649, + "code" : "_4.0_3.53", + "transmission" : "100.0", + "timeStart" : "2013-06-05 15:47:04.630129", + "bufferAcronym" : "B1", + "quality" : "0.742825", + "shapeDeterminationModelId" : null, + "expermientComments" : "[BsxCube] Generated from BsxCube", + "bufferId" : 422, + "isagregated" : "False", + "dmax" : "15.33973", + "bufferBeforeAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_066_ave.dat", + "exposureTemperature" : "4.0", + "subtractionId" : 3378, + "conc" : "3.5299999999999998", + "rapidShapeDeterminationModel" : null, + "experimentCreationDate" : "Jun 5, 2013 3:30:30 PM", + "lastPointUsed" : "61", + "modelListId" : null, + "framesMerge" : "10", + "rapidShapeDeterminationModelId" : null, + "bufferAfterAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_068_ave.dat", + "nsdFilePath" : null, + "bufferAfterFramesMerged" : "10", + "experimentId" : 700, + "macromoleculeAcronym" : "L9", + "i0stdev" : "0.1499898017", + "sampleMeasurementId" : 15050, + "measurementComments" : "[6]", + "priorityLevelId" : 12, + "bufferBeforeFramesMerged" : "10", + "substractionCreationTime" : "Jun 5, 2013 3:49:42 PM", + "proposalNumber" : "29", + "rgGnom" : "4.40615474861", + "volume" : "372.656", + "shapeDeterminationModel" : null, + "comments" : null, + "groupeField" : "L9 B1" + } ], + "frames_warning" : 0, + "calculation" : { + "rgGuinier" : { + "std" : 0, + "sum" : 4.38278, + "avg" : 4.38278, + "validNumber" : 1, + "totalNumber" : 1, + "values" : [ "4.38278" ] + }, + "i0Guinier" : { + "std" : 0, + "sum" : 160.023229462, + "avg" : 160.023229462, + "validNumber" : 1, + "totalNumber" : 1, + "values" : [ "160.023229462" ] + }, + "quality" : { + "std" : 0, + "sum" : 0.742825, + "avg" : 0.742825, + "validNumber" : 1, + "totalNumber" : 1, + "values" : [ "0.742825" ] + }, + "rgGnom" : { + "std" : 0, + "sum" : 4.40615474861, + "avg" : 4.40615474861, + "validNumber" : 1, + "totalNumber" : 1, + "values" : [ "4.40615474861" ] + }, + "dMax" : { + "std" : 0, + "sum" : 15.33973, + "avg" : 15.33973, + "validNumber" : 1, + "totalNumber" : 1, + "values" : [ "15.33973" ] + } + } + }, { + "concentration" : "1.75", + "id" : "1.75", + "bufferId" : "422.00", + "bufferAcronym" : "B1", + "rgGuinier" : [], + "frames" : [ { + "total" : "0.5538035065", + "bufferBeforeMeasurementId" : 15051, + "sampleMergeId" : 8180, + "averagedModelId" : null, + "I0" : "146.927428571", + "proposalCode" : "OPD", + "averagedModel" : null, + "bufferAfterMergeId" : 8181, + "framesCount" : "10", + "bufferBeforeMergeId" : 8179, + "averageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_069_ave.dat", + "bufferAfterMeasurementId" : 15054, + "rgGuinier" : "4.27139", + "subtractedFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_069_sub.dat", + "firstPointUsed" : "33", + "chi2RgFilePath" : null, + "abInitioModelId" : null, + "macromoleculeId" : 649, + "code" : "_4.0_1.75", + "transmission" : "100.0", + "timeStart" : "2013-06-05 15:50:09.395824", + "bufferAcronym" : "B1", + "quality" : "0.765999", + "shapeDeterminationModelId" : null, + "expermientComments" : "[BsxCube] Generated from BsxCube", + "bufferId" : 422, + "isagregated" : "False", + "dmax" : "14.949865", + "bufferBeforeAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_068_ave.dat", + "exposureTemperature" : "4.0", + "subtractionId" : 3379, + "conc" : "1.75", + "rapidShapeDeterminationModel" : null, + "experimentCreationDate" : "Jun 5, 2013 3:30:30 PM", + "lastPointUsed" : "62", + "modelListId" : null, + "framesMerge" : "6", + "rapidShapeDeterminationModelId" : null, + "bufferAfterAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_070_ave.dat", + "nsdFilePath" : null, + "bufferAfterFramesMerged" : "10", + "experimentId" : 700, + "macromoleculeAcronym" : "L9", + "i0stdev" : "0.191914285714", + "sampleMeasurementId" : 15053, + "measurementComments" : "[7]", + "priorityLevelId" : 14, + "bufferBeforeFramesMerged" : "10", + "substractionCreationTime" : "Jun 5, 2013 3:52:31 PM", + "proposalNumber" : "29", + "rgGnom" : "4.28379338749", + "volume" : "356.326", + "shapeDeterminationModel" : null, + "comments" : null, + "groupeField" : "L9 B1" + } ], + "frames_warning" : 1, + "calculation" : { + "rgGuinier" : { + "std" : null, + "sum" : 0, + "avg" : 0, + "validNumber" : 0, + "totalNumber" : 0, + "values" : [] + }, + "i0Guinier" : { + "std" : null, + "sum" : 0, + "avg" : 0, + "validNumber" : 0, + "totalNumber" : 0, + "values" : [] + }, + "quality" : { + "std" : null, + "sum" : 0, + "avg" : 0, + "validNumber" : 0, + "totalNumber" : 0, + "values" : [] + }, + "rgGnom" : { + "std" : null, + "sum" : 0, + "avg" : 0, + "validNumber" : 0, + "totalNumber" : 0, + "values" : [] + }, + "dMax" : { + "std" : null, + "sum" : 0, + "avg" : 0, + "validNumber" : 0, + "totalNumber" : 0, + "values" : [] + } + } + }, { + "concentration" : "0.91", + "id" : "0.91000000000000003", + "bufferId" : "422.00", + "bufferAcronym" : "B1", + "rgGuinier" : [], + "frames" : [ { + "total" : null, + "bufferBeforeMeasurementId" : 15054, + "sampleMergeId" : 8182, + "averagedModelId" : null, + "I0" : "0.0", + "proposalCode" : "OPD", + "averagedModel" : null, + "bufferAfterMergeId" : 8183, + "framesCount" : "10", + "bufferBeforeMergeId" : 8181, + "averageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_071_ave.dat", + "bufferAfterMeasurementId" : 15057, + "rgGuinier" : null, + "subtractedFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_071_sub.dat", + "firstPointUsed" : "0", + "chi2RgFilePath" : null, + "abInitioModelId" : null, + "macromoleculeId" : 649, + "code" : "_4.0_.91", + "transmission" : "100.0", + "timeStart" : "2013-06-05 15:52:58.133705", + "bufferAcronym" : "B1", + "quality" : "0.0", + "shapeDeterminationModelId" : null, + "expermientComments" : "[BsxCube] Generated from BsxCube", + "bufferId" : 422, + "isagregated" : "False", + "dmax" : null, + "bufferBeforeAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_070_ave.dat", + "exposureTemperature" : "4.0", + "subtractionId" : 3380, + "conc" : "0.91000000000000003", + "rapidShapeDeterminationModel" : null, + "experimentCreationDate" : "Jun 5, 2013 3:30:30 PM", + "lastPointUsed" : "0", + "modelListId" : null, + "framesMerge" : "10", + "rapidShapeDeterminationModelId" : null, + "bufferAfterAverageFilePath" : " /data/pyarch/bm29/opd29/700/1d/data_072_ave.dat", + "nsdFilePath" : null, + "bufferAfterFramesMerged" : "10", + "experimentId" : 700, + "macromoleculeAcronym" : "L9", + "i0stdev" : "0.0", + "sampleMeasurementId" : 15056, + "measurementComments" : "[8]", + "priorityLevelId" : 16, + "bufferBeforeFramesMerged" : "10", + "substractionCreationTime" : "Jun 5, 2013 3:55:35 PM", + "proposalNumber" : "29", + "rgGnom" : null, + "volume" : null, + "shapeDeterminationModel" : null, + "comments" : null, + "groupeField" : "L9 B1" + } ], + "frames_warning" : 1, + "calculation" : { + "rgGuinier" : { + "std" : null, + "sum" : 0, + "avg" : 0, + "validNumber" : 0, + "totalNumber" : 0, + "values" : [] + }, + "i0Guinier" : { + "std" : null, + "sum" : 0, + "avg" : 0, + "validNumber" : 0, + "totalNumber" : 0, + "values" : [] + }, + "quality" : { + "std" : null, + "sum" : 0, + "avg" : 0, + "validNumber" : 0, + "totalNumber" : 0, + "values" : [] + }, + "rgGnom" : { + "std" : null, + "sum" : 0, + "avg" : 0, + "validNumber" : 0, + "totalNumber" : 0, + "values" : [] + }, + "dMax" : { + "std" : null, + "sum" : 0, + "avg" : 0, + "validNumber" : 0, + "totalNumber" : 0, + "values" : [] + } } - subtractionKeys[selected[i].subtractionId] = true; - } - } + } ] + }, + "concentrationLabel" : "7.17 mg/ml ,3.53 mg/ml ,1.75 mg/ml ,0.91 mg/ml " } - - /** Refreshing Primary Data Reduction **/ - _this.subtractionCurveVisualizer.refresh(averagesId, subtractionIds); - - }); - return this.primaryDataProcessingGrid.getPanel(data); + }; }; -/** - * getAbinitioModellingContainer - */ -DataCollectionWidget.prototype.getAbinitioModellingContainer = function(data) { - var _this = this; - - this.abinitioGrid = new AbinitioGrid(); - this.abinitioGrid.onSelected.attach(function(sender, models) { - _this.modelViz.refresh(models); - - }); - /** It may be abinitio models linked to the buffers **/ - var abinitioIdList = []; - for (var i = 0; i < data.length; i++) { - abinitioIdList.push(data[i].abInitioId); - } - - var uniqueIds = []; - $.each(abinitioIdList, function(i, el) { - if ($.inArray(el, uniqueIds) === -1) - uniqueIds.push(el); - }); - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - _this.abinitioGrid.refresh(data); - }); - adapter.getAbinitioByIdsList(uniqueIds); - return this.abinitioGrid.getPanel([]); +ConcentrationHTMLTableWidget.prototype.test = function(targetId) { + var concentrationHTMLTableWidget = new ConcentrationHTMLTableWidget(); + document.getElementById(targetId).innerHTML = concentrationHTMLTableWidget.getPanel(concentrationHTMLTableWidget.input().data); }; +function DataCollectionWidget() { + +}; + +DataCollectionWidget.prototype.refresh = function(subtractionId) { + +}; + +DataCollectionWidget.prototype.getMacromolecule = function(data) { + for (var i = 0; i < data.length; i++) { + if (data[i].macromoleculeId != null) { + return BIOSAXS.proposal.getMacromoleculeById(data[i].macromoleculeId); + } + } + return null; +}; + +DataCollectionWidget.prototype.getMacromoleculeContainer = function(data) { + var macromolecule = this.getMacromolecule(data); + + var disabled = false; + if (macromolecule == null) { + disabled = true; + } + + var acronym = (macromolecule == null ? "" : macromolecule.acronym); + var mm = (macromolecule == null ? "" : macromolecule.molecularMass); + var comments = (macromolecule == null ? "" : macromolecule.comments); + + return Ext.create('Ext.Panel', { + width : 500, + height : 200, + disabled : disabled, + title : "Macromolecule", + layout : 'form', + bodyPadding : 5, + defaultType : 'textfield', + tbar : { + defaultButtonUI : 'default', + items : [ { + xtype : 'button', + text : 'Edit', + cls : 'btn-with-border', + handler : function() { + var macromoleculeWindow = new MacromoleculeWindow(); + macromoleculeWindow.draw(macromolecule); + /** TODO: update when save **/ + } + } ] + }, + items : [ { + fieldLabel : 'Acronym', + name : 'first', + readOnly : true, + value : acronym + }, { + fieldLabel : 'Molecular Mass', + name : 'last', + readOnly : true, + value : mm + }, { + xtype : 'textareafield', + fieldLabel : 'Comments', + value : '', + name : 'last', + readOnly : true, + value : comments + } ] + }); +}; + +DataCollectionWidget.prototype.getBufferContainer = function(data) { + var _this = this; + var buffer = BIOSAXS.proposal.getBufferById(data[0].bufferId); + + return Ext.create('Ext.Panel', { + width : 500, + height : 200, + title : "Buffer", + layout : 'form', + // collapsed : true, + // collapsible : true, + bodyPadding : 5, + defaultType : 'textfield', + style : { + padding : '0px 0px 0px 2px' + }, + tbar : { + defaultButtonUI : 'default', + items : [ { + xtype : 'button', + text : 'Edit', + cls : 'btn-with-border', + handler : function() { + var bufferWindow = new BufferWindow(); + bufferWindow.draw(BIOSAXS.proposal.getBufferById(data[0].bufferId)); + /** TODO: update when save **/ + } + + } ] + }, + items : [ { + fieldLabel : 'Buffer', + name : 'acronym', + readOnly : true, + value : buffer.acronym + }, { + fieldLabel : 'Composition', + name : 'last', + readOnly : true, + value : buffer.composition + }, { + xtype : 'textareafield', + fieldLabel : 'Comments', + value : buffer.comments, + name : 'last', + readOnly : true + + } ] + }); +}; + +DataCollectionWidget.prototype.getSpecimenContainer = function(data) { + return Ext.create('Ext.container.Container', { + layout : { + type : 'hbox' + }, + style : { + margin : '10px 10px 10px 10px' + }, + border : 0, + style : { + borderColor : '#000000', + borderStyle : 'solid', + borderWidth : '1px' + }, + defaults : { + labelWidth : 80, + // implicitly create Container by specifying xtype + xtype : 'datefield', + flex : 1, + + }, + items : [ this.getMacromoleculeContainer(data), this.getBufferContainer(data) ] + }); +}; + +DataCollectionWidget.prototype.getSeparator = function() { + return { + html : "
", + border : 0 + } +}; + +DataCollectionWidget.prototype.getFitStructurePanel = function(data) { + var _this = this; + + return Ext.create('Ext.container.Container', { + layout : { + type : 'hbox' + }, + style : { + margin : '10px 10px 10px 10px' + }, + border : 0, + style : { + borderColor : '#000000', + borderStyle : 'solid', + borderWidth : '1px' + }, + defaults : { + labelWidth : 80, + xtype : 'datefield', + flex : 1 + }, + items : [ + + ] + }); +}; + +DataCollectionWidget.prototype.getFitStructurePanelWorkflow = function(data) { + var _this = this; + var macromolecule = this.getMacromolecule(data); + + var items = []; + + /** Adding all the pdb files linked to the macromolecule **/ + // if (macromolecule.structure3VOs != null) { + // if (macromolecule.structure3VOs.length > 0) { + // + // items.push(); + // } + // } else { + // items.push({ + // html : "No apriori information added to this macromolecule. Apriori information needed for further analysis", + // margin : "5 5 5 5" + // }); + // } + var fitStructureToExperimentDataGrid = new FitStructureToExperimentDataGrid(); + + fitStructureToExperimentDataGrid.refresh(_this.data[0].subtractionId, _this.getMacromolecule(data)); + return Ext.create('Ext.container.Container', { + style : { + margin : '10px 10px 10px 10px' + }, + border : 0, + + style : { + borderColor : '#000000', + borderStyle : 'solid', + borderWidth : '1px' + }, + defaults : { + labelWidth : 80, + xtype : 'datefield', + flex : 1 + }, + items : [ fitStructureToExperimentDataGrid.getPanel() ], + listeners : { + afterrender : function() { + } + } + }); +}; +/** Static method **/ +DataCollectionWidget.prototype.RUNFitScattering = function(subtractionId, structureId) { + var _this = this; + /** Add to Workflow **/ + var adapter = new BiosaxsDataAdapter(); + var workflow = { + 'workflowTitle' : 'FitExperimentalDatatoStructure', + 'comments' : 'FitExperimentalDatatoStructure run from ISPyB for subtractionId: ' + subtractionId + ' and structureId ' + structureId + } + + var inputs = [ { + name : 'subtractionId', + value : subtractionId + }, { + name : 'structureId', + value : structureId + } ]; + + adapter.onSuccess.attach(function(sender, data) { + /** Add to Fit **/ + var adapter2 = new BiosaxsDataAdapter(); + var fit = { + 'workflowId' : data.workflowId, + 'subtractionId' : subtractionId, + 'structureId' : structureId, + 'comments' : 'Sent to workflow engine' + } + adapter2.onSuccess.attach(function(sender, fit) { + + }); + adapter2.addFitStructureData(fit); + + }); + adapter.addWorkflow(workflow, inputs); + +}; + +DataCollectionWidget.prototype.getSuperpositionTab = function(data) { + var _this = this; + + this.superpositionGrid = new SuperpositionGrid(); + + return Ext.create('Ext.container.Container', { + style : { + margin : '10px 10px 10px 10px' + }, + border : 0, + style : { + borderColor : '#000000', + borderStyle : 'solid', + borderWidth : '1px' + }, + items : [ _this.superpositionGrid.getPanel() ], + listeners : { + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + + }, + afterrender : function() { + /** Getting Rigid bodies **/ + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, result) { + _this.superpositionGrid.refresh(result); + }); + adapter.getSuperpositionBySubtractionId(data[1].subtractionId); + } + } + }); +}; + +DataCollectionWidget.prototype.getAdvancedTab = function(data) { + var _this = this; + return Ext.create('Ext.container.Container', { + style : { + margin : '10px 10px 10px 10px' + }, + border : 0, + style : { + borderColor : '#000000', + borderStyle : 'solid', + borderWidth : '1px' + }, + items : [ _this.getFitStructurePanel(data), _this.getFitStructurePanelWorkflow(data) ] + }); +}; + +DataCollectionWidget.prototype.getRigiBodyForm = function(data) { + var _this = this; + _this.rigiBodyGrid = new RigidModelGrid(); + return _this.rigiBodyGrid.getPanel(); + +}; + +DataCollectionWidget.prototype.getRigidBodyModelingTab = function(data) { + var _this = this; + return Ext.create('Ext.container.Container', { + style : { + margin : '10px 10px 10px 10px' + }, + border : 0, + style : { + borderColor : '#000000', + borderStyle : 'solid', + borderWidth : '1px' + }, + items : [ _this.getRigiBodyForm(data) ], + listeners : { + cellclick : function(grid, td, cellIndex, record, tr, rowIndex, e, eOpts) { + + }, + afterrender : function() { + /** Getting Rigid bodies **/ + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, result) { + _this.rigiBodyGrid.refresh(result); + }); + adapter.getRigidBodyModelingBySubtractionId(data[1].subtractionId); + } + } + }); +}; + +DataCollectionWidget.prototype.getTabs = function(data) { + var _this = this; + + this.subtractionCurveVisualizer = new SubtractionCurveVisualizer(); + + this.tabs = Ext.createWidget('tabpanel', { + activeTab : 1, + plain : true, + defaults : { + autoScroll : true, + bodyPadding : 10 + }, + items : [ { + title : 'Solution', + items : [ _this.getSpecimenContainer(data) ] + }, { + title : 'Primary Data Reduction', + active : true, + tabConfig : { + xtype : 'tab', + margins : '0 0 0 20', + }, + items : [ _this.subtractionCurveVisualizer.getPanel() ] + }, { + title : 'Abinitio', + items : [ _this.getAbinitioModellingContainer(data), _this.getSeparator(), _this.getModelViz(data) ] + }, { + title : 'Mixtures', + items : [ _this.getAdvancedTab(data) ] + }, { + title : 'Superpositions', + items : [ _this.getSuperpositionTab(data) ] + }, { + title : 'Rigid Body Modeling', + items : [ _this.getRigidBodyModelingTab(data) ] + } ] + }); + return this.tabs; +}; + +DataCollectionWidget.prototype.getPanel = function(data) { + var _this = this; + _this.data = data; + this.panel = Ext.create('Ext.container.Container', { + width : 1000, + layout : { + type : 'vbox', + align : 'stretch', + padding : 5 + }, + items : [ _this.getTabs(data) + + ] + }); + + this.panel.on("afterrender", function() { + _this.subtractionCurveVisualizer.refresh([ _this.data[1].mergeId ], [ _this.data[1].subtractionId ]); + }); + return this.panel; +}; + +DataCollectionWidget.prototype.getModelViz = function(data) { + this.modelViz = new ModelVisualizerForm({ + height : 800, + width : 1000 + }); + return this.modelViz.getPanel(); +}; + +/** + * PRIMARY DATA PROCESSING + */ +DataCollectionWidget.prototype.getPrimaryDataProcessingContainer = function(data) { + var _this = this; + this.primaryDataProcessingGrid = new PrimaryDataProcessingGrid({ + height : 250, + width : 1000, + title : 'Primary Data Processing' + }); + + this.primaryDataProcessingGrid.onSelected.attach(function(sender, selected) { + /** Refresh tabs **/ + var averagesId = []; + var subtractionIds = []; + + var subtractionKeys = {}; + for (var i = 0; i < selected.length; i++) { + if (selected[i].mergeId != null) { + averagesId.push(selected[i].mergeId); + } + + if (selected[i].subtractionId != null) { + if (selected[i].macromoleculeId != null) { + if (subtractionKeys[selected[i].subtractionId] == null) { + subtractionIds.push(selected[i].subtractionId); + } + subtractionKeys[selected[i].subtractionId] = true; + } + } + } + + /** Refreshing Primary Data Reduction **/ + _this.subtractionCurveVisualizer.refresh(averagesId, subtractionIds); + + }); + return this.primaryDataProcessingGrid.getPanel(data); +}; +/** + * getAbinitioModellingContainer + */ +DataCollectionWidget.prototype.getAbinitioModellingContainer = function(data) { + var _this = this; + + this.abinitioGrid = new AbinitioGrid(); + this.abinitioGrid.onSelected.attach(function(sender, models) { + _this.modelViz.refresh(models); + + }); + /** It may be abinitio models linked to the buffers **/ + var abinitioIdList = []; + for (var i = 0; i < data.length; i++) { + abinitioIdList.push(data[i].abInitioId); + } + + var uniqueIds = []; + $.each(abinitioIdList, function(i, el) { + if ($.inArray(el, uniqueIds) === -1) + uniqueIds.push(el); + }); + + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + _this.abinitioGrid.refresh(data); + }); + adapter.getAbinitioByIdsList(uniqueIds); + return this.abinitioGrid.getPanel([]); +}; + /** * Edit the information of a buffer * @@ -29163,258 +29163,258 @@ ShippingWidget.prototype.refresh = function() { }; -/** - * Widget container of Specimen grid and samplePlate widget - * Depending of the sample changer layout it may be displayed vertically or horizontally - * - * @param args - * - * #onExperimentChanged It happens when specimen are modified - */ -function SpecimenWidget(args){ - - this.width = 1000; - this.height = 600; - - if (args != null){ - if (args.width != null){ - this.width = args.width; - } - if (args.height != null){ - this.height = args.height; - } - } - - var _this = this; - - /** Specimen Grid **/ - this.specimenGrid = new SpecimenGrid({ - minHeight : 425, - selectionMode : "SINGLE", - editEnabled : false, - updateRowEnabled : true, - width : 900, - showTitle : false - }); - - - this.specimenGrid.onSpecimenChanged.attach(function(sender, specimen) { - _this.experiment.setSpecimenById(specimen); - _this.refresh(_this.experiment); - }); - - this.specimenGrid.onSelected.attach(function(sender, specimens) { - if (specimens.length > 0) { - _this.specimenSelected = specimens[0]; - } else { - _this.specimenSelected = null; - } - _this.samplePlateGroupWidget.selectSpecimens(specimens); - }); - - - /** Sample plate Widget **/ - this.samplePlateGroupWidget = new SamplePlateGroupWidget({ - showTitle : false, - height : 250, - margin : 5, - bbar : true - }); - - - this.samplePlateGroupWidget.onExperimentChanged.attach(function(sender, json) { - _this.refresh(new Experiment(json)); - }); - - this.samplePlateGroupWidget.onClick.attach(function(sender, args) { - /** Clicking on a plate * */ - var row = args.row; - var column = args.column; - var samplePlateId = args.samplePlate.samplePlateId; - - /** is specimen selected on the grid? * */ - if (_this.specimenSelected != null) { - /** Is position target empty * */ - if (_this.experiment.getSampleByPosition(args.samplePlate.samplePlateId, args.row, args.column).length == 0) { - var specimen = _this.experiment.getSampleById(_this.specimenSelected.specimenId); - if (specimen.sampleplateposition3VO == null) { - specimen.sampleplateposition3VO = {}; - } - - specimen.sampleplateposition3VO = { - columnNumber : column, - rowNumber : row, - samplePlateId : samplePlateId - }; - - _this.samplePlateGroupWidget.panel.setLoading("ISPyB: Saving specimen"); - var adapter = new BiosaxsDataAdapter(); - /** If success * */ - adapter.onSuccess.attach(function(sender, experiment) { - _this.samplePlateGroupWidget.panel.setLoading(false); - }); - - adapter.onError.attach(function(sender, error) { - _this.samplePlateGroupWidget.panel.setLoading(false); - showError(error); - }); - - adapter.saveSpecimen(specimen, _this.experiment); - - _this.samplePlateGroupWidget.refresh(_this.experiment); - _this.specimenGrid.refresh(_this.experiment); - //_this.refresh(_this.experiment); - _this.specimenGrid.deselectAll(); - - } else { - /** - * Can we merge? We can merge when specimen are the - * same. So, same buffer, macromolecule, concentration * - */ - var target = _this.experiment.getSampleByPosition(args.samplePlate.samplePlateId, args.row, args.column)[0]; - var specimen = _this.experiment.getSampleById(_this.specimenSelected.specimenId); - - if ((specimen.bufferId == target.bufferId) && (specimen.concentration == target.concentration)) { - if (((specimen.macromolecule3VO != null) && (target.macromolecule3VO != null) && (specimen.macromolecule3VO.macromoleculeId == target.macromolecule3VO.macromoleculeId)) || - ((specimen.macromolecule3VO == null) && (target.macromolecule3VO == null))) { - var adapter = new BiosaxsDataAdapter(); - adapter.onSuccess.attach(function(sender, data) { - _this.refresh(new Experiment(data)); - _this.samplePlateGroupWidget.panel.setLoading(false); - - _this.onExperimentChanged.notify(experiment); - }); - adapter.onError.attach(function(sender, error) { - _this.samplePlateGroupWidget.panel.setLoading(false); - showError(error); - }); - _this.samplePlateGroupWidget.panel.setLoading("ISPyB: Merging specimens"); - adapter.mergeSpecimens(specimen.specimenId, target.specimenId); - } - } else { - alert("Well is not empty. Select another well!"); - } - } - } else { - var specimen = _this.experiment.getSampleByPosition(args.samplePlate.samplePlateId, args.row, args.column)[0]; - if (specimen != null) { - _this.specimenGrid.selectById(specimen.specimenId); - } - } - }); - - /** Events **/ - this.onExperimentChanged = new Event(this); -}; - -/** - * Return vbox or hbox depending on the slot positions of the plates - */ -SpecimenWidget.prototype.getContainerLayoutConfiguration = function(experiment){ - var dimensions = this.samplePlateGroupWidget.getDimensions(experiment.getSamplePlates()); - if (dimensions.maxSlotPositionRow < dimensions.maxSlotPositionColumn){ - return { - layout : "vbox", - specimenGridWidth : this.width - 10, - specimenGridHeight : this.height - 260, - samplePlateGroupWidth : this.width - 10, - samplePlateGroupHeight : 250 - }; - } - return { - layout : "hbox", - samplePlateGroupWidth : this.width*1/3 -10, - samplePlateGroupHeight : this.height - 10, - specimenGridWidth : this.width*2/3, - specimenGridHeight : this.height - 10 - }; - -}; - - -SpecimenWidget.prototype.refresh = function(experiment){ - this.experiment = experiment; - - /** Removing all components **/ - this.panel.removeAll(); - - var layoutConfiguration = this.getContainerLayoutConfiguration(experiment); - - /** Setting new width and height for layout vbox and hbox **/ - this.specimenGrid.width = layoutConfiguration.specimenGridWidth; - this.specimenGrid.height = layoutConfiguration.specimenGridHeight; - - this.samplePlateGroupWidget.width = layoutConfiguration.samplePlateGroupWidth; - this.samplePlateGroupWidget.height = layoutConfiguration.samplePlateGroupHeight; - - if (layoutConfiguration.layout == "hbox"){ - this.specimenGrid.margin = "0 0 0 5"; - this.specimenGrid.width =this.specimenGrid.width - 5; - } - /** Insert container depending on layout [vertical|horizontal] */ - var container = Ext.create('Ext.container.Container', { - layout : layoutConfiguration.layout, - height : this.height, - width : this.width, - padding : '2px', - items : [ ] - }); - if (layoutConfiguration.layout == "vbox"){ - container.insert(this.specimenGrid.getPanel()); - container.insert(this.samplePlateGroupWidget.getPanel()); - } - else{ - container.insert(this.samplePlateGroupWidget.getPanel()); - container.insert(this.specimenGrid.getPanel()); - } - - /** Insert Widget **/ - this.panel.insert(container); - - /** Load data **/ - this.specimenGrid.refresh(experiment); - this.samplePlateGroupWidget.refresh(experiment); - - -}; - -/** It creates a dummy container to be inserted the plates once the method refresh has been called - * This is necessay because we can not know the sample changer layout before hand - * **/ -SpecimenWidget.prototype.getPanel = function(){ - this.panel = Ext.create('Ext.container.Container', { - layout : 'vbox', - height : this.height, - border : 0, - margin : 5, - width : this.width, - items : [] - }); - return this.panel; -}; - - -SpecimenWidget.prototype.input = function() { - return { - experiment : DATADOC.getExperiment_10(), - proposal : DATADOC.getProposal_10() - }; -}; - -SpecimenWidget.prototype.test = function(targetId) { - var specimenWidget = new SpecimenWidget({ - height : 500, - width : 1000 - }); - BIOSAXS.proposal = new Proposal(specimenWidget.input().proposal); - var experiment = new Experiment(specimenWidget.input().experiment); - var panel = specimenWidget.getPanel(); - panel.render(targetId); - specimenWidget.refresh(experiment); - -}; - - +/** + * Widget container of Specimen grid and samplePlate widget + * Depending of the sample changer layout it may be displayed vertically or horizontally + * + * @param args + * + * #onExperimentChanged It happens when specimen are modified + */ +function SpecimenWidget(args){ + + this.width = 1000; + this.height = 600; + + if (args != null){ + if (args.width != null){ + this.width = args.width; + } + if (args.height != null){ + this.height = args.height; + } + } + + var _this = this; + + /** Specimen Grid **/ + this.specimenGrid = new SpecimenGrid({ + minHeight : 425, + selectionMode : "SINGLE", + editEnabled : false, + updateRowEnabled : true, + width : 900, + showTitle : false + }); + + + this.specimenGrid.onSpecimenChanged.attach(function(sender, specimen) { + _this.experiment.setSpecimenById(specimen); + _this.refresh(_this.experiment); + }); + + this.specimenGrid.onSelected.attach(function(sender, specimens) { + if (specimens.length > 0) { + _this.specimenSelected = specimens[0]; + } else { + _this.specimenSelected = null; + } + _this.samplePlateGroupWidget.selectSpecimens(specimens); + }); + + + /** Sample plate Widget **/ + this.samplePlateGroupWidget = new SamplePlateGroupWidget({ + showTitle : false, + height : 250, + margin : 5, + bbar : true + }); + + + this.samplePlateGroupWidget.onExperimentChanged.attach(function(sender, json) { + _this.refresh(new Experiment(json)); + }); + + this.samplePlateGroupWidget.onClick.attach(function(sender, args) { + /** Clicking on a plate * */ + var row = args.row; + var column = args.column; + var samplePlateId = args.samplePlate.samplePlateId; + + /** is specimen selected on the grid? * */ + if (_this.specimenSelected != null) { + /** Is position target empty * */ + if (_this.experiment.getSampleByPosition(args.samplePlate.samplePlateId, args.row, args.column).length == 0) { + var specimen = _this.experiment.getSampleById(_this.specimenSelected.specimenId); + if (specimen.sampleplateposition3VO == null) { + specimen.sampleplateposition3VO = {}; + } + + specimen.sampleplateposition3VO = { + columnNumber : column, + rowNumber : row, + samplePlateId : samplePlateId + }; + + _this.samplePlateGroupWidget.panel.setLoading("ISPyB: Saving specimen"); + var adapter = new BiosaxsDataAdapter(); + /** If success * */ + adapter.onSuccess.attach(function(sender, experiment) { + _this.samplePlateGroupWidget.panel.setLoading(false); + }); + + adapter.onError.attach(function(sender, error) { + _this.samplePlateGroupWidget.panel.setLoading(false); + showError(error); + }); + + adapter.saveSpecimen(specimen, _this.experiment); + + _this.samplePlateGroupWidget.refresh(_this.experiment); + _this.specimenGrid.refresh(_this.experiment); + //_this.refresh(_this.experiment); + _this.specimenGrid.deselectAll(); + + } else { + /** + * Can we merge? We can merge when specimen are the + * same. So, same buffer, macromolecule, concentration * + */ + var target = _this.experiment.getSampleByPosition(args.samplePlate.samplePlateId, args.row, args.column)[0]; + var specimen = _this.experiment.getSampleById(_this.specimenSelected.specimenId); + + if ((specimen.bufferId == target.bufferId) && (specimen.concentration == target.concentration)) { + if (((specimen.macromolecule3VO != null) && (target.macromolecule3VO != null) && (specimen.macromolecule3VO.macromoleculeId == target.macromolecule3VO.macromoleculeId)) || + ((specimen.macromolecule3VO == null) && (target.macromolecule3VO == null))) { + var adapter = new BiosaxsDataAdapter(); + adapter.onSuccess.attach(function(sender, data) { + _this.refresh(new Experiment(data)); + _this.samplePlateGroupWidget.panel.setLoading(false); + + _this.onExperimentChanged.notify(experiment); + }); + adapter.onError.attach(function(sender, error) { + _this.samplePlateGroupWidget.panel.setLoading(false); + showError(error); + }); + _this.samplePlateGroupWidget.panel.setLoading("ISPyB: Merging specimens"); + adapter.mergeSpecimens(specimen.specimenId, target.specimenId); + } + } else { + alert("Well is not empty. Select another well!"); + } + } + } else { + var specimen = _this.experiment.getSampleByPosition(args.samplePlate.samplePlateId, args.row, args.column)[0]; + if (specimen != null) { + _this.specimenGrid.selectById(specimen.specimenId); + } + } + }); + + /** Events **/ + this.onExperimentChanged = new Event(this); +}; + +/** + * Return vbox or hbox depending on the slot positions of the plates + */ +SpecimenWidget.prototype.getContainerLayoutConfiguration = function(experiment){ + var dimensions = this.samplePlateGroupWidget.getDimensions(experiment.getSamplePlates()); + if (dimensions.maxSlotPositionRow < dimensions.maxSlotPositionColumn){ + return { + layout : "vbox", + specimenGridWidth : this.width - 10, + specimenGridHeight : this.height - 260, + samplePlateGroupWidth : this.width - 10, + samplePlateGroupHeight : 250 + }; + } + return { + layout : "hbox", + samplePlateGroupWidth : this.width*1/3 -10, + samplePlateGroupHeight : this.height - 10, + specimenGridWidth : this.width*2/3, + specimenGridHeight : this.height - 10 + }; + +}; + + +SpecimenWidget.prototype.refresh = function(experiment){ + this.experiment = experiment; + + /** Removing all components **/ + this.panel.removeAll(); + + var layoutConfiguration = this.getContainerLayoutConfiguration(experiment); + + /** Setting new width and height for layout vbox and hbox **/ + this.specimenGrid.width = layoutConfiguration.specimenGridWidth; + this.specimenGrid.height = layoutConfiguration.specimenGridHeight; + + this.samplePlateGroupWidget.width = layoutConfiguration.samplePlateGroupWidth; + this.samplePlateGroupWidget.height = layoutConfiguration.samplePlateGroupHeight; + + if (layoutConfiguration.layout == "hbox"){ + this.specimenGrid.margin = "0 0 0 5"; + this.specimenGrid.width =this.specimenGrid.width - 5; + } + /** Insert container depending on layout [vertical|horizontal] */ + var container = Ext.create('Ext.container.Container', { + layout : layoutConfiguration.layout, + height : this.height, + width : this.width, + padding : '2px', + items : [ ] + }); + if (layoutConfiguration.layout == "vbox"){ + container.insert(this.specimenGrid.getPanel()); + container.insert(this.samplePlateGroupWidget.getPanel()); + } + else{ + container.insert(this.samplePlateGroupWidget.getPanel()); + container.insert(this.specimenGrid.getPanel()); + } + + /** Insert Widget **/ + this.panel.insert(container); + + /** Load data **/ + this.specimenGrid.refresh(experiment); + this.samplePlateGroupWidget.refresh(experiment); + + +}; + +/** It creates a dummy container to be inserted the plates once the method refresh has been called + * This is necessay because we can not know the sample changer layout before hand + * **/ +SpecimenWidget.prototype.getPanel = function(){ + this.panel = Ext.create('Ext.container.Container', { + layout : 'vbox', + height : this.height, + border : 0, + margin : 5, + width : this.width, + items : [] + }); + return this.panel; +}; + + +SpecimenWidget.prototype.input = function() { + return { + experiment : DATADOC.getExperiment_10(), + proposal : DATADOC.getProposal_10() + }; +}; + +SpecimenWidget.prototype.test = function(targetId) { + var specimenWidget = new SpecimenWidget({ + height : 500, + width : 1000 + }); + BIOSAXS.proposal = new Proposal(specimenWidget.input().proposal); + var experiment = new Experiment(specimenWidget.input().experiment); + var panel = specimenWidget.getPanel(); + panel.render(targetId); + specimenWidget.refresh(experiment); + +}; + + function WarningWidget(args) { this.actions = []; From 19ac8a7c4ee8e6363e16b732b95a017fd0de52d9 Mon Sep 17 00:00:00 2001 From: delageniere Date: Tue, 31 Oct 2017 15:54:49 +0100 Subject: [PATCH 32/38] new release 5.3.4 --- ispyb-bcr-ear/pom.xml | 4 ++-- ispyb-bcr/pom.xml | 2 +- ispyb-ear/pom.xml | 6 +++--- ispyb-ejb/pom.xml | 2 +- ispyb-ui/pom.xml | 2 +- ispyb-ws/pom.xml | 4 ++-- pom.xml | 2 +- 7 files changed, 11 insertions(+), 11 deletions(-) diff --git a/ispyb-bcr-ear/pom.xml b/ispyb-bcr-ear/pom.xml index f68ff45ae..b727e8d4f 100644 --- a/ispyb-bcr-ear/pom.xml +++ b/ispyb-bcr-ear/pom.xml @@ -4,7 +4,7 @@ ispyb ispyb-parent - 5.3.2 + 5.3.4 ispyb-bcr-ear ear @@ -15,7 +15,7 @@ ispyb ispyb-ejb3 ejb - 5.3.2 + 5.3.4 provided diff --git a/ispyb-bcr/pom.xml b/ispyb-bcr/pom.xml index 7ec9b4460..b8c7744a4 100644 --- a/ispyb-bcr/pom.xml +++ b/ispyb-bcr/pom.xml @@ -31,7 +31,7 @@ ispyb ispyb-ejb3 - 5.3.2 + 5.3.4 provided diff --git a/ispyb-ear/pom.xml b/ispyb-ear/pom.xml index cbbe85d12..54fb40673 100644 --- a/ispyb-ear/pom.xml +++ b/ispyb-ear/pom.xml @@ -4,7 +4,7 @@ ispyb ispyb-parent - 5.3.2 + 5.3.4 ispyb-ear ear @@ -13,7 +13,7 @@ ispyb ispyb-ejb3 ejb - 5.3.2 + 5.3.4 @@ -26,7 +26,7 @@ ispyb ispyb-ws war - 5.3.2 + 5.3.4 diff --git a/ispyb-ejb/pom.xml b/ispyb-ejb/pom.xml index a2132d7f1..9fb47fee4 100644 --- a/ispyb-ejb/pom.xml +++ b/ispyb-ejb/pom.xml @@ -4,7 +4,7 @@ ispyb ispyb-parent - 5.3.2 + 5.3.4 ispyb-ejb3 jar diff --git a/ispyb-ui/pom.xml b/ispyb-ui/pom.xml index 0b3af3d9c..625170c04 100644 --- a/ispyb-ui/pom.xml +++ b/ispyb-ui/pom.xml @@ -22,7 +22,7 @@ ispyb ispyb-ejb3 - 5.3.2 + 5.3.4 provided diff --git a/ispyb-ws/pom.xml b/ispyb-ws/pom.xml index c05712229..d85dc8df3 100644 --- a/ispyb-ws/pom.xml +++ b/ispyb-ws/pom.xml @@ -4,7 +4,7 @@ ispyb ispyb-parent - 5.3.2 + 5.3.4 ispyb-ws war @@ -12,7 +12,7 @@ ispyb ispyb-ejb3 - 5.3.2 + 5.3.4 provided diff --git a/pom.xml b/pom.xml index 1d979d091..290b587c2 100644 --- a/pom.xml +++ b/pom.xml @@ -4,7 +4,7 @@ 4.0.0 ispyb ispyb-parent - 5.3.2 + 5.3.4 pom ispyb-ejb From 148eefba133cd58cde7dcd333a9bee718cb3ca5d Mon Sep 17 00:00:00 2001 From: delageniere Date: Tue, 31 Oct 2017 17:53:46 +0100 Subject: [PATCH 33/38] modifs for analysis report --- .../common/util/export/ExiPdfRtfExporter.java | 127 +++++++++--------- 1 file changed, 64 insertions(+), 63 deletions(-) diff --git a/ispyb-ejb/src/main/java/ispyb/common/util/export/ExiPdfRtfExporter.java b/ispyb-ejb/src/main/java/ispyb/common/util/export/ExiPdfRtfExporter.java index 347bca985..a823fea25 100644 --- a/ispyb-ejb/src/main/java/ispyb/common/util/export/ExiPdfRtfExporter.java +++ b/ispyb-ejb/src/main/java/ispyb/common/util/export/ExiPdfRtfExporter.java @@ -753,71 +753,13 @@ private void setDataAnalysisMapData(Document document, Map dataC Boolean strategy = getBoolean(dataCollectionMapItem, "ScreeningOutput_strategySuccess"); String autoprocSpaceGroup = getCellParam(dataCollectionMapItem, "AutoProc_spaceGroup", null); boolean existAutoProcSpaceGroup = (autoprocSpaceGroup != null && !autoprocSpaceGroup.isEmpty() ) - || ( dataCollectionMapItem.get("AutoProc_spaceGroups") != null && !((String)dataCollectionMapItem.get("AutoProc_spaceGroups")).isEmpty()); - + || ( dataCollectionMapItem.get("AutoProc_spaceGroups") != null && !((String)dataCollectionMapItem.get("AutoProc_spaceGroups")).isEmpty() + && dataCollectionMapItem.get("Autoprocessing_cell_a")!= null); p = new Paragraph(); String [] bestRmerge = null; - - if (indexing != null && strategy != null){ - // Cell 6 - parag = "\nIndexed: \n " - + "\nStrategy: \n"; - p = new Paragraph(parag, FONT_DOC_SMALL); - table.addCell(p); - - // Cell 7 - p = new Paragraph(); - Chunk chu2 = new Chunk( "KO", FONT_INDEXING_FAILED); - if (indexing.booleanValue() ){ - chu2 = new Chunk( "OK", FONT_INDEXING_SUCCESS); - } - p.add(chu2); - - chu2 = new Chunk( "KO", FONT_INDEXING_FAILED); - if (strategy.booleanValue() ){ - chu2 = new Chunk( "OK", FONT_INDEXING_SUCCESS); - } - p.add("\n"); - p.add(chu2); - table.addCell(p); - - // Cell 8 - parag = "Space group: \n" - + "Mosaicity: \n" ; - p = new Paragraph(parag, FONT_DOC_SMALL); - table.addCell(p); - - // Cell 9 - parag = getCellParam(dataCollectionMapItem, "ScreeningOutputLattice_spaceGroup", null) + "\n" - + getCellParam(dataCollectionMapItem, "ScreeningOutput_mosaicity", null)+ "\n" ; - p = new Paragraph(parag, FONT_DOC_SMALL_BOLD); - table.addCell(p); - - // Cell 10 - parag = "a \n" + getCellParam(dataCollectionMapItem, "ScreeningOutputLattice_unitCell_a", null) - + "\n alpha \n" + getCellParam(dataCollectionMapItem, "ScreeningOutputLattice_unitCell_alpha", null) ; - p = new Paragraph(parag, FONT_DOC_SMALL_CENTERED); - p.setAlignment(Element.ALIGN_CENTER); - table.addCell(p); - - // Cell 11 - parag = "b \n" + getCellParam(dataCollectionMapItem, "ScreeningOutputLattice_unitCell_b", null) - + "\n beta \n" + getCellParam(dataCollectionMapItem, "ScreeningOutputLattice_unitCell_beta", null) ; - p = new Paragraph(parag, FONT_DOC_SMALL_CENTERED); - p.setAlignment(Element.ALIGN_CENTER); - table.addCell(p); - - // Cell 12 - parag = "c \n" + getCellParam(dataCollectionMapItem, "ScreeningOutputLattice_unitCell_c", null) - + "\n gamma \n" + getCellParam(dataCollectionMapItem, "ScreeningOutputLattice_unitCell_gama", null) ; - - p = new Paragraph(parag, FONT_DOC_SMALL_CENTERED); - p.setAlignment(Element.ALIGN_CENTER); - table.addCell(p); - - } else if (existAutoProcSpaceGroup && extractBestAutoproc(dataCollectionMapItem) != null){ + if (existAutoProcSpaceGroup && extractBestAutoproc(dataCollectionMapItem) != null){ // Cell 6 bestRmerge = extractBestAutoproc(dataCollectionMapItem); parag = bestRmerge[0] + "\n" @@ -878,6 +820,63 @@ private void setDataAnalysisMapData(Document document, Map dataC p = new Paragraph(parag, FONT_DOC_SMALL_CENTERED); p.setAlignment(Element.ALIGN_CENTER); table.addCell(p); + + } else if (indexing != null && strategy != null){ + // Cell 6 + parag = "\nIndexed: \n " + + "\nStrategy: \n"; + p = new Paragraph(parag, FONT_DOC_SMALL); + table.addCell(p); + + // Cell 7 + p = new Paragraph(); + Chunk chu2 = new Chunk( "KO", FONT_INDEXING_FAILED); + if (indexing.booleanValue() ){ + chu2 = new Chunk( "OK", FONT_INDEXING_SUCCESS); + } + p.add(chu2); + + chu2 = new Chunk( "KO", FONT_INDEXING_FAILED); + if (strategy.booleanValue() ){ + chu2 = new Chunk( "OK", FONT_INDEXING_SUCCESS); + } + p.add("\n"); + p.add(chu2); + table.addCell(p); + + // Cell 8 + parag = "Space group: \n" + + "Mosaicity: \n" ; + p = new Paragraph(parag, FONT_DOC_SMALL); + table.addCell(p); + + // Cell 9 + parag = getCellParam(dataCollectionMapItem, "ScreeningOutputLattice_spaceGroup", null) + "\n" + + getCellParam(dataCollectionMapItem, "ScreeningOutput_mosaicity", null)+ "\n" ; + p = new Paragraph(parag, FONT_DOC_SMALL_BOLD); + table.addCell(p); + + // Cell 10 + parag = "a \n" + getCellParam(dataCollectionMapItem, "ScreeningOutputLattice_unitCell_a", null) + + "\n alpha \n" + getCellParam(dataCollectionMapItem, "ScreeningOutputLattice_unitCell_alpha", null) ; + p = new Paragraph(parag, FONT_DOC_SMALL_CENTERED); + p.setAlignment(Element.ALIGN_CENTER); + table.addCell(p); + + // Cell 11 + parag = "b \n" + getCellParam(dataCollectionMapItem, "ScreeningOutputLattice_unitCell_b", null) + + "\n beta \n" + getCellParam(dataCollectionMapItem, "ScreeningOutputLattice_unitCell_beta", null) ; + p = new Paragraph(parag, FONT_DOC_SMALL_CENTERED); + p.setAlignment(Element.ALIGN_CENTER); + table.addCell(p); + + // Cell 12 + parag = "c \n" + getCellParam(dataCollectionMapItem, "ScreeningOutputLattice_unitCell_c", null) + + "\n gamma \n" + getCellParam(dataCollectionMapItem, "ScreeningOutputLattice_unitCell_gama", null) ; + + p = new Paragraph(parag, FONT_DOC_SMALL_CENTERED); + p.setAlignment(Element.ALIGN_CENTER); + table.addCell(p); } else { table.addCell(" "); @@ -1136,6 +1135,8 @@ private String[] extractBestAutoproc(Map dataCollectionMapItem) int indexRmergeMin = 0; Set indexSet = new HashSet(); + //TODO select also no anom + for (Iterator iterator = scalingStatisticsTypesList.iterator(); iterator.hasNext();) { String type = (String) iterator.next(); if (type.contains("innerShell")){ @@ -1209,8 +1210,8 @@ private String[] extractBestAutoproc(Map dataCollectionMapItem) private Chunk getCompletenessChunk(String completeness) { Chunk chu = new Chunk( completeness, FONT_DOC_SMALL_BOLD); chu.setBackground(BLUE_COLOR); - if (completeness != null && new Double(completeness) < 80 ) { - if (new Double(completeness) < 10) { + if (completeness != null && new Double(completeness) < 90 ) { + if (new Double(completeness) < 50) { chu.setBackground(RED_COLOR); } else { chu.setBackground(LIGHT_YELLOW_COLOR); From f93b5d6da20a2ff1496110e51f0f4754c5ed634c Mon Sep 17 00:00:00 2001 From: delageniere Date: Mon, 6 Nov 2017 16:36:18 +0100 Subject: [PATCH 34/38] Explanation about site customization --- documentation/ISPyB_DevelopersGuide.doc | Bin 207360 -> 208896 bytes 1 file changed, 0 insertions(+), 0 deletions(-) diff --git a/documentation/ISPyB_DevelopersGuide.doc b/documentation/ISPyB_DevelopersGuide.doc index 65267a340e0591758ce0c0de5773e13591b99997..fee6b6457c4e83f84281775fb38c6676a9b2ee73 100644 GIT binary patch delta 11125 zcmb{234BcF-oWwanMoo@)UF~Js-;TAE~q83rj4a2N@*k$nd~wNqL^4>UqULUP2CDr zs)}k_Q%kMAReC8^t)+@mm)@e5_Fnt_{bzCr_wD`keLwHa=X=g`&OGOw|FfLuEJ^k^ z0okVlazh&}(8~KMuheU#W%2I4d-r7JTo&eGK62si8*E*!7g~a?&Y3!|wxw?1Lahom 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report --- .../common/util/export/ExiPdfRtfExporter.java | 108 +++++++++++------- 1 file changed, 67 insertions(+), 41 deletions(-) diff --git a/ispyb-ejb/src/main/java/ispyb/common/util/export/ExiPdfRtfExporter.java b/ispyb-ejb/src/main/java/ispyb/common/util/export/ExiPdfRtfExporter.java index a823fea25..8a4dabd52 100644 --- a/ispyb-ejb/src/main/java/ispyb/common/util/export/ExiPdfRtfExporter.java +++ b/ispyb-ejb/src/main/java/ispyb/common/util/export/ExiPdfRtfExporter.java @@ -753,8 +753,7 @@ private void setDataAnalysisMapData(Document document, Map dataC Boolean strategy = getBoolean(dataCollectionMapItem, "ScreeningOutput_strategySuccess"); String autoprocSpaceGroup = getCellParam(dataCollectionMapItem, "AutoProc_spaceGroup", null); boolean existAutoProcSpaceGroup = (autoprocSpaceGroup != null && !autoprocSpaceGroup.isEmpty() ) - || ( dataCollectionMapItem.get("AutoProc_spaceGroups") != null && !((String)dataCollectionMapItem.get("AutoProc_spaceGroups")).isEmpty() - && dataCollectionMapItem.get("Autoprocessing_cell_a")!= null); + || ( dataCollectionMapItem.get("AutoProc_spaceGroups") != null && dataCollectionMapItem.get("Autoprocessing_cell_a") != null); p = new Paragraph(); String [] bestRmerge = null; @@ -1117,17 +1116,19 @@ private String[] extractBestAutoproc(Map dataCollectionMapItem) listString.trim(); List completenessList = new ArrayList(Arrays.asList((listString.split(",")))); - LOG.info("completenessList = " + completenessList.toString()); + LOG.debug("completenessList = " + completenessList.toString()); List spaceGroupsList = new ArrayList(Arrays.asList(((String)dataCollectionMapItem.get("AutoProc_spaceGroups")).trim().split(","))); - LOG.info("spaceGroupsList = " + spaceGroupsList.size() + spaceGroupsList.toString()); + LOG.debug("spaceGroupsList = " + spaceGroupsList.size() + spaceGroupsList.toString()); List resolutionsLimitLowList = new ArrayList(Arrays.asList(((String)dataCollectionMapItem.get("resolutionsLimitLow")).trim().split(","))); - LOG.info("resolutionsLimitLowList = " + resolutionsLimitLowList.size() + resolutionsLimitLowList.toString()); + LOG.debug("resolutionsLimitLowList = " + resolutionsLimitLowList.size() + resolutionsLimitLowList.toString()); List resolutionsLimitHighList = new ArrayList(Arrays.asList(((String)dataCollectionMapItem.get("resolutionsLimitHigh")).trim().split(","))); - LOG.info("resolutionsLimitHighList = " + resolutionsLimitHighList.toString()); + LOG.debug("resolutionsLimitHighList = " + resolutionsLimitHighList.toString()); List rmergesList = new ArrayList(Arrays.asList(((String)dataCollectionMapItem.get("rMerges")).trim().split(","))); - LOG.info("rmergesList = " + rmergesList.size() + rmergesList.toString() ); + LOG.debug("rmergesList = " + rmergesList.size() + rmergesList.toString() ); List scalingStatisticsTypesList = new ArrayList(Arrays.asList(((String)dataCollectionMapItem.get("scalingStatisticsTypes")).trim().split(","))); - LOG.info("scalingStatisticsTypesList = " + scalingStatisticsTypesList.size() + scalingStatisticsTypesList.toString()); + LOG.debug("scalingStatisticsTypesList = " + scalingStatisticsTypesList.size() + scalingStatisticsTypesList.toString()); + List anomalousList = new ArrayList(Arrays.asList(((String)dataCollectionMapItem.get("Autoprocessing_anomalous")).trim().split(","))); + LOG.debug("anomalousList = " + anomalousList.size() + anomalousList.toString()); bestRmerge = new String[18]; int i = 0; @@ -1135,32 +1136,34 @@ private String[] extractBestAutoproc(Map dataCollectionMapItem) int indexRmergeMin = 0; Set indexSet = new HashSet(); - //TODO select also no anom - for (Iterator iterator = scalingStatisticsTypesList.iterator(); iterator.hasNext();) { String type = (String) iterator.next(); - if (type.contains("innerShell")){ + // select also no anom + if (type.contains("innerShell") && (new Integer(anomalousList.get(i).trim())).intValue() < 1) { double rm = new Double(rmergesList.get(i)).doubleValue(); - LOG.info("rm = " + rm); - if (rm > 0 && rm < rmergeMin) { + LOG.debug("rm = " + rm); + if (rm > 0 && rm < MIN_RMERGE) { + indexSet.add(i); + LOG.debug("index kept: " + i); + } else if (rm > 0 && rm < rmergeMin) { rmergeMin = rm; indexRmergeMin = i; - if (rmergeMin < MIN_RMERGE) - indexSet.add(i); } } i=i+1; } + // select higher symmetry if (!indexSet.isEmpty()) { String spgTemp; - Integer spgNb = 0; + int spgNb = 0; for (Iterator iterator = indexSet.iterator(); iterator.hasNext();) { - Integer index = (Integer) iterator.next(); - spgTemp = spaceGroupsList.get(index); - - if (spgMap.get(spgTemp)!= null && spgNb < spgMap.get(spgTemp)) { - spgNb = spgMap.get(spgTemp); + Integer index = (Integer) iterator.next(); + spgTemp = spaceGroupsList.get(index).trim(); + LOG.debug("index : " + index + " spgtemp: " + spgTemp); + if (spgMap.get(spgTemp)!= null && spgNb <= spgMap.get(spgTemp).intValue() ) { + spgNb = spgMap.get(spgTemp).intValue(); + LOG.debug("index : " + index + " spgNb: " + spgMap.get(spgTemp)); indexRmergeMin = index; } } @@ -1185,22 +1188,39 @@ private String[] extractBestAutoproc(Map dataCollectionMapItem) bestRmerge[9] = tmpList.get(indexRmergeMin); //outer - bestRmerge[10] = spaceGroupsList.get(indexRmergeMin+1); - bestRmerge[11] = rmergesList.get(indexRmergeMin+1); - bestRmerge[12]= completenessList.get(indexRmergeMin+1); - bestRmerge[13] = resolutionsLimitLowList.get(indexRmergeMin+1) + "/" + resolutionsLimitHighList.get(indexRmergeMin+1); + int outerIndex = -1; + if (scalingStatisticsTypesList.get(indexRmergeMin+1).contains("outerShell") ){ + outerIndex = indexRmergeMin+1; + } else if (indexRmergeMin+2 < scalingStatisticsTypesList.size() && scalingStatisticsTypesList.get(indexRmergeMin+2).contains("outerShell") ){ + outerIndex = indexRmergeMin+2; + } + if (outerIndex > -1) { + bestRmerge[10] = spaceGroupsList.get(outerIndex); + bestRmerge[11] = rmergesList.get(outerIndex); + bestRmerge[12]= completenessList.get(outerIndex); + bestRmerge[13] = resolutionsLimitLowList.get(outerIndex) + "/" + resolutionsLimitHighList.get(outerIndex); + } //overall - int overallIndex = indexRmergeMin-1; - if (overallIndex < 0 || scalingStatisticsTypesList.get(0).contains("innerShell")) { + int overallIndex=-1; + if (indexRmergeMin-1 >= 0 && scalingStatisticsTypesList.get(indexRmergeMin-1).contains("overall")) { + overallIndex = indexRmergeMin-1; + } else if (indexRmergeMin-2 >= 0 && scalingStatisticsTypesList.get(indexRmergeMin-2).contains("overall")) { + overallIndex = indexRmergeMin-2; + } else if (indexRmergeMin+2 < scalingStatisticsTypesList.size() && scalingStatisticsTypesList.get(indexRmergeMin+2).contains("overall")) { overallIndex = indexRmergeMin+2; + } else if (indexRmergeMin+3 < scalingStatisticsTypesList.size() && scalingStatisticsTypesList.get(indexRmergeMin+3).contains("overall")) { + overallIndex = indexRmergeMin+3; } - - bestRmerge[14] = spaceGroupsList.get(overallIndex); - bestRmerge[15] = rmergesList.get(overallIndex); - bestRmerge[16]= completenessList.get(overallIndex); - //TODO format to 2 figures after . - bestRmerge[17] = resolutionsLimitLowList.get(overallIndex) + "/" + resolutionsLimitHighList.get(overallIndex); + + if (overallIndex > -1) { + bestRmerge[14] = spaceGroupsList.get(overallIndex); + bestRmerge[15] = rmergesList.get(overallIndex); + bestRmerge[16]= completenessList.get(overallIndex); + //TODO format to 2 figures after . + bestRmerge[17] = resolutionsLimitLowList.get(overallIndex) + "/" + resolutionsLimitHighList.get(overallIndex); + } + LOG.info("bestRmerge = " + bestRmerge[0] + "- " + bestRmerge[1]+ "- " + bestRmerge[2]+ "- " + bestRmerge[3]); } @@ -1208,14 +1228,20 @@ private String[] extractBestAutoproc(Map dataCollectionMapItem) } private Chunk getCompletenessChunk(String completeness) { - Chunk chu = new Chunk( completeness, FONT_DOC_SMALL_BOLD); - chu.setBackground(BLUE_COLOR); - if (completeness != null && new Double(completeness) < 90 ) { - if (new Double(completeness) < 50) { - chu.setBackground(RED_COLOR); - } else { - chu.setBackground(LIGHT_YELLOW_COLOR); - } + + Chunk chu = new Chunk( " ", FONT_DOC_SMALL_BOLD); + + if (completeness != null && !completeness.isEmpty()) { + + chu = new Chunk( completeness, FONT_DOC_SMALL_BOLD); + chu.setBackground(BLUE_COLOR); + if (completeness != null && new Double(completeness) < 90 ) { + if (new Double(completeness) < 50) { + chu.setBackground(RED_COLOR); + } else { + chu.setBackground(LIGHT_YELLOW_COLOR); + } + } } return chu; } From 0959c267dfc45606ec352b66d6b97c6777b8e771 Mon Sep 17 00:00:00 2001 From: delageniere Date: Thu, 9 Nov 2017 11:25:28 +0100 Subject: [PATCH 36/38] documentation updated --- .../documentation/ISPyB_DevelopersGuide.doc | Bin 190464 -> 192000 bytes 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-624,12 +593,5 @@ - - - - - - - - + diff --git a/configuration/standalone.xml.simple b/configuration/standalone.xml.simple new file mode 100644 index 000000000..8b8e63f37 --- /dev/null +++ b/configuration/standalone.xml.simple @@ -0,0 +1,567 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + jdbc:mysql://ispydb-prod.esrf.fr:3306/pyconfig + mysql-connector-java-5.1.21.jar + + pxuser + ***** + + + + jdbc:mysql://ispydb-prod.esrf.fr:3306/pydb + mysql-connector-java-5.1.21.jar + + pxuser + ***** + + + + jdbc:mysql://ispydb-prod.esrf.fr:3306/pydb + mysql-connector-java-5.1.21.jar + + pxuser + ***** + + + + jdbc:h2:mem:test;DB_CLOSE_DELAY=-1;DB_CLOSE_ON_EXIT=FALSE + h2 + + sa + sa + + + + + + org.h2.jdbcx.JdbcDataSource + + + + + + + + + false + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 102400 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + jms.queue.DLQ + jms.queue.ExpiryQueue + 10485760 + 2097152 + 10 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ${jboss.bind.address:127.0.0.1} + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + From 0442a303af5f8041ffc978f83e09e0e831bda58f Mon Sep 17 00:00:00 2001 From: delageniere Date: Thu, 9 Nov 2017 11:35:18 +0100 Subject: [PATCH 37/38] cleanup documentation and configuration folders --- .../documentation/ISPyB_AdminGuide.doc | Bin 34816 -> 0 bytes .../documentation/ISPyB_DevelopersGuide.doc | Bin 192000 -> 0 bytes configuration/documentation/ISPyB_wildfly.doc | Bin 35840 -> 0 bytes .../MariaDB_installation_CentOS.txt | 131 ---- .../documentation/QuickAdaptToWildfly.docx | Bin 17293 -> 0 bytes .../database/ISPyB_DataModel.mwb | Bin 208613 -> 0 bytes .../database/ISPyB_DataModel_4-0-5.mwb | Bin 177110 -> 0 bytes .../database/ISPyB_DataModel_4-0-5.pdf | Bin 181455 -> 0 bytes .../database/ISPyB_DataModel_4-0-5.png | Bin 1188494 -> 0 bytes .../database/ISPyB_DataModel_BX.png | Bin 547230 -> 0 bytes .../database/ISPyB_DataModel_mx.png | Bin 1027413 -> 0 bytes .../database/ISPyB_DataModel_mx_autoproc.png | Bin 255751 -> 0 bytes .../documentation/settings.xml.example | 304 --------- .../documentation/standalone.xml.example | 597 ------------------ documentation/ISPyB_DevelopersGuide.doc | Bin 208896 -> 192000 bytes 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CentOS 7: --------------------------------------------------- - -0/ OS: CentOS Linux release 7.1.1503 (Core) x64 - [root@srvdb ~]# tail /etc/redhat-release - CentOS Linux release 7.1.1503 (Core) - -1/ Make sure that you have internet access: - [root@srvdb tmp]# wget http://google.fr - -2/ Adding the MariaDB YUM Repository: - [root@srvdb ~]# vi /etc/yum.repos.d/MariaDB.repo - [mariadb] - name = MariaDB - baseurl = http://yum.mariadb.org/10.1/centos7-amd64 - gpgkey=https://yum.mariadb.org/RPM-GPG-KEY-MariaDB - gpgcheck=1 - -3/ Installing MariaDB: - [root@srvdb ~]# yum install MariaDB-server MariaDB-client - -4/ Mariadb stat, start and Set to start on boot: - [root@srvdb ~]# systemctl status mariadb - [root@srvdb ~]# systemctl start mariadb - [root@srvdb ~]# systemctl enable mariadb - -5/ Login and View Existing Databases: - [root@srvdb ~]# mysql - -6/ First Installation of MariaDB: - [root@srvdb ~]# mysql_secure_installation - login: root - root password: PPPPPPPP - Remove anonymous user : Yes - disable root login remotely: Yes - remove test database and access to it: Yes - Reload privileges tables now: Yes - - [root@srvdb ~]# systemctl restart mariadb - -7/ Connection and set password: - [root@srvdb ~]# mysql -u root -p - Enter password: PPPPPPP - -8/ Importing ISPyB schema into MaraiDB - Create Database and User Account: - --------------------------------- - [root@srvdb ~]# mysql -u root -p - Enter password: PPPPPPPP - - MariaDB [(none)]> use mysql; - MariaDB [(none)]> CREATE DATABASE IF NOT EXISTS `ispyb_config` DEFAULT CHARACTER SET latin1 COLLATE latin1_swedish_ci; - MariaDB [(mysql)]> GRANT ALL PRIVILEGES ON *.* TO 'ispyb_config'@'localhost' IDENTIFIED BY 'PPPPPPPP' WITH GRANT OPTION; - - MariaDB [(none)]> CREATE DATABASE IF NOT EXISTS `ispyb_db` DEFAULT CHARACTER SET latin1 COLLATE latin1_swedish_ci; - MariaDB [(mysql)]> GRANT ALL PRIVILEGES ON *.* TO 'ispyb_db'@'localhost' IDENTIFIED BY 'PPPPPPPP' WITH GRANT OPTION; - - MariaDB [(mysql)]> GRANT ALL PRIVILEGES ON *.* TO 'root'@'localhost'; - - MariaDB [(mysql)]> FLUSH PRIVILEGES; - - MariaDB [mysql]> quit; - Bye - - See - ---- - MariaDB [(mysql)]> SELECT User,Host,Password FROM mysql.user; - +--------------+---------------+-------------------------------------------+ - | User | Host | Password | - +--------------+---------------+-------------------------------------------+ - | root | localhost | *DCDD362A8D61A6EF15DBC1FCA1D97E0B0F6F134B | - | root | 127.0.0.1 | *DCDD362A8D61A6EF15DBC1FCA1D97E0B0F6F134B | - | root | ::1 | *DCDD362A8D61A6EF15DBC1FCA1D97E0B0F6F134B | - | ispyb_db | 127.0.0.1 | *B659BF6BE0C776E1949529F99ADEE9D7E9061468 | - | ispyb_config | 127.0.0.1 | *6560351E4A775F27F05DD50F9E6C06BD79008276 | - | ispyb_config | localhost | *6560351E4A775F27F05DD50F9E6C06BD79008276 | - | ispyb_db | localhost | *B659BF6BE0C776E1949529F99ADEE9D7E9061468 | - +--------------+---------------+-------------------------------------------+ - 16 rows in set (0.00 sec) - - -9/ Log into new data: - [root@srvdb ~]# mysql -u ispyb_config -p - Enter password: PPPPPPPPP - -10/ Solve case sensitive issue in linux by declaring case sensitive attribute in the '/etc/my.conf' file - [root@srvdb ~]# vi /etc/my.cnf - ... - #added by IC to tell MySQL that table name comparaison should not be case sensitive - lower_case_table_names=1 - - # Disabling symbolic-links is recommended to prevent assorted security risks - symbolic-links=0 - -11/ Import ispyb_config and ispyb_db into the MaraiDB: - Before doing that you need to export ispyb schema and data from your MySQL database for instance into 'export_ispyb_config.sql' and 'export_ispyb_db.sql' files. - - [root@srvdb ~]# systemctl restart mariadb - [root@srvdb ~]# mysql -u ispyb_config -p --database=ispyb_config < /path_to/export_ispyb_config.sql - Enter password: PPPPPPPP - - [root@srvdb ~]# mysql -u ispyb_db -p --database=ispyb_db < /path_to/export_ispyb_db.sql - Enter password: PPPPPPPP - -12/ Test of MaraiDB: - In the ISPyB server: - 1/ Stop 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